RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780976|ref|YP_003065389.1| Holliday junction resolvase
YqgF [Candidatus Liberibacter asiaticus str. psy62]
         (160 letters)



>gnl|CDD|178870 PRK00109, PRK00109, Holliday junction resolvase-like protein;
           Reviewed.
          Length = 138

 Score =  150 bits (382), Expect = 1e-37
 Identities = 55/139 (39%), Positives = 78/139 (56%), Gaps = 1/139 (0%)

Query: 14  KPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFII 73
            P+  I  +D+GTKRIG+A+SDP    A P   + R   T     L   I        ++
Sbjct: 1   MPSGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVV 60

Query: 74  GLPLNMNGSEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRI 133
           GLPLNM+G+EGPR    R F  N ++ +  +P V  DERL+TV A++ L D+   +K R 
Sbjct: 61  GLPLNMDGTEGPRTERARKFA-NRLEGRFGLPVVLVDERLSTVEAERALADVGSRKKLRK 119

Query: 134 QKVDSIAAALILQEVLDRI 152
             +DS+AA +ILQ  LD +
Sbjct: 120 GVIDSLAAVIILQSYLDSL 138


>gnl|CDD|129352 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF.  This protein
           family, which exhibits an RNAse H fold in crystal
           structure, has been proposed as a putative Holliday
           junction resolvase, an alternate to RuvC.
          Length = 130

 Score = 96.0 bits (239), Expect = 4e-21
 Identities = 45/129 (34%), Positives = 63/129 (48%), Gaps = 1/129 (0%)

Query: 22  IDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNG 81
           +D GTK IG+A  D     A   P +  +        +   +        ++GLPLNM+G
Sbjct: 3   LDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDG 62

Query: 82  SEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAA 141
           +EGP     + F  N ++ +  VP V WDERL+TV A+  L      R  R  K+D  AA
Sbjct: 63  TEGPLTERAQKFA-NRLEGRFGVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAA 121

Query: 142 ALILQEVLD 150
            +ILQ  LD
Sbjct: 122 VIILQSYLD 130


>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold.  YqgF
           proteins are likely to function as an alternative to
           RuvC in most bacteria, and could be the principal
           holliday junction resolvases in low-GC Gram-positive
           bacteria. In Spt6p orthologues, the catalytic residues
           are substituted indicating that they lack enzymatic
           functions.
          Length = 99

 Score = 86.9 bits (216), Expect = 2e-18
 Identities = 32/97 (32%), Positives = 43/97 (44%), Gaps = 3/97 (3%)

Query: 22  IDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFITTENIAAFIIGLPLNMNG 81
           +D G K IG+A+ D   + A P   + R      A  L   I        +IGLPLNMNG
Sbjct: 6   LDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNG 65

Query: 82  SEGPRVHSTRAFVHNMIDRKVYVPFVFWDERLTTVSA 118
           +       T      ++  +  +P V  DERL TV A
Sbjct: 66  TASRE---TEEAFAELLKERFNLPVVLVDERLATVYA 99


>gnl|CDD|183978 PRK13328, PRK13328, pantothenate kinase; Reviewed.
          Length = 255

 Score = 27.3 bits (61), Expect = 1.8
 Identities = 11/26 (42%), Positives = 13/26 (50%)

Query: 18 PIASIDLGTKRIGLAISDPGRRFAHP 43
           I  ID G  RI  A +D GR + H 
Sbjct: 2  MILLIDAGNSRIKWAWADAGRPWVHS 27


>gnl|CDD|179960 PRK05192, PRK05192, tRNA uridine 5-carboxymethylaminomethyl
           modification enzyme GidA; Validated.
          Length = 618

 Score = 26.2 bits (59), Expect = 3.8
 Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 4/24 (16%)

Query: 80  NGSEGPRVHSTRAFVHNMIDRKVY 103
           N S+GP V + RA      DRK+Y
Sbjct: 83  NTSKGPAVRALRA----QADRKLY 102


>gnl|CDD|180771 PRK06947, PRK06947, glucose-1-dehydrogenase; Provisional.
          Length = 248

 Score = 26.3 bits (58), Expect = 3.9
 Identities = 11/38 (28%), Positives = 20/38 (52%)

Query: 116 VSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRIS 153
           V+    L DM+ +R +R+   + + A L  +E   R+S
Sbjct: 91  VAPSMPLADMDAARLRRMFDTNVLGAYLCAREAARRLS 128


