RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780822|ref|YP_003065235.1| thioredoxin [Candidatus Liberibacter asiaticus str. psy62] (107 letters) >gnl|CDD|162187 TIGR01068, thioredoxin, thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model. Length = 101 Score = 120 bits (304), Expect = 6e-29 Identities = 41/98 (41%), Positives = 66/98 (67%), Gaps = 1/98 (1%) Query: 6 VDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEI 65 + +FD + PV+VDFWA WC PC ++PI++++A E KVK KL+++E+ +I Sbjct: 1 LTDANFDETIASSDKPVLVDFWAPWCGPCKMIAPILEELAKEYEGKVKFVKLNVDENPDI 60 Query: 66 STRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 + +Y I SIPTL+LFK+GK +DR + GA ++ + + I Sbjct: 61 AAKYGIRSIPTLLLFKNGKEVDRSV-GALPKAALKQLI 97 >gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional. Length = 139 Score = 103 bits (260), Expect = 7e-24 Identities = 38/91 (41%), Positives = 62/91 (68%), Gaps = 1/91 (1%) Query: 13 SEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQIS 72 ++L+ PVV+DFWA WC PC +PI +D+A E + KV+ K++ E E+S R++I Sbjct: 46 DKLLQDDLPVVIDFWAPWCGPCRNFAPIFEDVAAERSGKVRFVKVNTEAERELSARFRIR 105 Query: 73 SIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 SIPT+++FK+G+V+D M+ GA ++ W+ Sbjct: 106 SIPTIMIFKNGQVVD-MLNGAVPKAPFDSWL 135 >gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional. Length = 109 Score = 82.8 bits (204), Expect = 2e-17 Identities = 40/94 (42%), Positives = 65/94 (69%), Gaps = 1/94 (1%) Query: 10 SFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRY 69 SFD++VL+ ++VDFWA WC PC ++PI+D+IADE K+ + KL+I+++ + +Y Sbjct: 12 SFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKY 71 Query: 70 QISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 I IPTL+LFK+G+V + GA S+ + E++ Sbjct: 72 GIRGIPTLLLFKNGEVAATKV-GALSKGQLKEFL 104 >gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional. Length = 98 Score = 72.2 bits (177), Expect = 3e-14 Identities = 31/84 (36%), Positives = 56/84 (66%), Gaps = 3/84 (3%) Query: 11 FDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQ 70 F+S L + V+VDF+A WC PC +++P ++ + E K+ K+D++E SE++ + Sbjct: 11 FES-TLSQNELVIVDFYAEWCGPCKRIAPFYEECSKEYT-KMVFVKVDVDELSEVAEKEN 68 Query: 71 ISSIPTLILFKDGKVIDRMMPGAS 94 I+S+PT +FK+G V+D ++ GA+ Sbjct: 69 ITSMPTFKVFKNGSVVDTLL-GAN 91 >gnl|CDD|162212 TIGR01126, pdi_dom, protein disulfide-isomerase domain. This model describes a domain of eukaryotic protein disulfide isomerases, generally found in two copies. The high cutoff for total score reflects the expectation of finding both copies. The domain is similar to thioredoxin but the redox-active disulfide region motif is APWCGHCK. Length = 102 Score = 68.8 bits (169), Expect = 3e-13 Identities = 28/97 (28%), Positives = 49/97 (50%), Gaps = 4/97 (4%) Query: 9 KSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELAD--KVKITKLDIEESSEIS 66 +FD VL + V+V+F+A WC C L+P + +A EL + + K+D +++ Sbjct: 4 SNFDDIVLS-NKDVLVEFYAPWCGHCKNLAPEYEKLAKELKGDPDIVLAKVDATAEKDLA 62 Query: 67 TRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 +R+ +S PT+ F GK G I+E++ Sbjct: 63 