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= 001325
(1100 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ETW|A Chain A, Principles Of Protein-Dna Recognition Revealed In The
Structural Analysis Of Ndt80-Mse Dna Complexes
pdb|2EUV|A Chain A, Principles Of Protein-Dna Recognition Revealed In The
Structural Analysis Of Ndt80-Mse Dna Complexes
pdb|2EUW|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma4t)
pdb|2EUX|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Variant Va4g)
pdb|2EUZ|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Mc5t)
pdb|2EVF|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma6t)
pdb|2EVG|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma7t)
pdb|2EVH|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma7g)
pdb|2EVI|A Chain A, Structure Of A Ndt80-Dna Complex (Mse Mutant Ma8t)
pdb|2EVJ|A Chain A, Structure Of An Ndt80-Dna Complex (Mse Mutant Ma9c)
Length = 345
Score = 34.7 bits (78), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 47/203 (23%), Positives = 74/203 (36%), Gaps = 39/203 (19%)
Query: 103 DLVPRYALYCPTALEAATEVVIYMHNSSVALINRGEDADGVAFQTASACIFGLGDICRTA 162
DLV +Y T E T V++ N N D + S F +G
Sbjct: 19 DLVSKYERELSTEQEEDTPVILTQLNEDGTTSNYF-DKRKLKIAPRSTLQFKVG------ 71
Query: 163 SSEVPTSSVIRGICSAVFHNVLDFFISSFDGKDIIHTVDKEITKMLDS-DEVFLGLKKKF 221
P ++R C V S G+ + + I + D DE ++G K+ +
Sbjct: 72 ----PPFELVRDYCPVV---------ESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNY 118
Query: 222 SDEDESSLIKLSKFRLLSLLQIFFSSPKNLLAACFELF-NPSVLEGIHKGQYFFSQITSR 280
F L+S + L + F+L S +EG + QYF +I ++
Sbjct: 119 -------------FTLVSTFETANCDLDTFLKSSFDLLVEDSSVEGRLRVQYFAIKIKAK 165
Query: 281 FDDD----NMTHSFIIKDDGPKF 299
DDD N+ +D GP+F
Sbjct: 166 NDDDDTEINLVQHTAKRDKGPQF 188
>pdb|1MNN|A Chain A, Structure Of The Sporulation Specific Transcription Factor
Ndt80 Bound To Dna
Length = 340
Score = 34.3 bits (77), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 47/203 (23%), Positives = 74/203 (36%), Gaps = 39/203 (19%)
Query: 103 DLVPRYALYCPTALEAATEVVIYMHNSSVALINRGEDADGVAFQTASACIFGLGDICRTA 162
DLV +Y T E T V++ N N D + S F +G
Sbjct: 14 DLVSKYERELSTEQEEDTPVILTQLNEDGTTSNYF-DKRKLKIAPRSTLQFKVG------ 66
Query: 163 SSEVPTSSVIRGICSAVFHNVLDFFISSFDGKDIIHTVDKEITKMLDS-DEVFLGLKKKF 221
P ++R C V S G+ + + I + D DE ++G K+ +
Sbjct: 67 ----PPFELVRDYCPVV---------ESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNY 113
Query: 222 SDEDESSLIKLSKFRLLSLLQIFFSSPKNLLAACFELF-NPSVLEGIHKGQYFFSQITSR 280
F L+S + L + F+L S +EG + QYF +I ++
Sbjct: 114 -------------FTLVSTFETANCDLDTFLKSSFDLLVEDSSVEGRLRVQYFAIKIKAK 160
Query: 281 FDDD----NMTHSFIIKDDGPKF 299
DDD N+ +D GP+F
Sbjct: 161 NDDDDTEINLVQHTAKRDKGPQF 183
>pdb|1YGA|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Yn9a
Protein, New York Structural Genomics Consortium
pdb|1YGA|B Chain B, Crystal Structure Of Saccharomyces Cerevisiae Yn9a
Protein, New York Structural Genomics Consortium
Length = 342
Score = 33.1 bits (74), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 43/185 (23%), Positives = 64/185 (34%), Gaps = 41/185 (22%)
Query: 481 PGD------FSCGRSSMPRDLPNPQMLSPAARTPLHFRNNSFEGRNHFPGRSSSEGA--- 531
PGD ++ + M D+ L TP++ N+S+ N S G
Sbjct: 137 PGDLEVTVKYTLNVAEMTLDMEYQAQLVRGDATPINMTNHSYFNLNKVKSEKSIRGTEVK 196
Query: 532 --SNALLSPNHHLPVPYASTTSQIVWYFD--------EDPAAMD---IFSASKQL----- 573
SN L +P + + FD ED D I A+K L
