analysis of sequence from tem21_2hypoth
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIPSGTVFSELDD
EKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTF
DLQTLPVDFVECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMAGMAFLGNFQD
NLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTL
LHFIALTVKEKYPDLANFWHELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE
GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQLA
QEAKKLDAKTPSQRNKWQQQELIAELRRRQAKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFC
DAAHHDESNC
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> Tem21.2_gi|7328133|emb|CAB82400.1|
. . . . .
1 LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFN 50
___________________EEEEEE___EEEEEE_______________E
. . . . .
51 WTALKPNQIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKT 100
EE___________________HHHHHHHHHHHHHHH____EEEEE____H
. . . . .
101 AQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTFDLQTLPVDFV 150
HHHHHHHHHHHHHHHHHHHHHHHHHH___HHHHHHHHHH________HHH
. . . . .
151 ECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMA 200
HHHHH_____HHHHHHHHHHHH___HHHHHHHHHHHHHHHHHHHHHHHHH
. . . . .
201 GMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMN 250
HHHHHH____HHHHHH_HHHHHHHHHHHHHHHHHHHHHHHHHHHH_____
. . . . .
251 SSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH 300
______EEEEE_HHHHHHHH_____HHHHHHHHHHHHHHH_____HHHHH
. . . . .
301 ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE 350
HHHHHHHHHHHHHHHHHHHHH_____HHHHHHHHH____HHHHHH_____
. . . . .
351 GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEA 400
___HHHHHHHHHHHHHHHHHEEEEE___________HHHHHHHHHHHHHH
. . . . .
401 EQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQ 450
HHHHHHHHHHHHHHHHHHHHHHHHHH_________HHHHHHHHHHHHHHH
. . . . .
451 AKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFCDAAHHDESNC 500
HHHH___________HHHHHHH______________EEEE__________
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 81.1 %
beta-contents : 0.0 %
coil-contents : 18.9 %
class : alpha
method : 2
alpha-contents : 52.0 %
beta-contents : 0.0 %
coil-contents : 48.0 %
class : alpha
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-21.87 -2.28 -0.17 0.00 -4.00 0.00 -4.00 0.00 0.00 -4.61 -3.54 0.00 -12.00 0.00 -12.00 0.00 -64.47
-3.25 -0.49 -0.29 -1.35 0.00 0.00 0.00 -0.13 -0.50 -6.73 -3.54 -12.00 -12.00 0.00 -12.00 0.00 -52.30
ID: Tem21.2_gi|7328133|emb|CAB82400.1| AC: xxx Len: 490 1:I 462 Sc: -52.30 Pv: 2.536860e-01 NO_GPI_SITE
GPI: learning from protozoa
-26.78 -0.48 -0.23 -0.13 -4.00 0.00 0.00 -0.35 -0.09 -5.83 -12.03 -12.00 -12.00 0.00 -12.00 0.00 -85.92
-26.85 0.00 -0.23 0.00 -4.00 0.00 0.00 -0.35 -0.09 -5.14 -12.03 -12.00 -12.00 0.00 -12.00 0.00 -84.69
ID: Tem21.2_gi|7328133|emb|CAB82400.1| AC: xxx Len: 490 1:I 461 Sc: -84.69 Pv: 5.955505e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
Tem21.2_gi| 0.537 162 Y 0.157 32 N 0.508 30 N 0.190 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
Tem21.2_gi| 0.421 222 N 0.280 496 N 0.726 104 N 0.134 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
Tem21.2_gi| 0.487 257 Y 0.359 485 Y 0.955 480 Y 0.223 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
1-1 L
ppppdkcppapplpgaap 2-19
20-31 SVVLTVPPGLSA
irikkpppik 32-41
42-220 TKFRLPVFNWTALKPNQIPSGTVFSELDDE
KILEDKFEELFKTKAQGPALDLICSKNKTA
QKAASKVTLLEANRAKNLAITLRKAGRSAE
EICRAIHTFDLQTLPVDFVECLMRFLPTEA
EVKLLRQYERERQPLEELAAEDRFMLLFSK
VERLTQRMAGMAFLGNFQDNLQMLTPQLN
aiiaasasvkss 221-232
233-260 QKLKQMLEIILALGNYMNSSKRGAVYGF
klqsldllldtkst 261-274
275-381 DRKMTLLHFIALTVKEKYPDLANFWHELHF
VEKAAAVSLENVLLDVKELGRGMELIRREC
SIHDNSVLRNFLSTNEGKLDKLQRDAKTAE
EAYNAVVRYFGESPKTT
ppsvffpvfv 382-391
392-500 RFIRSYKEAEQENEARKKQEEVMREKQLAQ
EAKKLDAKTPSQRNKWQQQELIAELRRRQA
KEHRPVYEGKDGTIEDIITVLKSVPFTART
AKRGSRFFCDAAHHDESNC
low complexity regions: SEG 25 3.0 3.3
>Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
lppppdkcppapplpgaapsvvltvppgls 1-49
airikkpppiktkfrlpvf
50-152 NWTALKPNQIPSGTVFSELDDEKILEDKFE
ELFKTKAQGPALDLICSKNKTAQKAASKVT
LLEANRAKNLAITLRKAGRSAEEICRAIHT
FDLQTLPVDFVEC
lmrflpteaevkllrqyererqpleelaae 153-188
drfmll
189-217 FSKVERLTQRMAGMAFLGNFQDNLQMLTP
qlnaiiaasasvkssqklkqmleiilal 218-245
246-397 GNYMNSSKRGAVYGFKLQSLDLLLDTKSTD
RKMTLLHFIALTVKEKYPDLANFWHELHFV
EKAAAVSLENVLLDVKELGRGMELIRRECS
IHDNSVLRNFLSTNEGKLDKLQRDAKTAEE
AYNAVVRYFGESPKTTPPSVFFPVFVRFIR
SY
keaeqenearkkqeevmrekqlaqeakkld 398-429
ak
430-500 TPSQRNKWQQQELIAELRRRQAKEHRPVYE
GKDGTIEDIITVLKSVPFTARTAKRGSRFF
CDAAHHDESNC
low complexity regions: SEG 45 3.4 3.75
>Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
lppppdkcppapplpgaapsvvltvppgls 1-60
airikkpppiktkfrlpvfnwtalkpnqip
61-397 SGTVFSELDDEKILEDKFEELFKTKAQGPA
LDLICSKNKTAQKAASKVTLLEANRAKNLA
ITLRKAGRSAEEICRAIHTFDLQTLPVDFV
ECLMRFLPTEAEVKLLRQYERERQPLEELA
AEDRFMLLFSKVERLTQRMAGMAFLGNFQD
NLQMLTPQLNAIIAASASVKSSQKLKQMLE
IILALGNYMNSSKRGAVYGFKLQSLDLLLD
TKSTDRKMTLLHFIALTVKEKYPDLANFWH
ELHFVEKAAAVSLENVLLDVKELGRGMELI
RRECSIHDNSVLRNFLSTNEGKLDKLQRDA
KTAEEAYNAVVRYFGESPKTTPPSVFFPVF
VRFIRSY
keaeqenearkkqeevmrekqlaqeakkld 398-455
aktpsqrnkwqqqeliaelrrrqakehr
