RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10107
(140 letters)
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 75.2 bits (186), Expect = 2e-19
Identities = 21/40 (52%), Positives = 26/40 (65%)
Query: 22 WLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61
WL EH NPYP++ EK LA T ++ Q+ WF NARRR
Sbjct: 1 WLLEHLHNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 57.3 bits (139), Expect = 4e-12
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 12 TEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
T L+ +KNPYP++ E+ LA +T QV WF N R +LK+
Sbjct: 8 TPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 54.2 bits (131), Expect = 6e-11
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 12 TEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
T L+ +KNPYP++ E+ LA ++ QV WF N R + K
Sbjct: 9 TPEQLEELEKEF---QKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 42.1 bits (100), Expect = 2e-06
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+KN YP+ E+ LA +T QV WF N R + K+
Sbjct: 20 EKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 39.7 bits (93), Expect = 1e-04
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 25 EHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
E + NPYP+ +I L+++ M V WF N R + KK+
Sbjct: 69 EFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111
>gnl|CDD|189002 cd09595, M1, Peptidase M1 family contains aminopeptidase N and
leukotriene A4 hydrolase. M1 Peptidase family includes
aminopeptidase N (APN) and leukotriene A4 hydrolase
(LTA4H). All peptidases in this family bind a single
catalytic zinc ion which is tetrahedrally co-ordinated
by three amino acid ligands and a water molecule that
forms the nucleophile on activation during catalysis.
APN consists of a small N-terminal cytoplasmic domain, a
single transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and is present in a variety
of human tissues and cell types. APN expression is
dysregulated in many inflammatory diseases and is
enhanced in numerous tumor cells, making it a lead
target in the development of anti-cancer and
anti-inflammatory drugs. LTA4H is a bifunctional enzyme,
possessing an aminopeptidase as well as an epoxide
hydrolase activity. The two activities occupy different,
but overlapping sites. The activity and physiological
relevance of the aminopeptidase in LTA4H is as yet
unknown while the epoxide hydrolase converts leukotriene
A4 (LTA4) into leukotriene B4 (LTB4), a potent
chemotaxin that is fundamental to the inflammatory
response of mammals.
Length = 407
Score = 29.3 bits (66), Expect = 0.60
Identities = 4/27 (14%), Positives = 14/27 (51%)
Query: 1 MFMNMVPEYVGTEIYKATLKAWLNEHK 27
+ + + + +G E + L+ ++ +H
Sbjct: 366 LVLRYLEKRLGDEAFFKGLRKYVEKHA 392
>gnl|CDD|220631 pfam10210, MRP-S32, Mitochondrial 28S ribosomal protein S32.
This entry is of a family of short, approximately 100
amino acid residues, proteins which are mitochondrial
28S ribosomal proteins named as MRP-S32. Their exact
function could not be confirmed.
Length = 96
Score = 27.8 bits (62), Expect = 0.77
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 12 TEIYKATLKAWLNEHK-KNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68
E ++ LK L + K K+P P + E ++K+ T W+ R R K+
Sbjct: 42 AETHEQVLKTALEKFKHKHPEPMREE------LSKVFFTTKHRWYPRGRDRRAKKTPP 93
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 28.8 bits (64), Expect = 0.98
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 57 NARRRLKKENKMTWEPKNKTDDDDDAIISDCDEKDKDDLMMDEE 100
NA R+L KE + + D++DD D DE D DD +++
Sbjct: 36 NAIRKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDD 79
>gnl|CDD|223857 COG0786, GltS, Na+/glutamate symporter [Amino acid transport and
metabolism].
Length = 404
Score = 28.4 bits (64), Expect = 1.2
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 60 RRLKKENKMTWEPKNKTDDDDDAIISDCDEKDKDDLMMDEEKMKQHHRMVKAVLGTSSIL 119
R L K+NK+ +P DDD + E K ++ E + + ++ L I+
Sbjct: 181 RWLIKKNKLKPDPTKDPDDDLVDVAF---EGPKSTRLITAEPLIETLAIIAICLAVGKII 237
Query: 120 T 120
Sbjct: 238 N 238
>gnl|CDD|236544 PRK09506, mrcB, bifunctional glycosyl transferase/transpeptidase;
Reviewed.
