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= 013511
(441 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NPI|A Chain A, Clp1-Atp-Pcf11 Complex
pdb|2NPI|B Chain B, Clp1-Atp-Pcf11 Complex
Length = 460
Score = 137 bits (344), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 129/443 (29%), Positives = 212/443 (47%), Gaps = 58/443 (13%)
Query: 24 QVKLERESELRIEVGEMPLRLRLLNGNAEIYGTELPPEIWLTFPPRLKFAVFTWYEATIE 83
Q+ L+ E +L ++V +G EI+GTEL + TF KF ++ E +
Sbjct: 50 QIDLKAEGKLIVKVN---------SGIVEIFGTELAVDDEYTFQ-NWKFPIYAVEETELL 99
Query: 84 MDGTPETDYTADETP--MVSYV-NVNAVLEGRRNHXXXXXXXXXXXXQGPRVIVVGPTDS 140
T T P Y+ N++ LE R +GPRV++VG + +
Sbjct: 100 WKCPDLTTNTITVKPNHTXKYIYNLHFXLEKIR----------XSNFEGPRVVIVGGSQT 149
Query: 141 GKSTLSRMLLSWAAKL-GWKPTFVDLDIGQGAITIPGCIAATPIELPID---PVEGIPL- 195
GK++LSR L S+A K ++P +++LD Q T+PGCI+ATPI +D P G L
Sbjct: 150 GKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLT 209
Query: 196 --------EMPLVYFFGHATPSNNVELYKVLVKELAQMLERQFNGNAESRAAGMVINTMG 247
+ P V FG + N +LY + +L Q++ ++ + + + R +G +++T
Sbjct: 210 SGATLLHNKQPXVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPS 269
Query: 248 WIEGVGYEL--LLHAIDTFKANVVLVLGQEK--LFSMLRDVL-KNRPNVDVVKLQKSGGV 302
I + L L H I+ N+ LVL E L+ ++ N ++ + K GV
Sbjct: 270 -ISQLDENLAELHHIIEKLNVNIXLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGV 328
Query: 303 VSRNSKVRQKARSYRIREYFYG-LTNDLSPHANVANFSDFLVYRIGGGPQAPRSALPIGA 361
+ + ++ + IREYFYG L LSP+A ++ D +++ P +
Sbjct: 329 SAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWK-------PSNVFDNEV 381
Query: 362 DPVA-NPLRIVPVNVDQELLHLVLAVSYA-KDADQ--IISSNVAGFIFVTNVDTQRKTIT 417
V P+ I P N L H ++A+++A + ADQ +I S + GF +T V+ +R+ +
Sbjct: 382 GRVELFPVTITPSN----LQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLR 437
Query: 418 YLAPSPGMLPSKYLIAGTLTWLE 440
L P PG LPSK I + +LE
Sbjct: 438 VLLPVPGRLPSKAXILTSYRYLE 460
>pdb|3QF4|B Chain B, Crystal Structure Of A Heterodimeric Abc Transporter In
Its Inward- Facing Conformation
Length = 598
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 10/41 (24%)
Query: 129 GPRVIVVGPTDSGKSTLSRMLLSWAAKLGWKPTFVDLDIGQ 169
G +V +VGPT SGK+T+ +L+ F D+D GQ
Sbjct: 381 GQKVALVGPTGSGKTTIVNLLMR----------FYDVDRGQ 411
>pdb|1K89|A Chain A, K89l Mutant Of Glutamate Dehydrogenase
Length = 449
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 390 KDADQIISSNVAGFIFVTNVDTQRKTITYLAPSPGML--PSKYLIAG 434
+ A +I+++NV +I V N+ T + + +L P M+ PSK + AG
Sbjct: 329 EQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAG 375
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 29.3 bits (64), Expect = 4.8, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 188 DPVEGIPLEMPLVYFFGHATPSNNVELYKVLVKEL 222
DPVEG P F G+ P+ +V KV + EL
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISEL 41
>pdb|1AUP|A Chain A, Glutamate Dehydrogenase
Length = 449
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 390 KDADQIISSNVAGFIFVTNVDTQRKTITYLAPSPGML--PSKYLIAG 434
+ A +I+++NV +I V N+ T + + +L P M+ PSK + AG
Sbjct: 329 EQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAG 375
>pdb|1HRD|A Chain A, Glutamate Dehydrogenase
pdb|1HRD|B Chain B, Glutamate Dehydrogenase
pdb|1HRD|C Chain C, Glutamate Dehydrogenase
pdb|1BGV|A Chain A, Glutamate Dehydrogenase
Length = 449
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 390 KDADQIISSNVAGFIFVTNVDTQRKTITYLAPSPGML--PSKYLIAG 434
+ A +I+++NV +I V N+ T + + +L P M+ PSK + AG
Sbjct: 329 EQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAG 375
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 128 QGPRVIVVGPTDSGKSTLSRMLLSWAAKLGWKPTFV 163
QG +V PT GK+T M W A+ G K V
Sbjct: 92 QGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALV 127
>pdb|2APJ|A Chain A, X-Ray Structure Of Protein From Arabidopsis Thaliana
At4g34215 At 1.6 Angstrom Resolution
pdb|2APJ|B Chain B, X-Ray Structure Of Protein From Arabidopsis Thaliana
At4g34215 At 1.6 Angstrom Resolution
pdb|2APJ|C Chain C, X-Ray Structure Of Protein From Arabidopsis Thaliana
At4g34215 At 1.6 Angstrom Resolution
