RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780620|ref|YP_003065033.1| iron-responsive transcriptional regulator [Candidatus Liberibacter asiaticus str. psy62] (144 letters) >gnl|CDD|171344 PRK11920, rirA, iron-responsive transcriptional regulator; Reviewed. Length = 153 Score = 261 bits (669), Expect = 4e-71 Identities = 87/144 (60%), Positives = 110/144 (76%) Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 M LTK+T+Y IR+LMYCA ++ +RI +IA A +SELFLFKILQPLV+AG+VETVRGR Sbjct: 1 MRLTKQTNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGR 60 Query: 61 RGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFD 120 GGVRL RPA I++ DVV+ TE+SF +AECF + +CPLV SCGL S LRKALNAFF Sbjct: 61 NGGVRLGRPAADISLFDVVRVTEDSFSMAECFENDASECPLVDSCGLNSALRKALNAFFA 120 Query: 121 VLTQYSIECLVRNRSSIKKIFNAG 144 VL++YSI LV+ R +I+ + Sbjct: 121 VLSKYSIADLVKARPNIRFLLGLD 144 >gnl|CDD|129821 TIGR00738, rrf2_super, rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency. Length = 132 Score = 118 bits (297), Expect = 7e-28 Identities = 52/133 (39%), Positives = 78/133 (58%), Gaps = 2/133 (1%) Query: 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 M LTK+T+Y +R L+ A++ D P + +IAE IS +L KIL+ L +AG+VE+VRG Sbjct: 1 MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRG 60 Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFF 119 GG RL RP ++IT+ DVV+A E +C + P C L +V R+ +A Sbjct: 61 PGGGYRLARPPEEITVGDVVRAVEGPLAPVQCIGLNG-CHPGEEVCLLHAVWRELEDAIE 119 Query: 120 DVLTQYSIECLVR 132 D L + ++ LV+ Sbjct: 120 DFLREITLADLVK 132 >gnl|CDD|182900 PRK11014, PRK11014, transcriptional repressor NsrR; Provisional. Length = 141 Score = 89.3 bits (222), Expect = 3e-19 Identities = 50/141 (35%), Positives = 72/141 (51%), Gaps = 5/141 (3%) Query: 1 MHLTKRTDYGIRVLMYCA-IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 M LT TDYG+R L+Y A + IS++ E +S + KI+ L +AG V VRG Sbjct: 1 MQLTSFTDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60 Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFF 119 + GG+RL +PA I I DVV+ E V C + C + +C L L KA+ +F Sbjct: 61 KNGGIRLGKPASTIRIGDVVRELEPLSLV-NCSSEF---CHITPACRLKQALSKAVQSFL 116 Query: 120 DVLTQYSIECLVRNRSSIKKI 140 L Y++ LV + K+ Sbjct: 117 KELDNYTLADLVEENQPLYKL 137 >gnl|CDD|131989 TIGR02944, suf_reg_Xantho, FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role. Length = 130 Score = 76.0 bits (187), Expect = 4e-15 Identities = 44/127 (34%), Positives = 65/127 (51%), Gaps = 1/127 (0%) Query: 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 + ++K TDY VL A ++ P ++IAE ++ + KIL+ L AGIV + RG Sbjct: 2 LKISKLTDYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGV 61 Query: 61 RGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFD 120 GG L R IT+ D+VKA E + EC K C L SCG+ S + + D Sbjct: 62 EGGYTLARAPRDITVADIVKAVEGPVALTECSDDQKK-CSLGNSCGVRSNWKVINSQVLD 120 Query: 121 VLTQYSI 127 +L+ S+ Sbjct: 121 LLSSVSL 127 >gnl|CDD|131065 TIGR02010, IscR, iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system. Length = 135 Score = 62.4 bits (152), Expect = 4e-11 Identities = 43/137 (31%), Positives = 71/137 (51%), Gaps = 5/137 (3%) Query: 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 M LT + Y + ++ A++ + P ++ I+E IS +L ++ L KAG+V++VRG Sbjct: 1 MRLTTKGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRG 60 Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNA-F 118 GG +L RPA+ I++ D++ A +ES C K +C C LT L L+ Sbjct: 61 PGGGYQLGRPAEDISVADIIDAVDESVDATRCQG--KGNCRHGTRC-LTHDLWADLSKHI 