RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780711|ref|YP_003065124.1| signal recognition particle protein [Candidatus Liberibacter asiaticus str. psy62] (461 letters) >gnl|CDD|30887 COG0541, Ffh, Signal recognition particle GTPase [Intracellular trafficking and secretion]. Length = 451 Score = 546 bits (1408), Expect = e-156 Identities = 232/459 (50%), Positives = 317/459 (69%), Gaps = 9/459 (1%) Query: 1 MFDNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAK 60 MF++L +RL + + + GKG ++E D+ LREIRR LEADV+L+VV+ F KR++E+A Sbjct: 1 MFESLSDRLSNALKKLRGKGRITEKDVKEALREIRRALLEADVNLKVVKDFIKRIKERAL 60 Query: 61 GEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120 GE++ + + PGQ IKIV++ELV++LG E+ EL+L P VI++VGLQGSGKTTT K+ Sbjct: 61 GEEVPKGLTPGQQFIKIVYEELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKL 120 Query: 121 AYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSAR 180 A +LK K KK+L+ + D +RPAA EQL+ L EQ+ V E+ P +IA A + A+ Sbjct: 121 AKYLKK-KGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKAALEKAK 179 Query: 181 DGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIV 240 + GYD VI+DTAGR HI++ LM E+ EIK + NP E LLV DA+ GQDAV+ A+ F++ + Sbjct: 180 EEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAVNTAKAFNEAL 239 Query: 241 DLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRILGMGDV 300 +TG+ILT++DGD RGGAALS R +TGKPIK IGTGEKI+DLE F PDR A+RILGMGDV Sbjct: 240 GITGVILTKLDGDARGGAALSARAITGKPIKFIGTGEKIDDLEPFHPDRFASRILGMGDV 299 Query: 301 VSLVEKAARNLNEKQAALTAKKIAKGKFDLEDLAEQFRQTQKIGGIGSILRMLPGMPSLK 360 +SL+EKA ++E++A A+K+ KGKF LED EQ Q +K+G + +L M+PGM +K Sbjct: 300 LSLIEKAEEVVDEEEAEKLAEKLKKGKFTLEDFLEQLEQMKKMGPLSKLLSMIPGM-GMK 358 Query: 361 QNIMPSSFDDKTINHHIAIIASMTKEERANPSIIKHSRKKRIAAGSGTNAAKINKLLKLH 420 + D+K + AII SMT EER NP II SRK+RIA GSGT+ +NKLLK Sbjct: 359 DSDKDIELDEKKLKRIEAIIDSMTPEERENPDIINASRKRRIARGSGTSVQDVNKLLKQF 418 Query: 421 RQVAEMMHSTQGLGGNALTQQIMGRLKSKIGFGKNGRFP 459 +Q+ +MM G GG G++ + G+FP Sbjct: 419 KQMKKMMKKMSGGGG-------KGKMMRGMKGMMGGKFP 450 >gnl|CDD|35999 KOG0780, KOG0780, KOG0780, Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]. Length = 483 Score = 314 bits (805), Expect = 5e-86 Identities = 156/457 (34%), Positives = 238/457 (52%), Gaps = 8/457 (1%) Query: 1 MFDNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAK 60 + L R+ S F ++ S+ ET ++ L+EI R LE+DV+ +V+ + +++ Sbjct: 2 VLAELGRRITSAFSRMSNATSIDETALNTMLKEICRALLESDVNPRLVKELRENIRKIIN 61 Query: 61 GEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120 EK+ + +++ K V DELV++L L P VIM VGLQGSGKTTT K+ Sbjct: 62 LEKLASGVNKRRIIQKAVFDELVKLLDPGKSALQPKKGKPSVIMFVGLQGSGKTTTCTKL 121 Query: 121 AYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSAR 180 AY+ K K K+ + D R A +QL+ + +V E P KIA + Sbjct: 122 AYYYKK-KGYKVALVCADTFRAGAFDQLKQNATKARVPFYGSYTEADPVKIASEGVDRFK 180 Query: 181 DGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIV 240 +D +I+DT+GR+ SL +E+ ++ P EI+ V DA GQ A AR F + V Sbjct: 181 KENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQAAEAQARAFKETV 240 Query: 241 DLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRILGMGDV 300 D+ +ILT++DG +GG ALS T PI IGTGE ++DLE F P +R+LGMGD+ Sbjct: 241 DVGAVILTKLDGHAKGGGALSAVAATKSPIIFIGTGEHMDDLEPFDPKPFVSRLLGMGDI 300 Query: 301 VSLVEKAARNLNEKQAALTAKKIAKGKFDLEDLAEQFRQTQKIGGIGSILRMLPGMPSL- 359 LVEK + L +K+ +GKF L D +QF+ K+G + +L M+PGM + Sbjct: 301 EGLVEKVQEVGKDDAKELV-EKLKQGKFTLRDFYDQFQNIMKMGPLSQVLGMIPGMSMMS 359 Query: 360 KQNIMPSSFDDKTINHHIAIIASMTKEERANPSII--KHSRKKRIAAGSGTNAAKINKLL 417 K N SS + + ++ SMT EE +P + + SR R+A GSGT+ ++ +LL Sbjct: 360 KGNEEESS---AKLKRMMTMMDSMTDEELDSPELFVEEPSRIMRVARGSGTSVQEVMELL 416 Query: 418 KLHRQVAEMMHSTQGLGGNALTQQIMGRLKSKIGFGK 454 +++ A MM G+ G + + K Sbjct: 417 AQYKKFAAMMKKIGGIKGIFGALGNPNKNMNPAPMAK 453 >gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins. Length = 196 Score = 250 bits (641), Expect = 6e-67 Identities = 99/197 (50%), Positives = 136/197 (69%), Gaps = 1/197 (0%) Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDT 159 P VI+LVGLQGSGKTTT AK+A +LK + KK+L+ + D R AA EQL+ L E++ V Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAYLK-KQGKKVLLVAADTFRAAAIEQLKQLAERLGVPV 59 Query: 160 LEVIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILL 219 P +A A + A+ YD V++DTAGR + +LM E+ +IK + P E+LL Sbjct: 60 FGSGTGSDPAAVAFDAVEKAKAENYDVVLVDTAGRLQNDKNLMDELKKIKRVIAPDEVLL 119 Query: 220 VADALTGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKI 279 V DA TGQ+A++ A+ F++ V +TG+ILT++DGD +GGAALS+ TGKPIK IG GEKI Sbjct: 120 VLDATTGQNALNQAKAFNEAVGITGVILTKLDGDAKGGAALSIAAETGKPIKFIGVGEKI 179 Query: 280 NDLENFFPDRIANRILG 296 +DLE F P+R +R+LG Sbjct: 180 DDLEPFDPERFVSRLLG 196 >gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.. Length = 173 Score = 226 bits (577), Expect = 1e-59 Identities = 98/173 (56%), Positives = 130/173 (75%), Gaps = 1/173 (0%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLE 161 VI+LVGLQG GKTTT AK+A +LK K KK+L+ + D +RPAA EQLR LGEQ+ V E Sbjct: 2 VILLVGLQGVGKTTTAAKLALYLKK-KGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFE 60 Query: 162 VIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVA 221 + P IA RA + AR+ +D VI+DTAGR I+++LM+E+ +IK + P E+LLV Sbjct: 61 EGEGKDPVSIAKRAIEHAREENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVV 120 Query: 222 DALTGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIG 274 DA+TGQDAV+ A+ F++ + +TG+ILT++DGD RGGAALS+R VTGKPIK IG Sbjct: 121 DAMTGQDAVNQAKAFNEALGITGVILTKLDGDARGGAALSIRAVTGKPIKFIG 173 >gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular trafficking and secretion]. Length = 340 Score = 212 bits (542), Expect = 1e-55 Identities = 107/312 (34%), Positives = 162/312 (51%), Gaps = 20/312 (6%) Query: 1 MFDNLQERLGSIFQNITGK------GSLSETDISNTLREIRRTFLEADVSLEVVQSFSKR 54 F+ L++ L +N + E + L E+ +EADV +E + + Sbjct: 33 WFERLKQGLSKTKKNFGKGIKGLFLKKIKEKLDEDLLEELEELLIEADVGVETAEEIIEE 92 Query: 55 VQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGK----ESIELDLNAPSPLVIMLVGLQG 110 ++ K E + I+ + V + + + L+E+L + P VI+ VG+ G Sbjct: 93 LR---KREGKKKKIKDEETVKEALREALIEILRPVDKVDLPLEIPKEKKPFVILFVGVNG 149 Query: 111 SGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEK 170 GKTTT AK+A +LK + K +L+A+ D R AA EQL GE++ V + P Sbjct: 150 VGKTTTIAKLAKYLKQ-QGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISGKEGADPAA 208 Query: 171 IAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTN------PHEILLVADAL 224 +A A Q+A+ G D V++DTAGR H +LM E+ +I + PHEILLV DA Sbjct: 209 VAFDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDAT 268 Query: 225 TGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDLEN 284 TGQ+A+ A+ F++ V L GIILT++DG +GG LS+ G PIK IG GE +DL Sbjct: 269 TGQNALSQAKIFNEAVGLDGIILTKLDGTAKGGIILSIAYELGIPIKFIGVGEGYDDLRP 328 Query: 285 FFPDRIANRILG 296 F + + +LG Sbjct: 329 FDAEWFVDALLG 340 >gnl|CDD|36000 KOG0781, KOG0781, KOG0781, Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]. Length = 587 Score = 145 bits (368), Expect = 2e-35 Identities = 94/306 (30%), Positives = 158/306 (51%), Gaps = 22/306 (7%) Query: 11 SIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQP 70 +F+ + G SLSE D++ L ++ + +V+ E+ + + V +G+K+ Sbjct: 282 GLFKGLVGSKSLSEEDLNPVLDKMTEHLITKNVAAEIAEKLCESVAASLEGKKVGSFSTV 341 Query: 71 GQMVIKIVHDELVEVLG-KESIEL--DLNAPS----PLVIMLVGLQGSGKTTTTAKIAYH 123 V + + D LV++L + S++L D+ + P VI VG+ G GK+T AKIAY Sbjct: 342 ESTVKEALRDALVQILTPQRSVDLLRDIMSARRRKRPYVISFVGVNGVGKSTNLAKIAYW 401 Query: 124 LKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIP------EQSPEKIAIRATQ 177 L K ++L+A+ D R A EQLR E++ ++ + +A A Q Sbjct: 402 L-LQNKFRVLIAACDTFRSGAVEQLRTHVERLSALHGTMVELFEKGYGKDAAGVAKEAIQ 460 Query: 178 SARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFD 237 AR+ G+D V++DTAGR H N LM ++++ + P IL V +AL G D+V + F+ Sbjct: 461 EARNQGFDVVLIDTAGRMHNNAPLMTSLAKLIKVNKPDLILFVGEALVGNDSVDQLKKFN 520 Query: 238 KIV-------DLTGIILTRMDG-DGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDR 289 + + + GI+LT+ D D + GAA+SM +TGKPI +G G+ +DL Sbjct: 521 RALADHSTPRLIDGILLTKFDTVDDKVGAAVSMVYITGKPILFVGVGQTYSDLRKLNVKA 580 Query: 290 IANRIL 295 + ++ Sbjct: 581 VVATLM 586 >gnl|CDD|145891 pfam02978, SRP_SPB, Signal peptide binding domain. Length = 100 Score = 127 bits (321), Expect = 8e-30 Identities = 47/101 (46%), Positives = 65/101 (64%), Gaps = 1/101 (0%) Query: 327 KFDLEDLAEQFRQTQKIGGIGSILRMLPGMPSLKQNIMPSSFDDKTINHHIAIIASMTKE 386 KF L D EQ +Q +K+G + +L M+PGM L + + D+K + AII SMT + Sbjct: 1 KFTLRDFLEQLQQIKKMGPLSKLLSMIPGMGKLPK-LAEQELDEKKLKRIEAIIDSMTPK 59 Query: 387 ERANPSIIKHSRKKRIAAGSGTNAAKINKLLKLHRQVAEMM 427 ER NP II SRK+RIA GSGT+ ++NKLLK +Q+ +MM Sbjct: 60 ERDNPEIINGSRKRRIAKGSGTSVQEVNKLLKQFKQMKKMM 100 >gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and secretion]. Length = 407 Score = 95.8 bits (238), Expect = 2e-20 Identities = 65/212 (30%), Positives = 108/212 (50%), Gaps = 10/212 (4%) Query: 88 KESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTL-KKKKILMASLDVHRPAAQE 146 S+ +L VI LVG G GKTTT AK+A L KKKK+ + + D +R A E Sbjct: 191 LLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVE 250 Query: 147 QLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEIS 206 QL+ + + V LEV+ SP+++A D +++DTAGR+ + ++E+ Sbjct: 251 QLKTYADIMGVP-LEVV--YSPKELAEAIEALRD---CDVILVDTAGRSQYDKEKIEELK 304 Query: 207 EIKSLTNPHEILLVADALT-GQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTV 265 E+ +++ E+ LV A T +D + + F + + G+I T++D G S+ Sbjct: 305 ELIDVSHSIEVYLVLSATTKYEDLKEIIKQF-SLFPIDGLIFTKLDETTSLGNLFSLMYE 363 Query: 266 TGKPIKAIGTGEKI-NDLENFFPDRIANRILG 296 T P+ + G+++ D+ PD + RILG Sbjct: 364 TRLPVSYVTNGQRVPEDIVVANPDYLVRRILG 395 >gnl|CDD|145830 pfam02881, SRP54_N, SRP54-type protein, helical bundle domain. Length = 77 Score = 57.2 bits (139), Expect = 8e-09 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 7/81 (8%) Query: 5 LQERLGSIFQNITGKGS---LSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKG 61 L+E L + GK L E I L E+ LEADV +E + +R++E Sbjct: 1 LKEGLSKTRSKLGGKIKDLFLGEKKIDELLEELEEALLEADVGVETTEKIIERLKELVGR 60 Query: 62 EKILRSIQPGQMVIKIVHDEL 82 + + + + K + +EL Sbjct: 61 ----KGLSDPEEIKKALKEEL 77 >gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.. Length = 217 Score = 38.7 bits (90), Expect = 0.003 Identities = 36/154 (23%), Positives = 55/154 (35%), Gaps = 40/154 (25%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLE 161 VI G G GKTT A A L + KK+L+ S D + + L L + V+ E Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRL-AEEGKKVLLVSTDPAHNLSDKGLPNLSDAFIVEDPE 59 Query: 162 VIPEQSPEKIA--------------------------------IRATQSARDGGYDAVIL 189 + P E++ + + +G YD ++ Sbjct: 60 IAPNLYREEVDATRRVERAWGGEGGLMLELAAALPGIEELASLLAVFREFSEGLYDVIVF 119 Query: 190 DTAGRNHINDSLMQEISEIKSLTNPHE--ILLVA 221 DTA H L++E+ LT+P LV Sbjct: 120 DTAPTGHTLRLLVREL-----LTDPERTSFRLVT 148 >gnl|CDD|38089 KOG2878, KOG2878, KOG2878, Predicted kinase [General function prediction only]. Length = 282 Score = 38.9 bits (90), Expect = 0.003 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 2/52 (3%) Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHL--KTLKKKKILMASLDVHRPAAQEQLR 149 PLVI G QGSGK+T + Y L K +++ S+D + Q Sbjct: 31 PLVIGFSGPQGSGKSTLVFALDYKLTKKYIQEYSSATISVDDFYLTHEGQAE 82 >gnl|CDD|33963 COG4240, COG4240, Predicted kinase [General function prediction only]. Length = 300 Score = 38.4 bits (89), Expect = 0.004 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 7/73 (9%) Query: 69 QPGQMVIKIVHDELVEVLGK---ESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLK 125 + + D + +L K + E PL++ + G QGSGK+T +A I L Sbjct: 20 RLPPAFAALAQDLHLPLLAKIAPWAQERG----RPLIVGISGPQGSGKSTLSALIVRLLA 