Sbjct: 197 VCSNKSLEVTEGALLPTGKIIERNIATFDSTKPTVLHEDTPVFDCTFIIDANKDLKTTDS 256
Query: 574 -----WLGSFGPEASEAHIRFQIDRFGPLEHFF--------FFPIKGFALVEYINIIDAI 620
+ F E+HI+F++ P H + F P GFA V+ +DAI
Sbjct: 257 VSVNKLVPVFKAYHPESHIKFEVSTTEPTVHLYTGDNLCGKFVPRSGFA-VQQGRYVDAI 315
Query: 621 RAREY 625
E+
Sbjct: 316 NRDEW 320
>pdb|3OTG|A Chain A, Crystal Structure Of Calg1, Calicheamicin
Glycostyltransferase, Tdp Bound Form
pdb|3OTH|A Chain A, Crystal Structure Of Calg1, Calicheamicin
Glycostyltransferase, Tdp And Calicheamicin Alpha3i
Bound Form
pdb|3OTH|B Chain B, Crystal Structure Of Calg1, Calicheamicin
Glycostyltransferase, Tdp And Calicheamicin Alpha3i
Bound Form
Length = 412
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 43/97 (44%), Gaps = 10/97 (10%)
Query: 8 LKKRKLYDLPPESPKPVEGPQSDVVPPQTPPPLSQDEIQSRRRNKDEIRSV-YECYRRLK 66
L +R DLPP P D+ PP L + E ++R R + E+R V + L
Sbjct: 178 LAQRLGLDLPPGRIDGFGNPFIDIFPPS----LQEPEFRARPR-RHELRPVPFAEQGDLP 232
Query: 67 ACIAQKDARRLPELEQAYLSLITASRGCTSVQRIVAD 103
A ++ +D R YL+L T+S G V R D
Sbjct: 233 AWLSSRDTAR----PLVYLTLGTSSGGTVEVLRAAID 265
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 570 SKQLWLGSFGPEASEAHIRFQIDRFGPLEHFFFFPIKGFALVEYINIIDAIRA 622
+ +LW+G GP S A + + DRFG + FA ++Y + +DA +A
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYES-LDAAQA 68
>pdb|1MN4|A Chain A, Structure Of Ndt80 (Residues 59-340) Dna-Binding Domain
Core
Length = 282
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 231 KLSKFRLLSLLQIFFSSPKNLLAACFELF-NPSVLEGIHKGQYFFSQITSRFDDD----N 285
K S F L+S + L + F+L S +EG + QYF +I ++ DDD N
Sbjct: 52 KRSYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVEGRLRVQYFAIKIKAKNDDDDTEIN 111
Query: 286 MTHSFIIKDDGPKF 299
+ +D GP+F
Sbjct: 112 LVQHTAKRDKGPQF 125
>pdb|3MIN|A Chain A, Nitrogenase Mofe Protein From Azotobacter Vinelandii,
Oxidized State
pdb|3MIN|C Chain C, Nitrogenase Mofe Protein From Azotobacter Vinelandii,
Oxidized State
pdb|2MIN|A Chain A, Nitrogenase Mofe Protein From Azotobacter Vinelandii,
Oxidized State
pdb|2MIN|C Chain C, Nitrogenase Mofe Protein From Azotobacter Vinelandii,
Oxidized State
pdb|1N2C|A Chain A, Nitrogenase Complex From Azotobacter Vinelandii Stabilized
By Adp-Tetrafluoroaluminate
pdb|1N2C|C Chain C, Nitrogenase Complex From Azotobacter Vinelandii Stabilized
By Adp-Tetrafluoroaluminate
pdb|1L5H|A Chain A, Femo-Cofactor Deficient Nitrogenase Mofe Protein
pdb|1M1N|A Chain A, Nitrogenase Mofe Protein From Azotobacter Vinelandii
pdb|1M1N|C Chain C, Nitrogenase Mofe Protein From Azotobacter Vinelandii
pdb|1M1N|E Chain E, Nitrogenase Mofe Protein From Azotobacter Vinelandii
pdb|1M1N|G Chain G, Nitrogenase Mofe Protein From Azotobacter Vinelandii
pdb|1M1Y|A Chain A, Chemical Crosslink Of Nitrogenase Mofe Protein And Fe
Protein
pdb|1M1Y|C Chain C, Chemical Crosslink Of Nitrogenase Mofe Protein And Fe
Protein
pdb|1M1Y|I Chain I, Chemical Crosslink Of Nitrogenase Mofe Protein And Fe
Protein
pdb|1M1Y|K Chain K, Chemical Crosslink Of Nitrogenase Mofe Protein And Fe
Protein
pdb|1M34|A Chain A, Nitrogenase Complex From Azotobacter Vinelandii Stabilized
By Adp- Tetrafluoroaluminate
pdb|1M34|C Chain C, Nitrogenase Complex From Azotobacter Vinelandii Stabilized
By Adp- Tetrafluoroaluminate
pdb|1M34|I Chain I, Nitrogenase Complex From Azotobacter Vinelandii Stabilized
By Adp- Tetrafluoroaluminate
pdb|1M34|K Chain K, Nitrogenase Complex From Azotobacter Vinelandii Stabilized
