RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= 537021.9.peg.409_1 (242 letters) >gnl|CDD|163018 TIGR02784, addA_alphas, double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. Length = 1141 Score = 229 bits (586), Expect = 5e-61 Identities = 94/196 (47%), Positives = 135/196 (68%), Gaps = 1/196 (0%) Query: 23 EQLLASDPTRSAWVSANAGSGKTHILVQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHRV 82 Q ASDP SAWVSANAGSGKTH+L QRV+RLLL PS +LCLT+TKAAAAEM +RV Sbjct: 2 RQARASDPKTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRV 61 Query: 83 LEIITAWSHLSDEILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEA 142 + + W+ L D L A + ++GK+P+ + +++AR L LETPGGLK+QTIHAFCE+ Sbjct: 62 FDRLGEWAVLDDAELRARLEALEGKRPDAAKLAEARRLFARALETPGGLKIQTIHAFCES 121 Query: 143 IMQQFPLEANITSHFAIADEEQSKKLIEEAKKSTLASIMLDNNEELKKAFYEILEISNDE 202 ++ QFPLEAN+ HF++ D+ + L+ EA+++ LA + ++ L A +LE + + Sbjct: 122 LLHQFPLEANVAGHFSVMDDRAAATLLAEARRALLAHVAAA-DDALADALATVLEAAGET 180 Query: 203 DIETLISDIISNRTAL 218 E L+++I++ R L Sbjct: 181 GFEALLAEIVARRAHL 196 Score = 26.2 bits (58), Expect = 8.8 Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 3/35 (8%) Query: 15 DLISQTKSEQLLASDPTRSAWVSANAGSGKTHILV 49 DLI ++ LLA P AWV G HILV Sbjct: 366 DLI--ERTVALLA-RPGAGAWVHYKLDRGIDHILV 397 >gnl|CDD|163019 TIGR02785, addA_Gpos, recombination helicase AddA, Firmicutes type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species. Length = 1232 Score = 77.8 bits (192), Expect = 2e-15 Identities = 52/204 (25%), Positives = 86/204 (42%), Gaps = 32/204 (15%) Query: 36 VSANAGSGKTHILVQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHRVLEIITAWSHLSDE 95 VSA+AGSGKT +LV+R+++ +L LL +T T AAA EM R+ E Sbjct: 19 VSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEE----------- 67 Query: 96 ILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEAIMQQFPLEANITS 155 + K ++PN + + LL T + T+H+FC ++++ ++ Sbjct: 68 ----ALQKALQQEPNSKHLRRQLALLNTA-------NISTLHSFCLKVIRKHYYLLDLDP 116 Query: 156 HFAIADEEQSKKLIEEAKKSTLASIMLDNNEELKKAFYEILE-ISNDEDIETLISDIISN 214 F I + + LI+E + + F+E+ + S D + L D+I Sbjct: 117 SFRILTDTEQLLLIKEVVDDVFEEEYYKED---NEGFFELTDNFSGDRSDDGL-RDLI-- 170 Query: 215 RTALKLIFFFFSYLWRRKIIEKSL 238 LKL F S K + Sbjct: 171 ---LKLYDFARSTPNPEKWLNNLA 191 >gnl|CDD|184388 PRK13909, PRK13909, putative recombination protein RecB; Provisional. Length = 910 Score = 74.2 bits (183), Expect = 3e-14 Identities = 52/167 (31%), Positives = 84/167 (50%), Gaps = 11/167 (6%) Query: 38 ANAGSGKTHILVQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHRVLEIITAWSHLSDEIL 97 A+AGSGKT L R L LL A+PS +L LT TK AA EM R+++ + +E Sbjct: 5 ASAGSGKTFALSVRFLALLFKGANPSEILALTFTKKAANEMKERIIDTLLNLEKEKEESE 64 Query: 98 SAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEAIMQQFPLEANITSHF 157 E+ + G + ++K + L + LK+ TI AF + I+++F L ++ F Sbjct: 65 LNELEEKLGLSKEEL-LNKRDKVYQEFLNS--ELKISTIDAFFQKILRKFCLNLGLSPDF 121 Query: 158 AIAD---EEQSKKLIEEAKK----STLASIMLDNNEELKKAFYEILE 197 +I + EE ++K + K LA I +++ F+E+LE Sbjct: 122 SIKEDTKEELNEKFLSALSKEELLELLAFIKQCESKKNNS-FFELLE 167 >gnl|CDD|161956 TIGR00609, recB, exodeoxyribonuclease V, beta subunit. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 1087 Score = 53.6 bits (129), Expect = 5e-08 Identities = 34/113 (30%), Positives = 52/113 (46%), Gaps = 3/113 (2%) Query: 38 ANAGSGKTHILVQRVLRLLL--ANAHPSTLLCLTHTKAAAAEMSHRVLE-IITAWSHLSD 94 A+AG+GKT + Q LRLLL +L +T T AA E+ R+ I A L Sbjct: 16 ASAGTGKTFTIAQLYLRLLLEGGPLTVEEILVVTFTNAATEELKTRIRGRIHQALRALKA 75 Query: 95 EILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEAIMQQF 147 + S E+ + + + +A L L T + TIH FC+ +++Q Sbjct: 76 ALTSQELPEPLKEAIQDEKVKQAITRLRNALATMDEAAIYTIHGFCQRMLEQH 128 >gnl|CDD|130147 TIGR01075, uvrD, DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily. Length = 715 Score = 52.1 bits (125), Expect = 1e-07 Identities = 35/147 (23%), Positives = 59/147 (40%), Gaps = 39/147 (26%) Query: 30 PTRSAWVSANAGSGKTHILVQRVLRLL-LANAHPSTLLCLTHTKAAAAEMSHRVLEIITA 88 P + V A AGSGKT +L R+ LL + NA P +++ +T T AAAEM HR+ ++ Sbjct: 16 PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLGT 75 Query: 89 WSHLSDEILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEAIMQQFP 148 + G+ + T H +++ Sbjct: 76 --------------------------------------SARGMWIGTFHGLAHRLLRAHH 97 Query: 149 LEANITSHFAIADEEQSKKLIEEAKKS 175 L+A + F I D + +L++ K+ Sbjct: 98 LDAGLPQDFQILDSDDQLRLLKRLIKA 124 >gnl|CDD|183307 PRK11773, uvrD, DNA-dependent helicase II; Provisional. Length = 721 Score = 49.5 bits (119), Expect = 8e-07 Identities = 25/58 (43%), Positives = 38/58 (65%), Gaps = 1/58 (1%) Query: 30 PTRSAWVSANAGSGKTHILVQRVLRLL-LANAHPSTLLCLTHTKAAAAEMSHRVLEII 86 P + V A AGSGKT +LV R+ L+ + NA P +++ +T T AAAEM HR+ +++ Sbjct: 21 PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLL 78 >gnl|CDD|162191 TIGR01073, pcrA, ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily. Length = 726 Score = 44.0 bits (104), Expect = 4e-05 Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 1/50 (2%) Query: 38 ANAGSGKTHILVQRVLRLLLA-NAHPSTLLCLTHTKAAAAEMSHRVLEII 86 A AGSGKT +L R+ L+ N P +L +T T AA EM RV +++ Sbjct: 24 AGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLL 73 >gnl|CDD|182930 PRK11054, helD, DNA helicase IV; Provisional. Length = 684 Score = 40.3 bits (95), Expect = 5e-04 Identities = 23/50 (46%), Positives = 27/50 (54%), Gaps = 1/50 (2%) Query: 36 VSANAGSGKTHILVQRVLRLLLAN-AHPSTLLCLTHTKAAAAEMSHRVLE 84 V A AGSGKT +LV R LL A P +L L + AA EM R+ E Sbjct: 214 VLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRE 263 >gnl|CDD|130146 TIGR01074, rep, ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily. Length = 664 Score = 38.6 bits (90), Expect = 0.001 Identities = 29/104 (27%), Positives = 45/104 (43%), Gaps = 14/104 (13%) Query: 36 VSANAGSGKTHILVQRVLRLLLANAH-PSTLLCLTHTKAAAAEMSHRVLE---------- 84 V A AGSGKT ++ ++ L+ + + +T T AA EM RV + Sbjct: 19 VLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLGKGEARGL 78 Query: 85 IITAWSHLSDEILSAEITKIQGKKPNKS--DMSKARHLLITILE 126 I+ + L +I+ E + G K N S D + LL + E Sbjct: 79 TISTFHTLGLDIIKREYNAL-GYKSNFSLFDETDQLALLKELTE 121 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 35.9 bits (83), Expect = 0.009 Identities = 18/91 (19%), Positives = 30/91 (32%), Gaps = 8/91 (8%) Query: 41 GSGKTHILVQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHRVLEIITAWSHLSDEILSAE 100 GSGKT + L L L L T+ A + + + + + Sbjct: 34 GSGKTLAALLPALEALKRGKGKRV-LVLVPTRELAEQWAEELKK----LGPSLGLKVVGL 88 Query: 101 ITKIQGKKPNKSDMSKARHLLITILETPGGL 131 ++ + S +L+T TPG L Sbjct: 89 YGGDSKREQLRKLESGKTDILVT---TPGRL 116 >gnl|CDD|182801 PRK10876, recB, exonuclease V subunit beta; Provisional. Length = 1181 Score = 34.6 bits (80), Expect = 0.026 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 9/60 (15%) Query: 36 VSANAGSGKTHILVQRVLRLLL----ANAHPSTL-----LCLTHTKAAAAEMSHRVLEII 86 + A+AG+GKT + LRLLL + A P L L +T T+AA E+ R+ I Sbjct: 22 IEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSNI 81 >gnl|CDD|182838 PRK10919, PRK10919, ATP-dependent DNA helicase Rep; Provisional. Length = 672 Score = 31.3 bits (71), Expect = 0.24 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%) Query: 36 VSANAGSGKTHILVQRVLRLLLANAH-PSTLLCLTHTKAAAAEMSHRV 82 V A AGSGKT ++ ++ L+ + + +T T AA EM RV Sbjct: 20 VLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERV 67 >gnl|CDD|132401 TIGR03358, VI_chp_5, type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. Length = 159 Score = 28.8 bits (65), Expect = 1.3 Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 2/33 (6%) Query: 182 LDNNEELKKAFYEILEISNDEDIETLISDIISN 214 LDNN +L+K E+L + + +E L+S++ + Sbjct: 129 LDNNPDLRKLLQELL--KDKDLLEKLLSELGAK 159 >gnl|CDD|161832 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR family. Members of this family are assumed to differ from each other in DNA site specificity. Length = 667 Score = 28.5 bits (64), Expect = 1.5 Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 10/100 (10%) Query: 94 DEILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEAIMQQFPLEANI 153 D L E +Q + + S A L + + GG+ + TI F + + ++ Sbjct: 306 DYQLMKEFQSLQKDCAERIE-SIA-ELKRLLEKDDGGIIITTIQKFDKKLKEEE------ 357 Query: 154 TSHFAIADEEQSKKLIEEAKKSTLASIMLDNNEELKKAFY 193 F + D ++ + +EA +S + + + LK A + Sbjct: 358 -EKFPV-DRKEVVVIFDEAHRSQYGELAKNLKKALKNASF 395 >gnl|CDD|178011 PLN02385, PLN02385, hydrolase; alpha/beta fold family protein. Length = 349 Score = 27.8 bits (62), Expect = 2.6 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 8/56 (14%) Query: 159 IADEEQSKKLIEEAKKSTLASIMLDNNEEL-KKAFYEILEISNDEDIETLISDIIS 213 + D SK L E+A S D +L + A++ ILE DE I ++ DIIS Sbjct: 292 VTDPSVSKFLYEKASSS-------DKKLKLYEDAYHSILEGEPDEMIFQVLDDIIS 340 >gnl|CDD|184801 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional. Length = 1627 Score = 27.9 bits (62), Expect = 2.8 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 7/55 (12%) Query: 161 DEEQSKKLIEEAKKSTLASIMLDNNEELKKAFYEILEISNDEDIETLISDIISNR 215 DEE+S+++ E + + EE K +YE+ E N E + I ++I+ R Sbjct: 287 DEEKSEEVKTE-------EVDEEFEEEEKGFYYELYEKVNIEANKKFIKEVIAGR 334 >gnl|CDD|128968 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases. Length = 216 Score = 27.4 bits (61), Expect = 3.4 Identities = 18/98 (18%), Positives = 39/98 (39%), Gaps = 12/98 (12%) Query: 127 TPGGLKVQTIHAFCEAIMQQFPLEANITSHFAIADEEQSKKLIEEAKKSTL--ASIMLD- 183 TP L + + EAI + L ++ +++L+E K++ + S+ + Sbjct: 61 TPTLLSPEQLEELLEAIREILGLADDVEITIETRPGTLTEELLEALKEAGVNRVSLGVQS 120 Query: 184 -NNEELKKA--------FYEILEISNDEDIETLISDII 212 ++E LK E +E + + +D+I Sbjct: 121 GSDEVLKAINRGHTVEDVLEAVEKLREAGPIKVSTDLI 158 >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 = 26.8 bits (60), Expect = 5.6 Identities = 10/26 (38%), Positives = 15/26 (57%) Query: 23 EQLLASDPTRSAWVSANAGSGKTHIL 48 QL A R ++ +GSGK+H+L Sbjct: 30 RQLAAGKGDRFLYLWGESGSGKSHLL 55 >gnl|CDD|132050 TIGR03005, ectoine_ehuA, ectoine/hydroxyectoine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins. Length = 252 Score = 26.7 bits (59), Expect = 5.7 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%) Query: 48 LVQRVLRLL--LANAHPSTLLCLTHTKAAAAEMSHRVL 83 LV VL ++ LA+ H T+L +TH A E + RV Sbjct: 181 LVGEVLNVIRRLASEHDLTMLLVTHEMGFAREFADRVC 218 >gnl|CDD|152382 pfam11947, DUF3464, Protein of unknown function (DUF3464). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 137 to 196 amino acids in length. Length = 149 Score = 26.5 bits (59), Expect = 5.8 Identities = 22/93 (23%), Positives = 32/93 (34%), Gaps = 14/93 (15%) Query: 161 DEEQSKKLIEEAKKST-LASIMLDNNEELKKAFYEILEISNDEDIETLISDIISNR---- 215 K+L E K+S + + S + E+ I ++SNR Sbjct: 1 MASSRKRLPFEPKRSRKKGYKAARKAAVAASKDKQKKKKSKRKASESGIPKVVSNRMIRR 60 Query: 216 --------TALKLIFFFFSY-LWRRKIIEKSLW 239 TAL + F SY L R II+ W Sbjct: 61 IAFFSGIPTALGMAVFVVSYLLVSRGIIDVPPW 93 >gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein. Length = 214 Score = 26.4 bits (59), Expect = 6.7 Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%) Query: 48 LVQRVLRLLLA-NAHPSTLLCLTHTKAAAAEMSHRVLEI 85 L +R+L LL N +T++ TH + ++HRV+ + Sbjct: 172 LSERILDLLKRLNKRGTTVIVATHDLSLVDRVAHRVIIL 210 >gnl|CDD|178475 PLN02887, PLN02887, hydrolase family protein. Length = 580 Score = 26.4 bits (58), Expect = 6.8 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 8/48 (16%) Query: 158 AIADEEQSKKLIEEAKKSTLAS--IMLDNNEELKKAFYEILEISNDED 203 AI D E ++++ LAS + L N E KA +++ +SNDED Sbjct: 528 AIGDGENDIEMLQ------LASLGVALSNGAEKTKAVADVIGVSNDED 569 >gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed. Length = 390 Score = 26.4 bits (59), Expect = 6.8 Identities = 25/127 (19%), Positives = 41/127 (32%), Gaps = 47/127 (37%) Query: 79 SHRVLEIITAWSHLSDEILSAEITKIQGKKPNKSDMSKARHLLITILETPGGL--KVQTI 136 S R LE AW L ++ E+ +++ + GGL V+ + Sbjct: 86 SKRRLEAEKAWDKLEEKFEEGEVVEVKVTE-----------------VVKGGLVVDVEGV 128 Query: 137 HAFCEAIM---------QQF---PLEANIT-----------SHFAIADEEQSKKLIEEAK 173 F A + F LE I S A+ +EE+ K Sbjct: 129 RGFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEER-----AAKK 183 Query: 174 KSTLASI 180 + L+S+ Sbjct: 184 EELLSSL 190 >gnl|CDD|184380 PRK13897, PRK13897, type IV secretion system component VirD4; Provisional. Length = 606 Score = 26.3 bits (58), Expect = 7.1 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 10/58 (17%) Query: 159 IADEEQSKKLIEEAKKSTLASIMLDNNEELKKAFYEILEISNDEDIETLISDIISNRT 216 I D EQ K + EEA N L + Y I +N+ + LIS ++ N+T Sbjct: 442 IQDTEQLKGIYEEAGM----------NSFLSNSTYRITFAANNIETANLISQLVGNKT 489 >gnl|CDD|185423 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional. Length = 202 Score = 25.8 bits (57), Expect = 9.8 Identities = 10/34 (29%), Positives = 16/34 (47%) Query: 160 ADEEQSKKLIEEAKKSTLASIMLDNNEELKKAFY 193 + + +K +EA+K LA + LKK Y Sbjct: 168 KKKVKLRKAWKEARKKALAKLPKAIVAVLKKFGY 201 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 0.129 0.360 Gapped Lambda K H 0.267 0.0793 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,763,099 Number of extensions: 228988 Number of successful extensions: 762 Number of sequences better than 10.0: 1 Number of HSP's gapped: 750 Number of HSP's successfully gapped: 57 Length of query: 242 Length of database: 5,994,473 Length adjustment: 91 Effective length of query: 151 Effective length of database: 4,028,145 Effective search space: 608249895 Effective search space used: 608249895 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: 56 (25.2 bits)