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= 041183
(760 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 35.8 bits (81), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 54/120 (45%), Gaps = 6/120 (5%)
Query: 529 IEDAKRAFRKICRDSLAGWNAMMMGYAQHGCYHEVSNLFNKMSKFGVKPDEITYLAVLTS 588
+ +R RK+ +L +NA+M+G+A+ G + E+ + + G+ PD ++Y A L
Sbjct: 152 VHHGQRQKRKLL--TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ- 208
Query: 589 CCHAGLVREARTYLSCMSDL--HGLIPQLEHYACIVDLLGRVGLLEGAKMTIDQMPIPPD 646
C ++A T C+ + GL Q A ++ R +L+ +PP
Sbjct: 209 -CMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQ 267
>pdb|4AV2|M Chain M, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|N Chain N, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|O Chain O, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|P Chain P, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|Q Chain Q, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|R Chain R, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|S Chain S, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|T Chain T, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|U Chain U, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|V Chain V, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|W Chain W, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis.
pdb|4AV2|X Chain X, Single Particle Electron Microscopy Of Pilq Dodecameric
Complexes From Neisseria Meningitidis
Length = 181
Score = 35.8 bits (81), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 291 ILRAGKQIQAFCYKVGFMEVVSIGNALISMYGKCGQVNDARSIFDYLIFKDSVSWNSMIA 350
IL++G+++ F G++ V +GN L YG+ + D + + LI + +W S A
Sbjct: 100 ILKSGQKVSGFIEAEGYVYTVGVGNYLGQNYGRIESITDDSIVLNELIEDSTGNWVSRKA 159
>pdb|2IVW|A Chain A, The Solution Structure Of A Domain From The Neisseria
Meningitidis Pilp Pilot Protein
Length = 113
Score = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 291 ILRAGKQIQAFCYKVGFMEVVSIGNALISMYGKCGQVNDARSIFDYLIFKDSVSWNS 347
IL++G+++ F G++ V +GN L YG+ + D + + LI + +W S
Sbjct: 32 ILKSGQKVSGFIEAEGYVYTVGVGNYLGQNYGRIESITDDSIVLNELIEDSTGNWVS 88
>pdb|3MKR|A Chain A, Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomplex Of
The Copi Vesicular Coat
Length = 291
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 52/237 (21%), Positives = 90/237 (37%), Gaps = 43/237 (18%)
Query: 434 VLSEIDKKNAVHINALASVLVYASCHAE----ALELYRTIWGSCREVNGSTFSIVLKAC- 488
VL EI +A + A+ Y + H+ EL R + S +V +TF ++ +
Sbjct: 53 VLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSV-DVTNTTFLLMAASIY 111
Query: 489 -------AAMTDLEQGKAIHCLA------------------LKARYDQD-----IFVESA 518
AA+ L QG ++ C+A LK DQD + +A
Sbjct: 112 FYDQNPDAALRTLHQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATA 171
Query: 519 VIDMYCKCGTIEDAKRAFRKI---CRDSLAGWNAMMMGYAQHGCYHEVSNLFNK-MSKFG 574
+ + ++DA F+++ C +L N + G + + + + K
Sbjct: 172 WVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDS 231
Query: 575 VKPDEITYLAVLTSCCHAGLVRE-ARTYLSCMSDLHGLIPQLEHYACIVDLLGRVGL 630
P+ + L VL+ H G E YLS + D H P ++ Y + R+ L
Sbjct: 232 GHPETLINLVVLSQ--HLGKPPEVTNRYLSQLKDAHRSHPFIKEYRAKENDFDRLVL 286
>pdb|4F7Z|A Chain A, Conformational Dynamics Of Exchange Protein Directly
Activated By Camp
Length = 999
Score = 29.3 bits (64), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 2/75 (2%)
Query: 99 IVHGVCLKLGFSSRVYLVSGFIENYAKSGEIVSAEMCFRDCLDLDNVAYTAMVCGYVWNG 158
+V VCL S RV L+ FI+ A E + F + L NVA + + W
Sbjct: 815 VVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRL--ALTWEK 872
Query: 159 EFDKSKEVFVEMRSL 173
K K+ + E SL
Sbjct: 873 LPSKFKKFYAEFESL 887
>pdb|2BYV|E Chain E, Structure Of The Camp Responsive Exchange Factor Epac2 In
Its Auto-Inhibited State
Length = 999
Score = 29.3 bits (64), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 2/75 (2%)
Query: 99 IVHGVCLKLGFSSRVYLVSGFIENYAKSGEIVSAEMCFRDCLDLDNVAYTAMVCGYVWNG 158
+V VCL S RV L+ FI+ A E + F + L NVA + + W
Sbjct: 815 VVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRL--ALTWEK 872
Query: 159 EFDKSKEVFVEMRSL 173
K K+ + E SL
Sbjct: 873 LPSKFKKFYAEFESL 887
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
0.323 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,556,067
Number of Sequences: 62578
Number of extensions: 846801
Number of successful extensions: 1572
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1566
Number of HSP's gapped (non-prelim): 11
length of query: 760
length of database: 14,973,337
effective HSP length: 106
effective length of query: 654
effective length of database: 8,340,069
effective search space: 5454405126
effective search space used: 5454405126
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)