RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780552|ref|YP_003064965.1| Holliday junction DNA helicase RuvB [Candidatus Liberibacter asiaticus str. psy62] (334 letters) >gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed. Length = 328 Score = 549 bits (1417), Expect = e-157 Identities = 201/322 (62%), Positives = 255/322 (79%), Gaps = 1/322 (0%) Query: 9 SRNVSQEDADISL-LRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGK 67 + +E+ +I LRP++L+EF GQ + NLK+FIEAAK R EALDHVL GPPGLGK Sbjct: 5 PETLEEEEDEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGK 64 Query: 68 TTLAQVVARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRLSIIVEEILYP 127 TTLA ++A E+GVN R TSGP + K GDLAA+LTNLE+ DVLFIDEIHRLS +VEEILYP Sbjct: 65 TTLANIIANEMGVNIRITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYP 124 Query: 128 AMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIRLNFYEIED 187 AMEDF+LD+M+G+GP+ARS++++L FTLI ATTR GLLT+PL+DRFGI RL FY +E+ Sbjct: 125 AMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEE 184 Query: 188 LKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRLLRRVRDFAEVAHAKTITREIAD 247 L+ IV+R A++ G+ + +E A EIA RSRGTPRIA RLLRRVRDFA+V IT+EIAD Sbjct: 185 LEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIAD 244 Query: 248 AALLRLAIDKMGFDQLDLRYLTMIARNFGGGPVGIETISAGLSEPRDAIEDLIEPYMIQQ 307 AL L +D++G D++D +YL I FGGGPVG++T++A L E RD IED+ EPY+IQQ Sbjct: 245 KALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQ 304 Query: 308 GFIQRTPRGRLLMPIAWQHLGI 329 GFIQRTPRGR+ P A++HLG+ Sbjct: 305 GFIQRTPRGRVATPKAYEHLGL 326 >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 = 427 bits (1099), Expect = e-120 Identities = 183/305 (60%), Positives = 236/305 (77%) Query: 25 RTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRS 84 + L EF GQ + L++FIEAAK R EALDH+L GPPGLGKTTLA ++A E+GVN + Sbjct: 1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKI 60 Query: 85 TSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSA 144 TSGP + K GDLAA+LTNLE+ DVLFIDEIHRLS VEE+LYPAMEDF+LD+++G+GPSA Sbjct: 61 TSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSA 120 Query: 145 RSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIRLNFYEIEDLKTIVQRGAKLTGLAVT 204 RSV+++L FTL+ ATTR G+LT+PL+DRFGI +RL FY +E+L IV R A L + + Sbjct: 121 RSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNVEIE 180 Query: 205 DEAACEIAMRSRGTPRIAGRLLRRVRDFAEVAHAKTITREIADAALLRLAIDKMGFDQLD 264 EAA EIA RSRGTPRIA RLLRRVRDFA+V K I R+IA AL L ID++G D++D Sbjct: 181 PEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDELGLDEID 240 Query: 265 LRYLTMIARNFGGGPVGIETISAGLSEPRDAIEDLIEPYMIQQGFIQRTPRGRLLMPIAW 324 + L+++ F GGPVG++T++A L E D IED+ EPY++Q GF+QRTPRGR+ +A+ Sbjct: 241 RKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRIATELAY 300 Query: 325 QHLGI 329 +HLG+ Sbjct: 301 EHLGL 305 >gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed. Length = 413 Score = 92.5 bits (231), Expect = 1e-19 Identities = 76/262 (29%), Positives = 114/262 (43%), Gaps = 62/262 (23%) Query: 21 LLRPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARE 77 +RP+TL+E GQ + L+ IEA + L ++ GPPG GKTTLA+++A Sbjct: 5 RMRPKTLDEVVGQEHLLGPGKPLRRMIEAGR-----LSSMILWGPPGTGKTTLARIIAGA 59 Query: 78 LGVNFRSTSGPVIAKAGDL------AALLTNLEDRDVLFIDEIHRLSIIVEEILYPAMED 131 F + S V + DL A + R +LFIDEIHR + ++ L P +ED Sbjct: 60 TDAPFEALSA-VTSGVKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED 118 Query: 132 FQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGI--PI--RLNFYEI-- 185 G TLI ATT NP F + + R +E+ Sbjct: 119 -------G-------------TITLIGATTE-----NPS---FEVNPALLSRAQVFELKP 150 Query: 186 ---EDLKTIVQRGAKLTG---LAVTDEAACEIAMRSRGTPRIAGRLLRRVRDFAEVAHAK 239 ED++ +++R + + + DEA +A + G R A LL + A Sbjct: 151 LSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLL----ELA-ALGVD 205 Query: 240 TITREIADAALLRLAI--DKMG 259 +IT E+ + AL + A DK G Sbjct: 206 SITLELLEEALQKRAARYDKDG 227 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 64.7 bits (158), Expect = 3e-11 Identities = 61/195 (31%), Positives = 84/195 (43%), Gaps = 55/195 (28%) Query: 20 SLLRPRTLEEFTGQVEACSNLKVFIEAAKA---RAEALDHV---LFVGPPGLGKTTLAQV 73 LRPRTLEEF GQ I RA D V + GPPG+GKTTLA++ Sbjct: 20 DRLRPRTLEEFVGQDH--------ILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARI 71 Query: 74 VARELGVNFRSTSGPVIAKAGDLAALLTNLED-------RDVLFIDEIHRLSIIVEEILY 126 +A +F S + V+A DL A + ++ R +LFIDE+HR + ++ L Sbjct: 72 IANHTRAHFSSLNA-VLAGVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALL 130 Query: 127 PAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNP-------LQDRFGIPIR 179 P +E+ + TLI ATT NP L R + R Sbjct: 131 PWVENGTI--------------------TLIGATTE-----NPYFEVNKALVSRSRL-FR 164 Query: 180 LNFYEIEDLKTIVQR 194 L EDL +++R Sbjct: 165 LKSLSDEDLHQLLKR 179 >gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed. Length = 319 Score = 56.0 bits (136), Expect = 1e-08 Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 5/56 (8%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 RPRTL+E GQ E LK +++ + + H+LF GPPG GKTT A +AREL Sbjct: 12 RPRTLDEIVGQEEIVERLKSYVKE-----KNMPHLLFAGPPGTGKTTAALALAREL 62 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 51.5 bits (124), Expect = 3e-07 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 9/61 (14%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEA----AKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 RP+TL + G +A L+ +IE+ +A +L GPPG+GKT+LA +A + Sbjct: 9 RPKTLSDVVGNEKAKEQLREWIESWLKGKPKKA-----LLLYGPPGVGKTSLAHALANDY 63 Query: 79 G 79 G Sbjct: 64 G 64 >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 = 49.6 bits (119), Expect = 1e-06 Identities = 36/139 (25%), Positives = 55/139 (39%), Gaps = 20/139 (14%) Query: 56 HVLFVGPPGLGKTTLAQVVARELG-------VNFRSTS-----GPVIAKAGDLA----AL 99 VL VGPPG GK+ LA+ +A L R T+ G G + L Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGPL 60 Query: 100 LTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAA 159 + + ++ +DEI+R + V L +++ +L L G + RF LIA Sbjct: 61 VRAAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAKRFRLIAT 120 Query: 160 TTRVGLLTN----PLQDRF 174 + N L+ RF Sbjct: 121 MNPLDRGLNELSPALRSRF 139 >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 = 47.5 bits (113), Expect = 5e-06 Identities = 24/58 (41%), Positives = 30/58 (51%), Gaps = 5/58 (8%) Query: 20 SLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARE 77 SLLRPR E GQ A L AK + H++ GPPG+GKTT A++ E Sbjct: 146 SLLRPRAFSEIVGQERAIKAL-----LAKVASPFPQHIILYGPPGVGKTTAARLALEE 198 >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 = 45.7 bits (108), Expect = 2e-05 Identities = 37/115 (32%), Positives = 51/115 (44%), Gaps = 16/115 (13%) Query: 26 TLEEFTGQVEACSNLKVFIEAAKARAEALDH--------VLFVGPPGLGKTTLAQVVARE 77 T E+ G EA ++ +E E +H VL GPPG GKT LA+ VA E Sbjct: 176 TYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE 235 Query: 78 LGVNFRSTSGPVIAKA------GDLAALLTNLEDR--DVLFIDEIHRLSIIVEEI 124 G F S +GP I L + E+ ++FIDEI ++ EE+ Sbjct: 236 AGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEV 290 Score = 42.2 bits (99), Expect = 2e-04 Identities = 20/34 (58%), Positives = 22/34 (64%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVI 90 VL GPPG GKT LA+ VA E G NF + GP I Sbjct: 490 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEI 523 >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 = 45.1 bits (106), Expect = 2e-05 Identities = 37/133 (27%), Positives = 51/133 (38%), Gaps = 27/133 (20%) Query: 56 HVLFVGPPGLGKTTLAQVVARELG--------------------------VNFRSTSGPV 89 +L VGPPG GKTTLA+ +ARELG V + SG Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63 Query: 90 IAKAGDLAALLTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKI 149 + AL DVL +DEI L +E L +E+ +L L++ + + Sbjct: 64 ELRLRLALALA-RKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122 Query: 150 NLSRFTLIAATTR 162 L A R Sbjct: 123 TNDEKDLGPALLR 135 >gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed. Length = 337 Score = 43.8 bits (104), Expect = 6e-05 Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 5/56 (8%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 RP LE+ GQ E L +++ L H+L GPPG GKT + +AREL Sbjct: 10 RPALLEDILGQDEVVERLSRAVDSPN-----LPHLLVQGPPGSGKTAAVRALAREL 60 >gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional. Length = 319 Score = 43.6 bits (103), Expect = 7e-05 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 6/62 (9%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARE-LGVN 