RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780766|ref|YP_003065179.1| recombination protein F [Candidatus Liberibacter asiaticus str. psy62] (375 letters) >gnl|CDD|31388 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]. Length = 363 Score = 288 bits (739), Expect = 2e-78 Identities = 122/366 (33%), Positives = 189/366 (51%), Gaps = 9/366 (2%) Query: 5 IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADV 64 + + L + FRNYA L L + VG+NG GKTN+LEAI L+ GR R + ++ Sbjct: 1 MYLLSLLLRNFRNYAELDLDLSPGVNVLVGENGQGKTNLLEAIYLLALGRSHRTSRDKEL 60 Query: 65 TRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISW 124 R G+ ARV+ + +++ + R VR IN R + EL HL + Sbjct: 61 IRTGADEAEI-SARVQRKGREGTLGLQISKKGRRRVR---INGTKARKLAELAGHLNVVL 116 Query: 125 LVPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCS 184 P + G +RRRFLD ++F I+P + + ++E+L++ RN LL + D +W Sbjct: 117 FTPEDLGLVKGSPSDRRRFLDWLLFQIEPVYLEALSNYEKLLKQRNALLKQLQGDYAWLD 176 Query: 185 SIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCALK 244 + Q+AELG +I AR E +NAL+ L + Q F SL+ F G D + ++ Sbjct: 177 VWDQQLAELGAEIAAARAEYLNALAPLAEKIHQL--FLPELESLSIFYRGSVDVTAWEIE 234 Query: 245 EEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHA 304 E+Y + L R+ D TL+GPHR DL+ K S G+QK + + + LA Sbjct: 235 EDYLEALAKRRERDLARGYTLVGPHRDDLLFRLNGKPA-ADFASQGQQKTLALALRLAEI 293 Query: 305 RLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDS-LNETAK 363 L+ TG PILLLD++++ LD+ +R AL ++G Q+F+T TD D L+E A+ Sbjct: 294 ELLREETGEYPILLLDDVASELDDGRRAALLDT-IELGVQVFVTTTDLEDIDDNLDENAQ 352 Query: 364 FMRISN 369 + + Sbjct: 353 MFHVED 358 >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 = 147 bits (372), Expect = 6e-36 Identities = 53/167 (31%), Positives = 89/167 (53%), Gaps = 4/167 (2%) Query: 7 IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTR 66 +K L + FRNYA L L F+ T+ VG+N GKTN+LEAIS L+ G+ R + ++ R Sbjct: 1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIR 60 Query: 67 IGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLV 126 G+ + A +E G + + + + R R +N + +R + +L L W Sbjct: 61 WGAEEAKIS-AVLERQGGELALELTIRSGGGRKAR---LNGIKVRRLSDLLGVLNAVWFA 116 Query: 127 PSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLL 173 P + G +RRRFLDR++ ++P + + ++++ +R RN LL Sbjct: 117 PEDLELVKGSPADRRRFLDRLLGQLEPAYAHVLSEYQKALRQRNALL 163 Score = 97.6 bits (243), Expect = 5e-21 Identities = 44/135 (32%), Positives = 67/135 (49%), Gaps = 3/135 (2%) Query: 236 FDQSFCALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVV 295 D+ L+ YA L + +K L GPHR DL+ DK GS G+Q+ + Sbjct: 134 LDRLLGQLEPAYAHVLSEYQKALRQRNALLKGPHRDDLLFFLNDKPAA-DFGSQGQQRTL 192 Query: 296 LVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVF 355 + + LA +LI +G P+LLLD++ A LD ++ AL + Q F+T TD + F Sbjct: 193 ALALKLAEIQLIKEVSGEYPVLLLDDVLAELDLGRQAALLDAIEGRV-QTFVTTTDLADF 251 Query: 356 DSL-NETAKFMRISN 369 D+L A+ R+ Sbjct: 252 DALWLRRAQIFRVDA 266 >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 = 48.4 bits (115), Expect = 3e-06 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 4/79 (5%) Query: 6 KIKFLNISEFRNYA-SLRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRASY 61 +K + I F++YA ++ L F T VG NG GK+NIL+AI F + R Sbjct: 1 YLKRIEIEGFKSYAKTVILPFSPGFTAIVGPNGSGKSNILDAILFVLGERSAKSLRSERL 60 Query: 62 ADVTRIGSPSFFSTFARVE 80 +D+ F A V Sbjct: 61 SDLIHYSKSGAFVNSAEVT 79 >gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]. Length = 908 Score = 41.6 bits (97), Expect = 4e-04 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 4/68 (5%) Query: 6 KIKFLNISEFRNYA--SLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPG--RGFRRASY 61 KI L + FR++ + +FD+ + VG NG GK++IL+AI+F G S Sbjct: 2 KILRLRLKNFRSFKDIDIEKLFDSGIFLIVGPNGAGKSSILDAITFALYGKTPRLGAFSL 61 Query: 62 ADVTRIGS 69 D+ R G Sbjct: 62 DDLIRAGE 69 Score = 35.0 bits (80), Expect = 0.032 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 1/78 (1%) Query: 272 DLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKR 331 ++V + I S GE+ + + + LA + L+ +L LDE LDE++ Sbjct: 801 VVVVYDGGEVRPIKTLSGGERFLASLALRLALSDLLQGRAR-LELLFLDEPFGTLDEERL 859 Query: 332 NALFRIVTDIGSQIFMTG 349 L I+ ++ S Sbjct: 860 EKLAEILEELLSDGRQII 877 >gnl|CDD|31303 COG1106, COG1106, Predicted ATPases [General function prediction only]. Length = 371 Score = 41.2 bits (96), Expect = 5e-04 Identities = 18/45 (40%), Positives = 25/45 (55%) Query: 7 IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLS 51 IK I F+++ L L + I G NG GK+N+LEA+ FL Sbjct: 2 IKSFKIKNFKSFRELELEDFGKINIIYGANGAGKSNLLEALYFLK 46 >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 = 38.1 bits (89), Expect = 0.003 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 4/67 (5%) Query: 7 IKFLNISEFRNYAS-LRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRASYA 62 +K L + F+++A + F T VG NG GK+NI++AI + + R + Sbjct: 1 LKKLELKGFKSFADKTTIPFPPGLTAIVGPNGSGKSNIIDAIRWVLGEQSAKSLRGEKMS 60 Query: 63 DVTRIGS 69 DV GS Sbjct: 61 DVIFAGS 67 >gnl|CDD|31389 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]. Length = 1163 Score = 38.1 bits (88), Expect = 0.004 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%) Query: 5 IKIKFLNISEFRNYAS-LRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRAS 60 + +K + + F+++A + F T VG NG GK+NI++AI F + R + Sbjct: 1 MYLKRIELKGFKSFADPTEINFSPGFTAIVGPNGSGKSNIVDAIRFVLGEQSAKNLRASK 60 Query: 61 YADVTRIGS 69 +D+ GS Sbjct: 61 MSDLIFAGS 69 >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 = 37.9 bits (88), Expect = 0.005 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 5/68 (7%) Query: 7 IKFLNISEFRNYAS-LRLVFDAQHTIFVGDNGVGKTNILEAISF----LSPGRGFRRASY 61 I L+I R++ + F + T+ VG NG GKT I+EA+ + P A Sbjct: 1 IDKLSIRNIRSFHERSEIEFFSPLTLIVGQNGAGKTTIIEALKYALTGELPPNSKGGAHD 60 Query: 62 ADVTRIGS 69 + R G Sbjct: 61 PKLIREGE 68 Score = 31.7 bits (72), Expect = 0.31 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 4/58 (6%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKR-NALFRIVTDIGSQ 344 S GE+ + + I LA A IL LDE + +LDE+ +L I+ + SQ Sbjct: 117 SGGEKVLASLIIRLALAETFG---SNCGILALDEPTTNLDEENIEESLAEIIEERKSQ 171 >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 = 36.7 bits (85), Expect = 0.010 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%) Query: 7 IKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50 IK + I F++Y ++ F +H + VG NG GK+N AI F+ Sbjct: 1 IKQVIIQGFKSYKDQTVIEPFSPKHNVVVGRNGSGKSNFFAAIRFV 46 Score = 27.9 bits (62), Expect = 5.2 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 6/73 (8%) Query: 279 DKAITIAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338 D+ + S G++ +V + + A + AP L DEI A LD R A+ ++ Sbjct: 151 DEQQEMQQLSGGQKSLVALALIFAIQKCDP-----APFYLFDEIDAALDAQYRTAVANMI 205 Query: 339 TDIGSQI-FMTGT 350 ++ F+T T Sbjct: 206 KELSDGAQFITTT 218 >gnl|CDD|33393 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]. Length = 581 Score = 36.1 bits (83), Expect = 0.015 Identities = 13/46 (28%), Positives = 26/46 (56%) Query: 5 IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFL 50 + ++ + I FR L L F+ + +G+N GK+++L+A+ L Sbjct: 1 MHLERVKIKNFRGINRLSLEFEEGLNVLIGENNSGKSSLLDALRLL 46 >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 = 36.1 bits (83), Expect = 0.016 Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 2/48 (4%) Query: 5 IKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50 + IK + + F++YA+ ++ FD Q G NG GK+NIL++I F+ Sbjct: 1 MHIKEIILDGFKSYATRTVISGFDPQFNAITGLNGSGKSNILDSICFV 48 >gnl|CDD|33697 COG3910, COG3910, Predicted ATPase [General function prediction only]. Length = 233 Score = 36.0 bits (83), Expect = 0.017 Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%) Query: 11 NISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAIS 48 ++ FR + RL F A T G+NG GK+ +LEAI+ Sbjct: 22 SLPAFR-HLEERLEFRAPITFITGENGSGKSTLLEAIA 58 >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 = 36.0 bits (83), Expect = 0.018 Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 2/48 (4%) Query: 5 IKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50 + IK + + F++YA+ ++ FD Q G NG GK+NIL+AI F+ Sbjct: 1 MHIKEIILDGFKSYATRTVISGFDPQFNAITGLNGSGKSNILDAICFV 48 >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 = 35.2 bits (81), Expect = 0.026 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%) Query: 7 IKFLNISEFRNYASLRLV-FDAQHTIFVGDNGVGKTNILEAISFLSPGR 54 IK + + F++Y +V VG NG GK+NI++AI F+ G+ Sbjct: 1 IKQITLKNFKSYRDETVVGGSNSFNAIVGPNGSGKSNIVDAICFVLGGK 49 >gnl|CDD|35241 KOG0018, KOG0018, KOG0018, Structural maintenance of chromosome protein 1 (sister chromatid cohesion complex Cohesin, subunit SMC1) [Cell cycle control, cell division, chromosome partitioning]. Length = 1141 Score = 35.3 bits (81), Expect = 0.027 Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 3/46 (6%) Query: 6 KIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISF 49 ++ L I F++Y +++ FD + T +G NG GK+N+++AISF Sbjct: 3 RLLTLEIENFKSYKGHQVIGPFD-RFTAIIGPNGSGKSNLMDAISF 47 >gnl|CDD|33731 COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]. Length = 440 Score = 35.0 bits (80), Expect = 0.035 Identities = 16/45 (35%), Positives = 29/45 (64%), Gaps = 1/45 (2%) Query: 5 IKIKFLNISEFRNYASLRLVFDAQH-TIFVGDNGVGKTNILEAIS 48 ++++ ++++ FR + +L + F TI