RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780270|ref|YP_003064683.1| ATP-dependent protease La [Candidatus Liberibacter asiaticus str. psy62] (820 letters) >gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock. Length = 775 Score = 960 bits (2484), Expect = 0.0 Identities = 385/775 (49%), Positives = 534/775 (68%), Gaps = 16/775 (2%) Query: 29 PLLPLRDIVVFPYMIVPLFVGREKSVRALDEAMNSHKKII-LVTQMNSNDENPIASSVYR 87 PLLPLR +FP MI P+ VGREKS++ + EA+ + + L Q + ++E P +Y Sbjct: 1 PLLPLRRRPLFPGMIKPIDVGREKSIKLIKEALRLKQPYLGLFLQKDDDNEEPEEDDIYS 60 Query: 88 IGTIVDIVQILRLPD---GTVKILVEGSVRARIVEYIEREDFLEAITQVLPD--PTEDPV 142 +G + I+++L LP T K++VEG R RI E ++ +L L + +D Sbjct: 61 VGVVAQILEMLPLPSSGTATYKVVVEGLRRIRIKELSDKGGYLVVRVDNLKEEPFDKDDE 120 Query: 143 ELEALSRSVIAEFSNYIKLNK--KISPEVIGITSQIEGFSKLADVIAANLSIK-VAERQK 199 E++AL+R + F I L+K + P ++ I+ +LAD +AA+L +K E Q+ Sbjct: 121 EIKALTREIKETFRELISLSKLFREQPALLSALEDIDEPGRLADFVAASLQLKEKDELQE 180 Query: 200 ILEAVSVKERLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELD 259 +LE V++++RL+ L ++ E+ +L+++ +I +V+ +MEKTQREYYL EQ+KAI+KEL Sbjct: 181 VLETVNIEKRLKKALELLKKELELLKLQNKITKKVEEKMEKTQREYYLREQLKAIKKELG 240 Query: 260 NGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLLGVP 319 ++ +DE+ + ++ +++L +E ++ EL KL + P S+E +V RNYLDWL +P Sbjct: 241 IEKDDKDELEKLKEKLEELKLPEEVKKVIEKELTKLSLLEPSSSEFTVTRNYLDWLTDLP 300 Query: 320 WDKKSKTKKNLDFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGK 379 W K SK +L A ILD+DH+GL+KVKERI+EYLAVQ K KG ILC VGPPGVGK Sbjct: 301 WGKYSKENLDLKRAKEILDEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGK 360 Query: 380 TSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLL 439 TSL +SIAKA R++VR SLGGV DEA+IRGHRRTY+G+MPGRIIQ LK+AK NPL LL Sbjct: 361 TSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNPLFLL 420 Query: 440 DEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTLN-IPLPL 498 DEIDK+GS RGDP++ALLEVLDP QN++F DHYL+V +DLS V+FI TAN+++ IP PL Sbjct: 421 DEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPL 480 Query: 499 MDRMEIIRIAGYTEEEKLQIAKNHLVKKVLTEHALKQEECCISDGVLLDIIRLFTHEAGV 558 +DRME+I ++GYTEEEKL+IAK +L+ K L +H LK +E I+D LL +I+ +T EAGV Sbjct: 481 LDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREAGV 540 Query: 559 RSFERALMKIARKAVTKIVK------NSDTTVSINENNLQDYLGVPRYKYGKIEGEDQVG 612 R+ ER + KI RKA K+V+ + +V I +NL+ YLG P + Y + G Sbjct: 541 RNLERQIEKICRKAAVKLVEQGEKKKSEAESVVITPDNLKKYLGKPVFTYERAYEVTPPG 600 Query: 613 IVTGLAWTEVGGEILTVEGVIMPGKGEITITGNLKEIMKESILAASSYVRSKATTFGIIP 672 +V GLAWT +GG+ L +E + GKG + +TG L ++MKES A +YVRS A GI P Sbjct: 601 VVMGLAWTPMGGDTLFIETTKVAGKGSLELTGQLGDVMKESAQIALTYVRSIAADLGISP 660 Query: 673 SAFNEINIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPI 732 + F + +IH+HVPEGATPKDGPSAGI MATA++S+ T PV +VAMTGE+TLRG+VLPI Sbjct: 661 NFFEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVLPI 720 Query: 733 GGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNGLEIIPVSFMGEVLKHAL 787 GGLKEK +AA RAG+ +++PE+N +DL ++PENVK GLEI V EVLK A Sbjct: 721 GGLKEKTIAAKRAGIKTIILPEKNRRDLEELPENVKEGLEIHFVKHYDEVLKKAF 775 >gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La; Provisional. Length = 784 Score = 947 bits (2450), Expect = 0.0 Identities = 449/764 (58%), Positives = 586/764 (76%), Gaps = 1/764 (0%) Query: 29 PLLPLRDIVVFPYMIVPLFVGREKSVRALDEAMNSHKKIILVTQMNSNDENPIASSVYRI 88 P+LPLRD+VV+P+M++PLFVGREKS+R L+ AM+ KKI+LV Q ++ + P + ++ + Sbjct: 12 PVLPLRDVVVYPHMVIPLFVGREKSIRCLEAAMDHDKKIMLVAQKEASTDEPGVNDLFTV 71 Query: 89 GTIVDIVQILRLPDGTVKILVEGSVRARIVEYIEREDFLEAITQVLPDPTEDPVELEALS 148 GT+ I+Q+L+LPDGTVK+LVEG RARI + + A + L PT D E E L Sbjct: 72 GTVASILQMLKLPDGTVKVLVEGLQRARISALSDNGEHFSAKAEYLESPTIDEREQEVLV 131 Query: 149 RSVIAEFSNYIKLNKKISPEVIGITSQIEGFSKLADVIAANLSIKVAERQKILEAVSVKE 208 R+ I++F YIKLNKKI PEV+ + I+ ++LAD IAA++ +K+A++Q +LE V E Sbjct: 132 RTAISQFEGYIKLNKKIPPEVLTSLNSIDDPARLADTIAAHMPLKLADKQSVLEMSDVNE 191 Query: 209 RLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEI 268 RLE L+ MESEI +LQVEKRIR+RVK+QMEK+QREYYL+EQMKAIQKEL ++ DE Sbjct: 192 RLEYLMAMMESEIDLLQVEKRIRNRVKKQMEKSQREYYLNEQMKAIQKELGEMDDAPDEN 251 Query: 269 SDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLLGVPWDKKSKTKK 328 + +I ++ KEA+EKA +ELQKL+ M+P+SAE++VVR Y+DW++ VPW+ +SK KK Sbjct: 252 EALKRKIDAAKMPKEAKEKAEAELQKLKMMSPMSAEATVVRGYIDWMVQVPWNARSKVKK 311 Query: 329 NLDFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAK 388 +L A ILD DH+GLE+VK+RI+EYLAVQ RV K KG ILC VGPPGVGKTSL QSIAK Sbjct: 312 DLRQAQEILDTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAK 371 Query: 389 ATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEIDKMGSD 448 ATGR+YVRM+LGGV DEA+IRGHRRTYIGSMPG++IQ + + NPL LLDEIDKM SD Sbjct: 372 ATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSD 431 Query: 449 LRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTLNIPLPLMDRMEIIRIA 508 +RGDP++ALLEVLDP QN +F DHYLEV+YDLSDVMF+ T+N++NIP PL+DRME+IR++ Sbjct: 432 MRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMNIPAPLLDRMEVIRLS 491 Query: 509 GYTEEEKLQIAKNHLVKKVLTEHALKQEECCISDGVLLDIIRLFTHEAGVRSFERALMKI 568 GYTE+EKL IAK HL+ K + +ALK+ E + D ++ IIR +T EAGVRS ER + K+ Sbjct: 492 GYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKL 551 Query: 569 ARKAVTKIVKNSDTT-VSINENNLQDYLGVPRYKYGKIEGEDQVGIVTGLAWTEVGGEIL 627 RKAV +++ + + IN +NL DYLGV R+ YG+ + E++VG VTGLAWTEVGG++L Sbjct: 552 CRKAVKQLLLDKSLKHIEINGDNLHDYLGVQRFDYGRADNENRVGQVTGLAWTEVGGDLL 611 Query: 628 TVEGVIMPGKGEITITGNLKEIMKESILAASSYVRSKATTFGIIPSAFNEINIHVHVPEG 687 T+E +PGKG++T TG+L E+M+ESI AA + VR++A GI P + + +IHVHVPEG Sbjct: 612 TIETACVPGKGKLTYTGSLGEVMQESIQAALTVVRARAEKLGINPDFYEKRDIHVHVPEG 671 Query: 688 ATPKDGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGV 747 ATPKDGPSAGIAM TA+VS +T PV +VAMTGE+TLRG+VLPIGGLKEKLLAA R G+ Sbjct: 672 ATPKDGPSAGIAMCTALVSCLTGNPVRADVAMTGEITLRGQVLPIGGLKEKLLAAHRGGI 731 Query: 748 TKVLIPEENIKDLMDIPENVKNGLEIIPVSFMGEVLKHALLRMP 791 VLIP EN +DL +IP+NV L+I PV + EVL AL P Sbjct: 732 KTVLIPFENKRDLEEIPDNVIADLDIHPVKRIEEVLTLALQNEP 775 >gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional. Length = 637 Score = 137 bits (346), Expect = 2e-32 Identities = 78/199 (39%), Positives = 121/199 (60%), Gaps = 13/199 (6%) Query: 599 RYKYGKIEGEDQVGIVTGLAWT-EVGGEILTVEGVIMPG----KGEITITGNLKEIMKES 653 Y+ EG +VG V GLA E G +L + + P +G++ TG LKEI KE+ Sbjct: 417 DYELFVTEGG-EVGRVNGLAVMGEDSGIVLPIMAEVTPAQSKEEGKVIATGKLKEIAKEA 475 Query: 654 ILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPV 713 + S+ ++ K T I + +IH+ + +G SA I++ATA++S + IPV Sbjct: 476 VQNVSAIIK-KFTGKDI-----SNYDIHIQFVQTYEGVEGDSASISVATAVISALENIPV 529 Query: 714 YKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNGLEI 773 ++VAMTG L++RG VLP+GG+ K+ AA AG+ KV+IP+ N +D+M I + ++ +EI Sbjct: 530 DQSVAMTGSLSVRGDVLPVGGVTYKIEAAAEAGIKKVIIPKSNEQDVM-IEDEYEDKIEI 588 Query: 774 IPVSFMGEVLKHALLRMPD 792 IPVS + EVL+HAL+ P+ Sbjct: 589 IPVSTISEVLEHALVGGPE 607 >gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein. Length = 608 Score = 126 bits (317), Expect = 3e-29 Identities = 74/194 (38%), Positives = 114/194 (58%), Gaps = 13/194 (6%) Query: 599 RYKYGKIEGEDQVGIVTGLAWT-EVGGEILTVEGVIMPG----KGEITITGNLKEIMKES 653 RYK EG +VG V GLA E G +L ++ ++ P +G I TG L EI KE+ Sbjct: 408 RYKVIVNEG-GEVGRVNGLAVIGEASGIVLPIKAIVAPAESKEEGRIIATGKLGEIAKEA 466 Query: 654 ILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPV 713 + S+ ++ + +IH+ + +G SA I++ATA++S + IPV Sbjct: 467 VTNVSALIKKYTGE------DISNYDIHIQFLQTYEGVEGDSASISVATAVISALEEIPV 520 Query: 714 YKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNGLEI 773 ++VAMTG L++RG VLP+GG+ EK+ AA+ AG+ KV+IP+ N+ D++ E + +EI Sbjct: 521 DQDVAMTGSLSVRGEVLPVGGVTEKIEAAIEAGIKKVIIPKSNMIDVILEKET-EGKIEI 579 Query: 774 IPVSFMGEVLKHAL 787 IPV + EVL+H L Sbjct: 580 IPVETLDEVLEHVL 593 >gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis. Length = 531 Score = 116 bits (291), Expect = 3e-26 Identities = 99/317 (31%), Positives = 141/317 (44%), Gaps = 43/317 (13%) Query: 488 TANTLNIPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVK--KVLTEHALKQEECCISDGVL 545 T N IP L R I +EE +IAKN K L +HAL+ S+G Sbjct: 241 TRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNG-- 298 Query: 546 LDIIRLFTHEAGVRSFERALMKIARKAVTKIVKNSDTTVSINENNLQDYLGVPRYKYGKI 605 + + + AG+ E RK + D N P+ K+ Sbjct: 299 REAVNIVQLAAGIALGE------GRKRILA----EDIEWVAENGNYH-----PKP-EIKL 342 