RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7947
(173 letters)
>gnl|CDD|176076 cd08694, C2_Dock-A, C2 domains found in Dedicator Of CytoKinesis
(Dock) class A proteins. Dock-A is one of 4 classes of
Dock family proteins. The members here include:
Dock180/Dock1, Dock2, and Dock5. Most of these members
have been shown to be GEFs specific for Rac. Dock5 has
not been well characterized to date, but most likely
also is a GEF specific for Rac. In addition to the C2
domain (AKA Dock homology region (DHR)-1, CED-5,
Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2
(AKA CZH2, or Docker), which all Dock180-related
proteins have, Dock-A members contain a proline-rich
region and a SH3 domain upstream of the C2 domain. DHR-2
has the catalytic activity for Rac and/or Cdc42, but is
structurally unrelated to the DH domain. The C2/DHR-1
domains of Dock180 and Dock4 have been shown to bind
phosphatidylinositol-3, 4, 5-triphosphate
(PtdIns(3,4,5)P3). 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 = 196
Score = 54.7 bits (132), Expect = 9e-10
Identities = 22/40 (55%), Positives = 28/40 (70%), Gaps = 4/40 (10%)
Query: 101 VRNDLYVTLVNAEF----KSSDKTIQVTVQVCTEAGVILK 136
VRNDLY+TLV +F K+SDK ++VTV VC E G I+
Sbjct: 1 VRNDLYLTLVQGDFDKGSKTSDKNVEVTVSVCNEDGKIIP 40
>gnl|CDD|176077 cd08695, C2_Dock-B, C2 domains found in Dedicator Of CytoKinesis
(Dock) class B proteins. Dock-B is one of 4 classes of
Dock family proteins. The members here include:
Dock3/MOCA (modifier of cell adhesion) and Dock4. Most
of these members have been shown to be GEFs specific for
Rac, although Dock4 has also been shown to interact
indirectly with the Ras family GTPase Rap1, probably
through Rap regulatory proteins. In addition to the C2
domain (AKA Dock homology region (DHR)-1, CED-5,
Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2
(AKA CZH2, or Docker), which all Dock180-related
proteins have, Dock-B members contain a SH3 domain
upstream of the C2 domain and a proline-rich region
downstream. DHR-2 has the catalytic activity for Rac
and/or Cdc42, but is structurally unrelated to the DH
domain. The C2/DHR-1 domains of Dock180 and Dock4 have
been shown to bind phosphatidylinositol-3, 4,
5-triphosphate (PtdIns(3,4,5)P3). 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 = 189
Score = 40.8 bits (96), Expect = 8e-05
Identities = 20/40 (50%), Positives = 25/40 (62%), Gaps = 4/40 (10%)
Query: 101 VRNDLYVTLVNAEF----KSSDKTIQVTVQVCTEAGVILK 136
VRNDLY+TL EF KS+ K I+VT+ V G +LK
Sbjct: 1 VRNDLYLTLERGEFEKGGKSTAKNIEVTMVVLDADGQVLK 40
>gnl|CDD|222580 pfam14180, DOCK_C2, GTP-GDP exchange factor. Dock proteins are
atypical GTP-GDP exchange factors for the small GTPases
Pac and Cdc42, and are implicated in biological roles
related to cell-migration and phagocytosis.
Length = 178
Score = 40.4 bits (95), Expect = 1e-04
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 100 DVRNDLYVTLVNAEF----KSSDKTIQVTVQVCTEAGVILKVNAEF 141
D RNDLYV + +F KS + I VTV++ G +L+
Sbjct: 1 DYRNDLYVYPKSLKFSKQPKSKARNIVVTVELRDSDGEVLEEGLPI 46
>gnl|CDD|222746 pfam14429, DOCK-C2, C2 domain in Dock180 and Zizimin proteins. The
Dock180/Dock1 and Zizimin proteins are atypical GTP/GDP
exchange factors for the small GTPases Rac and Cdc42 and
are implicated cell-migration and phagocytosis. Across
all Dock180 proteins, two regions are conserved:
C-terminus termed CZH2 or DHR2 (or the Dedicator of
cytokinesis) whereas CZH1/DHR1 contain a new family of
the C2 domain.
