analysis of sequence from tem35
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGCENVCYDAFAP
LSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMM
YPEMELESDKENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYGFQVHPFYVCS
RLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEMLHLGFGTIRDSLNSKRRELEDPGAYNYPFT
WNTPSAPPGYNIAVKPDQIQYTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD
LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|4885169|ref|NP_005488.1|
. . . . .
1 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSK 50
___HHHHHHHHHHH_____HHHHHHHHHHHHHHHHHH_____EEE_____
. . . . .
51 FVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIA 100
_______________________EEEHHHHHHHH____EEEEHHHHHHHH
. . . . .
101 KMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELESDK 150
HHH_____HHHHHHHHHHHHHHHHHHHHHHHH_________HHHHHHHHH
. . . . .
151 ENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYG 200
HHHHH__________EEEE____HHHHHHHHHHHHHHHHHHHHHHEEEEE
. . . . .
201 FQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEM 250
EE_____EEE________EEEE_____HHHHHHHHH_____HHHHHHHHH
. . . . .
251 LHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ 300
HH__________HHHHHHH_____________________EEEE____EE
. . . . .
301 YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD 350
EEE__HHHHHHHH___HHHHHHHH__________HHHHHHHHHHHHHHHH
. . . .
351 LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI 396
HHHHHHH__________HHHHHH_______________________
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 47.6 %
beta-contents : 14.5 %
coil-contents : 37.9 %
class : mixed
method : 2
alpha-contents : 36.4 %
beta-contents : 12.9 %
coil-contents : 50.7 %
class : mixed
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-29.22 -1.21 -0.14 0.00 -4.00 0.00 0.00 -0.56 -0.13 -7.81 -2.74 -12.00 -12.00 -12.00 -12.00 0.00 -93.81
-23.63 -0.96 -1.41 -1.27 -4.00 0.00 0.00 0.00 -0.57 -9.26 -2.74 -12.00 -12.00 -12.00 -12.00 0.00 -91.84
ID: gi|4885169|ref|NP_005488.1| AC: xxx Len: 350 1:I 333 Sc: -91.84 Pv: 9.521474e-01 NO_GPI_SITE
GPI: learning from protozoa
-35.28 -1.02 -0.74 -0.49 -4.00 0.00 0.00 -1.18 -0.24 -5.77 -9.80 -12.00 -12.00 -12.00 -12.00 0.00 -106.53
-14.54 -1.02 -0.03 -0.21 0.00 0.00 0.00 0.00 -0.11 -7.90 -9.80 -12.00 -12.00 -12.00 -12.00 0.00 -81.62
ID: gi|4885169|ref|NP_005488.1| AC: xxx Len: 350 1:I 333 Sc: -81.62 Pv: 5.383399e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|4885169| 0.727 41 Y 0.774 41 Y 0.956 29 Y 0.549 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|4885169| 0.347 346 N 0.318 40 N 0.927 31 Y 0.395 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|4885169| 0.389 96 N 0.401 40 Y 0.992 28 Y 0.517 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
1-127 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIV
FRIVLTAVGGESIYYDEQSKFVCNTEQPGC
ENVCYDAFAPLSHVRFWVFQIILVATPSVM
YLGYAIHKIAKMEHGEADKKAARSKPYAMR
WKQHRAL
eeteedneed 128-137
138-396 PMMYPEMELESDKENKEQSQPKPKHDGRRR
IREDGLMKIYVLQLLARTVFEVGFLIGQYF
LYGFQVHPFYVCSRLPCPHKIDCFISRPTE
KTIFLLIMYGVTGLCLLLNIWEMLHLGFGT
IRDSLNSKRRELEDPGAYNYPFTWNTPSAP
PGYNIAVKPDQIQYTELSNAKIAYKQNKAN
TAQEQQYGSHEENLPADLEALQREIRMAQE
RLDLAVQAYSHQNNPHGPREKKAKVGSKAG
SNKSTASSKSGDGKNSVWI
low complexity regions: SEG 25 3.0 3.3
>gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
1-126 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIV
FRIVLTAVGGESIYYDEQSKFVCNTEQPGC
ENVCYDAFAPLSHVRFWVFQIILVATPSVM
YLGYAIHKIAKMEHGEADKKAARSKPYAMR
WKQHRA
leeteedneedpmmypemelesdkenkeqs 127-159
qpk
160-367 PKHDGRRRIREDGLMKIYVLQLLARTVFEV
GFLIGQYFLYGFQVHPFYVCSRLPCPHKID
CFISRPTEKTIFLLIMYGVTGLCLLLNIWE
MLHLGFGTIRDSLNSKRRELEDPGAYNYPF
TWNTPSAPPGYNIAVKPDQIQYTELSNAKI
AYKQNKANTAQEQQYGSHEENLPADLEALQ
REIRMAQERLDLAVQAYSHQNNPHGPRE
kkakvgskagsnkstassksgdgkns 368-393
394-396 VWI
low complexity regions: SEG 45 3.4 3.75
>gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
1-396 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIV
FRIVLTAVGGESIYYDEQSKFVCNTEQPGC
ENVCYDAFAPLSHVRFWVFQIILVATPSVM
YLGYAIHKIAKMEHGEADKKAARSKPYAMR
WKQHRALEETEEDNEEDPMMYPEMELESDK
ENKEQSQPKPKHDGRRRIREDGLMKIYVLQ
LLARTVFEVGFLIGQYFLYGFQVHPFYVCS
RLPCPHKIDCFISRPTEKTIFLLIMYGVTG
LCLLLNIWEMLHLGFGTIRDSLNSKRRELE
DPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ
