RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780132|ref|YP_003064545.1| guanylate kinase [Candidatus Liberibacter asiaticus str. psy62] (186 letters) >gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and metabolism]. Length = 191 Score = 111 bits (279), Expect = 1e-25 Identities = 56/176 (31%), Positives = 85/176 (48%), Gaps = 8/176 (4%) Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKH 63 + VL G SGVGK+T+ K + L + L V TTR+PR E +DY F+++ +F+ Sbjct: 6 LIVLSGPSGVGKSTLVKAL-LEDDKLRFSVSATTRKPRPGEVDGVDYFFVTEEEFEELIE 64 Query: 64 TGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPP 123 F+E + YYG +E + + G D++L + QG +KK + V SIFI PP Sbjct: 65 RDEFLEWAEYHGNYYGTSREPVEQALAEGKDVILDIDVQGALQVKKKMPNAV-SIFILPP 123 Query: 124 SEAELIQRRIKRREDIPFNLDPDL------FGKNHSYSFTIVNNHLPTACRQVGLI 173 S EL +R R D + L + + IVN+ L A ++ I Sbjct: 124 SLEELERRLKGRGTDSEEVIARRLENAKKEISHADEFDYVIVNDDLEKALEELKSI 179 >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 = 92.5 bits (230), Expect = 5e-20 Identities = 44/121 (36%), Positives = 64/121 (52%), Gaps = 2/121 (1%) Query: 4 IFVLIGASGVGKTTIAKQVVLN-SEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62 + VL G SGVGK+T+ K+++ V TTR+PR E +DY F+S+ +F+ Sbjct: 1 LIVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHTTRKPRPGEVDGVDYHFVSKEEFERLI 60 Query: 63 HTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAP 122 G F+E + YYG K + + G ++L + QG +KK Y D V SIFI P Sbjct: 61 ENGEFLEWAEFHGNYYGTSKAAVEEALAEGKIVILEIDVQGARQVKKSYPDAV-SIFILP 119 Query: 123 P 123 P Sbjct: 120 P 120 >gnl|CDD|144280 pfam00625, Guanylate_kin, Guanylate kinase. Length = 182 Score = 84.3 bits (209), Expect = 2e-17 Identities = 57/175 (32%), Positives = 80/175 (45%), Gaps = 10/175 (5%) Query: 4 IFVLIGASGVGKTTIAKQVV-LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62 VL G SGVGK+ I K ++ E V TTR PR E DY F+S+ + + Sbjct: 3 PIVLSGPSGVGKSHIKKALLDEYPEKFGYSVSHTTRPPRPGEVDGKDYHFVSKEEMENDI 62 Query: 63 HTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAP 122 F+E + YYG KE I E G +L + QG+ L+K S+FI P Sbjct: 63 SANEFLEHAEFNGNYYGTSKEAIEQIAESGKICILDVDIQGVKQLRKAEL-SPISVFIKP 121 Query: 123 PSEAELIQRRIKRR-----EDIPFNLDP--DLFGKNHSYSFTIVNNHLPTACRQV 170 PS L QRR+K R E I ++ F + + IVN+ L A +++ Sbjct: 122 PSLKVL-QRRLKGRGTEQEEKINKRMEAAEQEFQHYAEFDYIIVNDDLDEAYKKL 175 >gnl|CDD|35829 KOG0609, KOG0609, KOG0609, Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]. Length = 542 Score = 75.0 bits (184), Expect = 1e-14 Identities = 49/179 (27%), Positives = 76/179 (42%), Gaps = 16/179 (8%) Query: 6 VLIGASGVGKTTIAKQVV-LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHT 64 VLIGA GVG+ + +++ LN + V TTR PR DE ++Y F+S+ + + Sbjct: 344 VLIGAQGVGRRELKNKLIELNPDRFGTAVPHTTRPPRSDEVDGVEYHFVSKEEMEADIRA 403 Query: 65 GLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPPS 124 G F+E + YG + + N + G +L + Q L L+ E + IFIAPPS Sbjct: 404 GKFLEYGEYEGNLYGTSLDSVRNVIASGKICVLDVEPQALKVLRTA-EFKPYVIFIAPPS 462 Query: 125 EAELIQRRIKRRE--DIPFNLDPDLFGK------------NHSYSFTIVNNHLPTACRQ 169 EL R + + + H + IVN+ L R+ Sbjct: 463 LEELRALRKVAVMSTIVAKQFTDEDLQEIIDESARIEQQYGHYFDLIIVNSDLDKTFRE 521 >gnl|CDD|35926 KOG0707, KOG0707, KOG0707, Guanylate kinase [Nucleotide transport and metabolism]. Length = 231 Score = 50.4 bits (120), Expect = 3e-07 Identities = 44/133 (33%), Positives = 57/133 (42%), Gaps = 6/133 (4%) Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVM---PVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62 VL G SGVGK+T+ K+ L E M V TTR PR E Y F + +F Sbjct: 41 VLSGPSGVGKSTLLKR--LREELGGMFGFSVSHTTRTPRAGEVHGKHYHFSTTEEFLSMI 98 Query: 63 HTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAP 122 FIE YG + M G +L + QG+ P++ D + IFI P Sbjct: 99 KNNEFIEFATFSGNKYGTSIAAVQRLMLSGKVCILDIDLQGVQPIRATSLDAIY-IFIKP 157 Query: 123 PSEAELIQRRIKR 135 PS L +R R Sbjct: 158 PSIKILEERLRAR 170 >gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism]. Length = 218 Score = 32.9 bits (75), Expect = 0.047 Identities = 33/143 (23%), Positives = 55/143 (38%), Gaps = 12/143 (8%) Query: 4 IFVLI-GASGVGKTTIAKQVV--LNSEYLVMPVG----VTTRRPRVDEKQYIDYRFISQS 56 I + I G SG GKTT+AK++ L E +V+ +E+ I+Y Sbjct: 9 IIIGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDDYYKDQSHLPFEERNKINYDHPEAF 68 Query: 57 QFKG-WKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPL--KKLYED 113 +H + V Y Y +++ +G+ L ++L + Sbjct: 69 DLDLLIEHLKDLKQGKPVDLPVYDYKTHTREPETIKVEPNDVVIV-EGILLLYDERLRDL 127 Query: 114 QVTSIFIAPPSEAELIQRRIKRR 136 IF+ ++ LI RRIKR Sbjct: 128 MDLKIFVDTDADVRLI-RRIKRD 149 >gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213 Score = 32.0 bits (74), Expect = 0.086 Identities = 9/27 (33%), Positives = 15/27 (55%) Query: 7 LIGASGVGKTTIAKQVVLNSEYLVMPV 33 + G SG GKT + + N++ V+ V Sbjct: 20 IFGGSGTGKTVLLGMIARNAKADVVEV 46 >gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members. Length = 268 Score = 32.1 bits (74), Expect = 0.10 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 7/40 (17%) Query: 5 FVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDE 44 L+G SG GKTT+A+ ++ + G R V++ Sbjct: 2 IALVGHSGSGKTTLAEALLYAT-------GAIDRLGSVED 34 >gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]. Length = 322 Score = 31.1 bits (70), Expect = 0.20 Identities = 11/19 (57%), Positives = 11/19 (57%) Query: 1 MAHIFVLIGASGVGKTTIA 19 M I G GVGKTTIA Sbjct: 1 MTRIVFFTGKGGVGKTTIA 19 >gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]. Length = 782 Score = 30.5 bits (69), Expect = 0.26 Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 2/33 (6%) Query: 4 IFVLIGASGVGKTTIAKQV--VLNSEYLVMPVG 34 I L+G GVGKT++ K + L +++ + +G Sbjct: 352 ILCLVGPPGVGKTSLGKSIAKALGRKFVRISLG 384 >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 = 30.5 bits (70), Expect = 0.27 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 5 FVLIGASGVGKTTIAKQ 21 VLIG SGVGKT++ + Sbjct: 3 IVLIGDSGVGKTSLLLR 19 >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 = 30.6 bits (69), Expect = 0.28 Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 2/28 (7%) Query: 4 IFVLIGASGVGKTTIAKQVV--LNSEYL 29 I V++G SG GK+T+ K + L + ++ Sbjct: 1 IIVVMGVSGSGKSTVGKALAERLGAPFI 28 >gnl|CDD|39131 KOG3928, KOG3928, KOG3928, Mitochondrial ribosome small subunit component, mediator of apoptosis DAP3 [Translation, ribosomal structure and biogenesis]. Length = 461 Score = 30.3 bits (68), Expect = 0.30 Identities = 24/143 (16%), Positives = 43/143 (30%), Gaps = 29/143 (20%) Query: 5 FVLIGASGVGKTTIAKQVV---LNSEYLVMPV----GVTTRRPRVDEKQYIDYRFISQSQ 57 FVL G G GK+ Q V + ++L++ + T R + + Sbjct: 182 FVLDGEPGTGKSIALAQAVHYAADQKWLILHIPYAELWTNGRKDYSYDSDLKGLWDQPLY 241 Query: 58 FKGW------KHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLY 111 K + + K +Y G PL ++ Sbjct: 242 AKKILKNFKKTNEPALKKQLKTSKDY----VWSKRESTLKG------------KPLVEIV 285 Query: 112 EDQVTSIFIAPPSEAELIQRRIK 134 E + SI AP + L++ + Sbjct: 286 ETGIASIKNAPDAVGILLRELKR 308 >gnl|CDD|30108 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle.. Length = 767 Score = 30.4 bits (68), Expect = 0.32 Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%) Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDE 44 + +G SG GKTT K + EYL + G R V++ Sbjct: 90 IFLGRSGAGKTTSCKHAL---EYLALAAGSVDGRVSVEK 125 >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 = 30.2 bits (68), Expect = 0.37 Identities = 8/21 (38%), Positives = 13/21 (61%), Gaps = 1/21 (4%) Query: 2 AHIFVLIGASGVGKTTIAKQV 22 ++ L G G GKTT+A+ + Sbjct: 20 KNLL-LYGPPGTGKTTLARAI 39 >gnl|CDD|147659 pfam05610, DUF779, Protein of unknown function (DUF779). This family consists of several bacterial proteins of unknown function. Length = 95 Score = 29.9 bits (68), Expect = 0.40 Identities = 12/23 (52%), Positives = 16/23 (69%) Query: 52 FISQSQFKGWKHTGLFIETTKVR 74 +IS+SQF+ WKHT L I+ R Sbjct: 53 YISKSQFEYWKHTQLIIDVVPGR 75 >gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 160 Score = 29.8 bits (68), Expect = 0.41 Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 3/26 (11%) Query: 6 VLIGASGVGKTTIAKQVVLN---SEY 28 V++GA GVGK+ I Q V EY Sbjct: 3 VVLGAGGVGKSAITIQFVKGTFVEEY 28 >gnl|CDD|133313 cd04113, Rab4, Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 161 Score = 29.9 bits (68), Expect = 0.47 Identities = 9/21 (42%), Positives = 15/21 (71%) Query: 5 FVLIGASGVGKTTIAKQVVLN 25 F++IG+SG GK+ + + V N Sbjct: 3 FIIIGSSGTGKSCLLHRFVEN 23 >gnl|CDD|33366 COG3564, COG3564, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 116 Score = 29.2 bits (65), Expect = 0.63 Identities = 10/23 (43%), Positives = 14/23 (60%) Query: 52 FISQSQFKGWKHTGLFIETTKVR 74 +IS Q++ WKHT L I+ R Sbjct: 67 YISGPQYEAWKHTQLIIDVVPGR 89 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 29.5 bits (66), Expect = 0.66 Identities = 7/19 (36%), Positives = 14/19 (73%) Query: 5 FVLIGASGVGKTTIAKQVV 23 +++G G GK+T+AK++ Sbjct: 3 ILILGPPGAGKSTLAKKLA 21 >gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]. Length = 906 Score = 29.1 bits (65), Expect = 0.67 Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 2/33 (6%) Query: 4 IFVLIGASGVGKTTIAKQVV--LNSEYLVMPVG 34 I +G GVGKT+IAK + LN ++ VG Sbjct: 440 ILCFVGPPGVGKTSIAKSIARALNRKFFRFSVG 472 >gnl|CDD|38419 KOG3209, KOG3209, KOG3209, WW domain-containing protein [General function prediction only]. Length = 984 Score = 29.2 bits (65), Expect = 0.70 Identities = 31/117 (26%), Positives = 44/117 (37%), Gaps = 17/117 (14%) Query: 20 KQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTGLFIETTKVRDEYYG 79 +Q + ++ YL V TTRR E + DY F + F + +G +E YYG Sbjct: 55 QQSIRDNLYL-FQVPCTTRRIL--EGEVPDYSFSTVPIFLCLEVSGCLLEFGTYESNYYG 111 Query: 80 YLKEDINNPMEHGYDILLILTHQ---GLAPLKKLYEDQVTSIF------IAPPSEAE 127 K P E D ++LT Q + Y + S I P E E Sbjct: 112 TPK-----PPECPADDDMMLTDQELLLPPNSAESYRKRTKSYSIMENAGITTPEEEE 163 >gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit [Posttranslational modification, protein turnover, chaperones]. Length = 786 Score = 29.1 bits (65), Expect = 0.71 Identities = 9/19 (47%), Positives = 14/19 (73%) Query: 4 IFVLIGASGVGKTTIAKQV 22 F+ +G +GVGKT +AK + Sbjct: 523 SFLFLGPTGVGKTELAKAL 541 Score = 27.2 bits (60), Expect = 2.6 Identities = 9/14 (64%), Positives = 10/14 (71%) Query: 6 VLIGASGVGKTTIA 19 VL+G GVGKT I Sbjct: 195 VLVGEPGVGKTAIV 208 >gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. Length = 161 Score = 29.1 bits (66), Expect = 0.73 Identities = 19/72 (26%), Positives = 27/72 (37%), Gaps = 26/72 (36%) Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62 VL G SGVGK+T+ ++ L + G IS+ +G + Sbjct: 36 KTSVLAGQSGVGKSTLLNALLPE---LDLRTGE-----------------ISEKLGRG-R 74 Query: 63 HTGLFIETTKVR 74 HT TT V Sbjct: 75 HT-----TTHVE 81 >gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and metabolism]. Length = 172 Score = 29.0 bits (65), Expect = 0.79 Identities = 9/22 (40%), Positives = 12/22 (54%) Query: 1 MAHIFVLIGASGVGKTTIAKQV 