RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780860|ref|YP_003065273.1| NADH dehydrogenase subunit H
[Candidatus Liberibacter asiaticus str. psy62]
         (348 letters)



>gnl|CDD|180386 PRK06076, PRK06076, NADH:ubiquinone oxidoreductase subunit H;
           Provisional.
          Length = 322

 Score =  423 bits (1090), Expect = e-119
 Identities = 178/330 (53%), Positives = 230/330 (69%), Gaps = 15/330 (4%)

Query: 11  PLFFMAIKSIVFLVGLLIFIAYVLLMDRKVWAAVQLRRGPNVVGPWGLLQSFADFLKFVF 70
            L  + +K++V LV +L+ +A+++  +RKV A +QLR GPN VGP+GLLQ  AD +K +F
Sbjct: 8   LLLLILLKAVVILVVVLLCVAFLIWFERKVLARMQLRYGPNRVGPFGLLQLVADGIKLLF 67

Query: 71  KEPIIPSKSNKILFLLAPLVSVILSLSAWAVVPVADGWIIADINVGILYILAISSLEIYG 130
           KE IIP+ ++K+LFLLAP+++ I +  AWAV+P     +IAD+NVGILYILAISSL +YG
Sbjct: 68  KEDIIPAGADKVLFLLAPVIAFIPAFLAWAVIPFGPELVIADLNVGILYILAISSLGVYG 127

Query: 131 IIIGGWASNSKYAFLGALRSAAQMISYEVSIGLVIVTVVLCAGSLNLTDIVYSQKSGLGT 190
           +I+ GWASN+KYA LGALR+AAQMISYEV +GL ++ VVL AGSLNL+DIV +Q      
Sbjct: 128 VILAGWASNNKYALLGALRAAAQMISYEVPLGLSLLAVVLLAGSLNLSDIVEAQ------ 181

Query: 191 FLGFPPSMLDWYWLALFPMFVVFFISLLAETNRPPFDLSEAESELVAGYMVEYSSTPYLL 250
                   L W  +   P FVVFFI+ +AETNR PFDL EAESELVAGY  EYS   + L
Sbjct: 182 -------FLSWNIIPQPPAFVVFFIAAVAETNRHPFDLPEAESELVAGYHTEYSGMKFGL 234

Query: 251 FMLAEYSTIVLMCTLASILFLGGWLPPFDISLFKSIPGFFWLVFKTLGLFFMVAMVKAFV 310
           F L EY  ++L+  L + LFLGGWLPPF +     IPG  W V K     F+   ++A +
Sbjct: 235 FFLGEYINMILVSALITTLFLGGWLPPFPLGGG--IPGAIWFVLKVAFFVFLFIWLRATL 292

Query: 311 PRYRYDQLMRLGWKVFLPLSFAMVLIVSFF 340
           PRYRYDQLMRLGWKV LPLS   +L+ +  
Sbjct: 293 PRYRYDQLMRLGWKVLLPLSLVNLLLTAAV 322


>gnl|CDD|169692 PRK09174, PRK09174, F0F1 ATP synthase subunit B'; Validated.
          Length = 204

 Score = 36.3 bits (84), Expect = 0.012
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 4/40 (10%)

Query: 273 GWLPPFDISLFKSIPGFFWLVFKTLGLFFMVAMVKAFVPR 312
           G  PPFD + + S     WL   T GLF++  M +  +PR
Sbjct: 42  GVFPPFDSTHYAS--QLLWLAI-TFGLFYL-FMSRVILPR 77


>gnl|CDD|177537 PHA03134, PHA03134, thymidine kinase; Provisional.
          Length = 340

 Score = 30.9 bits (70), Expect = 0.46
 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 186 SGLGTFLGFPPSMLDWYWLALFPMFVVFFISLLAETNRPPFDLSEAESELVAGYMVEYSS 245
           SG G  L FP  M   YW  LF   VV  I   A+  +    L+  ++  +  +     +
Sbjct: 38  SGGGPTLYFPEPMA--YWRTLFETDVVSGI-YDAQNRKQQGSLAAEDAAGITAHYQARFA 94

Query: 246 TPYLL 250
           TPYL+
Sbjct: 95  TPYLI 99


>gnl|CDD|178310 PLN02708, PLN02708, Probable pectinesterase/pectinesterase
           inhibitor.
          Length = 553

 Score = 30.6 bits (69), Expect = 0.57
 Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 6/44 (13%)

Query: 239 YMVEYSSTP-----YLLFMLAEYS-TIVLMCTLASILFLGGWLP 276
           YM  Y S P     +L     EYS T+ + C L +++   GW+P
Sbjct: 452 YMKLYRSNPKVHKNFLGRPWKEYSRTVFIGCNLEALITPQGWMP 495


>gnl|CDD|163055 TIGR02876, spore_yqfD, sporulation protein YqfD.  YqfD is part of
           the sigma-E regulon in the sporulation program of
           endospore-forming Gram-positive bacteria. Mutation
           results in a sporulation defect in Bacillus subtilis.
           Members are found in all currently known
           endospore-forming bacteria, including the genera
           Bacillus, Symbiobacterium, Carboxydothermus,
           Clostridium, and Thermoanaerobacter.
          Length = 382