117 Query: 119 FDVLTQYSIECLVRNRS 135 D L S+ LV ++ Sbjct: 118 RDYLESISLADLVNQQN 134 >gnl|CDD|182783 PRK10857, PRK10857, DNA-binding transcriptional regulator IscR; Provisional. Length = 164 Score = 49.9 bits (119), Expect = 2e-07 Identities = 39/136 (28%), Positives = 65/136 (47%), Gaps = 5/136 (3%) Query: 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 M LT + Y + ++ A++++ P ++ I+E IS +L ++ L K G+V +VRG Sbjct: 1 MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRG 60 Query: 60 RRGGVRLCRPADQITILDVVKATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNA-F 118 GG L + A I + +V+ A +ES C K C C LT L + L+ Sbjct: 61 PGGGYLLGKDASSIAVGEVISAVDESVDATRC--QGKGGCQGGDKC-LTHALWRDLSDRL 117 Query: 119 FDVLTQYSIECLVRNR 134 L ++ LV N+ Sbjct: 118 TGFLNNITLGELVNNQ 133 >gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional. Length = 588 Score = 29.2 bits (66), Expect = 0.38 Identities = 11/18 (61%), Positives = 12/18 (66%) Query: 48 LVKAGIVETVRGRRGGVR 65 L K GI T+ GRR GVR Sbjct: 4 LPKIGIRPTIDGRRMGVR 21 >gnl|CDD|184474 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional. Length = 392 Score = 28.5 bits (64), Expect = 0.71 Identities = 11/25 (44%), Positives = 17/25 (68%) Query: 49 VKAGIVETVRGRRGGVRLCRPADQI 73 VKA I RG+ GG++LCR +++ Sbjct: 45 VKAQIHSGARGKAGGIKLCRTYNEV 69 >gnl|CDD|162403 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4-->1,4-glucantransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site directed mutagenesis studies in S. cerevisiae indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this model belong to the larger alpha-amylase family. The model covers eukaryotic proteins with a seed composed of human, nematode and yeast sequences. Yeast seed sequence is well characterized. The model is quite rigorous; either query sequence yields large bit score or it fails to hit the model altogether. There doesn't appear to be any middle ground. Length = 1464 Score = 28.3 bits (63), Expect = 0.77 Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 1/34 (2%) Query: 86 FFVAECFA-SHKIDCPLVGSCGLTSVLRKALNAF 118 + VAE F S +D V G++S++R+A++A+ Sbjct: 537 YVVAELFTGSETLDNVFVNRLGISSLIREAMSAW 570 >gnl|CDD|181783 PRK09333, PRK09333, 30S ribosomal protein S19e; Provisional. Length = 150 Score = 27.1 bits (61), Expect = 1.6 Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%) Query: 43 KILQPLVKAGIVETV-RGRR 61 KILQ L KAG+VE +GR Sbjct: 100 KILQQLEKAGLVEKTKKGRV 119 >gnl|CDD|177992 PLN02363, PLN02363, phosphoribosylanthranilate isomerase. Length = 256 Score = 27.1 bits (60), Expect = 1.9 Identities = 13/30 (43%), Positives = 14/30 (46%), Gaps = 1/30 (3%) Query: 88 VAECFASHKIDCPLVGSCGLTSVLRKALNA 117 VA D PLV CG+TS R A A Sbjct: 35 VAPKDDERGKDRPLVKMCGITSA-RDAAMA 63 >gnl|CDD|130161 TIGR01089, fucI, L-fucose isomerase. This enzyme catalyzes the first step in fucose metabolism, and has been characterized in Escherichia coli and Bacteroides thetaiotaomicron. Length = 587 Score = 26.4 bits (58), Expect = 3.0 Identities = 11/18 (61%), Positives = 12/18 (66%) Query: 48 LVKAGIVETVRGRRGGVR 65 L K GI T+ GRR GVR Sbjct: 3 LPKIGIRPTIDGRRMGVR 20 >gnl|CDD|162205 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This model describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea. The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane. Length = 582 Score = 26.3 bits (58), Expect = 3.2 Identities = 7/23 (30%), Positives = 11/23 (47%) Query: 