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= 034229
(100 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 = 129 bits (324), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 62/76 (81%), Positives = 68/76 (89%), Gaps = 1/76 (1%)
Query: 8 FESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFN 67
FE+ +++GASKT+PQ AG IRK G+IVIK RPCKVVEVSTSKTGKHGHAKCHFV IDIF
Sbjct: 16 FEA-SESGASKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFT 74
Query: 68 GKKLEDIVPSSHNCDV 83
KKLEDIVPSSHNCDV
Sbjct: 75 AKKLEDIVPSSHNCDV 90
>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 = 127 bits (318), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 57/85 (67%), Positives = 70/85 (82%), Gaps = 1/85 (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 VGIDIFNGKKLEDIVPSSHNCDVLI 85
V IDIF GKKLED+ PS+HN +V +
Sbjct: 70 VAIDIFTGKKLEDLSPSTHNMEVPV 94
>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 = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 49/68 (72%), Positives = 56/68 (82%)
Query: 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIV 75
S TFP Q +RKNG++V+KGRPCK+VE+STSKTGKHGHAK H VGIDIF GKK EDI
Sbjct: 1 GSATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDIC 60
Query: 76 PSSHNCDV 83
PS+HN DV
Sbjct: 61 PSTHNMDV 68
>pdb|1X6O|A Chain A, Structural Analysis Of Leishmania Braziliensis
Eukaryotic Initiation Factor 5a
Length = 174
Score = 102 bits (255), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 47/84 (55%), Positives = 59/84 (70%), Gaps = 1/84 (1%)
Query: 1 MSDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCH 59
MSDE+H F + ASKT+P AG ++K GY+ I GRPCKV+++S SKTGKHGHAK
Sbjct: 9 MSDEDHDFSHQGGGDNASKTYPLAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVS 68
Query: 60 FVGIDIFNGKKLEDIVPSSHNCDV 83
V DIF G +LED PS+HN +V
Sbjct: 69 IVATDIFTGNRLEDQAPSTHNVEV 92
>pdb|1XTD|A Chain A, Structural Analysis Of Leishmania Mexicana Eukaryotic
Initiation Factor 5a
Length = 174
Score = 99.8 bits (247), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 46/83 (55%), Positives = 58/83 (69%), Gaps = 1/83 (1%)
Query: 2 SDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60
SDE+H F + ASKT+P AG ++K GY+ I GRPCKV+++S SKTGKHGHAK
Sbjct: 10 SDEDHDFAHQGGGDNASKTYPXAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSI 69
Query: 61 VGIDIFNGKKLEDIVPSSHNCDV 83
V DIF G +LED PS+HN +V
Sbjct: 70 VATDIFTGNRLEDQAPSTHNVEV 92
>pdb|1BKB|A Chain A, Initiation Factor 5a From Archebacterium Pyrobaculum
Aerophilum
Length = 136
Score = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 41/69 (59%)
Query: 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
+AG +++ Y+VI G PC+VVE+ SKTGKHG AK V + +F+G K +P +
Sbjct: 10 EAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVE 69
Query: 83 VLIYASLSA 91
V I +A
Sbjct: 70 VPIIEKFTA 78
>pdb|2EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 136
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 39/62 (62%)
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 LI 85
I
Sbjct: 73 PI 74
>pdb|1EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 135
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 39/62 (62%)
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 LI 85
I
Sbjct: 72 PI 73
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%)
Query: 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
Q ++ YI+I PC++V ++ S GKHG AK + IF+GK + P+S D
Sbjct: 8 QVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVD 67
Query: 83 VLIYASLSA 91
V I +A
Sbjct: 68 VPIIDKKTA 76
>pdb|1KHI|A Chain A, Crystal Structure Of Hex1
Length = 176
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 17/83 (20%)
Query: 3 DEEHHFESKADAGASKTFPQQAGT-----------IRKNGYIVIKGRPCKVVEVSTS-KT 50
D++ H +ADA T G+ IR ++++GRPC+V+ +STS T
Sbjct: 5 DDDAHGHVEADAAPRATTGTGTGSASQTVTIPCHHIRLGDILILQGRPCQVIRISTSAAT 64
Query: 51 GKHGHAKCHFVGIDIFNGKKLED 73
G+H ++G+D+F + E+
Sbjct: 65 GQH-----RYLGVDLFTKQLHEE 82
>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 = 28.9 bits (63), Expect = 0.68, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 15/50 (30%)
Query: 53 HGHAKCHFVGIDIFNGKKLEDIVPS---------------SHNCDVLIYA 87
H AK ++ + GKKLE+I PS S NCDVL A
Sbjct: 36 HPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTA 85
>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
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
0.322 0.138 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,106,619
Number of Sequences: 62578
Number of extensions: 108963
Number of successful extensions: 198
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 182
Number of HSP's gapped (non-prelim): 14
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)