YTELSNAKIAYKQNKANTAQEQQYGSHEEN
LPADLEALQREIRMAQERLDLAVQAYSHQN
NPHGPREKKAKVGSKAGSNKSTASSKSGDG
KNSVWI
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
>gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGC
ENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMR
WKQHRALeeteedneedpmmYPemelesdkenkeqsqpkpkHDGRRRIREDGLMKIYVLQ
LLARTVFEVGFLIGQYFLYGFQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTG
LCLLLNIWEMLHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ
YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLDLAVQAYSHQN
NPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI
1 - 127 MSWSFLTRLL EEIHNHSTFV GKIWLTVLIV FRIVLTAVGG ESIYYDEQSK FVCNTEQPGC
ENVCYDAFAP LSHVRFWVFQ IILVATPSVM YLGYAIHKIA KMEHGEADKK AARSKPYAMR
WKQHRAL
128 - 140 eet eedneedpmm
141 - 142 YP
143 - 161 emelesdk enkeqsqpkp k
162 - 396 HDGRRRIRE DGLMKIYVLQ LLARTVFEVG FLIGQYFLYG FQVHPFYVCS RLPCPHKIDC F
ISRPTEKTI FLLIMYGVTG LCLLLNIWEM LHLGFGTIRD SLNSKRRELE DPGAYNYPFT W
NTPSAPPGY NIAVKPDQIQ YTELSNAKIA YKQNKANTAQ EQQYGSHEEN LPADLEALQR E
IRMAQERLD LAVQAYSHQN NPHGPREKKA KVGSKAGSNK STASSKSGDG KNSVWI
low complexity regions: DUST
>gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGC
ENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMR
WKQHRALEETEEDNEEDPMMYPEMELESDKENKEQSQPKPKHDGRRRIREDGLMKIYVLQ
LLARTVFEVGFLIGQYFLYGFQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTG
LCLLLNIWEMLHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ
YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLDLAVQAYSHQN
NPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|4885169|ref|NP_005488.1|
sequence: 350 amino acids, 23 residue(s) in coiled coil state
Coil 1 * 327* 0*
. | . | . | . | . | . 60
MSWSFLTRLL EEIHNHSTFV GKIWLTVLIV FRIVLTAVGG ESIYYDEQSK FVCNTEQPGC
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
ENVCYDAFAP LSHVRFWVFQ IILVATPSVM YLGYAIHKIA KMEHGEADKK AARSKPYAMR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 180
WKQHRALEET EEDNEEDPMM YPEMELESDK ENKEQSQPKP KHDGRRRIRE DGLMKIYVLQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~677777777 7777773~~~ ~~44444444 4444442~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 240
LLARTVFEVG FLIGQYFLYG FQVHPFYVCS RLPCPHKIDC FISRPTEKTI FLLIMYGVTG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 300
LCLLLNIWEM LHLGFGTIRD SLNSKRRELE DPGAYNYPFT WNTPSAPPGY NIAVKPDQIQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~111 * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- -------efg * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~2444 4444444444 4~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . |
YTELSNAKIA YKQNKANTAQ EQQYGSHEEN LPADLEALQR EIRMAQERLD
1111111111 1111111111 111~~~2799 9999999999 9999999999
abgabcdefg abcdefgabc def---gabc defgabcdef gabcdefgab
~~~~~~~~~~ ~~~~~~~~~~ ~111136899 9999999999 9999999999
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~399 9999999999 9999999998
~~~~~~~~~~ ~~~~~~~~~~ ~444444444 4444444444 4444444444
~~~~~~~~~~ ~~~~~~~111 1111111155 5599999999 9999999999
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem35.___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: tem35.___inter___
(1 sequences)
MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSK
FVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIA
KMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELESDK
ENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYG
FQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEM
LHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ
YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD
LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI
(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 2 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 20 40 1.180 Certain
2 76 96 1.653 Certain
3 185 205 0.952 Putative
4 228 248 1.946 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4
Loop length 19 35 88 22 148
K+R profile 3.00 + +
2.00 4.00
CYT-EXT prof - -0.82 0.70
- -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -3.00
Tm probability: 0.88
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 2.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -0.12
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 2 4
Loop length 19 35 131 148
