RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780606|ref|YP_003065019.1| cell division protein [Candidatus Liberibacter asiaticus str. psy62] (744 letters) >gnl|CDD|31860 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]. Length = 858 Score = 473 bits (1219), Expect = e-134 Identities = 204/457 (44%), Positives = 269/457 (58%), Gaps = 17/457 (3%) Query: 290 LEKNAGSLETILEEFGIKGEIINVNPGPVVTLYEFEPAPGIKSSRVIGLADDIARSMSSL 349 L + L L I GP T +E G+K + L +D A ++ + Sbjct: 406 LLVSIARLGRSLGIHLILATQKPDGVGPSNTRFEIALKVGVKVDSIEILGNDDAAALVAK 465 Query: 350 SAR-VAVIPKRNAIGIELPN-ETRETVYLRQIIESRSFSHSKANLALCLGKTISGESVIA 407 S R +A IP ++ IG + PN LR++++ F + L K I E ++ Sbjct: 466 SRRYLAPIPGKSYIGFQSPNSGRPWLPPLRELLDLDEFLERFPLGVIDLPKDIRQEPIVI 525 Query: 408 DLANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPHLL 467 DLA H+L+AG TGSGKSVA+NTMI+SLLY P+E R ++DPKMLEL+ YDG+PHL Sbjct: 526 DLAKAGHLLIAGATGSGKSVALNTMILSLLYTHSPEEVRFYIIDPKMLELAAYDGLPHLG 585 Query: 468 TPVVTNPK-KAVMALKWAVREMEERYRKMSHLSVRNIKSYNERISTMYGEKPQGCGDDMR 526 PVVT+ K KA AL V EME RY+ S VRNI+ YNE+I+ ++ Sbjct: 586 DPVVTDEKEKAEKALAELVAEMERRYKLFSEKGVRNIEGYNEKIAGAIPDE--------- 636 Query: 527 PMPYIVIIVDEMADLMMVAGKEIEGAIQRLAQMARAAGIHLIMATQRPSVDVITGTIKAN 586 +PYIVII+DE ADLMMVAGKE+E I RLAQ RAAGIHLI+ATQRPSVDVITG IKAN Sbjct: 637 ELPYIVIIIDEYADLMMVAGKELEELIARLAQKGRAAGIHLILATQRPSVDVITG-IKAN 695 Query: 587 FPIRISFQVTSKIDSRTILGEHGAEQLLGRGDMLYM-SGGGRIQRVHGPLVSDIEIEKVV 645 P RI+ +++SKIDSR ILG+ GAE+LLGRGDML++ G + RV VSD E+E+VV Sbjct: 696 IPTRIALRLSSKIDSRLILGQDGAEKLLGRGDMLFLGPGDAKPVRVLPAFVSDEEVEEVV 755 Query: 646 QHLKKQGCPEYLNTVTTDTDTDKDGNNFD---SEEKKERSNLYAKAVDLVIDNQRCSTSF 702 +HLK Q P YL+ T E++ L+ +A +LV+ + STS Sbjct: 756 EHLKSQVEPVYLDLATNPHLLISGETTVLRAIDREEEAMDELFDEAKELVLPPPKASTSL 815 Query: 703 IQRRLQIGYNRAALLVERMEQEGLVSEADHVGKRHVF 739 +QR L +G NRAA L+E ME G+V + R + Sbjct: 816 LQRALDLGLNRAATLIESMELLGIVGPPNGPKGREIL 852 Score = 56.8 bits (136), Expect = 2e-08 Identities = 59/251 (23%), Positives = 96/251 (38%), Gaps = 30/251 (11%) Query: 366 LPNETRETVYLRQIIESRSFSHSKANLALCL-GKTISGESVIADLANMPHILVAGTTGSG 424 L I +S + L + + PH LVAGTTGSG Sbjct: 239 LARLRHTQTSENSIPGREDYSRLGVPIGLRGKKGELLNLDLHEKAEGGPHGLVAGTTGSG 298 Query: 425 KSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPHLLTPVVTNPKKAVMALKWA 484 KS + T I+SL P+E +++D K ++ H++ + ++ +A Sbjct: 299 KSE-LLTYILSLAINHSPEELNFLLIDYKGGSMANPFKGLHVVAVITNLAEERALAAIKG 357 Query: 485 VREMEERYRKMSHLSVRNIKSYNERISTMYGEKPQGCGDDMRPMPYIVIIVDEMADLMMV 544 +R ++ G D P+P++ +I DE A+L Sbjct: 358 ELARRQRNHINAYTKSYKR------------------GKDTPPLPHLFLIADEFAELK-S 398 Query: 545 AGKEIEGAIQRLAQMARAAGIHLIMATQRP--SVDVITGTIKANFPIRISFQVTSKIDSR 602 + + +A++ R+ GIHLI+ATQ+P T I+ +V K+DS Sbjct: 399 EHPDFAELLVSIARLGRSLGIHLILATQKPDGVGPSNTR-------FEIALKVGVKVDSI 451 Query: 603 TILGEHGAEQL 613 ILG A L Sbjct: 452 EILGNDDAAAL 462 >gnl|CDD|144975 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli and the stage III sporulation protein E SpoIIIE which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer. Length = 202 Score = 231 bits (590), Expect = 7e-61 