Query: 606 EGEDQVGIVTGLAWTEVG-GEILTVEGVIMP---GKGEITITGNLKEIMKESILAASSYV 661 E Q+G V GLA G +L VE G I +TG ++E E I + V Sbjct: 343 SSEPQIGRVNGLAVYGPNSGAVLEVEATAERAENLPGSINVTGIIEE---EEIGGSGKSV 399 Query: 662 RSKAT-------TFGIIPSAFNE----INIHVHVPEGATPKDGPSAGIAMATAIVSIMTC 710 R K++ ++ S F +IH++ P G P DGPSAG+A+A AI S + Sbjct: 400 RRKSSARGSVENVLAVLRSVFGINPQNYDIHINFP-GGIPVDGPSAGVAIAVAIYSAIFK 458 Query: 711 IPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNG 770 P+ VAMTGE++L G V P+GG+ K+ AA +AG KV+IP EN ++ + Sbjct: 459 CPIDNKVAMTGEISLNGLVKPVGGVPSKIEAAKKAGAKKVIIPYENWQESFGSISGIN-- 516 Query: 771 LEIIPVSFMGEVLKHAL 787 +IPV + E L +AL Sbjct: 517 --VIPVKNIDEALNYAL 531 >gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC. Length = 615 Score = 108 bits (271), Expect = 7e-24 Identities = 71/208 (34%), Positives = 121/208 (58%), Gaps = 18/208 (8%) Query: 584 VSINENNLQDYLGVPRYK-YGKIEGED--QVGIVTGLAWTEVGGEILTVEGVIM----PG 636 V+I ++++ + + + R Y K + +VG V GL + G +L +E V PG Sbjct: 416 VTITQDDVYEVIQISRLSPYEKRKASPTYEVGHVFGLGVSGFVGSVLEIEAVAFEAKEPG 475 Query: 637 KGEITITGNLKEIMKESILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSA 696 KG + + K+S+ A+S +R K T G S ++ IHV+V G DGPSA Sbjct: 476 KGTVRFNDTAGSMAKDSVFNAASVIR-KIT--GKDLSNYD---IHVNVIGGGR-IDGPSA 528 Query: 697 GIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEEN 756 G A+ ++S + P+ ++VA+TGE++LRG++ P+GG+ EK+ A +AG+ V+IPEEN Sbjct: 529 GAAITLCMISAILGKPIRQDVAITGEISLRGKIKPVGGIFEKIYGAKQAGIKTVVIPEEN 588 Query: 757 IKDLMDIPENVKNGLEIIPVSFMGEVLK 784 +K D+P+ + G+E+ VS + E+++ Sbjct: 589 LK---DVPQGLP-GIEVKFVSTIEELMR 612 >gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to Pfam model pfam05362, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of E. coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]. Length = 675 Score = 70.3 bits (172), Expect = 2e-12 Identities = 45/182 (24%), Positives = 82/182 (45%), Gaps = 5/182 (2%) Query: 587 NENNLQDYLGVPRYKYGKI--EGEDQVGIVTGLAWTEVGG-EILTVEGVIMPGKGEITIT 643 NE+ + ++ VP K+ G + G+V + E G + E + G G+ +++ Sbjct: 469 NESLEEFFVSVPEQGGSKLIPAGPPKPGVVYAVTQNESGKVGLYRFEVQVSAGSGKHSVS 528 Query: 644 GNLKEI-MKESILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSAGIAMAT 702 G KESI A Y + + F+E + H+HV + A +A Sbjct: 529 GLGSNTTAKESIRVAFDYFKGNLVRISA-SAKFSEHDYHLHVVDLHNTGPSTEASLAALI 587 Query: 703 AIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMD 762 A+ S + PV + + + G +T+ G + P+ L L A+ +G +VLIP + +D+ Sbjct: 588 ALCSALLKRPVQEQMVILGSMTIGGVINPVQDLAGSLQLAMDSGAKRVLIPMSSARDIPT 647 Query: 763 IP 764 +P Sbjct: 648 VP 649 >gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional. Length = 446 Score = 58.2 bits (142), Expect = 9e-09 Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 6/94 (6%) Query: 694 PSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIP 753 P+A +A+A AI S + P+ + + GE+ L G + P+ ++ +L A + G + ++P Sbjct: 357 PAADLAVALAIASSLRDRPLPPDTVVFGEVGLTGEIRPVPRIERRLKEAAKLGFKRAIVP 416 Query: 754 EENIKDLMDIPENVKNGLEIIPVSFMGEVLKHAL 787 + N +P+ G+E+I V + E L+ Sbjct: 417 KGN------LPKKPPKGIEVIGVKTLAEALELLF 444 >gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed. Length = 413 Score = 57.8 bits (141), Expect = 1e-08 Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 20/88 (22%) Query: 360 RVIKNKGLI-LCFVGPPGVGKTSLAQSIAKATGRQYVRMS--LGGVYDEADIRGHRRTYI 416 R+I+ L + GPPG GKT+LA+ IA AT + +S GV D+R Sbjct: 29 RMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGV---KDLR------- 78 Query: 417 GSMPGRIIQSLKRAKRS--NPLLLLDEI 442 +I+ ++ + + +L +DEI Sbjct: 79 -----EVIEEARQRRSAGRRTILFIDEI 101 >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 = 57.7 bits (140), Expect = 1e-08 Identities = 36/143 (25%), Positives = 55/143 (38%), Gaps = 14/143 (9%) Query: 369 LCFVGPPGVGKTSLAQSIAKAT-GRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSL 427 + VGPPG GK+ LA+ +A A R + L E D++G R + L Sbjct: 2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRN-IANGTTSWVDGPL 60 Query: 428 KRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPA---QNSSFVDHYLEVEYDLSDVM 484 RA R + +LDEI++ D+ +LL +LD + + Sbjct: 61 VRAAREGEIAVLDEINRANPDVLN----SLLSLLDERRLLLPEGGELVKVAPDDFAKRFR 116 Query: 485 FIMTANTLN-----IPLPLMDRM 502 I T N L+ + L R Sbjct: 117 LIATMNPLDRGLNELSPALRSRF 139 >gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA. Length = 731 Score = 52.4 bits (126), Expect = 5e-07 Identities = 44/130 (33%), Positives = 63/130 (48%), Gaps = 24/130 (18%) Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRT---YIGSMPGRIIQS- 426 F GP GVGKT LA+ +A+A G R + Y E + T IG+ PG + Sbjct: 489 FTGPTGVGKTELAKQLAEALGVHLERFDMSE-YME------KHTVSRLIGAPPGYVGFEQ 541 Query: 427 ---LKRAKRSNP--LLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLS 481 L A R +P +LLLDEI+K D+ LL+V+D ++ D+ D Sbjct: 542 GGLLTEAVRKHPHCVLLLDEIEKAHPDI----YNILLQVMD---YATLTDNNGRKA-DFR 593 Query: 482 DVMFIMTANT 491 +V+ IMT+N Sbjct: 594 NVILIMTSNA 603 Score = 33.5 bits (77), Expect = 0.21 Identities = 32/105 (30%), Positives = 47/105 (44%), Gaps = 12/105 (11%) Query: 343 GLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGG- 401 G E ER I+ L R KN L VG PGVGKT++A+ +A V +L Sbjct: 186 GREDELERTIQVLC---RRKKNNPL---LVGEPGVGKTAIAEGLALRIAEGKVPENLKNA 239 Query: 402 -VY--DEADIRGHRRTYIGSMPGRIIQSLKRAKR-SNPLLLLDEI 442 +Y D + + Y G R+ + ++ N +L +DEI Sbjct: 240 KIYSLDMGSLLAGTK-YRGDFEERLKAVVSEIEKEPNAILFIDEI 283 >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 = 51.2 bits (122), Expect = 9e-07 Identities = 34/147 (23%), Positives = 58/147 (39%), Gaps = 20/147 (13%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRM-------SLGGVYDEADIRGHRRTYIG 417 G ++ VGPPG GKT+LA+++A+ G + L V D+ + Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60 Query: 418 SMPGRII-QSLKRAKRSNP-LLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLE 475 + +L A++ P +L+LDEI + ALL +L+ L Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAE----QEALLLLLE-------ELRLLL 109 Query: 476 VEYDLSDVMFIMTANTLNIPLPLMDRM 502 + ++ I+T N P + R Sbjct: 110 LLKSEKNLTVILTTNDEKDLGPALLRR 136 >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 = 49.9 bits (120), Expect = 2e-06 Identities = 73/289 (25%), Positives = 116/289 (40%), Gaps = 50/289 (17%) Query: 176 IEGFSKLADVIAANLSIKVAERQKILEAVSVKERLEMLLVFMESEISVLQVE-KRIRSRV 234 +E + + L E + ERL L +E++ L+ E + +R Sbjct: 421 LEDLRRRIAALELELDALEREAALGAD---HDERLAEL----RAELAALEAELAALEARW 473 Query: 235 KRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQK 294 +++ E L E + A++ EL+ + D A +++ E AL+ Q Sbjct: 474 QQEKE-------LVEAILALRAELEADAD--APADDDAALRAQLA----ELEAALASAQG 520 Query: 295 -LRQMNPLSAESSVVRNYLDWLLGVPWDK--KSKTKKNLDFAI----RILDQDHFGLEKV 347 + P +V DW G+P + + + + L R++ QDH LE + Sbjct: 521 EEPLVFPEVDAQAVAEVVADWT-GIPVGRMVRDEIEAVLSLPDRLAERVIGQDH-ALEAI 578 Query: 348 KERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKAT--GRQY---VRMSLGGV 402 ERI A K G+ L VGP GVGKT A ++A+ G Q + MS Sbjct: 579 AERIRTARAGLEDPRKPLGVFL-LVGPSGVGKTETALALAELLYGGEQNLITINMS---E 634 Query: 403 YDEADIRGHR-RTYIGSMPGRIIQS----LKRAKRSNP--LLLLDEIDK 444 + EA H GS PG + L A R P ++LLDE++K Sbjct: 635 FQEA----HTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEK 679 >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 = 46.9 bits (112), Expect = 2e-05 Identities = 39/134 (29%), Positives = 69/134 (51%), Gaps = 20/134 (14%) Query: 323 KSKTKKNLDFAIRILDQDHFGLEKVKER---IIEYLAVQMRVIK-----NKGLILCFVGP 374 KSK K + ++ +D G+++ KE I+++L + K KG++L VGP Sbjct: 39 KSKAKLLNEEKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLL--VGP 96 Query: 375 PGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSN 434 PG GKT LA+++A G + +S G + E ++G R+ ++AK++ Sbjct: 97 PGTGKTLLAKAVAGEAGVPFFSIS-GSDFVE--------MFVGVGASRVRDLFEQAKKNA 147 Query: 435 P-LLLLDEIDKMGS 447 P ++ +DEID +G Sbjct: 148 PCIIFIDEIDAVGR 161 >gnl|CDD|128740 smart00464, LON, Found in ATP-dependent protease La (LON). N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs. Length = 92 Score = 46.7 bits (111), Expect = 3e-05 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%) Query: 29 PLLPLRDIVVFPYMIVPLFVGREKSVRALDEAMNSHKK--IILVTQMNSNDENPIAS 83 PLLP+R +FP ++P+ V R KSV A+ EA+ + I+ + Q + + S Sbjct: 3 PLLPIRRRPLFPGFVLPIPVKRPKSVAAIKEALRRSQPYVIVFLLQDDPTETPEPLS 59 >gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168 Score = 46.4 bits (111), Expect = 3e-05 Identities = 41/174 (23%), Positives = 68/174 (39%), Gaps = 40/174 (22%) Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTY---------IGSMPG 421 F+GP GVGKT LA+++A+ L + A IR Y IG+ PG Sbjct: 8 FLGPTGVGKTELAKALAE----------LLFGDERALIRIDMSEYMEEHSVSRLIGAPPG 57 Query: 422 RI------IQSLKRAKRSNPLLLLDEIDKMGSD-LRGDPSAALLEVLDPAQNSSFVDHYL 474 + + ++ ++L+DEI+K LL++L+ + D Sbjct: 58 YVGYEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQN-----DLLQILE---GGTLTDKQ- 108 Query: 475 EVEYDLSDVMFIMTANTLNIPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVKKVL 528 + D + +FIMT N + R+ + E L+ L+KK Sbjct: 109 GRKVDFRNTLFIMTGN-----FGSEKISDASRLGKSPDYELLKELVMDLLKKGF 157 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 44.9 bits (107), Expect = 9e-05 Identities = 41/132 (31%), Positives = 65/132 (49%), Gaps = 30/132 (22%) Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRM--SLGGV 402 EK KE++ E++ ++ K L+L GPPGVGKTSLA ++A G + + + S Sbjct: 20 EKAKEQLREWIESWLKGKPKKALLL--YGPPGVGKTSLAHALANDYGWEVIELNAS---- 73 Query: 403 YDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPL-------LLLDEIDKM-GSDLRGDPS 454 D+ RT I + A S L +LLDE+D + G++ RG + Sbjct: 74 -DQ-------RTA-----DVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNEDRGG-A 119 Query: 455 AALLEVLDPAQN 466 A+LE++ A+ Sbjct: 120 RAILELIKKAKQ 131 >gnl|CDD|161868 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). Length = 454 Score = 44.0 bits (104), Expect = 1e-04 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 6/92 (6%) Query: 692 DGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVL 751 P+A +A+ AIVS P+ ++ GE+ L G + P+ L+E+L A + G + + Sbjct: 369 SEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEERLKEAAKLGFKRAI 428 Query: 752 IPEENIKDLMDIPENVKNGLEIIPVSFMGEVL 783 +P+ N P+ G+++I V +G+ L Sbjct: 429 VPKAN------SPKTAPEGIKVIGVKKVGDAL 454 >gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed. Length = 644 Score = 43.9 bits (103), Expect = 2e-04 Identities = 40/131 (30%), Positives = 64/131 (48%), Gaps = 16/131 (12%) Query: 323 KSKTKKNLDFAIRILDQDHFGLEKVKERI---IEYLAVQMRVIKNKGLI---LCFVGPPG 376 KSK + + I+ D G ++ KE + +EYL R K G I + VGPPG Sbjct: 136 KSKARMLTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPG 195 Query: 377 VGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNP- 435 GKT LA++IA + +S G + E ++G R+ ++AK++ P Sbjct: 196 TGKTLLAKAIAGEAKVPFFTIS-GSDFVE--------MFVGVGASRVRDMFEQAKKAAPC 246 Query: 436 LLLLDEIDKMG 446 ++ +DEID +G Sbjct: 247 IIFIDEIDAVG 257 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 42.4 bits (100), Expect = 5e-04 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 16/77 (20%) Query: 369 LCFVGPPGVGKTSLAQSIAKATGRQYVRMS--LGGVYDEADIRGHRRTYIGSMPGRIIQS 426 L GPPGVGKT+LA+ IA T + ++ L GV D+R + R + Sbjct: 55 LILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAGV---KDLR--------AEVDRAKER 103 Query: 427 LKR-AKRSNPLLLLDEI 442 L+R KR+ +L +DE+ Sbjct: 104 LERHGKRT--ILFIDEV 118 >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 = 41.1 bits (97), Expect = 0.001 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%) Query: 335 RILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQY 394 R D D FG+E+ ER + Y + ++ + IL +GP G GK+SL + + + +Y Sbjct: 47 RFFDHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL-EEY 105 Query: 395 VRMSLGGVY 403 + G Y Sbjct: 106 SKTPEGRRY 114 >gnl|CDD|131926 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX. Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis. Length = 284 Score = 41.0 bits (96), Expect = 0.001 Identities = 37/115 (32%), Positives = 53/115 (46%), Gaps = 15/115 (13%) Query: 337 LDQDHFGLEKVKERIIEYLAV----QMR-----VIKNKGLILCFVGPPGVGKTSLAQSIA 387 LD++ GL+ VK RI E A+ ++R L + F G PG GKT++A +A Sbjct: 20 LDRELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMA 79 Query: 388 KATGR-QYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDE 441 + R YVR D+ G YIG + + LKRA +L +DE Sbjct: 80 QILHRLGYVRKGHLVSVTRDDLVGQ---YIGHTAPKTKEILKRAM--GGVLFIDE 129 >gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional. Length = 316 Score = 39.6 bits (93), Expect = 0.003 Identities = 47/200 (23%), Positives = 84/200 (42%), Gaps = 43/200 (21%) Query: 359 MRVIKNKGLI--LCFVGP-PGVGKTSLAQSIAKATGRQY--VRMSLGGVYDEADIRGHRR 413 + I KG I + P PG GKT++A+++ G + V S + +R Sbjct: 33 FKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCRI---DFVRNRLT 89 Query: 414 TYIGSMPGRIIQSLKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNS--SFVD 471 + ++ SL ++++DE D++G L AQ SF++ Sbjct: 90 RFASTV------SLT-GGGK--VIIIDEFDRLG--------------LADAQRHLRSFME 126 Query: 472 HYLEVEYDLSDVMFIMTANTLN-IPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVKKVLTE 530 Y + FI+TAN N I PL R +I T+EE++++ K +V+ + Sbjct: 127 AY------SKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVR---CK 177 Query: 531 HALKQEECCISDGVLLDIIR 550 L+ E + VL +++ Sbjct: 178 GILEAEGVEVDMKVLAALVK 197 >gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional. Length = 758 Score = 39.4 bits (92), Expect = 0.004 Identities = 39/129 (30%), Positives = 63/129 (48%), Gaps = 24/129 (18%) Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRT---YIGSMPGRI---- 423 F GP GVGKT + ++KA G + +R +D ++ R T IG+ PG + Sbjct: 493 FAGPTGVGKTEVTVQLSKALGIELLR------FDMSEY-MERHTVSRLIGAPPGYVGFDQ 545 Query: 424 --IQSLKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLS 481 + + K + +LLLDEI+K D+ LL+V+D N + D+ + D Sbjct: 546 GGLLTDAVIKHPHAVLLLDEIEKAHPDVFN----LLLQVMD---NGTLTDNNGR-KADFR 597 Query: 482 DVMFIMTAN 490 +V+ +MT N Sbjct: 598 NVVLVMTTN 606 >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 = 39.4 bits (92), Expect = 0.004 Identities = 19/50 (38%), Positives = 30/50 (60%) Query: 340 DHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKA 389 D FG+E+ ERI+ Y + ++ + IL +GP G GK+SLA+ + K Sbjct: 59 DFFGMEETIERIVNYFRHAAQGLEERKQILYLLGPVGGGKSSLAERLKKL 108 >gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed. Length = 328 Score = 38.2 bits (90), Expect = 0.008 Identities = 24/54 (44%), Positives = 30/54 (55%), Gaps = 11/54 (20%) Query: 343 GLEKVKERI---IEYLAVQMRVIKNKGL--ILCFVGPPGVGKTSLAQSIAKATG 391 G EKVKE + IE A + R + L +L GPPG+GKT+LA IA G Sbjct: 29 GQEKVKENLKIFIE--AAKKR---GEALDHVL-LYGPPGLGKTTLANIIANEMG 76 >gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated. Length = 268 Score = 38.1 bits (89), Expect = 0.010 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 11/83 (13%) Query: 363 KNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVR---MSLGGVYDEADIRGHRRTYIGSM 419 +N GL+L G G GKT LA IA + V ++ + + I+ ++ Sbjct: 113 ENVGLLLW--GSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNR--IKSTYKSSGKED 168 Query: 420 PGRIIQSLKRAKRSNPLLLLDEI 442 II+SL A LL+LD++ Sbjct: 169 ENEIIRSLVNA----DLLILDDL 187 >gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed. Length = 319 Score = 37.9 bits (89), Expect = 0.010 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 8/47 (17%) Query: 343 GLEKVKERIIEYLAVQMRVIKNKGLI-LCFVGPPGVGKTSLAQSIAK 388 G E++ ER+ Y +K K + L F GPPG GKT+ A ++A+ Sbjct: 21 GQEEIVERLKSY-------VKEKNMPHLLFAGPPGTGKTTAALALAR 60 >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 = 38.0 bits (88), Expect = 0.011 Identities = 50/204 (24%), Positives = 90/204 (44%), Gaps = 34/204 (16%) Query: 343 GLEKVKERIIEYLAVQ-----------MRVIKNKGLILCFVGPPGVGKTSLAQSIAKATG 391 GLE+VK+ + E AV+ M + KG++L GPPG GKT LA+++A +G Sbjct: 457 GLEEVKQELRE--AVEWPLKHPEIFEKMGIRPPKGVLL--FGPPGTGKTLLAKAVATESG 512 Query: 392 RQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNP-LLLLDEIDKMGSDLR 450 ++ + + + ++G I + ++A+++ P ++ DEID + Sbjct: 513 ANFIAVRGPEILSK---------WVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARG 563 Query: 451 GDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTLNIPLPLMDRM----EIIR 506 + V D N + ++ +LS+V+ I N +I P + R +I Sbjct: 564 ARFDTS---VTDRIVNQLLTE--MDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLIL 618 Query: 507 IAGYTEEEKLQIAKNHLVKKVLTE 530 + EE + +I K H L E Sbjct: 619 VPPPDEEARKEIFKIHTRSMPLAE 642 Score = 36.8 bits (85), Expect = 0.020 Identities = 32/115 (27%), Positives = 58/115 (50%), Gaps = 21/115 (18%) Query: 339 QDHFGLEKVKERIIEYLAVQMR---------VIKNKGLILCFVGPPGVGKTSLAQSIAKA 389 +D GL++ KE+I E + + M+ + KG++L GPPG GKT LA+++A Sbjct: 178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLL--YGPPGTGKTLLAKAVANE 235 Query: 390 TGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNP-LLLLDEID 443 G ++ ++ + + Y G R+ + K A+ + P ++ +DEID Sbjct: 236 AGAYFISINGPEIMSK---------YYGESEERLREIFKEAEENAPSIIFIDEID 281 >gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal. Length = 364 Score = 37.9 bits (88), Expect = 0.011 Identities = 56/223 (25%), Positives = 95/223 (42%), Gaps = 27/223 (12%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRII 424 KG++L GPPG GKT LA+++A T ++R+ V E R YIG + Sbjct: 157 KGVLL--YGPPGTGKTLLAKAVAHETNATFIRV----VGSEL-----VRKYIGEGARLVR 205 Query: 425 QSLKRAKRSNP-LLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVE-YD-LS 481 + + AK P ++ +DEID + + ++ EV + + E++ +D Sbjct: 206 EIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREV-----QRTLMQLLAELDGFDPRG 260 Query: 482 DVMFIMTANTLNIPLPLMDRM----EIIRIAGYTEEEKLQIAKNHLVKKVLTEHALKQEE 537 +V I N +I P + R II + E +L+I K H K L E + Sbjct: 261 NVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAI 320 Query: 538 CCISDGVLLDIIRLFTHEAGVRSFERALMKIA----RKAVTKI 576 +++G ++ EAG+ + + KAV K+ Sbjct: 321 AKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 >gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. Length = 282 Score = 37.3 bits (87), Expect = 0.017 Identities = 37/192 (19%), Positives = 68/192 (35%), Gaps = 30/192 (15%) Query: 207 KERLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRD 266 K+ +E+ E E++ E+ + ++ ++ A +E Sbjct: 42 KKFVEVTAAIDEEEVATASTEEEAKKALEPADPAKLSATAEPLELPAPLEEPAAPAAQAA 101 Query: 267 EISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLL--GVPWDKKS 324 E E ++ +E E+ L+ L L+ L+ LL GV + Sbjct: 102 EPLLPEELRKELEALRELLERLLAGLAWLQ-------RDPEGAKLLERLLRAGVSPE--- 151 Query: 325 KTKKNLDFAIRILD--QDHFGLEKVKERIIEYLAVQMRV------IKNKGLILCFVGPPG 376 A +L+ + E + E L + V I +G ++ VGP G Sbjct: 152 -------LARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTG 204 Query: 377 VGKTSLAQSIAK 388 VGKT+ ++AK Sbjct: 205 VGKTT---TLAK 213 >gnl|CDD|129401 TIGR00300, TIGR00300, conserved hypothetical protein TIGR00300. All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family. Length = 407 Score = 37.1 bits (86), Expect = 0.019 Identities = 20/57 (35%), Positives = 29/57 (50%) Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGG 401 E+ E +IE +A +M I++KG + V P V T AQ++A YV L G Sbjct: 180 ERPVETLIEQIAWEMYEIRDKGGKIGVVAGPAVIHTGAAQALAHLIREGYVDALLAG 236 >gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional. Length = 254 Score = 36.4 bits (84), Expect = 0.029 Identities = 28/105 (26%), Positives = 42/105 (40%), Gaps = 10/105 (9%) Query: 338 DQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRM 397 D DH +K I +L V + ++ F+GPPG GKT LA + + R+ Sbjct: 74 DFDH--QRSLKRDTIAHLGTLDFVTGKENVV--FLGPPGTGKTHLAIGLGIRACQAGHRV 129 Query: 398 SLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEI 442 R GR+ L + R PLL++DE+ Sbjct: 130 LFATAAQWVA-----RLAAAHHAGRLQAELVKLGRY-PLLIVDEV 168 >gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional. Length = 438 Score = 35.5 bits (82), Expect = 0.052 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 12/84 (14%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRII 424 KG+IL GPPG GKT LA+++A T ++R+ V E + Y+G P + Sbjct: 218 KGVIL--YGPPGTGKTLLAKAVANETSATFLRV----VGSEL-----IQKYLGDGPKLVR 266 Query: 425 QSLKRAKRSNP-LLLLDEIDKMGS 447 + + A+ + P ++ +DEID +G+ Sbjct: 267 ELFRVAEENAPSIVFIDEIDAIGT 290 >gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. Length = 305 Score = 35.4 bits (82), Expect = 0.063 Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 5/54 (9%) Query: 340 DHFGLEKVKERIIEYLAVQMRVIKNKGL--ILCFVGPPGVGKTSLAQSIAKATG 391 + G EKVKE++ L ++ ++ + L +L + GPPG+GKT+LA IA G Sbjct: 5 EFIGQEKVKEQL--QLFIEAAKMRQEALDHLLLY-GPPGLGKTTLAHIIANEMG 55 >gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional. Length = 880 Score = 35.4 bits (82), Expect = 0.064 Identities = 40/189 (21%), Positives = 80/189 (42%), Gaps = 14/189 (7%) Query: 114 RARIVEYIEREDFLEAITQVLPDPTEDPVELEALSRSVIAEFSNYIKLNKKISPEVIGIT 173 RI E + + LE + L + E E LS + Y+ ++I + + Sbjct: 265 EERIEELKKEIEELEEKVKELKELKEKAEEYIKLSE----FYEEYLDELREIEKRLSRLE 320 Query: 174 SQIEGFSKLADVIAANLSIKVAERQKILEAVS-VKERLEMLLVFMESEISVLQVEKRIRS 232 +I G + L K +++ + + +++RLE L E ++ + Sbjct: 321 EEINGIEERIK----ELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELER 376 Query: 233 RVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSEL 292 KR T + L ++++ ++K EE +EIS ARI +++ + +KA+ EL Sbjct: 377 LKKRLTGLTPEK--LEKELEELEKA---KEEIEEEISKITARIGELKKEIKELKKAIEEL 431 Query: 293 QKLRQMNPL 301 +K + P+ Sbjct: 432 KKAKGKCPV 440 Score = 30.0 bits (68), Expect = 2.6 Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 3/90 (3%) Query: 207 KERLEMLLVFMESEISVL--QVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEG 264 ERLE + I L + EK + ++ E + L E+++ ++KE+ EE Sbjct: 178 IERLEKFIK-RTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEEL 236 Query: 265 RDEISDFEARISKIRLSKEAREKALSELQK 294 ++EI + E + + SK E+ + EL++ Sbjct: 237 KEEIEELEKELESLEGSKRKLEEKIRELEE 266 >gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional. Length = 398 Score = 34.4 bits (79), Expect = 0.12 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 12/73 (16%) Query: 373 GPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKR 432 GPPG GKT LA+++A T ++R+ +G + + Y+G P R+++ + R R Sbjct: 186 GPPGTGKTMLAKAVAHHTTATFIRV-VGSEFVQ--------KYLGEGP-RMVRDVFRLAR 235 Query: 433 SN--PLLLLDEID 443 N ++ +DE+D Sbjct: 236 ENAPSIIFIDEVD 248 >gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group. Length = 261 Score = 34.3 bits (79), Expect = 0.14 Identities = 30/110 (27%), Positives = 53/110 (48%), Gaps = 17/110 (15%) Query: 343 GLEKVKERIIE---YLAVQMRVIK------NKGLILCFVGPPGVGKTSLAQSIAKATGRQ 393 GL++VK I E ++ + + + + L + F G PG GKT++A+ + K Sbjct: 10 GLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEM 69 Query: 394 YVRMSLGGVY--DEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDE 441 V +S G + + AD+ G YIG + + +K+A +L +DE Sbjct: 70 NV-LSKGHLIEVERADLVGE---YIGHTAQKTREVIKKA--LGGVLFIDE 113 >gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 131 Score = 34.1 bits (79), Expect = 0.17 Identities = 10/24 (41%), Positives = 17/24 (70%) Query: 373 GPPGVGKTSLAQSIAKATGRQYVR 396 G PG+ KT LA+++A++ G + R Sbjct: 6 GVPGLAKTLLARTLARSLGLDFRR 29 >gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional. Length = 880 Score = 33.9 bits (78), Expect = 0.17 Identities = 53/214 (24%), Positives = 85/214 (39%), Gaps = 51/214 (23%) Query: 124 EDFLEAITQVLPDPTEDPVELEALSRSV---IAEFSNYIKLNK--------KISPEVIGI 172 EDFLE + + + E ELEA R+ + E ++ K + SP V I Sbjct: 411 EDFLEELREERDELREREAELEATLRTARERVEEAEALLEAGKCPECGQPVEGSPHVETI 470 Query: 173 TSQIEGFSKLADVIAANLSIKVAERQKILEAVS-VKERLEML--LVFMESEISVLQ---- 225 E +L AE + + E V V+ERLE LV E I L+ Sbjct: 471 EEDRERVEELE-----------AELEDLEEEVEEVEERLERAEDLVEAEDRIERLEERRE 519 Query: 226 -VEKRIRSRVKRQMEKTQREYYLHEQM-----------KAIQKELDNGEEGRDEISDFEA 273 +E+ I R + EK +R L E+ +A + + EE R+E+++ + Sbjct: 520 DLEELIAERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNS 579 Query: 274 ----------RISKIRLSKEAREKALSELQKLRQ 297 + +IR A A E+++LR+ Sbjct: 580 KLAELKERIESLERIRTLLAAIADAEDEIERLRE 613 >gnl|CDD|185352 PRK15455, PRK15455, PrkA family serine protein kinase; Provisional. Length = 644 Score = 33.8 bits (78), Expect = 0.20 Identities = 16/45 (35%), Positives = 28/45 (62%) Query: 340 DHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQ 384 + +G+E+ E+I+ Y + ++ K IL +GP G GK+SLA+ Sbjct: 77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAE 121 >gnl|CDD|161686 TIGR00064, ftsY, signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein. Length = 272 Score = 33.4 bits (77), Expect = 0.24 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 10/51 (19%) Query: 345 EKVKERIIEYLAVQ-------MRVIKNKGLILCFVGPPGVGKTSLAQSIAK 388 E +KE + EYL + V +NK ++ FVG GVGKT+ +IAK Sbjct: 44 ELLKEILKEYLKEILKETDLELIVEENKPNVILFVGVNGVGKTT---TIAK 91 >gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 424 Score = 33.3 bits (77), Expect = 0.24 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 3/48 (6%) Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGR 392 + E + + V++ I +G ++ VGP GVGKT+ ++AK R Sbjct: 200 RYLLELLANMIPVRVEDILKQGGVVALVGPTGVGKTT---TLAKLAAR 244 >gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional. Length = 389 Score = 33.3 bits (77), Expect = 0.25 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 15/67 (22%) Query: 343 GLEKVKERIIEYLAVQMRVIKN-----------KGLILCFVGPPGVGKTSLAQSIAKATG 391 GLE+ + E AV++ + K KG++L GPPG GKT LA+++A T Sbjct: 135 GLEEQIREVRE--AVELPLKKPELFEEVGIEPPKGVLL--YGPPGTGKTLLAKAVAHETN 190 Query: 392 RQYVRMS 398 ++R+ Sbjct: 191 ATFIRVV 197 >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 = 33.4 bits (76), Expect = 0.26 Identities = 40/198 (20%), Positives = 74/198 (37%), Gaps = 17/198 (8%) Query: 268 ISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAE--SSVVRNYLDWLLGVPWDKKSK 325 IS S R+ + S R+ LS E + + + + PW +K K Sbjct: 20 ISTITKWSLSRPTSSHRRKNSPSTDIHARKRGFLSLEQDTGLELSSENLDGNEPWVEKYK 79 Query: 326 TKKNLDFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQS 385 + + A+ +E+V+ + A + + L++ GP G GK++ + Sbjct: 80 PETQHELAVH-----KKKIEEVETWL---KAQVLENAPKRILLIT--GPSGCGKSTTIKI 129 Query: 386 IAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLD--EID 443 ++K G Q S + D H+ T S+ + + + LL ++ Sbjct: 130 LSKELGIQVQEWSNPTLPDFQK-NDHKVTL--SLESCFSNFQSQIEVFSEFLLRATNKLQ 186 Query: 444 KMGSDLRGDPSAALLEVL 461 +G DL D L+E L Sbjct: 187 MLGDDLMTDKKIILVEDL 204 >gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728). Length = 262 Score = 33.2 bits (76), Expect = 0.27 Identities = 14/64 (21%), Positives = 27/64 (42%) Query: 352 IEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGH 411 ++ + + G + GP G GKT+LA +A+ R + ++ +D+ G Sbjct: 7 VKRVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGS 66 Query: 412 RRTY 415 Y Sbjct: 67 YAGY 70 >gnl|CDD|163196 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely. Length = 353 Score = 32.3 bits (74), Expect = 0.46 Identities = 12/23 (52%), Positives = 16/23 (69%) Query: 365 KGLILCFVGPPGVGKTSLAQSIA 387 KG +C +GP G GKT+L + IA Sbjct: 29 KGEFVCLLGPSGCGKTTLLRIIA 51 >gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein. Length = 383 Score = 32.4 bits (73), Expect = 0.46 Identities = 30/120 (25%), Positives = 48/120 (40%), Gaps = 14/120 (11%) Query: 373 GPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKR 432 G G GK +A+ IA+A + M+ + DE +++G +I + A + Sbjct: 126 GGAGSGKNHIAEQIAEALDLDFYFMN--AIMDEFELKG----FIDANGKFHETPFYEAFK 179 Query: 433 SNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTL 492 L +DEID P A ++ ++ A + F D E D I NTL Sbjct: 180 KGGLFFIDEIDA------SIPEALII--INSAIANKFFDFADERVTAHEDFRVISAGNTL 231 >gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional. Length = 602 Score = 32.5 bits (75), Expect = 0.48 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 12/55 (21%) Query: 334 IRILDQDHFGL-EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIA 387 + L + + L EK+KER+ E + +G+++ G PG GK++ AQ++A Sbjct: 235 VVKLSLEDYNLSEKLKERLEE---------RAEGILI--AGAPGAGKSTFAQALA 278 >gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed. Length = 175 Score = 32.1 bits (74), Expect = 0.56 Identities = 7/25 (28%), Positives = 15/25 (60%) Query: 371 FVGPPGVGKTSLAQSIAKATGRQYV 395 +G G GK+++ + +AK G ++ Sbjct: 9 LIGFMGAGKSTIGRLLAKRLGYDFI 33 >gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional. Length = 420 Score = 31.8 bits (72), Expect = 0.72 Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 13/90 (14%) Query: 349 ERIIEYLAVQMRVIKN-----KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGV- 402 ++ I L + +R I +G + +GP GVGKT+ + AK R +R V Sbjct: 169 KKTISLLTLNLRTIGGDEIIEQGGVYALIGPTGVGKTT---TTAKLAARAVIRHGADKVA 225 Query: 403 ---YDEADIRGHRRTYI-GSMPGRIIQSLK 428 D I GH + I G + G ++S+K Sbjct: 226 LLTTDSYRIGGHEQLRIYGKLLGVSVRSIK 255 >gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated. Length = 329 Score = 31.8 bits (73), Expect = 0.77 Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 4/45 (8%) Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKA 389 EK+ E+ ++ L F G G GKT L+ IAK Sbjct: 166 EKILEKCKNFIEN----FDKNNENLLFYGNTGTGKTFLSNCIAKE 206 >gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF; Provisional. Length = 432 Score = 31.9 bits (72), Expect = 0.80 Identities = 52/207 (25%), Positives = 93/207 (44%), Gaps = 35/207 (16%) Query: 220 EISVLQVEKRI-RSRVKRQMEK-----TQREYYLHEQMKAIQ------KELDNGEEGRDE 267 EI + EK+ R +++R+++ Q+ Y E+ K +Q + L+ E E Sbjct: 51 EIQIGIPEKQASREKIERKLQDLKELLKQKSYTEPERKKTLQTLKPLSERLEEKESAIYE 110 Query: 268 ISDFEARISKIRLSKEAREKALSELQKLRQMNPLS-AESSVVRNYLD---WLLGVPWDKK 323 I FE + ++ E R LS ++L + N +E+++VR D LG ++ Sbjct: 111 IESFE--LEEVITEPE-RPVGLSFEKELFEKNSFLESETTIVRKEKDSPLQRLGERLVRE 167 Query: 324 SKTKKNLDFAIRILDQ-----DHFGLEKVKERIIEYLAVQMRVI--------KNKGLILC 370 ++ ++ L++ D V ER + YL ++ V KN+ ++ Sbjct: 168 GMSQSYVEEMASKLEERLSPVDQGRNHNVTERAVTYLEERVSVDSDLFSGTGKNQRKVVF 227 Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRM 397 FVGP G GKT+ SIAK + ++ M Sbjct: 228 FVGPTGSGKTT---SIAKLAAKYFLHM 251 >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 = 31.5 bits (72), Expect = 0.82 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 5/53 (9%) Query: 356 AVQMRVIKNK---GLILCFVGPPGVGKTSLAQSIAKATGRQ--YVRMSLGGVY 403 V + +IK G + GPPG GKT+LA +I+K G + +S VY Sbjct: 37 GVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVY 89 Score = 30.4 bits (69), Expect = 1.9 Identities = 14/27 (51%), Positives = 17/27 (62%) Query: 494 IPLPLMDRMEIIRIAGYTEEEKLQIAK 520 IPL L+DR+ II YT EE QI + Sbjct: 329 IPLDLLDRLLIITTEPYTREEIKQILE 355 >gnl|CDD|162839 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis. Length = 355 Score = 31.4 bits (72), Expect = 0.86 Identities = 12/19 (63%), Positives = 14/19 (73%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F GP G GKTS+A+ AKA Sbjct: 41 FSGPRGTGKTSIARIFAKA 59 >gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau. Length = 188 Score = 31.4 bits (72), Expect = 0.88 Identities = 12/19 (63%), Positives = 14/19 (73%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F GP GVGK LA ++AKA Sbjct: 19 FAGPEGVGKELLALALAKA 37 >gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal 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. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. Length = 1164 Score = 31.2 bits (71), Expect = 1.0 Identities = 32/125 (25%), Positives = 57/125 (45%), Gaps = 26/125 (20%) Query: 194 VAERQKILEAVSVKERLEML---LVFMESEISVLQVEK-RIRSRV--------------- 234 A R IL + S L+ L L ++ E+S LQ E RI +R+ Sbjct: 660 RAPRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIG 719 Query: 235 ---KRQMEKTQREYYLHEQMKAIQKELDNGEEG----RDEISDFEARISKIRLSKEAREK 287 K + Q E L E+++ ++++L + E+ + E+ + EARI ++ E+ Sbjct: 720 EIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEE 779 Query: 288 ALSEL 292 AL++L Sbjct: 780 ALNDL 784 Score = 29.3 bits (66), Expect = 3.7 Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 3/68 (4%) Query: 227 EKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEARE 286 E R+R ++ T + YL ++++ +Q++ + +++I E I + KE E Sbjct: 811 EARLREIEQKLNRLTLEKEYLEKEIQELQEQRI---DLKEQIKSIEKEIENLNGKKEELE 867 Query: 287 KALSELQK 294 + L EL+ Sbjct: 868 EELEELEA 875 Score = 28.5 bits (64), Expect = 6.7 Identities = 24/102 (23%), Positives = 44/102 (43%), Gaps = 5/102 (4%) Query: 201 LEAVSVK-ERLEMLLVFMESEISVLQVEKRIRSRVKR-QMEKTQREYYLHEQMKAIQKEL 258 LE V ERL++++ ++ L+ E+ R + EK + E Y +K + Sbjct: 179 LEEVEENIERLDLIIDEKRQQLERLRREREKAERYQALLKEKREYEGYEL--LKEKEALE 236 Query: 259 DNGEEGRDEISDFEARISKIRLSKEAREKALSEL-QKLRQMN 299 E +++ E + K+ EK L E+ Q L ++N Sbjct: 237 RQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELN 278 >gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional. Length = 259 Score = 31.2 bits (71), Expect = 1.2 Identities = 30/117 (25%), Positives = 54/117 (46%), Gaps = 20/117 (17%) Query: 333 AIRILDQDHFGLEK-VKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATG 391 A++ ++ F ++ ++ L + +N+ ++L +GP GVGKT L A A G Sbjct: 70 AVKTFEEYDFTFATGAPQKQLQSLRSLSFIERNENIVL--LGPSGVGKTHL----AIALG 123 Query: 392 RQYVRMSLGGVY-DEADI-----RGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEI 442 + VR + + AD+ R+ GR +L+R + LL++DEI Sbjct: 124 YEAVRAGIKVRFTTAADLLLQLSTAQRQ-------GRYKTTLQRGVMAPRLLIIDEI 173 >gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional. Length = 585 Score = 30.9 bits (70), Expect = 1.2 Identities = 13/19 (68%), Positives = 15/19 (78%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F GP GVGKTS A+ +AKA Sbjct: 43 FTGPRGVGKTSTARILAKA 61 >gnl|CDD|181797 PRK09358, PRK09358, adenosine deaminase; Provisional. Length = 340 Score = 30.9 bits (71), Expect = 1.2 Identities = 