RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781215|ref|YP_003065628.1| putative phage terminase,
large subunit [Candidatus Liberibacter asiaticus str. psy62]
         (511 letters)



>gnl|CDD|162521 TIGR01763, MalateDH_bact, malate dehydrogenase, NAD-dependent.  The
           annotation of Botryococcus braunii as lactate
           dehydrogenase appears top be in error. This was
           initially annotated as MDH by Swiss-Prot and then
           changed. The rationale for either of these annotations
           is not traceable.
          Length = 305

 Score = 31.0 bits (70), Expect = 0.81
 Identities = 29/109 (26%), Positives = 48/109 (44%), Gaps = 15/109 (13%)

Query: 323 DIAEEGGDNTVVV---LRRGPVIEHLFDWSKTDLRTTNNKI----SGLVEKYRPDAIIID 375
           + A+    + VV+   L R P +      S+ DL + N  I    +G + ++ P+ II+ 
Sbjct: 63  NYADTANSDIVVITAGLPRKPGM------SREDLLSMNAGIVREVTGRIMEHSPNPIIVV 116

Query: 376 ANN-TGARTCDYLEMLGYHVYRVLGQKRAVDLEFCRNR-RTELHVKMAD 422
            +N   A T    +  G+   RV+GQ   +D    R     EL V + D
Sbjct: 117 VSNPLDAMTYVAWQKSGFPKERVIGQAGVLDSARFRTFIAMELGVSVQD 165


>gnl|CDD|178225 PLN02616, PLN02616, tetrahydrofolate dehydrogenase/cyclohydrolase,
           putative.
          Length = 364

 Score = 30.4 bits (68), Expect = 1.2
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 262 DPSFHEGIIARYGLDSDVTRVEVCGQFP-QQDIDSFIPLNIIEEAL-NREPCPDPYAPLI 319
           DPS H GI+ +  L S +    +      ++D+D F PLNI   A+  REP   P  P  
Sbjct: 159 DPSVH-GILVQLPLPSHMDEQNILNAVSIEKDVDGFHPLNIGRLAMRGREPLFVPCTP-- 215

Query: 320 MGC 322
            GC
Sbjct: 216 KGC 218


>gnl|CDD|184912 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 620

 Score = 29.9 bits (68), Expect = 1.7
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 8/44 (18%)

Query: 113 LANSETQLKTT----LWAEVSKWLSLLPNKHWFEMQSLSLHPAP 152
           L  SE QLK +    LW EV+  L LLP+     +  ++   AP
Sbjct: 335 LKGSEYQLKNSTQPRLWLEVT-LLGLLPSA---FISEIANASAP 374


>gnl|CDD|178131 PLN02516, PLN02516, methylenetetrahydrofolate dehydrogenase
           (NADP+).
          Length = 299

 Score = 29.5 bits (66), Expect = 2.1
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 262 DPSFHEGIIARYGLDSDVTRVEVCGQFP-QQDIDSFIPLNIIEEALN-REPCPDPYAPLI 319
           +P  H GI+ +  L   +   ++  +   ++D+D F PLNI + A+  REP   P  P  
Sbjct: 95  NPDVH-GILVQLPLPKHINEEKILNEISLEKDVDGFHPLNIGKLAMKGREPLFLPCTP-- 151

Query: 320 MGC 322
            GC
Sbjct: 152 KGC 154


>gnl|CDD|164931 PHA02535, P, terminase ATPase subunit; Provisional.
          Length = 581

 Score = 28.9 bits (65), Expect = 3.1
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 13/77 (16%)

Query: 348 WSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEMLGYHVYRVLGQKR--AVD 405
           W   D      +I  L EKY    I IDA  TG         +G  VY+++ +    AV 
Sbjct: 440 WRGLDFAEQAAEIRKLTEKYNVTYIGIDA--TG---------IGAGVYQLVKKFFPAAVA 488

Query: 406 LEFCRNRRTELHVKMAD 422
           + +    +T L +K  D
Sbjct: 489 INYSPEVKTRLVLKAHD 505


>gnl|CDD|181485 PRK08578, PRK08578, preprotein translocase subunit SecF; Reviewed.
          Length = 292

 Score = 28.7 bits (65), Expect = 3.3
 Identities = 9/21 (42%), Positives = 14/21 (66%)

Query: 91  TTLNAWLVLWLMSTRPGISVI 111
           TT+ A  VL+++ST P   V+
Sbjct: 236 TTIAAMAVLYIVSTIPQAEVL 256


>gnl|CDD|107088 PHA01818, PHA01818, hypothetical protein.
          Length = 458

 Score = 28.5 bits (63), Expect = 3.9
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 190 TYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIFNKPLDD-- 247
           + G+  +     G P  ++ G L    + N NR   +T      +GK Y    KP     
Sbjct: 165 SPGVYFVMGMTGGMPSGVSSGFLDLSVDANDNRLARLTDAE---TGKEYTSIKKPTGTYT 221

Query: 248 -WKRFQIDTRTVE 259
            WK+ + + + +E
Sbjct: 222 AWKK-EFEPKDME 233


>gnl|CDD|178166 PLN02551, PLN02551, aspartokinase.
          Length = 521

 Score = 28.5 bits (64), Expect = 4.1
 Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 10/34 (29%)

Query: 107 GISVICLANSETQLKTTLWAEVSKWLSLLPNKHW 140
           GISV  +A S          EVS  L+L P+K W
Sbjct: 394 GISVDVVATS----------EVSISLTLDPSKLW 417


