RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13820
(487 letters)
>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
Present in two copies in mammalian adenylyl cyclases.
Eubacterial homologues are known. Two residues (Asn,
Arg) are thought to be involved in catalysis. These
cyclases have important roles in a diverse range of
cellular processes.
Length = 194
Score = 267 bits (684), Expect = 7e-88
Identities = 104/186 (55%), Positives = 135/186 (72%), Gaps = 3/186 (1%)
Query: 139 IEKKKTEQLLNRMLPSSVAEKLKLG-MPVDPEDFREVTIYFSDIVGFTTISAYSTPFEVV 197
EKKKT++LL+++LP+SVAE+LK G PV E + VTI FSDIVGFT++ + STP +VV
Sbjct: 1 EEKKKTDRLLDQLLPASVAEQLKRGGSPVPAESYDNVTILFSDIVGFTSLCSTSTPEQVV 60
Query: 198 DLLNDLYTCFDATINAYNVYKVETIGDAYMVVGGLPVR-IPDHADQIATMALDLLHHSGR 256
+LLNDLY+ FD I+ + YKV+TIGDAYMV GLP + DHA+ IA ALD++
Sbjct: 61 NLLNDLYSRFDQIIDRHGGYKVKTIGDAYMVASGLPEEALVDHAELIADEALDMVEELKT 120
Query: 257 FKIRHLPYTPLRLRIGLHTGPCCAGVVGLTMPRYCLFGDTVNTASRLESTGAPWRIHLSA 316
++H LR+RIG+HTGP AGVVG+ MPRYCLFGDTVN ASR+ES G P +I +S
Sbjct: 121 VLVQH-REEGLRVRIGIHTGPVVAGVVGIRMPRYCLFGDTVNLASRMESAGDPGQIQVSE 179
Query: 317 DTKAKL 322
+T + L
Sbjct: 180 ETYSLL 185
>gnl|CDD|201086 pfam00211, Guanylate_cyc, Adenylate and Guanylate cyclase catalytic
domain.
Length = 184
Score = 259 bits (665), Expect = 3e-85
Identities = 95/186 (51%), Positives = 122/186 (65%), Gaps = 2/186 (1%)
Query: 166 VDPEDFREVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGDA 225
V + + VTI F+DIVGFT +S+ +P E+V LLNDLYT FD ++ + VYKV+TIGDA
Sbjct: 1 VYAQSYDNVTILFADIVGFTALSSRHSPEELVRLLNDLYTRFDELLDKHGVYKVKTIGDA 60
Query: 226 YMVVGGLPVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGPCCAGVVGL 285
YM GLP P HA +A MALD+L I LR+R+G+HTGP AGV+G
Sbjct: 61 YMAASGLPEPSPAHAQTLAEMALDMLEAIKSVNIHSFE--GLRVRVGIHTGPVVAGVIGA 118
Query: 286 TMPRYCLFGDTVNTASRLESTGAPWRIHLSADTKAKLDQVGDYQLEYRGETELKGKGKMP 345
PRY ++GDTVN ASR+ESTG P +IH+S +T L ++ RGE E+KGKGKM
Sbjct: 119 RRPRYDVWGDTVNLASRMESTGVPGKIHVSEETYRLLKTREQFEFTERGEVEVKGKGKME 178
Query: 346 TYWLLG 351
TY+L G
Sbjct: 179 TYFLNG 184
>gnl|CDD|143636 cd07302, CHD, cyclase homology domain. Catalytic domains of the
mononucleotidyl cyclases (MNC's), also called cyclase
homology domains (CHDs), are part of the class III
nucleotidyl cyclases. This class includes eukaryotic and
prokaryotic adenylate cyclases (AC's) and guanylate
cyclases (GC's). They seem to share a common catalytic
mechanism in their requirement for two magnesium ions to
bind the polyphosphate moiety of the nucleotide.
Length = 177
Score = 234 bits (598), Expect = 3e-75
Identities = 79/178 (44%), Positives = 101/178 (56%), Gaps = 2/178 (1%)
Query: 173 EVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGDAYMVVGGL 232
EVT+ F+DIVGFT +S P E+V+LLN+ ++ FD I + +TIGDA M V GL
Sbjct: 1 EVTVLFADIVGFTALSERLGPEELVELLNEYFSAFDEIIERHGGTVDKTIGDAVMAVFGL 60
Query: 233 PVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGPCCAGVVGLTMPRYCL 292
P DHA++ AL++ PLRLRIG+HTGP AGVVG P Y +
Sbjct: 61 PGAHEDHAERAVRAALEMQEALAELNAEREGGPPLRLRIGIHTGPVVAGVVGSERPEYTV 120
Query: 293 FGDTVNTASRLESTGAPWRIHLSADTKAKLDQVGDYQLEYRGETELKGK-GKMPTYWL 349
GDTVN A+RLES P +I +S T L ++ E GE ELKGK G + Y L
Sbjct: 121 IGDTVNLAARLESLAKPGQILVSEATYELLGD-AGFEFEELGEVELKGKSGPVRVYRL 177
>gnl|CDD|225025 COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain
HAMP domain) [Signal transduction mechanisms].
Length = 227
Score = 142 bits (359), Expect = 1e-39
Identities = 62/209 (29%), Positives = 87/209 (41%), Gaps = 18/209 (8%)
Query: 144 TEQLLNRMLPSSVAEKLKLGMPVDPEDFREVTIYFSDIVGFTTISAYSTPFEVVDLLNDL 203
++ +L L V L G R VT+ F+DIVG T +S +V+LLN
Sbjct: 21 SDLVLRLYLARVVGRLLARGG----AGDRRVTLLFADIVGSTELSESLGDEALVELLNLY 76
Query: 204 YTCFDATINAYNVYKVETIGDAYMVVGGLPVRIPDHADQIATMALDLLHHSGRFKIRHLP 263
+ + + V+ IGD ++ V G P + D + L L + R L
Sbjct: 77 FDAVAEVVARHGGRVVKFIGDGFLAVFGRPSPLEDAVACALDLQLALRNPLAR-----LR 131
Query: 264 YTPLRLRIGLHTGPCCAGVVGLTMPRYCLFGDTVNTASRLESTGAPWRIHLSADTKAKLD 323
LR+RIG+HTG G G Y + G VN A+RLES P ++ LS T D
Sbjct: 132 RESLRVRIGIHTGEVVVGNTG----GYTVVGSAVNQAARLESLAKPGQVLLSEAT---YD 184
Query: 324 QVGD--YQLEYRGETELKGKGKMPTYWLL 350
V D G LKG + + L
Sbjct: 185 LVRDLVDLFSGLGSHRLKGLARPVRVYQL 213
>gnl|CDD|143637 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases.
Class III nucleotidyl cyclases are the largest, most
diverse group of nucleotidyl cyclases (NC's) containing
prokaryotic and eukaryotic proteins. They can be divided
into two major groups; the mononucleotidyl cyclases
(MNC's) and the diguanylate cyclases (DGC's). The
MNC's, which include the adenylate cyclases (AC's) and
the guanylate cyclases (GC's), have a conserved cyclase
homology domain (CHD), while the DGC's have a conserved
GGDEF domain, named after a conserved motif within this
subgroup. Their products, cyclic guanylyl and adenylyl
nucleotides, are second messengers that play important
roles in eukaryotic signal transduction and prokaryotic
sensory pathways.
Length = 133
Score = 131 bits (331), Expect = 1e-36
Identities = 54/141 (38%), Positives = 76/141 (53%), Gaps = 8/141 (5%)
Query: 173 EVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGDAYMVVGGL 232
VTI F+DIVGFT+++ P E +LLN+L FD+ I K++TIGD +MVV G
Sbjct: 1 PVTILFADIVGFTSLADALGPDEGDELLNELAGRFDSLIRRSGDLKIKTIGDEFMVVSG- 59
Query: 233 PVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGPCCAGVVGLTMPRYCL 292
DH A D+ + P+R+RIG+HTGP GV+G P+Y +
Sbjct: 60 ----LDHPAAAVAFAEDMREAVSA--LNQSEGNPVRVRIGIHTGPVVVGVIGS-RPQYDV 112
Query: 293 FGDTVNTASRLESTGAPWRIH 313
+G VN ASR+ES ++
Sbjct: 113 WGALVNLASRMESQAKAGQVL 133
>gnl|CDD|219526 pfam07701, HNOBA, Heme NO binding associated. The HNOBA domain is
found associated with the HNOB domain and pfam00211 in
soluble cyclases and signalling proteins. The HNOB
domain is predicted to function as a heme-dependent
sensor for gaseous ligands, and transduce diverse
downstream signals, in both bacteria and animals.