81 RP L++ G +A S L+V AR + +++ GPPG GKTT +A E LG N Sbjct: 8 RPTKLDDIVGNEDAVSRLQVI-----ARDGNMPNLILSGPPGTGKTTSILALAHELLGPN 62 Query: 82 FR 83 ++ Sbjct: 63 YK 64 >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 = 43.4 bits (103), Expect = 8e-05 Identities = 21/31 (67%), Positives = 22/31 (70%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSG 87 VL VGPPG GKT LA+ VA E GV F S SG Sbjct: 91 VLLVGPPGTGKTLLAKAVAGEAGVPFFSISG 121 >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 = 43.2 bits (102), Expect = 9e-05 Identities = 54/208 (25%), Positives = 87/208 (41%), Gaps = 44/208 (21%) Query: 56 HVLFVGPPGLGKTTLAQVVAR---ELGVNFRSTSGPVI-AKAGDLAALL---TNLEDRD- 107 H++F G PG GKTT+A+++ + E+ V + G +I + DL T + R+ Sbjct: 44 HMIFKGNPGTGKTTVARILGKLFKEMNV---LSKGHLIEVERADLVGEYIGHTAQKTREV 100 Query: 108 -------VLFIDEIHRLSIIVE--------EILYPAMEDFQLDLMVGEGPSARSVKINLS 152 VLFIDE + L+ E + L MED + + ++ + Sbjct: 101 IKKALGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVL----ILAGYSDEMD 156 Query: 153 RFTLIAATTRVGLLTNP-LQDRFGIPIRLNFYEIEDLKTIVQRGAKLTGLAVTDEAACEI 211 F L NP L+ RF I I Y +E+L I +R K +T+EA ++ Sbjct: 157 YF----------LSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKL 206 Query: 212 AMRSRGTPRIAGRLL---RRVRDFAEVA 236 +++ R R VR+ E A Sbjct: 207 REHLYKVDQLSSREFSNARYVRNIIEKA 234 >gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau; Provisional. Length = 367 Score = 42.6 bits (100), Expect = 2e-04 Identities = 70/252 (27%), Positives = 100/252 (39%), Gaps = 65/252 (25%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82 RP+T ++ GQ + L IE A+AL LF GP G+GKTT A+++AR+ +N Sbjct: 12 RPQTFDDVVGQSHITNTLLNAIENNHL-AQAL---LFCGPRGVGKTTCARILARK--INQ 65 Query: 83 RSTSGPVIAKAGDLAAL----------LTNLEDR----------DVLFIDEIHRLSIIVE 122 P + ++ L + NL D+ + IDE+H LS Sbjct: 66 PGYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSAA- 124 Query: 123 EILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIRLNF 182 F L E P A ++ I ATT + IP L+ Sbjct: 125 ---------FNAFLKTLEEPPAHAI--------FILATTEKHKI---------IPTILSR 158 Query: 183 YEIEDLKTIVQRGAK--LTGLAVT------DEAACEIAMRSRGTPRIAGRLLRRVRDFAE 234 +I D K I + K L G+AV D+A IA ++ G R A + RV F Sbjct: 159 CQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFC- 217 Query: 235 VAHAKTITREIA 246 K ITR+ Sbjct: 218 ---GKNITRQAV 226 >gnl|CDD|179744 PRK04132, PRK04132, replication factor C small subunit; Provisional. Length = 846 Score = 42.5 bits (100), Expect = 2e-04 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 11/63 (17%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGK--TTLAQVVA----R 76 RP+ L++ GQ LK +++ ++ H+LF GPPG+GK T +V+A Sbjct: 14 RPQRLDDIVGQEHIVKRLKHYVKTG-----SMPHLLFAGPPGVGKCLTGDTKVIANGELF 68 Query: 77 ELG 79 E+G Sbjct: 69 EIG 71 >gnl|CDD|184926 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau; Provisional. Length = 472 Score = 42.1 bits (99), Expect = 2e-04 Identities = 66/256 (25%), Positives = 99/256 (38%), Gaps = 53/256 (20%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82 RP+T E GQ K+ I A K + + ++ F GP G GKTT+A+++A+ L Sbjct: 9 RPKTFSEVVGQDHV---KKLIINALKKNSISHAYI-FAGPRGTGKTTVARILAKSLNCEN 64 Query: 83 RSTSGPV----IAKAGDLAALLTNLE-----DRDVLFIDEIHRLS--------------I 119 R P ++ D + +E +R IDEI ++ Sbjct: 65 RKGVEPCNECRACRSIDEGTFMDVIELDAASNRG---IDEIRKIRDAVGYRPMEGKYKVY 121 Query: 120 IVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIR 179 I++E+ E F L E P + V + AT TN + I R Sbjct: 122 IIDEVHMLTKEAFNALLKTLEEPPSHVV--------FVLAT------TNLEKVPPTIISR 167 Query: 180 LNFYE-----IEDLKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRLLRRVRDFAE 234 E E + +Q A+ G+ + EA IA R+ G R A +L +V F+E Sbjct: 168 CQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSE 227 Query: 235 VAHAKTITREIADAAL 250 IT E AL Sbjct: 228 ----GKITLETVHEAL 239 >gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. Length = 413 Score = 42.1 bits (99), Expect = 2e-04 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 14/76 (18%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAG----DLAALLTNL--------- 103 +L +GP G GKT LAQ +AR L V F + +AG D+ +L L Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178 Query: 104 -EDRDVLFIDEIHRLS 118 + +++IDEI ++S Sbjct: 179 KAQKGIIYIDEIDKIS 194 >gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau; Validated. Length = 563 Score = 41.3 bits (97), Expect = 3e-04 Identities = 37/112 (33%), Positives = 51/112 (45%), Gaps = 15/112 (13%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82 RPR GQ LK IE+ K A A +F GP G+GKT+ A+ AR L Sbjct: 11 RPRDFNSLEGQDFVVETLKHSIESNKI-ANAY---IFSGPRGVGKTSSARAFARCLNC-- 64 Query: 83 RSTSGPVIAKAGDLAAL--LTNLEDRDVLFIDEIHRLSI-----IVEEILYP 127 +GP G+ ++ + N DV+ ID S+ I EEI++P Sbjct: 65 --VNGPTPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFP 114 >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 = 40.4 bits (95), Expect = 6e-04 Identities = 26/69 (37%), Positives = 32/69 (46%), Gaps = 3/69 (4%) Query: 22 LRPRTLEE-FTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELG- 79 R + E GQ +A V +E K A VL GPPG GKT LA +++ELG Sbjct: 17 GEARYVSEGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGE 76 Query: 80 -VNFRSTSG 87 F SG Sbjct: 77 DTPFCPISG 85 Score = 29.6 bits (67), Expect = 1.2 Identities = 31/112 (27%), Positives = 46/112 (41%), Gaps = 32/112 (28%) Query: 108 VLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLT 167 VLFIDE+H L I L A+E L+ +I AT R G+ T Sbjct: 278 VLFIDEVHMLDIECFSFLNRALES------------------ELAP-IVILATNR-GICT 317 Query: 168 ---NPLQDRFGIP---------IRLNFYEIEDLKTIVQRGAKLTGLAVTDEA 207 + GIP I Y E++K I++ A+ G+ +++EA Sbjct: 318 IRGTDIISPHGIPLDLLDRLLIITTEPYTREEIKQILEIRAQEEGVEISEEA 369 >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 = 40.2 bits (95), Expect = 8e-04 Identities = 17/28 (60%), Positives = 21/28 (75%) Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFR 83 HVL G PGL KT LA+ +AR LG++FR Sbjct: 1 HVLLEGVPGLAKTLLARTLARSLGLDFR 28 >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 = 39.4 bits (92), Expect = 0.001 Identities = 59/251 (23%), Positives = 86/251 (34%), Gaps = 71/251 (28%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEAL-----DHVLFVGPPGLGKTTLAQVVARE 77 RP++ +E GQ E I+A KA AL HV+ GPPG+GKT A++V E Sbjct: 60 RPKSFDEIIGQEEG-------IKALKA---ALCGPNPQHVIIYGPPGVGKTAAARLVLEE 109 Query: 78 LGVNFRSTSGPVIAKAGDLAALLTNLEDR------------------------------- 106 N S A ++ A ++R Sbjct: 110 AKKNPASPFKEG-AAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKP 168 Query: 107 --------DVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINL------- 151 VLFIDEI L + L +ED ++ L + S N+ Sbjct: 169 GAVTRAHGGVLFIDEIGELHPVQMNKLLKVLEDRKVFL---DSAYYNSENPNIPSHIHDI 225 Query: 152 ------SRFTLIAATTRVGLLTNPLQDRFGIPIRLNFYEIEDLKTIVQRGAKLTGLAVTD 205 + F LI ATTR P + I E++K I + A+ G+ + Sbjct: 226 FQNGLPADFRLIGATTRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEK 285 Query: 206 EAACEIAMRSR 216 A I + Sbjct: 286 HALELIVKYAS 296 >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 = 38.4 bits (89), Expect = 0.003 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 5/50 (10%) Query: 43 FIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAK 92 +E A R +L GP G GK+T +++++ELG+ + S P + Sbjct: 104 VLENAPKRI-----LLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPD 148 >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 = 38.0 bits (89), Expect = 0.004 Identities = 12/24 (50%), Positives = 17/24 (70%) Query: 59 FVGPPGLGKTTLAQVVARELGVNF 82 VGPPG+GKT+L + +A+ L F Sbjct: 352 LVGPPGVGKTSLGKSIAKALNRKF 375 >gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA. Length = 731 Score = 38.1 bits (89), Expect = 0.004 Identities = 14/25 (56%), Positives = 18/25 (72%) Query: 58 LFVGPPGLGKTTLAQVVARELGVNF 82 LF GP G+GKT LA+ +A LGV+ Sbjct: 488 LFTGPTGVGKTELAKQLAEALGVHL 512 Score = 31.6 bits (72), Expect = 0.33 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 20/78 (25%) Query: 58 LFVGPPGLGKTTLAQVVARELGVN-----------FRSTSGPVIAKA---GD----LAAL 99 L VG PG+GKT +A+ +A + + G ++A GD L A+ Sbjct: 207 LLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAV 266 Query: 100 LTNLEDRD--VLFIDEIH 115 ++ +E +LFIDEIH Sbjct: 267 VSEIEKEPNAILFIDEIH 284 >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 = 37.2 bits (87), Expect = 0.007 Identities = 27/96 (28%), Positives = 39/96 (40%), Gaps = 21/96 (21%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFR--------------STSGPVIAKAGDLAA---- 98 