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)