Length = 209
Score = 44.9 bits (107), Expect = 3e-05
Identities = 22/42 (52%), Positives = 27/42 (64%), Gaps = 4/42 (9%)
Query: 119 LEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPSSVAEKL 160
LEK + LE+ RE L+ EKKKT+ LL MLP SVA +L
Sbjct: 172 LEKLKDKLEEAHRE----LEEEKKKTDDLLYSMLPKSVANRL 209
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 39.8 bits (93), Expect = 0.003
Identities = 39/165 (23%), Positives = 59/165 (35%), Gaps = 22/165 (13%)
Query: 221 TIGDAYMVVGGLPVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRI--GLHTGPC 278
+GD + G P A + A AL+++ +GR R+ I G+HTG
Sbjct: 338 VLGDTLLFYFGYPSAAERDARRAARAALEMVRQAGRKGEAAAGEGKWRVEIAAGIHTGLV 397
Query: 279 CA---GVVGLTMPRYCLFGDTVNTASRLESTGAPWRIHLSADTKAKLDQVGDYQLEYRGE 335
A G T P N A R+++ P +I +S + L + D+ E
Sbjct: 398 LAQAPHASGGTTP---------NAAVRMQAQAEPGQILVSEAARKLLRRHADFD-PTALE 447
Query: 336 TELKGKGKMPTYWLLGKKGFYKELPTPPPLGDSHGLDENLILYGR 380
G P + LLG++ P S L GR
Sbjct: 448 EAAAGAESQPVFELLGER--AARTPF-----TSLDGGTTTPLVGR 485
>gnl|CDD|133191 cd05060, PTKc_Syk_like, Catalytic domain of Spleen Tyrosine
Kinase-like Protein Tyrosine Kinases. Protein Tyrosine
Kinase (PTK) family; Spleen Tyrosine Kinase (Syk)
subfamily; catalytic (c) domain. The Syk subfamily is
composed of Syk, ZAP-70, Shark, 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. Syk
subfamily kinases are cytoplasmic (or nonreceptor) tyr
kinases containing two Src homology 2 (SH2) domains
N-terminal to the catalytic tyr kinase domain. They are
involved in the signaling downstream of activated
receptors (including B-cell, T-cell, and Fc receptors)
that contain ITAMs (immunoreceptor tyr activation
motifs), leading to processes such as cell
proliferation, differentiation, survival, adhesion,
migration, and phagocytosis. Syk is important in B-cell
receptor (BCR) signaling, while Zap-70 is primarily
expressed in T-cells and NK cells, and is a crucial
component in T-cell receptor (TCR) signaling. Syk also
plays a central role in Fc receptor-mediated
phagocytosis in the adaptive immune system. Shark is
exclusively expressed in ectodermally derived epithelia,
and is localized preferentially to the apical surface of
the epithelial cells, it may play a role in a signaling
pathway for epithelial cell polarity.
Length = 257
Score = 36.6 bits (85), Expect = 0.019
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLFKT 24
M CW P+ RP F+E+ F+
Sbjct: 231 MLSCWKYRPEDRPTFSELESTFRR 254
>gnl|CDD|173624 cd00192, PTKc, Catalytic domain of Protein Tyrosine Kinases.
Protein Tyrosine Kinase (PTK) family, catalytic domain.
This PTKc family is part of a larger superfamily that
includes the catalytic domains of protein
serine/threonine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase (PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. They can be classified
into receptor and non-receptor tyr kinases. PTKs play
important roles in many cellular processes including,
lymphocyte activation, epithelium growth and
maintenance, metabolism control, organogenesis
regulation, survival, proliferation, differentiation,
migration, adhesion, motility, and morphogenesis.
Receptor tyr kinases (RTKs) are integral membrane
proteins which contain an extracellular ligand-binding
region, a transmembrane segment, and an intracellular
tyr kinase domain. RTKs are usually activated through
ligand binding, which causes dimerization and
autophosphorylation of the intracellular tyr kinase
catalytic domain, leading to intracellular signaling.
Some RTKs are orphan receptors with no known ligands.
Non-receptor (or cytoplasmic) tyr kinases are
distributed in different intracellular compartments and
are usually multi-domain proteins containing a catalytic
tyr kinase domain as well as various regulatory domains
such as SH3 and SH2. PTKs are usually autoinhibited and
require a mechanism for activation. In many PTKs, the
phosphorylation of tyr residues in the activation loop
is essential for optimal activity. Aberrant expression
of PTKs is associated with many development
abnormalities and cancers.
Length = 262
Score = 34.8 bits (81), Expect = 0.067
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 1 MRQCWAEPPDMRPDFNEV 18
M CW P+ RP F+E+
Sbjct: 240 MLSCWQLDPEDRPTFSEL 257
>gnl|CDD|219530 pfam07714, Pkinase_Tyr, Protein tyrosine kinase.
Length = 258
Score = 34.8 bits (81), Expect = 0.067
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLF 22
M QCWA P+ RP F+E+ +
Sbjct: 237 MLQCWAYDPEDRPTFSELVEDL 258
>gnl|CDD|214568 smart00221, STYKc, Protein kinase; unclassified specificity.
Phosphotransferases. The specificity of this class of
kinases can not be predicted. Possible dual-specificity
Ser/Thr/Tyr kinase.
Length = 258
Score = 34.4 bits (80), Expect = 0.098
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLF 22
M QCWAE P+ RP F+E+ ++
Sbjct: 237 MLQCWAEDPEDRPTFSELVEIL 258
>gnl|CDD|197581 smart00219, TyrKc, Tyrosine kinase, catalytic domain.
Phosphotransferases. Tyrosine-specific kinase subfamily.
Length = 257
Score = 33.7 bits (78), Expect = 0.15
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLF 22
M QCWAE P+ RP F+E+ ++
Sbjct: 236 MLQCWAEDPEDRPTFSELVEIL 257
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 33.7 bits (78), Expect = 0.20
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 15/69 (21%)
Query: 81 DLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIE 140
+LIRE E+L+ +K+ E LL L++ + + + E L+IE
Sbjct: 215 ELIREIKEELEEIEKERESLLEE---------------LKELAKKYLEELLALYEYLEIE 259
Query: 141 KKKTEQLLN 149
++ E L
Sbjct: 260 LERAEALSK 268
Score = 29.5 bits (67), Expect = 4.3
Identities = 7/31 (22%), Positives = 15/31 (48%)
Query: 72 LEKYSNNLEDLIRERTEQLDIEKKKTEQLLN 102
L++ + + + E L+IE ++ E L
Sbjct: 238 LKELAKKYLEELLALYEYLEIELERAEALSK 268
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 33.2 bits (76), Expect = 0.35
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 72 LEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIR 131
LE+ LE+L RE E + + L + + ++ + LEK LE L
Sbjct: 286 LEEKIERLEELEREIEELEEELEGLRALLEELE--ELLEKLKSLEERLEKLEEKLEKLES 343
Query: 132 ERTEQLDIEKKKTEQLLNR 150
E E+L EK + +LL
Sbjct: 344 E-LEELAEEKNELAKLLEE 361
Score = 28.6 bits (64), Expect = 9.4
Identities = 19/95 (20%), Positives = 42/95 (44%), Gaps = 13/95 (13%)
Query: 72 LEKYSNNLEDL-----IRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNL 126
LE Y LE+L + +L E ++ E+ L ++ L + L
Sbjct: 476 LELYELELEELEEELSREKEEAELREEIEELEKELRE--------LEEELIELLELEEAL 527
Query: 127 EDLIRERTEQLDIEKKKTEQLLNRMLPSSVAEKLK 161
++ + E+ E+L+ ++ E+L ++ + E+L+
Sbjct: 528 KEELEEKLEKLENLLEELEELKEKLQLQQLKEELR 562
>gnl|CDD|173631 cd05045, PTKc_RET, Catalytic domain of the Protein Tyrosine Kinase,
REarranged during Transfection protein. Protein
Tyrosine Kinase (PTK) family; RET (REarranged during
Transfection) protein; 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. RET is a
receptor tyr kinase (RTK) containing an extracellular
region with four cadherin-like repeats, a
calcium-binding site, and a cysteine-rich domain, a
transmembrane segment, and an intracellular catalytic
domain. It is part of a multisubunit complex that binds
glial-derived neurotropic factor (GDNF) family ligands
(GFLs) including GDNF, neurturin, artemin, and
persephin. GFLs bind RET along with four GPI-anchored
coreceptors, bringing two RET molecules together,
leading to autophosphorylation, activation, and
intracellular signaling. RET is essential for the
development of the sympathetic, parasympathetic and
enteric nervous systems, and the kidney. RET disruption
by germline mutations causes diseases in humans
including congenital aganglionosis of the
gastrointestinal tract (Hirschsprung's disease) and
three related inherited cancers: multiple endocrine
neoplasia type 2A (MEN2A), MEN2B, and familial medullary
thyroid carcinoma (FMTC).
Length = 290
Score = 32.6 bits (74), Expect = 0.40
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLFKTL 25
M CW + PD RP F +++ + +
Sbjct: 262 MLTCWKQEPDKRPTFADISKELEKM 286
>gnl|CDD|225871 COG3334, COG3334, Uncharacterized conserved protein [Function
unknown].
Length = 192
Score = 31.7 bits (72), Expect = 0.51
Identities = 26/142 (18%), Positives = 50/142 (35%), Gaps = 9/142 (6%)
Query: 35 LLLSLRYKNPHLGLRLKSLLYIDSPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEK 94
LLL + + L L + + + L + + I + +
Sbjct: 9 LLLLILIPSRFLLLLASAFALFAAKPVGAEAEDAAAELAEKKAAAQSEIEKFCANIADAA 68
Query: 95 KKTEQLLNRMLPRKVNF---VDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLN-- 149
L + L K+ V+ + LEK L+DL ER L ++ + +L+
Sbjct: 69 ADQLYALQKELLEKLKDLAEVNERLKALEKKKAELKDLEEEREGILRSKQAEDGKLVKIY 128
Query: 150 -RMLPSSVAEKLKLGMPVDPED 170
+M P + A L+ + E+
Sbjct: 129 SKMKPDAAAAILEN---LPDEE 147
>gnl|CDD|133192 cd05061, PTKc_InsR, Catalytic domain of the Protein Tyrosine
Kinase, Insulin Receptor. Protein Tyrosine Kinase (PTK)
family; Insulin Receptor (InsR); 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. InsR is a
receptor tyr kinase (RTK) that is composed of two
alphabeta heterodimers. Binding of the insulin ligand to
the extracellular alpha subunit activates the
intracellular tyr kinase domain of the transmembrane
beta subunit. Receptor activation leads to
autophosphorylation, stimulating downstream kinase
activities, which initiate signaling cascades and
biological function. InsR signaling plays an important
role in many cellular processes including glucose
homeostasis, glycogen synthesis, lipid and protein
metabolism, ion and amino acid transport, cell cycle and
proliferation, cell differentiation, gene transcription,
and nitric oxide synthesis. Insulin resistance, caused
by abnormalities in InsR signaling, has been described
in diabetes, hypertension, cardiovascular disease,
metabolic syndrome, heart failure, and female
infertility.
