RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780129|ref|YP_003064542.1| hypothetical protein CLIBASIA_00040 [Candidatus Liberibacter asiaticus str. psy62] (220 letters) >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 76.4 bits (188), Expect = 6e-15 Identities = 42/177 (23%), Positives = 70/177 (39%), Gaps = 14/177 (7%) Query: 5 LKPHQIVMVNWLLSHDR-CALWASMGSGKT-VSVLFALSTIKILDPRPVLIIAPLRVAQY 62 L+P+Q + LLS R L A GSGKT ++L AL +K + VL++ P R Sbjct: 9 LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAE 68 Query: 63 VWKDEVERWSAFSDMTVSSLIGS---ERQRIKALNTPAHLYIINFENIP-WLVKMKLDHW 118 W +E+++ + V L G Q K + + + + L L+ Sbjct: 69 QWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELS 128 Query: 119 DFATIVVDES--TKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLW 173 + +++DE+ F Q L K+ V+ + L+ TP L Sbjct: 129 NVDLVILDEAHRLLDGGFG-----DQLEKLLKLLPKNVQLLL-LSATPPEEIENLLE 179 >gnl|CDD|162193 TIGR01078, arcA, arginine deiminase. Arginine deiminase is the first enzyme of the arginine deiminase pathway of arginine degradation. Length = 405 Score = 31.6 bits (72), Expect = 0.16 Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 4/45 (8%) Query: 84 GSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATIVVDES 128 G E + + TP++L + F++IPW+ + +H FA + D Sbjct: 17 GRELENL----TPSNLDELLFDDIPWVEDAQKEHDQFANTLRDNG 57 >gnl|CDD|178452 PLN02861, PLN02861, long-chain-fatty-acid-CoA ligase. Length = 660 Score = 31.0 bits (70), Expect = 0.23 Identities = 14/38 (36%), Positives = 19/38 (50%) Query: 166 PNGLIDLWGQIWFLDKGKRLGLSFKSFVERWFHTQQVG 203 P G I L G F KR L+ + ++ WFHT +G Sbjct: 464 PRGEICLRGNTLFSGYHKRQDLTEEVLIDGWFHTGDIG 501 >gnl|CDD|178687 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional. Length = 1033 Score = 29.0 bits (65), Expect = 0.86 Identities = 47/195 (24%), Positives = 84/195 (43%), Gaps = 40/195 (20%) Query: 5 LKPHQIVMVNWLL---SHDRCALWA-SMGSGKTVSVLFALSTIKIL----DPR----PVL 52 ++ +Q+ +NWL+ + + A MG GKT L TI +L + R P + Sbjct: 170 MRDYQLAGLNWLIRLYENGINGILADEMGLGKT------LQTISLLGYLHEYRGITGPHM 223 Query: 53 IIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGS--ERQRIKALNTPAHLYIINFENIPWL 110 ++AP + W +E+ R+ + G+ ER + A + + + Sbjct: 224 VVAP-KSTLGNWMNEIRRFCPV--LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMA 280 Query: 111 VK----MKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVA--FSKVKRFIELTGTP 164 +K +K W + I++DE+ ++K+ + L K FS R + +TGTP Sbjct: 281 IKEKTALKRFSWRY--IIIDEAHRIKN--------ENSLLSKTMRLFSTNYRLL-ITGTP 329 Query: 165 SPNGLIDLWGQIWFL 179 N L +LW + FL Sbjct: 330 LQNNLHELWALLNFL 344 >gnl|CDD|179290 PRK01388, PRK01388, arginine deiminase; Provisional. Length = 406 Score = 28.6 bits (65), Expect = 1.2 Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 4/40 (10%) Query: 84 GSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATI 123 G E +R+ TP++ + F+++PW+ + + +H FA Sbjct: 24 GLELERL----TPSNCDELLFDDVPWVERAQKEHDAFAQT 59 >gnl|CDD|184388 PRK13909, PRK13909, putative recombination protein RecB; Provisional. Length = 910 Score = 28.4 bits (64), Expect = 1.3 Identities = 13/19 (68%), Positives = 13/19 (68%), Gaps = 4/19 (21%) Query: 23 ALWASMGSGKTVSVLFALS 41 AL AS GSGKT FALS Sbjct: 2 ALKASAGSGKT----FALS 