RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780855|ref|YP_003065268.1| NADH dehydrogenase subunit D
[Candidatus Liberibacter asiaticus str. psy62]
         (396 letters)



>gnl|CDD|30994 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7
           [Energy production and conversion].
          Length = 398

 Score =  629 bits (1623), Expect = 0.0
 Identities = 238/396 (60%), Positives = 296/396 (74%), Gaps = 4/396 (1%)

Query: 1   MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQ 60
             ++ + +  +NFGPQHP+ HGVLRLILELDGEIV   DP IG LHRG EKL E +T+LQ
Sbjct: 7   RSEENTENMFLNFGPQHPSTHGVLRLILELDGEIVVDADPDIGYLHRGMEKLAENRTYLQ 66

Query: 61  AVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQA 120
            +PY DRLDY++ MN E AY LAVEKLLGIE+P R Q IRV+ SE+ RI SHLL + T A
Sbjct: 67  NIPYTDRLDYLSAMNNELAYVLAVEKLLGIEVPERAQYIRVMLSELNRIASHLLWLGTFA 126

Query: 121 MDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSF 180
           +D+GA+TP L+ F EREK+M  +E  +G+RMH AYFRPGGV +D+P   +E I  + D F
Sbjct: 127 LDLGAMTPFLYAFREREKIMDLFEAITGARMHHAYFRPGGVRRDLPEGWLELIREFLDYF 186

Query: 181 PSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECY 240
           P  L++   LLT NRI++ R   +G +  E+A  WG +G M+R SG  +D+RK +PYE Y
Sbjct: 187 PKRLDEYEKLLTKNRIWRARLEGVGVLSKEEALEWGVTGPMLRASGVDYDVRKDEPYEAY 246

Query: 241 SELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPK 300
            ELDFD+P+GK+GDCY RYLVRM EMR+S++II QC+++L      GPV   DPK  PP 
Sbjct: 247 DELDFDVPVGKNGDCYARYLVRMEEMRQSIRIIEQCLDKLPK----GPVKNEDPKTTPPS 302

Query: 301 RADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAP 360
           +  MK SME+LIHHFKL TEG+ VP GEVYAAVEAPKGE GVY++SDG NKPYR KIRAP
Sbjct: 303 KERMKESMEALIHHFKLVTEGFKVPAGEVYAAVEAPKGELGVYIVSDGSNKPYRVKIRAP 362

Query: 361 GYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
            +AHLQA+  L KGH+LAD+ AILGS+DIV GEVDR
Sbjct: 363 SFAHLQALPELLKGHRLADLIAILGSIDIVMGEVDR 398


>gnl|CDD|38081 KOG2870, KOG2870, KOG2870, NADH:ubiquinone oxidoreductase,
           NDUFS2/49 kDa subunit [Energy production and
           conversion].
          Length = 452

 Score =  595 bits (1534), Expect = e-171
 Identities = 250/394 (63%), Positives = 313/394 (79%), Gaps = 4/394 (1%)

Query: 3   KKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAV 62
           +   R+  +NFGPQHPAAHGVLRL+LELDGE+V + +PHIGLLHRGTEKLIE KT+ QA+
Sbjct: 63  ETGKRNMILNFGPQHPAAHGVLRLVLELDGEVVVKAEPHIGLLHRGTEKLIEYKTYTQAL 122

Query: 63  PYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMD 122
           PYFDRLDYV+ M  E AY+LAVEKLL I++P+R + IRVL+ EI RI +H++ + T A+D
Sbjct: 123 PYFDRLDYVSMMCNEQAYSLAVEKLLNIDVPLRAKYIRVLFGEITRIANHIMALGTHALD 182

Query: 123 VGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPS 182
           VGA+TP  W FEEREKL  FYER SG+RMHA Y RPGGV QD+P  L++DI  +CD F  
Sbjct: 183 VGAMTPFFWLFEEREKLYEFYERVSGARMHANYIRPGGVAQDLPLGLMDDIYDFCDQFAE 242

Query: 183 ALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSE 242
            L+++ D+LT NRI+KQR ++IG V  E+A  WGFSGVM+RGSG  WDLRK+QPY+ Y E
Sbjct: 243 RLDELEDMLTRNRIWKQRTIDIGIVTAEEALNWGFSGVMLRGSGIKWDLRKTQPYDAYDE 302

Query: 243 LDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRA 302
           ++FD+P+G  GDCYDRYL R+ EMR+S++II+QC+N++      G +   D K+ PPKRA
Sbjct: 303 MEFDVPVGTKGDCYDRYLCRVEEMRQSLRIIQQCLNKMPP----GEIKVDDSKVCPPKRA 358

