RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781158|ref|YP_003065571.1| peptidyl prolyl cis-trans isomerase D signal peptide protein [Candidatus Liberibacter asiaticus str. psy62] (631 letters) >gnl|CDD|144291 pfam00639, Rotamase, PPIC-type PPIASE domain. Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline. Length = 95 Score = 35.3 bits (82), Expect = 0.053 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 7/79 (8%) Query: 280 QKEADEAFQSLKKGK-KFIQLA----EEQGKSLSDISLGSFSKEYIPDVSLADSIFSLAK 334 + +A+E + L+ G+ F +LA ++ + + LG F++ +P D++FSL K Sbjct: 17 KAKAEEILEQLQSGEDTFAELAREYSDDCPSAANGGDLGWFTRGQLPPE-FEDAVFSL-K 74 Query: 335 KGDFTPVIHGSFGYVIAHV 353 +G+ + + FGY I V Sbjct: 75 EGEISGPVKTPFGYHIIKV 93 >gnl|CDD|30890 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]. Length = 441 Score = 30.2 bits (68), Expect = 1.8 Identities = 23/103 (22%), Positives = 52/103 (50%), Gaps = 2/103 (1%) Query: 218 EKYKDNYRAPEYKRI-SYILFDVHEKEKKIEISNDELQAEYEKNKEKYFSPEIRTVEQLV 276 E+ ++ ++ KR+ +L + KE+K+E++ +E++AE E+ +Y + V +L Sbjct: 337 EELREEFKEEAEKRVKLGLLLEEIAKEEKLEVTEEEIKAEIEELARQYGGEQPEEVIKLY 396 Query: 277 FPNQKEADEAFQSLKKGKKF-IQLAEEQGKSLSDISLGSFSKE 318 + NQ+ D + + K + LA ++ + ++S E Sbjct: 397 YNNQELLDALKADILEEKAVDLLLANKKKVTEKEVSFEELMNE 439 >gnl|CDD|34165 COG4496, COG4496, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 100 Score = 29.9 bits (67), Expect = 2.5 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 5/61 (8%) Query: 495 TAEEVSSKANQL-VLEYSKEGKNFRDIGKNLGASLLTTNQINRMDNENKFFGYDGISQVF 553 T E+ S A +L V + KEG+ +RDI GAS T +++ R N +G DG + V Sbjct: 36 TINEIQSLAQRLQVAKMLKEGRTYRDIEDETGASTATISRVKRCLN----YGNDGYAMVL 91 Query: 554 S 554 Sbjct: 92 Q 92 >gnl|CDD|147705 pfam05698, Trigger_C, Bacterial trigger factor protein (TF) C-terminus. In the E. coli cytosol, a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the C-terminal region of the protein. Length = 162 Score = 29.5 bits (67), Expect = 2.6 Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 3/78 (3%) Query: 218 EKYKDNYRAPEYKRI-SYILFDVHEKEKKIEISNDELQAEYEKNKEKYFSPEIRTVEQLV 276 E+ ++ ++ KR+ ++ + KE+KIE++++E++ E E+ +Y E Sbjct: 80 EELREEFKEEAEKRVKLGLILEEIAKEEKIEVTDEEIKEEIEELASQYGMEPEEVKEF-- 137 Query: 277 FPNQKEADEAFQSLKKGK 294 + ++ + L + K Sbjct: 138 YKKNEQLSALKEDLLEEK 155 >gnl|CDD|99821 cd05778, DNA_polB_zeta_exo, inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. Length = 231 Score = 29.1 bits (66), Expect = 3.4 Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 10/54 (18%) Query: 187 FENRSVDYIVLNNRHVPAIADPSNAVLTQWFEKYKDN--YRAPEY--KRISYIL 236 EN V Y VL+ R I SN LT+W++ + +R EY KR+ L Sbjct: 180 LEN--VVYHVLHQR----IPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNL 227 >gnl|CDD|145500 pfam02388, FemAB, FemAB family. The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan. These proteins are also considered as a factor influencing the level of methicillin resistance. Length = 407 Score = 28.8 bits (65), Expect = 4.2 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 5/89 (5%) Query: 217 FEKYKDNYRAPEYKRISYILFD-----VHEKEKKIEISNDELQAEYEKNKEKYFSPEIRT 271 +EK D + ++Y+ FD + +K +K+E +L+A+ EKN ++ Sbjct: 219 YEKLLDTFGDKAEFTLAYLNFDEYLDELQQKLEKLEKDLAKLEADLEKNPNSKKKNKLAE 278 Query: 272 VEQLVFPNQKEADEAFQSLKKGKKFIQLA 300 +EQ + +K DEA + + K + LA Sbjct: 279 LEQQLASLEKRIDEAKELIAKYGNEVPLA 307 >gnl|CDD|145498 pfam02383, Syja_N, SacI homology domain. This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin. Length = 302 Score = 28.7 bits (65), Expect = 5.4 Identities = 12/38 (31%), Positives = 19/38 (50%) Query: 208 PSNAVLTQWFEKYKDNYRAPEYKRISYILFDVHEKEKK 245 S L++ +E+ + PE K+I Y FD H + K Sbjct: 260 GSEKKLSEAYEEAINYLNLPENKKIKYTWFDFHAECKG 297 >gnl|CDD|37128 KOG1917, KOG1917, KOG1917, Membrane-associated hematopoietic protein [General function prediction only]. Length = 1125 Score = 28.4 bits (63), Expect = 5.5 Identities = 15/78 (19%), Positives = 35/78 (44%), Gaps = 9/78 (11%) Query: 288 QSLKKGKKFIQLAEEQGKSLSDISLGSFSKEYIPDVSLADSIFSLAK------KGDFTPV 341 +S +K +K + + ++ +L+++ F+ Y+P + + + F+ + +G F Sbjct: 660 ESYRKNRKSLTMLDKLHTALTELC---FALNYVPPICVWEHTFAPREYLRQHLEGRFKRR 716 Query: 342 IHGSFGYVIAHVSNIKPS 359 + G Y KPS Sbjct: 717 LVGMLMYNQTTQEIAKPS 734 >gnl|CDD|37099 KOG1888, KOG1888, KOG1888, Putative phosphoinositide phosphatase [Lipid transport and metabolism]. Length = 868 Score = 28.4 bits (63), Expect = 5.7 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 5/69 (7%) Query: 181 QAKRFYFENRSVDY---IVLNNRHVPAIADPSNAVLTQWFEKYKD--NYRAPEYKRISYI 235 + +F+N Y I++ N P ++L + FE D N P R+ YI Sbjct: 322 ETAALHFDNLVQRYGNPIIILNLIKTNEKRPRESILREEFENAIDYLNQFLPPENRLKYI 381 Query: 236 LFDVHEKEK 244 +D+H+ K Sbjct: 382 HWDMHKHSK 390 >gnl|CDD|30630 COG0282, ackA, Acetate kinase [Energy production and conversion]. Length = 396 Score = 28.2 bits (63), Expect = 7.1 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 8/47 (17%) Query: 126 HGKDNKFSHDVFVSRLAREGINEKEYIDHYTKMLSRTDVVGMFVGGM 172 G + K + D+FV R+A+ YI Y L D + +F G+ Sbjct: 291 EGNEAKLALDMFVYRIAK-------YIGSYAAALGGLDAL-VFTAGI 329 >gnl|CDD|36377 KOG1162, KOG1162, KOG1162, Predicted small molecule transporter [Intracellular trafficking, secretion, and vesicular transport]. Length = 617 Score = 27.9 bits (62), Expect = 9.6 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 10/82 (12%) Query: 215 QWFEKYKDNYRAPEYKRISYILFDVHE-KEKKIEISNDELQAEYEKNKEKYFS---PEIR 270 +W + Y D YK + +L ++ E K E + + E + +E +F E+ Sbjct: 14 EWRQAYID------YKYLKKLLKEIIENKPSSEETTFLMVSEEGGEFEEVFFRRLDEELN 67 Query: 271 TVEQLVFPNQKEADEAFQSLKK 292 V + KEA E + L K Sbjct: 68 KVNKFYKEKVKEAREEAEELNK 89 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.317 0.135 0.381 Gapped Lambda K H 0.267 0.0790 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 7,510,755 Number of extensions: 410531 Number of successful extensions: 1220 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1220 Number of HSP's successfully gapped: 33 Length of query: 631 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 531 Effective length of database: 4,102,837 Effective search space: 2178606447 Effective search space used: 2178606447 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 (21.7 bits) S2: 60 (26.8 bits)