LF+GP G+GKT LA+ +A L + R S S + A G + Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65 Query: 99 LLTNLEDRD---VLFIDEIHRLSIIVEEILYPAMED 131 LT R ++ IDEI + V+ L +E Sbjct: 66 QLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEG 101 >gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional. Length = 389 Score = 36.7 bits (86), Expect = 0.008 Identities = 26/66 (39%), Positives = 35/66 (53%), Gaps = 8/66 (12%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKA--GDLAALLTNLED--RD----V 108 VL GPPG GKT LA+ VA E F G + + G+ A L+ L + R+ + Sbjct: 168 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSI 227 Query: 109 LFIDEI 114 +FIDEI Sbjct: 228 IFIDEI 233 >gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed. Length = 644 Score = 36.6 bits (84), Expect = 0.009 Identities = 18/31 (58%), Positives = 21/31 (67%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSG 87 VL VGPPG GKT LA+ +A E V F + SG Sbjct: 188 VLMVGPPGTGKTLLAKAIAGEAKVPFFTISG 218 >gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau; Provisional. Length = 486 Score = 36.7 bits (85), Expect = 0.009 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78 RP+ +E GQ LK ++ + + H +F GP G GKTT+A+++A+ L Sbjct: 11 RPKFFKEVIGQEIVVRILKNAVKLQR-----VSHAYIFAGPRGTGKTTIARILAKVL 62 >gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau; Provisional. Length = 702 Score = 36.2 bits (83), Expect = 0.011 Identities = 40/127 (31%), Positives = 52/127 (40%), Gaps = 36/127 (28%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81 RPR E GQ L +E + L H LF G G+GKTT+A+++A+ L Sbjct: 10 RPRNFNELVGQNHVSRALSSALERGR-----LHHAYLFTGTRGVGKTTIARILAKCLNCE 64 Query: 82 FRSTSGPVIAKAG----------DL----AALLTNLED-RDVL---------------FI 111 TS P A DL AA T +ED R++L I Sbjct: 65 TGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLI 124 Query: 112 DEIHRLS 118 DE+H LS Sbjct: 125 DEVHMLS 131 >gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional. Length = 614 Score = 36.3 bits (84), Expect = 0.012 Identities = 23/54 (42%), Positives = 28/54 (51%), Gaps = 4/54 (7%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAR 76 RP T E GQ + LK I K A A LF GP G+GKTT A++ A+ Sbjct: 12 RPSTFESVVGQEALTTTLKNAIATNKL-AHAY---LFCGPRGVGKTTCARIFAK 61 >gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated. Length = 329 Score = 36.0 bits (84), Expect = 0.014 Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 3/41 (7%) Query: 38 SNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 K FIE E L LF G G GKT L+ +A+EL Sbjct: 170 EKCKNFIENFDKNNENL---LFYGNTGTGKTFLSNCIAKEL 207 >gnl|CDD|180856 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau; Validated. Length = 725 Score = 35.9 bits (83), Expect = 0.015 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 6/57 (10%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78 RP+T ++ GQ LK I++ K + H LF GP G GKT++A++ A L Sbjct: 13 RPKTFDDIVGQDHIVQTLKNIIKSNK-----ISHAYLFSGPRGTGKTSVAKIFANAL 64 >gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. Length = 282 Score = 35.8 bits (83), Expect = 0.015 Identities = 32/142 (22%), Positives = 46/142 (32%), Gaps = 41/142 (28%) Query: 7 LLSRNVSQEDADISLLRPRTLEEFTGQVEAC-SNLKVFIEAAKARAEALDH---VLFVGP 62 LL VS E A L + + L+ + E L+ + VGP Sbjct: 143 LLRAGVSPELARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGP 202 Query: 63 PGLGKTT----LA----------------------------QVVARELGVNFRSTSGPVI 90 G+GKTT LA + A+ LGV + V Sbjct: 203 TGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVK-----VA 257 Query: 91 AKAGDLAALLTNLEDRDVLFID 112 +L L L D+D++ ID Sbjct: 258 RDPKELRKALDRLRDKDLILID 279 >gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed. Length = 175 Score = 35.9 bits (84), Expect = 0.016 Identities = 10/30 (33%), Positives = 21/30 (70%) Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRST 85 +++ +G G GK+T+ +++A+ LG +F T Sbjct: 6 NIVLIGFMGAGKSTIGRLLAKRLGYDFIDT 35 >gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional. Length = 438 Score = 35.5 bits (82), Expect = 0.018 Identities = 27/66 (40%), Positives = 34/66 (51%), Gaps = 8/66 (12%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNF-RSTSGPVIAK-AGDLAALLTNL----EDR--DV 108 V+ GPPG GKT LA+ VA E F R +I K GD L+ L E+ + Sbjct: 220 VILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSI 279 Query: 109 LFIDEI 114 +FIDEI Sbjct: 280 VFIDEI 285 >gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau; Provisional. Length = 546 Score = 35.4 bits (81), Expect = 0.019 Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 7/105 (6%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82 RP++ E GQ A ++L +E K LF G G+GKTTL +++A+ L Sbjct: 11 RPQSFAEVAGQQHALNSLVHALETQKVHHA----YLFTGTRGVGKTTLGRLLAKCLNCKT 66 Query: 83 RSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRLSI-IVEEILY 126 T+ P +A + N D++ ID R + +EIL Sbjct: 67 GVTAEPCNKCENCVA--INNNSFIDLIEIDAASRTGVEETKEILD 109 >gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau; Provisional. Length = 584 Score = 35.6 bits (82), Expect = 0.019 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 6/67 (8%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81 RP T E GQ L ++A + ++H LF GP G GKT+ A+++AR L Sbjct: 8 RPATFAEVVGQEHVTEPLSSALDAGR-----INHAYLFSGPRGCGKTSSARILARSLNCA 62 Query: 82 FRSTSGP 88 T+ P Sbjct: 63 QGPTATP 69 >gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional. Length = 412 Score = 35.1 bits (82), Expect = 0.023 Identities = 29/78 (37%), Positives = 37/78 (47%), Gaps = 26/78 (33%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIA------KAG----DLAALLTNL--- 103 +L +GP G GKT LAQ +AR L V F IA +AG D+ +L L Sbjct: 111 ILLIGPTGSGKTLLAQTLARILDVPF------AIADATTLTEAGYVGEDVENILLKLLQA 164 Query: 104 EDRDV-------LFIDEI 114 D DV ++IDEI Sbjct: 165 ADYDVEKAQRGIVYIDEI 182 >gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau; Validated. Length = 451 Score = 35.1 bits (81), Expect = 0.026 Identities = 24/59 (40%), Positives = 29/59 (49%), Gaps = 10/59 (16%) Query: 23 RPRTLEEFTGQVEACSNLK---VFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 RP+T E GQ + LK F AA A LF G G GKTTLA++ A+ L Sbjct: 12 RPQTFSEILGQDAVVAVLKNALRFNRAAHA-------YLFSGIRGTGKTTLARIFAKAL 63 >gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau; Provisional. Length = 624 Score = 34.7 bits (79), Expect = 0.036 Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 4/66 (6%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82 RP+T E GQ +K + A LF G G+GKTT+A++ A+ L Sbjct: 11 RPQTFAEVAGQ----ETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCET 66 Query: 83 RSTSGP 88 T P Sbjct: 67 APTGEP 72 >gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau; Provisional. Length = 527 Score = 34.3 bits (79), Expect = 0.045 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 12/60 (20%) Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78 RP++ E GQ V A +N + L H LF G G+GKTTLA+++A+ L Sbjct: 11 RPKSFSELVGQEHVVRALTN--------ALEQQRLHHAYLFTGTRGVGKTTLARILAKSL 62 >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 = 34.4 bits (79), Expect = 0.045 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 8/71 (11%) Query: 25 RTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRS 84 R +++ GQ EA +E K A+ +VL +G PG+GK+ LA+ +A EL + Sbjct: 15 RLIDQVIGQEEA-------VEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMA-ELLPDEEL 66 Query: 85 TSGPVIAKAGD 95 V D Sbjct: 67 EDILVYPNPED 77 Score = 28.3 bits (63), Expect = 3.1 Identities = 40/170 (23%), Positives = 67/170 (39%), Gaps = 36/170 (21%) Query: 106 RDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGP--SARSVKINL--SRFTLIAATT 161 + VL+IDEI + + V++ L A++D + + G+ S V+ F L+A+ Sbjct: 218 KGVLYIDEIKTMPLEVQQYLLTALQDKKFPI-TGQSENSSGAMVRTEPVPCDFILVASGN 276 Query: 162 RVGL--LTNPLQDRFGIPIRLNFYEI--------------EDLKTIVQRGAKLTGLA-VT 204 L + L+ R IR YE+ + ++ + Q K + T Sbjct: 277 LDDLEGMHPALRSR----IRGYGYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIPHFT 332 Query: 205 DEAACEI---AMRSRGTP-------RIAGRLLRRVRDFAEVAHAKTITRE 244 +A EI A R G R G L+R D A+ + +T E Sbjct: 333 RDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAE 382 >gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional. Length = 398 Score = 34.0 bits (78), Expect = 0.055 Identities = 14/26 (53%), Positives = 15/26 (57%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNF 82 VL GPPG GKT LA+ VA F Sbjct: 182 VLLYGPPGTGKTMLAKAVAHHTTATF 207 >gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional. Length = 637 