Query: 303 DMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGY 362
           +MK SMESLIHHFKL+TEG+ VP G  Y AVEAPKGEFGV+LISDG  +PYRCKIRAPG+
Sbjct: 359 EMKESMESLIHHFKLFTEGFQVPPGATYVAVEAPKGEFGVFLISDGSGRPYRCKIRAPGF 418

Query: 363 AHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
           AHL A++ + K H LADV AI+G+LDIVFGEVDR
Sbjct: 419 AHLAALDKMSKRHMLADVVAIIGTLDIVFGEVDR 452


>gnl|CDD|144077 pfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49
           Kd subunit. 
          Length = 272

 Score =  414 bits (1065), Expect = e-116
 Identities = 172/276 (62%), Positives = 211/276 (76%), Gaps = 5/276 (1%)

Query: 122 DVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFP 181
           DVGALTP  W FEEREKLM FYE  SG+RMHAAYFR GGV QD+P   ++D+  +CD F 
Sbjct: 1   DVGALTPFFWIFEEREKLMDFYEAVSGARMHAAYFRIGGVAQDLPYGWMDDLLEFCDYFL 60

Query: 182 SALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYS 241
             +++  +LLT NRIFK R   +G V  EDA  WG SGVM+RGSG  WDLRKSQPYECY 
Sbjct: 61  KRVDEYEELLTQNRIFKLRLRGVGFVTAEDALNWGLSGVMLRGSGIQWDLRKSQPYECYD 120

Query: 242 ELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGP-VSASDPKIVPPK 300
           + DFD+P+G +GDCYDRYL+R+ EMR+S++II+QC+N++ G    GP       K+ PPK
Sbjct: 121 QFDFDVPVGFNGDCYDRYLLRVEEMRQSLRIIQQCLNKMPG----GPGEKVEAFKLTPPK 176

Query: 301 RADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAP 360
           R++MK  +E+LIHHFKLY+ G+ VP GE YAAVEAPKGE GVYL+SDG   PYR KIRAP
Sbjct: 177 RSEMKDFIETLIHHFKLYSPGFKVPAGESYAAVEAPKGELGVYLVSDGSTFPYRWKIRAP 236

Query: 361 GYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
           G+AHLQ ++ L +GH LAD+ AILGS+DIVFGEVDR
Sbjct: 237 GFAHLQILDHLSRGHLLADLVAILGSIDIVFGEVDR 272


>gnl|CDD|176960 CHL00017, ndhH, NADH dehydrogenase subunit 7.
          Length = 393

 Score =  336 bits (863), Expect = 8e-93
 Identities = 167/400 (41%), Positives = 230/400 (57%), Gaps = 13/400 (3%)

Query: 1   MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQ 60
           +   +     +N GP HP+ HGVLRLI+ LDGE V   +P +G LHRG EK+ E +T +Q
Sbjct: 3   VPATRKDLMIVNMGPHHPSMHGVLRLIVTLDGEDVIDCEPILGYLHRGMEKIAENRTIIQ 62

Query: 61  AVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQA 120
            +PY  R DY+A M  E     A E+L  I++P R   IRV+  E+ RI SHLL +    
Sbjct: 63  YLPYVTRWDYLATMFTEAITVNAPEQLGNIQVPKRASYIRVIMLELSRIASHLLWLGPFM 122

Query: 121 MDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSF 180
            D+GA TP  + F ERE +   +E A+G RM   YFR GGV  D+P   ++    +CD F
Sbjct: 123 ADIGAQTPFFYIFRERELIYDLFEAATGMRMMHNYFRIGGVAADLPYGWIDKCLDFCDYF 182

Query: 181 PSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECY 240
            + + +   L+T N IF +R   +G +  E+A  WG SG M+R SG  WDLRK   YECY
Sbjct: 183 LTGVAEYQKLITRNPIFLERVEGVGIIGGEEAINWGLSGPMLRASGIQWDLRKVDHYECY 242

Query: 241 SELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPK 300
            E D+++   K GD   RYLVR+ EM ES+KII+Q +  + G    GP        +  +
Sbjct: 243 DEFDWEVQWQKEGDSLARYLVRIGEMTESIKIIQQALEGIPG----GPYEN-----LEAR 293

Query: 301 RADMKRSME--SLIHHF--KLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCK 356
           R D ++  E     + F  K  +  + +   E+Y  VEAPKGE G++LI D    P+R K
Sbjct: 294 RFDREKDSEWNDFEYRFISKKPSPTFELSKQELYVRVEAPKGELGIFLIGDDSVFPWRWK 353

