RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12057
(172 letters)
>gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase.
Length = 404
Score = 146 bits (370), Expect = 9e-43
Identities = 57/111 (51%), Positives = 74/111 (66%)
Query: 61 GKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCP 120
GKRRR GGF GA +I Q+K GVSR+R G S+G P R EI + + +++G +TSG
Sbjct: 294 GKRRRAEGGFLGADVILKQLKEGVSRRRVGFISSGAPARSHSEILDESGEKIGEVTSGGF 353
Query: 121 SPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHTPP 171
SP LKKNIAMGY++ + K G E+ V VR K D VTKMPF+ + Y+ PP
Sbjct: 354 SPCLKKNIAMGYVKSGFHKAGTEVKVEVRGKMYDAVVTKMPFVPTKYYKPP 404
>gnl|CDD|237435 PRK13579, gcvT, glycine cleavage system aminomethyltransferase T;
Provisional.
Length = 370
Score = 121 bits (305), Expect = 2e-33
Identities = 42/108 (38%), Positives = 60/108 (55%), Gaps = 1/108 (0%)
Query: 62 KRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGCP 120
K RRE GGFPGA I + + G SR+R GL G P+R G +F+ +G +TSG
Sbjct: 262 KARREAGGFPGAKAILAALAKGASRRRVGLKPEGRAPVREGAPLFDDAGTEIGTVTSGGF 321
Query: 121 SPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYH 168
PS+ +AMGY+ + + G ++ VR KR+ V V +PF+ Y
Sbjct: 322 GPSVGGPVAMGYVPASLAAPGTAVFAEVRGKRLPVTVHALPFVPHRYK 369
>gnl|CDD|219963 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 catalyzes the catabolism of glycine in
eukaryotes. The T-protein is an aminomethyl transferase.
Length = 95
Score = 107 bits (270), Expect = 4e-31
Identities = 37/95 (38%), Positives = 52/95 (54%), Gaps = 2/95 (2%)
Query: 68 GGFPGASIIQSQIKSGVSRKR-TGLTSTG-VPIRPGYEIFNANDQRVGAITSGCPSPSLK 125
G F G + Q GV R+R GL G P R G + A+ + VG +TSG SP+L
Sbjct: 1 GDFIGKEALARQKAEGVVRRRLVGLLLDGDGPPREGEPVLAADGEVVGEVTSGTYSPTLG 60
Query: 126 KNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKM 160
KNIA+ Y+ +++ G E+ V +R KRV V K+
Sbjct: 61 KNIALAYVRTEHAEPGTEVEVEIRGKRVPATVVKL 95
>gnl|CDD|223481 COG0404, GcvT, Glycine cleavage system T protein
(aminomethyltransferase) [Amino acid transport and
metabolism].
Length = 379
Score = 104 bits (262), Expect = 3e-27
Identities = 38/106 (35%), Positives = 56/106 (52%), Gaps = 3/106 (2%)
Query: 66 ETGGFPGASIIQSQIKSGVSRKRTGLT--STGVPIRPGYEIFNAN-DQRVGAITSGCPSP 122
+ F G + + + GV RK GL G +R G + +A+ + VG +TSG SP
Sbjct: 270 DKDDFIGKAALLREKAKGVRRKLVGLKLDDKGPVLRGGEPVLDADGEVEVGEVTSGTFSP 329
Query: 123 SLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYH 168
+L K+IA+ Y++ Y+K G EL V +R KRV +V K PF
Sbjct: 330 TLGKSIALAYVDSDYAKPGTELEVEIRGKRVPARVVKPPFYDPEGE 375
>gnl|CDD|234742 PRK00389, gcvT, glycine cleavage system aminomethyltransferase T;
Reviewed.
Length = 359
Score = 99.4 bits (249), Expect = 2e-25
Identities = 38/104 (36%), Positives = 58/104 (55%), Gaps = 7/104 (6%)
Query: 66 ETGGFPGASIIQSQIKSGVSRKRTGLTST--GVPIRPGYEIFNANDQRVGAITSGCPSPS 123
E F G +++Q ++GV RK GL G+P R GY + A+ + +G +TSG SP+
Sbjct: 260 EKRDFIGREALEAQKEAGVERKLVGLELEERGIP-RHGYPVL-ADGEEIGEVTSGTFSPT 317
Query: 124 LKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNY 167
L K+IA+ Y+ G E+ V +R K+V KV K PF++
Sbjct: 318 LGKSIALAYVPAGV---GDEVEVEIRGKQVPAKVVKPPFVRRGK 358
>gnl|CDD|233010 TIGR00528, gcvT, glycine cleavage system T protein. The glycine
cleavage system T protein (GcvT) is also known as
aminomethyltransferase (EC 2.1.2.10). It works with the
H protein (GcvH), the P protein (GcvP), and lipoamide
dehydrogenase. The reported sequence of the member from
Aquifex aeolicus starts about 50 residues downstream of
the start of other members of the family (perhaps in
error); it scores below the trusted cutoff. Eukaryotic
forms are mitochondrial and have an N-terminal transit
peptide [Energy metabolism, Amino acids and amines].