Length = 288
Score = 31.5 bits (71), Expect = 0.79
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLFK 23
MR CW P MRP F E+ +L K
Sbjct: 254 MRMCWQFNPKMRPTFLEIVNLLK 276
>gnl|CDD|133211 cd05080, PTKc_Tyk2_rpt2, Catalytic (repeat 2) domain of the Protein
Tyrosine Kinase, Tyrosine kinase 2. Protein Tyrosine
Kinase (PTK) family; Tyrosine kinase 2 (Tyk2); catalytic
(c) domain (repeat 2). 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. Tyk2 is a member of the
Janus kinase (Jak) subfamily of proteins, which are
cytoplasmic (or nonreceptor) tyr kinases containing an
N-terminal FERM domain, followed by a Src homology 2
(SH2) domain, a pseudokinase domain, and a C-terminal
tyr kinase catalytic domain. Jaks are crucial for
cytokine receptor signaling. They are activated by
autophosphorylation upon cytokine-induced receptor
aggregation, and subsequently trigger downstream
signaling events such as the phosphorylation of signal
transducers and activators of transcription (STATs).
Tyk2 is widely expressed in many tissues. It is involved
in signaling via the cytokine receptors IFN-alphabeta,
IL-6, IL-10, IL-12, IL-13, and IL-23. It mediates cell
surface urokinase receptor (uPAR) signaling and plays a
role in modulating vascular smooth muscle cell (VSMC)
functional behavior in response to injury. Tyk2 is also
important in dendritic cell function and T helper (Th)1
cell differentiation. A homozygous mutation of Tyk2 was
found in a patient with hyper-IgE syndrome (HIES), a
primary immunodeficiency characterized by recurrent skin
abscesses, pneumonia, and elevated serum IgE. This
suggests that Tyk2 may play important roles in multiple
cytokine signaling involved in innate and adaptive
immunity.
Length = 283
Score = 31.4 bits (71), Expect = 1.0
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLFKTL 25
M+ CW RP F + + K +
Sbjct: 257 MKNCWETEAKFRPTFRSLIPILKEM 281
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.4 bits (72), Expect = 1.0
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 72 LEKYSNNLEDLIRERTEQLDIEKKKTEQLLNR--MLPRKVNFVDTMFQMLEKYSNNLEDL 129
+ K LE ++ER +L ++ +LL R L RK+ +D + LEK E
Sbjct: 60 VHKLRAELERELKERRNEL---QRLERRLLQREETLDRKMESLDKKEENLEKK----EKE 112
Query: 130 IRERTEQLDIEKKKTEQLLNR 150
+ + + LD ++++ E+L+
Sbjct: 113 LSNKEKNLDEKEEELEELIAE 133
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 31.6 bits (72), Expect = 1.1
Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 10/94 (10%)
Query: 60 RKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQL------LNRMLPRKVNFVD 113
+K+N + + LEK L++ + EQ+ +K+ E L L L +
Sbjct: 819 QKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALR 878
Query: 114 TMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQL 147
LE +L+ E QL ++K E+L
Sbjct: 879 D----LESRLGDLKKERDELEAQLRELERKIEEL 908
Score = 31.2 bits (71), Expect = 1.4
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 72 LEKYSNNLED-LIRERTEQLDIEKKKTEQLLNRM------LPRKVNFVDTMFQMLEKYSN 124
LE+ N+LE L R ++ E K E+ ++R+ + +K+N + + LEK
Sbjct: 777 LEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQ 836
Query: 125 NLEDLIRERTEQLDIEKKKTEQL 147
L++ + EQ+ +K+ E L
Sbjct: 837 ELQEQRIDLKEQIKSIEKEIENL 859
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 31.6 bits (72), Expect = 1.2
Identities = 25/139 (17%), Positives = 43/139 (30%), Gaps = 12/139 (8%)
Query: 70 QMLEKYSNNLEDLIRER--TEQLDIEKKKTEQLLN-RMLPRKVNFVDTMFQMLEKYSNNL 126
+ + L+ L+ E IE K +L + K+ ++ L K S L
Sbjct: 924 EFKTELIARLKKLLNNIDLEEGPSIEYVKLPELNKLHEVESKLKETSEEYEDLLKKSTIL 983
Query: 127 EDLIRERTEQLDIEKKK-TEQLLNRMLPSSVAEKLKLGMPVDPEDFREVTIYFSDI-VGF 184
+ +L KK+ E ++LK E EV S +
Sbjct: 984 VREGNKANSELKNFKKELAELSKQYGALQESTKQLK-------ELPVEVAELQSASKIIS 1036
Query: 185 TTISAYSTPFEVVDLLNDL 203
+ + S + L L
Sbjct: 1037 SESTELSILKPLQKLKGLL 1055
>gnl|CDD|216842 pfam02009, Rifin_STEVOR, Rifin/stevor family. Several multicopy
gene families have been described in Plasmodium
falciparum, including the stevor family of subtelomeric
open reading frames and the rif interspersed repetitive
elements. Both families contain three predicted
transmembrane segments. It has been proposed that stevor
and rif are members of a larger superfamily that code
for variant surface antigens.
Length = 290
Score = 30.8 bits (70), Expect = 1.3
Identities = 13/55 (23%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 110 NFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLL-NRMLPSSVAEKLKLG 163
F Q ++Y ++D ++ EQ D K+ + +L +++ S+AEK++
Sbjct: 43 KFNRQTSQRFKEYDERMKDKRQKCKEQCD--KEIQKIILKDKLEKKSLAEKVEKE 95
>gnl|CDD|220614 pfam10174, Cast, RIM-binding protein of the cytomatrix active zone.
This is a family of proteins that form part of the CAZ
(cytomatrix at the active zone) complex which is
involved in determining the site of synaptic vesicle
fusion. The C-terminus is a PDZ-binding motif that binds
directly to RIM (a small G protein Rab-3A effector). The
family also contains four coiled-coil domains.
Length = 774
Score = 31.1 bits (70), Expect = 1.4
Identities = 30/158 (18%), Positives = 56/158 (35%), Gaps = 17/158 (10%)
Query: 17 EVNDLFKTLNQGRGRGHLLLLSLRYKNPHLGLRLKSLLYIDSPRKVNFVDTMFQMLEKYS 76
E+ L + R L L K++L + ++ L K +
Sbjct: 309 ELETLANQDSDMRQHLDKLKEDLTRAEQE-----KAILQTEVDALRYELERKHNTLTKKT 363
Query: 77 NNLEDLIRER-TEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRERTE 135
+L+ E+ T +IE + RK+ +L+K NL++ R +
Sbjct: 364 ASLQAAQEEKATYAGEIEDMRD---RYEKTERKLR-------VLQKKIENLQETFRRKER 413
Query: 136 QLDIEKKKTEQLLNRMLPSSVAEKLKLGMPVDPEDFRE 173
+L EK++ L + EKL+ + + E E
Sbjct: 414 RLKEEKERLRSLQTDTNTDTALEKLEKAL-AEKERIIE 450
Score = 30.4 bits (68), Expect = 3.0
Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 72 LEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLI- 130
L+K NL++ R + +L EK++ R L N DT + LEK E +I
Sbjct: 397 LQKKIENLQETFRRKERRLKEEKERL-----RSLQTDTN-TDTALEKLEKALAEKERIIE 450
Query: 131 ----------RERTEQLDIEKKKTEQLLN 149
R E+ + KK+ E L
Sbjct: 451 RLKEQRDRDERYEQEEFETYKKEFEDLKE 479
>gnl|CDD|173629 cd05041, PTKc_Fes_like, Catalytic domain of Fes-like Protein
Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family;
Fes subfamily; catalytic (c) domain. Fes subfamily
members include Fes (or Fps), Fer, 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. Fes
subfamily proteins are cytoplasmic (or nonreceptor) tyr
kinases containing an N-terminal region with FCH
(Fes/Fer/CIP4 homology) and coiled-coil domains,
followed by a SH2 domain, and a C-terminal catalytic
domain. The genes for Fes (feline sarcoma) and Fps
(Fujinami poultry sarcoma) were first isolated from
tumor-causing retroviruses. The viral oncogenes encode
chimeric Fes proteins consisting of Gag sequences at the
N-termini, resulting in unregulated tyr kinase activity.
Fes and Fer kinases play roles in haematopoiesis,
inflammation and immunity, growth factor signaling,
cytoskeletal regulation, cell migration and adhesion,
and the regulation of cell-cell interactions. Fes and
Fer show redundancy in their biological functions.
Length = 251
Score = 30.5 bits (69), Expect = 1.6
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 1 MRQCWAEPPDMRPDFNEVND 20
M QCWA P+ RP F+E+ +
Sbjct: 228 MLQCWAYDPENRPSFSEIYN 247
>gnl|CDD|217305 pfam02970, TBCA, Tubulin binding cofactor A.
