RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780854|ref|YP_003065267.1| NADH dehydrogenase subunit C
[Candidatus Liberibacter asiaticus str. psy62]
         (202 letters)



>gnl|CDD|180384 PRK06074, PRK06074, NADH dehydrogenase subunit C; Provisional.
          Length = 189

 Score =  255 bits (654), Expect = 6e-69
 Identities = 98/185 (52%), Positives = 126/185 (68%), Gaps = 10/185 (5%)

Query: 4   KIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGV 63
           K+E+L   ++     ++     + GEL+L V    ++ + +FLRDDP   F  +IDL GV
Sbjct: 3   KLEELVAKLLEKLPDAIGKVTVAFGELTLKVPAEKILEVLTFLRDDPELRFEQLIDLTGV 62

Query: 64  DFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIF 123
           D+  R  RF+VVYH LS K+N RLRVK+   E   VPS+V I+P A+W+ERE +D+YGI 
Sbjct: 63  DYPERGKRFEVVYHLLSYKHNVRLRVKVRAPEDPVVPSVVDIWPSANWYEREAYDLYGIV 122

Query: 124 FEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLS 183
           FEGHPDLRRILTDYGFEGHPLRKDFP+TG+VE+ YDD+ K+VVY PV           LS
Sbjct: 123 FEGHPDLRRILTDYGFEGHPLRKDFPLTGYVEVRYDDEQKRVVYEPVT----------LS 172

Query: 184 PWEGV 188
           PWEG 
Sbjct: 173 PWEGT 177


>gnl|CDD|162626 TIGR01961, NuoC_fam, NADH (or F420H2) dehydrogenase, subunit C.
           This model describes the C subunit of the NADH
           dehydrogenase complex I in bacteria, as well as many
           instances of the corresponding mitochondrial subunit
           (NADH dehydrogenase subunit 9) and of the F420H2
           dehydrogenase in Methanosarcina. Complex I contains
           subunits designated A-N. This C subunit often occurs as
           a fusion protein with the D subunit. This model excludes
           the NAD(P)H and plastoquinone-dependent form of
           chloroplasts and.
          Length = 121

 Score =  172 bits (437), Expect = 8e-44
 Identities = 61/119 (51%), Positives = 85/119 (71%), Gaps = 2/119 (1%)

Query: 34  VDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAV 93
           +    L+ + +FL+D P   F  + D+ GVD+  +  RF+VVYH LS K NRR+R+K+ +
Sbjct: 5   IKKEQLLEVLTFLKD-PALGFELLTDVSGVDY-PKEKRFEVVYHLLSIKKNRRIRLKVRL 62

Query: 94  AEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTG 152
           +E   VPS+  ++P A+W+ERE +DMYGI F+GHPDLRRIL    FEGHPLRKD+P+TG
Sbjct: 63  SEDDPVPSLTSVFPTANWYERETYDMYGIVFDGHPDLRRILMPDDFEGHPLRKDYPLTG 121


>gnl|CDD|183294 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase
           subunit C/D; Provisional.
          Length = 575

 Score =  137 bits (347), Expect = 2e-33
 Identities = 56/124 (45%), Positives = 78/124 (62%), Gaps = 9/124 (7%)

Query: 34  VDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNR-------FDVVYHFLSPKYNRR 86
           V    L+ +  FLR  P   +V + DL G+D   R++R       F V YH +S + NR 
Sbjct: 28  VKREQLLEVLRFLRKLP-KPYVMLFDLHGIDERLRTHREGLPAADFTVFYHLISIERNRD 86

Query: 87  LRVKIAVAEGK-SVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLR 145
           + +K+A++E    VP+I  I+P A+W+ERE WDM+GI F+GHP LRRIL    +EGHPLR
Sbjct: 87  IMLKVALSENDLHVPTITKIFPNANWYERETWDMFGITFDGHPHLRRILMPPTWEGHPLR 146

Query: 146 KDFP 149
           KD+P
Sbjct: 147 KDYP 150


>gnl|CDD|181115 PRK07785, PRK07785, NADH dehydrogenase subunit C; Provisional.
          Length = 235

 Score =  127 bits (321), Expect = 2e-30
 Identities = 57/143 (39%), Positives = 79/143 (55%), Gaps = 10/143 (6%)

Query: 16  FSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLC----GVDFL-SRSN 70
           F+ ++   V   GEL+L V    LV +   LRDDP   F    +LC    GV +      
Sbjct: 77  FADAIERVVVDRGELTLHVRREHLVEVAQTLRDDPALRF----ELCLGVSGVHYPHDTGR 132