>gnl|CDD|182415 PRK10370, PRK10370, formate-dependent nitrite reductase complex
           subunit NrfG; Provisional.
          Length = 198

 Score = 26.0 bits (57), Expect = 4.5
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 120 QILIDMNVSRKKRIQKVDSIAAALILQ 146
           Q ++D+N  R  R Q V+SI  A +LQ
Sbjct: 168 QKVLDLNSPRVNRTQLVESINMAKLLQ 194


>gnl|CDD|148572 pfam07034, ORC3_N, Origin recognition complex (ORC) subunit 3
           N-terminus.  This family represents the N-terminus
           (approximately 300 residues) of subunit 3 of the
           eukaryotic origin recognition complex (ORC). Origin
           recognition complex (ORC) is composed of six subunits
           that are essential for cell viability. They collectively
           bind to the autonomously replicating sequence (ARS) in a
           sequence-specific manner and lead to the chromatin
           loading of other replication factors that are essential
           for initiation of DNA replication.
          Length = 313

 Score = 25.8 bits (57), Expect = 5.0
 Identities = 14/49 (28%), Positives = 24/49 (48%)

Query: 104 VPFVFWDERLTTVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRI 152
           +PFV      T+ SA   L+  +VS    ++   S++    L  VLD++
Sbjct: 213 LPFVLVFGIATSPSAIHKLLPHHVSSLLCLELFQSLSPTQHLNAVLDKV 261


>gnl|CDD|147946 pfam06061, Baculo_ME53, Baculoviridae ME53.  ME53 is one of the
           major early-transcribed genes. The ME53 protein is
           reported to contain a putative zinc finger motif.
          Length = 326

 Score = 25.7 bits (57), Expect = 6.2
 Identities = 11/21 (52%), Positives = 14/21 (66%)

Query: 6   IEDLVKSLKPNQPIASIDLGT 26
           I D+V+  KPN+ I SI L T
Sbjct: 161 IRDIVREKKPNEQITSITLRT 181


>gnl|CDD|169558 PRK08719, PRK08719, ribonuclease H; Reviewed.
          Length = 147

 Score = 25.6 bits (56), Expect = 6.3
 Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 10 VKSLKPNQPIASIDLGTKRIGLAISDPGRRFAHPRPFLVRKKVTQTALELLSFI 63
          +    PN     +  G   IGL + D        +   V +      LELL+ I
Sbjct: 9  IDGAAPNNQHGCVRGG---IGLVVYDEAGEIVDEQSITVNRYTDNAELELLALI 59


>gnl|CDD|172390 PRK13870, PRK13870, transcriptional regulator TraR; Provisional.
          Length = 234

 Score = 25.3 bits (55), Expect = 6.6
 Identities = 12/44 (27%), Positives = 30/44 (68%), Gaps = 7/44 (15%)

Query: 115 TVSAQQILIDMNVSRKKRIQKVDSIAAALILQEVLDRISFLESS 158
           T+++++ +ID++       +++D++AAA  + ++  RISFL ++
Sbjct: 129 TLASEKPVIDLD-------REIDAVAAAATIGQIHARISFLRTT 165


>gnl|CDD|180805 PRK07042, PRK07042, amidase; Provisional.
          Length = 464

 Score = 25.3 bits (56), Expect = 6.9
 Identities = 14/29 (48%), Positives = 15/29 (51%), Gaps = 6/29 (20%)

Query: 17  QPIASIDLGTKR----IGLAISDPGRRFA 41
           QP ASI+ G  R    IGL I   G RF 
Sbjct: 411 QPAASINCGFTRDGLPIGLQIV--GPRFD 437


>gnl|CDD|182084 PRK09800, PRK09800, putative hypoxanthine oxidase; Provisional.
          Length = 956

 Score = 25.2 bits (55), Expect = 7.6
 Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 6/36 (16%)

Query: 119 QQILIDMNVSRKKRIQK-VDSIAAALILQEVLDRIS 153
           QQ ++D+ V     +Q   +  AAALI+ ++LDRI+
Sbjct: 87  QQAMVDVGV-----VQSGYNDPAAALIITDLLDRIA 117


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.323    0.138    0.385 

Gapped
Lambda     K      H
   0.267   0.0597    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,577,834
Number of extensions: 156787
Number of successful extensions: 317
Number of sequences better than 10.0: 1
Number of HSP's gapped: 314
Number of HSP's successfully gapped: 23
Length of query: 160
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 74
Effective length of database: 4,136,185
Effective search space: 306077690
Effective search space used: 306077690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.5 bits)