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= 004256
(765 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1G8P|A Chain A, Crystal Structure Of Bchi Subunit Of Magnesium Chelatase
pdb|2X31|G Chain G, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|H Chain H, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|I Chain I, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|J Chain J, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|K Chain K, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|L Chain L, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
Length = 350
Score = 201 bits (511), Expect = 1e-51, Method: Compositional matrix adjust.
Identities = 122/317 (38%), Positives = 173/317 (54%), Gaps = 13/317 (4%)
Query: 89 RQFFPLAAVVGQDAIKTALLLGAIDREIGGIAISGRRGTAKTVMARGLHAILPPIEVVVG 148
R FP +A+VGQ+ +K ALLL A+D IGG+ + G RGT K+ R L A+LP IE V G
Sbjct: 18 RPVFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEG 77
Query: 149 SIANADPTCPDEWEDGLDEKAEYDTAGNLKTQIAR--SPFVQIPLGVTEDRLIGSVDVEE 206
CP + + D A L T + R +P V +PLGV+EDR++G++D+E
Sbjct: 78 --------CP---VSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIER 126
Query: 207 SVKTGTTVFQPGLLAEAHRGVLYIDEINLLDEGISNLLLNVLTEGVNIVEREGISFKHPC 266
++ G F+PGLLA A+RG LYIDE NLL++ I +LLL+V G N+VER+G+S +HP
Sbjct: 127 AISKGEKAFEPGLLARANRGYLYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPA 186
Query: 267 KPLLIATYNPEEGVVREHLLDRIAINLSADLPMTFEDRVAAVGIATQFQERSNEVFKMVE 326
+ +L+ + NPEEG +R LLDR +++ P E RV + + +
Sbjct: 187 RFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWR 246
Query: 327 EETDLAKTQIILAREYLKDVAIGREQLKYLVMEALRGGCQGHRAELYAARVAKCLAALEG 386
+ + QI+ ARE L V L + G G R EL R A+ LAALEG
Sbjct: 247 PKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEG 306
Query: 387 REKVNVDDLKKAVELVI 403
V D LK+ + +
Sbjct: 307 ATAVGRDHLKRVATMAL 323
>pdb|2X31|A Chain A, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|B Chain B, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|C Chain C, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|D Chain D, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|E Chain E, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|F Chain F, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
Length = 189
Score = 88.6 bits (218), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 71/185 (38%), Positives = 100/185 (54%), Gaps = 16/185 (8%)
Query: 563 LVIFVVDASGSMALNRMQNAKGAALKLLAESYTCRDQVSIIPFRGDSAEVLLPPSRSIAM 622
++IF VDASGS A+ R+ AKGA LL +Y RD VS+I FRG +A+VLL PSRS+
Sbjct: 7 VLIFAVDASGSAAVARLSEAKGAVELLLGRAYAARDHVSLITFRGTAAQVLLQPSRSLTQ 66
Query: 623 ARKRLERLPCGGGSPLAHGLSMAVRVGLNAEKSGDVGRIMIVAITDGRANISLKRSTDPE 682
+++L+ LP GGG+PLA G+ MA+ A G I + +TDGR NI+L + + E
Sbjct: 67 TKRQLQGLPGGGGTPLASGMEMAMVTAKQARSRGMTPTIAL--LTDGRGNIALDGTANRE 124
Query: 683 ATASDAPRPSSQELKDEILEVAGKIYKAGMSLLVIDTENKFVSTGFAKEIARVAQGKYYY 742
A + VA I +GM ++IDT + ++AR Y
Sbjct: 125 LAGEQATK------------VARAIRASGMPAVIIDTAMR--PNPALVDLARTMDAHYIA 170
Query: 743 LPNAS 747
LP A+
Sbjct: 171 LPRAT 175
>pdb|3K1J|A Chain A, Crystal Structure Of Lon Protease From Thermococcus
Onnurineus Na1
pdb|3K1J|B Chain B, Crystal Structure Of Lon Protease From Thermococcus
Onnurineus Na1
Length = 604
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 216 QPGLLAEAHRGVLYIDEINLLDEGISNLLLNVLTE 250
+PG++ AH+GVL+IDEI L + LL + E
Sbjct: 193 EPGMIHRAHKGVLFIDEIATLSLKMQQSLLTAMQE 227
>pdb|3DZD|A Chain A, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
pdb|3DZD|B Chain B, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
Length = 368
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 189 IPLGVTEDRLIGSVDVEESVKTGTTVFQPGLLAEAHRGVLYIDEINLLDEGISNLLLNVL 248
IP + E L G E+ TG + G L A +G L++DE+ LD+ + LL VL
Sbjct: 190 IPQELAESELFGH---EKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVL 246
Query: 249 TEG 251
G
Sbjct: 247 ETG 249
