RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032537
(138 letters)
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 207 bits (530), Expect = 2e-66
Identities = 69/122 (56%), Positives = 86/122 (70%), Gaps = 1/122 (0%)
Query: 16 QGIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAKVAYFF 75
G+ GSRVEKVL+ HI NKN VPGD SA+VPGG+R+GTPA+TSRG VE+DF KVA F
Sbjct: 354 LGLTGSRVEKVLDLAHITLNKNAVPGDSSALVPGGVRIGTPAMTSRGLVEKDFEKVAEFL 413
Query: 76 DAAVKLTVKIKSETQGTKLKDFVATTQSANFQSEIAKRCHDVEEYAKQFPTIGFEKETMK 135
AV + +KI+ E G KLKDF +S +F +I +VEE+A FP GF+KE+MK
Sbjct: 414 HRAVTIALKIQKEH-GKKLKDFKKGLESNDFSKDIEALRAEVEEFATSFPMPGFDKESMK 472
Query: 136 YK 137
YK
Sbjct: 473 YK 474
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 140 bits (355), Expect = 1e-40
Identities = 56/114 (49%), Positives = 75/114 (65%), Gaps = 4/114 (3%)
Query: 16 QGIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAKVAYFF 75
GI GS++EK+L+AV+I+ NKNT+PGD SA+ P G+R+GTPALT+RG E+DF VA F
Sbjct: 343 FGITGSKMEKLLDAVNISVNKNTIPGDKSALNPSGVRLGTPALTTRGAKEKDFKFVADFL 402
Query: 76 DAAVKLTVKIKSETQGTKLKDFVATTQSANFQSEIAKRCHDVEEYAKQFPTIGF 129
D AVKL +I+ + G KL DF + E+ K +V E+A QFP G
Sbjct: 403 DRAVKLAQEIQKQV-GKKLVDFKK---ALEKNPELQKLRQEVVEFASQFPFPGI 452
>gnl|CDD|189558 pfam00464, SHMT, Serine hydroxymethyltransferase.
Length = 380
Score = 100 bits (252), Expect = 3e-26
Identities = 36/60 (60%), Positives = 43/60 (71%), Gaps = 1/60 (1%)
Query: 17 GIDGSRVEKVLEAVHIAANKNTVPGD-VSAMVPGGIRMGTPALTSRGFVEEDFAKVAYFF 75
G+DG R EK LE +I ANKNT+PGD S V G+R+GTPALTSRGF E DF +VA +
Sbjct: 321 GLDGKRAEKALERANITANKNTIPGDPKSPFVTSGLRLGTPALTSRGFGEADFEEVAGYI 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 = 100 bits (252), Expect = 4e-26
Identities = 34/84 (40%), Positives = 46/84 (54%), Gaps = 4/84 (4%)
Query: 17 GIDGSRVEKVLEAVHIAANKNTVPGDVS-AMVPGGIRMGTPALTSRGFVEEDFAKVAYFF 75
GI G E LE I NKNT+P D S VP GIR+GTPA+T+RG EE+ ++A F
Sbjct: 320 GITGKAAEDALEEAGITVNKNTLPWDPSSPFVPSGIRIGTPAMTTRGMGEEEMEEIADFI 379
Query: 76 DAAVKLTVKIKSETQGTKLKDFVA 99
A+K + +++ VA
Sbjct: 380 ARALKDA---EDVAVAEEVRKEVA 400
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 89.8 bits (224), Expect = 4e-22
Identities = 33/115 (28%), Positives = 52/115 (45%), Gaps = 23/115 (20%)
Query: 16 QGIDGSRVEKVLEAVHIAANKNTVPGDV-SAMVPGGIRMGTPALTSRGFVEEDFAKVAYF 74
+G+ G E LE +I NKN VP D S V GIR+GTPA+T+RGF E + ++A
Sbjct: 323 KGLTGKEAEAALEEANITVNKNAVPFDPRSPFVTSGIRIGTPAITTRGFKEAEMKEIAEL 382
Query: 75 FDAAVKLTVKIKSETQGTKLKDFVATTQSANFQSEIAKRCHDVEEYAKQFPTIGF 129
+ + + ++ I + +V+E K+FP +
Sbjct: 383 IADVLD----------------------NPDDEAVIEEVKEEVKELCKRFPLYKY 415
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 87.6 bits (218), Expect = 2e-21
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 2/86 (2%)
Query: 15 QQGIDGSRVEKVLEAVHIAANKNTVPGD-VSAMVPGGIRMGTPALTSRGFVEEDFAKVAY 73
+G+ G + E LE I NKN +P D S V GIR+GTPA+T+RGF E + ++A
Sbjct: 323 SKGLTGKKAEAALERAGITVNKNAIPFDPESPFVTSGIRIGTPAVTTRGFGEAEMEEIAD 382
Query: 74 FFDAAVKLTVKIKSETQGTKLKDFVA 99
+ + +E + ++ +
Sbjct: 383 LIADVLDGLKDVPAEVKE-EVAELCR 407
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 85.2 bits (211), Expect = 2e-20
