RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780567|ref|YP_003064980.1| hypothetical protein CLIBASIA_02270 [Candidatus Liberibacter asiaticus str. psy62] (246 letters) >gnl|CDD|169652 PRK09087, PRK09087, hypothetical protein; Validated. Length = 226 Score = 275 bits (706), Expect = 7e-75 Identities = 115/221 (52%), Positives = 146/221 (66%) Query: 24 KEEQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANI 83 EQL +F RDDLLV + AV L+D WP+WPS VV+L GP GSGK+ LA+I Sbjct: 4 APEQLPLNFSHDPAYGRDDLLVTESNRAAVSLVDHWPNWPSPVVVLAGPVGSGKTHLASI 63 Query: 84 WSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQLFHIINSIHQYDSSLLMT 143 W +KS + D+ PVL+EDID F++T LFH+INS+ Q +SLLMT Sbjct: 64 WREKSDALLIHPNEIGSDAANAAAEGPVLIEDIDAGGFDETGLFHLINSVRQAGTSLLMT 123 Query: 144 ARTFPVSWGVCLPDLCSRLKAATVVKISLPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQ 203 +R +P SW V LPDL SRLKAATVV+I PDD L +VI K+FADRQ+++D + Y+V Sbjct: 124 SRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVS 183 Query: 204 RMERSLVFAEKLVDKMDNLALSRGMGITRSLAAEVLKETQQ 244 RMERSL A+ +VD++D LAL R ITR+LAAEVL E Q Sbjct: 184 RMERSLFAAQTIVDRLDRLALERKSRITRALAAEVLNEMGQ 224 >gnl|CDD|168630 PRK06620, PRK06620, hypothetical protein; Validated. Length = 214 Score = 100 bits (251), Expect = 3e-22 Identities = 58/220 (26%), Positives = 112/220 (50%), Gaps = 11/220 (5%) Query: 26 EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSW----PSRVVILV-GPSGSGKSCL 80 +Q F F D+ +V S+ +QA +I +W P + +L+ GPS SGK+ L Sbjct: 1 QQYIFRFTTSSKYHPDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYL 60 Query: 81 ANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQLFHIINSIHQYDSSL 140 IW + S + +I + +++ ++EDI+ ++ + L HI N I++ L Sbjct: 61 TKIWQNLSNAYIIKDI--FFNEEILEKYNAFIIEDIE--NWQEPALLHIFNIINEKQKYL 116 Query: 141 LMTARTFPVSWGVCLPDLCSRLKAATVVKISLPDDDFLEKVIVKMFADRQIFIDKKLAAY 200 L+T+ ++ LPDL SR+K+ + ++ PDD+ ++ +I K F+ + I +++ + Sbjct: 117 LLTSSDKSRNF--TLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISSVTISRQIIDF 174 Query: 201 IVQRMERSLVFAEKLVDKMDNLALSRGMGITRSLAAEVLK 240 ++ + R ++++ ++ AL IT SL EVL Sbjct: 175 LLVNLPREYSKIIEILENINYFALISKRKITISLVKEVLN 214 >gnl|CDD|163254 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP. Length = 226 Score = 72.6 bits (179), Expect = 8e-14 Identities = 48/189 (25%), Positives = 77/189 (40%), Gaps = 14/189 (7%) Query: 65 RVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVL----------LE 114 R + L G SGSGKS L + S I L + L VL L+ Sbjct: 39 RFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPL-AELAQADPEVLEGLEQADLVCLD 97 Query: 115 DIDLLDFNDT---QLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKIS 171 D++ + LFH+ N + + LL+ R P + LPDL +RL V ++ Sbjct: 98 DVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLP 157 Query: 172 LPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGIT 231 D+ + A R + + ++A Y+++ R + L+D +D +L+ IT Sbjct: 158 PLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALLDALDRASLAAKRKIT 217 Query: 232 RSLAAEVLK 240 EVL Sbjct: 218 IPFVKEVLA 226 >gnl|CDD|181578 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated. Length = 227 Score = 51.1 bits (123), Expect = 3e-07 Identities = 43/188 (22%), Positives = 85/188 (45%), Gaps = 12/188 (6%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKS----RSTRFSNIAKSLDSILIDTRKPVL-LEDID 117 R L G +GSG+S L + R+ R+ + A L + D + ++D++ Sbjct: 41 ADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPLLAFDFDPEAELYAVDDVE 100 Query: 118 LLDFNDTQ--LFHIINSIHQY-DSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKI-SLP 173 LD + Q LF++ N + + +LL+ P++ + DL +RL V ++ L Sbjct: 101 RLD-DAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPL-REDLRTRLGWGLVYELKPLS 158 Query: 174 DDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGITRS 233 D D + + A+R + + ++ Y++ R + L+D +D +L + +T Sbjct: 159 DADKIA-ALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQKRPVTLP 217 Query: 234 LAAEVLKE 241 L E+L + Sbjct: 218 LLREMLAQ 225 >gnl|CDD|168147 PRK05642, PRK05642, DNA replication initiation factor; Validated. Length = 234 Score = 48.7 bits (116), Expect = 1e-06 Identities = 54/211 (25%), Positives = 94/211 (44%), Gaps = 22/211 (10%) Query: 47 SAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILID 106 +A+ RL ++ W ++ L G G G+S L + + R + A L + Sbjct: 28 AALGYVERLCEADAGWTESLIYLWGKDGVGRSHL--LQAACLRFEQRGEPAVYLPLAELL 85 Query: 107 TRKPVLLEDI---DLLDFNDTQ-----------LFHIINSIHQYDSSLLMTARTFPVSWG 152 R P LL+++ +L+ +D LFH+ N + LL+ A P Sbjct: 86 DRGPELLDNLEQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELP 145 Query: 153 VCLPDLCSRLKAATVVKI-SLPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVF 211 + LPDL SRL A V ++ L D+D L + ++ + R + + ++ +I+ R RS+ Sbjct: 146 IKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRA-SRRGLHLTDEVGHFILTRGTRSMSA 204 Query: 212 AEKLVDKMDNLALSRGMGITRSLAAEVLKET 242 L++++D +L R L LKET Sbjct: 205 LFDLLERLDQASLQA----QRKLTIPFLKET 231 >gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated. Length = 233 Score = 47.5 bits (113), Expect = 3e-06 Identities = 50/191 (26%), Positives = 88/191 (46%), Gaps = 20/191 (10%) Query: 67 VILVGPSGSGKSCLA-NIWSDKSRSTRFS----------NIAKSLDSILIDTRKPVLLED 115 + L GP+G+GK+ LA + + ++ R S + +L+++ + R V L+ Sbjct: 44 LYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGRLRDALEAL--EGRSLVALDG 101 Query: 116 IDLLDFN---DTQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKISL 172 ++ + + LF N +LL TAR P + LPDL SRL A ++I L Sbjct: 102 LESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRL--AQCIRIGL 159 Query: 173 P--DDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGI 230 P DD V+ + R + +D+ +++ ER L L+D++D +L+ + Sbjct: 160 PVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALLDRLDRESLAAKRRV 219 Query: 231 TRSLAAEVLKE 241 T VL+E Sbjct: 220 TVPFLRRVLEE 230 >gnl|CDD|168719 PRK06893, PRK06893, DNA replication initiation factor; Validated. Length = 229 Score = 39.4 bits (92), Expect = 0.001 Identities = 31/134 (23%), Positives = 65/134 (48%), Gaps = 4/134 (2%) Query: 111 VLLEDIDLLDFNDT---QLFHIINSIHQYDSSLLM-TARTFPVSWGVCLPDLCSRLKAAT 166 V L+D+ + N+ +F + N I + +LL+ +A P + + LPDL SRL Sbjct: 95 VCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGE 154 Query: 167 VVKISLPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSR 226 + +++ D+ V+ + R I + ++A ++++R++R + +D +D +L Sbjct: 155 IYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQA 214 Query: 227 GMGITRSLAAEVLK 240 +T E+L Sbjct: 215 QRKLTIPFVKEILG 228 >gnl|CDD|161840 TIGR00362, DnaA, chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006). Length = 405 Score = 37.9 bits (89), Expect = 0.002 