Length = 830
Score = 28.2 bits (63), Expect = 1.6
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 53 TWFANARRRLKKENKMTWEPKN 74
TW A+A L++ N W P+N
Sbjct: 529 TWIADAPISLRQPNGQVWSPQN 550
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 27.8 bits (62), Expect = 2.2
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 68 MTWEPKNKTDDDDDAIISD-CDEKDKDDLMMDEEKMKQHHRMVKAVLGTSSILTFPCSIV 126
M + K T D ++ D C+EK + DL + EK + ++ AVL S I
Sbjct: 156 MVKDEKTGTCFRADHLLKDFCEEKLEKDLTISAEKAAELKDVL-AVLDDLSAEELGAKIK 214
Query: 127 KLTI--PGNGSP 136
+ I P +P
Sbjct: 215 EYGIKAPDTKNP 226
>gnl|CDD|163260 TIGR03432, yjhG_yagF, putative dehydratase, YjhG/YagF family. This
homolog of dihydroxy-acid dehydratases has an odd,
sparse distribution. Members are found in two
Acidobacteria, two Planctomycetes, Bacillus clausii
KSM-K16, and (in two copies each) in strains K12-MG1655
and W3110 of Escherichia coli. The local context is not
well conserved, but a few members are adjacent to
homologs of the gluconate:H+ symporter (see TIGR00791)
[Unknown function, Enzymes of unknown specificity].
Length = 640
Score = 27.5 bits (61), Expect = 2.6
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 28/82 (34%)
Query: 43 ITKMTLTQVSTWFANARRR--LKKENKMTWEPKNKTDDDDDAIISDCDEKDKDDLMMDEE 100
+T TL + W+ N+ RR +K+ + + D D DD++M
Sbjct: 379 VTGETLGENLDWWENSERRARMKQR------------------LRERDGVDPDDVIMSPA 420
Query: 101 KMKQHHRMVKAVLGTSSILTFP 122
+ K G +S +TFP
Sbjct: 421 QAKAR--------GLTSTVTFP 434
>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional.
Length = 80
Score = 25.9 bits (57), Expect = 3.1
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 71 EPKNKTDDDDDAIISDCDEKDKDDLMMDEE 100
EP++ DD+DD D D+KD DD DE+
Sbjct: 49 EPEDDDDDEDDDDDDDKDDKDDDDDDDDED 78
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 27.0 bits (60), Expect = 3.3
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 77 DDDDDAIISDCDEKDKDDLMMDEE 100
DDD+DAI SD D+ D D D E
Sbjct: 259 DDDEDAIESDLDDSDDDVSDEDGE 282
>gnl|CDD|218661 pfam05622, HOOK, HOOK protein. This family consists of several
HOOK1, 2 and 3 proteins from different eukaryotic
organisms. The different members of the human gene
family are HOOK1, HOOK2 and HOOK3. Different domains
have been identified in the three human HOOK proteins,
and it was demonstrated that the highly conserved
NH2-domain mediates attachment to microtubules, whereas
the central coiled-coil motif mediates homodimerisation
and the more divergent C-terminal domains are involved
in binding to specific organelles (organelle-binding
domains). It has been demonstrated that endogenous HOOK3
binds to Golgi membranes, whereas both HOOK1 and HOOK2
are localised to discrete but unidentified cellular
structures. In mice the Hook1 gene is predominantly
expressed in the testis. Hook1 function is necessary for
the correct positioning of microtubular structures
within the haploid germ cell. Disruption of Hook1
function in mice causes abnormal sperm head shape and
fragile attachment of the flagellum to the sperm head.