Length = 179
Score = 38.8 bits (91), Expect = 3e-04
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 98 PGDVRNDLYVTLVNAEF----KSSDKTIQVTVQVCTEAGVI 134
P D RNDLYV L +A F KS + I+VTV++ G
Sbjct: 2 PTDYRNDLYVYLKSANFSKPKKSKARNIEVTVELRDSDGSS 42
>gnl|CDD|176061 cd08679, C2_DOCK180_related, C2 domains found in Dedicator Of
CytoKinesis 1 (DOCK 180) and related proteins. Dock180
was first identified as an 180kd proto-oncogene product
c-Crk-interacting protein involved in actin cytoskeletal
changes. It is now known that it has Rac-specific GEF
activity, but lacks the conventional Dbl homology (DH)
domain. There are 10 additional related proteins that
can be divided into four classes based on sequence
similarity and domain organization: Dock-A which
includes Dock180/Dock1, Dock2, and Dock5; Dock-B which
includes Dock3/MOCA (modifier of cell adhesion) and
Dock4; Dock-C which includes Dock6/Zir1, Dock7/Zir2, and
Dock8/Zir3; and Dock-D, which includes Dock9/Zizimin1,
Dock10/Zizimin3, and Dock11/Zizimin2/ACG (activated
Cdc42-associated GEF). Most of members of classes
Dock-A and Dock-B are the GEFs specific for Rac. Those
of Dock-D are Cdc42-specific GEFs while those of Dock-C
are the GEFs for both. All Dock180-related proteins have
two common homology domains: the C2 domain (AKA Dock
homology region (DHR)-1, CED-5, Dock180, MBC-zizimin
homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker).
DHR-2 has the catalytic activity for Rac and/or Cdc42,
but is structurally unrelated to the DH domain. The
C2/DHR-1 domains of Dock180 and Dock4 have been shown to
bind phosphatidylinositol-3, 4, 5-triphosphate
(PtdIns(3,4,5)P3). 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 = 178
Score = 35.8 bits (83), Expect = 0.004
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 102 RNDLYVTLVNAEF---KSSDKTIQVTVQV 127
RNDLYV + E KS + I++TV+V
Sbjct: 2 RNDLYVYPQSGELSKAKSKGRNIEITVEV 30
>gnl|CDD|149438 pfam08374, Protocadherin, Protocadherin. The structure of
protocadherins is similar to that of classic cadherins
(pfam00028), but particularly on the cytoplasmic domains
they also have some unique features. They are expressed
in a variety of organisms and are found in high
concentrations in the brain where they seem to be
localised mainly at cell-cell contact sites. Their
expression seems to be developmentally regulated.
Length = 223
Score = 32.9 bits (75), Expect = 0.058
Identities = 20/60 (33%), Positives = 30/60 (50%)
Query: 8 KKKKKKKKKKKKNVRPLSPYHSVVKLCEKDNLENTLKRLISSLKDISSQKSAGMYVSLKF 67
K+KKKKK KKKK+ + L V+ + D+ + K SL ++S G Y+ F
Sbjct: 90 KQKKKKKDKKKKSPKSLLLNFVTVEESKPDDEVHEQKSETLSLPIELEEQSMGRYLPTTF 149
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 31.8 bits (73), Expect = 0.15
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 3 VQKKKKKKKKKKKKKKKNV 21
++K+K K KK+ + KN+
Sbjct: 404 EKEKEKPKVKKRHRDTKNI 422
Score = 31.1 bits (71), Expect = 0.30
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 5 KKKKKKKKKKKKKKKNVR 22
K+ +KK+K+K+K K R
Sbjct: 398 KRAEKKEKEKEKPKVKKR 415
Score = 30.3 bits (69), Expect = 0.54
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 4 QKKKKKKKKKKKKKKK 19
+KK+K+K+K K KK+
Sbjct: 401 EKKEKEKEKPKVKKRH 416
Score = 29.5 bits (67), Expect = 0.88
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 4 QKKKKKKKKKKKKKKK 19
+ +KK+K+K+K K KK
Sbjct: 399 RAEKKEKEKEKPKVKK 414
Score = 29.5 bits (67), Expect = 0.99
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 4 QKKKKKKKKKKKKKKK 19
+K+K+K+K K KK+ +
Sbjct: 402 KKEKEKEKPKVKKRHR 417
Score = 29.1 bits (66), Expect = 1.1
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 4 QKKKKKKKKKKKKKKKNVR 22
K+ +KK+K+K+K V+
Sbjct: 395 VLAKRAEKKEKEKEKPKVK 413
Score = 28.8 bits (65), Expect = 1.3
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 3 VQKKKKKKKKKKKKKKK 19
V K+ +KK+K+K+K K
Sbjct: 395 VLAKRAEKKEKEKEKPK 411
Score = 27.2 bits (61), Expect = 4.6
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 5 KKKKKKKKKKKKKKKNVR 22
K K+ +KK+K+K+ +
Sbjct: 394 KVLAKRAEKKEKEKEKPK 411
Score = 26.8 bits (60), Expect = 7.2
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 4 QKKKKKKKKKKKKKKKNVRP 23
+ K KK+ + K K +P
Sbjct: 409 KPKVKKRHRDTKNIGKRRKP 428
Score = 26.8 bits (60), Expect = 7.6
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 5 KKKKKKKKKKKKKKKNVR 22
+K K KK+ + K R
Sbjct: 408 EKPKVKKRHRDTKNIGKR 425
>gnl|CDD|219901 pfam08555, DUF1754, Eukaryotic family of unknown function
(DUF1754). This is a eukaryotic protein family of
unknown function.