Query: 71  RFDVVYHFLSPKYNRRLRVKIAVAEGKS-VPSIVGIYPGADWFEREVWDMYGIFFEGHPD 129
               VYH  S  +NRR+R+++AV +    +PS+V +YP  DW ERE +D +GI F+GHP 
Sbjct: 133 ELHAVYHLTSITHNRRIRLEVAVPDADPHIPSLVSVYPTNDWHERETYDFFGIVFDGHPA 192

Query: 130 LRRILTDYGFEGHPLRKDFPVTG 152
           L RI     + GHP RKD+P+ G
Sbjct: 193 LTRIEMPDDWVGHPQRKDYPLGG 215


>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit
           B/C/D; Provisional.
          Length = 788

 Score =  109 bits (273), Expect = 7e-25
 Identities = 50/140 (35%), Positives = 70/140 (50%), Gaps = 6/140 (4%)

Query: 16  FSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNR---- 71
           F   VR    +   L+       +  +   L+      F  + DL  VD   R +R    
Sbjct: 232 FGDDVRLDEGATDMLTYRCPPELVPEVLRHLKKRASSPFRRLEDLAAVDESCRRDREKFP 291

Query: 72  -FDVVYHFLSPKYNRRLRVKIAV-AEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPD 129
            F V YH LS      +R+K  +      +PS  G++P A+W+ERE +DM+GI F GHP+
Sbjct: 292 DFTVNYHLLSFDTPGHVRIKTELRGRTPELPSATGVFPAANWYEREAFDMFGIRFAGHPN 351

Query: 130 LRRILTDYGFEGHPLRKDFP 149
           LRRIL    +EGHPLRK+ P
Sbjct: 352 LRRILMPPDWEGHPLRKEHP 371


>gnl|CDD|181449 PRK08491, PRK08491, NADH dehydrogenase subunit C; Provisional.
          Length = 263

 Score =  105 bits (265), Expect = 6e-24
 Identities = 48/155 (30%), Positives = 83/155 (53%), Gaps = 6/155 (3%)

Query: 26  SVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNR 85
            + +  + +   D   +   L+   H  +  + ++  +DFL++   F+V Y  LS    +
Sbjct: 55  ELDQAVIWIKKDDNFKVLKILK---HLGYECLSEMSAIDFLAKKGGFEVFYQLLSMSKRK 111

Query: 86  RLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLR 145
           R+RVK  + E +++ S+  ++  A+W ERE++DM+GI    HP L+RIL    + GHPL 
Sbjct: 112 RVRVKCFLKEKEALQSVSFLFKSANWSEREMYDMFGIVINNHPYLKRILMPDDWVGHPLL 171

Query: 146 KDFPVTG--FVELHYDDKVKKVVYRPVELMQEHRD 178
           K +P+ G  F + +  DK+    YR V +  E RD
Sbjct: 172 KSYPLKGDEFAQWYEVDKIFGKEYREV-VGPEQRD 205


>gnl|CDD|181096 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated.
          Length = 430

 Score = 97.0 bits (241), Expect = 3e-21
 Identities = 41/108 (37%), Positives = 60/108 (55%), Gaps = 10/108 (9%)

Query: 45  FLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRR----LRVKIAVAEGKSVP 100
            LR      F  + +L G DF++     +V  H  S  Y +R    ++VK+   E   V 
Sbjct: 322 LLRFHEQLAFDYLSELHGTDFVTH---MEVYVHLYS--YGKRQSVAVKVKLD-REAPQVE 375

Query: 101 SIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDF 148
           S+  ++ GA+W ERE +D+ GI F+GHP+L RIL    + GHPLRKD+
Sbjct: 376 SVTPLWKGANWPEREAYDLLGIVFKGHPNLSRILLPDDWVGHPLRKDY 423


>gnl|CDD|183557 PRK12494, PRK12494, NADH dehydrogenase subunit J; Provisional.
          Length = 172

 Score = 82.7 bits (205), Expect = 5e-17
 Identities = 40/87 (45%), Positives = 53/87 (60%), Gaps = 5/87 (5%)

Query: 75  VYHFLSPKYN----RRLRVKIAVA-EGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPD 129
            YH +    N    R +R+K+ +  +   VPS+  I+ GADW ERE +DMYGI FEGHP+
Sbjct: 82  FYHLIKVSDNADKPREVRLKVFLPRDDPRVPSVYWIWKGADWQERETYDMYGINFEGHPN 141

Query: 130 LRRILTDYGFEGHPLRKDFPVTGFVEL 156
           L+RIL    + G PLRKD+    F EL
Sbjct: 142 LKRILMPEDWVGWPLRKDYIQPDFYEL 168


>gnl|CDD|183818 PRK12893, PRK12893, allantoate amidohydrolase; Reviewed.
          Length = 412

 Score = 29.5 bits (67), Expect = 0.68
 Identities = 15/57 (26%), Positives = 18/57 (31%), Gaps = 8/57 (14%)

