RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|255764512|ref|YP_003065529.2| preprotein tranlocase protein [Candidatus Liberibacter asiaticus str. psy62] (108 letters) >gnl|CDD|180149 PRK05585, yajC, preprotein translocase subunit YajC; Validated. Length = 106 Score = 87.3 bits (217), Expect = 9e-19 Identities = 32/99 (32%), Positives = 59/99 (59%), Gaps = 3/99 (3%) Query: 9 SDAPAITSA--TSPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAA 66 S+A A +A S L V ++YFL+IRPQ+++ + +ML +L +GD +VT Sbjct: 4 SNAYAQAAAPAGSGLSSLLPLVVFFAIFYFLIIRPQQKRQKEHKKMLSSLAKGDEVVTNG 63 Query: 67 GIVGKVVRVIDDLELEVEIAENVRVRVVRSFVSEVQSKS 105 GI+GKV +V +D + +E+ ++ +++ +S ++ V K Sbjct: 64 GIIGKVTKVSEDF-VIIELNDDTEIKIQKSAIAAVLPKG 101 >gnl|CDD|162016 TIGR00739, yajC, preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas. Length = 84 Score = 66.6 bits (163), Expect = 1e-12 Identities = 23/85 (27%), Positives = 51/85 (60%), Gaps = 1/85 (1%) Query: 19 SPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDD 78 S L ++ +++YFL+IRPQR++ + +++ +L++GD ++T GI+G V + I + Sbjct: 1 SFLTTLLPLVLIFLIFYFLIIRPQRKRRKAHKKLIESLKKGDKVLTIGGIIGTVTK-IAE 59 Query: 79 LELEVEIAENVRVRVVRSFVSEVQS 103 + +E+ +N + ++ + EV Sbjct: 60 NTIVIELNDNTEITFSKNAIVEVLP 84 >gnl|CDD|180609 PRK06531, yajC, preprotein translocase subunit YajC; Validated. Length = 113 Score = 35.9 bits (83), Expect = 0.002 Identities = 17/50 (34%), Positives = 28/50 (56%) Query: 26 LFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRV 75 + FV+ + F + R Q++Q Q R L +++GD +VT G+ G V V Sbjct: 7 IMFVVMLGLIFFMQRQQKKQAQERQNQLNAIQKGDEVVTIGGLYGTVDEV 56 >gnl|CDD|168286 PRK05886, yajC, preprotein translocase subunit YajC; Validated. Length = 109 Score = 30.6 bits (69), Expect = 0.088 Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%) Query: 36 FLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDDLELEVEIAENV 89 + R QR+ +Q ++ +L+ GD + T +G+ +V + DD +++EIA V Sbjct: 19 YFASRRQRKAMQATIDLHESLQPGDRVHTTSGLQATIVGITDD-TVDLEIAPGV 71 >gnl|CDD|183890 PRK13200, psaA, photosystem I P700 chlorophyll a apoprotein A1; Provisional. Length = 766 Score = 26.7 bits (59), Expect = 1.4 Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%) Query: 5 VYAQSDAPAITSATSPLEMAGLFFVLA-VVWYFLLI 39 ++AQ+ + I S S L GL F+ A VW F L+ Sbjct: 665 LWAQA-SQVINSYGSALSAYGLMFLGAHFVWAFSLM 699 >gnl|CDD|179265 PRK01259, PRK01259, ribose-phosphate pyrophosphokinase; Provisional. Length = 309 Score = 26.2 bits (59), Expect = 1.9 Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 4/36 (11%) Query: 73 VRVIDDLELEVEIAENVRVRVVRSFVSEVQSKSEPV 108 V D E+ VEI ENVR + V F+ +QS P Sbjct: 29 VGRFSDGEISVEINENVRGKDV--FI--IQSTCAPT 60 >gnl|CDD|162278 TIGR01272, gluP, glucose/galactose transporter. Disruption of the loci leads to the total loss of glucose or galactose uptake in E.coli. Putative transporters in other bacterial species were isolated by functional complementation, which restored it functional activity. Length = 310 Score = 25.6 bits (56), Expect = 2.7 Identities = 13/54 (24%), Positives = 24/54 (44%) Query: 7 AQSDAPAITSATSPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGD 60 A ++A A T L +AG VLA+++ FL + ++ R ++ Sbjct: 82 ATANAEAAKVHTPYLLLAGALAVLAIIFAFLPLPELQEADVARVSSGDTTQKTS 135 >gnl|CDD|181802 PRK09367, PRK09367, histidine ammonia-lyase; Provisional. Length = 500 Score = 25.5 bits (57), Expect = 2.9 Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%) Query: 39 IRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKV 72 +R Q+ A LR L G SI+T++ +V Sbjct: 244 LRGHPGQIDV-AANLRALLEGSSIITSSHDCERV 276 >gnl|CDD|182846 PRK10929, PRK10929, putative mechanosensitive channel protein; Provisional. Length = 1109 Score = 25.4 bits (56), Expect = 3.2 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 15/43 (34%) Query: 33 VWYFLL-----IRP----QRQQL------QRRAEMLRNLRRGD 60 +W+ LL IR QR+++ QRRAE+L RG+ Sbjct: 709 IWFLLLVVYHIIRRWMLIQRRRIAFDRAKQRRAEILAQRARGE 751 >gnl|CDD|152094 pfam11658, DUF3260, Protein of unknown function (DUF3260). Some members in this family of proteins are annotated as YhjU however this cannot be confirmed. Currently this family has no known function. Length = 516 Score = 25.3 bits (56), Expect = 3.4 Identities = 6/18 (33%), Positives = 8/18 (44%) Query: 20 PLEMAGLFFVLAVVWYFL 37 +M FVL V + L Sbjct: 93 NWQMLLALFVLLVAYLLL 110 >gnl|CDD|150768 pfam10131, PTPS_related, 6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein. This domain is found in various bacterial hypothetical membrane