16 >gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed. Length = 402 Score = 28.7 bits (64), Expect = 1.4 Identities = 10/19 (52%), Positives = 14/19 (73%) Query: 72 SAFSDMTVSSLIGSERQRI 90 + F+D V+SL G ERQR+ Sbjct: 130 AQFADRPVTSLSGGERQRV 148 >gnl|CDD|140243 PTZ00216, PTZ00216, acyl-CoA synthetase; Provisional. Length = 700 Score = 28.4 bits (64), Expect = 1.5 Identities = 27/65 (41%), Positives = 31/65 (47%), Gaps = 13/65 (20%) Query: 161 TGTPSPNGLIDLWGQIWFLDKG--KRLGLSFKSFVER-WFHTQQVGSS--------IGAV 209 T TP P G I L G FL KG K+ L+ + E WFHT VGS IG V Sbjct: 501 TDTPEPRGEILLRGP--FLFKGYYKQEELTREVLDEDGWFHTGDVGSIAANGTLRIIGRV 558 Query: 210 KHIPK 214 K + K Sbjct: 559 KALAK 563 >gnl|CDD|181290 PRK08206, PRK08206, diaminopropionate ammonia-lyase; Provisional. Length = 399 Score = 27.5 bits (62), Expect = 3.1 Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 9/65 (13%) Query: 135 RTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDL--------WGQIWFLDKGKRLG 186 L + K + F + +P L+ L G I D+ R G Sbjct: 13 NKPYDGADLPLLSQEEAKKARAFHQSFPGYAPTPLVALPDLAAELGVGSILVKDESYRFG 72 Query: 187 L-SFK 190 L +FK Sbjct: 73 LNAFK 77 >gnl|CDD|161871 TIGR00420, trmU, tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase. tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU, asuE, or mnmA) is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in the wobble position of some tRNAs. This enzyme appears not to occur in the Archaea. Length = 352 Score = 27.4 bits (61), Expect = 3.3 Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 8/54 (14%) Query: 152 SKVKRFIELTGTPSPNGLIDLWGQ--------IWFLDKGKRLGLSFKSFVERWF 197 K + F++ P +I + GQ +WF G+R GL E WF Sbjct: 201 RKFRDFLKKYLPVKPGVIITVDGQSVIGEHDGLWFYTIGQRKGLGIGGAAEPWF 254 >gnl|CDD|132298 TIGR03254, oxalate_oxc, oxalyl-CoA decarboxylase. In a number of bacteria, including Oxalobacter formigenes from the human gut, a two-gene operon of oxc (oxalyl-CoA decarboxylase) and frc (formyl-CoA transferase) encodes a system for degrading and therefore detoxifying oxalate. Members of this family are the thiamine pyrophosphate (TPP)-containing enzyme oxalyl-CoA decarboxylase. Length = 554 Score = 27.1 bits (60), Expect = 3.9 Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 5/29 (17%) Query: 3 LVLKPHQIVMV-----NWLLSHDRCALWA 26 L +VM+ NWLLSH + LW Sbjct: 261 FALAEADVVMLVGARLNWLLSHGKGKLWG 289 >gnl|CDD|166255 PLN02614, PLN02614, long-chain acyl-CoA synthetase. Length = 666 Score = 26.9 bits (59), Expect = 4.3 Identities = 13/39 (33%), Positives = 20/39 (51%) Query: 165 SPNGLIDLWGQIWFLDKGKRLGLSFKSFVERWFHTQQVG 203 +P G I + G+ F KR L+ + ++ W HT VG Sbjct: 466 TPRGEICIRGKTLFSGYYKREDLTKEVLIDGWLHTGDVG 504 >gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter, ATP-binding protein. This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter. Length = 256 Score = 26.7 bits (59), Expect = 4.5 Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 3/35 (8%) Query: 72 SAFSDMTVSSLIGSERQRI---KALNTPAHLYIIN 103 S +D +S+L G ERQR+ +AL L +++ Sbjct: 128 SHLADRDMSTLSGGERQRVHVARALAQEPKLLLLD 162 >gnl|CDD|129256 TIGR00152, TIGR00152, dephospho-CoA kinase. This model produces scores in the range of 0-25 bits against