Length = 90
Score = 30.1 bits (68), Expect = 0.18
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 5 KKKKKKKKKKKKKKKNVRPLSPYHSVVKLCEKDNLENTLKRLISSLKDISSQKSAGMYVS 64
KK KKKKKKKKK + + + EK + E+ LK + ++
Sbjct: 14 GKKIDVKKKKKKKKKKNKSKEEVVTEKEEEEKSSAESDLKEGEEDEDNEKIEQEED---- 69
Query: 65 LKFHCGDNKTES 76
G N TE+
Sbjct: 70 -----GMNLTEA 76
>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19.
Med19 represents a family of conserved proteins which
are members of the multi-protein co-activator Mediator
complex. Mediator is required for activation of RNA
polymerase II transcription by DNA binding
transactivators.
Length = 178
Score = 31.0 bits (70), Expect = 0.19
Identities = 14/22 (63%), Positives = 17/22 (77%)
Query: 5 KKKKKKKKKKKKKKKNVRPLSP 26
K++KKKKK+KKKKKK P P
Sbjct: 153 KERKKKKKEKKKKKKRHSPEHP 174
Score = 27.9 bits (62), Expect = 2.5
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 4 QKKKKKKKKKKKKKKKNVRPLSPYH 28
+ K++KKKKK+KKKK R SP H
Sbjct: 150 EDDKERKKKKKEKKKKKKRH-SPEH 173
>gnl|CDD|180910 PRK07260, PRK07260, enoyl-CoA hydratase; Provisional.
Length = 255
Score = 30.9 bits (70), Expect = 0.28
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 27 YHSVVKLCEKDNLENTLKRLISSLKDISSQKSAGM 61
Y V ++ E + LE T ++L+ L+ SS A +
Sbjct: 177 YGFVYRVAESEKLEKTCEQLLKKLRRGSSNSYAAI 211
>gnl|CDD|217502 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognised by T cells.
Length = 603
Score = 30.5 bits (69), Expect = 0.42
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 3 VQKKKKKKKKKKKKKKKNVR 22
V+ KK KKKKKKKKK++
Sbjct: 273 VKFKKPKKKKKKKKKRRKDL 292
Score = 30.5 bits (69), Expect = 0.49
Identities = 13/19 (68%), Positives = 15/19 (78%)
Query: 1 MFVQKKKKKKKKKKKKKKK 19
M KK KKKKKKKKK++K
Sbjct: 272 MVKFKKPKKKKKKKKKRRK 290
>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
Length = 128
Score = 29.0 bits (66), Expect = 0.65
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 7 KKKKKKKKKKKKKNV 21
KKKK KKK KKN+
Sbjct: 1 AKKKKTVKKKVKKNI 15
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 28.9 bits (65), Expect = 0.75
Identities = 14/17 (82%), Positives = 15/17 (88%)
Query: 4 QKKKKKKKKKKKKKKKN 20
QKKK+KKKKKKK KK N
Sbjct: 91 QKKKQKKKKKKKAKKGN 107
Score = 26.9 bits (60), Expect = 4.4
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 6 KKKKKKKKKKKKKKNVR 22
KKK+KKKKKKK KK +
Sbjct: 92 KKKQKKKKKKKAKKGNK 108
>gnl|CDD|219564 pfam07771, TSGP1, Tick salivary peptide group 1. This contains a
group of peptides derived from a salivary gland cDNA
library of the tick Ixodes scapularis. Also present are
peptides from a related tick species, Ixodes ricinus.