10/35 (28%), Positives = 14/35 (40%) Query: 540 ISDGVLLDIIRLFTHEAGVRSFERALMKIARKAVT 574 IS ++L +R F EA R E + V Sbjct: 134 ISVRLILCFMRHFGEEAAARELEALAARYRDDGVV 168 >gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional. Length = 895 Score = 31.0 bits (70), Expect = 1.4 Identities = 40/205 (19%), Positives = 72/205 (35%), Gaps = 16/205 (7%) Query: 163 KKISPEVIGITSQIEGFSKLADVI---AANLS----IKVAERQKILEAVSVKERLEMLLV 215 KKI E++ I S + KL DVI A +S ++ + LE ++K+++ Sbjct: 152 KKILDEILEINSLERNYDKLKDVIDMLRAEISNIDYLEEKLKSSNLELENIKKQIADD-- 209 Query: 216 FMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARI 275 E S+ E S L + + D EI E+ + Sbjct: 210 --EKSHSITLKEIERLSIEYNNAMD--DYNNLKSALNELSSLEDMKNRYESEIKTAESDL 265 Query: 276 SKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLLGVPWDKKSKTKKNLDFAIR 335 S L K K L E +P+ + + +Y + + K + N+D I Sbjct: 266 SME-LEKNNYYKELEERHMKIINDPVYKNRNYINDY--FKYKNDIENKKQILSNIDAEIN 322 Query: 336 ILDQDHFGLEKVKERIIEYLAVQMR 360 L +++ +Y+ + R Sbjct: 323 KYHAIIKKLSVLQKDYNDYIKKKSR 347 >gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional. Length = 576 Score = 30.9 bits (70), Expect = 1.4 Identities = 12/19 (63%), Positives = 14/19 (73%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F G GVGKTS A+ +AKA Sbjct: 43 FTGARGVGKTSTARILAKA 61 >gnl|CDD|128712 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391 Score = 30.8 bits (70), Expect = 1.4 Identities = 32/131 (24%), Positives = 60/131 (45%), Gaps = 22/131 (16%) Query: 193 KVAERQKILEAVSVKERLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMK 252 K+ E+ K L+ + + +LL M S++ +++++S+ +R EK L ++K Sbjct: 281 KLQEKIKALKYQLKRLKKMILLFEMISDL-----KRKLKSKFERDNEK------LDAEVK 329 Query: 253 AIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYL 312 +KE E+ + +I E RI K+ + +E+ N A + NY+ Sbjct: 330 EKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEE-----------NKTVALGTSKINYI 378 Query: 313 DWLLGVPWDKK 323 D + V W KK Sbjct: 379 DPRITVAWCKK 389 >gnl|CDD|179009 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed. Length = 782 Score = 30.9 bits (71), Expect = 1.5 Identities = 23/122 (18%), Positives = 49/122 (40%), Gaps = 19/122 (15%) Query: 181 KLADVIAANLSIKVAERQKILEAVSVKERLEMLLVFMESEISVLQVEKRIRSRVKRQMEK 240 KL ++IA+ ++ QK EA ++ + E +++ ++ + EK Sbjct: 517 KLNELIASLEELERELEQKAEEAEALLKEAE-----------------KLKEELEEKKEK 559 Query: 241 TQREYY--LHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQM 298 Q E L E K Q+ + ++ DEI ++ K + + + ++L + Sbjct: 560 LQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKA 619 Query: 299 NP 300 N Sbjct: 620 NE 621 >gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional. Length = 857 Score = 30.6 bits (69), Expect = 1.6 Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 11/98 (11%) Query: 371 FVGPPGVGKTSLAQSIAK---ATGRQYVRMSLGGVYDEADIR---GHRRTYIGSMPGRII 424 F+GP GVGKT L +++A + VR+ + ++ + G Y+G G + Sbjct: 603 FLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYL 662 Query: 425 QSLKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLD 462 R +R ++LLDE++K D+ LL+VLD Sbjct: 663 TEAVR-RRPYSVILLDEVEKAHPDVFN----ILLQVLD 695 >gnl|CDD|184726 PRK14527, PRK14527, adenylate kinase; Provisional. Length = 191 Score = 30.5 bits (69), Expect = 2.0 Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 4/52 (7%) Query: 359 MRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRG 410 M KNK +I F+GPPG GK + A+ +A+ ++S G + + RG Sbjct: 1 MTQTKNKVVI--FLGPPGAGKGTQAERLAQE--LGLKKLSTGDILRDHVARG 48 >gnl|CDD|131325 TIGR02272, gentisate_1_2, gentisate 1,2-dioxygenase. This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases are excluded by a relatively high trusted cutoff score because they are too closely related to known examples of 1-hydroxy-2-naphthoate dioxygenase. Therefore some homologs may be bona fide gentisate 1,2-dioxygenases even if they score below the given cutoffs. Length = 335 Score = 30.1 bits (68), Expect = 2.1 Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 14/88 (15%) Query: 79 NPIASSVYRIGTIVDIVQIL---------RLPDGTVKILVEGSVRARIVEYIEREDFLEA 129 NP A+ Y + TI +Q+L R D TV +VEG + RI + F + Sbjct: 239 NP-ATGGYPMPTIGAFIQLLPKGFRTATYRSTDATVFCVVEGRGQVRIGD----AVFRFS 293 Query: 130 ITQVLPDPTEDPVELEALSRSVIAEFSN 157 V P+ PV EA +V+ FS+ Sbjct: 294 PKDVFVVPSWHPVRFEASDDAVLFSFSD 321 >gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional. Length = 180 Score = 30.2 bits (69), Expect = 2.1 Identities = 11/23 (47%), Positives = 18/23 (78%) Query: 373 GPPGVGKTSLAQSIAKATGRQYV 395 GPPG GKT++A+ +A+ G ++V Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHV 29 >gnl|CDD|181809 PRK09376, rho, transcription termination factor Rho; Provisional. Length = 416 Score = 30.1 bits (69), Expect = 2.1 Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 3/29 (10%) Query: 366 GLILCFVGPPGVGKTSLAQSIAKATGRQY 394 GLI V PP GKT L Q+IA + + Sbjct: 172 GLI---VAPPKAGKTVLLQNIANSITTNH 197 >gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional. Length = 504 Score = 30.2 bits (68), Expect = 2.1 Identities = 21/49 (42%), Positives = 26/49 (53%), Gaps = 5/49 (10%) Query: 343 GLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATG 391 G E VKE ++ L Q R+ G F GP GVGKT+ A+ IA A Sbjct: 18 GQEHVKEVLLAALR-QGRL----GHAYLFSGPRGVGKTTTARLIAMAVN 61 >gnl|CDD|178435 PLN02842, PLN02842, nucleotide kinase. Length = 505 Score = 30.2 bits (68), Expect = 2.5 Identities = 16/33 (48%), Positives = 25/33 (75%), Gaps = 4/33 (12%) Query: 85 VYRIGTIVDIVQILRLP---DGT-VKILVEGSV 113 VYRIGT++++V++L L DG VK+ V+GS+ Sbjct: 277 VYRIGTLMELVRVLALSFADDGKRVKVCVQGSM 309 >gnl|CDD|177370 PHA02530, pseT, polynucleotide kinase; Provisional. Length = 300 Score = 30.0 bits (68), Expect = 2.5 Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 6/41 (14%) Query: 368 ILCFVGPPGVGKTSLAQSIAKATG------RQYVRMSLGGV 402 I+ VG PG GK++ A+ A R +R SL G Sbjct: 4 IILTVGVPGSGKSTWAREFAAKNPKAVNVNRDDLRQSLFGH 44 >gnl|CDD|169983 PRK09579, PRK09579, multidrug efflux protein; Reviewed. Length = 1017 Score = 29.8 bits (67), Expect = 2.8 Identities = 25/65 (38%), Positives = 31/65 (47%), Gaps = 14/65 (21%) Query: 679 NIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEK 738 NIH H+ EG +P D A + A I +PV V+MT +TL PIG L Sbjct: 408 NIHRHIEEGKSPFD---AALEGAREI-----AMPV---VSMT--ITLAAVYAPIGFL-TG 453 Query: 739 LLAAL 743 L AL Sbjct: 454 LTGAL 458 >gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB; Provisional. Length = 225 Score = 29.8 bits (68), Expect = 2.9 Identities = 10/30 (33%), Positives = 15/30 (50%) Query: 364 NKGLILCFVGPPGVGKTSLAQSIAKATGRQ 393 +G I GPPG GKT++ +A + Sbjct: 21 ERGTITQIYGPPGSGKTNICLQLAVEAAKN 50 >gnl|CDD|185327 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator FhlA; Provisional. Length = 686 Score = 29.8 bits (67), Expect = 3.0 Identities = 34/104 (32%), Positives = 49/104 (47%), Gaps = 21/104 (20%) Query: 367 LILCFVGPPGVGKTSLAQSIAKATGRQYVRM------SLGGVYDEADIRGHRRTYIGSMP 420 LIL G G GK +A++I +GR RM ++ E+D+ GH R G+ Sbjct: 403 LIL---GETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHER---GAFT 456 Query: 421 GRIIQSLKR---AKRSNPLLLLDEIDKMGSDLRGDPSAALLEVL 461 G Q + R A +S+ L LDE+ M +L+ LL VL Sbjct: 457 GASAQRIGRFELADKSS--LFLDEVGDMPLELQ----PKLLRVL 494 >gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional. Length = 412 Score = 29.7 bits (68), Expect = 3.1 Identities = 10/17 (58%), Positives = 14/17 (82%) Query: 372 VGPPGVGKTSLAQSIAK 388 +GP G GKT LAQ++A+ Sbjct: 114 IGPTGSGKTLLAQTLAR 130 >gnl|CDD|183622 PRK12608, PRK12608, transcription termination factor Rho; Provisional. Length = 380 Score = 29.7 bits (67), Expect = 3.1 Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 3/30 (10%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQY 394 +GLI V PP GKT L Q IA A + Sbjct: 135 RGLI---VAPPRAGKTVLLQQIAAAVAANH 161 >gnl|CDD|184913 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional. Length = 944 Score = 29.7 bits (67), Expect = 3.1 Identities = 12/18 (66%), Positives = 13/18 (72%) Query: 371 FVGPPGVGKTSLAQSIAK 388 F G GVGKTSLA+ AK Sbjct: 43 FTGTRGVGKTSLARLFAK 60 >gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional. Length = 205 Score = 29.7 bits (68), Expect = 3.2 Identities = 8/23 (34%), Positives = 15/23 (65%) Query: 362 IKNKGLILCFVGPPGVGKTSLAQ 384 + +GL++ GP G GK++L + Sbjct: 1 MMRRGLLIVLSGPSGAGKSTLVK 23 >gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional. Length = 172 Score = 29.7 bits (67), Expect = 3.2 Identities = 12/25 (48%), Positives = 16/25 (64%) Query: 373 GPPGVGKTSLAQSIAKATGRQYVRM 397 G G GKT+LA ++A TG Q V + Sbjct: 22 GRSGSGKTTLAGALAARTGFQLVHL 46 >gnl|CDD|180345 PRK05995, PRK05995, enoyl-CoA hydratase; Provisional. Length = 262 Score = 29.5 bits (67), Expect = 3.2 Identities = 12/27 (44%), Positives = 19/27 (70%) Query: 268 ISDFEARISKIRLSKEAREKALSELQK 294 I+D +RI+ IR ++EARE + L+K Sbjct: 228 IADTASRIALIRATEEAREGVAAFLEK 254 >gnl|CDD|178078 PLN02459, PLN02459, probable adenylate kinase. Length = 261 Score = 29.8 bits (67), Expect = 3.3 Identities = 11/29 (37%), Positives = 17/29 (58%) Query: 363 KNKGLILCFVGPPGVGKTSLAQSIAKATG 391 K + + F+G PGVGK + A ++K G Sbjct: 26 KGRNVNWVFLGCPGVGKGTYASRLSKLLG 54 >gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed. Length = 668 Score = 29.7 bits (68), Expect = 3.3 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 372 VGPPGVGKTSLAQSIAKATGR 392 VG G GKT+L ++I TG Sbjct: 1 VGHSGAGKTTLTEAILFYTGA 21 >gnl|CDD|184937 PRK14974, PRK14974, cell division protein FtsY; Provisional. Length = 336 Score = 29.6 bits (67), Expect = 3.3 Identities = 36/170 (21%), Positives = 73/170 (42%), Gaps = 29/170 (17%) Query: 228 KRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREK 287 + +V+ ++E+ + E + + +++ EE + E F + + ++ E Sbjct: 10 SKFVEKVEEKIEEEEEEEAPEAEEEEEEED----EEEKKEKPGFFDKAKITEIKEKDIED 65 Query: 288 ALSELQKLRQMNPLSA--ESSVVRNYLDWLLGVPWDKKSKTKKNLDFAIRILDQDHFGLE 345 L EL+ + L + V L+ L KK K ++++ ++ Sbjct: 66 LLEELE----LELLESDVALEVAEEILESLKEKLVGKKVKRGEDVEEIVK---------N 112 Query: 346 KVKERIIEYLAV--QMRVI-----KNKGLILCFVGPPGVGKTSLAQSIAK 388 +KE ++E L+V +I K K +++ FVG G GKT+ +IAK Sbjct: 113 ALKEALLEVLSVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTT---TIAK 159 >gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau; Validated. Length = 563 Score = 29.7 bits (67), Expect = 3.4 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F GP GVGKTS A++ A+ Sbjct: 43 FSGPRGVGKTSSARAFARC 61 >gnl|CDD|162777 TIGR02237, recomb_radB, DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236). Length = 209 Score = 29.7 bits (67), Expect = 3.5 Identities = 12/29 (41%), Positives = 16/29 (55%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQ 393 +G I GPPG GKT++ +A RQ Sbjct: 11 RGTITQIYGPPGSGKTNICMILAVNAARQ 39 >gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional. Length = 614 Score = 29.4 bits (66), Expect = 3.6 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F GP GVGKT+ A+ AK Sbjct: 44 FCGPRGVGKTTCARIFAKT 62 >gnl|CDD|162744 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017. Length = 171 Score = 29.3 bits (66), Expect = 3.9 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 17/79 (21%) Query: 367 LILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQS 426 +I+ GPPG GKT++A+ +A+ + + S G ++ R M +I+ Sbjct: 1 MIITISGPPGSGKTTVAKILAEKLSLKLI--SAGDIF---------RELAAKMGLDLIEF 49 Query: 427 LKRAKRSNPLLLLDEIDKM 445 L A+ + EIDK Sbjct: 50 LNYAEENP------EIDKK 62 >gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional. Length = 174 Score = 29.5 bits (67), Expect = 3.9 Identities = 31/106 (29%), Positives = 45/106 (42%), Gaps = 37/106 (34%) Query: 373 GPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIR--GHR-----------------R 413 GPPGVGKT+L IA+ + + +GG Y E ++R G R R Sbjct: 7 GPPGVGKTTLVLKIAELLKEEGYK--VGGFYTE-EVREGGKRIGFKIIDLDTGEEGILAR 63 Query: 414 TYIGSMPGRI--------------IQSLKRAKRSNPLLLLDEIDKM 445 S P R+ I +L+RA ++++DEI KM Sbjct: 64 VGFPSRP-RVGKYVVNLEDLERIGIPALERALEEADVIIIDEIGKM 108 >gnl|CDD|149480 pfam08433, KTI12, Chromatin associated protein KTI12. This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II. The Elongator complex has histone acetyltransferase activity. Length = 266 Score = 29.2 bits (66), Expect = 4.1 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 16/82 (19%) Query: 367 LILCFVGPPGVGKTSLAQSIAK---ATGRQYVRMSLGGVYDEADIRGHRRTYIGS----- 418 +IL G P GK++ A+ +AK G + V + + Y S Sbjct: 2 IILT--GLPSSGKSTRAKELAKYLEEKGYDVI------VISDESLGIESDDYKDSKKEKF 53 Query: 419 MPGRIIQSLKRAKRSNPLLLLD 440 + G + ++KR N ++++D Sbjct: 54 LRGSLRSAVKRDLSKNTIVIVD 75 >gnl|CDD|162243 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA. This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c. Length = 198 Score = 29.3 bits (66), Expect = 4.2 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 6/62 (9%) Query: 364 NKGLILCFVGPPGVGKTSLAQSIA----KATGRQYVRMSLGGVYDEADIRGHRRTYIGSM 419 N G L GP G+GKT+L + +A +G VR + + ++ D Y+G + Sbjct: 24 NAGEALQVTGPNGIGKTTLLRILAGLLRPDSGE--VRWNGTALAEQRDEPHRNILYLGHL 81 Query: 420 PG 421 PG Sbjct: 82 PG 83 >gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional. Length = 459 Score = 29.3 bits (65), Expect = 4.4 Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 15/109 (13%) Query: 347 VKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAK-ATGR---QYVRM-SLGG 401 + E IE + ++ + KN + GPPGVGKT +A+ +A TG Q V M Sbjct: 179 IPETTIETILKRLTIKKN----IILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQ 234 Query: 402 VYDEAD-IRGHRRTYIG-----SMPGRIIQSLKRAKRSNPLLLLDEIDK 444 Y D I+G+R +G + Q K + ++DEI++ Sbjct: 235 SYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINR 283 >gnl|CDD|178179 PLN02566, PLN02566, amine oxidase (copper-containing). Length = 646 Score = 29.1 bits (65), Expect = 4.7 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 20/97 (20%) Query: 455 AALLEVLDP------------AQNSSFVD------HYLEV-EYDLSDVMFIMTANTLNIP 495 A+L LDP Q S + H+L++ E + DV+ +++N N Sbjct: 18 ASLYHPLDPLNPQEINKIRLIVQKSHLGNLPNLTFHFLDLEEPEKRDVLKWLSSNPSNKS 77 Query: 496 LPLMDRMEIIRIAGYTEEEKLQIAKNHLV-KKVLTEH 531 P ++R G T E + +A + +V T H Sbjct: 78 PPPRRAKVVVRAGGETYELIVDLATGSITSSRVYTGH 114 >gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed. Length = 307 Score = 28.9 bits (66), Expect = 4.8 Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 16/49 (32%) Query: 368 ILCFVGPPGVGKTSLAQSIAKATG--------RQYVRMSLGGVYDEADI 408 ++ VGP GKT+LA +AK Q VY DI Sbjct: 6 VIVIVGPTASGKTALAIELAKRLNGEIISADSMQ--------VYRGMDI 46 >gnl|CDD|183675 PRK12678, PRK12678, transcription termination factor Rho; Provisional. Length = 672 Score = 29.1 bits (66), Expect = 4.8 Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 3/24 (12%) Query: 366 GLILCFVGPPGVGKTSLAQSIAKA 389 GLI V PP GKT++ Q+IA A Sbjct: 419 GLI---VSPPKAGKTTILQNIANA 439 >gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. Length = 852 Score = 29.2 bits (66), Expect = 5.0 Identities = 11/17 (64%), Positives = 15/17 (88%) Query: 371 FVGPPGVGKTSLAQSIA 387 F+GP GVGKT LA+++A Sbjct: 600 FLGPTGVGKTELAKALA 616 >gnl|CDD|162135 TIGR00963, secA, preprotein translocase, SecA subunit. The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus. Length = 745 Score = 28.8 bits (65), Expect = 5.4 Identities = 27/122 (22%), Positives = 50/122 (40%), Gaps = 12/122 (9%) Query: 195 AERQKILEAVSVKER-LEMLLVFMESEISVLQVEKRIRSRVKRQ--MEKTQREYYLHEQM 251 AER++ILE+ + E L+ML ++ + E++ + +EK + + L Sbjct: 587 AERRRILESEDLSELILQMLESTLDEIVDAYINEQKPSEEWDLEGLIEKLKTLFLLDG-- 644 Query: 252 KAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNY 311 + E E E + KIR + + +E L E ++ M E V+ Sbjct: 645 -DLTPEDL---ENLTSEDLKELLLEKIRAAYDEKEAEL-ESERPGLMR--EFERYVLLQS 697 Query: 312 LD 313 +D Sbjct: 698 ID 699 >gnl|CDD|180504 PRK06277, PRK06277, hydrogenase subunit F; Validated. Length = 478 Score = 28.8 bits (65), Expect = 5.7 Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 5/32 (15%) Query: 29 PLLPLRDIVVFPY---MIVPLFVGREKSVRAL 57 LLPL +VVFP +I L G++K ++ L Sbjct: 2 NLLPL--MVVFPMICAIIFNLLHGKDKLIKYL 31 >gnl|CDD|148114 pfam06309, Torsin, Torsin. This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterized by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of (pfam00004) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia. Length = 127 Score = 28.9 bits (65), Expect = 5.8 Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 5/41 (12%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQ-----YVRMSLG 400 K L+L F G G GK +A+ IA R YV + Sbjct: 52 KPLVLSFHGWTGTGKNFVAEIIADNLYRDGLRSPYVHHFVA 92 >gnl|CDD|163043 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation. Length = 270 Score = 28.8 bits (65), Expect = 5.8 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 10/83 (12%) Query: 321 