RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780567|ref|YP_003064980.1| hypothetical protein CLIBASIA_02270 [Candidatus Liberibacter asiaticus str. psy62] (246 letters) >gnl|CDD|30938 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]. Length = 408 Score = 129 bits (325), Expect = 7e-31 Identities = 53/245 (21%), Positives = 101/245 (41%), Gaps = 25/245 (10%) Query: 22 KNKEEQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSW---PSWPSRVVILVGPSGSGKS 78 + QL + D+ +V + A + P + + G G GK+ Sbjct: 68 ASAPAQLPLPSGLNPKYTFDNFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKT 127 Query: 79 CLANIWSDKSR------------STRFSN-IAKSLDSILIDTRK------PVLLEDIDLL 119 L +++ S F+N K+L ++ K +L++DI L Sbjct: 128 HLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKYSLDLLLIDDIQFL 187 Query: 120 DFND---TQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKISLPDDD 176 + + FH N++ + +++T+ P L SRL+ VV+I PDD+ Sbjct: 188 AGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDE 247 Query: 177 FLEKVIVKMFADRQIFIDKKLAAYIVQRMERSLVFAEKLVDKMDNLALSRGMGITRSLAA 236 ++ K DR I I ++ ++ +R++R++ E ++++D AL IT L Sbjct: 248 TRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNVRELEGALNRLDAFALFTKRAITIDLVK 307 Query: 237 EVLKE 241 E+LK+ Sbjct: 308 EILKD 312 >gnl|CDD|35281 KOG0058, KOG0058, KOG0058, Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 716 Score = 35.7 bits (82), Expect = 0.013 Identities = 30/106 (28%), Positives = 44/106 (41%), Gaps = 29/106 (27%) Query: 30 FSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKSR 89 F++P +R D+ V + +R P VV LVGPSGSGKS +A++ Sbjct: 473 FAYP-----TRPDVPVLKNLSFTIR--------PGEVVALVGPSGSGKSTIASLL----- 514 Query: 90 STRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQLFHIINSIHQ 135 RF + IL+D + + D N L I + Q Sbjct: 515 -LRFYDPTSG--RILLD--------GVPISDINHKYLRRKIGLVGQ 549 >gnl|CDD|146043 pfam03215, Rad17, Rad17 cell cycle checkpoint protein. Length = 490 Score = 34.6 bits (79), Expect = 0.025 Identities = 30/129 (23%), Positives = 51/129 (39%), Gaps = 26/129 (20%) Query: 26 EQLFFSF-PRCLGISRDDLLVH----SAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCL 80 E + PR RD+L +H + ++ + S +++L GPSG GK Sbjct: 7 ELWTEKYKPRR----RDELAIHKKKIAEVDHWL-KAVFLESNKQLILLLTGPSGCGK--- 58 Query: 81 ANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLL----DFNDTQLFHIINSIHQY 136 ST ++K L +I+ P L + D DF + + ++ + Q+ Sbjct: 59 ---------STTVKVLSKELGIEIIEWSNPEYLHNPDNECQKPDFRGDCIVNSLSQMEQF 109 Query: 137 DSSLLMTAR 145 LL AR Sbjct: 110 REFLLRGAR 118 >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 = 34.2 bits (79), Expect = 0.033 Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 24/77 (31%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLD----SILIDTRKPVLLEDIDL 118 P V +VGPSGSGKS L + + + D ILID +DL Sbjct: 27 PGEKVAIVGPSGSGKSTLLKL------------LLRLYDPTSGEILID--------GVDL 66 Query: 119 LDFNDTQLFHIINSIHQ 135 D + L I + Q Sbjct: 67 RDLDLESLRKNIAYVPQ 83 >gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]. Length = 709 Score = 34.0 bits (78), Expect = 0.038 Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 16/73 (21%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122 P V +VG SGSGKS L K L + + +LL+ +DL D + Sbjct: 498 PGEKVAIVGRSGSGKSTL----------------LKLLLGLYKPQQGRILLDGVDLNDID 541 Query: 123 DTQLFHIINSIHQ 135 L + + Q Sbjct: 542 LASLRRQVGYVLQ 554 >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 = 33.6 bits (77), Expect = 0.058 Identities = 15/30 (50%), Positives = 16/30 (53%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTR 92 V +VGPSGSGKS L NI R T Sbjct: 29 KGEFVAIVGPSGSGKSTLLNILGGLDRPTS 58 >gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]. Length = 226 Score = 33.2 bits (76), Expect = 0.063 Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 16/66 (24%) Query: 66 VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQ 125 V +VGPSGSGKS L N+ L + T VL+ DL ++ + Sbjct: 33 FVAIVGPSGSGKSTLLNL----------------LGGLDKPTSGEVLINGKDLTKLSEKE 76 Query: 126 LFHIIN 131 L + Sbjct: 77 LAKLRR 82 >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 = 32.6 bits (74), Expect = 0.090 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 13/58 (22%) Query: 26 EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANI 83 + + F++P R D LV + + P V LVGPSGSGKS + + Sbjct: 15 QNVTFAYPT-----RPDTLVLQDVSFTLH--------PGEVTALVGPSGSGKSTVVAL 59 >gnl|CDD|37181 KOG1970, KOG1970, KOG1970, Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Energy production and conversion, Replication, recombination and repair]. Length = 634 Score = 32.7 bits (74), Expect = 0.091 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 10/59 (16%) Query: 26 EQLFFSF-PRCLGISRDDLLVH----SAIEQAVRLID-SWPSWPSRVVILVGPSGSGKS 78 E + PR L ++L VH S ++Q ++ + P SR+++L GPSG GKS Sbjct: 70 ELWVEKYKPRTL----EELAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKS 124 >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 = 32.6 bits (75), Expect = 0.11 Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 5/30 (16%) Query: 67 VILVGPSGSGKSCL-----ANIWSDKSRST 91 I++G SG+GKSCL N + + S+ T Sbjct: 3 FIIIGSSGTGKSCLLHRFVENKFKEDSQHT 32 >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 = 32.4 bits (74), Expect = 0.13 Identities = 11/32 (34%), Positives = 17/32 (53%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFS 94 P + ++GPSG+GKS L N + + S Sbjct: 34 PGELTAIMGPSGAGKSTLLNALAGRRTGLGVS 65 >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 = 31.8 bits (72), Expect = 0.18 Identities = 11/21 (52%), Positives = 13/21 (61%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 +V LVGP+GSGKS L Sbjct: 24 AGEIVALVGPNGSGKSTLLRA 44 >gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. Length = 161 Score = 31.8 bits (73), Expect = 0.19 Identities = 9/19 (47%), Positives = 11/19 (57%) Query: 64 SRVVILVGPSGSGKSCLAN 82 + +L G SG GKS L N Sbjct: 35 GKTSVLAGQSGVGKSTLLN 53 >gnl|CDD|35958 KOG0739, KOG0739, KOG0739, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 439 Score = 31.5 bits (71), Expect = 0.21 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 6/53 (11%) Query: 48 AIEQAVRLIDSWPSW------PSRVVILVGPSGSGKSCLANIWSDKSRSTRFS 94 A+++AV L +P P R ++L GP G+GKS LA + ++ ST FS Sbjct: 144 ALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANSTFFS 196 >gnl|CDD|35279 KOG0056, KOG0056, KOG0056, Heavy metal exporter HMT1, ABC superfamily [Inorganic ion transport and metabolism]. Length = 790 Score = 31.5 bits (71), Expect = 0.22 Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 19/78 (24%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILID-----------TRKPV 111 P + V LVGPSG+GKS + + RF ++ SI ID R + Sbjct: 563 PGKTVALVGPSGAGKSTIMRLL------FRFFDVNSG--SITIDGQDIRNVTQSSLRSSI 614 Query: 112 LLEDIDLLDFNDTQLFHI 129 + D + FNDT L++I Sbjct: 615 GVVPQDTVLFNDTILYNI 632 >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 = 31.3 bits (71), Expect = 0.28 Identities = 13/19 (68%), Positives = 14/19 (73%) Query: 65 RVVILVGPSGSGKSCLANI 83 V LVGPSGSGKS L N+ Sbjct: 29 ETVALVGPSGSGKSTLVNL 47 >gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast cancer resistance protein) [Secondary metabolites biosynthesis, transport and catabolism]. Length = 613 Score = 31.1 bits (70), Expect = 0.33 Identities = 10/21 (47%), Positives = 15/21 (71%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P ++ ++GPSGSGK+ L N Sbjct: 55 PGELLAIMGPSGSGKTTLLNA 75 >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 = 30.9 bits (70), Expect = 0.33 Identities = 10/18 (55%), Positives = 12/18 (66%) Query: 65 RVVILVGPSGSGKSCLAN 82 + +LVG SG GKS L N Sbjct: 162 KTSVLVGQSGVGKSTLIN 179 >gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]. Length = 338 Score = 30.6 bits (69), Expect = 0.36 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 67 VILVGPSGSGKSCLANI 83 V+L+GPSG GKS L + Sbjct: 32 VVLLGPSGCGKSTLLRM 48 >gnl|CDD|32436 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]. Length = 332 Score = 30.9 bits (70), Expect = 0.37 Identities = 26/74 (35%), Positives = 32/74 (43%), Gaps = 21/74 (28%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDL------LD 120 V+L GP G GK+ LA+I IA L L T P L + DL L+ Sbjct: 55 VLLFGPPGLGKTTLAHI------------IANELGVNLKITSGPALEKPGDLAAILTNLE 102 Query: 121 FNDTQLFHIINSIH 134 D LF I+ IH Sbjct: 103 EGDV-LF--IDEIH 113 >gnl|CDD|34624 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]. Length = 373 Score = 30.6 bits (69), Expect = 0.38 Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 6/67 (8%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNI---AKSLDSIL-IDTRKPVLLEDIDLLDFN 122 +++VG SG GK+ N S A+ L I K L ED L+ Sbjct: 26 IMVVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHLNLT 85 Query: 123 --DTQLF 127 DT F Sbjct: 86 VIDTPGF 92 >gnl|CDD|31323 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]. Length = 240 Score = 30.8 bits (70), Expect = 0.39 Identities = 11/18 (61%), Positives = 14/18 (77%) Query: 63 PSRVVILVGPSGSGKSCL 80 VV+++GPSGSGKS L Sbjct: 27 KGEVVVIIGPSGSGKSTL 44 >gnl|CDD|35957 KOG0738, KOG0738, KOG0738, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 491 Score = 30.7 bits (69), Expect = 0.39 Identities = 14/40 (35%), Positives = 25/40 (62%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDS 102 P + V++VGP G+GK+ LA + + +T F+ + +L S Sbjct: 244 PWKGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTS 283 >gnl|CDD|35278 KOG0055, KOG0055, KOG0055, Multidrug/pheromone exporter, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1228 Score = 30.6 bits (69), Expect = 0.40 Identities = 28/108 (25%), Positives = 41/108 (37%), Gaps = 29/108 (26%) Query: 28 LFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDK 87 + FS+P SR D+ + + + + V LVGPSGSGKS L + Sbjct: 356 VCFSYP-----SRPDVKILKGVSLKIP--------SGQTVALVGPSGSGKSTLIQLL--- 399 Query: 88 SRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQLFHIINSIHQ 135 RF + +LID D+ + N L I + Q Sbjct: 400 ---ARFYDPTSG--EVLID--------GEDIRNLNLKWLRSQIGLVSQ 434 Score = 29.0 bits (65), Expect = 1.3 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 13/53 (24%) Query: 26 EQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKS 78 + F++P +R D+ V + + ++R + V LVGPSGSGKS Sbjct: 991 RNVSFAYP-----TRPDVPVLNNLSLSIR--------AGQTVALVGPSGSGKS 1030 >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 = 30.5 bits (69), Expect = 0.41 Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 5/63 (7%) Query: 63 PSRVVILVGPSGSGKSCLAN----IWSDKSRSTRFSNIA-KSLDSILIDTRKPVLLEDID 117 P + ++GPSGSGKS LA + S R D + L +D + Sbjct: 27 PGESLAIIGPSGSGKSTLARLILGLLRPTSGRVRLDGADISQWDPNELGDHVGYLPQDDE 86 Query: 118 LLD 120 L Sbjct: 87 LFS 89 >gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]. Length = 539 Score = 30.5 bits (69), Expect = 0.42 Identities = 12/22 (54%), Positives = 13/22 (59%) Query: 62 WPSRVVILVGPSGSGKSCLANI 83 + LVG SGSGKS LA I Sbjct: 315 REGETLGLVGESGSGKSTLARI 336 Score = 29.8 bits (67), Expect = 0.68 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 12/67 (17%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122 P ++ +VG SGSGKS LA + L T V+L+ DLL + Sbjct: 34 PGEILGIVGESGSGKSTLALA------------LMGLLPEGGRITSGEVILDGRDLLGLS 81 Query: 123 DTQLFHI 129 + ++ + Sbjct: 82 EREMRKL 88 >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 = 30.4 bits (69), Expect = 0.43 Identities = 12/21 (57%), Positives = 12/21 (57%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 V LVGPSG GKS L I Sbjct: 29 EGEFVALVGPSGCGKSTLLRI 49 >gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein. Length = 219 Score = 30.3 bits (69), Expect = 0.44 Identities = 28/120 (23%), Positives = 53/120 (44%), Gaps = 11/120 (9%) Query: 93 FSNIAKSLDSILIDTRKPVLLEDIDLL-DFNDTQ--LFHIINSIHQYDSSLLMTARTFPV 149 F +++D +LID DI L TQ FH N++H+ + +++T+ P Sbjct: 91 FKKSYRNVDLLLID--------DIQFLAGKEKTQEEFFHTFNALHENNKQIVLTSDRPPK 142 Query: 150 SWGVCLPDLCSRLKAATVVKISLPDDDFLEKVIVKMFADRQIFIDKKLAAYIVQRMERSL 209 L SR + ++ I PD + ++ K + I I ++ +I QR+ ++ Sbjct: 143 ELEGFEDRLRSRFEWGLIIAIEPPDLETRLAILRKKAEEENINIPNEVLNFIAQRITDNV 202 >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 = 30.5 bits (69), Expect = 0.44 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 19/78 (24%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTR--KPVLLEDI---- 116 + V +VGPSGSGKS + + RF +++ SILID + + V L+ + Sbjct: 26 AGKKVAIVGPSGSGKSTILRLL------FRFYDVSSG--SILIDGQDIREVTLDSLRRAI 77 Query: 117 -----DLLDFNDTQLFHI 129 D + FNDT ++I Sbjct: 78 GVVPQDTVLFNDTIGYNI 95 >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 = 30.6 bits (69), Expect = 0.46 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 7/63 (11%) Query: 67 VILVGPSGSGKSCLANI----WSDKSRSTRFSNIA-KSLDSILIDTRKPVLLEDIDLLDF 121 V ++G SGSGKS L + W + S + + SLD + VL + + L F Sbjct: 367 VAILGRSGSGKSTLLQLLAGAWDPQQGSITLNGVEIASLDEQALRETISVLTQRVHL--F 424 Query: 122 NDT 124 + T Sbjct: 425 SGT 427 >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 = 30.3 bits (69), Expect = 0.46 Identities = 26/122 (21%), Positives = 43/122 (35%), Gaps = 24/122 (19%) Query: 67 VILVGPSGSGKSCLANIWS----DKSRSTRFSNIAK------------SLDSILID-TRK 109 ++L+GP G GK+ LA S F+ L L + Sbjct: 50 LLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTPDLVEQLKRARGDGRLARTLQRLAKA 109 Query: 110 PVL-LEDIDLLDFNDTQ---LFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAA 165 +L L+DI L + LF +I+ ++ S ++T+ W D L A Sbjct: 110 DLLILDDIGYLPLSQEAAHLLFELISDRYE-RRSTILTSNLPFGEWHEVFGD--PTLATA 166 Query: 166 TV 167 + Sbjct: 167 IL 168 >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 = 30.5 bits (69), Expect = 0.47 Identities = 11/15 (73%), Positives = 14/15 (93%) Query: 66 VVILVGPSGSGKSCL 80 VV+++GPSGSGKS L Sbjct: 28 VVVIIGPSGSGKSTL 42 >gnl|CDD|33731 COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]. Length = 440 Score = 30.4 bits (68), Expect = 0.49 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 7/55 (12%) Query: 63 PSRVVILVGPSGSGKSCL-------ANIWSDKSRSTRFSNIAKSLDSILIDTRKP 110 S I+VGP+GSGK+ + N + D RF ++ LD I + Sbjct: 23 ESETTIIVGPNGSGKTTVLDAIRNALNKFIDFFIYLRFKSLKIELDDIELCIMSQ 77 >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 = 30.1 bits (68), Expect = 0.53 Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 17/78 (21%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQL 126 V++VGP+GSGKS L + L+ +L T VL++ DL + +L Sbjct: 30 VLIVGPNGSGKSTLLRL----------------LNGLLGPTSGEVLVDGKDLTKLSLKEL 73 