They are characterized by a putative signal peptide
indicative of secretion and conserved cysteine residues.
Length = 120
Score = 28.3 bits (63), Expect = 0.98
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 4 QKKKKKKKKKKKKKKKN 20
+KKKK KK KK KK
Sbjct: 102 KKKKKSKKTKKPKKSSK 118
Score = 27.9 bits (62), Expect = 1.6
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 5 KKKKKKKKKKKKKKKN 20
KKKKKK KK KK KK+
Sbjct: 101 KKKKKKSKKTKKPKKS 116
Score = 26.8 bits (59), Expect = 4.3
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 3 VQKKKKKKKKKKKKKKK 19
+KKKKK KK KK KK
Sbjct: 100 PKKKKKKSKKTKKPKKS 116
Score = 26.0 bits (57), Expect = 7.8
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 4 QKKKKKKKKKKKKKKKN 20
+KK KK KK KK KK+
Sbjct: 104 KKKSKKTKKPKKSSKKD 120
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 29.5 bits (66), Expect = 1.2
Identities = 14/17 (82%), Positives = 16/17 (94%)
Query: 4 QKKKKKKKKKKKKKKKN 20
+KKKKKKK K+KKKKKN
Sbjct: 684 RKKKKKKKSKEKKKKKN 700
Score = 28.3 bits (63), Expect = 2.8
Identities = 14/21 (66%), Positives = 16/21 (76%)
Query: 5 KKKKKKKKKKKKKKKNVRPLS 25
+KKKKKKK K+KKKK R S
Sbjct: 684 RKKKKKKKSKEKKKKKNREAS 704
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 29.2 bits (66), Expect = 1.2
Identities = 12/16 (75%), Positives = 15/16 (93%)
Query: 4 QKKKKKKKKKKKKKKK 19
QK+KKKKK+KKK KK+
Sbjct: 393 QKRKKKKKRKKKGKKR 408
Score = 28.8 bits (65), Expect = 1.4
Identities = 12/16 (75%), Positives = 15/16 (93%)
Query: 4 QKKKKKKKKKKKKKKK 19
+KKKK+KKK KK+KKK
Sbjct: 396 KKKKKRKKKGKKRKKK 411
Score = 28.8 bits (65), Expect = 1.6
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 4 QKKKKKKKKKKKKKKKN 20
+ +K+KKKKK+KKK K
Sbjct: 391 KPQKRKKKKKRKKKGKK 407
Score = 28.8 bits (65), Expect = 1.7
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 4 QKKKKKKKKKKKKKKKNVRP 23
+K +K+KKKKK+KKK R
Sbjct: 390 KKPQKRKKKKKRKKKGKKRK 409
Score = 28.4 bits (64), Expect = 2.1
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 4 QKKKKKKKKKKKKKKK 19
+KK+KKK KK+KKK +
Sbjct: 398 KKKRKKKGKKRKKKGR 413
Score = 28.0 bits (63), Expect = 2.5
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 4 QKKKKKKKKKKKKKKKN 20
++KKKKK+KKK KK+K
Sbjct: 394 KRKKKKKRKKKGKKRKK 410
Score = 28.0 bits (63), Expect = 3.0
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 4 QKKKKKKKKKKKKKKKN 20
+KK +K+KKKKK+KKK
Sbjct: 389 EKKPQKRKKKKKRKKKG 405
Score = 27.6 bits (62), Expect = 3.4
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 4 QKKKKKKKKKKKKKKK 19
+K+KKK KK+KKK +K
Sbjct: 399 KKRKKKGKKRKKKGRK 414
Score = 27.2 bits (61), Expect = 4.2
Identities = 10/16 (62%), Positives = 15/16 (93%)
Query: 4 QKKKKKKKKKKKKKKK 19
++KK +K+KKKKK+KK
Sbjct: 388 EEKKPQKRKKKKKRKK 403
Score = 26.9 bits (60), Expect = 6.8
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 5 KKKKKKKKKKKKKKK 19
KKK+++KK +K+KKK
Sbjct: 384 KKKREEKKPQKRKKK 398
Score = 26.5 bits (59), Expect = 10.0
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 5 KKKKKKKKKKKKKKK 19
KK+++KK +K+KKKK
Sbjct: 385 KKREEKKPQKRKKKK 399
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 28.6 bits (65), Expect = 1.6
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 2 FVQKKKKKKKKKKKKKKKNVRP 23
+ + +KKK+K++ K K +P
Sbjct: 69 WHKAQKKKEKQEAKAAKAKSKP 90
Score = 26.7 bits (60), Expect = 7.6
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 4 QKKKKKKKKKKKKKKKNVR 22
QKKK+K++ K K K R
Sbjct: 73 QKKKEKQEAKAAKAKSKPR 91
>gnl|CDD|216819 pfam01973, MAF_flag10, Protein of unknown function DUF115. This
family of archaebacterial proteins has no known
function.
