RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 034072
(104 letters)
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 190 bits (486), Expect = 2e-60
Identities = 60/102 (58%), Positives = 76/102 (74%)
Query: 1 MGYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMG 60
GY+LV+GGT+NHLVL +L+ G+ GSRVEKVL+ HI NKN VPGD SA+VPGG+R+G
Sbjct: 333 KGYKLVTGGTDNHLVLWDLRPLGLTGSRVEKVLDLAHITLNKNAVPGDSSALVPGGVRIG 392
Query: 61 TPALTSRGFVEEDFAKVAYFFDAAVKLTVKIKSETQGSYQCF 102
TPA+TSRG VE+DF KVA F AV + +KI+ E + F
Sbjct: 393 TPAMTSRGLVEKDFEKVAEFLHRAVTIALKIQKEHGKKLKDF 434
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 153 bits (389), Expect = 2e-46
Identities = 56/93 (60%), Positives = 76/93 (81%)
Query: 2 GYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGT 61
GY+LV+GGT+NHLVLV+L+ GI GS++EK+L+AV+I+ NKNT+PGD SA+ P G+R+GT
Sbjct: 323 GYDLVTGGTDNHLVLVDLRPFGITGSKMEKLLDAVNISVNKNTIPGDKSALNPSGVRLGT 382
Query: 62 PALTSRGFVEEDFAKVAYFFDAAVKLTVKIKSE 94
PALT+RG E+DF VA F D AVKL +I+ +
Sbjct: 383 PALTTRGAKEKDFKFVADFLDRAVKLAQEIQKQ 415
>gnl|CDD|189558 pfam00464, SHMT, Serine hydroxymethyltransferase.
Length = 380
Score = 139 bits (352), Expect = 2e-41
Identities = 52/82 (63%), Positives = 63/82 (76%), Gaps = 1/82 (1%)
Query: 1 MGYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGD-VSAMVPGGIRM 59
GY+LVSGGT+NHLVLV+L+ KG+DG R EK LE +I ANKNT+PGD S V G+R+
Sbjct: 299 RGYKLVSGGTDNHLVLVDLRPKGLDGKRAEKALERANITANKNTIPGDPKSPFVTSGLRL 358
Query: 60 GTPALTSRGFVEEDFAKVAYFF 81
GTPALTSRGF E DF +VA +
Sbjct: 359 GTPALTSRGFGEADFEEVAGYI 380
>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 = 132 bits (334), Expect = 1e-38
Identities = 46/92 (50%), Positives = 61/92 (66%), Gaps = 1/92 (1%)
Query: 2 GYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDVS-AMVPGGIRMG 60
G+++VSGGT+NHLVLV+L+ KGI G E LE I NKNT+P D S VP GIR+G
Sbjct: 299 GFKVVSGGTDNHLVLVDLRPKGITGKAAEDALEEAGITVNKNTLPWDPSSPFVPSGIRIG 358
Query: 61 TPALTSRGFVEEDFAKVAYFFDAAVKLTVKIK 92
TPA+T+RG EE+ ++A F A+K +
Sbjct: 359 TPAMTTRGMGEEEMEEIADFIARALKDAEDVA 390
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 128 bits (325), Expect = 4e-37
Identities = 41/86 (47%), Positives = 56/86 (65%), Gaps = 1/86 (1%)
Query: 2 GYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDV-SAMVPGGIRMG 60
G+ +VSGGT+NHLVLV+L++KG+ G E LE +I NKN VP D S V GIR+G
Sbjct: 303 GFRVVSGGTDNHLVLVDLRSKGLTGKEAEAALEEANITVNKNAVPFDPRSPFVTSGIRIG 362
Query: 61 TPALTSRGFVEEDFAKVAYFFDAAVK 86
TPA+T+RGF E + ++A +
Sbjct: 363 TPAITTRGFKEAEMKEIAELIADVLD 388
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 121 bits (307), Expect = 1e-34
Identities = 40/86 (46%), Positives = 57/86 (66%), Gaps = 1/86 (1%)
Query: 2 GYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGD-VSAMVPGGIRMG 60
G+++VSGGT+NHLVLV+L++KG+ G + E LE I NKN +P D S V GIR+G
