RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (340 letters) >3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Length = 329 Score = 376 bits (966), Expect = e-105 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%) Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61 +Q + E +KP ++ Q + EPL RGF HTLGNALRR+L+SS+ G A+T Sbjct: 1 MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57 Query: 62 AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121 V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G VTA DI Sbjct: 58 EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117 Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177 D+E++ P HVIC+L D +A + M + V +G GYVPA + PIG + +DA Y Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177 Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237 SP+++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++ + Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237 Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297 ++ ++ + F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ N Sbjct: 238 RQPEVKE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294 Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331 G+KSL EIK VL + GL LGM L +WPP SI + Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328 >3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 329 Score = 346 bits (890), Expect = 3e-96 Identities = 146/334 (43%), Positives = 218/334 (65%), Gaps = 10/334 (2%) Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61 +Q + E +KP ++ Q + EPL RGF HTLGNALRR+L+SS+ G A+T Sbjct: 1 MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57 Query: 62 AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121 V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G VTA DI Sbjct: 58 EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117 Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 177 D+E++ P HVIC+L +A + M + V +G GYVPA H + PIG + +DA Y Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177 Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237 SP+++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++ + Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237 Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297 ++ ++ F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ N Sbjct: 238 RQPEVKEE---KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294 Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331 G+KSL EIK VL + GL LGM L +WPP SI + Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328 >2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A 1hqm_A ... Length = 315 Score = 297 bits (762), Expect = 2e-81 Identities = 115/316 (36%), Positives = 167/316 (52%), Gaps = 8/316 (2%) Query: 6 WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 +K G + EPL RGF TLGN LRR+L+SS+ G A+T+V I Sbjct: 2 LDSKLKAPVFTVRTQG---REYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYI 58 Query: 66 DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVN 123 + VLHE S+I GV ED+ +IILN+K + ++ S + VT+ + GP V A D V Sbjct: 59 EDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVA 118 Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183 D+E++NPD I L+ + ME+ V +G GYVPA+ H D I I +DA++SP+++V Sbjct: 119 DVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGI-KDRINAIPVDAVFSPVRRV 177 Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243 ++ VE R GQ D DKL++ I TDGS+T +++ A IL++ L F N + E Sbjct: 178 AFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPE 237 Query: 244 DINVKS--LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301 + L +EEL LS R + L+ E I + L+ D+ + G + Sbjct: 238 EAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGER 297 Query: 302 SLVEIKGVLGTMGLFL 317 SL EIK L G L Sbjct: 298 SLEEIKEALEKKGFTL 313 >1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Length = 235 Score = 241 bits (617), Expect = 1e-64 Identities = 99/237 (41%), Positives = 151/237 (63%), Gaps = 7/237 (2%) Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61 +Q + E +KP ++ Q + EPL RGF HTLGNALR +L+SS+ G A+T Sbjct: 1 MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVT 57 Query: 62 AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121 V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G