Query: 357 IRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
           IR PG+ +LQ +  L K  +LAD+  ILGS+DI+ GEVDR
Sbjct: 354 IRPPGFINLQILPQLVKRMKLADIMTILGSIDIIMGEVDR 393


>gnl|CDD|33072 COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Energy
           production and conversion].
          Length = 382

 Score =  225 bits (576), Expect = 1e-59
 Identities = 125/397 (31%), Positives = 182/397 (45%), Gaps = 31/397 (7%)

Query: 1   MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQ 60
           + K     F I  GP HP         L +DGE +   D  +G +HRG EK+ E   + +
Sbjct: 1   LGKGGEGEFEIPVGPVHPGLIEPGHFRLFVDGEKIVDADIRLGYVHRGIEKIAEGLPYNK 60

Query: 61  AVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQA 120
           A+   +R+  +       A+ LAVE  LGIE+P R Q IR +  E+ RI SHLLN+    
Sbjct: 61  ALFLAERVCGICSFAHAVAFVLAVEDALGIEVPERAQYIRAIILELERIHSHLLNLGLLC 120

Query: 121 MDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSF 180
            DVG  T  +  F  REK+M   E  +G+R+       GGV +DI    +E I    +  
Sbjct: 121 HDVGFETGFMQFFRLREKVMRLIELLTGNRVLYGLNVIGGVRRDILESDLEQILELIEDI 180

Query: 181 PSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECY 240
              + +I ++L  +   + R   +G +  EDA      G   R SG A D R   P   Y
Sbjct: 181 REEVKEIVEVLLSDPNIEDRLQGVGVLDKEDARKLSAVGPTARASGIADDARIDHPPVYY 240

Query: 241 SELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPK 300
            EL F++ +   GD + R+LVR+ E+ ES+K+I Q ++ L G                  
Sbjct: 241 DELPFEVIVRDEGDVFARFLVRIDEIFESLKLIEQALDNLPGGP---------------- 284

Query: 301 RADMKRSMESLIHHFKLYTEGYHV-PVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRA 359
                           L  E   +   GE    VEAP+GE   Y+      K  R KIR 
Sbjct: 285 --------------GGLLREKLELKGHGEGLGRVEAPRGELVHYVKLGDNGKIKRWKIRT 330

Query: 360 PGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
           P YA+L A++++ +G+ +AD   I+ SLD  +   DR
Sbjct: 331 PSYANLPALKYMLRGNTVADAPLIIASLDPCYSCTDR 367


>gnl|CDD|33070 COG3259, FrhA, Coenzyme F420-reducing hydrogenase, alpha subunit
           [Energy production and conversion].
          Length = 441

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 43/166 (25%), Positives = 66/166 (39%), Gaps = 15/166 (9%)

Query: 22  GVLRLILELDGE-IVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAY 80
           G  ++ +E+D + IVE    HI  + RG EK +  K   +A     R+  + P +   A 
Sbjct: 15  GHAKVTIEVDDDGIVEDARFHITEV-RGFEKFVLGKPIEEAPRIVPRICGICPASHHLAS 73

Query: 81  ALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLM 140
             A E  LG+EIP   + +R L +    I SH L++   A       P        E   
Sbjct: 74  VEAAEAALGVEIPEEAEKLRELLNIGNIIESHALHLYFLAAPDFLGPPDADPGMIDEYPE 133

Query: 141 VFYE----RASGSRM---------HAAYFRPGGVHQDIPPELVEDI 173
           +  E    R  G  +         H     PGGV +++  E  E +
Sbjct: 134 LAKEAIRLRKIGQTIVEVLGGKAIHPVNAVPGGVAKNLSEEAREKL 179


>gnl|CDD|30723 COG0374, HyaB, Ni,Fe-hydrogenase I large subunit [Energy production
           and conversion].
          Length = 545

 Score = 36.5 bits (84), Expect = 0.013
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 22  GVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYA 81
           G LR+ +E++  ++       G L RG E +++ +    A     R+  V   +   A  
Sbjct: 14  GHLRIEVEVEDGVITDAWSS-GTLFRGFEIILKGRDPRDAWAITQRICGVCTTSHALASV 72

