RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780856|ref|YP_003065269.1| NADH-quinone oxidoreductase, E subunit [Candidatus Liberibacter asiaticus str. psy62] (218 letters) >gnl|CDD|183479 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional. Length = 400 Score = 372 bits (956), Expect = e-104 Identities = 147/214 (68%), Positives = 170/214 (79%), Gaps = 2/214 (0%) Query: 2 SVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAI 61 +RRL E+ QP SF+F+ E+A W + I++YP R SAVIPLLMRAQEQEGWV+RAAI Sbjct: 1 MLRRLHED--QPDSFAFTPENAAWAEKQITKYPEGRQASAVIPLLMRAQEQEGWVTRAAI 58 Query: 62 EVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIH 121 E VA++LDMAYIRVLE+ATFYTQFQL PVGTRAH+QVCGTTPCMLRG E L+ VC++KIH Sbjct: 59 EKVADMLDMAYIRVLEVATFYTQFQLQPVGTRAHIQVCGTTPCMLRGSEALMAVCKSKIH 118 Query: 122 QKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIR 181 P N+DGTLSWEEVEC GACVNAPMV IGKD YEDLTPERLEEIIDAF+ G+G ++ Sbjct: 119 AHPHELNADGTLSWEEVECLGACVNAPMVQIGKDYYEDLTPERLEEIIDAFAAGKGPVVK 178 Query: 182 PGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDD 215 PGPQI R +S PAGGLTSL + K R K Sbjct: 179 PGPQIGRYASEPAGGLTSLTEEAGKARYNASKAL 212 >gnl|CDD|181024 PRK07539, PRK07539, NADH dehydrogenase subunit E; Validated. Length = 154 Score = 237 bits (608), Expect = 1e-63 Identities = 75/157 (47%), Positives = 95/157 (60%), Gaps = 3/157 (1%) Query: 17 SFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVL 76 S E + I++YP R SAVIP L QEQ GWV AIE VA+ L M I V Sbjct: 1 MLSAEELAAIEREIAKYPRPR--SAVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 Query: 77 EIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWE 136 E+ATFY+ PVG R +QVC +TPC LRG E ++ + K+ KP +DG + Sbjct: 59 EVATFYSMIFRQPVG-RHVIQVCTSTPCWLRGGEAILAALKKKLGIKPGETTADGRFTLL 117 Query: 137 EVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFS 173 EVEC GAC NAP+VMI DTYEDLTPE+++E++D Sbjct: 118 EVECLGACDNAPVVMINDDTYEDLTPEKIDELLDELK 154 >gnl|CDD|131013 TIGR01958, nuoE_fam, NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria. Length = 148 Score = 209 bits (533), Expect = 5e-55 Identities = 70/148 (47%), Positives = 98/148 (66%), Gaps = 1/148 (0%) Query: 25 WVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQ 84 + E+I++YP + +SA++P LM AQEQ+GWV+ AI VA +L + + V E+ATFY+ Sbjct: 1 LIEEIIAKYPDDQKRSAIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVATFYSM 60 Query: 85 FQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGAC 144 F PVG R H+QVC PC LRG E L++ NK+ KP DG + EVEC GAC Sbjct: 61 FDTEPVG-RYHLQVCTNVPCALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGAC 119 Query: 145 VNAPMVMIGKDTYEDLTPERLEEIIDAF 172 NAP++MI D YE LTPE+L+E+++ + Sbjct: 120 GNAPVMMINDDYYEFLTPEKLDELLERY 147 >gnl|CDD|136420 PRK07571, PRK07571, bidirectional hydrogenase complex protein HoxE; Reviewed. Length = 169 Score = 82.9 bits (205), Expect = 5e-17 Identities = 46/135 (34%), Positives = 65/135 (48%), Gaps = 1/135 (0%) Query: 39 QSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQV 98 Q A+I +L +AQE G++ R + VA L + RV +ATFY F L P G V V Sbjct: 35 QDALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFYHLFSLKPSGEHTCV-V 93 Query: 99 CGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYE 158 C T C ++G ++E N++ K +DG LS C GAC AP V+ Sbjct: 94 CTGTACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDGKVAG 153 Query: 159 DLTPERLEEIIDAFS 173 TPE + E + + Sbjct: 154 KQTPESVLEKVQGWL 168 >gnl|CDD|180339 PRK05988, PRK05988, formate dehydrogenase subunit gamma; Validated. Length = 156 Score = 66.9 bits (164), Expect = 4e-12 Identities = 38/135 (28%), Positives = 68/135 (50%), Gaps = 11/135 (8%) Query: 41 AVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHV-QVC 99 A++P+L Q++ G+V A+ V+A L+++ V + TFY F+ P G HV ++C Sbjct: 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPG--RHVLKLC 81 Query: 100 GTTPCMLRGCEKLIEVCRNKI----HQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKD 155 C G + L + ++ HQ +DG ++ E V C G C +P M+ + Sbjct: 82 RAEACQAMGGDALAAHAKARLGIDFHQ----TTADGAVTLEPVYCLGLCACSPAAMLDGE 137 Query: 156 TYEDLTPERLEEIID 170 + L P+RL+ ++ Sbjct: 138 VHGRLDPQRLDALLA 152 >gnl|CDD|185473 PTZ00139, PTZ00139, Succinate