Query: 127 FHIINSIHQY-DSSLLMT 143 + + Q D Sbjct: 74 RRKVGLVFQNPDDQFFGP 91 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 30.3 bits (68), Expect = 0.53 Identities = 9/23 (39%), Positives = 13/23 (56%) Query: 60 PSWPSRVVILVGPSGSGKSCLAN 82 ++ +L+G SG GKS L N Sbjct: 160 ELLAGKITVLLGQSGVGKSTLIN 182 >gnl|CDD|30812 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]. Length = 494 Score = 30.1 bits (67), Expect = 0.54 Identities = 16/44 (36%), Positives = 23/44 (52%) Query: 62 WPSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILI 105 P + V+L GP G+GK+ LA + +SRS S L S + Sbjct: 274 RPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWV 317 >gnl|CDD|33864 COG4107, PhnK, ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 258 Score = 30.3 bits (68), Expect = 0.56 Identities = 12/30 (40%), Positives = 18/30 (60%) Query: 58 SWPSWPSRVVILVGPSGSGKSCLANIWSDK 87 S+ +P V+ +VG SGSGK+ L S + Sbjct: 26 SFDLYPGEVLGIVGESGSGKTTLLKCISGR 55 >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 = 30.0 bits (68), Expect = 0.57 Identities = 10/17 (58%), Positives = 12/17 (70%) Query: 65 RVVILVGPSGSGKSCLA 81 R VIL G +GSGK+ L Sbjct: 1 RTVILQGEAGSGKTTLL 17 >gnl|CDD|33504 COG3709, COG3709, Uncharacterized component of phosphonate metabolism [Inorganic ion transport and metabolism]. Length = 192 Score = 30.3 bits (68), Expect = 0.58 Identities = 9/18 (50%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 R++ +VGPSG+GK L Sbjct: 4 MGRLIAVVGPSGAGKDTL 21 >gnl|CDD|31416 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General function prediction only]. Length = 368 Score = 29.9 bits (67), Expect = 0.58 Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 7/60 (11%) Query: 38 ISRDDLLVHSAIEQAVRLI-------DSWPSWPSRVVILVGPSGSGKSCLANIWSDKSRS 90 I+ DD++ ++ RLI + + W + V+ GP G+GK+ +A +++++ Sbjct: 118 ITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKV 177 >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 = 30.0 bits (68), Expect = 0.58 Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 1/55 (1%) Query: 65 RVVILVGPSGSGKSCL-ANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDL 118 V+L+GPS SGK+ L + + K RST S IL K +D+ Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKYRSTVTSIEPNVATFILNSEGKGKKFRLVDV 55 >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 = 30.1 bits (68), Expect = 0.60 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 9/46 (19%) Query: 66 VVILVGPSGSGKSCLAN-IWSDKSRSTRFSNIAKSLDSILIDTRKP 110 +++L GPSG GKS L + + + F S+ TRKP Sbjct: 1 LIVLSGPSGVGKSTLLKRLLEEFDPNFGF--------SVSHTTRKP 38 >gnl|CDD|31313 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 248 Score = 30.2 bits (68), Expect = 0.60 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 66 VVILVGPSGSGKSCLANI 83 V ++GPSG GKS L + Sbjct: 31 FVAILGPSGCGKSTLLRL 48 >gnl|CDD|34241 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]. Length = 580 Score = 30.2 bits (68), Expect = 0.61 Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%) Query: 63 PSRVVILVGPSGSGKSCLAN----IWSDKSRSTRF 93 + ++GPSGSGKS LA IW S S R Sbjct: 361 AGEALGIIGPSGSGKSTLARLLVGIWPPTSGSVRL 395 >gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]. Length = 231 Score = 29.9 bits (67), Expect = 0.64 Identities = 10/21 (47%), Positives = 15/21 (71%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 +V ++GPSG+GKS L N+ Sbjct: 24 AGEIVAILGPSGAGKSTLLNL 44 >gnl|CDD|35964 KOG0745, KOG0745, KOG0745, Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]. Length = 564 Score = 30.0 bits (67), Expect = 0.70 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 7/67 (10%) Query: 15 KQKNDQPKNKEEQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSG 74 K D+ E ++ S + R ++ V L S V+L+GP+G Sbjct: 184 KSAKDRDNPIELEISESNAQWPNNQRQIAKALDEDDEDVELEKS-------NVLLLGPTG 236 Query: 75 SGKSCLA 81 SGK+ LA Sbjct: 237 SGKTLLA 243 >gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]. Length = 219 Score = 30.0 bits (66), Expect = 0.70 Identities = 21/135 (15%), Positives = 42/135 (31%), Gaps = 16/135 (11%) Query: 67 VILVGPSGSGKSCLAN-----IWSDKSRSTRFSNIA--------KSLDSILIDTRKPVLL 113 ++++G G GK+ L N + + T + +++ L DT Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEY 67 Query: 114 EDIDLLDFNDTQLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKISLP 173 + + I+ +SS +T + D+ L KI L Sbjct: 68 RSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGN---KIDLF 124 Query: 174 DDDFLEKVIVKMFAD 188 D+ + I+ Sbjct: 125 DEQSSSEEILNQLNR 139 >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 = 29.9 bits (67), Expect = 0.74 Identities = 8/20 (40%), Positives = 13/20 (65%) Query: 63 PSRVVILVGPSGSGKSCLAN 82 + I+ GP+GSGKS + + Sbjct: 20 EGSLTIITGPNGSGKSTILD 39 >gnl|CDD|33845 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide transport and metabolism]. Length = 261 Score = 29.5 bits (66), Expect = 0.76 Identities = 29/116 (25%), Positives = 42/116 (36%), Gaps = 19/116 (16%) Query: 65 RVVILVGPSGSGKSCLANIWSDKSRSTRFSNI---AKSLDSILIDTRKPVLLEDID---- 117 ++IL G GSGK+ A + + R + I L IL D P+L E Sbjct: 2 PLIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLRGILWDESLPILKEVYRESFL 61 Query: 118 -----LLDFNDTQLFHIINSIHQYDS---SLLMTARTFPVSWGV----CLPDLCSR 161 LLD I++ + Y S L A+ +W + D C R Sbjct: 62 KSVERLLDSALKNYLVIVDDTNYYKSMRRQLACEAKERKTTWCIIYLRTPLDTCLR 117 >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 = 29.7 bits (67), Expect = 0.79 Identities = 11/21 (52%), Positives = 12/21 (57%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 + LVG SGSGKS LA Sbjct: 30 KGETLGLVGESGSGKSTLARA 50 >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 = 29.7 bits (67), Expect = 0.88 Identities = 11/21 (52%), Positives = 13/21 (61%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 V L+GP+GSGKS LA Sbjct: 25 KGEVHALMGPNGSGKSTLAKT 45 >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 = 29.4 bits (66), Expect = 0.91 Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 8/44 (18%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILID 106 P V +VGP+G+GK+ L N+ RF + K ILID Sbjct: 28 PGETVAIVGPTGAGKTTLINLL------MRFYDPQKG--QILID 63 >gnl|CDD|35309 KOG0086, KOG0086, KOG0086, GTPase Rab4, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 214 Score = 29.2 bits (65), Expect = 1.0 Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 5/30 (16%) Query: 67 VILVGPSGSGKSCL-----ANIWSDKSRST 91 +++G +G+GKSCL N + D S T Sbjct: 12 FLVIGSAGTGKSCLLHQFIENKFKDDSSHT 41 >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 = 29.0 bits (66), Expect = 1.1 Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 8/55 (14%) Query: 67 VILVGPSGSGKS------CLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLED 115 +++VG SG GKS + ++ I + K + E+ Sbjct: 7 IMVVGESGLGKSTFINTLFNTKLIPSDYPPDPAEEHIDK--TVEIKSSKAEIEEN 59 >gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]. Length = 254 Score = 29.2 bits (65), Expect = 1.1 Identities = 31/158 (19%), Positives = 59/158 (37%), Gaps = 27/158 (17%) Query: 13 PDKQKNDQPKNKEEQLFF-SFPRCLGISRDDL-LVHSAIEQAVRLIDSWPSWPSRV--VI 68 +++ + + E +L SFP D ++A+ + S + R ++ Sbjct: 50 EEEKLAREARKIERRLRSASFPAKKTFEEFDFEFQPGIDKKALEDLASLVEFFERGENLV 109 Query: 69 