RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781044|ref|YP_003065457.1| succinate dehydrogenase
iron-sulfur subunit [Candidatus Liberibacter asiaticus str. psy62]
         (259 letters)



>gnl|CDD|38259 KOG3049, KOG3049, KOG3049, Succinate dehydrogenase, Fe-S protein
           subunit [Energy production and conversion].
          Length = 288

 Score =  365 bits (937), Expect = e-102
 Identities = 157/241 (65%), Positives = 193/241 (80%), Gaps = 5/241 (2%)

Query: 19  NAPTGEKNLKEYRIYRWNPDNKGN-PCMDTYYVDLDNCGPMVLDGLLYIKNKIDPTLTLR 77
            A      LK + IYRWNPDN G+ P + TY VDL++CGPMVLD L+ IKN++DPTLT R
Sbjct: 38  TAAATGPRLKTFEIYRWNPDNPGDKPHLQTYEVDLNDCGPMVLDALIKIKNEMDPTLTFR 97

Query: 78  RSCREGICGSCGMNIDGTNTLACVKDMKDIKG-AIAVYPLPHMSVIKDLVVDMSHFYSQH 136
           RSCREGICGSC MNI+GTNTLAC+  +   +  +  +YPLPHM V+KDLV DM++FY+Q+
Sbjct: 98  RSCREGICGSCAMNINGTNTLACICKIDQNESKSTKIYPLPHMFVVKDLVPDMTNFYAQY 157

Query: 137 RSIEPWLKTVSP---KPAKELLQSHEDRQKIDGLYECVMCACCSTSCPSYWWNSDRYLGP 193
           +SIEPWL+  +P      K+ LQS EDR K+DGLYEC++CACCSTSCPSYWWNS++YLGP
Sbjct: 158 KSIEPWLQRKNPAKEPGKKQYLQSVEDRAKLDGLYECILCACCSTSCPSYWWNSEKYLGP 217

Query: 194 AILLQAYRWLIDSRDEFQGERLDNLEDPFRLYRCHTIMNCTQSCPKGLNPAKAIAKIKMM 253
           A+L+QAYRW+IDSRDE   ERL  L+DPF LYRCHTIMNCT++CPKGLNP KAIA+IK +
Sbjct: 218 AVLMQAYRWIIDSRDEATKERLAKLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKL 277

Query: 254 L 254
           L
Sbjct: 278 L 278


>gnl|CDD|30827 COG0479, FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S
           protein subunit [Energy production and conversion].
          Length = 234

 Score =  299 bits (768), Expect = 4e-82
 Identities = 127/235 (54%), Positives = 158/235 (67%), Gaps = 4/235 (1%)

Query: 26  NLKEYRIYRWNPDNKGNPCMDTYYVDLDNCGPMVLDGLLYIKNKIDPTLTLRRSCREGIC 85
              +++IYR+NPD    P   TY V  D  G  VLD LLYIK + DPTL+ RRSCREGIC
Sbjct: 1   MTLKFKIYRYNPD-DDKPYWQTYEVPYD-EGMTVLDALLYIKEEQDPTLSFRRSCREGIC 58

Query: 86  GSCGMNIDGTNTLACVKDMKDIK-GAIAVYPLPHMSVIKDLVVDMSHFYSQHRSIEPWLK 144
           GSC MNI+G   LAC   MKD++ G I + PLP+  VI+DLVVDM  FY + R I+P+L 
Sbjct: 59  GSCAMNINGKPRLACKTLMKDLEEGVITIEPLPNFPVIRDLVVDMEEFYEKLRKIKPYLI 118

Query: 145 TVSPKPAKELLQSHEDRQKIDGLYECVMCACCSTSCPSYWWNSDRYLGPAILLQAYRWLI 204
                   E LQS E+R+K+D L EC++C CC+ +CPS WWN D +LGPA L QAYR+L 
Sbjct: 119 RDDEPDPGERLQSPEEREKLDELSECILCGCCTAACPSIWWNPD-FLGPAALRQAYRFLA 177

Query: 205 DSRDEFQGERLDNLEDPFRLYRCHTIMNCTQSCPKGLNPAKAIAKIKMMLLDRKI 259
           DSRDE   ERL  LEDP  ++RC T  NCT+ CPKG+ PAKAIA++K  L  R +
Sbjct: 178 DSRDEGTAERLKILEDPDGVWRCTTCGNCTEVCPKGIPPAKAIAELKRRLAKRGL 232


>gnl|CDD|30596 COG0247, GlpC, Fe-S oxidoreductase [Energy production and
           conversion].
          Length = 388

 Score = 45.7 bits (107), Expect = 1e-05
 Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 8/88 (9%)