SRFGVSGFPTIKFFPKGKKPVD-YEGGRDLEAIVEFV 98 >gnl|CDD|185446 PTZ00102, PTZ00102, disulphide isomerase; Provisional. Length = 477 Score = 60.5 bits (147), Expect = 8e-11 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 5/85 (5%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADK---VKITKLDIEESSEISTRYQISSIPTLI 78 V+V F+A WC C +L+P A L +K + + +D E E++ + + PT+ Sbjct: 52 VLVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLASVDATEEMELAQEFGVRGYPTIK 111 Query: 79 LFKDGKVIDRMMPGASSQSDIIEWI 103 F G ++ G + I+ WI Sbjct: 112 FFNKGNPVN--YSGGRTADGIVSWI 134 Score = 42.8 bits (101), Expect = 2e-05 Identities = 17/78 (21%), Positives = 40/78 (51%), Gaps = 4/78 (5%) Query: 9 KSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELA--DKVKITKLDIEESSEIS 66 +F+ V + V+++ +A WC C L P+ +++ ++ D + + K++ ++E Sbjct: 365 NTFEEIVFKSDKDVLLEIYAPWCGHCKNLEPVYNELGEKYKDNDSIIVAKMN-GTANETP 423 Query: 67 TR-YQISSIPTLILFKDG 83 + S+ PT++ K G Sbjct: 424 LEEFSWSAFPTILFVKAG 441 >gnl|CDD|162215 TIGR01130, ER_PDI_fam, protein disulfide isomerases, eukaryotic. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs). Length = 462 Score = 59.3 bits (144), Expect = 2e-10 Identities = 30/107 (28%), Positives = 57/107 (53%), Gaps = 4/107 (3%) Query: 4 LKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADK---VKITKLDIE 60 L + +FD + ++ V+V+F+A WC C L+P + ADEL K +K+ K+D Sbjct: 4 LVLTKDNFD-DFIKSHEFVLVEFYAPWCGHCKSLAPEYEKAADELKKKGPPIKLAKVDAT 62 Query: 61 ESSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWILSRV 107 E +++ +Y +S PTL +F++G+ G I++++ + Sbjct: 63 EEKDLAQKYGVSGYPTLKIFRNGEDSVSDYNGPRDADGIVKYMKKQS 109 Score = 48.5 bits (116), Expect = 4e-07 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 5/79 (6%) Query: 9 KSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELAD---KVKITKLDIEESSEI 65 K+FD VL+ + V+V+F+A WC C L+PI +++A++ D V I K+D +++ Sbjct: 354 KNFDEIVLDETKDVLVEFYAPWCGHCKNLAPIYEELAEKYKDAESDVVIAKMDATA-NDV 412 Query: 66 STRYQISSIPTLILFKDGK 84 +++ PT+ GK Sbjct: 413 PP-FEVEGFPTIKFVPAGK 430 >gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein; Provisional. Length = 224 Score = 56.2 bits (135), Expect = 2e-09 Identities = 23/67 (34%), Positives = 37/67 (55%) Query: 19 SNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLI 78 + P V F+A WC C K++P + +A L +V + LD + ++ R+ I PTL+ Sbjct: 52 TGPWFVKFYAPWCSHCRKMAPAWERLAKALKGQVNVADLDATRALNLAKRFAIKGYPTLL 111 Query: 79 LFKDGKV 85 LF GK+ Sbjct: 112 LFDKGKM 118 >gnl|CDD|179545 PRK03147, PRK03147, thiol-disulfide oxidoreductase; Provisional. Length = 173 Score = 46.9 bits (112), Expect = 1e-06 Identities = 24/106 (22%), Positives = 52/106 (49%), Gaps = 25/106 (23%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADK-VKITKLDIEES------------------ 62 V ++FW +WC+PC K P ++++ + +K V+I ++++E+ Sbjct: 64 VFLNFWGTWCKPCEKEMPYMNELYPKYKEKGVEIIAVNVDETELAVKNFVNRYGLTFPVA 123 Query: 63 ----SEISTRYQISSIPTLILF-KDGKVIDRMMPGASSQSDIIEWI 103 ++ Y + +PT L KDGKV+ ++ G ++ + E++ Sbjct: 124 IDKGRQVIDAYGVGPLPTTFLIDKDGKVVK-VITGEMTEEQLEEYL 168 >gnl|CDD|129481 TIGR00385, dsbE, periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily. Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins. Length = 173 Score = 38.6 bits (90), Expect = 4e-04 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 3/63 (4%) Query: 2 SALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEE 61 +AL+ +++ E PV+++ WASWC PC P ++++A D + I +D ++ Sbjct: 46 AALREPLQAYTPEAFIQGKPVLLNVWASWCPPCRAEHPYLNELA---KDGLPIVGVDYKD 102 Query: 62 SSE 64 S+ Sbjct: 103 QSQ 105 >gnl|CDD|161873 TIGR00424, APS_reduc, 5'-adenylylsulfate reductase, thioredoxin-independent. This enzyme, involved in the assimilation of inorganic sulfate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulfate (APS) over 3'-phosphoadenylylsulfate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement E. coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis. Length = 463 Score = 35.8 bits (82), Expect = 0.003 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 3/63 (4%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELA---DKVKITKLDIEESSEISTRYQISSIPTL 77 +V +A WC C + ++A++LA KV + D ++ Q+ S PT+ Sbjct: 373 AWLVVLYAPWCPFCQAMEASYLELAEKLAGSGVKVAKFRADGDQKEFAKQELQLGSFPTI 432 Query: 78 ILF 80 + F Sbjct: 433 LFF 435 >gnl|CDD|162752 TIGR02187, GlrX_arch, Glutaredoxin-like domain protein. This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different. Length = 215 Score = 33.6 bits (77), Expect = 0.011 Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 3/65 (4%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVK--ITKLDIEESSEISTRYQISSIPTLIL 79 V D C+ C + ++++++ E++ K+K I D E E + +Y + +PT I+ Sbjct: 25 VFTDNDKEGCQYCKETEQLLEELS-EVSPKLKLEIYDFDTPEDKEEAEKYGVERVPTTII 83 Query: 80 FKDGK 84 ++GK Sbjct: 84 LEEGK 88 Score = 26.3 bits (58), Expect = 1.6 Identities = 13/59 (22%), Positives = 31/59 (52%), Gaps = 6/59 (10%) Query: 48 LADKVKITKLDIEESSEISTRYQISSIPTLILFKDG-KVIDRMMPGASSQSDIIEWILS 105 DK+ ++ E+ +++ +Y + S+P +++ K + + GA + +E+ILS Sbjct: 161 ANDKILGEMIEANENPDLAEKYGVMSVPKIVINKGVEEFV-----GAYPEEQFLEYILS 214 >gnl|CDD|129505 TIGR00411, redox_disulf_1, small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin. Length = 82 Score = 33.7 bits (77), Expect = 0.012 Identities = 17/78 (21%), Positives = 43/78 (55%), Gaps = 5/78 (6%) Query: 26 FWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFKDGKV 85 F + C C +++++A E+ D V++ +++ E+ + + Y I ++P +++ D + Sbjct: 6 FTSPTCPYCPAAKRVVEEVAKEMGDAVEVEYINVMENPQKAMEYGIMAVPAIVINGDVEF 65 Query: 86 IDRMMPGASSQSDIIEWI 103 I GA ++ +++E I Sbjct: 66 I-----GAPTKEELVEAI 78 >gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional. Length = 521 Score = 32.5 bits (74), Expect = 0.025 Identities = 10/23 (43%), Positives = 14/23 (60%) Query: 13 SEVLECSNPVVVDFWASWCRPCV 35 S L+ P ++ FWASWC C+ Sbjct: 50 SVYLKKDKPTLIKFWASWCPLCL 72 >gnl|CDD|133998 PHA02125, PHA02125, thioredoxin-like protein. Length = 75 Score = 32.3 bits (73), Expect = 0.029 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 6/53 (11%) Query: 26 FWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLI 78 F A WC C + P++ ++ D +D +E E++ ++ I S+PTL+ Sbjct: 5 