RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781032|ref|YP_003065445.1| hypothetical protein CLIBASIA_04670 [Candidatus Liberibacter asiaticus str. psy62] (118 letters) >gnl|CDD|163236 TIGR03367, queuosine_QueD, queuosine biosynthesis protein QueD. Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea. Length = 92 Score = 119 bits (302), Expect = 1e-28 Identities = 44/92 (47%), Positives = 65/92 (70%), Gaps = 2/92 (2%) Query: 2 KITQAFTFEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIEQYFSP 61 +IT+ FTF+AAHRLP P KC +HGH+Y+VE+ + G+V + G V DF +++ Sbjct: 1 EITKEFTFDAAHRLPGYPG--KCANLHGHTYKVEVTVSGEVLDEAGMVMDFSDLKAIVKE 58 Query: 62 LLEKLDHHCLNEIEELENPTAENIAIWIWKRL 93 ++++LDH LN++ LENPTAEN+A WI+ RL Sbjct: 59 VVDRLDHALLNDVPGLENPTAENLARWIYDRL 90 >gnl|CDD|161674 TIGR00039, 6PTHBS, 6-pyruvoyl tetrahydropterin synthase/QueD family protein. This model has been downgraded from hypothetical_equivalog to subfamily. The animal enzymes are known to be 6-pyruvoyl tetrahydropterin synthase. The function of the bacterial branch of the sequence lineage had been thought to be the same, but many are now taken to be QueD, and enzyme of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of some tRNAs in most species. A new model is built to be the QueD equivalog model. Length = 124 Score = 100 bits (252), Expect = 7e-23 Identities = 48/122 (39%), Positives = 74/122 (60%), Gaps = 7/122 (5%) Query: 1 MKITQAFTFEAAHRLPRVPKTHKCHRMHGHSYRVELVMEGDVDPKTGFVDDFFNIEQYFS 60 I + F+F AAHRLP KC +HGHSY+V++ + G+ DPKTG V DF ++++ Sbjct: 2 FGIHKEFSFSAAHRLPGHEG--KCGNLHGHSYKVDVEVSGERDPKTGMVMDFSDLKKIVK 59 Query: 61 PLLEK-LDHHCLN-EIEELENPTAENIAIWIW---KRLSTSLSILSSVRVYETPMSWVEY 115 ++++ LDH LN ++ LENPT+EN+A++I+ K + L V+ ETP Y Sbjct: 60 EVIDEPLDHKLLNDDVNYLENPTSENVAVYIFDNLKEYLIPVENLVKVKEEETPAEIRIY 119 Query: 116 QG 117 +G Sbjct: 120 RG 121 >gnl|CDD|179359 PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 498 Score = 28.9 bits (65), Expect = 0.30 Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 5/38 (13%) Query: 15 LPRVPKTHKCHRMHGHSYRVELVME-GDVDPKTGFVDD 51 LP P H G +RVELV VD + DD Sbjct: 337 LPAAPLLHGLREYRGEPHRVELVATIDGVD----YYDD 370 >gnl|CDD|180957 PRK07395, PRK07395, L-aspartate oxidase; Provisional. Length = 553 Score = 26.5 bits (59), Expect = 1.6 Identities = 9/13 (69%), Positives = 9/13 (69%) Query: 6 AFTFEAAHRLPRV 18 A T EAAH PRV Sbjct: 113 ALTLEAAHSRPRV 125 >gnl|CDD|179505 PRK02936, argD, acetylornithine aminotransferase; Provisional. Length = 377 Score = 26.1 bits (58), Expect = 2.3 Identities = 11/32 (34%), Positives = 17/32 (53%) Query: 55 IEQYFSPLLEKLDHHCLNEIEELENPTAENIA 86 I++ F PLL H N+I+ L+ E +A Sbjct: 138 IKEGFGPLLPGFTHVPFNDIKALKEVMNEEVA 169 >gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase. Length = 421 Score = 25.9 bits (57), Expect = 2.6 Identities = 9/24 (37%), Positives = 13/24 (54%) Query: 79 NPTAENIAIWIWKRLSTSLSILSS 102 +P A ++ W RL SL I+ S Sbjct: 169 DPKARSLPRNDWYRLRRSLEIIKS 192 >gnl|CDD|181430 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau; Validated. Length = 535 Score = 25.8 bits (57), Expect = 2.6 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 8/48 (16%) Query: 38 MEGDVDPKTGFVDDFFNIEQYFSPLLEKLDHHCLNEIEELENPTAENI 85 M G +DP +E +F +L + ++ELE+ AE + Sbjct: 238 MLGLLDPSK--------LEDFFQAILNQDKEKLFELLKELEDYEAEMV 277 >gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift. Length = 360 Score = 25.8 bits (57), Expect = 3.0 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 8/51 (15%) Query: 9 FEA-AHRLPRVPKTHKCHRMHGHSYRVELVM------EGDVDPKTGFVDDF 52 FE+ HR+ RVP T R+H + V VM E D++P +D F Sbjct: 179 FESGVHRVQRVPVTESQGRIHTSAATV-AVMPELEEVEVDINPADLRIDTF 228 >gnl|CDD|183863 PRK13107, PRK13107, preprotein translocase subunit SecA; Reviewed. Length = 908 Score = 25.7 bits (56), Expect = 3.1 Identities = 11/14 (78%), Positives = 11/14 (78%) Query: 73 EIEELENPTAENIA 86 EIE LENPTAE A Sbjct: 522 EIEALENPTAEQKA 535 >gnl|CDD|162005 TIGR00707, argD, acetylornithine and succinylornithine aminotransferases. Members