RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17234
(170 letters)
>gnl|CDD|218740 pfam05768, DUF836, Glutaredoxin-like domain (DUF836). These
proteins are related to the pfam00462 family.
Length = 76
Score = 52.2 bits (126), Expect = 9e-10
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 3/71 (4%)
Query: 68 MLNLFTKDPCPLCDELKLELTPY--LDRVHLEEVYLTPESYWYKLYRYEIPVLFLGG-RF 124
L L+ K C LC+ K L LE + + + + Y EIPVL L G
Sbjct: 1 TLTLYGKPGCHLCEGAKEVLAELEAALGFDLERIDIDDDEELFARYGLEIPVLALVGILE 60
Query: 125 VCRNRFNAQIL 135
+ R + + L
Sbjct: 61 ILSWRLDEEQL 71
>gnl|CDD|222442 pfam13899, Thioredoxin_7, Thioredoxin-like. Thioredoxins are small
enzymes that participate in redox reactions, via the
reversible oxidation of an active centre disulfide bond.
Length = 81
Score = 30.3 bits (69), Expect = 0.10
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 6/63 (9%)
Query: 64 QRKPMLNLFTKDPCPLCDELK--LELTPYL----DRVHLEEVYLTPESYWYKLYRYEIPV 117
+ KP+L F D CP C L P + ++ L V +T L +P
Sbjct: 16 EGKPLLVDFGADWCPTCQALDRDFLSDPRVKALAEKFVLLRVDVTTRDPNLLLDGQGVPH 75
Query: 118 LFL 120
+
Sbjct: 76 VVF 78
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis
of L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 304
Score = 30.5 bits (70), Expect = 0.34
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 29 DLK-AHQKGIVVYNTPES-TMSV 49
D++ A +GI+V N P + T+SV
Sbjct: 77 DVEAATARGILVVNAPGANTISV 99
>gnl|CDD|131709 TIGR02661, MauD, methylamine dehydrogenase accessory protein
MauD. This protein, MauD, appears critical to proper
formation of the small subunit of methylamine
dehydrogenase, which has both an unusual tryptophan
tryptophylquinone cofactor and multiple disulfide
bonds. MauD shares sequence similarity, including a
CPxC motif, with a number of thiol:disulfide
interchange proteins. In MauD mutants, the small
subunit apparently does not form properly and is
rapidly degraded [Protein fate, Protein folding and
stabilization, Energy metabolism, Amino acids and
amines].
Length = 189
Score = 29.1 bits (65), Expect = 0.85
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 55 PVKSNFITSQRKPMLNLFTKDPCPLCDEL 83
PV+ + +P L +FT CP+CD+L
Sbjct: 64 PVRIGGSIAPGRPTLLMFTAPSCPVCDKL 92
>gnl|CDD|211388 cd11302, O-FucT-1, GDP-fucose protein O-fucosyltransferase 1. The
protein O-fucosyltransferase 1 (Ofut1 or O-FucT-1) adds
O-fucose to EGF (epidermal growth factor-like) repeats.
The O-fucsosylation of the Notch receptor signaling
protein is dependent on this enzyme, which requires
GDP-fucose as a substrate. O-fucose residues added to
the target of O-FucT-1 may be further elongated by other
glycosyltransferases. On top of O-fucosylation, O-FucT-1
may have other functions such as the regulation of the
Notch receptor exit from the ER. Six highly conserved
cysteines are present in O-FucT-1, which is a soluble ER
protein, as well as a DXD-like motif (ERD), conserved in
mammals, Drosophila, and C. elegans. Both features are
characteristic of several glycosyltransferase families.
The membrane-bound pre-protein is released by
proteolysis and, as for most glycosyltransferases, is
strongly activated by manganese. O-FucT-1 is similar to
family 1 glycosyltransferases (GT1).
