BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 031432
(159 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HKS|A Chain A, Crystal Structure Of Eukaryotic Translation Initiation
Factor Eif-5a2 From Arabidopsis Thaliana
pdb|3HKS|B Chain B, Crystal Structure Of Eukaryotic Translation Initiation
Factor Eif-5a2 From Arabidopsis Thaliana
Length = 167
Score = 235 bits (599), Expect = 8e-63, Method: Compositional matrix adjust.
Identities = 112/150 (74%), Positives = 132/150 (88%), Gaps = 1/150 (0%)
Query: 8 FESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFN 67
FE+ +++GASKT+PQ AG IRK G+IVIK RPCKVVEVSTSKTGKHGHAKCHFV IDIF
Sbjct: 16 FEA-SESGASKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFT 74
Query: 68 GKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQI 127
KKLEDIVPSSHNCDVPHV R DYQLIDI+EDGFVSLLT++G TKDDL+LPTD+ L +Q+
Sbjct: 75 AKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQM 134
Query: 128 KDGFESGKDLVVSVQCAMGEEQINALKDIG 157
+ GF+ GKD+VVSV +MGEEQI A+K++G
Sbjct: 135 RLGFDEGKDIVVSVMSSMGEEQICAVKEVG 164
>pdb|3ER0|A Chain A, Crystal Structure Of The Full Length Eif5a From
Saccharomyces Cerevisiae
pdb|3ER0|B Chain B, Crystal Structure Of The Full Length Eif5a From
Saccharomyces Cerevisiae
Length = 167
Score = 186 bits (473), Expect = 4e-48, Method: Compositional matrix adjust.
Identities = 90/155 (58%), Positives = 119/155 (76%), Gaps = 3/155 (1%)
Query: 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60
MSDEEH FE+ ADAG+S T+P Q +RKNG++VIK RPCK+V++STSKTGKHGHAK H
Sbjct: 11 MSDEEHTFET-ADAGSSATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHL 69
Query: 61 VGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTD 120
V IDIF GKKLED+ PS+HN +VP V R +YQL+DI +DGF+SL+ +G+TKDD++ P
Sbjct: 70 VAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDI-DDGFLSLMNMDGDTKDDVKAPEG 128
Query: 121 ENLLSQIKDGFESGKDLVVSVQCAMGEEQINALKD 155
E L ++ F+ GKDL+V++ AMGEE + K+
Sbjct: 129 E-LGDSLQTAFDEGKDLMVTIISAMGEEAAISFKE 162
>pdb|3CPF|A Chain A, Crystal Structure Of Human Eukaryotic Translation
Initiation Factor Eif5a
pdb|3CPF|B Chain B, Crystal Structure Of Human Eukaryotic Translation
Initiation Factor Eif5a
Length = 138
Score = 164 bits (415), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 77/139 (55%), Positives = 107/139 (76%), Gaps = 2/139 (1%)
Query: 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIV 75
S TFP Q +RKNG++V+KGRPCK+VE+STSKTGKHGHAK H VGIDIF GKK EDI
Sbjct: 1 GSATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDIC 60
Query: 76 PSSHNCDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGK 135
PS+HN DVP++ R D+QLI I +DG++SLL ++G ++DLRLP + +L +I+ ++ G+
Sbjct: 61 PSTHNMDVPNIKRNDFQLIGI-QDGYLSLLQDSGEVREDLRLP-EGDLGKEIEQKYDCGE 118
Query: 136 DLVVSVQCAMGEEQINALK 154
+++++V AM EE A+K
Sbjct: 119 EILITVLSAMTEEAAVAIK 137
>pdb|1X6O|A Chain A, Structural Analysis Of Leishmania Braziliensis Eukaryotic
Initiation Factor 5a
Length = 174
Score = 154 bits (388), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 79/166 (47%), Positives = 108/166 (65%), Gaps = 7/166 (4%)
Query: 1 MSDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCH 59
MSDE+H F + ASKT+P AG ++K GY+ I GRPCKV+++S SKTGKHGHAK
Sbjct: 9 MSDEDHDFSHQGGGDNASKTYPLAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVS 68
Query: 60 FVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDI--SED----GFVSLLTENGNTKD 113
V DIF G +LED PS+HN +VP V Y ++DI +ED +SL+ + G +++
Sbjct: 69 IVATDIFTGNRLEDQAPSTHNVEVPFVKTYTYSVLDIQANEDPSLPAHLSLMDDEGESRE 128