75 Query: 126 TLKKKKILMASLD 138 ++ SLD Sbjct: 76 AKGLERTATLSLD 88 >gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.. Length = 99 Score = 36.2 bits (83), Expect = 0.017 Identities = 13/33 (39%), Positives = 19/33 (57%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILM 134 VI++ G G GKTT A +A L K+ +L+ Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33 >gnl|CDD|31385 COG1192, Soj, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]. Length = 259 Score = 34.4 bits (78), Expect = 0.071 Identities = 31/180 (17%), Positives = 57/180 (31%), Gaps = 42/180 (23%) Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDT---------- 159 G GKTTT +A L KK+L+ LD +LG + ++ Sbjct: 13 GVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSL----TSWLGLRPDLEGDLYNLLSGLK 68 Query: 160 --------------LEVIPE-------------QSPEKIAIRATQSARDGGYDAVILDTA 192 L++IP +++ ++ YD +I+DT Sbjct: 69 ERPDILDYTVVIEGLDLIPSNIDLAEGAEIELNAVAKELLLKRLLDPVKDDYDYIIIDTP 128 Query: 193 -GRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIVDLTGIILTRMD 251 + + + + P + L L + + + GI++TR D Sbjct: 129 PSLGVLTLNALAAADHVLIPVQPEFLDLEGLEQLLNTLEDLLKLRRNKLIVVGILITRFD 188 >gnl|CDD|110585 pfam01591, 6PF2K, 6-phosphofructo-2-kinase. This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyses both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. This enzyme contains a P-loop motif. Length = 223 Score = 33.8 bits (78), Expect = 0.10 Identities = 11/29 (37%), Positives = 17/29 (58%) Query: 99 SPLVIMLVGLQGSGKTTTTAKIAYHLKTL 127 S +I++VGL GKT + K+ +L L Sbjct: 12 SKTMIVMVGLPARGKTYISKKLTRYLNWL 40 >gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions. Length = 158 Score = 33.3 bits (77), Expect = 0.13 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 15/61 (24%) Query: 103 IMLVGLQGSGKTT------------TTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRY 150 I+++GL G+GKTT T I ++++T++ K + DV Q+++R Sbjct: 2 ILILGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVSFTVWDV---GGQDKIRP 58 Query: 151 L 151 L Sbjct: 59 L 59 >gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.. Length = 165 Score = 32.4 bits (73), Expect = 0.26 Identities = 27/133 (20%), Positives = 56/133 (42%), Gaps = 14/133 (10%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLE 161 +I++ G GSGKTT ++A ++ T K K++ ++ E+L + +D L Sbjct: 1 LILVFGPTGSGKTTLALQLALNIAT-KGGKVVYVDIEEEIEELTERLIGESLKGALDNLI 59 Query: 162 VI----PEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDS---------LMQEISEI 208 ++ + + ++ +A + GG D +ILD R L +E+ E+ Sbjct: 60 IVFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELREL 119 Query: 209 KSLTNPHEILLVA 221 + ++ Sbjct: 120 LERARKGGVTVIF 132 >gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]. Length = 299 Score = 32.2 bits (73), Expect = 0.35 Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 9/95 (9%) Query: 36 RTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKESIELDL 95 R+ A V ++ S + +QE+ K E I R + + I+ V+ +L+E E + L Sbjct: 22 RSLTAAGVDPDLAYSIAIEIQEELKKEGI-RLVTKDE--IREVYQKLLEKGDPEVAKRYL 78 Query: 96 ------NAPSPLVIMLVGLQGSGKTTTTAKIAYHL 124 PL+I++ G G GK+T ++A L Sbjct: 79 LWRRIRKMKRPLIILIGGASGVGKSTIAGELARRL 113 >gnl|CDD|144508 pfam00931, NB-ARC, NB-ARC domain. Length = 285 Score = 31.5 bits (72), Expect = 0.46 Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 4/41 (9%) Query: 80 DELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120 D + ++ K L + + V+ +VG+ G GKTT +I Sbjct: 3 DMIEALIEK----LLEMSENLGVVGIVGMGGVGKTTLAKQI 39 >gnl|CDD|36745 KOG1532, KOG1532, KOG1532, GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]. Length = 366 Score = 31.5 bits (71), Expect = 0.52 Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%) Query: 99 SPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQE 146 P++I++VG+ GSGKTT ++ HL KK + +LD PA + Sbjct: 18 RPVIILVVGMAGSGKTTFMQRLNSHLHA-KKTPPYVINLD---PAVRN 61 >gnl|CDD|31114 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]. Length = 448 Score = 31.4 bits (71), Expect = 0.57 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%) Query: 67 SIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGS-GKTTTTAKIAYHLK 125 I P +++ +E++G + L+ +P+V + G+ GKTTTT+ IA+ LK Sbjct: 78 GIPPTHPLVEAAKAAGIEIIGDIELFYRLSGEAPIV----AITGTNGKTTTTSLIAHLLK 133 Query: 126 TLKKKKILM 134 +L Sbjct: 134 AAGLDALLG 142 >gnl|CDD|73302 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.. Length = 104 Score = 31.0 bits (70), Expect = 0.69 Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 1/29 (3%) Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLD 138 G GKTTT +A L + K++L+ LD Sbjct: 10 GVGKTTTAVNLAAAL-ARRGKRVLLIDLD 37 >gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]. Length = 323 Score = 31.1 bits (70), Expect = 0.72 Identities = 26/114 (22%), Positives = 50/114 (43%), Gaps = 15/114 (13%) Query: 92 ELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYL 151 L + VI + G+ G+GK+T + L+ + ++ + ++D P + L Sbjct: 43 ALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRE-RGHRVAVLAVDPSSPFTGGSI--L 99 Query: 152 GEQIQVDTLEVIPEQSPEKIAIRAT-----QSARD-------GGYDAVILDTAG 193 G++I++ L V P R T ++ R+ GYD +I++T G Sbjct: 100 GDRIRMQRLAVDPGVFIRSSPSRGTLGGLSRATREAIKLLDAAGYDVIIVETVG 153 >gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. Length = 103 Score = 31.0 bits (71), Expect = 0.74 Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 4/47 (8%) Query: 103 IMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR 149 ++V GSGKT T AK+ L KKK + + V R EQ Sbjct: 21 GLIVMATGSGKTLTAAKLIARLLKGKKKVLFL----VPRKDLLEQAL 63 >gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop. Length = 122 Score = 30.8 bits (70), Expect = 0.77 Identities = 12/38 (31%), Positives = 22/38 (57%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDV 139 ++++VG + SGKTT K+ +LK + ++ LD