Identities = 38/152 (25%), Positives = 61/152 (40%), Gaps = 35/152 (23%) Query: 113 LEDIDLLDFNDTQ-----------LFHIINSIHQYDSSLLMTARTFPVSWGVCLPD---- 157 +DLL +D Q FH N++H+ +++T+ P LP Sbjct: 197 YRSVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKE----LPGLEER 252 Query: 158 LCSRLKAATVVKISLPDDDFLE---KVIVKMFADRQIFIDKKLAAYIVQRME---RSLVF 211 L SR + VV I PD LE ++ K + + + ++ +I + + R L Sbjct: 253 LRSRFEWGLVVDIEPPD---LETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEG 309 Query: 212 AEKLVDKMDNLALSRGMG--ITRSLAAEVLKE 241 A + LA + G IT LA E LK+ Sbjct: 310 ALNRL-----LAYASLTGKPITLELAKEALKD 336 >gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein. This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins. Length = 576 Score = 35.8 bits (83), Expect = 0.009 Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 13/55 (23%) Query: 26 EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCL 80 EQ+ F++P +R D + VR P V LVGPSG+GKS L Sbjct: 341 EQVNFAYP-----ARPDQPALDGLNLTVR--------PGETVALVGPSGAGKSTL 382 >gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes. Length = 571 Score = 35.5 bits (82), Expect = 0.012 Identities = 26/71 (36%), Positives = 30/71 (42%), Gaps = 15/71 (21%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKS---LDSI------LIDTRKPVLL 113 P V LVG SGSGKS L N+ RF LD L R+ V L Sbjct: 357 PGETVALVGRSGSGKSTLVNLI------PRFYEPDSGQILLDGHDLADYTLASLRRQVAL 410 Query: 114 EDIDLLDFNDT 124 D++ FNDT Sbjct: 411 VSQDVVLFNDT 421 >gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein; Provisional. Length = 582 Score = 33.8 bits (78), Expect = 0.040 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 8/40 (20%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILID 106 V LVG SGSGKS +AN+ TRF +I + IL+D Sbjct: 372 VALVGRSGSGKSTIANLL------TRFYDIDEG--EILLD 403 >gnl|CDD|162132 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein. Length = 711 Score = 33.5 bits (77), Expect = 0.055 Identities = 14/19 (73%), Positives = 15/19 (78%) Query: 63 PSRVVILVGPSGSGKSCLA 81 P VV LVGPSGSGKS +A Sbjct: 506 PGEVVALVGPSGSGKSTVA 524 >gnl|CDD|178750 PLN03211, PLN03211, ABC transporter G-25; Provisional. Length = 659 Score = 33.3 bits (76), Expect = 0.056 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 6/48 (12%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKP 110 P ++ ++GPSGSGKS L N + + + F+ +IL + RKP Sbjct: 93 PGEILAVLGPSGSGKSTLLNALAGRIQGNNFTG------TILANNRKP 134 >gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed. Length = 356 Score = 33.0 bits (76), Expect = 0.067 Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%) Query: 45 VHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLAN 82 V + + + ++ +W S + V L+G SG GKS L N Sbjct: 177 VSALDGEGLDVLAAWLS-GGKTVALLGSSGVGKSTLVN 213 >gnl|CDD|178902 PRK00149, dnaA, chromosomal replication initiation protein; Reviewed. Length = 450 Score = 32.8 bits (76), Expect = 0.075 Identities = 37/154 (24%), Positives = 61/154 (39%), Gaps = 43/154 (27%) Query: 115 DIDLLDFNDTQ-----------LFHIINSIHQYDSSLLMTARTFPVSWGVCLPD----LC 159 +D+L +D Q FH N++H+ +++T+ P LP L Sbjct: 211 SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKE----LPGLEERLR 266 Query: 160 SRLKAATVVKISLPDDDFLE---KVIVKMFADRQIFIDKKLAAYIVQRME---RSLVFAE 213 SR + V I PD LE ++ K + I + ++ +I + + R L E Sbjct: 267 SRFEWGLTVDIEPPD---LETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVREL---E 320 Query: 214 ----KLVDKMDNLALSRGMG--ITRSLAAEVLKE 241 +L+ A + G IT LA E LK+ Sbjct: 321 GALNRLI------AYASLTGKPITLELAKEALKD 348 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 33.0 bits (76), Expect = 0.083 Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%) Query: 48 AIEQAVRLIDSWPS-WPSRVVILVGPSGSGKSCLA 81 A EQ I+SW P + ++L GP G GK+ LA Sbjct: 22 AKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLA 56 >gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein; Reviewed. Length = 240 Score = 32.8 bits (75), Expect = 0.083 Identities = 11/15 (73%), Positives = 14/15 (93%) Query: 66 VVILVGPSGSGKSCL 80 VV+++GPSGSGKS L Sbjct: 29 VVVIIGPSGSGKSTL 43 >gnl|CDD|182733 PRK10790, PRK10790, putative multidrug transporter membrane\ATP-binding components; Provisional. Length = 592 Score = 32.8 bits (75), Expect = 0.096 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 17/59 (28%) Query: 26 EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSR-VVILVGPSGSGKSCLANI 83 + + F++ RDD LV I +V PSR V LVG +GSGKS LA++ Sbjct: 344 DNVSFAY-------RDDNLVLQNINLSV---------PSRGFVALVGHTGSGKSTLASL 386 >gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148 Score = 32.7 bits (74), Expect = 0.097 Identities = 16/63 (25%), Positives = 28/63 (44%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122 P V+++VGP GSGK+ LA + + I + IL + +LL + + Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60 Query: 123 DTQ 125 + Sbjct: 61 GSG 63 >gnl|CDD|181224 PRK08084, PRK08084, DNA replication initiation factor; Provisional. Length = 235 Score = 32.3 bits (74), Expect = 0.13 Identities = 27/117 (23%), Positives = 58/117 (49%), Gaps = 3/117 (2%) Query: 126 LFHIINSI-HQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKIS-LPDDDFLEKVIV 183 +F + N I + LL+T P + LPDL SRL + K+ L D++ L+ + + Sbjct: 119 IFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQL 178 Query: 184 KMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGITRSLAAEVLK 240 + R + + + ++++R++R + +D++D +++ +T E+LK Sbjct: 179 RA-RLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRKLTIPFVKEILK 234 >gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit, DevA family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts. Length = 220 Score = 32.3 bits (74), Expect = 0.13 Identities = 12/18 (66%), Positives = 14/18 (77%) Query: 63 PSRVVILVGPSGSGKSCL 80 P +VIL GPSGSGK+ L Sbjct: 30 PGEIVILTGPSGSGKTTL 47 >gnl|CDD|162555 TIGR01842, type_I_sec_PrtD, type I secretion system ABC transporter, PrtD family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. Length = 544 Score = 31.9 bits (73), Expect = 0.15 Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%) Query: 63 PSRVVILVGPSGSGKSCLAN----IWSDKSRSTRF 93 + ++GPSGSGKS LA IW S S R Sbjct: 343 AGEALAIIGPSGSGKSTLARLIVGIWPPTSGSVRL 377 >gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 637 Score = 31.9 bits (72), Expect = 0.16 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 5/48 (10%) Query: 42 DLLVH----SAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWS 85 +L VH +E + + P R++++ GPSG GKS I S Sbjct: 85 ELAVHKKKIEEVETWL-KAQVLENAPKRILLITGPSGCGKSTTIKILS 131 >gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking. Length = 164 Score = 31.7 bits (73), Expect = 0.20 Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 5/30 (16%) Query: 67 VILVGPSGSGKSCL-----ANIWSDKSRST 91 +IL+G SG GKS L +S++ +ST Sbjct: 3 IILIGDSGVGKSSLLSRFTDGKFSEQYKST 32 >gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed. Length = 307 Score = 31.3 bits (72), Expect = 0.23 Identities = 9/17 (52%), Positives = 15/17 (88%) Query: 65 RVVILVGPSGSGKSCLA 81 +V+++VGP+ SGK+ LA Sbjct: 5 KVIVIVGPTASGKTALA 21 >gnl|CDD|163508 TIGR03796, NHPM_micro_ABC1, NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin. Length = 710 Score = 31.1 bits (71), Expect = 0.28 Identities = 12/21 (57%), Positives = 15/21 (71%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P + V LVG SGSGKS +A + Sbjct: 504 PGQRVALVGGSGSGKSTIAKL 524 >gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD. Length = 529 Score = 30.7 bits (70), Expect = 0.31 Identities = 13/20 (65%), Positives = 14/20 (70%) Query: 63 PSRVVILVGPSGSGKSCLAN 82 P V LVGPSG+GKS L N Sbjct: 347 PGERVALVGPSGAGKSTLLN 366 >gnl|CDD|162807 TIGR02323, CP_lyasePhnK, phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se. Length = 253 Score = 31.0 bits (70), Expect = 0.33 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 62 WPSRVVILVGPSGSGKSCLANIWSDK 87 +P V+ +VG SGSGKS L + + Sbjct: 27 YPGEVLGIVGESGSGKSTLLGCLAGR 52 >gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed. Length = 298 Score = 30.9 bits (71), Expect = 0.33 Identities = 20/91 (21%), Positives = 28/91 (30%), Gaps = 27/91 (29%) Query: 34 RCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLAN----------- 82 L +S + ++ L +V +L G SG GKS L N Sbjct: 143 DVLELSAKEGEGLDELKP--LLAG-------KVTVLAGQSGVGKSTLLNALAPDLELKTG 193 Query: 83 -IWSDKSRS----TRFSN-IAKSLDSILIDT 107 I S+ T +LIDT Sbjct: 194 EI-SEALGRGKHTTTHVELYDLPGGGLLIDT 223 >gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK; Provisional. Length = 258 Score = 30.7 bits (70), Expect = 0.36 Identities = 11/21 (52%), Positives = 15/21 (71%) Query: 62 WPSRVVILVGPSGSGKSCLAN 82 +P V+ +VG SGSGK+ L N Sbjct: 30 YPGEVLGIVGESGSGKTTLLN 50 >gnl|CDD|178430 PLN02836, PLN02836, 3-oxoacyl-[acyl-carrier-protein] synthase. Length = 437 Score = 30.5 bits (69), Expect = 0.37 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 6/59 (10%) Query: 37 GISRDDL-LVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGK-SCLANIWSDKSRSTRF 93 +++DDL + E + +D PS RV LV P G+G +W + S+RF Sbjct: 39 ALTQDDLKMKSEDEETQLYTLDQLPS---RVAALV-PRGTGPGDFDEELWLNSRSSSRF 93 >gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed. Length = 352 Score = 30.8 bits (70), Expect = 0.39 Identities = 11/34 (32%), Positives = 18/34 (52%) Query: 49 IEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLAN 82 +E + L +++ ++ GPSG GKS L N Sbjct: 157 VETGIGLEALLEQLRNKITVVAGPSGVGKSSLIN 190 >gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase domain-containing protein; Reviewed. Length = 229 Score = 30.3 bits (69), Expect = 0.47 Identities = 9/25 (36%), Positives = 13/25 (52%) Query: 65 RVVILVGPSGSGKSCLANIWSDKSR 89 +V + GP G+GKS LA + Sbjct: 34 TIVGIAGPPGAGKSTLAEFLEALLQ 58 >gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed. Length = 588 Score = 29.8 bits (68), Expect = 0.62 Identities = 10/16 (62%), Positives = 13/16 (81%) Query: 67 VILVGPSGSGKSCLAN 82 + LVGPSG+GK+ L N Sbjct: 379 IALVGPSGAGKTSLLN 394 >gnl|CDD|182443 PRK10418, nikD, nickel transporter ATP-binding protein NikD; Provisional. Length = 254 Score = 30.1 bits (68), Expect = 0.64 Identities = 13/19 (68%), Positives = 14/19 (73%), Gaps = 2/19 (10%) Query: 65 RVVILVGPSGSGKS--CLA 81 RV+ LVG SGSGKS C A Sbjct: 30 RVLALVGGSGSGKSLTCAA 48 >gnl|CDD|183258 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding subunit; Provisional. Length = 356 Score = 29.8 bits (68), Expect = 0.65 Identities = 10/14 (71%), Positives = 12/14 (85%) Query: 67 VILVGPSGSGKSCL 80 ++LVGPSG GKS L Sbjct: 33 IVLVGPSGCGKSTL 46 >gnl|CDD|182226 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional. Length = 186 Score = 29.7 bits (67), Expect = 0.66 Identities = 9/18 (50%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 +++ L+GPSGSGK L Sbjct: 1 MGKLIWLMGPSGSGKDSL 18 >gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional. Length = 205 Score = 29.7 bits (68), Expect = 0.69 Identities = 10/30 (33%), Positives = 18/30 (60%) Query: 65 RVVILVGPSGSGKSCLANIWSDKSRSTRFS 94 +++L GPSG+GKS L ++ + + S Sbjct: 6 LLIVLSGPSGAGKSTLVKALLERDPNLQLS 35 >gnl|CDD|163509 TIGR03797, NHPM_micro_ABC2, NHPM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif. Length = 686 Score = 29.5 bits (67), Expect = 0.72 Identities = 12/18 (66%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 P V +VGPSGSGKS L Sbjct: 478 PGEFVAIVGPSGSGKSTL 495 >gnl|CDD|184133 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional. Length = 258 Score = 29.4 bits (67), Expect = 0.80 Identities = 10/18 (55%), Positives = 14/18 (77%) Query: 63 PSRVVILVGPSGSGKSCL 80 P VV ++GP+G+GKS L Sbjct: 27 PGEVVAILGPNGAGKSTL 44 >gnl|CDD|180064 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional. Length = 288 Score = 29.7 bits (68), Expect = 0.80 Identities = 10/16 (62%), Positives = 13/16 (81%) Query: 63 PSRVVILVGPSGSGKS 78 P R+VI+ G SG+GKS Sbjct: 5 PMRLVIVTGLSGAGKS 20 >gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Length = 529 Score = 29.3 bits (66), Expect = 0.91 Identities = 11/22 (50%), Positives = 14/22 (63%) Query: 63 PSRVVILVGPSGSGKSCLANIW 84 P V ++GPSGSGKS L + Sbjct: 360 PGERVAILGPSGSGKSTLLMLL 381 >gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional. Length = 172 Score = 29.3 bits (66), Expect = 0.92 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 65 RVVILVGPSGSGKSCLAN 82 V++ G SGSGK+ LA Sbjct: 16 ITVLIDGRSGSGKTTLAG 33 >gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed. Length = 175 Score = 29.4 bits (67), Expect = 0.93 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 12/45 (26%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDT 107 ++L+G G+GKS + + +AK L IDT Sbjct: 3 KGPNIVLIGFMGAGKSTIGRL------------LAKRLGYDFIDT 35 >gnl|CDD|132490 TIGR03449, mycothiol_MshA, UDP-N-acetylglucosamine: 1L-myo-inositol-1-phosphate 1-alpha-D-N-acetylglucosaminyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species. Length = 405 Score = 29.3 bits (66), Expect = 0.94 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 4/35 (11%) Query: 42 DLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSG 76 D+L+ + E L+D P RV+++ GPSGSG Sbjct: 235 DVLLRAVAE----LLDRDPDRNLRVIVVGGPSGSG 265 >gnl|CDD|178697 PLN03152, PLN03152, hypothetical protein; Provisional. Length = 241 Score = 29.4 bits (66), Expect = 0.94 Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 5/57 (8%) Query: 33 PRCL-GISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKS 88 P G SR D ++H+A A L P PS L PS K L+ I + KS Sbjct: 25 PLSRCGASRRDFILHTASLCASSLAAQNPLPPS----LADPSKPSKPLLSGIANTKS 77 >gnl|CDD|163352 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins. Length = 206 Score = 29.1 bits (66), Expect = 0.95 Identities = 10/18 (55%), Positives = 13/18 (72%) Query: 66 VVILVGPSGSGKSCLANI 83 + ++G SGSGKS L NI Sbjct: 26 MYAIIGESGSGKSTLLNI 43 >gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease protein; Provisional. Length = 648 Score = 29.3 bits (66), Expect = 0.99 Identities = 12/17 (70%), Positives = 13/17 (76%) Query: 67 VILVGPSGSGKSCLANI 83 V +VG SGSGKS L NI Sbjct: 37 VAIVGASGSGKSTLMNI 53 >gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit; Provisional. Length = 232 Score = 29.2 bits (66), Expect = 1.0 Identities = 13/19 (68%), Positives = 15/19 (78%), Gaps = 1/19 (5%) Query: 65 RVVILVGPSGSGKSCLANI 83 RV IL GPSG+GKS L N+ Sbjct: 27 RVAIL-GPSGAGKSTLLNL 44 >gnl|CDD|183063 PRK11264, PRK11264, putative amino-acid ABC transporter ATP-binding protein YecC; Provisional. Length = 250 Score = 28.9 bits (65), Expect = 1.1 Identities = 11/18 (61%), Positives = 14/18 (77%) Query: 63 PSRVVILVGPSGSGKSCL 80 P VV ++GPSGSGK+ L Sbjct: 28 PGEVVAIIGPSGSGKTTL 45 >gnl|CDD|130034 TIGR00960, 3a0501s02, Type II (General) Secretory Pathway (IISP) Family protein. Length = 216 Score = 28.9 bits (65), Expect = 1.3 Identities = 11/30 (36%), Positives = 15/30 (50%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTR 92 +V LVG SG+GKS + + TR Sbjct: 28 KGEMVFLVGHSGAGKSTFLKLILGIEKPTR 57 >gnl|CDD|167016 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional. Length = 1809 Score = 29.0 bits (65), Expect = 1.3 Identities = 12/19 (63%), Positives = 14/19 (73%) Query: 63 PSRVVILVGPSGSGKSCLA 81 P +V+L G SGSGKS LA Sbjct: 25 PREIVLLTGVSGSGKSSLA 43 >gnl|CDD|178349 PLN02748, PLN02748, tRNA dimethylallyltransferase. Length = 468 Score = 28.7 bits (64), Expect = 1.3 Identities = 11/17 (64%), Positives = 16/17 (94%) Query: 65 RVVILVGPSGSGKSCLA 81 +VV+++GP+GSGKS LA Sbjct: 23 KVVVVMGPTGSGKSKLA 39 >gnl|CDD|178800 PRK00023, cmk, cytidylate kinase; Provisional. Length = 225 Score = 28.9 bits (66), Expect = 1.3 Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 12/37 (32%) Query: 71 GPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDT 107 GP+GSGK +A I +AK L +DT Sbjct: 11 GPAGSGKGTVAKI------------LAKKLGFHYLDT 35 >gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional. Length = 412 Score = 29.0 bits (66), Expect = 1.4 Identities = 9/15 (60%), Positives = 14/15 (93%) Query: 67 VILVGPSGSGKSCLA 81 ++L+GP+GSGK+ LA Sbjct: 111 ILLIGPTGSGKTLLA 125 >gnl|CDD|161968 TIGR00630, uvra, excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 924 Score = 28.8 bits (65), Expect = 1.4 Identities = 10/19 (52%), Positives = 14/19 (73%) Query: 63 PSRVVILVGPSGSGKSCLA 81 ++V++ G SGSGKS LA Sbjct: 21 RDKLVVITGLSGSGKSSLA 39 Score = 26.1 bits (58), Expect = 9.3 Identities = 9/16 (56%), Positives = 10/16 (62%) Query: 67 VILVGPSGSGKSCLAN 82 + G SGSGKS L N Sbjct: 636 TCITGVSGSGKSTLIN 651 >gnl|CDD|178984 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed. Length = 943 Score = 28.5 bits (65), Expect = 1.5 Identities = 11/16 (68%), Positives = 11/16 (68%), Gaps = 1/16 (6%) Query: 66 VVILVGPSGSGKSCLA 81 VV G SGSGKS LA Sbjct: 29 VVF-TGLSGSGKSSLA 43 >gnl|CDD|162636 TIGR01978, sufC, FeS assembly ATPase SufC. SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA. Length = 243 Score = 28.8 bits (65), Expect = 1.5 Identities = 8/18 (44%), Positives = 13/18 (72%) Query: 66 VVILVGPSGSGKSCLANI 83 + ++GP+GSGKS L+ Sbjct: 28 IHAIMGPNGSGKSTLSKT 45 >gnl|CDD|184585 PRK14239, PRK14239, phosphate transporter ATP-binding protein; Provisional. Length = 252 Score = 28.6 bits (64), Expect = 1.6 Identities = 11/19 (57%), Positives = 15/19 (78%) Query: 62 WPSRVVILVGPSGSGKSCL 80 +P+ + L+GPSGSGKS L Sbjct: 29 YPNEITALIGPSGSGKSTL 47 >gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 139 Score = 28.4 bits (64), Expect = 1.6 Identities = 11/15 (73%), Positives = 13/15 (86%) Query: 67 VILVGPSGSGKSCLA 81 V+LVGP G+GKS LA Sbjct: 2 VLLVGPPGTGKSELA 16 >gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. Length = 395 Score = 28.4 bits (64), Expect = 1.7 Identities = 9/17 (52%), Positives = 13/17 (76%) Query: 65 RVVILVGPSGSGKSCLA 81 R V++ GP G+GK+ LA Sbjct: 51 RAVLIAGPPGTGKTALA 67 >gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional. Length = 632 Score = 28.4 bits (64), Expect = 1.7 Identities = 10/18 (55%), Positives = 11/18 (61%) Query: 65 RVVILVGPSGSGKSCLAN 82 V G SGSGKS +AN Sbjct: 461 ATVWFTGLSGSGKSTIAN 478 >gnl|CDD|163222 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system. Length = 852 Score = 28.4 bits (64), Expect = 1.8 Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 7/36 (19%) Query: 47 SAIEQAVR-----LIDSWPSWPSRVVILVGPSGSGK 77 AI + +R L D P P V +LVGPSG GK Sbjct: 576 EAIAERIRTARAGLED--PRKPLGVFLLVGPSGVGK 609 >gnl|CDD|162806 TIGR02322, phosphon_PhnN, phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN. Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP. Length = 179 Score = 28.1 bits (63), Expect = 1.9 Identities = 9/16 (56%), Positives = 13/16 (81%) Query: 65 RVVILVGPSGSGKSCL 80 R++ +VGPSG+GK L Sbjct: 2 RLIYVVGPSGAGKDTL 17 >gnl|CDD|162558 TIGR01846, type_I_sec_HlyB, type I secretion system ABC transporter, HlyB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. Length = 694 Score = 28.2 bits (63), Expect = 2.2 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 63 PSRVVILVGPSGSGKSCLA 81 P + +VGPSGSGKS L Sbjct: 482 PGEFIGIVGPSGSGKSTLT 500 >gnl|CDD|131817 TIGR02770, nickel_nikD, nickel import ATP-binding protein NikD. This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous. Length = 230 Score = 28.1 bits (63), Expect = 2.3 Identities = 21/57 (36%), Positives = 24/57 (42%), Gaps = 16/57 (28%) Query: 65 RVVILVGPSGSGKS--CLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLL 119 V+ LVG SGSGKS CLA I L L T +LL+ LL Sbjct: 13 EVLALVGESGSGKSLTCLA--------------ILGLLPPGLTQTSGEILLDGRPLL 55 >gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding protein; Provisional. Length = 369 Score = 28.1 bits (63), Expect = 2.3 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 67 VILVGPSGSGKSCL 80 V+ VGPSG GKS L Sbjct: 32 VVFVGPSGCGKSTL 45 >gnl|CDD|181651 PRK09105, PRK09105, putative aminotransferase; Provisional. Length = 370 Score = 28.1 bits (63), Expect = 2.4 Identities = 8/14 (57%), Positives = 10/14 (71%) Query: 58 SWPSWPSRVVILVG 71 SWP WP+ V + VG Sbjct: 339 SWPIWPNWVRVTVG 352 >gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed. Length = 413 Score = 27.7 bits (63), Expect = 2.4 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 12/36 (33%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDS 102 +IL GP G+GK+ LA I IA + D+ Sbjct: 39 MILWGPPGTGKTTLARI------------IAGATDA 62 >gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc. Length = 708 Score = 27.8 bits (62), Expect = 2.5 Identities = 20/70 (28%), Positives = 24/70 (34%), Gaps = 16/70 (22%) Query: 66 VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQ 125 +VG SGSGKS L AK L +LL L D + Sbjct: 502 KTTIVGMSGSGKSTL----------------AKLLVGFFQARSGEILLNGFSLKDIDRHT 545 Query: 126 LFHIINSIHQ 135 L IN + Q Sbjct: 546 LRQFINYLPQ 555 >gnl|CDD|184592 PRK14254, PRK14254, phosphate ABC transporter ATP-binding protein; Provisional. Length = 285 Score = 27.8 bits (62), Expect = 2.5 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%) Query: 38 ISRDDLLVHSAIEQAVRLID-SWPSWPSRVVILVGPSGSGKS 78 I DL V EQA+ + P ++V ++GPSG GKS Sbjct: 40 IEARDLNVFYGDEQALDDVSMDIPE--NQVTAMIGPSGCGKS 79 >gnl|CDD|184594 PRK14264, PRK14264, phosphate ABC transporter ATP-binding protein; Provisional. Length = 305 Score = 27.9 bits (62), Expect = 2.5 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 6/59 (10%) Query: 38 ISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKS----CLANIWSDKSRSTR 92 +S +DL V+ + A++ + S V L+GPSG GKS CL N +D+ ++ R Sbjct: 46 LSVEDLDVYYGDDHALKGV-SMDIPEKSVTALIGPSGCGKSTFLRCL-NRMNDRIKAAR 102 >gnl|CDD|132307 TIGR03263, guanyl_kin, guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP. Length = 180 Score = 27.8 bits (63), Expect = 2.5 Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 8/47 (17%) Query: 64 SRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKP 110 ++++ GPSG GKS L ++ + +F SI TRKP Sbjct: 1 GLLIVISGPSGVGKSTLVKALLEEDPNLKF--------SISATTRKP 39 >gnl|CDD|172578 PRK14088, dnaA, chromosomal replication initiation protein; Provisional. Length = 440 Score = 27.9 bits (62), Expect = 2.5 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 3/78 (3%) Query: 111 VLLEDIDLL---DFNDTQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATV 167 +L++D+ L T+LFH N +H +++ + P L SR + V Sbjct: 198 LLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLV 257 Query: 168 VKISLPDDDFLEKVIVKM 185 K+ PD++ +K+ KM Sbjct: 258 AKLEPPDEETRKKIARKM 275 >gnl|CDD|182980 PRK11124, artP, arginine transporter ATP-binding subunit; Provisional. Length = 242 Score = 27.7 bits (62), Expect = 2.7 Identities = 9/15 (60%), Positives = 13/15 (86%) Query: 66 VVILVGPSGSGKSCL 80 ++L+GPSG+GKS L Sbjct: 30 TLVLLGPSGAGKSSL 44 >gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit; Provisional. Length = 353 Score = 27.7 bits (62), Expect = 2.7 Identities = 11/17 (64%), Positives = 13/17 (76%) Query: 67 VILVGPSGSGKSCLANI 83 V L+GPSGSGK+ L I Sbjct: 31 VALLGPSGSGKTTLLRI 47 >gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional. Length = 259 Score = 27.7 bits (62), Expect = 2.8 Identities = 9/15 (60%), Positives = 13/15 (86%) Query: 67 VILVGPSGSGKSCLA 81 ++L+GPSG GK+ LA Sbjct: 105 IVLLGPSGVGKTHLA 119 >gnl|CDD|182342 PRK10261, PRK10261, glutathione transporter ATP-binding protein; Provisional. Length = 623 Score = 27.9 bits (62), Expect = 2.8 Identities = 12/21 (57%), Positives = 14/21 (66%) Query: 58 SWPSWPSRVVILVGPSGSGKS 78 S+ WP + LVG SGSGKS Sbjct: 344 SFDLWPGETLSLVGESGSGKS 364 >gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter; Provisional. Length = 588 Score = 27.6 bits (62), Expect = 3.0 Identities = 11/21 (52%), Positives = 16/21 (76%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P + V +VGP+G+GKS L N+ Sbjct: 360 PGQTVAIVGPTGAGKSTLINL 380 >gnl|CDD|178685 PLN03140, PLN03140, ABC transporter G family member; Provisional. Length = 1470 Score = 27.5 bits (61), Expect = 3.1 Identities = 10/18 (55%), Positives = 14/18 (77%) Query: 63 PSRVVILVGPSGSGKSCL 80 PSR+ +L+GP SGK+ L Sbjct: 190 PSRMTLLLGPPSSGKTTL 207 >gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. Length = 495 Score = 27.6 bits (62), Expect = 3.2 Identities = 10/15 (66%), Positives = 13/15 (86%) Query: 67 VILVGPSGSGKSCLA 81 V+LVGP G+GK+ LA Sbjct: 91 VLLVGPPGTGKTLLA 105 >gnl|CDD|150194 pfam09439, SRPRB, Signal recognition particle receptor beta subunit. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane. Length = 181 Score = 27.4 bits (61), Expect = 3.2 Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 1/53 (1%) Query: 64 SRVVILVGPSGSGKSCLAN-IWSDKSRSTRFSNIAKSLDSILIDTRKPVLLED 115 VI+ G SGK+ L + + R T S + + + + L D Sbjct: 3 QPAVIIAGLCDSGKTSLFTLLTTGSVRKTVTSQEPSAAYKYMNNKGNSLTLID 55 >gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF; Provisional. Length = 388 Score = 27.6 bits (61), Expect = 3.4 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%) Query: 65 RVVILVGPSGSGKSC----LANIWSDKSRSTRFSNIAKSLDSILIDTRKPV 111 RV ILVGP+G GK+ LA I+ S + ++D+ I +K + Sbjct: 175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQI 225 >gnl|CDD|182569 PRK10584, PRK10584, putative ABC transporter ATP-binding protein YbbA; Provisional. Length = 228 Score = 27.4 bits (61), Expect = 3.4 Identities = 10/21 (47%), Positives = 12/21 (57%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 + L+G SGSGKS L I Sbjct: 35 RGETIALIGESGSGKSTLLAI 55 >gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. Length = 282 Score = 27.3 bits (61), Expect = 3.5 Identities = 8/13 (61%), Positives = 10/13 (76%) Query: 65 RVVILVGPSGSGK 77 V+ LVGP+G GK Sbjct: 195 GVIALVGPTGVGK 207 >gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK). Important residue (active site in E.coli) is residue 100 of the seed alignment. Length = 184 Score = 27.4 bits (61), Expect = 3.5 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 64 SRVVILVGPSGSGKSCLAN 82 V+ L G SGSGKS +AN Sbjct: 18 GVVIWLTGLSGSGKSTIAN 36 >gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein; Provisional. Length = 445 Score = 27.5 bits (61), Expect = 3.6 Identities = 33/204 (16%), Positives = 79/204 (38%), Gaps = 40/204 (19%) Query: 30 FSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCL--------- 80 +F L ++ ++ L H +++ ++ + +P + L GP GSGK+ L Sbjct: 108 MTFANFL-VTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALR 166 Query: 81 ----------ANIWSDKSRS-------TRFSNIAKSLDSILIDTRKPVLLEDIDLLD--- 120 + ++++ S RF +++D++ I+ DI++ Sbjct: 167 ESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIE--------DIEVFSGKG 218 Query: 121 FNDTQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKIS-LPDDDFLE 