 Score = 30.4 bits (69), Expect = 0.65
 Identities = 10/30 (33%), Positives = 16/30 (53%)

Query: 12  LFFMAIKSIVFLVGLLIFIAYVLLMDRKVW 41
           LF    K    L+G+L+F+A V  +   +W
Sbjct: 77  LFKRLRKRPGILIGILLFLAIVYFLSNFIW 106


>gnl|CDD|148491 pfam06898, YqfD, Putative stage IV sporulation protein YqfD.  This
           family consists of several putative bacterial stage IV
           sporulation (SpoIV) proteins. YqfD of Bacillus subtilis
           is known to be essential for efficient sporulation
           although its exact function is unknown.
          Length = 383

 Score = 30.0 bits (68), Expect = 0.88
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 3   SFIEDFFVP-LFFMAIKSIVFLVGLLIFIAYVLLMDRKVW 41
            FIE   +P LFF   K    ++G+L+F+  +  +   +W
Sbjct: 70  KFIERKGLPFLFFRLRKRRGIVLGILLFVILLYFLSNFIW 109


>gnl|CDD|163111 TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl
           glycosylphosphotransferase.  Certain closely related
           transferase enzymes such as Sinorhizobium ExoY and
           Lactococcus EpsD lack the N-terminal domain and are not
           found by this model.
          Length = 445

 Score = 29.1 bits (66), Expect = 1.7
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 6/96 (6%)

Query: 253 LAEYSTIVLMCTLASILFLGGWLPPFDISLFKSIPGFFWLVFKTLGLFFMVAMVKAFVPR 312
           LA+   +VL   LA +L+ G  LPP        +      +     LF    + +++  R
Sbjct: 1   LADLLALVLALLLAYLLYGGLLLPPPSFYSLLILLLLLLFLI----LFAASGLYRSWRGR 56

Query: 313 YRYDQLMRLGWKVFLPLSFAMVLIVSFFLKIYTLIR 348
              ++L R+     L   F ++L ++F LK +   R
Sbjct: 57  SFLEELARVLLAWLL--VFLLLLALAFLLKGFDFSR 90


>gnl|CDD|178373 PLN02774, PLN02774, brassinosteroid-6-oxidase.
          Length = 463

 Score = 27.4 bits (61), Expect = 5.3
 Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 7/43 (16%)

Query: 159 VSIGLVIVTVVLCAGSLNLTDIVYSQKSGLGTFLGFPPSMLDW 201
           V +G++++ V LC+  L   ++ YS+K       G PP  + W
Sbjct: 4   VVLGVLVIIVCLCSALLRWNEVRYSKK-------GLPPGTMGW 39


>gnl|CDD|163172 TIGR03173, pbuX, xanthine permease.  All the seed members of this
           model are observed adjacent to genes for either xanthine
           phosphoribosyltransferase (for the conversion of
           xanthine to guanine, GenProp0696, ) or genes for the
           conversion of xanthine to urate and its concomitant
           catabolism (GenProp0640, GenProp0688, GenProp0686 and
           GenProp0687). A number of sequences scoring higher than
           trusted to this model are found in different genomic
           contexts, and the possibility exist that these transport
           related compounds in addition to or instead of xanthine
           itself. The outgroup to this family are sequences which
           are characterized as uracil permeases or are adjacent to
           established uracil phosphoribosyltransferases.
          Length = 406

 Score = 27.1 bits (61), Expect = 6.5
 Identities = 31/143 (21%), Positives = 63/143 (44%), Gaps = 19/143 (13%)

Query: 81  KILFLLAPLVS-VILSLSAWAVVPVADGWII---ADINVGILYILAISSLEIYGIIIGGW 136
           K++    P+V+  +++L   +++PVA  W        + G    L ++ L +  I++   
Sbjct: 105 KLVRFFPPVVTGTVITLIGLSLMPVAINWAAGGAGAPDFGSPQNLGLALLTLVIILLL-- 162

Query: 137 ASNSKYAFLGALRSAAQMISYEVSIGLVIVTVV-LCAGSLNLTDIVYSQKSGLGTFLGFP 195
                    G LRS A      V +GLV+ T+V    G ++ + +  +    L T   F 
Sbjct: 163 ----NRFGKGFLRSIA------VLLGLVVGTIVAAALGMVDFSGVAEAPWFALPTPFHF- 211

Query: 196 PSMLDWYWLALFPMFVVFFISLL 218
                +  +A+  M +V+ +S++
Sbjct: 212 -GAPTFDLVAILTMIIVYLVSMV 233


  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
   0.332    0.146    0.455 

Gapped
Lambda     K      H
   0.267   0.0753    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,908,575
Number of extensions: 399407
Number of successful extensions: 1443
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1429
Number of HSP's successfully gapped: 95
Length of query: 348
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 254
Effective length of database: 3,963,321
Effective search space: 1006683534
Effective search space used: 1006683534
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 58 (26.1 bits)