Length = 91
Score = 28.7 bits (65), Expect = 1.8
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 72 LEKYSNNLEDLIRERTEQLDIEK-----KKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNL 126
+E+ +E L E ++ D++K K+TE +L R V + + LE+Y L
Sbjct: 23 VEQQEERVEKLKAEGADEYDLKKQEEVLKETEMMLPDCKRRLQKAVADLEEYLEEYEEGL 82
Query: 127 EDL 129
E+L
Sbjct: 83 EEL 85
>gnl|CDD|183259 PRK11652, emrD, multidrug resistance protein D; Provisional.
Length = 394
Score = 30.6 bits (70), Expect = 1.9
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 272 GLHTGPCCAGVVGLTMPRYCLFGDTVNTASRLESTG 307
GL TG GV+ T+PR G + A+ L + G
Sbjct: 107 GLGTG--VGGVMARTLPRDLYEGTQLRHANSLLNMG 140
>gnl|CDD|217135 pfam02601, Exonuc_VII_L, Exonuclease VII, large subunit. This
family consist of exonuclease VII, large subunit
EC:3.1.11.6 This enzyme catalyzes exonucleolytic
cleavage in either 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. This exonuclease VII enzyme
is composed of one large subunit and 4 small ones.
Length = 295
Score = 30.0 bits (68), Expect = 2.5
Identities = 20/111 (18%), Positives = 48/111 (43%), Gaps = 9/111 (8%)
Query: 64 FVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRML---PRKVNFVDTMFQMLE 120
V ++L+K + L R +L+ E+ + L R+ R + + L
Sbjct: 141 LVPDRTELLQKLEGLEQRLSRALKNRLEKEQDRLNLLRERLKSLSRRLLEQHEERLAELR 200
Query: 121 -KYSNNLEDLIRERTEQLD-----IEKKKTEQLLNRMLPSSVAEKLKLGMP 165
+ +++++L+ + +L+ E +K L N++ +++ +LK P
Sbjct: 201 DRLISSIQNLLSRKQSRLERLILNRELEKNSLLENKLATANLTAQLKALSP 251
>gnl|CDD|173634 cd05053, PTKc_FGFR, Catalytic domain of the Protein Tyrosine
Kinases, Fibroblast Growth Factor Receptors. Protein
Tyrosine Kinase (PTK) family; Fibroblast Growth Factor
Receptor (FGFR) subfamily; catalytic (c) domain. The
FGFR subfamily consists of FGFR1, FGFR2, FGFR3, FGFR4,
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. FGFR subfamily members
are receptor tyr kinases (RTKs) containing an
extracellular ligand-binding region with three
immunoglobulin-like domains, a transmembrane segment,
and an intracellular catalytic domain. The binding of
FGFRs to their ligands, the FGFs, and to heparin/heparan
sulfate (HS) results in the formation of a ternary
complex, which leads to receptor dimerization and
activation, and intracellular signaling. There are at
least 23 FGFs and four types of FGFRs. The binding of
FGFs to FGFRs is promiscuous, in that a receptor may be
activated by several ligands and a ligand may bind to
more that one type of receptor. FGF/FGFR signaling is
important in the regulation of embryonic development,
homeostasis, and regenerative processes. Depending on
the cell type and stage, FGFR signaling produces diverse
cellular responses including proliferation, growth
arrest, differentiation, and apoptosis. Aberrant
signaling leads to many human diseases such as skeletal,
olfactory, and metabolic disorders, as well as cancer.
Length = 293
Score = 30.1 bits (68), Expect = 2.5
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 1 MRQCWAEPPDMRPDFNE-VNDLFKTL 25
MR CW E P RP F + V DL + L
Sbjct: 267 MRDCWHEVPSQRPTFKQLVEDLDRML 292
>gnl|CDD|173633 cd05052, PTKc_Abl, Catalytic domain of the Protein Tyrosine Kinase,
Abelson kinase. Protein Tyrosine Kinase (PTK) family;
Abelson (Abl) kinase; 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. Abl (or
c-Abl) is a ubiquitously-expressed cytoplasmic (or
nonreceptor) tyr kinase that contains SH3, SH2, and tyr
kinase domains in its N-terminal region, as well as
nuclear localization motifs, a putative DNA-binding
domain, and F- and G-actin binding domains in its
C-terminal tail. It also contains a short autoinhibitory
cap region in its N-terminus. Abl is normally inactive
and requires phosphorylation and myristoylation for
activation. Abl function depends on its subcellular
localization. In the cytoplasm, Abl plays a role in cell
proliferation and survival. In response to DNA damage or
oxidative stress, Abl is transported to the nucleus
where it induces apoptosis. In chronic myelogenous
leukemia (CML) patients, an aberrant translocation
results in the replacement of the first exon of Abl with
the BCR (breakpoint cluster region) gene. The resulting
BCR-Abl fusion protein is constitutively active and
associates into tetramers, resulting in a hyperactive
kinase sending a continuous signal. This leads to
uncontrolled proliferation, morphological transformation
and anti-apoptotic effects. BCR-Abl is the target of
selective inhibitors, such as imatinib (Gleevec), used
in the treatment of CML. Abl2, also known as ARG
(Abelson-related gene), is thought to play a cooperative
role with Abl in the proper development of the nervous
system. The Tel-ARG fusion protein, resulting from
reciprocal translocation between chromosomes 1 and 12,
is associated with acute myeloid leukemia (AML). The TEL
gene is a frequent fusion partner of other tyr kinase
oncogenes, including Tel/Abl, Tel/PDGFRbeta, and
Tel/Jak2, found in patients with leukemia and
myeloproliferative disorders.
Length = 263
Score = 29.8 bits (67), Expect = 2.6
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLFKTL 25
MR CW P RP F E++ F+T+
Sbjct: 238 MRACWQWNPSDRPSFAEIHQAFETM 262
>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production
and conversion].
Length = 161
Score = 29.2 bits (66), Expect = 2.7
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 15/86 (17%)
Query: 73 EKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRE 132
K +++L + E+ + EQ L + E+ S +E +E
Sbjct: 40 AKIADDLAE-AERLKEEAQALLAEYEQELE--------------EAREQASEIIEQAKKE 84
Query: 133 RTEQLDIEKKKTEQLLNRMLPSSVAE 158
+ + K + E+ L R+ ++ AE
Sbjct: 85 AEQIAEEIKAEAEEELERIKEAAEAE 110
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 30.4 bits (69), Expect = 2.7
Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 8/94 (8%)
Query: 72 LEKYSNNLEDLIRERTEQLDIEKKKTEQL-LNRMLPRKVNFVDTMFQMLEKYSNNLEDLI 130
LE+ LE+L ++ +E+ + E+ + E L L+R L ++ + + E+ LE L
Sbjct: 642 LEELRKELEELEKKYSEE-EYEELREEYLELSRELAGLRAELEELEKRREEIKKTLEKLK 700
Query: 131 RERTEQLDIEKKKTE-QLLNRMLP--SSVAEKLK 161
E E EK K E + L + L + EK+K
Sbjct: 701 EELEE---REKAKKELEKLEKALERVEELREKVK 731
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 30.5 bits (69), Expect = 2.8
Identities = 19/116 (16%), Positives = 39/116 (33%), Gaps = 8/116 (6%)
Query: 37 LSLRYKNPHLGLRLKSLL--YIDSPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEK 94
N + +K ID + +D +++ K N+ D I E + + +
Sbjct: 775 YLDLIDNLNDAREIKDKESKAIDL----DDIDFELELIGKQEINI-DYILELLQTFNDKN 829
Query: 95 KKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNR 150
E L + R + + +K L + I + + +K E+L
Sbjct: 830 GAYESLKEL-IERIIKEWIEDLRQKKKLIERLIEAINQYRAKKLDTAEKLEELYIL 884
>gnl|CDD|133172 cd05040, PTKc_Ack_like, Catalytic domain of the Protein Tyrosine
Kinase, Activated Cdc42-associated kinase. Protein
Tyrosine Kinase (PTK) family; Activated Cdc42-associated
kinase (Ack) subfamily; catalytic (c) domain. Ack
subfamily members include Ack1, thirty-eight-negative
kinase 1 (Tnk1), 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. Ack
subfamily members are cytoplasmic (or nonreceptor) tyr
kinases containing an N-terminal catalytic domain, an
SH3 domain, a Cdc42-binding CRIB domain, and a
proline-rich region. They are mainly expressed in brain
and skeletal tissues and are involved in the regulation
of cell adhesion and growth, receptor degradation, and
axonal guidance. Ack1 is also associated with
androgen-independent prostate cancer progression. Tnk1
regulates TNFalpha signaling and may play an important
role in cell death.
Length = 257
Score = 29.7 bits (67), Expect = 3.0
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLF 22
M QCWA P RP F + +
Sbjct: 234 MLQCWAHNPADRPTFAALREFL 255
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 30.0 bits (68), Expect = 3.0
Identities = 18/102 (17%), Positives = 41/102 (40%), Gaps = 21/102 (20%)
Query: 73 EKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRE 132
+K L +E ++ +I E + + ++LE+ + ++ +E
Sbjct: 33 DKLRK----LSKEYSQLEEIVDCYRE------YQQAQEDIKEAKEILEESDPEMREMAKE 82
Query: 133 RTEQLDIEKKKTEQLLNRMLPSSVAEKLKLGMPVDPEDFREV 174
E+L+ + ++ E+ L +L +P DP D + V
Sbjct: 83 ELEELEEKIEELEEQLKVLL-----------LPKDPNDEKNV 113
>gnl|CDD|213362 cd12828, TmCorA-like_1, Thermotoga maritima CorA_like subfamily.