Length = 170
Score = 28.0 bits (63), Expect = 2.0
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 79 VAMTNTFIARKMGFPEIILPG 99
VA +A +GF EIIL G
Sbjct: 142 VANRAVDLAVYLGFKEIILIG 162
>gnl|CDD|188606 TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis
protein DltB. Members of this protein family are DltB,
part of a four-gene operon for D-alanyl-lipoteichoic
acid biosynthesis that is present in the vast majority
of low-GC Gram-positive organisms. This protein may be
involved in transport of D-alanine across the plasma
membrane [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 380
Score = 28.3 bits (64), Expect = 2.2
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 4 QKKKKKKKKKKKKK 17
Q+K KK KK KK K
Sbjct: 342 QRKSKKYKKNKKNK 355
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 28.1 bits (64), Expect = 2.4
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 7/41 (17%)
Query: 4 QKKKKKKKKKKKKKKKNVRPLSPYHSVVKL--CEKDNLENT 42
Q + + KK K+KKK + L KL C + E T
Sbjct: 381 QARLRAAKKVKRKKKTSGPALPG-----KLADCTSQDPERT 416
>gnl|CDD|227507 COG5180, PBP1, Protein interacting with poly(A)-binding protein
[RNA processing and modification].
Length = 654
Score = 28.2 bits (62), Expect = 2.5
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 2 FVQKKKKKKKKKKKKKKKNVRPLSPYHS---VVKLCEKDNLENTLKRLISSLKDISSQ 56
+ K + ++K+K ++ + K NL +K SL DISS
Sbjct: 296 VSPQSKSEGPSSGQEKEKQIKEKKSFSYGWKHTKFDSSKNLLEVIKSKFKSLFDISSG 353
>gnl|CDD|222592 pfam14204, Ribosomal_L18_c, Ribosomal L18 C-terminal region.
This domain is the C-terminal end of ribosomal L18/L5
proteins.
Length = 93
Score = 26.7 bits (60), Expect = 2.6
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 5 KKKKKKKKKKKKKKKNVRPLS 25
KKK+KK+ K + K+ N + L+
Sbjct: 62 KKKEKKEVKAESKRYNAKKLT 82
>gnl|CDD|234717 PRK00293, dipZ, thiol:disulfide interchange protein precursor;
Provisional.
Length = 571
Score = 28.3 bits (64), Expect = 2.7
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 104 DLYVTLVNAEFKSSDKTIQVTVQVCTEAGV 133
DL V L A ++ T+ VT Q C +AG
Sbjct: 102 DLPVPLNQA---AAGATLTVTYQGCADAGF 128
>gnl|CDD|226685 COG4232, COG4232, Thiol:disulfide interchange protein
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 569
Score = 28.1 bits (63), Expect = 2.8
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 99 GDV-----RNDLYVTLVNAEFKSSDKTIQVTVQVCTEAGV 133
GDV + L + L A ++ T+ VT Q C EAG
Sbjct: 91 GDVEVYRHQLTLPLPLAQA---AAGATLVVTYQGCAEAGF 127
>gnl|CDD|236768 PRK10819, PRK10819, transport protein TonB; Provisional.
Length = 246
Score = 27.7 bits (62), Expect = 2.8
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 3 VQKKKKKKKKKKKKKKKNVRPLSP 26
+ K K KK +++ K+ V+P+ P
Sbjct: 103 PKPKPKPVKKVEEQPKREVKPVEP 126
>gnl|CDD|182670 PRK10715, flk, flagella biosynthesis regulator; Provisional.