Score = 33.8 bits (78), Expect = 0.055 Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 7/55 (12%) Query: 24 PRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 R +++ GQ A ++V +AAK R HV+ +G PG GK+ LA+ +A L Sbjct: 27 ERLIDQVIGQEHA---VEVIKKAAKQRR----HVMMIGSPGTGKSMLAKAMAELL 74 Score = 26.5 bits (59), Expect = 9.6 Identities = 11/24 (45%), Positives = 17/24 (70%) Query: 108 VLFIDEIHRLSIIVEEILYPAMED 131 VLFIDEI+ L + ++ L AM++ Sbjct: 229 VLFIDEINTLDLESQQSLLTAMQE 252 >gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional. Length = 576 Score = 33.9 bits (78), Expect = 0.060 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 RP+T + TGQ L+ I+ + A A LF G G+GKT+ A+++A+ L Sbjct: 11 RPQTFSDLTGQEHVSRTLQNAIDTGRV-AHAF---LFTGARGVGKTSTARILAKAL 62 >gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal. Length = 364 Score = 34.0 bits (78), Expect = 0.063 Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 8/66 (12%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKA--GDLAALLTNL------EDRDV 108 VL GPPG GKT LA+ VA E F G + + G+ A L+ + + + Sbjct: 159 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSI 218 Query: 109 LFIDEI 114 +FIDEI Sbjct: 219 IFIDEI 224 >gnl|CDD|178078 PLN02459, PLN02459, probable adenylate kinase. Length = 261 Score = 33.7 bits (77), Expect = 0.067 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 9/77 (11%) Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPV---IAKAGDLAALLTNLEDRDVLFID 112 + +F+G PG+GK T A +++ LGV +T V I +G L A L + ++ L D Sbjct: 31 NWVFLGCPGVGKGTYASRLSKLLGVPHIATGDLVREEIKSSGPLGAQLKEIVNQGKLVPD 90 Query: 113 EI------HRLSIIVEE 123 EI RL EE Sbjct: 91 EIIFSLLSKRLEAGEEE 107 >gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional. Length = 316 Score = 33.4 bits (77), Expect = 0.074 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 7/83 (8%) Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGP------VIAKAGDLAALLTNLEDRDVLFI 111 L PG GKTT+A+ + E+G +G V + A+ ++ V+ I Sbjct: 47 LHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCRIDFVRNRLTRFASTVSLTGGGKVIII 106 Query: 112 DEIHRLSI-IVEEILYPAMEDFQ 133 DE RL + + L ME + Sbjct: 107 DEFDRLGLADAQRHLRSFMEAYS 129 >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 = 33.3 bits (77), Expect = 0.087 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 12/60 (20%) Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78 RP+T E+ GQ V+ N I+ + + H LF GP G GKT++A++ A+ L Sbjct: 9 RPQTFEDVIGQEHIVQTLKNA---IKNGR-----IAHAYLFSGPRGTGKTSIARIFAKAL 60 >gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional. Length = 602 Score = 32.9 bits (76), Expect = 0.11 Identities = 10/20 (50%), Positives = 13/20 (65%) Query: 57 VLFVGPPGLGKTTLAQVVAR 76 +L G PG GK+T AQ +A Sbjct: 260 ILIAGAPGAGKSTFAQALAE 279 >gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional. Length = 585 Score = 32.9 bits (75), Expect = 0.12 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 4/54 (7%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAR 76 R +T E GQ L+ I + A A LF GP G+GKT+ A+++A+ Sbjct: 11 RSQTFAELVGQEHVVQTLRNAIAEGRV-AHAY---LFTGPRGVGKTSTARILAK 60 >gnl|CDD|184726 PRK14527, PRK14527, adenylate kinase; Provisional. Length = 191 Score = 32.8 bits (75), Expect = 0.13 Identities = 16/29 (55%), Positives = 22/29 (75%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85 V+F+GPPG GK T A+ +A+ELG+ ST Sbjct: 9 VIFLGPPGAGKGTQAERLAQELGLKKLST 37 >gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La; Provisional. Length = 784 Score = 32.6 bits (74), Expect = 0.16 Identities = 12/21 (57%), Positives = 16/21 (76%) Query: 59 FVGPPGLGKTTLAQVVARELG 79 VGPPG+GKT+L Q +A+ G Sbjct: 354 LVGPPGVGKTSLGQSIAKATG 374 >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 = 32.4 bits (74), Expect = 0.16 Identities = 12/24 (50%), Positives = 18/24 (75%) Query: 61 GPPGLGKTTLAQVVARELGVNFRS 84 GPPG GKTT+A+++A +L + S Sbjct: 7 GPPGSGKTTVAKILAEKLSLKLIS 30 >gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional. Length = 266 Score = 32.4 bits (74), Expect = 0.18 Identities = 23/68 (33%), Positives = 29/68 (42%), Gaps = 15/68 (22%) Query: 59 FVGPPGLGKTTLAQVVARELGVNFRSTSGPVI-----AKAGDLAALLTNLEDR------- 106 +G PG GKT L A EL R PV+ GDL LE + Sbjct: 122 LLGQPGSGKTHLLTAAANEL---MRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKV 178 Query: 107 DVLFIDEI 114 +VLFID++ Sbjct: 179 EVLFIDDL 186 >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 = 32.2 bits (74), Expect = 0.20 Identities = 10/24 (41%), Positives = 17/24 (70%) Query: 57 VLFVGPPGLGKTTLAQVVARELGV 80 ++ +GPPG GK T A+ +A + G+ Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYGL 25 >gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional. Length = 180 Score = 32.1 bits (74), Expect = 0.24 Identities = 13/24 (54%), Positives = 19/24 (79%) Query: 61 GPPGLGKTTLAQVVARELGVNFRS 84 GPPG GKTT+A+++A +LG+ S Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30 >gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional. Length = 484 Score = 31.8 bits (72), Expect = 0.25 Identities = 11/21 (52%), Positives = 18/21 (85%) Query: 58 LFVGPPGLGKTTLAQVVAREL 78 +F GP G+GKTT+A+++A+ L Sbjct: 44 IFFGPRGVGKTTIARILAKRL 64 >gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional. Length = 184 Score = 31.6 bits (72), Expect = 0.26 Identities = 14/29 (48%), Positives = 19/29 (65%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85 ++F+GPPG GK T A V+A L + ST Sbjct: 4 LIFLGPPGAGKGTQAVVLAEHLHIPHIST 32 >gnl|CDD|181180 PRK07952, PRK07952, DNA replication protein DnaC; Validated. Length = 244 Score = 31.7 bits (72), Expect = 0.27 Identities = 27/101 (26%), Positives = 41/101 (40%), Gaps = 23/101 (22%) Query: 33 QVEACSNLKVFIEAAKARAEALDH----VLFVGPPGLGKTTLAQVVARELGVNFRSTSGP 88 +VE + + A+ E D +F G PG GK LA + EL + +S Sbjct: 75 RVECEGQMNA-LSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSV--- 130 Query: 89 VIAKAGDLAA---------------LLTNLEDRDVLFIDEI 114 +I D+ + LL +L + D+L IDEI Sbjct: 131 LIITVADIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEI 171 >gnl|CDD|183438 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional. Length = 700 Score = 31.4 bits (71), Expect = 0.31 Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 6/71 (8%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81 RPR GQ L +E + L H LF G G+GKTTL++++A+ L Sbjct: 11 RPRDFTTLVGQEHVVRALTHALEQQR-----LHHAYLFTGTRGVGKTTLSRILAKSLNCT 65 Query: 82 FRSTSGPVIAK 92 G + A+ Sbjct: 66 GADGEGGITAQ 76 >gnl|CDD|184915 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional. Length = 618 Score = 31.6 bits (72), Expect = 0.31 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 12/60 (20%) Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78 RPR+ E GQ V+A +N + L H LF G G+GKTT+++++A+ L Sbjct: 11 RPRSFSEMVGQEHVVQALTNALT--------QQRLHHAYLFTGTRGVGKTTVSRILAKSL 62 >gnl|CDD|150510 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function. Length = 348 Score = 31.4 bits (72), Expect = 0.33 Identities = 25/90 (27%), Positives = 33/90 (36%), Gaps = 28/90 (31%) Query: 56 HVLFV-GPPGLGKTTLA-------QVVARELGVNFRSTSGPVIAK-----AGDL------ 96 V V G PG GKT +A F S + P++ AGDL Sbjct: 2 AVFLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVRKKK 61 Query: 97 -----AALLTNLEDR----DVLFIDEIHRL 117 + + NL DV+ +DE HRL Sbjct: 62 LFRKPTSFINNLHKAPPHEDVVIVDEAHRL 91 >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 = 31.3 bits (71), Expect = 0.33 Identities = 17/39 (43%), Positives = 19/39 (48%), Gaps = 7/39 (17%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGD 95 V GP G GKTTLA VAR+ PV+ GD Sbjct: 24 VHLRGPAGTGKTTLAMHVARKRD-------RPVMLINGD 55 >gnl|CDD|181191 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated. Length = 647 Score = 31.4 bits (72), Expect = 0.34 Identities = 42/140 (30%), Positives = 57/140 (40%), Gaps = 62/140 (44%) Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDH------VLFVGPPGLGKTTLAQV 73 RP+T E GQ + A +N ALD LF G G+GKTT+A++ Sbjct: 11 RPQTFAEVVGQEHVLTALAN-------------ALDLGRLHHAYLFSGTRGVGKTTIARL 57 Query: 74 VAR----ELGVNFRSTSGPV--------IAKAG---DL----AALLTNLED-RDVL---- 109 +A+ E G+ T+ P I G DL AA T +ED R++L Sbjct: 58 LAKGLNCETGI----TATPCGECDNCREIE-QGRFVDLIEIDAASRTKVEDTRELLDNVQ 112 Query: 110 -----------FIDEIHRLS 118 IDE+H LS Sbjct: 113 YAPARGRFKVYLIDEVHMLS 132 >gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 424 Score = 31.4 bits (72), Expect = 0.35 Identities = 13/21 (61%), Positives = 16/21 (76%), Gaps = 1/21 (4%) Query: 57 