RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781207|ref|YP_003065620.1| hypothetical protein CLIBASIA_05570 [Candidatus Liberibacter asiaticus str. psy62] (80 letters) >gnl|CDD|163264 TIGR03437, Soli_cterm, Solibacter uncharacterized C-terminal domain. This model describes a protein domain found in 90 proteins of Solibacter usitatus Ellin6076, nearly always as the C-terminal domain of a much larger protein. No homologs to this domain are detected outside of S. usitatus, a member of the Acidobacteria. Length = 215 Score = 29.2 bits (66), Expect = 0.23 Identities = 11/41 (26%), Positives = 18/41 (43%) Query: 11 AATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51 + G A ++ LA + V + GV A V+ AG + Sbjct: 134 PTSPAVADGAPAPSSPLAPALAPVTVTIGGVPATVLYAGLA 174 >gnl|CDD|151927 pfam11490, DNA_pol3_alph_N, DNA polymerase III polC-type N-terminus. This is an N-terminal domain of DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria. Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. The domain is associated with DNA_pol3_alpha pfam07733. Length = 180 Score = 28.1 bits (63), Expect = 0.59 Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%) Query: 50 ASDLAMHKMREQ-EEEEKKLLKKGLKKRQKN 79 +S+ + + EQ EEEE KL ++ L+ +K Sbjct: 140 SSEEEIEEFEEQKEEEEAKLAEEALEALKKK 170 >gnl|CDD|184359 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional. Length = 440 Score = 27.2 bits (61), Expect = 0.94 Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 1/38 (2%) Query: 15 GAVVGT-VATAAALATPIGWVGAAVAGVGAAVVGAGAS 51 GA VGT +A A G A G AA GA A+ Sbjct: 272 GAAVGTGLAAGGAAVAAAAGAGLAAGGGAAAAGGAAAA 309 Score = 26.0 bits (58), Expect = 2.2 Identities = 16/41 (39%), Positives = 17/41 (41%) Query: 11 AATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51 T A G AAA A GAA AG AA GA+ Sbjct: 275 VGTGLAAGGAAVAAAAGAGLAAGGGAAAAGGAAAAARGGAA 315 >gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional. Length = 472 Score = 26.5 bits (59), Expect = 1.5 Identities = 10/25 (40%), Positives = 20/25 (80%) Query: 56 HKMREQEEEEKKLLKKGLKKRQKNY 80 +K RE++E+EKK K+G ++R+ ++ Sbjct: 390 YKEREEKEKEKKAKKEGKEERRIHF 414 >gnl|CDD|173559 PTZ00366, PTZ00366, Surface antigen (SAG) superfamily; Provisional. Length = 392 Score = 26.5 bits (59), Expect = 1.6 Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 3/39 (7%) Query: 11 AATVGAVVGTV--ATAAALATPIGWVGAAVAGVGAAVVG 47 A + V+ TV A++A+ A+ V A +G AA+ G Sbjct: 349 ATSSCNVIVTVKAASSASSASSSLQVVATASGA-AALTG 386 >gnl|CDD|152276 pfam11840, DUF3360, Protein of unknown function (DUF3360). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 489 to 517 amino acids in length. Length = 491 Score = 26.2 bits (58), Expect = 2.1 Identities = 12/26 (46%), Positives = 17/26 (65%) Query: 7 ITSIAATVGAVVGTVATAAALATPIG 32 + ++AAT+G VV A AA A P+G Sbjct: 62 VPAMAATIGKVVMVSAVVAAFAAPLG 87 >gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional. Length = 112 Score = 26.0 bits (57), Expect = 2.3 Identities = 16/37 (43%), Positives = 17/37 (45%) Query: 32 GWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKKL 68 G AA GAA GA A K E+EEEE L Sbjct: 70 GVAAAAAPAAGAATAGAKAEAKKEEKKEEEEEEEDDL 106 >gnl|CDD|152736 pfam12301, CD99L2, CD99 antigen like protein 2. This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum. Length = 154 Score = 25.9 bits (57), Expect = 2.5 Identities = 9/32 (28%), Positives = 16/32 (50%) Query: 28 ATPIGWVGAAVAGVGAAVVGAGASDLAMHKMR 59 G + V+ V A++GA +S +A K + Sbjct: 107 GAETGTIAGIVSAVAVALLGAVSSYIAYQKKK 138 >gnl|CDD|149583 pfam08581, Tup_N, Tup N-terminal. The N-terminal domain