analysis of sequence from tem21_1
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
MGTLSAPPCTQRIKWKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKDVLLLVHNLPQNLTGYIWYKG
QMRDLYHYITSYVVDGEIIIYGPAYSGRETAYSNASLLIQNVTREDAGSYTLHIIKGDDGTRGVTGRFTF
TLHLETPKPSISSSNLNPRETMEAVSLTCDPETPDASYLWWMNGQSLPMTHSLKLSETNRTLFLLGVTKY
TAGPYECEIRNPVSASRSDPVTLNLLPKLPKPYITINNLNPRENKDVLNFTCEPKSENYTYIWWLNGQSL
PVSPRVKRPIENRILILPSVTRNETGPYQCEIRDRYGGVRSDPVTLNVLYGPDLPRIYPSFTYYRSGEVL
YLSCSADSNPPAQYSWTINEKFQLPGQKLFIRHITTKHSGLYVCSVRNSATGKESSKSMTVEVSEAL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> tem21_1gi|5902030|ref|NP_008836.1|
. . . . .
1 MGTLSAPPCTQRIKWKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKD 50
_________EEEEE_HHHHHHHHHHHH_________EEE__________E
. . . . .
51 VLLLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRET 100
EEEEE__________EEE_______EEEEEEEEE__EEEE__________
. . . . .
101 AYSNASLLIQNVTREDAGSYTLHIIKGDDGTRGVTGRFTFTLHLETPKPS 150
_____HHHHHHH_______EEEEEEE__________EEEEEEEE______
. . . . .
151 ISSSNLNPRETMEAVSLTCDPETPDASYLWWMNGQSLPMTHSLKLSETNR 200
_________HHHHHHHH_________EEEEE___________________
. . . . .
201 TLFLLGVTKYTAGPYECEIRNPVSASRSDPVTLNLLPKLPKPYITINNLN 250
___________________________________________EEE____
. . . . .
251 PRENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPRVKRPIENRILILPSV 300
______EEEE________EEEEEEE____________HHHHHEEEEE___
. . . . .
301 TRNETGPYQCEIRDRYGGVRSDPVTLNVLYGPDLPRIYPSFTYYRSGEVL 350
________________________EEEEEE__________EEEEE__EEE
. . . . .
351 YLSCSADSNPPAQYSWTINEKFQLPGQKLFIRHITTKHSGLYVCSVRNSA 400
EEEEE_______________________EEEEE_______EEEEEE____
.
401 TGKESSKSMTVEVSEAL 417
_________EEEE____
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 0.0 %
beta-contents : 41.2 %
coil-contents : 58.8 %
class : beta
method : 2
alpha-contents : 0.0 %
beta-contents : 27.8 %
coil-contents : 72.2 %
class : beta
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-13.89 -0.32 -1.15 -0.38 -4.00 0.00 -4.00 -0.03 0.00 -3.79 -1.06 -12.00 -12.00 0.00 -12.00 0.00 -64.63
0.28 -1.94 -2.54 -0.16 0.00 -4.00 -28.00 0.00 -0.65 -4.24 -1.06 -12.00 0.00 0.00 0.00 0.00 -54.32
ID: tem21_1gi|5902030|ref|NP_008836.1| AC: xxx Len: 350 1:I 340 Sc: -54.32 Pv: 2.810160e-01 NO_GPI_SITE
GPI: learning from protozoa
-11.75 -2.20 -1.78 -2.90 -4.00 -4.00 -28.00 0.00 -0.15 -3.78 -4.80 -12.00 0.00 0.00 0.00 0.00 -75.35
-21.75 -0.44 0.00 0.00 -4.00 0.00 0.00 0.00 -0.20 -4.18 -4.80 -12.00 -12.00 0.00 -12.00 0.00 -71.37
ID: tem21_1gi|5902030|ref|NP_008836.1| AC: xxx Len: 350 1:I 332 Sc: -71.37 Pv: 3.661824e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem21_1gi|5 0.739 35 Y 0.728 35 Y 0.921 25 Y 0.700 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem21_1gi|5 0.542 35 Y 0.527 35 Y 0.923 18 Y 0.494 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem21_1gi|5 0.448 37 Y 0.410 37 Y 0.934 27 N 0.629 Y
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
1-126 MGTLSAPPCTQRIKWKGLLLTASLLNFWNL
PTTAQVTIEAQPPKVSEGKDVLLLVHNLPQ
NLTGYIWYKGQMRDLYHYITSYVVDGEIII
YGPAYSGRETAYSNASLLIQNVTREDAGSY
TLHIIK
gddgtrgvtgrftft 127-141
142-417 LHLETPKPSISSSNLNPRETMEAVSLTCDP
ETPDASYLWWMNGQSLPMTHSLKLSETNRT
LFLLGVTKYTAGPYECEIRNPVSASRSDPV
TLNLLPKLPKPYITINNLNPRENKDVLNFT
CEPKSENYTYIWWLNGQSLPVSPRVKRPIE
NRILILPSVTRNETGPYQCEIRDRYGGVRS
DPVTLNVLYGPDLPRIYPSFTYYRSGEVLY
LSCSADSNPPAQYSWTINEKFQLPGQKLFI
RHITTKHSGLYVCSVRNSATGKESSKSMTV
EVSEAL
low complexity regions: SEG 25 3.0 3.3
>tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
1-417 MGTLSAPPCTQRIKWKGLLLTASLLNFWNL
PTTAQVTIEAQPPKVSEGKDVLLLVHNLPQ
NLTGYIWYKGQMRDLYHYITSYVVDGEIII
YGPAYSGRETAYSNASLLIQNVTREDAGSY
TLHIIKGDDGTRGVTGRFTFTLHLETPKPS
ISSSNLNPRETMEAVSLTCDPETPDASYLW
WMNGQSLPMTHSLKLSETNRTLFLLGVTKY
TAGPYECEIRNPVSASRSDPVTLNLLPKLP
KPYITINNLNPRENKDVLNFTCEPKSENYT
YIWWLNGQSLPVSPRVKRPIENRILILPSV
TRNETGPYQCEIRDRYGGVRSDPVTLNVLY
GPDLPRIYPSFTYYRSGEVLYLSCSADSNP
PAQYSWTINEKFQLPGQKLFIRHITTKHSG
LYVCSVRNSATGKESSKSMTVEVSEAL
low complexity regions: SEG 45 3.4 3.75
>tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
1-417 MGTLSAPPCTQRIKWKGLLLTASLLNFWNL
PTTAQVTIEAQPPKVSEGKDVLLLVHNLPQ
NLTGYIWYKGQMRDLYHYITSYVVDGEIII
YGPAYSGRETAYSNASLLIQNVTREDAGSY
TLHIIKGDDGTRGVTGRFTFTLHLETPKPS
ISSSNLNPRETMEAVSLTCDPETPDASYLW
WMNGQSLPMTHSLKLSETNRTLFLLGVTKY
TAGPYECEIRNPVSASRSDPVTLNLLPKLP
KPYITINNLNPRENKDVLNFTCEPKSENYT
YIWWLNGQSLPVSPRVKRPIENRILILPSV
TRNETGPYQCEIRDRYGGVRSDPVTLNVLY
GPDLPRIYPSFTYYRSGEVLYLSCSADSNP
PAQYSWTINEKFQLPGQKLFIRHITTKHSG
LYVCSVRNSATGKESSKSMTVEVSEAL
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_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
MGTLSAPPCTQRIKWKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKDVLLLVHNLPQ
NLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRETAYSNASLLIQNVTREDAGSY
TLHIIKGDDGTRGVTGRFTFTLHLETPKPSISSSNLNPRETMEAVSLTCDPETPDASYLW
WMNGQSLPMTHSLKLSETNRTLFLLGVTKYTAGPYECEIRNPVSASRSDPVTLNLLPKLP
KPYITINNLNPRENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPRVKRPIENRILILPSV
TRNETGPYQCEIRDRYGGVRSDPVTLNVLYGPDLPRIYPSFTYYRSGEVLYLSCSADSNP