456-500 PVYEGKDGTIEDIITVLKSVPFTARTAKRG
SRFFCDAAHHDESNC
low complexity regions: XNU
# Score cutoff = 21, Search from offsets 1 to 4
# both members of each repeat flagged
# lambda = 0.347, K = 0.200, H = 0.664
>Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIP
SGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLA
ITLRKAGRSAEEICRAIHTFDLQTLPVDFVECLMRFLPTEAEVKLLRQYERERQPLEELA
AEDRFMLLFSKVERLTQRMAGMAflgnfqdnlqmltpqlnaiiaasasvkssqklkqmle
iilalGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH
ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEGKLDKLQRDA
KTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQLA
QEAKKLDAKTPSQRNKWQQQELIAELRRRQAKEHRPVYEGKDGTIEDIITVLKSVPFTAR
TAKRGSRFFCDAAHHDESNC
1 - 203 LPPPPDKCPP APPLPGAAPS VVLTVPPGLS AIRIKKPPPI KTKFRLPVFN WTALKPNQIP
SGTVFSELDD EKILEDKFEE LFKTKAQGPA LDLICSKNKT AQKAASKVTL LEANRAKNLA
ITLRKAGRSA EEICRAIHTF DLQTLPVDFV ECLMRFLPTE AEVKLLRQYE RERQPLEELA
AEDRFMLLFS KVERLTQRMA GMA
204 - 245 flgnfqd nlqmltpqln aiiaasasvk ssqklkqmle iilal
246 - 500 GNYMN SSKRGAVYGF KLQSLDLLLD TKSTDRKMTL LHFIALTVKE KYPDLANFWH ELHFV
EKAAA VSLENVLLDV KELGRGMELI RRECSIHDNS VLRNFLSTNE GKLDKLQRDA KTAEE
AYNAV VRYFGESPKT TPPSVFFPVF VRFIRSYKEA EQENEARKKQ EEVMREKQLA QEAKK
LDAKT PSQRNKWQQQ ELIAELRRRQ AKEHRPVYEG KDGTIEDIIT VLKSVPFTAR TAKRG
SRFFC DAAHHDESNC
low complexity regions: DUST
>Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIP
SGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLA
ITLRKAGRSAEEICRAIHTFDLQTLPVDFVECLMRFLPTEAEVKLLRQYERERQPLEELA
AEDRFMLLFSKVERLTQRMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLE
IILALGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH
ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEGKLDKLQRDA
KTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQLA
QEAKKLDAKTPSQRNKWQQQELIAELRRRQAKEHRPVYEGKDGTIEDIITVLKSVPFTAR
TAKRGSRFFCDAAHHDESNC
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for Tem21.2_gi|7328133|emb|CAB82400.1|
sequence: 490 amino acids, 59 residue(s) in coiled coil state
Coil 1 * 345* 372* LSTNEGKLDKLQRDAKTAEEAYNAVVRY
Coil 2 * 394* 426* RSYKEAEQENEARKKQEEVMREKQLAQEAKKLD
. | . | . | . | . | . 60
LPPPPDKCPP APPLPGAAPS VVLTVPPGLS AIRIKKPPPI KTKFRLPVFN WTALKPNQIP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 120
SGTVFSELDD EKILEDKFEE LFKTKAQGPA LDLICSKNKT AQKAASKVTL LEANRAKNLA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~1111 1111111111 1111111111 * 21 M'95 -w border
---------- ---------- ---------- ------defg abcdefgabc dgabcdefga * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~122222222 * 21 M'95 +w polar
~~~~~11111 1111111111 1111111~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~111 1114444444 4444444~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~111111111 * 14 M'95 -w local
. | . | . | . | . | . 180
ITLRKAGRSA EEICRAIHTF DLQTLPVDFV ECLMRFLPTE AEVKLLRQYE RERQPLEELA
1111111111 11~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~1 1112222222 2222222222 * 21 M'95 -w border
bcdefgabcd ef-------- ---------- ---------b cdefgabcde fgabcdefgc * 21 M'95 -w register
2222222222 2221111~~~ ~~~~~~~~~~ ~~~~~~~~~1 1111111111 1111111125 * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~2 * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
11111~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~2 2222444444 4444444442 * 14 M'95 -w local
. | . | . | . | . | . 240
AEDRFMLLFS KVERLTQRMA GMAFLGNFQD NLQMLTPQLN AIIAASASVK SSQKLKQMLE
2222222222 2222222222 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
defgabcdef gabcdefgab ---------- ---------- ---------- ---------- * 21 M'95 -w register
5555555555 5555555555 31~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
2222222222 2222222222 11~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
22~~~~~~~1 1111111111 111~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 300
IILALGNYMN SSKRGAVYGF KLQSLDLLLD TKSTDRKMTL LHFIALTVKE KYPDLANFWH
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 360
ELHFVEKAAA VSLENVLLDV KELGRGMELI RRECSIHDNS VLRNFLSTNE GKLDKLQRDA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~1199999 9999999999 * 21 M'95 -w border
---------- ---------- ---------- ---------- ---fgabcde fgabcdefga * 21 M'95 -w register
~~~~~~~~~~ ~~11111111 1111111111 111~~~~~~~ 1111177779 9999999999 * 21 M'95 +w polar
~~~~~~~~~~ ~~11111111 1111111111 111~~~~~~~ ~~~~~88889 9999999999 * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~444 5888888888 8888888888 * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~22229 9999999999 * 14 M'95 -w local
. | . | . | . | . | . 420
KTAEEAYNAV VRYFGESPKT TPPSVFFPVF VRFIRSYKEA EQENEARKKQ EEVMREKQLA
9999999999 993~~~~~~~ ~~~~~~~~~~ ~333569999 9999999999 9999999999 * 21 M'95 -w border
bcdefgabcd efg------- ---------- -cdefgafga cdefgabcde fgabcdefga * 21 M'95 -w register
9999999999 995~~~~~~~ ~~~~~~~~~~ ~~~~~~~111 1166666666 6666666666 * 21 M'95 +w polar
9999999999 9951~~~~~~ ~~~~~~~~~~ ~~~~124666 6677888888 8888888888 * 21 MTK -w class
8888888884 111~~~~~~~ ~~~~~~~~~1 1113489999 9999999999 9999999999 * 28 M'95 -w signif.