22 VLIG G GK+TI + + Sbjct: 1 RNMNIVLIGFMGAGKSTIGRAL 22 >gnl|CDD|34258 COG4639, COG4639, Predicted kinase [General function prediction only]. Length = 168 Score = 28.8 bits (64), Expect = 0.81 Identities = 14/29 (48%), Positives = 18/29 (62%) Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYL 29 M + VL GASG GK+T AK+ L + L Sbjct: 1 MRILVVLRGASGSGKSTFAKENFLQNYVL 29 >gnl|CDD|112956 pfam04166, PdxA, Pyridoxal phosphate biosynthetic protein PdxA. In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesized de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate. Length = 299 Score = 28.8 bits (65), Expect = 0.82 Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%) Query: 87 NPMEHGYDILLILTH-QGLAPLKKLYEDQVTSIFIAPP 123 + YD +L + H QGL PLK L D+ ++ + P Sbjct: 229 PVLLGRYDAVLAMYHDQGLIPLKYLGFDRGVNVTLGLP 266 >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 = 28.8 bits (65), Expect = 0.85 Identities = 8/19 (42%), Positives = 14/19 (73%) Query: 6 VLIGASGVGKTTIAKQVVL 24 +L G +G GKTT+ +++ L Sbjct: 4 ILQGEAGSGKTTLLQKLAL 22 >gnl|CDD|144508 pfam00931, NB-ARC, NB-ARC domain. Length = 285 Score = 28.8 bits (65), Expect = 0.89 Identities = 10/17 (58%), Positives = 14/17 (82%) Query: 7 LIGASGVGKTTIAKQVV 23 ++G GVGKTT+AKQ+ Sbjct: 24 IVGMGGVGKTTLAKQIY 40 >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 = 29.0 bits (66), Expect = 0.89 Identities = 8/22 (36%), Positives = 13/22 (59%) Query: 5 FVLIGASGVGKTTIAKQVVLNS 26 VL+G GVGK+++ + N Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNK 23 >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 = 28.9 bits (65), Expect = 0.96 Identities = 9/20 (45%), Positives = 14/20 (70%) Query: 4 IFVLIGASGVGKTTIAKQVV 23 I +IG SG GK+T+ + +V Sbjct: 28 ILAIIGPSGSGKSTLLRLIV 47 >gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.. Length = 154 Score = 28.6 bits (64), Expect = 0.99 Identities = 9/17 (52%), Positives = 12/17 (70%) Query: 6 VLIGASGVGKTTIAKQV 22 VLIG G GKTT+ + + Sbjct: 3 VLIGMMGAGKTTVGRLL 19 >gnl|CDD|29990 cd01124, KaiC, KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.. Length = 187 Score = 28.7 bits (64), Expect = 1.0 Identities = 9/22 (40%), Positives = 11/22 (50%) Query: 4 IFVLIGASGVGKTTIAKQVVLN 25 +L G G GKTT A Q + Sbjct: 1 STLLSGGPGTGKTTFALQFLYA 22 >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 = 28.6 bits (64), Expect = 1.1 Identities = 7/20 (35%), Positives = 14/20 (70%) Query: 4 IFVLIGASGVGKTTIAKQVV 23 I ++G SG GK+T+ + ++ Sbjct: 36 ILAILGGSGSGKSTLLRLIL 55 >gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]. Length = 539 Score = 28.6 bits (64), Expect = 1.1 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 4 IFVLIGASGVGKTTIAK 20 L+G SG GK+T+A+ Sbjct: 319 TLGLVGESGSGKSTLAR 335 >gnl|CDD|36269 KOG1051, KOG1051, KOG1051, Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]. Length = 898 Score = 28.4 bits (63), Expect = 1.1 Identities = 30/104 (28%), Positives = 44/104 (42%), Gaps = 15/104 (14%) Query: 5 FVLIGASGVGKTTIAKQV---VLNSEYLVMPVGVTTRRPRVDEKQYI-DYRFI-SQSQFK 59 F+ +G GVGKT +AK + V SE + R+D ++ + I S + Sbjct: 594 FLFLGPDGVGKTELAKALAEYVFGSEENFI---------RLDMSEFQEVSKLIGSPPGYV 644 Query: 60 GWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQG 103 G + G E K R Y L E+I +ILL L +G Sbjct: 645 GKEEGGQLTEAVK-RRPYSVVLFEEIEKAHPDVLNILLQLLDRG 687 >gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131 Score = 28.3 bits (64), Expect = 1.3 Identities = 10/16 (62%), Positives = 11/16 (68%) Query: 7 LIGASGVGKTTIAKQV 22 L G G GKTT+AK V Sbjct: 3 LYGPPGTGKTTLAKAV 18 >gnl|CDD|30990 COG0645, COG0645, Predicted kinase [General function prediction only]. Length = 170 Score = 28.4 bits (63), Expect = 1.4 Identities = 6/20 (30%), Positives = 13/20 (65%) Query: 4 IFVLIGASGVGKTTIAKQVV 23 + ++ G G GK+T+A+ + Sbjct: 3 LVLVGGLPGSGKSTLARGLA 22 >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 = 28.2 bits (63), Expect = 1.4 Identities = 9/16 (56%), Positives = 12/16 (75%) Query: 3 HIFVLIGASGVGKTTI 18 VL+G SGVGK+T+ Sbjct: 162 KTSVLVGQSGVGKSTL 177 >gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction only]. Length = 296 Score = 28.0 bits (62), Expect = 1.4 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 8/82 (9%) Query: 2 AHIFVLI-GASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQY-------IDYRFI 53 + VL+ GA+G GK+++ + V VGV T Y D + Sbjct: 38 EPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGL 97 Query: 54 SQSQFKGWKHTGLFIETTKVRD 75 + K +H L+ + D Sbjct: 98 GDGKDKDAEHRQLYRDYLPKLD 119 >gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and secretion]. Length = 407 Score = 28.0 bits (62), Expect = 1.4 Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%) Query: 4 IFVLIGASGVGKTT-IAK 20 + L+G +GVGKTT +AK Sbjct: 205 VIALVGPTGVGKTTTLAK 222 >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 = 28.0 bits (62), Expect = 1.5 Identities = 7/19 (36%), Positives = 13/19 (68%) Query: 4 IFVLIGASGVGKTTIAKQV 22 I L+G +G GK+T+ + + Sbjct: 27 IVALVGPNGSGKSTLLRAI 45 >gnl|CDD|38564 KOG3354, KOG3354, KOG3354, Gluconate kinase [Carbohydrate transport and metabolism]. Length = 191 Score = 28.1 bits (62), Expect = 1.5 Identities = 9/19 (47%), Positives = 14/19 (73%) Query: 4 IFVLIGASGVGKTTIAKQV 22 + V++G SG GK+TI K + Sbjct: 14 VIVVMGVSGSGKSTIGKAL 32 >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 = 27.8 bits (62), Expect = 1.6 Identities = 7/17 (41%), Positives = 14/17 (82%) Query: 