RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780968|ref|YP_003065381.1| hypothetical protein CLIBASIA_04345 [Candidatus Liberibacter asiaticus str. psy62] (106 letters) >gnl|CDD|161841 TIGR00365, TIGR00365, monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation. Length = 97 Score = 181 bits (463), Expect = 2e-47 Identities = 57/97 (58%), Positives = 75/97 (77%) Query: 5 VNSIIQNEIKKNDVVLFMKGTPTSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIK 64 I+ +IK+N VVL+MKGTP P+CGFS + VQ+L + GV + ++VL D +RQ IK Sbjct: 1 TIERIKEQIKENPVVLYMKGTPQFPQCGFSARAVQILKACGVPFAYVNVLEDPEIRQGIK 60 Query: 65 EYSNWPTIPQLYVKGDFIGGCDIVCEMFESGELHEIL 101 EYSNWPTIPQLYVKG+F+GGCDI+ EM++SGEL +L Sbjct: 61 EYSNWPTIPQLYVKGEFVGGCDIIMEMYQSGELQTLL 97 >gnl|CDD|182759 PRK10824, PRK10824, glutaredoxin-4; Provisional. Length = 115 Score = 112 bits (282), Expect = 2e-26 Identities = 42/93 (45%), Positives = 66/93 (70%) Query: 9 IQNEIKKNDVVLFMKGTPTSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSN 68 IQ +I +N ++L+MKG+P P CGFS + VQ L + G + +D+L + +R + +Y+N Sbjct: 8 IQRQIAENPILLYMKGSPKLPSCGFSAQAVQALSACGERFAYVDILQNPDIRAELPKYAN 67 Query: 69 WPTIPQLYVKGDFIGGCDIVCEMFESGELHEIL 101 WPT PQL+V G+ +GGCDIV EM++ GEL +++ Sbjct: 68 WPTFPQLWVDGELVGGCDIVIEMYQRGELQQLI 100 >gnl|CDD|173357 PTZ00062, PTZ00062, glutaredoxin; Provisional. Length = 204 Score = 112 bits (281), Expect = 3e-26 Identities = 45/96 (46%), Positives = 65/96 (67%) Query: 9 IQNEIKKNDVVLFMKGTPTSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSN 68 I+ I+ + ++LFMKG+ T P C FS VV +L+S GV Y+ ++ D LR+ +K YSN Sbjct: 106 IERLIRNHKILLFMKGSKTFPFCRFSNAVVNMLNSSGVKYETYNIFEDPDLREELKVYSN 165 Query: 69 WPTIPQLYVKGDFIGGCDIVCEMFESGELHEILSID 104 WPT PQLYV G+ IGG DI+ E++ES L +++ D Sbjct: 166 WPTYPQLYVNGELIGGHDIIKELYESNSLRKVIPDD 201 >gnl|CDD|162749 TIGR02181, GRX_bact, Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides. Length = 79 Score = 50.3 bits (121), Expect = 1e-07 Identities = 24/75 (32%), Positives = 40/75 (53%) Query: 27 TSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSNWPTIPQLYVKGDFIGGCD 86 T P C + + +L S GV++ I V D ALR + + S T+PQ+++ +GGCD Sbjct: 5 TKPYCPYCTRAKALLSSKGVTFTEIRVDGDPALRDEMMQRSGRRTVPQIFIGDVHVGGCD 64 Query: 87 IVCEMFESGELHEIL 101 + + G+L +L Sbjct: 65 DLYALDREGKLDPLL 79 >gnl|CDD|162748 TIGR02180, GRX_euk, Glutaredoxin. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses. Length = 84 Score = 47.6 bits (114), Expect = 7e-07 Identities = 25/89 (28%), Positives = 47/89 (52%), Gaps = 10/89 (11%) Query: 18 VVLFMKGTPTSPRCGFSGKVVQVLDSLGVSYK----GIDVLAD-DALRQSIKEYSNWPTI 72 VV+F K C + K ++L L V +D L++ ++ ++E + T+ Sbjct: 1 VVVFSKSY-----CPYCKKAKEILAKLNVKPAYEVVELDQLSNGSEIQDYLEEITGQRTV 55 Query: 73 PQLYVKGDFIGGCDIVCEMFESGELHEIL 101 P +++ G FIGGC + +++SG+L E+L Sbjct: 56 PNIFINGKFIGGCSDLLALYKSGKLAELL 84 >gnl|CDD|182607 PRK10638, PRK10638, glutaredoxin 