Length = 335
Score = 27.7 bits (62), Expect = 2.8
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 42 TLKRLISSLKDISSQKSAGMYVSLKFHCG 70
TL+RLI+ + ++ QKSA ++ L+ G
Sbjct: 34 TLERLITRIMSLTQQKSAEVWAGLRHDLG 62
>gnl|CDD|238388 cd00763, Bacterial_PFK, Phosphofructokinase, a key regulatory
enzyme in glycolysis, catalyzes the phosphorylation of
fructose-6-phosphate to fructose-1,6-biphosphate. The
members belong to a subfamily of the PFKA family
(cd00363) and include bacterial ATP-dependent
phosphofructokinases. These are allosrterically
regulated homotetramers; the subunits are of about 320
amino acids.
Length = 317
Score = 27.8 bits (62), Expect = 3.1
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 89 KMGFPEIILPGDVRNDLYVT 108
+ GFP + LPG + ND+ T
Sbjct: 113 EHGFPCVGLPGTIDNDIPGT 132
>gnl|CDD|216547 pfam01518, PolyG_pol, Sigma NS protein. This viral protein has a
poly(C)-dependent poly(G) polymerase activity.
Length = 366
Score = 27.9 bits (62), Expect = 3.2
Identities = 16/73 (21%), Positives = 24/73 (32%), Gaps = 11/73 (15%)
Query: 21 VRPLSP--YHSVVKLCEKDNLENTLKRLISSLKDISSQKSAGMYVSLKFHCGDNKTESVA 78
++ LSP + + N+E L R I +D SL H GD +
Sbjct: 54 LKCLSPLQAAKRDRTLRQRNVERILTRDIKQTRD---------LHSLCHHTGDAPMSTHQ 104
Query: 79 VAMTNTFIARKMG 91
A + G
Sbjct: 105 AAEAARLVCSYFG 117
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
This domain is found to the N-terminus of bacterial
signal peptidases of the S49 family (pfam01343).
Length = 154
Score = 27.1 bits (61), Expect = 3.6
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 4 QKKKKKKKKKKKKKKKN 20
+K +KK +K K K +K
Sbjct: 72 EKAEKKAEKAKAKAEKK 88
Score = 26.7 bits (60), Expect = 4.9
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 4 QKKKKKKKKKKKKKKKNV 21
+KK +K K K +KKK
Sbjct: 75 EKKAEKAKAKAEKKKAKK 92
Score = 26.0 bits (58), Expect = 9.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 4 QKKKKKKKKKKKKKKK 19
+KK +K K K +KKK
Sbjct: 74 AEKKAEKAKAKAEKKK 89
>gnl|CDD|241511 cd13357, PH-GRAM_MTMR2_insect-like, Myotubularian related 2 protein
(MTMR2) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR2 is a member of the myotubularin protein
phosphatase gene family. MTMR2 binds to phosphoinositide
lipids through its PH-GRAM domain, and can hydrolyze
phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro.
Mutations in MTMR2 are a cause of Charcot-Marie-Tooth
disease type 4B, an autosomal recessive demyelinating
neuropathy. The protein can self-associate and form
heteromers with MTMR5 and MTMR12. MTMR2 contains a
N-terminal PH-GRAM domain, a Rac-induced recruitment
domain (RID) domain, an active PTP domain, a
SET-interaction domain, a coiled-coil region, and a
C-terminal PDZ domain. Myotubularin-related proteins are
a subfamily of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs
5, 9-13) contain naturally occurring substitutions of
residues required for catalysis by PTP family enzymes.
Although these proteins are predicted to be
enzymatically inactive, they are thought to function as
antagonists of endogenous phosphatase activity or
interaction modules. Most MTMRs contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, a PTP domain (which may be active or inactive),
a SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date. Members in this cd include Drosophila,
sea urchins, mosquitos, bees, ticks, and anemones.
Length = 148
Score = 27.0 bits (60), Expect = 3.8
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 99 GDVRNDLYVTLVNAEFKSSDKTIQVTVQVCTEAGVILKV 137
G VR L +T F+S DK V V GVI +V
Sbjct: 32 GPVRGTLTITNYKLYFRSLDKEPPFIVDV--PLGVIYRV 68
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 27.0 bits (60), Expect = 4.2
Identities = 13/20 (65%), Positives = 17/20 (85%)
Query: 4 QKKKKKKKKKKKKKKKNVRP 23
++KK+KKKKKKKKKKK +
Sbjct: 110 KQKKQKKKKKKKKKKKTSKK 129
>gnl|CDD|218148 pfam04557, tRNA_synt_1c_R2, Glutaminyl-tRNA synthetase,
non-specific RNA binding region part 2. This is a
region found N terminal to the catalytic domain of
glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes
but not in Escherichia coli. This region is thought to
bind RNA in a non-specific manner, enhancing
interactions between the tRNA and enzyme, but is not
essential for enzyme function.