Length = 362
Score = 90.7 bits (225), Expect = 4e-22
Identities = 41/107 (38%), Positives = 63/107 (58%), Gaps = 4/107 (3%)
Query: 62 KRRRETGGFPGASIIQSQIKSGVSRKRTGL--TSTGVPIRPGYEIFNAN-DQRVGAITSG 118
+ R+ F G +++ Q ++G +K GL G+ R GY IF N + VG +TSG
Sbjct: 257 SKSRQKYDFIGRAVLMEQKENGTEKKLVGLEMLEKGIA-RNGYPIFLPNGETEVGIVTSG 315
Query: 119 CPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKS 165
SP+L KNI + Y+ Y K+G +L V+VR+K +KV KMPF+++
Sbjct: 316 TASPTLGKNIGLAYVPKEYHKIGTKLLVQVRNKFYPIKVVKMPFVRT 362
>gnl|CDD|237113 PRK12486, dmdA, putative dimethyl sulfoniopropionate demethylase;
Reviewed.
Length = 368
Score = 43.6 bits (103), Expect = 2e-05
Identities = 17/59 (28%), Positives = 25/59 (42%)
Query: 104 IFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPF 162
A D RVG +TS SP + N+A+G + + G L V D V + +
Sbjct: 309 PLLAGDNRVGQVTSAAYSPDFQTNVAIGMVRMTHWDPGTGLEVETPDGMRPATVREGFW 367
>gnl|CDD|233382 TIGR01372, soxA, sarcosine oxidase, alpha subunit family,
heterotetrameric form. This model describes the alpha
subunit of a family of known and putative
heterotetrameric sarcosine oxidases. Five operons of
such oxidases are found in Mesorhizobium loti and three
in Agrobacterium tumefaciens, a high enough copy number
to suggest that not all members are share the same
function. The model is designated as subfamily rather
than equivalog for this reason.Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine to
glycine. The reaction converts tetrahydrofolate to
5,10-methylene-tetrahydrofolate. The enzyme is known in
monomeric and heterotetrameric (alpha,beta,gamma,delta)
forms [Energy metabolism, Amino acids and amines].
Length = 985
Score = 39.3 bits (92), Expect = 6e-04
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 92 TSTGVPIRPGYEIFNANDQR-----VGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWV 146
+ G I + + G +TS SP+L + IA+ ++ ++ G ++V
Sbjct: 900 LDPQRRLPEGAHIVADDAEAIPMNMQGHVTSSYFSPALGRTIALALVKGGRARHGETVYV 959
Query: 147 RVRDKRVDVKVTKMPF 162
+ + V++ F
Sbjct: 960 PDLGRFIAVEICDPVF 975
>gnl|CDD|130188 TIGR01118, lacA, galactose-6-phosphate isomerase, LacA subunit.
This family contains members from low GC gram-positive
bacteria. Galactose-6-phosphate isomerase is involved in
lactose catabolism by the tagatose-6-phosphate pathway
[Energy metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 141
Score = 28.0 bits (62), Expect = 1.5
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 11/71 (15%)
Query: 67 TGGFPGASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCPSPSLKK 126
G F A+ I+ I + VS +R+ + G N+ R+ + + L K
Sbjct: 67 AGSFMVATKIKGMIAAEVSDERSAYMTRG-----------HNNARMITVGAEIVGDELAK 115
Query: 127 NIAMGYIEPAY 137
NI ++E Y
Sbjct: 116 NIVKAFVEGKY 126
>gnl|CDD|184429 PRK13973, PRK13973, thymidylate kinase; Provisional.
Length = 213
Score = 27.2 bits (61), Expect = 3.8
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 65 RETGGFPGASIIQSQIKSGV 84
RE GG PGA I+ + SG
Sbjct: 38 REPGGSPGAEAIRHVLLSGA 57
>gnl|CDD|224593 COG1679, COG1679, Predicted aconitase [General function prediction
only].
