RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764512|ref|YP_003065529.2| preprotein tranlocase protein [Candidatus Liberibacter asiaticus str. psy62] (108 letters) >gnl|CDD|145709 pfam02699, YajC, Preprotein translocase subunit. See. Length = 83 Score = 92.5 bits (231), Expect = 2e-20 Identities = 33/83 (39%), Positives = 56/83 (67%), Gaps = 1/83 (1%) Query: 19 SPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDD 78 S L ++ ++YFLLIRPQ+++ + EML +L++GD +VT GI GK+V+ +DD Sbjct: 1 SGLSSLLPLVLIFAIFYFLLIRPQQKRQKEHKEMLSSLKKGDEVVTIGGIHGKIVK-VDD 59 Query: 79 LELEVEIAENVRVRVVRSFVSEV 101 + +EIA+ V+V+V +S ++ V Sbjct: 60 DTVVLEIADGVKVKVDKSAIARV 82 >gnl|CDD|32047 COG1862, YajC, Preprotein translocase subunit YajC [Intracellular trafficking and secretion]. Length = 97 Score = 84.5 bits (209), Expect = 5e-18 Identities = 29/94 (30%), Positives = 56/94 (59%), Gaps = 1/94 (1%) Query: 15 TSATSPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVR 74 S L + ++ ++YFL+IRPQR++++ E+L +L++GD +VT GIVG V + Sbjct: 3 MQGGSGLVLLLPLVLIFAIFYFLIIRPQRKRMKEHQELLNSLKKGDEVVTIGGIVGTVTK 62 Query: 75 VIDDLELEVEIAENVRVRVVRSFVSEVQSKSEPV 108 V DD +E+E+ + +++ + ++ V K + Sbjct: 63 VGDD-TVEIELGDGTKIKFEKEAIATVLEKGDLK 95 >gnl|CDD|32283 COG2100, COG2100, Predicted Fe-S oxidoreductase [General function prediction only]. Length = 414 Score = 27.2 bits (60), Expect = 0.90 Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 12/72 (16%) Query: 37 LLIRPQRQQLQRRAEMLRNLRRGDSI---VTAAGIV---------GKVVRVIDDLELEVE 84 L+++P + R + + +RG+ + V G + +V+ VI+ E + Sbjct: 333 LILKPGEFGMHPRPRLPKPFKRGEVVKAEVVLPGRLKGEMLAVARDRVIAVINSNEGALL 392 Query: 85 IAENVRVRVVRS 96 + + V+VR+VR+ Sbjct: 393 VGDRVKVRIVRT 404 >gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 509 Score = 26.7 bits (59), Expect = 1.5 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 2/48 (4%) Query: 56 LRRGDSIVTAAGIVGKVVRVIDDLELEVEIAENVRVRVVRSFVSEVQS 103 L++GD IV A G G+V ++DDL ++ A V +SEV + Sbjct: 208 LKKGDIIV-AGGEYGRVRTMVDDLGKPIKEAG-PSKPVEILGLSEVPA 253 >gnl|CDD|28760 cd03118, alpha_CA_V, Carbonic anhydrase alpha, CA isozyme V_like subgroup. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidines. This vertebrate subgroup comprises isozyme V. CA V is the mitochondrial isozyme, which may play a role in gluconeogenesis and ureagenesis and possibly also in lipogenesis.. Length = 236 Score = 26.1 bits (57), Expect = 2.2 Identities = 11/34 (32%), Positives = 19/34 (55%) Query: 30 LAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIV 63 LAV+ FL + + LQ+ + L +R D++V Sbjct: 117 LAVIGVFLKLGAHHEGLQKLVDALPEVRHKDTVV 150 >gnl|CDD|173935 cd08176, LPO, Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked oeprons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded Lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to L-lactaldehyde. FucO is induced regardless of the respiratory conditions of the culture, remains fully active in the absence of oxygen. In the presence of oxygen, this enzyme becomes oxidatively inactivated by a metal-catalyzed oxidation mechanism. FucO is an iron-dependent metalloenzyme that is inactivated by other metals, such as zinc, copper, or cadmium. This enzyme can also reduces glycol aldehyde with similar efficiency. Beside L-1,2-propanediol, the enzyme is also able to oxidize methanol as alternative substrates. Length = 377 Score = 25.6 bits (57), Expect = 3.2 Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 5/34 (14%) Query: 62 IVT-----AAGIVGKVVRVIDDLELEVEIAENVR 90 IVT G+V KV V+D+ ++ I + V+ Sbjct: 33 IVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVK 66 >gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members. This group contains a structure identified as an arginate lyase. Other members are identified quinone reductases, alginate lyases, and other proteins related to the zinc-dependent dehydrogenases/reductases. QOR catalyzes the conversion of a quinone and NAD(P)H to a hydroquinone and NAD(P+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 336 Score = 25.2 bits (56), Expect = 4.0 Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 28/89 (31%) Query: 13 AITSATSPLEMAGLFF-VLAVVWYFLLIRP---------QRQQLQRRAEML--------- 53 I PL++ L + W F+ R Q + L A++L Sbjct: 246 LIVDPQEPLDLGPLKSKSASFHWEFMFTRSMFQTPDMIEQHEILNEVADLLDAGKLKTTL 305 Query: 54 ---------RNLRRGDSIVTAAGIVGKVV 73 NLR +++ + +GK+V Sbjct: 306 TETLGPINAENLREAHALLESGKTIGKIV 334 >gnl|CDD|146989 pfam04612, GspM, General secretion pathway, M protein. This is a family of membrane proteins involved in the secretion of a number of molecules in Gram-negative bacteria. The precise function of these proteins is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers. Length = 159 Score = 25.3 bits (56), Expect = 4.1 Identities = 9/36 (25%), Positives = 15/36 (41%) Query: 23 MAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRR 58 +L V+ Y L +P Q+ R L+ R+ Sbjct: 20 AVLGAVLLLVLLYLGLWQPLSQRRARAQRRLQAARQ 55 >gnl|CDD|110924 pfam01972, SDH_sah, Serine dehydrogenase proteinase. This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan. Length = 286 Score = 24.8 bits (54), Expect = 4.9 Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 2/36 (5%) Query: 23 MAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRR 58 ++ LF+ L ++++L+I PQ + Q LR +R Sbjct: 10 LSSLFWFL--LFFYLIIAPQMKMRQLIMARLRCIRE 43 >gnl|CDD|132877 cd07180, RNaseH_typeII_Archaea_like, Archaeal ribonuclease HII. