RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 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* Length = 181 Score = 210 bits (535), Expect = 2e-55 Identities = 86/155 (55%), Positives = 117/155 (75%), Gaps = 2/155 (1%) Query: 26 FSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFA 85 F R E+ +G L T++++LV W R+ SL TFGLACCA+EMM ++ R DL RFG Sbjct: 7 FERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSE 66 Query: 86 -PRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVR 144 RASPRQ+DVMIVAG L+ KMA +RRV++QMP+P++VISMG+CA+ GG ++ +Y++V+ Sbjct: 67 VFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQ 125 Query: 145 GCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179 D +VPVD+YVPGCPP EALIY ++ LQKK+R Sbjct: 126 NVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRG 160 >1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 Length = 317 Score = 81.1 bits (200), Expect = 1e-16 Identities = 30/190 (15%), Positives = 57/190 (30%), Gaps = 41/190 (21%) Query: 25 DFSRISSEITHKGFLVTSVDQLVTWARTG----SLMWMTF-GLACCAVEMMQASMPRYDL 79 DF + + I + + V A G S++++ C+ +++A P D Sbjct: 25 DFLKFCTAIAVTMGMGPAFAPEVARALMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDT 84 Query: 80 ERFGFAP---------------------RASPRQSDVMIVAGTLTNKMA---------SA 109 + + +V G + + Sbjct: 85 LILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTM 144 Query: 110 LRRVYDQMPEPRYVISMGSCANGGGY------YHYSYSVVRGCDRIVPVDIYVPGCPPTA 163 L +P+ + VI+ G+CA GG + V + I + GCPP Sbjct: 145 LDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNP 204 Query: 164 EALIYGILLL 173 L+ I+ Sbjct: 205 YNLVGTIVYY 214 >1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S 1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S 1wuk_S 1wul_S 1e3d_A* Length = 267 Score = 80.0 bits (197), Expect = 3e-16 Identities = 25/161 (15%), Positives = 52/161 (32%), Gaps = 37/161 (22%) Query: 50 ARTGSLMWMTF-GLACCAVEMMQASMPRYDLERFG-----FAP----------------R 87 R S++++ C+ +++A P D + Sbjct: 4 PRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQA 63 Query: 88 ASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGYYH- 137 + + +V G + + L +P+ + VI+ G+CA GG Sbjct: 64 VNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAA 123 Query: 138 -YSYSVVRGCDRIVP----VDIYVPGCPPTAEALIYGILLL 173 + + +G + + I + GCPP L+ I+ Sbjct: 124 KPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYY 164 >1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A Length = 264 Score = 78.1 bits (192), Expect = 1e-15 Identities = 23/156 (14%), Positives = 51/156 (32%), Gaps = 37/156 (23%) Query: 54 SLMWMTFGLAC--CAVEMMQASMPRYDLERFGF-------------------APRASPRQ 92 S++++ C C+ +++ P D A + + Sbjct: 8 SVVYLHNA-ECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKG 66 Query: 93 SDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGG--YYHYSYS 141 V ++ G + + + P+ + VI++G+CA GG + + Sbjct: 67 DFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPT 126 Query: 142 VVRGCDRIVP----VDIYVPGCPPTAEALIYGILLL 173 G + + I + GCPP + ++ L Sbjct: 127 GTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHL 162 >1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} SCOP: e.19.1.1 Length = 283 Score = 70.4 bits (172), Expect = 2e-13 Identities = 16/131 (12%), Positives = 41/131 (31%), Gaps = 27/131 (20%) Query: 78 DLERFGFAPRASPRQSDVMIVAGTLTNKM-------------------ASALRRVYDQMP 118 + + ++V G + + + + D P Sbjct: 56 MALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKAHHHEVTMMELIRDLAP 115 Query: 119 EPRYVISMGSCANGGGYYHYSYSV--------VRGCDRIVPVDIYVPGCPPTAEALIYGI 170 + +++G+C+ GG +V ++I + + VPGCPP + ++ + Sbjct: 116 KSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTL 175 Query: 171 