VTA DI Sbjct: 58 EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117 Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 177 D+E++ P HVIC+L +A + M + V +G GYVPA H + PIG + +DA Y Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177 Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234 SP+++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++ Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 234 >2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D Length = 265 Score = 132 bits (334), Expect = 8e-32 Identities = 34/246 (13%), Positives = 77/246 (31%), Gaps = 44/246 (17%) Query: 32 AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDL 82 + + G+ NA+RR M + A+ V + + H ++ I + E+ Sbjct: 13 IDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEA 72 Query: 83 TDIILNIKGINLKMSGDSHKRVTIFKR-----GPGVVTAGDIQTVND-IEVLNPDHVICN 136 D + I+ P ++ + DI++ + + ++ D I Sbjct: 73 LDTYRWPEECIECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVL 132 Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRT---------------------ENDPIGLITI-- 173 L + + +E + G+G AK P G+ + Sbjct: 133 LGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVCPEGVFELKD 192 Query: 174 ------DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227 + L + + + DK + I++ GS+ E + A + + + Sbjct: 193 GKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRK 252 Query: 228 LGMFIN 233 + Sbjct: 253 IEELEK 258 >1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Length = 318 Score = 131 bits (331), Expect = 2e-31 Identities = 40/260 (15%), Positives = 81/260 (31%), Gaps = 43/260 (16%) Query: 37 RGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIIL 87 + N+LRRV+++ + AI +V++ + + H + I D+ + Sbjct: 23 SNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY 82 Query: 88 NIKGINLKMSGDSHK----RVTIFKRGPGVVTAGDIQTVND-----------IEVLNPDH 132 + + V + D+ V++ + Sbjct: 83 SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGV 142 Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAK-------------HHRTENDPIGLITIDALYSP 179 +IC L +++ KG AK ++ ++ A P Sbjct: 143 LICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP 202 Query: 180 IKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235 K + EG DY D M +++ GSI + V LQ ++ + Sbjct: 203 QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASIL--L 260 Query: 236 EPKKEVKEDINVKSLPFNPA 255 + ++ +N S N A Sbjct: 261 ALTQMDQDKVNFASGDNNTA 280 >3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 297 Score = 126 bits (316), Expect = 9e-30 Identities = 40/253 (15%), Positives = 84/253 (33%), Gaps = 45/253 (17%) Query: 37 RGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIIL 87 + + N+LRRV+++ + AI V+I + + H + I ++ + Sbjct: 22 TNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPP 81 Query: 88 NIKGINLKMSGDS---------HKRVTIFKRGPGVVTAGDIQTVNDIEVLNP-------- 130 D G + A D+ ++ + +P Sbjct: 82 VGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSR 141 Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHH-------------RTENDPIGLITIDALY 177 +IC L + + + KG AK + ++ Sbjct: 142 GPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAE 201 Query: 178 SPIKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 P K + E REG+ ++ + M +++ GSI + + RILQ++L + + Sbjct: 202 WPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVR 261 Query: 234 F--EEPKKEVKED 244 EE ++ + Sbjct: 262 DLDEEQPTQLSAN 274 >1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} SCOP: a.60.3.1 PDB: 1xs9_D Length = 84 Score = 120 bits (304), Expect = 3e-28 Identities = 46/80 (57%), Positives = 61/80 (76%) Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311 F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ N G+KSL EIK VL Sbjct: 4 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63 Query: 312 TMGLFLGMNLPDWPPESIEE 331 + GL LGM L +WPP SI + Sbjct: 64 SRGLSLGMRLENWPPASIAD 83 >1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} SCOP: a.60.3.1 PDB: 2jzb_A Length = 98 Score = 118 bits (298), Expect = 2e-27 Identities = 50/101 (49%), Positives = 71/101 (70%), Gaps = 5/101 (4%) Query: 232 INFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290 ++ + ++ EVKE+ F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE Sbjct: 1 MDLRDVREPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEV 56 Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331 ++L+ N G+KSL EIK VL + GL LGM L +WPP SI + Sbjct: 57 ELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 97 >3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} PDB: 1lb2_B* 1xs9_D Length = 86 Score = 117 bits (296), Expect = 3e-27 Identities = 44/80 (55%), Positives = 56/80 (70%) Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311 F+P LL+ V++LEL+VRS NCL E I Y+GDL+QRTE ++L N G SL EI VL Sbjct: 6 FDPILLRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLA 65 Query: 312 TMGLFLGMNLPDWPPESIEE 331 + GL LGM L +WPP SI + Sbjct: 66 SRGLSLGMRLENWPPASIAD 85 >3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Length = 79 Score = 95.1 bits (237), Expect = 2e-20 Identities = 30/70 (42%), Positives = 42/70 (60%) Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 L +EEL+LSVRS NCL+ I + +L +TE DM+++ N GRKSL E+K L Sbjct: 9 QKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKL 68 Query: 311 GTMGLFLGMN 320 +GL L + Sbjct: 69 EELGLGLRKD 78 >1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 Length = 73 Score = 94.3 bits (235), Expect = 3e-20 Identities = 30/68 (44%), Positives = 42/68 (61%) Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 L +EEL+LSVRS NCL+ I + +L +TE DM+++ N GRKSL E+K L Sbjct: 4 EKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE 63 Query: 313 MGLFLGMN 320 +GL L + Sbjct: 64 LGLGLRKD 71 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 34.9 bits (80), Expect = 0.023 Identities = 19/103 (18%), Positives = 33/103 (32%), Gaps = 35/103 (33%) Query: 202 SMTIDTDGSITGEDSVALASRI------LQDQLGMFIN-FEEPKKEVKEDINVKS----- 249 +T+ + GS+ E + + + LQ+Q F EP + D + Sbjct: 8 PLTL-SHGSL--EHVLLVPTASFFIASQLQEQ---FNKILPEPTEGFAADDEPTTPAELV 61 Query: 250 ---LPFNPALLKKVEE---------LELSVRS--TNCLRGENI 278 L + + VE L L + L G +I Sbjct: 62 GKFLGY---VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI 101 Score = 31.8 bits (72), Expect = 0.20 Identities = 53/383 (13%), Positives = 102/383 (26%), Gaps = 159/383 (41%) Query: 30 MIAEPLPRGFAHTLGNALRRVLMSSLRGAA-ITAV---Q--IDGVLHEISSIKGVHEDL- 82 M P + +AL R + G A + A+ Q D E+ + + L Sbjct: 132 MAKRPFDK--KSN--SALFR---AVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184 Query: 83 TDIILNIKGINLKMSGDSHKRVTIFKRG-------------PGV---VTA-------GDI 119 D+I ++ + +F +G P ++ G I Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVI 244 Query: 120 QTVNDIEVLNPDH--VIC-NLDVD-AVVRMELTVSKGH--GYVPAKHHRTENDPIGLITI 173 Q H V L +R L + GH G V A + I Sbjct: 245 QLA---------HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA------------VAI 283 Query: 174 ------DALYSPIKKV-------------SY--------TVESAR---EGQ------V-- 195 ++ + ++K +Y +E + EG + Sbjct: 284 AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN 343 Query: 196 LDYDKLSMTIDTDGSITGED---SVALA-SRILQDQL----------GMFINFEEPKKEV 241 L +++ ++ S ++L L G+ + + K Sbjct: 344 LTQEQVQDYVNKTNSHLPAGKQVEISLVNGA---KNLVVSGPPQSLYGLNLTLRKAKAPS 400 Query: 242 KEDIN--------VK--------SLPFNPALLKKVEE-----------------LELSVR 268 D + +K + PF+ LL + +++ V Sbjct: 401 GLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVY 460 Query: 269 STNC---LR--GENIVYMGDLIQ 286 T LR +I ++ Sbjct: 461 DTFDGSDLRVLSGSIS--ERIVD 481 Score = 31.1 bits (70), Expect = 0.42 Identities = 21/145 (14%), Positives = 37/145 (25%), Gaps = 70/145 (48%) Query: 25 ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84 NR L +A P F H+ L A+ I +DL Sbjct: 417 SNRFLPVASP----F-HS----------HLLVPAS-------------DLIN---KDLVK 445 Query: 85 IILNIKGINLKMSGDSHKRVTIFKRGPGVV----TAGDIQTVNDIEVLNPDHV--ICNLD 138 ++ ++++ P V D++ ++ ++ V I L Sbjct: 446 NNVSFNAKDIQI--------------P--VYDTFDGSDLRVLS--GSISERIVDCIIRLP 487 Query: 139 VD---AVVRMELTVSKGHGYVPAKH 160 V A H Sbjct: 488 VKWETTTQ------------FKATH 500 Score = 26.4 bits (58), Expect = 9.2 Identities = 8/29 (27%), Positives = 10/29 (34%), Gaps = 9/29 (31%) Query: 316 FLGMNLP--------DWPPESIEELAKKY 336 F LP D P + EL K+ Sbjct: 37 FN-KILPEPTEGFAADDEPTTPAELVGKF 64 >3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A* Length = 356 Score = 33.0 bits (75), Expect = 0.100 Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 16/86 (18%) Query: 65 IDGVLHEISSIKGVHEDLTDIILNIKG--------------INLKMSGDSHKRVTIFK-- 