RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= 537021.9.peg.473_1
         (165 letters)



>gnl|CDD|181656 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 598

 Score = 69.5 bits (171), Expect = 4e-13
 Identities = 32/113 (28%), Positives = 49/113 (43%), Gaps = 15/113 (13%)

Query: 66  QLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGEDW 125
            ++ L E+  D K+   ++R + +V FE GRLE +     P D  + LA KL+ WTG  W
Sbjct: 464 DIVALAEEKRDIKLKAAVERDVRLVRFEPGRLEFALAPGAPRDLAQRLARKLEEWTGRRW 523

Query: 126 EIRFSLGRCCEYF---------------EIDSDIKAVRTIFPTAQVVCIRTIP 163
            +  S                       E D  + AV   FP A++V +R + 
Sbjct: 524 VVSVSREGGQPTLAEQEAAAREEREAAAEADPLVAAVLAAFPGAKIVDVRDLA 576


>gnl|CDD|152797 pfam12362, DUF3646, DNA polymerase III gamma and tau subunits C
           terminal.  This domain family is found in bacteria, and
           is approximately 120 amino acids in length. The family
           is found in association with pfam00004. The proteins in
           this family are frequently annotated as the gamma and
           tau subunits of DNA polymerase III, however there is
           little accompanying literature to back this up.
          Length = 117

 Score = 69.5 bits (171), Expect = 4e-13
 Identities = 29/110 (26%), Positives = 44/110 (40%), Gaps = 15/110 (13%)

Query: 66  QLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGEDW 125
            L+ L     D K+   ++R + +VSFE GR+E       P D  + L  KL+ WTG  W
Sbjct: 8   DLVALARAKRDIKLKVEVERDVRLVSFEPGRIEFRPTPGAPRDLAQRLGRKLQEWTGRRW 67

Query: 126 EIRFSLGRCCEYF---------------EIDSDIKAVRTIFPTAQVVCIR 160
            +  S                            ++AV   FP A++V +R
Sbjct: 68  AVSLSNEGGAPTLAEQEAAAKEALRADARAHPLVQAVLAAFPGAKIVDVR 117


>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
          Length = 1170

 Score = 28.5 bits (64), Expect = 0.95
 Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 2/35 (5%)

Query: 86  FLHVVSFE--LGRLEVSFLKEIPEDFIENLATKLK 118
           +L  V+ +  L RL+++ L EI E++ E L+ +LK
Sbjct: 304 YLTEVTEQGLLKRLKLNSLDEIDENYKERLSYELK 338


>gnl|CDD|131978 TIGR02932, vnfK_nitrog, V-containing nitrogenase, beta subunit.
           Nitrogenase is the enzyme of biological nitrogen
           fixation. The most wide-spread and most efficient
           nitrogenase contains a molybdenum cofactor. This protein
           family, VnfK, represents the beta subunit of the
           vanadium (V)-containing alternative nitrogenase. It is
           homologous to NifK and AnfK, of the
           molybdenum-containing and the iron (Fe)-only types,
           respectively.
          Length = 457

 Score = 27.5 bits (61), Expect = 1.6
 Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 3/41 (7%)

Query: 113 LATKLKNWTGEDWEIRFSLGRCCEYFEIDSDIKAVRTIFPT 153
           L  ++K     D  +  S GR   Y  ID++I  VR  FPT
Sbjct: 375 LEKRIKAKLDIDLIMGHSKGR---YVAIDANIPMVRVGFPT 412


>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
           alpha; Validated.
          Length = 720

 Score = 26.6 bits (59), Expect = 3.0
 Identities = 9/23 (39%), Positives = 14/23 (60%)

Query: 97  LEVSFLKEIPEDFIENLATKLKN 119
           +E +F+K+   +FIE L   LK 
Sbjct: 66  IESAFIKKYRPEFIEKLYQFLKA 88


>gnl|CDD|183785 PRK12842, PRK12842, putative succinate dehydrogenase; Reviewed.
          Length = 574

 Score = 26.2 bits (58), Expect = 4.2
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 6/53 (11%)

Query: 106 PEDFIENLATKLKNWTGEDWE---IRFSLG---RCCEYFEIDSDIKAVRTIFP 152
             D  E   T LK+ TG  ++   +   L       E+FE ++++K V T++P
Sbjct: 68  VADSREAARTYLKHETGAFFDAAAVEAFLDNGPEMVEFFERETEVKFVPTLYP 120


