RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780762|ref|YP_003065175.1| recombination protein RecR
[Candidatus Liberibacter asiaticus str. psy62]
(201 letters)
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger,
toprim, walker B ATP binding motif; 2.50A {Deinococcus
radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
Length = 228
Score = 220 bits (561), Expect = 2e-58
Identities = 71/194 (36%), Positives = 110/194 (56%), Gaps = 2/194 (1%)
Query: 8 KEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVD 67
+ +LI+ L+R+PG GP+SA+R HL ++ + + LA A+ + +C IC N+
Sbjct: 5 PSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNIT 64
Query: 68 TTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGI 127
+ C +C D RD I VVE+ D+ ALERS LYHVL G LSP++ +GP+ + I
Sbjct: 65 DAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHI 124
Query: 128 QSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLD 187
V + E+I A T+EG TA Y+ L+ + I+R+AYG+P+G L+Y D
Sbjct: 125 --KPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTD 182
Query: 188 DGTIFEAIRSRTVL 201
+ T+ A+ R +
Sbjct: 183 EVTLGRALTGRQTV 196
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
recombination, helicase; 1.90A {Escherichia coli} SCOP:
a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A
1d8l_A
Length = 203
Score = 33.6 bits (77), Expect = 0.029
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 14 IKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANI 53
+ L ++PG G ++A R + + + + L G L A++
Sbjct: 107 VGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTPAADL 146
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 32.6 bits (74), Expect = 0.070
Identities = 30/134 (22%), Positives = 45/134 (33%), Gaps = 49/134 (36%)
Query: 97 LERSKAVN-ALY-----HVLGG---SL----SPLDRIGPEDIGI-QSLIERIEVKKIREL 142
L K V +L V+ G SL L + G+ QS RI + R+L
Sbjct: 360 LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPS-GLDQS---RIPFSE-RKL 414
Query: 143 IFA-----ISA---TIEGQTTAHY-------IMDKLKGIDVKITRLAYGIPM-----GSE 182
F+ +++ + H I L +V IP+ GS+
Sbjct: 415 KFSNRFLPVASPFHS-------HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD 467
Query: 183 L-DYLDDGTIFEAI 195
L G+I E I
Sbjct: 468 LRVL--SGSISERI 479
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.0 bits (66), Expect = 0.44
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 10/30 (33%)
Query: 132 ERIEVKKIR---EL-------IFAISATIE 151
E+ +KK++ +L AI AT+E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
>3e8x_A Putative NAD-dependent epimerase/dehydratase; structural genomics,
APC7755, NADP, PSI-2, protein structure initiative; HET:
MSE NAP; 2.10A {Bacillus halodurans}
Length = 236
Score = 29.7 bits (65), Expect = 0.46
Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 5/41 (12%)
Query: 86 IVVEDVAD--LWALERSKAVNALYHVLGGSLS---PLDRIG 121
I DVA +++ + + VL G ++++G
Sbjct: 195 ITRHDVAKVIAELVDQQHTIGKTFEVLNGDTPIAKVVEQLG 235
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 27.6 bits (61), Expect = 1.8
Identities = 11/63 (17%), Positives = 18/63 (28%), Gaps = 26/63 (41%)
Query: 51 ANIYNKVCLCSICGNVDT---TDP------CAICIDQQRDASVIIVVED-VADL---WAL 97
N+ + C C CA+C +V+ D + D W
Sbjct: 16 PNLNIVLT-CPECKVYPPKIVERFSEGDVVCALC---------GLVLSDKLVDTRSEW-- 63
Query: 98 ERS 100
R+
Sbjct: 64 -RT 65
>3jz4_A Succinate-semialdehyde dehydrogenase [NADP+]; tetramer, NADP
binding, oxidoreductase; HET: NAP; 2.30A {Escherichia
coli}
Length = 481
Score = 27.3 bits (61), Expect = 2.7
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 9/62 (14%)
Query: 82 ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRE 141
A+ + V + V D +A + +A++ L+ +G L IGP LI+ V K+ E
Sbjct: 291 ANRLYVQDGVYDRFAEKLQQAMSKLH--IGDGLDNGVTIGP-------LIDEKAVAKVEE 341
Query: 142 LI 143
I
Sbjct: 342 HI 343
>3eya_A Pyruvate dehydrogenase [cytochrome]; pyruvate oxidase,
membrane-associated flavoprotein dehydrogenase,
interactions with lipids cell membrane; HET: TDP FAD;
2.50A {Escherichia coli} PDB: 3ey9_A*
Length = 549