Sbjct: 304 GFKVVSGGTDNHLVLVDLRSKGLTGKKAEAALERAGITVNKNAIPFDPESPFVTSGIRIG 363
Query: 61 TPALTSRGFVEEDFAKVAYFFDAAVK 86
TPA+T+RGF E + ++A +
Sbjct: 364 TPAVTTRGFGEAEMEEIADLIADVLD 389
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 106 bits (266), Expect = 1e-28
Identities = 45/78 (57%), Positives = 57/78 (73%), Gaps = 1/78 (1%)
Query: 2 GYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDV-SAMVPGGIRMG 60
GY+LVSGGT+NHL+LV+L+ KG+ G E+ LE I NKNTVPGD S V GIR+G
Sbjct: 306 GYDLVSGGTDNHLLLVDLRPKGLSGKDAEQALERAGITVNKNTVPGDTESPFVTSGIRIG 365
Query: 61 TPALTSRGFVEEDFAKVA 78
TPA T+RGF E +F ++A
Sbjct: 366 TPAGTTRGFGEAEFREIA 383
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 96.4 bits (240), Expect = 9e-25
Identities = 43/99 (43%), Positives = 60/99 (60%)
Query: 5 LVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPAL 64
LV+GGT+NHL+L +L G+ G EKV E HI NK + GD + PGG+R+GTPA+
Sbjct: 458 LVTGGTDNHLLLWDLTTLGLTGKNYEKVCEMCHITLNKTAIFGDNGTISPGGVRIGTPAM 517
Query: 65 TSRGFVEEDFAKVAYFFDAAVKLTVKIKSETQGSYQCFL 103
TSRG +E DF +A F A ++ ++ E + FL
Sbjct: 518 TSRGCLESDFETIADFLLRAAQIASAVQREHGKLQKEFL 556
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 81.6 bits (202), Expect = 1e-19
Identities = 33/78 (42%), Positives = 50/78 (64%), Gaps = 1/78 (1%)
Query: 2 GYELVSGGTENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDVS-AMVPGGIRMG 60
G LV+GGT+NHLVL+++ + G+ G + E L I N+N++P D + A GIR+G
Sbjct: 359 GARLVTGGTDNHLVLIDVTSFGLTGRQAESALLDAGIVTNRNSIPSDPNGAWYTSGIRLG 418
Query: 61 TPALTSRGFVEEDFAKVA 78
TPALT+ G ++ +VA
Sbjct: 419 TPALTTLGMGSDEMDEVA 436
>gnl|CDD|219437 pfam07506, RepB, RepB plasmid partitioning protein. This family
includes proteins with sequence similarity to the RepB
partitioning protein of the large Ti (tumour-inducing)
plasmids of Agrobacterium tumefaciens.
Length = 185
Score = 27.4 bits (61), Expect = 1.3
Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 5/54 (9%)
Query: 11 ENHLVLVNLKNKGIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPAL 64
E L +G+ + + + + TV V+ +P GI AL
Sbjct: 9 ERARFAARLLERGVPRAEIAA-----ALGLDPQTVSKMVARAIPEGICPEEEAL 57
>gnl|CDD|224362 COG1445, FrwB, Phosphotransferase system fructose-specific
component IIB [Carbohydrate transport and metabolism].
Length = 122
Score = 26.9 bits (60), Expect = 1.5
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 83 AAVKLTVKIKSETQGS 98
AA KL V+IK ETQG+
Sbjct: 27 AAKKLGVEIKVETQGA 42
>gnl|CDD|179794 PRK04223, rpl22p, 50S ribosomal protein L22P; Reviewed.
Length = 153
Score = 26.8 bits (60), Expect = 2.0
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 18 NLKNKGIDGSRVEKVLEAVHIAANK 42
N + KG+D + L VHIAA+K
Sbjct: 100 NAEYKGLDTEK----LVIVHIAAHK 120
>gnl|CDD|235299 PRK04443, PRK04443, acetyl-lysine deacetylase; Provisional.
