RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1922
(159 letters)
>gnl|CDD|217394 pfam03155, Alg6_Alg8, ALG6, ALG8 glycosyltransferase family.
N-linked (asparagine-linked) glycosylation of proteins
is mediated by a highly conserved pathway in eukaryotes,
in which a lipid (dolichol phosphate)-linked
oligosaccharide is assembled at the endoplasmic
reticulum membrane prior to the transfer of the
oligosaccharide moiety to the target asparagine
residues. This oligosaccharide is composed of
Glc(3)Man(9)GlcNAc(2). The addition of the three glucose
residues is the final series of steps in the synthesis
of the oligosaccharide precursor. Alg6 transfers the
first glucose residue, and Alg8 transfers the second
one. In the human alg6 gene, a C->T transition, which
causes Ala333 to be replaced with Val, has been
identified as the cause of a congenital disorder of
glycosylation, designated as type Ic OMIM:603147.
Length = 463
Score = 59.7 bits (145), Expect = 3e-11
Identities = 29/81 (35%), Positives = 33/81 (40%), Gaps = 28/81 (34%)
Query: 77 VLGRLFPFDDRGLVHAYWAPNFWAFYNTADKAAVVLGKRFHLISSNVTNTMTRGLVENSQ 136
VL RLFPF RGL A NFW YN DK +
Sbjct: 244 VLSRLFPFA-RGLFEDKVA-NFWCLYNFVDKIK--------------------------E 275
Query: 137 HVVLPSIEPCTCFLLTLLGIL 157
V LP I+P F+LTL+G L
Sbjct: 276 VVPLPQIQPYISFILTLIGSL 296
>gnl|CDD|129282 TIGR00178, monomer_idh, isocitrate dehydrogenase, NADP-dependent,
monomeric type. The monomeric type of isocitrate
dehydrogenase has been found so far in a small number of
species, including Azotobacter vinelandii,
Corynebacterium glutamicum, Rhodomicrobium vannielii,
and Neisseria meningitidis. It is NADP-specific [Energy
metabolism, TCA cycle].
Length = 741
Score = 34.9 bits (80), Expect = 0.012
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 4 IALDAADGVDIAIVKKSGKVSALEDEIQTRIALDAADGVDIAIVKKSGKVSALEDEIQTR 63
+DAA V I ++ K G + L+ ++ L + +D +++ K + +E+EI+
Sbjct: 188 ATIDAAGSVKIELIAKDGSSTVLKAKLP----LLDGEIIDSSVMSKKALRNFIEEEIEDA 243
Query: 64 LKE 66
+E
Sbjct: 244 KEE 246
Score = 27.5 bits (61), Expect = 3.9
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 34 IALDAADGVDIAIVKKSGKVSALEDEIQTRLKEL 67
+DAA V I ++ K G + L+ ++ E+
Sbjct: 188 ATIDAAGSVKIELIAKDGSSTVLKAKLPLLDGEI 221
>gnl|CDD|238366 cd00714, GFAT, Glutamine amidotransferases class-II
(Gn-AT)_GFAT-type. This domain is found at the
N-terminus of glucosamine-6P synthase (GlmS, or GFAT in
humans). The glutaminase domain catalyzes amide
nitrogen transfer from glutamine to the appropriate
substrate. In this process, glutamine is hydrolyzed to
glutamic acid and ammonia. In humans, GFAT catalyzes
the first and rate-limiting step of hexosamine
metabolism, the conversion of D-fructose-6P (Fru6P)
into D-glucosamine-6P using L-glutamine as a nitrogen
source. The end product of this pathway, UDP-N-acetyl
glucosamine, is a major building block of the bacterial
peptidoglycan and fungal chitin.