DKKSKTKKNL-DFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGK 379 + K KT KN+ IRI + ++++ YL RV LI + PP GK Sbjct: 74 NGKVKTIKNVSSLNIRIARE----KLGAADKLLPYLVRNNRV--LNTLI---ISPPQCGK 124 Query: 380 TSLAQSIAKATGRQYVRMSLGGV 402 T+L + +A+ ++ L G Sbjct: 125 TTLLRDLARILSTGISQLGLRGK 147 >gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated. Length = 605 Score = 28.7 bits (64), Expect = 5.8 Identities = 12/19 (63%), Positives = 15/19 (78%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F GP G+GKTS+A+ AKA Sbjct: 43 FSGPRGIGKTSIAKIFAKA 61 >gnl|CDD|163553 TIGR03841, F420_Rv3093c, probable F420-dependent oxidoreductase, Rv3093c family. This model describes a small family of enzymes in the bacterial luciferase-like monooxygenase family, which includes F420-dependent enzymes such as N5,N10-methylenetetrahydromethanopterin reductase as well as FMN-dependent enzymes. All members of this family are from species that produce coenzyme F420; SIMBAL analysis suggests that members of this family bind F420 rather than FMN. Length = 301 Score = 28.6 bits (64), Expect = 6.1 Identities = 8/41 (19%), Positives = 17/41 (41%) Query: 387 AKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSL 427 A G + + G V A RR + ++P ++ ++ Sbjct: 231 APGYGEMFAWLGFGEVLRLARAAADRRELLAAVPDEVVDAV 271 >gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional. Length = 319 Score = 28.5 bits (64), Expect = 6.4 Identities = 32/107 (29%), Positives = 46/107 (42%), Gaps = 32/107 (29%) Query: 357 VQMRVIKNKG----LILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEA------ 406 +++VI G LIL GPPG GKT+ ++A LG Y EA Sbjct: 23 SRLQVIARDGNMPNLILS--GPPGTGKTTSILALA--------HELLGPNYKEAVLELNA 72 Query: 407 -DIRGHRRTYIGSMPGRIIQSLKRAKRSNP-----LLLLDEIDKMGS 447 D RG I + + I+ + K + P +++LDE D M S Sbjct: 73 SDDRG-----IDVVRNK-IKMFAQKKVTLPPGRHKIVILDEADSMTS 113 >gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 309 Score = 28.6 bits (64), Expect = 6.9 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 5/64 (7%) Query: 238 MEKTQR--EYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKL 295 +E T++ E Y E IQK N E+ E + E + + +E R L + ++ Sbjct: 115 LENTKKKIETYQKENKDVIQK---NKEKSTREQEELEEALEFEKEEEEQRRLLLQKEEEE 171 Query: 296 RQMN 299 +QMN Sbjct: 172 QQMN 175 >gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional. Length = 484 Score = 28.4 bits (63), Expect = 7.1 Identities = 11/18 (61%), Positives = 15/18 (83%) Query: 371 FVGPPGVGKTSLAQSIAK 388 F GP GVGKT++A+ +AK Sbjct: 45 FFGPRGVGKTTIARILAK 62 >gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed. Length = 449 Score = 28.5 bits (65), Expect = 7.2 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 6/60 (10%) Query: 329 NLDFA---IRILDQDHF--GLEKVKERIIEYLA-VQMRVIKNKGLILCFVGPPGVGKTSL 382 +DF I L + LE++ + LA + I +GL + G P VGK+SL Sbjct: 172 AIDFPEEDIEFLSDEKILEKLEELIAELEALLASARQGEILREGLKVVIAGRPNVGKSSL 231 >gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho. Members of this family differ in the specificity of RNA binding. Length = 415 Score = 28.5 bits (64), Expect = 7.2 Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 3/30 (10%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQY 394 +GLI V PP GKT L Q IA+A R + Sbjct: 170 RGLI---VAPPKAGKTVLLQKIAQAITRNH 196 >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 = 28.3 bits (64), Expect = 7.3 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 21/83 (25%) Query: 369 LCFVGPPGVGKTSLAQSI---AKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQ 425 L G G GK+ L Q+ A+ G+ + + L + +++ Sbjct: 41 LYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAE--------------LAQADPEVLE 86 Query: 426 SLKRAKRSNPLLLLDEIDKMGSD 448 L++A L+ LD+++ + Sbjct: 87 GLEQA----DLVCLDDVEAIAGQ 105 >gnl|CDD|162313 TIGR01351, adk, adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason. Length = 210 Score = 28.3 bits (64), Expect = 7.6 Identities = 10/25 (40%), Positives = 16/25 (64%) Query: 371 FVGPPGVGKTSLAQSIAKATGRQYV 395 +GPPG GK + A+ IA+ G ++ Sbjct: 4 LLGPPGSGKGTQAKRIAEKYGLPHI 28 >gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau; Provisional. Length = 527 Score = 28.2 bits (63), Expect = 8.1 Identities = 11/19 (57%), Positives = 15/19 (78%) Query: 371 FVGPPGVGKTSLAQSIAKA 389 F G GVGKT+LA+ +AK+ Sbjct: 43 FTGTRGVGKTTLARILAKS 61 >gnl|CDD|162618 TIGR01947, rnfG, electron transport complex, RnfABCDGE type, G subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit. Length = 186 Score = 28.5 bits (64), Expect = 8.3 Identities = 18/88 (20%), Positives = 26/88 (29%), Gaps = 7/88 (7%) Query: 107 ILVEGSVRARIVEYIEREDFLEAITQVLP------DPTEDPVELEALSRSVIAEFSNYIK 160 LV + I E E + LEA+ QVLP D E V + Sbjct: 16 ALVNQFTKEVIAE-AEAKQQLEALKQVLPQGLYDNDLLESTVPEVDEDLLGLGTILPVYG 74 Query: 161 LNKKISPEVIGITSQIEGFSKLADVIAA 188 K + G+S ++ Sbjct: 75 AKKGGQVVAYVLEVSAPGYSGPIQLLVG 102 >gnl|CDD|179397 PRK02256, PRK02256, putative aminopeptidase 1; Provisional. Length = 462 Score = 28.3 bits (64), Expect = 8.5 Identities = 10/18 (55%), Positives = 14/18 (77%) Query: 801 SIPLSVEGIVVGKDGRSV 818 +IPL++ G+VV KDG V Sbjct: 138 AIPLALHGVVVKKDGTKV 155 >gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding subunit. This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lactis functionally complements an E.coli proU mutant. The comlementing locus is similar to a opuA locus in B.sutlis. This clarifies the differences in nomenclature. Length = 363 Score = 28.3 bits (63), Expect = 9.3 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 4/57 (7%) Query: 365 KGLILCFVGPPGVGKTSLAQSIAK----ATGRQYVRMSLGGVYDEADIRGHRRTYIG 417 KG I +G G GK++ + + + G+ ++ ++R RR IG Sbjct: 18 KGEIFVIMGLSGSGKSTTVRMLNRLIEPTAGQIFIDGENIMKQSPVELREVRRKKIG 74 >gnl|CDD|178393 PLN02796, PLN02796, D-glycerate 3-kinase. Length = 347 Score = 28.2 bits (63), Expect = 9.5 Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 19/105 (18%) Query: 367 LILCFVGPPGVGKTSLAQSIA---KATGRQYVRMSLGGVY----DEADI----------- 408 L++ P G GKT+L ++ ATGR+ +S+ Y D+A + Sbjct: 101 LVIGISAPQGCGKTTLVFALVYLFNATGRRAASLSIDDFYLTAADQAKLAEANPGNALLE 160 Query: 409 -RGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEIDKMGSDLRGD 452 RG+ ++ ++ +++L++ + + + DK RGD Sbjct: 161 LRGNAGSHDLALGVETLEALRKLNKEGSKMKVPRYDKSAYGGRGD 205 >gnl|CDD|149775 pfam08822, DUF1804, Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized. Length = 165 Score = 28.1 bits (63), Expect = 9.8 Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 8/92 (8%) Query: 99 RLPDGTVKILVEGSVRARIVEYIEREDFLEAITQVLPDPTEDPVE-LEALSRSVIAEFSN 157 L G ++ L + +V+Y D L+ + P D + L +L+ S FS Sbjct: 58 TLAGGGIEDLARQMLTGFVVQYQATMDELQEDEDL---PPSDKAKLLASLADS----FSK 110 Query: 158 YIKLNKKISPEVIGITSQIEGFSKLADVIAAN 189 + +K++ PE + + +E +LAD + Sbjct: 111 TVAASKRVLPETSKLATALEVLQRLADFVQER 142 >gnl|CDD|150839 pfam10228, DUF2228, Uncharacterized conserved protein (DUF2228). This is a family of conserved proteins of approximately 700 residues found from worms to humans. Length = 253 Score = 28.2 bits (63), Expect = 9.8 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 14/86 (16%) Query: 217 MESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDN-GEEGRDEISDFEARI 275 E +S+ Q K ++ R K+ + KT H+ + +DN + G +S+ +A + Sbjct: 121 KELGLSLEQKTKVMKQRKKKVVTKT-----FHKGG--LVVPVDNKTDVGYRPLSESDANL 173 Query: 276 SKI------RLSKEAREKALSELQKL 295 KI KE R+KA ELQ+L Sbjct: 174 KKILKTIEEAEDKEERDKAFDELQEL 199 >gnl|CDD|172750 PRK14262, PRK14262, phosphate ABC transporter ATP-binding protein; Provisional. Length = 250 Score = 28.0 bits (62), Expect = 9.9 Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 2/32 (6%) Query: 357 VQMRVIKNKGLILCFVGPPGVGKTSLAQSIAK 388 V M++ KN+ I +GP G GKT+L +SI + Sbjct: 22 VTMKIFKNQ--ITAIIGPSGCGKTTLLRSINR 51 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 0.317 0.136 0.374 Gapped Lambda K H 0.267 0.0636 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 13,534,825 Number of extensions: 936636 Number of successful extensions: 2852 Number of sequences better than 10.0: 1 Number of HSP's gapped: 2811 Number of HSP's successfully gapped: 226 Length of query: 820 Length of database: 5,994,473 Length adjustment: 101 Effective length of query: 719 Effective length of database: 3,812,065 Effective search space: 2740874735 Effective search space used: 2740874735 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 (21.7 bits) S2: 61 (27.5 bits)