>gnl|CDD|182375 PRK10318, PRK10318, hypothetical protein; Provisional.
          Length = 121

 Score = 25.9 bits (57), Expect = 4.7
 Identities = 5/24 (20%), Positives = 14/24 (58%), Gaps = 1/24 (4%)

Query: 107 EDFIENLATKLKNWTGEDWEIRFS 130
           E FI+ +A+   + +G+ + ++  
Sbjct: 74  EQFIDKVASS-SSISGKPYIVKCP 96


>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
          Length = 637

 Score = 25.7 bits (57), Expect = 5.4
 Identities = 9/23 (39%), Positives = 18/23 (78%)

Query: 102 LKEIPEDFIENLATKLKNWTGED 124
           LKEI ++ ++N++  +K +TG+D
Sbjct: 468 LKEIAKEAVQNVSAIIKKFTGKD 490


>gnl|CDD|162191 TIGR01073, pcrA, ATP-dependent DNA helicase PcrA.  Designed to
           identify pcrA members of the uvrD/rep subfamily.
          Length = 726

 Score = 25.5 bits (56), Expect = 7.5
 Identities = 7/18 (38%), Positives = 11/18 (61%)

Query: 101 FLKEIPEDFIENLATKLK 118
           FL EIP + +E  +T  +
Sbjct: 628 FLNEIPAELLETASTGRR 645


>gnl|CDD|177962 PLN02328, PLN02328, lysine-specific histone demethylase 1 homolog.
          Length = 808

 Score = 25.3 bits (55), Expect = 7.5
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 5/49 (10%)

Query: 65  KQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENL 113
           KQ IEL E + D K  E L        F++  +    L +  E  I ++
Sbjct: 754 KQAIELGELDDDGKRNEYLYE-----KFQVVLVGRKGLSQEGESLISSI 797


>gnl|CDD|134000 PHA02142, PHA02142, putative RNA ligase.
          Length = 366

 Score = 25.3 bits (55), Expect = 8.0
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 98  EVSFLKEIPE-DFIENLATKLKNWTGEDWEIRFSLGRCCEYFEIDS 142
           +++ L+ IP  D IE     +  W     +  F +G  C YFEIDS
Sbjct: 14  KIADLQPIPGADAIE--VATIDGWEVVVKKGEFRVGDDCVYFEIDS 57


>gnl|CDD|178402 PLN02805, PLN02805, D-lactate dehydrogenase [cytochrome].
          Length = 555

 Score = 25.4 bits (55), Expect = 8.3
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 103 KEIPEDFIENLATKLKNWTGEDWEIRFSLGRCCEYFEIDSDIKAVRTIFPTAQ 155
           K +P++ I+ L   L++    D++ R+  G+    F    +I  V  +FP ++
Sbjct: 92  KLVPQELIDELKAILQDNMTLDYDERYFHGKPQNSFHKAVNIPDV-VVFPRSE 143


>gnl|CDD|179018 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase;
           Provisional.
          Length = 461

 Score = 25.1 bits (56), Expect = 8.3
 Identities = 7/21 (33%), Positives = 13/21 (61%)

Query: 139 EIDSDIKAVRTIFPTAQVVCI 159
           EI + +KA R  +P  ++V +
Sbjct: 336 EIKATLKAARQGYPDKRIVAV 356


>gnl|CDD|177932 PLN02295, PLN02295, glycerol kinase.
          Length = 512

 Score = 25.0 bits (55), Expect = 9.3
 Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 12/74 (16%)

Query: 1   LHAISWKKRKKKLDALNVSSFAIGENALPRNISSDECFPLAEAGITEKQDVLN-RLSACT 59
           L  + W   K  L+AL + +       LP+ +S+ E        I +   +    ++ C 
Sbjct: 199 LKTLDW--DKPTLEALGIPA-----EILPKIVSNSEVI----GTIAKGWPLAGVPIAGCL 247

Query: 60  PDNYTKQLIELCEK 73
            D +   L + C  
Sbjct: 248 GDQHAAMLGQRCRP 261


  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
   0.321    0.137    0.414 

Gapped
Lambda     K      H
   0.267   0.0689    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,676,965
Number of extensions: 157800
Number of successful extensions: 356
Number of sequences better than 10.0: 1
Number of HSP's gapped: 356
Number of HSP's successfully gapped: 26
Length of query: 165
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 79
Effective length of database: 4,136,185
Effective search space: 326758615
Effective search space used: 326758615
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: 53 (24.3 bits)