K+R profile 3.00 +
2.00 +
CYT-EXT prof - -0.42
- 0.70
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 2.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
"tem35" 396
20 40 #t 1.18021
76 96 #t 1.65313
185 205 #f 0.952083
228 248 #t 1.94583
************************************
*TOPPREDM with prokaryotic function*
************************************
tem35.___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: tem35.___inter___
(1 sequences)
MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSK
FVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIA
KMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELESDK
ENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYG
FQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEM
LHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ
YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD
LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI
(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 2 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 20 40 1.180 Certain
2 76 96 1.653 Certain
3 185 205 0.952 Putative
4 228 248 1.946 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4
Loop length 19 35 88 22 148
K+R profile 3.00 + +
2.00 4.00
CYT-EXT prof - -0.82 0.70
- -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -3.00
Tm probability: 0.88
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 2.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -0.12
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 2 4
Loop length 19 35 131 148
K+R profile 3.00 +
2.00 +
CYT-EXT prof - -0.42
- 0.70
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 2.0000
POS: 2.0000
-> Orientation: N-in
CYT-EXT difference: -1.12
-> Orientation: N-in
----------------------------------------------------------------------
"tem35" 396
20 40 #t 1.18021
76 96 #t 1.65313
185 205 #f 0.952083
228 248 #t 1.94583
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem35.___saps___
SAPS. Version of April 11, 1996.
Date run: Thu Dec 21 12:12:35 2000
File: /people/maria/tem35.___saps___
ID gi|4885169|ref|NP_005488.1|
DE gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
number of residues: 396; molecular weight: 45.5 kdal
1 MSWSFLTRLL EEIHNHSTFV GKIWLTVLIV FRIVLTAVGG ESIYYDEQSK FVCNTEQPGC
61 ENVCYDAFAP LSHVRFWVFQ IILVATPSVM YLGYAIHKIA KMEHGEADKK AARSKPYAMR
121 WKQHRALEET EEDNEEDPMM YPEMELESDK ENKEQSQPKP KHDGRRRIRE DGLMKIYVLQ
181 LLARTVFEVG FLIGQYFLYG FQVHPFYVCS RLPCPHKIDC FISRPTEKTI FLLIMYGVTG
241 LCLLLNIWEM LHLGFGTIRD SLNSKRRELE DPGAYNYPFT WNTPSAPPGY NIAVKPDQIQ
301 YTELSNAKIA YKQNKANTAQ EQQYGSHEEN LPADLEALQR EIRMAQERLD LAVQAYSHQN
361 NPHGPREKKA KVGSKAGSNK STASSKSGDG KNSVWI
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 27( 6.8%); C : 7( 1.8%); D : 15( 3.8%); E : 33( 8.3%); F : 16( 4.0%)
G : 23( 5.8%); H : 13( 3.3%); I : 23( 5.8%); K : 27( 6.8%); L : 34( 8.6%)
M : 11( 2.8%); N : 18( 4.5%); P : 21( 5.3%); Q : 19( 4.8%); R : 20( 5.1%)
S : 25( 6.3%); T : 17( 4.3%); V : 21( 5.3%); W : 7( 1.8%); Y : 19( 4.8%)
KR : 47 ( 11.9%); ED : 48 ( 12.1%); AGP : 71 ( 17.9%);
KRED : 95 ( 24.0%); KR-ED : -1 ( -0.3%); FIKMNY : 114 ( 28.8%);
LVIFM : 105 ( 26.5%); ST : 42 ( 10.6%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0000000+00 --00000000 0+00000000 0+00000000 -0000--00+ 00000-0000
61 -0000-0000 0000+00000 0000000000 0000000+00 +0-00-0-++ 00+0+0000+
121 0+00+00--0 ---0---000 00-0-0-0-+ -0+-0000+0 +0-0+++0+- -000+00000
181 000+000-00 0000000000 0000000000 +00000+0-0 000+00-+00 0000000000
241 00000000-0 00000000+- 0000+++-0- -000000000 0000000000 0000+0-000
301 00-0000+00 0+00+00000 -000000--0 000-0-000+ -0+000-+0- 0000000000
361 00000+-++0 +000+0000+ 00000+00-0 +00000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 10/30 or 14/45 or 17/60): none
Negative charge clusters (cmin = 10/30 or 14/45 or 17/60):
1)*From 128 to 149: EETEEDNEEDPMMYPEMELESD
--0---0---00000-0-0-0-
quartile: 2; size: 22, +count: 0, -count: 12, 0count: 10; t-value: 6.10 *
E: 9 (40.9%); D: 3 (13.6%); M: 3 (13.6%);
Mixed charge clusters (cmin = 16/30 or 22/45 or 27/60):
1)*From 98 to 171: see sequence above
see sequence above
quartile: 1; size: 74, +count: 17, -count: 20, 0count: 37; t-value: 5.24 *
K: 10 (13.5%); E: 14 (18.9%);