Query: 114 DLRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALKDIGPK 159
DL +P D L +QIK+ F+SGKD++V V AMG EQ+ K+ K
Sbjct: 129 DLDMPPDPALATQIKEQFDSGKDVLVVVVSAMGTEQVLQTKNAAEK 174
>pdb|1XTD|A Chain A, Structural Analysis Of Leishmania Mexicana Eukaryotic
Initiation Factor 5a
Length = 174
Score = 143 bits (360), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 76/165 (46%), Positives = 104/165 (63%), Gaps = 7/165 (4%)
Query: 2 SDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60
SDE+H F + ASKT+P AG ++K GY+ I GRPCKV+++S SKTGKHGHAK
Sbjct: 10 SDEDHDFAHQGGGDNASKTYPXAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSI 69
Query: 61 VGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDI--SED----GFVSLLTENGNTKDD 114
V DIF G +LED PS+HN +VP V Y ++DI +ED +SL + G +++D
Sbjct: 70 VATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNEDPSLPSHLSLXDDEGESRED 129
Query: 115 LRLPTDENLLSQIKDGFESGKDLVVSVQCAMGEEQINALKDIGPK 159
L P D L +QIK+ F+SGK+++V V A G EQ+ K+ K
Sbjct: 130 LDXPPDAALATQIKEQFDSGKEVLVVVVSAXGTEQVLQTKNAAEK 174
>pdb|2EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 136
Score = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 63/114 (55%), Gaps = 8/114 (7%)
Query: 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83
G+++ Y++I G PC++V++S SK GKHG AK VGI IF K E + P+S +V
Sbjct: 13 VGSLKVGQYVMIDGVPCEIVDISVSKPGKHGGAKARVVGIGIFEKVKKEFVAPTSSKVEV 72
Query: 84 PHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDL 137
P + R Q++ I D V ++ + T + L LP E + +G E G ++
Sbjct: 73 PIIDRRKGQVLAIMGD-MVQIM--DLQTYETLELPIPEGI-----EGLEPGGEV 118
>pdb|1EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 135
Score = 70.9 bits (172), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 63/114 (55%), Gaps = 8/114 (7%)
Query: 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83
G+++ Y++I G PC++V++S SK GKHG AK VGI IF K E + P+S +V
Sbjct: 12 VGSLKVGQYVMIDGVPCEIVDISVSKPGKHGGAKARVVGIGIFEKVKKEFVAPTSSKVEV 71
Query: 84 PHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESGKDL 137
P + R Q++ I D V ++ + T + L LP E + +G E G ++
Sbjct: 72 PIIDRRKGQVLAIMGD-MVQIM--DLQTYETLELPIPEGI-----EGLEPGGEV 117
>pdb|1BKB|A Chain A, Initiation Factor 5a From Archebacterium Pyrobaculum
Aerophilum
Length = 136
Score = 68.6 bits (166), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 47/77 (61%)
Query: 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
+AG +++ Y+VI G PC+VVE+ SKTGKHG AK V + +F+G K +P +
Sbjct: 10 EAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVE 69
Query: 83 VPHVTRTDYQLIDISED 99
VP + + Q++ +S D
Sbjct: 70 VPIIEKFTAQILSVSGD 86
>pdb|1IZ6|A Chain A, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
pdb|1IZ6|B Chain B, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
pdb|1IZ6|C Chain C, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
Length = 138
Score = 66.2 bits (160), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 57/112 (50%), Gaps = 3/112 (2%)
Query: 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
Q ++ YI+I PC++V ++ S GKHG AK + IF+GK + P+S D
Sbjct: 8 QVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVD 67
Query: 83 VPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGFESG 134
VP + + Q+I I+ D ++ + T + +P D + +I+D + G
Sbjct: 68 VPIIDKKTAQVIAITPD---TVQIMDMETYETFEVPIDTGVADEIRDQLKEG 116
>pdb|1KHI|A Chain A, Crystal Structure Of Hex1
Length = 176
Score = 57.8 bits (138), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 47/161 (29%), Positives = 82/161 (50%), Gaps = 30/161 (18%)