dehydrogenase [ubiquinone] flavoprotein subunit; Provisional. Length = 617 Score = 30.1 bits (68), Expect = 0.44 Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 9/64 (14%) Query: 95 HVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSW-----EEVECQGACVNAPM 149 H V + G EK+ E+ + K D +L W E +E + A Sbjct: 492 HAAVFRIGESLQEGVEKIKEIYSDFKDVKI----KDKSLVWNTDLIETLELENLLTQAKQ 547 Query: 150 VMIG 153 ++ Sbjct: 548 TILS 551 >gnl|CDD|161886 TIGR00456, argS, arginyl-tRNA synthetase. This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori. Length = 566 Score = 28.1 bits (63), Expect = 2.0 Identities = 10/30 (33%), Positives = 14/30 (46%) Query: 60 AIEVVANILDMAYIRVLEIATFYTQFQLSP 89 A E+V + I +E A + F LSP Sbjct: 57 AEEIVLKLKTGEIIEKVEAAGPFINFFLSP 86 >gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein; Provisional. Length = 267 Score = 27.8 bits (62), Expect = 2.1 Identities = 9/18 (50%), Positives = 10/18 (55%) Query: 54 GWVSRAAIEVVANILDMA 71 G V A E V IL+MA Sbjct: 16 GVVDPAHREEVKRILEMA 33 >gnl|CDD|178672 PLN03126, PLN03126, Elongation factor Tu; Provisional. Length = 478 Score = 27.3 bits (60), Expect = 3.0 Identities = 15/36 (41%), Positives = 20/36 (55%) Query: 182 PGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDDKI 217 PG I IS + L +L++N + KRG K DKI Sbjct: 233 PGDDIPIISGSALLALEALMENPNIKRGDNKWVDKI 268 >gnl|CDD|183390 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed. Length = 556 Score = 27.5 bits (62), Expect = 3.1 Identities = 10/20 (50%), Positives = 13/20 (65%) Query: 16 FSFSEESAIWVNEVISRYPP 35 FS S IWV++ + RYPP Sbjct: 335 FSKSRGWGIWVDDALERYPP 354 >gnl|CDD|180170 PRK05626, rpsO, 30S ribosomal protein S15; Reviewed. Length = 89 Score = 27.4 bits (62), Expect = 3.1 Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 13/58 (22%) Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQI----DRISSAPAGGLTSLLDNNSK----KRG 209 LT E+ EII + +GDT P Q+ +RI+ LT L + K +RG Sbjct: 3 LTKEKKAEIIKEYGRHEGDTGSPEVQVALLTERINH-----LTEHLKEHKKDHHSRRG 55 >gnl|CDD|162887 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines. Length = 295 Score = 27.3 bits (61), Expect = 3.5 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 7/83 (8%) Query: 108 GCEKLIEVCRNKIHQKPLHRNSDGTLSWEEV------ECQGACVNAPMVMIGKD-TYEDL 160 GC K +EVC + + + +C AC + + ++G++ T E++ Sbjct: 52 GCGKCVEVCPAGTARLSELADGRNRIIIRREKCTHCGKCTEACPSGALSIVGEEMTVEEV 111 Query: 161 TPERLEEIIDAFSTGQGDTIRPG 183 L + I ++G G T+ G Sbjct: 112 MRVVLRDSIFYRNSGGGVTLSGG 134 >gnl|CDD|177740 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone] iron-sulfur subunit. Length = 276 Score = 27.1 bits (60), Expect = 3.6 Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 11/46 (23%) Query: 155 DTYEDLTPERLEEIIDAFSTGQGDTIR-----------PGPQIDRI 189 D+ ++ T ERLE + D F + TIR P I +I Sbjct: 224 DSRDEYTKERLEALDDEFKLYRCHTIRNCSNACPKGLNPAKAIAKI 269 >gnl|CDD|177871 PLN02226, PLN02226, 2-oxoglutarate dehydrogenase E2 component. Length = 463 Score = 26.3 bits (57), Expect = 5.8 Identities = 9/25 (36%), Positives = 15/25 (60%) Query: 168 IIDAFSTGQGDTIRPGPQIDRISSA 192 +I F +GDT+ PG ++ IS + Sbjct: 144 VIQEFLVKEGDTVEPGTKVAIISKS 168 >gnl|CDD|178776 PLN03238, PLN03238, probable histone acetyltransferase MYST; Provisional. Length = 290 Score = 26.0 bits (57), Expect = 8.5 Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 11/55 (20%) Query: 119 KIHQKP----LHRNSDGTLSWEEVE-------CQGACVNAPMVMIGKDTYEDLTP 162 I Q P ++G LS EV+ CQ C+ A + + K Y D+ P Sbjct: 72 DIRQPPGGGIYGAVTEGPLSVFEVDGKKAKVYCQNLCLLAKLFLDHKTLYYDVDP 126 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 0.317 0.132 0.393 Gapped Lambda K H 0.267 0.0718 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,595,000 Number of extensions: 219092 Number of successful extensions: 489 Number of sequences better than 10.0: 1 Number of HSP's gapped: 484 Number of HSP's successfully gapped: 16 Length of query: 218 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 128 Effective length of database: 4,049,753 Effective search space: 518368384 Effective search space used: 518368384 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.0 bits)