This subfamily belongs to the Thermotoga maritima CorA
(TmCorA)-family of the MIT superfamily of essential
membrane proteins involved in transporting divalent
cations (uptake or efflux) across membranes. Members of
this subfamily are found in all three kingdoms of life.
It is functionally diverse subfamily, in addition to the
CorA Co2+ transporter from the hyperthermophilic
Thermotoga maritima, it includes Methanosarcina mazei
CorA which may be involved in transport of copper and/or
other divalent metal ions. Thermotoga maritima CorA
forms funnel-shaped homopentamers, the tip of the funnel
is formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by a related protein, Saccharomyces cerevisiae
Alr1p. Natural variants in this signature sequence may
be associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 294
Score = 29.7 bits (68), Expect = 3.2
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 63 NFVDTMFQMLEKYSNNLEDLIRERTEQLD--IEKKKTEQLLNRMLPRKVNFVDTMFQMLE 120
N+V + FQ E+ + + +RER I KK + L +L VD F +LE
Sbjct: 77 NYVIS-FQ--ERPGDVFDP-VRERLRNGKGRIRKKGADYLAYALLDA---IVDNYFPVLE 129
Query: 121 KYSNNLEDL 129
K + +EDL
Sbjct: 130 KLGDRIEDL 138
>gnl|CDD|215724 pfam00110, wnt, wnt family. Wnt genes have been identified in
vertebrates and invertebrates but not in plants,
unicellular eukaryotes or prokaryotes. In humans, 19 WNT
proteins are known. Because of their insolubility little
is known about Wnt protein structure, but all have 23 or
24 Cys residues whose spacing is highly conserved.
Signal transduction by Wnt proteins (including the
Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity
pathway) is mediated by receptors of the Frizzled and
LDL-receptor-related protein (LRP) families.
Length = 308
Score = 29.9 bits (68), Expect = 3.2
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 18/69 (26%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLFK---------TLNQGRGRGHLLLLSLRYKNPHLGLRLK 51
++ CW + PD R EV DL K +N R L+ + + K P
Sbjct: 174 LKTCWKQLPDFR----EVGDLLKEKYDGAIKVEVNNRGKRRRLVRKNPKSKPP----TST 225
Query: 52 SLLYI-DSP 59
L+Y+ DSP
Sbjct: 226 DLVYLEDSP 234
>gnl|CDD|133219 cd05088, PTKc_Tie2, Catalytic domain of the Protein Tyrosine
Kinase, Tie2. Protein Tyrosine Kinase (PTK) family;
Tie2; 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. Tie2 is a receptor tyr
kinase (RTK) containing an extracellular region, a
transmembrane segment, and an intracellular catalytic
domain. The extracellular region contains an
immunoglobulin (Ig)-like domain, three epidermal growth
factor (EGF)-like domains, a second Ig-like domain, and
three fibronectin type III repeats. Tie2 is expressed
mainly in endothelial cells and hematopoietic stem
cells. It is also found in a subset of tumor-associated
monocytes and eosinophils. The angiopoietins (Ang-1 to
Ang-4) serve as ligands for Tie2. The binding of Ang-1
to Tie2 leads to receptor autophosphorylation and
activation, promoting cell migration and survival. In
contrast, Ang-2 binding to Tie2 does not result in the
same response, suggesting that Ang-2 may function as an
antagonist. Tie2 signaling plays key regulatory roles in
vascular integrity and quiescence, and in inflammation.
Length = 303
Score = 29.6 bits (66), Expect = 3.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 1 MRQCWAEPPDMRPDFNEV 18
MRQCW E P RP F ++
Sbjct: 256 MRQCWREKPYERPSFAQI 273
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 30.0 bits (68), Expect = 3.4
Identities = 26/96 (27%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 36 LLSLRYKNPHLGLRLKSLLYIDSPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKK 95
L L K LG+ LK V + E+ +LE I+E E L+ +K
Sbjct: 40 LRKLESKIKKLGIPLKD---TGGKPDVPPSKEFLDLEEEI-LDLEAEIKEVEENLESLEK 95
Query: 96 KT---EQLLNRMLPRKVNFVDTMFQMLEKYSNNLED 128
+ E+ LN + K F+D + L + SN D
Sbjct: 96 EINELEEWLNVLDEEKS-FLDENLEELSELSNLDID 130
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.7 bits (68), Expect = 3.5
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 70 QMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDL 129
+ + K N E +RER +L ++L R+L +K +D ++LEK LE
Sbjct: 64 EEIHKLRNEFEKELRERRNEL-------QKLEKRLL-QKEENLDRKLELLEKREEELEKK 115
Query: 130 IRERTEQL-DIEKKKTE 145
+E ++ ++EKK+ E
Sbjct: 116 EKELEQKQQELEKKEEE 132
>gnl|CDD|133200 cd05069, PTKc_Yes, Catalytic domain of the Protein Tyrosine Kinase,
Yes. Protein Tyrosine Kinase (PTK) family; Yes kinase;
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. Yes (or c-Yes) is a
member of the Src subfamily of proteins, which are
cytoplasmic (or non-receptor) tyr kinases. Src kinases
contain an N-terminal SH4 domain with a myristoylation
site, followed by SH3 and SH2 domains, a tyr kinase
domain, and a regulatory C-terminal region containing a
conserved tyr. They are activated by autophosphorylation
at the tyr kinase domain, but are negatively regulated
by phosphorylation at the C-terminal tyr by Csk
(C-terminal Src Kinase). Src proteins are involved in
signaling pathways that regulate cytokine and growth
factor responses, cytoskeleton dynamics, cell
proliferation, survival, and differentiation. c-Yes
kinase is the cellular homolog of the oncogenic protein
(v-Yes) encoded by the Yamaguchi 73 and Esh sarcoma
viruses. It displays functional overlap with other Src
subfamily members, particularly Src. It also shows some
unique functions such as binding to occludins,
transmembrane proteins that regulate extracellular
interactions in tight junctions. Yes also associates
with a number of proteins in different cell types that
Src does not interact with, like JAK2 and gp130 in
pre-adipocytes, and Pyk2 in treated pulmonary vein
endothelial cells. Although the biological function of
Yes remains unclear, it appears to have a role in
regulating cell-cell interactions and vesicle
trafficking in polarized cells.
Length = 260
Score = 29.6 bits (66), Expect = 3.6
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 1 MRQCWAEPPDMRPDFNEVNDLFK 23
M+ CW + PD RP F + +
Sbjct: 236 MKLCWKKDPDERPTFEYIQSFLE 258
>gnl|CDD|185746 cd08915, V_Alix_like, Protein-interacting V-domain of mammalian
Alix and related domains. This superfamily contains the
V-shaped (V) domain of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), Bro1 and Rim20 (also known as PalA) from
Saccharomyces cerevisiae, and related domains. Alix,
HD-PTP, Bro1, and Rim20 all interact with the ESCRT
(Endosomal Sorting Complexes Required for Transport)
system. Alix, also known as apoptosis-linked gene-2
interacting protein 1 (AIP1), participates in membrane
remodeling processes during the budding of enveloped
viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), and the abscission
reactions of mammalian cell division. It also functions
in apoptosis. HD-PTP functions in cell migration and
endosomal trafficking, Bro1 in endosomal trafficking,
and Rim20 in the response to the external pH via the
Rim101 pathway. The Alix V-domain contains a binding
site, partially conserved in this superfamily, for the
retroviral late assembly (L) domain YPXnL motif. The
Alix V-domain is also a dimerization domain. Members of
this superfamily have an N-terminal Bro1-like domain,
which binds components of the ESCRT-III complex. The
Bro1-like domains of Alix and HD-PTP can also bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many
members, including Alix, HD-PTP, and Bro1, also have a
proline-rich region (PRR), which binds multiple partners
in Alix, including Tsg101 (tumor susceptibility gene
101, a component of ESCRT-1) and the apoptotic protein
ALG-2. The C-terminal portion (V-domain and PRR) of Bro1
interacts with Doa4, a ubiquitin thiolesterase needed to
remove ubiquitin from MVB cargoes; it interacts with a
YPxL motif in Doa4s catalytic domain to stimulate its
deubiquitination activity. Rim20 may bind the ESCRT-III
subunit Snf7, bringing the protease Rim13 (a
YPxL-containing transcription factor) into proximity
with Rim101, and promoting the proteolytic activation of
Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor
suppressor gene candidate often absent in human kidney,
breast, lung, and cervical tumors. HD-PTP has a
C-terminal catalytically inactive tyrosine phosphatase
domain.
Length = 342
Score = 29.6 bits (67), Expect = 3.6
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 62 VNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQL 100
++ ++ F+ L K N+E+L++E E L+ E + +QL
Sbjct: 72 LDNIEQSFKELSKLRQNVEELLQECEELLEEEAAEDDQL 110
Score = 29.6 bits (67), Expect = 3.6
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 109 VNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQL 147
++ ++ F+ L K N+E+L++E E L+ E + +QL
Sbjct: 72 LDNIEQSFKELSKLRQNVEELLQECEELLEEEAAEDDQL 110
>gnl|CDD|179149 PRK00872, PRK00872, hypothetical protein; Provisional.