Identities = 97/206 (47%), Positives = 138/206 (66%), Gaps = 8/206 (3%) Query: 375 YLRQIIESRSFSHSKANLALCLGKTISGESVIADLANMPHILVAGTTGSGKSVAINTMIM 434 L+++++ + F S++ L + LGK ISG V+ADL MPH+L+AG TGSGKS +NT+I+ Sbjct: 1 ELKELLDGKPFRGSRSRLTIALGKDISGNPVVADLVKMPHLLIAGATGSGKSTFLNTLIL 60 Query: 435 SLLYRLRPDECRMIMVDPKMLELSVYDGIPHLLTPVVTNPKKAVMALKWAVREMEERYRK 494 SL R P+E R+ ++DPK EL+ + +PHLL+ V T+P+ A+ AL+ V EME RY Sbjct: 61 SLAARHSPEEVRLYLIDPKGGELAALEDLPHLLSAVATDPEDALSALRALVAEMERRYAL 120 Query: 495 MSHLSVRNIKSYNERISTMYGEKPQGCGDDMRPMPYIVIIVDEMADLMMVAGKE----IE 550 + L VR+I+ YN I E G + +P IV+IVDE A+LM+ A K+ +E Sbjct: 121 LKQLGVRSIEEYNGEI----AEDILGGAGWLEELPPIVVIVDERAELMLAAPKDSEMRVE 176 Query: 551 GAIQRLAQMARAAGIHLIMATQRPSV 576 GA+ RLA+M RAAGIHL++ATQRP V Sbjct: 177 GALARLARMGRAAGIHLLLATQRPGV 202 >gnl|CDD|29993 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding domain. TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.. Length = 410 Score = 40.3 bits (94), Expect = 0.002 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 5/54 (9%) Query: 399 TISGESVIADLANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDP 452 TI+G D H ++ GTTG+GK+ I ++ S+ R R D R I+ DP Sbjct: 30 TIAGLPFPKDAEEA-HTMIIGTTGTGKTTQIRELLASI--RARGD--RAIIYDP 78 >gnl|CDD|29995 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.. Length = 264 Score = 37.9 bits (88), Expect = 0.011 Identities = 28/101 (27%), Positives = 41/101 (40%), Gaps = 10/101 (9%) Query: 341 DIARSMSSLSARVAVIPKRNAIGIE---LPNETRETVYLRQIIESRSFSHSKANLALCLG 397 DIA R+ + K I + LP E+V LR I++ ++ LG Sbjct: 9 DIAERRKPQDGRIRLKLKGREIDLRVSTLPTIYGESVVLR-ILDKKNQILDLE----KLG 63 Query: 398 KTISGESVIADLANMPH--ILVAGTTGSGKSVAINTMIMSL 436 + L PH ILV G TGSGK+ + + + L Sbjct: 64 LKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSEL 104 >gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.. Length = 151 Score = 36.0 bits (83), Expect = 0.037 Identities = 28/191 (14%), Positives = 57/191 (29%), Gaps = 55/191 (28%) Query: 406 IADLANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVD-PKMLELSVYDGIP 464 +L ++L+ G G+GK+ T+ ++ L + ++ +LE V + Sbjct: 13 ALELPPPKNLLLYGPPGTGKT----TLARAIANELFRPGAPFLYLNASDLLEGLVVAEL- 67 Query: 465 HLLTPVVTNPKKAVMALKWAVREMEERYRKMSHLSVRNIKSYNERISTMYGEKPQGCGDD 524 + R+ EK + Sbjct: 68 --------------------------------------FGHFLVRLLFELAEKAKPG--- 86 Query: 525 MRPMPYIVIIVDEMADLMMVAGKEIEGAIQRLAQM-ARAAGIHLIMATQRPSVDVITGTI 583 V+ +DE+ L A + ++ L + + +I AT RP + + + Sbjct: 87 -------VLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRAL 139 Query: 584 KANFPIRISFQ 594 IRI Sbjct: 140 YDRLDIRIVIP 150 >gnl|CDD|33254 COG3451, VirB4, Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]. Length = 796 Score = 36.1 bits (83), Expect = 0.041 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 6/63 (9%) Query: 393 ALCLGKTISGESVIADL---ANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIM 449 L + KT G + ++ H L+ G TG+GK+V ++ ++ L P +++ Sbjct: 414 PLTVLKTEDGSPFYFNFHVGEDVGHTLIIGPTGAGKTVLLSFLLAQALKYGNP---QIVA 470 Query: 450 VDP 452 D Sbjct: 471 FDK 473 >gnl|CDD|145224 