Score = 26.9 bits (58), Expect = 2.9
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 153 QTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLD 187
QT A YI L+ VK +G+ S D
Sbjct: 3 QTVAAYIAKTLESAGVKR---IWGVTGDSLNGLSD 34
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein
structure initiati midwest center for structural
genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}
Length = 382
Score = 26.5 bits (58), Expect = 4.1
Identities = 6/14 (42%), Positives = 7/14 (50%)
Query: 17 LARIPGFGPRSARR 30
L R GPR+ R
Sbjct: 28 LIRAENVGPRTFRS 41
>3ek1_A Aldehyde dehydrogenase; ssgcid, oxidoreductase, structural
genomics; HET: MES; 2.10A {Brucella melitensis biovar
ABORTUS2308}
Length = 504
Score = 26.5 bits (58), Expect = 4.2
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 9/62 (14%)
Query: 82 ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRE 141
A+ I V V D +A + + V L +G P IGP +IE + K++
Sbjct: 314 ANRIYVQRGVYDKFAEKLAAKVKEL--KVGNGTEPGVVIGP-------MIEEKAITKVKA 364
Query: 142 LI 143
I
Sbjct: 365 HI 366
>1am7_A Lysozyme; glycosidase, transglycosylase, evolution; HET: TRN; 2.30A
{Bacteriophage lambda} SCOP: d.2.1.4 PDB: 1d9u_A*
3d3d_A*
Length = 158
Score = 26.4 bits (58), Expect = 4.3
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 18 ARIPGFGPRSARRATLHLVKKKEQLL----GPLAEAMANIYN 55
+ F P+S L +K++ L G + +A+ N
Sbjct: 81 LGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSN 122
>2k16_A Transcription initiation factor TFIID subunit 3; protein,
alternative splicing, metal-binding, nucleus,
phosphoprotein, transcription regulation; NMR {Mus
musculus} PDB: 2k17_A*
Length = 75
Score = 26.5 bits (58), Expect = 4.8
Identities = 6/21 (28%), Positives = 9/21 (42%)
Query: 55 NKVCLCSICGNVDTTDPCAIC 75
N++ +C C D P C
Sbjct: 16 NQIWICPGCNKPDDGSPMIGC 36
>2vje_B MDM4 protein; protein, MDMX protein, double minute 4 protein;
proto-oncogene, phosphorylation, alternative splicing,
HOST-virus interaction; HET: FLC; 2.2A {Homo sapiens}
PDB: 2vjf_B*
Length = 63
Score = 26.2 bits (57), Expect = 5.7
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 67 DTTDPCAICIDQQRDASVII 86
+ PC++C + RD ++I
Sbjct: 5 NLLKPCSLCEKRPRDGNIIH 24
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex,
octameric RUVA, AAA-ATPase domain, complex with
nucleotide, hydrolase; HET: ANP; 3.30A {Thermus
thermophilus} SCOP: a.60.2.1 b.40.4.2
Length = 191
Score = 26.1 bits (57), Expect = 5.9
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 14 IKILARIPGFGPRSARRATLHLVKK 38
++L G G R A R L L K
Sbjct: 106 ARLLTSASGVGRRLAERIALELKGK 130
>2vje_A E3 ubiquitin-protein ligase MDM2; double minute 2 protein, HDM2,
MDM2; proto-oncogene, phosphorylation, alternative
splicing, HOST-virus interaction; HET: FLC; 2.2A {Homo
sapiens} PDB: 2vjf_A* 2hdp_A
Length = 64
Score = 25.9 bits (56), Expect = 5.9
Identities = 4/19 (21%), Positives = 11/19 (57%)
Query: 67 DTTDPCAICIDQQRDASVI 85
+ +PC IC + ++ ++
Sbjct: 6 NAIEPCVICQGRPKNGCIV 24
>3i44_A Aldehyde dehydrogenase; oxidoreductase, structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; 2.00A {Bartonella henselae}
Length = 497
Score = 26.1 bits (57), Expect = 6.0
Identities = 10/62 (16%), Positives = 23/62 (37%), Gaps = 9/62 (14%)
Query: 82 ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRE 141
+ ++V + + D +G + IGP ++ + + KI++
Sbjct: 306 PTRMLVEQAIYDKAIKTAKDIAEKT--QVGPGHQTGNHIGP-------VVSKEQYDKIQD 356
Query: 142 LI 143
LI
Sbjct: 357 LI 358
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.322 0.139 0.398
Gapped
Lambda K H
0.267 0.0576 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,774,370
Number of extensions: 82822
Number of successful extensions: 344
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 25
Length of query: 201
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 113
Effective length of database: 3,559,758
Effective search space: 402252654
Effective search space used: 402252654
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.9 bits)