179 + FH NS+H +++++ P L SR + + + L + L Sbjct: 219 ATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEG-LR 277 Query: 180 KVIVKMFADRQIFIDKKLAAYIVQ 203 + + I I++ ++++ Sbjct: 278 SFLERKAEALSIRIEETALDFLIE 301 >gnl|CDD|184193 PRK13633, PRK13633, cobalt transporter ATP-binding subunit; Provisional. Length = 280 Score = 27.4 bits (61), Expect = 3.6 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 17/59 (28%) Query: 66 VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDT 124 +VIL G +GSGKS IAK ++++LI + V ++ +D D + Sbjct: 39 LVIL-GRNGSGKS----------------TIAKHMNALLIPSEGKVYVDGLDTSDEENL 80 >gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding protein. Length = 237 Score = 27.5 bits (61), Expect = 3.7 Identities = 11/15 (73%), Positives = 13/15 (86%) Query: 66 VVILVGPSGSGKSCL 80 +V L+GPSGSGKS L Sbjct: 28 LVALLGPSGSGKSTL 42 >gnl|CDD|184582 PRK14236, PRK14236, phosphate transporter ATP-binding protein; Provisional. Length = 272 Score = 27.3 bits (61), Expect = 3.8 Identities = 10/16 (62%), Positives = 11/16 (68%) Query: 65 RVVILVGPSGSGKSCL 80 RV +GPSG GKS L Sbjct: 52 RVTAFIGPSGCGKSTL 67 >gnl|CDD|130045 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding protein. This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters. Length = 247 Score = 27.3 bits (61), Expect = 3.9 Identities = 10/15 (66%), Positives = 11/15 (73%) Query: 66 VVILVGPSGSGKSCL 80 V L+GPSG GKS L Sbjct: 29 VTALIGPSGCGKSTL 43 >gnl|CDD|161743 TIGR00174, miaA, tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine. Length = 287 Score = 27.4 bits (61), Expect = 3.9 Identities = 27/94 (28%), Positives = 36/94 (38%), Gaps = 32/94 (34%) Query: 66 VVILVGPSGSGKSCL---------ANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLED- 115 V+ ++GP+ GKS L A I S S I K +D I T KP L E Sbjct: 1 VIFIMGPTAVGKSQLAIQLAKKLNAEIISVDSMQ-----IYKGMD---IGTAKPSLQERE 52 Query: 116 ------IDLLDFND--------TQLFHIINSIHQ 135 ID+LD ++ T + I I Sbjct: 53 GIPHHLIDILDPSESYSAADFQTLALNAIADITA 86 >gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity. Length = 249 Score = 27.1 bits (60), Expect = 3.9 Identities = 11/38 (28%), Positives = 15/38 (39%) Query: 66 VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSI 103 ++IL G G GKS + + K I D I Sbjct: 1 LIILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLI 38 >gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood. Length = 143 Score = 27.2 bits (61), Expect = 4.0 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 13/47 (27%) Query: 67 VILVGPSGSGKSCLA------NIWSDKSRSTRFSNIAKSLDSILIDT 107 ++L+G SG GK+ L + K+++ FS+ IDT Sbjct: 4 IMLIGRSGCGKTTLTQALNGEELKYKKTQAIEFSDNM-------IDT 43 >gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. Length = 413 Score = 27.0 bits (60), Expect = 4.2 Identities = 9/15 (60%), Positives = 14/15 (93%) Query: 67 VILVGPSGSGKSCLA 81 ++L+GP+GSGK+ LA Sbjct: 119 ILLIGPTGSGKTLLA 133 >gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding protein. Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates. Length = 243 Score = 27.3 bits (61), Expect = 4.2 Identities = 10/18 (55%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 P V ++GPSG+GKS L Sbjct: 27 PGEFVAIIGPSGAGKSTL 44 >gnl|CDD|184583 PRK14237, PRK14237, phosphate transporter ATP-binding protein; Provisional. Length = 267 Score = 27.0 bits (60), Expect = 4.3 Identities = 16/44 (36%), Positives = 28/44 (63%), Gaps = 3/44 (6%) Query: 36 LGISRDDLLVHSAIEQAVRLID-SWPSWPSRVVILVGPSGSGKS 78 + +S DL V+ ++A++ ID + +++ L+GPSGSGKS Sbjct: 19 IALSTKDLHVYYGKKEAIKGIDMQFEK--NKITALIGPSGSGKS 60 >gnl|CDD|179632 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional. Length = 248 Score = 27.2 bits (61), Expect = 4.3 Identities = 9/15 (60%), Positives = 13/15 (86%) Query: 66 VVILVGPSGSGKSCL 80 ++ LVGP+G+GKS L Sbjct: 24 ILHLVGPNGAGKSTL 38 >gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. Length = 361 Score = 27.3 bits (61), Expect = 4.4 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 65 RVVILVGPSGSGKSCLA 81 +++ L+GP G GKS L Sbjct: 79 QILYLLGPVGGGKSSLV 95 >gnl|CDD|172749 PRK14261, PRK14261, phosphate ABC transporter ATP-binding protein; Provisional. Length = 253 Score = 27.1 bits (60), Expect = 4.4 Identities = 11/16 (68%), Positives = 12/16 (75%) Query: 65 RVVILVGPSGSGKSCL 80 RV L+GPSG GKS L Sbjct: 33 RVTALIGPSGCGKSTL 48 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 26.9 bits (60), Expect = 4.6 Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 1/29 (3%) Query: 68 ILVGPSGSGKSCLANIWSDKSRSTRFSNI 96 IL GP G GK+ LA I ++ +R+ FS++ Sbjct: 56 ILYGPPGVGKTTLARIIANHTRA-HFSSL 83 >gnl|CDD|178576 PLN02997, PLN02997, flavonol synthase. Length = 325 Score = 26.9 bits (59), Expect = 4.7 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 9/47 (19%) Query: 155 LPDLCSRLKAAT---------VVKISLPDDDFLEKVIVKMFADRQIF 192 LP L +L ++T VV +S+ D+DFL + +VK + +F Sbjct: 14 LPSLSKQLASSTLGGSAVDVPVVDLSVSDEDFLVREVVKASEEWGVF 60 >gnl|CDD|183056 PRK11248, tauB, taurine transporter ATP-binding subunit; Provisional. Length = 255 Score = 27.0 bits (60), Expect = 4.7 Identities = 8/21 (38%), Positives = 15/21 (71%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 +++++GPSG GK+ L N+ Sbjct: 26 SGELLVVLGPSGCGKTTLLNL 46 >gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed. Length = 251 Score = 27.0 bits (60), Expect = 4.9 Identities = 9/18 (50%), Positives = 15/18 (83%) Query: 63 PSRVVILVGPSGSGKSCL 80 P +++ L+GP+G+GKS L Sbjct: 29 PGKILTLLGPNGAGKSTL 46 >gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed. Length = 328 Score = 27.0 bits (61), Expect = 5.0 Identities = 11/17 (64%), Positives = 13/17 (76%) Query: 67 VILVGPSGSGKSCLANI 83 V+L GP G GK+ LANI Sbjct: 54 VLLYGPPGLGKTTLANI 70 >gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733 Score = 26.8 bits (59), Expect = 5.0 Identities = 10/19 (52%), Positives = 14/19 (73%) Query: 63 PSRVVILVGPSGSGKSCLA 81 P + V+L GP G+GK+ LA Sbjct: 211 PPKGVLLYGPPGTGKTLLA 229 Score = 26.8 bits (59), Expect = 5.7 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 11/51 (21%) Query: 49 IEQAVRLIDSWP-----------SWPSRVVILVGPSGSGKSCLANIWSDKS 88 ++Q +R WP P + V+L GP G+GK+ LA + +S Sbjct: 461 VKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATES 511 >gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional. Length = 438 Score = 27.0 bits (60), Expect = 5.1 Identities = 12/29 (41%), Positives = 20/29 (68%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRST 91 P + VIL GP G+GK+ LA ++++ +T Sbjct: 216 PPKGVILYGPPGTGKTLLAKAVANETSAT 244 >gnl|CDD|184131 PRK13546, PRK13546, teichoic acids export protein ATP-binding