of this family may also act on ornithine, like ornithine aminotransferase (EC 2.6.1.13) (see MEDLINE:90337349) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17, DapC, an enzyme of lysine biosynthesis) (see MEDLINE:99175097). Length = 379 Score = 25.4 bits (56), Expect = 3.4 Identities = 8/32 (25%), Positives = 15/32 (46%) Query: 55 IEQYFSPLLEKLDHHCLNEIEELENPTAENIA 86 ++ F PL+ + N+IE L+ + A Sbjct: 141 YQKGFEPLVPGFSYAPYNDIESLKKAIDDETA 172 >gnl|CDD|180865 PRK07178, PRK07178, pyruvate carboxylase subunit A; Validated. Length = 472 Score = 25.1 bits (55), Expect = 3.9 Identities = 8/19 (42%), Positives = 12/19 (63%) Query: 43 DPKTGFVDDFFNIEQYFSP 61 DPK F+ F I +Y++P Sbjct: 342 DPKNDFLPSFGKITRYYAP 360 >gnl|CDD|130122 TIGR01050, rpsS_bact, ribosomal protein S19, bacterial/organelle. the Archaea may be designated S15 or S19. Length = 92 Score = 25.0 bits (55), Expect = 4.3 Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%) Query: 66 LDHHCLNEIEELENPTAENIAIWIWKRLST 95 +DHH L ++E+L N + + I W R ST Sbjct: 11 VDHHLLKKVEKL-NESGKKKVIKTWSRRST 39 >gnl|CDD|179074 PRK00591, prfA, peptide chain release factor 1; Validated. Length = 359 Score = 25.0 bits (56), Expect = 4.7 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 25 HRMHGHSYRVELVMEGDVDP 44 HR++ Y+++ VMEGD+D Sbjct: 321 HRINLTLYKLDEVMEGDLDE 340 >gnl|CDD|148810 pfam07412, Geminin, Geminin. This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle. Length = 200 Score = 24.8 bits (54), Expect = 4.9 Identities = 6/23 (26%), Positives = 14/23 (60%) Query: 57 QYFSPLLEKLDHHCLNEIEELEN 79 QY + ++E+L + +E L++ Sbjct: 159 QYMAEMIERLTGEPPDNLESLKS 181 >gnl|CDD|179453 PRK02627, PRK02627, acetylornithine aminotransferase; Provisional. Length = 396 Score = 24.7 bits (55), Expect = 5.2 Identities = 9/30 (30%), Positives = 15/30 (50%) Query: 57 QYFSPLLEKLDHHCLNEIEELENPTAENIA 86 + F PL+E + N+IE L+ + A Sbjct: 155 EGFEPLVEGFIYVPFNDIEALKAAITDKTA 184 >gnl|CDD|151067 pfam10510, PIG-S, Phosphatidylinositol-glycan biosynthesis class S protein. PIG-S is one of several key, core, components of the glycosylphosphatidylinositol (GPI) trans-amidase complex that mediates GPI anchoring in the endoplasmic reticulum. Anchoring occurs when a protein's C-terminal GPI attachment signal peptide is replaced with a pre-assembled GPI. Mammalian GPITransamidase consists of at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and PIG-U, all five of which are required for function. It is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a tightly associated core that is only weakly associated with PIG-U. The exact function of PIG-S is unclear. Length = 500 Score = 24.2 bits (53), Expect = 7.2 Identities = 6/14 (42%), Positives = 9/14 (64%) Query: 55 IEQYFSPLLEKLDH 68 +++Y PLLE L Sbjct: 214 LKEYIQPLLEALSP 227 >gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional. Length = 493 Score = 24.2 bits (53), Expect = 7.8 Identities = 9/24 (37%), Positives = 10/24 (41%), Gaps = 8/24 (33%) Query: 27 MHGHSYRVELVMEGDVDPKTGFVD 50 H SY VDP TG +D Sbjct: 193 FHQRSY--------GVDPDTGLLD 208 >gnl|CDD|183035 PRK11199, tyrA, bifunctional chorismate mutase/prephenate dehydrogenase; Provisional. Length = 374 Score = 24.1 bits (53), Expect = 8.1 Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 3/26 (11%) Query: 34 VELVMEGDVDPKTGFVDDFFNIEQYF 59 +EL+ +GD K F+D F +E +F Sbjct: 328 LELLEQGD---KQAFIDSFRKVEHWF 350 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 0.322 0.136 0.430 Gapped Lambda K H 0.267 0.0787 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,006,288 Number of extensions: 114850 Number of successful extensions: 210 Number of sequences better than 10.0: 1 Number of HSP's gapped: 207 Number of HSP's successfully gapped: 28 Length of query: 118 Length of database: 5,994,473 Length adjustment: 81 Effective length of query: 37 Effective length of database: 4,244,225 Effective search space: 157036325 Effective search space used: 157036325 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: 51 (23.3 bits)