Length = 347
Score = 29.1 bits (66), Expect = 1.1
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 4 LLEKLPVKSTFITSQRKPMLNLFTKDLKAHQKGIVVYN 41
++K+ KS FI + M+ K LK+ + +V +
Sbjct: 264 AVKKIKAKSVFIATDNDHMIEELKKALKSLKVKVVHLD 301
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 28.0 bits (63), Expect = 2.2
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 8/28 (28%)
Query: 32 AHQKGIVVYNTP--------ESTMSVLL 51
A +KGI V NTP E T ++L
Sbjct: 84 AKEKGIPVTNTPAVSTEPTAELTFGLIL 111
>gnl|CDD|239249 cd02951, SoxW, SoxW family; SoxW is a bacterial periplasmic TRX,
containing a redox active CXXC motif, encoded by a
genetic locus (sox operon) involved in thiosulfate
oxidation. Sulfur bacteria oxidize sulfur compounds to
provide reducing equivalents for carbon dioxide fixation
during autotrophic growth and the respiratory electron
transport chain. It is unclear what the role of SoxW is,
since it has been found to be dispensable in the
oxidation of thiosulfate to sulfate. SoxW is
specifically kept in the reduced state by SoxV, which is
essential in thiosulfate oxidation.
Length = 125
Score = 26.9 bits (60), Expect = 3.0
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 66 KPMLNLFTKDPCPLCDELKLELTPYLD-RVHLEEVYLTPE 104
KP+L LF++ CP CD+LK + + ++ ++
Sbjct: 15 KPLLLLFSQPGCPYCDKLKRDYLNDPAVQAYIRAHFVVVY 54
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 27.6 bits (62), Expect = 3.1
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 29 DLK-AHQKGIVVYNTPE-STMSV 49
DL+ A ++GI V N P ST +V
Sbjct: 81 DLEAAKERGITVTNVPGYSTEAV 103
>gnl|CDD|225054 COG2143, COG2143, Thioredoxin-related protein [Posttranslational
modification, protein turnover, chaperones].
Length = 182
Score = 27.2 bits (60), Expect = 3.3
Identities = 20/63 (31%), Positives = 26/63 (41%), Gaps = 5/63 (7%)
Query: 61 ITSQRKPMLNLFTKDPCPLCDELKLELTPYLDRVHLEEVYLTPESYWYKLY-RYEIPVLF 119
I+ K +L +F + C C+ K +L L E YL Y L Y PVLF
Sbjct: 38 ISPNDKYLLLMFESNGCSYCERFKKDLKNVKR---LRE-YLKEHFSAYYLNISYSKPVLF 93
Query: 120 LGG 122
G
Sbjct: 94 KVG 96
>gnl|CDD|129395 TIGR00294, TIGR00294, GTP cyclohydrolase, MptA/FolE2 family.
This family includes type I GTP cyclohydrolases
involved in methanopterin in archaea (MptA) and de novo
tetrahydrofolate biosynthesis in bacteria (FolE2)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 308
Score = 27.1 bits (60), Expect = 4.5
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 19 RKPMLNLFTKD----LKAHQKGIVVYNTPESTMSVLLE 52
++P++ + T D L +HQKG+ + PE SVL E
Sbjct: 32 KRPIILISTFDVFVDLPSHQKGVHMSRNPEVITSVLEE 69
>gnl|CDD|188431 TIGR03916, rSAM_link_UDG, putative DNA modification/repair radical
SAM protein. This uncharacterized protein of about 400
amino acids in length contains a radical SAM protein in
the N-terminal half. Members are present in about twenty
percent of prokaryotic genomes, always paired with a
member of the conserved hypothetical protein TIGR03915.
Roughly forty percent of the members of that family
exist as fusions with a uracil-DNA glycosylase-like
region, TIGR03914. In DNA, uracil results from
deamidation of cytosine, forming U/G mismatches that
lead to mutation, and so uracil-DNA glycosylase is a DNA
repair enzyme. This indirect connection, and the
recurring role or radical SAM protein in modification
chemistries, suggest that this protein may act in DNA
modification, repair, or both [Unknown function, Enzymes
of unknown specificity].
Length = 415
Score = 27.3 bits (61), Expect = 5.1
Identities = 6/11 (54%), Positives = 9/11 (81%)
Query: 134 ILMSNECIFQC 144
IL++N CI+ C
Sbjct: 56 ILLTNHCIYDC 66
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 27.0 bits (61), Expect = 5.9
Identities = 8/19 (42%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 32 AHQKGIVVYNTPES-TMSV 49
A ++GI+V N P T+S
Sbjct: 83 ATRRGIIVVNAPTGNTISA 101
>gnl|CDD|237394 PRK13480, PRK13480, 3'-5' exoribonuclease YhaM; Provisional.