Length = 215
Score = 33.2 bits (77), Expect = 0.032
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 2 CGIALDAADGVDIAIVKKSGKVSALEDEIQTR 33
GIA+ + +VK GKV+ LE+++ +
Sbjct: 31 AGIAVIGDGS--LEVVKAVGKVANLEEKLAEK 60
Score = 29.0 bits (66), Expect = 1.0
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 34 IALDAADGVDIAIVKKSGKVSALEDEIQTR 63
IA+ + +VK GKV+ LE+++ +
Sbjct: 33 IAVIGDGS--LEVVKAVGKVANLEEKLAEK 60
>gnl|CDD|222785 PHA00368, PHA00368, internal virion protein D.
Length = 1315
Score = 32.4 bits (74), Expect = 0.098
Identities = 20/50 (40%), Positives = 29/50 (58%), Gaps = 7/50 (14%)
Query: 13 DIAIVKKSGKVSA-LEDEIQTRIALDAADGVDIAIVKKSGKVSALEDEIQ 61
DIAI+ +GK + L+DEI +ALD D K G+V AL+D ++
Sbjct: 808 DIAIMGGTGKTTKELKDEI---LALDKKAEGD---GKLKGEVEALKDTVK 851
>gnl|CDD|240047 cd04691, Nudix_Hydrolase_32, 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 = 117
Score = 29.8 bits (67), Expect = 0.32
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 51 GKVSALEDEIQTRLKE----LNVEESSATHVLGRLFPFDDRGLVHAYWAPNFWAFYNTAD 106
G + A E + + L+E L V+ S T++ P + L+H Y+ FW A
Sbjct: 34 GHIEAGESQEEALLREVQEELGVDPLSYTYLCSLYHPTSELQLLH-YYVVTFWQGEIPAQ 92
Query: 107 KAAVV 111
+AA V
Sbjct: 93 EAAEV 97
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 29.6 bits (67), Expect = 0.58
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 5 ALDAADGVDIAIVKKSGKVSALEDEIQ---TRIALDAADGVDIAIVKKSGKVSALEDEIQ 61
A + ++I + +VS LE EIQ RI ++ VK ++ AL EIQ
Sbjct: 43 LNKALEALEIELEDLENQVSQLESEIQEIRERIK---RAEEKLSAVKDERELRALNIEIQ 99
Query: 62 TRLKELNVEESSATHVLGRL 81
+ +N E ++ +
Sbjct: 100 IAKERINSLEDELAELMEEI 119
>gnl|CDD|225394 COG2838, Icd, Monomeric isocitrate dehydrogenase [Energy production
and conversion].
Length = 744
Score = 29.0 bits (65), Expect = 1.1
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 4 IALDAADGVDIAIVKKSGKVSALEDEIQTRIALDAADGVDIAIVKKSGKVSALEDEIQ 61
+ LD A V I K GK L+ +AL + +D + K + E+++Q
Sbjct: 190 MTLDQATDVRIEFTAKDGKKKVLKPP----VALQDGEIIDATFMSKKALCAFYEEQMQ 243
>gnl|CDD|234729 PRK00331, PRK00331, glucosamine--fructose-6-phosphate
aminotransferase; Reviewed.
Length = 604
Score = 28.1 bits (64), Expect = 2.1
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 2 CGIALDAADGVDIAIVKKSGKVSALEDEIQ 31
GIA+ D + + K GKV+ LE +++
Sbjct: 32 AGIAV--LDDGGLEVRKAVGKVANLEAKLE 59
>gnl|CDD|189016 cd09609, M3B_PepF_4, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 586
Score = 27.9 bits (63), Expect = 2.4
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 18/78 (23%)
Query: 5 ALDAADGVDIAIVKKS-GK-------VSALED--EIQTRIAL--------DAADGVDIAI 46
AL + KK GK +SAL+D EI I+ + DG D
Sbjct: 25 ALKKLKELAKDFKKKYKGKLTDAETILSALDDYEEILELISRLSHYASLPQSTDGTDPEN 84
Query: 47 VKKSGKVSALEDEIQTRL 64
++ K +L +I +L
Sbjct: 85 QARAAKFDSLAAKINAKL 102
>gnl|CDD|235437 PRK05380, pyrG, CTP synthetase; Validated.