PAQYSWTINEKFQLPGQKLFIRHITTKHSGLYVCSVRNSATGKESSKSMTVEVSEAL
1 - 417 MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLTGYIWYKG QMRDLYHYIT SYVVDGEIII YGPAYSGRET AYSNASLLIQ NVTREDAGSY
TLHIIKGDDG TRGVTGRFTF TLHLETPKPS ISSSNLNPRE TMEAVSLTCD PETPDASYLW
WMNGQSLPMT HSLKLSETNR TLFLLGVTKY TAGPYECEIR NPVSASRSDP VTLNLLPKLP
KPYITINNLN PRENKDVLNF TCEPKSENYT YIWWLNGQSL PVSPRVKRPI ENRILILPSV
TRNETGPYQC EIRDRYGGVR SDPVTLNVLY GPDLPRIYPS FTYYRSGEVL YLSCSADSNP
PAQYSWTINE KFQLPGQKLF IRHITTKHSG LYVCSVRNSA TGKESSKSMT VEVSEAL
low complexity regions: DUST
>tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
MGTLSAPPCTQRIKWKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKDVLLLVHNLPQ
NLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRETAYSNASLLIQNVTREDAGSY
TLHIIKGDDGTRGVTGRFTFTLHLETPKPSISSSNLNPRETMEAVSLTCDPETPDASYLW
WMNGQSLPMTHSLKLSETNRTLFLLGVTKYTAGPYECEIRNPVSASRSDPVTLNLLPKLP
KPYITINNLNPRENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPRVKRPIENRILILPSV
TRNETGPYQCEIRDRYGGVRSDPVTLNVLYGPDLPRIYPSFTYYRSGEVLYLSCSADSNP
PAQYSWTINEKFQLPGQKLFIRHITTKHSGLYVCSVRNSATGKESSKSMTVEVSEAL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for tem21_1gi|5902030|ref|NP_008836.1|
sequence: 350 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
NLTGYIWYKG QMRDLYHYIT SYVVDGEIII YGPAYSGRET AYSNASLLIQ NVTREDAGSY
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
TLHIIKGDDG TRGVTGRFTF TLHLETPKPS ISSSNLNPRE TMEAVSLTCD PETPDASYLW
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . | . 240
WMNGQSLPMT HSLKLSETNR TLFLLGVTKY TAGPYECEIR NPVSASRSDP VTLNLLPKLP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
KPYITINNLN PRENKDVLNF TCEPKSENYT YIWWLNGQSL PVSPRVKRPI ENRILILPSV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. | . | . | . | . |
TRNETGPYQC EIRDRYGGVR SDPVTLNVLY GPDLPRIYPS FTYYRSGEVL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
---------- ---------- ---------- ---------- ----------
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem21_1.___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_1.___inter___
(1 sequences)
MGTLSAPPCTQRIKWKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKD
VLLLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRET
AYSNASLLIQNVTREDAGSYTLHIIKGDDGTRGVTGRFTFTLHLETPKPS
ISSSNLNPRETMEAVSLTCDPETPDASYLWWMNGQSLPMTHSLKLSETNR
TLFLLGVTKYTAGPYECEIRNPVSASRSDPVTLNLLPKLPKPYITINNLN
PRENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPRVKRPIENRILILPSV
TRNETGPYQCEIRDRYGGVRSDPVTLNVLYGPDLPRIYPSFTYYRSGEVL
YLSCSADSNPPAQYSWTINEKFQLPGQKLFIRHITTKHSGLYVCSVRNSA
TGKESSKSMTVEVSEAL
(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 17 37 0.878 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 16 380
K+R profile 4.00
+
CYT-EXT prof -
1.02
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.70
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 4.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 3.0000
-> Orientation: N-in
CYT-EXT difference: -1.02
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment
Loop length 417
K+R profile +
CYT-EXT prof 0.92
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): -0.0513
NEG: 37.0000
POS: 41.0000
-> Orientation: undecided
CYT-EXT difference: 0.92
-> Orientation: N-out
----------------------------------------------------------------------
"tem21_1" 417
17 37 #f 0.878125
************************************
*TOPPREDM with prokaryotic function*
************************************
tem21_1.___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_1.___inter___
(1 sequences)
MGTLSAPPCTQRIKWKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKD
VLLLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRET
AYSNASLLIQNVTREDAGSYTLHIIKGDDGTRGVTGRFTFTLHLETPKPS
ISSSNLNPRETMEAVSLTCDPETPDASYLWWMNGQSLPMTHSLKLSETNR
TLFLLGVTKYTAGPYECEIRNPVSASRSDPVTLNLLPKLPKPYITINNLN
PRENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPRVKRPIENRILILPSV
TRNETGPYQCEIRDRYGGVRSDPVTLNVLYGPDLPRIYPSFTYYRSGEVL
YLSCSADSNPPAQYSWTINEKFQLPGQKLFIRHITTKHSGLYVCSVRNSA
TGKESSKSMTVEVSEAL
(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 17 37 0.878 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1
Loop length 16 380
K+R profile 4.00
+
CYT-EXT prof -
1.02
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.70
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 4.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 3.0000
-> Orientation: N-in
CYT-EXT difference: -1.02
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment
Loop length 417
K+R profile +
CYT-EXT prof 0.92
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 1.00
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): 0.00
(NEG-POS)/(NEG+POS): -0.0513
NEG: 37.0000
POS: 41.0000
-> Orientation: undecided
CYT-EXT difference: 0.92
-> Orientation: N-out
----------------------------------------------------------------------
"tem21_1" 417
17 37 #f 0.878125
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem21_1.___saps___
SAPS. Version of April 11, 1996.