7 LIGASGVGKTTIAKQVV 23 ++G SGVGKT++ +++ Sbjct: 1 VVGDSGVGKTSLLNRLL 17 >gnl|CDD|30759 COG0410, LivF, ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]. Length = 237 Score = 28.1 bits (63), Expect = 1.6 Identities = 9/17 (52%), Positives = 12/17 (70%) Query: 4 IFVLIGASGVGKTTIAK 20 I L+G +G GKTT+ K Sbjct: 31 IVALLGRNGAGKTTLLK 47 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 27.9 bits (62), Expect = 1.6 Identities = 12/39 (30%), Positives = 18/39 (46%) Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPR 41 I VL+G SGVGK+T+ ++ + R R Sbjct: 165 KITVLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGR 203 >gnl|CDD|30189 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.. Length = 194 Score = 27.9 bits (62), Expect = 1.7 Identities = 7/20 (35%), Positives = 12/20 (60%) Query: 4 IFVLIGASGVGKTTIAKQVV 23 +L+G G GK T A+++ Sbjct: 1 RILLLGPPGSGKGTQAERLA 20 >gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]. Length = 219 Score = 28.0 bits (61), Expect = 1.8 Identities = 12/43 (27%), Positives = 20/43 (46%) Query: 5 FVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQY 47 V++G GVGKTT+ ++V + P + P + Y Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPY 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 = 27.7 bits (62), Expect = 1.8 Identities = 10/27 (37%), Positives = 19/27 (70%) Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLV 30 + L+G +G GK+T+AK ++ + +Y V Sbjct: 28 VHALMGPNGSGKSTLAKTIMGHPKYEV 54 >gnl|CDD|145019 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family. Length = 212 Score = 27.8 bits (62), Expect = 1.9 Identities = 8/16 (50%), Positives = 10/16 (62%) Query: 4 IFVLIGASGVGKTTIA 19 I + GVGKTT+A Sbjct: 1 IAIAGTKGGVGKTTLA 16 >gnl|CDD|33504 COG3709, COG3709, Uncharacterized component of phosphonate metabolism [Inorganic ion transport and metabolism]. Length = 192 Score = 27.6 bits (61), Expect = 1.9 Identities = 28/145 (19%), Positives = 56/145 (38%), Gaps = 11/145 (7%) Query: 1 MAHIFVLIGASGVGKTTI----AKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQS 56 M + ++G SG GK T+ ++ + +T E D+ +S++ Sbjct: 4 MGRLIAVVGPSGAGKDTLLDAARARLAGRPRLHFVRRVITRPADAGGE----DHDALSEA 59 Query: 57 QFKGWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVT 116 +F G F + + YG + +I+ + G +L+ + L ++ Y + Sbjct: 60 EFNTRAGQGAFALSWQAHGLSYG-IPAEIDLWLAAGDVVLVNGSRAVLPQARRRYPQLLV 118 Query: 117 SIFIAPPS--EAELIQRRIKRREDI 139 A P L +R + RE+I Sbjct: 119 VCITASPEVLAQRLAERGRESREEI 143 >gnl|CDD|31322 COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]. Length = 309 Score = 27.6 bits (61), Expect = 2.0 Identities = 11/19 (57%), Positives = 12/19 (63%) Query: 4 IFVLIGASGVGKTTIAKQV 22 VLIG SG GKTT K + Sbjct: 29 FLVLIGPSGSGKTTTLKMI 47 >gnl|CDD|33052 COG3240, COG3240, Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]. Length = 370 Score = 27.3 bits (60), Expect = 2.2 Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 6/73 (8%) Query: 22 VVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTGLFIETTKVRDEYYGYL 81 V+ + + P G + Q + S + G I +R + Y L Sbjct: 213 VMTLPDLSLTPAGKAYGTEAIQASQATIA--FNASLTSQLEQLGGNI----IRIDTYTLL 266 Query: 82 KEDINNPMEHGYD 94 KE + NP E G Sbjct: 267 KEIMTNPAEFGLA 279 >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 = 27.4 bits (61), Expect = 2.4 Identities = 9/16 (56%), Positives = 11/16 (68%) Query: 3 HIFVLIGASGVGKTTI 18 IF L+G +G GKTT Sbjct: 29 EIFGLLGHNGAGKTTT 44 >gnl|CDD|133347 cd04147, Ras_dva, Ras-dva subfamily. Ras-dva (Ras - dorsal-ventral anterior localization) subfamily consists of a set of proteins characterized only in Xenopus leavis, to date. In Xenopus Ras-dva expression is activated by the transcription factor Otx2 and begins during gastrulation throughout the anterior ectoderm. Ras-dva expression is inhibited in the anterior neural plate by factor Xanf1. Downregulation of Ras-dva results in head development abnormalities through the inhibition of several regulators of the anterior neural plate and folds patterning, including Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation of Ras-dva also interferes with the FGF-8a signaling within the anterior ectoderm. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Length = 198 Score = 27.5 bits (61), Expect = 2.4 Identities = 8/21 (38%), Positives = 16/21 (76%) Query: 6 VLIGASGVGKTTIAKQVVLNS 26 V +GA+GVGKT + ++ + ++ Sbjct: 3 VFMGAAGVGKTALIQRFLYDT 23 >gnl|CDD|133271 cd01868, Rab11_like, Rab11-like. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 165 Score = 27.5 bits (62), Expect = 2.4 Identities = 9/13 (69%), Positives = 11/13 (84%) Query: 6 VLIGASGVGKTTI 18 VLIG SGVGK+ + Sbjct: 7 VLIGDSGVGKSNL 19 >gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]. Length = 258 Score = 27.5 bits (61), Expect = 2.6 Identities = 7/18 (38%), Positives = 12/18 (66%) Query: 3 HIFVLIGASGVGKTTIAK 20 I ++G +G GK+T+ K Sbjct: 29 EITGILGPNGSGKSTLLK 46 >gnl|CDD|133249 cd00066, G-alpha, G protein alpha subunit. The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute. Length = 317 Score = 27.1 bits (61), Expect = 2.7 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 7 LIGASGVGKTTIAKQ 21 L+GA GK+TI KQ Sbjct: 5 LLGAGESGKSTILKQ 19 >gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction mechanisms]. Length = 889 Score = 27.2 bits (60), Expect = 2.8 Identities = 9/16 (56%), Positives = 13/16 (81%) Query: 7 LIGASGVGKTTIAKQV 22 + G GVGKTT+A+Q+ Sbjct: 