Length = 83
Score = 25.8 bits (57), Expect = 4.9
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 3 VQKKKKKKKKKKKKKKKNV 21
+ KKKKKKKKKK +
Sbjct: 22 LVKKKKKKKKKKAEDTAAT 40
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both
non-LTR retrotransposons and non-LTR retrovirus RTs.
RTs catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA
polymerase and ribonuclease hybrid (RNase H)
activities.
Length = 220
Score = 26.9 bits (60), Expect = 5.4
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 10 KKKKKKKKKKNVRPLSPYHSVVKLCEK---DNLENTLKRLIS 48
KK K KN RP+S + KL EK + L L+ I
Sbjct: 8 PKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENIL 49
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 26.9 bits (60), Expect = 6.0
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 4 QKKKKKKKKKKKKKKKNVR 22
K KKKK K K K NV
Sbjct: 200 AAKGGKKKKGKAKAKLNVG 218
>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional.
Length = 470
Score = 27.0 bits (60), Expect = 6.1
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 4 QKKKKKKKKKKKKKKKNVRPLSP-YHSVVKLCEKDNLENTLKRLISS 49
KKKKKKKKKKKKK Y V +N+ R + +
Sbjct: 55 NNKKKKKKKKKKKKKNLGEAYDLAYDLPVVWSSAAFQDNSHIRKLGN 101
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 26.9 bits (60), Expect = 6.2
Identities = 13/15 (86%), Positives = 13/15 (86%)
Query: 7 KKKKKKKKKKKKKNV 21
KKKKKKKKKK KKN
Sbjct: 182 KKKKKKKKKKTKKNN 196
Score = 26.2 bits (58), Expect = 9.3
Identities = 13/15 (86%), Positives = 13/15 (86%)
Query: 6 KKKKKKKKKKKKKKN 20
KKKKKKKKKK KK N
Sbjct: 182 KKKKKKKKKKTKKNN 196
>gnl|CDD|212664 cd07792, FGGY_GK1-3_metazoa, Metazoan glycerol kinase 1 and 3-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
metazoan glycerol kinases (GKs), coded by X
chromosome-linked GK genes, and glycerol kinase
(GK)-like proteins, coded by autosomal testis-specific
GK-like genes (GK-like genes, GK1 and GK3). Sequence
comparison shows that metazoan GKs and GK-like proteins
in this family are closely related to the bacterial GKs,
which catalyze the Mg-ATP dependent phosphorylation of
glycerol to yield glycerol 3-phosphate (G3P). The
metazoan GKs do have GK enzymatic activity. However, the
GK-like metazoan proteins do not exhibit GK activity and
their biological functions are not yet clear. Some of
them lack important functional residues involved in the
binding of ADP and Mg2+, which may result in the loss of
GK catalytic function. Others that have conserved
catalytic residues have lost their GK activity as well;
the reason remains unclear. It has been suggested the
conserved catalytic residues might facilitate them
performing a distinct function. GKs belong to the FGGY
family of carbohydrate kinases, the monomers of which
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 504
Score = 26.9 bits (60), Expect = 6.9
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 11 KKKKKKKKKNVR-----PLSPYHSVVKLC-EKDNLEN 41
K K K ++ P+S Y S VKL DN+
Sbjct: 118 AKIPDKNKNYLKSICGLPISTYFSAVKLRWLLDNVPE 154
>gnl|CDD|240576 cd12932, RRP7_like, RRP7 domain ribosomal RNA-processing protein
7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A
(Rrp7A), and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by
YCL031C gene from Saccharomyces cerevisiae. It is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. Rrp7A, also termed gastric cancer antigen
Zg14, is the Rrp7p homolog mainly found in Metazoans.
The cellular function of Rrp7A remains unclear
currently. Both Rrp7p and Rrp7A harbor an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal RRP7 domain.