pdb|2APJ|D Chain D, X-Ray Structure Of Protein From Arabidopsis Thaliana
At4g34215 At 1.6 Angstrom Resolution
Length = 260
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 72/169 (42%), Gaps = 26/169 (15%)
Query: 149 LLSWAAKLGWK----PTFVDLDIGQGAITIPGCIAATPIELPIDPVEGIPLEMPLVYFFG 204
+L +A L W+ P VD+D G+ PG A ++ ++ + +P
Sbjct: 64 ILRLSADLRWEEAHEPLHVDIDTGKVCGVGPGMAFANAVKNRLETDSAVIGLVPC----- 118
Query: 205 HATPSNNVELYKVLVKELAQMLERQFNGNAESRAAGMVINTMGWIEGVGYELLLHAIDTF 264
A+ ++ ++ + + ER ESR G I + W +G L +H +++
Sbjct: 119 -ASGGTAIKEWE----RGSHLYERMVKRTEESRKCGGEIKAVLWYQGESDVLDIHDAESY 173
Query: 265 KANVVLVLGQEKLFSMLRDVLKNRPNVDVVK--LQKSGGVVSRNSKVRQ 311
N+ ++L LR L N P++ +++ + GG + KVR+
Sbjct: 174 GNNM------DRLIKNLRHDL-NLPSLPIIQVAIASGGGYI---DKVRE 212
>pdb|3C41|J Chain J, Abc Protein Artp In Complex With Amp-PnpMG2+
pdb|3C41|K Chain K, Abc Protein Artp In Complex With Amp-PnpMG2+
Length = 242
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 128 QGPRVIVVGPTDSGKSTLSRML 149
+G V+V+GP+ SGKST R L
Sbjct: 28 EGEVVVVIGPSGSGKSTFLRCL 49
>pdb|2OLJ|A Chain A, Abc Protein Artp In Complex With AdpMG2+
pdb|2OLJ|B Chain B, Abc Protein Artp In Complex With AdpMG2+
pdb|2OLK|A Chain A, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OLK|B Chain B, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OLK|C Chain C, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OLK|D Chain D, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OUK|A Chain A, Abc Protein Artp In Complex With Sulphate
pdb|2OUK|B Chain B, Abc Protein Artp In Complex With Sulphate
pdb|2OUK|C Chain C, Abc Protein Artp In Complex With Sulphate
pdb|2OUK|D Chain D, Abc Protein Artp In Complex With Sulphate
pdb|2Q0H|A Chain A, Abc Protein Artp In Complex With AdpMG2+, ATP-Gamma-S
Hydrolyzed
pdb|2Q0H|B Chain B, Abc Protein Artp In Complex With AdpMG2+, ATP-Gamma-S
Hydrolyzed
pdb|3C4J|A Chain A, Abc Protein Artp In Complex With Atp-Gamma-S
pdb|3C4J|B Chain B, Abc Protein Artp In Complex With Atp-Gamma-S
Length = 263
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 128 QGPRVIVVGPTDSGKSTLSRML 149
+G V+V+GP+ SGKST R L
Sbjct: 49 EGEVVVVIGPSGSGKSTFLRCL 70
>pdb|3P4Y|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
- P2 Form
Length = 415
Score = 28.5 bits (62), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 128 QGPRVIVVGPTDSGKSTLSRMLLSWAAKLGWKPTFV 163
QG +V PT GK+T M W A+ G K V
Sbjct: 36 QGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALV 71
>pdb|3OIY|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3OIY|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 414
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 128 QGPRVIVVGPTDSGKSTLSRMLLSWAAKLGWKPTFV 163
QG +V PT GK+T M W A+ G K V
Sbjct: 35 QGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALV 70
>pdb|3P4X|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3P4X|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 413
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 128 QGPRVIVVGPTDSGKSTLSRMLLSWAAKLGWKPTFV 163
QG +V PT GK+T M W A+ G K V
Sbjct: 34 QGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALV 69
>pdb|2PJZ|A Chain A, The Crystal Structure Of Putative Cobalt Transport Atp-
Binding Protein (cbio-2), St1066
Length = 263
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 99 MVSYVNVNAVLEGRRNHXXXXXXXXXXXXQGPRVIVVGPTDSGKSTLSR 147
M+ NV L G+ + G +VI++GP SGK+TL R
Sbjct: 1 MIQLKNVGITLSGK-GYERFSLENINLEVNGEKVIILGPNGSGKTTLLR 48
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
0.319 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,670,943
Number of Sequences: 62578
Number of extensions: 515373
Number of successful extensions: 1352
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1342
Number of HSP's gapped (non-prelim): 16
length of query: 441
length of database: 14,973,337
effective HSP length: 102
effective length of query: 339
effective length of database: 8,590,381
effective search space: 2912139159
effective search space used: 2912139159
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)