FGAEWCANCKMVKPMLANVEYTYVD------VDTDEGVELTAKHHIRSLPTLV 51 >gnl|CDD|185310 PRK15412, PRK15412, thiol:disulfide interchange protein DsbE; Provisional. Length = 185 Score = 32.3 bits (73), Expect = 0.032 Identities = 10/34 (29%), Positives = 21/34 (61%) Query: 1 MSALKVDTKSFDSEVLECSNPVVVDFWASWCRPC 34 + +L+ + + ++VL PV+++ WA+WC C Sbjct: 50 LESLENPGQFYQADVLTQGKPVLLNVWATWCPTC 83 >gnl|CDD|162114 TIGR00928, purB, adenylosuccinate lyase. This family consists of adenylosuccinate lyase, the enzyme that catalyzes step 8 in the purine biosynthesis pathway for de novo synthesis of IMP and also the final reaction in the two-step sequence from IMP to AMP. Length = 435 Score = 31.9 bits (73), Expect = 0.035 Identities = 10/42 (23%), Positives = 17/42 (40%) Query: 24 VDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEI 65 +D + R +L I + E+ K T +D+ EI Sbjct: 24 LDVEVALLRALAELGVIPAEAVKEIRAKANFTDVDLARIKEI 65 >gnl|CDD|149549 pfam08534, Redoxin, Redoxin. This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins. Length = 142 Score = 31.9 bits (73), Expect = 0.042 Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 1/32 (3%) Query: 21 PVVVDFWAS-WCRPCVKLSPIIDDIADELADK 51 VV++FW +C C P ++ ++ K Sbjct: 29 KVVLNFWPGAFCPTCSAEHPYLEKLSKLYKAK 60 >gnl|CDD|177804 PLN00410, PLN00410, U5 snRNP protein, DIM1 family; Provisional. Length = 142 Score = 31.3 bits (71), Expect = 0.059 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 2/83 (2%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFK 81 VV+ F W C+++ ++ +A+ + + I +DI E + +T Y++ T++ F Sbjct: 26 VVIRFGHDWDETCMQMDEVLASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFF 85 Query: 82 DGKVIDRMMPGASSQSDIIEWIL 104 K I M+ + ++ I W L Sbjct: 86 RNKHI--MIDLGTGNNNKINWAL 106 >gnl|CDD|131709 TIGR02661, MauD, methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded. Length = 189 Score = 31.0 bits (70), Expect = 0.069 Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 19/84 (22%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIAD-ELADKVKITKLDIEE-----------------S 62 P ++ F A C C KL PII IA E D V I+ E S Sbjct: 76 PTLLMFTAPSCPVCDKLFPIIKSIARAEETDVVMISDGTPAEHRRFLKDHELGGERYVVS 135 Query: 63 SEISTRYQISSIPTLILF-KDGKV 85 +EI +Q+ IP +L +DGK+ Sbjct: 136 AEIGMAFQVGKIPYGVLLDQDGKI 159 >gnl|CDD|147981 pfam06110, DUF953, Eukaryotic protein of unknown function (DUF953). This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 119 Score = 30.5 bits (69), Expect = 0.11 Identities = 20/116 (17%), Positives = 40/116 (34%), Gaps = 22/116 (18%) Query: 9 KSFDSEVLECSN---PVVVDFWA-------SWCRPCVKLSPIIDDIADELADKVKITKLD 58 + F+ V E N P+ F SWC CV+ P+I + + +D Sbjct: 6 EEFNKAVKESENGSKPIFALFTGSKDTTGESWCPDCVRAEPVIREALKHAPEDCHFIYVD 65 Query: 59 IEESS---------EISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWILS 105 + + +++ +PTL+ + + R+ S ++E Sbjct: 66 VGDRPYWKDPNNPFRKDPNLKLTGVPTLLRWGGPQ---RLDESQCLNSHLVEMFFE 118 >gnl|CDD|151456 pfam11009, DUF2847, Protein of unknown function (DUF2847). Some members in this bacterial family of proteins with unknown function are annotated as YtxJ, a putative general stress