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= 039455
(216 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PBR|A Chain A, Crystal Structure Of Thymidylate Kinase (Aq_969) From
Aquifex Aeolicus Vf5
pdb|2PBR|B Chain B, Crystal Structure Of Thymidylate Kinase (Aq_969) From
Aquifex Aeolicus Vf5
Length = 195
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 51 FIGICGMGGIGKTTLAKVLYNTLKDQFEASSFLANVREVSVTRGLVPLQEQLLSEVLMER 110
I G+ G GKTT AK LY LK + F++ RE T+ L+E LL+E L ER
Sbjct: 2 LIAFEGIDGSGKTTQAKKLYEYLKQK---GYFVSLYREPGGTKVGEVLREILLTEELDER 58
Query: 111 N-LIIWDVHKG 120
L++++ +
Sbjct: 59 TELLLFEASRS 69
>pdb|3PFI|A Chain A, 2.7 Angstrom Resolution Crystal Structure Of A Probable
Holliday Junction Dna Helicase (Ruvb) From
Campylobacter Jejuni Subsp. Jejuni Nctc 11168 In
Complex With Adenosine-5'-Diphosphate
pdb|3PFI|B Chain B, 2.7 Angstrom Resolution Crystal Structure Of A Probable
Holliday Junction Dna Helicase (Ruvb) From
Campylobacter Jejuni Subsp. Jejuni Nctc 11168 In
Complex With Adenosine-5'-Diphosphate
Length = 338
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 9/54 (16%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAG------LDDVRFIGICGMGGIGKTTLAKVL 69
PS DG +G S + +N ++ A LD + F G G+GKTTLA ++
Sbjct: 25 PSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILF---SGPAGLGKTTLANII 75
>pdb|3OZX|A Chain A, Crystal Structure Of Abce1 Of Sulfolubus Solfataricus
(-Fes Domain)
pdb|3OZX|B Chain B, Crystal Structure Of Abce1 Of Sulfolubus Solfataricus
(-Fes Domain)
Length = 538
Score = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 16/53 (30%)
Query: 52 IGICGMGGIGKTTLAKVLYNTLKDQFEASSFLANVREVSVTRGLVPLQEQLLS 104
IGI G GIGKTT A++L V E++ G V ++Q+LS
Sbjct: 297 IGILGPNGIGKTTFARIL----------------VGEITADEGSVTPEKQILS 333
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 37 KMNGYLEAGLDDVR---FIGICGMGGIGKTTLAKVL 69
K+NG+ GL + +G+ G G+GKTT+ K+L
Sbjct: 10 KVNGFKLFGLPTPKNNTILGVLGKNGVGKTTVLKIL 45
>pdb|1W5S|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp
Form)
pdb|1W5S|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp
Form)
pdb|1W5T|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein
(Adpnp-Adp Complexes)
pdb|1W5T|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein
(Adpnp-Adp Complexes)
pdb|1W5T|C Chain C, Structure Of The Aeropyrum Pernix Orc2 Protein
(Adpnp-Adp Complexes)
Length = 412
Score = 30.0 bits (66), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 21/39 (53%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 44 AGLDDVRFI-GICGMGGIGKTTLAKVLYNTLKDQFEASS 81
AGL DV I G G GIGKTTLAK T+K EA++
Sbjct: 46 AGLSDVNMIYGSIGRVGIGKTTLAKF---TVKRVSEAAA 81
>pdb|2IW3|A Chain A, Elongation Factor 3 In Complex With Adp
pdb|2IW3|B Chain B, Elongation Factor 3 In Complex With Adp
Length = 986
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 46 LDDVRFIGICGMGGIGKTTLAKVLYNTLKDQF 77
L R GICG G GK+TL + + N D F
Sbjct: 458 LKRARRYGICGPNGCGKSTLXRAIANGQVDGF 489
>pdb|2IX8|A Chain A, Model For Eef3 Bound To An 80s Ribosome
Length = 976
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 46 LDDVRFIGICGMGGIGKTTLAKVLYNTLKDQF 77
L R GICG G GK+TL + + N D F
Sbjct: 452 LKRARRYGICGPNGCGKSTLXRAIANGQVDGF 483
>pdb|1IXR|C Chain C, Ruva-Ruvb Complex
Length = 312
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAGL---DDVRFIGICGMGGIGKTTLAKVLYNTLKDQFE 78
P +D +G +K+ YLEA + + + + G G+GKTTLA V+ + L
Sbjct: 8 PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLR 67
Query: 79 ASS 81
+S
Sbjct: 68 VTS 70
>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii
Length = 318