Length = 713
Score = 27.1 bits (60), Expect = 4.1
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 38 IMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKNKTDDDDDAIISDCDEKDKDDLMM 97
+M AI M+ Q S+ + L ++ K E + ++ D + C E DK L++
Sbjct: 146 VMTAIQELMSKEQGSSPSRESAGNLDQQLKKALEDLKEAQEEKDELAQRCHELDKQVLLL 205
Query: 98 DEEK--MKQHHRMVKAVLG 114
EEK ++Q + ++ L
Sbjct: 206 QEEKNSLQQENEKLQERLA 224
>gnl|CDD|203444 pfam06424, PRP1_N, PRP1 splicing factor, N-terminal. This domain
is specific to the N-terminal part of the prp1 splicing
factor, which is involved in mRNA splicing (and possibly
also poly(A)+ RNA nuclear export and cell cycle
progression). This domain is specific to the N terminus
of the RNA splicing factor encoded by prp1. It is
involved in mRNA splicing and possibly also poly(A)and
RNA nuclear export and cell cycle progression.
Length = 131
Score = 26.1 bits (58), Expect = 4.7
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 56 ANARRRLKKENKMTWEPKNKTDDDDDAIISDCDEKDKDDLMMD------EEKMKQHHR 107
AR + +++ +PK D D++ + SD + D +D D +E+M + +
Sbjct: 23 GPARDGVDIDDEEDEDPKRYQDGDNEGLFSD-GKYDDEDEEADRIYESIDERMDERRK 79
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 26.7 bits (59), Expect = 4.8
Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 1/59 (1%)
Query: 2 FMNMVPEYVGTEIYKATLKAWLNEHK-KNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59
+ M+ +G E ++ L + H N K + K +W + A
Sbjct: 406 VLRMLETLLGEEAFRKGLSLYFKRHAGGNATTMDLWKALEDASGKDLSAFFESWLSQAG 464
>gnl|CDD|173635 cd05054, PTKc_VEGFR, Catalytic domain of the Protein Tyrosine
Kinases, Vascular Endothelial Growth Factor Receptors.
Protein Tyrosine Kinase (PTK) family; Vascular
Endothelial Growth Factor Receptor (VEGFR) subfamily;
catalytic (c) domain. The VEGFR subfamily consists of
VEGFR1 (Flt1), VEGFR2 (Flk1), VEGFR3 (Flt4), and similar
proteins. The PTKc family is part of a larger
superfamily that includes the catalytic domains of other
kinases such as protein serine/threonine kinases, RIO
kinases, and phosphoinositide 3-kinase (PI3K). PTKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to tyrosine (tyr) residues in protein substrates.
VEGFR subfamily members are receptor tyr kinases (RTKs)
containing an extracellular ligand-binding region with
seven immunoglobulin (Ig)-like domains, a transmembrane
segment, and an intracellular catalytic domain. In
VEGFR3, the fifth Ig-like domain is replaced by a
disulfide bridge. The binding of VEGFRs to their
ligands, the VEGFs, leads to receptor dimerization,
activation, and intracellular signaling. There are five
VEGF ligands in mammals, which bind, in an overlapping
pattern to the three VEGFRs, which can form homo or
heterodimers. VEGFRs regulate the cardiovascular system.
They are critical for vascular development during
embryogenesis and blood vessel formation in adults. They
induce cellular functions common to other growth factor
receptors such as cell migration, survival, and
proliferation. VEGFR1 binds VEGFA, VEGFB, and placenta
growth factor (PLGF). It regulates monocyte and
macrophage migration, vascular permeability,
haematopoiesis, and the recruitment of haematopietic
progenitor cells from the bone marrow.
Length = 337
Score = 26.4 bits (58), Expect = 6.0
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 7 PEYVGTEIYKATLKAWLNEHKKNPYPTK 34
PEY EIY L W N + P ++
Sbjct: 298 PEYATPEIYSIMLDCWHNNPEDRPTFSE 325
>gnl|CDD|237835 PRK14850, PRK14850, penicillin-binding protein 1b; Provisional.
Length = 764
Score = 26.3 bits (58), Expect = 7.5
Identities = 9/37 (24%), Positives = 18/37 (48%)
Query: 38 IMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 74
L +++ ++TW ++ +K +N W PKN
Sbjct: 460 TYLTALSQPEKYHLNTWISDTPISIKLDNGQYWTPKN 496
>gnl|CDD|173576 PTZ00384, PTZ00384, choline kinase; Provisional.