subunit; Provisional. Length = 264 Score = 26.7 bits (59), Expect = 5.2 Identities = 12/18 (66%), Positives = 15/18 (83%) Query: 66 VVILVGPSGSGKSCLANI 83 V+ LVG +GSGKS L+NI Sbjct: 52 VIGLVGINGSGKSTLSNI 69 >gnl|CDD|180683 PRK06762, PRK06762, hypothetical protein; Provisional. Length = 166 Score = 26.9 bits (60), Expect = 5.3 Identities = 8/20 (40%), Positives = 14/20 (70%) Query: 63 PSRVVILVGPSGSGKSCLAN 82 + ++I+ G SGSGK+ +A Sbjct: 1 MTTLIIIRGNSGSGKTTIAK 20 >gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit; Provisional. Length = 255 Score = 26.9 bits (60), Expect = 5.5 Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 16/64 (25%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122 ++ L+GP+G GKS L K +L V L D + + Sbjct: 27 TGKITALIGPNGCGKSTL----------------LKCFARLLTPQSGTVFLGDKPISMLS 70 Query: 123 DTQL 126 QL Sbjct: 71 SRQL 74 >gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional. Length = 327 Score = 26.9 bits (60), Expect = 5.6 Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%) Query: 63 PSRVVIL--VGPSGSGKSCLAN 82 P R V+L G SG GK+ Sbjct: 5 PDRPVLLGVAGDSGCGKTTFLR 26 >gnl|CDD|152038 pfam11602, NTPase_P4, ATPase P4 of dsRNA bacteriophage phi-12. P4 is a packaging motor which is involved in the packaging of phi-12 genome into preformed capsids using ATP. P4 is located at the vertices of the icosahedral capsid. ATP drives RNA translocation through cooperative conformational changes. Length = 320 Score = 26.9 bits (59), Expect = 5.7 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 12/72 (16%) Query: 62 WPSR-----VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLD----SILIDTRKPVL 112 W S +VI+ G +GSGKS N D + R+ + D ++ +D +L Sbjct: 104 WASEGIYSGMVIVTGKTGSGKSEALNG-KDPDVTIRWGEPLEGYDTLDFNVFVDDLAEML 162 Query: 113 LEDIDL--LDFN 122 + I L L Sbjct: 163 IVCIGLAMLQHR 174 >gnl|CDD|182182 PRK09984, PRK09984, phosphonate/organophosphate ester transporter subunit; Provisional. Length = 262 Score = 26.5 bits (58), Expect = 5.7 Identities = 11/15 (73%), Positives = 13/15 (86%) Query: 66 VVILVGPSGSGKSCL 80 +V L+GPSGSGKS L Sbjct: 32 MVALLGPSGSGKSTL 46 >gnl|CDD|182707 PRK10762, PRK10762, D-ribose transporter ATP binding protein; Provisional. Length = 501 Score = 26.5 bits (59), Expect = 5.9 Identities = 10/19 (52%), Positives = 15/19 (78%) Query: 62 WPSRVVILVGPSGSGKSCL 80 +P RV+ LVG +G+GKS + Sbjct: 28 YPGRVMALVGENGAGKSTM 46 >gnl|CDD|184126 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA; Provisional. Length = 207 Score = 26.8 bits (60), Expect = 6.0 Identities = 8/14 (57%), Positives = 12/14 (85%) Query: 67 VILVGPSGSGKSCL 80 ++L GP+GSGK+ L Sbjct: 31 LVLTGPNGSGKTTL 44 >gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein; Provisional. Length = 260 Score = 26.5 bits (59), Expect = 6.1 Identities = 9/16 (56%), Positives = 11/16 (68%) Query: 65 RVVILVGPSGSGKSCL 80 +V +GPSG GKS L Sbjct: 40 QVTAFIGPSGCGKSTL 55 >gnl|CDD|116881 pfam08298, AAA_PrkA, PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. Length = 358 Score = 26.7 bits (59), Expect = 6.1 Identities = 9/17 (52%), Positives = 13/17 (76%) Query: 65 RVVILVGPSGSGKSCLA 81 +++ L+GP G GKS LA Sbjct: 86 QILYLLGPVGGGKSSLA 102 >gnl|CDD|128968 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases. Length = 216 Score = 26.6 bits (59), Expect = 6.3 Identities = 21/112 (18%), Positives = 40/112 (35%), Gaps = 9/112 (8%) Query: 79 CLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDT-----QLFHIINSI 133 C K RS + + ++ + K +L+ + + T QL ++ +I Sbjct: 18 CSFPSARGKLRSRYLEALVREIELLAEKGEKEILVGTVFIGGGTPTLLSPEQLEELLEAI 77 Query: 134 HQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKISLP----DDDFLEKV 181 + T G +L LK A V ++SL D+ L+ + Sbjct: 78 REILGLADDVEITIETRPGTLTEELLEALKEAGVNRVSLGVQSGSDEVLKAI 129 >gnl|CDD|163576 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification. Length = 236 Score = 26.5 bits (59), Expect = 6.4 Identities = 10/18 (55%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 P V L+GP+G+GKS L Sbjct: 26 PGEFVALLGPNGAGKSTL 43 >gnl|CDD|130344 TIGR01277, thiQ, thiamine ABC transporter, ATP-binding protein. This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found. Length = 213 Score = 26.4 bits (58), Expect = 6.4 Identities = 10/17 (58%), Positives = 14/17 (82%) Query: 67 VILVGPSGSGKSCLANI 83 V ++GPSG+GKS L N+ Sbjct: 27 VAIMGPSGAGKSTLLNL 43 >gnl|CDD|162629 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. Length = 1283 Score = 26.7 bits (59), Expect = 6.6 Identities = 13/41 (31%), Positives = 22/41 (53%) Query: 108 RKPVLLEDIDLLDFNDTQLFHIINSIHQYDSSLLMTARTFP 148 R+ +L+++ L DF D +L IN+ +DS +R P Sbjct: 771 RRDILVDEQTLFDFYDGRLPEDINNARHFDSWWKKASRKQP 811 >gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding protein; Provisional. Length = 249 Score = 26.3 bits (58), Expect = 6.7 Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%) Query: 63 PSR-VVILVGPSGSGKSCL 80 P+R V L+GPSG GKS L Sbjct: 27 PARQVTALIGPSGCGKSTL 45 >gnl|CDD|149124 pfam07880, T4_gp9_10, Bacteriophage T4 gp9/10-like protein. The members of this family are similar to gene products 9 (gp9) and 10 (gp10) of bacteriophage T4. Both proteins are components of the viral baseplate. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains. The N-terminal domain consists of an extended polypeptide chain and two alpha helices. The alpha1 helix from each of the three monomers in the trimer interacts with its counterparts to form a coiled-coil structure. The middle domain is a seven-stranded beta-sandwich that is thought to be a novel protein fold. The C-terminal domain is thought to be essential for gp9 trimerisation and is organized into an eight- stranded antiparallel beta-barrel, which was found to resemble the 'jelly roll' fold found in many viral capsid proteins. The long flexible region between the N-terminal and middle domains may be required for the function of gp9 to transmit signals from the long tail fibres. Together with gp11, gp10 initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate. Length = 272 Score = 26.6 bits (59), Expect = 6.9 Identities = 19/71 (26%), Positives = 25/71 (35%), Gaps = 12/71 (16%) Query: 53 VRLIDSWPSW-PSRVVILVGPSG---SGKSCLANIWSDKSR--------STRFSNIAKSL 100 + I+S SW + V +V SG G S I S S S+ Sbjct: 102 IEFINSNGSWSVTNPVTIVPQSGDTIKGSSGNLEITKPYSDVELVCCSPGGSVSRWEYSI 161 Query: 101 DSILIDTRKPV 111 +SI D PV Sbjct: 162 ESIFGDDLSPV 172 >gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed. Length = 167 Score = 26.5 bits (59), Expect = 7.0 Identities = 10/15 (66%), Positives = 12/15 (80%) Query: 67 VILVGPSGSGKSCLA 81 +IL+G GSGKS LA Sbjct: 4 IILIGSGGSGKSTLA 