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= 028908
(202 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LTM|A Chain A, Solution Nmr Structure Of Nfu1 Iron-Sulfur Cluster
Scaffold Homolog From Homo Sapiens, Northeast Structural
Genomics Consortium (Nesg) Target Hr2876b
Length = 107
Score = 118 bits (296), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 56/93 (60%), Positives = 71/93 (76%), Gaps = 1/93 (1%)
Query: 1 MFIQTQPTPNPSSLMFYPGKPVMEVGSADFPNARAAMNSPLAKSLYGVDGITRVFFGSDF 60
MFIQTQ TPNP+SL F PGKPV+E + DFP AA SPLA+ L+ ++G+ VFFG D
Sbjct: 11 MFIQTQDTPNPNSLKFIPGKPVLETRTMDFPTPAAAFRSPLARQLFRIEGVKSVFFGPDS 70
Query: 61 ITVTK-SEDTSWDLLKPEIFAAIMDFYSSGQPL 92
ITVTK +E+ W+LLKP+I+A IMDF++SG PL
Sbjct: 71 ITVTKENEELDWNLLKPDIYATIMDFFASGLPL 103
>pdb|1VEH|A Chain A, Solution Structure Of Rsgi Ruh-018, A Nifu-Like Domain Of
Hirip5 Protein From Mouse Cdna
Length = 92
Score = 109 bits (272), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/74 (67%), Positives = 62/74 (83%), Gaps = 2/74 (2%)
Query: 113 TVAMIKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIEN 172
VAMIKELL+TRIRP VQ+DGGD+ YRGF E G V+L++QG+C+ CPSS +TLKSGI+N
Sbjct: 14 VVAMIKELLDTRIRPTVQEDGGDVIYRGF--EDGIVRLKLQGSCTSCPSSIITLKSGIQN 71
Query: 173 MLMHYVPEVKSVEQ 186
ML Y+PEV+ VEQ
Sbjct: 72 MLQFYIPEVEGVEQ 85
>pdb|1XHJ|A Chain A, Solution Structure Of The Staphylococcus Epidermidis
Protein Se0630. Northest Structural Genomics Consortium
Target Ser8
Length = 88
Score = 65.1 bits (157), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 35/70 (50%), Positives = 45/70 (64%), Gaps = 3/70 (4%)
Query: 117 IKELLETRIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMH 176
+ E++E R+RP + DGGD D E G VKL++ GAC CPSS++TLK+GIE L
Sbjct: 12 VAEVIE-RLRPFLLRDGGDCTL--VDVEDGIVKLQLHGACGTCPSSTITLKAGIERALHE 68
Query: 177 YVPEVKSVEQ 186
VP V VEQ
Sbjct: 69 EVPGVIEVEQ 78
>pdb|2Z51|A Chain A, Crystal Structure Of Arabidopsis Cnfu Involved In Iron-
Sulfur Cluster Biosynthesis
Length = 154
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/67 (43%), Positives = 42/67 (62%), Gaps = 2/67 (2%)
Query: 125 IRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKSV 184
IRP + DGG++ D V++++QGAC CPSS++T+K GIE LM +PE+ +V
Sbjct: 16 IRPYLMSDGGNVALHEID--GNVVRVKLQGACGSCPSSTMTMKMGIERRLMEKIPEIVAV 73
Query: 185 EQELDAE 191
E D E
Sbjct: 74 EALPDEE 80
>pdb|2JNV|A Chain A, Solution Structure Of C-Terminal Domain Of Nifu-Like
Protein From Oryza Sativa
Length = 91
Score = 61.2 bits (147), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 29/68 (42%), Positives = 42/68 (61%), Gaps = 2/68 (2%)
Query: 124 RIRPAVQDDGGDIEYRGFDPETGTVKLRMQGACSGCPSSSVTLKSGIENMLMHYVPEVKS 183
++RP + DGGD+ + V+L++QGAC CPSS +T+K GIE LM +P+V +
Sbjct: 16 QVRPYLTADGGDVAL--HEIAGNVVRLKLQGACGSCPSSLITIKRGIERRLMEKIPDVAA 73
Query: 184 VEQELDAE 191
VE D E
Sbjct: 74 VEPVTDKE 81
>pdb|2LTL|A Chain A, Solution Nmr Structure Of Nifu-Like Protein From
