RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781211|ref|YP_003065624.1| hypothetical protein CLIBASIA_05590 [Candidatus Liberibacter asiaticus str. psy62] (234 letters) >gnl|CDD|132216 TIGR03172, TIGR03172, probable selenium-dependent hydroxylase accessory protein YqeC. This uncharacterized protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis. Instead, this family, and families TIGR03309 and TIGR03310 appear to mark selenium-dependent molybdenum hydroxylase maturation systems. Length = 232 Score = 33.2 bits (76), Expect = 0.062 Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 9/67 (13%) Query: 50 SSTEEAGEPKPPIEDYTLSCPDYVSEAEVTAH--IEAFKEAGVDARVAQKV-------VD 100 ++T P+PP+ DY L+ D +VT A E RV+ KV VD Sbjct: 31 TTTTRMFLPEPPLYDYFLTSHDGWVRDQVTKDTPRIAGIEFSALPRVSGKVRGFTPSTVD 90 Query: 101 KLVDHGR 107 L D Sbjct: 91 DLSDFQH 97 >gnl|CDD|161973 TIGR00639, PurN, phosphoribosylglycinamide formyltransferase, formyltetrahydrofolate-dependent. In phylogenetic analyses, the member from Saccharomyces cerevisiae shows a long branch length but membership in the family, while the formyltetrahydrofolate deformylases form a closely related outgroup. Length = 190 Score = 32.3 bits (74), Expect = 0.11 Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 18/99 (18%) Query: 80 AHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQFGASLEEERKLLQTKLGSDYETR---E 136 A I+A KE + A V + +K +G + Q G +L K D+ +R + Sbjct: 16 AIIDACKEGKIPASVVLVISNKPDAYGLERAAQAGI----PTFVLSLK---DFPSREAFD 68 Query: 137 KDIARYFRKEKIPDNDVQSLISAWGFEK--TFNFFDRYA 173 + I R + D L+ GF + F R+A Sbjct: 69 QAIIEELRAHE-VD-----LVVLAGFMRILGPTFLSRFA 101 >gnl|CDD|162581 TIGR01887, dipeptidaselike, dipeptidase, putative. This model represents a clade of probable zinc dipeptidases, closely related to the characterized non-specific dipeptidase, PepV. Many enzymes in this clade have been given names including the terms "Xaa-His" and "carnosinase" due to the early mis-characterization of the Lactobacillus delbrueckii PepV enzyme. These names are likely too specific. Length = 447 Score = 31.6 bits (72), Expect = 0.17 Identities = 10/23 (43%), Positives = 12/23 (52%) Query: 128 LGSDYETREKDIARYFRKEKIPD 150 G+D ET I YF E+ PD Sbjct: 136 FGTDEETGWACIDYYFEHEEAPD 158 >gnl|CDD|178379 PLN02782, PLN02782, Branched-chain amino acid aminotransferase. Length = 403 Score = 29.4 bits (66), Expect = 0.82 Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 4/44 (9%) Query: 10 PLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTE 53 P PS+ + S SNP SK + SSSS TE Sbjct: 24 PPPSSLSLRHSNSSVSSNPISSKA----ISLTRCDAVSSSSYTE 63 >gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional. Length = 504 Score = 29.0 bits (65), Expect = 0.94 Identities = 16/113 (14%), Positives = 37/113 (32%), Gaps = 10/113 (8%) Query: 9 TPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRN-PSSSSSSTEEAGEPKPPIE---D 64 V + + + DP+ R P+ + + EA P Sbjct: 366 RLNRLEKEVRSLRSAPTAAATAAGAPLPDFDPRPRGPPAPEPARSAEAPPLVAPAAAPAG 425 Query: 65 YTLSCPDYVSEAEVTAHIEAF-KEAGV---DARVAQKVVDKLVDHGRKIGEQF 113 L D ++ ++ + AF +EA + V+ ++ H ++ ++ Sbjct: 426 LALRWRDVLAALKMQ--LRAFLREARPHVEEGYVSLTFPERASFHYKQAQKKL 476 >gnl|CDD|183854 PRK13042, PRK13042, superantigen-like protein; Reviewed. Length = 291 Score = 