B. HIGH SCORING (UN)CHARGED SEGMENTS.
There are no high scoring positive charge segments.
______________________________________
High scoring negative charge segments:
score= 2.00 frequency= 0.121 ( ED )
score= 0.00 frequency= 0.000 ( BZX )
score= -1.00 frequency= 0.760 ( LAGSVTIPNFQYHMCW )
score= -2.00 frequency= 0.119 ( KR )
Expected score/letter: -0.755
M_0.01= 11.19; M_0.05= 9.25
1) From 128 to 147: length= 20, score=13.00 **
(pocket at 138 to 142: length= 5, score=-5.00)
128 EETEEDNEED |PMMYP| EMELE
E: 9(45.0%); D: 2(10.0%); P: 2(10.0%); M: 3(15.0%);
There are no high scoring mixed charge segments.
There are no high scoring uncharged segments.
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 5 | 7 | 33 | 9 | 10 | 13 | 11 | 11 | 15 | 7 | 9 |
lmin1 6 | 6 | 9 | 40 | 12 | 12 | 16 | 14 | 14 | 18 | 9 | 11 |
lmin2 7 | 7 | 10 | 45 | 13 | 13 | 17 | 15 | 16 | 20 | 10 | 13 |
(Significance level: 0.010000; Minimal displayed length: 6)
(-) 8(2,0,0); at 128- 137: EETEEDNEED
(2. quartile) --0---0---
Run count statistics:
+ runs >= 3: 2, at 165; 265;
- runs >= 3: 2, at 131; 135;
* runs >= 5: 0
0
runs >= 22: 3, at 76; 189; 272;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
__________________________________
High scoring hydrophobic segments:
2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ)
-8.00 (KEDR)
Expected score/letter: -2.149
M_0.01= 23.07; M_0.05= 19.07
1) From 230 to 245: length= 16, score=22.00 *
230 IFLLIMYGVT GLCLLL
L: 6(37.5%); G: 2(12.5%); I: 2(12.5%);
____________________________________
High scoring transmembrane segments:
5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST)
-6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED)
Expected score/letter: -4.275
M_0.01= 51.17; M_0.05= 42.08; M_0.30= 31.26
1) From 23 to 40: length= 18, score=40.00
(pocket at 32 to 32: length= 1, score=-16.00)
23 IWLTVLIVF |R| IVLTAVGG
L: 3(16.7%); G: 2(11.1%); V: 4(22.2%); T: 2(11.1%);
I: 3(16.7%);
2) From 76 to 96: length= 21, score=35.00
(pocket at 86 to 88: length= 3, score=-10.00)
(pocket at 80 to 80: length= 1, score=-10.00)
76 FWVF |Q| IILVA |TPS| VMYLGYA I
V: 3(14.3%); I: 3(14.3%);
3) From 230 to 245: length= 16, score=52.00 **
230 IFLLIMYGVT GLCLLL
L: 6(37.5%); G: 2(12.5%); I: 2(12.5%);