>gnl|CDD|184560 PRK14190, PRK14190, bifunctional 5,10-methylene-tetrahydrofolate
           dehydrogenase/ 5,10-methylene-tetrahydrofolate
           cyclohydrolase; Provisional.
          Length = 284

 Score = 28.4 bits (64), Expect = 4.5
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 13/84 (15%)

Query: 262 DPSFHEGIIARYGLDSDVTRVEVCGQF-PQQDIDSFIPLNIIEEALNREPCPDPYAP--- 317
           DP  + GI+ +  L   +    V  +  P++D+D F P+N +   +  +    P  P   
Sbjct: 88  DPRIN-GILVQLPLPKHIDEKAVIERISPEKDVDGFHPIN-VGRMMLGQDTFLPCTPHGI 145

Query: 318 --LI--MGCDIAEEGGDNTVVVLR 337
             L+     DI+   G + VVV R
Sbjct: 146 LELLKEYNIDIS---GKHVVVVGR 166


>gnl|CDD|163456 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
           family.  Members of this protein family are predicted
           ATP-binding proteins apparently associated with DNA
           conjugal transfer. Members are found both in plasmids
           and in bacterial chromosomal regions that appear to
           derive from integrative elements such as conjugative
           transposons. More distant homologs, outside the scope of
           this family, include type IV secretion/conjugal transfer
           proteins such as TraC, VirB4 and TrsE. The granularity
           of this protein family definition is chosen so as to
           represent one distinctive clade and act as a marker
           through which to define and recognize the class of
           mobile element it serves.
          Length = 893

 Score = 28.1 bits (63), Expect = 5.1
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 355 TTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEMLGYHVYRV 397
           T  N +  ++  +RP   I++A N+     DY   LG  V RV
Sbjct: 491 TLTNLLMQVMAVHRPRLFIVEAGNSFGLLADYAARLGLSVNRV 533


>gnl|CDD|184549 PRK14167, PRK14167, bifunctional 5,10-methylene-tetrahydrofolate
           dehydrogenase/ 5,10-methylene-tetrahydrofolate
           cyclohydrolase; Provisional.
          Length = 297

 Score = 28.2 bits (63), Expect = 5.7
 Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 262 DPSFHEGIIARYGLDSDVTRVEVCGQF-PQQDIDSFIPLNI---IEEALNREPC-PDPYA 316
           D   H GI+ +  +   V   EV  +  P +D+D F P N+   +      +PC P    
Sbjct: 87  DEDVH-GILVQMPVPDHVDDREVLRRIDPAKDVDGFHPENVGRLVAGDARFKPCTPHGIQ 145

Query: 317 PLIMGCDIAEEGGDNTVV 334
            L+    +  EG D  VV
Sbjct: 146 KLLAAAGVDTEGADVVVV 163


>gnl|CDD|173376 PTZ00082, PTZ00082, L-lactate dehydrogenase; Provisional.
          Length = 321

 Score = 28.1 bits (63), Expect = 5.7
 Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 4/32 (12%)

Query: 347 DWSKTDLRTTNNKI----SGLVEKYRPDAIII 374
           +W++ DL   N KI    +  ++KY P+A +I
Sbjct: 94  EWNRDDLLPLNAKIMDEVAEGIKKYCPNAFVI 125


>gnl|CDD|181759 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
           Validated.
          Length = 395

 Score = 28.2 bits (64), Expect = 5.9
 Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 4/34 (11%)

Query: 363 LVEKYRPDAII--IDANNTGARTCDYLEMLGYHV 394
           ++E+ +PD I+  I+A  T A     LE  G++V
Sbjct: 70  VIEREKPDYIVPEIEAIATDA--LVELEKEGFNV 101


>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
          Length = 287

 Score = 27.9 bits (63), Expect = 6.1
 Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 1/22 (4%)

Query: 181 PDTFVGH-HNTYGMAIINDEAS 201
            +   GH H+TYG A+ N  AS
Sbjct: 199 AERLAGHFHDTYGQALANIYAS 220


>gnl|CDD|183474 PRK12362, PRK12362, germination protease; Provisional.
          Length = 318

 Score = 27.5 bits (62), Expect = 9.2
 Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 1/18 (5%)

Query: 360 ISGLVEKYRPDAII-IDA 376
           I G+VEK +PD +I IDA
Sbjct: 164 IKGVVEKIKPDLVIAIDA 181


>gnl|CDD|163039 TIGR02834, spo_ytxC, putative sporulation protein YtxC.  This
           uncharacterized protein is part of a panel of proteins
           conserved in all known endospore-forming Firmicutes
           (low-GC Gram-positive bacteria), including
           Carboxydothermus hydrogenoformans, and nowhere else.
          Length = 276

 Score = 27.3 bits (61), Expect = 9.4
 Identities = 8/29 (27%), Positives = 16/29 (55%)

Query: 408 FCRNRRTELHVKMADWLEFASLINHSGLI 436
           +  NR+ E+  ++ ++LE    IN  G +
Sbjct: 119 YKMNRKNEILDEINEFLEENDEINIEGFV 147


  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
   0.320    0.137    0.431 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 8,687,829
Number of extensions: 564981
Number of successful extensions: 1083
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1082
Number of HSP's successfully gapped: 21
Length of query: 511
Length of database: 5,994,473
Length adjustment: 98
Effective length of query: 413
Effective length of database: 3,876,889
Effective search space: 1601155157
Effective search space used: 1601155157
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 (21.8 bits)
S2: 59 (26.5 bits)