RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780559|ref|YP_003064972.1| thiamine transporter ATP-binding subunit [Candidatus Liberibacter asiaticus str. psy62] (234 letters) >gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]. Length = 231 Score = 294 bits (753), Expect = 2e-80 Identities = 122/230 (53%), Positives = 167/230 (72%) Query: 1 MIKLDHLIYCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNG 60 M+ LD + + Y +L M+FD V E + ILGPSGAGKSTLL+L+AGF+ P G I +NG Sbjct: 1 MLALDDVRFSYGHLPMRFDLTVPAGEIVAILGPSGAGKSTLLNLIAGFETPASGEILING 60 Query: 61 QNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLE 120 +HT S P++RP+S+LFQENNLF+HLTV QNI LG++P L+L+ Q +V+ +V L Sbjct: 61 VDHTASPPAERPVSMLFQENNLFAHLTVAQNIGLGLSPGLKLNAEQREKVEAAAAQVGLA 120 Query: 121 DFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQ 180 F R P ++SGGQRQRVALARCL+R++PILLLDEPF+ DPALR E+L L+ Q+CDER+ Sbjct: 121 GFLKRLPGELSGGQRQRVALARCLVREQPILLLDEPFSALDPALRAEMLALVSQLCDERK 180 Query: 181 LTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMNGLIPESTLLGI 230 +TLLM++H+ ED+ +IA R + + G+I G L++G + LLGI Sbjct: 181 MTLLMVTHHPEDAARIADRVVFLDNGRIAAQGSTQELLSGKASAAALLGI 230 >gnl|CDD|73057 cd03298, ABC_ThiQ_thiamine_transporter, ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP. Probably responsible for the translocation of thiamine across the membrane. 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 = 211 Score = 251 bits (642), Expect = 1e-67 Identities = 98/211 (46%), Positives = 142/211 (67%) Query: 2 IKLDHLIYCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQ 61 ++LD + + Y M FD + E I+GPSG+GKSTLL+L+AGF+ P G + +NG Sbjct: 1 VRLDKIRFSYGEQPMHFDLTFAQGEITAIVGPSGSGKSTLLNLIAGFETPQSGRVLINGV 60 Query: 62 NHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLED 121 + T + P+ RP+S+LFQENNLF+HLTV QN+ LG++P L+L ++ L +V L Sbjct: 61 DVTAAPPADRPVSMLFQENNLFAHLTVEQNVGLGLSPGLKLTAEDRQAIEVALARVGLAG 120 Query: 122 FFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQL 181 R P ++SGG+RQRVALAR L+R KP+LLLDEPFA DPALR E+L L+ + E ++ Sbjct: 121 LEKRLPGELSGGERQRVALARVLVRDKPVLLLDEPFAALDPALRAEMLDLVLDLHAETKM 180 Query: 182 TLLMISHNLEDSMQIATRFIVIAGGQIVYDG 212 T+LM++H ED+ ++A R + + G+I G Sbjct: 181 TVLMVTHQPEDAKRLAQRVVFLDNGRIAAQG 211 >gnl|CDD|73018 cd03259, ABC_Carb_Solutes_like, ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. 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 = 213 Score = 209 bits (535), Expect = 4e-55 Identities = 80/197 (40%), Positives = 121/197 (61%) Query: 16 MQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSI 75 V E + +LGPSG GK+TLL L+AG + P G I ++G++ T P +R + + Sbjct: 17 DDLSLTVEPGEFLALLGPSGCGKTTLLRLIAGLERPDSGEILIDGRDVTGVPPERRNIGM 76 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQR 135 +FQ+ LF HLTV +NIA G+ A+V+++LE V LE NR+P ++SGGQ+ Sbjct: 77 VFQDYALFPHLTVAENIAFGLKLRGVPKAEIRARVRELLELVGLEGLLNRYPHELSGGQQ 136 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQ 195 QRVALAR L R+ +LLLDEP + D LR E+ LK++ E +T + ++H+ E+++ Sbjct: 137 QRVALARALAREPSLLLLDEPLSALDAKLREELREELKELQRELGITTIYVTHDQEEALA 196 Query: 196 IATRFIVIAGGQIVYDG 212 +A R V+ G+IV G Sbjct: 197 LADRIAVMNEGRIVQVG 213 >gnl|CDD|33633 COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]. Length = 352 Score = 191 bits (487), Expect = 1e-49 Identities = 80/220 (36%), Positives = 134/220 (60%), Gaps = 3/220 (1%) Query: 1 MIKLDHLIYCYDNLK--MQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 +++ ++ + + + K E + +LGPSG GK+TLL ++AGF+ P+ G I L Sbjct: 5 ALEIRNVSKSFGDFTAVDDISLDIKKGEFVTLLGPSGCGKTTLLRMIAGFEQPSSGEILL 64 Query: 59 NGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRL-DHYQHAQVKQMLEKV 117 +G++ T P KRP+ ++FQ LF H+TV +N+A G+ +L A+V++ LE V Sbjct: 65 DGEDITDVPPEKRPIGMVFQSYALFPHMTVEENVAFGLKVRKKLKKAEIKARVEEALELV 124 Query: 118 FLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCD 177 LE F +R P Q+SGGQ+QRVALAR L+ + +LLLDEP + D LR ++ LK++ Sbjct: 125 GLEGFADRKPHQLSGGQQQRVALARALVPEPKVLLLDEPLSALDAKLREQMRKELKELQR 184 Query: 178 ERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 E +T + ++H+ E+++ ++ R V+ G+I G P+ + Sbjct: 185 ELGITFVYVTHDQEEALAMSDRIAVMNDGRIEQVGTPEEI 224 >gnl|CDD|31315 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]. Length = 345 Score = 189 bits (482), Expect = 5e-49 Identities = 80/224 (35%), Positives = 130/224 (58%), Gaps = 7/224 (3%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I+++++ + + E + +LGPSGAGKSTLL ++AG + P G I L Sbjct: 2 SIRINNVKKRFGAFGALDDISLDIKSGELVALLGPSGAGKSTLLRIIAGLETPDAGRIRL 61 Query: 59 NGQ---NHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIA-PNLRLDHYQ-HAQVKQM 113 NG+ + + + R + +FQ LF H+TV NIA G+ R + A+V+++ Sbjct: 62 NGRVLFDVSNLAVRDRKVGFVFQHYALFPHMTVADNIAFGLKVRKERPSEAEIRARVEEL 121 Query: 114 LEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLK 173 L V LE +R+P+Q+SGGQRQRVALAR L + +LLLDEPF D +R E+ L+ Sbjct: 122 LRLVQLEGLADRYPAQLSGGQRQRVALARALAVEPKVLLLDEPFGALDAKVRKELRRWLR 181 Query: 174 QVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 ++ D +T + ++H+ E+++++A R +V+ G+I G PD + Sbjct: 182 KLHDRLGVTTVFVTHDQEEALELADRVVVLNQGRIEQVGPPDEV 225 >gnl|CDD|31313 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 248 Score = 186 bits (475), Expect = 3e-48 Identities = 73/208 (35%), Positives = 125/208 (60%), Gaps = 5/208 (2%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 +++++ + + +++ + V K E + ILGPSG GKSTLL L+AG + PT G + L Sbjct: 3 LLEIEGVSKSFGGVEVLEDINLSVEKGEFVAILGPSGCGKSTLLRLIAGLEKPTSGEVLL 62 Query: 59 NGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF 118 +G+ T P + +FQE+ L LTV N+ALG+ + + K++LE V Sbjct: 63 DGRPVTGPGPD---IGYVFQEDALLPWLTVLDNVALGLELRGKSKAEARERAKELLELVG 119 Query: 119 LEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDE 178 L F +++P Q+SGG RQRVA+AR L + +LLLDEPF D R E+ L ++ +E Sbjct: 120 LAGFEDKYPHQLSGGMRQRVAIARALATRPKLLLLDEPFGALDALTREELQDELLRLWEE 179 Query: 179 RQLTLLMISHNLEDSMQIATRFIVIAGG 206 + T+L+++H++++++ +A R +V++ Sbjct: 180 TRKTVLLVTHDVDEAVYLADRVVVLSNR 207 >gnl|CDD|73052 cd03293, ABC_NrtD_SsuB_transporters, NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. 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 = 220 Score = 181 bits (461), Expect = 2e-46 Identities = 71/216 (32%), Positives = 118/216 (54%), Gaps = 11/216 (5%) Query: 2 IKLDHLIYCYDNLKMQF------DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGS 55 +++ ++ Y V + E + ++GPSG GKSTLL ++AG + PT G Sbjct: 1 LEVRNVSKTYGGGGGAVTALEDISLSVEEGEFVALVGPSGCGKSTLLRIIAGLERPTSGE 60 Query: 56 IFLNGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 + ++G+ T P +FQ++ L LTV N+ALG+ + +++LE Sbjct: 61 VLVDGEPVTGPGP---DRGYVFQQDALLPWLTVLDNVALGLELQGVPKAEARERAEELLE 117 Query: 116 KVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQV 175 V L F N +P Q+SGG RQRVALAR L +LLLDEPF+ D R ++ L + Sbjct: 118 LVGLSGFENAYPHQLSGGMRQRVALARALAVDPDVLLLDEPFSALDALTREQLQEELLDI 177 Query: 176 CDERQLTLLMISHNLEDSMQIATRFIVIAG--GQIV 209 E T+L+++H++++++ +A R +V++ G+IV Sbjct: 178 WRETGKTVLLVTHDIDEAVFLADRVVVLSARPGRIV 213 >gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]. Length = 338 Score = 178 bits (453), Expect = 1e-45 Identities = 80/223 (35%), Positives = 133/223 (59%), Gaps = 10/223 (4%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 ++L ++ + + ++ + + E +V+LGPSG GKSTLL ++AG + PT G I + Sbjct: 3 ELELKNVRKSFGSFEVLKDVNLDIEDGEFVVLLGPSGCGKSTLLRMIAGLEEPTSGEILI 62 Query: 59 NGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQ----VKQML 114 +G++ T P KR ++++FQ L+ H+TV++NIA G L+L A+ VK++ Sbjct: 63 DGRDVTDLPPEKRGIAMVFQNYALYPHMTVYENIAFG----LKLRGVPKAEIDKRVKEVA 118 Query: 115 EKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQ 174 + + LE NR P Q+SGGQRQRVALAR L+R+ + LLDEP + D LR + +K+ Sbjct: 119 KLLGLEHLLNRKPLQLSGGQRQRVALARALVRKPKVFLLDEPLSNLDAKLRVLMRSEIKK 178 Query: 175 VCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 + + T + ++H+ ++M +A R +V+ G+I G P L Sbjct: 179 LHERLGTTTIYVTHDQVEAMTLADRIVVMNDGRIQQVGTPLEL 221 >gnl|CDD|73059 cd03300, ABC_PotA_N, PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. 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 = 232 Score = 177 bits (451), Expect = 2e-45 Identities = 83/220 (37%), Positives = 130/220 (59%), Gaps = 2/220 (0%) Query: 2 IKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLN 59 I+L+++ Y + + E +LGPSG GK+TLL L+AGF+ PT G I L+ Sbjct: 1 IELENVSKFYGGFVALDGVSLDIKEGEFFTLLGPSGCGKTTLLRLIAGFETPTSGEILLD 60 Query: 60 GQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFL 119 G++ T P KRP++ +FQ LF HLTV++NIA G+ +V + L+ V L Sbjct: 61 GKDITNLPPHKRPVNTVFQNYALFPHLTVFENIAFGLRLKKLPKAEIKERVAEALDLVQL 120 Query: 120 EDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDER 179 E + NR PSQ+SGGQ+QRVA+AR L+ + +LLLDEP D LR ++ LK++ E Sbjct: 121 EGYANRKPSQLSGGQQQRVAIARALVNEPKVLLLDEPLGALDLKLRKDMQLELKRLQKEL 180 Query: 180 QLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 +T + ++H+ E+++ ++ R V+ G+I G P+ + Sbjct: 181 GITFVFVTHDQEEALTMSDRIAVMNKGKIQQIGTPEEIYE 220 >gnl|CDD|31326 COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]. Length = 293 Score = 174 bits (441), Expect = 3e-44 Identities = 70/223 (31%), Positives = 122/223 (54%), Gaps = 4/223 (1%) Query: 1 MIKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 +I++ +L Y K F+V E +LGP+GAGK+TLL ++AG PT G I Sbjct: 4 VIEVRNLTKKYGGDKTALDGVSFEVEPGEIFGLLGPNGAGKTTLLKILAGLLKPTSGEIL 63 Query: 58 LNGQNHTRSSPS-KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 + G + + +R + + QE +L+ LTV +N+ +++++LE Sbjct: 64 VLGYDVVKEPAKVRRRIGYVPQEPSLYPELTVRENLEFFARLYGLSKEEAEERIEELLEL 123 Query: 117 VFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVC 176 LED N+ +SGG +QR+++A L+ +L+LDEP + DP R EI LL+++ Sbjct: 124 FGLEDKANKKVRTLSGGMKQRLSIALALLHDPELLILDEPTSGLDPESRREIWELLRELA 183 Query: 177 DERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 E +T+L+ +H LE++ ++ R I++ G+I+ +G P+ L Sbjct: 184 KEGGVTILLSTHILEEAEELCDRVIILNDGKIIAEGTPEELKE 226 >gnl|CDD|73055 cd03296, ABC_CysA_sulfate_importer, Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). 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 = 239 Score = 170 bits (432), Expect = 3e-43 Identities = 75/205 (36%), Positives = 126/205 (61%), Gaps = 4/205 (1%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 + E + +LGPSG+GK+TLL L+AG + P G+I G++ T +R + +FQ Sbjct: 22 SLDIPSGELVALLGPSGSGKTTLLRLIAGLERPDSGTILFGGEDATDVPVQERNVGFVFQ 81 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVK----QMLEKVFLEDFFNRFPSQMSGGQ 134 LF H+TV+ N+A G+ R + A+++ ++L+ V L+ +R+P+Q+SGGQ Sbjct: 82 HYALFRHMTVFDNVAFGLRVKPRSERPPEAEIRAKVHELLKLVQLDWLADRYPAQLSGGQ 141 Query: 135 RQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSM 194 RQRVALAR L + +LLLDEPF D +R E+ L+++ DE +T + ++H+ E+++ Sbjct: 142 RQRVALARALAVEPKVLLLDEPFGALDAKVRKELRRWLRRLHDELHVTTVFVTHDQEEAL 201 Query: 195 QIATRFIVIAGGQIVYDGDPDRLMN 219 ++A R +V+ G+I G PD + + Sbjct: 202 EVADRVVVMNKGRIEQVGTPDEVYD 226 >gnl|CDD|73014 cd03255, ABC_MJ0796_Lo1CDE_FtsE, This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.. Length = 218 Score = 169 bits (431), Expect = 5e-43 Identities = 67/219 (30%), Positives = 116/219 (52%), Gaps = 13/219 (5%) Query: 2 IKLDHLIYCYDNLKMQF------DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGS 55 I+L +L Y + + K E + I+GPSG+GKSTLL+++ G PT G Sbjct: 1 IELKNLSKTYGGGGEKVQALKGVSLSIEKGEFVAIVGPSGSGKSTLLNILGGLDRPTSGE 60 Query: 56 IFLNGQNHTRSSPSKRP------LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQ 109 + ++G + ++ S + + +FQ NL LT +N+ L + + + Sbjct: 61 VRVDGTDISKLSEKELAAFRRRHIGFVFQSFNLLPDLTALENVELPLLLAGVPKKERRER 120 Query: 110 VKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEIL 169 +++LE+V L D N +PS++SGGQ+QRVA+AR L I+L DEP D E++ Sbjct: 121 AEELLERVGLGDRLNHYPSELSGGQQQRVAIARALANDPKIILADEPTGNLDSETGKEVM 180 Query: 170 GLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQI 208 LL+++ E T+++++H+ + + A R I + G+I Sbjct: 181 ELLRELNKEAGTTIVVVTHD-PELAEYADRIIELRDGKI 218 >gnl|CDD|31323 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]. Length = 240 Score = 167 bits (426), Expect = 2e-42 Identities = 76/223 (34%), Positives = 133/223 (59%), Gaps = 7/223 (3%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 MI++ +L + + ++ V K E +VI+GPSG+GKSTLL + G + P GSI + Sbjct: 2 MIEIKNLSKSFGDKEVLKGISLSVEKGEVVVIIGPSGSGKSTLLRCLNGLEEPDSGSITV 61 Query: 59 NGQNHTRSS---PSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQ-HAQVKQML 114 +G++ +R + ++FQ+ NLF HLTV +N+ L +L + + ++L Sbjct: 62 DGEDVGDKKDILKLRRKVGMVFQQFNLFPHLTVLENVTLAPVKVKKLSKAEAREKALELL 121 Query: 115 EKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQ 174 EKV L D + +P+Q+SGGQ+QRVA+AR L ++L DEP + DP L E+L ++K Sbjct: 122 EKVGLADKADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKD 181 Query: 175 VCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 + +E +T+++++H + + ++A R I + G+I+ +G P+ Sbjct: 182 LAEE-GMTMIIVTHEMGFAREVADRVIFMDQGKIIEEGPPEEF 223 >gnl|CDD|73020 cd03261, ABC_Org_Solvent_Resistant, ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; 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 = 235 Score = 167 bits (425), Expect = 2e-42 Identities = 75/208 (36%), Positives = 118/208 (56%), Gaps = 6/208 (2%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSK-----RP 72 D V + E + I+GPSG+GKSTLL L+ G P G + ++G++ + S ++ R Sbjct: 19 VDLDVRRGEILAIIGPSGSGKSTLLRLIVGLLRPDSGEVLIDGEDISGLSEAELYRLRRR 78 Query: 73 LSILFQENNLFSHLTVWQNIALGIAPNLRL-DHYQHAQVKQMLEKVFLEDFFNRFPSQMS 131 + +LFQ LF LTV++N+A + + RL + V + LE V L + +P+++S Sbjct: 79 MGMLFQSGALFDSLTVFENVAFPLREHTRLSEEEIREIVLEKLEAVGLRGAEDLYPAELS 138 Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLE 191 GG ++RVALAR L +LL DEP A DP I L++ + E LT +M++H+L+ Sbjct: 139 GGMKKRVALARALALDPELLLYDEPTAGLDPIASGVIDDLIRSLKKELGLTSIMVTHDLD 198 Query: 192 DSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + IA R V+ G+IV +G P+ L Sbjct: 199 TAFAIADRIAVLYDGKIVAEGTPEELRA 226 >gnl|CDD|73015 cd03256, ABC_PhnC_transporter, ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. 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 = 241 Score = 166 bits (422), Expect = 4e-42 Identities = 76/232 (32%), Positives = 125/232 (53%), Gaps = 16/232 (6%) Query: 2 IKLDHLIYCYDNLKMQFD---FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I++++L Y N K +N E + ++GPSGAGKSTLL + G PT GS+ + Sbjct: 1 IEVENLSKTYPNGKKALKDVSLSINPGEFVALIGPSGAGKSTLLRCLNGLVEPTSGSVLI 60 Query: 59 NGQNHTRSSPSK-----RPLSILFQENNLFSHLTVWQNI---ALGIAPNLR-----LDHY 105 +G + + R + ++FQ+ NL L+V +N+ LG R Sbjct: 61 DGTDINKLKGKALRQLRRQIGMIFQQFNLIERLSVLENVLSGRLGRRSTWRSLFGLFPKE 120 Query: 106 QHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALR 165 + + LE+V L D + Q+SGGQ+QRVA+AR L++Q ++L DEP A DPA Sbjct: 121 EKQRALAALERVGLLDKAYQRADQLSGGQQQRVAIARALMQQPKLILADEPVASLDPASS 180 Query: 166 HEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 +++ LLK++ E +T+++ H ++ + + A R + + G+IV+DG P L Sbjct: 181 RQVMDLLKRINREEGITVIVSLHQVDLAREYADRIVGLKDGRIVFDGPPAEL 232 >gnl|CDD|73058 cd03299, ABC_ModC_like, Archeal protein closely related to ModC. ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. 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 = 235 Score = 166 bits (421), Expect = 5e-42 Identities = 72/206 (34%), Positives = 119/206 (57%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 +V + + VILGP+G+GKS LL +AGF P G I LNG++ T P KR +S + Q Sbjct: 19 SLEVERGDYFVILGPTGSGKSVLLETIAGFIKPDSGKILLNGKDITNLPPEKRDISYVPQ 78 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRV 138 LF H+TV++NIA G+ +V ++ E + ++ NR P +SGG++QRV Sbjct: 79 NYALFPHMTVYKNIAYGLKKRKVDKKEIERKVLEIAEMLGIDHLLNRKPETLSGGEQQRV 138 Query: 139 ALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIAT 198 A+AR L+ ILLLDEPF+ D + ++ LK++ E +T+L ++H+ E++ +A Sbjct: 139 AIARALVVNPKILLLDEPFSALDVRTKEKLREELKKIRKEFGVTVLHVTHDFEEAWALAD 198 Query: 199 RFIVIAGGQIVYDGDPDRLMNGLIPE 224 + ++ G+++ G P+ + E Sbjct: 199 KVAIMLNGKLIQVGKPEEVFKKPKNE 224 >gnl|CDD|72988 cd03229, ABC_Class3, This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. 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 = 178 Score = 164 bits (416), Expect = 2e-41 Identities = 69/212 (32%), Positives = 111/212 (52%), Gaps = 40/212 (18%) Query: 2 IKLDHLIYCYDNLK--MQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLN 59 ++L ++ Y + E + +LGPSG+GKSTLL +AG + P GSI ++ Sbjct: 1 LELKNVSKRYGQKTVLNDVSLNIEAGEIVALLGPSGSGKSTLLRCIAGLEEPDSGSILID 60 Query: 60 GQNHTRSS----PSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 G++ T P +R + ++FQ+ LF HLTV +NIALG Sbjct: 61 GEDLTDLEDELPPLRRRIGMVFQDFALFPHLTVLENIALG-------------------- 100 Query: 116 KVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQV 175 +SGGQ+QRVALAR L +LLLDEP + DP R E+ LLK + Sbjct: 101 --------------LSGGQQQRVALARALAMDPDVLLLDEPTSALDPITRREVRALLKSL 146 Query: 176 CDERQLTLLMISHNLEDSMQIATRFIVIAGGQ 207 + +T+++++H+L+++ ++A R +V+ G+ Sbjct: 147 QAQLGITVVLVTHDLDEAARLADRVVVLRDGK 178 >gnl|CDD|31330 COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 339 Score = 163 bits (414), Expect = 4e-41 Identities = 83/229 (36%), Positives = 127/229 (55%), Gaps = 20/229 (8%) Query: 1 MIKLDHLIYCYDNLKMQF-------DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTR 53 MI+L+++ + ++ K E I+G SGAGKSTLL L+ + PT Sbjct: 1 MIELENVSKTFGQTGTGTVTALDDVSLEIPKGEIFGIIGYSGAGKSTLLRLINLLERPTS 60 Query: 54 GSIFLNGQNHTRSSPS-----KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHA 108 GS+F++GQ+ T S + ++ + ++FQ NL S TV++N+A L L A Sbjct: 61 GSVFVDGQDLTALSEAELRQLRQKIGMIFQHFNLLSSRTVFENVAFP----LELAGVPKA 116 Query: 109 QVKQ----MLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPAL 164 ++KQ +LE V L D +R+P+Q+SGGQ+QRVA+AR L ILL DE + DP Sbjct: 117 EIKQRVAELLELVGLSDKADRYPAQLSGGQKQRVAIARALANNPKILLCDEATSALDPET 176 Query: 165 RHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGD 213 IL LLK + E LT+++I+H +E +I R V+ G++V +G Sbjct: 177 TQSILELLKDINRELGLTIVLITHEMEVVKRICDRVAVLDQGRLVEEGT 225 >gnl|CDD|73017 cd03258, ABC_MetN_methionine_transporter, MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. 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 = 233 Score = 163 bits (413), Expect = 5e-41 Identities = 77/228 (33%), Positives = 122/228 (53%), Gaps = 19/228 (8%) Query: 1 MIKLDHLIYCYDNLKMQF------DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRG 54 MI+L ++ + + + V K E I+G SGAGKSTL+ + G + PT G Sbjct: 1 MIELKNVSKVFGDTGGKVTALKDVSLSVPKGEIFGIIGRSGAGKSTLIRCINGLERPTSG 60 Query: 55 SIFLNGQNHTRSSPSK-----RPLSILFQENNLFSHLTVWQNIALGIAPNLRLDH----Y 105 S+ ++G + T S + R + ++FQ NL S TV++N+AL L + Sbjct: 61 SVLVDGTDLTLLSGKELRKARRRIGMIFQHFNLLSSRTVFENVALP----LEIAGVPKAE 116 Query: 106 QHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALR 165 +V ++LE V LED + +P+Q+SGGQ+QRV +AR L +LL DE + DP Sbjct: 117 IEERVLELLELVGLEDKADAYPAQLSGGQKQRVGIARALANNPKVLLCDEATSALDPETT 176 Query: 166 HEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGD 213 IL LL+ + E LT+++I+H +E +I R V+ G++V +G Sbjct: 177 QSILALLRDINRELGLTIVLITHEMEVVKRICDRVAVMEKGEVVEEGT 224 >gnl|CDD|31322 COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]. Length = 309 Score = 161 bits (408), Expect = 2e-40 Identities = 72/227 (31%), Positives = 130/227 (57%), Gaps = 10/227 (4%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 MI+ +++ Y N K + + + E +V++GPSG+GK+T L ++ PT G I + Sbjct: 1 MIEFENVSKRYGNKKAVDDVNLTIEEGEFLVLIGPSGSGKTTTLKMINRLIEPTSGEILI 60 Query: 59 NGQNHTRSSPSKRPLSI--LFQENNLFSHLTVWQNIALGIAPNLR--LDHYQHAQVKQML 114 +G++ + P + I + Q+ LF HLTV +NIA P L + ++L Sbjct: 61 DGEDISDLDPVELRRKIGYVIQQIGLFPHLTVAENIAT--VPKLLGWDKERIKKRADELL 118 Query: 115 EKVFLE--DFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLL 172 + V L+ ++ +R+P ++SGGQ+QRV +AR L PILL+DEPF DP R ++ + Sbjct: 119 DLVGLDPSEYADRYPHELSGGQQQRVGVARALAADPPILLMDEPFGALDPITRKQLQEEI 178 Query: 173 KQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 K++ E T++ ++H++++++++A R V+ G+IV PD ++ Sbjct: 179 KELQKELGKTIVFVTHDIDEALKLADRIAVMDAGEIVQYDTPDEILA 225 >gnl|CDD|73056 cd03297, ABC_ModC_molybdenum_transporter, ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. 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 = 214 Score = 160 bits (405), Expect = 4e-40 Identities = 77/207 (37%), Positives = 122/207 (58%), Gaps = 9/207 (4%) Query: 12 DNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNG------QNHTR 65 + ++ DF +N E I G SGAGKSTLL +AG + P G+I LNG + Sbjct: 11 PDFTLKIDFDLN-EEVTGIFGASGAGKSTLLRCIAGLEKPDGGTIVLNGTVLFDSRKKIN 69 Query: 66 SSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNR 125 P +R + ++FQ+ LF HL V +N+A G+ + V ++L+ + L+ NR Sbjct: 70 LPPQQRKIGLVFQQYALFPHLNVRENLAFGLKRKRNREDRI--SVDELLDLLGLDHLLNR 127 Query: 126 FPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLM 185 +P+Q+SGG++QRVALAR L Q +LLLDEPF+ D ALR ++L LKQ+ + ++ Sbjct: 128 YPAQLSGGEKQRVALARALAAQPELLLLDEPFSALDRALRLQLLPELKQIKKNLNIPVIF 187 Query: 186 ISHNLEDSMQIATRFIVIAGGQIVYDG 212 ++H+L ++ +A R +V+ G++ Y G Sbjct: 188 VTHDLSEAEYLADRIVVMEDGRLQYIG 214 >gnl|CDD|73060 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.. Length = 213 Score = 158 bits (402), Expect = 9e-40 Identities = 70/214 (32%), Positives = 123/214 (57%), Gaps = 10/214 (4%) Query: 2 IKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLN 59 ++L+++ + N+ + + E +V+LGPSG GK+T L ++AG + PT G I++ Sbjct: 1 VELENVTKRFGNVTALDDLNLDIADGEFVVLLGPSGCGKTTTLRMIAGLEEPTSGRIYIG 60 Query: 60 GQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF- 118 G++ T P R ++++FQ L+ H+TV+ NIA G L+L ++ + + +V Sbjct: 61 GRDVTDLPPKDRDIAMVFQNYALYPHMTVYDNIAFG----LKLRKVPKDEIDERVREVAE 116 Query: 119 ---LEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQV 175 +E +R P Q+SGGQRQRVAL R ++R+ + L+DEP + D LR ++ LK++ Sbjct: 117 LLQIEHLLDRKPKQLSGGQRQRVALGRAIVREPKVFLMDEPLSNLDAKLRVQMRAELKRL 176 Query: 176 CDERQLTLLMISHNLEDSMQIATRFIVIAGGQIV 209 T + ++H+ ++M +A R V+ GQI Sbjct: 177 QQRLGTTTIYVTHDQVEAMTMADRIAVMNDGQIQ 210 >gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.. Length = 211 Score = 158 bits (402), Expect = 1e-39 Identities = 78/213 (36%), Positives = 128/213 (60%), Gaps = 10/213 (4%) Query: 3 KLDHLIYCYDNLKMQ----FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 +L +L + Y + + K E ++I+GP+G+GKSTLL L+ G PT G + + Sbjct: 1 ELKNLSFSYPDGARPALDDISLTIKKGEFVLIVGPNGSGKSTLLRLLNGLLGPTSGEVLV 60 Query: 59 NGQNHTRSSPSK--RPLSILFQE-NNLFSHLTVWQNIALGIAPNLRLDHYQ-HAQVKQML 114 +G++ T+ S + R + ++FQ ++ F TV + +A G+ NL L + +V++ L Sbjct: 61 DGKDLTKLSLKELRRKVGLVFQNPDDQFFGPTVEEEVAFGLE-NLGLPEEEIEERVEEAL 119 Query: 115 EKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQ 174 E V LE +R P +SGGQ+QRVA+A L ILLLDEP A DPA R E+L LLK+ Sbjct: 120 ELVGLEGLRDRSPFTLSGGQKQRVAIAGVLAMDPDILLLDEPTAGLDPAGRRELLELLKK 179 Query: 175 VCDERQLTLLMISHNLEDSMQIATRFIVIAGGQ 207 + E + T+++++H+L+ +++A R IV+ G+ Sbjct: 180 LKAEGK-TIIIVTHDLDLLLELADRVIVLEDGK 211 >gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]. Length = 226 Score = 158 bits (401), Expect = 1e-39 Identities = 74/221 (33%), Positives = 121/221 (54%), Gaps = 14/221 (6%) Query: 1 MIKLDHLIYCYDNLKMQ------FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRG 54 MI+L ++ Y + + ++ E + I+GPSG+GKSTLL+L+ G PT G Sbjct: 1 MIELKNVSKIYGLGGEKVEALKDVNLEIEAGEFVAIVGPSGSGKSTLLNLLGGLDKPTSG 60 Query: 55 SIFLNGQNHTRSSPSKRP------LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHA 108 + +NG++ T+ S + + +FQ NL LTV +N+ L + + + Sbjct: 61 EVLINGKDLTKLSEKELAKLRRKKIGFVFQNFNLLPDLTVLENVELPLLIAGKSAGRRKR 120 Query: 109 QVKQMLEKVFLEDFFN-RFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHE 167 +++LE + LED + PS++SGGQ+QRVA+AR LI I+L DEP D E Sbjct: 121 AAEELLEVLGLEDRLLKKKPSELSGGQQQRVAIARALINNPKIILADEPTGNLDSKTAKE 180 Query: 168 ILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQI 208 +L LL+++ ER T++M++H+ E + A R I + G+I Sbjct: 181 VLELLRELNKERGKTIIMVTHDPE-LAKYADRVIELKDGKI 220 >gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]. Length = 258 Score = 158 bits (400), Expect = 2e-39 Identities = 78/227 (34%), Positives = 129/227 (56%), Gaps = 8/227 (3%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 M+++++L + Y + F + K E ILGP+G+GKSTLL +AG P G + L Sbjct: 2 MLEVENLSFGYGGKPILDDLSFSIPKGEITGILGPNGSGKSTLLKCLAGLLKPKSGEVLL 61 Query: 59 NGQNHTRSSPS--KRPLSILFQENNLFSHLTVWQNIALGIAPNL----RLDHYQHAQVKQ 112 +G++ SP + L+ + Q + LTV++ + LG P+L R V++ Sbjct: 62 DGKDIASLSPKELAKKLAYVPQSPSAPFGLTVYELVLLGRYPHLGLFGRPSKEDEEIVEE 121 Query: 113 MLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLL 172 LE + LE +R ++SGG+RQRV +AR L ++ PILLLDEP + D A + E+L LL Sbjct: 122 ALELLGLEHLADRPVDELSGGERQRVLIARALAQETPILLLDEPTSHLDIAHQIEVLELL 181 Query: 173 KQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + + E+ LT++M+ H+L + + A I++ G+IV G P+ ++ Sbjct: 182 RDLNREKGLTVVMVLHDLNLAARYADHLILLKDGKIVAQGTPEEVLT 228 >gnl|CDD|31324 COG1127, Ttg2A, ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 263 Score = 157 bits (399), Expect = 2e-39 Identities = 75/226 (33%), Positives = 128/226 (56%), Gaps = 9/226 (3%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 +I++ + + + + D V + E + ILG SG+GKSTLL L+ G P +G I + Sbjct: 8 LIEVRGVTKSFGDRVILDGVDLDVPRGEILAILGGSGSGKSTLLRLILGLLRPDKGEILI 67 Query: 59 NGQNHTRSSPSK-----RPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQ-HAQVKQ 112 +G++ + S + + + +LFQ+ LFS LTV++N+A + + +L V Sbjct: 68 DGEDIPQLSEEELYEIRKRMGVLFQQGALFSSLTVFENVAFPLREHTKLPESLIRELVLM 127 Query: 113 MLEKVFL-EDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGL 171 LE V L + +PS++SGG R+RVALAR + +L LDEP + DP I L Sbjct: 128 KLELVGLRGAAADLYPSELSGGMRKRVALARAIALDPELLFLDEPTSGLDPISAGVIDEL 187 Query: 172 LKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 ++++ D LT++M++H+L+ + IA R V+A G+++ +G P+ L Sbjct: 188 IRELNDALGLTVIMVTHDLDSLLTIADRVAVLADGKVIAEGTPEEL 233 >gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 235 