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= 031057
(166 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C8O|A Chain A, The Crystal Structure Of Rraa From Pao1
pdb|3C8O|B Chain B, The Crystal Structure Of Rraa From Pao1
Length = 162
Score = 163 bits (412), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 81/161 (50%), Positives = 113/161 (70%), Gaps = 5/161 (3%)
Query: 6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
T ++CDA P+L+ + ++P+F +G R F G IVT+K FEDN L++E +++ G G+
Sbjct: 5 TPDLCDAYPELV-----QVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVDKDGKGK 59
Query: 66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
VLVVDGGGSLR A+LG +A NGW GIVV GCIRDVD I D+GV+ALASHP+K
Sbjct: 60 VLVVDGGGSLRRALLGDMLAEKAAKNGWEGIVVYGCIRDVDVIAQTDLGVQALASHPLKT 119
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
+K+GIG+ +V +T GG GE++YAD +GI++S L +
Sbjct: 120 DKRGIGDLNVAVTFGGVTFRPGEFVYADNNGIIVSPQALKM 160
>pdb|1J3L|A Chain A, Structure Of The Rna-Processing Inhibitor Rraa From
Thermus Thermophilis
pdb|1J3L|B Chain B, Structure Of The Rna-Processing Inhibitor Rraa From
Thermus Thermophilis
pdb|1J3L|C Chain C, Structure Of The Rna-Processing Inhibitor Rraa From
Thermus Thermophilis
pdb|1J3L|D Chain D, Structure Of The Rna-Processing Inhibitor Rraa From
Thermus Thermophilis
pdb|1J3L|E Chain E, Structure Of The Rna-Processing Inhibitor Rraa From
Thermus Thermophilis
pdb|1J3L|F Chain F, Structure Of The Rna-Processing Inhibitor Rraa From
Thermus Thermophilis
Length = 164
Score = 139 bits (351), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 73/154 (47%), Positives = 103/154 (66%), Gaps = 6/154 (3%)
Query: 6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
T ++ D P+ GE AL +F+ +G R F+G + TL+VFEDN L+R+ LEE+G G+
Sbjct: 5 TTDLSDLYPE----GE--ALPXVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQ 58
Query: 66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
VL VDGGGSLR A+LGGN +A GWAG+VV+G +RD +E+ IG+ ALA+ P K+
Sbjct: 59 VLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKS 118
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILI 159
K+G GE VP+ + G + G +L AD DG+L+
Sbjct: 119 AKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLL 152
>pdb|2PCN|A Chain A, Crystal Structure Of S-Adenosylmethionine:
2-Dimethylmenaquinone Methyltransferase (Gk_1813) From
Geobacillus Kaustophilus Hta426
Length = 161
Score = 130 bits (328), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 72/161 (44%), Positives = 102/161 (63%), Gaps = 5/161 (3%)
Query: 4 VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
+ TA++CD Q + EL+ + FQ YG +++FSGPI T+ VFEDNVL+RE LE
Sbjct: 1 MKTADLCD---QFL--DELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPP 55
Query: 64 GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
G VLVVDG GS R A+LG A G AG++++GCIRD EI IGV A+ + P+
Sbjct: 56 GTVLVVDGKGSRRVALLGDRLAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPV 115
Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
K+ K+G G + V + GG R G ++YAD DG++++ +L
Sbjct: 116 KSKKEGKGARDVVLEFGGVRWEPGAYVYADADGVVVANKDL 156
>pdb|1Q5X|A Chain A, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|1Q5X|B Chain B, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|1Q5X|C Chain C, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna
Processing
pdb|2YJT|A Chain A, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJT|B Chain B, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJT|C Chain C, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
pdb|2YJV|A Chain A, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|B Chain B, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|C Chain C, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|D Chain D, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|E Chain E, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|F Chain F, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|G Chain G, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|H Chain H, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|I Chain I, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|J Chain J, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|K Chain K, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
pdb|2YJV|L Chain L, Crystal Structure Of E. Coli Regulator Of Ribonuclease
Activity A (Rraa) Bound To Fragment Of Dead-Box Protein
Rhlb
Length = 161
Score = 129 bits (324), Expect = 7e-31, Method: Compositional matrix adjust.