28.8 bits (64), Expect = 1.1 Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 1/56 (1%) Query: 4 ETDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPK 59 E Q TP PST + + PP +K EA Q P PSS+ T ++ K Sbjct: 39 EAPQSTP-PSTKVEAPQSKPNATTPPSTKVEAPQQTPNATTPSSTKVETPQSPTTK 93 >gnl|CDD|180927 PRK07318, PRK07318, dipeptidase PepV; Reviewed. Length = 466 Score = 28.7 bits (65), Expect = 1.2 Identities = 9/23 (39%), Positives = 14/23 (60%) Query: 128 LGSDYETREKDIARYFRKEKIPD 150 +G+D E+ K + YF E+ PD Sbjct: 148 VGTDEESGWKCMDYYFEHEEAPD 170 >gnl|CDD|180107 PRK05472, PRK05472, redox-sensing transcriptional repressor Rex; Provisional. Length = 213 Score = 28.9 bits (66), Expect = 1.3 Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 7/33 (21%) Query: 83 EAFKEAGVD-------ARVAQKVVDKLVDHGRK 108 E KE ++ A AQ+V D+LV+ G K Sbjct: 140 EVVKENDIEIGILTVPAEAAQEVADRLVEAGIK 172 >gnl|CDD|132455 TIGR03414, ABC_choline_bnd, choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins. Length = 290 Score = 28.4 bits (64), Expect = 1.6 Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 13/50 (26%) Query: 65 YTLSCPDYVSEAEVT--AHIEAFK----------EAGVDA-RVAQKVVDK 101 YTL+ P YV++A + A I FK E G D R+ QK++DK Sbjct: 93 YTLAVPTYVADAGLKSFADIAKFKDKLDGKIYGIEPGNDGNRLIQKMIDK 142 >gnl|CDD|165700 PLN00131, PLN00131, hypothetical protein; Provisional. Length = 218 Score = 28.1 bits (62), Expect = 1.9 Identities = 30/133 (22%), Positives = 52/133 (39%), Gaps = 14/133 (10%) Query: 26 SNPPPSKEEAV--QSDPQGRNPSSSSSSTEEAGEPKPPIEDYTLSCPDYVSEAEVTAHIE 83 S+ PS+ + S PQ + ++ E+ EP PP++D L V+ + Sbjct: 88 SDAGPSRRPVLDLNSTPQPELDLNQPAAHEQEPEPAPPLDDQDL----LTKRKRVSEELR 143 Query: 84 AFKEAGVDARVAQKVVDKLVDHGRKIGEQFGASLEEERKLLQTKLGSDYETREKDIARYF 143 + G R K+ D+L+D G E +R LL Y+ E+ R Sbjct: 144 LLLQIGAVKR-KNKIADQLLD-------WMGLDNETDRTLLDDLYNHLYDLSEEQGRRVG 195 Query: 144 RKEKIPDNDVQSL 156 + + ++SL Sbjct: 196 QPQMFSSKGIKSL 208 >gnl|CDD|180861 PRK07157, PRK07157, acetate kinase; Provisional. Length = 400 Score = 28.2 bits (63), Expect = 1.9 Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 21/93 (22%) Query: 82 IEAFKEAGVDARVA-----QKVVDKLVDHGRKIGEQ-----FGASLEEE----RKLLQTK 127 I+A + A+ A QK+VD L ++ KIG++ F A + E R+L+ K Sbjct: 285 IKAAESGNKRAKFALDLYAQKIVDYLANYINKIGKKIDAIVFTAGVGENSAFVRELVINK 344 Query: 128 LGS-----DYETREKDIARYFRKEKI--PDNDV 153 + D E K I Y E I PD+D+ Sbjct: 345 INIPNIKLDKEKNLKKIGEYGPIELISTPDSDI 377 >gnl|CDD|169982 PRK09578, PRK09578, periplasmic multidrug efflux lipoprotein precursor; Reviewed. Length = 385 Score = 27.8 bits (62), Expect = 2.7 Identities = 10/35 (28%), Positives = 21/35 (60%) Query: 75 EAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKI 109 E+ ++A+++A V ARVA V + + G+++ Sbjct: 51 TVELPGRLDAYRQAEVRARVAGIVTARTYEEGQEV 85 >gnl|CDD|178748 PLN03209, PLN03209, translocon at the inner envelope of chloroplast subunit 62; Provisional. Length = 576 Score = 27.2 bits (60), Expect = 3.6 Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 11/105 (10%) Query: 2 SDETDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQG--------RNPSSSSSSTE 53 SD D P+P+ P E PP + +AV P + P+S + Sbjct: 333 SDAADGPKPVPTKPVTPEAPSPPIEEEPP-QPKAVVPRPLSPYTAYEDLKPPTSPIPTPP 391 Query: 54 EAGEPKPPIEDYT--LSCPDYVSEAEVTAHIEAFKEAGVDARVAQ 96 + D + PD V +++ + A V+A+ + Sbjct: 392 SSSPASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQVEAKKTR 436 >gnl|CDD|162811 TIGR02344, chap_CCT_gamma, T-complex protein 1, gamma subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT gamma chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. Length = 525 Score = 27.0 bits (60), Expect = 3.8 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 135 REKDIARYFRKEKIPDNDVQS 155 +E DI RY + EKIP D++ Sbjct: 187 KEIDIKRYAKVEKIPGGDIED 207 >gnl|CDD|181710 PRK09225, PRK09225, threonine synthase; Validated. Length = 462 Score = 27.0 bits (61), Expect = 4.2 Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 5/43 (11%) Query: 128 LGSDYETREKDIARYFRKEKIPDNDVQSLISAWGFEKTFNFFD 170 LG Y +I F + IP++D++++I + + FD Sbjct: 47 LGLSYAELAFEILSAFVGDDIPEDDLKAII-----ARAYTTFD 84 >gnl|CDD|177556 PHA03195, PHA03195, tegument protein VP11/12; Provisional. Length = 746 Score = 26.9 bits (59), Expect = 4.4 Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 3/59 (5%) Query: 2 SDETDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKP 60 S ET Q LPSTP +NP +E V + PQ +P S S+ + +P Sbjct: 539 STET-QYITLPSTPS--PTGEVVYTNPLLGPDEEVDASPQPVDPVSDYSAPKNPDYMRP 594 >gnl|CDD|149460 pfam08406, CbbQ_C, CbbQ/NirQ/NorQ C-terminal. This domain is found at the C-terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco. It is also found in the Thauera aromatica TutH protein which is similar to the CbbQ/NirQ/NorQ family, as well as in putative chaperones. The ATPase family associated with various cellular activities (AAA) pfam07728 is found in the same bacterial and archaeal proteins as the domain described here. Length = 86 Score = 27.1 bits (61), Expect = 4.6 Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 9/45 (20%) Query: 75 EAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQFGASLEE 119 EAE+ A E+GVD A K+V +L R + G LEE Sbjct: 1 EAEIVAK-----ESGVDEATAAKLV-RLAGRLRNLK---GHDLEE 36 >gnl|CDD|180169 PRK05625, PRK05625, 5-amino-6-(5-phosphoribosylamino)uracil reductase; Validated. Length = 217 Score = 26.7 bits (60), Expect = 5.3 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 7/42 (16%) Query: 72 YVSEAEVTAHIEAFKEAGVDARVA-------QKVVDKLVDHG 106 VSEA + +E ++ G + VA +++ L + G Sbjct: 99 AVSEAAPSEKVEELEKKGAEVIVAGGERVDLPDLLEDLYERG 140 >gnl|CDD|165506 PHA03247, PHA03247, large tegument protein UL36; Provisional. Length = 3151 Score = 26.5 bits (58), Expect = 5.8 Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 4/78 (5%) Query: 3 DETDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKPPI 62 D+T P+P++ P S PPP ++P S + +P P Sbjct: 403 DQTRPAAPVPASVPTPAPTPVPASAPPPPATPLPSAEP----GSDDGPAPPPERQPPAPA 458 Query: 63 EDYTLSCPDYVSEAEVTA 80 + PD + + A Sbjct: 459 TEPAPDDPDDATRKALDA 476 Score = 26.5 bits (58), Expect = 6.0 Identities = 17/59 (28%), Positives = 22/59 (37%), Gaps = 3/59 (5%) Query: 5 TDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQG--RNPSSSSSSTEEAGEPKPP 61 + P PS P V R + PP S D +G R P+ S + P PP Sbjct: 2570 PPRPAPRPSEPAVTSRAR-RPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP 2627 Score = 26.1 bits (57), Expect = 9.0 Identities = 11/54 (20%), Positives = 17/54 (31%) Query: 7 QLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKP 60 P P + PPP + P R + +T+ AG +P Sbjct: 2902 PDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEP 2955 >gnl|CDD|184075 PRK13478, PRK13478, phosphonoacetaldehyde hydrolase; Provisional. Length = 267 Score = 26.4 bits (59), Expect = 6.2 Identities = 9/26 (34%), Positives = 15/26 (57%) Query: 71 DYVSEAEVTAHIEAFKEAGVDARVAQ 96 D+ S A A +EAF + GV+ + + Sbjct: 17 DFGSFAPTQAFVEAFAQFGVEITLEE 42 >gnl|CDD|184913 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional. Length = 944 Score = 26.6 bits (59), Expect = 6.2 Identities = 6/46 (13%), Positives = 17/46 (36%) Query: 23 SQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKPPIEDYTLS 68 Q++ P + QS + +SS ++ + +++ Sbjct: 749 EQQATHQPQVQAEAQSPASTTALTQTSSEVQDTELNLVLLSSGSIT 794 >gnl|CDD|173619 PTZ00429, PTZ00429, beta-adaptin; Provisional. Length = 746 Score = 26.4 bits (58), Expect = 7.3 Identities = 19/86 (22%), Positives = 30/86 (34%), Gaps = 5/86 (5%) Query: 3 DETDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKPPI 62 E D LPSTP + + S + P+ + + G +S + P+ Sbjct: 613 TEDDDAVELPSTPSMGTQDGSPAPSAAPAGYDIFEFAGDGTGAPHPVASGSNGAQHADPL 672 Query: 63 EDYTLSCPDYVSEAEVTAHIEAFKEA 88 D P + V A AF+ A Sbjct: 673 GDLFSGLP-----STVGASSPAFQAA 693 >gnl|CDD|161747 TIGR00179, murB, UDP-N-acetylenolpyruvoylglucosamine reductase. This model describes MurB, UDP-N-acetylenolpyruvoylglucosamine reductase, which is also called UDP-N-acetylmuramate dehydrogenase. It is part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide that is a precursor of bacterial peptidoglycan. Length = 284 Score = 26.3 bits (58), Expect = 7.8 Identities = 11/31 (35%), Positives = 23/31 (74%), Gaps = 2/31 (6%) Query: 95 AQKVVDKLVDHGR-KIGEQFGASLEEERKLL 124 ++ V+D L++H + ++GE++G LE E K++ Sbjct: 254 SEDVLD-LIEHVKAEVGEKYGILLEPEVKII 283 >gnl|CDD|162812 TIGR02346, chap_CCT_theta, T-complex protein 1, theta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. Length = 531 Score = 26.2 bits (58), Expect = 7.8 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 11/61 (18%) Query: 75 EAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQFGASLEEERKLLQTKLGSDYET 134 E ++ A+I+A ++GV+ V V + H E+ ++ K+ S +E Sbjct: 265 ENQIEAYIKAIADSGVNVIVTGGSVGDMALH-----------YCEKYNIMVLKIPSKFEL 313 Query: 135 R 135 R Sbjct: 314 R 314 >gnl|CDD|165548 PHA03291, PHA03291, envelope glycoprotein I; Provisional. Length = 401 Score = 25.7 bits (56), Expect = 9.6 Identities = 9/61 (14%), Positives = 18/61 (29%), Gaps = 4/61 (6%) Query: 5 TDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPS----SSSSSTEEAGEPKP 60 D P P + + P + + + + + ++ E G P P Sbjct: 200 ADVFVPATPRPTPRTTASPETTPTPSTTTSPPSTTIPAPSTTIAAPQAGTTPEAEGTPAP 259 Query: 61 P 61 P Sbjct: 260 P 260 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 0.308 0.126 0.355 Gapped Lambda K H 0.267 0.0732 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,800,038 Number of extensions: 235391 Number of successful extensions: 628 Number of sequences better than 10.0: 1 Number of HSP's gapped: 620 Number of HSP's successfully gapped: 54 Length of query: 234 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 144 Effective length of database: 4,049,753 Effective search space: 583164432 Effective search space used: 583164432 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.6 bits) S2: 56 (25.3 bits)