LVGPSGSGKS----CLANIWSDKSRSTRFSNIAKSLDSILI----DTRKPVLLEDI---D 117 L+GP G GK+ + N S F L + + LL ++ D Sbjct: 110 LLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLEEKLLRELKKVD 169 Query: 118 LLDFND-----------TQLFHIINSIHQYDSSLLMTA 144 LL +D LF +I+ ++ SL++T+ Sbjct: 170 LLIIDDIGYEPFSQEEADLLFQLISRRYES-RSLIITS 206 >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 = 29.0 bits (65), Expect = 1.2 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 ++ LVG SG+GKS L N+ Sbjct: 346 AGQLTALVGASGAGKSTLLNL 366 >gnl|CDD|30875 COG0529, CysC, Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]. Length = 197 Score = 29.1 bits (65), Expect = 1.2 Identities = 11/25 (44%), Positives = 14/25 (56%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDK 87 V+ G SGSGKS +AN +K Sbjct: 22 KGAVIWFTGLSGSGKSTIANALEEK 46 >gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. Length = 207 Score = 29.0 bits (66), Expect = 1.2 Identities = 8/15 (53%), Positives = 13/15 (86%) Query: 67 VILVGPSGSGKSCLA 81 ++++GP GSGK+ LA Sbjct: 25 LLMIGPPGSGKTMLA 39 >gnl|CDD|30527 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication, recombination, and repair]. Length = 935 Score = 29.0 bits (65), Expect = 1.2 Identities = 10/17 (58%), Positives = 14/17 (82%) Query: 65 RVVILVGPSGSGKSCLA 81 ++V++ G SGSGKS LA Sbjct: 27 KLVVITGLSGSGKSSLA 43 >gnl|CDD|144280 pfam00625, Guanylate_kin, Guanylate kinase. Length = 182 Score = 28.9 bits (65), Expect = 1.2 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 64 SRVVILVGPSGSGKSCLAN 82 R ++L GPSG GKS + Sbjct: 1 RRPIVLSGPSGVGKSHIKK 19 >gnl|CDD|34177 COG4525, TauB, ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 259 Score = 29.1 bits (65), Expect = 1.2 Identities = 9/21 (42%), Positives = 15/21 (71%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 +V+++GPSG GK+ L N+ Sbjct: 30 SGELVVVLGPSGCGKTTLLNL 50 >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 = 29.0 bits (65), Expect = 1.3 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 V ++GP+GSGKS LA Sbjct: 29 EGEVHAIMGPNGSGKSTLAYT 49 >gnl|CDD|32733 COG2909, MalT, ATP-dependent transcriptional regulator [Transcription]. Length = 894 Score = 28.7 bits (64), Expect = 1.5 Identities = 7/26 (26%), Positives = 15/26 (57%) Query: 64 SRVVILVGPSGSGKSCLANIWSDKSR 89 R++++ P+G GK+ L W + + Sbjct: 37 YRLILISAPAGFGKTTLLAQWRELAA 62 >gnl|CDD|37203 KOG1992, KOG1992, KOG1992, Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport]. Length = 960 Score = 28.8 bits (64), Expect = 1.6 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 9/46 (19%) Query: 125 QLFHIINSIHQYDSSLLMTARTFPVSWGVCLPDLCSRLKAATVVKI 170 QL ++ I + D FP W LPDL +RL + I Sbjct: 107 QLSEALSLIGKRD---------FPDKWPTLLPDLVARLSSGDFNVI 143 >gnl|CDD|35216 COG5657, CSE1, CAS/CSE protein involved in chromosome segregation [Cell division and chromosome partitioning]. Length = 947 Score = 28.8 bits (64), Expect = 1.6 Identities = 28/130 (21%), Positives = 50/130 (38%), Gaps = 17/130 (13%) Query: 101 DSILIDTRKPVLLEDIDLLDFNDTQLF----HIINSIHQYDSSLLMTARTFPVSWGVCLP 156 +SIL D + E L+ + QL ++ I + D FP W +P Sbjct: 76 NSILPDENVLIRDELFSLIISSSNQLQIQNALAVSRIARLD---------FPDEWPTLVP 126 Query: 157 DLCSRLKAATVVKI--SLPDDDFLEKVIVKMFADRQIFIDKK--LAAYIVQRMERSLVFA 212 DL S L +V SL + K + ++F +F++ L + + + S F Sbjct: 127 DLLSLLSEKDMVTNENSLRVLHHIFKRLRRLFRSDALFLEIAPVLLSILCPFLFSSAYFW 186 Query: 213 EKLVDKMDNL 222 + ++L Sbjct: 187 SMSENLDESL 196 >gnl|CDD|177097 CHL00206, ycf2, Ycf2; Provisional. Length = 2281 Score = 28.7 bits (64), Expect = 1.7 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 3/84 (3%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122 PSR ++++G G+G+S L + ++ I L+ L + K L++DID+ D + Sbjct: 1629 PSRGILVIGSIGTGRSYLVK---YLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSD 1685 Query: 123 DTQLFHIINSIHQYDSSLLMTART 146 D I+ + +M A T Sbjct: 1686 DIDDSDDIDRDLDTELLTMMNALT 1709 >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 = 28.4 bits (64), Expect = 1.8 Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 4/29 (13%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSN 95 VI++G SG GK+ L N + +K +FSN Sbjct: 3 VIILGDSGVGKTSLMNQYVNK----KFSN 27 >gnl|CDD|30672 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]. Length = 308 Score = 28.3 bits (63), Expect = 1.9 Identities = 7/17 (41%), Positives = 14/17 (82%) Query: 65 RVVILVGPSGSGKSCLA 81 +++++ GP+ SGK+ LA Sbjct: 4 KLIVIAGPTASGKTALA 20 >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 = 2.0 Identities = 10/15 (66%), Positives = 12/15 (80%) Query: 67 VILVGPSGSGKSCLA 81 V++ GPSG GKS LA Sbjct: 17 VLITGPSGIGKSELA 31 >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 = 28.2 bits (64), Expect = 2.0 Identities = 7/14 (50%), Positives = 11/14 (78%) Query: 67 VILVGPSGSGKSCL 80 ++L+G SG GK+ L Sbjct: 3 IVLIGDSGVGKTSL 16 >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 = 28.3 bits (63), Expect = 2.0 Identities = 10/15 (66%), Positives = 12/15 (80%) Query: 69 LVGPSGSGKSCLANI 83 +VG SGSGKS LA + Sbjct: 38 IVGESGSGKSTLARL 52 >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 = 28.2 bits (63), Expect = 2.0 Identities = 11/18 (61%), Positives = 13/18 (72%) Query: 66 VVILVGPSGSGKSCLANI 83 +V L+GPSGSGKS L Sbjct: 28 IVALLGPSGSGKSTLLRC 45 >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 = 28.2 bits (63), Expect = 2.0 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 66 VVILVGPSGSGKSCL 80 + L+GPSG GKS L Sbjct: 28 ITALIGPSGCGKSTL 42 >gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]. Length = 845 Score = 28.4 bits (63), Expect = 2.1 Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 6/32 (18%) Query: 64 SRVVILVGPSGSGKS------CLANIWSDKSR 89 ++VVI+VG +GSGK+ L + Sbjct: 65 NQVVIIVGETGSGKTTQLPQFLLEEGLGIAGK 96 >gnl|CDD|36598 KOG1384, KOG1384, KOG1384, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]. Length = 348 Score = 28.4 bits (63), Expect = 2.1 Identities = 9/17 (52%), Positives = 15/17 (88%) Query: 65 RVVILVGPSGSGKSCLA 81 +VV+++G +G+GKS LA Sbjct: 8 KVVVIMGATGAGKSRLA 24 >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 = 28.4 bits (63), Expect = 2.1 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 65 RVVILVGPSGSGKSCLANI 83 + +VGPSGSGKS L N+ Sbjct: 25 EITAIVGPSGSGKSTLLNL 43 >gnl|CDD|73178 COG4608, AppF, ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]. Length = 268 Score = 28.3 bits (63), Expect = 2.2 Identities = 9/19 (47%), Positives = 11/19 (57%) Query: 65 RVVILVGPSGSGKSCLANI 83 + LVG SG GKS L + Sbjct: 40 ETLGLVGESGCGKSTLGRL 58 >gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and secretion]. Length = 407 Score = 28.0 bits (62), Expect = 2.3 Identities = 11/24 (45%), Positives = 16/24 (66%) Query: 55 LIDSWPSWPSRVVILVGPSGSGKS 78 LI++ RV+ LVGP+G GK+ Sbjct: 194 LIENLIVEQKRVIALVGPTGVGKT 217 >gnl|CDD|31412 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]. Length = 408 Score = 28.2 bits (63), Expect = 2.3 Identities = 9/15 (60%), Positives = 14/15 (93%) Query: 67 VILVGPSGSGKSCLA 81 ++L+GP+GSGK+ LA Sbjct: 100 ILLIGPTGSGKTLLA 114 >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 = 28.0 bits (63), Expect = 2.4 Identities = 9/17 (52%), Positives = 10/17 (58%) Query: 67 VILVGPSGSGKSCLANI 83 + L