RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781188|ref|YP_003065601.1| hypothetical protein CLIBASIA_05475 [Candidatus Liberibacter asiaticus str. psy62] (185 letters) >gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase. Length = 497 Score = 33.2 bits (76), Expect = 0.044 Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 11/76 (14%) Query: 17 GCIYYSPELFA-GILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQ-- 73 G IY SP LF G+L V GK++ V K + YR + DLKL A E L+ Sbjct: 340 GQIYLSPTLFELGVLPAVDVGKSVSRVGGKAQLAA----YRAVAGDLKLAYAQFEELETF 395 Query: 74 ----CRLDLLAEELLE 85 RLD + +E Sbjct: 396 ARFGARLDENTRKTIE 411 >gnl|CDD|162209 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum calcium-translocating P-type ATPase. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1, the latter of which is modelled by TIGR01522. Length = 917 Score = 31.3 bits (71), Expect = 0.15 Identities = 23/59 (38%), Positives = 30/59 (50%), Gaps = 6/59 (10%) Query: 25 LFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEEL 83 LF+G L V GKA G V+R GM ST I+ +++ E LQ +LD E L Sbjct: 152 LFSGTL--VVAGKARGVVVR-TGM---STEIGKIRDEMRAAEQEDTPLQKKLDEFGELL 204 >gnl|CDD|185239 PRK15339, PRK15339, type III secretion system outer membrane pore InvG; Provisional. Length = 559 Score = 29.4 bits (66), Expect = 0.66 Identities = 17/35 (48%), Positives = 18/35 (51%), Gaps = 7/35 (20%) Query: 94 LANPVFYSKMRDRKQRMGTF-------LLEKLSNQ 121 L PV SK+ RKQ G F LLEKLS Q Sbjct: 52 LKKPVIVSKLAARKQISGNFDLHDPNALLEKLSLQ 86 >gnl|CDD|132422 TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit. Members of this protein family are the membrane-anchoring, non-catalytic C subunit, product of the glpC gene, of a three-subunit, FAD-dependent, anaerobic glycerol-3-phosphate dehydrogenase. GlpC lasks classical hydrophobic transmembrane helices; Cole, et al suggest interaction with the membrane may involve amphipathic helices. GlcC has conserved Cys-containing motifs suggestive of iron-sulfur binding. This complex is found mostly in Escherichia coli and closely related species. Length = 397 Score = 28.2 bits (63), Expect = 1.4 Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 9/55 (16%) Query: 25 LFAGILDQVANGKALGHVLRKV-------GMPKYS--TFYRWIKKDLKLQEAYTE 70 FA I++ + K + +L K +PKYS TF RW KK+ Q Y Sbjct: 108 PFAPIVNAITGLKPVKKLLDKTLGVSKHRTLPKYSFGTFRRWYKKNATSQALYER 162 >gnl|CDD|183057 PRK11249, katE, hydroperoxidase II; Provisional. Length = 752 Score = 26.9 bits (60), Expect = 2.8 Identities = 9/11 (81%), Positives = 9/11 (81%) Query: 144 LREHYKHLKPI 154 L E YKHLKPI Sbjct: 684 LLEAYKHLKPI 694 >gnl|CDD|149086 pfam07820, TraC, TraC-like protein. The members of this family are sequences that are similar to TraC. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli CFN42 that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42a, which is also known as plasmid pSym as it carries most of the genes required for nodulation and nitrogen fixation by the symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58. Length = 92 Score = 26.6 bits (59), Expect = 3.5 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 5/55 (9%) Query: 132 KHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPL---EIVESSIAEQSIIEH 183 K + +R I +L+E K + ++ERI + + L EI E + Q+ E Sbjct: 2 KPSSKIREEIAKLQEQLKQAETREAERIGRIALKAGLGEIEIEEEEL--QAAFEE 54 >gnl|CDD|183822 PRK12900, secA, preprotein translocase subunit SecA; Reviewed. Length = 1025 Score = 26.7 bits (59), Expect = 4.2 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 9/56 (16%) Query: 131 SKHTID---LRPAIERLREHYKHLKPIDSERIPHKSTE------KPLEIVESSIAE 177 SKH D ++P I+R+ E L + + + K E LE +E + Sbjct: 11 SKHEKDIKKIQPIIDRINEIQASLASLSDDALREKGMELKSRVRGALEPIEQKKKD 66 >gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional. Length = 718 Score = 26.4 bits (58), Expect = 4.4 Identities = 26/90 (28%), Positives = 35/90 (38%), Gaps = 23/90 (25%) Query: 69 TEALQCRLDLLAE--ELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPR 126 T ALQC L+ E +LLEE A +QR F E + Sbjct: 249 TTALQCVLNTDIERTQLLEEEAQLVA--------------QQRELEFETETGKGK----- 289 Query: 127 VSVESKHTIDLRPAIERLREHYKHLKPIDS 156 +K +D +RL E YK L+ ID+ Sbjct: 290 --GANKDGVDKDAVSQRLEEIYKRLELIDA 317 >gnl|CDD|184034 PRK13405, bchH, magnesium chelatase subunit H; Provisional. Length = 1209 Score = 25.8 bits (57), Expect = 6.6 Identities = 6/13 (46%), Positives = 10/13 (76%) Query: 51 YSTFYRWIKKDLK 63 +S