RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16623
(93 letters)
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein
(UMSBP); Provisional.
Length = 148
Score = 46.0 bits (109), Expect = 1e-07
Identities = 17/44 (38%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
CYNC GH CP+ A CY C GH +REC
Sbjct: 55 CYNCGKTGHLSRECPE-----APPGSGPRSCYNCGQTGHISREC 93
Score = 44.4 bits (105), Expect = 5e-07
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 36 MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESP 92
+ CY C + GH CP S+ RG++ CY C GH +REC P
Sbjct: 22 AGAAKARPCYKCGEPGHLSRECP--SAPGGRGERS---CYNCGKTGHLSRECPEAPP 73
Score = 43.3 bits (102), Expect = 1e-06
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 39 TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE 90
+ CYNC GH CP ++ A CY C GH +R+C
Sbjct: 75 SGPRSCYNCGQTGHISRECPNRAKGGAARRA----CYNCGGEGHISRDCPNA 122
Score = 40.2 bits (94), Expect = 2e-05
Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
CYNC GH CP GDK CY C GH +R+C
Sbjct: 106 CYNCGGEGHISRDCPNAGKR-PGGDKT---CYNCGQTGHLSRDC 145
Score = 37.1 bits (86), Expect = 3e-04
Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
CY C GH CP + A A CYKC GH +REC
Sbjct: 3 CYRCGGVGHQSRECPNSAPAGAAK---ARPCYKCGEPGHLSREC 43
Score = 28.6 bits (64), Expect = 0.34
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 73 VCYKCNNYGHFARECATESP 92
VCY+C GH +REC +P
Sbjct: 2 VCYRCGGVGHQSRECPNSAP 21
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 39.1 bits (91), Expect = 6e-05
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 11/44 (25%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
CYNC GH CP+ CY C GH +R+C
Sbjct: 81 CYNCSWDGHRSNHCPKP-----------KKCYNCGETGHLSRDC 113
Score = 37.5 bits (87), Expect = 3e-04
Identities = 16/54 (29%), Positives = 20/54 (37%), Gaps = 4/54 (7%)
Query: 43 QCYNCFDFGHYQYSCPQ--KSSADARGDKVGI--VCYKCNNYGHFARECATESP 92
C++C H CP K GD I CY C + GHF +C
Sbjct: 122 SCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRS 175
Score = 34.8 bits (80), Expect = 0.002
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 7/49 (14%)
Query: 39 TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
+CYNC + GH C C+ CN+ H + +C
Sbjct: 95 PKPKKCYNCGETGHLSRDCNPSKD-------QQKSCFDCNSTRHSSEDC 136
Score = 25.2 bits (55), Expect = 5.4
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 51 GHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
G Y+ + SA + V C+ C GH R+C
Sbjct: 43 GRYEDRSVEDVSAIREENPV---CFNCGQNGHLRRDC 76
>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved
in eukaryotic gene regulation, such as C. elegans
GLH-1. Structure is an 18-residue zinc finger.
Length = 18
Score = 31.3 bits (72), Expect = 0.006
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 72 IVCYKCNNYGHFAREC 87
CY C GH AR+C
Sbjct: 1 RKCYNCGKEGHLARDC 16
Score = 23.6 bits (52), Expect = 4.7
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 42 IQCYNCFDFGHYQYSCPQ 59
+CYNC GH CP+
Sbjct: 1 RKCYNCGKEGHLARDCPE 18
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger.
Length = 17
Score = 29.3 bits (67), Expect = 0.027
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 73 VCYKCNNYGHFAREC 87
CY C GH AR+C
Sbjct: 1 KCYNCGKEGHIARDC 15
Score = 26.6 bits (60), Expect = 0.29
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 43 QCYNCFDFGHYQYSCPQ 59
+CYNC GH CP
Sbjct: 1 KCYNCGKEGHIARDCPS 17
>gnl|CDD|206088 pfam13917, zf-CCHC_3, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved
in eukaryotic gene regulation, such as C. elegans
GLH-1. Structure is an 18-residue zinc finger.
Length = 40
Score = 27.7 bits (62), Expect = 0.17
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 38 STSTIQCYNCFDFGHYQYSCPQKSSADAR 66
+ ++ +C C GH+ Y C + +R
Sbjct: 1 ANASARCQKCLKKGHWTYECKNERKYVSR 29
Score = 24.6 bits (54), Expect = 2.4
Identities = 7/20 (35%), Positives = 8/20 (40%)
Query: 68 DKVGIVCYKCNNYGHFAREC 87
C KC GH+ EC
Sbjct: 1 ANASARCQKCLKKGHWTYEC 20
>gnl|CDD|205872 pfam13696, zf-CCHC_2, Zinc knuckle. This is a zinc-binding
domain of the form CxxCxxxGHxxxxC from a variety of
different species.
Length = 32
Score = 26.7 bits (59), Expect = 0.42
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 43 QCYNCFDFGHYQYSCPQKS 61
C+ CF GHY CPQ S
Sbjct: 10 LCHLCFQKGHYISDCPQAS 28
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 28.2 bits (62), Expect = 0.61
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 71 GIVCYKCNNYGHFARECATES 91
G VCY+C GH+ + C T
Sbjct: 176 GYVCYRCGQKGHWIQNCPTNQ 196
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 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 = 334
Score = 26.9 bits (60), Expect = 1.5
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 5/25 (20%)
Query: 64 DARGDKVGIVCYKCNNYGHFARECA 88
D+ G +VGI+ YG R+ A
Sbjct: 130 DSVGKRVGIL-----GYGSIGRQTA 149
>gnl|CDD|176065 cd08683, C2_C2cd3, C2 domain found in C2 calcium-dependent domain
containing 3 (C2cd3) proteins. C2cd3 is a novel C2
domain-containing protein specific to vertebrates.