Length = 348
Score = 26.5 bits (59), Expect = 2.8
Identities = 24/70 (34%), Positives = 30/70 (42%), Gaps = 15/70 (21%)
Query: 23 GIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAK--VAYF 80
G G VL HI +TVPGD+ V G+ G RG V+ AK +A F
Sbjct: 53 GPAGDGPPLVLLLGHI----DTVPGDIPVRVEDGVLWG------RGSVD---AKGPLAAF 99
Query: 81 FDAAVKLTVK 90
AA +L
Sbjct: 100 AAAAARLEAL 109
>gnl|CDD|180715 PRK06828, PRK06828, amidase; Provisional.
Length = 491
Score = 26.3 bits (58), Expect = 3.5
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 20 KNKGIDGSRVEKVLEAV----HIAANKNTVPGDVSAMVPGG-IRMGTP---ALTSRGFVE 71
+ +GID + + L+A+ +I + G S +P G + G P L S F E
Sbjct: 409 QEQGIDFALEKYNLDAILFPSYIGSTICAKAGYPSIAIPAGYMEGGRPFGITLASTAFSE 468
Query: 72 EDFAKVAYFFDAAVKLTV 89
K+AY F+ A K
Sbjct: 469 GTLIKLAYAFEQATKHRK 486
>gnl|CDD|217909 pfam04121, Nup84_Nup100, Nuclear pore protein 84 / 107. Nup84p
forms a complex with five proteins, of which Nup120p,
Nup85p, Sec13p, and a Sec13p homologues. This Nup84p
complex in conjunction with Sec13-type proteins is
required for correct nuclear pore biogenesis.
Length = 685
Score = 26.2 bits (58), Expect = 3.7
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 76 KVAYFFDAAVKLTVKIKSETQGSYQCFLP 104
K+ F+ A++L ++ SE + Y F
Sbjct: 640 KIPKFYSEALRLADEVASEDRKLYLVFQS 668
>gnl|CDD|224884 COG1973, HypE, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 449
Score = 26.3 bits (58), Expect = 4.0
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 22 KGIDGSRVEKVLEAVHIAANKNTVP--GDVSAMVPGGIRMGTPALTSRG----FVEEDFA 75
K D R E++ +AV + KNT+ GD+ G+ MG + SRG FV E A
Sbjct: 38 KDWDRERAEEIADAV-LEEVKNTLKGLGDILGYPKSGVGMGEMGVGSRGEGDFFVHEKLA 96
Query: 76 KVA 78
++A
Sbjct: 97 ELA 99
>gnl|CDD|221485 pfam12246, MKT1_C, Temperature dependent protein affecting M2 dsRNA
replication. This domain family is found in eukaryotes,
and is typically between 231 and 255 amino acids in
length. There is a single completely conserved residue P
that may be functionally important. MKT1 is required for
maintenance of K2 toxin above 30 degrees C in strains
with the L-A-HN variant of the L-A double-stranded RNA
virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa
protein with serine-rich regions and the retroviral
protease signature, DTG. This family is the C terminal
region of MKT1.
Length = 243
Score = 25.4 bits (56), Expect = 6.6
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 70 VEEDFAKVAYFFDAAVKLTVKIKSE 94
++ED A+ F+DA K ++ E
Sbjct: 197 LKEDLARAFQFWDALYKAVQELAEE 221
>gnl|CDD|165443 PHA03172, PHA03172, UL37 tegument protein; Provisional.
Length = 951
Score = 25.4 bits (55), Expect = 6.7
Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 1/50 (2%)
Query: 29 VEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVE-EDFAKV 77
+ A+H A K+T G P L SR + ED
Sbjct: 8 LAACAAALHSACKKDTSSGSTRNSAPELTSALADILISRDDIPLEDLEAT 57
>gnl|CDD|190664 pfam03501, S10_plectin, Plectin/S10 domain. This presumed domain
is found at the N-terminus of some isoforms of the
cytoskeletal muscle protein plectin as well as the
ribosomal S10 protein. This domain may be involved in
RNA binding.