LLLQKKIRRVG 181 + + Sbjct: 176 VAAWSHVLNPT 186 >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 Length = 264 Score = 70.3 bits (172), Expect = 3e-13 Identities = 22/155 (14%), Positives = 45/155 (29%), Gaps = 36/155 (23%) Query: 54 SLMWMTFGLAC--CAVEMMQASMPRYDLERFGFAP---------------------RASP 90 S++W+ C C ++ P D Sbjct: 8 SVVWLHNA-ECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEG 66 Query: 91 RQSDVMIVAGTLTNKM---------ASALRRVYDQMPEPRYVISMGSCANGGGYYH--YS 139 + ++V G L + + + +I +G+C+ GG + Sbjct: 67 KDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPN 126 Query: 140 YSVVRGCDRIVPVDIY-VPGCPPTAEALIYGILLL 173 S +G + V +PGCPP + ++ + Sbjct: 127 PSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHV 161 >3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} Length = 269 Score = 69.2 bits (169), Expect = 5e-13 Identities = 23/108 (21%), Positives = 37/108 (34%), Gaps = 14/108 (12%) Query: 78 DLERFGFAPRASPRQSDVMIVAGTLTNKMA----------SALRRVYDQMPEPRYVISMG 127 E R ++IV G++ A S + + + VI++G Sbjct: 52 AAEAARLQAMDENRGQYLVIVDGSIPGPDANPGFSTVAGHSNYSILMETVEHAAAVIAVG 111 Query: 128 SCANGGGYY--HYSYSVVRGCDRIVP--VDIYVPGCPPTAEALIYGIL 171 +CA GG + + +V I VPGCPP + I Sbjct: 112 TCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPIPMVITGVIA 159 >2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Length = 317 Score = 46.9 bits (111), Expect = 3e-06 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%) Query: 100 GTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV--------VRGCDRIVP 151 G + S + + + P V+++G+CA GG S G + I Sbjct: 126 GEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKT 185 Query: 152 VDIYVPGCPPTAEALIYGILLL 173 + +PGCPP + ++ ++L Sbjct: 186 PVVNIPGCPPHPDWIVGTVVLA 207 >3nb0_A Glycogen [starch] synthase isoform 2; glycogen synthase, glucose-6-phosphate, yeast, allosteric AC transferase; HET: G6P; 2.41A {Saccharomyces cerevisiae} PDB: 3nch_A 3naz_A 3o3c_A* Length = 725 Score = 43.4 bits (101), Expect = 3e-05 Identities = 8/69 (11%), Positives = 15/69 (21%) Query: 104 NKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTA 163 +M + Y ++ G V + VPG P Sbjct: 620 KRMGLEYVKARQLALRRGYPDQFRELVGEELNDSNMDALAGGKKLKVARPLSVPGSPRDL 679 Query: 164 EALIYGILL 172 + + Sbjct: 680 RSNSTVYMT 688 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 32.3 bits (72), Expect = 0.059 Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 11/37 (29%) Query: 66 AVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTL 102 A++ +QAS+ Y A ++P + + T+ Sbjct: 21 ALKKLQASLKLY-------ADDSAP----ALAIKATM 46 >2wh6_A Early antigen protein R; mitochondrion, early protein, transmembrane, viral protein, apoptosis; 1.50A {Human herpesvirus 4} PDB: 2v6q_A 1q59_A Length = 173 Score = 29.1 bits (64), Expect = 0.69 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 11/60 (18%) Query: 20 EKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDL 79 E VD DF+ + EI H+G + R L WM + + C + Y + Sbjct: 90 EHVDLDFNSVFLEIFHRG--------DPSLGRA--LAWMAWCMHAC-RTLCCNQSTPYYV 138 >2c40_A Inosine-uridine preferring nucleoside hydrolase family protein; spine; 2.2A {Bacillus anthracis} Length = 312 Score = 27.1 bits (59), Expect = 2.5 Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%) Query: 95 VMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY 138 ++ G LT+ +A AL + + ++ MG G H Sbjct: 121 TLLFTGPLTD-LARALYEAPIIENKIKRLVWMGGTFRTAGNVHE 163 >2v6q_A BHRF1 protein; alternative splicing, membrane, apoptosis, epstein-BARR virus; 2.7A {Epstein-barr virus} PDB: 1q59_A Length = 173 Score = 26.9 bits (59), Expect = 2.7 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 >3ca8_A Protein YDCF; two domains, alpha/beta fold, helix