of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor. Length = 79 Score = 25.7 bits (57), Expect = 2.6 Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 2/27 (7%) Query: 52 DLAMH--KMREQEEEEKKLLKKGLKKR 76 +L KM+++ EEE LK+ L+ R Sbjct: 50 ELEQAHRKMKQKYEEEIARLKRELEAR 76 >gnl|CDD|148271 pfam06566, Chon_Sulph_att, Chondroitin sulphate attachment domain. This family represents the chondroitin sulphate attachment domain of vertebrate neural transmembrane proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis. This domain contains several potential sites of chondroitin sulphate attachment, as well as potential sites of N-linked glycosylation. Length = 253 Score = 25.7 bits (56), Expect = 2.7 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 2/51 (3%) Query: 4 WNSITSIAATVGAVVGTVA--TAAALATPIGWVGAAVAGVGAAVVGAGASD 52 + S A VG VG A+A TP W+ A+ G+G AG+ D Sbjct: 45 PEEVGSEEAPVGPGVGPEEGLEASAAVTPTAWLEASSPGLGGVTAEAGSGD 95 >gnl|CDD|177560 PHA03231, PHA03231, glycoprotein BALF4; Provisional. Length = 829 Score = 25.3 bits (56), Expect = 3.2 Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 9/39 (23%) Query: 3 FWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGV 41 F + ++ VG VV VA A VG+ V+GV Sbjct: 667 FMQGLGAVGKAVGNVVSGVAGA---------VGSIVSGV 696 >gnl|CDD|129854 TIGR00771, DcuC, c4-dicarboxylate anaerobic carrier family protein. catalyzing fumarate-succinate exchange and fumarate uptake. Length = 388 Score = 25.2 bits (55), Expect = 3.8 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 1/58 (1%) Query: 1 MGFWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVG-AGASDLAMHK 57 + F +I A +G + A+A +G + +AGV G A S + K Sbjct: 320 IAFNTAIPPHAVELGYTHVNLGMPMAIAGALGRTASPIAGVVVVCAGLAMVSPFEVVK 377 >gnl|CDD|173571 PTZ00378, PTZ00378, hypothetical protein; Provisional. Length = 518 Score = 25.2 bits (55), Expect = 3.9 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 3/61 (4%) Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKKL 68 ++ V + G ATAA LA +G G+ +A S LA R+ E ++ Sbjct: 427 AVTVLVQTLAGNAATAAHLAVAMGARFLCSGGLFSAHQCEVVSQLA---SRQDELTHSRM 483 Query: 69 L 69 L Sbjct: 484 L 484 >gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612 Score = 25.0 bits (54), Expect = 4.0 Identities = 20/44 (45%), Positives = 23/44 (52%), Gaps = 2/44 (4%) Query: 12 ATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAM 55 ATV A+ A AAA AT + AA A GAAV+G A A Sbjct: 292 ATVSAIPAAAAVAAAAAT--AKIMAAEAVAGAAVLGPRAQSPAT 333 >gnl|CDD|115462 pfam06805, Lambda_tail_I, Bacteriophage lambda tail assembly protein I. This family consists of several Bacteriophage lambda tail assembly protein I and related phage and bacterial sequences. Members of this family are typically around 200 residues in length. The function of this family is unknown. Length = 194 Score = 25.1 bits (55), Expect = 4.1 Identities = 13/36 (36%), Positives = 16/36 (44%) Query: 16 AVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51 ++G V A T GA AG GA + GAS Sbjct: 93 TILGAVLIVAGFFTAGASAGAGAAGAGAFLFSLGAS 128 >gnl|CDD|131845 TIGR02798, ligK_PcmE, 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase. Members of this protein family 4-carboxy-4-hydroxy-2-oxoadipate aldolase, also called 4-oxalocitramalate aldolase. This enzyme of the protocatechuate 4,5-cleavage pathway converts its substrate to pyruvate plus oxaloacetate. Protocatechuate is an intermediate in many pathways for degrading aromatic compounds, including lignin, fluorene, etc. Hara, et al. showed the LigK gene was not only a 4-carboxy-4-hydroxy-2-oxoadipate aldolase but