Identities = 67/161 (41%), Positives = 99/161 (61%), Gaps = 5/161 (3%)
Query: 6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
T+E+CD I ++ ++P+F +G R F G I+T+K FEDN L+ + LE+ G GR
Sbjct: 5 TSELCD-----IYQEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGR 59
Query: 66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
VLVVDGGGS+R A++ A N W G+V+ G +R VD++ DIG++A+A+ P+ A
Sbjct: 60 VLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGA 119
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
+GIGE V + GG G+ LYAD GI++S L +
Sbjct: 120 AGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSEDPLDI 160
>pdb|1NXJ|A Chain A, Structure Of Rv3853 From Mycobacterium Tuberculosis
pdb|1NXJ|B Chain B, Structure Of Rv3853 From Mycobacterium Tuberculosis
pdb|1NXJ|C Chain C, Structure Of Rv3853 From Mycobacterium Tuberculosis
Length = 183
Score = 120 bits (300), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 56/139 (40%), Positives = 89/139 (64%)
Query: 21 ELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAIL 80
++R+ F+ +G R F+GPI T++ F+DN L++ L + G VLV+DG GSL A++
Sbjct: 44 DVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALV 103
Query: 81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIG 140
G A++ GW G++V+G +RD + G DIG++AL ++P K+ K G GE+ V IT+G
Sbjct: 104 GDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLG 163
Query: 141 GTRISDGEWLYADTDGILI 159
G G+ Y+D DGI++
Sbjct: 164 GVTFVPGDIAYSDDDGIIV 182
>pdb|1VI4|A Chain A, Crystal Structure Of Regulator Of Ribonuclease Acivity A
Protein 1
Length = 174
Score = 111 bits (277), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 58/161 (36%), Positives = 90/161 (55%), Gaps = 5/161 (3%)
Query: 6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
T ++CD ++ L Q +G+R F G IVT++ + DN +R+ L + G G+
Sbjct: 8 TPDLCDK-----YESQVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGKGK 62
Query: 66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
VLVVDG GS A+ G + A N W G+++ G +RDV + D+G++AL + P K
Sbjct: 63 VLVVDGHGSCHKALXGDQLAILAIKNDWEGVIIYGAVRDVVAXSEXDLGIKALGTSPFKT 122
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
K+G G+ +V +T + G++LYAD +GIL S L V
Sbjct: 123 EKRGAGQVNVTLTXQNQIVEPGDYLYADWNGILXSETALDV 163
>pdb|3K4I|A Chain A, Crystal Structure Of Uncharacterized Protein Pspto_3204
From Pseudomonas Syringae Pv. Tomato Str. Dc3000
pdb|3K4I|B Chain B, Crystal Structure Of Uncharacterized Protein Pspto_3204
From Pseudomonas Syringae Pv. Tomato Str. Dc3000
pdb|3K4I|C Chain C, Crystal Structure Of Uncharacterized Protein Pspto_3204
From Pseudomonas Syringae Pv. Tomato Str. Dc3000
Length = 244
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/110 (24%), Positives = 49/110 (44%), Gaps = 1/110 (0%)
Query: 57 FLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVR 116
++++ +G V+V G C + G A NG G V++G RD+D + C+ +
Sbjct: 77 YIDQVPSGSVIVSSNSGRHDCTVWGDIXTHFALANGIKGTVIDGVARDIDTVINCNYPLF 136
Query: 117 ALASHPMKA-NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELS 165
+ A N+ + VP+ I G I G+ D G ++ +L+
Sbjct: 137 SRGRFXQSAKNRTQLKAVQVPLVIDGITIQPGDLXVCDGSGCVVVPQQLA 186
>pdb|3NOJ|A Chain A, The Structure Of HmgCHA ALDOLASE FROM THE PROTOCATECHUATE
DEGRADATION Pathway Of Pseudomonas Putida
Length = 238
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 45/111 (40%), Gaps = 1/111 (0%)
Query: 38 FSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGI 96
+G VT+ V DN + +E+ G VLVV G Q G +
Sbjct: 57 LAGSAVTVLVAPGDNWMFHVAVEQCRPGDVLVVSPSSPCTDGYFGDLLATSLQARGVRAL 116
Query: 97 VVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDG 147
+V+ +RD + V A A + K+ +G ++P+ GG I+ G
Sbjct: 117 IVDAGVRDTQTLRDMGFAVWARAINAQGTVKETLGSVNLPVICGGQLINPG 167
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
0.320 0.141 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,162,692
Number of Sequences: 62578
Number of extensions: 221457
Number of successful extensions: 548
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 540
Number of HSP's gapped (non-prelim): 9
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)