3; Provisional. Length = 83 Score = 46.4 bits (110), Expect = 2e-06 Identities = 24/76 (31%), Positives = 40/76 (52%) Query: 27 TSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSNWPTIPQLYVKGDFIGGCD 86 T C F + +L+S GVS++ I + D A R+ + + S T+PQ+++ IGGCD Sbjct: 8 TKATCPFCHRAKALLNSKGVSFQEIPIDGDAAKREEMIKRSGRTTVPQIFIDAQHIGGCD 67 Query: 87 IVCEMFESGELHEILS 102 + + G L +L Sbjct: 68 DLYALDARGGLDPLLK 83 >gnl|CDD|131245 TIGR02190, GlrX-dom, Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain. Length = 79 Score = 39.1 bits (91), Expect = 2e-04 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 6/73 (8%) Query: 14 KKNDVVLFMKGTPTSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSNWPTIP 73 K VV+F T P C F K L G ++ I L +DA +S++ + T+P Sbjct: 6 KPESVVVF-----TKPGCPFCAKAKATLKEKGYDFEEI-PLGNDARGRSLRAVTGATTVP 59 Query: 74 QLYVKGDFIGGCD 86 Q+++ G IGG D Sbjct: 60 QVFIGGKLIGGSD 72 >gnl|CDD|131251 TIGR02196, GlrX_YruB, Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system. Length = 74 Score = 32.0 bits (73), Expect = 0.033 Identities = 17/61 (27%), Positives = 29/61 (47%) Query: 27 TSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSNWPTIPQLYVKGDFIGGCD 86 T+P C K + L S G++++ IDV D A R+ + + +P + + I G D Sbjct: 6 TTPWCPPCKKAKEYLTSKGIAFEEIDVEKDSAAREEVLKVLGQRGVPVIVIGHKIIVGFD 65 Query: 87 I 87 Sbjct: 66 P 66 >gnl|CDD|183036 PRK11200, grxA, glutaredoxin 1; Provisional. Length = 85 Score = 29.2 bits (66), Expect = 0.23 Identities = 15/65 (23%), Positives = 31/65 (47%), Gaps = 7/65 (10%) Query: 29 PRCGFSGKVVQVLDSL-----GVSYKGIDVLADDALRQSIKEYSNWP--TIPQLYVKGDF 81 P C + + ++ + L Y+ +D+ A+ + +++ P T+PQ++V Sbjct: 9 PGCPYCVRAKELAEKLSEERDDFDYRYVDIHAEGISKADLEKTVGKPVETVPQIFVDQKH 68 Query: 82 IGGCD 86 IGGC Sbjct: 69 IGGCT 73 >gnl|CDD|184751 PRK14571, PRK14571, D-alanyl-alanine synthetase A; Provisional. Length = 299 Score = 28.6 bits (64), Expect = 0.32 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 6/46 (13%) Query: 11 NEIKKNDVVL-FMKGTPTSPRCGFSGKVVQVLDSLGVSYKGIDVLA 55 +++K DVV + GT G G + +LD LG+ Y G D + Sbjct: 49 DQLKSFDVVFNVLHGT-----FGEDGTLQAILDFLGIRYTGSDAFS 89 >gnl|CDD|131238 TIGR02183, GRXA, Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase. Length = 86 Score = 28.3 bits (63), Expect = 0.48 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 10/74 (13%) Query: 18 VVLFMKGTPTSPRC----GFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSNWP--T 71 VV+F G P P C + K+ ++ ID+ A+ + +++ P T Sbjct: 2 VVIF--GRPGCPYCVRAKQLAEKLAIERADF--EFRYIDIHAEGISKADLEKTVGKPVET 57 Query: 72 IPQLYVKGDFIGGC 85 +PQ++V +GGC Sbjct: 58 VPQIFVDEKHVGGC 71 >gnl|CDD|161986 TIGR00666, PBP4, D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family. In E. coli, this protein is known as penicillin binding protein 4 (dacB). A signal sequence is cleaved from a precursor form. The protein is