2. SPACINGS OF C.
H2N-52-C-6-C-3-C-144-C-4-C-5-C-21-C-154-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-13-H-1-H-36-C-6-C-3-C-8-H-23-H-6-H-19-H-37-H-41-H-4-C-4-C-1-H-3-C-21-C-9-H-74-H-30-H-4-H-33-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
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
Aligned matching blocks:
[ 22- 31] +iaioiiiii
[ 75- 84] +iaiiniiii
with superset:
[ 22- 29] +iaioiii
[ 75- 82] +iaiinii
[ 175- 182] +iaiinii
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 22 (Expected range: 7-- 35)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 7 (6-10) 3 (11-20) 5 (>=21) 8
3. Clusters of amino acid multiplets (cmin = 10/30 or 13/45 or 16/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 12 (Expected range: 0-- 20)
4 +plets (f+: 11.9%), 8 -plets (f-: 12.1%)
Total number of charge altplets: 10 (Critical number: 23)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 4 (6-10) 0 (11-20) 2 (>=21) 7
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
13- 52 10 I......... 4 4 0
378- 389 3 S.. 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9)
Location Period Element Copies Core Errors
23- 36 2 i. 7 7 0
101- 156 7 *...... 8 8 0
129- 138 2 -. 5 5 0
129- 176 8 *.*0..*. 6 6 /0/./2/2/././0/./
143- 152 2 -0 5 5 /0/1/
159- 172 2 *. 7 7 0
230- 235 1 i 6 6 0
232- 255 3 i.. 8 8 0
--------------------------------------------------------------------------------
SPACING ANALYSIS.
There are no unusual spacings.
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
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: tem35
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
connexin Connexin 510.0 1.7e-149 1
cytochr_b559 Cytochrome b559, alpha (gene psbE) and b 0.9 89 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
cytochr_b559 1/1 59 93 .. 1 33 [] 0.9 89
connexin 1/1 1 253 [. 1 246 [] 510.0 1.7e-149
Alignments of top-scoring domains:
cytochr_b559: domain 1 of 1, from 59 to 93: score 0.9, E = 89
*->ttntserpvtypIftvRwla..iHalaiPtvFflG<-*
+ ++ + p vR+++ +i +a P+v lG
gi|4885169 59 GCENVCYDAFAPLSHVRFWVfqIILVATPSVMYLG 93
connexin: domain 1 of 1, from 1 to 253: score 510.0, E = 1.7e-149
*->MGDWsfLgrLLegVnkHSTviGKvWLtVLFIFRILvLgvAAEsVWGD
M +WsfL+rLLe++++HST++GK+WLtVL++FRI++++v++Es+++D
gi|4885169 1 M-SWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYD 46
EQsdFvCNTqQPGCeNVCYDqaFPISHvRlWvLQiIFVSTPsLlYlgHVa
EQs+FvCNT+QPGCeNVCYD+++P+SHvR+Wv+QiI+V+TPs++Ylg
gi|4885169 47 EQSKFVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLG--- 93
YrvrreeKrkekeeelrrl.ask.lsveeakkqgaeeae.ekeedpplva
Y++++++K+ e+ e +++ +sk+ +++++++ +ee e+++eedp++++
gi|4885169 94 YAIHKIAKM-EHGEADKKAaRSKpYAMRWKQHRALEETEeDNEEDPMMYP 142
ek.........qklkikde.dGkvrir.GgLlwTYvlSilFKtifEvgFL
e + +++++++++ k+++dG++rir++gL+ +Yvl++l +t+fEvgFL
gi|4885169 143 EMelesdkenkEQSQPKPKhDGRRRIReDGLMKIYVLQLLARTVFEVGFL 192
ygQYlLYpGFtlsplyvCerayPCPhtVDCFvSRPTEKTIFiiFMLvVsa
+gQY+LY GF++ p yvC+r PCPh++DCF+SRPTEKTIF+++M++V +
gi|4885169 193 IGQYFLY-GFQVHPFYVCSRL-PCPHKIDCFISRPTEKTIFLLIMYGVTG 240
isLlLNlaElvhL<-*
++LlLN++E++hL
gi|4885169 241 LCLLLNIWEMLHL 253
//
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: tem35
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
connexin Connexin 508.1 6.5e-149 1
NifU_N NifU-like N terminal domain 1.9 38 1
cytochr_b559 Cytochrome b559, alpha (gene psbE) and 0.9 89 1