Date run: Mon Nov 13 19:53:09 2000
File: /people/maria/tem21_1.___saps___
ID tem21_1gi|5902030|ref|NP_008836.1|
DE pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
number of residues: 417; molecular weight: 46.9 kdal
1 MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
61 NLTGYIWYKG QMRDLYHYIT SYVVDGEIII YGPAYSGRET AYSNASLLIQ NVTREDAGSY
121 TLHIIKGDDG TRGVTGRFTF TLHLETPKPS ISSSNLNPRE TMEAVSLTCD PETPDASYLW
181 WMNGQSLPMT HSLKLSETNR TLFLLGVTKY TAGPYECEIR NPVSASRSDP VTLNLLPKLP
241 KPYITINNLN PRENKDVLNF TCEPKSENYT YIWWLNGQSL PVSPRVKRPI ENRILILPSV
301 TRNETGPYQC EIRDRYGGVR SDPVTLNVLY GPDLPRIYPS FTYYRSGEVL YLSCSADSNP
361 PAQYSWTINE KFQLPGQKLF IRHITTKHSG LYVCSVRNSA TGKESSKSMT VEVSEAL
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 16( 3.8%); C : 7( 1.7%); D : 14( 3.4%); E : 23( 5.5%); F : 8( 1.9%)
G : 25( 6.0%); H : 7( 1.7%); I : 23( 5.5%); K : 19( 4.6%); L : 46(11.0%)
M : 6( 1.4%); N : 25( 6.0%); P : 33( 7.9%); Q : 12( 2.9%); R : 22( 5.3%)
S : 38( 9.1%); T : 37( 8.9%); V : 24( 5.8%); W : 8( 1.9%); Y+ : 24( 5.8%)
KR : 41 ( 9.8%); ED : 37 ( 8.9%); AGP : 74 ( 17.7%);
KRED : 78 ( 18.7%); KR-ED : 4 ( 1.0%); FIKMNY : 105 ( 25.2%);
LVIFM : 107 ( 25.7%); ST : 75 ( 18.0%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0000000000 0+0+0+0000 0000000000 00000000-0 000+00-0+- 0000000000
61 00000000+0 00+-000000 0000-0-000 0000000+-0 0000000000 000+--0000
121 00000+0--0 0+0000+000 0000-00+00 00000000+- 00-000000- 0-00-00000
181 0000000000 000+00-00+ 00000000+0 00000-0-0+ 000000+0-0 0000000+00
241 +000000000 0+-0+-0000 00-0+0-000 0000000000 0000+0++00 -0+0000000
301 0+0-000000 -0+-+0000+ 0-00000000 00-00+0000 0000+00-00 000000-000
361 000000000- +000000+00 0+0000+000 000000+000 00+-00+000 0-00-00
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none
Negative charge clusters (cmin = 8/30 or 11/45 or 14/60): none
Mixed charge clusters (cmin = 14/30 or 18/45 or 23/60): 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.
There are no high scoring uncharged segments.
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 4 | 6 | 43 | 9 | 9 | 12 | 11 | 11 | 14 | 6 | 8 |
lmin1 6 | 6 | 8 | 52 | 11 | 11 | 14 | 14 | 13 | 17 | 8 | 10 |
lmin2 7 | 7 | 9 | 58 | 13 | 12 | 16 | 15 | 15 | 20 | 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 >= 3: 0
- runs >= 3: 0
* runs >= 4: 0
0 runs >= 29: 0
--------------------------------------------------------------------------------
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-8-C-159-C-47-C-44-C-47-C-43-C-39-C-23-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-8-C-46-H-20-H-45-H-19-H-25-C-21-H-25-C-44-C-47-C-43-C-28-H-4-H-5-C-23-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
Aligned matching blocks:
[ 22- 25] ASLL
[ 105- 108] ASLL
______________________________
[ 49- 52] KDVL
[ 255- 258] KDVL
______________________________
[ 155- 160]-(
19)-[ 180- 188]
[ 248- 253]-( 19)-[ 273- 281]
[ 155- 160] NLNPRE
[ 248- 253] NLNPRE
[ 180- 188] WWMNGQSLP
[ 273- 281] WWLNGQSLP
______________________________
[ 213- 220]-( 6)-[ 227- 234]
[ 306- 313]-( 6)-[ 320- 327]
[ 213- 220] GPYECEIR
[ 306- 313] GPYQCEIR
[ 227- 234] RSDPVTLN
[ 320- 327] RSDPVTLN
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: 22 (Expected range: 10-- 40)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 3 (6-10) 5 (11-20) 6 (>=21) 9
3. Clusters of amino acid multiplets (cmin = 10/30 or 13/45 or 15/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 3 (Expected range: 0-- 15)
1 +plets (f+: 9.8%), 2 -plets (f-: 8.9%)
Total number of charge altplets: 10 (Critical number: 17)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 0 (6-10) 0 (11-20) 1 (>=21) 3
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
127- 138 3 G.. 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8)
Location Period Element Copies Core Errors
There are no periodicities of the prescribed length.