Sbjct: 2 IVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDH 39 >gnl|CDD|109652 pfam00604, Flu_PB2, Influenza RNA-dependent RNA polymerase subunit PB2. PB2 can bind 5' end cap structure of RNA. Length = 759 Score = 31.0 bits (70), Expect = 0.78 Identities = 23/69 (33%), Positives = 28/69 (40%), Gaps = 4/69 (5%) Query: 245 IILTRMDGDGRGG---AALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRILGMGDVV 301 L + G A L V GK G IN+L N AN ++G GDVV Sbjct: 673 GALPEDPDEETMGVESAVLRGFLVLGKEDPRYGPALTINELSNLAKGEKANVLIGQGDVV 732 Query: 302 SLVEKAARN 310 LV K R+ Sbjct: 733 -LVMKRKRD 740 >gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]. Length = 845 Score = 30.7 bits (69), Expect = 0.85 Identities = 30/112 (26%), Positives = 44/112 (39%), Gaps = 16/112 (14%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILM------ASLDVHRPAAQEQLRYLGEQI 155 V+++VG GSGKTT + KI A+ V A+E LGE + Sbjct: 67 VVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETV 126 Query: 156 --------QVDTLEVIPEQSPEKIAIRATQSARD-GGYDAVILDTAGRNHIN 198 +V I + + I +R Q+ GY VI+D A +N Sbjct: 127 GYSIRFESKVSPRTRI-KVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLN 177 >gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria. Length = 374 Score = 30.6 bits (70), Expect = 1.0 Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 10/54 (18%) Query: 146 EQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVI-------LDTA 192 E LR G I+V + V E S E + A AR+ G D VI +D Sbjct: 41 EALRAAG--IEVTHVVVAGEPSVELVD-AAVAEARNAGCDVVIAIGGGSVIDAG 91 >gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional. Length = 489 Score = 30.4 bits (69), Expect = 1.1 Identities = 12/25 (48%), Positives = 18/25 (72%) Query: 98 PSPLVIMLVGLQGSGKTTTTAKIAY 122 P+P ++LVG+QG+GK+ T IA Sbjct: 257 PTPRGLLLVGIQGTGKSLTAKAIAN 281 >gnl|CDD|37264 KOG2053, KOG2053, KOG2053, Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]. Length = 932 Score = 30.3 bits (68), Expect = 1.1 Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 1/83 (1%) Query: 120 IAYHLKTLKKKKILMASLD-VHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQS 178 KTL K I +L + A+ R + + S ++ + Sbjct: 492 AYELYKTLDIKNIQTDTLGHLIFRRAETSGRSSFASNTFNEHLKFYDSSLKETPEYIALA 551 Query: 179 ARDGGYDAVILDTAGRNHINDSL 201 R G Y + A R+ + SL Sbjct: 552 YRRGAYSKIPEMLAFRDRLMHSL 574 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 30.2 bits (68), Expect = 1.3 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 8/64 (12%) Query: 103 IMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQ--VDTL 160 I+++G G+GK+T K+A KK + AA + LGE+I+ +D Sbjct: 3 ILILGPPGAGKSTLAKKLA------KKLGLPHLDTGDILRAAIAERTELGEEIKKYIDKG 56 Query: 161 EVIP 164 E++P Sbjct: 57 ELVP 60 >gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]. Length = 935 Score = 30.0 bits (67), Expect = 1.4 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 3/49 (6%) Query: 88 KESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMAS 136 +++ L P + ++ G G+GKT T+A I YHL +L+ + Sbjct: 416 SNAVKHVLQRP---LSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCA 461 >gnl|CDD|30812 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]. Length = 494 Score = 30.1 bits (67), Expect = 1.4 Identities = 22/100 (22%), Positives = 36/100 (36%), Gaps = 9/100 (9%) Query: 31 LREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKES 90 LRE+RR + V + + +K + + + I E + KE+ Sbjct: 198 LRELRRAIDLVGEYIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKEELKEA 257 Query: 91 IELDL---------NAPSPLVIMLVGLQGSGKTTTTAKIA 121 IE L P ++L G G+GKT +A Sbjct: 258 IETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVA 297 >gnl|CDD|73299 cd02036, MinD, Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.. Length = 179 Score = 29.8 bits (67), Expect = 1.5 Identities = 25/111 (22%), Positives = 45/111 (40%), Gaps = 20/111 (18%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL------MASLDVHRPAAQEQLRYLGEQI 155 +++ G G GKTTTTA + L L K +L + +LD+ L ++ Sbjct: 2 IVVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLI--------LGLENRV 53 Query: 156 QVDTLEVIPEQ-----SPEKIAIRATQSARDGGYDAVILDTAGRNHINDSL 201 +V+ SP I R +A +A+++ T + + D+ Sbjct: 54 VYTLHDVLAGDYILIDSPAGIE-RGFITAIAPADEALLVTTPEISSLRDAD 103 >gnl|CDD|36142 KOG0924, KOG0924, KOG0924, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]. Length = 1042 Score = 30.0 bits (67), Expect = 1.6 Identities = 44/215 (20%), Positives = 77/215 (35%), Gaps = 36/215 (16%) Query: 3 DNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGE 62 + G+ N+ G + E + V S+ V E A + Sbjct: 295 KKHWKLAGTALGNVMG--------LEKKNDEDGKVAYRGSVKFASHMKKSEAVSEFASKK 346 Query: 63 KILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAY 122 I Q + + D+L+ V+ + V+++VG GSGKTT A+ Y Sbjct: 347 SIRE--QRQYLPVFACRDQLLSVIRENQ-----------VVVIVGETGSGKTTQLAQYLY 393 Query: 123 HLKTLKKKKI------LMASLDVHRPAAQEQLRYLGEQI-------QVDTLEVIPEQSPE 169 I +A++ V + A+E LG+ + V + + + + Sbjct: 394 EDGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSEDTKIKYMTD 453 Query: 170 KIAIRATQSARD-GGYDAVILDTAGRNHIN-DSLM 202 I +R + RD Y +I+D A +N D L Sbjct: 454 GILLRESLKDRDLDKYSVIIMDEAHERSLNTDILF 488 >gnl|CDD|29614 cd01567, NAPRTase_PncB, Nicotinate phosphoribosyltransferase (NAPRTase) family. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.. Length = 343 Score = 29.9 bits (67), Expect = 1.6 Identities = 32/148 (21%), Positives = 47/148 (31%), Gaps = 30/148 (20%) Query: 212 TNPHEILLVADALTGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIK 271 T H + AL AR + GI L G Sbjct: 203 TMAHSWIQAFGALEEAAFEAFARWLPQFGGGLGIALIDTYDTDNG--------------- 247 Query: 272 AIGTGEKINDLENFFPDRIANRILGM----GDVVSLVEKAARNLNEKQAALTAKKI-AKG 326 +N L+ +LG+ GD V L++K ++L+E L KKI G Sbjct: 248 ------FLNALKLAKALGAGGGLLGVRLDSGDPVELIKKVRKHLDELGIDLNKKKIIISG 301 Query: 327 KFDLEDLAEQFRQTQKIG----GIGSIL 350 D E+ E + G+G+ L Sbjct: 302 DLDTEEAIELLLEQGASPNDAFGVGTSL 329 >gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.. Length = 159 Score = 29.8 bits (67), Expect = 1.8 Identities = 12/26 (46%), Positives = 13/26 (50%) Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHLK 125 VI VG GSGKTT K+ L Sbjct: 1 MKVIGFVGYSGSGKTTLLEKLIPALS 26 >gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.. Length = 116 Score = 29.4 bits (66), Expect = 2.0 Identities = 27/113 (23%), Positives = 41/113 (36%), Gaps = 13/113 (11%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLD--------VHRPAAQEQLRYLGE 153 I + G G GKTT A +A +L K K +L D + L +G Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAE-KGKPVLAIDADPDDLPERLSVEVGEIKLLLVMGM 59 Query: 154 QIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVILDT-AGRNHINDSLMQEI 205 PE + +R RD + V++DT AG H+ + + Sbjct: 60 GRPGGEGCYCPENALLNALLRHLVLTRD---EQVVVDTEAGLEHLGRGTAEGV 109 >gnl|CDD|145019 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family. Length = 212 Score = 29.3 bits (66), Expect = 2.1 Identities = 34/182 (18%), Positives = 60/182 (32%), Gaps = 47/182 (25%) Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAA---------QEQLRYLGEQIQ---- 156 G GKTT A +A L + ++L+ LD + L+ E + Sbjct: 9 GVGKTTLAANLARALA-KRGYRVLLIDLDPQANLTSSLGKGPDLIDVLKEGLEIVDAQPL 67 Query: 157 ------------VDTLEVIPE----QSPEKIAIRATQSAR--DGGYDAVILDTAGRNHIN 198 +D L +IP + E I YD VI+D A Sbjct: 68 QHIAAAIVPSRNLDPLLLIPSNLSLANFESELILEGGEEGLIKLAYDYVIIDGAP----- 122 Query: 199 DSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIV-----DLTGIILTRMDGD 253 L + +L +++ + AV A+ ++V + G++L ++D Sbjct: 123 -GLGELT--ANALVAADILVVPIEP--EGVAVLGAQRLLELVERLGLKILGVVLNKVDRG 177 Query: 254 GR 255 Sbjct: 178 DE 179 >gnl|CDD|32636 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 353 Score = 29.4 bits (66), Expect = 2.1 Identities = 26/109 (23%), Positives = 48/109 (44%), Gaps = 9/109 (8%) Query: 27 ISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDEL--VE 84 +++ R+I E D S + RV + +V++++ ++ +E Sbjct: 57 LNDDQRKILEENGELDFSYTLPGVARFRVN-------AFKQRGGYALVLRLIPSKIPTLE 109 Query: 85 VLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL 133 LG I +L +I++ G GSGK+TT A + ++ K K IL Sbjct: 110 ELGLPPIVRELAESPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHIL 158 >gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General function prediction only]. Length = 398 Score = 29.5 bits (66), Expect = 2.2 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%) Query: 81 ELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVH 140 E +E + +A V+M+VG SGK+T T +A L + +K+ + DV Sbjct: 54 EPLEEIADTWESKSESAGKVGVVMVVGPVDSGKSTLTTYLANKL-LARGRKVAIIDADVG 112 Query: 141 RP 142 + Sbjct: 113 QS 114 >gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved. Length = 159 Score = 29.2 bits (66), Expect = 2.2 Identities = 13/19 (68%), Positives = 13/19 (68%) Query: 103 IMLVGLQGSGKTTTTAKIA 121 I LVGLQ SGKTT IA Sbjct: 2 ITLVGLQNSGKTTLVNVIA 20 >gnl|CDD|31969 COG1783, XtmB, Phage terminase large subunit [General function prediction only]. Length = 414 Score = 29.2 bits (65), Expect = 2.3 Identities = 25/112 (22%), Positives = 42/112 (37%), Gaps = 6/112 (5%) Query: 103 IMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASL----DVHRPAAQEQLRYLGEQIQVD 158 + G +GS K+ TA K L + I + + + H+ + + ++ V Sbjct: 27 FIAKGGRGSSKSYATALKNI-EKLLSEPGIDVLVIREVENTHKQSTYALFKEALSELGVT 85 Query: 159 TLEVIPEQSPEKIA-IRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIK 209 I + SPE I + G D L + N I+D +E SE Sbjct: 86 KFFKISKSSPEIILKDTGQRIIFKGLDDPAKLKSIAVNWISDLWFEEASEFS 137 >gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.. Length = 180 Score = 29.2 bits (66), Expect = 2.3 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%) Query: 93 LDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLG 152 L L+ + ++ ++G G+GK+T +A LK +IL+ D+ + +E R + Sbjct: 18 LSLSIEAGEIVGILGPNGAGKSTLLKTLAGLLK-PSSGEILLDGKDLASLSPKELARKIA 76 >gnl|CDD|29991 cd01125, repA, Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.. Length = 239 Score = 29.2 bits (65), Expect = 2.3 Identities = 31/196 (15%), Positives = 53/196 (27%), Gaps = 57/196 (29%) Query: 102 VIMLVGLQGSGKTTTTAKIAYH-----------LKTLKKKKILMASLDVHRPAAQEQLRY 150 V LV G+GK++ +A LK + +++ S + R +L Sbjct: 3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRLEA 62 Query: 151 LGEQIQVDTLEV------------------IPEQSPEKIAIRATQSARDGGYDAVILDTA 192 + + ++ D PE I D V++D Sbjct: 63 ILQHLEPDDAGDRLFIDSGRIQPISIAREGRIIVVPEFERIIE--QLLIRRIDLVVIDPL 120 Query: 193 GRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIVDLT--------G 244 H S + + V AL +A + L Sbjct: 121 VSFH-----------GVSENDNGAMDAVIKALR-----RIAAQTGAAILLVHHVRKGSAK 164 Query: 245 IILTRMDGDGRGGAAL 260 T+ RG +AL Sbjct: 165 DGDTQ--EAARGASAL 178 >gnl|CDD|173952 cd08193, HVD, 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene. Length = 376 Score = 29.0 bits (66), Expect = 2.4 Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 16/88 (18%) Query: 118 AKIAYHLKTLKKKKIL------MASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKI 171 A++ L L K++L + + P L G ++ V +V + PE + Sbjct: 15 ARLGELLAALGAKRVLVVTDPGILKAGLIDPLLAS-LEAAGIEVTVFD-DVEAD-PPEAV 71 Query: 172 AIRATQSARDGGYDAVI-------LDTA 192 A ++AR G D VI +D A Sbjct: 72 VEAAVEAARAAGADGVIGFGGGSSMDVA 99 >gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism]. Length = 218 Score = 29.1 bits (65), Expect = 2.4 Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 3/41 (7%) Query: 98 PSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLD 138 ++I + G GSGKTT +++ + L +K+++ SLD Sbjct: 6 EKVIIIGIAGGSGSGKTTVAKELS---EQLGVEKVVVISLD 43 >gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication, recombination and repair]. Length = 1100 Score = 29.2 bits (65), Expect = 2.5 Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%) Query: 104 MLVGLQGSGKTTTTAKIAYHLKTLKKKKILMAS 136 +++G+ G+GKTTT + + L KK+L+ S Sbjct: 689 LILGMPGTGKTTTISLLIKIL-VALGKKVLLTS 720 >gnl|CDD|110578 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif. Length = 157 Score = 29.2 bits (66), Expect = 2.5 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 5/40 (12%) Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHL-KTLKKKKILMASLD 138 + GL GSGK+T IA L + L + I + LD Sbjct: 2 GCTVWFTGLSGSGKST----IANALERKLFAQGISVYVLD 37 >gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.. Length = 271 Score = 29.1 bits (65), Expect = 2.6 Identities = 12/37 (32%), Positives = 18/37 (48%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLD 138 +I+L G GKTT + A L T ++ SL+ Sbjct: 32 LIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLE 68 >gnl|CDD|33900 COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 352 Score = 29.1 bits (65), Expect = 2.9 Identities = 12/36 (33%), Positives = 19/36 (52%) Query: 86 LGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIA 121 LG +++ + P+ + L G GSGKT+ IA Sbjct: 10 LGNFALDANFTLPARGITALFGPSGSGKTSLINMIA 45 >gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).. Length = 200 Score = 28.7 bits (64), Expect = 3.0 Identities = 10/33 (30%), Positives = 18/33 (54%) Query: 101 LVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL 133 + I+ G+ G+GKTT +A L+ + +L Sbjct: 1 MFIVFEGIDGAGKTTLIELLAERLEARGYEVVL 33 >gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction mechanisms]. Length = 889 Score = 28.7 bits (64), Expect = 3.1 Identities = 21/88 (23%), Positives = 33/88 (37%), Gaps = 9/88 (10%) Query: 45 LEVVQSF-SKRVQEKAKGEKILRSIQ---PGQMVIKIVHDELVEVLGKESIELDLNAPSP 100 L V+S SK V E R P Q + + ++E L +E D Sbjct: 125 LREVESLGSKGVFEVVGESLDPREKVETRPIQSESDVGLETMLEKLWNRLMEDD-----V 179 Query: 101 LVIMLVGLQGSGKTTTTAKIAYHLKTLK 128 ++ + G+ G GKTT +I + Sbjct: 180 GIVGIYGMGGVGKTTLARQIFNKFDEVG 207 >gnl|CDD|30853 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]. Length = 696 Score = 28.9 bits (64), Expect = 3.3 Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 10/89 (11%) Query: 54 RVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPL-------VIMLV 106 E + + +++ VH L EV K + L L L V ML Sbjct: 284 ARAELRILDSLFVALKIRA---GTVHRLLGEVPAKVKLRLSLEQKEALDVLVVDEVSMLT 340 Query: 107 GLQGSGKTTTTAKIAYHLKTLKKKKILMA 135 G G+GKTT IA +K ++L A Sbjct: 341 GGPGTGKTTAIKAIARLIKEGDGDQLLAA 369 >gnl|CDD|133337 cd04137, RheB, Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that leads to cell growth and cell-cycle progression. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Length = 180 Score = 28.7 bits (65), Expect = 3.4 Identities = 13/34 (38%), Positives = 24/34 (70%), Gaps = 10/34 (29%) Query: 74 VIKIVHDELVEVLGKESIELDLNAPSPLVIMLVG 107 V+K+++D+++++LGKES+ P I+LVG Sbjct: 90 VVKVIYDKILDMLGKESV------P----IVLVG 113 >gnl|CDD|29997 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.. Length = 198 Score = 28.7 bits (64), Expect = 3.6 Identities = 11/32 (34%), Positives = 19/32 (59%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL 133 ++++ G GSGK+TT A + ++ K IL Sbjct: 3 LVLVTGPTGSGKSTTLAAMIDYINKNKTHHIL 34 >gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]. Length = 366 Score = 28.8 bits (64), Expect = 3.6 Identities = 10/37 (27%), Positives = 15/37 (40%) Query: 95 LNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKK 131 L P I++ G G+GKT T + L+ Sbjct: 37 LRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANV 73 >gnl|CDD|30201 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).. Length = 179 Score = 28.3 bits (63), Expect = 4.0 Identities = 10/26 (38%), Positives = 15/26 (57%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTL 127 V+ + G GSGKTT K++ L+ Sbjct: 1 VVGIAGPSGSGKTTFAKKLSNQLRVN 26 >gnl|CDD|30835 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]. Length = 265 Score = 28.5 bits (63), Expect = 4.1 Identities = 39/192 (20%), Positives = 65/192 (33%), Gaps = 44/192 (22%) Query: 102 VIMLV-GLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR----------- 149 VI + G G GK+T +A L K++L+ D+ P+ L Sbjct: 59 VIAVTSGKGGVGKSTVAVNLAAAL-AQLGKRVLLLDADLRGPSIPRMLGLENLPGLTELL 117 Query: 150 ---YLGEQIQVDTLEVI--------PEQSPEKIAIRATQ----SARDGGYDAVILDTAGR 194 L IQ D ++V+ P + +A G YD VI+DT Sbjct: 118 AGEALEPVIQHDGIKVLSILPLGPVPVIPRGLLGSKAMLQLLEDVLWGEYDYVIIDTPPG 177 Query: 195 NHIND-SLMQEISEIKSLTNPHEILLVA--DALTGQDAVHLARNFDKI-VDLTGIILTRM 250 D +++Q I P +++V +D +K + + G++ Sbjct: 178 TGDADATVLQRI--------PDGVVIVTTPGKTALEDVKKAIDMLEKAGIPVLGVVENMS 229 Query: 251 DG----DGRGGA 258 G GG Sbjct: 230 YFICPRCGEGGG 241 >gnl|CDD|31564 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]. Length = 398 Score = 28.5 bits (63), Expect = 4.6 Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 14/133 (10%) Query: 92 ELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDV--HRPAAQEQLR 149 + P +I+++G + GKTT + +K L ++ I + D+ R + LR Sbjct: 29 LIKKLDLRPFIILILGPRQVGKTTL---LKLLIKGLLEEIIYINFDDLRLDRIELLDLLR 85 Query: 150 YLGEQIQVDTLEVIPE--QSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISE 207 E + + + + Q+ RA + D G V++ G + S EISE Sbjct: 86 AYIELKEREKSYIFLDEIQNVPDW-ERALKYLYDRGNLDVLI--TGSSSSLLSK--EISE 140 Query: 208 IKSLTNPHEILLV 220 SL + L + Sbjct: 141 --SLAGRGKDLEL 151 >gnl|CDD|38335 KOG3125, KOG3125, KOG3125, Thymidine kinase [Nucleotide transport and metabolism]. Length = 234 Score = 28.4 bits (63), Expect = 4.7 Identities = 32/193 (16%), Positives = 62/193 (32%), Gaps = 27/193 (13%) Query: 98 PSPLVIM-------LVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRY 150 SPL M ++G SGKTT + ++ +L+ R + + + Sbjct: 18 NSPLCPMTRGTIHVILGPMFSGKTTELLRRIRREIIAGRRVLLIKYAKDTRYESSSIVTH 77 Query: 151 LGEQIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKS 210 G ++ L S + A +G D + +D A + Sbjct: 78 DGIEMPCWALPDASFLS------EFGKDALNGDVDVIGIDEA------QFFGDLYEFCRE 125 Query: 211 LTNPHEILLVADALTGQDAVHLARNFDKIVDLTGIILTRMDGDGR-----GGAALSMRTV 265 + + H ++ L G + F I+DL + + A ++R Sbjct: 126 VADVHGKTVIVAGLDGD---FKRKPFGAILDLVPLADSVTKLTAVCEECGADARFTLRKT 182 Query: 266 TGKPIKAIGTGEK 278 K ++ IG + Sbjct: 183 NDKEVEVIGGADV 195 >gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.. Length = 154 Score = 28.2 bits (63), Expect = 4.9 Identities = 10/23 (43%), Positives = 15/23 (65%) Query: 103 IMLVGLQGSGKTTTTAKIAYHLK 125 I+L+G+ G+GKTT +A L Sbjct: 2 IVLIGMMGAGKTTVGRLLAKALG 24 >gnl|CDD|35828 KOG0608, KOG0608, KOG0608, Warts/lats-like serine threonine kinases [Cell cycle control, cell division, chromosome partitioning]. Length = 1034 Score = 28.2 bits (62), Expect = 4.9 Identities = 30/123 (24%), Positives = 58/123 (47%), Gaps = 15/123 (12%) Query: 36 RTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLG-KES--IE 92 + F+E V V++S+ +R + K + EK + I+ +++ ++L KES I Sbjct: 566 KFFMEQHVE-NVLKSYQQREKRKKQLEKEMVKAGLPD----IMQNQMRKMLQQKESNYIR 620 Query: 93 L---DLNAPSPLVIMLVGLQGSGKTTTTAKI----AYHLKTLKKKKILMASLDVHRPAAQ 145 L ++ + I +G+ G+ K+ Y +KTL+K +LM + H A + Sbjct: 621 LKRAKMDKSMFVKIKTIGVGAFGEVCLVRKVDTRALYAMKTLRKADVLMRNQVAHVKAER 680 Query: 146 EQL 148 + L Sbjct: 681 DIL 683 >gnl|CDD|38801 KOG3595, KOG3595, KOG3595, Dyneins, heavy chain [Cytoskeleton]. Length = 1395 Score = 28.0 bits (62), Expect = 5.4 Identities = 25/125 (20%), Positives = 47/125 (37%), Gaps = 14/125 (11%) Query: 1 MFDNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAK 60 LQE L +F+ + + L D + +I L V+ ++ K Sbjct: 380 FDKKLQEVLLKLFEADSLQMPLLYGDFRSESHKIYEEVLS-------VELLRGVLEAYLK 432 Query: 61 GEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120 I + + ++ + +E + + I+ L P +LVG+ GSGK + T Sbjct: 433 QFNIEE----IRPMHLVLFRDAIEHVLR--IDRILRQPRGHA-LLVGVGGSGKQSLTRLA 485 Query: 121 AYHLK 125 A+ Sbjct: 486 AFING 490 >gnl|CDD|39108 KOG3905, KOG3905, KOG3905, Dynein light intermediate chain [Cell motility]. Length = 473 Score = 28.1 bits (62), Expect = 5.5 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 2/67 (2%) Query: 84 EVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL-MASLDVHRP 142 E+L + S PS ++++G GSGKT+ +K+ +T+KK L L VH Sbjct: 36 EILSEVSTRTRSKLPSGKNVLVLGDNGSGKTSLISKLQ-GSETVKKGSGLEYLYLHVHDE 94 Query: 143 AAQEQLR 149 + R Sbjct: 95 DRDDLTR 101 >gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]. Length = 260 Score = 28.1 bits (62), Expect = 5.5 Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 4/90 (4%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLG---EQIQVD 158 V+++ G G+GKT + Y + + +L S + E R G E Sbjct: 25 VVLITGPPGTGKTIFALQFLYEGAR-EGEPVLYVSTEESPEELLENARSFGWDLEVYIEK 83 Query: 159 TLEVIPEQSPEKIAIRATQSARDGGYDAVI 188 I + + + + + ++ Sbjct: 84 GKLAILDAFLSEKGLVSIVVGDPLDLEELL 113 >gnl|CDD|33657 COG3867, COG3867, Arabinogalactan endo-1,4-beta-galactosidase [Carbohydrate transport and metabolism]. Length = 403 Score = 28.1 bits (62), Expect = 5.5 Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 2/54 (3%) Query: 231 HLARNFDK--IVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDL 282 +A + K +V T T DGDG S G PI G + D+ Sbjct: 269 DIASRYHKDVMVVETAYTYTLEDGDGHENTFPSSEQTGGYPITVQGQATFVRDV 322 >gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1381 Score = 27.9 bits (62), Expect = 6.2 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 8/85 (9%) Query: 36 RTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKESIE--- 92 ++A VSL+ ++ F +E + G+ I+I ES E Sbjct: 481 SQLVQAKVSLKRLKEF-LLSEELDPDSVERSPDEAGENAIEI--KNGSFSWDSESPEPTL 537 Query: 93 --LDLNAPSPLVIMLVGLQGSGKTT 115 ++ ++ +VG GSGK++ Sbjct: 538 KDINFEIKKGQLVAVVGPVGSGKSS 562 >gnl|CDD|99868 cd06115, AthCS_per_like, Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains three Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3 which are involved in the glyoxylate cycle. AthCYS1, in addition to a peroxisomal targeting sequence, has a predicted secretory signal peptide; it may be targeted to both the secretory pathway and the peroxisomes and is thought to be located in the extracellular matrix. AthCSY1 is expressed only in siliques and specifically in developing seeds. AthCSY2 and 3 are active during seed germination and seedling development and are thought to participate in the beta-oxidation of fatty acids.. Length = 410 Score = 27.8 bits (62), Expect = 6.2 Identities = 13/56 (23%), Positives = 31/56 (55%), Gaps = 5/56 (8%) Query: 39 LEADVSLEVVQSFSKRVQEKAK-----GEKILRSIQPGQMVIKIVHDELVEVLGKE 89 L ++E + +F + V+ + + G ++ ++ P +IK + DE+ E++GK+ Sbjct: 265 LAEIGTVENIPAFIEGVKNRKRKLSGFGHRVYKNYDPRAKIIKKLADEVFEIVGKD 320 >gnl|CDD|30200 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.. Length = 149 Score = 27.7 bits (62), Expect = 6.6 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 5/38 (13%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHL-KTLKKKKILMASLD 138 VI L GL GSGK+T IA L + L ++ + LD Sbjct: 1 VIWLTGLSGSGKST----IARALEEKLFQRGRPVYVLD 34 >gnl|CDD|31393 COG1200, RecG, RecG-like helicase [DNA replication, recombination, and repair / Transcription]. Length = 677 Score = 27.9 bits (62), Expect = 6.7 Identities = 15/45 (33%), Positives = 19/45 (42%) Query: 91 IELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMA 135 I DL +P P+ +L G GSGKT + LMA Sbjct: 274 ILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMA 318 >gnl|CDD|31343 COG1149, COG1149, MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]. Length = 284 Score = 27.6 bits (61), Expect = 6.9 Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 2/41 (4%) Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRP 142 V + G G+GKTT A +A L K K+++A DV P Sbjct: 4 VAVASGKGGTGKTTVAANLAVLLG--DKYKLVLADCDVEAP 42 >gnl|CDD|38564 