GP G GKS LA Sbjct: 1 IWLYGPPGCGKSTLAKY 17 >gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.. Length = 151 Score = 27.9 bits (62), Expect = 2.4 Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 3/36 (8%) Query: 46 HSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLA 81 AIE ++ P + ++L GP G+GK+ LA Sbjct: 4 EEAIEALREALEL-PPPKN--LLLYGPPGTGKTTLA 36 >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 = 27.8 bits (62), Expect = 2.5 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P + V LVG SG GKS + ++ Sbjct: 28 PGKTVALVGSSGCGKSTVVSL 48 >gnl|CDD|30760 COG0411, LivG, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]. Length = 250 Score = 27.8 bits (62), Expect = 2.6 Identities = 10/21 (47%), Positives = 16/21 (76%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P +V L+GP+G+GK+ L N+ Sbjct: 29 PGEIVGLIGPNGAGKTTLFNL 49 >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 = 27.8 bits (62), Expect = 2.6 Identities = 11/18 (61%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 P V L+GPSG+GKS L Sbjct: 26 PGEFVALIGPSGAGKSTL 43 >gnl|CDD|33633 COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]. Length = 352 Score = 28.0 bits (62), Expect = 2.7 Identities = 9/18 (50%), Positives = 11/18 (61%) Query: 63 PSRVVILVGPSGSGKSCL 80 V L+GPSG GK+ L Sbjct: 30 KGEFVTLLGPSGCGKTTL 47 >gnl|CDD|37239 KOG2028, KOG2028, KOG2028, ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]. Length = 554 Score = 27.7 bits (61), Expect = 2.8 Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 12/58 (20%) Query: 42 DLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIW--SDKSRSTRFSNIA 97 D L+ S IEQ + PS +IL GP G+GK+ LA + + K S RF ++ Sbjct: 150 DGLLRSLIEQ-----NRIPS-----MILWGPPGTGKTTLARLIASTSKKHSYRFVELS 197 >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 = 27.7 bits (62), Expect = 2.8 Identities = 12/30 (40%), Positives = 18/30 (60%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTR 92 P + L+GP+G+GK+ L N+ S R T Sbjct: 25 PGEIHGLIGPNGAGKTTLFNLISGFLRPTS 54 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 27.9 bits (62), Expect = 2.8 Identities = 9/28 (32%), Positives = 15/28 (53%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFS 94 ++++GP G+GKS LA + K Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLGLPHLD 30 >gnl|CDD|147030 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B. Length = 230 Score = 27.9 bits (63), Expect = 2.8 Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 8/29 (27%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSN 95 V+L+G GSGKS + RS FSN Sbjct: 2 VLLMGLRGSGKSSM--------RSIIFSN 22 >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 = 27.8 bits (62), Expect = 2.9 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P + L+GPSG GK+ L + Sbjct: 25 PGEFLALLGPSGCGKTTLLRL 45 >gnl|CDD|37960 KOG2749, KOG2749, KOG2749, mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1 [RNA processing and modification]. Length = 415 Score = 27.9 bits (62), Expect = 2.9 Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%) Query: 45 VHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANI 83 +H+A+E+ R+ S V++VGP+ GKS L I Sbjct: 85 LHAALEK-RRMQAEEESSYGPRVMVVGPTDVGKSTLCRI 122 >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 = 27.9 bits (62), Expect = 3.0 Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 12/41 (29%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDT 107 ++L+G G+GK+ + + +AK+L +D Sbjct: 2 IVLIGMMGAGKTTVGRL------------LAKALGLPFVDL 30 >gnl|CDD|31314 COG1117, PstB, ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 253 Score = 27.8 bits (62), Expect = 3.0 Identities = 10/18 (55%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 ++V L+GPSG GKS L Sbjct: 32 KNKVTALIGPSGCGKSTL 49 >gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and metabolism]. Length = 191 Score = 27.8 bits (62), Expect = 3.0 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 9/46 (19%) Query: 65 RVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKP 110 +++L GPSG GKS L + RF S+ TRKP Sbjct: 5 LLIVLSGPSGVGKSTLVKALLEDD-KLRF--------SVSATTRKP 41 >gnl|CDD|32265 COG2082, CobH, Precorrin isomerase [Coenzyme metabolism]. Length = 210 Score = 27.5 bits (61), Expect = 3.2 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 1/63 (1%) Query: 175 DDFLEKVIVKMFADRQIFIDKKL-AAYIVQRMERSLVFAEKLVDKMDNLALSRGMGITRS 233 +E + A I +D + AA I +R +L VD L++ GITRS Sbjct: 56 PGAIEAGREALKAGCPIVVDVNMVAAGITRRRLPALNPVICYVDDPRVAELAKEEGITRS 115 Query: 234 LAA 236 A Sbjct: 116 AAG 118 >gnl|CDD|110578 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif. Length = 157 Score = 27.6 bits (62), Expect = 3.2 Identities = 10/17 (58%), Positives = 11/17 (64%) Query: 66 VVILVGPSGSGKSCLAN 82 V G SGSGKS +AN Sbjct: 4 TVWFTGLSGSGKSTIAN 20 >gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]. Length = 531 Score = 27.6 bits (61), Expect = 3.2 Identities = 10/24 (41%), Positives = 13/24 (54%) Query: 67 VILVGPSGSGKSCLANIWSDKSRS 90 + +VG GKS L N S + RS Sbjct: 271 IAIVGRPNVGKSSLLNALSREDRS 294 >gnl|CDD|144365 pfam00735, Septin, Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis. Length = 280 Score = 27.6 bits (62), Expect = 3.3 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 23/94 (24%) Query: 67 VILVGPSGSGKS------CLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLD 120 +++VG SG GK+ L +++ ++ I K+++ I + ED L+ Sbjct: 7 LMVVGESGLGKTTLINTLFLTDLYPERGIPGPSEKIKKTVE---IKATTVEIEEDGVKLN 63 Query: 121 FN--DTQLFH-----------IINSI-HQYDSSL 140 DT F I+ I Q++ L Sbjct: 64 LTVIDTPGFGDAIDNSNCWKPIVEYIDEQFEQYL 97 >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 = 27.6 bits (61), Expect = 3.5 Identities = 11/18 (61%), Positives = 12/18 (66%) Query: 63 PSRVVILVGPSGSGKSCL 80 V +VGPSGSGKS L Sbjct: 35 RGETVAIVGPSGSGKSTL 52 >gnl|CDD|143926 pfam00158, Sigma54_activat, Sigma-54 interaction domain. Length = 168 Score = 27.3 bits (62), Expect = 3.7 Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 5/35 (14%) Query: 48 AIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLAN 82 +E A R+ + + V+I G SG+GK A Sbjct: 11 VLELAKRVAPT----DATVLIT-GESGTGKELFAR 40 >gnl|CDD|33892 COG4136, COG4136, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 213 Score = 27.6 bits (61), Expect = 3.7 Identities = 10/18 (55%), Positives = 12/18 (66%) Query: 63 PSRVVILVGPSGSGKSCL 80 +V L+GPSG GKS L Sbjct: 27 KGEIVTLMGPSGCGKSTL 44 >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 = 27.5 bits (61), Expect = 3.7 Identities = 10/19 (52%), Positives = 15/19 (78%) Query: 63 PSRVVILVGPSGSGKSCLA 81 +++V++ G SGSGKS LA Sbjct: 20 RNKLVVITGVSGSGKSSLA 38 >gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism]. Length = 218 Score = 27.5 bits (61), Expect = 3.7 Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 6/72 (8%) Query: 60 PSWPSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLE----D 115 ++ + G SGSGK+ +A S++ + I SLD D E + Sbjct: 4 KPEKVIIIGIAGGSGSGKTTVAKELSEQLGVEKVVVI--SLDDYYKDQSHLPFEERNKIN 61 Query: 116 IDLLDFNDTQLF 127 D + D L Sbjct: 62 YDHPEAFDLDLL 73 >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 = 27.4 bits (61), Expect = 3.7 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 13/72 (18%) Query: 69 LVGPSGSGKSCLANIWSDK------SRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN 122 +VG SG GK+ L N +T +K +I +D +K + + D Sbjct: 1 VVGDSGVGKTSLLNRLLGGEFVPEEYETTIIDFYSK---TIEVDGKK----VKLQIWDTA 53 Query: 123 DTQLFHIINSIH 134 + F + ++ Sbjct: 54 GQERFRSLRRLY 65 >gnl|CDD|34201 COG4559, COG4559, ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 259 Score = 27.6 bits (61), Expect = 3.7 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 5/45 (11%) Query: 38 ISRDDLLVHSAIEQAVRLID--SWPSWPSRVVILVGPSGSGKSCL 80 I ++L RL+D S P V+ ++GP+G+GKS L Sbjct: 2 IRAENLSYSL---AGRRLLDGVSLDLRPGEVLAILGPNGAGKSTL 43 >gnl|CDD|33681 COG3893, COG3893, Inactivated superfamily I helicase [DNA replication, recombination, and repair]. Length = 697 Score = 27.3 bits (60), Expect = 3.7 Identities = 12/44 (27%), Positives = 20/44 (45%) Query: 19 DQPKNKEEQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSW 62 D+ + E + F LG R LL + ++A+R + SW Sbjct: 249 DEWQAIEGHPQYGFHSLLGAERQLLLEIAEADEALRPAELTASW 292 >gnl|CDD|35880 KOG0661, KOG0661, KOG0661, MAPK related serine/threonine protein kinase [Signal transduction mechanisms]. Length = 538 Score = 27.3 bits (60), Expect = 3.8 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 1/50 (2%) Query: 13 PDKQKNDQPKNKEEQLFFSFPRCLGISRDDLLVHSAIEQAVRLIDSWPSW 62 PDK + N + F FP+ DLL +A +A LI+ +W Sbjct: 229 PDKDSWPEGYNLASAMNFRFPQVKPSPLKDLL-PNASSEAASLIERLLAW 277 >gnl|CDD|32710 COG2884, FtsE, Predicted ATPase involved in cell division [Cell division and chromosome partitioning]. Length = 223 Score = 27.5 bits (61), Expect = 3.9 Identities = 13/30 (43%), Positives = 16/30 (53%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRSTR 92 V L GPSG+GKS L + + R TR Sbjct: 27 KGEFVFLTGPSGAGKSTLLKLIYGEERPTR 56 >gnl|CDD|133270 cd01867, Rab8_Rab10_Rab13_like, Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. 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 = 167 Score = 27.2 bits (61), Expect = 3.9 Identities = 12/27 (44%), Positives = 18/27 (66%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRF 93 ++L+G SG GKSCL +S+ S + F Sbjct: 6 LLLIGDSGVGKSCLLLRFSEDSFNPSF 32 >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 = 27.1 bits (61), Expect = 4.0 Identities = 10/15 (66%), Positives = 12/15 (80%) Query: 67 VILVGPSGSGKSCLA 81 + LVG SGSGK+ LA Sbjct: 2 IALVGHSGSGKTTLA 16 >gnl|CDD|31682 COG1493, HprK, Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]. Length = 308 Score = 27.1 bits (60), Expect = 4.1 Identities = 10/15 (66%), Positives = 13/15 (86%) Query: 67 VILVGPSGSGKSCLA 81 V++ GPSG+GKS LA Sbjct: 148 VLITGPSGAGKSELA 162 >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 = 27.2 bits (60), Expect = 4.1 Identities = 12/21 (57%), Positives = 14/21 (66%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P VV +VG SGSGKS L + Sbjct: 27 PGEVVGIVGRSGSGKSTLTKL 47 >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 = 27.2 bits (60), Expect = 4.2 Identities = 12/26 (46%), Positives = 15/26 (57%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTR 92 V LVGPSG+GKS L + + T Sbjct: 30 VFLVGPSGAGKSTLLKLIYKEELPTS 55 >gnl|CDD|35952 KOG0733, KOG0733, KOG0733, Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]. Length = 802 Score = 27.3 bits (60), Expect = 4.3 Identities = 12/20 (60%), Positives = 14/20 (70%) Query: 63 PSRVVILVGPSGSGKSCLAN 82 P R V+L GP G GK+ LAN Sbjct: 222 PPRGVLLHGPPGCGKTSLAN 241 >gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]. Length = 366 Score = 27.2 bits (60), Expect = 4.3 Identities = 21/138 (15%), Positives = 44/138 (31%), Gaps = 40/138 (28%) Query: 49 IEQAVRLIDSW-PSWPSRVVILVGPSGSGKSCLA-------------------NIWSDKS 88 I Q + +I+ GP+G+GK+ N ++ Sbjct: 26 INQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRT 85 Query: 89 RSTRFSNIAKSLDSI-----------------LIDTRKPVL--LEDID-LLDFNDTQLFH 128 S I L + L K V+ L+++D L+D + L+ Sbjct: 86 PYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYS 145 Query: 129 IINSIHQYDSSLLMTART 146 ++ + + + + A + Sbjct: 146 LLRAPGENKVKVSIIAVS 163 >gnl|CDD|31417 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein [Transcription]. Length = 450 Score = 27.1 bits (60), Expect = 4.3 Identities = 9/17 (52%), Positives = 14/17 (82%) Query: 65 RVVILVGPSGSGKSCLA 81 R +++VGP G+GK+ LA Sbjct: 66 RGILIVGPPGTGKTALA 82 >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 = 4.4 Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 8/48 (16%) Query: 36 LGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANI 83 L R + + S + + + + GP+G+GK+ L I Sbjct: 8 LSCERGERTLFSDLSFTLN--------AGEALQITGPNGAGKTTLLRI 47 >gnl|CDD|31315 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]. Length = 345 Score = 27.2 bits (60), Expect = 4.6 Identities = 11/20 (55%), Positives = 14/20 (70%) Query: 64 SRVVILVGPSGSGKSCLANI 83 +V L+GPSG+GKS L I Sbjct: 28 GELVALLGPSGAGKSTLLRI 47 >gnl|CDD|37866 KOG2655, KOG2655, KOG2655, Septin family protein (P-loop GTPase) [Cell cycle control, cell division, chromosome partitioning, Nuclear structure, Intracellular trafficking, secretion, and vesicular transport]. Length = 366 Score = 27.2 bits (60), Expect = 4.6 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 5/66 (7%) Query: 67 VILVGPSGSGKSCLANIWSDKSRS---TRFSNIAKSLDSILIDTRKPVLLEDIDLLDFN- 122 +++VG SG GKS N S + +++ I++ K + E+ L+ Sbjct: 24 LMVVGESGLGKSTFINSLFLTDLSGNREVPGASERIKETVEIESTKVEIEENGVKLNLTV 83 Query: 123 -DTQLF 127 DT F Sbjct: 84 IDTPGF 89 >gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]. Length = 258 Score = 27.1 bits (60), Expect = 4.6 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 16/70 (22%) Query: 66 VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDTQ 125 + ++GP+GSGKS L K L +L VLL+ D+ + + Sbjct: 30 ITGILGPNGSGKSTL----------------LKCLAGLLKPKSGEVLLDGKDIASLSPKE 73 Query: 126 LFHIINSIHQ 135 L + + Q Sbjct: 74 LAKKLAYVPQ 83 >gnl|CDD|144904 pfam01482, DUF13, DUF13. This domain is found in nematode proteins and is thought to be involved in nematode larval development and have a positive regulation on growth rate. It is currently of unknown function. Length = 87 Score = 27.1 bits (61), Expect = 4.7 Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 8/28 (28%) Query: 22 KNKEEQLFFSFPRC--------LGISRD 41 KN +E + P+C LGI D Sbjct: 7 KNSDETKYVILPKCQEPLTMVTLGIGHD 34 >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 = 27.1 bits (61), Expect = 4.9 Identities = 8/14 (57%), Positives = 10/14 (71%) Query: 67 VILVGPSGSGKSCL 80 ++LVG G GKS L Sbjct: 2 LVLVGDGGVGKSSL 15 >gnl|CDD|37167 KOG1956, KOG1956, KOG1956, DNA topoisomerase III alpha [Replication, recombination and repair]. Length = 758 Score = 26.9 bits (59), Expect = 5.0 Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 4/50 (8%) Query: 125 QLFHIINSIHQYDSSLL----MTARTFPVSWGVCLPDLCSRLKAATVVKI 170 + F + H + L F V L ++C K ATVVK+ Sbjct: 231 EEFWTLKFKHTHKGGLTEFNWKRGHLFDRLSVVILYEICVEEKEATVVKV 280 >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 = 27.1 bits (60), Expect = 5.2 Identities = 8/25 (32%), Positives = 16/25 (64%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDK 87 P + L+G SG+GK+ L ++ + + Sbjct: 32 PGTLTALMGESGAGKTTLLDVLAGR 56 >gnl|CDD|146469 