9999999984 ~~~~~~~~~~ ~~~~~~~~~~ 1666668899 9999999999 9999887777 * 14 M'95 -w local
. | . | . | . | . | . 480
QEAKKLDAKT PSQRNKWQQQ ELIAELRRRQ AKEHRPVYEG KDGTIEDIIT VLKSVPFTAR
999997322~ ~122222222 2222222222 222~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
bcdefgefg- -dgabcdefg abcdefgabc def------- ---------- ---------- * 21 M'95 -w register
666431~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
888884322~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
9999999999 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
7776555553 ~~11111444 4444444444 433~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. |
TAKRGSRFFC
~~~~~~~~~~
----------
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem21_2hypoth.___inter___ is a single sequence
Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale
Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok
Using sequence file: tem21_2hypoth.___inter___
(1 sequences)
LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFN
WTALKPNQIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKT
AQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTFDLQTLPVDFV
ECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMA
GMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMN
SSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH
ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE
GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEA
EQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQ
AKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFCDAAHHDESNC
(p)rokaryotic or (e)ukaryotic: e
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 1 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 12 32 1.316 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 11 468
K+R profile 2.00
+
CYT-EXT prof -
-0.55
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -6.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.55
-> Orientation: N-out
----------------------------------------------------------------------
"tem21_2hypoth" 500
12 32 #t 1.31563
************************************
*TOPPREDM with prokaryotic function*
************************************
tem21_2hypoth.___inter___ is a single sequence
Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale
Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok
Using sequence file: tem21_2hypoth.___inter___
(1 sequences)
LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFN
WTALKPNQIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKT
AQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTFDLQTLPVDFV
ECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMA
GMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMN
SSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH
ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE
GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEA
EQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQ
AKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFCDAAHHDESNC
(p)rokaryotic or (e)ukaryotic: p
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 1 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 12 32 1.316 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 11 468
K+R profile 2.00
+
CYT-EXT prof -
-0.55
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -6.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.55
-> Orientation: N-out
----------------------------------------------------------------------
"tem21_2hypoth" 500
12 32 #t 1.31563
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
SAPS. Version of April 11, 1996.
Date run: Fri Jan 19 18:07:46 2001
File: /people/maria/tem21_2hypoth.___saps___
ID Tem21.2_gi|7328133|emb|CAB82400.1|
DE hypothetical protein [Homo sapiens]
number of residues: 500; molecular weight: 56.7 kdal
1 LPPPPDKCPP APPLPGAAPS VVLTVPPGLS AIRIKKPPPI KTKFRLPVFN WTALKPNQIP
61 SGTVFSELDD EKILEDKFEE LFKTKAQGPA LDLICSKNKT AQKAASKVTL LEANRAKNLA
121 ITLRKAGRSA EEICRAIHTF DLQTLPVDFV ECLMRFLPTE AEVKLLRQYE RERQPLEELA
181 AEDRFMLLFS KVERLTQRMA GMAFLGNFQD NLQMLTPQLN AIIAASASVK SSQKLKQMLE
241 IILALGNYMN SSKRGAVYGF KLQSLDLLLD TKSTDRKMTL LHFIALTVKE KYPDLANFWH
301 ELHFVEKAAA VSLENVLLDV KELGRGMELI RRECSIHDNS VLRNFLSTNE GKLDKLQRDA
361 KTAEEAYNAV VRYFGESPKT TPPSVFFPVF VRFIRSYKEA EQENEARKKQ EEVMREKQLA
421 QEAKKLDAKT PSQRNKWQQQ ELIAELRRRQ AKEHRPVYEG KDGTIEDIIT VLKSVPFTAR
481 TAKRGSRFFC DAAHHDESNC
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 47( 9.4%); C : 7( 1.4%); D : 22( 4.4%); E : 43( 8.6%); F : 25( 5.0%)
G : 17( 3.4%); H : 8( 1.6%); I : 21( 4.2%); K : 45( 9.0%); L : 58(11.6%)
M : 10( 2.0%); N : 19( 3.8%); P : 31( 6.2%); Q : 23( 4.6%); R : 33( 6.6%)
S : 27( 5.4%); T : 26( 5.2%); V : 27( 5.4%); W : 3( 0.6%); Y : 8( 1.6%)
KR : 78 ( 15.6%); ED : 65 ( 13.0%); AGP : 95 ( 19.0%);
KRED : 143 ( 28.6%); KR-ED : 13 ( 2.6%); FIKMNY : 128 ( 25.6%);
LVIFM : 141 ( 28.2%); ST : 53 ( 10.6%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 00000-+000 0000000000 0000000000 00+0++0000 +0+0+00000 0000+00000
61 000000-0-- -+00--+0-- 00+0+00000 0-0000+0+0 00+000+000 0-00+0+000
121 000++00+00 --00+00000 -000000-00 -000+0000- 0-0+00+00- +-+000--00
181 0--+000000 +0-+000+00 000000000- 0000000000 000000000+ 000+0+000-
241 0000000000 00++000000 +0000-000- 0+00-++000 00000000+- +00-000000
301 -0000-+000 000-0000-0 +-00+00-00 ++-0000-00 00+000000- 0+0-+00+-0
361 +00--00000 0+000-00+0 0000000000 0+00+00+-0 -0-0-0+++0 --00+-+000
421 0-0++0-0+0 000+0+0000 -000-0+++0 0+-0+000-0 +-000--000 00+000000+
481 00++00+000 -0000--000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 12/30 or 16/45 or 20/60): none
Negative charge clusters (cmin = 11/30 or 14/45 or 18/60): none
Mixed charge clusters (cmin = 18/30 or 24/45 or 31/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
There are no high scoring positive charge segments.
There are no high scoring negative charge segments.
There are no high scoring mixed charge segments.