VG NG GKT +L+AI Sbjct: 1 MRLRKISLNNFRCFLNLDITFGESETTIIVGPNGSGKTTVLDAIR 45 >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 = 34.9 bits (80), Expect = 0.038 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 14/102 (13%) Query: 25 FDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTR---IGSPSFFSTFARVE- 80 + TI G NG GK+ IL+AI G + V + + S F R++ Sbjct: 19 GEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAELIFTRLQL 78 Query: 81 --GMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHL 120 G + L+ +++ L + + ++DE+++ L Sbjct: 79 SGGEKELSALALILALAS--------LKPRPLYILDEIDRGL 112 Score = 29.5 bits (66), Expect = 1.5 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 5/51 (9%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338 S GE+++ + + LA A + P+ +LDEI LD AL + Sbjct: 79 SGGEKELSALALILALA-----SLKPRPLYILDEIDRGLDPRDGQALAEAI 124 >gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning]. Length = 1293 Score = 34.9 bits (80), Expect = 0.041 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 5/58 (8%) Query: 2 TNRIKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFLSPGRGFR 57 R+ I + + F++YA +++ F T VG NG GK+N+++++ F+ GFR Sbjct: 81 GPRLMITEIVVENFKSYAGKQILGPFHKSFTAIVGPNGSGKSNVIDSMLFVF---GFR 135 >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 = 34.6 bits (79), Expect = 0.050 Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 2/48 (4%) Query: 5 IKIKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFL 50 + IK + I FR+Y +V F H + VG NG GK+N AI F+ Sbjct: 1 MYIKQVIIKGFRSYRDETVVDPFSPHHNVIVGRNGSGKSNFFHAIRFV 48 >gnl|CDD|30843 COG0497, RecN, ATPase involved in DNA repair [DNA replication, recombination, and repair]. Length = 557 Score = 34.4 bits (79), Expect = 0.055 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 5/55 (9%) Query: 1 MTNRIKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRG 55 M + IK I E L L F+ T+ G+ G GK+ I++A+ L GR Sbjct: 1 MLLELSIKNFAIIE-----ELELEFEKGLTVLTGETGAGKSIIIDALGLLLGGRA 50 >gnl|CDD|73000 cd03241, ABC_RecN, RecN ATPase involved in DNA repair; 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 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 = 276 Score = 34.0 bits (78), Expect = 0.067 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 5/59 (8%) Query: 10 LNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIG 68 L+I F L L F+ T+ G+ G GK+ +L+A+S L GR + AD+ R G Sbjct: 4 LSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLLLGGR-----ASADLIRSG 57 >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 = 33.7 bits (77), Expect = 0.077 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 13/87 (14%) Query: 275 VDYCDKAITIAHG-STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNA 333 V K + S GEQ+ V + AR I N+ IL+ DE + +LD D Sbjct: 124 VGLSHKHRALPAELSGGEQQRVAI------ARAIVNS---PTILIADEPTGNLDPDTTWE 174 Query: 334 LFRIVTDI---GSQIFMTGTDKSVFDS 357 + ++ I G+ + + K + D+ Sbjct: 175 IMNLLKKINKAGTTVVVATHAKELVDT 201 >gnl|CDD|73034 cd03275, ABC_SMC1_euk, Eukaryotic SMC1 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 = 247 Score = 33.2 bits (76), Expect = 0.10 Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%) Query: 7 IKFLNISEFRNYASLRLV-FDAQHTIFVGDNGVGKTNILEAISF 49 +K L + F++Y ++ + T +G NG GK+N+++AISF Sbjct: 1 LKRLELENFKSYKGRHVIGPFDRFTCIIGPNGSGKSNLMDAISF 44 >gnl|CDD|34256 COG4637, COG4637, Predicted ATPase [General function prediction only]. Length = 373 Score = 32.6 bits (74), Expect = 0.20 Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 1/45 (2%) Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFL 50 + + + +R++ SL L + + +G NG GK+N +A+ L Sbjct: 2 MLVSIKVKNYRSFRSLDLEI-RRVNVIIGANGAGKSNFYDALRLL 45 >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 = 32.2 bits (73), Expect = 0.23 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 12/64 (18%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI---GSQ 344 S G+++ V + L +LLLDE ++ LD R L ++ ++ G Sbjct: 82 SGGQRQRVALARALLLN---------PDLLLLDEPTSGLDPASRERLLELLRELAEEGRT 132 Query: 345 IFMT 348 + + Sbjct: 133 VIIV 136 Score = 30.3 bits (68), Expect = 0.87 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 1/62 (1%) Query: 24 VFDAQHTIFVGDNGVGKTNILEAISFL-SPGRGFRRASYADVTRIGSPSFFSTFARVEGM 82 + + VG NG GK+ +L AI+ L P G D+ ++ V + Sbjct: 22 LKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQL 81 Query: 83 EG 84 G Sbjct: 82 SG 83 >gnl|CDD|73033 cd03274, ABC_SMC4_euk, Eukaryotic SMC4 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 = 212 Score = 31.7 bits (72), Expect = 0.33 Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 5/53 (9%) Query: 7 IKFLNISEFRNYASLRLV--FDAQHTIFVGDNGVGKTNILEAISFLSPGRGFR 57 I L + F++YA +++ F + VG NG GK+N+++++ F+ GFR Sbjct: 3 ITKLVLENFKSYAGEQVIGPFHKSFSAIVGPNGSGKSNVIDSMLFVF---GFR 52 >gnl|CDD|33894 COG4138, BtuD, ABC-type cobalamin transport system, ATPase component [Coenzyme metabolism]. Length = 248 Score = 31.5 bits (71), Expect = 0.43 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%) Query: 283 TIAHGSTGE-QKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341 + S GE Q+V L + L ++ + +LLLDE LD +++AL R+++ + Sbjct: 122 STNQLSGGEWQRVRLAAVVL---QITPDANPAGQLLLLDEPMNSLDVAQQSALDRLLSAL 178 Query: 342 ---GSQIFMTGTD 351 G I M+ D Sbjct: 179 CQQGLAIVMSSHD 191 >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 = 30.5 bits (69), Expect = 0.84 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 9/61 (14%) Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGS 343 S G+++ V + LA ILLLDE +A LD R L ++ + + Sbjct: 132 PFTLSGGQKQRVAIAGVLAMD---------PDILLLDEPTAGLDPAGRRELLELLKKLKA 182 Query: 344 Q 344 + Sbjct: 183 E 183 >gnl|CDD|36180 KOG0962, KOG0962, KOG0962, DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]. Length = 1294 Score = 29.9 bits (67), Expect = 1.1 Identities = 16/53 (30%), Positives = 27/53 (50%) Query: 1 MTNRIKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPG 53 M++ K+ I F + + F + T+ VG NG GKT I+E + + + G Sbjct: 1 MSSIDKLSIRGIRSFDDKDRNTIEFFSPLTLIVGANGTGKTTIIECLKYATTG 53 >gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]. Length = 500 Score = 29.7 bits (67), Expect = 1.3 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 15/94 (15%) Query: 251 LFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNT 310 L D + M +R L + D + S ++++V + L+ Sbjct: 116 LIDRKAMRRRARELL------ARLGLDIDPDTLVGDLSIAQRQMVEIARALSFD------ 163 Query: 311 TGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQ 344 A +L+LDE +A L + LF ++ + +Q Sbjct: 164 ---ARVLILDEPTAALTVKETERLFDLIRRLKAQ 194 >gnl|CDD|177026 CHL00094, dnaK, heat shock protein 70. Length = 621 Score = 29.7 bits (67), Expect = 1.4 Identities = 16/48 (33%), Positives = 24/48 (50%) Query: 181 SWCSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSL 228 S C E Q+ EL KI+ + E I L + + +Q +N+ IK L Sbjct: 536 SLCYQAEKQLKELKDKISEEKKEKIENLIKKLRQALQNDNYESIKSLL 583 >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 = 29.5 bits (66), Expect = 1.4 Identities = 14/34 (41%), Positives = 20/34 (58%) Query: 315 PILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348 P+LLLDE A LD R + +V D+ ++ MT Sbjct: 148 PVLLLDEPFAALDPALRAEMLDLVLDLHAETKMT 181 >gnl|CDD|31298 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 263 Score = 29.5 bits (66), Expect = 1.5 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%) Query: 24 VFDAQHTIFVGDNGVGKTNILEAIS-FLSPGRGFRRASYADVTRIGSPSFFSTFARV 79 + + +G NG GK+ +L AI+ L P G DVT+ + ARV Sbjct: 29 IAEGDFVTVIGSNGAGKSTLLNAIAGDLKPTSGQILIDGVDVTKKSVAKRANLLARV 85 >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 = 29.4 bits (67), Expect = 1.6 Identities = 8/14 (57%), Positives = 13/14 (92%) Query: 31 IFVGDNGVGKTNIL 44 + +GD+GVGKT++L Sbjct: 4 VLIGDSGVGKTSLL 17 >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 = 29.3 bits (66), Expect = 1.7 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 9/62 (14%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFM 347 S GEQ+ LA ARL+ + F LDE ++ LDE+ + L++++ ++G + Sbjct: 93 SGGEQQR------LAFARLLLHKPKFV---FLDEATSALDEESEDRLYQLLKELGITVIS 143 Query: 348 TG 349 G Sbjct: 144 VG 145 >gnl|CDD|35471 KOG0250, KOG0250, KOG0250, DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]. Length = 1074 Score = 29.1 bits (65), Expect = 2.0 Identities = 36/153 (23%), Positives = 66/153 (43%), Gaps = 25/153 (16%) Query: 6 KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGF---RRASYA 62 KI+ ++++ F +++L + F + VG+NG GK+ IL A++ GR R +S Sbjct: 41 KIESIHLTNFMCHSNLLIEFGPRVNFIVGNNGSGKSAILTALTLGLGGRASATNRGSSLK 100 Query: 63 DVTRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRI 122 D+ + G S A ISI L + + + +I + + +R Sbjct: 101 DLIKDGCSS--------------AKISITLSNSGLDAFKPEIYGNSII-----IERTIRR 141 Query: 123 SWLVPSMDRIFSGLSMERRRF-LDRMV--FAID 152 S + R +G + ++ LD +V F I Sbjct: 142 SSSTYYLLRSANGRVVSTKKEDLDTVVDHFNIQ 174 >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 = 29.1 bits (65), Expect = 2.1 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 9/67 (13%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFM 347 S GEQ+ LA ARL + FA +LDE ++ + ED AL+R ++G Sbjct: 572 SPGEQQR------LAFARLFYHKPKFA---ILDECTSAVTEDVEGALYRKCREMGITFIS 622 Query: 348 TGTDKSV 354 G KS+ Sbjct: 