Saccharomyces Cerevisiae, Northeast Structural Genomics
Consortium (Nesg) Target Yr313a
Length = 119
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 1 MFIQTQPTPNPSSLMFYP--GKPVMEVGSADF----PNARAAMNSPLAKSLY-GVDGITR 53
+ I+T TPN ++L F G+ + GS + +S LA+ ++ G+
Sbjct: 17 IHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVES 76
Query: 54 VFFGSDFITVTKSEDTSWDLLKPEIF 79
+ G DF+T+ K W+ +KPEI
Sbjct: 77 LMIGDDFLTINKDRMVHWNSIKPEII 102
>pdb|2K1H|A Chain A, Solution Nmr Structure Of Ser13 From Staphylococcus
Epidermidis. Northeast Structural Genomics Consortium
Target Ser13
Length = 94
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 24/34 (70%)
Query: 45 LYGVDGITRVFFGSDFITVTKSEDTSWDLLKPEI 78
L+ ++G+ +F+ DFI++ K ++ +W+ L P+I
Sbjct: 45 LFEIEGVKSIFYVLDFISIDKEDNANWNELLPQI 78
>pdb|2FFM|A Chain A, X-Ray Crystal Structure Of Protein Sav1430 From
Staphylococcus Aureus. Northeast Structural Genomics
Consortium Target Zr18
Length = 91
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 45 LYGVDGITRVFFGSDFITVTKSEDTSWDLLKPEIFAA 81
+ V+G+ +F DFI+V K D +W+ + P++ A
Sbjct: 45 ILKVEGVKSIFHVXDFISVDKENDANWETVLPKVEAV 81
>pdb|1PQX|A Chain A, Solution Nmr Structure Of Staphylococcus Aureus Protein
Sav1430. Northeast Strucutral Genomics Consortium
Target Zr18
Length = 91
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 45 LYGVDGITRVFFGSDFITVTKSEDTSWDLLKPEIFAA 81
+ V+G+ +F DFI+V K D +W+ + P++ A
Sbjct: 45 ILKVEGVKSIFHVMDFISVDKENDANWETVLPKVEAV 81
>pdb|4FSJ|A Chain A, Crystal Structure Of The Virus Like Particle Of Flock
House Virus
pdb|4FSJ|B Chain B, Crystal Structure Of The Virus Like Particle Of Flock
House Virus
pdb|4FSJ|C Chain C, Crystal Structure Of The Virus Like Particle Of Flock
House Virus
pdb|4FTB|A Chain A, Crystal Structure Of The Authentic Flock House Virus
Particle
pdb|4FTB|B Chain B, Crystal Structure Of The Authentic Flock House Virus
Particle
pdb|4FTB|C Chain C, Crystal Structure Of The Authentic Flock House Virus
Particle
Length = 363
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 59/145 (40%), Gaps = 18/145 (12%)
Query: 12 SSLMFYPG-----KPVMEVGSADFPNARAAMNSPLAKSLYGVDGITRV---FFGSDFI-- 61
S+LM + G K +++ + FP A S L +L G+DG+ V F FI
Sbjct: 179 SNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKG 238
Query: 62 TVTKSEDTSWDLLKPEIFAAI-------MDFYSSGQPLFLDSETAAAKDTAINEDDSETV 114
++S D +I I + S+GQP +DS A A + + +T+
Sbjct: 239 VFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSG-AEATSGVVGWGNMDTI 297
Query: 115 AMIKELLETRIRPAVQDDGGDIEYR 139
+ E + A+ IEYR
Sbjct: 298 VIRVSAPEGAVNSAILKAWSCIEYR 322
>pdb|4FTS|A Chain A, Crystal Structure Of The N363t Mutant Of The Flock House
Virus Capsid
pdb|4FTS|B Chain B, Crystal Structure Of The N363t Mutant Of The Flock House
Virus Capsid
pdb|4FTS|C Chain C, Crystal Structure Of The N363t Mutant Of The Flock House
Virus Capsid
Length = 407