By Adp- Tetrafluoroaluminate
pdb|2AFH|A Chain A, Crystal Structure Of Nucleotide-Free Av2-Av1 Complex
pdb|2AFH|C Chain C, Crystal Structure Of Nucleotide-Free Av2-Av1 Complex
pdb|2AFI|A Chain A, Crystal Structure Of Mgadp Bound Av2-Av1 Complex
pdb|2AFI|C Chain C, Crystal Structure Of Mgadp Bound Av2-Av1 Complex
pdb|2AFI|I Chain I, Crystal Structure Of Mgadp Bound Av2-Av1 Complex
pdb|2AFI|K Chain K, Crystal Structure Of Mgadp Bound Av2-Av1 Complex
pdb|2AFK|A Chain A, Crystal Structure Of Mgamppcp-Bound Av2-Av1 Complex
pdb|2AFK|C Chain C, Crystal Structure Of Mgamppcp-Bound Av2-Av1 Complex
Length = 491
Score = 30.4 bits (67), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 187 FISSFDGKDIIHTVDKEITKMLDSDEVFLGLKKKFSDEDE 226
F S F KDI+ DK++ K++D E L K S + E
Sbjct: 113 FTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSE 152
>pdb|1FP4|A Chain A, Crystal Structure Of The Alpha-H195q Mutant Of Nitrogenase
pdb|1FP4|C Chain C, Crystal Structure Of The Alpha-H195q Mutant Of Nitrogenase
Length = 492
Score = 30.0 bits (66), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 187 FISSFDGKDIIHTVDKEITKMLDSDEVFLGLKKKFSDEDE 226
F S F KDI+ DK++ K++D E L K S + E
Sbjct: 114 FTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSE 153
>pdb|1G20|A Chain A, Mgatp-Bound And Nucleotide-Free Structures Of A
Nitrogenase Protein Complex Between Leu127del-Fe Protein
And The Mofe Protein
pdb|1G20|C Chain C, Mgatp-Bound And Nucleotide-Free Structures Of A
Nitrogenase Protein Complex Between Leu127del-Fe Protein
And The Mofe Protein
pdb|1G21|A Chain A, Mgatp-Bound And Nucleotide-Free Structures Of A
Nitrogenase Protein Complex Between Leu127del-Fe Protein
And The Mofe Protein
pdb|1G21|C Chain C, Mgatp-Bound And Nucleotide-Free Structures Of A
Nitrogenase Protein Complex Between Leu127del-Fe Protein
And The Mofe Protein
pdb|3U7Q|A Chain A, A. Vinelandii Nitrogenase Mofe Protein At Atomic
Resolution
pdb|3U7Q|C Chain C, A. Vinelandii Nitrogenase Mofe Protein At Atomic
Resolution
Length = 492
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 187 FISSFDGKDIIHTVDKEITKMLDSDEVFLGLKKKFSDEDE 226
F S F KDI+ DK++ K++D E L K S + E
Sbjct: 114 FTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSE 153
>pdb|3K1A|A Chain A, Insights Into Substrate Binding At Femo-Cofactor In
Nitrogenase From The Structure Of An Alpha-70ile Mofe
Protein Variant
pdb|3K1A|C Chain C, Insights Into Substrate Binding At Femo-Cofactor In
Nitrogenase From The Structure Of An Alpha-70ile Mofe
Protein Variant
Length = 491
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 187 FISSFDGKDIIHTVDKEITKMLDSDEVFLGLKKKFSDEDE 226
F S F KDI+ DK++ K++D E L K S + E
Sbjct: 113 FTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSE 152
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 0.133 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,335,868
Number of Sequences: 62578
Number of extensions: 1262025
Number of successful extensions: 2627
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2622
Number of HSP's gapped (non-prelim): 12
length of query: 1100
length of database: 14,973,337
effective HSP length: 109
effective length of query: 991
effective length of database: 8,152,335
effective search space: 8078963985
effective search space used: 8078963985
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: 57 (26.6 bits)