--------------------------------------------------------------------------------
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: tem21_1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ig Immunoglobulin domain 55.7 1e-15 4
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
ig 1/4 105 121 .. 26 42 .. 6.0 2.8
ig 2/4 162 219 .. 1 45 [] 6.7 1.6
ig 3/4 255 312 .. 1 45 [] 17.2 0.00093
ig 4/4 347 396 .. 1 45 [] 26.5 1.2e-06
Alignments of top-scoring domains:
ig: domain 1 of 4, from 105 to 121: score 6.0, E = 2.8
*->lslti.svtpeDsgGtYt<-*
+sl+i++vt+eD+ G Yt
tem21_1gi| 105 ASLLIqNVTREDA-GSYT 121
ig: domain 2 of 4, from 162 to 219: score 6.7, E = 1.6
*->GesvtLtCsvsgfgpp.p.vtWlrngk...............lslti
e v+LtC p++++ W+ ng++ + +++ + ++++++ +++
tem21_1gi| 162 MEAVSLTCDPE---TPdAsYLWWMNGQslpmthslklsetnrTLFLL 205
.svtpeDsgGtYtCvv<-*
+ +++ G Y C+
tem21_1gi| 206 gVTKYTA--GPYECEI 219
ig: domain 3 of 4, from 255 to 312: score 17.2, E = 0.00093
*->GesvtLtCsvsgfgpp.p.vtWlrngk..............lslti.
+ +++tC+ + + ++++ W+ ng++ + +++ +++ ++ l ++
tem21_1gi| 255 KDVLNFTCEPK---SEnYtYIWWLNGQslpvsprvkrpienRILILp 298
svtpeDsgGtYtCvv<-*
svt++ + G Y C+
tem21_1gi| 299 SVTRNET-GPYQCEI 312
ig: domain 4 of 4, from 347 to 396: score 26.5, E = 1.2e-06
*->GesvtLtCsvsgfgpp.p.vtWlrngk.....lslti.svtpeDsgG
Ge + L+Cs+ ++p+++++W+ n k + ++ l i+ t +s G
tem21_1gi| 347 GEVLYLSCSAD--SNPpAqYSWTINEKfqlpgQKLFIrHITTKHS-G 390
tYtCvv<-*
Y C v
tem21_1gi| 391 LYVCSV 396
//
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_1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ig Immunoglobulin domain 55.7 1e-15 4
Herpes_gE Alphaherpesvirus glycoprotein E -1.4 35 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
ig 1/4 105 121 .. 26 42 .. 6.0 2.8
Herpes_gE 1/1 107 133 .. 108 135 .. -1.4 35
ig 2/4 162 219 .. 1 45 [] 6.7 1.6
ig 3/4 255 312 .. 1 45 [] 17.2 0.00093
ig 4/4 347 396 .. 1 45 [] 26.5 1.2e-06
Alignments of top-scoring domains:
ig: domain 1 of 4, from 105 to 121: score 6.0, E = 2.8
*->lslti.svtpeDsgGtYt<-*
+sl+i++vt+eD+ G Yt
tem21_1gi| 105 ASLLIqNVTREDA-GSYT 121
Herpes_gE: domain 1 of 1, from 107 to 133: score -1.4, E = 35
*->ltilnAtpqnaGvYtlydRLiGDrgdtr<-*
l i+n+t ++aG Ytl+ + GD+g+ +
tem21_1gi| 107 LLIQNVTREDAGSYTLHI-IKGDDGTRG 133
ig: domain 2 of 4, from 162 to 219: score 6.7, E = 1.6
*->GesvtLtCsvsgfgpp.p.vtWlrngk...............lslti
e v+LtC p++++ W+ ng++ + +++ + ++++++ +++
tem21_1gi| 162 MEAVSLTCDPE---TPdAsYLWWMNGQslpmthslklsetnrTLFLL 205
.svtpeDsgGtYtCvv<-*
+ +++ G Y C+
tem21_1gi| 206 gVTKYTA--GPYECEI 219
ig: domain 3 of 4, from 255 to 312: score 17.2, E = 0.00093
*->GesvtLtCsvsgfgpp.p.vtWlrngk..............lslti.
+ +++tC+ + + ++++ W+ ng++ + +++ +++ ++ l ++
tem21_1gi| 255 KDVLNFTCEPK---SEnYtYIWWLNGQslpvsprvkrpienRILILp 298
svtpeDsgGtYtCvv<-*
svt++ + G Y C+
tem21_1gi| 299 SVTRNET-GPYQCEI 312
ig: domain 4 of 4, from 347 to 396: score 26.5, E = 1.2e-06
*->GesvtLtCsvsgfgpp.p.vtWlrngk.....lslti.svtpeDsgG
Ge + L+Cs+ ++p+++++W+ n k + ++ l i+ t +s G
tem21_1gi| 347 GEVLYLSCSAD--SNPpAqYSWTINEKfqlpgQKLFIrHITTKHS-G 390
tYtCvv<-*
Y C v
tem21_1gi| 391 LYVCSV 396
//
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_1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [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: Mon Nov 13 19:54:49 2000
Sequence file: tem21_1
----------------------------------------
Sequence tem21_1gi|5902030|ref|NP_008836.1| (417 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
61: NLTG
104: NASL
111: NVTR
199: NRTL
259: NFTC
268: NYTY
303: NETG
Total matches: 7
Matching pattern PS00005 PKC_PHOSPHO_SITE:
10: TQR
96: SGR
135: TGR
146: TPK
192: SLK
198: TNR
283: SPR
385: TTK
395: SVR
401: TGK
405: SSK
Total matches: 11
Matching pattern PS00006 CK2_PHOSPHO_SITE:
96: SGRE
113: TRED
226: SRSD
301: TRNE
367: TINE
401: TGKE
Total matches: 6
Matching pattern PS00008 MYRISTYL:
17: GLLLTA
317: GGVRSD
390: GLYVCS
Total matches: 3
Matching pattern PS00019 ACTININ_1:
267: ENYTYIWWLN
Total matches: 1
Total no of hits in this sequence: 28
========================================
1314 pattern(s) searched in 1 sequence(s), 417 residues.
