RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10666
(240 letters)
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 171 bits (435), Expect = 7e-51
Identities = 67/122 (54%), Positives = 82/122 (67%), Gaps = 28/122 (22%)
Query: 11 EGKYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL------- 63
+YYGGN+ +D+IE + Q+R+L+AF LDPE+WG NVQPYSGSPANFAVYT L
Sbjct: 68 GNRYYGGNEVVDKIENLCQKRALEAFGLDPEEWGVNVQPYSGSPANFAVYTALLQPHDRI 127
Query: 64 --------------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLI 103
K+SATSI+FESLPY+VN E GLIDYDKL E A+ F+P+LI
Sbjct: 128 MGLDLPSGGHLTHGFYTAKKKVSATSIYFESLPYQVN-EKGLIDYDKLEELAKAFRPKLI 186
Query: 104 IA 105
IA
Sbjct: 187 IA 188
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 170 bits (434), Expect = 2e-50
Identities = 65/120 (54%), Positives = 82/120 (68%), Gaps = 27/120 (22%)
Query: 13 KYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL--------- 63
+YYGGN++ID+IE + Q+R+L+AF LDPE+WG NVQP SGSPANFAVYT L
Sbjct: 70 RYYGGNEYIDQIETLCQKRALEAFRLDPEKWGVNVQPLSGSPANFAVYTALLQPHDRIMG 129
Query: 64 ------------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
KISATSI+FES+PY+++ TGLIDYDKL + A LF+P+LIIA
Sbjct: 130 LDLPHGGHLSHGYQTDGKKISATSIYFESMPYRLDESTGLIDYDKLEKKAMLFRPKLIIA 189
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 145 bits (368), Expect = 2e-40
Identities = 60/120 (50%), Positives = 74/120 (61%), Gaps = 28/120 (23%)
Query: 13 KYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL--------- 63
+YY GNQ+ID+IE + +R+L AF LD E+WG NVQPYS + ANFAVYTGL
Sbjct: 184 RYYTGNQYIDQIERLCCERALAAFGLDSEKWGVNVQPYSCTSANFAVYTGLLLPGDRIMG 243
Query: 64 -------------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLII 104
K+S SIFFESLPYKVN +TG IDYDKL E A F+P+++I
Sbjct: 244 LDSPSGGHMSHGYYTPGGKKVSGASIFFESLPYKVNPQTGYIDYDKLEEKALDFRPKILI 303
>gnl|CDD|189558 pfam00464, SHMT, Serine hydroxymethyltransferase.
Length = 380
Score = 138 bits (350), Expect = 4e-39
Identities = 52/117 (44%), Positives = 72/117 (61%), Gaps = 26/117 (22%)
Query: 13 KYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL--------- 63
+YYGG +++DE+E +AQ R+ + F LD G NVQP SGS AN AVYT L
Sbjct: 56 RYYGGCEYVDEVETLAQDRAKELFGLD----GVNVQPLSGSQANLAVYTALLNPGDRIMG 111
Query: 64 -------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIAET 107
++ + FFES+PY V+ +TGLIDYD+L ++A+LFKP+LI+A T
Sbjct: 112 LDLPHGGHLTHGYPVNFSGKFFESMPYGVDPDTGLIDYDQLEKNAKLFKPKLIVAGT 168
>gnl|CDD|99733 cd00378, SHMT, Serine-glycine hydroxymethyltransferase (SHMT). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). SHMT
carries out interconversion of serine and glycine; it
catalyzes the transfer of hydroxymethyl group of N5,
N10-methylene tetrahydrofolate to glycine resulting in
the formation of serine and tetrahydrofolate. Both
eukaryotic and prokaryotic SHMT enzymes form tight
obligate homodimers; the mammalian enzyme forms a
homotetramer comprising four pyridoxal phosphate-bound
active sites.
