RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780554|ref|YP_003064967.1| Holliday junction resolvase [Candidatus Liberibacter asiaticus str. psy62] (169 letters) >gnl|CDD|178813 PRK00039, ruvC, Holliday junction resolvase; Reviewed. Length = 164 Score = 232 bits (594), Expect = 4e-62 Identities = 78/157 (49%), Positives = 111/157 (70%), Gaps = 1/157 (0%) Query: 5 IRIIGIDPGLRRTGWGIVDVAGDNLCFVSSGTIVSCVRQSLAFRLCQLYEGLTDVIKNWR 64 +RI+GIDPGLRRTG+G+++V G L +V+SG I + L RL Q+Y+GL+++I ++ Sbjct: 2 MRILGIDPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEYQ 61 Query: 65 PEEAAVEQVFVNKDAVATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVIGVGHGDKK 124 P+E A+E+VF NK+ + LKLGQAR +AIL+ A +PV+EY P +KKAV+G G DK+ Sbjct: 62 PDEVAIEEVFFNKNPQSALKLGQARGVAILAAAQRGLPVAEYTPLQVKKAVVGYGRADKE 121 Query: 125 QIHMMLKMLMP-ESFFKGKDAADALAIAVCHAYHANS 160 Q+ M+K L+ K DAADALAIA+CHA+ S Sbjct: 122 QVQHMVKRLLNLPEIPKPDDAADALAIAICHAHRRQS 158 >gnl|CDD|129331 TIGR00228, ruvC, crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC. Length = 156 Score = 130 bits (327), Expect = 3e-31 Identities = 64/150 (42%), Positives = 96/150 (64%), Gaps = 1/150 (0%) Query: 7 IIGIDPGLRRTGWGIVDVAGDNLCFVSSGTIVSCVRQSLAFRLCQLYEGLTDVIKNWRPE 66 I+GIDPG R TG+G++ G L ++ SG I + V L RL +Y G+T++I ++P Sbjct: 1 ILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKV-DDLPSRLKLIYAGVTEIITQFQPN 59 Query: 67 EAAVEQVFVNKDAVATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVIGVGHGDKKQI 126 A+EQVF+ K+A + LKLGQAR +AI++ +PV EYA +K+ V+G+G +K Q+ Sbjct: 60 YFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQV 119 Query: 127 HMMLKMLMPESFFKGKDAADALAIAVCHAY 156 M++ L+ DAADALAIA+ HA+ Sbjct: 120 QHMVRRLLKLPANPQADAADALAIAITHAH 149 >gnl|CDD|185216 PRK15316, PRK15316, RatA-like protein; Provisional. Length = 2683 Score = 29.6 bits (66), Expect = 0.38 Identities = 13/37 (35%), Positives = 24/37 (64%), Gaps = 1/37 (2%) Query: 80 VATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVI 116 AT+++ Q++ + + +P L +PV+ Y PNT+ VI Sbjct: 813 FATVEIKQSQGVGLSTP-LNIVPVNSYIPNTVNYNVI 848 >gnl|CDD|149657 pfam08672, APC2, Anaphase promoting complex (APC) subunit 2. The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein. Length = 60 Score = 28.0 bits (63), Expect = 1.4 Identities = 6/11 (54%), Positives = 7/11 (63%) Query: 125 QIHMMLKMLMP 135 +IH MLKM Sbjct: 16 RIHSMLKMFPK 26 >gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions. Length = 99 Score = 27.9 bits (63), Expect = 1.4 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 9/66 (13%) Query: 5 IRIIGIDPGLRRTGWGIVDVAGDNLCFVSSGTIVSCVRQSLAFRLCQLYEGLTDVIKNWR 64 R++G+DPG + G +VD G ++ + L +IK ++ Sbjct: 1 KRVLGLDPGRKGIGVAVVDETGK---LADPLEVIPRTNKEADAAR------LKKLIKKYQ 51 Query: 65 PEEAAV 70 P+ + Sbjct: 52 PDLIVI 57 >gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this model. Length = 678 Score = 27.6 bits (62), Expect = 1.7 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 6/64 (9%) Query: 37 IVSCVRQSLAFRLCQLYEGLTDVIKNWRPEEAAVEQVFVNKDAVATLKLGQARAIAILSP 96 +V VRQ L ++ Q Y V+ + +E L+ + L P Sbjct: 558 LVEHVRQRLGRQITQQYLDEDGVLPVIT-LDPDLEAALAEA-----LQRDGEGELLDLEP 611 Query: 97 ALAR 100 AL Sbjct: 612 ALLE 615 >gnl|CDD|168156 