RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780715|ref|YP_003065128.1| 50S ribosomal protein L19 [Candidatus Liberibacter asiaticus str. psy62] (141 letters) >gnl|CDD|180025 PRK05338, rplS, 50S ribosomal protein L19; Provisional. Length = 116 Score = 180 bits (460), Expect = 1e-46 Identities = 70/121 (57%), Positives = 92/121 (76%), Gaps = 5/121 (4%) Query: 1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGIN 60 MN+I E++ E++ ++ +P+F PGDT+ V + EG+K RIQA+EGV IAR GRG+N Sbjct: 1 MNLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLN 55 Query: 61 KNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENTGK 120 + FTVRKISYG G+ R FPL+SP I I V+RRGKVRR+KLYYL++LRGKAARIKE Sbjct: 56 ETFTVRKISYGVGVERTFPLHSPRIDSIEVVRRGKVRRAKLYYLRELRGKAARIKERRDA 115 Query: 121 R 121 + Sbjct: 116 K 116 >gnl|CDD|130096 TIGR01024, rplS_bact, ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs. Length = 113 Score = 145 bits (368), Expect = 4e-36 Identities = 67/116 (57%), Positives = 84/116 (72%), Gaps = 5/116 (4%) Query: 1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGIN 60 N+I +++ E++ K+ LP F GDT+ V I EG K RIQ +EGV IAR G GI Sbjct: 1 QNLIKQIEQEQL-----KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIG 55 Query: 61 KNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKE 116 + FTVRKISYG G+ R+FPL+SP I I V+RRGKVRR+KLYYL++ RGKAARIKE Sbjct: 56 ETFTVRKISYGVGVERIFPLHSPNIDSIEVVRRGKVRRAKLYYLRERRGKAARIKE 111 >gnl|CDD|167649 PRK03963, PRK03963, V-type ATP synthase subunit E; Provisional. Length = 198 Score = 26.6 bits (59), Expect = 2.2 Identities = 14/40 (35%), Positives = 24/40 (60%) Query: 102 YYLQDLRGKAARIKENTGKRAKALNEEVRRAALPEKEMSK 141 Y L++ + +A +IKE KRA++ E + R A + E+ K Sbjct: 21 YILEEAQKEAEKIKEEARKRAESKAEWILRKAKTQAELEK 60 >gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated. Length = 156 Score = 26.3 bits (59), Expect = 2.9 Identities = 13/35 (37%), Positives = 17/35 (48%) Query: 104 LQDLRGKAARIKENTGKRAKALNEEVRRAALPEKE 138 L + R +AA I E KRA + EE + A E Sbjct: 65 LAEARAEAAEIIEQAKKRAAQIIEEAKAEAEAEAA 99 >gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase. Length = 147 Score = 26.2 bits (58), Expect = 3.0 Identities = 12/35 (34%), Positives = 19/35 (54%) Query: 104 LQDLRGKAARIKENTGKRAKALNEEVRRAALPEKE 138 L++ + +A I EN KR + EE + A E+E Sbjct: 56 LKEAKDEAQEIIENANKRGSEILEEAKAEAREERE 90 >gnl|CDD|150429 pfam09754, PAC2, PAC2 family. This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits. Length = 177 Score = 25.3 bits (56), Expect = 5.4 Identities = 6/31 (19%), Positives = 13/31 (41%) Query: 3 IIDELDHEEMVRIESKRSLPKFSPGDTLCVK 33 +I+ L+ E++ I+S P + Sbjct: 19 LIESLEAEKVGEIDSDELFPFRGRRPQVTFD 49 >gnl|CDD|149655 pfam08670, MEKHLA, MEKHLA domain. The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins. Length = 148 Score = 25.3 bits (56), Expect = 5.5 Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 14/48 (29%) Query: 10 EEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR 57 EE R E L K ++ +G Y GV I+ GR Sbjct: 83 EESGRKERCSELAK-----------VMQQG---FACLYSGVRISSMGR 116 >gnl|CDD|184421 PRK13961, PRK13961, phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional. Length = 296 Score = 25.2 bits (56), Expect = 5.7 Identities = 6/19 (31%), Positives = 10/19 (52%) Query: 79 PLYSPMIQDITVIRRGKVR 97 L + + ++ RGKVR Sbjct: 3 TLMESDLPSLPLLGRGKVR 21 >gnl|CDD|152495 pfam12060, DUF3541, Domain of unknown function (DUF3541). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 230 amino acids in length. Length = 228 Score = 25.0 bits (55), Expect = 6.7 Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 6/47 (12%) Query: 101 LYYLQDLRGKAARIKEN--TGKRAKALNEEVRRA----ALPEKEMSK 141 LY DL AR E L E +RR L +K M + Sbjct: 107 LYLGDDLLRFMARADEYGLKHPCDDKLREVLRRYDFKKYLTDKAMIE 153 >gnl|CDD|128878 smart00630, Sema, semaphorin domain. Length = 390 Score = 25.0 bits (55), Expect = 6.9 Identities = 6/25 (24%), Positives = 9/25 (36%) Query: 78 FPLYSPMIQDITVIRRGKVRRSKLY 102 P Y +Q ++ G LY Sbjct: 207 SPFYFNELQAAFLLPPGSESDDVLY 231 >gnl|CDD|167593 PRK03732, PRK03732, hypothetical protein; Provisional. Length = 114 Score = 24.9 bits (54), Expect = 7.1 Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 2/50 (4%) Query: 90 VIRRGKVRRSKLYYLQDLRGKAARIKENTGKRAKALNEEVRRAALPEKEM 139 +++ + R + L++++G +KE T A+A E +RR AL KE+ Sbjct: 32 IVKATHLGRDIMALLRNIKG--GEVKEYTQMMAEAREEALRRMALHAKEL 79 >gnl|CDD|180656 PRK06680, PRK06680, D-amino acid aminotransferase; Reviewed. Length = 286 Score = 24.5 bits (54), Expect = 8.9 Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 1/24 (4%) Query: 90 VIRRGKVRRSKLYYLQDLRGKAAR 113 +IRR +VR L YLQ RG A R Sbjct: 78 LIRRNRVR-EGLVYLQVTRGVARR 100 >gnl|CDD|162540 TIGR01809, Shik-DH-AROM, shikimate-5-dehydrogenase, fungal AROM-type. This model represents a clade of shikimate-5-dehydrogenases found in Corynebacterium, Mycobacteria and fungi. The fungal sequences are pentafunctional proteins known as AroM which contain the central five seven steps in the chorismate biosynthesis pathway. The Corynebacterium and Mycobacterial sequences represent the sole shikimate-5-dehydrogenases in species which otherwise have every enzyme of the chorismate biosynthesis pathway. Length = 282 Score = 24.5 bits (53), Expect = 9.2 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%) Query: 77 LFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENTGKRAKALNEEVR 130 ++ L S + DITVI R + S+L L G R++ ++G A+ + Sbjct: 141 VYALASLGVTDITVINRNPDKLSRLVDLGVQVGVITRLEGDSG--GLAIEKAAE 192 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 0.318 0.136 0.377 Gapped Lambda K H 0.267 0.0705 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,325,068 Number of extensions: 138117 Number of successful extensions: 254 Number of sequences better than 10.0: 1 Number of HSP's gapped: 252 Number of HSP's successfully gapped: 26 Length of query: 141 Length of database: 5,994,473 Length adjustment: 84 Effective length of query: 57 Effective length of database: 4,179,401 Effective search space: 238225857 Effective search space used: 238225857 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: 52 (23.9 bits)