49 VKAGIVETVRGRRGGVRLCRPAD 71 + A + + G + CRPAD Sbjct: 375 INAELQRKILGDEKPIVDCRPAD 397 >gnl|CDD|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase N; Provisional. Length = 343 Score = 25.9 bits (57), Expect = 4.1 Identities = 6/21 (28%), Positives = 12/21 (57%) Query: 112 RKALNAFFDVLTQYSIECLVR 132 R+ + F ++L + IE +R Sbjct: 300 RERIERFKEILLKNGIEAEIR 320 >gnl|CDD|170049 PRK09692, PRK09692, integrase; Provisional. Length = 413 Score = 25.8 bits (56), Expect = 4.5 Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 6/35 (17%) Query: 41 LFKILQPLVKAGIVETVRGRRGGVRLCRPADQITI 75 L + +QP+ G +ETVR RLC+ +++ I Sbjct: 155 LVQAVQPVQARGALETVR------RLCQRINEVMI 183 >gnl|CDD|171489 PRK12423, PRK12423, LexA repressor; Provisional. Length = 202 Score = 25.9 bits (57), Expect = 4.5 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 7/50 (14%) Query: 36 ISELFLF-------KILQPLVKAGIVETVRGRRGGVRLCRPADQITILDV 78 I++ F F K +Q L +AG++E V + G+RL A + +L++ Sbjct: 31 IAQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIRLPGGAGRPELLEL 80 >gnl|CDD|184952 PRK14990, PRK14990, anaerobic dimethyl sulfoxide reductase subunit A; Provisional. Length = 814 Score = 25.4 bits (55), Expect = 5.2 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 3/61 (4%) Query: 87 FVAECFASHKIDCPLVGSCGLTSVL---RKALNAFFDVLTQYSIECLVRNRSSIKKIFNA 143 + +C AS ++D L SCG S + + + F+ T Y + + R +++ F Sbjct: 526 LLPDCTASEQMDFALDASCGNMSYVIFNDQVIKPRFECKTIYEMTSELAKRLGVEQQFTE 585 Query: 144 G 144 G Sbjct: 586 G 586 >gnl|CDD|184448 PRK14010, PRK14010, potassium-transporting ATPase subunit B; Provisional. Length = 673 Score = 25.4 bits (55), Expect = 5.4 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 3/57 (5%) Query: 45 LQPLVKAGIVETVRGRRG-GVR--LCRPADQITILDVVKATEESFFVAECFASHKID 98 L+ ++K G+VE R R G+ +C +++T + K FVAEC KI+ Sbjct: 438 LKDVIKDGLVERFRELREMGIETVMCTGDNELTAATIAKEAGVDRFVAECKPEDKIN 494 >gnl|CDD|116493 pfam07881, Fucose_iso_N1, L-fucose isomerase, first N-terminal domain. The members of this family are similar to L-fucose isomerase expressed by E. coli (EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta-sheets with surrounding alpha helices. Domain 1 demonstrates the beta-alpha-beta-alpha- beta Rossman fold. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues, and domain 1 from the adjacent subunit contributing some other residues. Length = 171 Score = 25.0 bits (55), Expect = 6.9 Identities = 11/16 (68%), Positives = 12/16 (75%) Query: 50 KAGIVETVRGRRGGVR 65 K GI T+ GRRGGVR Sbjct: 5 KIGIRPTIDGRRGGVR 20 >gnl|CDD|182200 PRK10026, PRK10026, arsenate reductase; Provisional. Length = 141 Score = 24.8 bits (54), Expect = 8.8 Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 2/28 (7%) Query: 63 GVRLCRPADQITILDVVKATEESFFVAE 90 G RLCRP++ +L+++ ++ F E Sbjct: 102 GTRLCRPSE--VVLEILPDAQKGAFTKE 127 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 0.329 0.141 0.428 Gapped Lambda K H 0.267 0.0639 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,209,520 Number of extensions: 126646 Number of successful extensions: 313 Number of sequences better than 10.0: 1 Number of HSP's gapped: 309 Number of HSP's successfully gapped: 27 Length of query: 144 Length of database: 5,994,473 Length adjustment: 84 Effective length of query: 60 Effective length of database: 4,179,401 Effective search space: 250764060 Effective search space used: 250764060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.0 bits)