Score = 157 bits (399), Expect = 2e-39 Identities = 83/228 (36%), Positives = 133/228 (58%), Gaps = 11/228 (4%) Query: 1 MIKLDHLIYCYDNLKMQFD---FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 MI+ ++L + Y K ++ K ER++++GP+G+GKSTLL L+ G PT G + Sbjct: 3 MIEAENLSFRYPGRKAALKDVSLEIEKGERVLLIGPNGSGKSTLLKLLNGLLKPTSGEVL 62 Query: 58 LNGQNHTRSSPSK---RPLSILFQ--ENNLFSHLTVWQNIALGIAPNLRLDHYQ-HAQVK 111 ++G + + + + ++FQ ++ LF TV +A G NL L + +V Sbjct: 63 VDGLDTSSEKSLLELRQKVGLVFQNPDDQLFG-PTVEDEVAFG-LENLGLPREEIEERVA 120 Query: 112 QMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGL 171 + LE V LE+ +R P +SGGQ+QRVA+A L ILLLDEP A DP R E+L L Sbjct: 121 EALELVGLEELLDRPPFNLSGGQKQRVAIAGVLAMGPEILLLDEPTAGLDPKGRRELLEL 180 Query: 172 LKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 LK++ +E T+++++H+LE ++ A R +V+ G+I+ DGDP + N Sbjct: 181 LKKLKEEGGKTIIIVTHDLELVLEYADRVVVLDDGKILADGDPAEIFN 228 >gnl|CDD|73021 cd03262, ABC_HisP_GlnQ_permeases, HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQMP system of S. typhimurium, where HisJ is the extracellular solute binding proteins and HisP is the ABC protein.. Length = 213 Score = 156 bits (395), Expect = 7e-39 Identities = 70/195 (35%), Positives = 117/195 (60%), Gaps = 6/195 (3%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS----KRPLS 74 D V K E +VI+GPSG+GKSTLL + + P G+I ++G T + ++ + Sbjct: 20 DLTVKKGEVVVIIGPSGSGKSTLLRCINLLEEPDSGTIIIDGLKLTDDKKNINELRQKVG 79 Query: 75 ILFQENNLFSHLTVWQNIALGIAPNLRLDHYQ-HAQVKQMLEKVFLEDFFNRFPSQMSGG 133 ++FQ+ NLF HLTV +NI L + + + ++LEKV L D + +P+Q+SGG Sbjct: 80 MVFQQFNLFPHLTVLENITLAPIKVKGMSKAEAEERALELLEKVGLADKADAYPAQLSGG 139 Query: 134 QRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDS 193 Q+QRVA+AR L ++L DEP + DP L E+L ++K + +E +T+++++H + + Sbjct: 140 QQQRVAIARALAMNPKVMLFDEPTSALDPELVGEVLDVMKDLAEE-GMTMVVVTHEMGFA 198 Query: 194 MQIATRFIVIAGGQI 208 ++A R I + G+I Sbjct: 199 REVADRVIFMDDGRI 213 >gnl|CDD|30760 COG0411, LivG, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]. Length = 250 Score = 154 bits (390), Expect = 3e-38 Identities = 65/217 (29%), Positives = 120/217 (55%), Gaps = 15/217 (6%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRP---LS 74 +V E + ++GP+GAGK+TL +L+ GF P+ G++ G++ T P + ++ Sbjct: 23 VSLEVRPGEIVGLIGPNGAGKTTLFNLITGFYKPSSGTVIFRGRDITGLPPHRIARLGIA 82 Query: 75 ILFQENNLFSHLTVWQNIALG------IAPNLRLDHYQH------AQVKQMLEKVFLEDF 122 FQ LF LTV +N+A+G ++ L + + +++LE V L + Sbjct: 83 RTFQITRLFPGLTVLENVAVGAHARLGLSGLLGRPRARKEEREARERARELLEFVGLGEL 142 Query: 123 FNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLT 182 +R +S GQ++R+ +AR L Q +LLLDEP A +P E+ L++++ D +T Sbjct: 143 ADRPAGNLSYGQQRRLEIARALATQPKLLLLDEPAAGLNPEETEELAELIRELRDRGGVT 202 Query: 183 LLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 +L+I H+++ M +A R +V+ G+++ +G P+ + N Sbjct: 203 ILLIEHDMKLVMGLADRIVVLNYGEVIAEGTPEEVRN 239 >gnl|CDD|72978 cd03219, ABC_Mj1267_LivG_branched, The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (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).. Length = 236 Score = 153 bits (389), Expect = 3e-38 Identities = 68/214 (31%), Positives = 119/214 (55%), Gaps = 14/214 (6%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRP---LSI 75 F V E ++GP+GAGK+TL +L++GF PT GS+ +G++ T P + + Sbjct: 20 SFSVRPGEIHGLIGPNGAGKTTLFNLISGFLRPTSGSVLFDGEDITGLPPHEIARLGIGR 79 Query: 76 LFQENNLFSHLTVWQNIALG----------IAPNLRLDHYQHAQVKQMLEKVFLEDFFNR 125 FQ LF LTV +N+ + +A R + + +++LE+V L D +R Sbjct: 80 TFQIPRLFPELTVLENVMVAAQARTGSGLLLARARREEREARERAEELLERVGLADLADR 139 Query: 126 FPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLM 185 ++S GQ++R+ +AR L +LLLDEP A +P E+ L++++ ER +T+L+ Sbjct: 140 PAGELSYGQQRRLEIARALATDPKLLLLDEPAAGLNPEETEELAELIREL-RERGITVLL 198 Query: 186 ISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + H+++ M +A R V+ G+++ +G PD + N Sbjct: 199 VEHDMDVVMSLADRVTVLDQGRVIAEGTPDEVRN 232 >gnl|CDD|33436 COG3638, COG3638, ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 258 Score = 152 bits (386), Expect = 6e-38 Identities = 77/233 (33%), Positives = 121/233 (51%), Gaps = 16/233 (6%) Query: 1 MIKLDHLIYCYDNLK---MQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 MI++ +L Y + ++N+ E + I+GPSGAGKSTLL + G PT G I Sbjct: 3 MIEVKNLSKTYPGGHQALKDVNLEINQGEMVAIIGPSGAGKSTLLRSLNGLVDPTSGEIL 62 Query: 58 LNGQNHTRSSPS-----KRPLSILFQENNLFSHLTVWQNIALGIAPNL--------RLDH 104 NG T+ +R + ++FQ+ NL L+V +N+ LG Sbjct: 63 FNGVQITKLKGKELRKLRRDIGMIFQQFNLVPRLSVLENVLLGRLGYTSTWRSLFGLFSK 122 Query: 105 YQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPAL 164 AQ LE+V + D + S +SGGQ+QRVA+AR L++Q I+L DEP A DP Sbjct: 123 EDKAQALDALERVGILDKAYQRASTLSGGQQQRVAIARALVQQPKIILADEPVASLDPES 182 Query: 165 RHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 +++ +LK + E +T+++ H ++ + + A R I + G+IV+DG L Sbjct: 183 AKKVMDILKDINQEDGITVIVNLHQVDLAKKYADRIIGLKAGRIVFDGPASEL 235 >gnl|CDD|73016 cd03257, ABC_NikE_OppD_transporters, The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.. Length = 228 Score = 151 bits (384), Expect = 1e-37 Identities = 71/205 (34%), Positives = 118/205 (57%), Gaps = 10/205 (4%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPL---- 73 F + K E + ++G SG+GKSTL + G PT GSI +G++ + S R + Sbjct: 24 VSFSIKKGETLGLVGESGSGKSTLARAILGLLKPTSGSIIFDGKDLLKLSRRLRKIRRKE 83 Query: 74 -SILFQE--NNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFL---EDFFNRFP 127 ++FQ+ ++L +T+ + IA + + +L + + +L V + E+ NR+P Sbjct: 84 IQMVFQDPMSSLNPRMTIGEQIAEPLRIHGKLSKKEARKEAVLLLLVGVGLPEEVLNRYP 143 Query: 128 SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMIS 187 ++SGGQRQRVA+AR L +L+ DEP + D +++ +IL LLK++ +E LTLL I+ Sbjct: 144 HELSGGQRQRVAIARALALNPKLLIADEPTSALDVSVQAQILDLLKKLQEELGLTLLFIT 203 Query: 188 HNLEDSMQIATRFIVIAGGQIVYDG 212 H+L +IA R V+ G+IV +G Sbjct: 204 HDLGVVAKIADRVAVMYAGKIVEEG 228 >gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. 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 = 269 Score = 151 bits (382), Expect = 2e-37 Identities = 67/207 (32%), Positives = 116/207 (56%), Gaps = 6/207 (2%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS------KRP 72 V + E VI+G SG+GKSTLL + PT G + ++GQ+ S ++ Sbjct: 44 SLDVREGEIFVIMGLSGSGKSTLLRCINRLIEPTSGKVLIDGQDIAAMSRKELRELRRKK 103 Query: 73 LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSG 132 +S++FQ L H TV +N+A G+ + + + LE V LE + +++P ++SG Sbjct: 104 ISMVFQSFALLPHRTVLENVAFGLEVQGVPRAEREERAAEALELVGLEGWEHKYPDELSG 163 Query: 133 GQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLED 192 G +QRV LAR L ILL+DE F+ DP +R E+ L ++ E Q T++ I+H+L++ Sbjct: 164 GMQQRVGLARALAVDPDILLMDEAFSALDPLIRREMQDELLRLQAELQKTIVFITHDLDE 223 Query: 193 SMQIATRFIVIAGGQIVYDGDPDRLMN 219 ++++ R ++ G++V G P+ ++ Sbjct: 224 ALRLGDRIAIMKDGRLVQVGTPEEILT 250 >gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]. Length = 386 Score = 150 bits (381), Expect = 2e-37 Identities = 68/207 (32%), Positives = 121/207 (58%), Gaps = 6/207 (2%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS------KRP 72 V + E VI+G SG+GKSTL+ L+ PTRG I ++G++ + S + ++ Sbjct: 48 SLDVEEGEIFVIMGLSGSGKSTLVRLLNRLIEPTRGEILVDGKDIAKLSAAELRELRRKK 107 Query: 73 LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSG 132 +S++FQ L H TV +N+A G+ + + + LE V LE + +++P+++SG Sbjct: 108 ISMVFQSFALLPHRTVLENVAFGLEVQGVPKAEREERALEALELVGLEGYADKYPNELSG 167 Query: 133 GQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLED 192 G +QRV LAR L ILL+DE F+ DP +R E+ L ++ + + T++ I+H+L++ Sbjct: 168 GMQQRVGLARALANDPDILLMDEAFSALDPLIRTEMQDELLELQAKLKKTIVFITHDLDE 227 Query: 193 SMQIATRFIVIAGGQIVYDGDPDRLMN 219 +++I R ++ G+IV G P+ ++ Sbjct: 228 ALRIGDRIAIMKDGEIVQVGTPEEILL 254 >gnl|CDD|31321 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]. Length = 252 Score = 149 bits (377), Expect = 8e-37 Identities = 79/238 (33%), Positives = 130/238 (54%), Gaps = 14/238 (5%) Query: 1 MIKLDHLIYCYDNLKMQF------DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRG 54 ++ + +L Y K F ++ + E + I+G SG+GKSTL L+AG + P+ G Sbjct: 3 LLSVRNLSIVYGGGKFAFHALNNVSLEIERGETLGIVGESGSGKSTLARLLAGLEKPSSG 62 Query: 55 SIFLNGQ---NHTRSSPSKRPLSILFQ--ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQ 109 SI L+G+ R+ RP+ ++FQ ++L TV + ++ + P+ Q Sbjct: 63 SILLDGKPLAPKKRAKAFYRPVQMVFQDPYSSLNPRRTVGRILSEPLRPHGLSKSQQRIA 122 Query: 110 VKQMLEKVFL-EDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEI 168 ++L++V L F +R P ++SGGQRQR+A+AR LI + +L+LDEP + D +++ +I Sbjct: 123 --ELLDQVGLPPSFLDRRPHELSGGQRQRIAIARALIPEPKLLILDEPTSALDVSVQAQI 180 Query: 169 LGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMNGLIPEST 226 L LL ++ ER LT L ISH+L + R V+ GQIV G + L++ T Sbjct: 181 LNLLLELKKERGLTYLFISHDLALVEHMCDRIAVMDNGQIVEIGPTEELLSHPSHPYT 238 >gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]. Length = 539 Score = 149 bits (377), Expect = 9e-37 Identities = 74/211 (35%), Positives = 121/211 (57%), Gaps = 10/211 (4%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN----HTRSSPSKRPL 73 F + + E + ++G SG+GKSTL ++AG P+ GSI +GQ+ +R + Sbjct: 310 VSFDLREGETLGLVGESGSGKSTLARILAGLLPPSSGSIIFDGQDLDLTGGELRRLRRRI 369 Query: 74 SILFQ--ENNLFSHLTVWQNIA--LGIAPNLRLDHYQHAQVKQMLEKVFL-EDFFNRFPS 128 ++FQ ++L +TV +A L I + A+V ++LE V L +F +R+P Sbjct: 370 QMVFQDPYSSLNPRMTVGDILAEPLRIHGGGSGA-ERRARVAELLELVGLPPEFLDRYPH 428 Query: 129 QMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISH 188 ++SGGQRQRVA+AR L + +L+LDEP + D +++ ++L LLK + +E LT L ISH Sbjct: 429 ELSGGQRQRVAIARALALEPKLLILDEPVSALDVSVQAQVLNLLKDLQEELGLTYLFISH 488 Query: 189 NLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 +L IA R V+ G+IV +G +++ Sbjct: 489 DLAVVRYIADRVAVMYDGRIVEEGPTEKVFE 519 Score = 129 bits (325), Expect = 9e-31 Identities = 67/220 (30%), Positives = 111/220 (50%), Gaps = 21/220 (9%) Query: 18 FDFQVNKAERIVILGPSGAGKSTL-LSLMAGFKYP---TRGSIFLNGQN------HTRSS 67 F+V E + I+G SG+GKSTL L+LM T G + L+G++ Sbjct: 28 VSFEVEPGEILGIVGESGSGKSTLALALMGLLPEGGRITSGEVILDGRDLLGLSEREMRK 87 Query: 68 PSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQ------HAQVKQMLEKVFLED 121 + ++++FQ+ + L I I LRL H + + ++LE+V L D Sbjct: 88 LRGKRIAMIFQDP--MTSLNPVMTIGDQIREALRL-HGKGSRAEARKRAVELLEQVGLPD 144 Query: 122 --FFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDER 179 +R+P Q+SGG RQRV +A L + +L+ DEP D + +IL LLK + E Sbjct: 145 PERRDRYPHQLSGGMRQRVMIAMALALKPKLLIADEPTTALDVTTQAQILDLLKDLQREL 204 Query: 180 QLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + +L I+H+L ++A R +V+ G+IV G + +++ Sbjct: 205 GMAVLFITHDLGVVAELADRVVVMYKGEIVETGPTEEILS 244 >gnl|CDD|30759 COG0410, LivF, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]. Length = 237 Score = 146 bits (371), Expect = 4e-36 Identities = 68/237 (28%), Positives = 124/237 (52%), Gaps = 9/237 (3%) Query: 1 MIKLDHLIYCYDNLKMQF--DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 M+++++L Y ++ +V + E + +LG +GAGK+TLL + G P G I Sbjct: 3 MLEVENLSAGYGKIQALRGVSLEVERGEIVALLGRNGAGKTTLLKTIMGLVRPRSGRIIF 62 Query: 59 NGQNHTRSSPSKRP---LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 +G++ T P +R ++ + + +F LTV +N+ LG R Q ++++ E Sbjct: 63 DGEDITGLPPHERARLGIAYVPEGRRIFPRLTVEENLLLGAYA-RRDKEAQERDLEEVYE 121 Query: 116 KVF--LEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLK 173 +F L++ N+ +SGG++Q +A+AR L+ + +LLLDEP P + EI +K Sbjct: 122 -LFPRLKERRNQRAGTLSGGEQQMLAIARALMSRPKLLLLDEPSEGLAPKIVEEIFEAIK 180 Query: 174 QVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMNGLIPESTLLGI 230 ++ E +T+L++ N +++IA R V+ G+IV G L+ LG+ Sbjct: 181 ELRKEGGMTILLVEQNARFALEIADRGYVLENGRIVLSGTAAELLADPDVREAYLGV 237 >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 = 146 bits (371), Expect = 4e-36 Identities = 64/209 (30%), Positives = 111/209 (53%), Gaps = 15/209 (7%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRP---LSI 75 V + E + +LG +GAGK+TLL + G P GSI +G++ T P +R + Sbjct: 20 SLTVPEGEIVALLGRNGAGKTTLLKTIMGLLPPRSGSIRFDGRDITGLPPHERARAGIGY 79 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF-----LEDFFNRFPSQM 130 + + +F LTV +N+ LG R A+ K LE+V+ L++ + + Sbjct: 80 VPEGRRIFPELTVEENLLLGAYARRR------AKRKARLERVYELFPRLKERRKQLAGTL 133 Query: 131 SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNL 190 SGG++Q +A+AR L+ + +LLLDEP P + EI ++++ DE +T+L++ N Sbjct: 134 SGGEQQMLAIARALMSRPKLLLLDEPSEGLAPKIVEEIFEAIRELRDE-GVTILLVEQNA 192 Query: 191 EDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 +++IA R V+ G++V +G L+ Sbjct: 193 RFALEIADRAYVLERGRVVLEGTAAELLA 221 >gnl|CDD|32710 COG2884, FtsE, Predicted ATPase involved in cell division [Cell division and chromosome partitioning]. Length = 223 Score = 144 bits (364), Expect = 2e-35 Identities = 75/228 (32%), Positives = 125/228 (54%), Gaps = 17/228 (7%) Query: 1 MIKLDHLIYCYDNLKMQFD---FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 MI+ +++ Y + F + K E + + GPSGAGKSTLL L+ G + PTRG I Sbjct: 1 MIRFENVSKAYPGGREALRDVSFHIPKGEFVFLTGPSGAGKSTLLKLIYGEERPTRGKIL 60 Query: 58 LNGQNHTRSSPS-----KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQ 112 +NG + +R +R + ++FQ+ L TV++N+AL LR+ ++++ Sbjct: 61 VNGHDLSRLKGREIPFLRRQIGVVFQDFRLLPDRTVYENVALP----LRVIGKPPREIRR 116 Query: 113 ----MLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEI 168 +L+ V L+ PSQ+SGG++QRVA+AR ++ Q +LL DEP DP L EI Sbjct: 117 RVSEVLDLVGLKHKARALPSQLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEI 176 Query: 169 LGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDR 216 + L +++ + T+LM +H+LE ++ R + + G++V D Sbjct: 177 MRLFEEI-NRLGTTVLMATHDLELVNRMRHRVLALEDGRLVRDESRGV 223 >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 = 144 bits (364), Expect = 2e-35 Identities = 69/225 (30%), Positives = 126/225 (56%), Gaps = 7/225 (3%) Query: 2 IKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I+ +++ Y K + ++ K E +V++GPSG+GK+T + ++ PT G IF+ Sbjct: 1 IEFENVTKRYGGGKKAVNNLNLEIAKGEFLVLIGPSGSGKTTTMKMINRLIEPTSGEIFI 60 Query: 59 NGQNHTRSSPSK--RPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 +G++ P + R + + Q+ LF H+TV +NIAL + ++L Sbjct: 61 DGEDIREQDPVELRRKIGYVIQQIGLFPHMTVEENIALVPKLLKWPKEKIRERADELLAL 120 Query: 117 VFLED--FFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQ 174 V L+ F +R+P ++SGGQ+QRV +AR L P+LL+DEPF DP R ++ K+ Sbjct: 121 VGLDPAEFADRYPHELSGGQQQRVGVARALAADPPLLLMDEPFGALDPITRDQLQEEFKR 180 Query: 175 VCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + E T++ ++H+++++ ++A R ++ G+IV G PD ++ Sbjct: 181 LQQELGKTIVFVTHDIDEAFRLADRIAIMKNGEIVQVGTPDEILR 225 >gnl|CDD|34177 COG4525, TauB, ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 259 Score = 143 bits (361), Expect = 5e-35 Identities = 78/226 (34%), Positives = 118/226 (52%), Gaps = 19/226 (8%) Query: 1 MIKLDHLIYCYDNLKM----QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSI 56 M+ + HL Y+ + E +V+LGPSG GK+TLL+L+AGF P+RGSI Sbjct: 3 MLNVSHLSLSYEGKPRSALEDVSLTIASGELVVVLGPSGCGKTTLLNLIAGFVTPSRGSI 62 Query: 57 FLNGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIAL-----GIAPNLRLDHYQHAQVK 111 LNG+ + ++FQ L L V N+A GI R + Sbjct: 63 QLNGRRIEGPGAER---GVVFQNEALLPWLNVIDNVAFGLQLRGIEKAQRRE-----IAH 114 Query: 112 QMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGL 171 QML V LE +++ Q+SGG RQRV +AR L + +LLLDEPF D R ++ L Sbjct: 115 QMLALVGLEGAEHKYIWQLSGGMRQRVGIARALAVEPQLLLLDEPFGALDALTREQMQEL 174 Query: 172 LKQVCDERQLTLLMISHNLEDSMQIATRFIVIAG--GQIVYDGDPD 215 L + E +L+I+H++E+++ +ATR +V++ G++V D Sbjct: 175 LLDLWQETGKQVLLITHDIEEALFLATRLVVLSPGPGRVVERLPLD 220 >gnl|CDD|72977 cd03218, ABC_YhbG, The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.. Length = 232 Score = 141 bits (356), Expect = 2e-34 Identities = 63/204 (30%), Positives = 109/204 (53%), Gaps = 4/204 (1%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRP---LSI 75 V + E + +LGP+GAGK+T ++ G P G I L+GQ+ T+ KR + Sbjct: 20 SLSVKQGEIVGLLGPNGAGKTTTFYMIVGLVKPDSGKILLDGQDITKLPMHKRARLGIGY 79 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQR 135 L QE ++F LTV +NI + + +++++LE+ + S +SGG+R Sbjct: 80 LPQEASIFRKLTVEENILAVLEIRGLSKKEREEKLEELLEEFHITHLRKSKASSLSGGER 139 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQ 195 +RV +AR L LLLDEPFA DP +I ++K + +R + +L+ HN+ +++ Sbjct: 140 RRVEIARALATNPKFLLLDEPFAGVDPIAVQDIQKIIKIL-KDRGIGVLITDHNVRETLS 198 Query: 196 IATRFIVIAGGQIVYDGDPDRLMN 219 I R +I G+++ +G P+ + Sbjct: 199 ITDRAYIIYEGKVLAEGTPEEIAA 222 >gnl|CDD|31318 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]. Length = 254 Score = 139 bits (353), Expect = 4e-34 Identities = 74/229 (32%), Positives = 114/229 (49%), Gaps = 15/229 (6%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 MI++++L Y N + V K E ++GP+GAGKSTLL + G P+ G I + Sbjct: 4 MIEVENLTVSYGNRPVLEDISLSVEKGEITALIGPNGAGKSTLLKAILGLLKPSSGEIKI 63 Query: 59 NGQNHTRSSPSKR----PLSILFQENNLFSHLTVWQNIALGIAPNL----RLDHYQHAQV 110 G+ + R P + +TV + LG RL+ +V Sbjct: 64 FGKPVRKRRKRLRIGYVPQKSSV---DRSFPITVKDVVLLGRYGKKGWFRRLNKKDKEKV 120 Query: 111 KQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILG 170 + LE+V +ED +R ++SGGQ+QRV LAR L + +LLLDEPF D A + EI Sbjct: 121 DEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYD 180 Query: 171 LLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 LLK++ E T+LM++H+L M R I + ++ G P+ ++ Sbjct: 181 LLKELRQE-GKTVLMVTHDLGLVMAYFDRVICLNRH-LIASGPPEEVLT 227 >gnl|CDD|33892 COG4136, COG4136, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 213 Score = 139 bits (352), Expect = 5e-34 Identities = 66/182 (36%), Positives = 102/182 (56%), Gaps = 4/182 (2%) Query: 14 LKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGF---KYPTRGSIFLNGQNHTRSSPSK 70 L +F + K E + ++GPSG GKSTLLS M G ++ G ++LN Q ++ Sbjct: 17 LLANVNFTIAKGEIVTLMGPSGCGKSTLLSWMIGALAGQFSCTGELWLNEQRLDMLPAAQ 76 Query: 71 RPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQM 130 R + ILFQ+ LF HL+V QN+ + L+ + ++A LE+ L+ F++ P+ + Sbjct: 77 RQIGILFQDALLFPHLSVGQNLLFALPATLKGNARRNA-ANAALERSGLDGAFHQDPATL 135 Query: 131 SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNL 190 SGGQR RVAL R L+ Q LLLDEPF+ D ALR + + + + ++H+L Sbjct: 136 SGGQRARVALLRALLAQPKALLLDEPFSRLDVALRDQFRQWVFSEVRAAGIPTVQVTHDL 195 Query: 191 ED 192 +D Sbjct: 196 QD 197 >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 = 138 bits (349), Expect = 1e-33 Identities = 70/212 (33%), Positives = 108/212 (50%), Gaps = 34/212 (16%) Query: 3 KLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNG 60 ++++L Y + + E + ILGP+GAGKSTLL +AG P+ G I L+G Sbjct: 1 EVENLSVGYGGRTVLDDLSLSIEAGEIVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDG 60 Query: 61 QNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLE 120 ++ SP + + IA V Q LE + L Sbjct: 61 KDLASLSPKELA-----------------RKIAY---------------VPQALELLGLA 88 Query: 121 DFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQ 180 +R +++SGG+RQRV LAR L ++ PILLLDEP + D A + E+L LL+++ ER Sbjct: 89 HLADRPFNELSGGERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERG 148 Query: 181 LTLLMISHNLEDSMQIATRFIVIAGGQIVYDG 212 T++M+ H+L + + A R I++ G+IV G Sbjct: 149 KTVVMVLHDLNLAARYADRVILLKDGRIVAQG 180 >gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]. Length = 500 Score = 136 bits (345), Expect = 4e-33 Identities = 58/203 (28%), Positives = 102/203 (50%), Gaps = 8/203 (3%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS---KRPLSI 75 V E +LG +GAGKSTL+ +++G P G I ++G+ SSP ++ Sbjct: 28 SLTVRPGEVHALLGENGAGKSTLMKILSGVYPPDSGEILIDGKPVAFSSPRDALAAGIAT 87 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLR---LDH-YQHAQVKQMLEKVFLEDFFNRFPSQMS 131 + QE +L +L+V +NI LG P R +D + +++L ++ L+ + +S Sbjct: 88 VHQELSLVPNLSVAENIFLGREPTRRFGLIDRKAMRRRARELLARLGLDIDPDTLVGDLS 147 Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLE 191 QRQ V +AR L +L+LDEP A + L++++ + + ++ ISH L+ Sbjct: 148 IAQRQMVEIARALSFDARVLILDEPTAALTVKETERLFDLIRRL-KAQGVAIIYISHRLD 206 Query: 192 DSMQIATRFIVIAGGQIVYDGDP 214 + +IA R V+ G++V Sbjct: 207 EVFEIADRITVLRDGRVVGTRPT 229 Score = 92.5 bits (230), Expect = 9e-20 Identities = 55/207 (26%), Positives = 93/207 (44%), Gaps = 21/207 (10%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKR-PLSILF 77 F V E + I G GAG++ L + G + + G I L+G+ SP I + Sbjct: 279 SFTVRAGEILGIAGLVGAGRTELARALFGARPASSGEILLDGKPVRIRSPRDAIKAGIAY 338 Query: 78 -----QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRF------ 126 + L +++ +NI L +LR + + + E+ E + R Sbjct: 339 VPEDRKSEGLVLDMSIAENITL---ASLR-RFSRRGLIDRRKERALAERYIRRLRIKTPS 394 Query: 127 ----PSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLT 182 +SGG +Q+V LAR L +L+LDEP D + EI L++++ E Sbjct: 395 PEQPIGTLSGGNQQKVVLARWLATDPKVLILDEPTRGIDVGAKAEIYRLIRELAAE-GKA 453 Query: 183 LLMISHNLEDSMQIATRFIVIAGGQIV 209 +LMIS L + + ++ R +V+ G+IV Sbjct: 454 ILMISSELPELLGLSDRILVMREGRIV 480 >gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]. Length = 709 Score = 136 bits (344), Expect = 5e-33 Identities = 71/235 (30%), Positives = 116/235 (49%), Gaps = 27/235 (11%) Query: 2 IKLDHLIYCYDNLKMQ----FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 I+ +++ + Y ++ E++ I+G SG+GKSTLL L+ G P +G I Sbjct: 472 IEFENVSFRYGPDDPPVLEDLSLEIPPGEKVAIVGRSGSGKSTLLKLLLGLYKPQQGRIL 531 Query: 58 LNGQNHTRSSPS--KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 L+G + + +R + + Q+ LFS ++ +NIALG P + ++ + + Sbjct: 532 LDGVDLNDIDLASLRRQVGYVLQDPFLFSG-SIRENIALG-NPEATDE-----EIIEAAQ 584 Query: 116 KVFLEDFFNRFPSQM-----------SGGQRQRVALARCLIRQKPILLLDEPFAVFDPAL 164 +F P SGGQRQR+ALAR L+ + ILLLDE + DP Sbjct: 585 LAGAHEFIENLPMGYDTPVGEGGANLSGGQRQRLALARALLSKPKILLLDEATSALDPET 644 Query: 165 RHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 IL L Q+ R T+++I+H L +++ A R IV+ G+IV G + L+ Sbjct: 645 EAIILQNLLQILQGR--TVIIIAHRLS-TIRSADRIIVLDQGKIVEQGSHEELLA 696 >gnl|CDD|33900 COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 352 Score = 135 bits (342), Expect = 9e-33 Identities = 69/218 (31%), Positives = 122/218 (55%), Gaps = 13/218 (5%) Query: 1 MIKLDHLIYCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNG 60 M++L+ N + +F + + GPSG+GK++L++++AG P G I LNG Sbjct: 1 MLELN-FRQRLGNFALDANFTLPARGITALFGPSGSGKTSLINMIAGLTRPDEGRIELNG 59 Query: 61 QNHTRSS------PSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQML 114 + + P KR + +FQ+ LF H TV N+ G+ ++R AQ Q++ Sbjct: 60 RVLVDAEKGIFLPPEKRRIGYVFQDARLFPHYTVRGNLRYGMWKSMR------AQFDQLV 113 Query: 115 EKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQ 174 + +E +R+P +SGG++QRVA+ R L+ +LL+DEP A D + EIL L++ Sbjct: 114 ALLGIEHLLDRYPGTLSGGEKQRVAIGRALLTAPELLLMDEPLASLDLPRKREILPYLER 173 Query: 175 VCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDG 212 + DE + +L +SH+L++ +++A R +V+ G++ G Sbjct: 174 LRDEINIPILYVSHSLDEVLRLADRVVVLENGKVKASG 211 >gnl|CDD|72989 cd03230, ABC_DR_subfamily_A, This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter 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 = 173 Score = 134 bits (338), Expect = 3e-32 Identities = 60/210 (28%), Positives = 99/210 (47%), Gaps = 40/210 (19%) Query: 2 IKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLN 59 I++ +L Y V K E +LGP+GAGK+TL+ ++ G P G I + Sbjct: 1 IEVRNLSKRYGKKTALDDISLTVEKGEIYGLLGPNGAGKTTLIKIILGLLKPDSGEIKVL 60 Query: 60 GQNHTRSSPS-KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF 118 G++ + KR + L +E +L+ +LTV +N+ L Sbjct: 61 GKDIKKEPEEVKRRIGYLPEEPSLYENLTVRENLKL------------------------ 96 Query: 119 LEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDE 178 SGG +QR+ALA+ L+ +L+LDEP + DP R E LL+++ E Sbjct: 97 ------------SGGMKQRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKE 144 Query: 179 RQLTLLMISHNLEDSMQIATRFIVIAGGQI 208 T+L+ SH LE++ ++ R ++ G+I Sbjct: 145 -GKTILLSSHILEEAERLCDRVAILNNGRI 173 >gnl|CDD|35278 KOG0055, KOG0055, KOG0055, Multidrug/pheromone exporter, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1228 Score = 133 bits (335), Expect = 6e-32 Identities = 60/215 (27%), Positives = 106/215 (49%), Gaps = 23/215 (10%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN-HTRSSPSKRP-LSI 75 ++ + + ++GPSG+GKSTL+ L+A F PT G + ++G++ + R + + Sbjct: 372 VSLKIPSGQTVALVGPSGSGKSTLIQLLARFYDPTSGEVLIDGEDIRNLNLKWLRSQIGL 431 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP-------- 127 + QE LF+ T+ +NI G ++++ + DF + P Sbjct: 432 VSQEPVLFA-TTIRENIRYG------KPDATREEIEEAAKAANAHDFILKLPDGYDTLVG 484 Query: 128 ---SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 Q+SGGQ+QR+A+AR L+R ILLLDE + D + L + R T + Sbjct: 485 ERGVQLSGGQKQRIAIARALVRNPKILLLDEATSALDAESERVVQEALDKASKGR--TTI 542 Query: 185 MISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 +++H L +++ A + V+ G+IV G D L+ Sbjct: 543 VVAHRLS-TIRNADKIAVMEEGKIVEQGTHDELIA 576 Score = 111 bits (278), Expect = 2e-25 Identities = 59/236 (25%), Positives = 111/236 (47%), Gaps = 28/236 (11%) Query: 2 IKLDHLIYCYDNLKMQ-----FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSI 56 I+ ++ + Y + + + ++GPSG+GKST++SL+ F P G + Sbjct: 988 IEFRNVSFAYPTRPDVPVLNNLSLSIRAGQTVALVGPSGSGKSTVISLLERFYDPDAGKV 1047 Query: 57 FLNGQNHTRSSPS--KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQML 114 ++G + + ++ + ++ QE LF+ T+ +NIA G + ++ + Sbjct: 1048 KIDGVDIKDLNLKWLRKQIGLVSQEPVLFN-GTIRENIAYG------SEEVSEEEIIEAA 1100 Query: 115 EKVFLEDFFNRFP-----------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPA 163 + +F + P Q+SGGQ+QR+A+AR ++R ILLLDE + D Sbjct: 1101 KLANAHNFISSLPQGYDTRVGERGVQLSGGQKQRIAIARAILRNPKILLLDEATSALDSE 1160 Query: 164 LRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + L + + R T ++I+H L ++Q A V+ G++V G D L+ Sbjct: 1161 SERVVQEALDRAMEGR--TTIVIAHRLS-TIQNADVIAVLKNGKVVEQGTHDELLA 1213 >gnl|CDD|34593 COG4988, CydD, ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]. Length = 559 Score = 131 bits (330), Expect = 2e-31 Identities = 74/232 (31%), Positives = 120/232 (51%), Gaps = 25/232 (10%) Query: 2 IKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I L++L + Y + K + + + ++G SGAGKSTLL+L+ GF PT+G I + Sbjct: 321 ISLENLSFRYPDGKPALSDLNLTIKAGQLTALVGASGAGKSTLLNLLLGFLAPTQGEIRV 380 Query: 59 NGQNHTRSSPS--KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 NG + SP ++ +S + Q LF+ T+ +NI L P+ ++ L++ Sbjct: 381 NGIDLRDLSPEAWRKQISWVSQNPYLFAG-TIRENILLA-RPDA-----SDEEIIAALDQ 433 Query: 117 VFLEDFFNRFP----------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRH 166 L +F + + +SGGQ QR+ALAR L+ +LLLDEP A D Sbjct: 434 AGLLEFVPKPDGLDTVIGEGGAGLSGGQAQRLALARALLSPASLLLLDEPTAHLDAETEQ 493 Query: 167 EILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 IL L+++ ++ T+L+I+H LED A R +V+ G++V G + L Sbjct: 494 IILQALQELAKQK--TVLVITHRLED-AADADRIVVLDNGRLVEQGTHEELS 542 >gnl|CDD|72994 cd03235, ABC_Metallic_Cations, ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.. Length = 213 Score = 131 bits (330), Expect = 2e-31 Identities = 69/222 (31%), Positives = 117/222 (52%), Gaps = 21/222 (9%) Query: 3 KLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNG 60 +++ L Y + F+V E + I+GP+GAGKSTLL + G PT GSI + G Sbjct: 1 EVEDLTVSYGGHPVLEDVSFEVKPGEFLAIVGPNGAGKSTLLKAILGLLKPTSGSIRVFG 60 Query: 61 QNHTRSS------PSKRPLSILFQENNLFSHLTVWQNIALGIAPNL----RLDHYQHAQV 110 + + P +R + F ++V + +G+ + RL A+V Sbjct: 61 KPLEKERKRIGYVPQRRSIDRDFP-------ISVRDVVLMGLYGHKGLFRRLSKADKAKV 113 Query: 111 KQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILG 170 + LE+V L + +R ++SGGQ+QRV LAR L++ +LLLDEPFA DP + +I Sbjct: 114 DEALERVGLSELADRQIGELSGGQQQRVLLARALVQDPDLLLLDEPFAGVDPKTQEDIYE 173 Query: 171 LLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDG 212 LL+++ E +T+L+++H+L ++ R +++ +V G Sbjct: 174 LLRELRREG-MTILVVTHDLGLVLEYFDRVLLLNRT-VVASG 213 >gnl|CDD|34592 COG4987, CydC, ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]. Length = 573 Score = 130 bits (329), Expect = 3e-31 Identities = 74/234 (31%), Positives = 121/234 (51%), Gaps = 27/234 (11%) Query: 2 IKLDHLIYCYDNLKMQ----FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 ++L ++ + Y + + F+ + + E++ ILG SG+GKSTLL L+AG P +GSI Sbjct: 337 LELRNVSFTYPGQQTKALKNFNLTLAQGEKVAILGRSGSGKSTLLQLLAGAWDPQQGSIT 396 Query: 58 LNGQN--HTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 LNG + +S+L Q +LFS T+ N+ L P+ ++ L+ Sbjct: 397 LNGVEIASLDEQALRETISVLTQRVHLFSG-TLRDNLRLA-NPDA-----SDEELWAALQ 449 Query: 116 KVFLEDFFNRFPS-----------QMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPAL 164 +V LE P ++SGG+R+R+ALAR L+ P+ LLDEP DP Sbjct: 450 QVGLEKLLESAPDGLNTWLGEGGRRLSGGERRRLALARALLHDAPLWLLDEPTEGLDPIT 509 Query: 165 RHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 ++L LL + + + TLLM++H L ++ R IV+ G+I+ +G L+ Sbjct: 510 ERQVLALLFEHAEGK--TLLMVTHRLR-GLERMDRIIVLDNGKIIEEGTHAELL 560 >gnl|CDD|73023 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. 