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)