MOZ_SAS MOZ/SAS family 0.6 37 1
AAA ATPases associated with various cellula -0.9 1e+02 1
Synaptophysin Synaptophysin / synaptoporin -1.2 66 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Synaptophysin 1/1 63 86 .. 1 26 [. -1.2 66
cytochr_b559 1/1 59 93 .. 1 33 [] 0.9 89
MOZ_SAS 1/1 168 180 .. 192 204 .] 0.6 37
connexin 1/1 1 253 [. 1 246 [] 508.1 6.5e-149
AAA 1/1 333 348 .. 201 216 .] -0.9 1e+02
NifU_N 1/1 344 363 .. 110 129 .] 1.9 38
Alignments of top-scoring domains:
Synaptophysin: domain 1 of 1, from 63 to 86: score -1.2, E = 66
*->qfrvvkePLgfvkvlqwvFAiFAFAt<-*
+ ++PL +v wvF i At
gi|4885169 63 VCYDAFAPL--SHVRFWVFQIILVAT 86
cytochr_b559: domain 1 of 1, from 59 to 93: score 0.9, E = 89
*->ttntserpvtypIftvRwla..iHalaiPtvFflG<-*
+ ++ + p vR+++ +i +a P+v lG
gi|4885169 59 GCENVCYDAFAPLSHVRFWVfqIILVATPSVMYLG 93
MOZ_SAS: domain 1 of 1, from 168 to 180: score 0.6, E = 37
*->ikyykgqylqvLn<-*
i+++++ +++vL+
gi|4885169 168 IREDGLMKIYVLQ 180
connexin: domain 1 of 1, from 1 to 253: score 508.1, E = 6.5e-149
*->MGDWsfLgrLLegVnkHSTviGKvWLtVLFIFRILvLgvAAEsVWGD
M +WsfL+rLLe++++HST++GK+WLtVL++FRI++++v++Es+++D
gi|4885169 1 M-SWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYD 46
EQsdFvCNTqQPGCeNVCYDqaFPISHvRlWvLQiIFVSTPsLlYlgHVa
EQs+FvCNT+QPGCeNVCYD+++P+SHvR+Wv+QiI+V+TPs++Ylg
gi|4885169 47 EQSKFVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLG--- 93
YrvrreeKrkekeeelrrl.ask.lsveeakkqgaeeae.ekeedpplva
Y++++++K+ e+ e +++ +sk+ +++++++ +ee e+++eedp++++
gi|4885169 94 YAIHKIAKM-EHGEADKKAaRSKpYAMRWKQHRALEETEeDNEEDPMMYP 142
ek.........qklkikde.dGkvrir.GgLlwTYvlSilFKtifEvgFL
e + +++++++++ k+++dG++rir++gL+ +Yvl++l +t+fEvgFL
gi|4885169 143 EMelesdkenkEQSQPKPKhDGRRRIReDGLMKIYVLQLLARTVFEVGFL 192
ygQYlLYpGFtlsplyvCerayPCPhtVDCFvSRPTEKTIFiiFMLvVsa
+gQY+LY GF++ p yvC+r PCPh++DCF+SRPTEKTIF+++M++V +
gi|4885169 193 IGQYFLY-GFQVHPFYVCSRL-PCPHKIDCFISRPTEKTIFLLIMYGVTG 240
isLlLNlaElvhL<-*
++LlLN++E++hL
gi|4885169 241 LCLLLNIWEMLHL 253
AAA: domain 1 of 1, from 333 to 348: score -0.9, E = 1e+02
*->adlaalcreAalralr<-*
adl+al re +++ r
gi|4885169 333 ADLEALQREIRMAQER 348
NifU_N: domain 1 of 1, from 344 to 363: score 1.9, E = 38
*->LgqdalkaAiadYkgknlka<-*
++q++l A+ +Y + n+ +
gi|4885169 344 MAQERLDLAVQAYSHQNNPH 363
//
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: tem35
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [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: Thu Dec 21 12:14:34 2000
Sequence file: tem35
----------------------------------------
Sequence gi|4885169|ref|NP_005488.1| (396 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
15: NHST
379: NKST
Total matches: 2
Matching pattern PS00005 PKC_PHOSPHO_SITE:
148: SDK
226: TEK
257: TIR
264: SKR
378: SNK
384: SSK
Total matches: 6
Matching pattern PS00006 CK2_PHOSPHO_SITE:
130: TEED
148: SDKE
185: TVFE
257: TIRD
318: TAQE
326: SHEE
Total matches: 6
Matching pattern PS00007 TYR_PHOSPHO_SITE:
267: RELEDPGAY
Total matches: 1
Matching pattern PS00008 MYRISTYL:
373: GSKAGS
377: GSNKST
Total matches: 2
Matching pattern PS00009 AMIDATION:
163: DGRR
Total matches: 1
Matching pattern PS00407 CONNEXINS_1:
53: CNTEQPGCENVCYD
Total matches: 1
Matching pattern PS00408 CONNEXINS_2:
209: CSRLPCPHKIDCFISRP
Total matches: 1
Total no of hits in this sequence: 20
========================================
1314 pattern(s) searched in 1 sequence(s), 396 residues.