KOG3354, KOG3354, KOG3354, Gluconate kinase [Carbohydrate transport and metabolism]. Length = 191 Score = 27.7 bits (61), Expect = 7.5 Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 5/54 (9%) Query: 96 NAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR 149 P VI+++G+ GSGK+T ++ L K + D+H PA E++ Sbjct: 8 MGPFKYVIVVMGVSGSGKSTIGKALSEEL----GLKFIDGD-DLHPPANVEKMT 56 >gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 179 Score = 27.5 bits (61), Expect = 7.6 Identities = 13/24 (54%), Positives = 17/24 (70%) Query: 101 LVIMLVGLQGSGKTTTTAKIAYHL 124 +VI + GL GSGKTT ++A HL Sbjct: 1 MVITISGLPGSGKTTVARELAEHL 24 >gnl|CDD|30597 COG0248, GppA, Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]. Length = 492 Score = 27.6 bits (61), Expect = 7.6 Identities = 23/121 (19%), Positives = 46/121 (38%), Gaps = 14/121 (11%) Query: 320 AKKIAKGKFDLEDLAEQFRQTQKIGGIGS------ILRMLPGMPSLKQNIMP-SSFDDKT 372 A+ + + LE++A+++R G +G+ + ++ S ++ + Sbjct: 182 ARDAVREE--LEEIAKEYRIAGWAGLVGTSGTIRALAKLHMAQGSYPLRVLHGYEITAEE 239 Query: 373 INHHIAIIASMTKEERANPSIIKHSRKKRIAAGSGTNAAKINKLLKLHRQVAEMMHSTQG 432 + + + MT EER + R I AG+ A L + M+ S G Sbjct: 240 LEKLLERLIRMTSEERLKLEGLSKDRADVILAGAAILEAVFEAL-----SIERMIVSDGG 294 Query: 433 L 433 L Sbjct: 295 L 295 >gnl|CDD|72983 cd03224, ABC_TM1139_LivF_branched, LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.. Length = 222 Score = 27.7 bits (62), Expect = 7.7 Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 1/57 (1%) Query: 93 LDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR 149 + L P ++ L+G G+GKTT I L + I D+ E+ R Sbjct: 19 VSLTVPEGEIVALLGRNGAGKTTLLKTIMGLLPP-RSGSIRFDGRDITGLPPHERAR 74 >gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.. Length = 151 Score = 27.5 bits (61), Expect = 7.8 Identities = 12/33 (36%), Positives = 15/33 (45%) Query: 98 PSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKK 130 P P ++L G G+GKTT IA L Sbjct: 17 PPPKNLLLYGPPGTGKTTLARAIANELFRPGAP 49 >gnl|CDD|35293 KOG0070, KOG0070, KOG0070, GTP-binding ADP-ribosylation factor Arf1 [Intracellular trafficking, secretion, and vesicular transport]. Length = 181 Score = 27.5 bits (61), Expect = 8.0 Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 4/24 (16%) Query: 103 IMLVGLQGSGKTTTTAKIAYHLKT 126 I++VGL +GKTT I Y LK Sbjct: 20 ILMVGLDAAGKTT----ILYKLKL 39 >gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Bacillus subtilis addA and Escherichia coli exodeoxyribonuclease V beta have large insertions near to the carboxy-terminus relative to other members of the family. Length = 494 Score = 27.7 bits (62), Expect = 8.0 Identities = 8/18 (44%), Positives = 11/18 (61%), Gaps = 1/18 (5%) Query: 110 GSGKTTT-TAKIAYHLKT 126 G+GKT T +IAY + Sbjct: 23 GTGKTRVLTERIAYLILE 40 >gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]. Length = 386 Score = 27.6 bits (61), Expect = 8.1 Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%) Query: 85 VLGKESIELDLNAPSPLVIMLVGLQGSGKTT 115 V+G LD+ VIM GL GSGK+T Sbjct: 41 VVGVNDASLDVEEGEIFVIM--GLSGSGKST 69 >gnl|CDD|145224 pfam01935, DUF87, Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands. Length = 218 Score = 27.3 bits (61), Expect = 8.2 Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%) Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLDVH 140 GSGK+ T A + L K +L+ D H Sbjct: 33 GSGKSNTVAVLLEELLEKKGATVLI--FDPH 61 >gnl|CDD|73054 cd03295, ABC_OpuCA_Osmoprotection, OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 242 Score = 27.5 bits (61), Expect = 8.3 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 1/65 (1%) Query: 92 ELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYL 151 L+L ++L+G GSGKTTT K+ L +I + D+ E R + Sbjct: 19 NLNLEIAKGEFLVLIGPSGSGKTTTM-KMINRLIEPTSGEIFIDGEDIREQDPVELRRKI 77 Query: 152 GEQIQ 156 G IQ Sbjct: 78 GYVIQ 82 >gnl|CDD|31396 COG1203, COG1203, Predicted helicases [General function prediction only]. Length = 733 Score = 27.4 bits (60), Expect = 8.4 Identities = 25/130 (19%), Positives = 44/130 (33%), Gaps = 8/130 (6%) Query: 6 QERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKIL 65 L S + LS++ R R + D+ QE + +L Sbjct: 122 LSSLISEKSFLADWEGLSDSLF----RFFFRLLEKMDIKDTR-NFTELAKQEARLLKPLL 176 Query: 66 RSIQPGQMVIKIV--HDELVEVLGKESIELDLNAPSP-LVIMLVGLQGSGKTTTTAKIAY 122 + + K + L ++++EL L L+++L G GKT + +A Sbjct: 177 LLLSAIARINKFKSFIEHEGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILAL 236 Query: 123 HLKTLKKKKI 132 L K K Sbjct: 237 ALLDEKIKLK 246 >gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]. Length = 161 Score = 27.2 bits (60), Expect = 8.7 Identities = 10/27 (37%), Positives = 15/27 (55%) Query: 99 SPLVIMLVGLQGSGKTTTTAKIAYHLK 125 ++ +VG + SGKTT K+ LK Sbjct: 1 MMKILGIVGYKNSGKTTLIEKLVRKLK 27 >gnl|CDD|38349 KOG3139, KOG3139, KOG3139, N-acetyltransferase [General function prediction only]. Length = 165 Score = 27.2 bits (60), Expect = 9.9 Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 13/68 (19%) Query: 132 ILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAI----RATQSARDGGYDAV 187 ++ LD HR + + L V E + I +A + R GY V Sbjct: 71 AIVCKLDTHRNTLRGYIAMLA---------VDSEYRGQGIGKALVRKAIDAMRSRGYSEV 121 Query: 188 ILDTAGRN 195 +L+T N Sbjct: 122 VLETEVTN 129 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.316 0.134 0.361 Gapped Lambda K H 0.267 0.0775 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,132,969 Number of extensions: 270094 Number of successful extensions: 1250 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1222 Number of HSP's successfully gapped: 151 Length of query: 461 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 364 Effective length of database: 4,167,664 Effective search space: 1517029696 Effective search space used: 1517029696 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 59 (26.4 bits)