Total no of hits in all sequences: 28.
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 tem21_1
***** 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, 417 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_1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [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_1
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem21_1gi|5902030|ref|NP_008836.1| pregnancy specific beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [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_1gi|5902030|ref|NP_008836.1| pregnancy specific
beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo
sapiens]
(417 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
AP2 A plant specific DNA binding domain (Apetala 2 like) 25 0.16
CAD Cadherin domain (A calcium dependent adhesion module) 22 0.97
UBHYD Ubiquitin C-terminal hydrolase domain 22 1.5
SNARE Alpha helical domains which are involved in vesicle fu... 22 1.7
LAMNT Lamin N-terminal domain 21 2.0
CATH Cathepsin like protease domain 21 2.2
KIN Protein kinase domain 20 4.1
MATH The Meprin associated TRAF homology domain 20 4.9
ZNF Classic C2H2 Zinc finger domain 20 5.1
ACTIN Actin ATPase/ Cytoskeletal ATPase domain 20 5.3
SWIB SWIB domain (A chromatin associated domain) 20 6.5
DSP Dual specificity protein phosphatase 20 6.6
PTP Phospho-tyrosine Phosphatase domain 20 6.6
DHHC Novel zinc finger domain with DHHC signature 20 7.2
KELCH Kelch repeat- beta propeller like domain 20 7.9
JAB JAB1 associated domain involved in proteolysis 19 9.2
>AP2 A plant specific DNA binding domain (Apetala 2 like)
Length = 218
Score = 25.2 bits (54), Expect = 0.16
Identities = 10/22 (45%), Positives = 11/22 (49%)
Query: 206 GVTKYTAGPYECEIRNPVSASR 227
GV K G + EIR P SR
Sbjct: 38 GVRKRNWGKWVSEIREPRKKSR 59
Score = 24.8 bits (53), Expect = 0.24
Identities = 6/21 (28%), Positives = 9/21 (42%)
Query: 300 VTRNETGPYQCEIRDRYGGVR 320
V + G + EIR+ R
Sbjct: 39 VRKRNWGKWVSEIREPRKKSR 59
Score = 19.3 bits (39), Expect = 9.0
Identities = 4/22 (18%), Positives = 9/22 (40%)
Query: 382 RHITTKHSGLYVCSVRNSATGK 403
R + ++ G +V +R
Sbjct: 37 RGVRKRNWGKWVSEIREPRKKS 58
>CAD Cadherin domain (A calcium dependent adhesion module)
Length = 84
Score = 22.5 bits (48), Expect = 0.97
Identities = 6/38 (15%), Positives = 12/38 (30%)
Query: 108 LIQNVTREDAGSYTLHIIKGDDGTRGVTGRFTFTLHLE 145
+ + + RE YTL + V + +
Sbjct: 40 VTEQLDREKIDRYTLLSHAVSASGQPVEDPMEIIITVM 77
>UBHYD Ubiquitin C-terminal hydrolase domain
Length = 884
Score = 21.9 bits (46), Expect = 1.5
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 380 FIRHITTKHSGLYVCSVRNSATGK 403
+ H H G YV + GK
Sbjct: 235 VLVHSGDNHGGHYVVYLNPKGDGK 258
>SNARE Alpha helical domains which are involved in vesicle fusion
Length = 254
Score = 21.8 bits (46), Expect = 1.7
Identities = 5/33 (15%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 340 SFTYYRSGEVLYLSCSADSNPPAQYSWTINEKF 372
+ + S V Y+ N P +++ ++
Sbjct: 59 NINFISSLGVSYM-MLCTENYPNVLAFSFLDEL 90
>LAMNT Lamin N-terminal domain
Length = 256
Score = 21.4 bits (45), Expect = 2.0
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 180 WWMNGQSLPMTHSLKLSETNRTLFL 204
WW S P++ L+ +E N T+ L
Sbjct: 101 WW---MSPPLSRGLQHNEVNITIDL 122
>CATH Cathepsin like protease domain
Length = 371
Score = 21.4 bits (45), Expect = 2.2
Identities = 9/51 (17%), Positives = 19/51 (36%), Gaps = 4/51 (7%)
Query: 342 TYYRSGEVLYLSCSADSNPPAQYSWTINEK-FQLPGQKLFIRHITTKHSGL 391
G+ L C S+ P + + K + L + ++ +T + L
Sbjct: 276 KPIIKGQ-YMLPCDKLSSLPN-VNLVLGGKSYALTPNQ-YVLKVTVQGETL 323
>KIN Protein kinase domain
Length = 313
Score = 20.4 bits (42), Expect = 4.1
Identities = 13/82 (15%), Positives = 28/82 (33%), Gaps = 8/82 (9%)
Query: 179 LWWMNGQSLPMTHSLKLSETNRTLFLLGVTKYTAGPYECEIRNPVSASRSDPVTLNLLPK 238
+ G+ + + L+ T + P E +I N + + L
Sbjct: 224 FAELLGRKPLFQG----KDYIHQITLIIETIGS--PSEEDICNIANEQARQ--FIRSLNM 275
Query: 239 LPKPYITINNLNPRENKDVLNF 260
+P + N+ P+ N D ++
Sbjct: 276 GNQPKVNFANMFPKANPDAIDL 297
Score = 19.6 bits (40), Expect = 7.3