Length = 402
Score = 128 bits (325), Expect = 3e-35
Identities = 50/116 (43%), Positives = 65/116 (56%), Gaps = 28/116 (24%)
Query: 14 YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL---------- 63
YYGG +++DEIE +A +R+ K F + NVQP+SGS AN AVY L
Sbjct: 56 YYGGCEYVDEIEDLAIERAKKLFGAE----YANVQPHSGSQANLAVYFALLEPGDTIMGL 111
Query: 64 --------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
K+SA+ FES+PY V+ ETGLIDYD L + A FKP+LI+A
Sbjct: 112 DLSHGGHLTHGSFTKVSASGKLFESVPYGVDPETGLIDYDALEKMALEFKPKLIVA 167
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 110 bits (277), Expect = 3e-28
Identities = 47/129 (36%), Positives = 67/129 (51%), Gaps = 31/129 (24%)
Query: 1 MNR-AEMSSDEEGK-YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFA 58
N+ AE GK YYGG +++DE+E +A +R+ K F + NVQP+SGS AN A
Sbjct: 51 TNKYAEG---YPGKRYYGGCEYVDEVEELAIERAKKLFGAE----YANVQPHSGSQANQA 103
Query: 59 VYTGL----------------------KISATSIFFESLPYKVNTETGLIDYDKLAESAR 96
VY L ++ + F + Y V+ ETGLIDYD++ + A+
Sbjct: 104 VYLALLQPGDTIMGLDLSHGGHLTHGSPVNFSGKLFNVVSYGVDPETGLIDYDEVEKLAK 163
Query: 97 LFKPRLIIA 105
KP+LIIA
Sbjct: 164 EVKPKLIIA 172
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 98.6 bits (247), Expect = 5e-24
Identities = 41/121 (33%), Positives = 61/121 (50%), Gaps = 30/121 (24%)
Query: 11 EGK----YYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGL--- 63
EG YYGG +++D +E +A R+ + F + + NVQP+SGS AN AVY L
Sbjct: 55 EGYPGKRYYGGCEYVDVVEQLAIDRAKELFGAE---Y-ANVQPHSGSQANAAVYFALLKP 110
Query: 64 -------------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLII 104
++ + + + Y V+ ETGLIDYD++ + A KP+LII
Sbjct: 111 GDTILGMDLAHGGHLTHGSPVNFSGKLYNVVSYGVDEETGLIDYDEVEKLALEHKPKLII 170
Query: 105 A 105
A
Sbjct: 171 A 171
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 89.6 bits (223), Expect = 8e-21
Identities = 45/118 (38%), Positives = 65/118 (55%), Gaps = 32/118 (27%)
Query: 13 KYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGC---NVQPYSGSPANFAVYTGL------ 63
+YYGG +F+DE+E +A +R+ + F GC NVQP+SGS AN AVY L
Sbjct: 64 RYYGGCEFVDEVEALAIERAKQLF-------GCDYANVQPHSGSQANGAVYLALLKPGDT 116
Query: 64 ----------------KISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
K+S + ++ ++ Y V+ TGLIDYD++ E A+ KP+LIIA
Sbjct: 117 ILGMSLSHGGHLTHGAKVSLSGKWYNAVQYGVDRLTGLIDYDEVEELAKEHKPKLIIA 174
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 52.0 bits (125), Expect = 8e-08
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 62 GLKISATSIFFESLPYKVNTETGLIDYDKLAESARLFKPRLIIA 105
G + + + F Y V+ +TGL+DYD++A AR FKP +++A
Sbjct: 183 GFRPNISGKMFHQRSYGVDPDTGLLDYDEIAALAREFKPLILVA 226
Score = 31.2 bits (71), Expect = 0.48
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 10/51 (19%)
Query: 13 KYYGGNQFIDEIEIVAQQRSLKAFNLDPEQWGCN---VQPYSGSPANFAVY 60
++Y G Q +D +E A + + + F G VQP+SG+ AN +
Sbjct: 85 RFYAGCQNVDTVEWEAAEHAKELF-------GAEHAYVQPHSGADANLVAF 128
>gnl|CDD|99742 cd01494, AAT_I, Aspartate aminotransferase (AAT) superfamily (fold
type I) of pyridoxal phosphate (PLP)-dependent enzymes.
PLP combines with an alpha-amino acid to form a compound
called a Schiff base or aldimine intermediate, which
depending on the reaction, is the substrate in four
kinds of reactions (1) transamination (movement of amino
groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
Structure and sequence analysis has revealed that the
PLP dependent enzymes can be classified into four major
groups of different evolutionary origin: aspartate
aminotransferase superfamily (fold type I), tryptophan
synthase beta superfamily (fold type II), alanine
racemase superfamily (fold type III), and D-amino acid
superfamily (fold type IV) and Glycogen phophorylase
family (fold type V).
Length = 170
Score = 33.1 bits (76), Expect = 0.060
Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 21/99 (21%)
Query: 30 QRSLKAFNLDPEQWGCNVQPYSGSPANFAVYTGLK------------------ISATSIF 71
+ L L P P SG+ AN A L ++A
Sbjct: 6 EEKLARL-LQPGNDKAVFVP-SGTGANEAALLALLGPGDEVIVDANGHGSRYWVAAELAG 63
Query: 72 FESLPYKVN-TETGLIDYDKLAESARLFKPRLIIAETIE 109
+ +P V+ G +D L E LI+
Sbjct: 64 AKPVPVPVDDAGYGGLDVAILEELKAKPNVALIVITPNT 102
>gnl|CDD|218210 pfam04679, DNA_ligase_A_C, ATP dependent DNA ligase C terminal
region. This region is found in many but not all
ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is
thought to constitute part of the catalytic core of ATP
dependent DNA ligase.
