RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780853|ref|YP_003065266.1| NADH dehydrogenase subunit B [Candidatus Liberibacter asiaticus str. psy62] (185 letters) >3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_6* 3iam_6* 3ias_6* (6:) Length = 181 Score = 167 bits (425), Expect = 7e-43 Identities = 86/160 (53%), Positives = 118/160 (73%), Gaps = 2/160 (1%) Query: 21 KVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLE 80 + F R E+ +G L T++++LV W R+ SL TFGLACCA+EMM ++ R DL Sbjct: 2 ALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLA 61 Query: 81 RFGFAP-RASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYS 139 RFG RASPRQ+DVMIVAG L+ KMA +RRV++QMP+P++VISMG+CA+ GG ++ + Sbjct: 62 RFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-N 120 Query: 140 YSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179 Y++V+ D +VPVD+YVPGCPP EALIY ++ LQKK+R Sbjct: 121 YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRG 160 >1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} (S:1-198) Length = 198 Score = 159 bits (403), Expect = 2e-40 Identities = 20/160 (12%), Positives = 54/160 (33%), Gaps = 17/160 (10%) Query: 34 THKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQS 93 + + +++ ++M A+ M +++ F A P Sbjct: 28 AVHPRIKEILLDVISLEFHPTVM---ASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAK 84 Query: 94 DVM------IVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV----- 142 + + + + + + D P+ +++G+C+ GG +V Sbjct: 85 EGRYCIVGETLDAKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKS 144 Query: 143 ---VRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179 ++I + + VPGCPP + ++ ++ + Sbjct: 145 VRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLN 184 >2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} (A:1-240) Length = 240 Score = 156 bits (395), Expect = 2e-39 Identities = 27/158 (17%), Positives = 55/158 (34%), Gaps = 9/158 (5%) Query: 31 SEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASP 90 S + D L+ + A+E M+ ++ + F + P Sbjct: 56 SVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVP 115 Query: 91 -RQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV------- 142 + G + S + + + P V+++G+CA GG S Sbjct: 116 VEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVS 175 Query: 143 -VRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179 G + I + +PGCPP + ++ ++L I++ Sbjct: 176 KFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKK 213 >1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} (A:1-177) Length = 177 Score = 145 bits (366), Expect = 4e-36 Identities = 24/168 (14%), Positives = 49/168 (29%), Gaps = 34/168 (20%) Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGF-------------------AP 86 L R + C+ +++ P D A Sbjct: 1 LTAKKRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEAL 60 Query: 87 RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGYY- 136 + + V ++ G + + + P+ + VI++G+CA GG Sbjct: 61 HEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQA 120 Query: 137 -HYSYSVVRGCDR----IVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179 + + G + + I + GCPP + ++ L K Sbjct: 121 AKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKGMP 168 >1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S (A:1-182) Length = 182 Score = 145 bits (366), Expect = 5e-36 Identities = 23/166 (13%), Positives = 44/166 (26%), Gaps = 33/166 (19%) Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAP------------------- 86 L R + C ++ P D Sbjct: 1 LTAKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAAL 60 Query: 87 --RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGY 135 + ++V G L + + + +I +G+C+ GG Sbjct: 61 HQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGV 120 Query: 136 Y--HYSYSVVRGCDRIVPVD-IYVPGCPPTAEALIYGILLLQKKIR 178 + S +G + V I +PGCPP + ++ + K Sbjct: 121 QKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGI 166 >1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} (S:1-180) Length = 180 Score = 142 bits (358), Expect = 4e-35 Identities = 26/170 (15%), Positives = 50/170 (29%), Gaps = 36/170 (21%) Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAP------------------- 86 L+ R + C+ +++A P D Sbjct: 1 LMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAAL 60 Query: 87 --RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGY 135 + + +V G + + L +P+ + VI+ G+CA GG Sbjct: 61 EQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGV 120 Query: 136 Y--HYSYSVVRGCDRIVPV----DIYVPGCPPTAEALIYGILLLQKKIRR 179 + + +G + + I + GCPP L+ I+ K Sbjct: 121 QAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAA 170 >1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} (S:1-236) Length = 236 Score = 141 bits (356), Expect = 7e-35 Identities = 27/180 (15%), Positives = 51/180 (28%), Gaps = 36/180 (20%) Query: 36 KGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAP--------- 86 F L+ R + C+ +++A P D Sbjct: 41 PAFAPEVARALMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMA 100 Query: 87 ------------RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVIS 125 + + +V G + + L +P+ + VI+ Sbjct: 101 AAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIA 160 Query: 126 MGSCANGGGYY--HYSYSVVRGCDRIVP----VDIYVPGCPPTAEALIYGILLLQKKIRR 179 G+CA GG + + +G + + I + GCPP L+ I+ K Sbjct: 161 YGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAA 220 >3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation termination, ATP-binding, cytoplasm, hydrolase, membrane; 2.80A {Schizosaccharomyces pombe} (A:1-326) Length = 326 Score = 29.7 bits (66), Expect = 0.27 Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 4/35 (11%) Query: 94 DVMIVAGTLTNKMAS----ALRRVYDQMPEPRYVI 124 +++ + + T K A+ L RV +P+P+ + Sbjct: 160 NMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAIC 194 >3i4a_A N(G),N(G)-dimethylarginine dimethylaminohydrolase 1; DDAH, nitric oxide synthase regulation, acetylation, metal-binding, zinc; HET: LN5; 1.90A {Homo sapiens} PDB: 3i2e_A* (A:1-96,A:292-308) Length = 113 Score = 27.9 bits (62), Expect = 0.85 Identities = 6/29 (20%), Positives = 14/29 (48%) Query: 117 MPEPRYVISMGSCANGGGYYHYSYSVVRG 145 +P ++ SM + + +++VVR Sbjct: 15 VPRGSHMASMAGLGHPAAFGRATHAVVRA 43 >3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, 4Fe-4S, iron-sulfur, metal-binding, oxidoreductase; HET: HCN; 1.39A {Clostridium pasteurianum} (A:210-268,A:344-406) Length = 122 Score = 27.7 bits (62), Expect = 0.98 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 21/70 (30%) Query: 67 VEMMQASMPRYDL-ERFGFAPRASPRQSDVMIVAGTLT-NKMASALRR-----VYDQMPE 119 V + A R + E F G K+ +ALR+ ++D +P+ Sbjct: 16 VIVAMAPSVRASIGELFNMGF-------------GVDVTGKIYTALRQLGFDKIFD-IPK 61 Query: 120 PRYVISMGSC 129 + +++ C Sbjct: 62 NVFTVTVMPC 71 >2v6q_A BHRF1 protein; alternative splicing, membrane, apoptosis, epstein-BARR virus; 2.7A {Epstein-barr virus} PDB: 1q59_A (A:) Length = 173 Score = 27.3 bits (60), Expect = 1.4 Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 10/58 (17%) Query: 20 EKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRY 77 E VD DF+ + EI H+G + R +L WM + + C S P Y Sbjct: 90 EHVDLDFNSVFLEIFHRGD--------PSLGR--ALAWMAWCMHACRTLCCNQSTPYY 137 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006) Length = 120 Score = 27.0 bits (60), Expect = 1.6 Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 17/39 (43%) Query: 40 VTSVDQLVTWARTGSLMWMTF--GLACCAVEMMQASMPR 76 V S++ LV ++ F G+ MQ ++PR Sbjct: 5 VMSIESLV------EVV---FYRGMT------MQVAVPR 28 >1m1n_A Nitrogenase molybdenum-iron protein alpha chain; atomic resolution, FEMO cofactor, nitrogen fixation, central nitrogen ligand; HET: HCA CLF CFN; 1.16A {Azotobacter vinelandii} (A:56-212) Length = 157 Score = 26.5 bits (58), Expect = 2.1 Identities = 13/87 (14%), Positives = 23/87 (26%), Gaps = 4/87 (4%) Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRY---DLERFGFAPRASPRQSDVMIVAGTL 102 V W ++ ++ G C Y + + IV G Sbjct: 13 GVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGG- 71 Query: 103 TNKMASALRRVYDQMPEPRYVISMGSC 129 K+A + V P + + C Sbjct: 72 DKKLAKLIDEVETLFPLNKGISVQSEC 98 >3beo_A UDP-N-acetylglucosamine 2-epimerase; UDP-GLCNAC, allosteric, regulation, isomerase; HET: UD1 UDP; 1.70A {Bacillus anthracis} PDB: 1o6c_A (A:1-192,A:357-375) Length = 211 Score = 26.3 bits (57), Expect = 2.5 Identities = 14/98 (14%), Positives = 27/98 (27%), Gaps = 10/98 (10%) Query: 85 APRASPRQSDVMIVAGTL--TNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV 142 P + VM + GT KMA + + + +++ + Sbjct: 1 GPVDMTERLKVMTIFGTRPEAIKMAPLVLELQKHPEKIESIVT------VTAQHRQMLDQ 54 Query: 143 VRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRV 180 V I P + LI + + +V Sbjct: 55 VLSIFGITPDFDLNIMKDR--QTLIDITTRGLEGLDKV 90 >1dku_A Protein (phosphoribosyl pyrophosphate synthetase); open alpha-beta structure, domain duplication, phosphoribosyltransferase type I fold; HET: AP2 ABM; 2.20A {Bacillus subtilis} (A:1-153,A:296-317) Length = 175 Score = 25.3 bits (55), Expect = 5.8 Identities = 15/89 (16%), Positives = 32/89 (35%), Gaps = 4/89 (4%) Query: 92 QSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVP 151 ++ I + ++A + + D + S+ ++G + S+ RGCD + Sbjct: 7 DKNLKIFSLNSNPELA---KEIADIVGVQLGKCSVTRFSDGEVQINIEESI-RGCDCYII 62 Query: 152 VDIYVPGCPPTAEALIYGILLLQKKIRRV 180 P E LI L + + + Sbjct: 63 QSTSDPVNEHIMELLIMVDALKRASAKTI 91 >3fz0_A Nucleoside hydrolase, putative; NH fold, open alpha/beta structure, glycosidase; HET: BTB; 2.50A {Trypanosoma brucei} (A:) Length = 360 Score = 24.9 bits (53), Expect = 7.8 Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 2/46 (4%) Query: 94 DVMIVA-GTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY 138 +VA G LTN +A ALR D + G G Sbjct: 128 VYQLVALGPLTN-VALALRLNPDLFSKLGTDTIPGIVIMNGTSESK 172 >1bd0_A Alanine racemase; isomerase, pyridoxal phosphate, alanine phosphonate; HET: IN5; 1.60A {Bacillus stearothermophilus} (A:15-232) Length = 218 Score = 24.5 bits (52), Expect = 9.1 Identities = 4/42 (9%), Positives = 17/42 (40%) Query: 103 TNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVR 144 + + + + +P ++ + A + ++++VR Sbjct: 164 FSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVR 205 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.323 0.136 0.417 Gapped Lambda K H 0.267 0.0534 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,453,342 Number of extensions: 64572 Number of successful extensions: 214 Number of sequences better than 10.0: 1 Number of HSP's gapped: 191 Number of HSP's successfully gapped: 19 Length of query: 185 Length of database: 4,956,049 Length adjustment: 83 Effective length of query: 102 Effective length of database: 2,150,234 Effective search space: 219323868 Effective search space used: 219323868 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 52 (24.3 bits)