pfam03853, YjeF_N, YjeF-related protein N-terminus. Length = 170 Score = 26.8 bits (60), Expect = 5.3 Identities = 13/46 (28%), Positives = 20/46 (43%) Query: 36 LGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLA 81 GIS L+ ++ A + RV++L GP +G LA Sbjct: 1 AGISSLILMENAGRAVARVIRKLLSPAGKRVLVLCGPGNNGGDGLA 46 >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 = 26.7 bits (59), Expect = 5.3 Identities = 9/28 (32%), Positives = 15/28 (53%) Query: 56 IDSWPSWPSRVVILVGPSGSGKSCLANI 83 S + ++ L G +G+GK+ LA I Sbjct: 18 DLSLDLYAGEIIALTGKNGAGKTTLAKI 45 >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 = 26.8 bits (59), Expect = 5.4 Identities = 11/33 (33%), Positives = 15/33 (45%) Query: 64 SRVVILVGPSGSGKSCLANIWSDKSRSTRFSNI 96 V+LVG S SGK+ L S ++I Sbjct: 38 QNAVLLVGLSDSGKTSLFTQLITGSHRGTVTSI 70 >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 = 26.6 bits (59), Expect = 5.8 Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 8/45 (17%) Query: 36 LGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCL 80 L S V ++ VR ++ ++GPSGSGKS L Sbjct: 6 LTKSFGGRTVLKGVDLDVR--------RGEILAIIGPSGSGKSTL 42 >gnl|CDD|30201 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).. Length = 179 Score = 26.8 bits (59), Expect = 5.8 Identities = 16/45 (35%), Positives = 23/45 (51%) Query: 66 VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKP 110 VV + GPSGSGK+ A S++ R + SLD + + P Sbjct: 1 VVGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYYVPRKTP 45 >gnl|CDD|31316 COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]. Length = 257 Score = 26.8 bits (59), Expect = 5.9 Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 8/48 (16%) Query: 36 LGISRDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLANI 83 + + R+ + + V + W +VGP+G+GK+ L ++ Sbjct: 37 VSVRRNGKKILGDLSWQVNPGEHW--------AIVGPNGAGKTTLLSL 76 >gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop. Length = 122 Score = 26.6 bits (59), Expect = 6.0 Identities = 8/16 (50%), Positives = 12/16 (75%) Query: 65 RVVILVGPSGSGKSCL 80 +V++VGP SGK+ L Sbjct: 1 PIVLVVGPKDSGKTTL 16 >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 = 26.7 bits (59), Expect = 6.1 Identities = 8/18 (44%), Positives = 12/18 (66%) Query: 63 PSRVVILVGPSGSGKSCL 80 ++ ++G SGSGKS L Sbjct: 33 RGEILAILGGSGSGKSTL 50 >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 = 26.7 bits (59), Expect = 6.1 Identities = 10/20 (50%), Positives = 13/20 (65%) Query: 63 PSRVVILVGPSGSGKSCLAN 82 ++ +VG SGSGKS LA Sbjct: 30 KGEILGIVGESGSGKSVLAK 49 >gnl|CDD|31326 COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]. Length = 293 Score = 26.9 bits (59), Expect = 6.1 Identities = 9/23 (39%), Positives = 15/23 (65%) Query: 63 PSRVVILVGPSGSGKSCLANIWS 85 P + L+GP+G+GK+ L I + Sbjct: 30 PGEIFGLLGPNGAGKTTLLKILA 52 >gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit [Posttranslational modification, protein turnover, chaperones]. Length = 786 Score = 26.8 bits (59), Expect = 6.4 Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%) Query: 45 VHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKSCLA 81 V AI +A + P+ P + +GP+G GK+ LA Sbjct: 503 VSDAIRRARAGLGD-PNRPIGSFLFLGPTGVGKTELA 538 >gnl|CDD|133269 cd01866, Rab2, Rab2 subfamily. Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. 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 = 168 Score = 26.6 bits (59), Expect = 6.5 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 4/29 (13%) Query: 68 ILVGPSGSGKSCLANIWSDKSRSTRFSNI 96 I++G +G GKSCL ++DK RF + Sbjct: 8 IIIGDTGVGKSCLLLQFTDK----RFQPV 32 >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 = 26.6 bits (59), Expect = 6.5 Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 12/42 (28%) Query: 66 VVILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDT 107 ++ + GP+GSGKS +A + +AK L +DT Sbjct: 1 IIAIDGPAGSGKSTVAKL------------LAKKLGLPYLDT 30 >gnl|CDD|177080 CHL00176, ftsH, cell division protein; Validated. Length = 638 Score = 26.6 bits (59), Expect = 6.6 Identities = 10/15 (66%), Positives = 13/15 (86%) Query: 67 VILVGPSGSGKSCLA 81 V+LVGP G+GK+ LA Sbjct: 219 VLLVGPPGTGKTLLA 233 >gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General function prediction only]. Length = 398 Score = 26.4 bits (58), Expect = 6.7 Identities = 10/17 (58%), Positives = 12/17 (70%) Query: 66 VVILVGPSGSGKSCLAN 82 VV++VGP SGKS L Sbjct: 75 VVMVVGPVDSGKSTLTT 91 >gnl|CDD|146942 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria. Length = 200 Score = 26.4 bits (59), Expect = 6.8 Identities = 8/16 (50%), Positives = 12/16 (75%) Query: 67 VILVGPSGSGKSCLAN 82 ++LVG +G+GKS N Sbjct: 3 IVLVGKTGNGKSATGN 18 >gnl|CDD|37180 KOG1969, KOG1969, KOG1969, DNA replication checkpoint protein CHL12/CTF18 [Energy production and conversion, Replication, recombination and repair]. Length = 877 Score = 26.5 bits (58), Expect = 6.8 Identities = 9/21 (42%), Positives = 16/21 (76%) Query: 63 PSRVVILVGPSGSGKSCLANI 83 P ++++L GP G GK+ LA++ Sbjct: 325 PKKILLLCGPPGLGKTTLAHV 345 >gnl|CDD|36328 KOG1112, KOG1112, KOG1112, Ribonucleotide reductase, alpha subunit [Nucleotide transport and metabolism]. Length = 796 Score = 26.5 bits (58), Expect = 6.9 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 9/43 (20%) Query: 155 LPDLCSRLKA--ATVVKISLPDDDFLEKVIVKMFADRQIFIDK 195 +P++ LK TV +IS +K ++ M ADR FID+ Sbjct: 669 IPEIPQDLKELYKTVWEIS-------QKTVIDMAADRGAFIDQ 704 >gnl|CDD|30200 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.. Length = 149 Score = 26.6 bits (59), Expect = 6.9 Identities = 10/17 (58%), Positives = 12/17 (70%) Query: 66 VVILVGPSGSGKSCLAN 82 V+ L G SGSGKS +A Sbjct: 1 VIWLTGLSGSGKSTIAR 17 >gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]. Length = 403 Score = 26.5 bits (58), Expect = 7.2 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 5/76 (6%) Query: 10 FFVPDKQKNDQPKNKEEQLFFSFPRCLGISRDDLLV--HSAIEQAVRLIDSWPSWPSRVV 67 F+P + + + + L L D L+ ++++ I ++ PS + Sbjct: 46 IFLPSEAFSMSELTELQALLPQARPYLKSEALDDLIGESPSLQELREQIKAYA--PSGLP 103 Query: 68 ILV-GPSGSGKSCLAN 82 +L+ G +G+GK A Sbjct: 104 VLIIGETGTGKELFAR 119 >gnl|CDD|39610 KOG4409, KOG4409, KOG4409, Predicted hydrolase/acyltransferase (alpha/beta hydrolase superfamily) [General function prediction only]. Length = 365 Score = 26.4 bits (58), Expect = 7.5 Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 2/39 (5%) Query: 61 SWPSRV--VILVGPSGSGKSCLANIWSDKSRSTRFSNIA 97 +P RV +ILV P G + + K + + Sbjct: 180 KYPERVEKLILVSPWGFPEKPDSEPEFTKPPPEWYKALF 218 >gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing and modification]. Length = 674 Score = 26.4 bits (58), Expect = 7.6 Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 7/52 (13%) Query: 29 FFSFPRCLGIS--RDDLLVHSAIEQAVRLIDSWPSWPSRVVILVGPSGSGKS 78 + L I R+ L ++ +Q + ++ ++V+I++G +GSGKS Sbjct: 34 SYGKSTNLSIQEQRESLPIYKYRDQILYAVED-----NQVLIVIGETGSGKS 80 >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 = 26.5 bits (59), Expect = 7.8 Identities = 8/18 (44%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 +V ++GP+G+GKS L Sbjct: 24 AGEIVGILGPNGAGKSTL 41 >gnl|CDD|34291 COG4674, COG4674, Uncharacterized ABC-type transport system, ATPase component [General function