pfam01935, DUF87, Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands. Length = 218 Score = 35.4 bits (82), Expect = 0.065 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 7/63 (11%) Query: 394 LCLGKTISGESVIA--DLANM--PHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIM 449 + +G+ + G V DL + H + G+TGSGKS + ++ LL + +++ Sbjct: 1 IEIGRLLDGSEVPVYLDLNKLVSRHFAILGSTGSGKSNTVAVLLEELLEKKG---ATVLI 57 Query: 450 VDP 452 DP Sbjct: 58 FDP 60 >gnl|CDD|36209 KOG0991, KOG0991, KOG0991, Replication factor C, subunit RFC2 [Replication, recombination and repair]. Length = 333 Score = 34.9 bits (80), Expect = 0.079 Identities = 15/39 (38%), Positives = 25/39 (64%) Query: 399 TISGESVIADLANMPHILVAGTTGSGKSVAINTMIMSLL 437 T+ SVIA NMP+++++G G+GK+ +I + LL Sbjct: 35 TVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELL 73 >gnl|CDD|32635 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 500 Score = 34.6 bits (79), Expect = 0.11 Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 2/33 (6%) Query: 406 IADLANMPH--ILVAGTTGSGKSVAINTMIMSL 436 + L N P ILV G TGSGK+ + + L Sbjct: 250 LLRLLNRPQGLILVTGPTGSGKTTTLYAALSEL 282 >gnl|CDD|30782 COG0433, COG0433, Predicted ATPase [General function prediction only]. Length = 520 Score = 33.8 bits (76), Expect = 0.16 Identities = 33/154 (21%), Positives = 47/154 (30%), Gaps = 17/154 (11%) Query: 325 EPAPGIKSSRVIGLADDIARSMSSLSARVAVIPKRNAIGI--------ELPNETRETVYL 376 + I + L I S+ L I KR +G P VY Sbjct: 67 DRITSIDLEALADLEAFIISSVLDLEGSYVGIAKRRVLGELEPELLPPRSPVRPGSPVYR 126 Query: 377 -RQIIESRSFSHSKANLALCLGKTISGESVIADL-----ANMPHILVAGTTGSGKSVAIN 430 + + L LG + G V L HI + G+TGSGKS N Sbjct: 127 ASDEVLEKILGFDVDGRGLLLGALLDGGEVPVYLDLNKLVLARHIAILGSTGSGKS---N 183 Query: 431 TMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIP 464 + L L D +++ DP + Sbjct: 184 LAKVLLEELLGKDGATVVIFDPHGEYDLLRLDRA 217 Score = 30.3 bits (67), Expect = 1.7 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 11/77 (14%) Query: 529 PYIVIIVDEMADLMMVAGKE-IEGAIQRLAQMARAAGIHLIMATQRPSVDVITGTIKANF 587 ++I+++E + + K ++ I+R+A+ R G+ L++ATQRPS + Sbjct: 391 GPLLIVIEEAHNFAPSSRKAPVKDIIERIAREGRKFGVGLVLATQRPS----------DL 440 Query: 588 PIRISFQVTSKIDSRTI 604 + Q +KI R + Sbjct: 441 DDLVLSQANTKIILRLV 457 >gnl|CDD|36372 KOG1157, KOG1157, KOG1157, Predicted guanosine polyphosphate pyrophosphohydrolase/synthase [Signal transduction mechanisms]. Length = 543 Score = 33.1 bits (75), Expect = 0.27 Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 11/112 (9%) Query: 204 DLAPHMSTEYLHNKKIRTDSTPTTAGDQQKKSSIDHKPSSSNTMTEHM----FQDTSQEI 259 ++ + E L K P A D ++++ + HK SS + + + Q Sbjct: 35 EMDSVLVDEALGFKMEVELVGPY-ARDLERRAQLWHKTFSSELVIKALYEAAKAHRGQMR 93 Query: 260 AKGQKQYEQPCS------SFLQVQSNVNLQGITHEILEKNAGSLETILEEFG 305 A + Y C + + S V + I H++++ S E IL FG Sbjct: 94 ADDDRPYLNHCIETAMILADIGADSTVVVAAILHDVVDDTFMSYEEILRHFG 145 >gnl|CDD|73322 cd02755, MopB_Thiosulfate-R-like, The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Members of the MopB_Thiosulfate-R-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.. Length = 454 Score = 32.9 bits (75), Expect = 0.29 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 3/57 (5%) Query: 402 GESVIADLANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELS 458 G V D N +I++ G + AI + L + + ++++VDP+ EL+ Sbjct: 147 GGEVNPDFENARYIILFGRNLAE---AIIVVDARRLMKALENGAKVVVVDPRFSELA 200 >gnl|CDD|112562 pfam03753, HHV6-IE, Human herpesvirus 6 immediate early protein. The proteins in this family are poorly characterized, but an investigation has indicated that the immediate early protein is required the down-regulation of MHC class I expression in dendritic cells. Human herpesvirus 6 immediate early protein is also referred to as U90. Length = 993 Score = 33.1 bits (75), Expect = 0.30 Identities = 22/113 (19%), Positives = 40/113 (35%), Gaps = 2/113 (1%) Query: 130 ETIEPSLDVIEEVNTDTASNVSD-QINQNPDTLSWLSDFAFFEGLSTPHSFLSFNDHHQY 188 E IE D + + ++ + I N + S + D STP F+DH +Y Sbjct: 294 EQIEKLYDDTGLIKPLNSISIMEGYITGNKNRSSSICDSNLDPSDSTPLELEDFDDHGKY 353 Query: 189 T-PIPIQSAEDLSDHTDLAPHMSTEYLHNKKIRTDSTPTTAGDQQKKSSIDHK 240 + I+S + D+ ++ + N + T ID + Sbjct: 354 SEESSIESIHEDDDNLAVSQASDESHSKNTTGKNPEVCTREYKLDFFEEIDTQ 406 >gnl|CDD|146673 pfam04157, EAP30, EAP30/Vps36 family. This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. Length = 219 Score = 32.6 bits (75), Expect = 0.40 Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 8/94 (8%) Query: 635 LVSDIEIEKVVQHLKKQGCPEYLNTVTTDTDTDKDGNNF-DSEEKKERSNLYAKAVDLVI 693 LVS ++ K + L+K G L V G S E S K ++L Sbjct: 130 LVSPDDLLKACKKLEKLGLGFKLVKV-------GSGVLVVQSVPDSELSTDQTKILELAE 182 Query: 694 DNQRCSTSFIQRRLQIGYNRAALLVERMEQEGLV 727 + + S + +L RA ++E+ E+EGL+ Sbjct: 183 ELGGVTASELAEKLGWSIGRAKEVLEKAEKEGLL 216 >gnl|CDD|35548 KOG0327, KOG0327, KOG0327, Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]. Length = 397 Score = 32.2 bits (73), Expect = 0.54 Identities = 33/141 (23%), Positives = 46/141 (32%), Gaps = 12/141 (8%) Query: 327 APGIKSSRVIGLADDIARSM--SSLSARVAVIPKRNAIGIELPNETRETVYLRQIIESRS 384 P IK VI A +S + + TRE Q + Sbjct: 58 LPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRAL 117 Query: 385 FSHSKANLALCLGKTISGESVIADLANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDE 444 H ++ C+G T A L + PHI+V GT G M L D Sbjct: 118 GDHMDVSVHACIGGTNVRREDQALLKDKPHIVV-GTPG-------RVFDMLNRGSLSTDG 169 Query: 445 CRMIMVDP--KMLELSVYDGI 463 +M ++D +ML D I Sbjct: 170 IKMFVLDEADEMLSRGFKDQI 190 >gnl|CDD|32636 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 353 Score = 32.1 bits (73), Expect = 0.60 Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 2/31 (6%) Query: 405 VIADLANMPH--ILVAGTTGSGKSVAINTMI 433 ++ +LA P ILV G TGSGKS + MI Sbjct: 116 IVRELAESPRGLILVTGPTGSGKSTTLAAMI 146 >gnl|CDD|109493 pfam00437, GSPII_E, Type II/IV secretion system protein. This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection. Length = 283 Score = 31.9 bits (73), Expect = 0.66 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 5/45 (11%) Query: 415 ILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMV-DPKMLELS 458 ILV+G TGSGK+ + LL + D+ R++ + DP ++L Sbjct: 142 ILVSGGTGSGKTTLLYA----LLNEINTDDERIVTIEDPVEIQLE 182 >gnl|CDD|113806 pfam05049, IIGP, Interferon-inducible GTPase (IIGP). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing. Length = 375 Score = 31.3 bits (71), Expect = 0.87 Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%) Query: 396 LGKTISG-ESVIADLANMP-HILVAGTTGSGKSVAINTM 432 L K +S + I ++++ P I V G +G+GKS IN + Sbjct: 17 LQKVVSIIKKAIQEISSAPLKIAVTGDSGNGKSSFINAL 55 >gnl|CDD|30975 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 312 Score = 30.7 bits (69), Expect = 1.3 Identities = 31/154 (20%), Positives = 55/154 (35%), Gaps = 18/154 (11%) Query: 295 GSLETILEEFGIKGEIINVN-PGPVVTLYEFEPAPGIKSSRVIGLADDIARSMSSLSARV 353 G LE +L + I E I VN PGPV ++ + ++ +++ L+ R Sbjct: 16 GKLEPLLRDPRI--EDIVVNGPGPVYVEHKGGGS--YVTNIPFLTEEELDSLAIRLAQRS 71 Query: 354 A--VIPKRNAIGIELPNETRETVYLRQIIES-------RSFSHSKANLALCLGKTISGES 404 + + LP+ +R + L + R FS + Sbjct: 72 GKPISEANPILDATLPDGSRIQIVLGPEVSPNGSSFTIRKFSDEPITPEDLIEYGTISPE 131 Query: 405 VIADLA----NMPHILVAGTTGSGKSVAINTMIM 434 A L I++ G T SGK+ +N ++ Sbjct: 132 QAAYLWLAIEARKSIIICGGTASGKTTLLNALLD 165 >gnl|CDD|145645 pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyses the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2, 3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl beta-phosphate <=> ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS). The family contains a P-loop motif at the N terminus. Length = 318 Score = 31.0 bits (71), Expect = 1.4 Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 4/41 (9%) Query: 169 FFEGLS----TPHSFLSFNDHHQYTPIPIQSAEDLSDHTDL 205 FF+ L + L+F DHH +T + E + L Sbjct: 236 FFDTLRALGLEVVATLAFPDHHPFTAADLAFLEAEAKEPGL 276 >gnl|CDD|133259 cd01850, CDC_Septin, CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities. Length = 276 Score = 30.6 bits (70), Expect = 1.5 Identities = 11/30 (36%), Positives = 15/30 (50%) Query: 415 ILVAGTTGSGKSVAINTMIMSLLYRLRPDE 444 I+V G +G GKS INT+ + L Sbjct: 7 IMVVGESGLGKSTFINTLFNTKLIPSDYPP 36 >gnl|CDD|35566 KOG0345, KOG0345, KOG0345, ATP-dependent RNA helicase [RNA processing and modification]. Length = 567 Score = 30.7 bits (69), Expect = 1.7 Identities = 42/201 (20%), Positives = 79/201 (39%), Gaps = 18/201 (8%) Query: 404 SVIADLANMPHILVAGTTGSGKSVAINTMIMSLLYR----LRPDECRMIMVDPKMLELSV 459 + I L ++V TGSGK++A ++ ++YR P + +++ P EL+ Sbjct: 35 ATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTR-ELAR 93 Query: 460 YDGIPHLLTPVVTNPKKAVMALKWAVREMEERYRKMSHLSVRNIKSYNERISTMYGEKPQ 519 I + P + + L R +EE + + R+ + + + Sbjct: 94 Q--IREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAE 151 Query: 520 GCGDDMRPMPYIVIIVDEMADLMMVAG--KEIEGAIQRLAQMARAAGIHLIMATQRPSVD 577 R + +V+ DE AD ++ G + + L + R L ATQ V+ Sbjct: 152 KL--SFRSLEILVL--DE-ADRLLDMGFEASVNTILSFLPKQRRTG---LFSATQTQEVE 203 Query: 578 VITGTIKANFPIRISFQVTSK 598 + N P+R+S + SK Sbjct: 204 DLARAGLRN-PVRVSVKEKSK 223 >gnl|CDD|48072 cd01968, Nitrogenase_NifE_I, Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).. Length = 410 Score = 30.2 bits (68), Expect = 2.2 Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 1/48 (2%) Query: 508 