also the enzyme of the following step, oxaloacetate decarboxylase. Length = 222 Score = 24.8 bits (54), Expect = 5.0 Identities = 19/59 (32%), Positives = 26/59 (44%) Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKK 67 ++ AT+G+V V A AL P V A GV + L + RE EE K+ Sbjct: 137 TVKATLGSVNIPVVCANALVNPGDVVVADDDGVVVVPRANAGAVLDAAQAREANEEAKR 195 >gnl|CDD|149170 pfam07946, DUF1682, Protein of unknown function (DUF1682). The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322 Score = 24.9 bits (55), Expect = 5.3 Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 6/28 (21%) Query: 57 KMREQE------EEEKKLLKKGLKKRQK 78 + RE + EE++K +K KK + Sbjct: 294 EEREAKLAKLSPEEQRKYEEKERKKEAR 321 Score = 23.7 bits (52), Expect = 9.5 Identities = 9/26 (34%), Positives = 15/26 (57%) Query: 54 AMHKMREQEEEEKKLLKKGLKKRQKN 79 A + R++E +EKK KK ++ K Sbjct: 275 AAEEERQEEAQEKKEEKKKEEREAKL 300 >gnl|CDD|151650 pfam11208, DUF2992, Protein of unknown function (DUF2992). This bacterial family of proteins has no known function. Length = 132 Score = 24.5 bits (54), Expect = 5.4 Identities = 9/22 (40%), Positives = 15/22 (68%) Query: 57 KMREQEEEEKKLLKKGLKKRQK 78 K +++EE+E+K K KK+ K Sbjct: 107 KEKKEEEKERKRQLKQQKKKAK 128 >gnl|CDD|149683 pfam08703, PLC-beta_C, PLC-beta C terminal. This domain corresponds to the alpha helical C terminal domain of phospholipase C beta. Length = 185 Score = 24.4 bits (53), Expect = 6.5 Identities = 10/25 (40%), Positives = 17/25 (68%) Query: 55 MHKMREQEEEEKKLLKKGLKKRQKN 79 + K++E E+EKK LKK L +++ Sbjct: 58 LKKLKEICEKEKKELKKKLDRKRLE 82 >gnl|CDD|163530 TIGR03818, MotA1, flagellar motor stator protein MotA. This model represents one family of MotA proteins which are often not identified by the "transporter, MotA/TolQ/ExbB proton channel family" model, pfam01618. Length = 282 Score = 24.4 bits (54), Expect = 6.6 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%) Query: 14 VGAVVGTVATAAALATPIGWVGAAVAGVGAAVVG 47 V AV+G V T ++ P +G +A AA+VG Sbjct: 178 VAAVLGVVITMGSIDGPPEVLGVLIA---AALVG 208 >gnl|CDD|177761 PLN00162, PLN00162, transport protein sec23; Provisional. Length = 761 Score = 24.1 bits (53), Expect = 7.4 Identities = 11/25 (44%), Positives = 15/25 (60%) Query: 22 ATAAALATPIGWVGAAVAGVGAAVV 46 T AAL+ G +GA V G GA ++ Sbjct: 263 CTGAALSVAAGLLGACVPGTGARIM 287 >gnl|CDD|150600 pfam09946, DUF2178, Predicted membrane protein (DUF2178). This domain, found in various hypothetical archaeal proteins, has no known function. Length = 111 Score = 24.2 bits (53), Expect = 7.6 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 10/58 (17%) Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEK 66 I +GA+VG A G + V A + G A ++ E+E+ Sbjct: 9 LIVIIMGAIVG-------WAVSSGN---PLVAVLAVIAGILAIYFLKSRVDGVVEDER 56 >gnl|CDD|184041 PRK13413, mpi, multiple promoter invertase; Provisional. Length = 200 Score = 24.3 bits (53), Expect = 8.0 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 56 HKMREQEEEEKKLLKKGLKKR 76 +K+ +EE+ KKLL KG K Sbjct: 156 YKLTGKEEKIKKLLDKGTSKS 176 >gnl|CDD|163311 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3. Length = 251 Score = 24.0 bits (53), Expect = 8.1 Identities = 9/30 (30%), Positives = 14/30 (46%) Query: 51 SDLAMHKMREQEEEEKKLLKKGLKKRQKNY 80 +DL +H +E EE + L +R K Sbjct: 15 TDLLLHPEKELTPEELARFEALLARRAKGE 44 >gnl|CDD|151929 pfam11492, Dicistro_VP4, Cricket paralysis virus, VP4. This is a family of minor capsid proteins, known as VP4, from the dicistroviridae. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome. Length = 56 Score = 24.2 bits (53), Expect = 8.2 Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 3/40 (7%) Query: 5 NSITSIAATVGAVVGTVATA---AALATPIGWVGAAVAGV 41 I+ A+TV V +++ +A WV AV + Sbjct: 11 GVISKPASTVSEVASALSSIPVIGNIAKATSWVSDAVGDI 50 >gnl|CDD|147912 pfam06011, TRP, Transient receptor potential (TRP) ion channel. This family of proteins are transient receptor potential (TRP) ion channels. They are essential for cellular viability and are involved in cell growth and cell wall synthesis. The genes for these proteins are homologous to polycystic kidney disease related ion channel genes. Length = 532 Score = 24.1 bits (53), Expect = 8.5 Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 18/69 (26%) Query: 6 SITSIAATVGAVVGTVATAAALA------TP--------IGWVGAAVAGVGAAVVGA--- 48 ++ + ATV V + T LA + + W A +AG+G Sbjct: 106 TVPDLDATVRVGVYSTDTGTVLACVQATLSNGKTVSQKAVKWATAVIAGLGLLASAFASI 165 Query: 49 -GASDLAMH 56 G S+ A H Sbjct: 166 YGPSNTAAH 174 >gnl|CDD|162094 TIGR00893, 2A0114, d-galactonate transporter. Length = 399 Score = 23.8 bits (52), Expect = 8.8 Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 1/33 (3%) Query: 10 IAATVGAVVGTVATAAALATPIGWVGAAVAGVG 42 IA G ++ ++ + PI +GA A G Sbjct: 344 IAGLTGGLINSLGNLGGIVGPIV-IGAIAATTG 375 >gnl|CDD|178188 PLN02576, PLN02576, protoporphyrinogen oxidase. Length = 496 Score = 23.8 bits (52), Expect = 8.9 Identities = 12/26 (46%), Positives = 14/26 (53%) Query: 29 TPIGWVGAAVAGVGAAVVGAGASDLA 54 + I AA + AVVGAG S LA Sbjct: 1 SAIAEGSAAASSKDVAVVGAGVSGLA 26 >gnl|CDD|165416 PHA03145, PHA03145, helicase-primase primase subunit; Provisional. Length = 1058 Score = 23.8 bits (51), Expect = 8.9 Identities = 12/35 (34%), Positives = 15/35 (42%) Query: 17 VVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51 ++G +A A L P GW A G GA A Sbjct: 454 MLGRLAEAERLLVPHGWPAFAPPKPGEGDGGATAP 488 >gnl|CDD|173158 PRK14695, PRK14695, serine/threonine transporter SstT; Provisional. Length = 319 Score = 23.9 bits (51), Expect = 9.6 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 2/49 (4%) Query: 6 SITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLA 54 ++ +A T+ + T+ T L P+ + A V V AA+ GAS +A Sbjct: 211 NMAGVAITINLL--TLVTVNTLGIPVDFATAFVLSVVAAISACGASGIA 257 >gnl|CDD|177542 PHA03144, PHA03144, helicase-primase primase subunit; Provisional. Length = 746 Score = 23.9 bits (52), Expect = 9.8 Identities = 14/42 (33%), Positives = 17/42 (40%) Query: 3 FWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAA 44 WN T VG + + A AA A + AAVA A Sbjct: 572 LWNRRTDTEDFVGFPLRSAAARAAKAALRALLRAAVADSADA 613 >gnl|CDD|151469 pfam11022, DUF2611, Protein of unknown function (DUF2611). This family is conserved in the Dikarya of Fungi. The function is not known. Length = 70 Score = 23.9 bits (52), Expect = 9.8 Identities = 16/50 (32%), Positives = 24/50 (48%) Query: 31 IGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKKLLKKGLKKRQKNY 80 IG +G+ GV A G A A + ++E+K +K+ LKK K Sbjct: 19 IGTLGSLFGGVALATGGKKAPKPATPPINASSKDEEKFIKEFLKKHSKEE 68 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.313 0.126 0.355 Gapped Lambda K H 0.267 0.0827 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,278,754 Number of extensions: 75067 Number of successful extensions: 619 Number of sequences better than 10.0: 1 Number of HSP's gapped: 590 Number of HSP's successfully gapped: 189 Length of query: 80 Length of database: 5,994,473 Length adjustment: 50 Effective length of query: 30 Effective length of database: 4,914,073 Effective search space: 147422190 Effective search space used: 147422190 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (22.9 bits)