Query: 164 IDGLYECVMCACCSTSCPSYWWNSDRYLGPAILLQAYRWLIDSRDEFQGERLDNLEDPFR 223
            + L +CV C  C+  CPSY   +   L P   +   R ++  +         + E    
Sbjct: 5   FESLDKCVHCGFCTNVCPSY--RATEALSPRGRIVLVREVLRGKAPG------DEEVYEA 56

Query: 224 LYRCHTIMNCTQSCPKGLNPAKAIAKIK 251
           L  C     C  +CP G++    I + +
Sbjct: 57  LDTCLACGACATACPSGIDIGDLIREAR 84


>gnl|CDD|31344 COG1150, HdrC, Heterodisulfide reductase, subunit C [Energy
           production and conversion].
          Length = 195

 Score = 35.3 bits (81), Expect = 0.018
 Identities = 23/107 (21%), Positives = 42/107 (39%), Gaps = 17/107 (15%)

Query: 153 ELLQSHEDRQKIDGLYECVMCACCSTSCPSYWWNSDRY--LGPAILLQAYRWLIDSRDEF 210
           E  +  +   ++D L  C  C  C+ SCPS      R+    P  +++  R         
Sbjct: 24  ERTEEVKGEGRLDYLEGCYQCGTCTGSCPS-----GRFTDYSPRKIIRKAR--------- 69

Query: 211 QGERLDNLEDPFRLYRCHTIMNCTQSCPKGLNPAKAIAKIKMMLLDR 257
            G     L     L+ C T   CT+ CP+G+   + +  ++ + +  
Sbjct: 70  LGLVDLILSSE-SLWACVTCYTCTERCPRGVKIVEVVKALRNIAVKE 115


>gnl|CDD|31334 COG1139, COG1139, Uncharacterized conserved protein containing a
           ferredoxin-like domain [Energy production and
           conversion].
          Length = 459

 Score = 31.8 bits (72), Expect = 0.20
 Identities = 19/95 (20%), Positives = 32/95 (33%), Gaps = 17/95 (17%)

Query: 170 CVMCACCSTSCPSY-----WWNSDRYLGPAILLQAYRWLIDSRDEFQGERLDNLEDPFRL 224
           C+ C  C   CP Y           Y GP  ++ +   ++           D   D    
Sbjct: 310 CIRCGACLNHCPVYRHIGGHAYGSIYPGPIGVVWSP--ILGG--------YDAAGDL--P 357

Query: 225 YRCHTIMNCTQSCPKGLNPAKAIAKIKMMLLDRKI 259
           Y C     CT+ CP  +   + I K++ +  +   
Sbjct: 358 YACSLCGACTEVCPVKIPLPELIRKLRRVAAESGG 392



 Score = 26.0 bits (57), Expect = 9.5
 Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 2/42 (4%)

Query: 142 WLKTVSPKPAKELLQSHEDRQK--IDGLYECVMCACCSTSCP 181
              ++ P P   +            D  Y C +C  C+  CP
Sbjct: 330 AYGSIYPGPIGVVWSPILGGYDAAGDLPYACSLCGACTEVCP 371


>gnl|CDD|99816 cd06220, DHOD_e_trans_like2, FAD/NAD binding domain in the electron
           transfer subunit of dihydroorotate dehydrogenase-like
           proteins. Dihydroorotate dehydrogenases (DHODs) catalyze
           the only redox reaction in pyrimidine de novo
           biosynthesis. They catalyze the oxidation of
           (S)-dihydroorotate to orotate coupled with the reduction
           of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is
           co-expressed with pyrK and both gene products are
           required for full activity, as well as 3 cofactors: FMN,
           FAD, and an [2Fe-2S] cluster..
          Length = 233

 Score = 30.3 bits (69), Expect = 0.60
 Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 13/56 (23%)

Query: 46  DTYYVDLDNCGP--M---VLDGLLYIKNKIDPTLTLRRS--CREGICGSCGMNIDG 94
           D  YV    CGP  M   VL+ L   +  +    +L R   C  GICGSC ++  G
Sbjct: 168 DAIYV----CGPEIMMYKVLEIL--DERGVRAQFSLERYMKCGIGICGSCCIDPTG 217


>gnl|CDD|39680 KOG4480, KOG4480, KOG4480, Heme oxygenase [Inorganic ion transport
           and metabolism].
          Length = 283

 Score = 28.8 bits (64), Expect = 1.4
 Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 5/51 (9%)

Query: 2   VEIMLPKRSRVKRGKIWNAPTGEKNLKEYRIYRWNPDNKGNPCMDTYYVDL 52
           V +  P    +   +       E++ +E+    W    +G P    Y VD 
Sbjct: 77  VAMRFPSTEELHEKE-----ALEQDPEEFFGENWEETIEGEPAYQKYLVDS 122