ERISTMYGEKPQGCGDDMRPMPYIVIIVDEMADLMMVAGKEIEGAIQR 555 ERI + GE DD P ++ ++ ADL++ GKE A++ Sbjct: 327 ERIKELLGEG-TVIVDDANPRELKKLLKEKKADLLVAGGKERYLALKL 373 >gnl|CDD|34569 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]. Length = 355 Score = 29.9 bits (67), Expect = 2.6 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 15/84 (17%) Query: 415 ILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPH---LLT--P 469 IL++G TGSGK+ T++ +L + DE + + D L+L PH L T P Sbjct: 176 ILISGGTGSGKT----TLLNALSGFIDSDERVITIEDTAELQL----AHPHVVRLETRPP 227 Query: 470 VVTNPKKAVMA--LKWAVREMEER 491 V + M +K A+R +R Sbjct: 228 NVEGTGEVTMRDLVKNALRMRPDR 251 >gnl|CDD|35954 KOG0735, KOG0735, KOG0735, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 952 Score = 30.0 bits (67), Expect = 2.7 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 3/60 (5%) Query: 413 PHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPHLLTPVVT 472 +IL+ G GSGK+ + + Y + + +V L+ S + I L V + Sbjct: 432 GNILLNGPKGSGKTNLVKALFD---YYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFS 488 >gnl|CDD|31846 COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]. Length = 286 Score = 29.8 bits (67), Expect = 2.7 Identities = 9/21 (42%), Positives = 15/21 (71%) Query: 412 MPHILVAGTTGSGKSVAINTM 432 M ++V G +G+GKSVA+ + Sbjct: 1 MRLVIVTGLSGAGKSVALRVL 21 >gnl|CDD|58523 cd04501, SGNH_hydrolase_like_4, Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.. Length = 183 Score = 29.5 bits (66), Expect = 3.8 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 1/71 (1%) Query: 523 DDMRPMPYIVIIVDEMADLMM-VAGKEIEGAIQRLAQMARAAGIHLIMATQRPSVDVITG 581 D + P +VII+ D+++ + + I+ I+ + ++A A GI +I+A+ P D Sbjct: 54 DVIALKPAVVIIMGGTNDIIVNTSLEMIKDNIRSMVELAEANGIKVILASPLPVDDYPWK 113 Query: 582 TIKANFPIRIS 592 ++ Sbjct: 114 PQWLRPANKLK 124 >gnl|CDD|37246 KOG2035, KOG2035, KOG2035, Replication factor C, subunit RFC3 [Energy production and conversion, Replication, recombination and repair]. Length = 351 Score = 29.5 bits (66), Expect = 3.9 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 13/73 (17%) Query: 406 IADLANMPHILVAGTTGSGKSVAINTMIMSLL--------YRLRPDECRMIMVDPKMLEL 457 ++ + PH+LV G +G+GK T IM LL +L+ + K LE+ Sbjct: 28 LSSTGDFPHLLVYGPSGAGK----KTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEI 83 Query: 458 SVYDGIPHL-LTP 469 S HL +TP Sbjct: 84 STVSSNYHLEITP 96 >gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]. Length = 845 Score = 29.2 bits (65), Expect = 4.4 Identities = 49/263 (18%), Positives = 89/263 (33%), Gaps = 64/263 (24%) Query: 409 LANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPHLLT 468 + +++ G TGSGK+ + ++ ++ P+ L Sbjct: 62 IEQNQVVIIVGETGSGKTTQLPQFLLEEGLG---IAGKIGCTQPRRLA------------ 106 Query: 469 PVVTNPKKAVMALKWAVREMEERYRKMSHLSVR--NIKSYNERISTMY-GEKPQGCGDDM 525 A + E+ E+ + S+R + S RI M G + +D Sbjct: 107 --------ARSVAERVAEELGEKLGETVGYSIRFESKVSPRTRIKVMTDGILLREIQNDP 158 Query: 526 RPMPYIVIIVDE------MADLMMVAGKEIEGAIQRLAQMARAAGIHLIM-ATQ------ 572 Y V+I+DE D+++ G ++ L R +IM AT Sbjct: 159 LLSGYSVVIIDEAHERSLNTDILL-------GLLKDLLARRRDDLKLIIMSATLDAERFS 211 