Length = 157
Score = 28.9 bits (65), Expect = 3.6
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 11/53 (20%)
Query: 150 RMLPSSVAEKLKLGMPVDPEDFREVTIYFSDIVGFTTISAYSTPFEVVDLLND 202
R P V ++L G PVDP++ YF T+ + T D L
Sbjct: 94 RHGPPEVLQRLARGEPVDPKE-----YYFR------TVPRFETGHPKYDWLMR 135
>gnl|CDD|151614 pfam11172, DUF2959, Protein of unknown function (DUF2959). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 201
Score = 29.1 bits (66), Expect = 3.7
Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 78 NLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFV-DTMF----QMLEKYSNNLEDLIRE 132
+LED+ + ++ + + E++ +R+ V V + +F L++YSN L R
Sbjct: 61 DLEDVYNQLNDEYEDSEAAAEEVSDRI--DAVEDVAEALFDEWEDELDQYSNA--SLRRS 116
Query: 133 RTEQLDIEKKKTEQLLNRM 151
+L +++ QL+ M
Sbjct: 117 SQRKLRETRRQYRQLIRAM 135
>gnl|CDD|227038 COG4694, COG4694, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 758
Score = 29.9 bits (67), Expect = 4.0
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 6/93 (6%)
Query: 68 MFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVD---TMFQMLEKYSN 124
+ L K +N ER + + +KK +++ L + L + + LEK N
Sbjct: 396 AIKDLIKKANAQVVNHNERIKNFEKQKKSSKEQLEKFLVNEFKSDVQEYNKYCGLEKKIN 455
Query: 125 NLEDLI---RERTEQLDIEKKKTEQLLNRMLPS 154
NLE I +E ++L E K+ E+ L + P
Sbjct: 456 NLEKEIKNNQEEVKKLSNEIKEIEKFLVSIKPI 488
>gnl|CDD|133189 cd05058, PTKc_Met_Ron, Catalytic domain of the Protein Tyrosine
Kinases, Met and Ron. Protein Tyrosine Kinase (PTK)
family; Met and Ron; 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. Met and
Ron are receptor tyr kinases (RTKs) composed of an
alpha-beta heterodimer. The extracellular alpha chain is
disulfide linked to the beta chain, which contains an
extracellular ligand-binding region with a sema domain,
a PSI domain and four IPT repeats, a transmembrane
segment, and an intracellular catalytic domain. Binding
to their ligands leads to receptor dimerization,
autophosphorylation, activation, and intracellular
signaling. Met binds to the ligand, hepatocyte growth
factor/scatter factor (HGF/SF), and is also called the
HGF receptor. HGF/Met signaling plays a role in growth,
transformation, cell motility, invasion, metastasis,
angiogenesis, wound healing, and tissue regeneration.
Aberrant expression of Met through mutations or gene
amplification is associated with many human cancers
including hereditary papillary renal and gastric
carcinomas. The ligand for Ron is macrophage stimulating
protein (MSP). Ron signaling is important in regulating
cell motility, adhesion, proliferation, and apoptosis.
Aberrant Ron expression is implicated in tumorigenesis
and metastasis.
Length = 262
Score = 29.4 bits (66), Expect = 4.3
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 1 MRQCWAEPPDMRPDFNEV 18
M CW P+MRP F+E+
Sbjct: 235 MLSCWHPKPEMRPTFSEL 252
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 29.5 bits (66), Expect = 4.5
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 12/61 (19%)
Query: 80 EDLIRER-TEQLDIEKKKTEQLLNRMLPRKVNFVD-------TMFQMLEKYSNNLEDLIR 131
++L R R +Q+++ K+K E+LLN ++ N D + M +++ + L L +
Sbjct: 23 DELRRRREEQQVELRKQKREELLN----KRRNLADVSEEAESSFIPMEQQFYSELPQLTQ 78
Query: 132 E 132
+
Sbjct: 79 Q 79
>gnl|CDD|133193 cd05062, PTKc_IGF-1R, Catalytic domain of the Protein Tyrosine
Kinase, Insulin-like Growth Factor-1 Receptor. Protein
Tyrosine Kinase (PTK) family; Insulin-like Growth
Factor-1 Receptor (IGF-1R); 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. IGF-1R is
a receptor tyr kinases (RTK) that is composed of two
alphabeta heterodimers. Binding of the ligand (IGF-1 or
IGF-2) to the extracellular alpha subunit activates the
intracellular tyr kinase domain of the transmembrane
beta subunit. Receptor activation leads to
autophosphorylation, which stimulates downstream kinase
activities and biological function. IGF-1R signaling is
important in the differentiation, growth, and survival
of normal cells. In cancer cells, where it is frequently
overexpressed, IGF-1R is implicated in proliferation,
the suppression of apoptosis, invasion, and metastasis.
IGF-1R is being developed as a therapeutic target in
cancer treatment.
Length = 277
Score = 29.2 bits (65), Expect = 4.7
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 1 MRQCWAEPPDMRPDFNEV 18
MR CW P MRP F E+
Sbjct: 254 MRMCWQYNPKMRPSFLEI 271
>gnl|CDD|153358 cd07674, F-BAR_FCHO1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only 1
protein. F-BAR domains are dimerization modules that
bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
FCH domain Only 1 (FCHO1) may be involved in
clathrin-coated vesicle formation. It contains an
N-terminal F-BAR domain and a C-terminal domain of
unknown function named SAFF which is also present in
FCHO2 and endophilin interacting protein 1. F-BAR
domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 261
Score = 29.1 bits (65), Expect = 4.8
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 9/84 (10%)
Query: 69 FQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNN--- 125
+++ K ++ ++D+ R EQ+ I KK E+ + + V + Q L+K N
Sbjct: 77 LELMRKLNDLIKDINRYGDEQVKIHKKTKEEAIGTL--EAVQSLQVQSQHLQKSRENYHS 134
Query: 126 ----LEDLIRERTEQLDIEKKKTE 145
E L RE Q ++EK + +
Sbjct: 135 KCVEQERLRREGVPQKELEKAELK 158
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 29.2 bits (66), Expect = 4.8
Identities = 14/63 (22%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 70 QMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDL 129
QM+E + ++ +++ E+++ E++K RML K+ + + + E + E L
Sbjct: 232 QMMEAQERSYQEHVKQLIEKMEAEREKLLAEQERMLEHKLQEQEEL--LKEGFKTEAESL 289
Query: 130 IRE 132
+E
Sbjct: 290 QKE 292
Score = 28.8 bits (65), Expect = 6.1
Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 15/78 (19%)
Query: 84 RERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKK 143
R + E + E++ + QM+E + ++ +++ E+++ E++K
Sbjct: 210 RAKAEAAEAEQELLREKQKEEE-----------QMMEAQERSYQEHVKQLIEKMEAEREK 258
Query: 144 TEQLLNRMLPSSVAEKLK 161
RML KL+
Sbjct: 259 LLAEQERML----EHKLQ 272
>gnl|CDD|185466 PTZ00130, PTZ00130, heat shock protein 90; Provisional.
Length = 814
Score = 29.2 bits (65), Expect = 5.5
Identities = 26/107 (24%), Positives = 54/107 (50%), Gaps = 11/107 (10%)
Query: 43 NPHLGLRLKSL-LYIDSPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQ-- 99
N HL + S+ LY+ R+V D + L +Y + ++ ++ L++ +++ +Q
Sbjct: 383 NDHLFTKQNSIKLYV---RRVLVADEFVEFLPRYMSFVKGVVDSDDLPLNVSREQLQQNK 439
Query: 100 ---LLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKK 143
+++ + RK+ +DT + ++ N E L E ++ D EKKK
Sbjct: 440 ILKAVSKRIVRKI--LDTFRTLYKEGKKNKETLRAELAKETDEEKKK 484
>gnl|CDD|224188 COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase subunit I [Energy
production and conversion].
Length = 660
Score = 29.3 bits (66), Expect = 5.5
Identities = 27/160 (16%), Positives = 58/160 (36%), Gaps = 23/160 (14%)
Query: 47 GLRLKSLLYIDSPRKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLP 106
L++ + I ++ V + + K ++ E E+L+ E K E+++
Sbjct: 48 KLKVAEVAQISLSSLLSEVLDYLRSV-KGLEGRLFILPEEVEKLEAELKSLEEVI----- 101
Query: 107 RKVNFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPSSVAEKLK-LGMP 165
+ EK+S+ +E+L R+ E+L ++ E L + + E L L
Sbjct: 102 ----------KPAEKFSSEVEELTRKLEERLSELDEELEDLEDLLE---ELEPLAYLDFD 148
Query: 166 VDPEDFREVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYT 205
+ + + +G V++ LY
Sbjct: 149 LSLLRGLKFLLV---RLGLVRREKLEALVGVIEDEVALYG 185
>gnl|CDD|192109 pfam08640, U3_assoc_6, U3 small nucleolar RNA-associated protein 6.
This is a family of U3 nucleolar RNA-associated
proteins which are involved in nucleolar processing of
pre-18S ribosomal RNA.