adenylate, guanylate, uridine, and thymidylate kinases. Length = 188 Score = 26.6 bits (59), Expect = 5.6 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 4/86 (4%) Query: 60 AQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWD 119 + V+ D E +++ LI +++ A Y++ ++P L + KL Sbjct: 69 GERVFNDPEEL-KWLNNLL-HPLIREWMKKLLAQFQSKLAYVL--LDVPLLFENKLRSLC 124 Query: 120 FATIVVDESTKLKSFRTHQGTKQTRA 145 IVVD S +L+ R Q T Sbjct: 125 DRVIVVDVSPQLQLERLMQRDNLTEE 150 >gnl|CDD|150299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is a conserved membrane protein. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family. Length = 835 Score = 26.4 bits (59), Expect = 6.4 Identities = 8/26 (30%), Positives = 14/26 (53%) Query: 59 VAQYVWKDEVERWSAFSDMTVSSLIG 84 + + ++KD RW F +SSL+ Sbjct: 198 LYRLIFKDIKSRWKQFLRFIISSLLS 223 >gnl|CDD|161832 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR family. Members of this family are assumed to differ from each other in DNA site specificity. Length = 667 Score = 26.2 bits (58), Expect = 6.8 Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 14/66 (21%) Query: 3 LVLKPHQIVMVNWLL--------------SHDRCALWASMGSGKTVSVLFALSTIKILDP 48 LV KP+Q M + +W + GSGKT+++LFA L Sbjct: 233 LVTKPYQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLK 292 Query: 49 RPVLII 54 P + Sbjct: 293 NPKVFF 298 >gnl|CDD|183924 PRK13258, PRK13258, 7-cyano-7-deazaguanine reductase; Provisional. Length = 115 Score = 26.3 bits (59), Expect = 7.2 Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 12/32 (37%) Query: 119 DFATIVVD--------ESTKLK----SFRTHQ 138 DFATIV+D E LK SFR H Sbjct: 36 DFATIVIDYIPDKKCVELKSLKLYLFSFRNHG 67 >gnl|CDD|149650 pfam08664, YcbB, YcbB domain. YcbB is a DNA-binding domain. Length = 133 Score = 26.1 bits (58), Expect = 7.4 Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 5/24 (20%) Query: 88 QRI-----KALNTPAHLYIINFEN 106 QRI KALN A L + ++ N Sbjct: 68 QRIRRAIKKALNNLASLGLEDYSN 91 >gnl|CDD|163398 TIGR03686, pupylate_PafA, proteasome accessory factor PafA. Members of this family are PafA (proteasome accessory factor A), a protein shown to regulate steady-state levels of certain proteasome targets in Mycobacterium tuberculosis. Iyer, et al (2008) suggest that PafA is the ligase for Pup, a ubiquitin analog attached to an epsilon-amino group of a Lys side-chain to direct the target to the proteasome. Length = 453 Score = 25.9 bits (57), Expect = 7.7 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 6/40 (15%) Query: 141 KQTRALG--KVAFSKVKRFIELTGTPSPNGLI----DLWG 174 + AL + + KVK F+E G +PN I DLWG Sbjct: 269 RSASALEIQREYYEKVKAFLETRGDGTPNAEIPRVVDLWG 308 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 0.426 Gapped Lambda K H 0.267 0.0636 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,612,891 Number of extensions: 220968 Number of successful extensions: 355 Number of sequences better than 10.0: 1 Number of HSP's gapped: 353 Number of HSP's successfully gapped: 23 Length of query: 220 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 130 Effective length of database: 4,049,753 Effective search space: 526467890 Effective search space used: 526467890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 55 (25.2 bits)