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 = 211 Score = 130 bits (328), Expect = 4e-31 Identities = 55/185 (29%), Positives = 103/185 (55%), Gaps = 5/185 (2%) Query: 30 ILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS-KRPLSILFQENNLFSHLTV 88 +LGP+GAGK+TL+ ++A P+ G+I ++GQ+ + +R + L QE ++ + TV Sbjct: 30 LLGPNGAGKTTLMRILATLTPPSSGTIRIDGQDVLKQPQKLRRRIGYLPQEFGVYPNFTV 89 Query: 89 WQNIA-LGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQ 147 + + + + A+V ++LE V L D + +SGG R+RV +A+ L+ Sbjct: 90 REFLDYIAWLKGIP-SKEVKARVDEVLELVNLGDRAKKKIGSLSGGMRRRVGIAQALVGD 148 Query: 148 KPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQ 207 IL++DEP A DP R LL ++ ++R +++ +H +ED + + V+ G+ Sbjct: 149 PSILIVDEPTAGLDPEERIRFRNLLSELGEDR--IVILSTHIVEDVESLCNQVAVLNKGK 206 Query: 208 IVYDG 212 +V++G Sbjct: 207 LVFEG 211 >gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). 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 = 171 Score = 129 bits (327), Expect = 5e-31 Identities = 59/212 (27%), Positives = 98/212 (46%), Gaps = 47/212 (22%) Query: 2 IKLDHLIYCYDNLKMQ----FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 I+ ++ + Y + E++ I+GPSG+GKSTLL L+ PT G I Sbjct: 1 IEFKNVSFSYPGRPKPVLKDVSLTIKPGEKVAIVGPSGSGKSTLLKLLLRLYDPTSGEIL 60 Query: 58 LNGQNHTRSSPS--KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 ++G + ++ ++ + Q+ LFS T+ +NI Sbjct: 61 IDGVDLRDLDLESLRKNIAYVPQDPFLFS-GTIRENI----------------------- 96 Query: 116 KVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQV 175 +SGGQRQR+A+AR L+R PIL+LDE + DP IL L+ + Sbjct: 97 --------------LSGGQRQRIAIARALLRDPPILILDEATSALDPETEALILEALRAL 142 Query: 176 CDERQLTLLMISHNLEDSMQIATRFIVIAGGQ 207 + T+++I+H L +++ A R IV+ G+ Sbjct: 143 AKGK--TVIVIAHRLS-TIRDADRIIVLDDGR 171 >gnl|CDD|73051 cd03292, ABC_FtsE_transporter, FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane. The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.. Length = 214 Score = 128 bits (323), Expect = 1e-30 Identities = 62/194 (31%), Positives = 104/194 (53%), Gaps = 6/194 (3%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN----HTRSSPS-KRPLS 74 ++ E + ++GPSGAGKSTLL L+ + PT G+I +NGQ+ R+ P +R + Sbjct: 22 ISISAGEFVFLVGPSGAGKSTLLKLIYKEELPTSGTIRVNGQDVSDLRGRAIPYLRRKIG 81 Query: 75 ILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQ 134 ++FQ+ L V++N+A + +V LE V L P+++SGG+ Sbjct: 82 VVFQDFRLLPDRNVYENVAFALEVTGVPPREIRKRVPAALELVGLSHKHRALPAELSGGE 141 Query: 135 RQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSM 194 +QRVA+AR ++ IL+ DEP DP EI+ LLK++ ++ T+++ +H E Sbjct: 142 QQRVAIARAIVNSPTILIADEPTGNLDPDTTWEIMNLLKKI-NKAGTTVVVATHAKELVD 200 Query: 195 QIATRFIVIAGGQI 208 R I + G++ Sbjct: 201 TTRHRVIALERGKL 214 >gnl|CDD|73022 cd03263, ABC_subfamily_A, The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.. Length = 220 Score = 128 bits (323), Expect = 2e-30 Identities = 58/203 (28%), Positives = 105/203 (51%), Gaps = 5/203 (2%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN-HTRSSPSKRPLSI 75 V K E +LG +GAGK+T L ++ G PT G+ ++NG + T +++ L Sbjct: 20 DLSLNVYKGEIFGLLGHNGAGKTTTLKMLTGELRPTSGTAYINGYSIRTDRKAARQSLGY 79 Query: 76 LFQENNLFSHLTVWQNIAL-GIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQ 134 Q + LF LTV +++ L +V+ +L + L D N+ +SGG Sbjct: 80 CPQFDALFDELTVREHLRFYARLKGLPKSEI-KEEVELLLRVLGLTDKANKRARTLSGGM 138 Query: 135 RQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSM 194 +++++LA LI +LLLDEP + DPA R I L+ +V R ++++ +H+++++ Sbjct: 139 KRKLSLAIALIGGPSVLLLDEPTSGLDPASRRAIWDLILEVRKGR--SIILTTHSMDEAE 196 Query: 195 QIATRFIVIAGGQIVYDGDPDRL 217 + R +++ G++ G P L Sbjct: 197 ALCDRIAIMSDGKLRCIGSPQEL 219 >gnl|CDD|73178 COG4608, AppF, ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]. Length = 268 Score = 125 bits (316), Expect = 8e-30 Identities = 64/202 (31%), Positives = 101/202 (50%), Gaps = 36/202 (17%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 F + + E + ++G SG GKSTL L+ G + PT G I G++ T+ S +R Sbjct: 33 SFSIKEGETLGLVGESGCGKSTLGRLILGLEEPTSGEILFEGKDITKLSKEER------- 85 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFL-EDFFNRFPSQMSGGQRQR 137 +V ++LEKV L E+F R+P ++SGGQRQR Sbjct: 86 ----------------------------RERVLELLEKVGLPEEFLYRYPHELSGGQRQR 117 Query: 138 VALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIA 197 + +AR L +++ DEP + D +++ +IL LLK + +E LT L ISH+L I+ Sbjct: 118 IGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYIS 177 Query: 198 TRFIVIAGGQIVYDGDPDRLMN 219 R V+ G+IV G + + + Sbjct: 178 DRIAVMYLGKIVEIGPTEEVFS 199 >gnl|CDD|73019 cd03260, ABC_PstB_phosphate_transporter, Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).. Length = 227 Score = 125 bits (315), Expect = 1e-29 Identities = 64/230 (27%), Positives = 116/230 (50%), Gaps = 17/230 (7%) Query: 2 IKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGF-----KYPTRG 54 I+L L Y + + K E ++GPSG GKSTLL L+ P G Sbjct: 1 IELRDLNVYYGDKHALKDISLDIPKGEITALIGPSGCGKSTLLRLLNRLNDLIPGAPDEG 60 Query: 55 SIFLNGQNHTRSSPS----KRPLSILFQENNLFSHLTVWQNIALGIAPN-LRLDHYQHAQ 109 + L+G++ +R + ++FQ+ N F +++ N+A G+ + ++L + Sbjct: 61 EVLLDGKDIYDLDVDVLELRRRVGMVFQKPNPF-PGSIYDNVAYGLRLHGIKLKEELDER 119 Query: 110 VKQMLEKVFLEDFFNR--FPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHE 167 V++ L K L D +SGGQ+QR+ LAR L + +LLLDEP + DP + Sbjct: 120 VEEALRKAALWDEVKDRLHALGLSGGQQQRLCLARALANEPEVLLLDEPTSALDPISTAK 179 Query: 168 ILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 I L+ ++ E T+++++HN++ + ++A R + G++V G +++ Sbjct: 180 IEELIAELKKE--YTIVIVTHNMQQAARVADRTAFLLNGRLVEFGPTEQI 227 >gnl|CDD|33907 COG4161, ArtP, ABC-type arginine transport system, ATPase component [Amino acid transport and metabolism]. Length = 242 Score = 124 bits (312), Expect = 2e-29 Identities = 74/229 (32%), Positives = 133/229 (58%), Gaps = 12/229 (5%) Query: 2 IKLDHLIYCYDNLKMQFD--FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLN 59 I+L+ + Y + FD + E +V+LGPSGAGKS+LL ++ + P G++ + Sbjct: 3 IQLNGINCFYGAHQALFDITLDCPEGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLNIA 62 Query: 60 GQNHTRS-SPS-------KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQ-HAQV 110 G + S +PS +R + ++FQ+ NL+ HLTV +N+ L L Q A+ Sbjct: 63 GNHFDFSKTPSDKAIRDLRRNVGMVFQQYNLWPHLTVQENLIEAPCRVLGLSKDQALARA 122 Query: 111 KQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILG 170 +++L+++ L+ + +R+P +SGGQ+QRVA+AR L+ + +LL DEP A DP + +I+ Sbjct: 123 EKLLKRLRLKPYADRYPLHLSGGQQQRVAIARALMMEPQVLLFDEPTAALDPEITAQIVS 182 Query: 171 LLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 ++K++ E +T ++++H +E + + A+R + + G IV GD Sbjct: 183 IIKEL-AETGITQVIVTHEVEVARKTASRVVYMENGHIVEQGDASCFTE 230 >gnl|CDD|31327 COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]. Length = 567 Score = 124 bits (312), Expect = 2e-29 Identities = 73/234 (31%), Positives = 116/234 (49%), Gaps = 26/234 (11%) Query: 2 IKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I+ +++ + Y K F + E++ I+GPSG+GKSTL+ L+ PT G I + Sbjct: 329 IEFENVSFSYPGKKPVLKDISFSIEPGEKVAIVGPSGSGKSTLIKLLLRLYDPTSGEILI 388 Query: 59 NGQNHTRSSPSKRP--LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 +G + S + I+ Q+ LFS T+ +NIALG ++++ L+ Sbjct: 389 DGIDIRDISLDSLRKRIGIVSQDPLLFS-GTIRENIALG------RPDATDEEIEEALKL 441 Query: 117 VFLEDFFNRFP-----------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALR 165 +F P +SGGQRQR+A+AR L+R PIL+LDE + D Sbjct: 442 ANAHEFIANLPDGYDTIVGERGVNLSGGQRQRLAIARALLRNPPILILDEATSALDTETE 501 Query: 166 HEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 I LK++ R T L+I+H L +++ A R IV+ G+IV G + L+ Sbjct: 502 ALIQDALKKLLKGR--TTLIIAHRL-STIKNADRIIVLDNGRIVERGTHEELLA 552 >gnl|CDD|73004 cd03245, ABCC_bacteriocin_exporters, ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.. Length = 220 Score = 124 bits (312), Expect = 3e-29 Identities = 72/207 (34%), Positives = 108/207 (52%), Gaps = 25/207 (12%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSILF 77 + E++ I+G G+GKSTLL L+AG PT GS+ L+G + + P+ +R + + Sbjct: 25 LTIRAGEKVAIIGRVGSGKSTLLKLLAGLYKPTSGSVLLDGTDIRQLDPADLRRNIGYVP 84 Query: 78 QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP---------- 127 Q+ LF T+ NI LG AP ++ + E + DF N+ P Sbjct: 85 QDVTLFYG-TLRDNITLG-AP-----LADDERILRAAELAGVTDFVNKHPNGLDLQIGER 137 Query: 128 -SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMI 186 +SGGQRQ VALAR L+ PILLLDEP + D + L+Q+ ++ TL++I Sbjct: 138 GRGLSGGQRQAVALARALLNDPPILLLDEPTSAMDMNSEERLKERLRQLLGDK--TLIII 195 Query: 187 SHNLEDSM-QIATRFIVIAGGQIVYDG 212 +H S+ + R IV+ G+IV DG Sbjct: 196 THRP--SLLDLVDRIIVMDSGRIVADG 220 >gnl|CDD|31332 COG1137, YhbG, ABC-type (unclassified) transport system, ATPase component [General function prediction only]. Length = 243 Score = 124 bits (312), Expect = 3e-29 Identities = 66/226 (29%), Positives = 117/226 (51%), Gaps = 8/226 (3%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 + ++L Y K+ +VN E + +LGP+GAGK+T ++ G P G I L Sbjct: 4 TLVAENLAKSYKKRKVVNDVSLEVNSGEIVGLLGPNGAGKTTTFYMIVGLVRPDSGKILL 63 Query: 59 NGQNHTRSSPSKRP---LSILFQENNLFSHLTVWQNI--ALGIAPNLRLDHYQHAQVKQM 113 + ++ T+ KR + L QE ++F LTV NI L I + ++ + Sbjct: 64 DDEDITKLPMHKRARLGIGYLPQEASIFRKLTVEDNIMAVLEIREKDLKKAERKEELDAL 123 Query: 114 LEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLK 173 LE+ + + +SGG+R+RV +AR L +LLDEPFA DP +I ++K Sbjct: 124 LEEFHITHLRDSKAYSLSGGERRRVEIARALAANPKFILLDEPFAGVDPIAVIDIQRIIK 183 Query: 174 QVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + +R + +L+ HN+ +++ I R +I+ G+++ +G P+ ++N Sbjct: 184 HL-KDRGIGVLITDHNVRETLDICDRAYIISDGKVLAEGSPEEIVN 228 >gnl|CDD|34199 COG4555, NatA, ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]. Length = 245 Score = 123 bits (311), Expect = 3e-29 Identities = 59/221 (26%), Positives = 111/221 (50%), Gaps = 5/221 (2%) Query: 1 MIKLDHLIYCYDNLKMQFD---FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 M+++ L Y + F+ + E +LG +GAGK+TLL ++A P G + Sbjct: 1 MLEVTDLTKSYGSKVQAVRDVSFEAEEGEITGLLGENGAGKTTLLRMIATLLIPDSGKVT 60 Query: 58 LNGQNHTR-SSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 ++G + R S +R + +LF E L++ LT +N+ N A++ ++ ++ Sbjct: 61 IDGVDTVRDPSFVRRKIGVLFGERGLYARLTARENLKYFARLNGLSRKEIKARIAELSKR 120 Query: 117 VFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVC 176 + L ++ +R + S G +Q+VA+AR L+ IL+LDEP + D R + +KQ Sbjct: 121 LQLLEYLDRRVGEFSTGMKQKVAIARALVHDPSILVLDEPTSGLDIRTRRKFHDFIKQ-L 179 Query: 177 DERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 ++ SH +++ + R IV+ G++V +G + L Sbjct: 180 KNEGRAVIFSSHIMQEVEALCDRVIVLHKGEVVLEGSIEAL 220 >gnl|CDD|30793 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]. Length = 316 Score = 122 bits (307), Expect = 9e-29 Identities = 61/217 (28%), Positives = 110/217 (50%), Gaps = 18/217 (8%) Query: 19 DFQVNKAERIVILGPSGAGKSTL-LSLMAGFKYP----TRGSIFLNGQNHTRSSPSKRP- 72 F++ K E + I+G SG+GKS L ++M P G I +G++ S + Sbjct: 25 SFELKKGEILGIVGESGSGKSVLAKAIMGLLPKPNARIVGGEILFDGKDLLSLSEKELRK 84 Query: 73 -----LSILFQE--NNLFSHLTVWQNIALGIAPNLRLDHYQHA--QVKQMLEKVFLED-- 121 ++++FQ+ +L +T+ IA + + + + A + ++LE V + D Sbjct: 85 IRGKEIAMIFQDPMTSLNPVMTIGDQIAEVLRLHGKGLSKKEAKERAIELLELVGIPDPE 144 Query: 122 -FFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQ 180 +P ++SGG RQRV +A L +L+ DEP D ++ +IL LLK++ E+ Sbjct: 145 RRLKSYPHELSGGMRQRVMIAMALALNPKLLIADEPTTALDVTVQAQILDLLKELQREKG 204 Query: 181 LTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 L++I+H+L +IA R V+ G+IV +G + + Sbjct: 205 TALILITHDLGVVAEIADRVAVMYAGRIVEEGPVEEI 241 >gnl|CDD|34201 COG4559, COG4559, ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 259 Score = 121 bits (306), Expect = 1e-28 Identities = 69/231 (29%), Positives = 109/231 (47%), Gaps = 13/231 (5%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 MI+ ++L Y ++ + E + ILGP+GAGKSTLL ++G P G + L Sbjct: 1 MIRAENLSYSLAGRRLLDGVSLDLRPGEVLAILGPNGAGKSTLLKALSGELSPDSGEVTL 60 Query: 59 NGQNHTRSSPSK--RPLSILFQENNLFSHLTVWQNIALGIAPNL--RLDHYQHAQVKQML 114 NG P + R ++L Q ++L TV + + +G P+ R Q L Sbjct: 61 NGVPLNSWPPEELARHRAVLPQNSSLAFPFTVQEVVQMGRIPHRSGREPEEDERIAAQAL 120 Query: 115 EKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKP------ILLLDEPFAVFDPALRHEI 168 L R +SGG++QRV LAR L + P L LDEP + D A +H Sbjct: 121 AATDLSGLAGRDYRTLSGGEQQRVQLARVLAQLWPPVPSGRWLFLDEPTSALDIAHQHHT 180 Query: 169 LGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 L L +Q+ E +L + H+L + Q A R +++ G+++ G P ++ Sbjct: 181 LRLARQLAREG-GAVLAVLHDLNLAAQYADRIVLLHQGRVIASGSPQDVLT 230 >gnl|CDD|34233 COG4598, HisP, ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]. Length = 256 Score = 120 bits (302), Expect = 4e-28 Identities = 62/213 (29%), Positives = 118/213 (55%), Gaps = 17/213 (7%) Query: 21 QVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN-------HTRSSPSKRP- 72 Q N + I I+G SG+GKST L + + P+ GSI +NG+ + P+ + Sbjct: 28 QANAGDVISIIGSSGSGKSTFLRCINFLEKPSAGSIRVNGEEIRLKRDKDGQLKPADKRQ 87 Query: 73 -------LSILFQENNLFSHLTVWQNIALGIAPNLRLD-HYQHAQVKQMLEKVFLEDFFN 124 L ++FQ NL+SH+TV +N+ L + + ++ L KV + + + Sbjct: 88 LQRLRTRLGMVFQHFNLWSHMTVLENVIEAPVHVLGVSKAEAIERAEKYLAKVGIAEKAD 147 Query: 125 RFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 +P+ +SGGQ+QRVA+AR L + ++L DEP + DP L E+L +++ + +E + T++ Sbjct: 148 AYPAHLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPELVGEVLKVMQDLAEEGR-TMV 206 Query: 185 MISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 +++H + + +++ I + G+I +G P+++ Sbjct: 207 VVTHEMGFARDVSSHVIFLHQGKIEEEGPPEQV 239 >gnl|CDD|31298 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 263 Score = 119 bits (301), Expect = 5e-28 Identities = 67/213 (31%), Positives = 113/213 (53%), Gaps = 24/213 (11%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRP--LS 74 ++ + + + ++G +GAGKSTLL+ +AG PT G I ++G + T+ S +KR L+ Sbjct: 24 GLSLEIAEGDFVTVIGSNGAGKSTLLNAIAGDLKPTSGQILIDGVDVTKKSVAKRANLLA 83 Query: 75 ILFQ--ENNLFSHLTVWQNIAL--------GIAPNL---RLDHYQHAQVKQMLEKVFLED 121 +FQ LT+ +N+AL G++ L R ++ + L ++ L Sbjct: 84 RVFQDPLAGTAPELTIEENLALAESRGKKRGLSSALNERRRSSFR-----ERLARLGL-G 137 Query: 122 FFNRFPSQM---SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDE 178 NR ++ SGGQRQ ++L + ILLLDE A DP ++ L ++ +E Sbjct: 138 LENRLSDRIGLLSGGQRQALSLLMATLHPPKILLLDEHTAALDPKTAEFVMELTAKIVEE 197 Query: 179 RQLTLLMISHNLEDSMQIATRFIVIAGGQIVYD 211 +LT LM++HN+ED++ R I++ G+IV D Sbjct: 198 HKLTTLMVTHNMEDALDYGNRLIMLHSGKIVLD 230 >gnl|CDD|33636 COG3845, COG3845, ABC-type uncharacterized transport systems, ATPase components [General function prediction only]. Length = 501 Score = 119 bits (300), Expect = 7e-28 Identities = 68/217 (31%), Positives = 111/217 (51%), Gaps = 16/217 (7%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS---KRPLSI 75 V K E +LG +GAGKSTL+ ++ G P G I ++G+ SP + + + Sbjct: 24 SLSVKKGEIHALLGENGAGKSTLMKILFGLYQPDSGEIRVDGKEVRIKSPRDAIRLGIGM 83 Query: 76 LFQENNLFSHLTVWQNIALGIAP--NLRLDHYQ-HAQVKQMLEKVFLEDFFNRFPSQMSG 132 + Q L LTV +NI LG+ P +D Q A++K++ E+ L + + +S Sbjct: 84 VHQHFMLVPTLTVAENIILGLEPSKGGLIDRRQARARIKELSERYGLPVDPDAKVADLSV 143 Query: 133 GQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLED 192 G++QRV + + L R +L+LDEP AV P E+ +L+++ E T++ I+H L++ Sbjct: 144 GEQQRVEILKALYRGARLLILDEPTAVLTPQEADELFEILRRLAAE-GKTIIFITHKLKE 202 Query: 193 SMQIATRFIVIAGGQIV--YDGDPD-------RLMNG 220 M IA R V+ G++V D + LM G Sbjct: 203 VMAIADRVTVLRRGKVVGTVDPVAETTEEELAELMVG 239 Score = 77.5 bits (191), Expect = 3e-15 Identities = 60/213 (28%), Positives = 103/213 (48%), Gaps = 18/213 (8%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN-HTRSSPSKRPLSILF 77 F+V E + I G +G G+S L+ ++G + P G I LNG++ R SP +R L Sbjct: 278 SFEVRAGEIVGIAGVAGNGQSELVEAISGLRKPASGRILLNGKDVLGRLSPRERRRLGLA 337 Query: 78 ------QENNLFSHLTVWQNIALG---IAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPS 128 + L L++ +N+ LG P R +++ ++ +E+F R PS Sbjct: 338 YVPEDRHGHGLVLDLSLAENLVLGRHDKKPFSRGGFLDRRAIRKFAREL-IEEFDVRAPS 396 Query: 129 ------QMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLT 182 +SGG +Q++ LAR L R+ +L+ +P D I L ++ D + Sbjct: 397 PDAPARSLSGGNQQKLILARELARRPDLLIAAQPTRGLDVGAIEFIHERLLELRDAGKAV 456 Query: 183 LLMISHNLEDSMQIATRFIVIAGGQIVYDGDPD 215 LL IS +L++ ++++ R VI G+IV P+ Sbjct: 457 LL-ISEDLDEILELSDRIAVIYEGRIVGIVPPE 488 >gnl|CDD|73008 cd03249, ABC_MTABC3_MDL1_MDL2, MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.. Length = 238 Score = 117 bits (295), Expect = 2e-27 Identities = 64/214 (29%), Positives = 102/214 (47%), Gaps = 23/214 (10%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSI 75 + + + ++G SG GKST++SL+ F PT G I L+G + + + + + Sbjct: 22 LSLTIPPGKTVALVGSSGCGKSTVVSLLERFYDPTSGEILLDGVDIRDLNLRWLRSQIGL 81 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP-------- 127 + QE LF T+ +NI G +V++ +K + DF P Sbjct: 82 VSQEPVLFD-GTIAENIRYGKPDA------TDEEVEEAAKKANIHDFIMSLPDGYDTLVG 134 Query: 128 ---SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 SQ+SGGQ+QR+A+AR L+R ILLLDE + D + L + R T + Sbjct: 135 ERGSQLSGGQKQRIAIARALLRNPKILLLDEATSALDAESEKLVQEALDRAMKGR--TTI 192 Query: 185 MISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 +I+H L +++ A V+ GQ+V G D LM Sbjct: 193 VIAHRLS-TIRNADLIAVLQNGQVVEQGTHDELM 225 >gnl|CDD|73025 cd03266, ABC_NatA_sodium_exporter, NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.. Length = 218 Score = 117 bits (294), Expect = 3e-27 Identities = 58/224 (25%), Positives = 108/224 (48%), Gaps = 18/224 (8%) Query: 1 MIKLDHLIYCYDNLKMQF------DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRG 54 MI D L + ++K F V E +LGP+GAGK+T L ++AG P G Sbjct: 1 MITADALTKRFRDVKKTVQAVDGVSFTVKPGEVTGLLGPNGAGKTTTLRMLAGLLEPDAG 60 Query: 55 SIFLNGQN-HTRSSPSKRPLSILFQENNLFSHLTVWQNIAL-----GIAPNLRLDHYQHA 108 ++G + + ++R L + L+ LT +N+ G+ A Sbjct: 61 FATVDGFDVVKEPAEARRRLGFVSDSTGLYDRLTARENLEYFAGLYGLKG-----DELTA 115 Query: 109 QVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEI 168 +++++ +++ +E+ +R S G RQ+VA+AR L+ P+LLLDEP D + Sbjct: 116 RLEELADRLGMEELLDRRVGGFSTGMRQKVAIARALVHDPPVLLLDEPTTGLDVMATRAL 175 Query: 169 LGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDG 212 ++Q+ +L +H +++ ++ R +V+ G++VY+G Sbjct: 176 REFIRQLRAL-GKCILFSTHIMQEVERLCDRVVVLHRGRVVYEG 218 >gnl|CDD|73024 cd03265, ABC_DrrA, DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin. In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. 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 = 220 Score = 116 bits (292), Expect = 5e-27 Identities = 63/223 (28%), Positives = 122/223 (54%), Gaps = 11/223 (4%) Query: 2 IKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLN 59 I++++L+ Y + + F+V + E +LGP+GAGK+T + ++ PT G + Sbjct: 1 IEVENLVKKYGDFEAVRGVSFRVRRGEIFGLLGPNGAGKTTTIKMLTTLLKPTSGRATVA 60 Query: 60 GQNHTRSSPS-KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQ----ML 114 G + R +R + I+FQ+ ++ LT W+N+ + + RL A+ ++ +L Sbjct: 61 GHDVVREPREVRRRIGIVFQDLSVDDELTGWENLYI----HARLYGVPGAERRERIDELL 116 Query: 115 EKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQ 174 + V L + +R SGG R+R+ +AR L+ + +L LDEP DP R + +++ Sbjct: 117 DFVGLLEAADRLVKTYSGGMRRRLEIARSLVHRPEVLFLDEPTIGLDPQTRAHVWEYIEK 176 Query: 175 VCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 + +E +T+L+ +H +E++ Q+ R +I G+I+ +G P+ L Sbjct: 177 LKEEFGMTILLTTHYMEEAEQLCDRVAIIDHGRIIAEGTPEEL 219 >gnl|CDD|72971 cd00267, ABC_ATPase, 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 = 157 Score = 115 bits (290), Expect = 8e-27 Identities = 55/190 (28%), Positives = 87/190 (45%), Gaps = 50/190 (26%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILF 77 + E + ++GP+G+GKSTLL +AG PT G I ++G++ + + I + Sbjct: 18 VSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGY 77 Query: 78 QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQR 137 V Q+SGGQRQR Sbjct: 78 ---------------------------------------VP----------QLSGGQRQR 88 Query: 138 VALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIA 197 VALAR L+ +LLLDEP + DPA R +L LL+++ +E T+++++H+ E + A Sbjct: 89 VALARALLLNPDLLLLDEPTSGLDPASRERLLELLRELAEE-GRTVIIVTHDPELAELAA 147 Query: 198 TRFIVIAGGQ 207 R IV+ G+ Sbjct: 148 DRVIVLKDGK 157 >gnl|CDD|31316 COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]. Length = 257 Score = 113 bits (285), Expect = 3e-26 Identities = 58/237 (24%), Positives = 106/237 (44%), Gaps = 37/237 (15%) Query: 1 MIKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 +I+L ++ + K+ +QVN E I+GP+GAGK+TLLSL+ G P+ G + L Sbjct: 31 LIELKNVSVRRNGKKILGDLSWQVNPGEHWAIVGPNGAGKTTLLSLLTGEHPPSSGDVTL 90 Query: 59 NGQNHTR-------------SSPSKRPLSILFQENNL---------FSHLTVWQNIALGI 96 G+ + S L F+ F+ + ++Q Sbjct: 91 LGRRFGKGETIFELRKRIGLVSSE---LHERFRVRETVRDVVLSGFFASIGIYQE----- 142 Query: 97 APNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEP 156 L A + +LE + + +R +S G+++RV +AR L++ +L+LDEP Sbjct: 143 ----DLTAEDLAAAQWLLELLGAKHLADRPFGSLSQGEQRRVLIARALVKDPELLILDEP 198 Query: 157 FAVFDPALRHEILGLLKQVC-DERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDG 212 D R ++L L+++ LL ++H+ E+ T +++ G++V G Sbjct: 199 AQGLDLIAREQLLNRLEELAASPGAPALLFVTHHAEEIPPCFTHRLLLKEGEVVAQG 255 >gnl|CDD|34235 COG4604, CeuD, ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 252 Score = 113 bits (284), Expect = 4e-26 Identities = 72/226 (31%), Positives = 120/226 (53%), Gaps = 8/226 (3%) Query: 1 MIKLDHLIYCYDNLKMQFD--FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 MI ++++ Y + D + K I+GP+GAGKSTLLS+M+ G I + Sbjct: 1 MITIENVSKSYGTKVVLDDVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITI 60 Query: 59 NGQNHTRSSPSK---RPLSILFQENNLFSHLTVWQNIALGIAP--NLRLDHYQHAQVKQM 113 +G T S+PSK + LSIL QEN++ S LTV + G P RL + + Sbjct: 61 DGLELT-STPSKELAKKLSILKQENHINSRLTVRDLVGFGRFPYSQGRLTKEDRRIINEA 119 Query: 114 LEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLK 173 +E + LED +R+ ++SGGQRQR +A L + +LLDEP D +I+ +L+ Sbjct: 120 IEYLHLEDLSDRYLDELSGGQRQRAFIAMVLAQDTDYVLLDEPLNNLDMKHSVQIMKILR 179 Query: 174 QVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 ++ DE T++++ H++ + + + + G++V G PD ++ Sbjct: 180 RLADELGKTIVVVLHDINFASCYSDHIVALKNGKVVKQGSPDEIIQ 225 >gnl|CDD|33919 COG4181, COG4181, Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 228 Score = 113 bits (283), Expect = 5e-26 Identities = 66/201 (32%), Positives = 107/201 (53%), Gaps = 7/201 (3%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQ------NHTRSSPSK 70 + V + E + I+GPSG+GKSTLL+++AG P+ G + L GQ R++ Sbjct: 28 GVELVVKRGETVAIVGPSGSGKSTLLAVLAGLDDPSSGEVRLLGQPLHKLDEDARAALRA 87 Query: 71 RPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQM 130 R + +FQ +L +LT +N+AL + A K +LE V L +P+Q+ Sbjct: 88 RHVGFVFQSFHLIPNLTALENVALPLELRGESSADSRAGAKALLEAVGLGKRLTHYPAQL 147 Query: 131 SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNL 190 SGG++QRVALAR + +L DEP D A +I LL + ER TL++++H+ Sbjct: 148 SGGEQQRVALARAFAGRPDVLFADEPTGNLDRATGDKIADLLFALNRERGTTLVLVTHDP 207 Query: 191 EDSMQIATRFIVIAGGQIVYD 211 + + + R + + G++V D Sbjct: 208 QLAAR-CDRQLRLRSGRLVED 227 >gnl|CDD|73012 cd03253, ABCC_ATM1_transporter, ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. 