623 VGHRKSL 629 >gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]. Length = 591 Score = 29.0 bits (65), Expect = 2.2 Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 5/42 (11%) Query: 314 APILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVF 355 A + LLDE SA+LD ++R + +++ + F+ +K+ Sbjct: 474 ADLYLLDEPSAYLDVEQRIIVAKVI-----RRFIENNEKTAL 510 >gnl|CDD|36372 KOG1157, KOG1157, KOG1157, Predicted guanosine polyphosphate pyrophosphohydrolase/synthase [Signal transduction mechanisms]. Length = 543 Score = 28.9 bits (64), Expect = 2.3 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 3/69 (4%) Query: 203 EMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCALKEEYAKKLFDGRKMDSMSR 262 I L+ K FP + ++ L+ FD+ A+ +KL K +S Sbjct: 227 LGIGTNKVLLENLDFKHLFPCQHIEMSSMLEDSFDE---AMITSAIEKLEQALKKAGISY 283 Query: 263 RTLIGPHRS 271 + G H+S Sbjct: 284 HVIKGRHKS 292 >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 = 29.0 bits (65), Expect = 2.3 Identities = 26/158 (16%), Positives = 49/158 (31%), Gaps = 22/158 (13%) Query: 12 ISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPS 71 I R L ++ + G G GKT + AI+ G + + Sbjct: 7 IEALREALELP---PPKNLLLYGPPGTGKTTLARAIANELFRPGAP------FLYLNASD 57 Query: 72 FFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDR 131 V + G + + E + L +DE++ R ++ R Sbjct: 58 LLEG-LVVAELFGHFLVRLLFELAEKAKPGVL--------FIDEIDSLSR--GAQNALLR 106 Query: 132 IFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGR 169 + L+ R + V +R + D +R + R Sbjct: 107 VLETLNDLRIDRENVRVIGA--TNRPLLGDLDRALYDR 142 >gnl|CDD|35286 KOG0063, KOG0063, KOG0063, RNAse L inhibitor, ABC superfamily [RNA processing and modification]. Length = 592 Score = 28.7 bits (64), Expect = 2.4 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 9/55 (16%) Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338 + S GE + V L A + L+DE SA+LD ++R +++ Sbjct: 454 VQGLSGGELQRV---------ALALCLGKPADVYLIDEPSAYLDSEQRIIASKVI 499 >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 = 28.9 bits (65), Expect = 2.4 Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 18/105 (17%) Query: 251 LFDGRKMDSMSRRTL---IG--PHRSDL--IVDYCDKAITIAHGSTGEQKVVLVGIFLAH 303 L DG+ + S+S + L I P +L + D+ S GE++ VL+ Sbjct: 57 LLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFN--ELSGGERQRVLL------ 108 Query: 304 ARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348 AR ++ PILLLDE ++HLD + L ++ + + T Sbjct: 109 ARALAQEP---PILLLDEPTSHLDIAHQIELLELLRRLARERGKT 150 >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 = 2.6 Identities = 8/14 (57%), Positives = 13/14 (92%) Query: 31 IFVGDNGVGKTNIL 44 + +GD+GVGK+N+L Sbjct: 7 VLIGDSGVGKSNLL 20 >gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]. Length = 231 Score = 28.7 bits (64), Expect = 2.7 Identities = 13/34 (38%), Positives = 19/34 (55%) Query: 315 PILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348 PILLLDE + LD R + +V+ + + MT Sbjct: 149 PILLLDEPFSALDPALRAEMLALVSQLCDERKMT 182 >gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]. Length = 258 Score = 28.6 bits (64), Expect = 3.0 Identities = 30/133 (22%), Positives = 48/133 (36%), Gaps = 9/133 (6%) Query: 28 QHTIFVGDNGVGKTNILEAIS-FLSPGRGFRRASYADVTRIGSPSFFSTFARV----EGM 82 + T +G NG GK+ +L+ ++ L P G D+ + A V Sbjct: 29 EITGILGPNGSGKSTLLKCLAGLLKPKSGEVLLDGKDIASLSPKELAKKLAYVPQSPSAP 88 Query: 83 EGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSM-ERR 141 GL + L R + + +V+E + L + L DR LS ER+ Sbjct: 89 FGLTVYELVLLGRYPHLGLFGRPSKEDEEIVEEALELLGLEHLA---DRPVDELSGGERQ 145 Query: 142 RFLDRMVFAIDPR 154 R L A + Sbjct: 146 RVLIARALAQETP 158 Score = 28.6 bits (64), Expect = 3.1 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 11/67 (16%) Query: 283 TIAHGSTGEQKVVLVGIFLAHAR-LISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341 + S GE++ VL+ AR L T PILLLDE ++HLD + + ++ D+ Sbjct: 135 PVDELSGGERQRVLI------ARALAQET----PILLLDEPTSHLDIAHQIEVLELLRDL 184 Query: 342 GSQIFMT 348 + +T Sbjct: 185 NREKGLT 191 >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 = 28.7 bits (64), Expect = 3.0 Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 10/71 (14%) Query: 289 TGEQKVVLVGIFLAHARLISNTTGFAP-ILLLDEISAHLDEDKRNALFRIVTDIGSQIFM 347 +G QK + + T P +L+LDE + HLD D AL + + + + + Sbjct: 484 SGGQKSRVA---------FAACTWNNPHLLVLDEPTNHLDRDSLGALAKALKNFNGGVVL 534 Query: 348 TGTDKSVFDSL 358 D+ SL Sbjct: 535 VSHDEEFISSL 545 Score = 28.4 bits (63), Expect = 3.0 Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%) Query: 17 NYASLRLVFDAQHTIFVGDNGVGKTNILEAIS 48 N A+L L ++ + VG NG+GK+ +L AI+ Sbjct: 97 NKANLTLSRGRRYGL-VGRNGIGKSTLLRAIA 