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= 033076
(128 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 = 199 bits (506), Expect = 4e-52, Method: Compositional matrix adjust.
Identities = 94/120 (78%), Positives = 107/120 (89%), Gaps = 1/120 (0%)
Query: 8 FESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFN 67
FE+ +++GASKT+PQ AG IRK G+IVIK RPCKVVEVSTSKTGKHGHAKCHFV IDIF
Sbjct: 16 FEA-SESGASKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFT 74
Query: 68 GKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQV 127
KKLEDIVPSSHNCDVPHV R DYQLIDI+EDGFVSLLT++G TKDDL+LPTD+ L +Q+
Sbjct: 75 AKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQM 134
>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 = 166 bits (421), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 77/121 (63%), Positives = 98/121 (80%), Gaps = 2/121 (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 E 121
E
Sbjct: 129 E 129
>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 = 150 bits (380), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 67/103 (65%), Positives = 84/103 (81%), Gaps = 1/103 (0%)
Query: 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIV 75
S TFP Q +RKNG++V+KGRPCK+VE+STSKTGKHGHAK H VGIDIF GKK EDI
Sbjct: 1 GSATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDIC 60
Query: 76 PSSHNCDVPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLP 118
PS+HN DVP++ R D+QLI I +DG++SLL ++G ++DLRLP
Sbjct: 61 PSTHNMDVPNIKRNDFQLIGI-QDGYLSLLQDSGEVREDLRLP 102
>pdb|1X6O|A Chain A, Structural Analysis Of Leishmania Braziliensis Eukaryotic
Initiation Factor 5a
Length = 174
Score = 127 bits (318), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 63/134 (47%), Positives = 87/134 (64%), Gaps = 7/134 (5%)
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 DLRLPTDENLLSQV 127
DL +P D L +Q+
Sbjct: 129 DLDMPPDPALATQI 142
>pdb|1XTD|A Chain A, Structural Analysis Of Leishmania Mexicana Eukaryotic
Initiation Factor 5a
Length = 174
Score = 120 bits (302), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 62/133 (46%), Positives = 84/133 (63%), Gaps = 7/133 (5%)
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 LRLPTDENLLSQV 127
L P D L +Q+
Sbjct: 130 LDXPPDAALATQI 142
>pdb|2EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 136
Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 37/100 (37%), Positives = 57/100 (57%), Gaps = 3/100 (3%)
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 PHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENL 123
P + R Q++ I D V ++ + T + L LP E +
Sbjct: 73 PIIDRRKGQVLAIMGD-MVQIM--DLQTYETLELPIPEGI 109
>pdb|1EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 135
Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 37/100 (37%), Positives = 57/100 (57%), Gaps = 3/100 (3%)
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 PHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENL 123
P + R Q++ I D V ++ + T + L LP E +
Sbjct: 72 PIIDRRKGQVLAIMGD-MVQIM--DLQTYETLELPIPEGI 108
>pdb|1BKB|A Chain A, Initiation Factor 5a From Archebacterium Pyrobaculum
Aerophilum
Length = 136
Score = 68.9 bits (167), Expect = 7e-13, 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 = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 53/105 (50%), Gaps = 3/105 (2%)
Query: 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
Q ++ YI+I PC++V ++ S GKHG AK + IF+GK + P+S D
Sbjct: 8 QVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVD 67
Query: 83 VPHVTRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDENLLSQV 127
VP + + Q+I I+ D ++ + T + +P D + ++
Sbjct: 68 VPIIDKKTAQVIAITPD---TVQIMDMETYETFEVPIDTGVADEI 109
>pdb|1KHI|A Chain A, Crystal Structure Of Hex1
Length = 176
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 71/144 (49%), Gaps = 26/144 (18%)
Query: 3 DEEHHFESKADAGASKTFPQQAGT-----------IRKNGYIVIKGRPCKVVEVSTS-KT 50
D++ H +ADA T G+ 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 LLTENGNTKDDLRLPTDENLLSQV 127
+TE G+ K +L + +L +++
Sbjct: 118 AMTETGDVKQNLPVIDQSSLWNRL 141
>pdb|1PEX|A Chain A, Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain
Length = 207
Score = 27.3 bits (59), Expect = 2.4, 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 = 2.9, 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|1VKN|A Chain A, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
pdb|1VKN|B Chain B, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
pdb|1VKN|C Chain C, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
pdb|1VKN|D Chain D, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
Length = 351
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 15/46 (32%)
Query: 53 HGHAKCHFVGIDIFNGKKLEDIVPS---------------SHNCDV 83
H AK ++ + GKKLE+I PS S NCDV
Sbjct: 36 HPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDV 81
>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 = 6.2, 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 = 6.2, 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|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 = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 96 ISEDGFVSLLTENGNTKDDLRLPTDENLLSQ 126
+SE G+ LLT N D+ R ENLLSQ
Sbjct: 41 LSEQGYSMLLTSTNNNPDNERRGL-ENLLSQ 70
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 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,163,086
Number of Sequences: 62578
Number of extensions: 162574
Number of successful extensions: 255
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 235
Number of HSP's gapped (non-prelim): 18
length of query: 128
length of database: 14,973,337
effective HSP length: 87
effective length of query: 41
effective length of database: 9,529,051
effective search space: 390691091
effective search space used: 390691091
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)