VLFVGPPGLGKTT-LAQVVAR 76 V VGP G+GKTT LA++ AR Sbjct: 224 VALVGPTGVGKTTTLAKLAAR 244 >gnl|CDD|139997 PRK13938, PRK13938, phosphoheptose isomerase; Provisional. Length = 196 Score = 31.2 bits (70), Expect = 0.42 Identities = 28/91 (30%), Positives = 39/91 (42%), Gaps = 6/91 (6%) Query: 42 VFIEAAKARAEALDHVLFVGPPGLGKTTL-AQVVARELGVNFRSTSGPVIAKAGDLAALL 100 VF A + A D + + G + L A ARELGV + +G + + A L Sbjct: 102 VFARALEGSARPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQLAEFADFL 161 Query: 101 TNLEDRDVLFIDE-----IHRLSIIVEEILY 126 N+ RD I E IH +S VE L+ Sbjct: 162 INVPSRDTGRIQESHIVFIHAISEHVEHALF 192 >gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau; Provisional. Length = 491 Score = 30.9 bits (70), Expect = 0.42 Identities = 56/216 (25%), Positives = 75/216 (34%), Gaps = 81/216 (37%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGP-----------------VIAKAGDLAAL 99 +L VG G+GKTT A++++ L + TS P VI AA Sbjct: 38 ILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEID---AAS 94 Query: 100 LTNLEDRDVLF----------------IDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPS 143 T+++D V+ IDE+H LS F L E P Sbjct: 95 NTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSN----------SAFNALLKTLEEP- 143 Query: 144 ARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPI-------RLNFYEI------EDLKT 190 A VK I ATT V IP+ R + +I E L Sbjct: 144 APHVK-------FILATTEVK----------KIPVTIISRCQRFDLQKIPTDKLVEHLVD 186 Query: 191 IVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRLL 226 I AK + +E+ IA S G+ R A LL Sbjct: 187 I----AKKENIEHDEESLKLIAENSSGSMRNALFLL 218 >gnl|CDD|161840 TIGR00362, DnaA, chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006). Length = 405 Score = 31.0 bits (71), Expect = 0.43 Identities = 35/127 (27%), Positives = 50/127 (39%), Gaps = 21/127 (16%) Query: 9 SRNVSQEDADISLLRPR-TLEEFTGQVEACSNLKVFIEAAKARAEALDHV---LFV-GPP 63 S E + S L P+ T + F V SN ++ AA A AE LF+ G Sbjct: 90 PPEASAEPTNNSPLNPKYTFDNF---VVGKSN-RLAHAAALAVAENPGKAYNPLFIYGGV 145 Query: 64 GLGKTTLAQVVARELGVNFRS-----------TSGPVIA-KAGDLAALLTNLEDRDVLFI 111 GLGKT L + E+ N + T+ V A + + D+L I Sbjct: 146 GLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLI 205 Query: 112 DEIHRLS 118 D+I L+ Sbjct: 206 DDIQFLA 212 >gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional. Length = 174 Score = 31.0 bits (71), Expect = 0.47 Identities = 11/18 (61%), Positives = 13/18 (72%) Query: 61 GPPGLGKTTLAQVVAREL 78 GPPG+GKTTL +A L Sbjct: 7 GPPGVGKTTLVLKIAELL 24 >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 = 30.7 bits (70), Expect = 0.51 Identities = 11/21 (52%), Positives = 14/21 (66%) Query: 58 LFVGPPGLGKTTLAQVVAREL 78 LF GP G+GK LA +A+ L Sbjct: 18 LFAGPEGVGKELLALALAKAL 38 >gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated. Length = 268 Score = 30.8 bits (70), Expect = 0.53 Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 5/35 (14%) Query: 58 LFVGPPGLGKTTLAQVVAREL-----GVNFRSTSG 87 L G G GKT LA +A EL V F + Sbjct: 118 LLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQ 152 >gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau; Provisional. Length = 509 Score = 30.5 bits (68), Expect = 0.58 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 6/67 (8%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81 RPR +E GQ L ++ + L H LF G G+GKTT+++++A+ L Sbjct: 11 RPRCFQEVIGQAPVVRALSNALDQ-----QYLHHAYLFTGTRGVGKTTISRILAKCLNCE 65 Query: 82 FRSTSGP 88 ++ P Sbjct: 66 KGVSANP 72 >gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed. Length = 394 Score = 30.6 bits (70), Expect = 0.59 Identities = 13/22 (59%), Positives = 14/22 (63%) Query: 57 VLFVGPPGLGKTTLAQVVAREL 78 VL GPPG GKTT + V EL Sbjct: 58 VLIYGPPGTGKTTTVKKVFEEL 79 >gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional. Length = 211 Score = 30.6 bits (69), Expect = 0.59 Identities = 13/29 (44%), Positives = 21/29 (72%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85 ++F+GPPG GK T+A++++ EL ST Sbjct: 3 LVFLGPPGSGKGTIAKILSNELNYYHIST 31 >gnl|CDD|178957 PRK00279, adk, adenylate kinase; Reviewed. Length = 215 Score = 30.5 bits (70), Expect = 0.62 Identities = 12/29 (41%), Positives = 19/29 (65%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85 ++ +GPPG GK T A+ +A + G+ ST Sbjct: 3 LILLGPPGAGKGTQAKFIAEKYGIPHIST 31 >gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional. Length = 504 Score = 30.6 bits (69), Expect = 0.63 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 4/53 (7%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVA 75 RP T +E GQ ++K + AA + LF GP G+GKTT A+++A Sbjct: 9 RPITFDEVVGQ----EHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIA 57 >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 = 30.6 bits (70), Expect = 0.64 Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 8/104 (7%) Query: 18 DISLLRPRTLEEF--TGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVA 75 D+ L T + F G E L + A + + + G G GK+ L Q Sbjct: 5 DVGLPDDPTFDNFYAGGNAEL---LAALRQLAAGKGD--RFLYLWGESGSGKSHLLQAAC 59 Query: 76 RELGVNFRSTS-GPVIAKAGDLAALLTNLEDRDVLFIDEIHRLS 118 +S P+ A +L LE D++ +D++ ++ Sbjct: 60 AAAEERGKSAIYLPLAELAQADPEVLEGLEQADLVCLDDVEAIA 103 >gnl|CDD|163401 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. Length = 512 Score = 30.5 bits (69), Expect = 0.70 Identities = 13/22 (59%), Positives = 15/22 (68%) Query: 57 VLFVGPPGLGKTTLAQVVAREL 78 VL GPPG GKT +A+ VA L Sbjct: 219 VLLYGPPGCGKTLIAKAVANSL 240 >gnl|CDD|180131 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated. Length = 559 Score = 30.2 bits (69), Expect = 0.78 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 6/57 (10%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAK-ARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 RP+T E+ GQ LK I+ K + A LF GP G GKT+ A++ A+ + Sbjct: 11 RPQTFEDVVGQEHITKTLKNAIKQGKISHA-----YLFSGPRGTGKTSAAKIFAKAV 62 >gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau; Provisional. Length = 363 Score = 30.2 bits (68), Expect = 0.85 Identities = 38/129 (29%), Positives = 51/129 (39%), Gaps = 40/129 (31%) Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELG 79 RP+ + GQ V A SN A L G G+GKTT+A+++A+ L Sbjct: 11 RPQYFRDIIGQKHIVTAISNGLSLGRIHHA-------WLLSGTRGVGKTTIARLLAKSLN 63 Query: 80 VNFRSTSGPV--------IAKAG--DL----AALLTNLED-RDVL--------------- 109 TS P I K DL AA T +E+ R++L Sbjct: 64 CQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVY 123 Query: 110 FIDEIHRLS 118 IDE+H LS Sbjct: 124 LIDEVHMLS 132 >gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional. Length = 773 Score = 30.2 bits (69), Expect = 0.86 Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 12/55 (21%) Query: 21 LLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVA 75 L++P T+E Q L AA A + L V P GLGKT +A +V Sbjct: 8 LIKPNTIEARLYQQ----LL-----AATALK---KNTLVVLPTGLGKTAIALLVI 50 >gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional. Length = 259 Score = 30.1 bits (68), Expect = 0.95 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 17/57 (29%) Query: 24 PRTLEEF-----TG----QVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLA 71 +T EE+ TG Q+++ +L FIE R E +++ +GP G+GKT LA Sbjct: 71 VKTFEEYDFTFATGAPQKQLQSLRSLS-FIE----RNE---NIVLLGPSGVGKTHLA 119 >gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional. Length = 169 Score = 29.7 bits (67), Expect = 1.1 Identities = 14/26 (53%), Positives = 19/26 (73%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNF 82 + VG G GKTTL + +ARELG++F Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSF 29 >gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional. Length = 254 Score = 29.5 bits (66), Expect = 1.3 Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 10/70 (14%) Query: 55 DHVLFVGPPGLGKTTLA---QVVARELG--VNFRSTSGPV-----IAKAGDLAALLTNLE 104 ++V+F+GPPG GKT LA + A + G V F + + V AG L A L L Sbjct: 99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLG 158 Query: 105 DRDVLFIDEI 114 +L +DE+ Sbjct: 159 RYPLLIVDEV 168 >gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain. Length = 499 Score = 29.4 bits (66), Expect = 1.5 Identities = 39/163 (23%), Positives = 57/163 (34%), Gaps = 42/163 (25%) Query: 57 VLFVGPPGLGKTTLAQ----------------------VVARELGVN------FR----S 84 +L GPPG GKT LA +V + + FR S Sbjct: 214 LLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSLVGKLIDRKQIKQRPFRSPHHS 273 Query: 85 TSGPVIAKAGDLAAL-LTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPS 143 S P + G + +L VLF+DE+ V + L +ED + + S