RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780591|ref|YP_003065004.1| aminomethyltransferase protein (glycine cleavage) [Candidatus Liberibacter asiaticus str. psy62] (273 letters) >gnl|CDD|163214 TIGR03317, ygfZ_signature, folate-binding protein YgfZ. YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein. Length = 67 Score = 79.5 bits (197), Expect = 8e-16 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 1/68 (1%) Query: 142 KTYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIR 201 + + LRI GI + + P + +D L G+S KGCY+GQEVV+R+ +R ++ Sbjct: 1 EAWELLRIAAGIPEGGAE-TSGEFLPQELNLDALGGVSFKKGCYVGQEVVARMHYRGKVK 59 Query: 202 KRPMIITG 209 +R + + Sbjct: 60 RRLVRLRL 67 >gnl|CDD|149654 pfam08669, GCV_T_C, Glycine cleavage T-protein C-terminal barrel domain. This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. Length = 95 Score = 52.2 bits (126), Expect = 1e-07 Identities = 28/98 (28%), Positives = 46/98 (46%), Gaps = 22/98 (22%) Query: 183 GCYIGQEVVSRIQHRNIIRKRPMIITGTDDLPP-SGSPILTDDIEIGTLGVVVG------ 235 G +IG+E ++R + + ++R+R + + D PP G P+L D G VVG Sbjct: 1 GDFIGKEALARQKAKGVVRRRLVGLLLDGDGPPREGEPVLAAD------GEVVGEVTSGT 54 Query: 236 -----KKALAIARIDKVDHAIKKGMALTVH--GVRVKA 266 K +A+A + + A + G + V G RV A Sbjct: 55 YSPTLGKNIALAYVRT-EAA-EPGTEVEVEIRGKRVPA 90 >gnl|CDD|181953 PRK09559, PRK09559, putative global regulator; Reviewed. Length = 327 Score = 43.5 bits (103), Expect = 6e-05 Identities = 57/234 (24%), Positives = 87/234 (37%), Gaps = 43/234 (18%) Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKIL--LYFLISKIEED 63 L + + + G + +LQ +TADV L +A +GK+ L D Sbjct: 24 LDDWALATITGADSEKYLQGQVTADVSQLTEDQHLLAAHCDAKGKMWSNLRLFR---RGD 80 Query: 64 TFILEIDRSKRDSLIDKLLFYKLRSNVIIEIQPINGVVLSW-----------------NQ 106 F RS R++ + +L Y + S V I V+L + Sbjct: 81 GFAWIERRSVRENQLTELKKYAVFSKVTIAPDD-ERVLLGVAGFQARAALANLFSELPDA 139 Query: 107 EH--------TFSNSSFIDERF------SIADVLLHRTWGHNEKIASDIKTYHELRINHG 152 E T ERF + A++L + G + ++ + + L I G Sbjct: 140 EKPVVQEGATTLLWFEHPAERFLLVTDEATANMLTEKLRGEAQ--LNNSQQWLALDIEAG 197 Query: 153 IVDPNTDFLPSTIF-PHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPM 205 P D S F P + L GIS KGCY GQE+V+R + R KR + Sbjct: 198 F--PVIDAANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRG-ANKRAL 248 >gnl|CDD|129619 TIGR00528, gcvT, glycine cleavage system T protein. Eukaryotic forms are mitochondrial and have an N-terminal transit peptide. Length = 361 Score = 35.6 bits (82), Expect = 0.014 Identities = 20/70 (28%), Positives = 37/70 (52%) Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTF 65 +S+ + + G ++ FLQ ++ DV L A+ S +L PQG ++ +I ED F Sbjct: 48 VSHMGIVDLSGSRSLEFLQRLLPNDVAALTPGKAQYSVLLNPQGGVVDDLIIYYFGEDRF 107 Query: 66 ILEIDRSKRD 75 L ++ + R+ Sbjct: 108 RLVVNAATRE 117 >gnl|CDD|178995 PRK00389, gcvT, glycine cleavage system aminomethyltransferase T; Reviewed. Length = 359 Score = 32.0 bits (74), Expect = 0.17 Identities = 16/56 (28%), Positives = 30/56 (53%) Query: 12 IKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFIL 67 + V G A+ FLQ ++ DV L A+ + +L G ++ ++ K+ ED ++L Sbjct: 55 VDVTGPDALAFLQYLLANDVSKLKPGKAQYTCMLNEDGGVIDDLIVYKLSEDEYLL 110 >gnl|CDD|183048 PRK11239, PRK11239, hypothetical protein; Provisional. Length = 215 Score = 27.8 bits (62), Expect = 2.9 Identities = 10/21 (47%), Positives = 12/21 (57%) Query: 107 EHTFSNSSFIDERFSIADVLL 127 E F NS F D + S A+V L Sbjct: 82 EQRFCNSEFGDLKLSAAEVAL 102 >gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase. Length = 404 Score = 27.4 bits (61), Expect = 4.0 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 8/64 (12%) Query: 16 GKSAIPFLQAIITADVLTLPYKIARGSAILT----PQGKILLYFLISKIEEDTFILEIDR 71 GK AIPFL+ ++ AD+ L G+ L+ +G I+ +I+K+ +D L ++ Sbjct: 90 GKDAIPFLETLVVADIAGL----KDGTGTLSVFTNEKGGIIDDTVITKVTDDHIYLVVNA 145 Query: 72 SKRD 75 RD Sbjct: 146 GCRD 149 >gnl|CDD|177906 PLN02265, PLN02265, probable phenylalanyl-tRNA synthetase beta chain. Length = 597 Score = 27.3 bits (61), Expect = 4.4 Identities = 9/18 (50%), Positives = 13/18 (72%) Query: 196 HRNIIRKRPMIITGTDDL 213 H+NI R+R ++ GT DL Sbjct: 152 HQNICRRRTLVAIGTHDL 169 >gnl|CDD|128754 smart00478, ENDO3c, endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases. Length = 149 Score = 26.8 bits (60), Expect = 6.2 Identities = 8/29 (27%), Positives = 16/29 (55%) Query: 66 ILEIDRSKRDSLIDKLLFYKLRSNVIIEI 94 + D + + LI L FY+ ++ +IE+ Sbjct: 27 LAAADEEELEELIRPLGFYRRKAKYLIEL 55 >gnl|CDD|163018 TIGR02784, addA_alphas, double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. Length = 1141 Score = 26.2 bits (58), Expect = 8.6 Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 11/64 (17%) Query: 29 ADVLTLPYKIA------RGSAILTPQGKI-LLYFLISKI----EEDTFILEIDRSKRDSL 77 AD L L IA G +L P+ + L L S + EED F L RS +SL Sbjct: 615 ADRLKLTSHIAVQDLMALGRFVLQPEDDLSLAALLKSPLFGLDEEDLFALAAGRSGGESL 674 Query: 78 IDKL 81 +L Sbjct: 675 WARL 678 >gnl|CDD|183552 PRK12486, dmdA, putative dimethyl sulfoniopropionate demethylase; Reviewed. Length = 368 Score = 26.3 bits (58), Expect = 9.2 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 4/50 (8%) Query: 185 YIGQEVVSRIQHRNIIRK-RPMIITGTDDLPPSGS--PILTDDIEIGTLG 231 IG++ + R+ ++ R + I G + +PP P+L D +G + Sbjct: 273 CIGKDALLRVAKEGPQKQIRGIKIGG-ERIPPCDRAWPLLAGDNRVGQVT 321 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 0.323 0.140 0.410 Gapped Lambda K H 0.267 0.0805 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,554,566 Number of extensions: 302536 Number of successful extensions: 478 Number of sequences better than 10.0: 1 Number of HSP's gapped: 478 Number of HSP's successfully gapped: 20 Length of query: 273 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 181 Effective length of database: 4,006,537 Effective search space: 725183197 Effective search space used: 725183197 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: 56 (25.2 bits)