described as periplasmic in E. coli (Gram-negative) and extracellular in Actinomadura R39 (Gram-positive). Unlike some other proteins with similar activity, it does not form transpeptidation. It is not essential for viability. This family is related to class A beta-lactamases. Length = 345 Score = 28.2 bits (63), Expect = 0.50 Identities = 18/65 (27%), Positives = 25/65 (38%), Gaps = 1/65 (1%) Query: 6 NSIIQNEIKKNDVVLFMKGTPTSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKE 65 ++N K ++VL G PT R +V L GV +VL D + S Sbjct: 45 KGNVENGNLKGNLVLRFGGDPTLKRQDI-RNLVATLKKSGVKQIDGNVLVDTSAFSSHDR 103 Query: 66 YSNWP 70 WP Sbjct: 104 APGWP 108 >gnl|CDD|180081 PRK05437, PRK05437, isopentenyl pyrophosphate isomerase; Provisional. Length = 352 Score = 27.4 bits (62), Expect = 0.79 Identities = 8/23 (34%), Positives = 10/23 (43%), Gaps = 2/23 (8%) Query: 31 CGFSGKVVQVLDSLGVSYKGIDV 53 G S + + L GV IDV Sbjct: 196 FGISKETAKRLADAGVKA--IDV 216 >gnl|CDD|131255 TIGR02200, GlrX_actino, Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif. Length = 77 Score = 27.1 bits (60), Expect = 0.98 Identities = 9/32 (28%), Positives = 20/32 (62%) Query: 27 TSPRCGFSGKVVQVLDSLGVSYKGIDVLADDA 58 + CG+ ++++ LD LG +Y+ +D+ D+ Sbjct: 6 GTTWCGYCAQLMRTLDKLGAAYEWVDIEEDEG 37 >gnl|CDD|162754 TIGR02189, GlrX-like_plant, Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa. Length = 99 Score = 26.6 bits (59), Expect = 1.4 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 8/96 (8%) Query: 9 IQNEIKKNDVVLFMKGTPTSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKEYSN 68 ++ + + VV+F + + C V ++L +LGV+ ++ + A + S Sbjct: 1 VRRMVSEKAVVIFSRSS-----CCMCHVVKRLLLTLGVNPAVHEIDKEPAGKDIENALSR 55 Query: 69 W---PTIPQLYVKGDFIGGCDIVCEMFESGELHEIL 101 P +P ++V G +GG + V + SG L +L Sbjct: 56 LGCSPAVPAVFVGGKLVGGLENVMALHISGSLVPML 91 >gnl|CDD|162450 TIGR01617, arsC_related, transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B. Length = 117 Score = 26.2 bits (58), Expect = 1.9 Identities = 11/39 (28%), Positives = 20/39 (51%) Query: 27 TSPRCGFSGKVVQVLDSLGVSYKGIDVLADDALRQSIKE 65 SP C K + L++ G+ Y+ ID+ D R+ + + Sbjct: 5 GSPNCTTCKKARRWLEANGIEYQFIDIGEDGPTREELLD 43 >gnl|CDD|165101 PHA02734, PHA02734, coat protein; Provisional. Length = 149 Score = 26.0 bits (56), Expect = 2.5 Identities = 9/20 (45%), Positives = 14/20 (70%) Query: 78 KGDFIGGCDIVCEMFESGEL 97 KGD+ GG + + FE+G+L Sbjct: 8 KGDYAGGAAKILDGFEAGQL 27 >gnl|CDD|150118 pfam09342, DUF1986, Domain of unknown function (DUF1986). This domain is found in serine proteases and is predicted to contain disulphide bonds. Length = 267 Score = 25.8 bits (56), Expect = 2.7 Identities = 9/29 (31%), Positives = 18/29 (62%) Query: 54 LADDALRQSIKEYSNWPTIPQLYVKGDFI 82 + + Q+ KE +WP I ++YV+G++ Sbjct: 1 NRETEVVQTFKEELHWPWIAKVYVEGNYR 29 >gnl|CDD|183126 PRK11414, PRK11414, colanic acid/biofilm transcriptional