Length = 314
Score = 26.9 bits (60), Expect = 6.1
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 35 KGIVVYNTPESTMSVLLEKLPVKSNFITSQRKPMLNLFTKD 75
KGI E LL K K + S KP L L +D
Sbjct: 3 KGIEELEVGEQVDHFLLIKSATKG--VASNGKPFLTLILQD 41
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding
and catalytic domains. Phosphoglycerate dehydrogenase
(PGDH) catalyzes the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDH comes in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 301
Score = 26.7 bits (60), Expect = 6.7
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 32 AHQKGIVVYNTPE-STMSV 49
A +KGI V NTP S+ SV
Sbjct: 82 AKKKGIKVINTPGASSNSV 100
>gnl|CDD|215242 PLN02441, PLN02441, cytokinin dehydrogenase.
Length = 525
Score = 26.4 bits (59), Expect = 7.9
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 25/61 (40%)
Query: 44 ESTMSVLLEKLPVKSNFITSQRKPMLNLFTKDPCPLCDELKLELTPY---LDRVHLEEVY 100
+ + LL++L +FI LFT D Y LDRVH+EE+
Sbjct: 333 DQEVESLLKRL----SFIPGL------LFTTD------------VSYVDFLDRVHVEELK 370
Query: 101 L 101
L
Sbjct: 371 L 371
>gnl|CDD|182309 PRK10213, nepI, ribonucleoside transporter; Reviewed.
Length = 394
Score = 26.4 bits (58), Expect = 8.5
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 119 FLGGRFVCRNRFNAQILMSNECIF 142
FLG RN FNA +M CIF
Sbjct: 166 FLGELIGWRNVFNAAAVMGVLCIF 189
>gnl|CDD|236985 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 409
Score = 26.3 bits (59), Expect = 9.1
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 12/42 (28%)
Query: 29 DLK-AHQKGIVVYNTPES-TMSV----------LLEKLPVKS 58
DL A ++GI V+N P S T SV LL +P K+
Sbjct: 90 DLDAAAKRGIPVFNAPFSNTRSVAELVIGEIILLLRGIPEKN 131
>gnl|CDD|234548 TIGR04331, o_ant_LIC12162, putative transferase, LIC12162 family.
This protein family shows C-terminal sequence similarity
to various surface carbohydrate biosynthesis enzymes:
spore coat polysaccharide biosynthesis protein SpsB,
UDP-N-acetyl-D-glucosamine 2-epimerase, lipid A
disaccharide synthetase LpxB, etc. It may occur in
O-antigen biosythesis regions.
Length = 585
Score = 26.6 bits (59), Expect = 9.2
Identities = 26/153 (16%), Positives = 46/153 (30%), Gaps = 39/153 (25%)
Query: 2 SVLLEKLPVKSTFITSQRKPMLNLFTKDLKAHQKGIVVYNTPESTMSVLLEKLPVKSNFI 61
LE + R F + + + ++V + +T LE L
Sbjct: 456 QRWLEDFFPRLRLDDGNRS-----FEELMARCR--LIVCDYLSTTF---LEAL------- 498
Query: 62 TSQRKPMLNLFTKDPCPLCDELKLELTPYLDRV---------------HLEEVYLTPESY 106
+ KP + + ++ L E + PY DR+ H+ +++ PE +
Sbjct: 499 -AANKPTILFWDREAWELRPEAE----PYFDRLREAGILFEDPESAAAHVNQIWDDPEGW 553
Query: 107 WYKLYRYEIPVLFLGGRFVCRNRFNAQILMSNE 139
W LF R N E
Sbjct: 554 WNSPEVQAARKLFC--AQYARESGNPFKYWKQE 584
>gnl|CDD|227005 COG4658, RnfD, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfD [Energy production and conversion].
Length = 338
Score = 26.2 bits (58), Expect = 9.7
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 106 YWYKLYRYEIPVLFLGGRFVC 126
W K R+ IPV FL F+
Sbjct: 221 LWVKAIRWHIPVSFLVTLFLL 241
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
0.323 0.136 0.406
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,379,418
Number of extensions: 744865
Number of successful extensions: 539
Number of sequences better than 10.0: 1
Number of HSP's gapped: 538
Number of HSP's successfully gapped: 27
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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 (22.0 bits)
S2: 55 (24.9 bits)