________________________________
High scoring uncharged segments:
score= 1.00 frequency= 0.714 ( LAGSVTIPNFQYHMCW )
score= 0.00 frequency= 0.000 ( BZX )
score= -8.00 frequency= 0.286 ( KEDR )
Expected score/letter: -1.574
M_0.01= 29.58; M_0.05= 24.38
1) From 8 to 32: length= 25, score=25.00 *
8 CPPAPPLPGA APSVVLTVPP GLSAI
L: 3(12.0%); A: 4(16.0%); V: 3(12.0%); P: 8(32.0%);
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 6 | 5 | 8 | 28 | 10 | 10 | 14 | 12 | 11 | 16 | 6 | 8 |
lmin1 7 | 7 | 10 | 34 | 13 | 12 | 17 | 15 | 14 | 19 | 8 | 10 |
lmin2 8 | 8 | 12 | 38 | 14 | 13 | 19 | 17 | 16 | 21 | 9 | 11 |
(Significance level: 0.010000; Minimal displayed length: 6)
There are no charge runs or patterns exceeding the given minimal lengths.
Run count statistics:
+ runs >= 4: 0
- runs >= 3: 1, at 69;
* runs >= 6: 0
0 runs >= 19: 2, at 8; 211;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
There are no high scoring hydrophobic segments.
There are no high scoring transmembrane segments.
2. SPACINGS OF C.
H2N-7-C-86-C-38-C-17-C-181-C-155-C-9-C-0-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-7-C-86-C-38-C-3-H-13-C-129-H-17-H-2-H-30-C-2-H-116-H-35-C-3-H-H-4-C-0-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[ 355- 362] KLQRDAKT
[ 425- 430] KL__DAKT
B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet.
(i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C)
Repeat core block length: 8
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 41 (Expected range: 14-- 47)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 16 (6-10) 10 (11-20) 9 (>=21) 7
3. Clusters of amino acid multiplets (cmin = 13/30 or 17/45 or 21/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 19 (Expected range: 5-- 30)
9 +plets (f+: 15.6%), 10 -plets (f-: 13.0%)
Total number of charge altplets: 17 (Critical number: 34)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 5 (6-10) 1 (11-20) 4 (>=21) 10
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
2- 5 1 P 4 4 0
5- 32 7 P...... 4 4 0
67- 82 4 E... 4 4 0
360- 371 3 A.. 4 4 0
399- 406 2 E. 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 7)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core:10)
Location Period Element Copies Core Errors
399- 418 2 *. 9 7 1
401- 442 7 *0.0... 6 6 /0/2/./2/./././
427- 468 7 *0.0*.. 6 6 /0/2/./1/2/././
445- 493 7 *....00 7 7 /0/././././2/2/
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
6- 67 (1.) -( 61)- 1 of 66 0.0074 large maximal spacing
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Pfam (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/Pfam
Sequence file: tem21_2hypoth
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
FH2 Formin Homology 2 Domain 487.7 8.9e-143 1
SMC_C SMC family, C-terminal domain -146.8 66 1
IPT Isopentenyl transferase -163.9 13 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
SMC_C 1/1 130 262 .. 1 210 [] -146.8 66
IPT 1/1 121 303 .. 1 240 [] -163.9 13
FH2 1/1 36 467 .. 1 503 [] 487.7 8.9e-143
Alignments of top-scoring domains:
SMC_C: domain 1 of 1, from 130 to 262: score -146.8, E = 66
*->lekeikeLgpVlnElqvNlkAi.eEYaeveeRyeelvekledleeer
+e+ ++ + +l ++ ++ e+ R+ ++++ l + +
Tem21.2_gi 130 AEEICRAIHTF------DLQTLpVDFVECLMRFLPTEAEVKLLRQYE 170
kkllevieeldkkrleeFmeaFnkInknfkevFqeLtgGGdAeLrLtDpd
++ ++ +eel ++Fm F k+++ ++++ + + G + D +
Tem21.2_gi 171 RE-RQPLEEL--AAEDRFMLLFSKVERLTQRMAGMAFLGN-----FQDNL 212
DPFssGieisArPPgKkwknlelLSGGEKtLtALALlFAIhkykPsPFYv
+++ +l+ A + A ++k s
Tem21.2_gi 213 QMLTP--------------QLN------------AIIAASASVKSS---- 232
lDEvDAALDeaNVsRvAnyIkrersknaQFIVIsLRnnmmekADaLvGVy
+++ ++++ I+ L n m + +
Tem21.2_gi 233 -------------QKLKQMLE---------IILALGNYMNS--------S 252
mqddgvskVislkL<-*
+++ V + kL
Tem21.2_gi 253 KRG----AVYGFKL 262
IPT: domain 1 of 1, from 121 to 303: score -163.9, E = 13
*->mklYLIwGATcTGKTaeAiaLAksT....GwPVivLDRvQCcsqLat
+ l+ G +ae i A T + + +PV D v C +
Tem21.2_gi 121 ITLR------KAGRSAEEICRAIHTfdlqTLPV---DFVECLMRFL- 157
GSGRPlpaELqgTrRiYLdPnR.slseGvIdAeeAndrLiaeVtshkdre
P++aE+ ++ R Y +R++l e + Ae+ + +L+++V+++
Tem21.2_gi 158 ----PTEAEV-KLLRQYER-ERqPLEE--LAAEDRFMLLFSKVERLTQ-- 197
gglILEGGSISLLkrMaqdpyWnadFeWhvkrlrLpdrdvFlaqAKkRvr
rMa ++ F+ +
Tem21.2_gi 198 --------------RMAGMAFL-GNFQDNL-------------------- 212
qMLrpdsggpSlLdELvelWkepaaraiLEdIDGYRyiidyArahqltid
qML p + + ++ +++ + +++ LE I + ++ +
Tem21.2_gi 213 QMLTP--QLNAIIAASASVKSSQKLKQMLEIILALGNYMNSSKRGAVYGF 260
qLtnldt.....tTdqeeeLiegIAqEYleHAlwQEqeFPltPAtalewg
+L +ld+ +++ Td++ +L + I Al ++ P a +w
Tem21.2_gi 261 KLQSLDLlldtkSTDRKMTLLHFI-------ALTVKEKYPDL---ANFWH 300
rgp<-*
+