127 >gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 591 Score = 28.7 bits (64), Expect = 3.1 Identities = 11/27 (40%), Positives = 17/27 (62%) Query: 314 APILLLDEISAHLDEDKRNALFRIVTD 340 APILLLDE ++ LD + + ++ D Sbjct: 506 APILLLDEATSALDSETEREILDMIMD 532 >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 = 28.6 bits (64), Expect = 3.3 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%) Query: 310 TTGFAPILLLDEISAHLDEDKRNALFRIVTDI--GSQIFMT 348 G +LLLDE ++ LD R A++ ++ ++ G I +T Sbjct: 148 LIGGPSVLLLDEPTSGLDPASRRAIWDLILEVRKGRSIILT 188 >gnl|CDD|35442 KOG0221, KOG0221, KOG0221, Mismatch repair ATPase MSH5 (MutS family) [Replication, recombination and repair]. Length = 849 Score = 28.1 bits (62), Expect = 3.7 Identities = 12/40 (30%), Positives = 20/40 (50%) Query: 336 RIVTDIGSQIFMTGTDKSVFDSLNETAKFMRISNHQALCI 375 RI T I S ++ + LN+ AK +R + Q+L + Sbjct: 644 RIFTRIHSCESVSLGQSTFMIDLNQVAKALRNATAQSLVL 683 >gnl|CDD|32710 COG2884, FtsE, Predicted ATPase involved in cell division [Cell division and chromosome partitioning]. Length = 223 Score = 28.2 bits (63), Expect = 3.7 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 12/75 (16%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI---GSQ 344 S GEQ+ V A AR I N +LL DE + +LD D + R+ +I G+ Sbjct: 139 SGGEQQRV------AIARAIVNQ---PAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTT 189 Query: 345 IFMTGTDKSVFDSLN 359 + M D + + + Sbjct: 190 VLMATHDLELVNRMR 204 >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 = 28.2 bits (63), Expect = 4.0 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 1/29 (3%) Query: 28 QHTIFVGDNGVGKTNILEAIS-FLSPGRG 55 Q T VG +G GK+ +L + FL+P +G Sbjct: 348 QLTALVGASGAGKSTLLNLLLGFLAPTQG 376 >gnl|CDD|33903 COG4152, COG4152, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 300 Score = 27.9 bits (62), Expect = 4.3 Identities = 40/169 (23%), Positives = 56/169 (33%), Gaps = 40/169 (23%) Query: 32 FVGDNGVGKTNILEAI-SFLSPGRGF-----RRASYADVTRIG-------------SPSF 72 +G NG GKT I L P G S RIG Sbjct: 33 LLGPNGAGKTTTFRMILGLLEPTEGEITWNGGPLSQEIKNRIGYLPEERGLYPKMTVEDQ 92 Query: 73 FSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNK--HLRISWLV---- 126 A ++GM A+I KL+ +R L+I + + EL+K +I ++ Sbjct: 93 LKYLAELKGMP-KAEIQKKLQAWLER----LEIVGKKTKKIKELSKGNQQKIQFISAVIH 147 Query: 127 -PS---MDRIFSGLSMERRRFLDRMVFAIDPR------HRRRMIDFERL 165 P +D FSGL L +F + RM E L Sbjct: 148 EPELLILDEPFSGLDPVNVELLKDAIFELKEEGATIIFSSHRMEHVEEL 196 >gnl|CDD|36004 KOG0785, KOG0785, KOG0785, Isocitrate dehydrogenase, alpha subunit [Amino acid transport and metabolism]. Length = 365 Score = 28.0 bits (62), Expect = 4.6 Identities = 9/43 (20%), Positives = 21/43 (48%) Query: 233 DGKFDQSFCALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIV 275 DG F + + ++Y F+ + +D+ + + P D++V Sbjct: 212 DGLFLECCREVAKKYPDIKFEEQYLDTCCLKLVRNPSCFDVLV 254 >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 = 27.9 bits (62), Expect = 4.7 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%) Query: 24 VFDAQHTIFVGDNGVGKTNILEAIS-FLSPGRGFRRASYADVT 65 V + + +G G GK+ +LE I+ F+ P G + D+T Sbjct: 22 VERGDYFVILGPTGSGKSVLLETIAGFIKPDSGKILLNGKDIT 64 >gnl|CDD|31318 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]. Length = 254 Score = 27.9 bits (62), Expect = 4.8 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 11/68 (16%) Query: 274 IVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNA 333 + D D+ I S G+++ V LA A L N +LLLDE +D + Sbjct: 129 MEDLRDR--QIGELSGGQKQRV----LLARA-LAQN----PDLLLLDEPFTGVDVAGQKE 177 Query: 334 LFRIVTDI 341 ++ ++ ++ Sbjct: 178 IYDLLKEL 185 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 27.9 bits (62), Expect = 5.2 Identities = 9/40 (22%), Positives = 20/40 (50%) Query: 9 FLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAIS 48 F++ L + + T+ +G +GVGK+ ++ A+ Sbjct: 146 FVSAKNGDGLEELAELLAGKITVLLGQSGVGKSTLINALL 185 >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 = 27.7 bits (62), Expect = 5.3 Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 5/42 (11%) Query: 301 LAHAR-LISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341 +A AR L+ + PIL+LDE ++ LD + + + + Sbjct: 105 IAIARALLRD----PPILILDEATSALDPETEALILEALRAL 142 >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 = 27.5 bits (61), Expect = 5.7 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 2/47 (4%) Query: 5 IKIKFLNISEFRNYASLRLVFDAQHTIFV--GDNGVGKTNILEAISF 49 +K++ N FR + + +F+ G G GK+ IL+AI++ Sbjct: 4 LKLELKNFGPFREEQVIDFTGLDNNGLFLICGPTGAGKSTILDAITY 50 >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 = 27.6 bits (61), Expect = 6.3 Identities = 11/25 (44%), Positives = 17/25 (68%) Query: 314 APILLLDEISAHLDEDKRNALFRIV 338 A I LLDE SA+LD ++R +++ Sbjct: 134 ADIYLLDEPSAYLDVEQRLMASKVI 158 >gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. Length = 161 Score = 27.5 bits (62), Expect = 6.7 Identities = 8/39 (20%), Positives = 19/39 (48%) Query: 9 FLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAI 47 ++ L+ + + ++ G +GVGK+ +L A+ Sbjct: 17 VVSAKTGEGIEELKPLLKGKTSVLAGQSGVGKSTLLNAL 55 >gnl|CDD|39094 KOG3891, KOG3891, KOG3891, Secretory vesicle-associated protein ICA69, contains Arfaptin domain [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 436 Score = 27.4 bits (60), Expect = 6.8 Identities = 11/27 (40%), Positives = 16/27 (59%) Query: 248 AKKLFDGRKMDSMSRRTLIGPHRSDLI 274 AK+ FD KMD + L+G R +L+ Sbjct: 197 AKENFDKLKMDVCQKVDLLGASRCNLL 223 >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 = 27.4 bits (61), Expect = 6.9 Identities = 9/43 (20%), Positives = 20/43 (46%) Query: 5 IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAI 47 + ++ LR + ++ VG +GVGK+ ++ A+ Sbjct: 139 YPVLAVSAKTGEGLDELREYLKGKTSVLVGQSGVGKSTLINAL 181 >gnl|CDD|37542 KOG2331, KOG2331, KOG2331, Predicted glycosylhydrolase [General function prediction only]. Length = 526 Score = 27.3 bits (60), Expect = 6.9 Identities = 14/92 (15%), Positives = 30/92 (32%), Gaps = 18/92 (19%) Query: 134 SGLSMERRRFLDRMVFAIDPRHRRRM------IDFERLMRGRNRLLTEGYFDSSWCSSIE 187 + L ++ + F D + + + +N+ + D+ W ++ Sbjct: 372 TTLVLDGGTLTEISAFCYDSDNLTTLTITCETSLLIGHISLKNQQKMDKTGDAEW-WIVK 430 Query: 188 AQMAELGVKINIARVEMINALSSLIMEYVQKE 219 A VE++ LSS V+ E Sbjct: 431 AH-----------NVELVPGLSSSKSLTVRLE 451 >gnl|CDD|72983 cd03224, ABC_TM1139_LivF_branched, LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.. Length = 222 Score = 27.3 bits (61), Expect = 7.0 Identities = 11/23 (47%), Positives = 14/23 (60%) Query: 33 VGDNGVGKTNILEAISFLSPGRG 55 +G NG GKT +L+ I L P R Sbjct: 32 LGRNGAGKTTLLKTIMGLLPPRS 54 >gnl|CDD|144183 pfam00493, MCM, MCM2/3/5 family. Length = 327 Score = 27.1 bits (61), Expect = 7.1 Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 5/33 (15%) Query: 29 HTIFVGDNGVGKTNILEAISFLSPGRGFRRASY 61 + + VGD G K+ +L+ ++ L+P RA Y Sbjct: 59 NVLLVGDPGTAKSQLLKYVAKLAP-----RAVY 86 >gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]. Length = 4600 Score = 27.4 bits (60), Expect = 7.2 Identities = 7/24 (29%), Positives = 15/24 (62%) Query: 28 QHTIFVGDNGVGKTNILEAISFLS 51 + T+ VG+ G GKT +++ ++ Sbjct: 465 EPTLLVGETGTGKTTMIQYLALKL 488 >gnl|CDD|31240 COG1038, PycA, Pyruvate carboxylase [Energy production and conversion]. Length = 1149 Score = 27.1 bits (60), Expect = 7.4 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 10/68 (14%) Query: 58 RASYADVTRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIR----VV 113 R +Y DV+ + +P+FF G+ +I +++E ++ I + + V Sbjct: 994 RETYGDVSVLPTPTFFY------GLRPGEEIEVEIEKGKTLIIKLQAIGEPDEKGMRTVY 1047 Query: 114 DELNKHLR 121 ELN R Sbjct: 1048 FELNGQPR 1055 >gnl|CDD|30759 COG0410, LivF, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]. Length = 237 Score = 27.4 bits (61), Expect = 7.4 Identities = 10/23 (43%), Positives = 13/23 (56%) Query: 33 VGDNGVGKTNILEAISFLSPGRG 55 +G NG GKT +L+ I L R Sbjct: 35 LGRNGAGKTTLLKTIMGLVRPRS 57 >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 = 27.3 bits (61), Expect = 7.4 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 11/48 (22%) Query: 288 STGEQ-KVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNAL 334 S GE+ ++ L + L + +LLLDE + HLD + AL Sbjct: 72 SGGEKMRLALAKLLLENP----------NLLLLDEPTNHLDLESIEAL 109 >gnl|CDD|173865 cd08500, PBP2_NikA_DppA_OppA_like_4, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 499 Score = 27.2 bits (61), Expect = 7.9 Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 7/37 (18%) Query: 318 LLDEISAHLDEDKRNALF----RIVTDIGSQIFMTGT 350 L D+ + LD++KR AL+ +I + + + GT Sbjct: 450 LYDKGAVELDQEKRKALYAEIQKIAAE---NLPVIGT 483 >gnl|CDD|147747 pfam05762, VWA_CoxE, VWA domain containing CoxE-like protein. This family is annotated by SMART as containing a VWA type domain. The exact function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon is several bacteria. Length = 223 Score = 27.0 bits (60), Expect = 7.9 Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 8/43 (18%) Query: 125 LVPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMR 167 L ++ + GL+ RRR R R ID R +R Sbjct: 1 LARALAALLLGLARRRRRRK--------RRRRGGRIDLRRTLR 35 >gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins (PDR1-15), ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1391 