RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781064|ref|YP_003065477.1| FeS assembly scaffold SufA [Candidatus Liberibacter asiaticus str. psy62] (116 letters) >gnl|CDD|131052 TIGR01997, sufA_proteo, FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria. Length = 107 Score = 139 bits (352), Expect = 2e-34 Identities = 53/108 (49%), Positives = 78/108 (72%), Gaps = 2/108 (1%) Query: 4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDG 63 ++T+T+AA I+E+V + +A GIR+ +KK GCAG+EY++DLV+ P DDLIE DG Sbjct: 2 VITLTDAAAIHIRELV-AKRPEAVGIRLGVKKTGCAGMEYVLDLVS-EPKKDDDLIEHDG 59 Query: 64 VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111 KV++ ++L++LGT++DF L GF F+NPN SACGCG+S E+ Sbjct: 60 AKVFVAPEAVLFILGTQVDFVRTTLRQGFKFNNPNATSACGCGESFEL 107 >gnl|CDD|161681 TIGR00049, TIGR00049, Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry. Length = 105 Score = 123 bits (312), Expect = 8e-30 Identities = 46/103 (44%), Positives = 67/103 (65%), Gaps = 1/103 (0%) Query: 6 TMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVK 65 T+T++A RIK ++ G+R+ +K GGC+GL+Y ++ D P + D++ E+DGVK Sbjct: 1 TLTDSAAKRIKALLAGEGEPNLGLRVGVKGGGCSGLQYGLEFD-DEPNEDDEVFEQDGVK 59 Query: 66 VWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQS 108 V +D SL Y+ G+EID+ E L SGF F NPN CGCG+S Sbjct: 60 VVVDPKSLPYLDGSEIDYVEELLGSGFTFTNPNAKGTCGCGKS 102 >gnl|CDD|131066 TIGR02011, IscA, iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria. Length = 105 Score = 95.3 bits (237), Expect = 3e-21 Identities = 44/107 (41%), Positives = 66/107 (61%), Gaps = 2/107 (1%) Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGV 64 +T+T++A R+ + N +GK G+R+ +K GC+G+ Y+++ V D P D + E GV Sbjct: 1 ITLTDSAAARVNTFLAN-RGKGFGLRLGVKTSGCSGMAYVLEFV-DEPTPDDIVFEDKGV 58 Query: 65 KVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111 K+ ID SL Y+ GT++DF E L GF F NPN CGCG+S + Sbjct: 59 KIVIDGKSLQYLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 105 >gnl|CDD|181914 PRK09502, iscA, iron-sulfur cluster assembly protein; Provisional. Length = 107 Score = 91.5 bits (227), Expect = 5e-20 Identities = 40/107 (37%), Positives = 66/107 (61%), Gaps = 2/107 (1%) Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGV 64 +T++++A R+ + ++GK G+R+ ++ GC+G+ Y+++ V D P D + E GV Sbjct: 3 ITLSDSAAARVNTFL-ANRGKGFGLRLGVRTSGCSGMAYVLEFV-DEPTPEDIVFEDKGV 60 Query: 65 KVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQSVEI 111 KV +D SL ++ GT++DF E L GF F NPN CGCG+S + Sbjct: 61 KVVVDGKSLQFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESFHV 107 >gnl|CDD|181915 PRK09504, sufA, iron-sulfur cluster assembly scaffold protein; Provisional. Length = 122 Score = 88.3 bits (219), Expect = 4e-19 Identities = 39/104 (37%), Positives = 65/104 (62%), Gaps = 2/104 (1%) Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGV 64 +T+T AA I+E++ Q +G+R+ +K+ GCAG Y++D V++ P D + E DG Sbjct: 18 LTLTPAAAAHIRELM-AKQPGMKGVRLGVKQTGCAGFGYVLDSVSE-PDKDDLVFEHDGA 75 Query: 65 KVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGCGQS 108 K+++ ++ ++ GTE+D+ E L F FHNP + CGCG+S Sbjct: 76 KLFVPLQAMPFIDGTEVDYVREGLNQIFKFHNPKAQNECGCGES 119 >gnl|CDD|184186 PRK13623, PRK13623, iron-sulfur cluster insertion protein ErpA; Provisional. Length = 115 Score = 74.6 bits (184), Expect = 5e-15 Identities = 42/108 (38%), Positives = 60/108 (55%), Gaps = 5/108 (4%) Query: 6 TMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDL-IEKDGV 64 T+AA ++KE++ +R+ + GGC+G +Y D V+ DD IEK GV Sbjct: 11 VFTDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTF--DEQVNEDDTTIEKQGV 68 Query: 65 KVWIDSASLLYMLGTEIDFKTEKLY-SGFVFHNPNQVSACGCGQSVEI 111 + +D SL Y++G E+D+ TE L S FV NPN + CGCG S I Sbjct: 69 TLVVDPMSLQYLVGAEVDY-TEGLEGSRFVIKNPNAKTTCGCGSSFSI 115 >gnl|CDD|178631 PLN03082, PLN03082, Iron-sulfur cluster assembly; Provisional. Length = 163 Score = 71.1 bits (174), Expect = 6e-14 Identities = 41/114 (35%), Positives = 68/114 (59%), Gaps = 7/114 (6%) Query: 3 DIVTMTEAAVYRIKEIVFNSQGKAQG--IRISLKKGGCAGLEYMVDLVTDNPVDGDDLI- 59 D V MT+ + R+KE+ S+ A+ +R+S++ GGC+G +Y+ +L D+ + DD + Sbjct: 53 DAVHMTDNCIRRLKEL-QTSEPSAEDKMLRLSVETGGCSGFQYVFEL--DDKTNSDDRVF 109 Query: 60 EKDGVKVWIDSASLLYMLGTEIDFKTEKLYSGFVFH-NPNQVSACGCGQSVEIK 112 EKDGVK+ +D+ S ++ G +D+ E + S FV NP+ V C C S +K Sbjct: 110 EKDGVKLVVDNISYDFVKGATVDYVEELIRSAFVVSTNPSAVGGCSCKSSFMVK 163 >gnl|CDD|132384 TIGR03341, YhgI_GntY, IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization. Length = 190 Score = 38.5 bits (90), Expect = 4e-04 Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 2/95 (2%) Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDL-IEKDG 63 +T+TEAA + +++ Q + GIR+ + G E V + V+ D+ +E +G Sbjct: 1 ITITEAAQAYLAKLL-AKQNEGTGIRVFVVNPGTPYAECCVSYCPPDEVEPSDIKLEFNG 59 Query: 64 VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPN 98 ++D+ S ++ IDF T+++ PN Sbjct: 60 FSAYVDALSAPFLEDAVIDFVTDRMGGQLTLKAPN 94 >gnl|CDD|183027 PRK11190, PRK11190, Fe/S biogenesis protein NfuA; Provisional. Length = 192 Score = 29.6 bits (67), Expect = 0.16 Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 2/95 (2%) Query: 5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDL-IEKDG 63 +T+++AA +++ +Q + IR+ + G E V + V+ D ++ DG Sbjct: 2 ITISDAAQAHFAKLL-ANQEEGTQIRVFVINPGTPNAECGVSYCPPDAVEATDTELKFDG 60 Query: 64 VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPN 98 ++D S ++ EIDF T++L S PN Sbjct: 61 FSAYVDELSAPFLEDAEIDFVTDQLGSQLTLKAPN 95 >gnl|CDD|130966 TIGR01911, HesB_rel_seleno, HesB-like selenoprotein. This model represents a family of small proteins related to HesB and its close homologs, which are likely to be invovlved in iron-sulfur cluster assembly (See TIGR00049 and pfam01521). Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain. A variable Cys/Ser/Gly-rich C-terminal region is not included in the seed alignment and model. Length = 92 Score = 29.1 bits (65), Expect = 0.24 Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 2/90 (2%) Query: 3 DIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKD 62 IV M++ A K+ + + IRI GC G M +L+ D +GD++ + Sbjct: 2 KIVAMSDDAYEEFKDFLKENDIDNDVIRIHFAGMGCMGP--MFNLIADEEKEGDEIEKIH 59 Query: 63 GVKVWIDSASLLYMLGTEIDFKTEKLYSGF 92 + ID + G I+ E +GF Sbjct: 60 DLTFLIDKNLIDQFGGFSIECAEENFGAGF 89 >gnl|CDD|72638 pfam09222, Fim-adh_lectin, Fimbrial adhesin F17-AG, lectin domain. Members of this family are carbohydrate-specific lectin domains found in bacterial fimbrial adhesins. They adopt a compact, elongated structure consisting of a beta-sandwich with two major sheets: one consisting of five long strands in mixed orientations, and a front sheet with four antiparallel strands, forming an immunoglobin-like fold. Length = 170 Score = 28.9 bits (64), Expect = 0.26 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 6/68 (8%) Query: 33 LKKGGCAGLEYMVDLVTDNPVDGDD---LIEKDGVKVWIDSASLLYMLGTEIDFKT-EKL 88 + G C GL+ VDL +DG L E+ G+ +W+ + Y GT + + E + Sbjct: 47 ISGGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTN--YSRGTAMSGNSWENV 104 Query: 89 YSGFVFHN 96 +SG+ N Sbjct: 105 FSGWCVGN 112 >gnl|CDD|178732 PLN03190, PLN03190, aminophospholipid translocase; Provisional. Length = 1178 Score = 26.8 bits (59), Expect = 1.2 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 1/69 (1%) Query: 14 RIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASL 73 ++ +I+ NS K + R SL+ + G D V + ID SL Sbjct: 769 KMTQIIINSNSK-ESCRKSLEDALVMSKKLTTVSGISQNTGGSSAAASDPVALIIDGTSL 827 Query: 74 LYMLGTEID 82 +Y+L +E++ Sbjct: 828 VYVLDSELE 836 >gnl|CDD|180640 PRK06608, PRK06608, threonine dehydratase; Provisional. Length = 338 Score = 26.7 bits (59), Expect = 1.4 Identities = 12/21 (57%), Positives = 13/21 (61%) Query: 68 IDSASLLYMLGTEIDFKTEKL 88 + S SL MLG EI FK E L Sbjct: 27 VHSESLNEMLGHEIFFKVESL 47 >gnl|CDD|181426 PRK08444, PRK08444, hypothetical protein; Provisional. Length = 353 Score = 25.8 bits (57), Expect = 2.4 Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 5/46 (10%) Query: 54 DGDDLIEKDGVKVW-IDSASLLYMLGTEIDFKTEKLYSGFVFHNPN 98 + + L +++ VK++ +D L+ LG D K KL+ V+ N N Sbjct: 9 NNERLNQEEAVKLYDLD----LFTLGKYADKKRTKLHGKKVYFNVN 50 >gnl|CDD|161885 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer. Length = 442 Score = 25.5 bits (56), Expect = 2.7 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 5/62 (8%) Query: 4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISL-----KKGGCAGLEYMVDLVTDNPVDGDDL 58 I+ ++ I + + N A G+RI C E + V N G+D+ Sbjct: 11 IIRLSGPDSLSILKKITNKLNTASGMRIQYGHIIDSNNKCKDDELLFKFVAPNSYTGEDV 70 Query: 59 IE 60 IE Sbjct: 71 IE 72 >gnl|CDD|149840 pfam08902, DUF1848, Domain of unknown function (DUF1848). This family of proteins are functionally uncharacterized. The C-terminus contains a cluster of cysteines that are similar to the iron-sulfur cluster found at the N-terminus of pfam04055. Length = 264 Score = 24.9 bits (55), Expect = 4.5 Identities = 6/16 (37%), Positives = 9/16 (56%) Query: 96 NPNQVSACGCGQSVEI 111 + Q CGC +S +I Sbjct: 234 DKGQRKECGCVESRDI 249 >gnl|CDD|177494 PHA02878, PHA02878, ankyrin repeat protein; Provisional. Length = 477 Score = 24.8 bits (54), Expect = 4.8 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 10/61 (16%) Query: 42 EYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEIDFKTEKLYSG---FVFHNPN 98 +DLV + DD+IE + K LL G +I+ K + + N + Sbjct: 128 IQTIDLVYIDKKSKDDIIEAEITK-------LLLSYGADINMKDRHKGNTALHYATENKD 180 Query: 99 Q 99 Q Sbjct: 181 Q 181 >gnl|CDD|179992 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed. Length = 344 Score = 24.7 bits (55), Expect = 5.0 Identities = 5/16 (31%), Positives = 8/16 (50%) Query: 88 LYSGFVFHNPNQVSAC 103 +YSG ++ P V Sbjct: 317 IYSGLIYEGPGLVKEI 332 >gnl|CDD|180889 PRK07217, PRK07217, replication factor A; Reviewed. Length = 311 Score = 24.6 bits (54), Expect = 5.5 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 10/74 (13%) Query: 2 SDIVTMTEAAVYRIKEIVFNS-QGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIE 60 SD+ + E Y +K +V + QG R S+K +E +L D V GDD +E Sbjct: 123 SDLPELEEGKSYLLKNVVTDEYQG-----RFSVKLNRTTSIE---ELDEDIEV-GDDEVE 173 Query: 61 KDGVKVWIDSASLL 74 +G V I S S L Sbjct: 174 VEGALVDIQSGSGL 187 >gnl|CDD|184036 PRK13407, bchI, magnesium chelatase subunit I; Provisional. Length = 334 Score = 24.4 bits (53), Expect = 5.9 Identities = 7/25 (28%), Positives = 19/25 (76%) Query: 42 EYMVDLVTDNPVDGDDLIEKDGVKV 66 +++VDL+ D G++++E++G+ + Sbjct: 142 DHIVDLLLDVAQSGENVVEREGLSI 166 >gnl|CDD|184379 PRK13896, PRK13896, cobyrinic acid a,c-diamide synthase; Provisional. Length = 433 Score = 24.3 bits (53), Expect = 6.7 Identities = 12/24 (50%), Positives = 15/24 (62%) Query: 41 LEYMVDLVTDNPVDGDDLIEKDGV 64 L D+VT +PV GD L + DGV Sbjct: 255 LRERADVVTFSPVAGDPLPDCDGV 278 >gnl|CDD|178069 PLN02450, PLN02450, 1-aminocyclopropane-1-carboxylate synthase. Length = 468 Score = 23.9 bits (52), Expect = 8.5 Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 8/30 (26%) Query: 81 IDFKTEK--------LYSGFVFHNPNQVSA 102 +DF T K +YSG VF +P VS Sbjct: 217 VDFITAKNIHLISDEIYSGTVFDSPGFVSV 246 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 0.137 0.398 Gapped Lambda K H 0.267 0.0702 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,840,825 Number of extensions: 104111 Number of successful extensions: 205 Number of sequences better than 10.0: 1 Number of HSP's gapped: 194 Number of HSP's successfully gapped: 31 Length of query: 116 Length of database: 5,994,473 Length adjustment: 81 Effective length of query: 35 Effective length of database: 4,244,225 Effective search space: 148547875 Effective search space used: 148547875 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)