RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2972
(143 letters)
>gnl|CDD|130398 TIGR01331, bisphos_cysQ, 3'(2'),5'-bisphosphate nucleotidase,
bacterial. Sulfate is incorporated into
3-phosphoadenylylsulfate, PAPS, for utilization in
pathways such as methionine biosynthesis. Transfer of
sulfate from PAPS to an acceptor leaves adenosine
3'-5'-bisphosphate, APS. This model describes a form
found in bacteria of the enzyme 3'(2'),5'-bisphosphate
nucleotidase, which removes the 3'-phosphate from APS to
regenerate AMP and help drive the cycle [Central
intermediary metabolism, Sulfur metabolism].
Length = 249
Score = 28.2 bits (63), Expect = 1.3
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 15/79 (18%)
Query: 45 GQSIMCCIQADNKKFDIVISPKNTRVSDLKRTIERQITMQMK----------RKGLSKQI 94
G+ I+ Q K+ + N+ V++ R R I ++ + S +
Sbjct: 13 GEEILPVYQ---KELAVAQKADNSPVTEADRAAHRFILEGLRALTPDIPVLSEEDASIPL 69
Query: 95 SWRHVWKSYWL--SFDGIK 111
+ R W+ +WL DG K
Sbjct: 70 TPRQTWQRFWLVDPLDGTK 88
>gnl|CDD|241264 cd01230, PH1_Tiam1_2, T-lymphoma invasion and metastasis 1 and 2
Pleckstrin Homology (PH) domain, N-terminal domain.
Tiam1 activates Rac GTPases to induce membrane ruffling
and cell motility while Tiam2 (also called STEF (SIF
(still life) and Tiam1 like-exchange factor) contributes
to neurite growth. Tiam1/2 are Dbl-family of GEFs that
possess a Dbl(DH) domain with a PH domain in tandem.
DH-PH domain catalyzes the GDP/GTP exchange reaction in
the GTPase cycle and facillitating the switch between
inactive GDP-bound and active GTP-bound states. Tiam1/2
possess two PH domains, which are often referred to as
PHn and PHc domains. The DH-PH tandem domain is made up
of the PHc domain while the PHn is part of a novel
N-terminal PHCCEx domain which is made up of the PHn
domain, a coiled coil region(CC), and an extra region
(Ex). PHCCEx mediates binding to plasma membranes and
signalling proteins in the activation of Rac GTPases.
The PH domain resembles the beta-spectrin PH domain,
suggesting non-canonical phosphatidylinositol binding.
CC and Ex form a positively charged surface for protein
binding. There are 2 motifs in Tiam1/2-interacting
proteins that bind to the PHCCEx domain: Motif-I in
CD44, ephrinBs, and the NMDA receptor and Motif-II in
Par3 and JIP2.Neither of these fall in the PHn domain.
PH domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 127
Score = 27.8 bits (62), Expect = 1.4
Identities = 9/40 (22%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 87 RKGLSKQISWRHVWKSYWLSFDGIKL----TNEKSLLSEL 122
+K +++ R WK YW++ G L +E++ + +
Sbjct: 18 KKKKKLELASRRKWKKYWVTLKGCTLLFYECDERTGIDDN 57
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 28.4 bits (64), Expect = 1.4
Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 6/92 (6%)
Query: 1 MKDLDQLLTETKEAIKNIRTQNTLSHLPQDVTVEEIKSEMELLHGQSIMCCIQADNKKFD 60
+D DQ + E I ++ L L E I M + ++ + ++ D
Sbjct: 319 PEDTDQWVELADENNNLIALEHPLEALALAAEAELILDAM-----EDLVQHLGLPDEYQD 373
Query: 61 IVISPKNTRVSDLKRTIERQITMQMKRKGLSK 92
++ +++D ++T+ ++ Q+K++
Sbjct: 374 LIKQ-LKEQLTDPEKTLSGRLLKQIKQESYVA 404
>gnl|CDD|217527 pfam03387, Herpes_UL46, Herpesvirus UL46 protein.