Length = 83
Score = 27.2 bits (61), Expect = 6.0
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 11/79 (13%)
Query: 72 LEKYSNNLEDLIR----ERTEQLDIEKKKT--EQLLNRMLPRKVNFVDTMFQMLEKYSNN 125
LE+ LEDL R + E I KK+T E L R +F+ + +Y N
Sbjct: 1 LEQSVPELEDLERKGLFTKDEIRSIVKKRTDFEYRLQRRGSSLSDFLRYI-----QYELN 55
Query: 126 LEDLIRERTEQLDIEKKKT 144
LE L R+R +++ +K
Sbjct: 56 LEKLRRKRRKRIGYKKNSI 74
>gnl|CDD|133229 cd05098, PTKc_FGFR1, Catalytic domain of the Protein Tyrosine
Kinase, Fibroblast Growth Factor Receptor 1. Protein
Tyrosine Kinase (PTK) family; Fibroblast Growth Factor
Receptor 1 (FGFR1); 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. FGFR1 is
part of the FGFR subfamily, which are receptor tyr
kinases (RTKs) containing an extracellular
ligand-binding region with three immunoglobulin-like
domains, a transmembrane segment, and an intracellular
catalytic domain. The binding of FGFRs to their ligands,
the FGFs, results in receptor dimerization and
activation, and intracellular signaling. The binding of
FGFs to FGFRs is promiscuous, in that a receptor may be
activated by several ligands and a ligand may bind to
more that one type of receptor. Alternative splicing of
FGFR1 transcripts produces a variety of isoforms, which
are differentially expressed in cells. FGFR1 binds the
ligands, FGF1 and FGF2, with high affinity and has also
been reported to bind FGF4, FGF6, and FGF9. FGFR1
signaling is critical in the control of cell migration
during embryo development. It promotes cell
proliferation in fibroblasts. Nuclear FGFR1 plays a role
in the regulation of transcription. Mutations,
insertions or deletions of FGFR1 have been identified in
patients with Kallman's syndrome (KS), an inherited
disorder characterized by hypogonadotropic hypogonadism
and loss of olfaction. Aberrant FGFR1 expression has
been found in some human cancers including 8P11
myeloproliferative syndrome (EMS), breast cancer, and
pancreatic adenocarcinoma.
Length = 307
Score = 28.8 bits (64), Expect = 6.1
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 1 MRQCWAEPPDMRPDFNE-VNDLFKTL 25
MR CW P RP F + V DL + L
Sbjct: 275 MRDCWHAVPSQRPTFKQLVEDLDRIL 300
>gnl|CDD|133248 cd05148, PTKc_Srm_Brk, Catalytic domain of the Protein Tyrosine
Kinases, Srm and Brk. Protein Tyrosine Kinase (PTK)
family; Src-related kinase lacking C-terminal regulatory
tyrosine and N-terminal myristylation sites (Srm) and
breast tumor kinase (Brk, also called protein tyrosine
kinase 6); catalytic (c) domains. 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. Srm and
Brk are a member of the Src subfamily of proteins, which
are cytoplasmic (or non-receptor) tyr kinases. Src
kinases in general contain an N-terminal SH4 domain with
a myristoylation site, followed by SH3 and SH2 domains,
a tyr kinase domain, and a regulatory C-terminal region
containing a conserved tyr; they are activated by
autophosphorylation at the tyr kinase domain, but are
negatively regulated by phosphorylation at the
C-terminal tyr by Csk (C-terminal Src Kinase). Srm and
Brk however, lack the N-terminal myristylation sites.
Src proteins are involved in signaling pathways that
regulate cytokine and growth factor responses,
cytoskeleton dynamics, cell proliferation, survival, and
differentiation. Brk has been found to be overexpressed
in a majority of breast tumors.
Length = 261
Score = 28.6 bits (64), Expect = 6.9
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1 MRQCWAEPPDMRPDF 15
M +CWA P+ RP F
Sbjct: 237 MLECWAAEPEDRPSF 251
>gnl|CDD|133186 cd05055, PTKc_PDGFR, Catalytic domain of the Protein Tyrosine
Kinases, Platelet Derived Growth Factor Receptors.
Protein Tyrosine Kinase (PTK) family; Platelet Derived
Growth Factor Receptor (PDGFR) subfamily; catalytic (c)
domain. The PDGFR subfamily consists of PDGFR alpha,
PDGFR beta, KIT, CSF-1R, the mammalian FLT3, 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.
PDGFR subfamily members are receptor tyr kinases (RTKs)
containing an extracellular ligand-binding region with
five immunoglobulin-like domains, a transmembrane
segment, and an intracellular catalytic domain. PDGFR
kinase domains are autoinhibited by their juxtamembrane
regions containing tyr residues. The binding to their
ligands leads to receptor dimerization, trans
phosphorylation and activation, and intracellular
signaling. PDGFR subfamily receptors are important in
the development of a variety of cells. PDGFRs are
expressed in a many cells including fibroblasts,
neurons, endometrial cells, mammary epithelial cells,
and vascular smooth muscle cells. PDGFR signaling is
critical in normal embryonic development, angiogenesis,
and wound healing. PDGFRs transduce mitogenic signals
for connective tissue cells and are important for cell
shape and motility. Kit is important in the development
of melanocytes, germ cells, mast cells, hematopoietic
stem cells, the interstitial cells of Cajal, and the
pacemaker cells of the GI tract. CSF-1R signaling is
critical in the regulation of macrophages and
osteoclasts. Mammalian FLT3 plays an important role in
the survival, proliferation, and differentiation of stem
cells.
Length = 302
Score = 28.6 bits (64), Expect = 6.9
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 1 MRQCWAEPPDMRPDFNEVNDL 21
M+ CW P RP F ++ L
Sbjct: 277 MKTCWDADPLKRPTFKQIVQL 297
>gnl|CDD|203945 pfam08439, Peptidase_M3_N, Oligopeptidase F. This domain is found
to the N-terminus of the pfam01432 domain in bacterial
and archaeal proteins including Oligoendopeptidase F. An
example of this protein is Lactococcus lactis PepF.
Length = 70
Score = 26.4 bits (59), Expect = 7.3
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 72 LEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLP 106
L+ Y LE++ R++ L ++ E+LL +
Sbjct: 20 LKPYRFYLEEIRRQKPHTLS---EEEEKLLAALSD 51
Score = 26.4 bits (59), Expect = 7.3
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 119 LEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLP 153
L+ Y LE++ R++ L ++ E+LL +
Sbjct: 20 LKPYRFYLEEIRRQKPHTLS---EEEEKLLAALSD 51
>gnl|CDD|213509 TIGR00134, gatE_arch, glutamyl-tRNA(Gln) amidotransferase, subunit
E. This peptide is found only in the Archaea. It is
paralogous to the gatB-encoded subunit of Glu-tRNA(Gln)
amidotransferase. The GatABC system operates in many
bacteria to convert Glu-tRNA(Gln) into Gln-tRNA(Gln).
However, the homologous system in archaea instead
converts Asp-tRNA(Asn) to Asn-tRNA(Asn). Glu-tRNA(Gln)
is converted to Gln-tRNA(Gln) by a heterodimeric
amidotransferase of GatE (this protein) and GatD. The
Archaea have an Asp-tRNA(Asn) amidotransferase instead
of an Asp--tRNA ligase, but the genes have not been
identified. It is likely that this protein replaces gatB
in Asp-tRNA(Asn) amidotransferase but that both enzymes
share gatA [Protein synthesis, tRNA aminoacylation].
Length = 620
Score = 28.7 bits (64), Expect = 7.5
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 70 QMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKY------- 122
++LE NL +L E+ E++ E +E L ++++ N+VD + EK+
Sbjct: 435 ELLEGIRRNLPELPEEKKERIMREYGLSEDLASQLVKS--NYVDEFEALTEKFRVDPTVI 492
Query: 123 SNNLEDLIRE-RTEQLDIEK 141
++ L +RE R E DI+
Sbjct: 493 ASLLAYTLRELRREGHDIDG 512
>gnl|CDD|236869 PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C;
Provisional.
Length = 396
Score = 28.7 bits (65), Expect = 7.5
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 232 LPVRIPDHADQI--ATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGPCCAGVVGLTMP 288
L V D I AT L L G+ LP PL L++ HT PC G +
Sbjct: 255 LGVDNAGVRDHIEDATEFLRRLLDQGKL----LPLKPLPLKVAYHT-PCHLEKQGWGLY 308
>gnl|CDD|173640 cd05067, PTKc_Lck_Blk, Catalytic domain of the Protein Tyrosine
Kinases, Lymphocyte-specific kinase and Blk. Protein
Tyrosine Kinase (PTK) family; Lck and Blk kinases;
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. Lck (lymphocyte-specific
kinase) and Blk are members of the Src subfamily of
proteins, which are cytoplasmic (or non-receptor) tyr
kinases. Src kinases contain an N-terminal SH4 domain
with a myristoylation site, followed by SH3 and SH2
domains, a tyr kinase domain, and a regulatory
C-terminal region containing a conserved tyr. They are
activated by autophosphorylation at the tyr kinase
domain, but are negatively regulated by phosphorylation
at the C-terminal tyr by Csk (C-terminal Src Kinase).
Src proteins are involved in signaling pathways that
regulate cytokine and growth factor responses,
cytoskeleton dynamics, cell proliferation, survival, and
differentiation. Lck is expressed in T-cells and natural
killer (NK) cells. It plays a critical role in T-cell
maturation, activation, and T-cell receptor (TCR)
signaling. Lck phosphorylates ITAM (immunoreceptor tyr
activation motif) sequences on several subunits of TCRs,
leading to the activation of different second messenger
cascades. Phosphorylated ITAMs serve as binding sites
for other signaling factor such as Syk and ZAP-70,
leading to their activation and propagation of
downstream events. In addition, Lck regulates
drug-induced apoptosis by interfering with the
mitochondrial death pathway. The apototic role of Lck is
independent of its primary function in T-cell signaling.
Blk is expressed specifically in B-cells. It is involved
in pre-BCR (B-cell receptor) signaling.
Length = 260
Score = 28.3 bits (63), Expect = 7.6
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 1 MRQCWAEPPDMRPDF 15
MR CW E P+ RP F
Sbjct: 236 MRLCWKEKPEERPTF 250
>gnl|CDD|173626 cd05034, PTKc_Src_like, Catalytic domain of Src kinase-like Protein
Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family;
Src kinase subfamily; catalytic (c) domain. Src
subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr,
Fyn, Yrk, and Yes. 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.
