RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780236|ref|YP_003064649.1| 50S ribosomal protein L17 [Candidatus Liberibacter asiaticus str. psy62] (136 letters) >gnl|CDD|180154 PRK05591, rplQ, 50S ribosomal protein L17; Validated. Length = 113 Score = 191 bits (487), Expect = 6e-50 Identities = 72/111 (64%), Positives = 88/111 (79%) Query: 6 SGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRL 65 GRKL RTSSHRKAM N+A S+I HE+I TTLPKAKELR +VEKL+TL KKG LH+ R Sbjct: 3 KGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQ 62 Query: 66 AISKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFV 116 A +++ D + V+KLF IA RY+DR+GGY RI+K GFR GD+APMA+IE V Sbjct: 63 AFARLRDKEAVHKLFDEIAPRYADRNGGYTRILKLGFRRGDNAPMAIIELV 113 >gnl|CDD|129169 TIGR00059, L17, ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model. Length = 112 Score = 138 bits (349), Expect = 5e-34 Identities = 62/112 (55%), Positives = 82/112 (73%) Query: 6 SGRKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRL 65 S RKL RTS+HRKA+ N+A+++I HE+I TTL KAKELR +VEKL+TL K ++ R Sbjct: 1 SYRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRRE 60 Query: 66 AISKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKRGFRYGDSAPMAVIEFVD 117 A + I + ++V+KLF IA RY+ R GGY RI+K G R GD+A MA+IE VD Sbjct: 61 AKAYIRNKEIVHKLFSEIAPRYAQRPGGYTRILKLGPRRGDAAEMAIIELVD 112 >gnl|CDD|173371 PTZ00076, PTZ00076, 60S ribosomal protein L17; Provisional. Length = 253 Score = 59.0 bits (143), Expect = 4e-10 Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 1/112 (0%) Query: 8 RKLNRTSSHRKAMFSNMAASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAI 67 R+ + HR N ++ + ++ TLP+AKEL+ E+L+ L KK S Sbjct: 20 RRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVE 79 Query: 68 SKIGDVDVVNKLFGIIAKRYSDRSGGYLRIMKR-GFRYGDSAPMAVIEFVDR 118 S + KL+ Y DR + R++ + R D+APMA IEFVDR Sbjct: 80 SMLRTPQGRRKLYEKYVPLYRDRPFFFTRVVNQWRLRLRDAAPMAYIEFVDR 131 >gnl|CDD|181674 PRK09148, PRK09148, aminotransferase; Validated. Length = 405 Score = 30.8 bits (70), Expect = 0.14 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 12/83 (14%) Query: 43 ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNK------LFGIIAKRYSDRS----- 91 +L P + + TLG K G ++ AI+ GDV + FG I RS Sbjct: 88 KLNPDTQVVATLGSKEGFANMAQAITAPGDVILCPNPSYPIHAFGFIMAGGVIRSVPAEP 147 Query: 92 -GGYLRIMKRGFRYGDSAPMAVI 113 + ++R R+ P+A+I Sbjct: 148 DEEFFPALERAVRHSIPKPIALI 170 >gnl|CDD|181268 PRK08175, PRK08175, aminotransferase; Validated. Length = 395 Score = 28.9 bits (65), Expect = 0.50 Identities = 14/34 (41%), Positives = 19/34 (55%) Query: 43 ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVV 76 ++ P E +VT+G K GL L LA GD +V Sbjct: 87 DIDPESEAIVTIGSKEGLAHLMLATLDHGDTVLV 120 >gnl|CDD|181511 PRK08636, PRK08636, aspartate aminotransferase; Provisional. Length = 403 Score = 27.0 bits (60), Expect = 1.5 Identities = 14/34 (41%), Positives = 19/34 (55%) Query: 43 ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVV 76 +L P E + T+G K G L AI+ GDV +V Sbjct: 91 DLDPETEVVATMGSKEGYVHLVQAITNPGDVAIV 124 >gnl|CDD|147801 pfam05843, Suf, Suppressor of forked protein (Suf). This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and an important role of the GU-rich sequence for this regulation to occur. Length = 275 Score = 27.3 bits (61), Expect = 1.5 Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 16/57 (28%) Query: 32 EQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVVNKLFGIIAKRYS 88 E +VT L E +P+ +K SK GD+ + KL KR Sbjct: 94 ETVVTKLTPEPEAKPLWKKF---------IKYE---SKYGDLSSILKL----EKRMF 134 >gnl|CDD|162665 TIGR02025, BchH, magnesium chelatase, H subunit. This model represents the H subunit of the magnesium chelatase complex responsible for magnesium insertion into the protoporphyrin IX ring in the biosynthesis of both chlorophyll and bacteriochlorophyll. In chlorophyll-utilizing species, this gene is known as ChlH, while in bacteriochlorophyll-utilizing spoecies it is called BchH. Subunit H is the largest (~140kDa) of the three subunits (the others being BchD/ChlD and