RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780440|ref|YP_003064853.1| transcription elongation factor GreA [Candidatus Liberibacter asiaticus str. psy62] (158 letters) >gnl|CDD|31125 COG0782, GreA, Transcription elongation factor [Transcription]. Length = 151 Score = 146 bits (369), Expect = 3e-36 Identities = 70/152 (46%), Positives = 101/152 (66%), Gaps = 1/152 (0%) Query: 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAEL 66 +T +GF K+++EL + + ERP I++ I++AR GDLSENAEY+AAKE Q E R+ L Sbjct: 1 LTDEGFRKLKEELEYLKPVERPEIVEEIADARELGDLSENAEYRAAKEEQAFIERRIRLL 60 Query: 67 ENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPI 126 E ++ A+VID D + FG+TV+L + G++ Y IVG EAD G +S+ SP+ Sbjct: 61 EELLRNAQVIDDEKPP-DVVTFGSTVTLENLDDGEEVTYTIVGPDEADPAKGKISVDSPL 119 Query: 127 ARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 RAL+GK++GD + VN PGGEK EIL + + Sbjct: 120 GRALLGKKVGDTVEVNTPGGEKEVEILSIEYQ 151 >gnl|CDD|146205 pfam03449, GreA_GreB_N, domain. This domain adopts a long alpha-hairpin structure. Length = 71 Score = 96.4 bits (241), Expect = 3e-21 Identities = 40/71 (56%), Positives = 53/71 (74%) Query: 5 IPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMA 64 P+T +G++K+Q+EL + ERP IIKAI+EAR +GDLSENAEY AAKE Q E R+ Sbjct: 1 NPITPEGYEKLQEELERLKNVERPEIIKAIAEAREHGDLSENAEYHAAKEEQREIEARIR 60 Query: 65 ELENIITRAEV 75 ELE+ + RAE+ Sbjct: 61 ELEDRLARAEI 71 >gnl|CDD|144753 pfam01272, GreA_GreB, Transcription elongation factor, GreA/GreB, C-term. This domain has a FKBP-like fold. Length = 77 Score = 95.3 bits (238), Expect = 7e-21 Identities = 35/75 (46%), Positives = 53/75 (70%) Query: 81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIIS 140 + D + FG+TV+L + + G+++ Y IVG EAD G +S+ SP+ RAL+GK++GD + Sbjct: 1 LPADVVTFGSTVTLEDLDDGEEETYTIVGPDEADPSKGKISVLSPLGRALLGKKVGDEVE 60 Query: 141 VNAPGGEKTYEILQV 155 V AP GEK YEIL++ Sbjct: 61 VTAPSGEKKYEILKI 75 >gnl|CDD|143439 cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like. Coenzyme A acylating aldehyde dehydrogenase (ACDH), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, acetylating (EC=1.2.1.10), converts acetaldehyde into acetyl-CoA. This CD is limited to such monofunctional enzymes as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium. Mutations in eutE abolish the ability to utilize ethanolamine as a carbon source. Length = 429 Score = 28.0 bits (63), Expect = 1.3 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 12/77 (15%) Query: 16 QQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR----MAELENIIT 71 Q++ R +R +II+AI EA L NAE A ++ GR +A+ Sbjct: 17 QKQYRKCTLADREKIIEAIREA-----LLSNAEELAEMAVEETGMGRVEDKIAKNHLAAE 71 Query: 72 RA---EVIDISTMSGDR 85 + E + + SGD Sbjct: 72 KTPGTEDLTTTAWSGDN 88 >gnl|CDD|147187 pfam04890, DUF648, Family of unknown function (DUF648). Family of hypothetical Chlamydia proteins. This family may well comprise of two domains, as some members only match the N-terminus. Length = 288 Score = 27.1 bits (60), Expect = 2.1 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 3/30 (10%) Query: 71 TRAEVIDISTMSGDRIAF---GATVSLVEK 97 R +VI +ST +G RIA G +VS EK Sbjct: 31 KRTKVISLSTENGLRIAAKQEGVSVSTTEK 60 >gnl|CDD|112956 pfam04166, PdxA, Pyridoxal phosphate biosynthetic protein PdxA. In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesized de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate. Length = 299 Score = 26.2 bits (58), Expect = 4.4 Identities = 9/17 (52%), Positives = 11/17 (64%) Query: 25 EERPRIIKAISEARAYG 41 EE II A+ +ARA G Sbjct: 198 EEIEEIIPALEQARAEG 214 >gnl|CDD|146701 pfam04199, Cyclase, Putative cyclase. Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site. Length = 162 Score = 25.8 bits (57), Expect = 5.7 Identities = 3/20 (15%), Positives = 8/20 (40%) Query: 65 ELENIITRAEVIDISTMSGD 84 LE + ++D++ Sbjct: 69 PLEWFVGPGVLLDVAHKLPP 88 >gnl|CDD|99711 cd05828, Sortase_D_4, Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.. Length = 127 Score = 25.6 bits (57), Expect = 6.0 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 134 ELGDIISVNAPGGEKTYEI 152 E GDII++ GG TY + Sbjct: 63 EPGDIITLQTLGGTYTYRV 81 >gnl|CDD|37834 KOG2623, KOG2623, KOG2623, Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 467 Score = 25.7 bits (56), Expect = 6.2 Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 1/46 (2%) Query: 57 NLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDK 102 G + NI ++I M FG T L+ ++G K Sbjct: 229 RFQLGGSDQWGNITAGTDLIR-KIMPIQAFVFGLTFPLLTSSTGAK 273 >gnl|CDD|145100 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis. Length = 165 Score = 25.2 bits (56), Expect = 7.5 Identities = 9/48 (18%), Positives = 24/48 (50%) Query: 27 RPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAE 74 R + + ++SE+ +A KE+Q L + + +++ ++ + E Sbjct: 114 RRDANDKLKKLEKDKEISEDEVKKAEKEIQKLTDKYIKKIDELLKKKE 161 >gnl|CDD|36896 KOG1683, KOG1683, KOG1683, Hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase [Lipid transport and metabolism]. Length = 380 Score = 25.3 bits (55), Expect = 7.5 Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 12/82 (14%) Query: 8 TSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNL------NEG 61 T KG + L ++ +R + + + + ++ NE Sbjct: 255 TGKGIYPYARGLT--KKMKRDEMEALLRRLSLTPNPRVADD----EDFVEFLLSPFVNEA 308 Query: 62 RMAELENIITRAEVIDISTMSG 83 LE + DI+++ G Sbjct: 309 LRCLLEGLKASPSDGDIASVFG 330 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 0.312 0.131 0.354 Gapped Lambda K H 0.267 0.0721 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,740,163 Number of extensions: 80299 Number of successful extensions: 175 Number of sequences better than 10.0: 1 Number of HSP's gapped: 174 Number of HSP's successfully gapped: 25 Length of query: 158 Length of database: 6,263,737 Length adjustment: 86 Effective length of query: 72 Effective length of database: 4,405,363 Effective search space: 317186136 Effective search space used: 317186136 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 53 (24.2 bits)