PRK05656, PRK05656, acetyl-CoA acetyltransferase; Provisional. Length = 393 Score = 26.8 bits (59), Expect = 3.3 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%) Query: 75 VNKDAVATLKLGQARAIAILSPALARIPVSEYAPNTIKKAVIGVG 119 +N A A L + A+A A+ P LA+I + YA + A++G+G Sbjct: 250 LNDGAAAVLLMSAAKAKALGLPVLAKI--AAYANAGVDPAIMGIG 292 >gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon; Provisional. Length = 232 Score = 26.5 bits (59), Expect = 3.4 Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%) Query: 78 DAVATLKLGQARAIAILSPALARIPVSE 105 DA+A ++ A A+A P LA + +E Sbjct: 165 DALAAARV--AWALARRFPELAALSPAE 190 >gnl|CDD|180448 PRK06182, PRK06182, short chain dehydrogenase; Validated. Length = 273 Score = 26.5 bits (59), Expect = 3.9 Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%) Query: 5 IRIIGIDPGLRRTGWGIVDVAGDNLCFVSSGT 36 I ++ I+PG +T WG D+A D+L S Sbjct: 169 IDVVVIEPGGIKTEWG--DIAADHLLKTSGNG 198 >gnl|CDD|165505 PHA03246, PHA03246, large tegument protein UL36; Provisional. Length = 3095 Score = 26.1 bits (57), Expect = 4.7 Identities = 13/29 (44%), Positives = 17/29 (58%) Query: 32 VSSGTIVSCVRQSLAFRLCQLYEGLTDVI 60 +S G+ VSC+R SLAF GL V+ Sbjct: 89 LSPGSSVSCLRSSLAFLRIVFAYGLDTVL 117 >gnl|CDD|162567 TIGR01865, cas_Csn1, CRISPR-associated protein, Csn1 family. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only. Length = 805 Score = 25.5 bits (56), Expect = 6.7 Identities = 8/18 (44%), Positives = 12/18 (66%) Query: 6 RIIGIDPGLRRTGWGIVD 23 I+G+D G+ GW IV+ Sbjct: 2 YILGLDIGIASVGWAIVE 19 >gnl|CDD|178870 PRK00109, PRK00109, Holliday junction resolvase-like protein; Reviewed. Length = 138 Score = 25.5 bits (57), Expect = 7.3 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 13/66 (19%) Query: 4 SIRIIGIDPGLRRTGWGIVDVA-GDNLCFVSSG-TIVSCVRQSLAFRLCQLYEGLTDVIK 61 S RI+G+D G +R G VA D L + + + + L +IK Sbjct: 3 SGRILGLDVGTKRIG-----VAVSDPLGGTAQPLETIKRNNGTPDWDR------LEKLIK 51 Query: 62 NWRPEE 67 W+P+ Sbjct: 52 EWQPDG 57 >gnl|CDD|132144 TIGR03100, hydr1_PEP, hydrolase, ortholog 1, exosortase system type 1 associated. This group of proteins are members of the alpha/beta hydrolase superfamily. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present in the vicinity of a second, relatively unrelated enzyme (ortholog 2, TIGR03101) of the same superfamily. Length = 274 Score = 25.2 bits (55), Expect = 8.1 Identities = 12/49 (24%), Positives = 18/49 (36%) Query: 47 FRLCQLYEGLTDVIKNWRPEEAAVEQVFVNKDAVATLKLGQARAIAILS 95 L GL D + R + V + + A L+ Q + ILS Sbjct: 167 VNLGSSLRGLGDALLKARQKGDEVAHGGLAERMKAGLERFQGPVLFILS 215 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 0.323 0.136 0.406 Gapped Lambda K H 0.267 0.0637 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,794,783 Number of extensions: 171822 Number of successful extensions: 316 Number of sequences better than 10.0: 1 Number of HSP's gapped: 313 Number of HSP's successfully gapped: 20 Length of query: 169 Length of database: 5,994,473 Length adjustment: 87 Effective length of query: 82 Effective length of database: 4,114,577 Effective search space: 337395314 Effective search space used: 337395314 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 (22.0 bits) S2: 53 (24.4 bits)