Sbjct: 274 ASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFKRSVLDALREPIEDGSISI------S 327 Query: 144 ARSVKINL-SRFTLIAAT--TRVGLLTNPLQDRFGIPIRLNFY 183 S KI +RF L+AA G P +++ Y Sbjct: 328 RASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRY 370 >gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated. Length = 709 Score = 29.3 bits (65), Expect = 1.5 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 6/67 (8%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81 RP+T + GQ L+ ++ + L H L G G+GKTT+A+++A+ L Sbjct: 11 RPKTFADLVGQEHVVKALQNALDEGR-----LHHAYLLTGTRGVGKTTIARILAKSLNCE 65 Query: 82 FRSTSGP 88 P Sbjct: 66 NAQHGEP 72 >gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated. Length = 351 Score = 29.2 bits (66), Expect = 1.5 Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 1/27 (3%) Query: 46 AAKARAEALDH-VLFVGPPGLGKTTLA 71 A R L H +LF GP G+GK TLA Sbjct: 36 AQAYREGKLHHALLFEGPEGIGKATLA 62 >gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding protein; Provisional. Length = 369 Score = 29.2 bits (66), Expect = 1.5 Identities = 11/19 (57%), Positives = 16/19 (84%) Query: 57 VLFVGPPGLGKTTLAQVVA 75 V+FVGP G GK+TL +++A Sbjct: 32 VVFVGPSGCGKSTLLRMIA 50 >gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau; Provisional. Length = 620 Score = 29.1 bits (65), Expect = 1.6 Identities = 50/198 (25%), Positives = 81/198 (40%), Gaps = 31/198 (15%) Query: 108 VLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLT 167 V IDE+H LS F L E P ++ I ATT + + Sbjct: 130 VYIIDEVHMLSTAA----------FNAFLKTLEEPPPHAI--------FIFATTELHKIP 171 Query: 168 NPLQDRFGIPIRLNFYEI--EDLKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRL 225 + R R NF I +++++ +Q + G+ + +A IA +++G+ R A + Sbjct: 172 ATIASRCQ---RFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSI 228 Query: 226 LRRVRDFAEVAHAKTITREIADAALLRLAIDKMGFDQLDLRYLTMIARNFGGGPVGIE-- 283 L +V F+ + A+ + A LL D+ FD D IA N + + Sbjct: 229 LDQVIAFSVGSEAEKVIAYQGVAELLNYIDDEQFFDVTD-----AIAENDAVKMLEVARF 283 Query: 284 TISAGLSEPRDAIEDLIE 301 I G E +D +E LIE Sbjct: 284 VIDNGYDE-QDFLEKLIE 300 >gnl|CDD|184912 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional. Length = 620 Score = 29.2 bits (66), Expect = 1.8 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 10/70 (14%) Query: 23 RPRTLEEFTGQVEACS-NLKVFIEAAK-ARAEALDHVLFVGPPGLGKTTLAQVVARELGV 80 RP+ +E GQ EA + LK + + + A A LF GP G GKT+ A+++A+ L Sbjct: 11 RPQRFDELVGQ-EAIATTLKNALISNRIAPA-----YLFTGPRGTGKTSSARILAKSL-- 62 Query: 81 NFRSTSGPVI 90 N ++ P Sbjct: 63 NCLNSDKPTP 72 >gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional. Length = 180 Score = 28.9 bits (65), Expect = 1.9 Identities = 10/22 (45%), Positives = 18/22 (81%) Query: 61 GPPGLGKTTLAQVVARELGVNF 82 G PG+GKTT+++++A +LG + Sbjct: 7 GTPGVGKTTVSKLLAEKLGYEY 28 >gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated. Length = 233 Score = 28.7 bits (64), Expect = 2.0 Identities = 46/167 (27%), Positives = 75/167 (44%), Gaps = 15/167 (8%) Query: 47 AKARAEALDHVLFVGPPGLGKTTLA-QVVARELGVNFRSTSGPVIAKAGDLAALLTNLED 105 A A ++ D + GP G GKT LA + A S P+ A AG L L LE Sbjct: 34 ALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGRLRDALEALEG 93 Query: 106 RDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGL 165 R ++ +D + ++ E+ + A+ DF AR+ I L +T + L Sbjct: 94 RSLVALDGLESIAGQREDEV--ALFDFH--------NRARAAGITL-LYTARQMPDGLAL 142 Query: 166 LTNPLQDRFGIPIRLNFYEIEDL--KTIVQRGAKLTGLAVTDEAACE 210 + L+ R IR+ ++D+ +++ A+ GLA+ DEAA + Sbjct: 143 VLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRRGLAL-DEAAID 188 >gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site. Length = 142 Score = 28.9 bits (65), Expect = 2.1 Identities = 21/84 (25%), Positives = 30/84 (35%), Gaps = 15/84 (17%) Query: 57 VLFVGPPGLGKTTLAQVV-----------ARELGVNFRSTSGPVIAKAGDLAALLTNLED 105 ++F+G G GKTTL Q + A E T G + +AL+ D Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEILYKKTQAVEYNDGAIDTPGEYVENRRLYSALIVTAAD 62 Query: 106 RDVLFIDEIHRLSIIVEEILYPAM 129 DV+ S E +P Sbjct: 63 ADVI----ALVQSATDPESRFPPG 82 >gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated. Length = 605 Score = 28.7 bits (64), Expect = 2.2 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 4/56 (7%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 RP ++ GQ +K + A + +F GP G+GKT++A++ A+ + Sbjct: 11 RPHNFKQIIGQ----ELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAI 62 >gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional. Length = 172 Score = 28.6 bits (64), Expect = 2.2 Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 4/41 (9%) Query: 44 IEAAKARAEALDH----VLFVGPPGLGKTTLAQVVARELGV 80 + A A VL G G GKTTLA +A G Sbjct: 1 MLVALIAARLCGGGMITVLIDGRSGSGKTTLAGALAARTGF 41 >gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated. Length = 365 Score = 28.5 bits (64), Expect = 2.3 Identities = 20/64 (31%), Positives = 26/64 (40%), Gaps = 6/64 (9%) Query: 14 QEDADISLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQ 72 + D + PR G A + L R+ L H L GP G+GK TLA Sbjct: 5 EADREEGAPHPRETTALFGHAAAEAAL-----LDAYRSGRLHHAWLIGGPQGIGKATLAY 59 Query: 73 VVAR 76 +AR Sbjct: 60 RMAR 63 >gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors. Length = 217 Score = 28.5 bits (64), Expect = 2.4 Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 4/51 (7%) Query: 61 GPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAALL--TNLEDRDVL 109 GP G GK+T+A+ VA +LG + + + +A LAAL +L D L Sbjct: 9 GPSGAGKSTVAKAVAEKLGYAYLDSGA--MYRAIALAALQNRVDLTSEDAL 57 >gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood. Length = 143 Score = 28.7 bits (65), Expect = 2.4 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 57 VLFVGPPGLGKTTLAQVVARE 77 ++ +G G GKTTL Q + E Sbjct: 4 IMLIGRSGCGKTTLTQALNGE 24 >gnl|CDD|184582 PRK14236, PRK14236, phosphate transporter ATP-binding protein; Provisional. Length = 272 Score = 28.5 bits (64), Expect = 2.5 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 10/70 (14%) Query: 1 MMDREGLLSRNVSQEDADISLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFV 60 +M L N+S E + + R L F G +A ++ + I K R A F+ Sbjct: 8 LMALPLLDVLNLSDEQTALEV---RNLNLFYGDKQALFDISMRI--PKNRVTA-----FI 57 Query: 61 GPPGLGKTTL 70 GP G GK+TL Sbjct: 58 GPSGCGKSTL 67 >gnl|CDD|184913 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional. Length = 944 Score = 28.6 bits (64), Expect = 2.6 Identities = 30/95 (31%), Positives = 39/95 (41%), Gaps = 38/95 (40%) Query: 58 LFVGPPGLGKTTLAQVVAR----ELGVNFRSTSGPV--------IA-------------- 91 LF G G+GKT+LA++ A+ E GV T+ P IA Sbjct: 42 LFTGTRGVGKTSLARLFAKGLNCEQGV----TATPCGVCSSCVEIAQGRFVDLIEVDAAS 97 Query: 92 --KAGDLAALLTNLEDR------DVLFIDEIHRLS 118 K D LL N++ R V IDE+H LS Sbjct: 98 RTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLS 132 >gnl|CDD|184728 PRK14530, PRK14530, adenylate kinase; Provisional. Length = 215 Score = 28.6 bits (64), Expect = 2.6 Identities = 12/30 (40%), Positives = 17/30 (56%) Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRST 85 +L +G PG GK T + +A E GV +T Sbjct: 5 RILLLGAPGAGKGTQSSNLAEEFGVEHVTT 34 >gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated. Length = 830 Score = 28.3 bits (63), Expect = 2.7 Identities = 14/31 (45%), Positives = 19/31 (61%) Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGP 88 LF G G+GKTTL+++ A+ L TS P Sbjct: 42 LFTGTRGVGKTTLSRIFAKALNCETGVTSQP 72 >gnl|CDD|178902 PRK00149, dnaA, chromosomal replication initiation protein; Reviewed. Length = 450 Score = 28.2 bits (64), Expect = 2.7 Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 4/37 (10%) Query: 46 AAKARAEALDHV---LFV-GPPGLGKTTLAQVVAREL 78 AA A AE LF+ G GLGKT L + + Sbjct: 136 AALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYI 172 >gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional. Length = 590 Score = 28.2 bits (64), Expect = 2.8 Identities = 11/19 (57%), Positives = 15/19 (78%) Query: 60 VGPPGLGKTTLAQVVAREL 78 VGP G+GKTT A+++A L Sbjct: 371 VGPNGIGKTTFAKLLAGVL 389 >gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase domain-containing protein; Reviewed. Length = 229 Score = 28.4 bits (64), Expect = 2.8 Identities = 11/23 (47%), Positives = 14/23 (60%) Query: 57 VLFVGPPGLGKTTLAQVVARELG 79 V GPPG GK+TLA+ + L Sbjct: 36 VGIAGPPGAGKSTLAEFLEALLQ 58 >gnl|CDD|181106 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated. Length = 824 Score = 28.4 bits (64), Expect = 2.9 Identities = 12/21 (57%), Positives = 16/21 (76%) Query: 58 