Length = 443
Score = 28.1 bits (63), Expect = 1.5
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 85 MKRKGLSKQISWRHVWKSYW 104
+ R GLSK WR SYW
Sbjct: 93 LARAGLSKDAVWRAYLASYW 112
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 26.8 bits (60), Expect = 1.5
Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 17/83 (20%)
Query: 53 QADNKKFDIVISPKNTRVSDLKRTIERQITMQMKRKGLSKQISWRHVWKSYWLSFDGIKL 112
D K + + P +T VS+LK I + +++ L + G L
Sbjct: 7 TLDGKTITLEVKPSDT-VSELKEKIAELTGIPPEQQ---------------RLIYKGKVL 50
Query: 113 TNEKSLLSELGIESQCEITFVKR 135
++++L ++ GI+ I V R
Sbjct: 51 EDDRTL-ADYGIQDGSTIHLVLR 72
>gnl|CDD|176405 cd01810, ISG15_repeat2, ISG15 ubiquitin-like protein, second repeat
of 2. ISG15 is a ubiquitin-like protein containing two
ubiquitin homology domains and becomes conjugated to a
variety of proteins when cells are treated with type I
interferon or lipopolysaccharide. Although ISG15 has
properties similar to those of other ubiquitin-like
molecules, it is a unique member of the ubiquitin-like
superfamily, whose expression and conjugation to target
proteins are tightly regulated by specific signaling
pathways, indicating it may have specialized functions
in the immune system.
Length = 74
Score = 26.8 bits (59), Expect = 1.8
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 90 LSKQISWRHVWKS--YWLSFDGIKLTNEKSLLSELGIESQCEITFVKRLK 137
L +Q+S R ++ +WLSF+G + ++ L E G++ C + RL+
Sbjct: 24 LKQQVSQRERVQADQFWLSFEG-RPMEDEHPLGEYGLKPGCTVFMNLRLR 72
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 27.7 bits (62), Expect = 2.7
Identities = 9/37 (24%), Positives = 15/37 (40%)
Query: 59 FDIVISPKNTRVSDLKRTIERQITMQMKRKGLSKQIS 95
F+I I P R D+ + ++ KR +I
Sbjct: 488 FEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKID 524
>gnl|CDD|185087 PRK15133, PRK15133, microcin C ABC transporter permease YejB;
Provisional.
Length = 364
Score = 27.0 bits (60), Expect = 3.4
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 77 IERQITMQMKRKGLS-KQISWRHVWKSYWL 105
I +Q + + KG+S K I W+HV+++ L
Sbjct: 255 IRKQYVVTARAKGVSEKNILWKHVFRNAML 284
>gnl|CDD|214594 smart00273, ENTH, Epsin N-terminal homology (ENTH) domain.
Length = 127
Score = 26.4 bits (59), Expect = 3.7
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 83 MQMKRKGLSKQISWRHVWKS 102
M + + L+ +WR V+K+
Sbjct: 41 MAVLWRRLNDTKNWRVVYKA 60
>gnl|CDD|225251 COG2376, DAK1, Dihydroxyacetone kinase [Carbohydrate transport and
metabolism].
Length = 323
Score = 26.1 bits (58), Expect = 7.0
Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 3/46 (6%)
Query: 3 DLDQLLTETKEAIKNIRT---QNTLSHLPQDVTVEEIKSEMELLHG 45
LD++ +AI N + T +P E L HG
Sbjct: 169 SLDEVKAVALKAIDNAASIGVALTPCTVPTKGRASLGLGERSLGHG 214
>gnl|CDD|240716 cd12270, RRM_MTHFSD, RNA recognition motif in vertebrate
methenyltetrahydrofolate synthetase domain-containing
proteins. This subfamily corresponds to
methenyltetrahydrofolate synthetase domain (MTHFSD), a
putative RNA-binding protein found in various
vertebrate species. It contains an N-terminal
5-formyltetrahydrofolate cyclo-ligase domain and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The biological role of MTHFSD remains unclear. .
Length = 74
Score = 25.0 bits (55), Expect = 7.2
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 65 PKNTRVSDLKRTI-ERQIT-MQMKRKG 89
+N RVSDLK + ER + +++ +G
Sbjct: 8 SRNLRVSDLKSALRERGVKPLRITWQG 34
>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 = 24.9 bits (55), Expect = 7.5
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 17/83 (20%)
Query: 55 DNKKFDIVISPKNTRVSDLKRTIERQITMQMKRKGLSKQISWRHVWKSYWLSFDGIKLTN 114
D K + + P +T VS+LK IE + + + + L F G L +
Sbjct: 4 DGKTITLEVDPSDT-VSELKEKIEDKEGIPVDQ---------------QRLIFSGKVLED 47
Query: 115 EKSLLSELGIESQCEITFVKRLK 137
+ +L SE GI+ + V RL+
Sbjct: 48 DTTL-SEYGIQDGSTLHLVLRLR 69
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 0.372
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,949,473
Number of extensions: 596918
Number of successful extensions: 645
Number of sequences better than 10.0: 1
Number of HSP's gapped: 645
Number of HSP's successfully gapped: 38
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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 (21.7 bits)
S2: 54 (24.6 bits)