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= 000449
(1497 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form I
pdb|3BZK|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form 2
Length = 785
Score = 53.1 bits (126), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/109 (28%), Positives = 59/109 (54%), Gaps = 13/109 (11%)
Query: 1357 SDLSTDVDTPGKH-------------LEKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLD 1403
+D+ ++D PG+ +E ++DL P M+++G V NVT+ G F+ + D
Sbjct: 620 TDILKELDKPGRDPRPEFKTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQD 679
Query: 1404 AKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452
V +S LS+ +V+ P + G +V +V+ V+ RV ++++ SD+
Sbjct: 680 GLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSDT 728
Score = 35.8 bits (81), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 481 LKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSE------F 534
K + F+ V + D+KPGMV++G V V +FGA V L + +SE +
Sbjct: 637 FKTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPY 696
Query: 535 EIVKPGKKFKV 545
E+VK G KV
Sbjct: 697 EVVKAGDIVKV 707
>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From
Pseudomonas Aeruginosa
Length = 780
Score = 53.1 bits (126), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/109 (28%), Positives = 59/109 (54%), Gaps = 13/109 (11%)
Query: 1357 SDLSTDVDTPGKH-------------LEKIEDLSPNMIVQGYVKNVTSKGCFIMLSRKLD 1403
+D+ ++D PG+ +E ++DL P M+++G V NVT+ G F+ + D
Sbjct: 621 TDILKELDKPGRDPRPEFKTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQD 680
Query: 1404 AKVLLSNLSDGYVESPEKEFPIGKLVAGRVLSVEPLSKRVEVTLKTSDS 1452
V +S LS+ +V+ P + G +V +V+ V+ RV ++++ SD+
Sbjct: 681 GLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSDT 729
Score = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 481 LKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSE------F 534
K + F+ V + D+KPGMV++G V V +FGA V L + +SE +
Sbjct: 638 FKTAEFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPY 697
Query: 535 EIVKPGKKFKV 545
E+VK G KV
Sbjct: 698 EVVKAGDIVKV 708
>pdb|1WI5|A Chain A, Solution Structure Of The S1 Rna Binding Domain From Human
Hypothetical Protein Baa11502
Length = 119
Score = 46.6 bits (109), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 5/97 (5%)
Query: 228 ETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAE-----NSGIDVKPGLLLQG 282
E ++ GM+LT V S+EDHGY++ G+ FLP E N G +K G L
Sbjct: 17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNC 76
Query: 283 VVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLL 319
+V + VV LS VS + + + +++ L
Sbjct: 77 IVEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNNL 113
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 36.2 bits (82), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNI 816
+ I V G V I++ G FV G G S+ D + ++ +GQ V +
Sbjct: 623 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 682
Query: 817 LDVNSETGRITLSLKQSCCSS 837
L+V+ + GRI LS+K++ S
Sbjct: 683 LEVDRQ-GRIRLSIKEATEQS 702
Score = 33.5 bits (75), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 51/105 (48%), Gaps = 10/105 (9%)
Query: 479 GILKASAFEGLVFTHS---------DVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLP 529
G +K +A +G H+ +++ G V GKV + FGA V GG + L +
Sbjct: 599 GTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHIS 658
Query: 530 HMSEFEIVKPGKKFKVGAELVFRVLGV-KSKRITVTHKKTLVKSK 573
+++ + K ++G E+ +VL V + RI ++ K+ +S+
Sbjct: 659 QIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEATEQSQ 703
>pdb|2CQO|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Hypothetical Protein Flj11067
Length = 119
Score = 33.9 bits (76), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 501 VVKGKVIAVDSFGAIVQFPGGVK-ALCPLPHMSEFEIVKPGKKFKVGAELVFRVLG--VK 557
+ +G+V V +GA ++ PG K L HMS + KP + VG ++ +++G +K
Sbjct: 25 IFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMK 84
Query: 558 SKRITVT 564
+ RI V+
Sbjct: 85 NDRIKVS 91
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 33.5 bits (75), Expect = 1.0, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNI 816
+ I V G V I++ G FV G G S+ D + ++ +GQ V +
Sbjct: 1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 60
Query: 817 LDVNSETGRITLSLKQS 833
L+V+ + GRI LS+K++
Sbjct: 61 LEVDRQ-GRIRLSIKEA 76
Score = 32.7 bits (73), Expect = 1.6, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 494 SDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRV 553
++++ G V GKV + FGA V GG + L + +++ + K ++G E+ +V
Sbjct: 1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 60
Query: 554 LGV-KSKRITVTHKK 567
L V + RI ++ K+
Sbjct: 61 LEVDRQGRIRLSIKE 75
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 9/90 (10%)
Query: 479 GILKASAFEGLVFTHS---------DVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLP 529
G++K SA +G + + + G + GKV+ V FGA V F G L +
Sbjct: 609 GVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVS 668
Query: 530 HMSEFEIVKPGKKFKVGAELVFRVLGVKSK 559
+S + KP K G + ++LG +
Sbjct: 669 QISNERVAKPSDVLKEGQMVKVKLLGFDDR 698