Score = 27.1 bits (60), Expect = 8.0 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 4/65 (6%) Query: 30 TIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGMEGLADIS 89 T +G++G GKT +L+ ++ GR D+ G P TFARV G DI Sbjct: 820 TALMGESGAGKTTLLDVLA----GRKTGGYIEGDILISGFPKDQETFARVSGYVEQQDIH 875 Query: 90 IKLET 94 T Sbjct: 876 SPELT 880 >gnl|CDD|34390 COG4778, PhnL, ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 235 Score = 27.2 bits (60), Expect = 8.6 Identities = 11/24 (45%), Positives = 15/24 (62%) Query: 315 PILLLDEISAHLDEDKRNALFRIV 338 PILLLDE +A LD R + ++ Sbjct: 172 PILLLDEPTASLDATNRAVVVELI 195 >gnl|CDD|33889 COG4133, CcmA, ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]. Length = 209 Score = 27.2 bits (60), Expect = 8.8 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 9/52 (17%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVT 339 S G+Q+ V A ARL AP+ +LDE LD++ L ++ Sbjct: 132 SAGQQRRV------ALARLW---LSPAPLWILDEPFTALDKEGVALLTALMA 174 >gnl|CDD|173868 cd08503, PBP2_NikA_DppA_OppA_like_17, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 460 Score = 26.8 bits (60), Expect = 9.3 Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 4/32 (12%) Query: 318 LLDEISAHLDEDKRNALF----RIVTDIGSQI 345 LLD A LDE KR L+ +I+ D G I Sbjct: 411 LLDAARAELDEAKRKELYAEMQQILHDEGGII 442 >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 = 27.0 bits (60), Expect = 9.3 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 9/55 (16%) Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338 I S G+Q+ V LA A L+ + +LLLDE A +D + ++ ++ Sbjct: 130 IGELSGGQQQRV----LLARA-LVQD----PDLLLLDEPFAGVDPKTQEDIYELL 175 >gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]. Length = 906 Score = 26.8 bits (59), Expect = 9.4 Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%) Query: 32 FVGDNGVGKTNILEAISFLSPGRGFRRASYADVT 65 FVG GVGKT+I ++I+ + R F R S +T Sbjct: 443 FVGPPGVGKTSIAKSIA-RALNRKFFRFSVGGMT 475 >gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]. Length = 226 Score = 27.0 bits (60), Expect = 9.6 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 9/54 (16%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341 S G+Q+ V A AR + N I+L DE + +LD + ++ ++ Sbjct: 144 SGGQQQRV------AIARALINN---PKIILADEPTGNLDSKTAKEVLELLREL 188 >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 = 26.8 bits (60), Expect = 9.7 Identities = 25/92 (27%), Positives = 33/92 (35%), Gaps = 25/92 (27%) Query: 33 VGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFA----RVEGMEG---L 85 +G G GK+ +L A FL GR F +Y SP+ +A V G E L Sbjct: 10 LGAKGSGKSALLRA--FL--GRSFSLNAY-------SPTIKPRYAVNTVEVYGQEKYLIL 58 Query: 86 ADISIKLE---TRDDRSVRCLQINDVVIRVVD 114 ++ D C DV V D Sbjct: 59 REVGEDEVAILLNDAELAAC----DVACLVYD 86 >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 = 26.9 bits (59), Expect = 9.8 Identities = 12/14 (85%), Positives = 12/14 (85%) Query: 314 APILLLDEISAHLD 327 A ILLLDE SAHLD Sbjct: 157 AKILLLDEPSAHLD 170 >gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. Length = 530 Score = 26.8 bits (59), Expect = 9.9 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 9/47 (19%) Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNAL 334 S G ++ V LA A L+ +LLLDE + HLD + L Sbjct: 155 SGGWRRRVA----LARA-LLEE----PDLLLLDEPTNHLDLESIEWL 192 >gnl|CDD|153337 cd07653, F-BAR_CIP4-like, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein 4 and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory response. CIP4 may also play a role in phagocytosis. Members of this subfamily typically contain an N-terminal F-BAR domain and a C-terminal SH3 domain. In addition, some members such as FNBP1L contain a central Cdc42-binding HR1 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. Length = 251 Score = 26.8 bits (60), Expect = 10.0 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 2/24 (8%) Query: 230 GFLD--GKFDQSFCALKEEYAKKL 251 FL+ GKF + A+++EYAKKL Sbjct: 19 DFLERYGKFVKERAAIEQEYAKKL 42 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 0.326 0.139 0.402 Gapped Lambda K H 0.267 0.0696 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,503,495 Number of extensions: 247431 Number of successful extensions: 1174 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1165 Number of HSP's successfully gapped: 140 Length of query: 375 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 280 Effective length of database: 4,210,882 Effective search space: 1179046960 Effective search space used: 1179046960 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: 58 (26.2 bits)