Query: 573 --RPSVDVITGTIKANFPIRISFQVTSKIDS------RTILGEHGAEQLLGRGDML-YMS 623 + VI + +P+ I + ++ D + H E G G +L ++ Sbjct: 212 AYFGNAPVIEIEGRT-YPVEIRYLPEAEADYILLDAIVAAVDIHLRE---GSGSILVFLP 267 Query: 624 GGGRIQRVHG-----PLVSDIEI 641 G I+R L D+EI Sbjct: 268 GQREIERTAEWLEKAELGDDLEI 290 >gnl|CDD|29996 cd01130, VirB11-like_ATPase, Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.. Length = 186 Score = 29.1 bits (65), Expect = 4.6 Identities = 16/37 (43%), Positives = 26/37 (70%), Gaps = 5/37 (13%) Query: 415 ILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVD 451 IL++G TGSGK+ T++ +LL + PDE R+I ++ Sbjct: 28 ILISGGTGSGKT----TLLNALLAFIPPDE-RIITIE 59 >gnl|CDD|144365 pfam00735, Septin, Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis. Length = 280 Score = 29.2 bits (66), Expect = 4.7 Identities = 11/27 (40%), Positives = 18/27 (66%) Query: 415 ILVAGTTGSGKSVAINTMIMSLLYRLR 441 ++V G +G GK+ INT+ ++ LY R Sbjct: 7 LMVVGESGLGKTTLINTLFLTDLYPER 33 >gnl|CDD|32537 COG2401, COG2401, ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]. Length = 593 Score = 28.8 bits (64), Expect = 5.1 Identities = 42/180 (23%), Positives = 69/180 (38%), Gaps = 39/180 (21%) Query: 415 ILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPHLLTPVVT-- 472 + V G +G+GK+ + MI+ ++ R ++ + +V IP P Sbjct: 412 VAVVGQSGAGKTTLLR-MILGAQKGRGEEKYRPDSGKVEVPKNTVSALIPGEYEPEFGEV 470 Query: 473 -----------NPKKAVMALKWAVREMEERYR-KMSHLSVRNIKSYNERISTMYGEKPQG 520 + AV L A YR K S LS + +++ + E+P Sbjct: 471 TILEHLRSKTGDLNAAVEILNRAGLSDAVLYRRKFSELSTG--QKERAKLAKLLAERPN- 527 Query: 521 CGDDMRPMPYIVIIVDEMADLMMVAGKEIEGAIQRLA----QMARAAGIHLIMATQRPSV 576 V+++DE A + E R+A ++AR AGI LI+ T RP V Sbjct: 528 -----------VLLIDEFAAHLD------ELTAVRVARKISELAREAGITLIVVTHRPEV 570 >gnl|CDD|37142 KOG1931, KOG1931, KOG1931, Putative transmembrane protein [General function prediction only]. Length = 1156 Score = 28.8 bits (64), Expect = 5.3 Identities = 20/126 (15%), Positives = 39/126 (30%), Gaps = 29/126 (23%) Query: 8 NLHWLET---PHKQVDLKSFVPPWHEAFLLA-----------PNVRFTRTPENDLNRYRN 53 N+ W + K + L P+ E L P + D+++Y+ Sbjct: 36 NIEWRRSYGRVPKVIRLPIEFIPFGEEELDQDKSGDKSLLEFPFLHILIVECIDIDQYKA 95 Query: 54 N----STLQQPKETEHSIGDYLHTKAVTESLKSTSSLVYLKNRFMMNRNSVADQ----FN 105 T +S D++ + +S S + SV D+ F Sbjct: 96 TVRPLVTKWLKNLESNSSSDWMIVIVEYAAKRSNDS-------NLFPVKSVMDKIRKDFP 148 Query: 106 SQKTPH 111 +++T Sbjct: 149 TKQTDR 154 >gnl|CDD|29997 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.. Length = 198 Score = 29.0 bits (65), Expect = 5.3 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 415 ILVAGTTGSGKSVAINTMI 433 +LV G TGSGKS + MI Sbjct: 4 VLVTGPTGSGKSTTLAAMI 22 >gnl|CDD|146942 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria. Length = 200 Score = 28.7 bits (65), Expect = 6.2 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 17/62 (27%) Query: 415 ILVAGTTGSGKSVAINTMI----------------MSLLYRLRPDECRMIMVD-PKMLEL 457 I++ G TG+GKS N+++ L D + ++D P + +L Sbjct: 3 IVLVGKTGNGKSATGNSILGRKAFESKLRAQGVTKTCQLVSRTWDGRIINVIDTPGLFDL 62 Query: 458 SV 459 SV Sbjct: 63 SV 64 >gnl|CDD|35422 