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 = 236 Score = 112 bits (283), Expect = 6e-26 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 28/235 (11%) Query: 2 IKLDHLIYCYDNLKMQFD---FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I+ +++ + YD + F + +++ I+GPSG+GKST+L L+ F + GSI + Sbjct: 1 IEFENVTFAYDPGRPVLKDVSFTIPAGKKVAIVGPSGSGKSTILRLLFRFYDVSSGSILI 60 Query: 59 NGQ---NHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 +GQ T S +R + ++ Q+ LF + T+ NI G R D +V + + Sbjct: 61 DGQDIREVTLDS-LRRAIGVVPQDTVLF-NDTIGYNIRYG-----RPD-ATDEEVIEAAK 112 Query: 116 KVFLEDFFNRFPSQ-----------MSGGQRQRVALARCLIRQKPILLLDEPFAVFDPAL 164 + D RFP +SGG++QRVA+AR +++ PILLLDE + D Sbjct: 113 AAQIHDKIMRFPDGYDTIVGERGLKLSGGEKQRVAIARAILKNPPILLLDEATSALDTHT 172 Query: 165 RHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 EI L+ V R T ++I+H L + A + IV+ G+IV G + L+ Sbjct: 173 EREIQAALRDVSKGR--TTIVIAHRLSTIVN-ADKIIVLKDGRIVERGTHEELLA 224 >gnl|CDD|73010 cd03251, ABCC_MsbA, MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. 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 = 234 Score = 110 bits (276), Expect = 4e-25 Identities = 61/214 (28%), Positives = 107/214 (50%), Gaps = 23/214 (10%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSI 75 + E + ++GPSG+GKSTL++L+ F G I ++G + + + +R + + Sbjct: 21 ISLDIPAGETVALVGPSGSGKSTLVNLIPRFYDVDSGRILIDGHDVRDYTLASLRRQIGL 80 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP-------- 127 + Q+ LF+ TV +NIA G P +V++ +F P Sbjct: 81 VSQDVFLFND-TVAENIAYG-RPGA-----TREEVEEAARAANAHEFIMELPEGYDTVIG 133 Query: 128 ---SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 ++SGGQRQR+A+AR L++ PIL+LDE + D + L+++ R T Sbjct: 134 ERGVKLSGGQRQRIAIARALLKDPPILILDEATSALDTESERLVQAALERLMKNR--TTF 191 Query: 185 MISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 +I+H L +++ A R +V+ G+IV G + L+ Sbjct: 192 VIAHRLS-TIENADRIVVLEDGKIVERGTHEELL 224 >gnl|CDD|73013 cd03254, ABCC_Glucan_exporter_like, Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). 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 = 229 Score = 110 bits (276), Expect = 4e-25 Identities = 67/233 (28%), Positives = 121/233 (51%), Gaps = 26/233 (11%) Query: 2 IKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I+ +++ + YD K +F + E + I+GP+GAGK+TL++L+ F P +G I + Sbjct: 3 IEFENVNFSYDEKKPVLKDINFSIKPGETVAIVGPTGAGKTTLINLLMRFYDPQKGQILI 62 Query: 59 NGQN-HTRSSPSKRP-LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 +G + S S R + ++ Q+ LFS T+ +NI LG PN + +V + ++ Sbjct: 63 DGIDIRDISRKSLRSMIGVVLQDTFLFSG-TIMENIRLG-RPNATDE-----EVIEAAKE 115 Query: 117 VFLEDFFNRFP-----------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALR 165 DF + P +S G+RQ +A+AR ++R IL+LDE + D Sbjct: 116 AGAHDFIMKLPNGYDTVLGENGGNLSQGERQLLAIARAMLRDPKILILDEATSNIDTETE 175 Query: 166 HEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 I L+++ R T ++I+H L +++ A + +V+ G+I+ +G D L+ Sbjct: 176 KLIQEALEKLMKGR--TSIIIAHRL-STIKNADKILVLDDGKIIEEGTHDELL 225 >gnl|CDD|33913 COG4172, COG4172, ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]. Length = 534 Score = 108 bits (272), Expect = 1e-24 Identities = 65/214 (30%), Positives = 113/214 (52%), Gaps = 17/214 (7%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSS-----PSKRPL 73 + + + + ++G SG+GKSTL + P++G I +GQ+ S P +R + Sbjct: 307 SLTLRRGQTLGLVGESGSGKSTLGLALLRL-IPSQGEIRFDGQDIDGLSRKEMRPLRRRM 365 Query: 74 SILFQENNLFSHLTVWQNIALGIAPNLRLDHYQH-------AQVKQMLEKVFLE-DFFNR 125 ++FQ+ + L+ + I LR+ H +V + LE+V L+ NR Sbjct: 366 QVVFQDP--YGSLSPRMTVGQIIEEGLRV-HEPKLSAAERDQRVIEALEEVGLDPATRNR 422 Query: 126 FPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLM 185 +P + SGGQRQR+A+AR LI + ++LLDEP + D +++ ++L LL+ + + L+ L Sbjct: 423 YPHEFSGGQRQRIAIARALILKPELILLDEPTSALDRSVQAQVLDLLRDLQQKHGLSYLF 482 Query: 186 ISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 ISH+L + R IV+ G+IV G + + Sbjct: 483 ISHDLAVVRALCHRVIVMRDGKIVEQGPTEAVFA 516 Score = 100 bits (250), Expect = 4e-22 Identities = 65/219 (29%), Positives = 108/219 (49%), Gaps = 23/219 (10%) Query: 19 DFQVNKAERIVILGPSGAGKS-TLLSLMAGFKYPTR----GSIFLNGQNHTRSSPSKR-- 71 F + E + ++G SG+GKS T LS++ P GSI +G++ +S + Sbjct: 30 SFDIEAGETLALVGESGSGKSVTALSILGLLPSPAAAHPSGSILFDGEDLLAASERQLRG 89 Query: 72 ----PLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQ------HAQVKQMLEKVFLED 121 + ++FQE + L I +A LRL H A+ ++LE V + + Sbjct: 90 VRGNKIGMIFQEP--MTSLNPLHTIGKQLAEVLRL-HRGLSRAAARARALELLELVGIPE 146 Query: 122 ---FFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDE 178 + +P ++SGGQRQRV +A L + +L+ DEP D ++ +IL LLK++ E Sbjct: 147 PEKRLDAYPHELSGGQRQRVMIAMALANEPDLLIADEPTTALDVTVQAQILDLLKELQAE 206 Query: 179 RQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 + +L I+H+L + A R V+ G+IV G + L Sbjct: 207 LGMAILFITHDLGIVRKFADRVYVMQHGEIVETGTTETL 245 >gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 591 Score = 108 bits (272), Expect = 1e-24 Identities = 64/214 (29%), Positives = 106/214 (49%), Gaps = 24/214 (11%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSI 75 F + K E++ I+G +G+GKST+L L+ F + GSI ++GQ+ S ++ + + Sbjct: 371 VSFTIPKGEKVAIVGSNGSGKSTILRLLLRF-FDYSGSILIDGQDIKEVSLESLRQSIGV 429 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQ------ 129 + Q++ LF + T+ NI G N + V + ++ L D +R P Sbjct: 430 VPQDSVLF-NDTILYNIKYG---NPSASDEE---VVEACKRAGLHDVISRLPDGYQTLVG 482 Query: 130 -----MSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 +SGG++QRV+LAR ++ PILLLDE + D EIL ++ V R T++ Sbjct: 483 ERGLMLSGGEKQRVSLARAFLKDAPILLLDEATSALDSETEREILDMIMDVMSGR--TVI 540 Query: 185 MISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 MI H L+ + IV+ G + G L+ Sbjct: 541 MIVHRLDLLKD-FDKIIVLDNGTVKEYGTHSELL 573 >gnl|CDD|72985 cd03226, ABC_cobalt_CbiO_domain2, Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.. Length = 205 Score = 108 bits (271), Expect = 2e-24 Identities = 54/194 (27%), Positives = 100/194 (51%), Gaps = 11/194 (5%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 + E I + G +GAGK+TL ++AG + GSI LNG+ +R SI + Sbjct: 20 SLDLYAGEIIALTGKNGAGKTTLAKILAGLIKESSGSILLNGKP---IKAKERRKSIGYV 76 Query: 79 ENNLFSHL---TVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQR 135 ++ L +V + + LG L+ + Q + +L+ + L R P +SGGQ+ Sbjct: 77 MQDVDYQLFTDSVREELLLG----LKELDAGNEQAETVLKDLDLYALKERHPLSLSGGQK 132 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQ 195 QR+A+A L+ K +L+ DEP + D + L++++ + + +++I+H+ E + Sbjct: 133 QRLAIAAALLSGKDLLIFDEPTSGLDYKNMERVGELIRELAAQGK-AVIVITHDYEFLAK 191 Query: 196 IATRFIVIAGGQIV 209 + R +++A G IV Sbjct: 192 VCDRVLLLANGAIV 205 >gnl|CDD|35281 KOG0058, KOG0058, KOG0058, Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 716 Score = 108 bits (270), Expect = 2e-24 Identities = 69/235 (29%), Positives = 119/235 (50%), Gaps = 28/235 (11%) Query: 2 IKLDHLIYCYDNLKMQ-----FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSI 56 I+ + + + Y F + E + ++GPSG+GKST+ SL+ F PT G I Sbjct: 466 IEFEDVSFAYPTRPDVPVLKNLSFTIRPGEVVALVGPSGSGKSTIASLLLRFYDPTSGRI 525 Query: 57 FLNGQNHTRSSPS--KRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQML 114 L+G + + +R + ++ QE LFS ++ +NIA G LD+ +++ Sbjct: 526 LLDGVPISDINHKYLRRKIGLVGQEPVLFSG-SIRENIAYG------LDNATDEEIEAAA 578 Query: 115 EKVFLEDFFNRFP-----------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPA 163 + +F FP SQ+SGGQ+QR+A+AR L+R +L+LDE + D Sbjct: 579 KMANAHEFITNFPDGYNTVVGEKGSQLSGGQKQRIAIARALLRNPRVLILDEATSALDAE 638 Query: 164 LRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 + + L ++ R T+L+I+H L +++ A + +VI G++V G D L+ Sbjct: 639 SEYLVQEALDRLMQGR--TVLVIAHRLS-TVRHADQIVVIDKGRVVEMGTHDELL 690 >gnl|CDD|34242 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 223 Score = 107 bits (269), Expect = 2e-24 Identities = 58/193 (30%), Positives = 96/193 (49%), Gaps = 8/193 (4%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSILF 77 V E I I GPSG GKSTLL ++A PT G++ G++ + P ++ +S Sbjct: 24 LSVRAGEFIAITGPSGCGKSTLLKIVASLISPTSGTLLFEGEDVSTLKPEAYRQQVSYCA 83 Query: 78 QENNLFSHLTVWQNIALGIAP-NLRLDHYQHAQVKQMLEKVFLED-FFNRFPSQMSGGQR 135 Q LF TV N+ I P +R A +L + L D + +++SGG++ Sbjct: 84 QTPALFGD-TVEDNL---IFPWQIRNRRPDRAAALDLLARFALPDSILTKNITELSGGEK 139 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQ 195 QR+AL R L ILLLDE + D + + I ++ + E+ + +L I+H+ + +++ Sbjct: 140 QRIALIRNLQFMPKILLLDEITSALDESNKRNIEEMIHRYVREQNVAVLWITHDKDQAIR 199 Query: 196 IATRFIVIAGGQI 208 A + I + G Sbjct: 200 HADKVITLQPGHA 212 >gnl|CDD|143798 pfam00005, ABC_tran, ABC transporter. ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong in different polypeptide chains. Length = 119 Score = 107 bits (268), Expect = 4e-24 Identities = 51/124 (41%), Positives = 75/124 (60%), Gaps = 9/124 (7%) Query: 39 STLLSLMAGFKYPTRGSIFLNGQNHTRSSPSK---RPLSILFQENNLFSHLTVWQNIALG 95 STLL L+ G PT G+I L+G++ T S K + + ++FQ+ LF LTV +N+ G Sbjct: 1 STLLKLITGLLQPTSGTILLDGEDGTDLSSRKALRKRIGVVFQDPQLFPELTVRENLFFG 60 Query: 96 IAPNLRLDHYQHAQVKQMLEKVFLEDFFNR-FPSQMSGGQRQRVALARCLIRQKPILLLD 154 D A+ ++ LE+V L DF +R +SGGQ+QRVA+AR L+++ +LLLD Sbjct: 61 -----LRDKEADARAEEALERVGLPDFLDRSPVGTLSGGQKQRVAIARALLKKPKLLLLD 115 Query: 155 EPFA 158 EP A Sbjct: 116 EPTA 119 >gnl|CDD|72975 cd03216, ABC_Carb_Monos_I, This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.. Length = 163 Score = 105 bits (265), Expect = 9e-24 Identities = 50/193 (25%), Positives = 84/193 (43%), Gaps = 49/193 (25%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 V + E +LG +GAGKSTL+ +++G P G I ++G+ + +SP Sbjct: 20 SLSVRRGEVHALLGENGAGKSTLMKILSGLYKPDSGEILVDGKEVSFASPRDA------- 72 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRV 138 GIA V+ Q+S G+RQ V Sbjct: 73 -------------RRAGIAM------------------VY----------QLSVGERQMV 91 Query: 139 ALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIAT 198 +AR L R +L+LDEP A PA + +++++ + + ++ ISH L++ +IA Sbjct: 92 EIARALARNARLLILDEPTAALTPAEVERLFKVIRRLR-AQGVAVIFISHRLDEVFEIAD 150 Query: 199 RFIVIAGGQIVYD 211 R V+ G++V Sbjct: 151 RVTVLRDGRVVGT 163 >gnl|CDD|73027 cd03268, ABC_BcrA_bacitracin_resist, The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.. Length = 208 Score = 105 bits (264), Expect = 9e-24 Identities = 54/196 (27%), Positives = 101/196 (51%), Gaps = 5/196 (2%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSIL 76 V K E LGP+GAGK+T + ++ G P G I +G+++ ++ + R + L Sbjct: 18 DISLHVKKGEIYGFLGPNGAGKTTTMKIILGLIKPDSGEITFDGKSYQKNIEALRRIGAL 77 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQ 136 + + +LT +N+ L RL + ++ ++L+ V L+D + S G +Q Sbjct: 78 IEAPGFYPNLTARENLRL----LARLLGIRKKRIDEVLDVVGLKDSAKKKVKGFSLGMKQ 133 Query: 137 RVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQI 196 R+ +A L+ +L+LDEP DP E+ L+ + D+ +T+L+ SH L + ++ Sbjct: 134 RLGIALALLGNPDLLILDEPTNGLDPDGIKELRELILSLRDQ-GITVLISSHLLSEIQKV 192 Query: 197 ATRFIVIAGGQIVYDG 212 A R +I G+++ +G Sbjct: 193 ADRIGIINKGKLIEEG 208 >gnl|CDD|73026 cd03267, ABC_NatA_like, Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.. Length = 236 Score = 105 bits (264), Expect = 1e-23 Identities = 62/197 (31%), Positives = 102/197 (51%), Gaps = 4/197 (2%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN-HTRSSPSKRPLSILF 77 F + K E + +GP+GAGK+T L +++G PT G + + G R R + ++F Sbjct: 41 SFTIEKGEIVGFIGPNGAGKTTTLKILSGLLQPTSGEVRVAGLVPWKRRKKFLRRIGVVF 100 Query: 78 -QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQ-VKQMLEKVFLEDFFNRFPSQMSGGQR 135 Q+ L+ L V + L +A L + + + ++ E + LE+ + Q+S GQR Sbjct: 101 GQKTQLWWDLPVIDSFYL-LAAIYDLPPARFKKRLDELSELLDLEELLDTPVRQLSLGQR 159 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQ 195 R +A L+ + IL LDEP D + I LK+ ER T+L+ SH ++D Sbjct: 160 MRAEIAAALLHEPEILFLDEPTIGLDVVAQENIRNFLKEYNRERGTTVLLTSHYMKDIEA 219 Query: 196 IATRFIVIAGGQIVYDG 212 +A R +VI G+++YDG Sbjct: 220 LARRVLVIDKGRLLYDG 236 >gnl|CDD|34224 COG4586, COG4586, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 325 Score = 104 bits (261), Expect = 2e-23 Identities = 64/216 (29%), Positives = 99/216 (45%), Gaps = 14/216 (6%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQE 79 F++ K E + LG +GAGKST L ++ G PT G + +NG++ P +R L Sbjct: 45 FEIPKGEIVGFLGANGAGKSTTLKMLTGLLLPTSGKVRVNGKD-----PFRRREEYLRSI 99 Query: 80 NNLFSHLT--VWQNIALGIAPNLRL------DHYQHAQVKQMLEKVFLEDFFNRFPSQMS 131 + W AL L+L D + ++ + E + LE F ++S Sbjct: 100 GLVMGQKLQLWWDLPALDSLEVLKLIYEIPDDEF-AERLDFLTEILDLEGFLKWPVRKLS 158 Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLE 191 GQR R LA L+ +L LDEP D + I LK+ +ERQ T+L+ +H + Sbjct: 159 LGQRMRAELAAALLHPPKVLFLDEPTVGLDVNAQANIREFLKEYNEERQATVLLTTHIFD 218 Query: 192 DSMQIATRFIVIAGGQIVYDGDPDRLMNGLIPESTL 227 D + R ++I GQ+V+DG +L P Sbjct: 219 DIATLCDRVLLIDQGQLVFDGTLAQLQEQFGPYKEF 254 >gnl|CDD|34291 COG4674, COG4674, Uncharacterized ABC-type transport system, ATPase component [General function prediction only]. Length = 249 Score = 103 bits (259), Expect = 3e-23 Identities = 59/229 (25%), Positives = 111/229 (48%), Gaps = 23/229 (10%) Query: 12 DNLKMQFD---------FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN 62 D + + F F V+ E V++GP+GAGK+TL+ ++ G P G + +G Sbjct: 9 DGVSVSFGGFKALNDLSFSVDPGELRVLIGPNGAGKTTLMDVITGKTRPQEGEVLFDGDT 68 Query: 63 HTRSSP----SKRPLSILFQENNLFSHLTVWQNIAL------GIAPNL--RLDHYQHAQV 110 P ++ + FQ+ +F +LTV +N+ L + +L RL + ++ Sbjct: 69 DLTKLPEHRIARAGIGRKFQKPTVFENLTVRENLELALNRDKSVFASLFARLRAEERRRI 128 Query: 111 KQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILG 170 ++L + L D +R + +S GQ+Q + + L + +LLLDEP A A + Sbjct: 129 DELLATIGLGDERDRLAALLSHGQKQWLEIGMLLAQDPKLLLLDEPVAGMTDAETEKTAE 188 Query: 171 LLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 LLK + + ++L++ H++ +IA + V+ G ++ +G D + N Sbjct: 189 LLKSL--AGKHSILVVEHDMGFVREIADKVTVLHEGSVLAEGSLDEVQN 235 >gnl|CDD|73006 cd03247, ABCC_cytochrome_bd, The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.. Length = 178 Score = 102 bits (256), Expect = 7e-23 Identities = 59/216 (27%), Positives = 101/216 (46%), Gaps = 43/216 (19%) Query: 2 IKLDHLIYCYDNLKMQ----FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 + ++++ + Y + Q ++ + E+I +LG SG+GKSTLL L+ G P +G I Sbjct: 1 LSINNVSFSYPEQEQQVLKNLSLELKQGEKIALLGRSGSGKSTLLQLLTGDLKPQQGEIT 60 Query: 58 LNGQN-HTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 L+G +S+L Q LF T+ N+ Sbjct: 61 LDGVPVSDLEKALSSLISVLNQRPYLFDT-TLRNNLGR---------------------- 97 Query: 117 VFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVC 176 + SGG+RQR+ALAR L++ PI+LLDEP DP ++L L+ +V Sbjct: 98 ------------RFSGGERQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVL 145 Query: 177 DERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDG 212 ++ TL+ I+H+L ++ + + + G+I+ G Sbjct: 146 KDK--TLIWITHHLT-GIEHMDKILFLENGKIIMQG 178 >gnl|CDD|31329 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]. Length = 249 Score = 102 bits (256), Expect = 7e-23 Identities = 60/207 (28%), Positives = 101/207 (48%), Gaps = 21/207 (10%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILF 77 F++ K ER+ I+G +GAGKSTLL L+AG PT G + + G+ ++ L Sbjct: 46 ISFEIYKGERVGIIGHNGAGKSTLLKLIAGIYKPTSGKVKVTGK-----------VAPLI 94 Query: 78 QENNLFSH-LTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF----LEDFFNRFPSQMSG 132 + F LT +NI L + ++ + ++++ L DF ++ S Sbjct: 95 ELGAGFDPELTGRENIYL----RGLILGLTRKEIDEKVDEIIEFAELGDFIDQPVKTYSS 150 Query: 133 GQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLED 192 G R+A + + ILLLDE AV D A + + L L ++ E+ T++++SH+L Sbjct: 151 GMYARLAFSVATHVEPDILLLDEVLAVGDAAFQEKCLERLNELV-EKNKTIVLVSHDLGA 209 Query: 193 SMQIATRFIVIAGGQIVYDGDPDRLMN 219 Q R I + GQI +G P+ ++ Sbjct: 210 IKQYCDRAIWLEHGQIRMEGSPEEVIP 236 >gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast cancer resistance protein) [Secondary metabolites biosynthesis, transport and catabolism]. Length = 613 Score = 101 bits (254), Expect = 1e-22 Identities = 58/207 (28%), Positives = 102/207 (49%), Gaps = 16/207 (7%) Query: 26 ERIVILGPSGAGKSTLLSLMAGFKYP---TRGSIFLNGQNHTRSSPSKRPLSILFQENNL 82 E + I+GPSG+GK+TLL+ +AG G I LNG+ S K + Q++ L Sbjct: 57 ELLAIMGPSGSGKTTLLNALAGRLNGGLKLSGEILLNGRPRDSRSFRKIS-GYVQQDDVL 115 Query: 83 FSHLTVWQNIALGIAPNLRLDHYQHAQ-----VKQMLEKVFLED-----FFNRFPSQMSG 132 LTV + L + LRL + V++++ ++ LE N +SG Sbjct: 116 LPTLTVRET--LRFSALLRLPSSLSKEEKRERVEEVISELGLEKCADTLIGNPGIRGLSG 173 Query: 133 GQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLED 192 G+R+RV++A L+ IL LDEP + D +++ LLK++ + + I + Sbjct: 174 GERKRVSIALELLTDPSILFLDEPTSGLDSFSALQVVQLLKRLARSGRTVICTIHQPSSE 233 Query: 193 SMQIATRFIVIAGGQIVYDGDPDRLMN 219 ++ + ++++ G++VY G P L+ Sbjct: 234 LFELFDKLLLLSEGEVVYSGSPRELLE 260 >gnl|CDD|73011 cd03252, ABCC_Hemolysin, The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E. coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.. Length = 237 Score = 101 bits (252), Expect = 2e-22 Identities = 63/209 (30%), Positives = 107/209 (51%), Gaps = 15/209 (7%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSIL 76 ++ E + I+G SG+GKSTL L+ F P G + ++G + + P+ +R + ++ Sbjct: 22 SLRIKPGEVVGIVGRSGSGKSTLTKLIQRFYVPENGRVLVDGHDLALADPAWLRRQVGVV 81 Query: 77 FQENNLFSHLTVWQNIALG-IAPNLRLDHY------QHAQVKQMLEKVFLEDFFNRFPSQ 129 QEN LF+ ++ NIAL ++ H + ++ E + + Sbjct: 82 LQENVLFNR-SIRDNIALADPGMSMERVIEAAKLAGAHDFISELPEG--YDTIVGEQGAG 138 Query: 130 MSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHN 189 +SGGQRQR+A+AR LI IL+ DE + D H I+ + +C R T+++I+H Sbjct: 139 LSGGQRQRIAIARALIHNPRILIFDEATSALDYESEHAIMRNMHDICAGR--TVIIIAHR 196 Query: 190 LEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 L +++ A R IV+ G+IV G D L+ Sbjct: 197 LS-TVKNADRIIVMEKGRIVEQGSHDELL 224 >gnl|CDD|73003 cd03244, ABCC_MRP_domain2, Domain 2 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.. Length = 221 Score = 99.4 bits (248), Expect = 7e-22 Identities = 63/230 (27%), Positives = 108/230 (46%), Gaps = 28/230 (12%) Query: 2 IKLDHLIYCY-DNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 I+ ++ Y NL F + E++ I+G +G+GKS+LL + + GSI Sbjct: 3 IEFKNVSLRYRPNLPPVLKNISFSIKPGEKVGIVGRTGSGKSSLLLALFRLVELSSGSIL 62 Query: 58 LNGQNHTRSSPSK--RPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 ++G + ++ +SI+ Q+ LFS T+ N+ Y ++ Q LE Sbjct: 63 IDGVDISKIGLHDLRSRISIIPQDPVLFSG-TIRSNLDP-------FGEYSDEELWQALE 114 Query: 116 KVFLEDFFNRFP-----------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPAL 164 +V L++F P +S GQRQ + LAR L+R+ IL+LDE A DP Sbjct: 115 RVGLKEFVESLPGGLDTVVEEGGENLSVGQRQLLCLARALLRKSKILVLDEATASVDPET 174 Query: 165 RHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDP 214 I +++ + T+L I+H L+ + + R +V+ G++V P Sbjct: 175 DALIQKTIREAFKDC--TVLTIAHRLDTIID-SDRILVLDKGRVVEFDSP 221 >gnl|CDD|72972 cd03213, ABCG_EPDR, ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.. Length = 194 Score = 97.5 bits (243), Expect = 3e-21 Identities = 51/196 (26%), Positives = 93/196 (47%), Gaps = 34/196 (17%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFK--YPTRGSIFLNGQNHTRSSPSKRPLSILF 77 + E I+GPSGAGKSTLL+ +AG + G + +NG+ + S K + + Sbjct: 30 GKAKPGELTAIMGPSGAGKSTLLNALAGRRTGLGVSGEVLINGRPLDKRSFRKI-IGYVP 88 Query: 78 QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQR 137 Q++ L LTV + L A LR +SGG+R+R Sbjct: 89 QDDILHPTLTVRE--TLMFAAKLR---------------------------GLSGGERKR 119 Query: 138 VALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSM-QI 196 V++A L+ +L LDEP + D + +++ LL+++ D T++ H + ++ Sbjct: 120 VSIALELVSNPSLLFLDEPTSGLDSSSALQVMSLLRRLADT-GRTIICSIHQPSSEIFEL 178 Query: 197 ATRFIVIAGGQIVYDG 212 + ++++ G+++Y G Sbjct: 179 FDKLLLLSQGRVIYFG 194 >gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. Length = 530 Score = 96.5 bits (240), Expect = 6e-21 Identities = 55/220 (25%), Positives = 106/220 (48%), Gaps = 24/220 (10%) Query: 1 MIKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 +++ +++ YD ++ F++++ +RI I+GP+GAGKSTLL L+AG P G++ Sbjct: 321 VLEFENVSKGYDGGRLLLKDLSFRIDRGDRIAIVGPNGAGKSTLLKLLAGELGPLSGTV- 379 Query: 58 LNGQNHTRSSPSKRPLSILFQENN-LFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEK 116 + Q + L TV + ++ G P+ V+ L + Sbjct: 380 --------KVGETVKIGYFDQHRDELDPDKTVLEELSEG-FPDGDEQE-----VRAYLGR 425 Query: 117 V-FLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQV 175 F + + +SGG++ R+ LA+ L++ +LLLDEP D E L L++ Sbjct: 426 FGFTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDI----ESLEALEEA 481 Query: 176 CDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPD 215 + + T+L++SH+ ++ATR ++ ++G + Sbjct: 482 LLDFEGTVLLVSHDRYFLDRVATRIWLVEDKVEEFEGGYE 521 Score = 83.8 bits (207), Expect = 4e-17 Identities = 64/250 (25%), Positives = 100/250 (40%), Gaps = 45/250 (18%) Query: 1 MIKLDHLIYCYDNLKMQFD--FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 MI L++L Y + + + +N ERI ++G +GAGKSTLL ++AG P G + Sbjct: 3 MITLENLSLAYGDRPLLENVSLTLNPGERIGLVGRNGAGKSTLLKILAGELEPDSGEVTR 62 Query: 59 NGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQM----- 113 P + L QE L TV + G L + Sbjct: 63 ---------PKGLRVGYLSQEPPLDPEKTVLDYVIEGFGELRELLAELEEAYALLADPDD 113 Query: 114 -----LEKVFLE-------------------DFFNRFPSQMSGGQRQRVALARCLIRQKP 149 LE + E +R S +SGG R+RVALAR L+ + Sbjct: 114 ELLAELEALLEELDGWTLEARAEEALLGLGFPDEDRPVSSLSGGWRRRVALARALLEEPD 173 Query: 150 ILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQI- 208 +LLLDEP D E + L+ T++++SH+ +AT + + G++ Sbjct: 174 LLLLDEPTNHLD----LESIEWLEDYLKRYPGTVIVVSHDRYFLDNVATHILELDRGKLT 229 Query: 209 VYDGDPDRLM 218 Y G+ + Sbjct: 230 PYKGNYSSYL 239 >gnl|CDD|72979 cd03220, ABC_KpsT_Wzt, ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.. Length = 224 Score = 96.4 bits (240), Expect = 6e-21 Identities = 58/198 (29%), Positives = 99/198 (50%), Gaps = 19/198 (9%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 F+V + ERI ++G +GAGKSTLL L+AG P G++ + G R S+L Sbjct: 42 SFEVPRGERIGLIGRNGAGKSTLLRLLAGIYPPDSGTVTVRG----------RVSSLLGL 91 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF----LEDFFNRFPSQMSGGQ 134 LT +NI L N RL ++ + ++++ L DF + S G Sbjct: 92 GGGFNPELTGRENIYL----NGRLLGLSRKEIDEKIDEIIEFSELGDFIDLPVKTYSSGM 147 Query: 135 RQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSM 194 + R+A A + ILL+DE AV D A + + L+++ ++ T++++SH+ Sbjct: 148 KARLAFAIATALEPDILLIDEVLAVGDAAFQEKCQRRLRELL-KQGKTVILVSHDPSSIK 206 Query: 195 QIATRFIVIAGGQIVYDG 212 ++ R +V+ G+I +DG Sbjct: 207 RLCDRALVLEKGKIRFDG 224 >gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8), the human homolog of the Drosophila white gene is induced in monocyte-derived macrophages during cholesterol influx mediated by acetylated low-density lipoprotein. It is possible that human ABCG1 forms heterodimers with several heterologous partners.. Length = 226 Score = 95.7 bits (238), Expect = 1e-20 Identities = 52/202 (25%), Positives = 93/202 (46%), Gaps = 12/202 (5%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAG---FKYPTRGSIFLNGQNHTRSSPSKRPLSIL 76 V + + ILG SG+GK+TLL ++G T G I NGQ ++ ++ + Sbjct: 28 LHVESGQVMAILGSSGSGKTTLLDAISGRVEGGGTTSGQILFNGQPRKPDQ-FQKCVAYV 86 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF------LEDFFNRFPSQM 130 Q++ L LTV + + LRL +++ + L + Sbjct: 87 RQDDILLPGLTVRETLTY--TAILRLPRKSSDAIRKKRVEDVLLRDLALTRIGGNLVKGI 144 Query: 131 SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNL 190 SGG+R+RV++A L+ +L+LDEP + D ++ L Q+ ++ +L I Sbjct: 145 SGGERRRVSIAVQLLWDPKVLILDEPTSGLDSFTALNLVSTLSQLARRNRIVILTIHQPR 204 Query: 191 EDSMQIATRFIVIAGGQIVYDG 212 D ++ R ++++ G+IVY G Sbjct: 205 SDLFRLFDRILLLSSGEIVYSG 226 >gnl|CDD|33894 COG4138, BtuD, ABC-type cobalamin transport system, ATPase component [Coenzyme metabolism]. Length = 248 Score = 95.1 bits (236), Expect = 1e-20 Identities = 61/215 (28%), Positives = 105/215 (48%), Gaps = 26/215 (12%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSK--RPLSI 75 +V E + ++GP+GAGKSTLL+ MAG GSI GQ S ++ R + Sbjct: 18 LSGEVRAGEILHLVGPNGAGKSTLLARMAGM-TSGSGSIQFAGQPLEAWSATELARHRAY 76 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQ-----VKQMLEKVFLEDFFNRFPSQM 130 L Q+ + VW + L +Q + + + + L+D R +Q+ Sbjct: 77 LSQQQTPPFAMPVWHYLTL----------HQPDKTRTELLNDVAGALALDDKLGRSTNQL 126 Query: 131 SGGQRQRVALARCLIRQKP-------ILLLDEPFAVFDPALRHEILGLLKQVCDERQLTL 183 SGG+ QRV LA +++ P +LLLDEP D A + + LL +C ++ L + Sbjct: 127 SGGEWQRVRLAAVVLQITPDANPAGQLLLLDEPMNSLDVAQQSALDRLLSALC-QQGLAI 185 Query: 184 LMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 +M SH+L +++ A R ++ G+++ G + ++ Sbjct: 186 VMSSHDLNHTLRHAHRAWLLKRGKLLASGRREEVL 220 >gnl|CDD|73007 cd03248, ABCC_TAP, TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.. Length = 226 Score = 95.0 bits (236), Expect = 2e-20 Identities = 61/204 (29%), Positives = 102/204 (50%), Gaps = 23/204 (11%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQ--NHTRSSPSKRPLSI 75 F ++ E ++GPSG+GKST+++L+ F P G + L+G+ + +S+ Sbjct: 33 VSFTLHPGEVTALVGPSGSGKSTVVALLENFYQPQGGQVLLDGKPISQYEHKYLHSKVSL 92 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP-------- 127 + QE LF+ ++ NIA G L VK+ +K F + Sbjct: 93 VGQEPVLFAR-SLQDNIAYG------LQSCSFECVKEAAQKAHAHSFISELASGYDTEVG 145 Query: 128 ---SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 SQ+SGGQ+QRVA+AR LIR +L+LDE + D ++ L + T+L Sbjct: 146 EKGSQLSGGQKQRVAIARALIRNPQVLILDEATSALDAESEQQVQQALY--DWPERRTVL 203 Query: 185 MISHNLEDSMQIATRFIVIAGGQI 208 +I+H L +++ A + +V+ GG+I Sbjct: 204 VIAHRLS-TVERADQILVLDGGRI 226 >gnl|CDD|73005 cd03246, ABCC_Protease_Secretion, This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substrates ranges from inorganic ions, nutrients such as amino acids, sugars, or peptides, hydrophobic drugs, to large polypeptides, such as HlyA.. Length = 173 Score = 93.7 bits (233), Expect = 4e-20 Identities = 53/192 (27%), Positives = 86/192 (44%), Gaps = 42/192 (21%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSIL 76 F + E + I+GPSG+GKSTL L+ G PT G + L+G + ++ P+ + L Sbjct: 22 SFSIEPGESLAIIGPSGSGKSTLARLILGLLRPTSGRVRLDGADISQWDPNELGDHVGYL 81 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQ 136 Q++ LFS ++ +NI +SGGQRQ Sbjct: 82 PQDDELFSG-SIAENI-------------------------------------LSGGQRQ 103 Query: 137 RVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQI 196 R+ LAR L IL+LDEP + D + + + T ++I+H E ++ Sbjct: 104 RLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAAL-KAAGATRIVIAHRPE-TLAS 161 Query: 197 ATRFIVIAGGQI 208 A R +V+ G++ Sbjct: 162 ADRILVLEDGRV 173 >gnl|CDD|72990 cd03231, ABC_CcmA_heme_exporter, CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.. Length = 201 Score = 93.5 bits (232), Expect = 4e-20 Identities = 57/180 (31%), Positives = 87/180 (48%), Gaps = 11/180 (6%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS-KRPLSI 75 F + E + + GP+G+GK+TLL ++AG P G + LNG S R L Sbjct: 18 GLSFTLAAGEALQVTGPNGSGKTTLLRILAGLSPPLAGRVLLNGGPLDFQRDSIARGLLY 77 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHA--QVKQMLEKVFLEDFFNRFPSQMSGG 133 L + + L+V +N LR H H+ QV++ L +V L F +R +Q+S G Sbjct: 78 LGHAPGIKTTLSVLEN--------LRFWHADHSDEQVEEALARVGLNGFEDRPVAQLSAG 129 Query: 134 QRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDS 193 Q++RVALAR L+ +P+ +LDEP D A + C + +L +L S Sbjct: 130 QQRRVALARLLLSGRPLWILDEPTTALDKAGVARFAEAMAGHCARGGMVVLTTHQDLGLS 189 >gnl|CDD|31314 COG1117, PstB, ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 253 Score = 93.7 bits (233), Expect = 4e-20 Identities = 55/203 (27%), Positives = 109/203 (53%), Gaps = 20/203 (9%) Query: 30 ILGPSGAGKSTLLS-------LMAGFKYPTRGSIFLNGQNHTRSSPS----KRPLSILFQ 78 ++GPSG GKSTLL L+ G + G + L+G+N +R + ++FQ Sbjct: 38 LIGPSGCGKSTLLRCLNRMNDLIPGARV--EGEVLLDGKNIYDPKVDVVELRRRVGMVFQ 95 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFL----EDFFNRFPSQMSGGQ 134 + N F ++++ N+A G+ + D V+ L+K L +D ++ +SGGQ Sbjct: 96 KPNPFP-MSIYDNVAYGLRLHGIKDKELDEIVESSLKKAALWDEVKDRLHKSALGLSGGQ 154 Query: 135 RQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSM 194 +QR+ +AR L + +LL+DEP + DP +I L+ ++ +++ T+++++HN++ + Sbjct: 155 QQRLCIARALAVKPEVLLMDEPTSALDPISTLKIEELITEL--KKKYTIVIVTHNMQQAA 212 Query: 195 QIATRFIVIAGGQIVYDGDPDRL 217 +++ G++V G D++ Sbjct: 213 RVSDYTAFFYLGELVEFGPTDKI 235 >gnl|CDD|73028 cd03269, ABC_putative_ATPase, This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity. In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. 