184 IYGMGGVGKTTLARQI 199 >gnl|CDD|30813 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]. Length = 596 Score = 27.2 bits (60), Expect = 2.8 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 10/45 (22%) Query: 7 LIGASGVGKTTIAKQVVLN----------SEYLVMPVGVTTRRPR 41 L+G G GKT +AK V S+++ M VGV R R Sbjct: 188 LVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVR 232 >gnl|CDD|30672 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]. Length = 308 Score = 27.1 bits (60), Expect = 2.8 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 13/61 (21%) Query: 4 IFVLIGASGVGKTTIAKQVV--LNSE---------YLVMPVGVTTRRPRVDEKQYIDYRF 52 + V+ G + GKT +A + L E Y + +G T +P ++E + + Sbjct: 5 LIVIAGPTASGKTALAIALAKRLGGEIISLDSMQVYRGLDIG--TAKPSLEELAGVPHHL 62 Query: 53 I 53 I Sbjct: 63 I 63 >gnl|CDD|73178 COG4608, AppF, ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]. Length = 268 Score = 27.1 bits (60), Expect = 2.8 Identities = 7/20 (35%), Positives = 13/20 (65%) Query: 4 IFVLIGASGVGKTTIAKQVV 23 L+G SG GK+T+ + ++ Sbjct: 41 TLGLVGESGCGKSTLGRLIL 60 >gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]. Length = 709 Score = 27.1 bits (60), Expect = 2.8 Identities = 7/15 (46%), Positives = 11/15 (73%) Query: 6 VLIGASGVGKTTIAK 20 ++G SG GK+T+ K Sbjct: 503 AIVGRSGSGKSTLLK 517 >gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.. Length = 99 Score = 27.0 bits (59), Expect = 2.9 Identities = 9/16 (56%), Positives = 12/16 (75%) Query: 4 IFVLIGASGVGKTTIA 19 + V+ G GVGKTT+A Sbjct: 1 VIVVTGKGGVGKTTLA 16 >gnl|CDD|33633 COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]. Length = 352 Score = 27.2 bits (60), Expect = 2.9 Identities = 8/15 (53%), Positives = 10/15 (66%) Query: 4 IFVLIGASGVGKTTI 18 L+G SG GKTT+ Sbjct: 33 FVTLLGPSGCGKTTL 47 >gnl|CDD|177027 CHL00095, clpC, Clp protease ATP binding subunit. Length = 821 Score = 26.9 bits (60), Expect = 3.5 Identities = 10/15 (66%), Positives = 12/15 (80%) Query: 6 VLIGASGVGKTTIAK 20 +LIG GVGKT IA+ Sbjct: 204 ILIGEPGVGKTAIAE 218 >gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]. Length = 531 Score = 26.9 bits (59), Expect = 3.6 Identities = 10/33 (30%), Positives = 17/33 (51%) Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTR 38 ++G VGK+++ + +V PV TTR Sbjct: 272 AIVGRPNVGKSSLLNALSREDRSIVSPVPGTTR 304 >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 = 27.0 bits (60), Expect = 3.6 Identities = 8/15 (53%), Positives = 10/15 (66%) Query: 4 IFVLIGASGVGKTTI 18 L+G SG GKTT+ Sbjct: 28 FLALLGPSGCGKTTL 42 >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 = 26.7 bits (59), Expect = 3.7 Identities = 8/15 (53%), Positives = 12/15 (80%) Query: 6 VLIGASGVGKTTIAK 20 +IG SG GK+T+A+ Sbjct: 32 AIIGPSGSGKSTLAR 46 >gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]. Length = 299 Score = 26.8 bits (59), Expect = 3.7 Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%) Query: 1 MAHIFVLIG-ASGVGKTTIAKQV 22 + +LIG ASGVGK+TIA ++ Sbjct: 87 KRPLIILIGGASGVGKSTIAGEL 109 >gnl|CDD|133348 cd04148, RGK, RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ras superfamily members. The N-terminal extension is not conserved among family members; the C-terminal extension is reported to be conserved among the family and lack the CaaX prenylation motif typical of membrane-associated Ras proteins. However, a putative CaaX motif has been identified in the alignment of the C-terminal residues of this CD. Length = 221 Score = 26.6 bits (59), Expect = 3.9 Identities = 8/16 (50%), Positives = 14/16 (87%) Query: 6 VLIGASGVGKTTIAKQ 21 V++G+ GVGK+++A Q Sbjct: 4 VMLGSPGVGKSSLASQ 19 >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 = 26.7 bits (59), Expect = 3.9 Identities = 8/27 (29%), Positives = 18/27 (66%) Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLV 30 + ++G +G GK+T+A ++ + +Y V Sbjct: 32 VHAIMGPNGSGKSTLAYTIMGHPKYEV 58 >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 = 26.5 bits (59), Expect = 4.0 Identities = 7/15 (46%), Positives = 11/15 (73%) Query: 6 VLIGASGVGKTTIAK 20 ++G SG GK+T+ K Sbjct: 32 AIVGPSGSGKSTLLK 46 >gnl|CDD|72983 cd03224, ABC_TM1139_LivF_branched, LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.. Length = 222 Score = 26.6 bits (59), Expect = 4.0 Identities = 9/20 (45%), Positives = 14/20 (70%) Query: 4 IFVLIGASGVGKTTIAKQVV 23 I L+G +G GKTT+ K ++ Sbjct: 28 IVALLGRNGAGKTTLLKTIM 47 >gnl|CDD|35953 KOG0734, KOG0734, KOG0734, AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]. Length = 752 Score = 26.5 bits (58), Expect = 4.1 Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 10/46 (21%) Query: 6 VLIGASGVGKTTIAKQV----------VLNSEYLVMPVGVTTRRPR 41 +L+G G GKT +A+ V SE+ M VGV RR R Sbjct: 341 LLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMFVGVGARRVR 386 >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 = 26.5 bits (59), Expect = 4.3 Identities = 9/18 (50%), Positives = 14/18 (77%) Query: 6 VLIGASGVGKTTIAKQVV 23 +++G SGVGKT++ Q V Sbjct: 4 IILGDSGVGKTSLMNQYV 21 >gnl|CDD|32641 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]. Length = 515 Score = 26.6 bits (58), Expect = 4.3 Identities = 11/20 (55%), Positives = 15/20 (75%) Query: 1 MAHIFVLIGASGVGKTTIAK 20 +AH ++ G GVGKTTIA+ Sbjct: 37 IAHAYLFSGPRGVGKTTIAR 56 >gnl|CDD|31326 COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]. Length = 293 Score = 26.5 bits (58), Expect = 4.5 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 4 IFVLIGASGVGKTTIAK 20 IF L+G +G GKTT+ K Sbjct: 33 IFGLLGPNGAGKTTLLK 49 >gnl|CDD|133263 cd01860, Rab5_related, Rab5-related subfamily. This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. 