Tem21.2_gi 301 ELH 303
FH2: domain 1 of 1, from 36 to 467: score 487.7, E = 8.9e-143
*->pkkvpkpkkpLKqLhWdkletlkqpdapPsekskgtvWgttlndeld
++ ++k+k++L+ ++W++l+ P+++++gtv+ eld
Tem21.2_gi 36 KPPPIKTKFRLPVFNWTALK--------PNQIPSGTVF-----SELD 69
etklLenegdldeleelFatkektksakkgdvsetksklmkkkvkknlki
++k+ + d++eelF k+k++++ d+ ++k k ++k+++k +++
Tem21.2_gi 70 DEKI-----LEDKFEELF--KTKAQGPAL-DLICSKNKTAQKAASK-VTL 110
ldpkrsqnppleIllrslhcdmsieetvikvailevDevkvlsedlleqL
l ++r++n l+I+lr+ s+ee i+ ai+++D ++l++d++e+L
Tem21.2_gi 111 LEANRAKN--LAITLRKA--GRSAEE--ICRAIHTFDL-QTLPVDFVECL 153
lkfaPYsktkeelkklrevkedkekdleeLsraeqiFllllsnLipylee
++f+P t+ e+k+lr+++++ + +leeL+ +++ F+ll+s+ + +l +
Tem21.2_gi 154 MRFLP---TEAEVKLLRQYERE-RQPLEELAAEDR-FMLLFSK-VERLTQ 197
RlkallfklnfeeevedLkpklekvtaAseeLreSkkFkklLeliLaiGN
R+ + f++nf +++++L p+l++++aAs ++++S k+k++Le+iLa+GN
Tem21.2_gi 198 RMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGN 247
yMNggsrrrgqAkGFkLssLtkLsdvKsadnktTLLHylvkiirekypel
yMN +s+r g+++GFkL+sL+ L+d+Ks+d+k+TLLH+++ +++ekyp+l
Tem21.2_gi 248 YMN-SSKR-GAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDL 295
ldFysdlhhvdeaSsrkvnleelekdvkslekqiknlEtsldlgnlsdpe
++F +lh+v++a+ v+le+++ dvk+l++ ++E l +++s+
Tem21.2_gi 296 ANFWHELHFVEKAA--AVSLENVLLDVKELGR---GME--LIRRECSI-- 336
lhpdDkflevmrpFlkaAkekfdkLqkdlkdmktrleslveyygedpkdd
h+ v+r Fl + k+dkLq d+k+++++++ +v+y+ge+pk+
Tem21.2_gi 337 -HD----NSVLRNFLSTNEGKLDKLQRDAKTAEEAYNAVVRYFGESPKT- 380
lspneFFkdfneFleefkkarkenlAEeqrkekeeelkrrrklalkalsk
++p FF f++F+ ++k+a +en + ++k+ee +r ++la +
Tem21.2_gi 381 TPPSVFFPVFVRFIRSYKEAEQEN----EARKKQEEVMREKQLA-----Q 421
eklereqgkskqkentlerrkernplmdgeaekeqdfkgvldsllkalrt
e ++ ++++ q + + ++++++a e+ +++++ + + ++++
Tem21.2_gi 422 EAKKLDAKTPSQRN--------KWQQQELIA--ELRRRQAKEHRPVYEGK 461
dssfrr<-*
d+ +++
Tem21.2_gi 462 DGTIED 467
//
Start with PfamFrag (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/PfamFrag
Sequence file: tem21_2hypoth
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
FH2 Formin Homology 2 Domain 485.9 3.3e-142 1
cofilin_ADF Cofilin/tropomyosin-type actin-bindin 4.3 7.7 1
HNH HNH endonuclease 2.1 77 1
Auxin_BP Auxin binding protein -0.8 54 1
GTP_cyclohydroI GTP cyclohydrolase I -0.9 90 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
cofilin_ADF 1/1 63 79 .. 134 150 .] 4.3 7.7
HNH 1/1 210 227 .. 35 52 .] 2.1 77
Auxin_BP 1/1 332 344 .. 1 14 [. -0.8 54
GTP_cyclohydroI 1/1 357 372 .. 169 184 .] -0.9 90
FH2 1/1 36 467 .. 1 503 [] 485.9 3.3e-142
Alignments of top-scoring domains:
cofilin_ADF: domain 1 of 1, from 63 to 79: score 4.3, E = 7.7
*->gDaselsDeealleklk<-*
+++sel+De++l++k
Tem21.2_gi 63 TVFSELDDEKILEDKFE 79
HNH: domain 1 of 1, from 210 to 227: score 2.1, E = 77
*->dNLvlltpkeNsrkhatk<-*
dNL++ltp+ N +++a
Tem21.2_gi 210 DNLQMLTPQLNAIIAASA 227
Auxin_BP: domain 1 of 1, from 332 to 344: score -0.8, E = 54
*->askcsikglplvRn<-*
+csi+++++ Rn
Tem21.2_gi 332 -RECSIHDNSVLRN 344
GTP_cyclohydroI: domain 1 of 1, from 357 to 372: score -0.9, E = 90
*->redqkTReEfLrlirk<-*
+ d+kT eE+++++ +
Tem21.2_gi 357 QRDAKTAEEAYNAVVR 372
FH2: domain 1 of 1, from 36 to 467: score 485.9, E = 3.3e-142
*->pkkvpkpkkpLKqLhWdkletlkqpdapPsekskgtvWgttlndeld
++ ++k+k++L+ ++W++l+ P+++++gtv+ eld
Tem21.2_gi 36 KPPPIKTKFRLPVFNWTALK--------PNQIPSGTVF-----SELD 69
etklLenegdldeleelFatkektksakkgdvsetksklmkkkvkknlki
++k+ + d++eelF k+k++++ d+ ++k k ++k+++k +++
Tem21.2_gi 70 DEKI-----LEDKFEELF--KTKAQGPAL-DLICSKNKTAQKAASK-VTL 110
ldpkrsqnppleIllrslhcdmsieetvikvailevDevkvlsedlleqL
l ++r++n l+I+lr+ s+ee i+ ai+++D ++l++d++e+L
Tem21.2_gi 111 LEANRAKN--LAITLRKA--GRSAEE--ICRAIHTFDL-QTLPVDFVECL 153
lkfaPYsktkeelkklrevkedkekdleeLsraeqiFllllsnLipylee
++f+P t+ e+k+lr+++++ + +leeL+ +++ F+ll+s+ + +l +
Tem21.2_gi 154 MRFLP---TEAEVKLLRQYERE-RQPLEELAAEDR-FMLLFSK-VERLTQ 197
RlkallfklnfeeevedLkpklekvtaAseeLreSkkFkklLeliLaiGN
R+ + f++nf +++++L p+l++++aAs ++++S k+k++Le+iLa+GN
Tem21.2_gi 198 RMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGN 247
yMNggsrrrgqAkGFkLssLtkLsdvKsadnktTLLHylvkiirekypel
yMN +s+r g+++GFkL+sL+ L+d+Ks+d+k+TLLH+++ +++ekyp+l
Tem21.2_gi 248 YMN-SSKR-GAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDL 295
ldFysdlhhvdeaSsrkvnleelekdvkslekqiknlEtsldlgnlsdpe
++F +lh+v++a+ v+le+++ dvk+l++ ++E l +++s+
Tem21.2_gi 296 ANFWHELHFVEKAA--AVSLENVLLDVKELGR---GME--LIRRECSI-- 336
lhpdDkflevmrpFlkaAkekfdkLqkdlkdmktrleslveyygedpkdd
h+ v+r Fl + k+dkLq d+k+++++++ +v+y+ge+pk+
Tem21.2_gi 337 -HD----NSVLRNFLSTNEGKLDKLQRDAKTAEEAYNAVVRYFGESPKT- 380
lspneFFkdfneFleefkkarkenlAEeqrkekeeelkrrrklalkalsk
++p FF f++F+ ++k+a +en + ++k+ee +r ++la +
Tem21.2_gi 381 TPPSVFFPVFVRFIRSYKEAEQEN----EARKKQEEVMREKQLA-----Q 421