Identities = 12/52 (23%), Positives = 26/52 (49%), Gaps = 2/52 (3%)
Query: 353 SCSADSNPPAQYSWTINEKFQLPGQKLFIRHITTKHSGLYVCSVRNSATGKE 404
S +++ N Y + +F +P + ++ I G VCS +++ TG++
Sbjct: 7 SDTSNFNDNISY-FVYGSQFTVPRRYSIVKCIGHGAYG-VVCSAKDNLTGEK 56
>MATH The Meprin associated TRAF homology domain
Length = 209
Score = 20.2 bits (42), Expect = 4.9
Identities = 7/39 (17%), Positives = 11/39 (27%), Gaps = 4/39 (10%)
Query: 336 RIYPSFTYYRSGEVLYLSCSADSNPPAQYSWTINEKFQL 374
R+ P YLS + + KF+
Sbjct: 70 RVNPK--GLDEESKDYLSLYLLLV--SCPKSEVRAKFKF 104
>ZNF Classic C2H2 Zinc finger domain
Length = 162
Score = 20.3 bits (42), Expect = 5.1
Identities = 6/19 (31%), Positives = 7/19 (36%), Gaps = 2/19 (10%)
Query: 380 FIRHITTKHSGL--YVCSV 396
+H HS YVC
Sbjct: 119 RAKHQNRTHSNEKPYVCKA 137
>ACTIN Actin ATPase/ Cytoskeletal ATPase domain
Length = 376
Score = 20.2 bits (42), Expect = 5.3
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 3 TLSAPPCTQRIKWKGLLLTASLLNF 27
+ APP + W G + ASL F
Sbjct: 329 KVVAPPERKYSVWIGGSILASLSTF 353
>SWIB SWIB domain (A chromatin associated domain)
Length = 81
Score = 19.9 bits (41), Expect = 6.5
Identities = 5/17 (29%), Positives = 7/17 (40%)
Query: 243 YITINNLNPRENKDVLN 259
YI +N L + N
Sbjct: 63 YIHLNELLTNDESAFEN 79
>DSP Dual specificity protein phosphatase
Length = 185
Score = 19.9 bits (41), Expect = 6.6
Identities = 10/51 (19%), Positives = 18/51 (34%), Gaps = 7/51 (13%)
Query: 226 SRSDPVTLNLLPKLPKPYITINNLNPRENKDVLNFTCEP---KSENYTYIW 273
+ S + L KL ++ LN E + ++ K TY+
Sbjct: 41 NASVAQDIPKLQKLGITHV----LNAAEGRSFMHVNTNANFYKDSGITYLG 87
>PTP Phospho-tyrosine Phosphatase domain
Length = 102
Score = 20.0 bits (41), Expect = 6.6
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 59 PQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRETAYSNASLLIQNVTREDAG 118
P++ G I + Q+ +Y + G I+++ A GR LIQ + ED+
Sbjct: 16 PEHPHGIIKFIRQINSVYS-----LQRGPILVHCSAGVGRTGTLVALDSLIQQLEEEDSV 70
Query: 119 S 119
S
Sbjct: 71 S 71
>DHHC Novel zinc finger domain with DHHC signature
Length = 217
Score = 19.7 bits (40), Expect = 7.2
Identities = 5/47 (10%), Positives = 10/47 (20%), Gaps = 1/47 (2%)
Query: 15 WKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKDVLLLVHNLPQN 61
+ + T A + L + N Q+
Sbjct: 82 GYACMGAIFAGHLVVHLTAVS-IDPADDNVRDKSYAGPLPIFNRSQH 127
>KELCH Kelch repeat- beta propeller like domain
Length = 319
Score = 19.5 bits (40), Expect = 7.9
Identities = 5/23 (21%), Positives = 9/23 (38%)
Query: 70 GQMRDLYHYITSYVVDGEIIIYG 92
+ Y + V+ +I I G
Sbjct: 206 ATCPQPWRYTAAAVLGNQIFIMG 228
>JAB JAB1 associated domain involved in proteolysis
Length = 136
Score = 19.4 bits (40), Expect = 9.2
Identities = 5/25 (20%), Positives = 10/25 (40%)
Query: 149 PSISSSNLNPRETMEAVSLTCDPET 173
I+ + L R +V + D +
Sbjct: 97 NDIAINELMKRYCPNSVLVIIDVKP 121
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 16
Number of calls to ALIGN: 19
Length of query: 417
Total length of test sequences: 20182
Effective length of test sequences: 16536.0
Effective search space size: 6332000.6
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_1gi|5902030|ref|NP_008836.1| pregnancy specific
beta-1-glycoprotein 1; Pregnancy-specific beta-1-glycoprotein-1 [Homo
sapiens]
(417 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|462182 [68..563] alpha/beta-Hydrolases 29 0.15
gi|1431878 [342..581] Carbonic anhydrase 28 0.40
gi|1633321 [7..184] (Phosphotyrosine) protein phosphatases II 26 1.4
gi|1001372 [10..242] Sugar phosphatases 26 1.5
gi|2209100 [9..467] PLP-dependent transferases 26 1.7
gi|1945717 [15..256] alpha/beta-Hydrolases 25 2.9
gi|2392378 [1..380] Periplasmic binding protein-like II 25 3.0
gi|2494396 [4..243] alpha/beta-Hydrolases 24 3.9
gi|2313908 [466..823] Aconitase, first 3 domains 24 4.2
gi|2652959 [169..353] P-loop containing nucleotide triphosph... 24 4.4
gi|1827635 [121..432] Metallo-dependent phosphatases 24 4.8
gi|297485 [55..186] Glutaminase/Asparaginase 23 6.6
gi|1145791 [40..633] alpha/beta-Hydrolases 23 7.9
gi|2228580 [283..484] beta-Prism I 23 8.2
gi|2828820 [148..443] Periplasmic binding protein-like II 23 9.0