C2cd3 functions in regulator of cilia formation,
Hedgehog signaling, and mouse embryonic development.
Mutations in C2cd3 mice resulted in lethality in some
cases and exencephaly, a twisted body axis, and
pericardial edema in others. The presence of
calcium-dependent lipid-binding domains in C2cd3
suggests a potential role in vesicular transport. C2cd3
is also an interesting candidate for ciliopathy because
of its orthology to certain cilia-related genetic
disease loci on chromosome. The C2 domain was first
identified in PKC. C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of
piccolo/aczonin and intersectin which only have a
single C2 domain. C2 domains with a calcium binding
region have negatively charged residues, primarily
aspartates, that serve as ligands for calcium ions.
Length = 143
Score = 26.2 bits (58), Expect = 2.4
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 28 LLFVLRVEMSSTSTIQCYNCFDFG-HYQYSCP---QKSSADA 65
L F+ E+ T T+ C +F H ++ C Q++S +A
Sbjct: 41 LSFLPEKELRRTRTVARSFCPEFNHHVEFPCNLVVQRNSGEA 82
>gnl|CDD|233674 TIGR01992, PTS-IIBC-Tre, PTS system, trehalose-specific IIBC
component. This model represents the fused enzyme II B
and C components of the trehalose-specific PTS sugar
transporter system. Trehalose is converted to
trehalose-6-phosphate in the process of translocation
into the cell. These transporters lack their own IIA
domains and instead use the glucose IIA protein (IIAglc
or Crr). The exceptions to this rule are Staphylococci
and Streptococci which contain their own A domain as a
C-terminal fusion. This family is closely related to the
sucrose transporting PTS IIBC enzymes and the B and C
domains of each are described by subfamily-domain level
TIGRFAMs models (TIGR00826 and TIGR00852, respectively).
In E. coli, B. subtilis and P. fluorescens the presence
of this gene is associated with the presence of
trehalase which degrades T6P to glucose and glucose-6-P.
Trehalose may also be transported (in Salmonella) via
the mannose PTS or galactose permease systems, or (in
Sinorhizobium, Thermococcus and Sulfolobus, for
instance) by ABC transporters.
Length = 462
Score = 26.2 bits (58), Expect = 2.7
Identities = 9/32 (28%), Positives = 13/32 (40%), Gaps = 7/32 (21%)
Query: 14 VLGILLIIKQRNEGLLFVLRVEMSSTSTIQCY 45
LGI+ + + E +S TS I Y
Sbjct: 356 ALGIIFMSRNEKEK-------GLSLTSAISAY 380
>gnl|CDD|185108 PRK15186, PRK15186, AraC family transcriptional regulator;
Provisional.
Length = 291
Score = 25.4 bits (55), Expect = 4.4
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 17 ILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCP 58
I + +++ +E L + L +E+ S S YN F + H +S P
Sbjct: 75 IHITMEETHEQLNYNL-IELDSASIKNAYNFFLYEHADFSAP 115
>gnl|CDD|219797 pfam08326, ACC_central, Acetyl-CoA carboxylase, central region.
The region featured in this family is found in various
eukaryotic acetyl-CoA carboxylases, N-terminal to the
catalytic domain (pfam01039). This enzyme (EC:6.4.1.2)
is involved in the synthesis of long-chain fatty acids,
as it catalyzes the rate-limiting step in this process.
Length = 707
Score = 25.4 bits (56), Expect = 4.8
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 1 MHQRLENSLWNNYVLG--ILLIIKQRNEGLLFVLRVEMSSTS----TIQCY 45
+R LW V + + ++ + G LRV +++ S ++ Y
Sbjct: 634 FLERFGRRLWRLRVTQAEVRIRLRDPSTGAPVPLRVIITNVSGYVVKVELY 684
>gnl|CDD|202098 pfam02035, Coagulin, Coagulin.
Length = 172
Score = 25.0 bits (54), Expect = 5.8
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 43 QCYNCFDFGHYQYSCPQKSSA 63
+CYN F H++ CP +
Sbjct: 72 RCYNFPPFTHFKSECPVSTRD 92
>gnl|CDD|232841 TIGR00131, gal_kin, galactokinase. Galactokinase is a member of
the GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase) and shares
with them an amino-terminal domain probably related to
ATP binding.The galactokinases found by This model are
divided into two sets. Prokaryotic forms are generally
shorter. The eukaryotic forms are longer because of
additional central regions and in some cases are known
to be bifunctional, with regulatory activities that are
independent of galactokinase activity [Energy
metabolism, Sugars].
Length = 386
Score = 25.2 bits (55), Expect = 6.8
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 6 ENSLWNNYVLGILLIIKQRN 25
E S W NY G+L + ++R
Sbjct: 85 EVSDWANYFKGVLHVAQERF 104
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 0.438
Gapped
Lambda K H
0.267 0.0869 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,294,904
Number of extensions: 308389
Number of successful extensions: 319
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 28
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (23.9 bits)