RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780291|ref|YP_003064704.1| hypothetical protein CLIBASIA_00880 [Candidatus Liberibacter asiaticus str. psy62] (475 letters) >gnl|CDD|179784 PRK04204, PRK04204, RNA 3'-terminal-phosphate cyclase; Provisional. Length = 343 Score = 30.6 bits (70), Expect = 0.92 Identities = 8/16 (50%), Positives = 10/16 (62%) Query: 420 TGRPVRVYNINKNSKN 435 TG+P R+ NI N N Sbjct: 27 TGKPFRITNIRANRPN 42 >gnl|CDD|150358 pfam09669, Phage_pRha, Phage regulatory protein Rha (Phage_pRha). Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that Rha is a phage regulatory protein. Length = 86 Score = 30.2 bits (69), Expect = 1.2 Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 3/31 (9%) Query: 412 PESYIKDSTGRPVRVYNINKNSKNEFILLEM 442 ES DS GR +Y + K+ F+LL M Sbjct: 34 IESSYTDSRGRKYPMYLLT---KDGFMLLVM 61 >gnl|CDD|182838 PRK10919, PRK10919, ATP-dependent DNA helicase Rep; Provisional. Length = 672 Score = 29.8 bits (67), Expect = 1.4 Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 4/34 (11%) Query: 387 QKRMFEKFLTQSKISTIFT--TRFTSSPESYIKD 418 Q R+FEKFL Q++I + T F S PE IKD Sbjct: 354 QSRVFEKFLMQNRIPYKISGGTSFFSRPE--IKD 385 >gnl|CDD|149078 pfam07811, TadE, TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues. Length = 43 Score = 30.0 bits (69), Expect = 1.5 Identities = 9/41 (21%), Positives = 21/41 (51%) Query: 17 GNITILTAIIIPLIITLITISTTCANILYHRASIEASADEA 57 G + A+++P+++ L+ + Y R ++ +A EA Sbjct: 1 GAAAVEFALVLPVLLLLLFGIVELGRLFYARQVLQNAAREA 41 >gnl|CDD|162399 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase. This alignment encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512. Length = 556 Score = 29.5 bits (67), Expect = 1.8 Identities = 35/197 (17%), Positives = 66/197 (33%), Gaps = 40/197 (20%) Query: 9 KTIFLSKKGNIT----ILTAIIIPLIITLITISTTCANILYHRASIEASADEALNHGIVL 64 KT+ K G +T + + + +IS +L A++E S+ L IV Sbjct: 247 KTVVFDKTGTLTTGKPTVVDV---EPLDDASISEEE--LLALAAALEQSSSHPLARAIVR 301 Query: 65 LCKDSDLTPQDITPPVLKDLET---SLIKNDFSIKEAAQIKKESSINYQGKIPLSQGTYL 121 K + + P +D+E ++ +E +I + + + L Sbjct: 302 YAKK-----RGLELPKQEDVEEVPGKGVEATVDGQEEVRIGNPRLLELAAEPISASPDLL 356 Query: 122 NLHAVYHVPLNSLERILLPHKQNMDIVVDVNKILNCHHKGIAVIADPWYKADTPMFVEAI 181 N + + + G+ + D + + EAI Sbjct: 357 NEGESQGKTVVFVAV-------------------DGELLGVIALRDQ-LRPEAK---EAI 393 Query: 182 NSLKSSKNIILGILTGD 198 +LK + I L +LTGD Sbjct: 394 AALKRAGGIKLVMLTGD 410 >gnl|CDD|163249 TIGR03399, RNA_3prim_cycl, RNA 3'-phosphate cyclase. Members of this protein family are RNA 3'-phosphate cyclase (6.5.1.4), an enzyme whose function is conserved from E. coli to human. The modification this enzyme performs enables certain RNA ligations to occur, although the full biological roll for this enzyme is not fully described. This model separates this enzyme from a related protein, present only in eukaryotes, localized to the nucleolus, and involved in ribosomal modification. Length = 326 Score = 28.8 bits (65), Expect = 2.8 Identities = 9/16 (56%), Positives = 11/16 (68%) Query: 420 TGRPVRVYNINKNSKN 435 TG+PVR+YNI N Sbjct: 25 TGKPVRIYNIRANRPK 40 >gnl|CDD|182203 PRK10034, PRK10034, fructuronate transporter; Provisional. Length = 447 Score = 28.7 bits (64), Expect = 3.1 Identities = 13/22 (59%), Positives = 17/22 (77%) Query: 23 TAIIIPLIITLITISTTCANIL 44 T+I++PLI +I ISTT ANI Sbjct: 227 TSILVPLIPAIIMISTTIANIW 248 >gnl|CDD|130575 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type ATPase. One member from Halobacterium is annotated as "molybdenum-binding protein" although no evidence can be found for this classification. Length = 562 Score = 28.4 bits (64), Expect = 3.7 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 9/52 (17%) Query: 147 IVVDVNKILNCHHKGIAVIADPWYKADTPMFVEAINSLKSSKNIILGILTGD 198 ++V VN G+ + D + + E I +LK + I +LTGD Sbjct: 388 VLVAVNG----ELAGVFALEDQ-LRPEA---KEVIQALKR-RGIEPVMLTGD 430 >gnl|CDD|182907 PRK11023, PRK11023, outer