Query: 82  LAVEKLLGIEIPIRGQLIRVL 102
            A+E  LGI +P+   LIR +
Sbjct: 73  RALEDALGITVPVNALLIRNI 93


>gnl|CDD|145066 pfam01717, Meth_synt_2, Cobalamin-independent synthase, Catalytic
           domain.  This is a family of vitamin-B12 independent
           methionine synthases or
           5-methyltetrahydropteroyltriglutamate--homocysteine
           methyltransferases, EC:2.1.1.14 from bacteria and
           plants. Plants are the only higher eukaryotes that have
           the required enzymes for methionine synthesis. This
           enzyme catalyses the last step in the production of
           methionine by transferring a methyl group from
           5-methyltetrahydrofolate to homocysteine. The aligned
           region makes up the carboxy region of the approximately
           750 amino acid protein except in some hypothetical
           archaeal proteins present in the family, where this
           region corresponds to the entire length. This domain
           contains the catalytic residues of the enzyme.
          Length = 324

 Score = 28.5 bits (64), Expect = 2.9
 Identities = 6/36 (16%), Positives = 16/36 (44%)

Query: 65  FDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIR 100
               +Y   +      A+  ++ LG+++ + G+  R
Sbjct: 27  ISEEEYEDAIKGAIERAVRDQERLGVDVLVHGEPER 62


>gnl|CDD|37222 KOG2011, KOG2011, KOG2011, Sister chromatid cohesion complex
           Cohesin, subunit STAG/IRR1/SCC3 [Cell cycle control,
           cell division, chromosome partitioning].
          Length = 1048

 Score = 28.0 bits (62), Expect = 4.8
 Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 6/46 (13%)

Query: 151 MHAAYFRPGGVHQ--DIPPEL----VEDIGCWCDSFPSALNDISDL 190
           M    F    VH+  D+ P++    ++++G W  S+P      S L
Sbjct: 283 MINDIFDSVFVHRYRDVDPDIRAICIQELGIWIKSYPEIFLSDSYL 328


>gnl|CDD|145468 pfam02333, Phytase, Phytase.  Phytase is a secreted enzyme which
           hydrolyses phytate to release inorganic phosphate. This
           family appears to represent a novel enzyme that shows
           phytase activity and has been shown to have a six-
           bladed propeller folding architecture.
          Length = 353

 Score = 27.7 bits (61), Expect = 5.6
 Identities = 23/79 (29%), Positives = 30/79 (37%), Gaps = 12/79 (15%)

Query: 278 NRLLGKNKVGPVSASDPK------IVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYA 331
           NR  GKN +  + A D        I  P         E  ++ F LY   +    G  YA
Sbjct: 93  NRSEGKNTI-EIYAIDGDKGKLKSITDPNHPIASAIDE--VYGFSLY---HSQKTGAFYA 146

Query: 332 AVEAPKGEFGVYLISDGGN 350
            V   +GEF  Y I+  G 
Sbjct: 147 LVTGKEGEFEQYEINADGK 165


>gnl|CDD|144094 pfam00374, NiFeSe_Hases, Nickel-dependent hydrogenase. 
          Length = 504

 Score = 27.8 bits (62), Expect = 5.9
 Identities = 15/27 (55%), Positives = 17/27 (62%), Gaps = 2/27 (7%)

Query: 78  HAYA--LAVEKLLGIEIPIRGQLIRVL 102
           HA A   AVE  LGI+IP   +LIR L
Sbjct: 30  HALASVRAVEDALGIKIPKNARLIRNL 56


>gnl|CDD|33569 COG3774, OCH1, Mannosyltransferase OCH1 and related enzymes [Cell
           envelope biogenesis, outer membrane].
          Length = 347

 Score = 27.7 bits (61), Expect = 6.4
 Identities = 12/43 (27%), Positives = 17/43 (39%)

Query: 159 GGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRN 201
           GG++ DI   LV+ I    D   + L     L  GN +     
Sbjct: 160 GGIYLDIDTGLVKPIDPLLDDAEAWLRRTIPLGVGNGVMGSAP 202


>gnl|CDD|36611 KOG1397, KOG1397, KOG1397, Ca2+/H+ antiporter VCX1 and related
           proteins [Inorganic ion transport and metabolism].
          Length = 441

 Score = 27.2 bits (60), Expect = 9.0
 Identities = 14/44 (31%), Positives = 24/44 (54%)

Query: 83  AVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGAL 126
           A+E ++ I     G++  V  S +G ILS+LL V   ++  G +
Sbjct: 139 AIELIIYILALKNGKVRIVQGSLLGSILSNLLLVLGLSLFCGGI 182


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.322    0.141    0.433 

Gapped
Lambda     K      H
   0.267   0.0766    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,037,096
Number of extensions: 275551
Number of successful extensions: 581
Number of sequences better than 10.0: 1
Number of HSP's gapped: 574
Number of HSP's successfully gapped: 19
Length of query: 396
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 300
Effective length of database: 4,189,273
Effective search space: 1256781900
Effective search space used: 1256781900
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: 58 (26.0 bits)