RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12858
(131 letters)
>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 = 75.3 bits (186), Expect = 5e-19
Identities = 34/101 (33%), Positives = 48/101 (47%), Gaps = 16/101 (15%)
Query: 8 FIGKAALQRQKDQGV-QKRLVMFVAEDLDPDTDVWLWGSEPIYRND-QFVGTITSAGYGF 65
FIGK AL RQK +GV ++RLV + + D EP+ D + VG +TS Y
Sbjct: 3 FIGKEALARQKAEGVVRRRLVGLLLDG-----DGPPREGEPVLAADGEVVGEVTSGTYSP 57
Query: 66 TMKKLIGLGYIRHPSEQNVTNDFVTEGT-YTLDVAGNRFQA 105
T+ K I L Y+R + GT +++ G R A
Sbjct: 58 TLGKNIALAYVR--------TEHAEPGTEVEVEIRGKRVPA 90
>gnl|CDD|223481 COG0404, GcvT, Glycine cleavage system T protein
(aminomethyltransferase) [Amino acid transport and
metabolism].
Length = 379
Score = 73.1 bits (180), Expect = 3e-16
Identities = 38/111 (34%), Positives = 54/111 (48%), Gaps = 15/111 (13%)
Query: 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRND--QFVGTITSAG 62
KD FIGKAAL R+K +GV+++LV +D P L G EP+ D VG +TS
Sbjct: 271 KDDFIGKAALLREKAKGVRRKLVGLKLDDKGPV----LRGGEPVLDADGEVEVGEVTSGT 326
Query: 63 YGFTMKKLIGLGYIRHPSEQNVTNDFVTEGT-YTLDVAGNRFQASAHIYPP 112
+ T+ K I L Y+ +D+ GT +++ G R A P
Sbjct: 327 FSPTLGKSIALAYVD--------SDYAKPGTELEVEIRGKRVPARVVKPPF 369
>gnl|CDD|234742 PRK00389, gcvT, glycine cleavage system aminomethyltransferase T;
Reviewed.
Length = 359
Score = 54.0 bits (131), Expect = 1e-09
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 11/78 (14%)
Query: 2 FTVKDYFIGKAALQRQKDQGVQKRLVMFVAED---LDPDTDVWLWGSEPIYRNDQFVGTI 58
K FIG+ AL+ QK+ GV+++LV E+ P+ + + +G +
Sbjct: 258 LEEKRDFIGREALEAQKEAGVERKLVGLELEERGIPRHGY--------PVLADGEEIGEV 309
Query: 59 TSAGYGFTMKKLIGLGYI 76
TS + T+ K I L Y+
Sbjct: 310 TSGTFSPTLGKSIALAYV 327
>gnl|CDD|237113 PRK12486, dmdA, putative dimethyl sulfoniopropionate demethylase;
Reviewed.
Length = 368
Score = 41.7 bits (98), Expect = 3e-05
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 8 FIGKAALQRQKDQGVQK--RLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGF 65
IGK AL R +G QK R + E + P W P+ D VG +TSA Y
Sbjct: 273 CIGKDALLRVAKEGPQKQIRGIKIGGERIPPCDRAW-----PLLAGDNRVGQVTSAAYSP 327
Query: 66 TMKKLIGLGYIR 77
+ + +G +R
Sbjct: 328 DFQTNVAIGMVR 339
>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 = 39.0 bits (91), Expect = 2e-04
Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 5 KDYFIGKAALQRQKDQGVQKRLVMFV-AEDLDPDTDVWLWGSEPIYRND--QFVGTITSA 61
K FIG+A L QK+ G +K+LV E PI+ + VG +TS
Sbjct: 262 KYDFIGRAVLMEQKENGTEKKLVGLEMLEKGIARNGY------PIFLPNGETEVGIVTSG 315
Query: 62 GYGFTMKKLIGLGYI 76
T+ K IGL Y+
Sbjct: 316 TASPTLGKNIGLAYV 330
>gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase.
Length = 404
Score = 33.9 bits (78), Expect = 0.016
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTM 67
F+G + +Q +GV +R V F++ + SE + + + +G +TS G+ +
Sbjct: 303 FLGADVILKQLKEGVSRRRVGFISSGAPARS-----HSEILDESGEKIGEVTSGGFSPCL 357
Query: 68 KKLIGLGYI 76
KK I +GY+
Sbjct: 358 KKNIAMGYV 366
>gnl|CDD|237435 PRK13579, gcvT, glycine cleavage system aminomethyltransferase T;
Provisional.
Length = 370
Score = 32.2 bits (74), Expect = 0.051
Identities = 28/120 (23%), Positives = 46/120 (38%), Gaps = 25/120 (20%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRND-QFVGTITSAGYGFT 66
F G A+ +G +R V L P+ + P++ + +GT+TS G+G +
Sbjct: 270 FPGAKAILAALAKGASRRRV-----GLKPEGRAPVREGAPLFDDAGTEIGTVTSGGFGPS 324
Query: 67 MKKLIGLGYIRHPSEQNVTNDFVTEGT-YTLDVAGNRFQASAHIYPPLSNVQVARPYVPQ 125
+ + +GY V GT +V G R + H A P+VP
Sbjct: 325 VGGPVAMGY--------VPASLAAPGTAVFAEVRGKRLPVTVH----------ALPFVPH 366
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1034
Score = 28.3 bits (63), Expect = 1.3
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 8/48 (16%)
Query: 37 DTDVWLWGSEPIYRN----DQFVGTITSAGY----GFTMKKLIGLGYI 76
D+D+WL+G+ +Y+N ++FV G KLI L Y+
Sbjct: 815 DSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYL 862
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region. domain in
nucleases.