eklereqgkskqkentlerrkernplmdgeaekeqdfkgvldsllkalrt
e ++ ++++ q + + ++++++a e+ +++++ + + ++++
Tem21.2_gi 422 EAKKLDAKTPSQRN--------KWQQQELIA--ELRRRQAKEHRPVYEGK 461
dssfrr<-*
d+ +++
Tem21.2_gi 462 DGTIED 467
//
Start with Repeat Library (from /data/patterns/repeats-Miguel-Andrade/hmm)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/repeats-Miguel-Andrade/hmm/repeats.hmm-lib
Sequence file: tem21_2hypoth
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Prosite
---------------------------------------------------------
| ppsearch (c) 1994 EMBL Data Library |
| based on MacPattern (c) 1990-1994 R. Fuchs |
---------------------------------------------------------
PROSITE pattern search started: Fri Jan 19 18:09:57 2001
Sequence file: tem21_2hypoth
----------------------------------------
Sequence Tem21.2_gi|7328133|emb|CAB82400.1| (500 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
50: NWTA
98: NKTA
250: NSSK
Total matches: 3
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
276: RKMT
483: KRGS
Total matches: 2
Matching pattern PS00005 PKC_PHOSPHO_SITE:
122: TLR
196: TQR
228: SVK
232: SQK
251: SSK
252: SKR
274: TDR
287: TVK
377: SPK
396: SYK
432: SQR
478: TAR
481: TAK
Total matches: 13
Matching pattern PS00006 CK2_PHOSPHO_SITE:
66: SELD
109: TLLE
129: SAEE
159: TEAE
190: SKVE
287: TVKE
335: SIHD
347: STNE
362: TAEE
396: SYKE
464: TIED
Total matches: 11
Matching pattern PS00008 MYRISTYL:
16: GAAPSV
62: GTVFSE
246: GNYMNS
255: GAVYGF
Total matches: 4
Matching pattern PS00290 IG_MHC:
488: FFCDAAH
Total matches: 1
Total no of hits in this sequence: 34
========================================
1314 pattern(s) searched in 1 sequence(s), 500 residues.
Total no of hits in all sequences: 34.
Search time: 00:00 min
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Profile Search
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with motif search against own library
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
SeqTyp=2 : PROTEIN search;
>APC D-Box is the MOTIF name
>STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 500 units
>ER-GOLGI-traffic signal is the MOTIF name
>STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 500 units
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~ ~~~
Start with HMM-search search against own library
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm.lib
Sequence file: tem21_2hypoth
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm-f.lib
Sequence file: tem21_2hypoth
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
L. Aravind's signalling DB
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo
sapiens]
(500 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
ARM Armadillo repeat 26 0.10
ARR Arrestin domain 24 0.34
PDE cyclic NMP phosphodiesterase domain 23 0.75
PAIRED Paired domain (A HTH domain) 22 1.6
KIN Protein kinase domain 22 2.2
SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 21 2.3
CALC Calcineurin like Phosphoesterase domain 21 2.8
INSL Insulinase like Metallo protease domain 21 3.1
UBHYD Ubiquitin C-terminal hydrolase domain 21 3.8
SH3 Src Homology domain 3 21 4.6
14-3-3 14-3-3 protein alpha Helical domain 20 6.4
CYCLIN Cyclin/TFIIB domain 20 7.9
RHOGAP RHO-type GTPase GTP hydrolysis activating protein 19 9.5
>ARM Armadillo repeat
Length = 532
Score = 26.1 bits (57), Expect = 0.10
Identities = 14/81 (17%), Positives = 14/81 (17%), Gaps = 10/81 (12%)
Query: 394 IRSYKEAEQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQAKE 453
Sbjct: 13 RNRYKVAVDAEEGRRRREDNMVEIRKSKREESLMKK----RREGMQALQGFPSASAASVD 68
Query: 454 HRPVYEGKDGTIEDIITVLKS 474
Sbjct: 69 KKL------DSLKDMVAGVWS 83
Score = 23.4 bits (50), Expect = 0.66
Identities = 15/74 (20%), Positives = 15/74 (20%), Gaps = 11/74 (14%)
Query: 307 KAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEG--KLDKLQR--DAKT 362
Sbjct: 430 TVCLEGLENILKV----GEAEKNLGHT---GDMNYYAQLIDDAEGLEKIENLQSHDNNEI 482
Query: 363 AEEAYNAVVRYFGE 376
Sbjct: 483 YEKAVKILETYWLE 496
Score = 19.5 bits (40), Expect = 9.5
Identities = 11/86 (12%), Positives = 11/86 (12%), Gaps = 4/86 (4%)
Query: 165 LLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMAGMAFLGN---FQDNLQMLTPQLNA 221
Sbjct: 269 LSDGTNDKIQTVIQAGVVPKLVELLLHHSPSVLIPALRT-VGNIVTGDDIQTQCVINSGA 327
Query: 222 IIAASASVKSSQKLKQMLEIILALGN 247
Sbjct: 328 LPCLANLLTQNHKKSIKKEACWTISN 353
>ARR Arrestin domain
Length = 454
Score = 24.5 bits (53), Expect = 0.34
Identities = 11/74 (14%), Positives = 11/74 (14%), Gaps = 15/74 (20%)
Query: 19 PSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIPSGTVFSELDDEKILEDK- 77
Sbjct: 374 PFTLTHSKPPESPERTDRGLPSIEAT-----------NGSEPVDIDLIQLHEELEPRYDD 422
Query: 78 ---FEELFKTKAQG 88
Sbjct: 423 DLIFEDFARMRLHG 436
Score = 19.8 bits (41), Expect = 7.7
Identities = 5/22 (22%), Positives = 5/22 (22%)
Query: 3 PPPDKCPPAPPLPGAAPSVVLT 24
Sbjct: 197 LAIRKLTYAPFESRPQPMVDVS 218
>PDE cyclic NMP phosphodiesterase domain
Length = 350
Score = 23.2 bits (49), Expect = 0.75
Identities = 28/149 (18%), Positives = 28/149 (18%), Gaps = 7/149 (4%)
Query: 168 QYERERQPLEELAAEDRFMLLFSKVERLTQRMAGMAFLGNFQDNLQMLTPQLNAIIAASA 227
Sbjct: 163 QYKELRRSVVQLILATDMQNHFEHTNKFQHHLNNLPFDRNKKEDRQMI---LNFLIKCGD 219
Query: 228 SVKSSQKLKQMLEIILALGN-YMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIAL 286
Sbjct: 220 ISNIARPWHLNFEWSLRVSDEFFQQSHYETICGYPVTP---FMDKTKTTRARIAADFIDF 276
Query: 287 TVKEKYPDLANFWHELHFVEKAAAVSLEN 315
Sbjct: 277 VASPLFQSMAKFLKESQFLLKVISKNREN 305
>PAIRED Paired domain (A HTH domain)
Length = 127
Score = 22.4 bits (47), Expect = 1.6
Identities = 10/27 (37%), Positives = 10/27 (37%), Gaps = 5/27 (18%)
Query: 375 GESPKTTPPSVFFPVFVRFIRSYKEAE 401
Sbjct: 70 GSKPRVTTPTV-----VKHIRTYKQRD 91
>KIN Protein kinase domain
Length = 313
Score = 21.6 bits (45), Expect = 2.2
Identities = 10/53 (18%), Positives = 10/53 (18%), Gaps = 1/53 (1%)
Query: 300 HELH-FVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEG 351
Sbjct: 117 TDLHQIITSPQPLSDDHCQYFVYQMLRGLKHIHSANVLHRDLKPSNLLINEDC 169
>SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain)
Length = 219
Score = 21.5 bits (45), Expect = 2.3
Identities = 5/20 (25%), Positives = 5/20 (25%)
Query: 393 FIRSYKEAEQENEARKKQEE 412
Sbjct: 200 YGPLYWKHRKKREEFVPQEE 219
>CALC Calcineurin like Phosphoesterase domain
Length = 274
Score = 21.3 bits (44), Expect = 2.8
Identities = 18/103 (17%), Positives = 18/103 (17%), Gaps = 6/103 (5%)
Query: 242 ILALGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWHE 301
Sbjct: 123 ALLLDSQVYGVPHGQLSQHQLDLLKETLGKNPERYTLVVLHHHLLPTNSAWLD----QHN 178
Query: 302 LHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRN 344
Sbjct: 179 LRNSHELAEVLAPF--TNVKAILYGHIHQEVNSEWNGYQVMAT 219
>INSL Insulinase like Metallo protease domain
Length = 433
Score = 21.4 bits (45), Expect = 3.1
Identities = 7/25 (28%), Positives = 7/25 (28%)
Query: 364 EEAYNAVVRYFGESPKTTPPSVFFP 388
Sbjct: 214 KEVEEEVMKTFGKEEGRPVPKVQIP 238
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 20.7 bits (43), Expect = 3.8
Identities = 26/108 (24%), Positives = 26/108 (24%), Gaps = 26/108 (24%)
Query: 388 PVFVRFIRS--YKEAEQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAE 445
Sbjct: 616 PMLLQFFKSQGYRDG-PGNPLRHNYEGTLRD--LLQFFK------PRQPKKLYYQQLKMK 666
Query: 446 L----RRRQAK----------EHRPVYEGKDGTIEDII-TVLKSVPFT 478
Sbjct: 667 ITDFENRRSFKCIWLNSQFREEEITLYPDKHGCVRDLLEECKKAVELG 714
Score = 19.6 bits (40), Expect = 9.8
Identities = 8/35 (22%), Positives = 8/35 (22%)
Query: 67 ELDDEKILEDKFEELFKTKAQGPALDLICSKNKTA 101
Sbjct: 261 KFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNA 295
>SH3 Src Homology domain 3
Length = 90
Score = 20.5 bits (43), Expect = 4.6
Identities = 4/16 (25%), Positives = 4/16 (25%)
Query: 2 PPPPDKCPPAPPLPGA 17
Sbjct: 1 PRVQAWSPPVRGIPQL 16
>14-3-3 14-3-3 protein alpha Helical domain
Length = 270
Score = 20.3 bits (42), Expect = 6.4
Identities = 6/30 (20%), Positives = 6/30 (20%)
Query: 399 EAEQENEARKKQEEVMREKQLAQEAKKLDA 428
Sbjct: 241 AAAAGGNTEGAQENAPSNAPEGEAEPKADA 270
>CYCLIN Cyclin/TFIIB domain
Length = 317
Score = 19.9 bits (41), Expect = 7.9
Identities = 13/112 (11%), Positives = 13/112 (11%), Gaps = 6/112 (5%)
Query: 308 AAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEGKLDKLQRDAKTAEEAY 367
Sbjct: 208 LTAILSSASRAGITMESYLSESLMLK----ENRTCLSQLLDIMKSMRNLVKKYEPPRSEE 263
Query: 368 NAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQL 419
Sbjct: 264 VAVLKQKLERCHSAELALNVI--TKKRKGYEDDDYVSKKSKHEEEEWTDDDL 313
>RHOGAP RHO-type GTPase GTP hydrolysis activating protein
Length = 194
Score = 19.4 bits (40), Expect = 9.5
Identities = 9/79 (11%), Positives = 9/79 (11%), Gaps = 9/79 (11%)
Query: 384 SVFFPVFVRFIRSYKEA----EQENEARKKQEEVMREKQLAQEAKKLDAKT----PSQRN 435
Sbjct: 95 EQMCKTYSEFCSRHSKALKFYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQR- 153
Query: 436 KWQQQELIAELRRRQAKEH 454
Sbjct: 154 ITKYPLLISRILQHSHGIE 172
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 13
Number of calls to ALIGN: 17
Length of query: 500
Total length of test sequences: 20182
Effective length of test sequences: 16235.0
Effective search space size: 7512734.8
Initial X dropoff for ALIGN: 25.0 bits
Y. Wolf's SCOP PSSM
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo
sapiens]
(500 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2131476 [80..370] Zn-dependent exopeptidases 29 0.15
gi|628630 [25..232] Ribosome inactivating proteins (RIP) 28 0.50
gi|1001472 [191..704] N-terminal nucleophile aminohydrolases... 26 1.9
gi|576299 [1..317] alpha/beta-Hydrolases 24 3.7
gi|442637 [1..263] Trypsin-like serine proteases 24 4.2
gi|417068 [395..693] Ribonuclease H-like motif 24 4.3
gi|2809057 [242..451] Metzincin-like 24 7.3
gi|629488 [18..291] Ribosome inactivating proteins (RIP) 23 8.1
>gi|2131476 [80..370] Zn-dependent exopeptidases
Length = 291
Score = 29.3 bits (65), Expect = 0.15
Identities = 8/82 (9%), Positives = 8/82 (9%), Gaps = 9/82 (10%)
Query: 58 QIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLI--CSKNKTAQKAASKVTL----L 111
Sbjct: 15 NIDKGSMHKNLAK---FTSFYTRYYKSDHGFESAEWLAATIANITKDIPQDTLTIEHFDH 71
Query: 112 EANRAKNLAITLRKAGRSAEEI 133
Sbjct: 72 KEWKQYSIIVRVTGSTTPEDII 93
>gi|628630 [25..232] Ribosome inactivating proteins (RIP)
Length = 208
Score = 27.6 bits (60), Expect = 0.50
Identities = 17/46 (36%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 136 AIHTFDLQTLPVDFVECLMRFLPTEAEVKLLRQYERE-RQPLEELA 180
Sbjct: 140 ALMEFSGNTMTRDASRAVLRFVTVTAEALRFRQIQREFRQALSETA 185
>gi|1001472 [191..704] N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Length = 514
Score = 25.7 bits (56), Expect = 1.9
Identities = 27/125 (21%), Positives = 27/125 (21%), Gaps = 19/125 (15%)
Query: 203 AFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMNSSKRGAVYGFKL 262
Sbjct: 294 QFKQKVFDSQMELGDRIVPLLVSAAKVLANPIGIEAAEVLQAWDKQANPDSRGAVL-FML 352
Query: 263 QSLDLLLDT------------------KSTDRKMTLLHFIALTVKEKYPDLANFWHELHF 304
Sbjct: 353 WALTIGADKVLGGQWNPADPLNTPSGMADINKFMAVLEGVAAQVKFLYDDLAISWGEVVQ 412
Query: 305 VEKAA 309
Sbjct: 413 MQVGN 417
>gi|576299 [1..317] alpha/beta-Hydrolases
Length = 317
Score = 24.4 bits (52), Expect = 3.7
Identities = 22/171 (12%), Positives = 22/171 (12%), Gaps = 21/171 (12%)
Query: 183 DRFMLLFSKVERLTQRMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEII 242
Sbjct: 145 DALAVSAPSVWQQTTGSALTTALRNAGGLTQIVPTTNLYSATDEIVQPQVSNSPLDSSYL 204
Query: 243 LALGNYMNSSKRGAVYGFKLQSL---------------DLLLDTKSTD---RKMTLLHFI 284
Sbjct: 205 FNGKNVQAQAVCGPLFVIDHAGSLTSQFSYVVGRSALRSTTGQARSADYGITDCNPLPAN 264
Query: 285 ALTVKEKYPDLANFWHELHFVEKAAAVSLENVLLDVKELGRGMELIRRECS 335
Sbjct: 265 DLTPEQKVAAAALLAPAAAAIVAGPKQNCEP---DLMPYARPFAVGKRTCS 312
>gi|442637 [1..263] Trypsin-like serine proteases
Length = 263
Score = 24.5 bits (52), Expect = 4.2
Identities = 14/27 (51%), Positives = 14/27 (51%)
Query: 101 AQKAASKVTLLEANRAKNLAITLRKAG 127
Sbjct: 107 ATYATSDFTLLELNNAANPAFNLFWAG 133
>gi|417068 [395..693] Ribonuclease H-like motif
Length = 299
Score = 24.2 bits (52), Expect = 4.3
Identities = 4/85 (4%), Positives = 4/85 (4%), Gaps = 11/85 (12%)
Query: 70 DEKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLAITLRKAGRS 129
Sbjct: 67 VAGAVVQWLRDNLRLIDK----SEDVGPIASTVPDSGGVVFVPAFSGLFAPYWD------ 116
Query: 130 AEEICRAIHTFDLQTLPVDFVECLM 154
Sbjct: 117 -PDARATIMGMSQFTTASHIARAAV 140
>gi|2809057 [242..451] Metzincin-like
Length = 210
Score = 23.7 bits (51), Expect = 7.3
Identities = 10/62 (16%), Positives = 10/62 (16%), Gaps = 5/62 (8%)
Query: 325 RGMELIRRECSIHDNS----VLRNFLSTNEGKLDKLQRDAKTAEEAYNAVVRYF-GESPK 379
Sbjct: 51 KILVIYEEQKGPEVTSNAALTLRNFCNWQKQHNSPSDRDPEHYDTAILFTRQDLCGSHTC 110
Query: 380 TT 381
Sbjct: 111 DT 112
>gi|629488 [18..291] Ribosome inactivating proteins (RIP)
Length = 274
Score = 23.3 bits (50), Expect = 8.1
Identities = 15/94 (15%), Positives = 15/94 (15%), Gaps = 7/94 (7%)
Query: 346 LSTNEGKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENE 405
Sbjct: 128 MESKGGARTKLGLGKITLKSRMGKIYGKDATDQKQYQKNEAEFLLI-AVQMVTEA----- 181
Query: 406 ARKKQ-EEVMREKQLAQEAKKLDAKTPSQRNKWQ 438
Sbjct: 182 SRFKYIENKVKAKFDDANGYQPDPKAISLEKNWD 215
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 8
Number of calls to ALIGN: 8
Length of query: 500
Total length of test sequences: 256703
Effective length of test sequences: 204927.0
Effective search space size: 93454301.3
Initial X dropoff for ALIGN: 25.0 bits
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
calculation of internal repeats with prospero
***** PROSPERO v1.3 Fri Jan 19 18:10:42 2001 *****
Copyright 2000, Richard Mott, Wellcome Trust Centre for Human Genetics, University of Oxford
For help see http://www.well.ox.ac.uk/ariadne For usage use -help
using gap penalty 11+1k
using matrix BLOSUM62
printing all alignments with eval < 0.100000
using sequence1 Tem21.2_gi|7328133|emb|CAB82400.1|
using self-comparison