BchI/ChlI), and is known to bind protoporphyrin IX. Subunit H is homologous to the CobN subunit of cobaltochelatase and by anology with that enzyme, subunit H is believed to also bind the magnesium ion which is inserted into the ring. In conjunction with the hydrolysis of ATP by subunits I and D, a conformation change is believed to happen in subunit H causing the magnesium ion insertion into the distorted protoporphyrin ring. Length = 1216 Score = 27.0 bits (60), Expect = 1.7 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 4/75 (5%) Query: 30 WHEQIVTTLPKAKELRPIVE---KLVTLGKKGGLHSLRLAISKIGDVDVVNKLFGIIAKR 86 W ++++ + ++ + E +L+ L K G ++ K G V K+ R Sbjct: 73 WLREVLSQIRNQEDTVVVFESMPELMKLTKLGSF-AMGKPAEKSGMPKPVKKIADKSNGR 131 Query: 87 YSDRSGGYLRIMKRG 101 D+ GY++++K Sbjct: 132 GEDKLAGYMKLLKIV 146 >gnl|CDD|180317 PRK05942, PRK05942, aspartate aminotransferase; Provisional. Length = 394 Score = 26.2 bits (58), Expect = 3.2 Identities = 17/34 (50%), Positives = 18/34 (52%) Query: 43 ELRPIVEKLVTLGKKGGLHSLRLAISKIGDVDVV 76 EL P E L LG K GL L LA GDV +V Sbjct: 93 ELDPDSEALPLLGSKEGLTHLALAYVNPGDVVLV 126 >gnl|CDD|182898 PRK11010, ampG, muropeptide transporter; Validated. Length = 491 Score = 25.8 bits (57), Expect = 3.8 Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 2/30 (6%) Query: 71 GDVDVVNKLFGIIAKRYSDRSGGYLRIMKR 100 G+V +VNK G++A GG L M+R Sbjct: 258 GEVGLVNKTLGLLATIVGALYGGIL--MQR 285 >gnl|CDD|172445 PRK13932, PRK13932, stationary phase survival protein SurE; Provisional. Length = 257 Score = 24.7 bits (54), Expect = 7.1 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 59 GLHSLRLAISKIGDVDVV 76 G+H L ++ KIG V VV Sbjct: 20 GIHVLAASMKKIGRVTVV 37 >gnl|CDD|163500 TIGR03788, marine_srt_targ, marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092). Length = 596 Score = 24.7 bits (54), Expect = 7.9 Identities = 10/32 (31%), Positives = 16/32 (50%) Query: 7 GRKLNRTSSHRKAMFSNMAASIIWHEQIVTTL 38 G+K R +F+N A+I E +V T+ Sbjct: 77 GKKAALVEQQRPNLFTNKVANIGPGETVVVTI 108 >gnl|CDD|182374 PRK10316, PRK10316, hypothetical protein; Provisional. Length = 209 Score = 24.9 bits (54), Expect = 8.2 Identities = 15/41 (36%), Positives = 20/41 (48%) Query: 26 ASIIWHEQIVTTLPKAKELRPIVEKLVTLGKKGGLHSLRLA 66 AS+ E V T K ++ EK+ KKG + LRLA Sbjct: 113 ASVGISEDYVATPEKEAAIKIANEKMAKGDKKGAMEELRLA 153 >gnl|CDD|140343 PTZ00322, PTZ00322, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional. Length = 664 Score = 24.5 bits (53), Expect = 8.4 Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 4/36 (11%) Query: 88 SDRSGGYLRIMKRGFRYGDSAPMAVIEFVDRDLSAK 123 S R GG R+ +RG Y A+ E+ +++S Sbjct: 435 SGRIGGNSRLTERGRAYSR----ALFEYFQKEISTT 466 >gnl|CDD|131381 TIGR02328, TIGR02328, conserved hypothetical protein. Members of this protein are found in a small number of taxonomically well separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the Firmicutes. The function of this protein is unknown. Length = 120 Score = 24.4 bits (53), Expect = 9.5 Identities = 6/16 (37%), Positives = 12/16 (75%) Query: 29 IWHEQIVTTLPKAKEL 44 +WH+ ++T LP+ + L Sbjct: 3 LWHQSLITKLPRQQLL 18 >gnl|CDD|184052 PRK13435, PRK13435, response regulator; Provisional. Length = 145 Score = 24.6 bits (54), Expect = 9.8 Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 4/36 (11%) Query: 81 GIIAKRYSDRSG----GYLRIMKRGFRYGDSAPMAV 112 G+IAK YS R YL + G R PM V Sbjct: 100 GVIAKPYSPRGVARALSYLSARRVGDRASGPTPMGV 135 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 0.321 0.135 0.382 Gapped Lambda K H 0.267 0.0694 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,181,563 Number of extensions: 131043 Number of successful extensions: 259 Number of sequences better than 10.0: 1 Number of HSP's gapped: 258 Number of HSP's successfully gapped: 26 Length of query: 136 Length of database: 5,994,473 Length adjustment: 83 Effective length of query: 53 Effective length of database: 4,201,009 Effective search space: 222653477 Effective search space used: 222653477 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: 52 (23.9 bits)