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAGL---DDVRFIGICGMGGIGKTTLAKVLYNTLKDQFE 78
P +D +G +K+ YLEA + + + + G G+GKTTLA V+ + L
Sbjct: 8 PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLR 67
Query: 79 ASS 81
+S
Sbjct: 68 VTS 70
>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8
pdb|1HQC|B Chain B, Structure Of Ruvb From Thermus Thermophilus Hb8
Length = 324
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAGL---DDVRFIGICGMGGIGKTTLAKVLYNTLKDQFE 78
P +D +G +K+ YLEA + + + + G G+GKTTLA V+ + L
Sbjct: 8 PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLR 67
Query: 79 ASS 81
+S
Sbjct: 68 VTS 70
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 41 YLEAGLDDVRFIGICGMGGIGKTTLAKVLYNTLKDQF 77
Y + G+D R + + G G GKT L K + N+ K F
Sbjct: 198 YEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAF 234
>pdb|2IWH|A Chain A, Structure Of Yeast Elongation Factor 3 In Complex With
Adpnp
pdb|2IWH|B Chain B, Structure Of Yeast Elongation Factor 3 In Complex With
Adpnp
pdb|2IX3|A Chain A, Structure Of Yeast Elongation Factor 3
pdb|2IX3|B Chain B, Structure Of Yeast Elongation Factor 3
Length = 986
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 46 LDDVRFIGICGMGGIGKTTLAKVLYNTLKDQF 77
L R GICG G GK+TL + + N D F
Sbjct: 458 LKRARRYGICGPNGCGKSTLMRAIANGQVDGF 489
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAG------LDDVRFIGICGMGGIGKTTLAKVLYNTLKD 75
P ++D +G + +K++ LEA LD V + G G+GKTTLA ++ + L+
Sbjct: 21 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVL---LAGPPGLGKTTLAHIIASELQT 77
Query: 76 QFEASS 81
+S
Sbjct: 78 NIHVTS 83
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAG------LDDVRFIGICGMGGIGKTTLAKVLYNTLKD 75
P ++D +G + +K++ LEA LD V + G G+GKTTLA ++ + L+
Sbjct: 21 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVL---LAGPPGLGKTTLAHIIASELQT 77
Query: 76 QFEASS 81
+S
Sbjct: 78 NIHVTS 83
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
Migration Motor
Length = 334
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAG------LDDVRFIGICGMGGIGKTTLAKVLYNTLKD 75
P ++D +G + +K++ LEA LD V + G G+GKTTLA ++ + L+
Sbjct: 21 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVL---LAGPPGLGKTTLAHIIASELQT 77
Query: 76 QFEASS 81
+S
Sbjct: 78 NIHVTS 83
>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
Length = 334
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAG------LDDVRFIGICGMGGIGKTTLAKVLYNTLKD 75
P ++D +G + +K++ LEA LD V + G G+GKTTLA ++ + L+
Sbjct: 21 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVL---LAGPPGLGKTTLAHIIASELQT 77
Query: 76 QFEASS 81
+S
Sbjct: 78 NIHVTS 83
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAG------LDDVRFIGICGMGGIGKTTLAKVLYNTLKD 75
P ++D +G + +K++ LEA LD V + G G+GKTTLA ++ + L+
Sbjct: 21 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVL---LAGPPGLGKTTLAHIIASELQT 77
Query: 76 QFEASS 81
+S
Sbjct: 78 NIHVTS 83
>pdb|1Z6G|A Chain A, Crystal Structure Of Guanylate Kinase From Plasmodium
Falciparum
Length = 218
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 44 AGLDDVRFIGICGMGGIGKTTLAKVLYNTLKDQFEAS 80
++++ + ICG G+GK TL K L N + F S
Sbjct: 18 GSMNNIYPLVICGPSGVGKGTLIKKLLNEFPNYFYFS 54
>pdb|3LV8|A Chain A, 1.8 Angstrom Resolution Crystal Structure Of A
Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Tmp,
Thymidine-5'-Diphosphate And Adp
pdb|3N2I|A Chain A, 2.25 Angstrom Resolution Crystal Structure Of A
Thymidylate Kinase (tmk) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Thymidine
pdb|3N2I|B Chain B, 2.25 Angstrom Resolution Crystal Structure Of A
Thymidylate Kinase (tmk) From Vibrio Cholerae O1 Biovar
Eltor Str. N16961 In Complex With Thymidine
Length = 236