protein. This cannot be confirmed. Length = 104 Score = 27.9 bits (63), Expect = 0.65 Identities = 14/49 (28%), Positives = 30/49 (61%), Gaps = 9/49 (18%) Query: 45 ADELADKVKITKLDIEE----SSEISTRYQI---SSIPTLILFKDGKVI 86 A+E + + + LD++E S+EI+ ++ + S P +I+ K+G+V+ Sbjct: 44 AEEDEEDLPVYYLDVQEYRDVSNEIAEKFGVKHES--PQVIVIKNGEVV 90 >gnl|CDD|131789 TIGR02742, TrbC_Ftype, type-F conjugative transfer system pilin assembly protein TrbC. This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins are heterogeneous and are not covered by this model. Length = 130 Score = 27.7 bits (62), Expect = 0.67 Identities = 8/34 (23%), Positives = 17/34 (50%) Query: 67 TRYQISSIPTLILFKDGKVIDRMMPGASSQSDII 100 ++ I+++P ++ KDG P S D++ Sbjct: 65 KQFDITAVPAFVVVKDGLACLPEQPCPESDYDVV 98 >gnl|CDD|178965 PRK00293, dipZ, thiol:disulfide interchange protein precursor; Provisional. Length = 571 Score = 27.5 bits (62), Expect = 0.91 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 9/75 (12%) Query: 21 PVVVDFWASWCRPCVKLSPII---DDIADELAD----KVKITKLDIEESSEISTRYQISS 73 PV++D +A WC C + + LAD + +T + E + Y + Sbjct: 476 PVMLDLYADWCVACKEFEKYTFSDPQVQQALADTVLLQADVTANN-AEDVALLKHYNVLG 534 Query: 74 IPTLILF-KDGKVID 87 +PT++ F G+ I Sbjct: 535 LPTILFFDAQGQEIP 549 >gnl|CDD|163278 TIGR03465, HpnD, squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. Length = 266 Score = 26.9 bits (60), Expect = 1.2 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 8/31 (25%) Query: 29 SWCRPCVKLSPIIDDIADELAD-KVKITKLD 58 ++CR +DDI DE +D +V KL Sbjct: 28 AFCR-------EVDDIVDEDSDPEVAQAKLA 51 >gnl|CDD|148829 pfam07449, HyaE, Hydrogenase-1 expression protein HyaE. This family contains bacterial hydrogenase-1 expression proteins approximately 120 residues long. This includes the E. coli protein HyaE, and the homologous proteins HoxO of R. eutropha and HupG of R. leguminosarum. Deletion of the hoxO gene in R. eutropha led to complete loss of the uptake [NiFe] hydrogenase activity, suggesting that it has a critical role in hydrogenase assembly. Length = 107 Score = 25.0 bits (55), Expect = 4.1 Identities = 8/35 (22%), Positives = 19/35 (54%), Gaps = 3/35 (8%) Query: 60 EESSEISTRYQISSIPTLILFKDGK---VIDRMMP 91 E+ ++ R+ + P+L+ F+DG+ V+ + Sbjct: 69 EQEEALAARFGVRRFPSLLFFRDGRYLGVLAGIRD 103 >gnl|CDD|183290 PRK11720, PRK11720, galactose-1-phosphate uridylyltransferase; Provisional. Length = 346 Score = 25.3 bits (56), Expect = 4.2 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 18/56 (32%) Query: 22 VVVDFWASWC--------RPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRY 69 VV +WA+W ++L+ + D D+LA +K ++++RY Sbjct: 221 AVVPYWAAWPFETLLLPKAHVLRLTDLTDAQRDDLALALK----------KLTSRY 266 >gnl|CDD|132187 TIGR03143, AhpF_homolog, putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140). Length = 555 Score = 24.7 bits (54), Expect = 5.1 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 2/50 (4%) Query: 35 VKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTL-ILFKDG 83 +L + + A L++K+ ++ E E T +I+ +PT+ +L DG Sbjct: 382 AELQSFLGEFAS-LSEKLNSEAVNRGEEPESETLPKITKLPTVALLDDDG 430 >gnl|CDD|128689 smart00411, BHL, bacterial (prokaryotic) histone like domain. Length = 90 Score = 24.8 bits (55), Expect = 5.6 Identities = 5/22 (22%), Positives = 14/22 (63%) Query: 43 DIADELADKVKITKLDIEESSE 64 ++ D +A+K ++K D + + + Sbjct: 5 ELIDAIAEKAGLSKKDAKAAVD 26 >gnl|CDD|177806 PLN00412, PLN00412, NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Provisional. Length = 496 Score = 24.7 bits (54), Expect = 5.7 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 9/64 (14%) Query: 35 VKLSPIIDDIADELADKV--KITKLDI---EESSEISTRYQISSIPTLILFKDGKVIDRM 89 VK+ +++ +AD L +KV K+ KL + E+ +I+ SS F +G V+D Sbjct: 301 VKVVLVMESVADALVEKVNAKVAKLTVGPPEDDCDITPVVSESSAN----FIEGLVMDAK 356 Query: 90 MPGA 93 GA Sbjct: 357 EKGA 360 >gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional. Length = 253 Score = 24.5 bits (54), Expect = 6.3 Identities = 7/13 (53%), Positives = 9/13 (69%) Query: 77 LILFKDGKVIDRM 89 L+ KDGKV +M Sbjct: 98 LVKAKDGKVTSKM 110 >gnl|CDD|162289 TIGR01295, PedC_BrcD, bacteriocin transport accessory protein, putative. This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris. Length = 122 Score = 24.5 bits (53), Expect = 6.7 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 13/82 (15%) Query: 31 CRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISS-------------IPTL 77 C C K S + + + + + S E+S+ +++ PT Sbjct: 35 CPYCRKFSGTLSGVVAQTKAPIYYIDSENNGSFEMSSLNDLTAFRSRFGIPTSFMGTPTF 94 Query: 78 ILFKDGKVIDRMMPGASSQSDI 99 + DGK + +++ ++ Sbjct: 95 VHITDGKQVSVRCGSSTTAQEL 116 >gnl|CDD|177357 PHA02278, PHA02278, thioredoxin-like protein. Length = 103 Score = 24.3 bits (52), Expect = 6.9 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 4/70 (5%) Query: 31 CRPCVKLSPIIDDIADE--LADKVKITKLDIEES--SEISTRYQISSIPTLILFKDGKVI 86 C C L +I + + + LD E+ + + I S P LI +KDG+++ Sbjct: 26 CGKCEILKSVIPMFQESGDIKKPILTLNLDAEDVDREKAVKLFDIMSTPVLIGYKDGQLV 85 Query: 87 DRMMPGASSQ 96 + + Sbjct: 86 KKYEDQVTPM 95 >gnl|CDD|177812 PLN02151, PLN02151, trehalose-phosphatase. Length = 354 Score = 23.9 bits (51), Expect = 9.9 Identities = 7/25 (28%), Positives = 15/25 (60%) Query: 31 CRPCVKLSPIIDDIADELADKVKIT 55 C+P + P+I+++ +L +K K Sbjct: 186 CQPATEFLPVINEVYKKLVEKTKSI 210 >gnl|CDD|182822 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional. Length = 427 Score = 24.0 bits (53), Expect = 10.0 Identities = 6/16 (37%), Positives = 10/16 (62%) Query: 47 ELADKVKITKLDIEES 62 ELA + ++ LDI+ Sbjct: 264 ELAPQAQVVALDIDAQ 279 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 0.318 0.133 0.392 Gapped Lambda K H 0.267 0.0744 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,698,709 Number of extensions: 90905 Number of successful extensions: 261 Number of sequences better than 10.0: 1 Number of HSP's gapped: 256 Number of HSP's successfully gapped: 58 Length of query: 107 Length of database: 5,994,473 Length adjustment: 73 Effective length of query: 34 Effective length of database: 4,417,089 Effective search space: 150181026 Effective search space used: 150181026 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.0 bits)