LFVGPPGLGKTTLAQVVAREL 78 LF GP G GKT+ A+++AR L Sbjct: 41 LFSGPRGCGKTSSARILARSL 61 >gnl|CDD|179638 PRK03731, aroL, shikimate kinase II; Reviewed. Length = 171 Score = 28.4 bits (64), Expect = 3.1 Identities = 12/26 (46%), Positives = 15/26 (57%) Query: 60 VGPPGLGKTTLAQVVARELGVNFRST 85 VG G GKTT+ +A+ LG F T Sbjct: 8 VGARGCGKTTVGMALAQALGYRFVDT 33 >gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity. Length = 249 Score = 28.2 bits (63), Expect = 3.2 Identities = 8/22 (36%), Positives = 17/22 (77%) Query: 57 VLFVGPPGLGKTTLAQVVAREL 78 ++ G PG+GK+T ++ +A++L Sbjct: 2 IILTGLPGVGKSTFSKELAKKL 23 >gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional. Length = 718 Score = 27.9 bits (62), Expect = 3.5 Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 4/29 (13%) Query: 60 VGPPGLGKTTLAQVVAREL----GVNFRS 84 VGP G+GK+T+ ++++ EL G FRS Sbjct: 541 VGPNGIGKSTILKLISGELQPSSGTVFRS 569 >gnl|CDD|147939 pfam06048, DUF927, Domain of unknown function (DUF927). Family of bacterial proteins of unknown function. Length = 284 Score = 28.0 bits (63), Expect = 3.5 Identities = 22/75 (29%), Positives = 29/75 (38%), Gaps = 15/75 (20%) Query: 59 FVGPPGLGKTTLAQVVA------RELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFID 112 FVG GKTT ++ A L ++RST A L A + D L +D Sbjct: 196 FVGDSSTGKTTALKLAASVWGNPDTLIRSWRST-------ANGLEATASEHNDT-PLILD 247 Query: 113 EIHRLS-IIVEEILY 126 EI V +Y Sbjct: 248 EISEADPREVGGAVY 262 >gnl|CDD|183622 PRK12608, PRK12608, transcription termination factor Rho; Provisional. Length = 380 Score = 28.1 bits (63), Expect = 3.6 Identities = 24/97 (24%), Positives = 32/97 (32%), Gaps = 36/97 (37%) Query: 58 LFVGPPGLGKTTLAQVVARELGVNF---------------------RSTSGPVIAKAGD- 95 L V PP GKT L Q +A + N RS G V A D Sbjct: 137 LIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDR 196 Query: 96 -------LAALLTNLEDRD-------VLFIDEIHRLS 118 +A L+ R V+ +D + RL+ Sbjct: 197 PPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRLA 233 >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 = 28.0 bits (63), Expect = 3.6 Identities = 8/22 (36%), Positives = 14/22 (63%) Query: 57 VLFVGPPGLGKTTLAQVVAREL 78 ++ G P GK+T A+ +A+ L Sbjct: 2 IILTGLPSSGKSTRAKELAKYL 23 >gnl|CDD|181675 PRK09162, PRK09162, hypoxanthine-guanine phosphoribosyltransferase; Provisional. Length = 181 Score = 27.9 bits (63), Expect = 3.7 Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 4/29 (13%) Query: 101 TNLEDRDVLFIDEI----HRLSIIVEEIL 125 +L+ R VL +D+I H L+ I + L Sbjct: 93 ESLKGRTVLVVDDILDEGHTLAAIRDRCL 121 >gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase. Length = 421 Score = 27.9 bits (62), Expect = 3.8 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%) Query: 46 AAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAALLTNLED 105 A+K + E + ++ GP G GK+ LA +A+ L S + + D+ + +L + Sbjct: 15 ASKTKKEKV--IVISGPTGAGKSRLALELAKRLNGEIISADSVQVYRGLDVGSAKPSLSE 72 Query: 106 RDVL---FIDEIH 115 R + ID +H Sbjct: 73 RKEVPHHLIDILH 85 >gnl|CDD|177370 PHA02530, pseT, polynucleotide kinase; Provisional. Length = 300 Score = 27.7 bits (62), Expect = 3.9 Identities = 10/22 (45%), Positives = 13/22 (59%) Query: 58 LFVGPPGLGKTTLAQVVARELG 79 L VG PG GK+T A+ A + Sbjct: 6 LTVGVPGSGKSTWAREFAAKNP 27 >gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown. Length = 220 Score = 27.8 bits (62), Expect = 4.4 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 14/100 (14%) Query: 57 VLFVGPPGLGKTTLA-QVVARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIH 115 L G PG GKT+ + + L ++F +S +L E+ D+ D++ Sbjct: 15 YLIYGKPGTGKTSTIKYLPGKTLVLSFDMSS-----------KVLIGDENVDIADHDDMP 63 Query: 116 RLSIIVEEILYPAMEDFQLDLMVGEGPSA--RSVKINLSR 153 + +VE + ++ + D +V + SA N+ R Sbjct: 64 PIQAMVEFYVMQNIQAVKYDNIVIDNISALQNLWLENIGR 103 >gnl|CDD|181578 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated. Length = 227 Score = 27.6 bits (62), Expect = 4.5 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 9/61 (14%) Query: 61 GPPGLGKTTLAQVV---ARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRL 117 G G G++ L Q + A G N R + A L A + E ++ +D++ RL Sbjct: 49 GEAGSGRSHLLQALVADASYGGRNAR-----YLDAASPLLAFDFDPEA-ELYAVDDVERL 102 Query: 118 S 118 Sbjct: 103 D 103 >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 = 27.5 bits (61), Expect = 4.6 Identities = 12/23 (52%), Positives = 16/23 (69%) Query: 56 HVLFVGPPGLGKTTLAQVVAREL 78 H+ F G PG GKTT+A +A+ L Sbjct: 60 HMSFTGNPGTGKTTVALRMAQIL 82 >gnl|CDD|172994 PRK14528, PRK14528, adenylate kinase; Provisional. Length = 186 Score = 27.7 bits (61), Expect = 4.7 Identities = 12/32 (37%), Positives = 21/32 (65%) Query: 54 LDHVLFVGPPGLGKTTLAQVVARELGVNFRST 85 + +++F+GPPG GK T A+++ L + ST Sbjct: 1 MKNIIFMGPPGAGKGTQAKILCERLSIPQIST 32 >gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau; Provisional. Length = 397 Score = 27.5 bits (61), Expect = 4.8 Identities = 36/144 (25%), Positives = 61/144 (42%), Gaps = 25/144 (17%) Query: 108 VLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLT 167 V IDE+H LSI F L E P ++ I ATT + + Sbjct: 130 VYIIDEVHMLSIAA----------FNAFLKTLEEPPPHAI--------FIFATTELHKIP 171 Query: 168 NPLQDRFGIPIRLNFYEI--EDLKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRL 225 + R R NF I E+++ +Q + G++V +A I +++G+ R A + Sbjct: 172 ATIASRCQ---RFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSI 228 Query: 226 LRRVRDFA-EVAHAKTIT-REIAD 247 L +V F+ E +I ++A+ Sbjct: 229 LDQVIAFSVESEGEGSIRYDKVAE 252 >gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein; Provisional. Length = 445 Score = 27.5 bits (61), Expect = 4.9 Identities = 23/68 (33%), Positives = 30/68 (44%), Gaps = 10/68 (14%) Query: 61 GPPGLGKTTLAQVVA---RELGVN---FRS---TSGPVIA-KAGDLAALLTNLEDRDVLF 110 GP G GKT L Q RE G RS T V A ++G++ + D LF Sbjct: 148 GPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALF 207 Query: 111 IDEIHRLS 118 I++I S Sbjct: 208 IEDIEVFS 215 >gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional. Length = 758 Score = 27.5 bits (61), Expect = 5.0 Identities = 28/84 (33%), Positives = 36/84 (42%), Gaps = 32/84 (38%) Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGPV---IAKA-----------------GDL- 96 L VG G+GKT +A+ G+ +R G V +A GD Sbjct: 211 LLVGESGVGKTAIAE------GLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFE 264 Query: 97 ---AALLTNLE-DRD-VLFIDEIH 115 ALL LE D + +LFIDEIH Sbjct: 265 KRFKALLKQLEQDTNSILFIDEIH 288 >gnl|CDD|162636 TIGR01978, sufC, FeS assembly ATPase SufC. SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA. Length = 243 Score = 27.2 bits (61), Expect = 5.4 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%) Query: 56 HVLFVGPPGLGKTTLAQVVA-RELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFI 111 H + +GP G GK+TL++ +A ++ TSG ++ K DL L + R LF+ Sbjct: 29 HAI-MGPNGSGKSTLSKTIAGHP---SYEVTSGTILFKGQDLLELEPDERARAGLFL 81 >gnl|CDD|178749 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional. Length = 1153 Score = 27.5 bits (61), Expect = 5.6 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 3/67 (4%) Query: 19 ISLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78 ++L E+F G + + + + +E + V G G+GKTT+A+ + L Sbjct: 175 LNLTPSNDFEDFVGIEDHIAKMSSLLHLE---SEEVRMVGIWGSSGIGKTTIARALFSRL 231 Query: 79 GVNFRST 85 F+S+ Sbjct: 232 SRQFQSS 238 >gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein YbbL; Provisional. Length = 225 Score = 27.4 bits (61), Expect = 6.2 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 4/42 (9%) Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAAL 99 L GP G GK+TL ++VA + TSG ++ + D++ L Sbjct: 37 LITGPSGCGKSTLLKIVASLIS----PTSGTLLFEGEDISTL 74 >gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. Length = 361 Score = 27.3 bits (61), Expect = 6.3 Identities = 12/44 (27%), Positives = 21/44 (47%) Query: 46 AAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPV 89 AA+ E + +GP G GK++L + + R L ++ G Sbjct: 70 AAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRR 113 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 27.1 bits (60), Expect = 6.5 Identities = 13/35 (37%), Positives = 16/35 (45%) Query: 45 EAAKARAEALDHVLFVGPPGLGKTTLAQVVARELG 79 EA +A L V+ P G GKT A + A E Sbjct: 15 EAIEALLSGLRDVILAAPTGSGKTLAALLPALEAL 49 >gnl|CDD|179724 PRK04040, PRK04040, adenylate kinase; Provisional. Length = 188 Score = 27.2 bits (61), Expect = 6.7 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 13/68 (19%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTS-GPV---IAKAGDLAALLTNLEDRDVLF-- 