RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8588
(265 letters)
>gnl|CDD|241491 cd13337, PX-FERM_C_SNX17, sorting nexin 17 Phox FERM-like domain
C-lobe. SNX17 is a beta1-integrin-tail-binding protein
that interacts with the free kindlin-binding site in
endosomes to stabilize beta1 integrins, resulting in
their recycling to the cell surface where they can be
reused. SNX17 contains a N-terminal PX domain, a
FERM-like domain, and a unique C-terminal region. SNX17
binds Ras GTPase through its FERM-like domains. The PX
domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. These interactions place the
PX-FERM-like proteins at a hub of endosomal sorting and
signaling processes. These proteins participate in a
network of interactions that will impact on both
endosomal protein trafficking and compartment specific
Ras signaling cascades. The FERM domain has a cloverleaf
tripart structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3
within the FERM domain is part of the PH domain family.
The FERM domain is found in the cytoskeletal-associated
proteins such as ezrin, moesin, radixin, 4.1R, and
merlin. These proteins provide a link between the
membrane and cytoskeleton and are involved in signal
transduction pathways. The FERM domain is also found in
protein tyrosine phosphatases (PTPs) , the tyrosine
kinases FAK and JAK, in addition to other proteins
involved in signaling. This domain is structurally
similar to the PH and PTB domains and consequently is
capable of binding to both peptides and phospholipids at
different sites.
Length = 114
Score = 173 bits (440), Expect = 3e-55
Identities = 69/123 (56%), Positives = 96/123 (78%), Gaps = 10/123 (8%)
Query: 128 DLARKLKYYGFIEFEPCTCDFPKPNTKVVVNIGLREINFRIRSSEGEIREGTFKVTRMRC 187
LAR LKYYG+I+FEPC CD+PKPNT+V+V+IG RE+NFR++ + +++EG+F+VTRMRC
Sbjct: 2 RLARTLKYYGYIQFEPCICDYPKPNTRVLVSIGNRELNFRVKLEDDKVKEGSFRVTRMRC 61
Query: 188 WKITINKEEDNDASNARHNTSQANQTQLSFEYLLAKNKLQWITIQSNQAILMSNLLQSII 247
W+IT +E++D +LSFEYL++K+KLQWIT++S QAILMS LQS++
Sbjct: 62 WRITSTHDEESDEVG----------LELSFEYLMSKDKLQWITLRSEQAILMSMCLQSMV 111
Query: 248 DEL 250
DEL
Sbjct: 112 DEL 114
Score = 52.3 bits (126), Expect = 7e-09
Identities = 19/26 (73%), Positives = 22/26 (84%)
Query: 18 DLARKLKYYGFIEFEPCTCDFPKPNI 43
LAR LKYYG+I+FEPC CD+PKPN
Sbjct: 2 RLARTLKYYGYIQFEPCICDYPKPNT 27
>gnl|CDD|241361 cd13207, PX-FERM_C_SNX, sorting nexin family Phox FERM-like domain
C-lobe. Sorting nexins function in regulating recycling
from endosomes to the cell surface. SNX17, SNX27, and
SNX31 contain a N-terminal PX domain, a FERM-like
domain, and a unique C-terminal region. All three
proteins are able to bind the Ras GTPase through their
FERM-like domains. The PX domain of SNXs binds PIs and
targets the protein to PI-enriched membranes. These
interactions place the PX-FERM-like proteins at a hub of
endosomal sorting and signaling processes. These
proteins participate in a network of interactions that
will impact on both endosomal protein trafficking and
compartment specific Ras signaling cascades. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 121
Score = 119 bits (300), Expect = 4e-34
Identities = 53/124 (42%), Positives = 87/124 (70%), Gaps = 3/124 (2%)
Query: 127 VDLARKLKYYGFIEFEPCTCDFPKPNTKVVVNIGLREINFRIRSSEGEIREGTFKVTRMR 186
++LA+ L++YG+I F+ C+CDFP+ V V+ G E++ +I+ + EG+FKVTRMR
Sbjct: 1 LNLAQTLEHYGYIIFDHCSCDFPEKGCIVAVSAGNNELSAQIKLPCTQEGEGSFKVTRMR 60
Query: 187 CWKITINKEEDNDASNARHNTSQANQTQLSFEYLLAKNKLQWITIQSNQAILMSNLLQSI 246
CW++T + D S+++ + +L+FEYL++K++LQW+TI + QAI+MS LQS+
Sbjct: 61 CWRVTSSWPLDEG-SDSQQTLEV--RLELAFEYLMSKDRLQWVTIFTPQAIMMSICLQSM 117
Query: 247 IDEL 250
+DEL
Sbjct: 118 VDEL 121
Score = 42.2 bits (99), Expect = 3e-05