Length = 118
Score = 26.1 bits (58), Expect = 6.9
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 5 KKKKKKKKKKKKKKKN 20
K+K+KKKKKKK+ ++
Sbjct: 75 AKEKEKKKKKKKELED 90
>gnl|CDD|188353 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC
transporter, lactococcin 972 group. A gene pair with a
fairly wide distribution consists of a polypeptide
related to the lactococcin 972 (see TIGR01653) and
multiple-membrane-spanning putative immunity protein
(see TIGR01654). This model represents a small clade
within the ABC transporters that regularly are found
adjacent to these bacteriocin system gene pairs and are
likely serve as export proteins [Cellular processes,
Toxin production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 206
Score = 26.4 bits (59), Expect = 6.9
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 12/55 (21%)
Query: 5 KKKKKKKKKKKKKKKNVRPLSPYHSVVKLCEKDNLENTLKRLISSLKDISSQKSA 59
K KK KK+K++KKK EK L LK+ I L Q+ A
Sbjct: 102 KYKKLSKKEKREKKKEA------------LEKVGLNLKLKQKIYELSGGEQQRVA 144
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 26.4 bits (59), Expect = 7.0
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 3 VQKKKKKKKKKKKKKKKNV 21
+K KK+K+K++K+ +K
Sbjct: 17 AKKAKKEKRKQRKQARKGA 35
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase components
[Carbohydrate transport and metabolism].
Length = 338
Score = 26.8 bits (60), Expect = 7.0
Identities = 13/98 (13%), Positives = 36/98 (36%), Gaps = 11/98 (11%)
Query: 83 NTFIARKMGFPEI-ILPGDVRNDLYVTLVNAEFKSSDKTIQVTV-----QVCTEAGVILK 136
N F+A +G P + L +V+ D + + K + + + + + + ++
Sbjct: 227 NLFVAGFIGSPPMNFLKAEVKADGNGLSIPEDKKVALEQVILGIRPEHISLSASGIILGT 286
Query: 137 V-NAEFKSSDKTIQVT----VQVCTEAGVILKAHDQFW 169
V E S+ + V ++ ++ ++
Sbjct: 287 VEVVEPLGSETIVYVRLGGELKARVPEDSKIEPGEEVR 324
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 26.5 bits (59), Expect = 7.3
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 37 DNLENTLKRLISSLKDISSQK 57
D+LE+ LK+L +L+ + +Q+
Sbjct: 34 DSLESQLKKLYKALELLVNQR 54
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 26.7 bits (59), Expect = 7.6
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 5 KKKKKKKKKKKKKKKNVRPLSP 26
KKK K K KK KK+ +P
Sbjct: 769 KKKSKAKSKKTTKKRAGPLYTP 790
>gnl|CDD|197876 smart00792, Agouti, Agouti protein. The agouti protein regulates
pigmentation in the mouse hair follicle producing a
black hair with a subapical yellow band. A highly
homologous protein agouti signal protein (ASIP) is
present in humans and is expressed at highest levels in
adipose tissue where it may play a role in energy
homeostasis and possibly human pigmentation.
Length = 124
Score = 26.0 bits (57), Expect = 7.6
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 4 QKKKKKKKKKKKKKKKNV---RPLSP 26
+ +KK +KK+KK NV P SP
Sbjct: 61 EAEKKLLQKKEKKALTNVLRPEPRSP 86
>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p
homolog [Translation, ribosomal structure and
biogenesis].
Length = 395
Score = 26.6 bits (59), Expect = 7.6
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 3 VQKKKKKKKKKKKKKKKNVRPLS 25
++ KK++ + ++KKK + S
Sbjct: 366 PERDKKERPGRYRRKKKEKKAKS 388
>gnl|CDD|222918 PHA02687, PHA02687, ORF061 late transcription factor VLTF-4;
Provisional.
Length = 231
Score = 26.5 bits (58), Expect = 7.6
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 8 KKKKKKKKKKKKNVRPLSPYHSVVKLCEKDNLENTL 43
K K++ KKK K +P +V KLC D+ ++
Sbjct: 84 KTPKRRTKKKAKADKPEKSPKAVEKLCPPDDRDDKN 119
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
0.315 0.128 0.357
Gapped
Lambda K H
0.267 0.0603 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,014,669
Number of extensions: 699960
Number of successful extensions: 4310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3681
Number of HSP's successfully gapped: 318
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
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: 55 (25.2 bits)