prediction only]. Length = 249 Score = 26.4 bits (58), Expect = 7.8 Identities = 10/29 (34%), Positives = 20/29 (68%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRST 91 P + +L+GP+G+GK+ L ++ + K+R Sbjct: 30 PGELRVLIGPNGAGKTTLMDVITGKTRPQ 58 >gnl|CDD|35301 KOG0078, KOG0078, KOG0078, GTP-binding protein SEC4, small G protein superfamily, and related Ras family GTP-binding proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 207 Score = 26.3 bits (58), Expect = 7.9 Identities = 13/27 (48%), Positives = 19/27 (70%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRF 93 ++L+G SG GK+CL +SD S +T F Sbjct: 15 LLLIGDSGVGKTCLLLRFSDDSFNTSF 41 >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 = 26.3 bits (58), Expect = 8.1 Identities = 8/14 (57%), Positives = 11/14 (78%) Query: 67 VILVGPSGSGKSCL 80 V+L+GPSG GK+ Sbjct: 29 VVLLGPSGCGKTTT 42 >gnl|CDD|145608 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation. Length = 205 Score = 26.3 bits (59), Expect = 8.1 Identities = 8/16 (50%), Positives = 13/16 (81%) Query: 66 VVILVGPSGSGKSCLA 81 +V +GP+G+GK+ LA Sbjct: 21 IVFGIGPAGTGKTYLA 36 >gnl|CDD|35615 KOG0394, KOG0394, KOG0394, Ras-related GTPase [General function prediction only]. Length = 210 Score = 26.5 bits (58), Expect = 8.2 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 4/58 (6%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDTRKPVLLEDIDLLDFNDT 124 VI++G SG GK+ L N + +K +FS K+ T++ + + L DT Sbjct: 12 VIILGDSGVGKTSLMNQYVNK----KFSQQYKATIGADFLTKEVQVDDRSVTLQIWDT 65 >gnl|CDD|35954 KOG0735, KOG0735, KOG0735, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 952 Score = 26.1 bits (57), Expect = 8.3 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 20/73 (27%) Query: 67 VILVGPSGSGKSCLANIWSD----------------KSRSTRFSNIAKSLDSILIDT--R 108 ++L GP GSGK+ L D + I K L+++ + Sbjct: 434 ILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWY 493 Query: 109 KP--VLLEDIDLL 119 P ++L+D+D L Sbjct: 494 APSIIVLDDLDCL 506 >gnl|CDD|33436 COG3638, COG3638, ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 258 Score = 26.3 bits (58), Expect = 8.5 Identities = 9/14 (64%), Positives = 12/14 (85%) Query: 67 VILVGPSGSGKSCL 80 V ++GPSG+GKS L Sbjct: 33 VAIIGPSGAGKSTL 46 >gnl|CDD|133319 cd04119, RJL, RJL (RabJ-Like) subfamily. RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. 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. Length = 168 Score = 26.2 bits (58), Expect = 8.6 Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 6/40 (15%) Query: 67 VILVGPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILID 106 VI +G SG GKSC+ + + RF ++K L +I ID Sbjct: 3 VISMGNSGVGKSCIIKRYCEG----RF--VSKYLPTIGID 36 >gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 179 Score = 26.4 bits (58), Expect = 8.7 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 6/48 (12%) Query: 65 RVVILVGPSGSGKSCLANIWSDK------SRSTRFSNIAKSLDSILID 106 V+ + G GSGK+ +A ++ S T F +A+ L + Sbjct: 1 MVITISGLPGSGKTTVARELAEHLGLKLVSAGTIFREMARERGMSLEE 48 >gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins (PDR1-15), ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1391 Score = 26.4 bits (58), Expect = 8.7 Identities = 8/18 (44%), Positives = 13/18 (72%) Query: 63 PSRVVILVGPSGSGKSCL 80 P + +++GP GSGK+ L Sbjct: 140 PGEMTLVLGPPGSGKTTL 157 >gnl|CDD|35945 KOG0726, KOG0726, KOG0726, 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]. Length = 440 Score = 26.1 bits (57), Expect = 8.9 Identities = 11/29 (37%), Positives = 19/29 (65%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRST 91 P + VIL G G+GK+ LA ++++ +T Sbjct: 218 PPKGVILYGEPGTGKTLLAKAVANQTSAT 246 >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 = 26.0 bits (57), Expect = 8.9 Identities = 7/16 (43%), Positives = 13/16 (81%) Query: 66 VVILVGPSGSGKSCLA 81 +++++G SGSGKS + Sbjct: 1 IIVVMGVSGSGKSTVG 16 >gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 235 Score = 26.0 bits (57), Expect = 9.1 Identities = 10/17 (58%), Positives = 14/17 (82%) Query: 67 VILVGPSGSGKSCLANI 83 V+L+GP+GSGKS L + Sbjct: 33 VLLIGPNGSGKSTLLKL 49 >gnl|CDD|30631 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 222 Score = 25.9 bits (57), Expect = 9.2 Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 12/37 (32%) Query: 71 GPSGSGKSCLANIWSDKSRSTRFSNIAKSLDSILIDT 107 GP+GSGKS +A I +A+ L +DT Sbjct: 11 GPAGSGKSTVAKI------------LAEKLGFHYLDT 35 >gnl|CDD|33907 COG4161, ArtP, ABC-type arginine transport system, ATPase component [Amino acid transport and metabolism]. Length = 242 Score = 26.1 bits (57), Expect = 9.2 Identities = 9/14 (64%), Positives = 13/14 (92%) Query: 67 VILVGPSGSGKSCL 80 ++L+GPSG+GKS L Sbjct: 31 LVLLGPSGAGKSSL 44 >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 = 25.9 bits (57), Expect = 9.3 Identities = 8/12 (66%), Positives = 12/12 (100%) Query: 67 VILVGPSGSGKS 78 ++L+GPSGSGK+ Sbjct: 30 LVLIGPSGSGKT 41 >gnl|CDD|35871 KOG0652, KOG0652, KOG0652, 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]. Length = 424 Score = 26.1 bits (57), Expect = 9.5 Identities = 9/29 (31%), Positives = 19/29 (65%) Query: 63 PSRVVILVGPSGSGKSCLANIWSDKSRST 91 P + V++ GP G+GK+ +A + ++ +T Sbjct: 204 PPKGVLMYGPPGTGKTLMARACAAQTNAT 232 >gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]. Length = 591 Score = 25.9 bits (57), Expect = 9.5 Identities = 10/23 (43%), Positives = 15/23 (65%) Query: 63 PSRVVILVGPSGSGKSCLANIWS 85 P +VV ++GP+G GKS I + Sbjct: 99 PGKVVGILGPNGIGKSTALKILA 121 >gnl|CDD|31318 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]. Length = 254 Score = 25.9 bits (57), Expect = 9.5 Identities = 8/18 (44%), Positives = 12/18 (66%) Query: 63 PSRVVILVGPSGSGKSCL 80 + L+GP+G+GKS L Sbjct: 29 KGEITALIGPNGAGKSTL 46 >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 = 26.0 bits (57), Expect = 9.6 Identities = 10/18 (55%), Positives = 14/18 (77%) Query: 66 VVILVGPSGSGKSCLANI 83 +V L+GPSGSGK+ L + Sbjct: 30 LVALLGPSGSGKTTLLRL 47 >gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]. Length = 386 Score = 26.1 bits (57), Expect = 9.7 Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 12/59 (20%) Query: 65 RVVILVGPSGSGKSCLANIWSDKSRSTRFSN--IAKSLDSILIDTRKPVLLEDIDLLDF 121 + +++G SGSGKS L R N I + IL+D + L +L + Sbjct: 55 EIFVIMGLSGSGKSTLV----------RLLNRLIEPTRGEILVDGKDIAKLSAAELREL 103 >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 = 25.9 bits (57), Expect = 9.9 Identities = 8/32 (25%), Positives = 16/32 (50%), Gaps = 1/32 (3%) Query: 52 AVRLIDSWPSWPSRVVILVGPSGSGKSCLANI 83 AV + S + + L+G +G+GK+ + Sbjct: 17 AVDDL-SLNVYKGEIFGLLGHNGAGKTTTLKM 47 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 0.322 0.136 0.401 Gapped Lambda K H 0.267 0.0724 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,944,882 Number of extensions: 151507 Number of successful extensions: 885 Number of sequences better than 10.0: 1 Number of HSP's gapped: 884 Number of HSP's successfully gapped: 231 Length of query: 246 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 155 Effective length of database: 4,297,318 Effective search space: 666084290 Effective search space used: 666084290 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 56 (25.4 bits)