Identities = 43/114 (37%), Positives = 63/114 (55%), Gaps = 4/114 (3%)
Query: 17 GIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAKVAYFFD 76
G+ G EKV E HI NK + GD + PGG+R+GTPA+TSRG +E DF +A F
Sbjct: 476 GLTGKNYEKVCEMCHITLNKTAIFGDNGTISPGGVRIGTPAMTSRGCLESDFETIADFLL 535
Query: 77 AAVKLTVKIKSETQGTKLKDFVATTQSANFQSEIAKRCHDVEEYAKQFPTIGFE 130
A ++ ++ E G K+F+ Q+ +I + + VE +A QF GF+
Sbjct: 536 RAAQIASAVQRE-HGKLQKEFLKGLQNNK---DIVELRNRVEAFASQFAMPGFD 585
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 71.5 bits (176), Expect = 1e-15
Identities = 30/61 (49%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 13 FHQQGIDGSRVEKVLEAVHIAANKNTVPGDV-SAMVPGGIRMGTPALTSRGFVEEDFAKV 71
+G+ G E+ LE I NKNTVPGD S V GIR+GTPA T+RGF E +F ++
Sbjct: 323 LRPKGLSGKDAEQALERAGITVNKNTVPGDTESPFVTSGIRIGTPAGTTRGFGEAEFREI 382
Query: 72 A 72
A
Sbjct: 383 A 383
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 58.5 bits (142), Expect = 5e-11
Identities = 32/111 (28%), Positives = 50/111 (45%), Gaps = 9/111 (8%)
Query: 17 GIDGSRVEKVLEAVHIAANKNTVPGDVS-AMVPGGIRMGTPALTSRGFVEEDFAKVAYFF 75
G+ G + E L I N+N++P D + A GIR+GTPALT+ G ++ +VA
Sbjct: 380 GLTGRQAESALLDAGIVTNRNSIPSDPNGAWYTSGIRLGTPALTTLGMGSDEMDEVA--- 436
Query: 76 DAAVKLTVKIKSETQGTKLKDFVATTQSANFQSEIAKRCHD-VEEYAKQFP 125
+L VK+ S T + + +A+ V E +FP
Sbjct: 437 ----ELIVKVLSNTTPGTTAEGAPSKAKYELDEGVAQEVRARVAELLARFP 483
>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 = 30.2 bits (68), Expect = 0.31
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 10/62 (16%)
Query: 10 AKMFHQQGIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFA 69
+H +G++G+R + +H K+ V V + A G +E D +
Sbjct: 474 ELRYHSEGLEGAR-KLGKSIIHWLPAKDAVKVKV---------IMPDASIVEGVIEADAS 523
Query: 70 KV 71
++
Sbjct: 524 EL 525
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 28.1 bits (62), Expect = 1.4
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 118 EEYAKQFPTIGFEKETMKYKS 138
+E+ + PTIGF ET++YK+
Sbjct: 22 DEFMQPIPTIGFNVETVEYKN 42
>gnl|CDD|178782 PLN03244, PLN03244, alpha-amylase; Provisional.
Length = 872
Score = 28.4 bits (63), Expect = 1.5
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 101 TQSANFQSEIAKRCHDVEEYAKQFPTIGFEKETMK 135
S NF +A RC D+ E F+K+ M
Sbjct: 723 MPSNNFSFSLANRCWDLLENEVHHHLFSFDKDLMD 757
>gnl|CDD|235299 PRK04443, PRK04443, acetyl-lysine deacetylase; Provisional.
Length = 348
Score = 28.0 bits (63), Expect = 1.7
Identities = 24/70 (34%), Positives = 30/70 (42%), Gaps = 15/70 (21%)
Query: 17 GIDGSRVEKVLEAVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAK--VAYF 74
G G VL HI +TVPGD+ V G+ G RG V+ AK +A F
Sbjct: 53 GPAGDGPPLVLLLGHI----DTVPGDIPVRVEDGVLWG------RGSVD---AKGPLAAF 99
Query: 75 FDAAVKLTVK 84
AA +L
Sbjct: 100 AAAAARLEAL 109
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 27.6 bits (61), Expect = 2.4
Identities = 19/75 (25%), Positives = 25/75 (33%), Gaps = 18/75 (24%)
Query: 58 LTSRGFVEEDFAKVAYFFDAAVKLTVKIKSETQGTKLKDFVATTQSANFQSEIAKRCHDV 117
L GF + + Y E Q +L F N +S K +
Sbjct: 554 LKHLGFDSAIISALIY--------------ENQVEQLIKFQLN----NIESLAKKGYLSL 595
Query: 118 EEYAKQFPTIGFEKE 132
+E KQF IG KE
Sbjct: 596 DEIKKQFKAIGIIKE 610
>gnl|CDD|180715 PRK06828, PRK06828, amidase; Provisional.