Length = 95
Score = 29.0 bits (66), Expect = 0.69
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 105 AETIEDLKLLTKVLLEETSKWRIKHNREIRDLYNEPDVVGEIK------SGRLR 152
+ +L+ + L + S + E D++ EP++V E++ SGRLR
Sbjct: 31 DADLAELRERLEPLERKKSPFAEPVPAERPDVWVEPELVAEVEFAEWTASGRLR 84
>gnl|CDD|217176 pfam02670, DXP_reductoisom, 1-deoxy-D-xylulose 5-phosphate
reductoisomerase. This is a family of
1-deoxy-D-xylulose 5-phosphate reductoisomerases. This
enzyme catalyzes the formation of
2-C-methyl-D-erythritol 4-phosphate from
1-deoxy-D-xylulose-5-phosphate in the presence of NADPH.
This reaction is part of the terpenoid biosynthesis
pathway.
Length = 129
Score = 27.5 bits (62), Expect = 3.1
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 88 YDKLAESARLFKPRLIIAETIEDLKLLTKVLLEETSKWRIKHNRE-IRDL--YNEPDVV 143
+ LAE + FKP+ + E + L + L K + E + +L E D+V
Sbjct: 36 VELLAEQIKEFKPKYVAVADEEAAEELKEALAGAGLKTEVLAGEEGLCELAALPEADIV 94
>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3. This family
of proteins are membrane localised chaperones that are
required for correct plasma membrane localisation of
amino acid permeases (AAPs). SH3 prevents AAPs proteins
from aggregating and assists in their correct folding.
In the absence of SH3, AAPs are retained in the ER.
Length = 196
Score = 27.7 bits (62), Expect = 4.1
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 58 AVYTGLKISATS----IFFESLPYKVNT 81
+V T L I ATS + F + PY NT
Sbjct: 6 SVGTALIIGATSFFLGVLFANFPYDYNT 33
>gnl|CDD|233993 TIGR02745, ccoG_rdxA_fixG, cytochrome c oxidase accessory protein
FixG. Member of this ferredoxin-like protein family are
found exclusively in species with an operon encoding the
cbb3 type of cytochrome c oxidase (cco-cbb3), and near
the cco-cbb3 operon in about half the cases. The
cco-cbb3 is found in a variety of proteobacteria and
almost nowhere else, and is associated with oxygen use
under microaerobic conditions. Some (but not all) of
these proteobacteria are also nitrogen-fixing, hence the
gene symbol fixG. FixG was shown essential for
functional cco-cbb3 expression in Bradyrhizobium
japonicum.
Length = 434
Score = 27.7 bits (62), Expect = 6.2
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 5/32 (15%)
Query: 78 KVNTETGLIDYDKLA-----ESARLFKPRLII 104
K+ GLI Y A + RL +PR I
Sbjct: 273 KMGKPKGLISYTSEAALEGRKKVRLLRPRTIG 304
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 27.6 bits (61), Expect = 7.9
Identities = 21/105 (20%), Positives = 31/105 (29%), Gaps = 18/105 (17%)
Query: 150 RLRWAGHVQRREEDSNIRSIWEHQPE--------GRRPRGRPKNRWKDQVR--------K 193
R R + RE+ RR R RP+ R + +
Sbjct: 37 RHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLR 96
Query: 194 DMTILNLTTEDSFNRALWRQKVGEAKYLLGNYLLLKMSGLRQVSA 238
D + N +D R+LW + Y L K S + V
Sbjct: 97 DRSPSNQWRKDDKKRSLW--DIKPPGYELVTADQAKASQVFSVPG 139
>gnl|CDD|236281 PRK08517, PRK08517, DNA polymerase III subunit epsilon;
Provisional.
Length = 257
Score = 26.9 bits (60), Expect = 9.2
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 65 ISATSIF---FESLPYKVNTETGLIDYDKLAESARLFKPR 101
++A IF +LP + T LID+ K A++ + KPR
Sbjct: 218 LAAYEIFKICLLNLPSYIKTTEDLIDFSKTAKTLKKKKPR 257
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
0.317 0.134 0.397
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,457,903
Number of extensions: 1188365
Number of successful extensions: 1023
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1009
Number of HSP's successfully gapped: 31
Length of query: 240
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 146
Effective length of database: 6,768,326
Effective search space: 988175596
Effective search space used: 988175596
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.8 bits)