gi|2120680 [21..211] alpha/beta-Hydrolases 23 9.0
gi|1722978 [130..632] beta-Glucosyltransferase & glycogen ph... 23 9.4
gi|1653619 [107..344] Periplasmic binding protein-like II 23 9.7
>gi|462182 [68..563] alpha/beta-Hydrolases
Length = 496
Score = 28.9 bits (64), Expect = 0.15
Identities = 9/66 (13%), Positives = 21/66 (31%), Gaps = 1/66 (1%)
Query: 43 PKVSEGKDVLLLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRETAY 102
P+ + VL+ VH G + + ++ + +G + +
Sbjct: 86 PEGANQLPVLVFVHGEMLFDGGSEEAQPDYVLEKDVLL-VSINYRLAPFGFLSALTDELP 144
Query: 103 SNASLL 108
N +L
Sbjct: 145 GNVALS 150
>gi|1431878 [342..581] Carbonic anhydrase
Length = 240
Score = 27.5 bits (60), Expect = 0.40
Identities = 12/41 (29%), Positives = 23/41 (55%), Gaps = 1/41 (2%)
Query: 2 GTLSAPPCTQRIKWKGLLLTASLLNFWNLPTTAQVTIEAQP 42
G+L+ PPC++ +KW + L ++ + A VT+ + P
Sbjct: 183 GSLTTPPCSEIVKWH-VFLEPRTVSVEQMEVFADVTLNSNP 222
>gi|1633321 [7..184] (Phosphotyrosine) protein phosphatases II
Length = 178
Score = 25.9 bits (56), Expect = 1.4
Identities = 6/66 (9%), Positives = 12/66 (18%), Gaps = 3/66 (4%)
Query: 243 YITINNLNPRENKDVLNFTCEPKS-ENYTYIWWLNGQSLPVSPRVKRPIENRILILPSVT 301
+ N + +N TY+ E +
Sbjct: 49 ITHVLNAAEGRSFMHVNTNANFYKDSGITYLGI-KANDTQEFNLSA-YFERAADFIDQAL 106
Query: 302 RNETGP 307
+ G
Sbjct: 107 AQKNGR 112
>gi|1001372 [10..242] Sugar phosphatases
Length = 233
Score = 25.7 bits (56), Expect = 1.5
Identities = 6/45 (13%), Positives = 17/45 (37%)
Query: 273 WWLNGQSLPVSPRVKRPIENRILILPSVTRNETGPYQCEIRDRYG 317
+ ++ ++P +P + V+R+ ++ DR
Sbjct: 138 CFRETKAGAITPVKVKPKTELESLTLVVSRSHRDQRFQDLIDRLP 182
>gi|2209100 [9..467] PLP-dependent transferases
Length = 459
Score = 25.6 bits (55), Expect = 1.7
Identities = 6/85 (7%), Positives = 22/85 (25%), Gaps = 8/85 (9%)
Query: 47 EGKDVLLLVHNLPQNLTGYIWYKGQMRDLYHYITSY----VVD----GEIIIYGPAYSGR 98
++ + G ++ +Y Y ++D E +
Sbjct: 177 AHNVPYIVCTITCNSAGGQPVSIANLKGMYEIARKYDIPVIMDSARFAENAYFVQQREEA 236
Query: 99 ETAYSNASLLIQNVTREDAGSYTLH 123
++ + ++ D + +
Sbjct: 237 YKDWTIEQITYESYRYADGLAMSAK 261
>gi|1945717 [15..256] alpha/beta-Hydrolases
Length = 242
Score = 24.8 bits (52), Expect = 2.9
Identities = 7/68 (10%), Positives = 15/68 (21%), Gaps = 7/68 (10%)
Query: 47 EGKDVLLLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRETAYSNAS 106
GK ++ + +W + D G +S N
Sbjct: 2 SGKASIMFAPGFGCD--QSVWN-AVAPAFEEDHRVILFD----YVGSGHSDLRAYDLNRY 54
Query: 107 LLIQNVTR 114
+ +
Sbjct: 55 QTLDGYAQ 62
>gi|2392378 [1..380] Periplasmic binding protein-like II
Length = 380
Score = 24.6 bits (53), Expect = 3.0
Identities = 22/177 (12%), Positives = 40/177 (22%), Gaps = 20/177 (11%)
Query: 14 KWKGLLLTASLLNFWNLPTTAQVTIEAQPPKVSEGKDVLLLVHNLPQNLTGYIWYKGQMR 73
K L+ ++ P A A + ++ + ++ + G +
Sbjct: 152 PGKSALMFNLQEPYFTWPLIA-----ADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLV 206
Query: 74 DLYHYITSYVVDGEIIIYGPAYSGRETAYSNASLLIQNVTREDA--GSYTLHIIKGDDGT 131
DL I G N N+ G L KG
Sbjct: 207 DLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSK 266
Query: 132 RGVTGRFTFTLHLETPKPSISSSNLNPRETMEAVSLTCDPETPDASYLWWMNGQSLP 188
V I++++ N E + D + L
Sbjct: 267 PFVGVLSA----------GINAASPNKELAKEFLENY---LLTDEGLEAVNKDKPLG 310
>gi|2494396 [4..243] alpha/beta-Hydrolases
Length = 240
Score = 24.2 bits (52), Expect = 3.9
Identities = 7/46 (15%), Positives = 13/46 (28%), Gaps = 1/46 (2%)
Query: 322 DPVTLNVLYGPDLPRIYPSFTYYRSGEVLYLSCSADSNPPAQYSWT 367
+ L + P P F + G L + + P +
Sbjct: 78 ECSNLMI-TRPQGATNLPVFVWIHGGGNLAGNGYCSDHNPVPFVKH 122
>gi|2313908 [466..823] Aconitase, first 3 domains
Length = 358
Score = 24.1 bits (52), Expect = 4.2
Identities = 8/64 (12%), Positives = 20/64 (30%), Gaps = 12/64 (18%)
Query: 28 WNLPTTAQVTIEAQPPKVSEGKDVLLLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVD-- 85
N+P + V + + +D++ + +Y + L +
Sbjct: 53 LNMPESVLVRFKGEMNPGITLRDLVNAI----------PYYAIKKGLLTVEKKGKINVFN 102
Query: 86 GEII 89
G I+
Sbjct: 103 GRIL 106
>gi|2652959 [169..353] P-loop containing nucleotide triphosphate hydrolases
Length = 185
Score = 24.2 bits (51), Expect = 4.4