110 V+ G PG+GKTT+ +L +++ + G V +AK L E RD + Sbjct: 5 VVVTGVPGVGKTTVLNKALEKLKEDYKIVNFGDVMLEVAKEEGLV------EHRDEMRKL 58 Query: 111 -IDEIHRL 117 +E L Sbjct: 59 PPEEQKEL 66 >gnl|CDD|172997 PRK14531, PRK14531, adenylate kinase; Provisional. Length = 183 Score = 27.1 bits (60), Expect = 6.8 Identities = 13/29 (44%), Positives = 17/29 (58%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85 +LF+GPPG GK T A + G+ ST Sbjct: 5 LLFLGPPGAGKGTQAARLCAAHGLRHLST 33 >gnl|CDD|180357 PRK06031, PRK06031, phosphoribosyltransferase; Provisional. Length = 233 Score = 27.0 bits (60), Expect = 7.1 Identities = 19/34 (55%), Positives = 20/34 (58%), Gaps = 3/34 (8%) Query: 46 AAKARAEALDHVLFVGPPGLGKTTLAQVVARELG 79 A KARA D V G P LG TLA VAR+LG Sbjct: 77 AEKARAFDPDVV--AGLPTLG-LTLAAAVARKLG 107 >gnl|CDD|181430 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau; Validated. Length = 535 Score = 26.9 bits (60), Expect = 7.1 Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 16/62 (25%) Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDH------VLFVGPPGLGKTTLAQVVAR 76 RP+ +E GQ E+ S K + ALD+ LF G G GKT+ A++ AR Sbjct: 9 RPKHFDELIGQ-ESVS---------KTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFAR 58 Query: 77 EL 78 L Sbjct: 59 AL 60 >gnl|CDD|171510 PRK12452, PRK12452, cardiolipin synthetase; Reviewed. Length = 509 Score = 26.8 bits (59), Expect = 7.4 Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 2/41 (4%) Query: 267 YLTMIARNFGGGPVGIETISAGLSEPRDAIEDLIEPYMIQQ 307 +LT + + FGGGP T + L+ ++++ I+Q Sbjct: 123 HLTEVVQKFGGGPAADRTTTKLLTNGDQTFSEILQ--AIEQ 161 >gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Length = 529 Score = 27.0 bits (60), Expect = 7.6 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 5/58 (8%) Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDE 113 V +GP G GK+TL ++ + G + L + R + + Sbjct: 363 RVAILGPSGSGKSTLLMLLTG-----LLDPLQGEVTLDGVSVSSLQDELRRRISVFAQ 415 >gnl|CDD|183342 PRK11860, PRK11860, bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional. Length = 661 Score = 26.9 bits (60), Expect = 7.8 Identities = 13/40 (32%), Positives = 20/40 (50%) Query: 43 FIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82 A+A A+ + + GP GK T+A VA LG ++ Sbjct: 431 LFSVAQADADRVPVICIDGPTASGKGTVAARVAEALGYHY 470 >gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated. Length = 325 Score = 26.8 bits (59), Expect = 8.1 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 58 LFVGPPGLGKTTLAQVVAREL 78 LF G G+GKT A+ A+ L Sbjct: 25 LFAGKKGIGKTAFARFAAQAL 45 >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 = 26.8 bits (60), Expect = 8.3 Identities = 12/21 (57%), Positives = 16/21 (76%) Query: 58 LFVGPPGLGKTTLAQVVAREL 78 LF+GP G+GKT LA+ +A L Sbjct: 599 LFLGPTGVGKTELAKALAEFL 619 >gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional. Length = 184 Score = 26.8 bits (60), Expect = 8.3 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%) Query: 47 AKARAEALDH--VLFVGPPGLGKTTLAQVVARELGVNFR 83 + AL V+ VG G GK+T+ + +A LG+ F Sbjct: 1 EERARAALGKRTVVLVGLMGAGKSTVGRRLATMLGLPFL 39 >gnl|CDD|129254 TIGR00150, HI0065_YjeE, ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity. Length = 133 Score = 26.6 bits (59), Expect = 8.4 Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 3/50 (6%) Query: 40 LKVFIEAAKARAEALDH---VLFVGPPGLGKTTLAQVVARELGVNFRSTS 86 K + KA A+ LD VL G G GKTTL Q + + LG+ TS Sbjct: 5 EKAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGLGIQGNVTS 54 >gnl|CDD|181965 PRK09580, sufC, cysteine desulfurase ATPase component; Reviewed. Length = 248 Score = 26.7 bits (59), Expect = 8.4 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 4/41 (9%) Query: 60 VGPPGLGKTTLAQVVA-RELGVNFRSTSGPVIAKAGDLAAL 99 +GP G GK+TL+ +A RE ++ T G V K DL L Sbjct: 33 MGPNGSGKSTLSATLAGRE---DYEVTGGTVEFKGKDLLEL 70 >gnl|CDD|182623 PRK10657, PRK10657, isoaspartyl dipeptidase; Provisional. Length = 388 Score = 26.7 bits (60), Expect = 8.5 Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%) Query: 139 GE-GPSARSVKINLSRFTLIAATTRVGLL 166 GE G S R+ ++ LS T TT VGLL Sbjct: 70 GEGGFSTRTPEVQLSDLTEAGITTVVGLL 98 >gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein; Provisional. Length = 260 Score = 26.5 bits (59), Expect = 9.0 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 7/52 (13%) Query: 25 RTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAR 76 R L + G+ A N+ + I + A F+GP G GK+TL + R Sbjct: 17 RNLNFYYGKFHALKNINLDIAKNQVTA-------FIGPSGCGKSTLLRTFNR 61 >gnl|CDD|178800 PRK00023, cmk, cytidylate kinase; Provisional. Length = 225 Score = 26.6 bits (60), Expect = 9.2 Identities = 10/19 (52%), Positives = 16/19 (84%) Query: 61 GPPGLGKTTLAQVVARELG 79 GP G GK T+A+++A++LG Sbjct: 11 GPAGSGKGTVAKILAKKLG 29 >gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional. Length = 197 Score = 26.7 bits (59), Expect = 9.2 Identities = 8/25 (32%), Positives = 15/25 (60%) Query: 57 VLFVGPPGLGKTTLAQVVARELGVN 81 G PG+GKT+++ +AR ++ Sbjct: 6 HFIGGIPGVGKTSISGYIARHRAID 30 >gnl|CDD|131030 TIGR01975, isoAsp_dipep, isoaspartyl dipeptidase IadA. The L-isoaspartyl derivative of Asp arises non-enzymatically over time as a form of protein damage. In this isomerization, the connectivity of the polypeptide changes to pass through the beta-carboxyl of the side chain. Much but not all of this damage can be repaired by protein-L-isoaspartate (D-aspartate) O-methyltransferase. This model describes the isoaspartyl dipeptidase IadA, apparently one of two such enzymes in E. coli, an enzyme that degrades isoaspartyl dipeptides and may unblock degradation of proteins that cannot be repaired. This model also describes closely related proteins from other species (e.g. Clostridium perfringens, Thermoanaerobacter tengcongensis) that we assume to be equivalent in function. This family shows homology to dihydroorotases. Length = 389 Score = 26.7 bits (59), Expect = 9.3 Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 1/29 (3%) Query: 139 GE-GPSARSVKINLSRFTLIAATTRVGLL 166 GE GP+ R+ ++ LS T TT VGLL Sbjct: 70 GEGGPTTRTPELTLSDITKGGVTTVVGLL 98 >gnl|CDD|173382 PTZ00088, PTZ00088, adenylate kinase 1; Provisional. Length = 229 Score = 26.7 bits (59), Expect = 9.3 Identities = 7/21 (33%), Positives = 16/21 (76%) Query: 57 VLFVGPPGLGKTTLAQVVARE 77 ++ G PG+GK T A++++++ Sbjct: 9 IVLFGAPGVGKGTFAEILSKK 29 >gnl|CDD|163375 TIGR03649, ergot_EASG, ergot alkaloid biosynthesis protein, AFUA_2G17970 family. This family consists of fungal proteins of unknown function associated with secondary metabolite biosynthesis, such as of the ergot alkaloids such as ergovaline. Nomenclature differs because gene order differs - this is EasG in Neotyphodium lolii but is designated ergot alkaloid biosynthetic protein A in several other fungi. Length = 285 Score = 26.5 bits (59), Expect = 9.4 Identities = 26/93 (27%), Positives = 33/93 (35%), Gaps = 18/93 (19%) Query: 57 VLFVGPPGLGKTTLAQV---VARELGVN-FRSTSGPVIAKAGD----LAALLTNLEDRD- 107 V V PP AR GV F S +I K G + A L +L + Sbjct: 71 VYLVAPPIPDLAPPMIKFIDFARSKGVRRFVLLSASIIEKGGPAMGQVHAHLDSLGGVEY 130 Query: 108 -VL--------FIDEIHRLSIIVEEILYPAMED 131 VL F +E H +I E +Y A D Sbjct: 131 TVLRPTWFMENFSEEFHVEAIRKENKIYSATGD 163 >gnl|CDD|184719 PRK14511, PRK14511, maltooligosyl trehalose synthase; Provisional. Length = 879 Score = 26.5 bits (59), Expect = 9.6 Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 7/57 (12%) Query: 44 IEAAKARAEALDHVLF------VGPPGLGKTTLAQVVAR-ELGVNFRSTSGPVIAKA 93 A+ R D + + + + R E V F+ +GPV+AK Sbjct: 462 AARARRRLPEADWPVLDFLEDVLLGRAARELPRGRRKLRLEFAVRFQQLTGPVMAKG 518 >gnl|CDD|165405 PHA03133, PHA03133, thymidine kinase; Provisional. Length = 368 Score = 26.4 bits (58), Expect = 10.0 Identities = 15/32 (46%), Positives = 19/32 (59%) Query: 48 KARAEALDHVLFVGPPGLGKTTLAQVVARELG 79 + +A AL + GP GLGKTT A +A LG Sbjct: 34 QQKASALLRIYVDGPHGLGKTTTAAALAAALG 65 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 0.323 0.140 0.396 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: 5,730,176 Number of extensions: 396975 Number of successful extensions: 1434 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1403 Number of HSP's successfully gapped: 233 Length of query: 334 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 240 Effective length of database: 3,963,321 Effective search space: 951197040 Effective search space used: 951197040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 57 (25.9 bits)