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. Some archaeal RNase HII show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. Length = 204 Score = 24.5 bits (54), Expect = 5.9 Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%) Query: 62 IVTAAGIVGKVVR--VIDDLELE 82 +V+AA I+ KV R I++L+ E Sbjct: 139 VVSAASIIAKVERDREIEELKEE 161 >gnl|CDD|173650 cd05094, PTKc_TrkC, Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase C (TrkC); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some non-neural tissues including the developing heart. NT3/TrkC signaling plays an important role in the innervation of the cardiac conducting system and the development of smooth muscle cells. Mice deficient with NT3 and TrkC have multiple heart defects. NT3/TrkC signaling is also critical for the development and maintenance of enteric neurons that are important for the control of gut peristalsis. Length = 291 Score = 24.6 bits (53), Expect = 6.4 Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%) Query: 43 RQQLQRRAEMLRNLRRGDSIVTAAGIVG 70 R+ QR AE+L NL+ + IV G+ G Sbjct: 51 RKDFQREAELLTNLQH-EHIVKFYGVCG 77 >gnl|CDD|173769 cd08229, STKc_Nek7, Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A-related kinase 7. Serine/Threonine Kinases (STKs), Never In Mitosis gene A (NIMA)-related kinase 7 (Nek7) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek7 subfamily is one of a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Nek7 is required for mitotic spindle formation and cytokinesis. It is enriched in the centrosome and is critical for microtubule nucleation. Nek7 is activated by Nek9 during mitosis, and may regulate the p70 ribosomal S6 kinase. Length = 267 Score = 24.6 bits (53), Expect = 6.5 Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%) Query: 33 VW-YFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIV 69 VW YF+ + + + R M R+++ + +TA G+V Sbjct: 108 VWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVV 145 >gnl|CDD|132878 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication. Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with two other accessory proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. Length = 216 Score = 24.5 bits (54), Expect = 7.3 Identities = 9/13 (69%), Positives = 10/13 (76%) Query: 62 IVTAAGIVGKVVR 74 IV+AA IV KV R Sbjct: 145 IVSAASIVAKVTR 157 >gnl|CDD|39694 KOG4494, KOG4494, KOG4494, Cell surface ATP diphosphohydrolase Apyrase [Nucleotide transport and metabolism]. Length = 352 Score = 24.2 bits (52), Expect = 7.3 Identities = 11/80 (13%), Positives = 31/80 (38%), Gaps = 4/80 (5%) Query: 27 FFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDDLELEVEIA 86 FV A+++Y + R+ E + + GI ++ +I DL+ + + Sbjct: 16 GFVTAILFYSG---SHFNKSGRQEEHIAHANLYSPKKFDDGIEYRIA-LIADLDTDSKDG 71 Query: 87 ENVRVRVVRSFVSEVQSKSE 106 + + + + +++ Sbjct: 72 KTWKSYLKKGYLTVSADHKH 91 >gnl|CDD|143978 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. Length = 682 Score = 24.3 bits (53), Expect = 7.6 Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%) Query: 6 YAQSDAPAITSATSPLEMAGLFFVLA-VVWYF 36 +A S + I S S L + GL F+ A VW F Sbjct: 588 WANS-SQVINSYGSLLSVYGLMFLGAHFVWAF 618 >gnl|CDD|145017 pfam01654, Bac_Ubq_Cox, Bacterial Cytochrome Ubiquinol Oxidase. This family are the alternative oxidases found in many bacteria which oxidize ubiquinol and reduce oxygen as part of the electron transport chain. This family is the subunit I of the oxidase E. coli has two copies of the oxidase, bo and bd', both of which are represented here In some nitrogen fixing bacteria, e.g. Klebsiella pneumoniae this oxidase is responsible for removing oxygen in microaerobic conditions, making the oxidase required for nitrogen fixation. This subunit binds a single b-haem, through ligands at His186 and Met393 (using SW:P11026 numbering). In addition His19 is a ligand for the haem b found in subunit II. Length = 430 Score = 24.0 bits (53), Expect = 9.2 Identities = 13/44 (29%), Positives = 19/44 (43%) Query: 1 MFTTVYAQSDAPAITSATSPLEMAGLFFVLAVVWYFLLIRPQRQ 44 + T A S A S + L+ VL V +LL+R R+ Sbjct: 383 LLRTADAVSPVSAGQVLFSLIGFTLLYAVLFVAEVYLLLRYARK 426 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 0.324 0.135 0.368 Gapped Lambda K H 0.267 0.0748 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,199,201 Number of extensions: 58268 Number of successful extensions: 340 Number of sequences better than 10.0: 1 Number of HSP's gapped: 337 Number of HSP's successfully gapped: 39 Length of query: 108 Length of database: 6,263,737 Length adjustment: 75 Effective length of query: 33 Effective length of database: 4,643,062 Effective search space: 153221046 Effective search space used: 153221046 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (23.4 bits)