>gnl|CDD|99815 cd06219, DHOD_e_trans_like1, FAD/NAD binding domain in the electron
           transfer subunit of dihydroorotate dehydrogenase-like
           proteins. Dihydroorotate dehydrogenases (DHODs) catalyze
           the only redox reaction in pyrimidine de novo
           biosynthesis. They catalyze the oxidation of
           (S)-dihydroorotate to orotate coupled with the reduction
           of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is
           co-expressed with pyrK and both gene products are
           required for full activity, as well as NAD binding.
           NAD(P) binding domain of ferredoxin reductase-like
           proteins catalyze electron transfer between an
           NAD(P)-binding domain of the alpha/beta class and a
           discrete (usually N-terminal) domain which vary in
           orientation with respect to the NAD(P) binding domain.
           The N-terminal domain may contain a flavin prosthetic
           group, as in flavoenzymes, or use flavin as a substrate.
           Ferredoxin is reduced in the final stage of photosystem
           I. The flavoprotein Ferredoxin-NADP+ reductase transfers
           electrons from reduced ferredoxin to FAD, forming FADH2
           via a semiquinone intermediate, and then transfers a
           hydride ion to convert NADP+ to NADPH..
          Length = 248

 Score = 28.7 bits (65), Expect = 1.6
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 83  GICGSCGMNIDGTNTLACV 101
           G+CG+C + + G    ACV
Sbjct: 219 GMCGACRVTVGGETKFACV 237


>gnl|CDD|31839 COG1653, UgpB, ABC-type sugar transport system, periplasmic
           component [Carbohydrate transport and metabolism].
          Length = 433

 Score = 28.5 bits (62), Expect = 2.0
 Identities = 13/32 (40%), Positives = 14/32 (43%)

Query: 86  GSCGMNIDGTNTLACVKDMKDIKGAIAVYPLP 117
           G   M IDGT  +   K     K  I V PLP
Sbjct: 266 GKVAMTIDGTWAIGYFKKAAGPKFDIGVAPLP 297


>gnl|CDD|29262 cd00207, fer2, 2Fe-2S iron-sulfur cluster binding domain.
          Iron-sulfur proteins play an important role in electron
          transfer processes and in various enzymatic reactions.
          The family includes plant and algal ferredoxins, which
          act as electron carriers in photosynthesis and
          ferredoxins, which participate in redox chains (from
          bacteria to mammals). Fold is ismilar to thioredoxin..
          Length = 84

 Score = 28.1 bits (62), Expect = 2.6
 Identities = 7/20 (35%), Positives = 12/20 (60%)

Query: 74 LTLRRSCREGICGSCGMNID 93
          + +  SCR G CG+C + + 
Sbjct: 29 IDIPYSCRAGACGTCKVEVV 48


>gnl|CDD|32263 COG2080, CoxS, Aerobic-type carbon monoxide dehydrogenase, small
           subunit CoxS/CutS homologs [Energy production and
           conversion].
          Length = 156

 Score = 27.9 bits (62), Expect = 2.8
 Identities = 8/25 (32%), Positives = 15/25 (60%)

Query: 77  RRSCREGICGSCGMNIDGTNTLACV 101
           ++ C  G CG+C + +DG    +C+
Sbjct: 37  KKGCGHGQCGACTVLVDGEAVNSCL 61


>gnl|CDD|29678 cd01916, ACS_1, Acetyl-CoA synthase (ACS), also known as acetyl-CoA
           decarbonylase, is found in acetogenic and methanogenic
           organisms and is responsible for the synthesis and
           breakdown of acetyl-CoA.  ACS forms a heterotetramer
           with carbon monoxide dehydrogenase (CODH) consisting of
           two ACS and two CODH subunits. CODH reduces carbon
           dioxide to carbon monoxide and ACS then synthesizes
           acetyl-CoA from carbon monoxide, CoA, and a methyl group
           donated by another protein (CoFeSP).  ACS has three
           structural domains, an N-terminal rossman fold domain
           with a helical region at its N-terminus which interacts
           with CODH, and two alpha + beta fold domains.  A Ni-Fe-S
           center referred to as the A-cluster is located in the
           C-terminal domain. A large cavity exists between the
           three domains which may bind CoA..
          Length = 731

 Score = 27.5 bits (61), Expect = 3.5
 Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 19/83 (22%)

Query: 159 EDRQKIDGLYECVMCACCSTSCPSYWWNSDRYLGPAILLQAYRWLIDSRDEFQGERLDNL 218
            D +  +   +C  C  C+ +CP+        +  A+             E     L +L
Sbjct: 356 TDEEFQELAAKCTDCGWCTRACPN-----SLRIKEAMEAAK---------EGDFSGLADL 401