bundle, structural genomics, structure 2 function project, S2F, unknown function; 1.80A {Escherichia coli K12} Length = 266 Score = 26.9 bits (59), Expect = 2.7 Identities = 13/81 (16%), Positives = 23/81 (28%), Gaps = 8/81 (9%) Query: 86 PRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRG 145 P Q+D +I+AG A ++ P + GG H + + Sbjct: 30 SGEVPYQADCVILAGNAVMPTIDAACKIARDQQIPLLIS--------GGIGHSTTFLYSA 81 Query: 146 CDRIVPVDIYVPGCPPTAEAL 166 + + A L Sbjct: 82 IAQHPHYNTIRTTGRAEATIL 102 >2k4z_A DSRR; ISCA/SUFA/HESB like fold, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Allochromatium vinosum} Length = 125 Score = 26.9 bits (59), Expect = 2.8 Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 3/52 (5%) Query: 90 PRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYS 141 PR S +M LT A + + Q + + + N G Y Sbjct: 16 PRGSHMMF---KLTPAAAEQVLKAAKQGGTEGMCLRLAAGRNPDGSIDYRMG 64 >2x3d_A SSO6206; unknown function; 2.70A {Sulfolobus solfataricus} Length = 96 Score = 26.7 bits (59), Expect = 2.9 Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 7/43 (16%) Query: 5 TVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLV 47 T+ II +E +F I + +G + S+D++V Sbjct: 47 TMGLMII-------IEGTSLNFDDIRKMLEEEGCAIHSIDEVV 82 >1ddg_A Sulfite reductase (NADPH) flavoprotein alpha- component; cytochrome P450 reductase, FNR, modular protein, oxidoreductase; HET: FAD; 2.01A {Escherichia coli} SCOP: b.43.4.1 c.25.1.4 PDB: 1ddi_A* Length = 374 Score = 26.7 bits (58), Expect = 3.6 Identities = 15/118 (12%), Positives = 33/118 (27%), Gaps = 6/118 (5%) Query: 23 DADFSRISSEITHKG--FLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLE 80 +S SS+ + + V + R + +F + + + Sbjct: 160 PRLYSIASSQAEVENEVHVTVGVVRYDVEGRARAGGASSF---LADRVEEEGEVRVFIEH 216 Query: 81 RFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY 138 F A+P +MI GT + +++ P + + Y Sbjct: 217 NDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADE-APGKNWLFFGNPHFTEDFLY 273 >1j1l_A Pirin; beta sandwich, cupin, iron, metatl binding protein; 2.10A {Homo sapiens} SCOP: b.82.1.12 Length = 290 Score = 26.2 bits (57), Expect = 4.2 Identities = 19/119 (15%), Positives = 30/119 (25%), Gaps = 5/119 (4%) Query: 51 RTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASAL 110 G L WMT G E MP + G + R S+ M+ K Sbjct: 86 NPGDLQWMTAGRGILHAE-----MPCSEEPAHGLQLWVNLRSSEKMVEPQYQELKSEEIP 140 Query: 111 RRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYG 169 + D + + + + D +P + I G Sbjct: 141 KPSKDGVTVAVISGEALGIKSKVYTRTPTLYLDFKLDPGAKHSQPIPKGWTSFIYTISG 199 >1q14_A HST2 protein; histone deacetylase, hydrolase; 2.50A {Saccharomyces cerevisiae} SCOP: c.31.1.5 Length = 361 Score = 26.3 bits (57), Expect = 4.3 Identities = 10/87 (11%), Positives = 28/87 (32%), Gaps = 5/87 (5%) Query: 68 EMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPE--PRYVIS 125 + + + R Q ++IV GT + + + +++P R + + Sbjct: 195 SFSETWLNDSEWLREKITTSGKHPQQPLVIVVGT-SLAVYPF-ASLPEEIPRKVKRVLCN 252 Query: 126 MGSCANGGGYYHYSYSVVRG-CDRIVP 151 + + + + +V D Sbjct: 253 LETVGDFKANKRPTDLIVHQYSDEFAE 279 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.323 0.136 0.417 Gapped Lambda K H 0.267 0.0436 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,630,635 Number of extensions: 73131 Number of successful extensions: 251 Number of sequences better than 10.0: 1 Number of HSP's gapped: 241 Number of HSP's successfully gapped: 22 Length of query: 185 Length of database: 5,693,230 Length adjustment: 87 Effective length of query: 98 Effective length of database: 3,584,002 Effective search space: 351232196 Effective search space used: 351232196 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: 54 (25.3 bits)