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 = 163 Score = 26.3 bits (59), Expect = 4.5 Identities = 7/14 (50%), Positives = 11/14 (78%) Query: 6 VLIGASGVGKTTIA 19 VL+G S VGK+++ Sbjct: 5 VLLGDSSVGKSSLV 18 >gnl|CDD|145101 pfam01767, Birna_VP3, Birnavirus VP3 protein. VP3 is a minor structural component of the virus. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C). Length = 229 Score = 26.4 bits (58), Expect = 4.5 Identities = 25/100 (25%), Positives = 41/100 (41%), Gaps = 15/100 (15%) Query: 49 DYRFISQSQFKGWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGL---A 105 YR S QFK + TG + D+Y Y+ I P + L + GL Sbjct: 133 GYRGPSPGQFKYYLITGRDPDPG---DDYEDYIPPPITRPTDENKIRRLANSIYGLPHQE 189 Query: 106 PLKKLYEDQVTSIFIAP----PSEAE-----LIQRRIKRR 136 P + D+V +++ P++ + L+ RR+K R Sbjct: 190 PAPDAFYDEVAAVYAENQGRGPNQEQMRDLRLLARRMKSR 229 >gnl|CDD|37566 KOG2355, KOG2355, KOG2355, Predicted ABC-type transport, ATPase component/CCR4 associated factor [General function prediction only, Transcription]. Length = 291 Score = 26.5 bits (58), Expect = 4.5 Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 4/41 (9%) Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMP--VGVTTRRPRVDE 44 +L+GA+G GKTT+ K +L+ +++V V V R D Sbjct: 44 LLVGANGAGKTTLLK--ILSGKHMVGGGVVQVLGRSAFHDT 82 >gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular trafficking and secretion]. Length = 340 Score = 26.4 bits (58), Expect = 4.5 Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 1/19 (5%) Query: 3 HIFVLIGASGVGKTT-IAK 20 + + +G +GVGKTT IAK Sbjct: 140 FVILFVGVNGVGKTTTIAK 158 >gnl|CDD|73174 COG0470, HolB, ATPase involved in DNA replication [DNA replication, recombination, and repair]. Length = 325 Score = 26.4 bits (57), Expect = 4.6 Identities = 30/146 (20%), Positives = 58/146 (39%), Gaps = 19/146 (13%) Query: 1 MAHIFVLIGASGVGKTT----IAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQS 56 + H + G GVGKTT +AK+++ + ++P G + + D+ ++ S Sbjct: 23 LPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPS 82 Query: 57 QFKGWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGL------APLKKL 110 + + ++ + +P+E GY +++I L A LK L Sbjct: 83 DLRKIDI---------IVEQVRELAEFLSESPLEGGYKVVIIDEADKLTEDAANALLKTL 133 Query: 111 YEDQVTSIFIAPPSEAELIQRRIKRR 136 E + FI ++ I I+ R Sbjct: 134 EEPPKNTRFILITNDPSKILPTIRSR 159 >gnl|CDD|38232 KOG3022, KOG3022, KOG3022, Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]. Length = 300 Score = 26.4 bits (58), Expect = 4.6 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 4 IFVLIGASGVGKTTIAKQVVL 24 I VL G GVGK+T+ + L Sbjct: 50 ILVLSGKGGVGKSTVTVNLAL 70 >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 = 4.7 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 5/56 (8%) Query: 6 VLIGASGVGKTTIAKQVV-----LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQS 56 +IG SG GK+T+ + + + E L V +T + + K D I Q Sbjct: 34 AIIGPSGAGKSTLLRSLNGLVDPTSGEILFNGVQITKLKGKELRKLRRDIGMIFQQ 89 >gnl|CDD|34241 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]. Length = 580 Score = 26.4 bits (58), Expect = 4.8 Identities = 9/17 (52%), Positives = 14/17 (82%) Query: 7 LIGASGVGKTTIAKQVV 23 +IG SG GK+T+A+ +V Sbjct: 367 IIGPSGSGKSTLARLLV 383 >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 = 26.2 bits (58), Expect = 4.8 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 4 IFVLIGASGVGKTTIAK 20 L+G SG GK+T+A+ Sbjct: 33 TLGLVGESGSGKSTLAR 49 >gnl|CDD|37180 KOG1969, KOG1969, KOG1969, DNA replication checkpoint protein CHL12/CTF18 [Energy production and conversion, Replication, recombination and repair]. Length = 877 Score = 26.2 bits (57), Expect = 5.0 Identities = 12/36 (33%), Positives = 20/36 (55%) Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRR 39 I +L G G+GKTT+A + + Y V+ + + R Sbjct: 328 ILLLCGPPGLGKTTLAHVIAKQAGYSVVEINASDER 363 >gnl|CDD|35315 KOG0092, KOG0092, KOG0092, GTPase Rab5/YPT51 and related small G protein superfamily GTPases [Intracellular trafficking, secretion, and vesicular transport]. Length = 200 Score = 26.4 bits (58), Expect = 5.2 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 6 VLIGASGVGKTTIAKQVVLN 25 VL+G SGVGK+++ + V + Sbjct: 9 VLLGDSGVGKSSLVLRFVKD 28 >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 = 26.3 bits (59), Expect = 5.6 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 3 HIFVLIGASGVGKTTIAK 20 H ++IG G GKT +AK Sbjct: 23 HNLLMIGPPGSGKTMLAK 40 >gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.. Length = 165 Score = 26.2 bits (57), Expect = 5.6 Identities = 10/20 (50%), Positives = 15/20 (75%) Query: 6 VLIGASGVGKTTIAKQVVLN 25 ++ G +G GKTT+A Q+ LN Sbjct: 3 LVFGPTGSGKTTLALQLALN 22 >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 = 26.3 bits (58), Expect = 5.7 Identities = 8/16 (50%), Positives = 11/16 (68%) Query: 3 HIFVLIGASGVGKTTI 18 I L+G SG GK+T+ Sbjct: 27 EIVALLGPSGSGKSTL 42 >gnl|CDD|133342 cd04142, RRP22, RRP22 subfamily. RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated. Length = 198 Score = 26.0 bits (57), Expect = 5.7 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 7 LIGASGVGKTTIAKQVVLN 25 ++GA GVGKT I +Q + Sbjct: 5 VLGAPGVGKTAIVRQFLAQ 23 >gnl|CDD|72989 