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 = 210 Score = 93.0 bits (231), Expect = 7e-20 Identities = 51/197 (25%), Positives = 94/197 (47%), Gaps = 11/197 (5%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQE 79 F V K E +LGP+GAGK+T + ++ G P G + +G ++ + L +E Sbjct: 21 FSVEKGEIFGLLGPNGAGKTTTIRMILGIILPDSGEVLFDG--KPLDIAARNRIGYLPEE 78 Query: 80 NNLFSHLTVWQN-IALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRV 138 L+ + V + L L+ ++ + LE++ L ++ N+ ++S G +Q+V Sbjct: 79 RGLYPKMKVIDQLVYLAQLKGLKK-EEARRRIDEWLERLELSEYANKRVEELSKGNQQKV 137 Query: 139 ALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDE---RQLTLLMISHNLEDSMQ 195 +I +L+LDEPF+ DP LLK V E T+++ +H +E + Sbjct: 138 QFIAAVIHDPELLILDEPFSGLDPVNVE----LLKDVIRELARAGKTVILSTHQMELVEE 193 Query: 196 IATRFIVIAGGQIVYDG 212 + R +++ G+ V G Sbjct: 194 LCDRVLLLNKGRAVLYG 210 >gnl|CDD|33889 COG4133, CcmA, ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]. Length = 209 Score = 92.3 bits (229), Expect = 1e-19 Identities = 48/172 (27%), Positives = 78/172 (45%), Gaps = 8/172 (4%) Query: 16 MQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN-HTRSSPSKRPLS 74 F +N E + I GP+GAGK+TLL ++AG P G ++ G+ + L Sbjct: 19 SDLSFTLNAGEALQITGPNGAGKTTLLRILAGLLRPDAGEVYWQGEPIQNVRESYHQALL 78 Query: 75 ILFQENNLFSHLTVWQNIALGIAPNLRLDHYQH--AQVKQMLEKVFLEDFFNRFPSQMSG 132 L + + + LT +N+ + H A + + L +V L + Q+S Sbjct: 79 YLGHQPGIKTELTALENLHF-----WQRFHGSGNAATIWEALAQVGLAGLEDLPVGQLSA 133 Query: 133 GQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 GQ++RVALAR + P+ +LDEPF D + L+ + + LL Sbjct: 134 GQQRRVALARLWLSPAPLWILDEPFTALDKEGVALLTALMAAHAAQGGIVLL 185 >gnl|CDD|72974 cd03215, ABC_Carb_Monos_II, This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.. Length = 182 Score = 91.3 bits (227), Expect = 2e-19 Identities = 55/197 (27%), Positives = 86/197 (43%), Gaps = 39/197 (19%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKR-PLSIL 76 F+V E + I G G G++ L + G + P G I L+G+ TR SP I Sbjct: 19 VSFEVRAGEIVGIAGLVGNGQTELAEALFGLRPPASGEITLDGKPVTRRSPRDAIRAGIA 78 Query: 77 F-----QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMS 131 + + L L+V +NIAL S +S Sbjct: 79 YVPEDRKREGLVLDLSVAENIAL--------------------------------SSLLS 106 Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLE 191 GG +Q+V LAR L R +L+LDEP D + EI L++++ D +L+IS L+ Sbjct: 107 GGNQQKVVLARWLARDPRVLILDEPTRGVDVGAKAEIYRLIRELADAG-KAVLLISSELD 165 Query: 192 DSMQIATRFIVIAGGQI 208 + + + R +V+ G+I Sbjct: 166 ELLGLCDRILVMYEGRI 182 >gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1381 Score = 90.7 bits (225), Expect = 3e-19 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 34/217 (15%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN------HT-RSSPSKRP 72 F + E++ I+G +GAGKS+L+ + P G I ++G + H RS Sbjct: 1161 FTIKPGEKVGIVGRTGAGKSSLILALFRLVEPAEGEILIDGVDISKIGLHDLRSR----- 1215 Query: 73 LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP----- 127 LSI+ Q+ LFS TV N+ P D Y ++ + LE+ L+D + P Sbjct: 1216 LSIIPQDPVLFSG-TVRFNLD----P---FDEYSDDEIWEALERCQLKDVVSSLPGGLDS 1267 Query: 128 ------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQL 181 S GQRQ + LAR L+R+ IL+LDE A DP I +++ + Sbjct: 1268 EVSEGGENFSVGQRQLLCLARALLRKSKILVLDEATASVDPETDALIQKTIREEFKDC-- 1325 Query: 182 TLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 T+L I+H L M + R +V+ G++V P L+ Sbjct: 1326 TVLTIAHRLNTVMD-SDRVLVLDAGRVVEFDSPAELL 1361 Score = 83.8 bits (207), Expect = 4e-17 Identities = 58/219 (26%), Positives = 102/219 (46%), Gaps = 46/219 (21%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILF- 77 +F++ K + + ++GP G+GKS+LLS + G GS+ +NG S+ + Sbjct: 541 NFEIKKGQLVAVVGPVGSGKSSLLSAILGEMPKLSGSVAVNG-------------SVAYV 587 Query: 78 -QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP--------- 127 Q+ + + TV +NI G D ++ +V ++ L+ P Sbjct: 588 PQQPWIQN-GTVRENILFG----SPYDEERYDKV---IKACALKKDLEILPFGDLTEIGE 639 Query: 128 --SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDP-----ALRHEILGLLKQVCDERQ 180 +SGGQ+QR++LAR + + I LLD+P + D I GLL R Sbjct: 640 RGINLSGGQKQRISLARAVYQDADIYLLDDPLSAVDAHVGKHIFEECIRGLL------RG 693 Query: 181 LTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 T+++++H L+ + A + IV+ G+IV G + L+ Sbjct: 694 KTVILVTHQLQ-FLPHADQIIVLKDGKIVESGTYEELLK 731 >gnl|CDD|34241 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]. Length = 580 Score = 90.7 bits (225), Expect = 3e-19 Identities = 64/234 (27%), Positives = 107/234 (45%), Gaps = 36/234 (15%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSK--RPLSILF 77 F + E + I+GPSG+GKSTL L+ G PT GS+ L+G + + + R + L Sbjct: 357 FALQAGEALGIIGPSGSGKSTLARLLVGIWPPTSGSVRLDGADLRQWDREQLGRHIGYLP 416 Query: 78 QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFL---EDFFNRFP------- 127 Q+ LF T+ +NIA R + A ++++E L + R P Sbjct: 417 QDVELFDG-TIAENIA-------RFG--EEADPEKVIEAARLAGVHELILRLPQGYDTRI 466 Query: 128 ----SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDP----ALRHEILGLLKQVCDER 179 + +SGGQRQR+ALAR L +++LDEP + D AL IL + Sbjct: 467 GEGGATLSGGQRQRIALARALYGDPFLVVLDEPNSNLDSEGEAALAAAILAAKARGG--- 523 Query: 180 QLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMNGLIPESTLLGIPSR 233 T+++I+H ++ + +V+ G+I G + ++ ++ P Sbjct: 524 --TVVVIAHRPS-ALASVDKILVLQDGRIAAFGPREEVLAKVLRPPPRQAKPGT 574 >gnl|CDD|33909 COG4167, SapF, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]. Length = 267 Score = 89.6 bits (222), Expect = 6e-19 Identities = 55/205 (26%), Positives = 111/205 (54%), Gaps = 6/205 (2%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQ--NHTRSSPSKRPLSILF 77 F + + + + I+G +G+GKSTL ++AG PT G I +N + S + + ++F Sbjct: 34 FTLREGQTLAIIGENGSGKSTLAKMLAGMIEPTSGEILINDHPLHFGDYSFRSKRIRMIF 93 Query: 78 QENN--LFSHLTVWQNIALGIAPNLRLDHYQHAQ-VKQMLEKV-FLEDFFNRFPSQMSGG 133 Q+ N L L + Q + + N L+ Q + + + L V L D N +P ++ G Sbjct: 94 QDPNTSLNPRLRIGQILDFPLRLNTDLEPEQRRKQIFETLRMVGLLPDHANYYPHMLAPG 153 Query: 134 QRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDS 193 Q+QRVALAR LI + I++ DE A D ++R +++ L+ ++ +++ ++ + ++ ++ Sbjct: 154 QKQRVALARALILRPKIIIADEALASLDMSMRSQLINLMLELQEKQGISYIYVTQHIGMI 213 Query: 194 MQIATRFIVIAGGQIVYDGDPDRLM 218 I+ + +V+ G++V G ++ Sbjct: 214 KHISDQVLVMHEGEVVERGSTADVL 238 >gnl|CDD|33903 COG4152, COG4152, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 300 Score = 88.0 bits (218), Expect = 2e-18 Identities = 53/220 (24%), Positives = 103/220 (46%), Gaps = 15/220 (6%) Query: 1 MIKLDHLIYCYDNLKMQFD--FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 ++++ + + + K + F+V E +LGP+GAGK+T ++ G PT G I Sbjct: 2 ALEIEGVTKSFGDKKAVDNISFEVPPGEIFGLLGPNGAGKTTTFRMILGLLEPTEGEITW 61 Query: 59 NGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIA-LGIAPNLRLDHYQHAQVKQMLEKV 117 NG ++ ++ + L +E L+ +TV + L + Q +++ LE++ Sbjct: 62 NGGPLSQEIKNR--IGYLPEERGLYPKMTVEDQLKYLAELKGMPKAEIQ-KKLQAWLERL 118 Query: 118 FLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDP----ALRHEILGLLK 173 + + ++S G +Q++ +I + +L+LDEPF+ DP L+ I L Sbjct: 119 EIVGKKTKKIKELSKGNQQKIQFISAVIHEPELLILDEPFSGLDPVNVELLKDAIFEL-- 176 Query: 174 QVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGD 213 E T++ SH +E ++ R +++ GQ V G Sbjct: 177 ---KEEGATIIFSSHRMEHVEELCDRLLMLKKGQTVLYGT 213 >gnl|CDD|35282 KOG0059, KOG0059, KOG0059, Lipid exporter ABCA1 and related proteins, ABC superfamily [Lipid transport and metabolism, General function prediction only]. Length = 885 Score = 87.8 bits (217), Expect = 2e-18 Identities = 55/224 (24%), Positives = 102/224 (45%), Gaps = 7/224 (3%) Query: 2 IKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 + L++L Y F V E +LG +GAGK+T ++ G PT G + Sbjct: 565 LVLNNLSKVYGGKDGAVRGLSFAVPPGECFGLLGVNGAGKTTTFKMLTGETKPTSGEALI 624 Query: 59 NGQNHTRSSPSKRPLSILF---QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 G + T S+ ++ L Q + L+ LT +++ + ++++L Sbjct: 625 KGHDITVSTDFQQVRKQLGYCPQFDALWEELTGREHLEFYARLRGLPRSDIGSAIEKLLR 684 Query: 116 KVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQV 175 V L + N+ SGG ++R++ A LI ++LLDEP DP R + ++ ++ Sbjct: 685 LVGLGPYANKQVRTYSGGNKRRLSFAIALIGDPSVILLDEPSTGLDPKARRHLWDIIARL 744 Query: 176 CDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 + +L SH++E++ + TR ++ GQ+ G P L + Sbjct: 745 RKNGKAIIL-TSHSMEEAEALCTRTAIMVIGQLRCIGSPQELKS 787 >gnl|CDD|34862 COG5265, ATM1, ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]. Length = 497 Score = 87.2 bits (216), Expect = 4e-18 Identities = 66/213 (30%), Positives = 104/213 (48%), Gaps = 23/213 (10%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN--HTRSSPSKRPLSIL 76 F + + + I+G SGAGKST+L L+ F GSI ++GQ+ +R + I+ Sbjct: 283 SFTIPLGKTVAIVGESGAGKSTILRLLFRFYDVNSGSITIDGQDIRDVTQQSLRRAIGIV 342 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPS-------- 128 Q+ LF+ T+ NI G P+ +V E + DF P Sbjct: 343 PQDTVLFND-TIAYNIKYG-RPDA-----TAEEVGAAAEAAQIHDFIQSLPEGYDTGVGE 395 Query: 129 ---QMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLM 185 ++SGG++QRVA+AR +++ PIL+LDE + D I L++V R T L+ Sbjct: 396 RGLKLSGGEKQRVAIARTILKNPPILILDEATSALDTHTEQAIQAALREVSAGR--TTLV 453 Query: 186 ISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 I+H L ++ A IV+ G+IV G + L+ Sbjct: 454 IAHRLS-TIIDADEIIVLDNGRIVERGTHEELL 485 >gnl|CDD|35279 KOG0056, KOG0056, KOG0056, Heavy metal exporter HMT1, ABC superfamily [Inorganic ion transport and metabolism]. Length = 790 Score = 85.5 bits (211), Expect = 1e-17 Identities = 68/228 (29%), Positives = 118/228 (51%), Gaps = 16/228 (7%) Query: 2 IKLDHLIYCYDNLKM---QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I+ ++ + YD K F V + + ++GPSGAGKST++ L+ F GSI + Sbjct: 538 IEFSNVTFAYDPGKPVLSDISFTVQPGKTVALVGPSGAGKSTIMRLLFRFFDVNSGSITI 597 Query: 59 NGQ---NHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLE 115 +GQ N T+SS + + ++ Q+ LF+ T+ NI + Y A+ Q+ + Sbjct: 598 DGQDIRNVTQSS-LRSSIGVVPQDTVLFND-TILYNIRYAKPSASNEEVYAAAKAAQIHD 655 Query: 116 KV--FLEDFFNRFPS---QMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILG 170 ++ F E + R ++SGG++QRVA+AR +++ I+LLDE + D I Sbjct: 656 RILQFPEGYNTRVGERGLKLSGGEKQRVAIARTILKAPSIILLDEATSALDTNTERAIQA 715 Query: 171 LLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 L ++C R T ++++H L + A +VI+ G+IV G + L+ Sbjct: 716 ALARLCANR--TTIVVAHRLSTIVN-ADLILVISNGRIVERGRHEELL 760 >gnl|CDD|73009 cd03250, ABCC_MRP_domain1, Domain 1 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.. Length = 204 Score = 83.2 bits (206), Expect = 6e-17 Identities = 54/205 (26%), Positives = 93/205 (45%), Gaps = 41/205 (20%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 + +V K E + I+GP G+GKS+LLS + G GS+ + G ++ + Q Sbjct: 25 NLEVPKGELVAIVGPVGSGKSSLLSALLGELEKLSGSVSVPGS-----------IAYVSQ 73 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP----------- 127 E + + T+ +NI G D ++ +V ++ LE P Sbjct: 74 EPWIQN-GTIRENILFG----KPFDEERYEKV---IKACALEPDLEILPDGDLTEIGEKG 125 Query: 128 SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPA-----LRHEILGLLKQVCDERQLT 182 +SGGQ+QR++LAR + I LLD+P + D + ILGLL T Sbjct: 126 INLSGGQKQRISLARAVYSDADIYLLDDPLSAVDAHVGRHIFENCILGLLL-----NNKT 180 Query: 183 LLMISHNLEDSMQIATRFIVIAGGQ 207 ++++H L+ + A + +V+ G+ Sbjct: 181 RILVTHQLQ-LLPHADQIVVLDNGR 204 >gnl|CDD|72996 cd03237, ABC_RNaseL_inhibitor_domain2, The ATPase domain 2 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.. Length = 246 Score = 81.1 bits (200), Expect = 3e-16 Identities = 57/210 (27%), Positives = 99/210 (47%), Gaps = 23/210 (10%) Query: 22 VNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENN 81 ++++E I ILGP+G GK+T + ++AG P G I + + S +P Q Sbjct: 22 ISESEVIGILGPNGIGKTTFIKMLAGVLKPDEGDIEIE-----LDTVSYKP-----QYIK 71 Query: 82 LFSHLTVWQNIALGIAPNLRLDHYQHAQVK-QMLEKVFLEDFFNRFPSQMSGGQRQRVAL 140 TV +++ I D Y H K ++ + + +E +R ++SGG+ QRVA+ Sbjct: 72 ADYEGTV-RDLLSSITK----DFYTHPYFKTEIAKPLQIEQILDREVPELSGGELQRVAI 126 Query: 141 ARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRF 200 A CL + I LLDEP A D R ++++ + + T ++ H++ +A R Sbjct: 127 AACLSKDADIYLLDEPSAYLDVEQRLMASKVIRRFAENNEKTAFVVEHDIIMIDYLADRL 186 Query: 201 IVIAGGQIVYDGDPDRLMNGLIPESTLLGI 230 IV++G+P P+S G+ Sbjct: 187 -------IVFEGEPSVNGVANPPQSLRSGM 209 >gnl|CDD|34240 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]. Length = 546 Score = 79.2 bits (195), Expect = 8e-16 Identities = 58/198 (29%), Positives = 96/198 (48%), Gaps = 20/198 (10%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPS--KRPLSIL 76 + + + E + ++G +G+GKSTL L+ G P G I L+G+ + ++ S + Sbjct: 343 NLTIKRGELVFLIGGNGSGKSTLAMLLTGLYQPQSGEILLDGKPVSAEQLEDYRKLFSAV 402 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRF-PSQMSGGQR 135 F + +LF L + A +P L Q ++ L D RF ++S GQ+ Sbjct: 403 FSDYHLFDQLLGPEGKA---SPQLIEKWLQRLELAHKTS---LND--GRFSNLKLSTGQK 454 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALR----HEILGLLKQVCDERQLTLLMISHNLE 191 +R+AL L+ ++ IL+LDE A DPA R +L LLK E+ T+ ISH+ + Sbjct: 455 KRLALLLALLEERDILVLDEWAADQDPAFRREFYQVLLPLLK----EQGKTIFAISHD-D 509 Query: 192 DSMQIATRFIVIAGGQIV 209 A R + + GQ+ Sbjct: 510 HYFIHADRLLEMRNGQLS 527 >gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]. Length = 591 Score = 77.6 bits (191), Expect = 3e-15 Identities = 52/185 (28%), Positives = 84/185 (45%), Gaps = 16/185 (8%) Query: 21 QVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQEN 80 ++ E I ILGP+G GK+T + L+AG P GS S +P I + Sbjct: 363 EIYDGEVIGILGPNGIGKTTFVKLLAGVIKPDEGSE-------EDLKVSYKPQYISPDYD 415 Query: 81 NLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVAL 140 TV + + Y ++ + L LED R ++SGG+ QRVA+ Sbjct: 416 G-----TVEDLLR-SAIRSAFGSSYFKTEIVKPLN---LEDLLERPVDELSGGELQRVAI 466 Query: 141 ARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRF 200 A L R+ + LLDEP A D R + ++++ + + T L++ H++ ++ R Sbjct: 467 AAALSREADLYLLDEPSAYLDVEQRIIVAKVIRRFIENNEKTALVVDHDIYMIDYVSDRL 526 Query: 201 IVIAG 205 IV G Sbjct: 527 IVFEG 531 Score = 56.4 bits (136), Expect = 7e-09 Identities = 44/178 (24%), Positives = 79/178 (44%), Gaps = 26/178 (14%) Query: 30 ILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENNLFSHLT-- 87 ILGP+G GKST L ++AG P G PS + F+ L ++ Sbjct: 105 ILGPNGIGKSTALKILAGELKPNLGR--------YEDPPSWDEVIKRFRGTELQNYFKKL 156 Query: 88 VWQNIALGIAPNL--RLDHYQHAQVKQMLEKVF-------------LEDFFNRFPSQMSG 132 + P + +V ++L+KV LE+ +R S++SG Sbjct: 157 YEGELRAVHKPQYVDLIPKVVKGKVGELLKKVDERGKFDEVVERLGLENVLDRDVSELSG 216 Query: 133 GQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNL 190 G+ QRVA+A L+R + DEP + D R +++++ ++ + ++++ H+L Sbjct: 217 GELQRVAIAAALLRDADVYFFDEPSSYLDIRQRLNAARVIRELAEDGK-YVIVVEHDL 273 >gnl|CDD|30745 COG0396, SufC, ABC-type transport system involved in Fe-S cluster assembly, ATPase component [Posttranslational modification, protein turnover, chaperones]. Length = 251 Score = 77.1 bits (190), Expect = 4e-15 Identities = 58/218 (26%), Positives = 97/218 (44%), Gaps = 30/218 (13%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGF-KY-PTRGSIFLNGQNHTRSSPSKRP--- 72 + V + E I+GP+G+GKSTL + G KY T G I +G++ SP +R Sbjct: 23 VNLTVKEGEVHAIMGPNGSGKSTLAYTIMGHPKYEVTEGEILFDGEDILELSPDERARAG 82 Query: 73 LSILFQEN------NLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFL-EDFFNR 125 + + FQ L N G L ++K+ E + L E+F R Sbjct: 83 IFLAFQYPVEIPGVTNSDFLRAAMNARRGARGILPEF---IKELKEKAELLGLDEEFLER 139 Query: 126 FPSQ-MSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCD------E 178 + ++ SGG+++R + + L+ + + +LDEP + D + LK V + E Sbjct: 140 YVNEGFSGGEKKRNEILQLLLLEPKLAILDEPDSGLD-------IDALKIVAEGINALRE 192 Query: 179 RQLTLLMISHNLEDSMQIATRFI-VIAGGQIVYDGDPD 215 +L+I+H I + V+ G+IV GDP+ Sbjct: 193 EGRGVLIITHYQRLLDYIKPDKVHVLYDGRIVKSGDPE 230 >gnl|CDD|34390 COG4778, PhnL, ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 235 Score = 76.9 bits (189), Expect = 5e-15 Identities = 55/198 (27%), Positives = 89/198 (44%), Gaps = 12/198 (6%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSIL 76 VN E +V+ GPSG+GKSTLL + P G I + + + P +L Sbjct: 29 NVSLSVNAGECVVLHGPSGSGKSTLLRSLYANYLPDEGQILVRHEGEWVDLVTAEPREVL 88 Query: 77 FQENNLFSHLTVWQNI-----ALGIAPNLRLD-----HYQHAQVKQMLEKVFL-EDFFNR 125 +++ + + AL + L A+ +L ++ L E ++ Sbjct: 89 EVRRTTIGYVSQFLRVIPRVSALDVVAEPLLARGVPREVARAKAADLLTRLNLPERLWSL 148 Query: 126 FPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLM 185 P+ SGG++QRV +AR I PILLLDEP A D R ++ L+++ R L+ Sbjct: 149 APATFSGGEQQRVNIARGFIVDYPILLLDEPTASLDATNRAVVVELIREA-KARGAALVG 207 Query: 186 ISHNLEDSMQIATRFIVI 203 I H+ E +A R + + Sbjct: 208 IFHDEEVREAVADRLLDV 225 >gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins (PDR1-15), ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1391 Score = 75.7 bits (186), Expect = 1e-14 Identities = 53/218 (24%), Positives = 92/218 (42%), Gaps = 20/218 (9%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAG----FKYPTRGSIFLNGQNHTRSSPSKRPL 73 + E ++LGP G+GK+TLL +AG F + G I NG + P K+ + Sbjct: 134 ISGIIKPGEMTLVLGPPGSGKTTLLKALAGKLDNFLKSS-GEITYNGHDLKEFVP-KKTV 191 Query: 74 SILFQENNLFSHLTVWQNIALGIA---PNLRLD-----HYQHAQVKQMLEKVFLEDFF-- 123 + +++ F LTV + + P R D A +L+ + L+ Sbjct: 192 AYNSEQDVHFPELTVRETLDFAARCKGPGSRYDEVSRREKLAAMTDYLLKILGLDHCADT 251 Query: 124 ---NRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQ 180 N +SGG+R+RV++ L+ IL DE D + +I+ L+Q+ Sbjct: 252 LVGNDMVRGVSGGERKRVSIGEMLVGPASILFWDEITRGLDSSTAFQIIKALRQLAHITG 311 Query: 181 LTLLM-ISHNLEDSMQIATRFIVIAGGQIVYDGDPDRL 217 T L+ I + + I+++ G +Y G D + Sbjct: 312 ATALVSILQPSPEIYDLFDDVILLSEGYQIYQGPRDEV 349 Score = 65.3 bits (159), Expect = 2e-11 Identities = 52/201 (25%), Positives = 96/201 (47%), Gaps = 18/201 (8%) Query: 30 ILGPSGAGKSTLLSLMAGFKYP--TRGSIFLNGQNHTRSSPSKRPLSILFQENNLFS-HL 86 ++G SGAGK+TLL ++AG K G I ++G + + ++ S ++ ++ S L Sbjct: 822 LMGESGAGKTTLLDVLAGRKTGGYIEGDILISGFPKDQETFARV--SGYVEQQDIHSPEL 879 Query: 87 TVWQNIALGIAPNLRLDHY-----QHAQVKQMLEKVFLEDFFNRF----PSQMSGGQRQR 137 TV + +L + LRL ++ V++++E + L+++ + S +S QR+R Sbjct: 880 TVRE--SLRFSAALRLPKEVSDEEKYEYVEEVIELLELKEYADALVGLPGSGLSTEQRKR 937 Query: 138 VALARCLI-RQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQI 196 + + L+ IL LDEP + D ++ L+++ D Q L I D + Sbjct: 938 LTIGVELVANPSSILFLDEPTSGLDSQAAAIVMRFLRKLADTGQTILCTIHQPSIDIFEA 997 Query: 197 ATRFIVIA-GGQIVYDGDPDR 216 +++ GGQ VY G Sbjct: 998 FDELLLLKRGGQTVYFGPLGE 1018 >gnl|CDD|33864 COG4107, PhnK, ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 258 Score = 75.4 bits (185), Expect = 1e-14 Identities = 56/223 (25%), Positives = 106/223 (47%), Gaps = 29/223 (13%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSI--L 76 F + E + I+G SG+GK+TLL ++G P G++ T +P + + Sbjct: 26 SFDLYPGEVLGIVGESGSGKTTLLKCISGRLTPDAGTV-------TYRMRDGQPRDLYTM 78 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLD-----------------HYQH--AQVKQMLEKV 117 + T W + LR+ HY + A+ + LE+V Sbjct: 79 SEAERRRLLRTEWGFVHQNPRDGLRMQVSAGGNIGERLMAIGARHYGNIRAEAQDWLEEV 138 Query: 118 FLE-DFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVC 176 ++ D + P SGG +QR+ +AR L+ + ++ +DEP D +++ +L LL+ + Sbjct: 139 EIDLDRIDDLPRTFSGGMQQRLQIARNLVTRPRLVFMDEPTGGLDVSVQARLLDLLRGLV 198 Query: 177 DERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMN 219 E L +++++H+L + +A R +V+ GQ+V G DR+++ Sbjct: 199 RELGLAVVIVTHDLAVARLLADRLMVMKQGQVVESGLTDRVLD 241 >gnl|CDD|73061 cd03369, ABCC_NFT1, Domain 2 of NFT1 (New full-length MRP-type transporter 1). NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.. Length = 207 Score = 72.6 bits (178), Expect = 8e-14 Identities = 53/197 (26%), Positives = 91/197 (46%), Gaps = 20/197 (10%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQN--HTRSSPSKRPLSILF 77 F+V E+I I+G +GAGKSTL+ + F G I ++G + + L+I+ Sbjct: 29 FKVKAGEKIGIVGRTGAGKSTLILALFRFLEAEEGKIEIDGIDISTIPLEDLRSSLTIIP 88 Query: 78 QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQR 137 Q+ LFS T+ N+ D Y ++ L + +S GQRQ Sbjct: 89 QDPTLFSG-TIRSNLD-------PFDEYSDEEIYGALR-------VSEGGLNLSQGQRQL 133 Query: 138 VALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIA 197 + LAR L+++ +L+LDE A D A I +++ + T+L I+H L ++ Sbjct: 134 LCLARALLKRPRVLVLDEATASIDYATDALIQKTIRE--EFTNSTILTIAHRLR-TIIDY 190 Query: 198 TRFIVIAGGQIVYDGDP 214 + +V+ G++ P Sbjct: 191 DKILVMDAGEVKEYDHP 207 >gnl|CDD|36145 KOG0927, KOG0927, KOG0927, Predicted transporter (ABC superfamily) [General function prediction only]. Length = 614 Score = 72.7 bits (178), Expect = 9e-14 Identities = 46/218 (21%), Positives = 90/218 (41%), Gaps = 24/218 (11%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQE 79 ++N+ R ++GP+G+GKST L +AG + P I + K+ + + E Sbjct: 96 LELNRGRRYGLIGPNGSGKSTFLRAIAGREVPIPEHIDFYLLSREIEPSEKQAVQAVVME 155 Query: 80 N------------------NLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLED 121 + + + + + A++ + FL + Sbjct: 156 TDHERKRLEYLAEDLAQACDDKEKDELDELYERLDEMDNDTFEAKAAKI--LHGLGFLSE 213 Query: 122 FFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQL 181 ++ +SGG R R ALAR L ++ +LLLDEP D + L + ++ Sbjct: 214 MQDKKVKDLSGGWRMRAALARALFQKPDLLLLDEPTNHLDLEAIVWLEEYLAK---YDRI 270 Query: 182 TLLMISHNLEDSMQIATRFIVIAGGQ-IVYDGDPDRLM 218 L+++SH+ + + T I + + I Y+G+ D+ + Sbjct: 271 ILVIVSHSQDFLNGVCTNIIHLDNKKLIYYEGNYDQYV 308 Score = 68.1 bits (166), Expect = 2e-12 Identities = 57/217 (26%), Positives = 98/217 (45%), Gaps = 21/217 (9%) Query: 2 IKLDHLIYCYDNLKMQF---DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I + ++ + Y + M + +F ++ R+ ++GP+GAGKSTLL L+ G PT G + Sbjct: 390 IMVQNVSFGYSDNPMIYKKLNFGIDLDSRVALVGPNGAGKSTLLKLITGDLQPTIGMVSR 449 Query: 59 NGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF 118 + N P L + + + L+ +++ +L + Sbjct: 450 HSHNKL-------PRYNQHLAEQLDLDKSSLEFMMPKFPDEKELE-----EMRSILGRFG 497 Query: 119 LE-DFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCD 177 L D SQ+S GQR+RV AR ++Q +LLLDEP D E + L + + Sbjct: 498 LTGDAQVVPMSQLSDGQRRRVLFARLAVKQPHLLLLDEPTNHLDI----ETIDALAEAIN 553 Query: 178 ERQLTLLMISHNLEDSMQIATRFIVIAGGQIV-YDGD 213 E ++++SH+ Q+A V G + +DGD Sbjct: 554 EFPGGVVLVSHDFRLISQVAEEIWVCENGTVTKWDGD 590 >gnl|CDD|32537 COG2401, COG2401, ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]. Length = 593 Score = 70.8 bits (173), Expect = 3e-13 Identities = 47/196 (23%), Positives = 83/196 (42%), Gaps = 36/196 (18%) Query: 9 YCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKY--------PTRGSIFLNG 60 Y NL + ++ + + ++G SGAGK+TLL ++ G + P G + + Sbjct: 397 YVLRNL----NLEIKPGDVVAVVGQSGAGKTTLLRMILGAQKGRGEEKYRPDSGKVEVPK 452 Query: 61 QNHTRSSPSKRPLSILFQENNLFSHL---TVWQNIALGIAPNLRLDHYQHAQVKQMLEKV 117 + P + F E + HL T N A+ I L + Sbjct: 453 NTVSALIPGE--YEPEFGEVTILEHLRSKTGDLNAAVEI-----------------LNRA 493 Query: 118 FLED--FFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQV 175 L D + R S++S GQ++R LA+ L + +LL+DE A D + + ++ Sbjct: 494 GLSDAVLYRRKFSELSTGQKERAKLAKLLAERPNVLLIDEFAAHLDELTAVRVARKISEL 553 Query: 176 CDERQLTLLMISHNLE 191 E +TL++++H E Sbjct: 554 AREAGITLIVVTHRPE 569 >gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]. Length = 604 Score = 70.3 bits (172), Expect = 5e-13 Identities = 49/178 (27%), Positives = 78/178 (43%), Gaps = 22/178 (12%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSIL 76 + +F+V ER++I G SGAGK++LL +AG G I + + P +RP Sbjct: 411 ELNFEVRPGERLLITGESGAGKTSLLRALAGLWPWGSGRISMPADSALLFLP-QRPY--- 466 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRF------PSQM 130 + L L PN + A++ +L KV L D R + Sbjct: 467 LPQGTLREAL---------CYPNA-APDFSDAELVAVLHKVGLGDLAERLDEEDRWDRVL 516 Query: 131 SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISH 188 SGG++QR+A AR L+ + + LDE + D + LLK+ T++ + H Sbjct: 517 SGGEQQRLAFARLLLHKPKWVFLDEATSALDEETEDRLYQLLKEEL--PDATVISVGH 572 >gnl|CDD|37566 KOG2355, KOG2355, KOG2355, Predicted ABC-type transport, ATPase component/CCR4 associated factor [General function prediction only, Transcription]. Length = 291 Score = 69.3 bits (169), Expect = 8e-13 Identities = 53/215 (24%), Positives = 97/215 (45%), Gaps = 8/215 (3%) Query: 2 IKLDHLIYCY---DNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I++ L + Y D + F+ + R +++G +GAGK+TLL +++G G + + Sbjct: 14 IEVSGLQFKYKVSDPIFFDFNLDLPAGSRCLLVGANGAGKTTLLKILSGKHMVGGGVVQV 73 Query: 59 NGQN--HTRSSPSKRPLSILFQE--NNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQML 114 G++ H S S LS L E + V + + + ++ L Sbjct: 74 LGRSAFHDTSLESSGDLSYLGGEWSKTVGIAGEVPLQGDISAEHMIFGVGGDDPERREKL 133 Query: 115 EKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQ 174 + D R ++S GQR+RV + L++ +LLLDE D R ++L LK+ Sbjct: 134 IDILDIDLRWRM-HKVSDGQRRRVQICMGLLKPFKVLLLDEVTVDLDVLARADLLEFLKE 192 Query: 175 VCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIV 209 C++R T++ +H + T + I G++V Sbjct: 193 ECEQRGATIVYATHIFDGLETWPTHLVYIKSGKLV 227 >gnl|CDD|72976 cd03217, ABC_FeS_Assembly, ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.. Length = 200 Score = 66.3 bits (162), Expect = 6e-12 Identities = 50/204 (24%), Positives = 84/204 (41%), Gaps = 38/204 (18%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAGF-KY-PTRGSIFLNGQNHTRSSPSKRPLSI 75 + + K E ++GP+G+GKSTL + G KY T G I G++ T P +R Sbjct: 19 VNLTIKKGEVHALMGPNGSGKSTLAKTIMGHPKYEVTEGEILFKGEDITDLPPEERARLG 78 Query: 76 LFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQR 135 +F +Q + V DF SGG++ Sbjct: 79 IF---------LAFQYPP-------------------EIPGVKNADFLRYVNEGFSGGEK 110 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCD---ERQLTLLMISHNLED 192 +R + + L+ + + +LDEP D L + L L+ +V + E ++L+I+H Sbjct: 111 KRNEILQLLLLEPDLAILDEP----DSGLDIDALRLVAEVINKLREEGKSVLIITHYQRL 166 Query: 193 SMQIATRFI-VIAGGQIVYDGDPD 215 I + V+ G+IV GD + Sbjct: 167 LDYIKPDRVHVLYDGRIVKSGDKE 190 >gnl|CDD|73050 cd03291, ABCC_CFTR1, The CFTR subfamily domain 1. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.. Length = 282 Score = 63.9 bits (155), Expect = 4e-11 Identities = 60/228 (26%), Positives = 105/228 (46%), Gaps = 37/228 (16%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 + ++ K E + I G +G+GK++LL L+ G P+ G I +G R S S + I+ Sbjct: 57 NLKIEKGEMLAITGSTGSGKTSLLMLILGELEPSEGKIKHSG----RISFSSQFSWIMPG 112 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQ--------- 129 T+ +NI G++ D Y++ V + + LE+ +FP + Sbjct: 113 --------TIKENIIFGVS----YDEYRYKSVVKACQ---LEEDITKFPEKDNTVLGEGG 157 Query: 130 --MSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCD-ERQLTLLMI 186 +SGGQR R++LAR + + + LLD PF D EI VC T +++ Sbjct: 158 ITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEKEIFE--SCVCKLMANKTRILV 215 Query: 187 SHNLEDSMQIATRFIVIAGGQIVYDGDPDRLMNGLIPE--STLLGIPS 232 + +E ++ A + +++ G + G L L P+ S L+G + Sbjct: 216 TSKME-HLKKADKILILHEGSSYFYGTFSEL-QSLRPDFSSKLMGYDT 261 >gnl|CDD|72992 cd03233, ABC_PDR_domain1, The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters. PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including 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 = 202 Score = 63.7 bits (155), Expect = 4e-11 Identities = 43/200 (21%), Positives = 80/200 (40%), Gaps = 28/200 (14%) Query: 18 FDFQVNKAERIVILGPSGAGKSTLLSLMAG---FKYPTRGSIFLNG-QNHTRSSPSKRPL 73 F V E +++LG G+G STLL +A G I NG + + Sbjct: 26 FSGVVKPGEMVLVLGRPGSGCSTLLKALANRTEGNVSVEGDIHYNGIPYKEFAEKYPGEI 85 Query: 74 SILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGG 133 + +E+ F LTV + LD + + + + SGG Sbjct: 86 IYVSEEDVHFPTLTVRET----------LDFALRCKGNEFVRGI-------------SGG 122 Query: 134 QRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLM-ISHNLED 192 +R+RV++A L+ + +L D D + EIL ++ + D + T + + ++ Sbjct: 123 ERKRVSIAEALVSRASVLCWDNSTRGLDSSTALEILKCIRTMADVLKTTTFVSLYQASDE 182 Query: 193 SMQIATRFIVIAGGQIVYDG 212 + + +V+ G+ +Y G Sbjct: 183 IYDLFDKVLVLYEGRQIYYG 202 >gnl|CDD|72981 cd03222, ABC_RNaseL_inhibitor, The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.. Length = 177 Score = 63.5 bits (154), Expect = 5e-11 Identities = 48/209 (22%), Positives = 77/209 (36%), Gaps = 65/209 (31%) Query: 22 VNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENN 81 V + E I I+GP+G GK+T + ++AG P + + +P +P Sbjct: 22 VKEGEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWD-----GITPVYKP--------- 67 Query: 82 LFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALA 141 Q I L SGG+ QRVA+A Sbjct: 68 --------QYIDL------------------------------------SGGELQRVAIA 83 Query: 142 RCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFI 201 L+R L DEP A D R ++++ +E + T L++ H+L ++ R Sbjct: 84 AALLRNATFYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLAVLDYLSDRI- 142 Query: 202 VIAGGQIVYDGDPDRLMNGLIPESTLLGI 230 V++G+P P+ T GI Sbjct: 143 ------HVFEGEPGVYGIASQPKGTREGI 165 >gnl|CDD|73048 cd03289, ABCC_CFTR2, The CFTR subfamily domain 2. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.. Length = 275 Score = 62.7 bits (152), Expect = 9e-11 Identities = 57/202 (28%), Positives = 97/202 (48%), Gaps = 25/202 (12%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSK--RPLSILF 77 F ++ +R+ +LG +G+GKSTLLS T G I ++G + K + ++ Sbjct: 25 FSISPGQRVGLLGRTGSGKSTLLSAFLRLLN-TEGDIQIDGVSWNSVPLQKWRKAFGVIP 83 Query: 78 QENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQM------- 130 Q+ +FS T +N+ P + ++ ++ E+V L+ +FP Q+ Sbjct: 84 QKVFIFSG-TFRKNLD----PY---GKWSDEEIWKVAEEVGLKSVIEQFPGQLDFVLVDG 135 Query: 131 ----SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMI 186 S G +Q + LAR ++ + ILLLDEP A DP I LKQ + T+++ Sbjct: 136 GCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPITYQVIRKTLKQAFAD--CTVILS 193 Query: 187 SHNLEDSMQIATRFIVIAGGQI 208 H +E +M RF+VI ++ Sbjct: 194 EHRIE-AMLECQRFLVIEENKV 214 >gnl|CDD|35289 KOG0066, KOG0066, KOG0066, eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]. Length = 807 Score = 62.0 bits (150), Expect = 1e-10 Identities = 48/179 (26%), Positives = 78/179 (43%), Gaps = 19/179 (10%) Query: 12 DNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKR 71 L + DF ++ RI I+GP+G GKSTLL L+ G P G + +NH Sbjct: 600 KPLFKKLDFGIDMDSRIAIVGPNGVGKSTLLKLLIGKLDPNDGEL---RKNHR------- 649 Query: 72 PLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFP-SQM 130 L I + + + L + + L + + ++ L L + + Sbjct: 650 -LRIGWFDQHANEALNGEETPVEYLQRKFNLP---YQEARKQLGTFGLASHAHTIKIKDL 705 Query: 131 SGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHN 189 SGGQ+ RVALA + +L+LDEP D E + L + +E ++M+SH+ Sbjct: 706 SGGQKARVALAELALGGPDVLILDEPTNNLDI----ESIDALAEAINEYNGGVIMVSHD 760 Score = 42.8 bits (100), Expect = 8e-05 Identities = 53/189 (28%), Positives = 83/189 (43%), Gaps = 22/189 (11%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMA--GFKYPTRGSIFLNGQNHTRSSPS------- 69 + R ++GP+G GK+TLL +A P + L Q S S Sbjct: 284 SLTIVYGRRYGLVGPNGMGKTTLLKHIAARALAIPPNIDVLLCEQEVVADSTSAIDTVLK 343 Query: 70 --KRPLSILFQENNLFSHLTVWQNIAL----GIAPNLRL--DHYQHAQVKQMLEKV-FLE 120 K+ L++L +E L S + A +A LR A+ +++L + F + Sbjct: 344 ADKKRLALLEEEAKLMSQIEEGDTTAAERLKEVADELRAIGADSAEARARRILAGLGFSK 403 Query: 121 DFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQ 180 + R ++ SGG R RV+LAR L + +L+LDEP D L I L + Sbjct: 404 EMQERPTTKFSGGWRMRVSLARALFLEPTLLMLDEPTNHLD--LNAVI--WLDNYLQGWK 459 Query: 181 LTLLMISHN 189 TLL++SH+ Sbjct: 460 KTLLIVSHD 468 >gnl|CDD|73049 cd03290, ABCC_SUR1_N, The SUR domain 1. The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.. Length = 218 Score = 60.5 bits (146), Expect = 4e-10 Identities = 48/192 (25%), Positives = 93/192 (48%), Gaps = 28/192 (14%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRS------SPSKRP 72 + ++ + +I+G G GKS+LL + G G + + +N + S ++ Sbjct: 21 NIRIPTGQLTMIVGQVGCGKSSLLLAILGEMQTLEGKVHWSNKNESEPSFEATRSRNRYS 80 Query: 73 LSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPS---- 128 ++ Q+ L + TV +NI G +P + + K + + L+ + P Sbjct: 81 VAYAAQKPWLLN-ATVEENITFG-SP------FNKQRYKAVTDACSLQPDIDLLPFGDQT 132 Query: 129 -------QMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEIL--GLLKQVCDER 179 +SGGQRQR+ +AR L + I+ LD+PF+ D L ++ G+LK + D++ Sbjct: 133 EIGERGINLSGGQRQRICVARALYQNTNIVFLDDPFSALDIHLSDHLMQEGILKFLQDDK 192 Query: 180 QLTLLMISHNLE 191 + TL++++H L+ Sbjct: 193 R-TLVLVTHKLQ 203 >gnl|CDD|35286 KOG0063, KOG0063, KOG0063, RNAse L inhibitor, ABC superfamily [RNA processing and modification]. Length = 592 Score = 58.4 bits (141), Expect = 2e-09 Identities = 54/207 (26%), Positives = 90/207 (43%), Gaps = 24/207 (11%) Query: 25 AERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENNLFS 84 +E IV+LG +G GK+T + ++AG P G + S +P I + Sbjct: 367 SEIIVMLGENGTGKTTFIRMLAGRLKPDEGGEI------PVLNVSYKPQKISPKREGTVR 420 Query: 85 HLTVWQNIALGIAPNLRLDHYQHAQ-VKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARC 143 L D Y H Q V +++ + +E+ ++ +SGG+ QRVALA C Sbjct: 421 QL----------LHTKIRDAYMHPQFVNDVMKPLQIENIIDQEVQGLSGGELQRVALALC 470 Query: 144 LIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVI 203 L + + L+DEP A D R ++K+ + T ++ H+ + +A R Sbjct: 471 LGKPADVYLIDEPSAYLDSEQRIIASKVIKRFILHAKKTAFVVEHDFIMATYLADRV--- 527 Query: 204 AGGQIVYDGDPDRLMNGLIPESTLLGI 230 IV++G P P+S L G+ Sbjct: 528 ----IVFEGQPSVNTVANSPQSLLAGM 550 Score = 41.4 bits (97), Expect = 2e-04 Identities = 34/150 (22%), Positives = 67/150 (44%), Gaps = 27/150 (18%) Query: 30 ILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENNLFSHLT-- 87 ++G +G GKST L ++AG + P G + P + + F+ + L ++ T Sbjct: 105 LVGTNGIGKSTALKILAGKQKPNLGRY--------DNPPDWQEILTYFRGSELQNYFTKI 156 Query: 88 VWQNIALGIAPNLRLDHYQHA----------------QVKQMLEKVFLEDFFNRFPSQMS 131 + N+ I P +D A +++ +++ L + +R Q+S Sbjct: 157 LEDNLKAIIKPQY-VDQIPRAVKGTVGSLLDRKDERDNKEEVCDQLDLNNLLDREVEQLS 215 Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFD 161 GG+ QR A+A +++ + + DEP + D Sbjct: 216 GGELQRFAIAMVCVQKADVYMFDEPSSYLD 245 >gnl|CDD|35285 KOG0062, KOG0062, KOG0062, ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism, Translation, ribosomal structure and biogenesis]. Length = 582 Score = 56.1 bits (135), Expect = 8e-09 Identities = 41/177 (23%), Positives = 67/177 (37%), Gaps = 20/177 (11%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSIL 76 Q RI +G +G GKSTLL ++ G PTRG + + + + Sbjct: 382 QLGLDRESDSRISRVGENGDGKSTLLKILKGDLTPTRGIVGRHP---------RLRIKYF 432 Query: 77 FQ-ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLE-DFFNRFPSQMSGGQ 134 Q + + P + + L L + + + +SGGQ Sbjct: 433 AQHHVDFLDKNVNAVDFMEKSFPGKTEEEIRRH-----LGSFGLSGELALQSIASLSGGQ 487 Query: 135 RQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLE 191 + RVA A C +L+LDEP D + LG L + ++++SH+ E Sbjct: 488 KSRVAFAACTWNNPHLLVLDEPTNHLD----RDSLGALAKALKNFNGGVVLVSHDEE 540 Score = 47.6 bits (113), Expect = 3e-06 Identities = 36/134 (26%), Positives = 53/134 (39%), Gaps = 14/134 (10%) Query: 24 KAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSK-RPLSILFQENNL 82 + R ++G +G GKSTLL +A NGQ + R ++ L Sbjct: 105 RGRRYGLVGRNGIGKSTLLRAIA------------NGQVSGFHVEQEVRGDDTEALQSVL 152 Query: 83 FSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALAR 142 S +A L + K + F + + +SGG R R+ALAR Sbjct: 153 ESDTERLDFLAEEKELLAGL-TLEEIYDKILAGLGFTPEMQLQPTKSLSGGWRMRLALAR 211 Query: 143 CLIRQKPILLLDEP 156 L + +LLLDEP Sbjct: 212 ALFAKPDLLLLDEP 225 Score = 35.3 bits (81), Expect = 0.016 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 4/46 (8%) Query: 16 MQFDFQVNKAE----RIVILGPSGAGKSTLLSLMAGFKYPTRGSIF 57 +F + +A RI +LG A KSTL+ ++ GF +PT G + Sbjct: 313 DKFRYNAARASSVQSRIKMLGKLPALKSTLIEVLIGFLFPTEGEVL 358 >gnl|CDD|33911 COG4170, SapD, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]. Length = 330 Score = 55.0 bits (132), Expect = 2e-08 Identities = 52/220 (23%), Positives = 101/220 (45%), Gaps = 25/220 (11%) Query: 22 VNKAERIVILGPSGAGKSTLLSLMAGFKYP----TRGSIFLNGQNHTRSSPSKR------ 71 +N+ E ++G SG+GKS + + G T + + + R SP +R Sbjct: 30 LNEGEIRGLVGESGSGKSLIAKAICGVNKDNWRVTADRMRFDDIDLLRLSPRERRKLVGH 89 Query: 72 PLSILFQENNLFSHLTVWQNIALGIAPNL----------RLDHYQHAQVKQMLEKVFL-- 119 +S++FQE S L + + + N+ + ++ + ++L +V + Sbjct: 90 NVSMIFQEPQ--SCLDPSERVGRQLIQNIPAWTYKGRWWQRFGWRKRRAIELLHRVGIKD 147 Query: 120 -EDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDE 178 +D +P +++ G+ Q+V +A L Q +L+ DEP +P + +I LL ++ Sbjct: 148 HKDIMRSYPYELTEGECQKVMIAIALANQPRLLIADEPTNSMEPTTQAQIFRLLSRLNQN 207 Query: 179 RQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 T+L+ISH+L+ Q A + V+ GQ V + L+ Sbjct: 208 SNTTILLISHDLQMISQWADKINVLYCGQTVESAPSEELV 247 >gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).. Length = 166 Score = 54.0 bits (130), Expect = 4e-08 Identities = 47/190 (24%), Positives = 75/190 (39%), Gaps = 47/190 (24%) Query: 2 IKLDHLIYCYDN---LKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFL 58 I+L++L + L F++ +R++I GPSG GKS+L +AG G I + Sbjct: 1 IELENLSLATPDGRVLLKDLSFEIKPGDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGM 60 Query: 59 NGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVF 118 P +RP + LG LR Q+ + V Sbjct: 61 PEGEDLLFLP-QRPY------------------LPLG---TLR------EQLIYPWDDVL 92 Query: 119 LEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDE 178 SGG++QR+A AR L+ + + LDE + D E L Q+ E Sbjct: 93 ------------SGGEQQRLAFARLLLHKPKFVFLDEATSALDE----ESEDRLYQLLKE 136 Query: 179 RQLTLLMISH 188 +T++ + H Sbjct: 137 LGITVISVGH 146 >gnl|CDD|35283 KOG0060, KOG0060, KOG0060, Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism, General function prediction only]. Length = 659 Score = 53.8 bits (129), Expect = 4e-08 Identities = 45/208 (21%), Positives = 79/208 (37%), Gaps = 35/208 (16%) Query: 1 MIKLDHLIYCYDN----LKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSI 56 I+ + + L +V + ++I GPSG GK++LL ++ G T G + Sbjct: 433 AIEFEEVSLSTPTNGDLLIENLSLEVPSGQNLLITGPSGCGKTSLLRVLGGLWPSTGGKL 492 Query: 57 FLNGQNHTRSSPSKRPLSILFQENNLFSHL-TVWQNIALGIAPNLRLDHYQHA----QVK 111 T P + F + L T+ + I P D + + Sbjct: 493 ----TKPTDGGPK----DLFFLPQRPYMTLGTLRDQV---IYPLKAEDMDSKSASDEDIL 541 Query: 112 QMLEKVFLEDFFNRFP-----------SQMSGGQRQRVALARCLIRQKPILLLDEPFAVF 160 ++LE V L R +S G++QR+A AR + +LDE + Sbjct: 542 RILENVQLGHLLEREGGLDQQVDWDWMDVLSPGEQQRLAFARLFYHKPKFAILDECTS-- 599 Query: 161 DPALRHEILGLLKQVCDERQLTLLMISH 188 A+ ++ G L + C E +T + + H Sbjct: 600 --AVTEDVEGALYRKCREMGITFISVGH 625 >gnl|CDD|30527 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication, recombination, and repair]. Length = 935 Score = 51.3 bits (123), Expect = 2e-07 Identities = 38/142 (26%), Positives = 67/142 (47%), Gaps = 25/142 (17%) Query: 99 NLRLDHYQHAQVKQMLEKV-----FLEDF------FNRFPSQMSGGQRQRVALARCLIRQ 147 NL+L + + +L+++ FL D +R +SGG+ QR+ LA + Sbjct: 440 NLKLSEKEKKIAEPILKEIKERLGFLVDVGLGYLTLSRSAGTLSGGEAQRIRLATQIGSG 499 Query: 148 KPILL--LDEPFAVFDPALRHEILGLLKQVCDERQL--TLLMISHNLEDSMQIATRFIVI 203 +L LDEP ++ LK++ R L T++++ H+ ED+++ A I I Sbjct: 500 LTGVLYVLDEPSIGLHQRDNERLIETLKRL---RDLGNTVIVVEHD-EDTIRAADHIIDI 555 Query: 204 A------GGQIVYDGDPDRLMN 219 GG+IV +G P+ L+ Sbjct: 556 GPGAGEHGGEIVAEGTPEELLA 577 Score = 40.9 bits (96), Expect = 3e-04 Identities = 31/99 (31%), Positives = 54/99 (54%), Gaps = 11/99 (11%) Query: 128 SQMSGGQRQRVALARCLIRQ---KPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLL 184 + +SGG+ QRV LA+ L ++ K + +LDEP ++L +L ++ D+ T++ Sbjct: 821 TTLSGGEAQRVKLAKELSKRSTGKTLYILDEPTTGLHFDDIKKLLEVLHRLVDKGN-TVI 879 Query: 185 MISHNLEDSMQIATRFIVI------AGGQIVYDGDPDRL 217 +I HNL D ++ A I + GG+IV G P+ + Sbjct: 880 VIEHNL-DVIKTADWIIDLGPEGGDGGGEIVASGTPEEV 917 Score = 29.8 bits (67), Expect = 0.60 Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 1/29 (3%) Query: 13 NLKMQFDFQVNKAERIVILGPSGAGKSTL 41 NLK D ++ + + +VI G SG+GKS+L Sbjct: 15 NLK-NIDLEIPRNKLVVITGLSGSGKSSL 42 Score = 26.7 bits (59), Expect = 6.4 Identities = 8/16 (50%), Positives = 12/16 (75%) Query: 28 IVILGPSGAGKSTLLS 43 + G SG+GKSTL++ Sbjct: 630 TCVTGVSGSGKSTLIN 645 >gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.. Length = 144 Score = 50.8 bits (122), Expect = 3e-07 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 4/80 (5%) Query: 128 SQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMIS 187 Q+SGG++ R+ALA+ L+ +LLLDEP D + LK E T++++S Sbjct: 69 EQLSGGEKMRLALAKLLLENPNLLLLDEPTNHLDLESIEALEEALK----EYPGTVILVS 124 Query: 188 HNLEDSMQIATRFIVIAGGQ 207 H+ Q+AT+ I + G+ Sbjct: 125 HDRYFLDQVATKIIELEDGK 144 Score = 50.1 bits (120), Expect = 5e-07 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 2/57 (3%) Query: 2 IKLDHLIYCYDNLKM--QFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSI 56 I+L++L Y + +N +RI ++G +GAGKSTLL L+AG P G + Sbjct: 1 IELENLSKTYGGKLLLKDISLTINPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIV 57 >gnl|CDD|72991 cd03232, ABC_PDR_domain2, The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters. PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including 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 = 192 Score = 49.4 bits (118), Expect = 8e-07 Identities = 54/225 (24%), Positives = 89/225 (39%), Gaps = 51/225 (22%) Query: 6 HLIYCYDNLKMQFDFQVNKAERIVI---------------LGPSGAGKSTLLSLMAGFKY 50 + + NL + V +R ++ +G SGAGK+TLL ++AG K Sbjct: 1 GSVLTWKNL--NYTVPVKGGKRQLLNNISGYVKPGTLTALMGESGAGKTTLLDVLAGRKT 58 Query: 51 P--TRGSIFLNGQNHTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHA 108 G I +NG+ ++ R + Q++ +LTV + AL + LR Sbjct: 59 AGVITGEILINGRPLDKNFQ--RSTGYVEQQDVHSPNLTVRE--ALRFSALLR------- 107 Query: 109 QVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEI 168 +S QR+R+ + L + IL LDEP + D + I Sbjct: 108 --------------------GLSVEQRKRLTIGVELAAKPSILFLDEPTSGLDSQAAYNI 147 Query: 169 LGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIA-GGQIVYDG 212 + LK++ D Q L I + R +++ GG+ VY G Sbjct: 148 VRFLKKLADSGQAILCTIHQPSASIFEKFDRLLLLKRGGKTVYFG 192 >gnl|CDD|72995 cd03236, ABC_RNaseL_inhibitor_domain1, The ATPase domain 1 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI s are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLIs have an N-terminal Fe-S domain and two nucleotide binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.. Length = 255 Score = 49.5 bits (118), Expect = 8e-07 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 28/179 (15%) Query: 30 ILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENNLFSHLTVW 89 ++GP+G GKST L ++AG P G P + F+ + L ++ T Sbjct: 31 LVGPNGIGKSTALKILAGKLKPNLGKF--------DDPPDWDEILDEFRGSELQNYFTKL 82 Query: 90 QN--IALGIAPNLRLDHYQHA---QVKQMLEKV-------------FLEDFFNRFPSQMS 131 + + + P +D A +V ++L+K L +R Q+S Sbjct: 83 LEGDVKVIVKPQY-VDLIPKAVKGKVGELLKKKDERGKLDELVDQLELRHVLDRNIDQLS 141 Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNL 190 GG+ QRVA+A L R DEP + D R L++++ ++ +L++ H+L Sbjct: 142 GGELQRVAIAAALARDADFYFFDEPSSYLDIKQRLNAARLIRELAEDDN-YVLVVEHDL 199 >gnl|CDD|72999 cd03240, ABC_Rad50, The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.. Length = 204 Score = 46.7 bits (111), Expect = 5e-06 Identities = 39/194 (20%), Positives = 71/194 (36%), Gaps = 27/194 (13%) Query: 11 YDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSK 70 ++ +++F + +I+G +GAGK+T++ KY G + N + Sbjct: 13 HERSEIEFFSPLT-----LIVGQNGAGKTTIIE---ALKYALTGELPPN-----SKGGAH 59 Query: 71 RPLSILFQENNLFSHLTVWQNIALGIAPNLRLDHYQHA-QVKQMLEKVFLEDFFNRFPSQ 129 P I E L L ++ Q L D + Sbjct: 60 DPKLIREGEVRAQVKLAFENANGKKYTITRSLAILENVIFCHQGESNWPLLDM----RGR 115 Query: 130 MSGGQRQ------RVALARCLIRQKPILLLDEPFAVFDPA-LRHEILGLLKQVCDERQLT 182 SGG++ R+ALA IL LDEP D + + ++++ ++ Sbjct: 116 CSGGEKVLASLIIRLALAETFGSNCGILALDEPTTNLDEENIEESLAEIIEERKSQKNFQ 175 Query: 183 LLMISH--NLEDSM 194 L++I+H L D+ Sbjct: 176 LIVITHDEELVDAA 189 >gnl|CDD|73047 cd03288, ABCC_SUR2, The SUR domain 2. The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.. Length = 257 Score = 47.0 bits (111), Expect = 5e-06 Identities = 62/237 (26%), Positives = 108/237 (45%), Gaps = 34/237 (14%) Query: 2 IKLDHLIYCYDN-LK---MQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPT--RGS 55 IK+ L Y+N LK + +++ I G +G+GKS+L +A F+ G Sbjct: 20 IKIHDLCVRYENNLKPVLKHVKAYIKPGQKVGICGRTGSGKSSLS--LAFFRMVDIFDGK 77 Query: 56 IFLNGQN------HTRSSPSKRPLSILFQENNLFSHLTVWQNIALGIAPNLRL------D 103 I ++G + HT S LSI+ Q+ LFS +I + P + + Sbjct: 78 IVIDGIDISKLPLHTLRSR----LSIILQDPILFS-----GSIRFNLDPECKCTDDRLWE 128 Query: 104 HYQHAQVKQMLEKV--FLEDFFNRFPSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFD 161 + AQ+K M++ + L+ S GQRQ LAR +R+ IL++DE A D Sbjct: 129 ALEIAQLKNMVKSLPGGLDAVVTEGGENFSVGQRQLFCLARAFVRKSSILIMDEATASID 188 Query: 162 PALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQIVYDGDPDRLM 218 A + + ++ +R T++ I+H + + A +V++ G +V P+ L+ Sbjct: 189 MATENILQKVVMTAFADR--TVVTIAHRVSTILD-ADLVLVLSRGILVECDTPENLL 242 >gnl|CDD|73038 cd03279, ABC_sbcCD, SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.. Length = 213 Score = 45.6 bits (108), Expect = 1e-05 Identities = 45/206 (21%), Positives = 74/206 (35%), Gaps = 31/206 (15%) Query: 18 FDF-QVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSIL 76 DF ++ +I GP+GAGKST+L + Y + +P + + Sbjct: 20 IDFTGLDNNGLFLICGPTGAGKSTILDAITYALYGKTPRYGRQENLRSVFAPGEDTAEVS 79 Query: 77 FQENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFL-----EDFFNRFPSQMS 131 F LG R++ + Q V L + F R S +S Sbjct: 80 FT-------------FQLGGK-KYRVERSRGLDYDQFTRIVLLPQGEFDRFLARPVSTLS 125 Query: 132 GGQRQRVALARCLIRQKPI----------LLLDEPFAVFDPALRHEILGLLKQVCDERQL 181 GG+ +L+ L + + L +DE F DP + L+ + E ++ Sbjct: 126 GGETFLASLSLALALSEVLQNRGGARLEALFIDEGFGTLDPEALEAVATALELIRTENRM 185 Query: 182 TLLMISHNLEDSMQIATRFIVIAGGQ 207 + +ISH E +I R VI Sbjct: 186 -VGVISHVEELKERIPQRLEVIKTPG 210 >gnl|CDD|35287 KOG0064, KOG0064, KOG0064, Peroxisomal long-chain acyl-CoA transporter, ABC superfamily [Lipid transport and metabolism]. Length = 728 Score = 44.6 bits (105), Expect = 2e-05 Identities = 44/182 (24%), Positives = 74/182 (40%), Gaps = 30/182 (16%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQE 79 FQ+ ++I GP+G GKS+L ++ G G + + N+ P +RP Sbjct: 503 FQIEPGMHLLITGPNGCGKSSLFRILGGLWPVYNGLLSIPRPNNIFYIP-QRP------- 554 Query: 80 NNLFSHLTVWQNIALGIAPNLRLD----HYQHAQVKQMLEKVFLEDFFNR---------F 126 S T+ I I P+ Y ++ +L+ V LE R + Sbjct: 555 --YMSGGTLRDQI---IYPDSSEQMKRKGYTDQDLEAILDIVHLEHILQREGGWDAVRDW 609 Query: 127 PSQMSGGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMI 186 +SGG++QR+ +AR + LLDE + + +I K ++LL I Sbjct: 610 KDVLSGGEKQRMGMARMFYHRPKYALLDECTSAVSIDVEGKIFQAAKDA----GISLLSI 665 Query: 187 SH 188 +H Sbjct: 666 TH 667 >gnl|CDD|72997 cd03238, ABC_UvrA, The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.. Length = 176 Score = 43.7 bits (103), Expect = 5e-05 Identities = 48/202 (23%), Positives = 79/202 (39%), Gaps = 48/202 (23%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQ 78 D + +V+ G SG+GKSTL++ G + + S+ L + Q Sbjct: 15 DVSIPLNVLVVVTGVSGSGKSTLVN--EGLYASGKARL-----ISFLPKFSRNKLIFIDQ 67 Query: 79 ENNLFSHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRV 138 L I +G+ L L + S +SGG+ QRV Sbjct: 68 LQFL---------IDVGLG-YLTL---------------------GQKLSTLSGGELQRV 96 Query: 139 ALARCLIRQKP--ILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQI 196 LA L + P + +LDEP +++L ++K + D T+++I HN D + Sbjct: 97 KLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGN-TVILIEHN-LDVLSS 154 Query: 197 ATRFIVIA------GGQIVYDG 212 A I GG++V+ G Sbjct: 155 ADWIIDFGPGSGKSGGKVVFSG 176 >gnl|CDD|73029 cd03270, ABC_UvrA_I, The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.. Length = 226 Score = 42.9 bits (101), Expect = 8e-05 Identities = 58/233 (24%), Positives = 99/233 (42%), Gaps = 49/233 (21%) Query: 13 NLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQ---NHTRSSPS 69 NLK D + + + +VI G SG+GKS+L F +I+ GQ + S+ + Sbjct: 10 NLK-NVDVDIPRNKLVVITGVSGSGKSSL-----AF-----DTIYAEGQRRYVESLSAYA 58 Query: 70 KRPLSILFQEN-----NLFSHLTVWQNIA-----------LGIAPNLRLDHYQHAQVKQM 113 ++ L + + + L + + Q I LRL + +++ Sbjct: 59 RQFLGQMDKPDVDSIEGLSPAIAIDQKTTSRNPRSTVGTVTEIYDYLRL-LFARVGIRER 117 Query: 114 LEKVFLEDF------FNRFPSQMSGGQRQRVALARCLIRQ--KPILLLDEPFAVFDPALR 165 L FL D +R +SGG+ QR+ LA + + +LDEP P Sbjct: 118 LG--FLVDVGLGYLTLSRSAPTLSGGEAQRIRLATQIGSGLTGVLYVLDEPSIGLHPRDN 175 Query: 166 HEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIA------GGQIVYDG 212 ++ LK++ D T+L++ H+ ED+++ A I I GG+IV G Sbjct: 176 DRLIETLKRLRDLGN-TVLVVEHD-EDTIRAADHVIDIGPGAGVHGGEIVAQG 226 >gnl|CDD|177053 CHL00131, ycf16, sulfate ABC transporter protein; Validated. Length = 252 Score = 42.3 bits (100), Expect = 1e-04 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 6/57 (10%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFKYP----TRGSIFLNGQNHTRSSPSKR 71 + +NK E I+GP+G+GKSTL ++AG +P G I G++ P +R Sbjct: 27 NLSINKGEIHAIMGPNGSGKSTLSKVIAG--HPAYKILEGDILFKGESILDLEPEER 81 >gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]. Length = 908 Score = 41.2 bits (96), Expect = 2e-04 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 9/86 (10%) Query: 125 RFPSQMSGGQRQ------RVALARCLIRQKPI--LLLDEPFAVFDPALRHEILGLLKQVC 176 R +SGG+R R+AL+ L + + L LDEPF D ++ +L+++ Sbjct: 811 RPIKTLSGGERFLASLALRLALSDLLQGRARLELLFLDEPFGTLDEERLEKLAEILEEL- 869 Query: 177 DERQLTLLMISHNLEDSMQIATRFIV 202 +++ISH E + R V Sbjct: 870 LSDGRQIIIISHVEELKERADVRIRV 895 Score = 27.7 bits (61), Expect = 2.6 Identities = 9/14 (64%), Positives = 14/14 (100%) Query: 29 VILGPSGAGKSTLL 42 +I+GP+GAGKS++L Sbjct: 29 LIVGPNGAGKSSIL 42 >gnl|CDD|73030 cd03271, ABC_UvrA_II, The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins and UvrB having one ATP binding site that is structurally related to that of helicases.. Length = 261 Score = 41.3 bits (97), Expect = 2e-04 Identities = 30/94 (31%), Positives = 52/94 (55%), Gaps = 11/94 (11%) Query: 130 MSGGQRQRVALARCLIRQ---KPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMI 186 +SGG+ QR+ LA+ L ++ K + +LDEP ++L +L+++ D+ T+++I Sbjct: 170 LSGGEAQRIKLAKELSKRSTGKTLYILDEPTTGLHFHDVKKLLEVLQRLVDKGN-TVVVI 228 Query: 187 SHNLEDSMQIATRFIVI------AGGQIVYDGDP 214 HNL D ++ A I + GGQ+V G P Sbjct: 229 EHNL-DVIKCADWIIDLGPEGGDGGGQVVASGTP 261 Score = 26.3 