Length = 533
Score = 27.3 bits (62), Expect = 3.6
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 28 DEIQTRIALDAADGVDIAIV 47
DEI+ RI L A D+ IV
Sbjct: 120 DEIKERI-LAAGTDADVVIV 138
>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin)
oxidoreductase, homodimeric. This model represents a
single chain form of pyruvate:ferredoxin (or flavodoxin)
oxidoreductase. This enzyme may transfer electrons to
nitrogenase in nitrogen-fixing species. Portions of this
protein are homologous to gamma subunit of the four
subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
Length = 1165
Score = 27.0 bits (60), Expect = 4.9
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 100 AFYNTADKAAVVLGKRFHLISSNVTNTMTRGLVEN 134
AFY + V+LG R+ L S T M + + +N
Sbjct: 343 AFYEMGEAMPVILGGRYGLGSKEFTPAMVKAVFDN 377
>gnl|CDD|236579 PRK09585, anmK, anhydro-N-acetylmuramic acid kinase; Reviewed.
Length = 365
Score = 26.6 bits (60), Expect = 6.5
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 14/65 (21%)
Query: 39 ADGVDIAIVKKSGKVSALE----------DEIQTRLKELNVEESSATHVLGRLFPFDDRG 88
DGVD A+V+ G+ + +E DE++ L L + L L D
Sbjct: 13 LDGVDAALVEIDGEGTKVELLASATVPYPDELRAALLALLQGGADELERLAEL----DTA 68
Query: 89 LVHAY 93
L +
Sbjct: 69 LGRLF 73
>gnl|CDD|188995 cd06456, M3A_DCP, Peptidase family M3 dipeptidyl carboxypeptidase
(DCP). Peptidase family M3 dipeptidyl carboxypeptidase
(DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This
metal-binding M3A family also includes oligopeptidase A
(OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off
the C-termini of various peptides and proteins, the
smallest substrate being N-blocked tripeptides and
unblocked tetrapeptides. DCP from E. coli is inhibited
by the anti-hypertensive drug captopril, an inhibitor of
the mammalian angiotensin converting enzyme (ACE, also
called peptidyl dipeptidase A). Oligopeptidase A (OpdA)
may play a specific role in the degradation of signal
peptides after they are released from precursor forms of
secreted proteins. It can also cleave N-acetyl-L-Ala.
Length = 654
Score = 26.6 bits (60), Expect = 7.6
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 55 ALEDEIQTRLKELNVEESSAT 75
AL++E + RL+E+N E + +
Sbjct: 124 ALDEEKKERLREINEELAELS 144
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A
number of them are thought to carry a distinctive
five-residue motif termed the proteasome-interacting
motif (PIM), which may have a biologically significant
role in protein delivery to proteasomes and recruitment
of proteasomes to transcription sites.
Length = 69
Score = 24.5 bits (54), Expect = 9.3
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 4/32 (12%)
Query: 50 SGKVSALEDEIQTRLKELNVEESSATHVLGRL 81
SGKV LED+ T L E +++ S H++ RL
Sbjct: 41 SGKV--LEDD--TTLSEYGIQDGSTLHLVLRL 68
>gnl|CDD|185053 PRK15098, PRK15098, beta-D-glucoside glucohydrolase; Provisional.
Length = 765
Score = 26.2 bits (58), Expect = 9.9
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 9/41 (21%)
Query: 4 IALDAADGVDIAIVKKSGKVSALEDEIQTRIALDAADGVDI 44
I+L A D+ V G+VSA E A DG+++
Sbjct: 122 ISLGLASSWDLDAVATVGRVSAYE---------AADDGLNM 153
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 0.136 0.394
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,996,743
Number of extensions: 728631
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 780
Number of HSP's successfully gapped: 25
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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 (25.0 bits)