Identities = 12/88 (13%), Positives = 21/88 (23%), Gaps = 7/88 (7%)
Query: 88 IIIYGPAYSGRETAYSNASLLIQNVTREDAGSYTLHIIKGDDGTRGVTGRFTFTLHLETP 147
I+ G G+ + V A + +HI D + +
Sbjct: 4 ILFMGGPGGGK-------TRHAARVADSLADNGLVHICMPDIIRTALGKYKDKYPEWKEA 56
Query: 148 KPSISSSNLNPRETMEAVSLTCDPETPD 175
L P + + PD
Sbjct: 57 NEHYIRGELIPNQLALTLLKAEMGRHPD 84
>gi|1827635 [121..432] Metallo-dependent phosphatases
Length = 312
Score = 23.9 bits (51), Expect = 4.8
Identities = 23/135 (17%), Positives = 43/135 (31%), Gaps = 18/135 (13%)
Query: 28 WNLPTTAQVTIEAQPPKVSEGKD--VLLLVHNLPQNLTGYIWYKGQMRD------LYHYI 79
+ T ++ + KV + +++L+H+ N + + +G+ Y
Sbjct: 136 YGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYK 195
Query: 80 TSYVVDGEIIIYGPAYSGR-ETAYSNASLLIQNVTREDAGSYTLHIIKGDDGTRGVTGRF 138
V G + Y + L T S ++I GD G GV
Sbjct: 196 VDVVFAGHVHAYERSERVSNIAYKITDGL----CTPVKDQSAPVYITIGDAGNYGVIDSN 251
Query: 139 TFTLHLETPKPSISS 153
P+P S+
Sbjct: 252 M-----IQPQPEYSA 261
>gi|297485 [55..186] Glutaminase/Asparaginase
Length = 132
Score = 23.4 bits (50), Expect = 6.6
Identities = 12/76 (15%), Positives = 24/76 (30%), Gaps = 7/76 (9%)
Query: 32 TTAQVTIEAQPPKVSEGKDVL-----LLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVDG 86
++Q+ I + +V L + N L Y R + I G
Sbjct: 16 ESSQLQIIVRGGQVPITNSSLTHTNYTRLFNSSSALNITELYN-VARVVNETIQDKSSAG 74
Query: 87 EIIIYGPAYSGRETAY 102
+++ A S ++
Sbjct: 75 AVVVAN-AKSLEAVSF 89
>gi|1145791 [40..633] alpha/beta-Hydrolases
Length = 594
Score = 23.1 bits (49), Expect = 7.9
Identities = 10/69 (14%), Positives = 23/69 (32%), Gaps = 2/69 (2%)
Query: 42 PPKVSEGKD--VLLLVHNLPQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRE 99
+ + V++ +H G + Y + ++ + + G +G +
Sbjct: 152 DEDIRDSGAKPVMVYIHGGSYMEGTGNMIDGSVLASYGNVIVITLNYRVGVLGFLSTGDQ 211
Query: 100 TAYSNASLL 108
A N LL
Sbjct: 212 AAKGNYGLL 220
>gi|2228580 [283..484] beta-Prism I
Length = 202
Score = 23.2 bits (49), Expect = 8.2
Identities = 17/64 (26%), Positives = 27/64 (41%), Gaps = 10/64 (15%)
Query: 59 PQNLTGYIWYKGQMRDLYHYITSYVVDGEIIIYGPAYSGRET-AYSNASLLIQNVTREDA 117
P N+ Y W Q +++ +G +YG GR T SN + N+T
Sbjct: 60 PHNIPRYYWSGNQ---------NFLSNGTSNLYGYRSDGRTTFNVSNIDIFRVNMTTHIG 110
Query: 118 GSYT 121
G++T
Sbjct: 111 GAFT 114
>gi|2828820 [148..443] Periplasmic binding protein-like II
Length = 296
Score = 23.0 bits (49), Expect = 9.0
Identities = 16/104 (15%), Positives = 28/104 (26%), Gaps = 15/104 (14%)
Query: 196 SETNRTLFLLG-VTKYTAGPYECEIRNPVSASRSDPVTLNLLPKLP----KPYITINNL- 249
E R +F G PY + N + V + LP P + ++
Sbjct: 132 EEPVRLMFQQGNAAFERNWPYAWGLHNADDSPVKGKVGVAPLPHFPGHKSAATLGGWHIG 191
Query: 250 ------NPRENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPRVK 287
N + + F + + +N P V
Sbjct: 192 ISKYSDNKALAWEFVKFVESYSVQKG---FAMNLGWNPGRVDVY 232
>gi|2120680 [21..211] alpha/beta-Hydrolases
Length = 191
Score = 23.0 bits (48), Expect = 9.0
Identities = 8/62 (12%), Positives = 15/62 (23%), Gaps = 9/62 (14%)
Query: 51 VLLLVHNLPQNLTGYIWYKGQMRDL--YHYITSYVVDGEIIIYGPAYSGRETAYSNASLL 108
LL++ ++ Y Y L +VD + + A
Sbjct: 2 RLLVLPDIYGCNGFYRGY---AAYLAEQGASEVLLVDP----FAAFGELPQATREAAFQR 54
Query: 109 IQ 110
Sbjct: 55 RH 56
>gi|1722978 [130..632] beta-Glucosyltransferase & glycogen phosphorylase
Length = 503
Score = 23.0 bits (49), Expect = 9.4
Identities = 10/53 (18%), Positives = 15/53 (27%), Gaps = 10/53 (18%)
Query: 68 YKGQMRDLYHYITSY------VVDGEIIIYGPAYSGRETAYSNASLLIQNVTR 114
YK L ++I+ G ++ LIQ V R
Sbjct: 392 YKRLTLMLRDPDRLEQLLLDEQRPIQLIVAGKSHPA----DDGGKALIQQVVR 440
>gi|1653619 [107..344] Periplasmic binding protein-like II
Length = 238
Score = 23.0 bits (49), Expect = 9.7
Identities = 5/42 (11%), Positives = 10/42 (22%), Gaps = 3/42 (7%)
Query: 250 NPRENKDVLNFTCEPKSENYTYIWWLNGQSLPVSPRVKRPIE 291
+ LNF+ + +L V +
Sbjct: 199 AAEITYEWLNFS---AQPSSLEQMATFSNALAVPYQNLEVSA 237
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 18
Number of calls to ALIGN: 18
Length of query: 417
Total length of test sequences: 256703
Effective length of test sequences: 208388.0
Effective search space size: 78500663.2
Initial X dropoff for ALIGN: 25.0 bits