Query: 101 SIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELH 157
              G  P  D   R   D  GI       L   L   G+ G        V  ++ELH
Sbjct: 143 VFTGALPLDDALARRDAD--GI------TLGEALARIGYRGTARVGRRAVDAYLELH 191


>gnl|CDD|183093 PRK11346, PRK11346, hypothetical protein; Provisional.
          Length = 285

 Score = 28.7 bits (64), Expect = 0.93
 Identities = 9/38 (23%), Positives = 17/38 (44%)

Query: 53  CFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVK 90
           C+    DL  +++L R   FD+   F S     +++  
Sbjct: 241 CYYKRPDLFNLNYLGRGKWFDLFRCFRSNTLGAKMQAL 278


>gnl|CDD|177611 PHA03374, PHA03374, hypothetical protein; Provisional.
          Length = 730

 Score = 28.9 bits (65), Expect = 1.0
 Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 3/32 (9%)

Query: 39  LVSLCSFLRDDPHCCFVNIIDLCGV-DFLSRS 69
           L   CSFLR DPH   VN +   G+ DF  R 
Sbjct: 617 LYECCSFLRLDPHA--VNRLAQEGLFDFSKRI 646


>gnl|CDD|163324 TIGR03560, F420_Rv1855c, probable F420-dependent oxidoreductase,
           Rv1855c family.  Coenzyme F420 has a limited
           phylogenetic distribution, including methanogenic
           archaea, Mycobacterium tuberculosis and related species,
           Colwellia psychrerythraea 34H, Rhodopseudomonas
           palustris HaA2, and others. Partial phylogenetic
           profiling identifies protein subfamilies, within the
           larger family called luciferase-like monooxygenanases
           (pfam00296), that appear only in F420-positive genomes
           and are likely to be F420-dependent. This model
           describes one such subfamily, exemplified by Rv1855c
           from Mycobacterium tuberculosis.
          Length = 227

 Score = 28.4 bits (64), Expect = 1.2
 Identities = 10/17 (58%), Positives = 11/17 (64%), Gaps = 1/17 (5%)

Query: 108 GADWFEREVWDMYGIFF 124
           GA W+ERE    YGI F
Sbjct: 103 GAGWYERE-HRAYGIPF 118


>gnl|CDD|178446 PLN02855, PLN02855, Bifunctional selenocysteine lyase/cysteine
           desulfurase.
          Length = 424

 Score = 28.6 bits (64), Expect = 1.3
 Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 18/58 (31%)

Query: 141 GHPLRKDFPVTGFVELHYDDKVKKVVY--------RPVELMQEHRDYDFLSPWEGVNS 190
           G   R DFP+     L       K+VY        +P  ++   +DY     +E  NS
Sbjct: 14  GAETRPDFPI-----LDQTVNGSKLVYLDNAATSQKPAAVLDALQDY-----YEEYNS 61


>gnl|CDD|183403 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
          Length = 368

 Score = 26.4 bits (59), Expect = 5.1
 Identities = 14/33 (42%), Positives = 15/33 (45%), Gaps = 5/33 (15%)

Query: 121 GIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGF 153
           GI F GH D  +IL  Y   G P       TGF
Sbjct: 46  GIIF-GHRDYDKILEAYR-NGKPF---AVYTGF 73


>gnl|CDD|173557 PTZ00364, PTZ00364, dipeptidyl-peptidase I precursor; Provisional.
          Length = 548

 Score = 26.4 bits (58), Expect = 5.5
 Identities = 4/13 (30%), Positives = 7/13 (53%)

Query: 100 PSIVGIYPGADWF 112
           P    +Y  +DW+
Sbjct: 355 PVPASVYANSDWY 367


>gnl|CDD|162140 TIGR00970, leuA_yeast, 2-isopropylmalate synthase, yeast type.  A
           larger family of homologous proteins includes
           homocitrate synthase, distinct lineages of
           2-isopropylmalate synthase, several distinct,
           uncharacterized, orthologous sets in the Archaea, and
           other related enzymes. This model describes a family of
           2-isopropylmalate synthases as found in yeasts and in a
           minority of studied bacteria.
          Length = 564

 Score = 25.6 bits (56), Expect = 9.5
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 9   GDYIVNSFSGSVRFAVNS-VGELSLDVDCGDLVSLCSFLRDDPH 51
           GD +  +FSGS + A+N  +  + LD    D++    +L  DP 
Sbjct: 326 GDLVYTAFSGSHQDAINKGLDAMKLDAAAADMLWQVPYLPLDPR 369


  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
   0.325    0.144    0.457 

Gapped
Lambda     K      H
   0.267   0.0725    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,545,905
Number of extensions: 231685
Number of successful extensions: 599
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 21
Length of query: 202
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 113
Effective length of database: 4,071,361
Effective search space: 460063793
Effective search space used: 460063793
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.0 bits)