Query: 219 EDPFRLYRCHTIMNCTQSCPKGL 241
            D     +C     C Q CPK +
Sbjct: 402 FD-----QCVGCGRCEQECPKEI 419


>gnl|CDD|114309 pfam05579, Peptidase_S32, Equine arteritis virus serine
           endopeptidase S32.  Serine peptidases involved in
           processing nidovirus polyprotein.
          Length = 426

 Score = 27.4 bits (61), Expect = 3.8
 Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 5/35 (14%)

Query: 71  DPTLTLRR----SCREGICGSCGMNIDG-TNTLAC 100
           D    LR     + REG+  SCGM  +  T  LAC
Sbjct: 342 DAAFFLRYFAEGNLREGVSQSCGMTPESLTAALAC 376


>gnl|CDD|30978 COG0633, Fdx, Ferredoxin [Energy production and conversion].
          Length = 102

 Score = 27.3 bits (60), Expect = 4.5
 Identities = 12/61 (19%), Positives = 28/61 (45%), Gaps = 7/61 (11%)

Query: 48  YYVDLDNCGPMVLDGLLYIKNKIDPTLTLRRSCREGICGSC-GMNIDGTNTLACVKDMKD 106
              +  N G  +L+     +N I     +  +CR G CG+C    ++G + ++  ++ ++
Sbjct: 14  DVTEAVNEGETLLEAAE--RNGIP----IEYACRGGACGTCRVKVLEGFDEVSPPEESEE 67

Query: 107 I 107
            
Sbjct: 68  D 68


>gnl|CDD|30696 COG0348, NapH, Polyferredoxin [Energy production and conversion].
          Length = 386

 Score = 26.9 bits (59), Expect = 4.9
 Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 6/53 (11%)

Query: 144 KTVSPKPAKELLQSHEDRQKIDGLYECVMCACCSTSCP------SYWWNSDRY 190
           K V P+P    +Q       I    EC+ C  C  +C       +  +    Y
Sbjct: 221 KKVCPEPIPLWVQVCPAGIDIRDGLECIGCGRCIDACDDDMLKFNLPFGLIAY 273


>gnl|CDD|143888 pfam00111, Fer2, 2Fe-2S iron-sulfur cluster binding domain.
          Several members of the Prosite family are not included
          since they only contain the active site.
          Length = 78

 Score = 26.7 bits (59), Expect = 5.8
 Identities = 7/13 (53%), Positives = 9/13 (69%)

Query: 76 LRRSCREGICGSC 88
          +  SCR G CG+C
Sbjct: 30 IPYSCRGGGCGTC 42


>gnl|CDD|31346 COG1152, CdhA, CO dehydrogenase/acetyl-CoA synthase alpha subunit
           [Energy production and conversion].
          Length = 772

 Score = 26.9 bits (59), Expect = 6.4
 Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 26/111 (23%)

Query: 146 VSPKPAKELLQSHEDRQKI-------DGLYECVMCACCSTSCPSYWWNSDRYLGPAILLQ 198
           V+ + A+ +    + R++        +   +C  C  C  +CP+     +  +  A+   
Sbjct: 371 VAVEVAEAVEPIRKGRKEKPDDEEFMEYARKCTYCGNCMRACPN-----ELDIPEAMEYA 425

Query: 199 AYRWLIDSRDEFQGERLDNLEDPFRLYRCHTIMNCTQSCPKGLNPAKAIAK 249
           A         +    +L++L D      C     C Q CPK +     I K
Sbjct: 426 A---------KGDFSKLEDLHD-----VCIGCGRCEQVCPKNIPILNMIEK 462


>gnl|CDD|35651 KOG0430, KOG0430, KOG0430, Xanthine dehydrogenase [Nucleotide
          transport and metabolism].
          Length = 1257

 Score = 26.4 bits (58), Expect = 7.2
 Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 13/42 (30%)

Query: 60 LDGLLYIKNKIDPTLTL-------------RRSCREGICGSC 88
          ++G       + P LTL             +  C EG CG+C
Sbjct: 7  INGKRVEVELLPPDLTLNTFLREKLGLTGTKLGCGEGGCGAC 48


  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
   0.323    0.139    0.454 

Gapped
Lambda     K      H
   0.267   0.0652    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,358,693
Number of extensions: 174384
Number of successful extensions: 419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 403
Number of HSP's successfully gapped: 26
Length of query: 259
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 167
Effective length of database: 4,275,709
Effective search space: 714043403
Effective search space used: 714043403
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: 56 (25.5 bits)