Total no of hits in all sequences: 20.
Search time: 00:00 min
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Profile Search
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with motif search against own library
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
argv[1]=P
argv[2]=-m /data/patterns/own/motif.fa
argv[4]=-seq tem35
***** 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, 396 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: tem35
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [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: tem35
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [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= gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD
(connexin 45) [Homo sapiens]
(396 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
CHROMO Chromodomain- A chromatin associated domain 26 0.12
KIN Protein kinase domain 22 1.6
ARR Arrestin domain 21 2.5
TBC Probable RAB-type GTPase GTP hydrolysis activating prote... 21 2.6
DHHC Novel zinc finger domain with DHHC signature 21 3.5
CALC Calcineurin like Phosphoesterase domain 21 3.6
UBA Ubiquitin pathway associated domain 20 4.0
ARM Armadillo repeat 20 6.5
S1 S1 RNA binding domain 19 7.9
KELCH Kelch repeat- beta propeller like domain 20 8.8
>CHROMO Chromodomain- A chromatin associated domain
Length = 66
Score = 25.6 bits (56), Expect = 0.12
Identities = 14/71 (19%), Positives = 14/71 (19%), Gaps = 9/71 (12%)
Query: 94 YAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEETEE--DNEEDPMMYPEMELESDKE 151
Sbjct: 2 FVVEKV------LDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFL-NSQKA 54
Query: 152 NKEQSQPKPKH 162
Sbjct: 55 GKEKDGTKRKS 65
>KIN Protein kinase domain
Length = 313
Score = 22.0 bits (46), Expect = 1.6
Identities = 14/58 (24%), Positives = 14/58 (24%), Gaps = 5/58 (8%)
Query: 94 YAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEE-----TEEDNEEDPMMYPEMEL 146
Sbjct: 57 VAIKKISKAFDNLKDTKRTLREIHLLRHFKHENLISIKDILKPNSKEQFEDVYIVSEL 114
>ARR Arrestin domain
Length = 454
Score = 21.4 bits (45), Expect = 2.5
Identities = 5/27 (18%), Positives = 5/27 (18%), Gaps = 1/27 (3%)
Query: 265 KRRELEDPGAYNYPFTWNTP-SAPPGY 290
Sbjct: 126 QERLKRKLGANAFPFWFEVAPKSASSV 152
>TBC Probable RAB-type GTPase GTP hydrolysis activating protein
Length = 225
Score = 21.0 bits (44), Expect = 2.6
Identities = 10/122 (8%), Positives = 10/122 (8%), Gaps = 30/122 (24%)
Query: 109 KKAARSKPYAMRWKQHRALEETEEDNEED-PMMYPEMELESDKENKEQSQPKPKHDGRRR 167
Sbjct: 21 SMEASTQRYLALLKLGPPSTTIYQKIKNDTSRTFQTDPNFRNRVSEDAL---------IR 71
Query: 168 IREDGLMKIY-------VLQLLARTVFEVGFLIGQYFLYGFQVHPFYVCSRLPCPHKIDC 220
Sbjct: 72 C-----LSCFAWQTQQRRQKTRFGRIPVSTYVQGMNVL----LAPLL----YSCPSEPMA 118
Query: 221 FI 222
Sbjct: 119 YQ 120
>DHHC Novel zinc finger domain with DHHC signature
Length = 217
Score = 20.9 bits (43), Expect = 3.5
Identities = 13/55 (23%), Positives = 13/55 (23%)
Query: 154 EQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYGFQVHPFYV 208
Sbjct: 26 QPSGPSPELQGQRSRRNGWSWPPHPLQIVAWLLYLFFAVIGFGILVPLLPHHWVP 80
>CALC Calcineurin like Phosphoesterase domain
Length = 274
Score = 20.5 bits (42), Expect = 3.6
Identities = 3/40 (7%), Positives = 3/40 (7%)
Query: 339 QREIRMAQERLDLAVQAYSHQNNPHGPREKKAKVGSKAGS 378
Sbjct: 183 HELAEVLAPFTNVKAILYGHIHQEVNSEWNGYQVMATPAT 222
>UBA Ubiquitin pathway associated domain
Length = 255
