RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780375|ref|YP_003064788.1| hypothetical protein CLIBASIA_01300 [Candidatus Liberibacter asiaticus str. psy62] (175 letters) >gnl|CDD|33143 COG3334, COG3334, Uncharacterized conserved protein [Function unknown]. Length = 192 Score = 94.3 bits (234), Expect = 1e-20 Identities = 41/144 (28%), Positives = 78/144 (54%), Gaps = 5/144 (3%) Query: 26 FLQGFANQSYGDPTLVDREIQQYCTNVIDSVRERDYLSQKKVLEDLQK--DIEQRVILLE 83 + A + EI+++C N+ D+ ++ Y QK++LE L+ ++ +R+ LE Sbjct: 38 EAEDAAAELAEKKAAAQSEIEKFCANIADAAADQLYALQKELLEKLKDLAEVNERLKALE 97 Query: 84 NHKKEYNLWFQKYDSFIMSYNK---NILDIYKKMDSDSAALQLEQIDPDISSHILMRLSP 140 K E ++ + + S ++ IY KM D+AA LE + + ++ ILM+L P Sbjct: 98 KKKAELKDLEEEREGILRSKQAEDGKLVKIYSKMKPDAAAAILENLPDEEAAAILMKLKP 157 Query: 141 RQSSLIMSKMNPKSATMITNVVAN 164 R+ LI++KM+P+ A +T ++A+ Sbjct: 158 RKLGLILAKMDPEKAATLTELIAS 181 >gnl|CDD|58628 cd03687, Dehydratase_LU, Dehydratase large subunit. This family contains the large (alpha) subunit of B12-dependent glycerol dehydratases (GDHs) and B12-dependent diol dehydratases (DDHs). GDH is isofunctional with DDH. These enzymes can each catalyze the conversion of 1,2-propanediol, glycerol, and 1,2-ethanediol to the corresponding aldehydes via a coenzyme B12 (adenosylcobalamin)-dependent radical mechanism. Both enzymes exhibit a subunit composition of alpha2beta2gamma2. The enzymes differ in substrate specificity; glycerol is the preferred substrate for GDH and 1,2-propanediol for DDH. GDH shows almost equal affinity for both (R) and (S)-isomers while DDH prefers the (S) isomer. GDH plays a key role in the dihydroxyacetone (DHA) pathway and DDH in the anaerobic degradation of 1,2-diols. The radical mechanism has been well studied for Klebsiella oxytoca DDH and involves binding of 1,2-propanediol to the enzyme to induce hemolytic cleavage of the Co-C5' bond of the coenzyme to form cob(II)alamin and the adenosyl radical. Hydrogen abstraction from the substrate follows producing a substrate generated radical and 5'-deoxyadenosine. Rearrangement to the product radical is then followed by abstraction of a hydrogen atom from 5'-deoxyadenosine to produce the hydrated propionaldehyde and regenerate the adenosyl radical. After the Co-C5' bond is reformed and the hydrated aldehyde dehydrated, the process is complete. GDH has a higher affinity for coenzyme B12 than DDH. Both GDH and DDH are activated by various monovalent cations with K+, NH4+, and Rb+ being the most effective. However, DDH differs from GDH in that it is partially active with Cs+ and Na+. In general, the alpha and beta subunits for both enzymes are on different chains. However, for a subset of the GDHs, alpha and beta subunits appear to be on a single chain.. Length = 545 Score = 31.1 bits (70), Expect = 0.16 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 4/69 (5%) Query: 93 FQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRL----SPRQSSLIMS 148 F D FI Y N+ + M DS L +DP++ ++RL +P + ++S Sbjct: 52 FDMIDHFIARYGINLERAEEAMALDSVKLARMLVDPNVPREEIVRLTTAMTPAKLVEVVS 111 Query: 149 KMNPKSATM 157 +MN M Sbjct: 112 QMNVVEMMM 120 >gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit [Transcription]. Length = 1386 Score = 29.5 bits (66), Expect = 0.54 Identities = 24/96 (25%), Positives = 41/96 (42%), Gaps = 6/96 (6%) Query: 74 DIEQRVILLENHKKEYNLWFQKYDSFIMSYNKNILDIYKKMDSDSA-----ALQLEQIDP 128 D++ IL + ++ N + K D I YNK L + + + +L I Sbjct: 700 DVQPGEILSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIRE 759 Query: 129 DISSHILMRLSPRQSSLIMSKMNPKSATM-ITNVVA 163 + + L PR S LIM+ K + + I+ +VA Sbjct: 760 EAGKICIRELHPRNSPLIMALCGSKGSKINISQMVA 795 >gnl|CDD|146204 pfam03448, MgtE_N, MgtE intracellular N domain. This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family pfam01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains. Length = 102 Score = 26.7 bits (60), Expect = 3.7 Identities = 6/54 (11%), Positives = 23/54 (42%) Query: 107 ILDIYKKMDSDSAALQLEQIDPDISSHILMRLSPRQSSLIMSKMNPKSATMITN 160 I ++ +++ + L + P+ ++ +L L + ++ + P+ + Sbjct: 6 IAELLEELPPEERLALLRLLPPERAAEVLEELDEDVQAELLEALPPEELAELLE 59 >gnl|CDD|34518 COG4909, PduC, Propanediol dehydratase, large subunit [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 554 Score = 26.2 bits (57), Expect = 4.9 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 13/84 (15%) Query: 93 FQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRL----SPRQSSLIMS 148 F D FI Y ++ + M DS L DP++ ++RL +P + ++S Sbjct: 59 FDLIDHFIARYGIDLERAEEVMAMDSVKLANMLCDPNVPRETIVRLTTAMTPAKIVEVVS 118 Query: 149 KMNPKSATMITNVVANMLKFKKLK 172 +M NVV M+ +K++ Sbjct: 119 QM---------NVVEMMMAMQKMR 133 >gnl|CDD|32420 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]. Length = 451 Score = 26.0 bits (57), Expect = 5.2 Identities = 20/119 (16%), Positives = 48/119 (40%), Gaps = 15/119 (12%) Query: 50 TNVIDSVRERDYLSQKKVLEDLQK----------DIEQRVILLENHKKEYNLWFQKYDSF 99 N+ID + ++D +K+L L +RV++ KE + Sbjct: 10 ENLIDLLEDKDLSVLRKLLARLHPADVAEILEELPGRERVVVWRLLPKE-----DAAEVL 64 Query: 100 IMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRLSPRQSSLIMSKMNPKSATMI 158 ++ +I + + + A +E++D D ++ +L L ++S ++P+ + Sbjct: 65 GELDDEVREEIIEALSDEELAAAIEELDIDDAADLLDELPDEVRDELLSLLDPEERARV 123 >gnl|CDD|145440 pfam02286, Dehydratase_LU, Dehydratase large subunit. This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances. Length = 554 Score = 26.2 bits (58), Expect = 5.4 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 4/69 (5%) Query: 93 FQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRL----SPRQSSLIMS 148 F D FI Y ++ + M DS L +DP++ ++RL +P + + ++S Sbjct: 59 FDLIDRFIARYGIDLERAEEAMAMDSVKLARMLVDPNVPREEIVRLTTGMTPAKLAEVVS 118 Query: 149 KMNPKSATM 157 ++N M Sbjct: 119 QLNVVEMMM 127 >gnl|CDD|58174 cd03508, Delta4-sphingolipid-FADS-like, The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase (MLD), reported to modulate biosynthesis of the epidermal growth factor receptor; and other related proteins. These proteins are found in various eukaryotes including vertebrates, higher plants, and fungi. Studies show that MLD is localized to the endoplasmic reticulum. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase.. Length = 289 Score = 25.9 bits (57), Expect = 5.9 Identities = 12/34 (35%), Positives = 17/34 (50%) Query: 1 MILLPIIYYYKKRDMLSQLLFLLFFFLQGFANQS 34 ++LL II Y RD + L+ +F G N S Sbjct: 25 VVLLQIITAYLLRDSSWWKILLVAYFFGGTINHS 58 >gnl|CDD|37502 KOG2291, KOG2291, KOG2291, Oligosaccharyltransferase, alpha subunit (ribophorin I) [Posttranslational modification, protein turnover, chaperones]. Length = 602 Score = 25.7 bits (56), Expect = 7.9 Identities = 23/166 (13%), Positives = 54/166 (32%), Gaps = 20/166 (12%) Query: 6 IIYYYKKRDMLSQLLFLLFFFLQGFANQSYGDPTLVDREIQQYCTNVIDSVRERDYLSQK 65 + Y + K ML + L ++ F F Y + + + + Sbjct: 425 VHYTFSKSSMLQEPLLIIAAFFILFFAVIV------------YVRLDFNISSDPSMSATR 472 Query: 66 KV---LEDLQKDIEQRVILLENHKKEYNLWFQKYDSFIMSYNKNILDIYKKMDSDSAALQ 122 +V L L ++ + ++ + + + + + K + KK + Sbjct: 473 RVFQILLQLALEVNKCDVMYCSLSEGRFRYKNTENIPTLGGAKKSSPLEKKDLASELVPL 532 Query: 123 LEQIDPDISSHILMRLSPRQSSLIMS-KMNPKSATMITNVVANMLK 167 + S+ + + + L S K+ PK++ M + V K Sbjct: 533 PSPLKTSDSTCV----ANKLPELSCSVKLVPKTSVMQKHGVEGNGK 574 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.322 0.136 0.379 Gapped Lambda K H 0.267 0.0713 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,109,407 Number of extensions: 108462 Number of successful extensions: 363 Number of sequences better than 10.0: 1 Number of HSP's gapped: 359 Number of HSP's successfully gapped: 36 Length of query: 175 Length of database: 6,263,737 Length adjustment: 87 Effective length of query: 88 Effective length of database: 4,383,754 Effective search space: 385770352 Effective search space used: 385770352 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 (21.9 bits) S2: 54 (24.6 bits)