RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (340 letters) >gnl|CDD|30551 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]. Length = 317 Score = 303 bits (777), Expect = 5e-83 Identities = 148/319 (46%), Positives = 206/319 (64%), Gaps = 5/319 (1%) Query: 9 LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68 +KP ++ + + + EPL RGF TLGNALRRVL+SS+ GAA+TAV+IDGV Sbjct: 1 FLKPKKVKIE---ELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGV 57 Query: 69 LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128 LHE SI+GV ED+ LN+K + +K+ GD + + K GPG VTA DI D+EV+ Sbjct: 58 LHEFDSIEGVQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVV 117 Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188 NPDHVI L DA + MEL V G GYVPA+ +R ++ P+G I +DA +SP++KV Y VE Sbjct: 118 NPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPVGPIAVDAPFSPVRKVQYIVE 177 Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248 AR GQ D D L +T+GSI E+++A+A++IL + L +F+ E++E+ Sbjct: 178 EARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEE--KP 235 Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308 P L ++EL+LSVRS NCL+ E I +G+L+QRTE ++L++ N G+KSL EIK Sbjct: 236 EFPILLVLEAPIDELDLSVRSYNCLKREGIETIGELVQRTEEELLKVENLGKKSLEEIKE 295 Query: 309 VLGTMGLFLGMNLPDWPPE 327 L +GL LGM L +WPP Sbjct: 296 KLAELGLELGMELENWPPS 314 >gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD. Length = 215 Score = 288 bits (740), Expect = 1e-78 Identities = 108/211 (51%), Positives = 149/211 (70%), Gaps = 1/211 (0%) Query: 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81 + EN + EPL RG TLGNALRRVL+SSL GAAITAV+I+GVLHE S+I GV ED Sbjct: 5 NKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVRED 64 Query: 82 LTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140 + +I+LN+K I K S D + + + +GPGVVTA DI+ + +E++NPD I L D Sbjct: 65 VLEILLNLKEIVFKSDSEDEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTED 124 Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200 A + MEL + KG GYVPA+ +++E PIG I IDA++SP++KV+Y+VES R GQ DY+K Sbjct: 125 ASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFSPVRKVNYSVESTRVGQRTDYEK 184 Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMF 231 L + I T+GSI+ E+++A A++IL + F Sbjct: 185 LILEIWTNGSISPEEALAQAAKILINHFSPF 215 >gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit. Length = 327 Score = 195 bits (499), Expect = 1e-50 Identities = 105/307 (34%), Positives = 165/307 (53%), Gaps = 22/307 (7%) Query: 31 IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90 I PL +G A T+G ALRR L+ + G IT +I+GV HE S+I G+ E + +I+LN+K Sbjct: 25 ILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILLNLK 84 Query: 91 GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150 I LK + ++ +I +GP VTA DI +E+++P I + + +EL + Sbjct: 85 EIVLKSNLYGPQKASICVQGPKYVTAQDIILPPSVEIVDPTQHIATITEPIDLEIELKIE 144 Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210 KG GY + +N G IDA++ P++ V+Y++ S G + L + I T+GS Sbjct: 145 KGRGY---RLKTPKNFQDGSFPIDAVFMPVRNVNYSIHSYGNGNEKQ-EILFLEIWTNGS 200 Query: 211 ITGEDSVALASRILQDQLGMFINFEEP--KKEVKEDINVKSLPFNPALLKK--------- 259 IT ++++ ASR L D F++ EE K E E+ F+ L Sbjct: 201 ITPKEALHEASRNLIDLFIPFLHAEEENLKLENNENRVTLLFTFHDRLTDLKKNKKEIAL 260 Query: 260 ----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315 +E+LELSVR+ NCL+ NI + DL+ ++ D+L++ NFG+KS K VL + Sbjct: 261 KQIFIEQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKS---AKEVLEALQK 317 Query: 316 FLGMNLP 322 G++LP Sbjct: 318 RFGIDLP 324 >gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain. Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal. Length = 117 Score = 126 bits (319), Expect = 7e-30 Identities = 47/118 (39%), Positives = 72/118 (61%), Gaps = 3/118 (2%) Query: 63 VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQ 120 V I+GV HE I GV ED+ +IILN+K + K+ G VT+ +GPG VTAGD++ Sbjct: 1 VYINGVAHEFGLIPGVSEDVLEIILNLKELVCKIEGCEECSVTLTLDVKGPGEVTAGDLE 60 Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178 + D+E++NPD +I L + +E KG GYV AK ++ + + G I +D+++S Sbjct: 61 SDPDVEIVNPDILIATLRKGQELELEAYAKKGRGYVHAKENKEDEEE-GRIPVDSIFS 117 >gnl|CDD|145976 pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal. Length = 62 Score = 84.1 bits (209), Expect = 5e-17 Identities = 30/60 (50%), Positives = 40/60 (66%) Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 L +EELELSVRS NCL+ I +GDL+ ++E D+L++ NFG+KSL EIK L Sbjct: 1 EELALLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEKL 60 >gnl|CDD|144693 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerization domain. The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Length = 91 Score = 62.3 bits (152), Expect = 2e-10 Identities = 32/63 (50%), Positives = 44/63 (69%) Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230 I DA +SP+KKV+Y VE R GQ DYDKL + I+TDGSIT E+++ A++IL D+L Sbjct: 29 IAGDAKFSPVKKVNYRVEPTRVGQNTDYDKLILEIETDGSITPEEALLEAAKILIDKLDE 88 Query: 231 FIN 233 + Sbjct: 89 LLE 91 Score = 50.3 bits (121), Expect = 7e-07 Identities = 17/31 (54%), Positives = 20/31 (64%) Query: 32 AEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62 E L G HTLGNALRR+L+S + G AI Sbjct: 1 IEFLLEGEDHTLGNALRRILLSEVPGVAIAG 31 >gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Length = 86 Score = 40.1 bits (94), Expect = 0.001 Identities = 20/56 (35%), Positives = 31/56 (55%) Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231 L SP++ +Y VE + Q D DK + I+T GSI E+++ A IL+ +L Sbjct: 31 LKSPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKLEHL 86 Score = 30.1 bits (68), Expect = 0.97 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 12/68 (17%) Query: 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81 ++E+N + E HTLGN+LRR+L+ S A ++ +K D Sbjct: 5 EKEKNYVDFVLENED----HTLGNSLRRILLKS--PVEFAAYYVE------HPVKLQRTD 52 Query: 82 LTDIILNI 89 IL I Sbjct: 53 EDKFILRI 60 >gnl|CDD|35413 KOG0192, KOG0192, KOG0192, Tyrosine kinase specific for activated (GTP-bound) p21cdc42Hs [Signal transduction mechanisms]. Length = 362 Score = 30.5 bits (68), Expect = 0.73 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 8/92 (8%) Query: 12 PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGV-- 68 PN +++ ++ E +P G L + R+ + L+ A+ I G+ Sbjct: 99 PNIVQFYGACTSPPGSLCIVTEYMPGGSLSVLLHKKRKRKL-PLKVRLRIALDIARGMEY 157 Query: 69 LHEISSIKGVHEDL--TDIILNIKGINLKMSG 98 LH I +H DL +I++++KG LK++ Sbjct: 158 LHSEGPI--IHRDLKSDNILVDLKGKTLKIAD 187 >gnl|CDD|31955 COG1769, COG1769, Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) [DNA replication, recombination, and repair]. Length = 335 Score = 30.4 bits (68), Expect = 0.82 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 4/90 (4%) Query: 155 YVPAKHHRTENDPI-GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213 YVP+ + + D + ++ ID LY P Y ++S + + S + Sbjct: 79 YVPSPRNVYKTDSVTPIVEIDGLYLPWL-PEYKMDSKESTN--GFIEFSDLELLRSNGIC 135 Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKE 243 + + A +I + + + I E+ +K+VKE Sbjct: 136 KFDLVSAEKIFKKETRVGIALEKNRKKVKE 165 >gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer. Length = 259 Score = 29.9 bits (68), Expect = 0.90 Identities = 59/268 (22%), Positives = 105/268 (39%), Gaps = 58/268 (21%) Query: 14 NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI--------TAVQI 65 IE + L +++R + E +P FA NA+RR ++S + AI T+V Sbjct: 2 EIEVLEL---DDDRARFVLEGVPPAFA----NAIRRAIISEVPTLAIDDVNIYENTSVLF 54 Query: 66 DGVL-HEISSIKGVHEDLTDIILN--IKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQ 120 D +L H + I TD+ L + +G VT + GPG V +GD++ Sbjct: 55 DEMLAHRLGLIPLR----TDLDLYKYRSECSCGGAGCPLCTVTLTLSVEGPGTVYSGDLK 110 Query: 121 TVN-DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGLI--T 172 + + D++ + + I L + +E G G AK T + P+ I Sbjct: 111 SSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYKYYPVIEIDED 170 Query: 173 IDALYSPIKKVSYTVESAREGQVL--------------------------DYDKLSMTID 206 D +++ V EG+V+ D D+ ++ Sbjct: 171 CDGCGKCVEECPRGVLELEEGKVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVE 230 Query: 207 TDGSITGEDSVALASRILQDQLGMFINF 234 +DGS+ ++ + A RIL+++ I Sbjct: 