bits (58), Expect = 7.4 Identities = 7/15 (46%), Positives = 11/15 (73%) Query: 28 IVILGPSGAGKSTLL 42 + G SG+GKS+L+ Sbjct: 24 TCVTGVSGSGKSSLI 38 >gnl|CDD|72986 cd03227, ABC_Class2, ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.. Length = 162 Score = 37.6 bits (87), Expect = 0.003 Identities = 18/86 (20%), Positives = 39/86 (45%), Gaps = 6/86 (6%) Query: 122 FFNRFPSQMSGGQRQRVALA----RCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCD 177 Q+SGG+++ ALA ++ +P+ +LDE DP + + + Sbjct: 70 ELIFTRLQLSGGEKELSALALILALASLKPRPLYILDEIDRGLDPRDGQALAEAILEHLV 129 Query: 178 ERQLTLLMISHNLEDSMQIATRFIVI 203 + +++I+H + ++A + I I Sbjct: 130 K-GAQVIVITHL-PELAELADKLIHI 153 >gnl|CDD|36182 KOG0964, KOG0964, KOG0964, Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]. Length = 1200 Score = 36.1 bits (83), Expect = 0.008 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 4/56 (7%) Query: 129 QMSGGQRQRVALARCLIRQK----PILLLDEPFAVFDPALRHEILGLLKQVCDERQ 180 Q+SGGQ+ VALA Q+ P L DE A D R + L+K++ D Q Sbjct: 1097 QLSGGQKSVVALALIFAIQRCDPAPFYLFDEIDAALDAQYRTAVADLIKELSDSAQ 1152 >gnl|CDD|73031 cd03272, ABC_SMC3_euk, Eukaryotic SMC3 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).. Length = 243 Score = 35.6 bits (82), Expect = 0.012 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 4/56 (7%) Query: 129 QMSGGQRQRVALARCLIRQK----PILLLDEPFAVFDPALRHEILGLLKQVCDERQ 180 Q+SGGQ+ VALA QK P L DE A D R + ++K++ D Q Sbjct: 158 QLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDAALDAQYRTAVANMIKELSDGAQ 213 >gnl|CDD|73037 cd03278, ABC_SMC_barmotin, Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).. Length = 197 Score = 35.0 bits (81), Expect = 0.019 Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 7/78 (8%) Query: 128 SQMSGGQRQRVALARC----LIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTL 183 S +SGG++ ALA +R P +LDE A D A LLK+ E Q Sbjct: 112 SLLSGGEKALTALALLFAIFRVRPSPFCVLDEVDAALDDANVERFARLLKEFSKETQ--F 169 Query: 184 LMISHNLEDSMQIATRFI 201 ++I+H + +M+ A R Sbjct: 170 IVITHR-KGTMEAADRLY 186 >gnl|CDD|73180 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.. Length = 137 Score = 34.7 bits (80), Expect = 0.021 Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 1/30 (3%) Query: 28 IVILGPSGAGKSTLLS-LMAGFKYPTRGSI 56 IV+ GPSG GKSTLL L+ F S+ Sbjct: 2 IVLSGPSGVGKSTLLKRLLEEFDPNFGFSV 31 >gnl|CDD|30002 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.. Length = 326 Score = 34.0 bits (78), Expect = 0.031 Identities = 13/27 (48%), Positives = 17/27 (62%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMA 46 V K +R+ I SG GKSTLL ++A Sbjct: 64 LTVGKGQRLGIFAGSGVGKSTLLGMIA 90 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 34.1 bits (78), Expect = 0.032 Identities = 13/15 (86%), Positives = 14/15 (93%) Query: 27 RIVILGPSGAGKSTL 41 RI+ILGP GAGKSTL Sbjct: 2 RILILGPPGAGKSTL 16 >gnl|CDD|143815 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a number of different Prosite families together. Length = 174 Score = 33.7 bits (78), Expect = 0.041 Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 3/32 (9%) Query: 11 YDNLKMQFDFQVNKAERIVILGPSGAGKSTLL 42 LK+ +NK RI+ILG AGK+T+L Sbjct: 3 SILLKL---LGLNKEMRILILGLDNAGKTTIL 31 >gnl|CDD|31389 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]. Length = 1163 Score = 33.8 bits (77), Expect = 0.041 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 7/80 (8%) Query: 128 SQMSGGQRQRVALARCLIRQK----PILLLDEPFAVFDPALRHEILGLLKQVCDERQLTL 183 S +SGG++ ALA QK P +LDE A D A + L+K++ E Q Sbjct: 1065 SLLSGGEKSLTALALLFAIQKYRPAPFYVLDEVDAALDDANVERVARLIKEMSKETQ--F 1122 Query: 184 LMISHNLEDSMQIATRFIVI 203 ++I+H + +M+ A R + + Sbjct: 1123 IVITHR-KGTMEAADRLVGV 1141 >gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]. Length = 219 Score = 33.8 bits (76), Expect = 0.044 Identities = 12/26 (46%), Positives = 19/26 (73%) Query: 27 RIVILGPSGAGKSTLLSLMAGFKYPT 52 +IV+LG G GK+TLL+ + G ++P Sbjct: 7 KIVVLGDGGVGKTTLLNRLVGDEFPE 32 >gnl|CDD|73032 cd03273, ABC_SMC2_euk, Eukaryotic SMC2 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).. Length = 251 Score = 33.3 bits (76), Expect = 0.056 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 8/53 (15%) Query: 128 SQMSGGQRQRVALARCLI------RQKPILLLDEPFAVFDPALRHEILGLLKQ 174 +++SGGQR VAL LI + P+ +LDE A D + I ++K Sbjct: 165 TELSGGQRSLVAL--SLILALLLFKPAPMYILDEVDAALDLSHTQNIGRMIKT 215 >gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. Length = 161 Score = 32.9 bits (76), Expect = 0.074 Identities = 10/20 (50%), Positives = 13/20 (65%) Query: 28 IVILGPSGAGKSTLLSLMAG 47 V+ G SG GKSTLL+ + Sbjct: 38 SVLAGQSGVGKSTLLNALLP 57 >gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.. Length = 287 Score = 32.5 bits (74), Expect = 0.093 Identities = 10/24 (41%), Positives = 16/24 (66%) Query: 24 KAERIVILGPSGAGKSTLLSLMAG 47 K + V++G SG GKSTL++ + Sbjct: 160 KGKTSVLVGQSGVGKSTLINALLP 183 >gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer. Length = 203 Score = 32.7 bits (75), Expect = 0.097 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 2/51 (3%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYP-TRGSIFLNGQNHTRSSPSKRPLSILF 77 +++LGPS +GK+ L + + KY T SI N + + Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKYRSTVTSIEPN-VATFILNSEGKGKKFRL 52 >gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction only]. Length = 604 Score = 32.5 bits (74), Expect = 0.100 Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 1/35 (2%) Query: 22 VNKAERIVILGPSGAGKSTLLSLMAGFKYPTRGSI 56 +AE I+I G GAGKST +A F Y ++G I Sbjct: 260 EERAEGILIAGAPGAGKSTFAQALAEF-YASQGKI 293 >gnl|CDD|30631 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 222 Score = 32.5 bits (74), Expect = 0.11 Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%) Query: 28 IVILGPSGAGKSTLLSLMA---GFKYPTRGSIF 57 I I GP+G+GKST+ ++A GF Y G+++ Sbjct: 7 IAIDGPAGSGKSTVAKILAEKLGFHYLDTGAMY 39 >gnl|CDD|33254 COG3451, VirB4, Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]. Length = 796 Score = 32.2 bits (73), Expect = 0.11 Identities = 10/17 (58%), Positives = 14/17 (82%) Query: 30 ILGPSGAGKSTLLSLMA 46 I+GP+GAGK+ LLS + Sbjct: 441 IIGPTGAGKTVLLSFLL 457 >gnl|CDD|33697 COG3910, COG3910, Predicted ATPase [General function prediction only]. Length = 233 Score = 32.2 bits (73), Expect = 0.12 Identities = 50/215 (23%), Positives = 73/215 (33%), Gaps = 57/215 (26%) Query: 24 KAERIVILGPSGAGKSTLL-SLMAGFKYPTRGSIFLNGQNHTRSS-PSKRPLSILFQENN 81 +A I G +G+GKSTLL ++ AG + G G+N S L Sbjct: 36 RAPITFITGENGSGKSTLLEAIAAGMGFNAAG----GGKNFKGELDASHSALV------- 84 Query: 82 LFSHLTVWQNIALGIAPNLRLDHYQHAQ----VKQMLEKVFLE-DFFNRFPSQMSGGQR- 135 L + + A+ V L++ E ++ R MS G+ Sbjct: 85 --------DYAKLHKRKKPPIGFFLRAESFYNVASYLDEADGEANYGGRSLHHMSHGESF 136 Query: 136 QRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQ 195 + R + I +LDEP A P RQL LL I +L DS Sbjct: 137 LAIFHNRF--NGQGIYILDEPEAALSP---------------SRQLELLAILRDLADS-- 177 Query: 196 IATRFIVIAGGQIVYDGDPDRLMNGLIPESTLLGI 230 G QI+ L+ IP + + I Sbjct: 178 ---------GAQIIIATHSPILLA--IPGAEIYEI 201 >gnl|CDD|133364 cd04164, trmE, TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance. Length = 157 Score = 32.1 bits (74), Expect = 0.12 Identities = 10/21 (47%), Positives = 16/21 (76%) Query: 27 RIVILGPSGAGKSTLLSLMAG 47 ++VI+G GKS+LL+ +AG Sbjct: 3 KVVIVGKPNVGKSSLLNALAG 23 >gnl|CDD|39383 KOG4181, KOG4181, KOG4181, Uncharacterized conserved protein [Function unknown]. Length = 491 Score = 32.0 bits (72), Expect = 0.13 Identities = 17/36 (47%), Positives = 20/36 (55%), Gaps = 5/36 (13%) Query: 12 DNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAG 47 L DF V I +LG G+GKSTLLSL+A Sbjct: 180 KLLHKTTDFTV-----IGVLGGQGSGKSTLLSLLAA 210 >gnl|CDD|73296 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.. Length = 147 Score = 32.0 bits (73), Expect = 0.14 Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 3/33 (9%) Query: 27 RIVILGPSGAGKSTLLSLMA---GFKYPTRGSI 56 I I GP+G+GKST+ L+A G Y G I Sbjct: 1 IIAIDGPAGSGKSTVAKLLAKKLGLPYLDTGGI 33 >gnl|CDD|37414 KOG2203, KOG2203, KOG2203, GTP-binding protein [General function prediction only]. Length = 772 Score = 31.9 bits (72), Expect = 0.15 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 5/44 (11%) Query: 4 LDHLIYCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAG 47 LD+ C + V + ++G +GKSTLL+ + G Sbjct: 21 LDYFQQCVGLRDCGLSYHV-----VAVMGSQSSGKSTLLNHLFG 59 >gnl|CDD|39108 KOG3905, KOG3905, KOG3905, Dynein light intermediate chain [Cell motility]. Length = 473 Score = 31.9 bits (72), Expect = 0.15 Identities = 14/53 (26%), Positives = 32/53 (60%), Gaps = 4/53 (7%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPTRGS----IFLNGQNHTRSSPSKRPLSIL 76 +++LG +G+GK++L+S + G + +GS ++L+ + R ++ + IL Sbjct: 55 VLVLGDNGSGKTSLISKLQGSETVKKGSGLEYLYLHVHDEDRDDLTRCNVWIL 107 >gnl|CDD|31351 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 441 Score = 31.7 bits (72), Expect = 0.16 Identities = 13/25 (52%), Positives = 16/25 (64%) Query: 22 VNKAERIVILGPSGAGKSTLLSLMA 46 K +RI I SG GKSTLL ++A Sbjct: 160 CGKGQRIGIFAGSGVGKSTLLGMIA 184 >gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 179 Score = 31.8 bits (72), Expect = 0.17 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 10/52 (19%) Query: 27 RIVILGPSGAGKSTLLSLMA---GFKYPTRGSIFLNGQNHTRSSPSKRPLSI 75 I I G G+GK+T+ +A G K + G+IF R +R +S+ Sbjct: 2 VITISGLPGSGKTTVARELAEHLGLKLVSAGTIF-------REMARERGMSL 46 >gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members. Length = 268 Score = 31.8 bits (73), Expect = 0.17 Identities = 8/15 (53%), Positives = 12/15 (80%) Query: 28 IVILGPSGAGKSTLL 42 I ++G SG+GK+TL Sbjct: 2 IALVGHSGSGKTTLA 16 >gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and metabolism]. Length = 191 Score = 31.3 bits (71), Expect = 0.21 Identities = 13/23 (56%), Positives = 16/23 (69%), Gaps = 1/23 (4%) Query: 28 IVILGPSGAGKSTLLS-LMAGFK 49 IV+ GPSG GKSTL+ L+ K Sbjct: 7 IVLSGPSGVGKSTLVKALLEDDK 29 >gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only]. Length = 454 Score = 31.3 bits (71), Expect = 0.26 Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 5/45 (11%) Query: 3 KLDHLIYCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAG 47 +LD L+ K+ + + ++VI+G GKS+LL+ + G Sbjct: 200 ELDELLATAKQGKI-----LREGLKVVIIGRPNVGKSSLLNALLG 239 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 31.0 bits (70), Expect = 0.27 Identities = 10/19 (52%), Positives = 14/19 (73%) Query: 29 VILGPSGAGKSTLLSLMAG 47 V+LG SG GKSTL++ + Sbjct: 168 VLLGQSGVGKSTLINALLP 186 >gnl|CDD|35502 KOG0281, KOG0281, KOG0281, Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown]. Length = 499 Score = 31.1 bits (70), Expect = 0.29 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 6/77 (7%) Query: 58 LNGQNHTRSSPSKRPLSILFQENN--LFSHLTVW-QNIALGIAPNL--RLDHYQHAQVKQ 112 NG + RP S +Q+ + W ++ + +L R+ HYQH + Sbjct: 6 DNGTSSV-IVVRDRPSSCSYQKEKELCIKYFPQWSESDQVDFVEHLISRMCHYQHGHINN 64 Query: 113 MLEKVFLEDFFNRFPSQ 129 L+ + DF P Q Sbjct: 65 YLKPMLQRDFITALPEQ 81 >gnl|CDD|35471 KOG0250, KOG0250, KOG0250, DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]. Length = 1074 Score = 30.7 bits (69), Expect = 0.35 Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 5/37 (13%) Query: 10 CYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMA 46 C+ NL ++F +VN I+G +G+GKS +L+ + Sbjct: 52 CHSNLLIEFGPRVN-----FIVGNNGSGKSAILTALT 83 >gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213 Score = 30.5 bits (70), Expect = 0.44 Identities = 11/20 (55%), Positives = 14/20 (70%) Query: 27 RIVILGPSGAGKSTLLSLMA 46 RI I G SG GK+ LL ++A Sbjct: 17 RIGIFGGSGTGKTVLLGMIA 36 >gnl|CDD|133365 cd04165, GTPBP1_like, GTPBP1-like. Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and survival. This fusion product may contribute to the onset of GBM. Length = 224 Score = 30.3 bits (69), Expect = 0.46 Identities = 9/17 (52%), Positives = 12/17 (70%) Query: 27 RIVILGPSGAGKSTLLS 43 R+ ++G AGKSTLL Sbjct: 1 RVAVVGNVDAGKSTLLG 17 >gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning]. Length = 1174 Score = 30.3 bits (68), Expect = 0.48 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 8/53 (15%) Query: 128 SQMSGGQRQRVALARCLI------RQKPILLLDEPFAVFDPALRHEILGLLKQ 174 S++SGGQR VAL LI + P+ +LDE A D + I ++K Sbjct: 1081 SELSGGQRSLVAL--SLILAMLKFKPAPLYILDEVDAALDLSHTQNIGRMIKT 1131 >gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function. Length = 178 Score = 29.9 bits (68), Expect = 0.59 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 22 VNKAERIVILGPSGAGKSTL 41 + +AE +++LGP G GK+ L Sbjct: 44 IEQAENLLLLGPPGVGKTHL 63 >gnl|CDD|33504 COG3709, COG3709, Uncharacterized component of phosphonate metabolism [Inorganic ion transport and metabolism]. Length = 192 Score = 29.9 bits (67), Expect = 0.63 Identities = 11/16 (68%), Positives = 13/16 (81%) Query: 28 IVILGPSGAGKSTLLS 43 I ++GPSGAGK TLL Sbjct: 8 IAVVGPSGAGKDTLLD 23 >gnl|CDD|144080 pfam00350, Dynamin_N, Dynamin family. Length = 168 Score = 29.9 bits (68), Expect = 0.64 Identities = 10/29 (34%), Positives = 16/29 (55%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPTRGSI 56 I ++G AGKS++L+ + G RG Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDILPRGPG 29 >gnl|CDD|107274 cd06279, PBP1_LacI_like_3, Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Length = 283 Score = 29.9 bits (68), Expect = 0.64 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 13/72 (18%) Query: 151 LLLDE--PFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATR------FIV 202 ++L + +A DP + L + +V D + LL++ + EDS FIV Sbjct: 4 VVLTDSLSYAFSDPVAS-QFLAGVAEVLDAAGVNLLLLPASSEDSDSALVVSALVDGFIV 62 Query: 203 IAGGQIVYDGDP 214 V DP Sbjct: 63 YG----VPRDDP 70 >gnl|CDD|147025 pfam04665, Pox_A32, Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging. Length = 241 Score = 29.7 bits (67), Expect = 0.65 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 9/51 (17%) Query: 9 YCYDNLKMQFDFQVNKAERIVILGPSGAGKST-LLSLMAGFKYPTRGSIFL 58 + D+L R+ I+G SG+GK+T LLSL+ + IFL Sbjct: 4 FDRDSLL-------AAPFRMAIVGGSGSGKTTYLLSLLRTLVRKFK-HIFL 46 >gnl|CDD|144489 pfam00910, RNA_helicase, RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses. Length = 105 Score = 29.9 bits (68), Expect = 0.65 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 5/35 (14%) Query: 28 IVILGPSGAGKSTL-----LSLMAGFKYPTRGSIF 57 I + GP G GKSTL +L+ P + S++ Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLDHLGLPKKDSVY 35 >gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Length = 267 Score = 29.6 bits (67), Expect = 0.65 Identities = 11/20 (55%), Positives = 14/20 (70%) Query: 24 KAERIVILGPSGAGKSTLLS 43 +A R+ I G GAGKSTL+ Sbjct: 28 RAHRVGITGVPGAGKSTLIE 47 >gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General function prediction only]. Length = 398 Score = 29.5 bits (66), Expect = 0.74 Identities = 9/24 (37%), Positives = 16/24 (66%) Query: 23 NKAERIVILGPSGAGKSTLLSLMA 46 K ++++GP +GKSTL + +A Sbjct: 71 GKVGVVMVVGPVDSGKSTLTTYLA 94 >gnl|CDD|133358 cd04158, ARD1, ARD1 subfamily. ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization. Length = 169 Score = 29.5 bits (66), Expect = 0.77 Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 4/32 (12%) Query: 27 RIVILGPSGAGKSTLLSLMAGFKY----PTRG 54 R+V LG GAGK+T+L + ++ PT G Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIG 32 >gnl|CDD|35962 KOG0743, KOG0743, KOG0743, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 457 Score = 29.5 bits (66), Expect = 0.78 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 32 GPSGAGKSTLLSLMAGF 48 GP G GKS+ ++ MA + Sbjct: 242 GPPGTGKSSFIAAMANY 258 >gnl|CDD|133313 cd04113, Rab4, Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 161 Score = 29.5 bits (67), Expect = 0.80 Identities = 9/16 (56%), Positives = 12/16 (75%) Query: 27 RIVILGPSGAGKSTLL 42 + +I+G SG GKS LL Sbjct: 2 KFIIIGSSGTGKSCLL 17 >gnl|CDD|73035 cd03276, ABC_SMC6_euk, Eukaryotic SMC6 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).. Length = 198 Score = 29.4 bits (66), Expect = 0.81 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 21/87 (24%) Query: 10 CYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLS-LMAGF----KYPTRGS----IFLNG 60 C+ +L+++F +VN I+G +G+GKS +L+ L G RGS + +G Sbjct: 11 CHRHLQIEFGPRVN-----FIVGNNGSGKSAILTALTIGLGGKASDTNRGSSLKDLIKDG 65 Query: 61 QNHTR-------SSPSKRPLSILFQEN 80 ++ + PL +L Q+ Sbjct: 66 ESSAKITVTLKNQGLDANPLCVLSQDM 92 >gnl|CDD|33731 COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]. Length = 440 Score = 29.6 bits (66), Expect = 0.82 Identities = 10/26 (38%), Positives = 18/26 (69%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLL 42 D ++E +I+GP+G+GK+T+L Sbjct: 16 NLDITFGESETTIIVGPNGSGKTTVL 41 >gnl|CDD|144280 pfam00625, Guanylate_kin, Guanylate kinase. Length = 182 Score = 29.6 bits (67), Expect = 0.84 Identities = 9/16 (56%), Positives = 11/16 (68%) Query: 28 IVILGPSGAGKSTLLS 43 IV+ GPSG GKS + Sbjct: 4 IVLSGPSGVGKSHIKK 19 >gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]. Length = 323 Score = 29.5 bits (66), Expect = 0.89 Identities = 11/20 (55%), Positives = 12/20 (60%) Query: 24 KAERIVILGPSGAGKSTLLS 43 A I I G GAGKSTL+ Sbjct: 50 NAHVIGITGVPGAGKSTLIE 69 >gnl|CDD|30189 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.. Length = 194 Score = 29.4 bits (66), Expect = 0.92 Identities = 10/20 (50%), Positives = 14/20 (70%) Query: 27 RIVILGPSGAGKSTLLSLMA 46 RI++LGP G+GK T +A Sbjct: 1 RILLLGPPGSGKGTQAERLA 20 >gnl|CDD|133255 cd00879, Sar1, Sar1 subfamily. Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation. Length = 190 Score = 29.1 bits (66), Expect = 1.1 Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%) Query: 11 YDNLKMQFDFQVNKAERIVILGPSGAGKSTLL 42 Y+ L + NK +I+ LG AGK+TLL Sbjct: 7 YNVLSSLGLY--NKEAKILFLGLDNAGKTTLL 36 >gnl|CDD|145545 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162 Score = 29.2 bits (65), Expect = 1.1 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 11/80 (13%) Query: 128 SQMSGGQRQRVALARCLI------RQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQL 181 +SGG++ VALA LI R P LLDE A D + LK++ Q Sbjct: 1077 DNLSGGEKTLVALA--LIFAIQKYRPAPFYLLDEIDAALDDQNVSRVANYLKELSKNAQ- 1133 Query: 182 TLLMISHNLEDSMQIATRFI 201 ++IS E+ ++ A R + Sbjct: 1134 -FIVISLR-EEMLEKADRLV 1151 >gnl|CDD|35926 KOG0707, KOG0707, KOG0707, Guanylate kinase [Nucleotide transport and metabolism]. Length = 231 Score = 29.2 bits (65), Expect = 1.1 Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 4/41 (9%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSP 68 IV+ GPSG GKSTLL + + G +F +HT +P Sbjct: 40 IVLSGPSGVGKSTLLKRL--REEL--GGMFGFSVSHTTRTP 76 >gnl|CDD|37181 KOG1970, KOG1970, KOG1970, Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Energy production and conversion, Replication, recombination and repair]. Length = 634 Score = 28.9 bits (64), Expect = 1.2 Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%) Query: 17 QFDFQVNKAERIVIL--GPSGAGKSTLLSLMA 46 Q K ++L GPSG GKST + +++ Sbjct: 100 QVAEFTPKLGSRILLLTGPSGCGKSTTVKVLS 131 >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 = 29.0 bits (65), Expect = 1.2 Identities = 10/20 (50%), Positives = 15/20 (75%) Query: 27 RIVILGPSGAGKSTLLSLMA 46 IV++G GAGK+T+ L+A Sbjct: 1 NIVLIGMMGAGKTTVGRLLA 20 >gnl|CDD|34613 COG5008, PilU, Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 375 Score = 28.8 bits (64), Expect = 1.3 Identities = 11/31 (35%), Positives = 21/31 (67%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMAGFK 49 D + K ++I+G +G+GKST ++ M G++ Sbjct: 121 DLALAKRGLVIIVGATGSGKSTTMAAMIGYR 151 >gnl|CDD|133250 cd00154, Rab, Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible. Length = 159 Score = 29.0 bits (66), Expect = 1.3 Identities = 9/17 (52%), Positives = 14/17 (82%) Query: 27 RIVILGPSGAGKSTLLS 43 +IV++G SG GK++LL Sbjct: 2 KIVLIGDSGVGKTSLLL 18 >gnl|CDD|30191 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.. Length = 193 Score = 28.7 bits (64), Expect = 1.3 Identities = 11/20 (55%), Positives = 13/20 (65%) Query: 27 RIVILGPSGAGKSTLLSLMA 46 IV+ G GAGKSTL +A Sbjct: 1 VIVVEGNIGAGKSTLAKELA 20 >gnl|CDD|35668 KOG0447, KOG0447, KOG0447, Dynamin-like GTP binding protein [General function prediction only]. Length = 980 Score = 28.9 bits (64), Expect = 1.3 Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 5/48 (10%) Query: 27 RIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLS 74 R+V++G AGK+++L ++A + RGS G+ TR SP K LS Sbjct: 310 RVVVVGDQSAGKTSVLEMIAQARIFPRGS----GEMMTR-SPVKVTLS 352 >gnl|CDD|147760 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo. Length = 490 Score = 28.7 bits (64), Expect = 1.3 Identities = 10/28 (35%), Positives = 21/28 (75%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPTRGS 55 +++LG G+GK+TL++ + G ++P +G Sbjct: 48 VLVLGEDGSGKTTLIAKLQGVEHPKKGR 75 >gnl|CDD|133293 cd01893, Miro1, Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 166 Score = 28.8 bits (65), Expect = 1.4 Identities = 10/26 (38%), Positives = 17/26 (65%) Query: 27 RIVILGPSGAGKSTLLSLMAGFKYPT 52 RIV++G G GKS+L+ + ++P Sbjct: 2 RIVLIGDEGVGKSSLIMSLVSEEFPE 27 >gnl|CDD|30194 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.. Length = 150 Score = 28.7 bits (64), Expect = 1.4 Identities = 10/19 (52%), Positives = 15/19 (78%) Query: 28 IVILGPSGAGKSTLLSLMA 46 IV++G SG+GKST+ +A Sbjct: 2 IVVMGVSGSGKSTVGKALA 20 >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 = 28.7 bits (65), Expect = 1.4 Identities = 11/16 (68%), Positives = 14/16 (87%) Query: 27 RIVILGPSGAGKSTLL 42 RI+ILG GAGK+T+L Sbjct: 1 RILILGLDGAGKTTIL 16 >gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]. Length = 531 Score = 28.8 bits (64), Expect = 1.4 Identities = 8/19 (42%), Positives = 13/19 (68%) Query: 28 IVILGPSGAGKSTLLSLMA 46 I I+G GKS+LL+ ++ Sbjct: 271 IAIVGRPNVGKSSLLNALS 289 >gnl|CDD|133271 cd01868, Rab11_like, Rab11-like. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 165 Score = 28.7 bits (65), Expect = 1.5 Identities = 11/17 (64%), Positives = 14/17 (82%) Query: 27 RIVILGPSGAGKSTLLS 43 +IV++G SG GKS LLS Sbjct: 5 KIVLIGDSGVGKSNLLS 21 >gnl|CDD|29620 cd01573, modD_like, ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.. Length = 272 Score = 28.7 bits (64), Expect = 1.6 Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 6/52 (11%) Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTL 183 G R+ L+ + IL+ E A + L L+ E+++ + Sbjct: 143 GAVPHRLGLS------ETILVFAEHRAFLGGPEPLKALARLRATAPEKKIVV 188 >gnl|CDD|31617 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport and metabolism]. Length = 216 Score = 28.7 bits (64), Expect = 1.6 Identities = 14/25 (56%), Positives = 16/25 (64%) Query: 22 VNKAERIVILGPSGAGKSTLLSLMA 46 +N A IVI G GAGKSTL +A Sbjct: 1 MNVAMVIVIEGMIGAGKSTLAQALA 25 >gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. Length = 168 Score = 28.3 bits (64), Expect = 1.6 Identities = 10/16 (62%), Positives = 12/16 (75%) Query: 27 RIVILGPSGAGKSTLL 42 RI I GP G GK+TL+ Sbjct: 1 RIFITGPPGVGKTTLV 16 >gnl|CDD|73295 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.. Length = 69 Score = 28.4 bits (63), Expect = 1.7 Identities = 10/20 (50%), Positives = 13/20 (65%) Query: 27 RIVILGPSGAGKSTLLSLMA 46 I I G SG+GKST+ +A Sbjct: 1 IIAITGGSGSGKSTVAKKLA 20 >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 = 28.3 bits (63), Expect = 1.7 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 28 IVILGPSGAGKSTLLSLMA 46 IV G GAGK+TL+ L+A Sbjct: 3 IVFEGIDGAGKTTLIELLA 21 >gnl|CDD|133302 cd04102, RabL3, RabL3 (Rab-like3) subfamily. RabL3s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown. Length = 202 Score = 28.6 bits (64), Expect = 1.7 Identities = 9/20 (45%), Positives = 16/20 (80%) Query: 27 RIVILGPSGAGKSTLLSLMA 46 R++++G SG GKS+L+ L+ Sbjct: 2 RVLVVGDSGVGKSSLVHLIC 21 >gnl|CDD|34791 COG5192, BMS1, GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]. Length = 1077 Score = 28.2 bits (62), Expect = 1.8 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENNLFSHLT 87 + ++GP G GKSTL+ + + T+ +I T S R ++ L ++L + Sbjct: 72 VAVVGPPGTGKSTLIRSLV--RRFTKQTIDEIRGPITVVSGKTRRITFLECPSDLHQMID 129 Query: 88 V 88 V Sbjct: 130 V 130 >gnl|CDD|29996 cd01130, VirB11-like_ATPase, Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.. Length = 186 Score = 28.3 bits (63), Expect = 1.8 Identities = 10/21 (47%), Positives = 16/21 (76%) Query: 28 IVILGPSGAGKSTLLSLMAGF 48 I+I G +G+GK+TLL+ + F Sbjct: 28 ILISGGTGSGKTTLLNALLAF 48 >gnl|CDD|36598 KOG1384, KOG1384, KOG1384, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]. Length = 348 Score = 28.4 bits (63), Expect = 1.9 Identities = 10/18 (55%), Positives = 14/18 (77%) Query: 24 KAERIVILGPSGAGKSTL 41 K + +VI+G +GAGKS L Sbjct: 6 KDKVVVIMGATGAGKSRL 23 >gnl|CDD|72998 cd03239, ABC_SMC_head, The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.. Length = 178 Score = 28.3 bits (63), Expect = 2.0 Identities = 36/173 (20%), Positives = 63/173 (36%), Gaps = 49/173 (28%) Query: 29 VILGPSGAGKSTLL-SLMAGFKYPT----RGSIFLNGQNHTRSSPSKRPLSILFQENNLF 83 I+GP+G+GKS ++ ++ RGS+ ++ + + I F ++ Sbjct: 26 AIVGPNGSGKSNIVDAICFVLGGKAAKLRRGSLLFLAGGGVKAGINSASVEITFDKSYFL 85 Query: 84 SHLTVWQNIALGIAPNLRLDHYQHAQVKQMLEKVFLEDFFNRFPSQMSGGQRQRVALARC 143 V Q +V+Q+L SGG++ ALA Sbjct: 86 ----VLQ-----------------GKVEQIL----------------SGGEKSLSALALI 108 Query: 144 L----IRQKPILLLDEPFAVFDPALRHEILGLLK-QVCDERQLTLLMISHNLE 191 I+ P +LDE A DP R + ++K Q ++I+ E Sbjct: 109 FALQEIKPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQ--FIVITLKKE 159 >gnl|CDD|36760 KOG1547, KOG1547, KOG1547, Septin CDC10 and related P-loop GTPases [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms, Cytoskeleton]. Length = 336 Score = 28.0 bits (62), Expect = 2.0 Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 6/30 (20%) Query: 14 LKMQFDFQVNKAERIVILGPSGAGKSTLLS 43 +K FDF I+++G SG GKSTL++ Sbjct: 41 MKTGFDFN------IMVVGQSGLGKSTLIN 64 >gnl|CDD|133351 cd04151, Arl1, Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability. Length = 158 Score = 28.1 bits (63), Expect = 2.1 Identities = 10/16 (62%), Positives = 13/16 (81%) Query: 27 RIVILGPSGAGKSTLL 42 RI+ILG AGK+T+L Sbjct: 1 RILILGLDNAGKTTIL 16 >gnl|CDD|29833 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.. Length = 149 Score = 28.3 bits (63), Expect = 2.1 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 28 IVILGPSGAGKSTL 41 ++I GPSG GKS L Sbjct: 17 VLITGPSGIGKSEL 30 >gnl|CDD|35296 KOG0073, KOG0073, KOG0073, GTP-binding ADP-ribosylation factor-like protein ARL2 [Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton]. Length = 185 Score = 27.9 bits (62), Expect = 2.2 Identities = 8/16 (50%), Positives = 13/16 (81%) Query: 27 RIVILGPSGAGKSTLL 42 RI+ILG +GK+T++ Sbjct: 18 RILILGLDNSGKTTIV 33 >gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]. Length = 254 Score = 28.0 bits (62), Expect = 2.2 Identities = 9/30 (30%), Positives = 14/30 (46%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMA 46 + E +V+LGP G GK+ L + Sbjct: 97 SLVEFFERGENLVLLGPPGVGKTHLAIAIG 126 >gnl|CDD|111395 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans. Length = 174 Score = 28.0 bits (63), Expect = 2.3 Identities = 8/16 (50%), Positives = 11/16 (68%) Query: 27 RIVILGPSGAGKSTLL 42 V+ G G+GK+TLL Sbjct: 2 VTVLTGFLGSGKTTLL 17 >gnl|CDD|35194 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal transduction mechanisms]. Length = 824 Score = 28.1 bits (62), Expect = 2.3 Identities = 10/23 (43%), Positives = 16/23 (69%) Query: 24 KAERIVILGPSGAGKSTLLSLMA 46 K +++ILG G+GK+T L +A Sbjct: 221 KYAKLLILGAPGSGKTTFLQRLA 243 >gnl|CDD|34569 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]. Length = 355 Score = 28.0 bits (62), Expect = 2.4 Identities = 11/26 (42%), Positives = 18/26 (69%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPTR 53 I+I G +G+GK+TLL+ ++GF Sbjct: 176 ILISGGTGSGKTTLLNALSGFIDSDE 201 >gnl|CDD|73043 cd03284, ABC_MutS1, MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 216 Score = 27.9 bits (62), Expect = 2.4 Identities = 12/35 (34%), Positives = 23/35 (65%), Gaps = 7/35 (20%) Query: 19 DFQVNKAERIVIL-GPSGAGKST------LLSLMA 46 D +++ +I+++ GP+ AGKST L++L+A Sbjct: 23 DTELDPERQILLITGPNMAGKSTYLRQVALIALLA 57 >gnl|CDD|133261 cd01852, AIG1, AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins). Length = 196 Score = 27.9 bits (63), Expect = 2.6 Identities = 8/14 (57%), Positives = 12/14 (85%) Query: 27 RIVILGPSGAGKST 40 R+V++G +GAGKS Sbjct: 2 RLVLVGKTGAGKSA 15 >gnl|CDD|133348 cd04148, RGK, RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ras superfamily members. The N-terminal extension is not conserved among family members; the C-terminal extension is reported to be conserved among the family and lack the CaaX prenylation motif typical of membrane-associated Ras proteins. However, a putative CaaX motif has been identified in the alignment of the C-terminal residues of this CD. Length = 221 Score = 27.7 bits (62), Expect = 2.6 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 27 RIVILGPSGAGKSTLLSLMAG 47 R+V+LG G GKS+L S Sbjct: 2 RVVMLGSPGVGKSSLASQFTS 22 >gnl|CDD|146043 pfam03215, Rad17, Rad17 cell cycle checkpoint protein. Length = 490 Score = 27.7 bits (61), Expect = 2.6 Identities = 11/32 (34%), Positives = 21/32 (65%), Gaps = 1/32 (3%) Query: 16 MQFDFQVNKAERIVIL-GPSGAGKSTLLSLMA 46 ++ F + + I++L GPSG GKST + +++ Sbjct: 35 LKAVFLESNKQLILLLTGPSGCGKSTTVKVLS 66 >gnl|CDD|133282 cd01882, BMS1, Bms1. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes. Length = 225 Score = 27.6 bits (62), Expect = 2.6 Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 4/30 (13%) Query: 28 IVILGPSGAGKSTLL-SLMAGFKYPTRGSI 56 + ++GP G GK+TL+ SL+ K T+ +I Sbjct: 42 VAVVGPPGVGKTTLIKSLV---KNYTKQNI 68 >gnl|CDD|30084 cd00124, MYSc, Myosin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.. Length = 679 Score = 27.9 bits (62), Expect = 2.7 Identities = 9/38 (23%), Positives = 19/38 (50%) Query: 8 IYCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLM 45 ++ + + + + + I+I G SGAGK+ L+ Sbjct: 69 VFAIADRAYRNMLRDRRNQSIIISGESGAGKTENTKLI 106 >gnl|CDD|33698 COG3911, COG3911, Predicted ATPase [General function prediction only]. Length = 183 Score = 27.7 bits (61), Expect = 2.7 Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 2/31 (6%) Query: 16 MQFDFQVNKAERIVILGPSGAGKSTLLSLMA 46 F N+ +R ++ G GAGK+TLL+ +A Sbjct: 2 RVRPF--NRHKRFILTGGPGAGKTTLLAALA 30 >gnl|CDD|143853 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices. Length = 162 Score = 27.9 bits (63), Expect = 2.8 Identities = 8/16 (50%), Positives = 13/16 (81%) Query: 27 RIVILGPSGAGKSTLL 42 ++V++G G GKS+LL Sbjct: 1 KLVLVGDGGVGKSSLL 16 >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 = 2.8 Identities = 9/20 (45%), Positives = 14/20 (70%) Query: 23 NKAERIVILGPSGAGKSTLL 42 K RI+++G AGK+T+L Sbjct: 15 KKEMRILMVGLDAAGKTTIL 34 >gnl|CDD|133296 cd01896, DRG, The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding. Length = 233 Score = 27.9 bits (63), Expect = 2.8 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 27 RIVILGPSGAGKSTLLSLMAG 47 R+ ++G GKSTLLS + Sbjct: 2 RVALVGFPSVGKSTLLSKLTN 22 >gnl|CDD|35310 KOG0087, KOG0087, KOG0087, GTPase Rab11/YPT3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 222 Score = 27.6 bits (61), Expect = 3.0 Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 2/46 (4%) Query: 27 RIVILGPSGAGKSTLLS--LMAGFKYPTRGSIFLNGQNHTRSSPSK 70 +IV++G S GKS LLS F ++ +I + T + K Sbjct: 16 KIVLIGDSAVGKSNLLSRFTRNEFSLESKSTIGVEFATRTVNVDGK 61 >gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]. Length = 625 Score = 27.6 bits (61), Expect = 3.0 Identities = 8/26 (30%), Positives = 16/26 (61%) Query: 27 RIVILGPSGAGKSTLLSLMAGFKYPT 52 RIV++G G GK++L+ + ++ Sbjct: 11 RIVLIGDEGVGKTSLIMSLLEEEFVD 36 Score = 26.9 bits (59), Expect = 5.1 Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 4/36 (11%) Query: 19 DFQVNKAERIV----ILGPSGAGKSTLLSLMAGFKY 50 D + + +R V ++GP GKS LL G Sbjct: 415 DRKKKQTDRKVFQCFVVGPKNCGKSALLQSFLGRSM 450 >gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]. Length = 845 Score = 27.6 bits (61), Expect = 3.1 Identities = 7/21 (33%), Positives = 16/21 (76%) Query: 22 VNKAERIVILGPSGAGKSTLL 42 + + + ++I+G +G+GK+T L Sbjct: 62 IEQNQVVIIVGETGSGKTTQL 82 >gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop. Length = 122 Score = 27.7 bits (62), Expect = 3.2 Identities = 6/20 (30%), Positives = 14/20 (70%) Query: 27 RIVILGPSGAGKSTLLSLMA 46 ++++GP +GK+TL+ + Sbjct: 2 IVLVVGPKDSGKTTLIRKLL 21 >gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction only]. Length = 200 Score = 27.5 bits (61), Expect = 3.3 Identities = 10/28 (35%), Positives = 14/28 (50%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPTRGS 55 I G S GKS+L++ + K R S Sbjct: 27 IAFAGRSNVGKSSLINALTNQKNLARTS 54 >gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and secretion]. Length = 407 Score = 27.6 bits (61), Expect = 3.3 Identities = 9/21 (42%), Positives = 15/21 (71%) Query: 28 IVILGPSGAGKSTLLSLMAGF 48 I ++GP+G GK+T L+ +A Sbjct: 206 IALVGPTGVGKTTTLAKLAAR 226 >gnl|CDD|34333 COG4717, COG4717, Uncharacterized conserved protein [Function unknown]. Length = 984 Score = 27.3 bits (60), Expect = 3.5 Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%) Query: 20 FQVNKAERIVILGPSGAGKSTLLSLMAG--FKYPTRGSI 56 F +++ VI G + AGKSTL S + F +PT Sbjct: 19 FDFGESKFQVIYGENEAGKSTLFSFIHSMLFGFPTSSKY 57 >gnl|CDD|143847 pfam00063, Myosin_head, Myosin head (motor domain). Length = 679 Score = 27.3 bits (61), Expect = 3.5 Identities = 9/21 (42%), Positives = 12/21 (57%) Query: 28 IVILGPSGAGKSTLLSLMAGF 48 IVI G SGAGK+ + + Sbjct: 88 IVISGESGAGKTENTKKLMQY 108 >gnl|CDD|38564 KOG3354, KOG3354, KOG3354, Gluconate kinase [Carbohydrate transport and metabolism]. Length = 191 Score = 27.3 bits (60), Expect = 3.5 Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 3/26 (11%) Query: 28 IVILGPSGAGKSTLLSLMA---GFKY 50 IV++G SG+GKST+ ++ G K+ Sbjct: 15 IVVMGVSGSGKSTIGKALSEELGLKF 40 >gnl|CDD|31564 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]. Length = 398 Score = 27.3 bits (60), Expect = 3.5 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 28 IVILGPSGAGKSTLLSLMA 46 I+ILGP GK+TLL L+ Sbjct: 40 ILILGPRQVGKTTLLKLLI 58 >gnl|CDD|32119 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]. Length = 180 Score = 27.5 bits (61), Expect = 3.6 Identities = 9/25 (36%), Positives = 12/25 (48%) Query: 27 RIVILGPSGAGKSTLLSLMAGFKYP 51 I I G G GK+T+ L+ Y Sbjct: 2 LIAITGTPGVGKTTVCKLLRELGYK 26 >gnl|CDD|133265 cd01862, Rab7, Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 172 Score = 27.2 bits (61), Expect = 3.8 Identities = 8/16 (50%), Positives = 14/16 (87%) Query: 27 RIVILGPSGAGKSTLL 42 +++ILG SG GK++L+ Sbjct: 2 KVIILGDSGVGKTSLM 17 >gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and metabolism]. Length = 208 Score = 27.2 bits (60), Expect = 3.8 Identities = 10/19 (52%), Positives = 12/19 (63%) Query: 28 IVILGPSGAGKSTLLSLMA 46 IVI G GAGK+T L+ Sbjct: 6 IVIEGIDGAGKTTQAELLK 24 >gnl|CDD|73001 cd03242, ABC_RecF, RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including 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 with 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 = 270 Score = 27.1 bits (60), Expect = 4.1 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 19/81 (23%) Query: 131 SGGQRQRVALA---------RCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQL 181 S GQ++ +ALA + + + P+LLLD+ A D + +L + + R Sbjct: 185 SQGQQRTLALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALLDAI----EGRVQ 240 Query: 182 TLL------MISHNLEDSMQI 196 T + QI Sbjct: 241 TFVTTTDLADFDALWLRRAQI 261 >gnl|CDD|39063 KOG3859, KOG3859, KOG3859, Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning]. Length = 406 Score = 27.3 bits (60), Expect = 4.3 Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 15/91 (16%) Query: 11 YDNLKMQFDFQVNKAER------IVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHT 64 +D+L Q VNK+ I+ +G +G GKSTL+ + K+ + S HT Sbjct: 25 FDSLPDQL---VNKSVSQGFCFNILCVGETGLGKSTLMDTLFNTKFESEPS------THT 75 Query: 65 RSSPSKRPLSILFQENNLFSHLTVWQNIALG 95 + + + QE+N+ LT+ + G Sbjct: 76 LPNVKLQANTYELQESNVRLKLTIVDTVGFG 106 >gnl|CDD|100271 CHL00171, cpcB, phycocyanin beta subunit; Reviewed. Length = 172 Score = 26.9 bits (59), Expect = 4.4 Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 6/41 (14%) Query: 194 MQIATRFI---VIAGGQIVYDGDPDRLMNGLIPESTLLGIP 231 M+I R++ +IAG V D DR +NGL LG+P Sbjct: 86 MEIVLRYVSYAMIAGDSSVLD---DRCLNGLRETYQALGVP 123 >gnl|CDD|133258 cd00882, Ras_like_GTPase, Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulate initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions. Length = 157 Score = 27.1 bits (60), Expect = 4.4 Identities = 7/14 (50%), Positives = 12/14 (85%) Query: 30 ILGPSGAGKSTLLS 43 ++G SG GK++LL+ Sbjct: 1 VVGDSGVGKTSLLN 14 >gnl|CDD|31307 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair]. Length = 1187 Score = 27.2 bits (60), Expect = 4.4 Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 6/30 (20%) Query: 25 AERIV------ILGPSGAGKSTLLSLMAGF 48 A+R+V I+ P+G GK+T LM+ + Sbjct: 91 AKRLVRGKSFAIIAPTGVGKTTFGLLMSLY 120 >gnl|CDD|35294 KOG0071, KOG0071, KOG0071, GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport]. Length = 180 Score = 26.9 bits (59), Expect = 4.4 Identities = 11/21 (52%), Positives = 15/21 (71%) Query: 23 NKAERIVILGPSGAGKSTLLS 43 NK RI++LG AGK+T+L Sbjct: 15 NKEMRILMLGLDAAGKTTILY 35 >gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and metabolism]. Length = 172 Score = 27.1 bits (60), Expect = 4.4 Identities = 10/23 (43%), Positives = 15/23 (65%) Query: 24 KAERIVILGPSGAGKSTLLSLMA 46 + IV++G GAGKST+ +A Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALA 23 >gnl|CDD|145008 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family. Length = 223 Score = 26.9 bits (60), Expect = 4.5 Identities = 8/15 (53%), Positives = 10/15 (66%) Query: 28 IVILGPSGAGKSTLL 42 IV+ GP GK+ LL Sbjct: 23 IVVYGPRRCGKTALL 37 >gnl|CDD|37984 KOG2773, KOG2773, KOG2773, Apoptosis antagonizing transcription factor/protein transport protein [Transcription, Intracellular trafficking, secretion, and vesicular transport]. Length = 483 Score = 26.9 bits (59), Expect = 4.7 Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 2/48 (4%) Query: 48 FKYPTRGSIFLNGQNHTRSSPSKRPLSILFQE-NNLFSHLTVWQNIAL 94 KYP I +N + S KR L E N+L L ++N L Sbjct: 258 TKYPNTTKI-VNAKKSFESGKFKRSLKEFSLEINSLDFFLLEYRNKVL 304 >gnl|CDD|30598 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]. Length = 843 Score = 26.8 bits (59), Expect = 4.8 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 7/35 (20%) Query: 19 DFQVNKAERI-VILGPSGAGKST------LLSLMA 46 D ++ RI +I GP+ GKST L+ ++A Sbjct: 600 DIDLSGNRRIILITGPNMGGKSTYLRQVALIVILA 634 >gnl|CDD|147726 pfam05729, NACHT, NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931. Length = 165 Score = 26.9 bits (60), Expect = 4.9 Identities = 7/16 (43%), Positives = 13/16 (81%) Query: 27 RIVILGPSGAGKSTLL 42 +++ G +G+GK+TLL Sbjct: 2 TVILQGEAGSGKTTLL 17 >gnl|CDD|31388 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]. Length = 363 Score = 26.7 bits (59), Expect = 5.0 Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 5/33 (15%) Query: 10 CYDNLKMQFDFQVNKAERIVILGPSGAGKSTLL 42 Y L + VN V++G +G GK+ LL Sbjct: 13 NYAELDLDLSPGVN-----VLVGENGQGKTNLL 40 >gnl|CDD|109493 pfam00437, GSPII_E, Type II/IV secretion system protein. This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection. Length = 283 Score = 26.8 bits (60), Expect = 5.1 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 5/43 (11%) Query: 4 LDHLIYCYDNLKMQFDFQVNKAER----IVILGPSGAGKSTLL 42 LD L + +A + I++ G +G+GK+TLL Sbjct: 115 LDDLGM-TGAFDADIAEFLRQAVQARGNILVSGGTGSGKTTLL 156 >gnl|CDD|114021 pfam05272, VirE, Virulence-associated protein E. This family contains several bacterial virulence-associated protein E like proteins. Length = 198 Score = 27.0 bits (60), Expect = 5.2 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 6/31 (19%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMAG 47 +FD +++ G G+GKST L + G Sbjct: 50 KFDHV------LILQGAQGSGKSTFLKKLGG 74 >gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Length = 163 Score = 26.9 bits (60), Expect = 5.2 Identities = 7/13 (53%), Positives = 10/13 (76%) Query: 30 ILGPSGAGKSTLL 42 + G + AGKS+LL Sbjct: 1 LFGRTNAGKSSLL 13 >gnl|CDD|35104 COG5545, COG5545, Predicted P-loop ATPase and inactivated derivatives [General function prediction only]. Length = 517 Score = 27.0 bits (59), Expect = 5.3 Identities = 10/20 (50%), Positives = 14/20 (70%) Query: 28 IVILGPSGAGKSTLLSLMAG 47 +V+ GP G+ KST LS + G Sbjct: 205 LVLEGPQGSHKSTFLSELFG 224 >gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only]. Length = 365 Score = 26.7 bits (59), Expect = 5.5 Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 2/34 (5%) Query: 18 FDFQVNK--AERIVILGPSGAGKSTLLSLMAGFK 49 F V K + ++G GKSTLL+ + K Sbjct: 54 SGFAVKKSGDATVALVGFPSVGKSTLLNKLTNTK 87 >gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date. Length = 164 Score = 26.6 bits (59), Expect = 5.5 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 28 IVILGPSGAGKSTLLSLMAG 47 I++LG GAGK++LL ++ Sbjct: 2 ILVLGLDGAGKTSLLHSLSS 21 >gnl|CDD|144409 pfam00800, PDT, Prephenate dehydratase. This protein is involved in Phenylalanine biosynthesis. This protein catalyses the decarboxylation of prephenate to phenylpyruvate. Length = 181 Score = 26.7 bits (60), Expect = 5.6 Identities = 7/19 (36%), Positives = 13/19 (68%) Query: 186 ISHNLEDSMQIATRFIVIA 204 ++ N+ED+ TRF+V+ Sbjct: 159 LAENIEDNKNNTTRFLVLG 177 >gnl|CDD|133251 cd00157, Rho, Rho (Ras homology) family. Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho 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 Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy. Length = 171 Score = 26.8 bits (60), Expect = 5.8 Identities = 10/25 (40%), Positives = 14/25 (56%) Query: 28 IVILGPSGAGKSTLLSLMAGFKYPT 52 IV++G GK+ LL K+PT Sbjct: 3 IVVVGDGAVGKTCLLISYTTGKFPT 27 >gnl|CDD|36699 KOG1486, KOG1486, KOG1486, GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]. Length = 364 Score = 26.8 bits (59), Expect = 5.9 Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%) Query: 20 FQVNKA--ERIVILGPSGAGKSTLLSLMAGFK 49 F+V K+ R+ ++G GKSTLLS + Sbjct: 55 FEVLKSGDARVALIGFPSVGKSTLLSKITSTH 86 >gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only]. Length = 298 Score = 26.7 bits (59), Expect = 6.0 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 24 KAERIVILGPSGAGKSTLLSLMAGFK 49 K+ + I+G GKSTLL+ + G K Sbjct: 5 KSGFVAIIGRPNVGKSTLLNALVGQK 30 >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 = 26.4 bits (58), Expect = 6.1 Identities = 34/177 (19%), Positives = 57/177 (32%), Gaps = 28/177 (15%) Query: 24 KAERIVILGPSGAGKSTLLSLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENNLF 83 K E I++ +G GK+T L A G + +L Q Sbjct: 29 KGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTIS--LEEPVVRTARRLLGQYAGKR 86 Query: 84 SHLTVWQNI-----------ALGIAPNLRL-DHYQHAQVKQMLEKVFLEDFFNRFPSQMS 131 HL I L + D + + +LEKV R+ + Sbjct: 87 LHLPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKV-------RYMAVSH 139 Query: 132 GGQRQRVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISH 188 G Q +I I++ DE + + EI+ L+ E + + ++SH Sbjct: 140 GIQ-------HIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHITLVSH 189 >gnl|CDD|144975 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli and the stage III sporulation protein E SpoIIIE which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer. Length = 202 Score = 26.6 bits (59), Expect = 6.4 Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 1/29 (3%) Query: 20 FQVNKAERIVILGPSGAGKST-LLSLMAG 47 + K ++I G +G+GKST L +L+ Sbjct: 33 ADLVKMPHLLIAGATGSGKSTFLNTLILS 61 >gnl|CDD|35299 KOG0076, KOG0076, KOG0076, GTP-binding ADP-ribosylation factor-like protein yARL3 [Intracellular trafficking, secretion, and vesicular transport]. Length = 197 Score = 26.4 bits (58), Expect = 6.6 Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 8/42 (19%) Query: 1 MIKLDHLIYCYDNLKMQFDFQVNKAERIVILGPSGAGKSTLL 42 M L +Y Y K + ++ILG AGK+T L Sbjct: 1 MFTLMSGLYKYMFKKEDYS--------VLILGLDNAGKTTFL 34 >gnl|CDD|133329 cd04129, Rho2, Rho2 subfamily. Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho 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 proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors). Length = 187 Score = 26.3 bits (58), Expect = 6.9 Identities = 9/26 (34%), Positives = 17/26 (65%) Query: 27 RIVILGPSGAGKSTLLSLMAGFKYPT 52 ++VI+G GK++LLS+ ++P Sbjct: 3 KLVIVGDGACGKTSLLSVFTLGEFPE 28 >gnl|CDD|133259 cd01850, CDC_Septin, CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities. Length = 276 Score = 26.3 bits (59), Expect = 6.9 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%) Query: 28 IVILGPSGAGKSTLL-SLMAGFKYPTRGSIFLNGQNHTRSSPSKRPLSILFQENNLFSHL 86 I+++G SG GKST + +L P+ ++ ++ K + + +EN + L Sbjct: 7 IMVVGESGLGKSTFINTLFNTKLIPSDYPPDPAEEHIDKTVEIKSSKAEI-EENGVKLKL 65 Query: 87 TV 88 TV Sbjct: 66 TV 67 >gnl|CDD|35313 KOG0090, KOG0090, KOG0090, Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]. Length = 238 Score = 26.5 bits (58), Expect = 7.0 Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 1/38 (2%) Query: 20 FQVNKAERIVILGPSGAGKSTLLS-LMAGFKYPTRGSI 56 F+ +K ++++G S +GK++L + L+ G T SI Sbjct: 33 FRRSKQNAVLLVGLSDSGKTSLFTQLITGSHRGTVTSI 70 >gnl|CDD|73042 cd03283, ABC_MutS-like, MutS-like homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 199 Score = 26.4 bits (58), Expect = 7.0 Identities = 10/28 (35%), Positives = 15/28 (53%) Query: 19 DFQVNKAERIVILGPSGAGKSTLLSLMA 46 D + K I+I G + +GKST L + Sbjct: 19 DIDMEKKNGILITGSNMSGKSTFLRTIG 46 >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 = 26.3 bits (58), Expect = 7.1 Identities = 9/21 (42%), Positives = 16/21 (76%) Query: 28 IVILGPSGAGKSTLLSLMAGF 48 +++ GP+G+GKST L+ M + Sbjct: 4 VLVTGPTGSGKSTTLAAMIDY 24 >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 = 26.3 bits (58), Expect = 7.1 Identities = 8/19 (42%), Positives = 13/19 (68%) Query: 28 IVILGPSGAGKSTLLSLMA 46 +++ GP G GK+TL +A Sbjct: 22 LLLYGPPGTGKTTLARAIA 40 >gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 160 Score = 26.3 bits (59), Expect = 7.2 Identities = 7/15 (46%), Positives = 11/15 (73%) Query: 27 RIVILGPSGAGKSTL 41 ++V+LG G GKS + Sbjct: 1 KVVVLGAGGVGKSAI 15 >gnl|CDD|144180 pfam00488, MutS_V, MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters. Length = 234 Score = 26.4 bits (59), Expect = 7.3 Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 6/25 (24%) Query: 28 IVILGPSGAGKST------LLSLMA 46 ++I GP+ GKST L+ +MA Sbjct: 45 LLITGPNMGGKSTYLRQVALIVIMA 69 >gnl|CDD|36180 KOG0962, KOG0962, KOG0962, DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]. Length = 1294 Score = 26.4 bits (58), Expect = 7.7 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 11/79 (13%) Query: 131 SGGQRQ------RVALARCLIRQKPILLLDEPFAVFDPALRHEILGLLKQVCDERQ---- 180 S GQ+ R+ALA +L LDEP D + L ++ +ER+ Sbjct: 1185 SAGQKVLASLIIRLALAETFGSNCGVLALDEPTTNLDRENIESLAKALSRIIEERRRQRN 1244 Query: 181 LTLLMISHNLEDSMQIATR 199 L++I+H+ ED +Q+ R Sbjct: 1245 FQLIVITHD-EDFVQLLGR 1262 >gnl|CDD|32636 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 353 Score = 26.4 bits (58), Expect = 7.8 Identities = 10/18 (55%), Positives = 15/18 (83%) Query: 28 IVILGPSGAGKSTLLSLM 45 I++ GP+G+GKST L+ M Sbjct: 128 ILVTGPTGSGKSTTLAAM 145 >gnl|CDD|38288 KOG3078, KOG3078, KOG3078, Adenylate kinase [Nucleotide transport and metabolism]. Length = 235 Score = 26.1 bits (57), Expect = 7.9 Identities = 11/30 (36%), Positives = 14/30 (46%) Query: 17 QFDFQVNKAERIVILGPSGAGKSTLLSLMA 46 FD K R V+LG G+GK T + Sbjct: 7 GFDEDEKKGVRAVLLGAPGSGKGTQAPRLT 36 >gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 379 Score = 26.1 bits (57), Expect = 8.0 Identities = 9/23 (39%), Positives = 13/23 (56%) Query: 27 RIVILGPSGAGKSTLLSLMAGFK 49 + ++G GKSTL + M G K Sbjct: 74 YVAVIGAPNVGKSTLTNQMIGQK 96 >gnl|CDD|133266 cd01863, Rab18, Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 161 Score = 26.1 bits (58), Expect = 8.0 Identities = 9/16 (56%), Positives = 14/16 (87%) Query: 27 RIVILGPSGAGKSTLL 42 +I+++G SG GKS+LL Sbjct: 2 KILLIGDSGVGKSSLL 17 >gnl|CDD|35295 KOG0072, KOG0072, KOG0072, GTP-binding ADP-ribosylation factor-like protein ARL1 [Intracellular trafficking, secretion, and vesicular transport]. Length = 182 Score = 26.1 bits (57), Expect = 8.2 Identities = 11/23 (47%), Positives = 15/23 (65%) Query: 20 FQVNKAERIVILGPSGAGKSTLL 42 + RI+ILG GAGK+T+L Sbjct: 13 QGPEREMRILILGLDGAGKTTIL 35 >gnl|CDD|133356 cd04156, ARLTS1, ARLTS1 subfamily. ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer. Length = 160 Score = 26.2 bits (58), Expect = 8.3 Identities = 9/16 (56%), Positives = 13/16 (81%) Query: 27 RIVILGPSGAGKSTLL 42 ++++LG AGKSTLL Sbjct: 1 QVLLLGLDSAGKSTLL 16 >gnl|CDD|32985 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]. Length = 187 Score = 26.1 bits (57), Expect = 8.5 Identities = 9/22 (40%), Positives = 15/22 (68%) Query: 25 AERIVILGPSGAGKSTLLSLMA 46 + + ILG +GKSTL++ +A Sbjct: 8 VKTVAILGGESSGKSTLVNKLA 29 >gnl|CDD|31805 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide transport and metabolism]. Length = 179 Score = 26.0 bits (57), Expect = 8.5 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 27 RIVILGPSGAGKSTLLSLMAG 47 +I I G G GK+TL+ +A Sbjct: 7 KIFITGRPGVGKTTLVLKIAE 27 >gnl|CDD|31546 COG1355, COG1355, Predicted dioxygenase [General function prediction only]. Length = 279 Score = 26.0 bits (57), Expect = 9.0 Identities = 7/24 (29%), Positives = 14/24 (58%) Query: 23 NKAERIVILGPSGAGKSTLLSLMA 46 + + +VILGP+ G + +S+ Sbjct: 73 GEPDTVVILGPNHTGLGSPVSVSP 96 >gnl|CDD|133292 cd01892, Miro2, Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 169 Score = 26.0 bits (58), Expect = 9.1 Identities = 9/18 (50%), Positives = 11/18 (61%) Query: 30 ILGPSGAGKSTLLSLMAG 47 +LG G+GKS LL G Sbjct: 9 VLGAKGSGKSALLRAFLG 26 >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 = 25.8 bits (56), Expect = 9.6 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 28 IVILGPSGAGKSTLLSLMA 46 IV+ G G GK+TL + +A Sbjct: 2 IVVTGKGGVGKTTLAANLA 20 >gnl|CDD|37960 KOG2749, KOG2749, KOG2749, mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1 [RNA processing and modification]. Length = 415 Score = 26.0 bits (57), Expect = 9.8 Identities = 10/37 (27%), Positives = 23/37 (62%) Query: 12 DNLKMQFDFQVNKAERIVILGPSGAGKSTLLSLMAGF 48 + +MQ + + + R++++GP+ GKSTL ++ + Sbjct: 90 EKRRMQAEEESSYGPRVMVVGPTDVGKSTLCRILLNY 126 >gnl|CDD|133349 cd04149, Arf6, Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection. Length = 168 Score = 25.9 bits (57), Expect = 10.0 Identities = 11/20 (55%), Positives = 15/20 (75%) Query: 23 NKAERIVILGPSGAGKSTLL 42 NK RI++LG AGK+T+L Sbjct: 7 NKEMRILMLGLDAAGKTTIL 26 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 0.325 0.141 0.420 Gapped Lambda K H 0.267 0.0626 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,929,326 Number of extensions: 154202 Number of successful extensions: 1349 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1111 Number of HSP's successfully gapped: 380 Length of query: 234 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 143 Effective length of database: 4,297,318 Effective search space: 614516474 Effective search space used: 614516474 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 56 (25.6 bits)