Length = 491
Score = 27.5 bits (61), Expect = 2.7
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 11/85 (12%)
Query: 7 LLFAKMFHQQGIDGSRVEKVLEAV----HIAANKNTVPGDVSAMVPGG-IRMGTP---AL 58
+ F++ +QGID + + L+A+ +I + G S +P G + G P L
Sbjct: 405 IYFSQ---EQGIDFALEKYNLDAILFPSYIGSTICAKAGYPSIAIPAGYMEGGRPFGITL 461
Query: 59 TSRGFVEEDFAKVAYFFDAAVKLTV 83
S F E K+AY F+ A K
Sbjct: 462 ASTAFSEGTLIKLAYAFEQATKHRK 486
>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 = 27.4 bits (61), Expect = 2.8
Identities = 9/62 (14%), Positives = 22/62 (35%)
Query: 37 NTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAKVAYFFDAAVKLTVKIKSETQGTKLKD 96
G++S++ G+ + G + Y+ K+ + K + ++ D
Sbjct: 574 TEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGD 633
Query: 97 FV 98
V
Sbjct: 634 RV 635
>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 = 26.5 bits (59), Expect = 4.7
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 64 VEEDFAKVAYFFDAAVKLTVKIKSE--TQGTKLKDFVATTQ 102
++ED A+ F+DA K ++ E LK F +
Sbjct: 197 LKEDLARAFQFWDALYKAVQELAEEDLISADDLKLFEEADE 237
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in the
GDP-bound state. GDP/GTP exchange exposes the helix,
which anchors to the membrane. Following GTP hydrolysis,
the helix dissociates from the membrane and folds back
into the protein. A general feature of Arf1-5 signaling
may be the cooperation of two Arfs at the same site.
Arfs1-5 are generally considered to be interchangeable
in function and location, but some specific functions
have been assigned. Arf1 localizes to the
early/cis-Golgi, where it is activated by GBF1 and
recruits the coat protein COPI. It also localizes to the
trans-Golgi network (TGN), where it is activated by
BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally function
interchangeably with Arf1. Human Arf4 in the activated
(GTP-bound) state has been shown to interact with the
cytoplasmic domain of epidermal growth factor receptor
(EGFR) and mediate the EGF-dependent activation of
phospholipase D2 (PLD2), leading to activation of the
activator protein 1 (AP-1) transcription factor. Arf4
has also been shown to recognize the C-terminal sorting
signal of rhodopsin and regulate its incorporation into
specialized post-Golgi rhodopsin transport carriers
(RTCs). There is some evidence that Arf5 functions at
the early-Golgi and the trans-Golgi to affect
Golgi-associated alpha-adaptin homology Arf-binding
proteins (GGAs).
Length = 159
Score = 26.2 bits (58), Expect = 5.0
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 125 PTIGFEKETMKYK 137
PTIGF ET++YK
Sbjct: 30 PTIGFNVETVEYK 42
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 26.0 bits (58), Expect = 6.6
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 125 PTIGFEKETMKYK 137
PTIGF ET++YK
Sbjct: 29 PTIGFNVETVEYK 41
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 26.0 bits (57), Expect = 7.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 119 EYAKQFPTIGFEKETMKYKS 138
E PTIGF ET++YK+
Sbjct: 41 EVVTTIPTIGFNVETVEYKN 60
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 25.8 bits (57), Expect = 7.5
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 125 PTIGFEKETMKYK 137
PTIGF ET+ YK
Sbjct: 29 PTIGFNVETVTYK 41
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 25.7 bits (56), Expect = 8.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 119 EYAKQFPTIGFEKETMKYKS 138
E PTIGF ET++YK+
Sbjct: 41 EIVTTIPTIGFNVETVEYKN 60
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
0.318 0.131 0.371
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,774,012
Number of extensions: 575564
Number of successful extensions: 584
Number of sequences better than 10.0: 1
Number of HSP's gapped: 576
Number of HSP's successfully gapped: 38
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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: 54 (24.9 bits)