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 39 NGYLEAGLDDVRFIGICGMGGIGKTTLAKVLYNTLK 74
N Y ++ + +FI I G+ G GK+T +V+ TL+
Sbjct: 17 NLYFQSNAMNAKFIVIEGLEGAGKSTAIQVVVETLQ 52
>pdb|1RZ3|A Chain A, Structure Of A Possible Uridine Kinase From Bacillus
Stearothermophilus
Length = 201
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 52 IGICGMGGIGKTTLAKVLYNTLKDQ 76
+GI G+ GKTTLA L TL++Q
Sbjct: 25 LGIDGLSRSGKTTLANQLSQTLREQ 49
>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant
Length = 334
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 22 PSAVDGLVGIASRMEKMNGYLEAG------LDDVRFIGICGMGGIGKTTLAKVLYNTLKD 75
P ++D +G + +K++ LEA LD V + G G+G+TTLA ++ + L+
Sbjct: 21 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVL---LAGPPGLGRTTLAHIIASELQT 77
Query: 76 QFEASS 81
+S
Sbjct: 78 NIHVTS 83
>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
Length = 543
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 54 ICGMGGIGKTTLAKVLYNTLKDQFEASSFLANVREVSVTRG 94
+ G G+GKT+LAK + +L +F S L VR+ S RG
Sbjct: 113 LAGPPGVGKTSLAKSIAKSLGRKFVRIS-LGGVRDESEIRG 152
>pdb|1UGK|A Chain A, Solution Structure Of The First C2 Domain Of Synaptotagmin
Iv From Human Fetal Brain (Kiaa1342)
Length = 138
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 8/65 (12%)
Query: 68 VLYNTLKDQFEASSFLANVREVSVTRGLVPLQEQ-LLSEVLMERNLIIWDVHKGINLIRW 126
L+ +L+ FE +F+ N++E RGL + EQ + S+ ++ ++ HK ++
Sbjct: 10 TLFFSLEYNFERKAFVVNIKEA---RGLPAMDEQSMTSDPYIKMTILPEKKHK----VKT 62
Query: 127 RLCRK 131
R+ RK
Sbjct: 63 RVLRK 67
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 27.3 bits (59), Expect = 7.1, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 40 GYLEAGLDDVRFIGICGMGGIGKT-TLAKVL 69
G +EA D RF+ + G G GKT T+AKV+
Sbjct: 20 GLVEALRDGERFVTLLGATGTGKTVTMAKVI 50
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 27.3 bits (59), Expect = 7.1, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 40 GYLEAGLDDVRFIGICGMGGIGKT-TLAKVL 69
G +EA D RF+ + G G GKT T+AKV+
Sbjct: 19 GLVEALRDGERFVTLLGATGTGKTVTMAKVI 49
>pdb|1YQT|A Chain A, Rnase-L Inhibitor
Length = 538
Score = 26.9 bits (58), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 12 EISKRLNPTFPSAVDGLVGIASRMEKMNGYLEAGLDDVRFIGICGMGGIGKTTLAKVL 69
EI + T+P V R+E G ++ G IGI G GIGKTT K L
Sbjct: 281 EIERETLVTYPRLVKDYGSF--RLEVEPGEIKKG----EVIGIVGPNGIGKTTFVKXL 332
>pdb|3BK7|A Chain A, Structure Of The Complete Abce1RNAASE-L Inhibitor Protein
From Pyrococcus Abysii
Length = 607
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 52 IGICGMGGIGKTTLAKVL 69
IGI G GIGKTT K+L
Sbjct: 385 IGIVGPNGIGKTTFVKML 402
>pdb|3J15|B Chain B, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 593
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 52 IGICGMGGIGKTTLAKVL 69
IGI G GIGKTT K+L
Sbjct: 371 IGIVGPNGIGKTTFVKML 388
>pdb|3TXO|A Chain A, Pkc Eta Kinase In Complex With A Naphthyridine
Length = 353
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 45 GLDDVRFIGICGMGGIGKTTLAKV 68
G+D+ FI + G G GK LA+V
Sbjct: 21 GIDNFEFIRVLGKGSFGKVMLARV 44
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 0.140 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,702,192
Number of Sequences: 62578
Number of extensions: 203566
Number of successful extensions: 735
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 714
Number of HSP's gapped (non-prelim): 41
length of query: 216
length of database: 14,973,337
effective HSP length: 95
effective length of query: 121
effective length of database: 9,028,427
effective search space: 1092439667
effective search space used: 1092439667
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: 49 (23.5 bits)