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 59/145 (40%), Gaps = 18/145 (12%)
Query: 12 SSLMFYPG-----KPVMEVGSADFPNARAAMNSPLAKSLYGVDGITRV---FFGSDFI-- 61
S+LM + G K +++ + FP A S L +L G+DG+ V F FI
Sbjct: 179 SNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKG 238
Query: 62 TVTKSEDTSWDLLKPEIFAAI-------MDFYSSGQPLFLDSETAAAKDTAINEDDSETV 114
++S D +I I + S+GQP +DS A A + + +T+
Sbjct: 239 VFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSG-AEATSGVVGWGNMDTI 297
Query: 115 AMIKELLETRIRPAVQDDGGDIEYR 139
+ E + A+ IEYR
Sbjct: 298 VIRVSAPEGAVNSAILKAWSCIEYR 322
>pdb|4FTE|A Chain A, Crystal Structure Of The D75n Mutant Capsid Of Flock House
Virus
pdb|4FTE|B Chain B, Crystal Structure Of The D75n Mutant Capsid Of Flock House
Virus
pdb|4FTE|C Chain C, Crystal Structure Of The D75n Mutant Capsid Of Flock House
Virus
Length = 407
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 59/145 (40%), Gaps = 18/145 (12%)
Query: 12 SSLMFYPG-----KPVMEVGSADFPNARAAMNSPLAKSLYGVDGITRV---FFGSDFI-- 61
S+LM + G K +++ + FP A S L +L G+DG+ V F FI
Sbjct: 179 SNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKG 238
Query: 62 TVTKSEDTSWDLLKPEIFAAI-------MDFYSSGQPLFLDSETAAAKDTAINEDDSETV 114
++S D +I I + S+GQP +DS A A + + +T+
Sbjct: 239 VFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSG-AEATSGVVGWGNMDTI 297
Query: 115 AMIKELLETRIRPAVQDDGGDIEYR 139
+ E + A+ IEYR
Sbjct: 298 VIRVSAPEGAVNSAILKAWSCIEYR 322
>pdb|1RW9|A Chain A, Crystal Structure Of The Arthrobacter Aurescens
Chondroitin Ac Lyase
Length = 757
Score = 26.9 bits (58), Expect = 6.9, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 19 GKPVMEVGSADFPNARAAMNSPLAKSLYGVD---GITRVF 55
G+ V++ G DF A A+N+ A SL +D G T VF
Sbjct: 22 GRNVIQAGDPDFAKAITALNNKAADSLAKLDVKKGRTSVF 61
>pdb|1RWA|A Chain A, Crystal Structure Of Arthrobacter Aurescens Chondroitin
Ac Lyase
pdb|1RWC|A Chain A, Crystal Structure Of Arthrobacter Aurescens Chondroitin
Ac Lyase
pdb|1RWF|A Chain A, Crystal Structure Of Arthrobacter Aurescens Chondroitin
Ac Lyase In Complex With Chondroitin Tetrasaccharide
pdb|1RWG|A Chain A, Crystal Structure Of Arthrobacter Aurescens Chondroitin
Ac Lyase In Complex With Chondroitin Tetrasaccharide
pdb|1RWH|A Chain A, Crystal Structure Of Arthrobacter Aurescens Chondroitin
Ac Lyase In Complex With Chondroitin Tetrasaccharide
Length = 757
Score = 26.9 bits (58), Expect = 7.2, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 19 GKPVMEVGSADFPNARAAMNSPLAKSLYGVD---GITRVF 55
G+ V++ G DF A A+N+ A SL +D G T VF
Sbjct: 22 GRNVIQAGDPDFAKAITALNNKAADSLAKLDAAAGRTSVF 61
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 0.131 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,007,426
Number of Sequences: 62578
Number of extensions: 238606
Number of successful extensions: 547
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 535
Number of HSP's gapped (non-prelim): 14
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)