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 588 ITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIM 641
I G + K+ G FV F+ G S++ + +PS + GQ+VK +++
Sbjct: 640 IYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLL 693
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 33.1 bits (74), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 9/90 (10%)
Query: 479 GILKASAFEGLVFTHS---------DVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLP 529
G++K SA +G + + + G + GKV+ V FGA V F G L +
Sbjct: 600 GVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVS 659
Query: 530 HMSEFEIVKPGKKFKVGAELVFRVLGVKSK 559
+S + KP K G + ++LG +
Sbjct: 660 QISNERVAKPSDVLKEGQMVKVKLLGFDDR 689
Score = 31.6 bits (70), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 588 ITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIM 641
I G + K+ G FV F+ G S++ + +PS + GQ+VK +++
Sbjct: 631 IYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLL 684
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 33.1 bits (74), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 9/90 (10%)
Query: 479 GILKASAFEGLVFTHS---------DVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLP 529
G++K SA +G + + + G + GKV+ V FGA V F G L +
Sbjct: 609 GVVKVSASDGAKIKAAIDWIKSITDEAEIGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVS 668
Query: 530 HMSEFEIVKPGKKFKVGAELVFRVLGVKSK 559
+S + KP K G + ++LG +
Sbjct: 669 QISNERVAKPSDVLKEGQMVKVKLLGFDDR 698
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 588 ITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIM 641
I G + K+ G FV F+ G S++ + +PS + GQ+VK +++
Sbjct: 640 IYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLL 693
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 32.3 bits (72), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 767 GYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADL--SKTYYVGQSVRSNILDVNSETG 824
G V N+ + GCFV + G S+ +D ++ SK VG V +LD++ E
Sbjct: 36 GRVTNLTDYGCFVEIEEGVEGLVHVSE-MDWTNKNIHPSKVVNVGDVVEVMVLDIDEERR 94
Query: 825 RITLSLKQSCCSSTDASFMQEH 846
RI+L LKQ C ++ F + H
Sbjct: 95 RISLGLKQ-CKANPWQQFAETH 115
>pdb|2KHJ|A Chain A, Nmr Structure Of The Domain 6 Of The E. Coli Ribosomal
Protein S1
Length = 109
Score = 32.0 bits (71), Expect = 2.5, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 30/68 (44%)
Query: 497 KPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGV 556
K G +V GKV AVD+ GA V+ GV+ S + VG E+ + GV
Sbjct: 30 KKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGV 89
Query: 557 KSKRITVT 564
K ++
Sbjct: 90 DRKNRAIS 97
>pdb|2X3D|A Chain A, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
pdb|2X3D|B Chain B, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
pdb|2X3D|C Chain C, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
pdb|2X3D|D Chain D, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
pdb|2X3D|E Chain E, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
pdb|2X3D|F Chain F, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
pdb|2X3D|G Chain G, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
pdb|2X3D|H Chain H, Crystal Structure Of Sso6206 From Sulfolobus Solfataricus P2
Length = 96
Score = 32.0 bits (71), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 1320 GQFVKCKVLEISRTVRGTFHVELSLR-SSLDGMSSTNSSDLSTDVDTPGKHLEKIEDLSP 1378
G ++ VL++ + +RGT V+L+ R S LDG+ N S DV+T G + IE S
Sbjct: 1 GMAIRRLVLDVLKPIRGTSIVDLAERISKLDGVEGVNISVTDMDVETMGLMI-IIEGTSL 59
Query: 1379 NMIVQGYVKNVTSKGCFI 1396
N K + +GC I
Sbjct: 60 NF--DDIRKMLEEEGCAI 75
>pdb|1IOK|A Chain A, Crystal Structure Of Chaperonin-60 From Paracoccus
Denitrificans
pdb|1IOK|B Chain B, Crystal Structure Of Chaperonin-60 From Paracoccus
Denitrificans
pdb|1IOK|C Chain C, Crystal Structure Of Chaperonin-60 From Paracoccus
Denitrificans
pdb|1IOK|D Chain D, Crystal Structure Of Chaperonin-60 From Paracoccus
Denitrificans
pdb|1IOK|E Chain E, Crystal Structure Of Chaperonin-60 From Paracoccus
Denitrificans
pdb|1IOK|F Chain F, Crystal Structure Of Chaperonin-60 From Paracoccus
Denitrificans
pdb|1IOK|G Chain G, Crystal Structure Of Chaperonin-60 From Paracoccus
Denitrificans
Length = 545
Score = 30.4 bits (67), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 10/56 (17%)
Query: 875 GSVIEGKVHESND--FGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVA 928
G+V+ GKV ES+D FG EE+ D++ F ++ V++ A+ D A
Sbjct: 462 GAVVAGKVRESSDKAFGFNAQTEEYGDMFKF--------GVIDPAKVVRTALEDAA 509
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
0.318 0.135 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 38,733,025
Number of Sequences: 62578
Number of extensions: 1482514
Number of successful extensions: 3433
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 3376
Number of HSP's gapped (non-prelim): 60
length of query: 1497
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1386
effective length of database: 8,027,179
effective search space: 11125670094
effective search space used: 11125670094
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)