Length = 96
Score = 24.5 bits (54), Expect = 7.1
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 63 ALTSRGFVEEDFA 75
+L SRG+V+E FA
Sbjct: 46 SLKSRGYVKEQFA 58
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases
[Transcription, Degradation of RNA].
Length = 654
Score = 25.4 bits (56), Expect = 7.2
Identities = 7/54 (12%), Positives = 18/54 (33%)
Query: 43 NTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAKVAYFFDAAVKLTVKIKSETQ 96
G++S++ G+ + G + Y+ K+ + K +
Sbjct: 574 TEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGK 627
>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. This gene is part of the type I restriction and
modification system which is composed of three
polypeptides R (restriction endonuclease), M
(modification) and S (specificity). This group of
enzymes recognize specific short DNA sequences and have
an absolute requirement for ATP (or dATP) and
S-adenosyl-L-methionine. They also catalyse the
reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
site specificity.(J. Mol. Biol. 271 (3), 342-348
(1997)). Members of this family are assumed to differ
from each other in DNA site specificity [DNA metabolism,
Restriction/modification].
Length = 667
Score = 25.1 bits (55), Expect = 8.2
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 4/41 (9%)
Query: 15 VLVNLKNKGIDGSRVEKVLEAV--HIAANKNTVPGDVSAMV 53
L K + R+E + + + H A K AMV
Sbjct: 481 KLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFK--AMV 519
>gnl|CDD|232985 TIGR00463, gltX_arch, glutamyl-tRNA synthetase, archaeal and
eukaryotic family. The glutamyl-tRNA synthetases of the
eukaryotic cytosol and of the Archaea are more similar
to glutaminyl-tRNA synthetases than to bacterial
glutamyl-tRNA synthetases. This model models just the
eukaryotic cytosolic and archaeal forms of the enzyme.
In some eukaryotes, the glutamyl-tRNA synthetase is part
of a longer, multifunctional aminoacyl-tRNA ligase. In
many species, the charging of tRNA(gln) proceeds first
through misacylation with Glu and then transamidation.
For this reason, glutamyl-tRNA synthetases, including
all known archaeal enzymes (as of 2010) may act on both
tRNA(gln) and tRNA(glu) [Protein synthesis, tRNA
aminoacylation].
Length = 556
Score = 25.2 bits (55), Expect = 8.5
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 10/55 (18%)
Query: 23 GIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAKV 77
G++G+R + +H K+ V V + A G +E D +++
Sbjct: 481 GLEGAR-KLGKSIIHWLPAKDAVKVKV---------IMPDASIVEGVIEADASEL 525
>gnl|CDD|217061 pfam02482, Ribosomal_S30AE, Sigma 54 modulation protein / S30EA
ribosomal protein. This Pfam family contains the
sigma-54 modulation protein family and the S30AE family
of ribosomal proteins which includes the light-
repressed protein (lrtA).
Length = 94
Score = 24.3 bits (54), Expect = 9.1
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 61 TPALTSRGFVEEDFAKVAYFFDAAVKLTVKIKSE 94
T AL R +VEE K+ +FD + V + E
Sbjct: 12 TDAL--REYVEEKLEKLEKYFDRIISADVTLSKE 43
>gnl|CDD|240023 cd04665, Nudix_Hydrolase_8, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity and
contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability,
thereby serving as surveillance & "house-cleaning"
enzymes. Substrate specificity is used to define
families within the superfamily. Differences in
substrate specificity are determined by the N-terminal
extension or by residues in variable loop regions.
Mechanistically, substrate hydrolysis occurs by a
nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 118
Score = 24.6 bits (54), Expect = 9.8
Identities = 8/23 (34%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 10 TENHLVLVNLKNKGID--GSRVE 30
++ L+LV K++G + G VE
Sbjct: 9 YDDGLLLVRHKDRGWEFPGGHVE 31
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 0.135 0.381
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,105,717
Number of extensions: 429554
Number of successful extensions: 414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 35
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
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: 53 (24.2 bits)