>pdb|2BJW|A Chain A, Pspf Aaa Domain
pdb|2C96|A Chain A, Structural Basis Of The Nucleotide Driven Conformational
Changes In The Aaa Domain Of Transcription Activator
Pspf
pdb|2C98|A Chain A, Structural Basis Of The Nucleotide Driven Conformational
Changes In The Aaa Domain Of Transcription Activator
Pspf
pdb|2C99|A Chain A, Structural Basis Of The Nucleotide Driven Conformational
Changes In The Aaa Domain Of Transcription Activator
Pspf
Length = 265
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/125 (26%), Positives = 50/125 (40%), Gaps = 10/125 (8%)
Query: 183 RSPFVQIPLGVTEDRLIGS--VDVEESVKTGTTVFQPGLLAEAHRGVLYIDEINLLDEGI 240
+ PF+ + + L+ S E TG PG A G L++DE+ +
Sbjct: 57 QGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMV 116
Query: 241 SNLLLNVLTEGVNIVEREGISFKHPCKPLLIATYNPE------EGVVREHLLDRIAINLS 294
LL V+ G +ER G S L+ N + EG R LLDR+A ++
Sbjct: 117 QEKLLRVIEYGE--LERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVV 174
Query: 295 ADLPM 299
P+
Sbjct: 175 QLPPL 179
>pdb|2VII|A Chain A, Pspf1-275-mg-amp
Length = 259
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/125 (26%), Positives = 50/125 (40%), Gaps = 10/125 (8%)
Query: 183 RSPFVQIPLGVTEDRLIGS--VDVEESVKTGTTVFQPGLLAEAHRGVLYIDEINLLDEGI 240
+ PF+ + + L+ S E TG PG A G L++DE+ +
Sbjct: 57 QGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMV 116
Query: 241 SNLLLNVLTEGVNIVEREGISFKHPCKPLLIATYNPE------EGVVREHLLDRIAINLS 294
LL V+ G +ER G S L+ N + EG R LLDR+A ++
Sbjct: 117 QEKLLRVIEYGE--LERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVV 174
Query: 295 ADLPM 299
P+
Sbjct: 175 QLPPL 179
>pdb|2C9C|A Chain A, Structural Basis Of The Nucleotide Driven Conformational
Changes In The Aaa Domain Of Transcription Activator
Pspf
Length = 265
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 33/125 (26%), Positives = 50/125 (40%), Gaps = 10/125 (8%)
Query: 183 RSPFVQIPLGVTEDRLIGS--VDVEESVKTGTTVFQPGLLAEAHRGVLYIDEINLLDEGI 240
+ PF+ + + L+ S E TG PG A G L++DE+ +
Sbjct: 57 QGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMV 116
Query: 241 SNLLLNVLTEGVNIVEREGISFKHPCKPLLIATYNPE------EGVVREHLLDRIAINLS 294
LL V+ G +ER G S L+ N + EG R LLDR+A ++
Sbjct: 117 QEKLLRVIEYGE--LERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVV 174
Query: 295 ADLPM 299
P+
Sbjct: 175 QLPPL 179
>pdb|3P9D|C Chain C, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9D|K Chain K, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|CC Chain c, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|KK Chain k, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|4D8Q|C Chain C, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8Q|K Chain K, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|CC Chain c, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|KK Chain k, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
Length = 590
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 49/110 (44%), Gaps = 17/110 (15%)
Query: 296 DLPMTFEDRVAAVGIATQFQERSNEVFKMVEEETDLAKTQIILAREYLKDVAIGREQL-- 353
D P+ ++ + I + +E N + ++ EE+ L QI+ R L G L
Sbjct: 247 DCPLEYKKGESQTNIEIEKEEDWNRILQIEEEQVQLMCEQILAVRPTLVITEKGVSDLAQ 306
Query: 354 KYLVMEALRGGCQGHRAELYAARVAKC----LAALEGREKVN-VDDLKKA 398
YL L+GGC R RV K +A + G VN V+DLK++
Sbjct: 307 HYL----LKGGCSVLR------RVKKSDNNRIARVTGATIVNRVEDLKES 346
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 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,045,092
Number of Sequences: 62578
Number of extensions: 635580
Number of successful extensions: 1760
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1748
Number of HSP's gapped (non-prelim): 19
length of query: 765
length of database: 14,973,337
effective HSP length: 106
effective length of query: 659
effective length of database: 8,340,069
effective search space: 5496105471
effective search space used: 5496105471
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: 55 (25.8 bits)