Score = 20.4 bits (42), Expect = 4.0
Identities = 14/42 (33%), Positives = 14/42 (33%), Gaps = 2/42 (4%)
Query: 316 ANTAQEQQYGSHEENL-PADLEALQREIRMAQERLDLAVQAY 356
Sbjct: 211 AGLGQGEGEGSFQVDYTPEDDQAISRLCELGFER-DLVIQVY 251
>ARM Armadillo repeat
Length = 532
Score = 19.9 bits (41), Expect = 6.5
Identities = 5/19 (26%), Positives = 5/19 (26%)
Query: 271 DPGAYNYPFTWNTPSAPPG 289
Sbjct: 509 DGSQAGFQFGGNQAPVPSG 527
>S1 S1 RNA binding domain
Length = 305
Score = 19.5 bits (40), Expect = 7.9
Identities = 7/51 (13%), Positives = 7/51 (13%), Gaps = 1/51 (1%)
Query: 288 PGYNIAVKPD-QIQYTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEA 337
Sbjct: 143 PRSHLMHKDNMDALVGQVLKAHILEANQDNNKLVLTQRRIQQAESMGKIAA 193
>KELCH Kelch repeat- beta propeller like domain
Length = 319
Score = 19.5 bits (40), Expect = 8.8
Identities = 5/25 (20%), Positives = 5/25 (20%), Gaps = 2/25 (8%)
Query: 3 WSFLTRLLEEIHNHSTFV--GKIWL 25
Sbjct: 154 WTMVAPLREGVSNAAVVSAKLKLFA 178
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 10
Number of calls to ALIGN: 10
Length of query: 396
Total length of test sequences: 20182
Effective length of test sequences: 16637.0
Effective search space size: 6025420.2
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= gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD
(connexin 45) [Homo sapiens]
(396 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|1817676 [157..389] Protein kinases (PK), catalytic core 26 1.1
gi|2493387 [94..456] Cytochrome P450 25 2.1
gi|1127061 [6..559] Single-stranded right-handed beta-helix 24 5.0
gi|730275 [335..617] beta-Lactamase/D-ala carboxypeptidase 23 6.1
>gi|1817676 [157..389] Protein kinases (PK), catalytic core
Length = 233
Score = 25.8 bits (55), Expect = 1.1
Identities = 4/55 (7%), Positives = 4/55 (7%)
Query: 94 YAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELES 148
Sbjct: 21 PVVLKGLVHSGDAEAQAMAMAERQFLAEVVHPSIVQIFNFVEHTDRHGDPVGYIV 75
>gi|2493387 [94..456] Cytochrome P450
Length = 363
Score = 25.1 bits (54), Expect = 2.1
Identities = 9/151 (5%), Positives = 9/151 (5%), Gaps = 9/151 (5%)
Query: 5 FLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGCENVC 64
Sbjct: 35 FCEQLRQKARTGTVFQLEPLTLRL-TVDTICSVTLYVVTPVGRWPFLTPDLEI---HSST 90
Query: 65 YDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMRWKQH 124
Sbjct: 91 TKLRTTPLPQRCNGRSN----GPRLELPSTPLRRYLTVRPLVMWYNNRLMNRFIDQEVDR 146
Query: 125 RALEETEEDNEEDPMMYPEMELESDKENKEQ 155
Sbjct: 147 A-YREQSGRQSKSVISLALRDYMKEKDGSLE 176
>gi|1127061 [6..559] Single-stranded right-handed beta-helix
Length = 554
Score = 24.0 bits (51), Expect = 5.0
Identities = 19/73 (26%), Positives = 19/73 (26%), Gaps = 1/73 (1%)
Query: 314 NKANTAQEQQYGSHEENLPADLEALQREIRMAQERLDLAVQAYSHQNNPHGPREKKAKVG 373
Sbjct: 424 NVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGA-LYSHINGGAGSGSAYTQLT 482
Query: 374 SKAGSNKSTASSK 386
Sbjct: 483 AISGSTPDAVSLK 495
>gi|730275 [335..617] beta-Lactamase/D-ala carboxypeptidase
Length = 283
Score = 23.4 bits (50), Expect = 6.1
Identities = 5/31 (16%), Positives = 5/31 (16%)
Query: 286 APPGYNIAVKPDQIQYTELSNAKIAYKQNKA 316
Sbjct: 230 QVPGVEVAGKTGTTNFDDNEVKRYNIASGGA 260
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 4
Number of calls to ALIGN: 4
Length of query: 396
Total length of test sequences: 256703
Effective length of test sequences: 208388.0
Effective search space size: 74181392.3
Initial X dropoff for ALIGN: 25.0 bits