Query: 3 DEEHHFESKADAG-----------ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTS-KT 50
D++ H +ADA AS+T IR ++++GRPC+V+ +STS T
Sbjct: 5 DDDAHGHVEADAAPRATTGTGTGSASQTVTIPCHHIRLGDILILQGRPCQVIRISTSAAT 64
Query: 51 GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRT-------DYQLIDISEDGFVS 103
G+H ++G+D+F K+L + N V +T Y+++D+ +DG +
Sbjct: 65 GQH-----RYLGVDLFT-KQLHEESSFVSNPAPSVVVQTMLGPVFKQYRVLDM-QDGSIV 117
Query: 104 LLTENGNTKDDLRLPTDENLLSQIKDGFESGKD----LVVS 140
+TE G+ K +L + +L ++++ FESG+ LVVS
Sbjct: 118 AMTETGDVKQNLPVIDQSSLWNRLQKAFESGRGSVRVLVVS 158
>pdb|3TB6|A Chain A, Structure Of The Effector-binding Domain Of Arabinose
Repressor Arar From Bacillus Subtilis
pdb|3TB6|B Chain B, Structure Of The Effector-binding Domain Of Arabinose
Repressor Arar From Bacillus Subtilis
Length = 298
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 96 ISEDGFVSLLTENGNTKDDLRLPTDENLLSQIKDGF 131
+SE G+ LLT N D+ R ENLLSQ DG
Sbjct: 41 LSEQGYSMLLTSTNNNPDNERRGL-ENLLSQHIDGL 75
>pdb|1PEX|A Chain A, Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain
Length = 207
Score = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60
NGY +++G P K+ E+ K K A HF
Sbjct: 94 NGYDILEGYPKKISELGLPKEVKKISAAVHF 124
>pdb|1R61|A Chain A, The Structure Of Predicted Metal-Dependent Hydrolase From
Bacillus Stearothermophilus
pdb|1R61|B Chain B, The Structure Of Predicted Metal-Dependent Hydrolase From
Bacillus Stearothermophilus
pdb|3KRV|A Chain A, The Structure Of Potential Metal-Dependent Hydrolase With
Cyclase Activity
pdb|3KRV|B Chain B, The Structure Of Potential Metal-Dependent Hydrolase With
Cyclase Activity
Length = 207
Score = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 50 TGKHGHAKCHFV-GIDIFNGKKLEDIVPSSHNCDVPHV----TRTDYQLIDISEDGFVSL 104
TG H A H V G F L D+V D+ HV T+ D +DI E FV
Sbjct: 48 TGTHIDAPLHMVEGGATFETIPLNDLVGPCKLFDLTHVNDRITKDDIAHLDIQEGDFVLF 107
Query: 105 LTEN 108
T+N
Sbjct: 108 KTKN 111
>pdb|2XBB|A Chain A, Nedd4 Hect:ub Complex
pdb|2XBB|B Chain B, Nedd4 Hect:ub Complex
pdb|2XBF|A Chain A, Nedd4 Hect Structure
Length = 386
Score = 26.9 bits (58), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 10/86 (11%)
Query: 62 GIDIFNGKKLEDIVPSSHNCDVPH--VTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPT 119
G+ +++GK L+ + H +T D + +D + + EN T+ DLR
Sbjct: 129 GMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTELDLRFII 188
Query: 120 DENLLSQ-----IKDGFESGKDLVVS 140
DE L Q +K+G G ++VV+
Sbjct: 189 DEELFGQTHQHELKNG---GSEIVVT 211
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase
Iii Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase
Iii Alpha-Subunit
Length = 1220
Score = 25.8 bits (55), Expect = 10.0, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 41 KVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTD 90
+V+EV+ G + HA H G+ + + L D+VP + + VT+ D
Sbjct: 557 QVIEVAMRLEGLNRHASVHAAGV-VIAAEPLTDLVPLMRDQEGRPVTQYD 605
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 25.8 bits (55), Expect = 10.0, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 41 KVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTD 90
+V+EV+ G + HA H G+ + + L D+VP + + VT+ D
Sbjct: 557 QVIEVAMRLEGLNRHASVHAAGV-VIAAEPLTDLVPLMRDQEGRPVTQYD 605
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.314 0.134 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,173,400
Number of Sequences: 62578
Number of extensions: 213175
Number of successful extensions: 374
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 355
Number of HSP's gapped (non-prelim): 24
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)