regulator; Provisional. Length = 221 Score = 25.2 bits (55), Expect = 3.5 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 4/30 (13%) Query: 53 VLADDALRQSIKEYSNWPT----IPQLYVK 78 + A+ R +I SN P I QL+V+ Sbjct: 132 INANRLFRLAIYHRSNMPILCEMIEQLWVR 161 >gnl|CDD|115203 pfam06531, DUF1108, Protein of unknown function (DUF1108). This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown. Length = 86 Score = 25.2 bits (55), Expect = 3.6 Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 7/36 (19%) Query: 38 VQVLDSLGVSYKGIDV-------LADDALRQSIKEY 66 +QV D V KGI V A D L QSI E+ Sbjct: 33 IQVKDMNNVPIKGIHVIDENDLYTALDILNQSIYEW 68 >gnl|CDD|181617 PRK09034, PRK09034, aspartate kinase; Reviewed. Length = 454 Score = 25.1 bits (56), Expect = 3.8 Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 4/25 (16%) Query: 32 GFSGKVVQVLDSLGVSYK----GID 52 GF KV+Q+L+ G+SY+ GID Sbjct: 323 GFGRKVLQILEDHGISYEHMPSGID 347 >gnl|CDD|149148 pfam07910, Peptidase_C78, Peptidase family C78. This family formerly known as DUF1671 has been shown to be a cysteine peptidase called (Ufm1)-specific protease. Length = 208 Score = 25.3 bits (56), Expect = 3.9 Identities = 23/101 (22%), Positives = 35/101 (34%), Gaps = 25/101 (24%) Query: 1 MNSSVNSI--IQNEIKKNDVVLFMKGTPTSPR---CGFSG--------KVVQVLDSLGVS 47 + V +I IQ ++ KG R GF G + VL SLGV Sbjct: 52 TSKPVPTIPEIQQMLEDAW----DKGFDAQGRAETGGFVGTRKWIGTTEASAVLTSLGVP 107 Query: 48 YK------GIDVLADDALRQSIKEY--SNWPTIPQLYVKGD 80 K G ++ L + Y S +P +Y++ Sbjct: 108 CKIVDFHSGSELETHPELFDEVANYFESAGGLLPPIYLQHQ 148 >gnl|CDD|184295 PRK13745, PRK13745, anaerobic sulfatase-maturase; Provisional. Length = 412 Score = 25.2 bits (55), Expect = 3.9 Identities = 11/23 (47%), Positives = 17/23 (73%) Query: 53 VLADDALRQSIKEYSNWPTIPQL 75 V++D+ L + IKEY N T+PQ+ Sbjct: 47 VMSDELLEKFIKEYINSQTMPQV 69 >gnl|CDD|181519 PRK08644, PRK08644, thiamine biosynthesis protein ThiF; Provisional. Length = 212 Score = 25.2 bits (56), Expect = 4.2 Identities = 7/17 (41%), Positives = 10/17 (58%) Query: 80 DFIGGCDIVCEMFESGE 96 + CDIV E F++ E Sbjct: 113 ELFKDCDIVVEAFDNAE 129 >gnl|CDD|180500 PRK06270, PRK06270, homoserine dehydrogenase; Provisional. Length = 341 Score = 24.8 bits (55), Expect = 5.5 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 4/44 (9%) Query: 19 VLFMKGTPTSPRCGFSGKVVQVLDSLGVSYK--GIDVLADDALR 60 +L K R G KVV + DS G + G+D + AL+ Sbjct: 20 LLAEKREYLKKRYGLDLKVVAIADSSGSAIDPDGLD--LELALK 61 >gnl|CDD|163456 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706 family. Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves. Length = 893 Score = 24.6 bits (54), Expect = 5.7 Identities = 8/24 (33%), Positives = 12/24 (50%) Query: 57 DALRQSIKEYSNWPTIPQLYVKGD 80 DAL+ S E P + Q Y + + Sbjct: 67 DALQDSFDELDEAPWVVQFYCQDE 90 >gnl|CDD|179600 PRK03584, PRK03584, acetoacetyl-CoA synthetase; Provisional. Length = 655 Score = 24.8 bits (55), Expect = 5.8 Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 14/44 (31%) Query: 36 KVVQVLDSL--GVSYKGID-------VLA-----DDALRQSIKE 65 + +VLDSL G + D VLA DDALR I+ Sbjct: 542 ALPEVLDSLVIGQEWPDGDVRMPLFVVLAEGVTLDDALRARIRT 585 >gnl|CDD|135627 PRK05863, PRK05863, sulfur carrier protein ThiS; Provisional. Length = 65 Score = 24.4 bits (53), Expect = 7.3 Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%) Query: 37 VVQVLDSLGVSYKGIDVLADDALRQSIKEYSNWPT 71 V +LDSLG KGI V D S+ S+W T Sbjct: 18 VAALLDSLGFPEKGIAVAVDW----SVLPRSDWAT 48 >gnl|CDD|183852 PRK13030, PRK13030, 2-oxoacid ferredoxin oxidoreductase; Provisional. Length = 1159 Score = 24.2 bits (53), Expect = 7.8 Identities = 10/22 (45%), Positives = 13/22 (59%) Query: 35 GKVVQVLDSLGVSYKGIDVLAD 56 GK VLD G++ KG VL+ Sbjct: 745 GKSASVLDFTGLAQKGGAVLSH 766 >gnl|CDD|167141 PRK01021, lpxB, lipid-A-disaccharide synthase; Reviewed. Length = 608 Score = 24.0 bits (52), Expect = 8.7 Identities = 11/38 (28%), Positives = 18/38 (47%) Query: 65 EYSNWPTIPQLYVKGDFIGGCDIVCEMFESGELHEILS 102 EY+N +P L+ K +GG + +G+ IL Sbjct: 163 EYNNQSALPALFWKASLLGGSLALLYFIRTGDPVNILC 200 >gnl|CDD|163035 TIGR02826, RNR_activ_nrdG3, anaerobic ribonucleoside-triphosphate reductase activating protein. Members of this family represent a set of proteins related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of this protein as an RNR activitating protein is partly from pairing with a candidate RNR. It is further supported by our finding that upstream of these operons are examples of a conserved regulatory element (described Rodionov and Gelfand) that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes. Length = 147 Score = 23.9 bits (52), Expect = 8.9 Identities = 10/35 (28%), Positives = 15/35 (42%) Query: 63 IKEYSNWPTIPQLYVKGDFIGGCDIVCEMFESGEL 97 I E + +P Y +I GC + C+ S E Sbjct: 3 INEIIVFQEVPNEYSLAFYITGCPLGCKGCHSPES 37 >gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional. Length = 293 Score = 23.9 bits (53), Expect = 10.0 Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 7/25 (28%) Query: 39 QVLDSLGVSYKGID---VL--ADDA 58 Q+L++LGV Y ID VL AD+ Sbjct: 90 QILEALGVDY--IDESEVLTPADEE 112 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 0.319 0.138 0.407 Gapped Lambda K H 0.267 0.0710 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,715,946 Number of extensions: 96693 Number of successful extensions: 226 Number of sequences better than 10.0: 1 Number of HSP's gapped: 226 Number of HSP's successfully gapped: 45 Length of query: 106 Length of database: 5,994,473 Length adjustment: 72 Effective length of query: 34 Effective length of database: 4,438,697 Effective search space: 150915698 Effective search space used: 150915698 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 (21.7 bits) S2: 50 (23.1 bits)