KOG0201, KOG0201, KOG0201, Serine/threonine protein kinase [Signal transduction mechanisms]. Length = 467 Score = 28.1 bits (62), Expect = 8.6 Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 6/91 (6%) Query: 231 QQKKSSIDHKPSSSNTMTEHMFQDTSQEIAKGQKQYEQPCSSFLQVQSNVNLQGITHEIL 290 Q+ S +PSS T + F ++ + + +Y QP S+ + + ++ Sbjct: 346 QRTSSPSGSQPSSGTTASGSGFNKSTSL--QNESEYAQPDSACPSPIPSPVFGLLNCKLS 403 Query: 291 EK----NAGSLETILEEFGIKGEIINVNPGP 317 +AGS + N PG Sbjct: 404 STIRDPSAGSSGALDSLRNAFSSAENSCPGI 434 >gnl|CDD|35571 KOG0350, KOG0350, KOG0350, DEAD-box ATP-dependent RNA helicase [RNA processing and modification]. Length = 620 Score = 28.1 bits (62), Expect = 8.6 Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%) Query: 415 ILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDP-KMLELSVYD 461 I V TGSGK++A I+ LL R +++ P + L L VYD Sbjct: 186 ICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYD 233 >gnl|CDD|30033 cd00530, PTE, Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal center, at the C-terminal end of a TIM alpha- beta barrel motif. The native enzyme contains two zinc ions at the active site however these can be replaced with other metals such as cobalt, cadmium, nickel or manganese and the enzyme remains active.. Length = 293 Score = 28.3 bits (63), Expect = 8.7 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 9/64 (14%) Query: 516 EKPQGCGDDMRPMPYIVIIVDEMADLMMVAGKEIEGA--------IQRLAQMARAAGIHL 567 + DD +E+ G+ I A +++LA++ARA G+++ Sbjct: 17 VRDPPEVDDFDLADVEAAK-EELKRFRAHGGRTIVDATPPGIGRDVEKLAEVARATGVNI 75 Query: 568 IMAT 571 + AT Sbjct: 76 VAAT 79 >gnl|CDD|31921 COG1735, Php, Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]. Length = 316 Score = 28.3 bits (63), Expect = 8.8 Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 8/47 (17%) Query: 533 IIVDEMADLMMVAGKEIEGA--------IQRLAQMARAAGIHLIMAT 571 + + E+ LM G+ I A + ++ ++A A G++++ AT Sbjct: 49 LAIAELKRLMARGGQTIVDATNIGIGRDVLKMRRVAEATGLNIVAAT 95 >gnl|CDD|107296 cd06301, PBP1_rhizopine_binding_like, Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Length = 272 Score = 28.0 bits (63), Expect = 8.9 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 12/74 (16%) Query: 552 AIQRLAQMARAAGIHLIMATQRPSVDVITGTIKANFPIRISFQVTSK-IDSRTILGEHGA 610 A + + A AAGI L+ +RP N P +++ V S + + + E+ A Sbjct: 69 ATAPIVKAANAAGIPLVYVNRRPE----------NAPKGVAY-VGSDEVVAGRLQAEYVA 117 Query: 611 EQLLGRGDMLYMSG 624 ++L G+G++ + G Sbjct: 118 DKLGGKGNVAILMG 131 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 0.315 0.131 0.372 Gapped Lambda K H 0.267 0.0648 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,640,502 Number of extensions: 454442 Number of successful extensions: 1478 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1466 Number of HSP's successfully gapped: 57 Length of query: 744 Length of database: 6,263,737 Length adjustment: 101 Effective length of query: 643 Effective length of database: 4,081,228 Effective search space: 2624229604 Effective search space used: 2624229604 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: 61 (27.4 bits)