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= 007077
(619 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 33.1 bits (74), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 33/135 (24%), Positives = 62/135 (45%), Gaps = 22/135 (16%)
Query: 363 IEMYAKCGLIEKALEIFYELREKDAASWTSI-------ICGLA-------MNGKINKALE 408
++M +K G + +AL ++ E R ++ + +C LA N +++ +
Sbjct: 33 LDMCSKKGDVLEALRLYDEAR-RNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFD 91
Query: 409 LFSQMISGGAKPDDITFI-GVLSACSHGGLVDEGRRFFNTMTEV--YQIQPKLEHYGCLI 465
+F QMI P++ TF G A + D+ F+ + ++ + IQP+L YG +
Sbjct: 92 IFKQMIVDKVVPNEATFTNGARLAVAK----DDPEMAFDMVKQMKAFGIQPRLRSYGPAL 147
Query: 466 DLLGRAGLLDEAEEL 480
R G D+A E+
Sbjct: 148 FGFCRKGDADKAYEV 162
>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 = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 32/65 (49%)
Query: 93 FVFKAVGWLGEVKKGEKVHGYVVKTGLEFDTYVCNSIMDMYGVLGKICNVKKLFDEMPDK 152
F + + ++G +K G+KV G++ G + V N + YG + I + + +E+ +
Sbjct: 90 FSLENMRYVGILKSGQKVSGFIEAEGYVYTVGVGNYLGQNYGRIESITDDSIVLNELIED 149
Query: 153 DVVSW 157
+W
Sbjct: 150 STGNW 154
>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 934
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 34/135 (25%), Positives = 65/135 (48%), Gaps = 16/135 (11%)
Query: 478 EELIRKIPNENN-EIIVPLYGALLSAC-RIYGNVDMGEKLAALLEKIESKDSSFHTLLAN 535
E+L+R+ P+ N A L C R+Y ++ +L +++ +E + LL
Sbjct: 378 EDLLRRFPDLNRLAKKFQRQAANLQDCYRLYQGIN---QLPNVIQALEKHEGKHQKLLLA 434
Query: 536 IYASANRWEDVTNVRQKMKEMGVRKVPGCSSIEINGIIHEFLVG---DPSHSEMKEIYSM 592
++ + D+ + K +EM + +E HEFLV DP+ SE++EI +
Sbjct: 435 VFVTP--LTDLRSDFSKFQEM-IETTLDMDQVEN----HEFLVKPSFDPNLSELREIMND 487
Query: 593 LD-RMAKTLLDSKQN 606
L+ +M TL+ + ++
Sbjct: 488 LEKKMQSTLISAARD 502
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 34/135 (25%), Positives = 65/135 (48%), Gaps = 16/135 (11%)
Query: 478 EELIRKIPNENN-EIIVPLYGALLSAC-RIYGNVDMGEKLAALLEKIESKDSSFHTLLAN 535
E+L+R+ P+ N A L C R+Y ++ +L +++ +E + LL
Sbjct: 378 EDLLRRFPDLNRLAKKFQRQAANLQDCYRLYQGIN---QLPNVIQALEKHEGKHQKLLLA 434
Query: 536 IYASANRWEDVTNVRQKMKEMGVRKVPGCSSIEINGIIHEFLVG---DPSHSEMKEIYSM 592
++ + D+ + K +EM + +E HEFLV DP+ SE++EI +
Sbjct: 435 VFVTP--LTDLRSDFSKFQEM-IETTLDMDQVEN----HEFLVKPSFDPNLSELREIMND 487
Query: 593 LD-RMAKTLLDSKQN 606
L+ +M TL+ + ++
Sbjct: 488 LEKKMQSTLISAARD 502
>pdb|2IVW|A Chain A, The Solution Structure Of A Domain From The Neisseria
Meningitidis Pilp Pilot Protein
Length = 113
Score = 29.3 bits (64), Expect = 7.2, Method: Composition-based stats.
Identities = 15/65 (23%), Positives = 32/65 (49%)
Query: 93 FVFKAVGWLGEVKKGEKVHGYVVKTGLEFDTYVCNSIMDMYGVLGKICNVKKLFDEMPDK 152
F + + ++G +K G+KV G++ G + V N + YG + I + + +E+ +
Sbjct: 22 FSLENMRYVGILKSGQKVSGFIEAEGYVYTVGVGNYLGQNYGRIESITDDSIVLNELIED 81
Query: 153 DVVSW 157
+W
Sbjct: 82 STGNW 86
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 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,742,440
Number of Sequences: 62578
Number of extensions: 723906
Number of successful extensions: 1713
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1704
Number of HSP's gapped (non-prelim): 18
length of query: 619
length of database: 14,973,337
effective HSP length: 105
effective length of query: 514
effective length of database: 8,402,647
effective search space: 4318960558
effective search space used: 4318960558
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: 54 (25.4 bits)