FYRW+++D Sbjct: 584 FSAFYRWLREDFG 596 >gnl|CDD|177911 PLN02271, PLN02271, serine hydroxymethyltransferase. Length = 586 Score = 25.5 bits (56), Expect = 7.6 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 6/42 (14%) Query: 38 ALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEAL---QCRL 76 AL L++V P+Y + + +KK+ + A AL +CRL Sbjct: 420 ALAIALKQVATPEYKAYMQQVKKNAQ---ALASALLRRKCRL 458 >gnl|CDD|183283 PRK11706, PRK11706, TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional. Length = 375 Score = 25.6 bits (57), Expect = 8.0 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 6/61 (9%) Query: 62 LKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANP-VFYSKMRDRKQRMGTFLLEKLSN 120 L L + Y +AL L +E P+ + N +FY K+RD + R + L+ L Sbjct: 257 LALWQRYYDALA---PLAEAGRIELPSIPDDCKHNAHMFYIKLRDLEDR--SALINFLKE 311 Query: 121 Q 121 Sbjct: 312 A 312 >gnl|CDD|115557 pfam06907, Latexin, Latexin. This family consists of several animal specific latexin proteins. Latexin is a carboxypeptidase A inhibitor and is expressed in a cell type-specific manner in both central and peripheral nervous systems in the rat. Length = 220 Score = 25.6 bits (56), Expect = 8.4 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%) Query: 120 NQKYGPRVSVESKHTIDLRPAIE---RLREHYKHLK-PIDSERIP 160 NQK P V+V + I + E R + K LK P++++ IP Sbjct: 77 NQKPRPEVNVTCERLIGKKKRQEEDYRFYKQLKQLKRPLEAQSIP 121 >gnl|CDD|161784 TIGR00238, TIGR00238, KamA family protein. Note that the E. coli homolog was expressed in E. coli and purified and found not to display display lysine 2,3-aminomutase activity. Active site residues are found in 100 residue extension in B. subtilis. Name changed to KamA family protein. Length = 331 Score = 25.6 bits (56), Expect = 8.7 Identities = 13/55 (23%), Positives = 21/55 (38%) Query: 1 MSNLVKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFY 55 ++ +A K +R + L G+ D+ L L KVG+ Y Y Sbjct: 235 ITEEFAEAMKKLRTVNVTLLNQSVLLRGVNDRAQILAKLSIALFKVGIIPYYLHY 289 >gnl|CDD|162665 TIGR02025, BchH, magnesium chelatase, H subunit. This model represents the H subunit of the magnesium chelatase complex responsible for magnesium insertion into the protoporphyrin IX ring in the biosynthesis of both chlorophyll and bacteriochlorophyll. In chlorophyll-utilizing species, this gene is known as ChlH, while in bacteriochlorophyll-utilizing spoecies it is called BchH. Subunit H is the largest (~140kDa) of the three subunits (the others being BchD/ChlD and BchI/ChlI), and is known to bind protoporphyrin IX. Subunit H is homologous to the CobN subunit of cobaltochelatase and by anology with that enzyme, subunit H is believed to also bind the magnesium ion which is inserted into the ring. In conjunction with the hydrolysis of ATP by subunits I and D, a conformation change is believed to happen in subunit H causing the magnesium ion insertion into the distorted protoporphyrin ring. Length = 1216 Score = 25.5 bits (56), Expect = 9.4 Identities = 6/15 (40%), Positives = 11/15 (73%) Query: 49 PKYSTFYRWIKKDLK 63 +++ FYRW+ +D K Sbjct: 562 HQFAAFYRWLDRDFK 576 >gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. Length = 654 Score = 25.4 bits (56), Expect = 9.5 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 5/62 (8%) Query: 69 TEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQR-----MGTFLLEKLSNQKY 123 + LQ L+ LAE L P AE + +R+ K R + T LL LS +Y Sbjct: 425 KKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEY 484 Query: 124 GP 125 P Sbjct: 485 SP 486 >gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. Length = 495 Score = 25.3 bits (56), Expect = 9.6 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 6/37 (16%) Query: 64 LQEAYTEALQC------RLDLLAEELLEEPAPTAEEL 94 ++EAY A Q L+LLA+ LLE+ T EE+ Sbjct: 454 IEEAYKRAKQILTENRDELELLAKALLEKETITREEI 490 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 0.316 0.133 0.375 Gapped Lambda K H 0.267 0.0658 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,056,938 Number of extensions: 194148 Number of successful extensions: 462 Number of sequences better than 10.0: 1 Number of HSP's gapped: 462 Number of HSP's successfully gapped: 33 Length of query: 185 Length of database: 5,994,473 Length adjustment: 88 Effective length of query: 97 Effective length of database: 4,092,969 Effective search space: 397017993 Effective search space used: 397017993 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 54 (24.7 bits)