108 +DG + I+ H+ + +I +I + ++ G + RV F Sbjct: 30 VDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQN 89 Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVI 134 RG G V V +E L V Sbjct: 90 RGAGAVFRTIPSKVLTMEELGMGEVF 115 >1qfg_A FHUA, protein (ferric hydroxamate uptake receptor); TONB-dependent receptor, integral outer membrane protein, ferrichrome-iron receptor; HET: PA1 GCN KDO GMH GLC GLA FTT DAO MYR DDQ; 2.50A {Escherichia coli} SCOP: f.4.3.3 PDB: 1qff_A* 1qjq_A* 1qkc_A* 2grx_A* 1fi1_A* 2fcp_A* 1by5_A* 1by3_A* 1fcp_A* Length = 725 Score = 32.1 bits (71), Expect = 0.21 Identities = 10/72 (13%), Positives = 27/72 (37%), Gaps = 2/72 (2%) Query: 81 DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140 + + + G+++ G S+ + RG +N +++ + +D Sbjct: 65 SVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPY 124 Query: 141 AVVRMELTVSKG 152 + R E + +G Sbjct: 125 MLERAE--IMRG 134 >3cz1_A Pheromone-binding protein Asp1; honey BEE, signal transduction, queen mandibular pheromone; HET: NBB; 1.50A {Apis mellifera} PDB: 2h8v_A* 3bfa_A* 3bfb_A* 3bfh_A* 3cab_A 3cdn_A 3cyz_A* 3cz0_A* 3bjh_A* 3cz2_A 3d78_A* 3d75_A* 3d76_A* 3d77_A* 3d73_A* 3d74_A* Length = 119 Score = 29.5 bits (66), Expect = 1.0 Identities = 6/19 (31%), Positives = 11/19 (57%) Query: 322 PDWPPESIEELAKKYEDKC 340 PDW P + +L + + +C Sbjct: 2 PDWVPPEVFDLVAEDKARC 20 >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 = 29.2 bits (64), Expect = 1.2 Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 11/32 (34%) Query: 192 EGQVLDYDKL--SMTIDTDGSITGEDSV-ALA 220 E Q L KL S+ + D DS ALA Sbjct: 18 EKQALK--KLQASLKLYAD------DSAPALA 41 >3k9v_A 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial; mitochondrial cytochrome P450, monotopic membrane protein, monooxygenase; HET: HEM CPS; 2.50A {Rattus norvegicus} PDB: 3k9y_A* Length = 482 Score = 27.7 bits (60), Expect = 3.8 Identities = 7/41 (17%), Positives = 18/41 (43%), Gaps = 5/41 (12%) Query: 301 KSLVEIKG-----VLGTMGLFLGMNLPDWPPESIEELAKKY 336 +++ ++ G +LG++ +++ E KKY Sbjct: 21 RNVTDLPGPTNWPLLGSLLEIFWKGGLKKQHDTLAEYHKKY 61 >3ogn_A Odorant-binding protein; helix bundle, transport protein; HET: 3OG; 1.30A {Culex quinquefasciatus} PDB: 2erb_A* 3k1e_A* Length = 124 Score = 27.7 bits (61), Expect = 4.0 Identities = 6/19 (31%), Positives = 9/19 (47%) Query: 322 PDWPPESIEELAKKYEDKC 340 ++PP + E K D C Sbjct: 7 AEYPPPELLEALKPLHDIC 25 >1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Length = 120 Score = 27.1 bits (60), Expect = 6.4 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 7/49 (14%) Query: 11 KPNNIEYIVLGQEEENRTLMIAEPLPRGF-------AHTLGNALRRVLM 52 P+ E +LG+ E + P HTLGN +R L+ Sbjct: 3 APDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELL 51 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 26.7 bits (58), Expect = 6.8 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 7/57 (12%) Query: 287 RTEADMLRMANFGRKSLVEIKG----VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339 RT A+M R A R +E +G ++ L L M +P + I +A DK Sbjct: 1161 RTPAEMSRPATTTRNGFMEAQGAGIQIIMQADLALKMGVPIY---GIVAMAATATDK 1214 >2vcc_A Alpha-N-acetylglucosaminidase; GH89, naGlu, sanfilippo disease, hydrolase, mucopolysaccharidosis, family 89 glycoside hydrolase; 2.0A {Clostridium perfringens} PDB: 2vc9_A* 2vcb_A* 2vca_A Length = 891 Score = 26.8 bits (59), Expect = 7.6 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 7/57 (12%) Query: 172 TIDALYSPIKKV-------SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221 T++ + + + +V + E + D ++S + D I G + V+LAS Sbjct: 170 TLNEIKNLVGRVIGREFKDKFIFEIRDQLNGNDVFEVSDSGDGKVLIKGNNGVSLAS 226 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 0.317 0.136 0.386 Gapped Lambda K H 0.267 0.0541 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,897,589 Number of extensions: 135416 Number of successful extensions: 394 Number of sequences better than 10.0: 1 Number of HSP's gapped: 375 Number of HSP's successfully gapped: 37 Length of query: 340 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 247 Effective length of database: 3,438,538 Effective search space: 849318886 Effective search space used: 849318886 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 (21.6 bits) S2: 57 (26.2 bits)