Length = 73
Score = 26.4 bits (59), Expect = 1.8
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 36 PDTDVWLWGSEPIYRNDQFVGT 57
D+D+ L+G+ +YRN F G
Sbjct: 33 EDSDLLLFGAPRLYRNLFFSGK 54
>gnl|CDD|218969 pfam06277, EutA, Ethanolamine utilisation protein EutA. This
family consists of several bacterial EutA ethanolamine
utilisation proteins. The EutA protein is thought to
protect the lyase (EutBC) from inhibition by CNB12.
Length = 473
Score = 27.2 bits (61), Expect = 2.9
Identities = 9/30 (30%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 92 GTYTLDVAGNRFQASAHIYPPLSNVQVARP 121
G++T +++G+ +A + PL N+ V +P
Sbjct: 315 GSHTTELSGSTITYTADLL-PLKNLPVLKP 343
>gnl|CDD|189026 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuclease-1
(FEN1)-like, structure-specific, divalent-metal-ion
dependent, 5' nucleases. PIN (PilT N terminus) domain
of Flap Endonuclease-1 (FEN1)-like nucleases: FEN1, Gap
endonuclease 1 (GEN1) and Xeroderma pigmentosum
complementation group G (XPG) nuclease are members of
the structure-specific, 5' nuclease family that
catalyzes hydrolysis of DNA duplex-containing nucleic
acid structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 30 to 800 residues) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Most nucleases within this
family also have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). Some nucleases in this family
have C-terminal extensions that act as interaction sites
for other proteins.
Length = 207
Score = 26.3 bits (58), Expect = 5.5
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 37 DTDVWLWGSEPIYRN 51
D+D L+G+E +YRN
Sbjct: 138 DSDTLLFGAEKVYRN 152
>gnl|CDD|237634 PRK14179, PRK14179, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 25.9 bits (57), Expect = 7.4
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 84 VTNDFVTEGTYTLDVAGNR 102
VT +FV EG +DV NR
Sbjct: 215 VTKEFVKEGAVVIDVGMNR 233
>gnl|CDD|183218 PRK11590, PRK11590, hypothetical protein; Provisional.
Length = 211
Score = 25.8 bits (57), Expect = 7.8
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 15/55 (27%)
Query: 22 VQKRLVMFVAEDLDPDTDVWL-WGS-----EPIYRNDQF------VGTITSAGYG 64
VQ+RL ++ D DVWL GS E +Y + + + + YG
Sbjct: 100 VQERLTTYLLS---SDADVWLITGSPQPLVEQVYFDTPWLPRVNLIASQMQRRYG 151
>gnl|CDD|233667 TIGR01982, UbiB, 2-polyprenylphenol 6-hydroxylase. This model
represents the enzyme (UbiB) which catalyzes the first
hydroxylation step in the ubiquinone biosynthetic
pathway in bacteria. It is believed that the reaction is
2-polyprenylphenol -> 6-hydroxy-2-polyprenylphenol. This
model finds hits primarily in the proteobacteria. The
gene is also known as AarF in certain species
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 437
Score = 25.7 bits (57), Expect = 8.2
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 23 QKRLVMF--VAEDLDPDTDVW 41
QK L+ V LDPD ++W
Sbjct: 396 QKTLLTVEGVGRQLDPDLNMW 416
>gnl|CDD|132471 TIGR03430, trp_dimet_allyl, tryptophan dimethylallyltransferase.
Members of this family are the enzyme tryptophan
dimethylallyltransferase (EC 2.5.1.34), a distinct clade
within a larger group of aromatic prenyltransferases
that may act on on trp-containing cyclic dipeptides, or
on tyrosine or other related substrates. Tryptophan
dimethylallyltransferase and related enzymes typically
are of fungal origin are involved in the biosynthesis of
secondary metabolites such as ergot alkaloids.
Length = 419
Score = 26.0 bits (57), Expect = 8.4
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 86 NDFVTEGTYT-----LDVAGNRFQASAHIYPPLSNV 116
ND V E T LD+ G+RF +IYP L +V
Sbjct: 151 NDLVNEQIKTQNKLALDLKGDRFALKVYIYPHLKSV 186
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving DNA
bubble structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 25.7 bits (57), Expect = 9.2
Identities = 7/15 (46%), Positives = 14/15 (93%)
Query: 37 DTDVWLWGSEPIYRN 51
D+DV+L+G++ +Y+N
Sbjct: 179 DSDVFLFGAKRVYKN 193
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
0.321 0.138 0.417
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,771,545
Number of extensions: 588048
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 417
Number of HSP's successfully gapped: 25
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
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 (21.8 bits)
S2: 53 (24.1 bits)