Length = 383
Score = 25.9 bits (57), Expect = 7.8
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 44 TKMTLTQVSTWFANARRRLKKEN 66
T M LT++STW + R +KK N
Sbjct: 172 TPMFLTKISTWSQHVERIIKKYN 194
>gnl|CDD|189010 cd09603, M1_APN_4, Peptidase M1 family Aminopeptidase N. This
family contains mostly bacterial and some archaeal
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN consists of a
small N-terminal cytoplasmic domain, a single
transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and, in higher eukaryotes,
is present in a variety of human tissues and cell types
(leukocyte, fibroblast, endothelial and epithelial
cells). APN expression is dysregulated in inflammatory
diseases such as chronic pain, rheumatoid arthritis,
multiple sclerosis, systemic sclerosis, systemic lupus
erythematosus, polymyositis/dermatomyosytis and
pulmonary sarcoidosis, and is enhanced in tumor cells
such as melanoma, renal, prostate, pancreas, colon,
gastric and thyroid cancers. It is predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 415
Score = 26.0 bits (58), Expect = 8.1
Identities = 6/27 (22%), Positives = 15/27 (55%)
Query: 1 MFMNMVPEYVGTEIYKATLKAWLNEHK 27
+ ++ + +G E + L+ +L EH+
Sbjct: 354 LVLHALRRLLGDEAFFRLLRTYLAEHR 380
>gnl|CDD|133234 cd05103, PTKc_VEGFR2, Catalytic domain of the Protein Tyrosine
Kinase, Vascular Endothelial Growth Factor Receptor 2.
Protein Tyrosine Kinase (PTK) family; Vascular
Endothelial Growth Factor Receptor 2 (VEGFR2); catalytic
(c) domain. The PTKc family is part of a larger
superfamily that includes the catalytic domains of other
kinases such as protein serine/threonine kinases, RIO
kinases, and phosphoinositide 3-kinase (PI3K). PTKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to tyrosine (tyr) residues in protein substrates.
VEGFR2 (or Flk1) is a member of the VEGFR subfamily of
proteins, which are receptor tyr kinases (RTKs)
containing an extracellular ligand-binding region with
seven immunoglobulin (Ig)-like domains, a transmembrane
segment, and an intracellular catalytic domain. The
binding of VEGFRs to their ligands, the VEGFs, leads to
receptor dimerization, activation, and intracellular
signaling. The carboxyl terminus of VEGFR2 plays an
important role in its autophosphorylation and
activation. VEGFR2 binds the ligands VEGFA, VEGFC, VEGFD
and VEGFE. VEGFR2 signaling is implicated in all aspects
of normal and pathological vascular endothelial cell
biology. It induces a variety of cellular effects
including migration, survival, and proliferation. It is
critical in regulating embryonic vascular development
and angiogenesis. VEGFR2 is the major signal transducer
in pathological angiogenesis including cancer and
diabetic retinopathy, and is a target for inhibition in
cancer therapy.
Length = 343
Score = 26.1 bits (57), Expect = 8.2
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 7 PEYVGTEIYKATLKAWLNEHKKNP 30
P+Y E+Y+ L W E + P
Sbjct: 304 PDYTTPEMYQTMLDCWHGEPSQRP 327
>gnl|CDD|152005 pfam11569, Homez, Homeodomain leucine-zipper encoding, Homez.
Homez contains two leucine zipper-like motifs and an
acidic domain and belongs to the superfamily of
homeobox-containing proteins. The presence of leucine
zippers suggests that Homez can function as a homo or
heterodimer in the nucleus. It is thought that the
first leucine zipper and homeodomain 1 (HD1)of Homez is
responsible for dimerisation and HD2 has a specific
DNA-binding activity. Homez is also thought to function
as a transcriptional repressor due to the acidic region
in its C-terminal domain. Homez is involved in a
complex regulatory network.
Length = 57
Score = 24.3 bits (53), Expect = 8.9
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 44 TKMTLTQVSTWFA 56
+ M+ QV WFA
Sbjct: 36 SGMSYEQVRDWFA 48
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
0.316 0.131 0.398
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,005,375
Number of extensions: 606092
Number of successful extensions: 697
Number of sequences better than 10.0: 1
Number of HSP's gapped: 683
Number of HSP's successfully gapped: 39
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.6 bits)