cd03230, ABC_DR_subfamily_A, This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 173 Score = 26.1 bits (58), Expect = 6.0 Identities = 9/17 (52%), Positives = 13/17 (76%) Query: 4 IFVLIGASGVGKTTIAK 20 I+ L+G +G GKTT+ K Sbjct: 28 IYGLLGPNGAGKTTLIK 44 >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 = 26.0 bits (57), Expect = 6.0 Identities = 7/20 (35%), Positives = 13/20 (65%) Query: 4 IFVLIGASGVGKTTIAKQVV 23 ++G SG GK+T+A+ + Sbjct: 35 TLGIVGESGSGKSTLARLLA 54 >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 = 26.0 bits (57), Expect = 6.1 Identities = 10/17 (58%), Positives = 12/17 (70%) Query: 4 IFVLIGASGVGKTTIAK 20 I L G +G GKTT+AK Sbjct: 28 IIALTGKNGAGKTTLAK 44 >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 = 6.1 Identities = 8/15 (53%), Positives = 12/15 (80%) Query: 6 VLIGASGVGKTTIAK 20 +LIG +G GK+T+ K Sbjct: 34 LLIGPNGSGKSTLLK 48 >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 = 6.2 Identities = 9/19 (47%), Positives = 15/19 (78%) Query: 4 IFVLIGASGVGKTTIAKQV 22 IFV++G SG GK+T+ + + Sbjct: 56 IFVIMGLSGSGKSTLVRLL 74 >gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. Length = 168 Score = 26.0 bits (58), Expect = 6.3 Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 1/21 (4%) Query: 3 HIFVLIGASGVGKTTIAKQVV 23 IF + G GVGKTT+ K+V+ Sbjct: 1 RIF-ITGPPGVGKTTLVKKVI 20 >gnl|CDD|32178 COG1995, PdxA, Pyridoxal phosphate biosynthesis protein [Coenzyme metabolism]. Length = 332 Score = 26.0 bits (57), Expect = 6.5 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 1/38 (2%) Query: 87 NPMEHGYDILLILTH-QGLAPLKKLYEDQVTSIFIAPP 123 YD +L + H QGL PLK L D+ ++ + P Sbjct: 253 PAYLANYDAVLAMYHDQGLIPLKYLGFDRGVNVTLGLP 290 >gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.. Length = 173 Score = 25.9 bits (57), Expect = 6.7 Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 3/41 (7%) Query: 3 HIFVLIGASGVGKTT-IAK--QVVLNSEYLVMPVGVTTRRP 40 + +L+G GVGKTT AK + V+ V T RP Sbjct: 1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRP 41 >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 = 25.9 bits (57), Expect = 6.8 Identities = 7/14 (50%), Positives = 10/14 (71%) Query: 7 LIGASGVGKTTIAK 20 L+G SG GK+T+ Sbjct: 33 LVGPSGSGKSTLVN 46 >gnl|CDD|143879 pfam00102, Y_phosphatase, Protein-tyrosine phosphatase. Length = 234 Score = 25.7 bits (57), Expect = 6.9 Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 1/45 (2%) Query: 21 QVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTG 65 V L SE T R + + R ++ + GW G Sbjct: 103 TVTLVSEETKEA-DYTVRTLELSNSGDDESRTVTHFHYTGWPDHG 146 >gnl|CDD|109737 pfam00693, Herpes_TK, Thymidine kinase from herpesvirus. Length = 279 Score = 25.7 bits (57), Expect = 6.9 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 9 GASGVGKTTIAKQVVLNSE 27 GA G+GKTT A+ + S Sbjct: 1 GAHGIGKTTTARALAAASS 19 >gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 269 Score = 25.9 bits (57), Expect = 7.0 Identities = 9/15 (60%), Positives = 13/15 (86%) Query: 4 IFVLIGASGVGKTTI 18 IFV++G SG GK+T+ Sbjct: 52 IFVIMGLSGSGKSTL 66 >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 = 25.9 bits (57), Expect = 7.0 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 4 IFVLIGASGVGKTTI 18 I LIG SG GK+T+ Sbjct: 28 ITALIGPSGCGKSTL 42 >gnl|CDD|35305 KOG0082, KOG0082, KOG0082, G-protein alpha subunit (small G protein superfamily) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 354 Score = 25.9 bits (57), Expect = 7.0 Identities = 9/18 (50%), Positives = 13/18 (72%) Query: 5 FVLIGASGVGKTTIAKQV 22 +L+GA GK+TI KQ+ Sbjct: 36 LLLLGAGESGKSTIVKQM 53 >gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]. Length = 338 Score = 26.0 bits (57), Expect = 7.1 Identities = 8/14 (57%), Positives = 10/14 (71%) Query: 4 IFVLIGASGVGKTT 17 VL+G SG GK+T Sbjct: 31 FVVLLGPSGCGKST 44 >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 = 25.8 bits (57), Expect = 7.3 Identities = 7/15 (46%), Positives = 10/15 (66%) Query: 4 IFVLIGASGVGKTTI 18 L+G SG GK+T+ Sbjct: 32 FVALVGPSGCGKSTL 46 >gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 744 Score = 25.7 bits (56), Expect = 7.3 Identities = 9/23 (39%), Positives = 16/23 (69%) Query: 6 VLIGASGVGKTTIAKQVVLNSEY 28 +L G G GKT +A ++ L+S++ Sbjct: 542 LLEGPPGSGKTALAAKIALSSDF 564 >gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.. Length = 271 Score = 25.6 bits (56), Expect = 7.3 Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 3/34 (8%) Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTT 37 + +L +GVGKTT ++ L L+ GV Sbjct: 32 LIILTAGTGVGKTTFLREYAL---DLITQHGVRV 62 >gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain [Cytoskeleton]. Length = 1930 Score = 26.0 bits (57), Expect = 7.4 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 4/44 (9%) Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYID 49 ++ G SG GKT K+V+ +YL V ++ + E D Sbjct: 172 LITGESGAGKTENTKKVI---QYLAS-VASSSTKKVKIEGTLED 211 >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 = 25.8 bits (57), Expect = 7.4 Identities = 5/15 (33%), Positives = 12/15 (80%) Query: 6 VLIGASGVGKTTIAK 20 +++G +G GK+T+ + Sbjct: 31 LIVGPNGSGKSTLLR 45 >gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]. Length = 366 Score = 25.7 bits (56), Expect = 7.5 Identities = 20/153 (13%), Positives = 47/153 (30%), Gaps = 16/153 (10%) Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDY----RFISQS 56 ++ G +G GKT K V+ E V V Y + + Sbjct: 41 RPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKV 100 Query: 57 QFKGWKHTGLFIETTKVRDEYYGYL---KEDINNPMEHGYDILLILTHQGLAPLKKLYED 113 G + + + ++++ ++ ++L L + Sbjct: 101 PLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLR-----APGENKV 155 Query: 114 QVTSIFIAPPSE-AELIQRRIKRR---EDIPFN 142 +V+ I ++ + + + R+K +I F Sbjct: 156 KVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFP 188 >gnl|CDD|37239 KOG2028, KOG2028, KOG2028, ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]. Length = 554 Score = 25.8 bits (56), Expect = 7.5 Identities = 9/22 (40%), Positives = 14/22 (63%) Query: 6 VLIGASGVGKTTIAKQVVLNSE 27 +L G G GKTT+A+ + S+ Sbjct: 166 ILWGPPGTGKTTLARLIASTSK 187 >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 = 25.9 bits (57), Expect = 7.6 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 4 IFVLIGASGVGKTTIAK 20 I ++G SG GK+ +AK Sbjct: 33 ILGIVGESGSGKSVLAK 49 >gnl|CDD|31323 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]. Length = 240 Score = 25.8 bits (57), Expect = 7.8 Identities = 8/16 (50%), Positives = 12/16 (75%) Query: 3 HIFVLIGASGVGKTTI 18 + V+IG SG GK+T+ Sbjct: 29 EVVVIIGPSGSGKSTL 44 >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 = 25.7 bits (56), Expect = 8.0 Identities = 7/22 (31%), Positives = 13/22 (59%) Query: 3 HIFVLIGASGVGKTTIAKQVVL 24 + ++ G +G GK+TI + L Sbjct: 22 SLTIITGPNGSGKSTILDAIGL 43 >gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.. Length = 217 Score = 25.6 bits (56), Expect = 8.0 Identities = 9/16 (56%), Positives = 10/16 (62%) Query: 4 IFVLIGASGVGKTTIA 19 + G GVGKTTIA Sbjct: 1 VIFFTGKGGVGKTTIA 16 >gnl|CDD|31413 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]. Length = 444 Score = 25.6 bits (56), Expect = 8.0 Identities = 9/17 (52%), Positives = 15/17 (88%) Query: 6 VLIGASGVGKTTIAKQV 22 ++IG +GVGKT IA+++ Sbjct: 54 LMIGPTGVGKTEIARRL 70 >gnl|CDD|36143 KOG0925, KOG0925, KOG0925, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]. Length = 699 Score = 25.7 bits (56), Expect = 8.0 Identities = 18/39 (46%), Positives = 21/39 (53%), Gaps = 1/39 (2%) Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPR 41 I VL+G +G GKTT Q VL E L GV +PR Sbjct: 63 QIIVLVGETGSGKTTQIPQFVLEYE-LSHLTGVACTQPR 100 >gnl|CDD|31624 COG1435, Tdk, Thymidine kinase [Nucleotide transport and metabolism]. Length = 201 Score = 25.6 bits (56), Expect = 8.2 Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 2/43 (4%) Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVD 43 M + + G GKT + + M V V P +D Sbjct: 3 MGWLEFIYGPMFSGKTEELLRRARRYKEAGMKVLVFK--PAID 43 >gnl|CDD|31330 COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 339 Score = 25.6 bits (56), Expect = 8.3 Identities = 9/15 (60%), Positives = 12/15 (80%) Query: 4 IFVLIGASGVGKTTI 18 IF +IG SG GK+T+ Sbjct: 34 IFGIIGYSGAGKSTL 48 >gnl|CDD|133344 cd04144, Ras2, Ras2 subfamily. The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Length = 190 Score = 25.6 bits (56), Expect = 8.4 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 6 VLIGASGVGKTTIAKQVVLNS 26 V++G GVGKT + Q+ LN Sbjct: 3 VVLGDGGVGKTALTIQLCLNH 23 >gnl|CDD|35304 KOG0081, KOG0081, KOG0081, GTPase Rab27, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 219 Score = 25.7 bits (56), Expect = 8.6 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 4/41 (9%) Query: 5 FVLIGASGVGKTTIAKQVV---LNSEYLVMPVGVTTRRPRV 42 F+ +G SGVGKT+ Q N+++ + VG+ R RV Sbjct: 12 FLALGDSGVGKTSFLYQYTDGKFNTQF-ISTVGIDFREKRV 51 >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 = 25.5 bits (56), Expect = 8.9 Identities = 7/14 (50%), Positives = 11/14 (78%) Query: 9 GASGVGKTTIAKQV 22 G +G GK+T+AK + Sbjct: 6 GPAGSGKSTVAKLL 19 >gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]. Length = 908 Score = 25.4 bits (55), Expect = 9.5 Identities = 7/17 (41%), Positives = 14/17 (82%) Query: 2 AHIFVLIGASGVGKTTI 18 + IF+++G +G GK++I Sbjct: 25 SGIFLIVGPNGAGKSSI 41 >gnl|CDD|73300 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.. Length = 169 Score = 25.4 bits (56), Expect = 9.6 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 4 IFVLIGASGVGKTTIAKQVVL 24 I V+ G GVGK+T+A + L Sbjct: 2 IAVMSGKGGVGKSTVAVNLAL 22 >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 = 25.5 bits (56), Expect = 9.7 Identities = 8/13 (61%), Positives = 10/13 (76%) Query: 6 VLIGASGVGKTTI 18 LIG SG GK+T+ Sbjct: 31 ALIGPSGAGKSTL 43 >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 = 25.3 bits (56), Expect = 9.9 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 2 AHIFVLIGASGVGKTTIA 19 A +L+G GVGKT +A Sbjct: 47 AENLLLLGPPGVGKTHLA 64 >gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]. Length = 161 Score = 25.3 bits (55), Expect = 9.9 Identities = 8/23 (34%), Positives = 14/23 (60%) Query: 1 MAHIFVLIGASGVGKTTIAKQVV 23 M I ++G GKTT+ +++V Sbjct: 1 MMKILGIVGYKNSGKTTLIEKLV 23 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 0.140 0.414 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: 2,374,858 Number of extensions: 126665 Number of successful extensions: 781 Number of sequences better than 10.0: 1 Number of HSP's gapped: 772 Number of HSP's successfully gapped: 184 Length of query: 186 Length of database: 6,263,737 Length adjustment: 88 Effective length of query: 98 Effective length of database: 4,362,145 Effective search space: 427490210 Effective search space used: 427490210 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: 54 (24.6 bits)