231 SDGSLPPKEILLEALRILKEKADELIEA 258 >gnl|CDD|132907 cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to associate with the RPB3 counterpart, AC40, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. Length = 85 Score = 29.5 bits (67), Expect = 1.5 Identities = 9/12 (75%), Positives = 11/12 (91%) Query: 41 HTLGNALRRVLM 52 HTLGN+LR V+M Sbjct: 20 HTLGNSLRYVIM 31 >gnl|CDD|146686 pfam04177, TAP42, TAP42-like family. The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 (pfam04176) interacts with TAP42 and negatively regulates the TOR signaling pathway. Length = 335 Score = 28.0 bits (63), Expect = 4.1 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 17/82 (20%) Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231 ++ L+ K+ +E + DK+ TI+ + A+R++ QL +F Sbjct: 1 SLSELFDEALKLFDELEESASDSEEYQDKVKKTIE---------LLEKATRLV-SQLSLF 50 Query: 232 -INFEEPKKEVKEDINVKSLPF 252 N E EDI+ SL + Sbjct: 51 SSN------ETLEDISTSSLKY 66 >gnl|CDD|36735 KOG1522, KOG1522, KOG1522, RNA polymerase II, subunit POLR2C/RPB3 [Transcription]. Length = 285 Score = 27.6 bits (61), Expect = 5.1 Identities = 47/230 (20%), Positives = 86/230 (37%), Gaps = 44/230 (19%) Query: 43 LGNALRRVLMSSLRGAAITAVQID---GVLHE--ISSIKGVHEDLTDIILNIK------- 90 + N+LRRV+++ + AI V+I+ VL + I+ G+ ++D I+ ++ Sbjct: 29 VANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVELQYTRDCEC 88 Query: 91 -----------GINLKMSGDSHKRVT---IFKRGPGVVTAGDIQTVNDIEVLNPDH-VIC 135 +++K + D + VT + P V + + +I Sbjct: 89 DEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLDPTVTPVDSNRGSEIDDDSESKGILIV 148 Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGLI--------TIDALYSPIKK 182 L +++ KG G AK T E DP + D + P K Sbjct: 149 KLRKGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDLIEWPKSK 208 Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQL 228 S E EG D DK +++ G++ V + IL+++L Sbjct: 209 NSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKL 258 >gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. Length = 265 Score = 27.2 bits (61), Expect = 6.4 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 20/64 (31%) Query: 10 IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG-- 67 + + +++I+ EN L +A N+LRRV+++ + AI V+I+ Sbjct: 8 LTDDKVKFIL-----ENTDLSVA------------NSLRRVMIAEVPTLAIDLVEIEENT 50 Query: 68 -VLH 70 VLH Sbjct: 51 SVLH 54 >gnl|CDD|36604 KOG1390, KOG1390, KOG1390, Acetyl-CoA acetyltransferase [Lipid transport and metabolism]. Length = 396 Score = 26.8 bits (59), Expect = 8.3 Identities = 10/23 (43%), Positives = 13/23 (56%) Query: 102 KRVTIFKRGPGVVTAGDIQTVND 124 K +FK G VTA + T+ND Sbjct: 233 KLRPVFKEDGGTVTAANASTLND 255 >gnl|CDD|112628 pfam03824, NicO, High-affinity nickel-transport protein. High affinity nickel transporters involved in the incorporation of nickel into H2-uptake hydrogenase and urease enzymes. Essential for the expression of catalytically active hydrogenase and urease. Ion uptake is dependent on proton motive force. HoxN in Alcaligenes eutrophus is thought to be an integral membrane protein with seven transmembrane helices. The family also includes a cobalt transporter. Length = 278 Score = 27.0 bits (60), Expect = 8.3 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 2/53 (3%) Query: 27 RTLMIA--EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77 R+ M A PL G +LG++ L++ L + V L EI S G Sbjct: 28 RSYMQAGKTPLKVGILFSLGHSSVVGLVALLLALGVKLVLRLPSLQEIGSTIG 80 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 0.317 0.136 0.386 Gapped Lambda K H 0.267 0.0737 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,963,820 Number of extensions: 205796 Number of successful extensions: 508 Number of sequences better than 10.0: 1 Number of HSP's gapped: 500 Number of HSP's successfully gapped: 21 Length of query: 340 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 246 Effective length of database: 4,232,491 Effective search space: 1041192786 Effective search space used: 1041192786 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: 58 (26.1 bits)