18 >gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit. This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux. Length = 190 Score = 26.2 bits (58), Expect = 7.1 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 64 SRVVILVGPSGSGKSCL 80 V+ L+G +G+GKS L Sbjct: 18 GEVLALLGANGAGKSTL 34 >gnl|CDD|180254 PRK05782, PRK05782, bifunctional sirohydrochlorin cobalt chelatase/precorrin-8X methylmutase; Validated. Length = 335 Score = 26.3 bits (58), Expect = 7.2 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 10/76 (13%) Query: 162 LKAATVVKISLPDDDFLEKVIVKMFADRQIFIDKKL-AAYIVQRMERSLVFAEKLVDKMD 220 L+ A VKIS +D L+ I + A+ +I D K+ +A I R ++ ++D Sbjct: 182 LELAKYVKIS---NDLLDAGIEAIRAESEIVADVKMVSAGI--RWKK----VTCMIDAER 232 Query: 221 NLALSRGMGITRSLAA 236 L++ +GITR+ AA Sbjct: 233 TKELAKELGITRAAAA 248 >gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP) Family protein. Length = 617 Score = 26.2 bits (58), Expect = 7.3 Identities = 9/27 (33%), Positives = 17/27 (62%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSR 89 P ++ ++G SG+GK+ L N + +S Sbjct: 50 PGELLAVMGSSGAGKTTLMNALAFRSP 76 >gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein PhnL. Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se. Length = 224 Score = 26.2 bits (58), Expect = 7.3 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 67 VILVGPSGSGKSCL 80 V L GPSG+GKS L Sbjct: 37 VALSGPSGAGKSTL 50 >gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed. Length = 394 Score = 26.4 bits (59), Expect = 7.4 Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 20/57 (35%) Query: 63 PSRVVILVGPSGSGKSCLA-------------------NIWSDKSRSTRFSNIAKSL 100 P V+I GP G+GK+ N D++R FS IA+ L Sbjct: 55 PLNVLIY-GPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQL 110 >gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF; Provisional. Length = 432 Score = 26.1 bits (57), Expect = 8.1 Identities = 9/14 (64%), Positives = 12/14 (85%) Query: 65 RVVILVGPSGSGKS 78 +VV VGP+GSGK+ Sbjct: 224 KVVFFVGPTGSGKT 237 >gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 424 Score = 26.0 bits (58), Expect = 8.2 Identities = 9/33 (27%), Positives = 14/33 (42%) Query: 45 VHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGK 77 + + + + VV LVGP+G GK Sbjct: 202 LLELLANMIPVRVEDILKQGGVVALVGPTGVGK 234 >gnl|CDD|184315 PRK13768, PRK13768, GTPase; Provisional. Length = 253 Score = 26.0 bits (58), Expect = 8.3 Identities = 7/16 (43%), Positives = 11/16 (68%) Query: 66 VVILVGPSGSGKSCLA 81 +V +G +GSGK+ L Sbjct: 4 IVFFLGTAGSGKTTLT 19 >gnl|CDD|150662 pfam10014, DUF2257, Uncharacterized protein conserved in bacteria (DUF2257). Members of this family of hypothetical bacterial proteins have no known function. Length = 196 Score = 26.0 bits (58), Expect = 8.3 Identities = 10/28 (35%), Positives = 15/28 (53%) Query: 112 LLEDIDLLDFNDTQLFHIINSIHQYDSS 139 LLE D L +D +L+H + I D + Sbjct: 157 LLEPGDTLLLDDRRLWHYVTPIKPIDPA 184 >gnl|CDD|179060 PRK00549, PRK00549, competence damage-inducible protein A; Provisional. Length = 414 Score = 26.3 bits (59), Expect = 8.4 Identities = 7/20 (35%), Positives = 14/20 (70%) Query: 174 DDDFLEKVIVKMFADRQIFI 193 D+D LE+V+ K+ ++ + I Sbjct: 255 DEDSLEEVVAKLLKEKGLTI 274 >gnl|CDD|172735 PRK14247, PRK14247, phosphate ABC transporter ATP-binding protein; Provisional. Length = 250 Score = 26.0 bits (57), Expect = 8.7 Identities = 10/18 (55%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 + + L+GPSGSGKS L Sbjct: 28 DNTITALMGPSGSGKSTL 45 >gnl|CDD|178835 PRK00064, recF, recombination protein F; Reviewed. Length = 361 Score = 25.9 bits (58), Expect = 9.0 Identities = 7/14 (50%), Positives = 9/14 (64%) Query: 64 SRVVILVGPSGSGK 77 V +LVG +G GK Sbjct: 23 PGVNVLVGENGQGK 36 >gnl|CDD|172730 PRK14242, PRK14242, phosphate transporter ATP-binding protein; Provisional. Length = 253 Score = 25.9 bits (57), Expect = 9.1 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 65 RVVILVGPSGSGKS 78 +V L+GPSG GKS Sbjct: 33 QVTALIGPSGCGKS 46 >gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal. Length = 364 Score = 25.9 bits (57), Expect = 9.1 Identities = 11/29 (37%), Positives = 19/29 (65%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRST 91 P + V+L GP G+GK+ LA + ++ +T Sbjct: 155 PPKGVLLYGPPGTGKTLLAKAVAHETNAT 183 >gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional. Length = 637 Score = 26.1 bits (58), Expect = 9.3 Identities = 9/17 (52%), Positives = 13/17 (76%) Query: 65 RVVILVGPSGSGKSCLA 81 R V+++G G+GKS LA Sbjct: 51 RHVMMIGSPGTGKSMLA 67 >gnl|CDD|132050 TIGR03005, ectoine_ehuA, ectoine/hydroxyectoine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins. Length = 252 Score = 25.9 bits (57), Expect = 9.5 Identities = 11/21 (52%), Positives = 13/21 (61%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 V L+GPSGSGKS + I Sbjct: 25 AGEKVALIGPSGSGKSTILRI 45 >gnl|CDD|182348 PRK10270, PRK10270, putative aminodeoxychorismate lyase; Provisional. Length = 340 Score = 26.0 bits (57), Expect = 9.6 Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 2/33 (6%) Query: 147 FPVSW--GVCLPDLCSRLKAATVVKISLPDDDF 177 FP+ G+ L D +L+ A +K +L DD + Sbjct: 110 FPLRLVEGMRLSDYLKQLREAPYIKHTLSDDKY 142 >gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase. Length = 421 Score = 25.9 bits (57), Expect = 9.8 Identities = 9/17 (52%), Positives = 15/17 (88%) Query: 65 RVVILVGPSGSGKSCLA 81 +V+++ GP+G+GKS LA Sbjct: 22 KVIVISGPTGAGKSRLA 38 >gnl|CDD|161735 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). Length = 245 Score = 25.8 bits (57), Expect = 10.0 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 64 SRVVILVGPSGSGKSCLAN 82 +R+ + G SG GKS L N Sbjct: 120 NRISVFAGQSGVGKSSLIN 138 >gnl|CDD|162739 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. Length = 1179 Score = 25.8 bits (57), Expect = 10.0 Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 3/21 (14%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 + +VGP+G GKS NI Sbjct: 22 DKGITGIVGPNGCGKS---NI 39 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 0.322 0.136 0.401 Gapped Lambda K H 0.267 0.0738 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,950,515 Number of extensions: 246237 Number of successful extensions: 959 Number of sequences better than 10.0: 1 Number of HSP's gapped: 949 Number of HSP's successfully gapped: 182 Length of query: 246 Length of database: 5,994,473 Length adjustment: 91 Effective length of query: 155 Effective length of database: 4,028,145 Effective search space: 624362475 Effective search space used: 624362475 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 56 (25.3 bits)