Length = 403
Score = 27.3 bits (61), Expect = 4.2
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 98 IRPGYEIFNANDQRVGAITSGCPSPSLK--KNIAMGYIEPAYSKVGVELWV 146
I +E N D I GCP SL+ + +A ++ GV L+V
Sbjct: 276 IDDAWERLNTADGEPDLIALGCPHASLEELRRLA-ELLKGRKRPAGVPLYV 325
>gnl|CDD|130874 TIGR01815, TrpE-clade3, anthranilate synthase, alpha
proteobacterial clade. This model represents a small
clade of anthranilate synthases from alpha
proteobacteria and Nostoc (a cyanobacterium). This
enzyme is the first step in the pathway for the
biosynthesis of tryprophan from chorismate [Amino acid
biosynthesis, Aromatic amino acid family].
Length = 717
Score = 27.2 bits (60), Expect = 5.0
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 84 VSRKRTGLT-STGVPIRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEP--AYSKV 140
V+R+ T L T + I + +R ++SG P + A+G+++P A S
Sbjct: 9 VTRRATALDPRTALD---PV-IDALDRRRGLLLSSGYEYPGRYRRWALGFVDPPVALSAR 64
Query: 141 GVELWVRVRDKRVDV 155
G L + ++R V
Sbjct: 65 GRTLRIDALNERGQV 79
>gnl|CDD|181505 PRK08621, PRK08621, galactose-6-phosphate isomerase subunit LacA;
Reviewed.
Length = 142
Score = 26.6 bits (59), Expect = 5.4
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 11/70 (15%)
Query: 68 GGFPGASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCPSPSLKKN 127
G F A+ I+ + + VS +R+ + G N+ R+ + S L KN
Sbjct: 68 GSFMVATKIKGMVAAEVSDERSAYMTRG-----------HNNARMITMGSEIVGDGLAKN 116
Query: 128 IAMGYIEPAY 137
I G++E Y
Sbjct: 117 IIKGFVEGKY 126
>gnl|CDD|236230 PRK08304, PRK08304, stage V sporulation protein AD; Validated.
Length = 337
Score = 26.7 bits (60), Expect = 7.5
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 101 GYEIFNANDQRVGAITSGC 119
G I+++ Q V A SGC
Sbjct: 263 GLMIYDSEQQDVFAGGSGC 281
>gnl|CDD|132313 TIGR03269, met_CoM_red_A2, methyl coenzyme M reductase system,
component A2. The enzyme that catalyzes the final step
in methanogenesis, methyl coenzyme M reductase, contains
alpha, beta, and gamma chains. In older literature, the
complex of alpha, beta, and gamma chains was termed
component C, while this single chain protein was termed
methyl coenzyme M reductase system component A2 [Energy
metabolism, Methanogenesis].
Length = 520
Score = 26.7 bits (59), Expect = 8.8
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 116 TSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDV 155
TSG +L K I G +EP +V VRV D+ VD+
Sbjct: 318 TSGAGKTTLSK-IIAGVLEPTSGEV----NVRVGDEWVDM 352
>gnl|CDD|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin is
an insoluble storage polymer for carbon, nitrogen, and
energy, found in most Cyanobacteria. The polymer has a
backbone of L-aspartic acid, with most Asp side chain
carboxyl groups attached to L-arginine. The polymer is
made by this enzyme, cyanophycin synthetase, and
degraded by cyanophycinase. Heterologously expressed
cyanophycin synthetase in E. coli produces a closely
related, water-soluble polymer with some Arg replaced by
Lys. It is unclear whether enzymes that produce soluble
cyanophycin-like polymers in vivo in non-Cyanobacterial
species should be designated as cyanophycin synthetase
itself or as a related enzyme. This model makes the
designation as cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions [Cellular
processes, Biosynthesis of natural products].
Length = 864
Score = 26.7 bits (59), Expect = 8.9
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 12/53 (22%)
Query: 101 GYEIFNANDQRVGAITSGCP-----------SPSLKKNIAMGYIEPAYSKVGV 142
GY + NA+D V A+ C +P++ +IA G Y + G
Sbjct: 604 GYAVLNADDPMVAAMAEKCKGKIAYFSMDPNNPTVAAHIADGGR-AVYYENGY 655
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.136 0.422
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,662,245
Number of extensions: 773126
Number of successful extensions: 498
Number of sequences better than 10.0: 1
Number of HSP's gapped: 491
Number of HSP's successfully gapped: 17
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
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: 55 (24.9 bits)