proteins, as well as in tetratricopeptide TPR_2 repeat protein. The exact function of the domain has not, as yet, been established. Length = 620 Score = 25.1 bits (55), Expect = 4.4 Identities = 9/18 (50%), Positives = 11/18 (61%) Query: 27 FFVLAVVWYFLLIRPQRQ 44 FFV A+ WYF R R+ Sbjct: 34 FFVGALGWYFWGRRTGRR 51 >gnl|CDD|132411 TIGR03368, cellulose_yhjU, cellulose synthase operon protein YhjU. This protein was identified by the partial phylogenetic profiling algorithm (PubMed:16930487) as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation (PubMed:11929533). Length = 518 Score = 25.0 bits (55), Expect = 5.0 Identities = 5/18 (27%), Positives = 8/18 (44%) Query: 20 PLEMAGLFFVLAVVWYFL 37 +M FV+ V + L Sbjct: 94 NWQMLLAIFVVLVAYLLL 111 >gnl|CDD|184397 PRK13922, PRK13922, rod shape-determining protein MreC; Provisional. Length = 276 Score = 24.6 bits (54), Expect = 6.0 Identities = 6/20 (30%), Positives = 14/20 (70%) Query: 56 LRRGDSIVTAAGIVGKVVRV 75 +++G ++ G+VG+V+ V Sbjct: 146 VKKGMPVIDPGGLVGRVIEV 165 >gnl|CDD|169384 PRK08330, PRK08330, biotin--protein ligase; Provisional. Length = 236 Score = 24.7 bits (54), Expect = 6.0 Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 7/45 (15%) Query: 46 LQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDDLELEVE-IAENV 89 L+ E+L ++ S+ I+GK V++I D E+ VE IAE++ Sbjct: 170 LEGPGEILEEVKG-RSM-----ILGKRVKIIGDGEILVEGIAEDI 208 >gnl|CDD|163029 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid synthase PfaA. Members of the seed for this alignment are involved in omega-3 polyunsaturated fatty acid biosynthesis, such as the protein PfaA from the eicosapentaenoic acid biosynthesis operon in Photobacterium profundum strain SS9. PfaA is encoded together with PfaB, PfaC, and PfaD, and the functions of the individual polypeptides have not yet been described. More distant homologs of PfaA, also included with the reach of this model, appear to be involved in polyketide-like biosynthetic mechanisms of polyunsaturated fatty acid biosynthesis, an alternative to the more familiar iterated mechanism of chain extension and desaturation, and in most cases are encoded near genes for homologs of PfaB, PfaC, and/or PfaD. Length = 2582 Score = 24.6 bits (53), Expect = 6.6 Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 1/57 (1%) Query: 49 RAEMLRNLRRGDSIVTAAGIVGKVVRVIDDLELEVEIAENVRVRVVRSFVSEVQSKS 105 R +M +L G + A V +VV I + +E E V V + +V S Sbjct: 952 RKKMDDSLNDGW-TIKQATSVPQVVEKIVEKIVEKERIVEVERIVYLTADVKVFDGS 1007 >gnl|CDD|180380 PRK06066, PRK06066, acetyl-CoA acetyltransferase; Provisional. Length = 385 Score = 24.3 bits (53), Expect = 8.1 Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%) Query: 20 PLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAE 51 PLE +GL +L V Y +R + Q +AE Sbjct: 335 PLEASGLSLLLDAVEY---LRGEAGARQGKAE 363 >gnl|CDD|165951 PLN02310, PLN02310, triacylglycerol lipase. Length = 405 Score = 24.2 bits (52), Expect = 8.6 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%) Query: 46 LQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDDLELEVEIAENVRVRVVRSFVSEVQSKS 105 + R E R RR D +V G V DLE ++E +N V+V F+ +SK Sbjct: 120 VSRDEESQRIGRR-DIMVAWRGTVA-PSEWFLDLETKLEHIDNTNVKVQEGFLKIYKSKD 177 Query: 106 E 106 E Sbjct: 178 E 178 >gnl|CDD|129897 TIGR00816, tdt, C4-dicarboxylate transporter/malic acid transport protein. spanners (TMSs). Length = 320 Score = 23.9 bits (52), Expect = 8.9 Identities = 6/30 (20%), Positives = 10/30 (33%) Query: 11 APAITSATSPLEMAGLFFVLAVVWYFLLIR 40 IT L +A + + + IR Sbjct: 220 GEFITIKEPFLILAIILWGFGLWQLLFAIR 249 >gnl|CDD|171762 PRK12839, PRK12839, hypothetical protein; Provisional. Length = 572 Score = 24.0 bits (52), Expect = 9.2 Identities = 9/29 (31%), Positives = 18/29 (62%) Query: 57 RRGDSIVTAAGIVGKVVRVIDDLELEVEI 85 RRG +V + G+++R DDL +++ + Sbjct: 205 RRGMQLVNGTALTGRLLRSADDLGVDLRV 233 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 0.324 0.135 0.368 Gapped Lambda K H 0.267 0.0704 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,727,206 Number of extensions: 104989 Number of successful extensions: 455 Number of sequences better than 10.0: 1 Number of HSP's gapped: 454 Number of HSP's successfully gapped: 61 Length of query: 108 Length of database: 5,994,473 Length adjustment: 74 Effective length of query: 34 Effective length of database: 4,395,481 Effective search space: 149446354 Effective search space used: 149446354 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: 50 (23.1 bits)