Src (or c-Src) proteins are cytoplasmic (or
non-receptor) tyr kinases which are anchored to the
plasma membrane. They contain an N-terminal SH4 domain
with a myristoylation site, followed by SH3 and SH2
domains, a tyr kinase domain, and a regulatory
C-terminal region containing a conserved tyr. They are
activated by autophosphorylation at the tyr kinase
domain, but are negatively regulated by phosphorylation
at the C-terminal tyr by Csk (C-terminal Src Kinase).
Src proteins are involved in signaling pathways that
regulate cytokine and growth factor responses,
cytoskeleton dynamics, cell proliferation, survival, and
differentiation. They were identified as the first
proto-oncogene products, and they regulate cell
adhesion, invasion, and motility in cancer cells and
tumor vasculature, contributing to cancer progression
and metastasis. Src kinases are overexpressed in a
variety of human cancers, making them attractive targets
for therapy. They are also implicated in acute
inflammatory responses and osteoclast function. Src,
Fyn, Yes, and Yrk are widely expressed, while Blk, Lck,
Hck, Fgr, and Lyn show a limited expression pattern.
Length = 261
Score = 28.4 bits (64), Expect = 7.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1 MRQCWAEPPDMRPDF 15
M QCW + P+ RP F
Sbjct: 237 MLQCWDKDPEERPTF 251
>gnl|CDD|217899 pfam04108, APG17, Autophagy protein Apg17. Apg17 is required for
activating Apg1 protein kinases.
Length = 408
Score = 28.8 bits (65), Expect = 7.9
Identities = 30/168 (17%), Positives = 60/168 (35%), Gaps = 15/168 (8%)
Query: 63 NFVDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKY 122
+ T+ L + L DL+ T D + T P D + ++L+
Sbjct: 188 PLISTIPSELNSLEHELADLLESLTNHFD--QCVTAVKHTEGDPLDDAEYDELLEVLKND 245
Query: 123 SNNLEDLIRERTEQLDI----EKKKTEQLLNRMLPSSVAEKLKLGMPVDPEDFREV---- 174
+ L D+++E +D EK+ + L + M E+L E+ +
Sbjct: 246 AAELPDVVKELHTVIDEIENNEKRVKKFLSSHMSKI---EELHSATKELLEELEKYKERL 302
Query: 175 TIYFSDIVGFTT-ISAYSTPFEV-VDLLNDLYTCFDATINAYNVYKVE 220
Y + + P + + L++L +D +N+Y +E
Sbjct: 303 PRYLAIFADIRALWEDFKEPIQQYIQELSELCEFYDNFLNSYKGLLLE 350
>gnl|CDD|227548 COG5223, COG5223, Uncharacterized conserved protein [Function
unknown].
Length = 240
Score = 28.5 bits (63), Expect = 7.9
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 7/73 (9%)
Query: 40 RYKNPHLGLRLKSLLYIDSPRKVNFVDTMFQM----LEKYSNNLEDLIRERTEQLDIEKK 95
RYK G + + +S FVD F E++ E+L+ R +L+ ++
Sbjct: 111 RYKPMPCG---TQIKFEESSLHTIFVDMRFGQKEFIPEEFFRTTEELVVRRENRLEKDQI 167
Query: 96 KTEQLLNRMLPRK 108
+ +L + + K
Sbjct: 168 ENNELEDSVFSGK 180
>gnl|CDD|133181 cd05050, PTKc_Musk, Catalytic domain of the Protein Tyrosine
Kinase, Muscle-specific kinase. Protein Tyrosine Kinase
(PTK) family; Muscle-specific kinase (Musk); 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.
Musk is a receptor tyr kinase (RTK) containing an
extracellular region with four immunoglobulin-like
domains and a cysteine-rich cluster, a transmembrane
segment, and an intracellular catalytic domain. Musk is
expressed and concentrated in the postsynaptic membrane
in skeletal muscle. It is essential for the
establishment of the neuromuscular junction (NMJ), a
peripheral synapse that conveys signals from motor
neurons to muscle cells. Agrin, a large proteoglycan
released from motor neurons, stimulates Musk
autophosphorylation and activation, leading to the
clustering of acetylcholine receptors (AChRs). To date,
there is no evidence to suggest that agrin binds
directly to Musk. Mutations in AChR, Musk and other
partners are responsible for diseases of the NMJ, such
as the autoimmune syndrome myasthenia gravis.
Length = 288
Score = 28.3 bits (63), Expect = 8.3
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 1 MRQCWAEPPDMRPDFNEVN 19
MR CW++ P RP F +N
Sbjct: 265 MRLCWSKLPSDRPSFASIN 283
>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 438
Score = 28.6 bits (64), Expect = 8.4
Identities = 16/101 (15%), Positives = 41/101 (40%), Gaps = 5/101 (4%)
Query: 55 YIDSPRKVNFVDTMF--QMLEKYSN-NLEDLIRERTEQLDIEKKKTEQLLNRMLPRKVNF 111
I S +++ V M ++ + N ++L + + + TE+ +
Sbjct: 314 TICSYKEMYGVRPMLFIALIGLFRNRAAQELALTKVQIIYY--YLTEKEFEAFVEAIDEK 371
Query: 112 VDTMFQMLEKYSNNLEDLIRERTEQLDIEKKKTEQLLNRML 152
++ LEK + ++R ++++ + TE +L +L
Sbjct: 372 LENTQLDLEKEKKAIIRAWKKREKEIEKLIESTENMLGSLL 412
>gnl|CDD|133171 cd05039, PTKc_Csk_like, Catalytic domain of C-terminal Src
kinase-like Protein Tyrosine Kinases. Protein Tyrosine
Kinase (PTK) family; C-terminal Src kinase (Csk)
subfamily; catalytic (c) domain. The Csk subfamily is
composed of Csk, Chk, 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. Csk
subfamily kinases are cytoplasmic (or nonreceptor) tyr
kinases containing the Src homology domains, SH3 and
SH2, N-terminal to the catalytic tyr kinase domain. They
negatively regulate the activity of Src kinases that are
anchored to the plasma membrane. To inhibit Src kinases,
Csk and Chk are translocated to the membrane via binding
to specific transmembrane proteins, G-proteins, or
adaptor proteins near the membrane. Csk catalyzes the
tyr phosphorylation of the regulatory C-terminal tail of
Src kinases, resulting in their inactivation. Chk
inhibit Src kinases using a noncatalytic mechanism by
simply binding to them. As negative regulators of Src
kinases, Csk and Chk play important roles in cell
proliferation, survival, and differentiation, and
consequently, in cancer development and progression.
Length = 256
Score = 28.1 bits (63), Expect = 8.5
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 1 MRQCWAEPPDMRPDFNEV 18
M+ CW P RP F ++
Sbjct: 232 MKDCWELDPAKRPTFKQL 249
>gnl|CDD|225593 COG3051, CitF, Citrate lyase, alpha subunit [Energy production and
conversion].
Length = 513
Score = 28.6 bits (64), Expect = 8.5
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 216 VYKVETIGDAYMVVGGLPVRIPDHADQ--IATMALDLLHHSGRFK 258
V +V+ +GD + G R+ + + IA A D++ +SG FK
Sbjct: 229 VVQVDAVGDPKKIGAG-ATRMTTNPRELLIARSAADVIVNSGYFK 272
>gnl|CDD|173625 cd05032, PTKc_InsR_like, Catalytic domain of Insulin Receptor-like
Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK)
family; Insulin Receptor (InsR) subfamily; 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). The InsR subfamily
is composed of InsR, Insulin-like Growth Factor-1
Receptor (IGF-1R), and similar proteins. PTKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. InsR and
IGF-1R are receptor tyr kinases (RTKs) composed of two
alphabeta heterodimers. Binding of the ligand (insulin,
IGF-1, or IGF-2) to the extracellular alpha subunit
activates the intracellular tyr kinase domain of the
transmembrane beta subunit. Receptor activation leads to
autophosphorylation, stimulating downstream kinase
activities, which initiate signaling cascades and
biological function. InsR and IGF-1R, which share 84%
sequence identity in their kinase domains, display
physiologically distinct yet overlapping functions in
cell growth, differentiation, and metabolism. InsR
activation leads primarily to metabolic effects while
IGF-1R activation stimulates mitogenic pathways. In
cells expressing both receptors, InsR/IGF-1R hybrids are
found together with classical receptors. Both receptors
can interact with common adaptor molecules such as IRS-1
and IRS-2.
Length = 277
Score = 28.5 bits (64), Expect = 8.7
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 1 MRQCWAEPPDMRPDFNEV 18
MR CW P MRP F E+
Sbjct: 254 MRMCWQYNPKMRPTFLEI 271
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 28.3 bits (64), Expect = 9.8
Identities = 21/99 (21%), Positives = 45/99 (45%), Gaps = 10/99 (10%)
Query: 79 LEDLIRE---RTEQLDIEKKKTEQLLNRMLPRKVNFVDTMFQMLEKYSNNLEDLIRERTE 135
L++ R+ E+L E+ + + + R L R + + + +++ L++L
Sbjct: 34 LDEERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKEL----EA 89
Query: 136 QLDIEKKKTEQLLNRMLPSSVAEKLKLGMPVDPEDFREV 174
LD + + + LL +P+ E + +G D +D EV
Sbjct: 90 ALDELEAELDTLLLT-IPNIPHESVPVG--KDEDDNVEV 125
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 0.136 0.399
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,889,497
Number of extensions: 2444600
Number of successful extensions: 2650
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2618
Number of HSP's successfully gapped: 117
Length of query: 487
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 386
Effective length of database: 6,457,848
Effective search space: 2492729328
Effective search space used: 2492729328
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: 61 (27.1 bits)