membrane lipoprotein; Provisional. Length = 191 Score = 28.1 bits (63), Expect = 5.2 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 3/36 (8%) Query: 83 DLETSLIKNDFSIKEAAQIKKESSIN---YQGKIPL 115 D T ++ + ++ + QIKKE+ IN YQGK+ L Sbjct: 46 DDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLL 81 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 27.7 bits (62), Expect = 6.1 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 4/34 (11%) Query: 358 IRDDVFQAQ----REGKYIILFADDIDRFSSIDQ 387 +R +V +A+ R GK ILF D++ RF+ Q Sbjct: 93 LRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQ 126 >gnl|CDD|128865 smart00602, VPS10, VPS10 domain. Length = 612 Score = 27.8 bits (62), Expect = 6.3 Identities = 8/50 (16%), Positives = 16/50 (32%), Gaps = 3/50 (6%) Query: 298 SQSYSWNIDNVHFIQANYSMFHSVYFNDEWSNIFTVAVPEHISKQDLPSH 347 S ++ + + I +F S +DE + +P L Sbjct: 38 SDFFNSSANKFKTILVKGYIFIS---SDEGKSFQKFTLPFPPLPSLLYHP 84 >gnl|CDD|181587 PRK08939, PRK08939, primosomal protein DnaI; Reviewed. Length = 306 Score = 27.9 bits (63), Expect = 6.4 Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 19/44 (43%) Query: 353 EISQWIRDDVFQAQREGKYIILFADDIDRFSSIDQKRMFEKFLT 396 ++S W+RD+V IL Q RM E+ T Sbjct: 230 QMSSWVRDEVLGV-------IL------------QYRMQEELPT 254 >gnl|CDD|183981 PRK13333, PRK13333, pantothenate kinase; Reviewed. Length = 206 Score = 27.6 bits (62), Expect = 6.5 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 9/60 (15%) Query: 393 KFLTQSKISTIFTTRFTSSPESYIKDSTGRPVRVYNINKNSKNEFILLEMTPHYINVTAY 452 F KI ++ F I +Y I+ N + E LL+ P+ IN+ Y Sbjct: 12 HFYQNGKIFSLSIEEFKRF---KIDQ------EIYYISVNEELEKKLLKCYPNAINLEPY 62 >gnl|CDD|181028 PRK07559, PRK07559, 2'-deoxycytidine 5'-triphosphate deaminase; Provisional. Length = 365 Score = 27.6 bits (62), Expect = 6.9 Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 2/29 (6%) Query: 112 KIPLSQGTYLNLHAVYHVPLNSLERILLP 140 +I L+ G L VY VPL LE + LP Sbjct: 75 EIDLTDGAVLETGCVYIVPL--LESLALP 101 >gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed. Length = 505 Score = 27.7 bits (61), Expect = 7.0 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%) Query: 411 SPESYIKD-STGRPVRVYNINKNSKNEFILLEMTPHYINVTAY 452 +PE Y+K G RV+ IN+N +NE I + P + + Y Sbjct: 239 APELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELY 281 >gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase. Length = 421 Score = 27.5 bits (61), Expect = 7.1 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 7/39 (17%) Query: 158 HHKGIA---VIADPWYKADTPMFVEAIN--SLKSSKNII 191 H KG A VI+ P AD PMFV +N + K + NI+ Sbjct: 194 HLKGGAKKVVISAP--SADAPMFVVGVNEKTYKPNMNIV 230 >gnl|CDD|128867 smart00604, MD, MD domain. Length = 145 Score = 27.5 bits (61), Expect = 8.2 Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 2/50 (4%) Query: 234 RPCRDPYTL--TPSIYGCAFIAINDISQQINDHYPQIKSIKEFNGDSQRY 281 R C L GCA+ ++ + I + E + +R Sbjct: 96 RFCTYAPVLERLSLTDGCAYEFVSTSDFSCDYFVVLIDGVDENGYNFRRT 145 >gnl|CDD|162366 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. Length = 720 Score = 27.1 bits (60), Expect = 9.6 Identities = 8/52 (15%), Positives = 18/52 (34%), Gaps = 4/52 (7%) Query: 214 IYSLKFPFFRGLGSQEYIGNRP----CRDPYTLTPSIYGCAFIAINDISQQI 261 + L ++ +DPY L + G F+ + ++Q + Sbjct: 150 LQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQAL 201 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 0.319 0.135 0.395 Gapped Lambda K H 0.267 0.0747 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,655,801 Number of extensions: 489117 Number of successful extensions: 1029 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1028 Number of HSP's successfully gapped: 30 Length of query: 475 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 378 Effective length of database: 3,898,497 Effective search space: 1473631866 Effective search space used: 1473631866 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 (21.8 bits) S2: 59 (26.5 bits)