Identities = 12/25 (48%), Positives = 21/25 (84%)
Query: 17 VDLARKLKYYGFIEFEPCTCDFPKP 41
++LA+ L++YG+I F+ C+CDFP+
Sbjct: 1 LNLAQTLEHYGYIIFDHCSCDFPEK 25
>gnl|CDD|241490 cd13336, PX-FERM_C_SNX31, sorting nexin family Phox FERM-like
domain C-lobe. SNX31 functions in regulating recycling
from endosomes to the cell surface. SNX31 contain a
N-terminal PX domain, a FERM-like domain, and a unique
C-terminal region. It bind Ras GTPase through its
FERM-like domains. The PX domain of SNXs binds PIs and
targets the protein to PI-enriched membranes. These
interactions place the PX-FERM-like proteins at a hub of
endosomal sorting and signaling processes. These
proteins participate in a network of interactions that
will impact on both endosomal protein trafficking and
compartment specific Ras signaling cascades. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 118
Score = 87.2 bits (216), Expect = 8e-22
Identities = 38/125 (30%), Positives = 81/125 (64%), Gaps = 10/125 (8%)
Query: 127 VDLARKLKYYGFIEFEPCTCDFPKPNTKVVVNIGLREINFRIRSSEGEIREGTFKVTRMR 186
++LA+++++YG+++ +PCTCD+P+ ++V V++G EI+ I+ + + +E FK++R++
Sbjct: 1 LELAQEVQHYGYLQLDPCTCDYPECGSEVNVSVGNNEISCCIKLPDNQTQEVRFKISRVK 60
Query: 187 CWKITI--NKEEDNDASNARHNTSQANQTQLSFEYLLAKNKLQWITIQSNQAILMSNLLQ 244
CW++T +++ ++ ++ +L FEY + +WITI + QA L+S+ L+
Sbjct: 61 CWQVTFLGTLKQEVMSTLNQN-------LELKFEY-NESSSWKWITIYTKQAFLLSSCLK 112
Query: 245 SIIDE 249
+I E
Sbjct: 113 KMISE 117
Score = 38.3 bits (89), Expect = 7e-04
Identities = 15/58 (25%), Positives = 34/58 (58%), Gaps = 8/58 (13%)
Query: 17 VDLARKLKYYGFIEFEPCTCDFPKPNISSYWDLEYDLELMCYVAL-------ISFNMS 67
++LA+++++YG+++ +PCTCD+P+ + + E+ C + L + F +S
Sbjct: 1 LELAQEVQHYGYLQLDPCTCDYPECGSEVNVSVGNN-EISCCIKLPDNQTQEVRFKIS 57
>gnl|CDD|241492 cd13338, PX-FERM_C_SNX27, sorting nexin family Phox FERM-like
domain C-lobe. SNX27 is localized to early endosomes
and known to regulate the intracellular trafficking of
ion channels and receptors. SNX27 contain a N-terminal
PDZ domain, a PX domain, and a FERM-like domain. SNX27
regulates trafficking of a PAK interacting exchange
factor-G protein-coupled receptor kinase interacting
protein complex via its PDZ domain interaction. Sorting
nexin 27 interacts with multidrug resistance-associated
protein 4 (MRP4). SNX27 binds Ras GTPase through its
FERM-like domains. The PX domain of SNXs binds PIs and
targets the protein to PI-enriched membranes. These
interactions place the PX-FERM-like proteins at a hub of
endosomal sorting and signaling processes. These
proteins participate in a network of interactions that
will impact on both endosomal protein trafficking and
compartment specific Ras signaling cascades. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 107
Score = 31.9 bits (73), Expect = 0.095
Identities = 22/122 (18%), Positives = 43/122 (35%), Gaps = 17/122 (13%)
Query: 129 LARKLKYYGFIEFEPCTCDFPKPNTKVVVNIGLREINFRIRSSEGEIREGTFKVTRMRCW 188
LAR L+ Y + F C CD K V+ ++ ++ + +G++ + W
Sbjct: 3 LARTLEGYNEVVFPHCACDSRK-EGHVIPSVSIKAFKLHACTEDGQLESQEIEFE----W 57
Query: 189 KITINKEEDNDASNARHNTSQANQTQLSFEYLLAKNKLQWITIQSNQAILMSNLLQSIID 248
E D + FEY + K +W+ + + M + + +
Sbjct: 58 DEIQRWETDEEG------------MAFCFEYSRPEKKPRWVKVFTPYYNYMHECFERVQE 105
Query: 249 EL 250
E
Sbjct: 106 ER 107
Score = 27.7 bits (62), Expect = 2.6
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 19 LARKLKYYGFIEFEPCTCD 37
LAR L+ Y + F C CD
Sbjct: 3 LARTLEGYNEVVFPHCACD 21
>gnl|CDD|205234 pfam13053, DUF3914, Protein of unknown function (DUF3914). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 110 amino acids in length.
There are two conserved sequence motifs: KFDIR and DLW.
Length = 92
Score = 28.7 bits (64), Expect = 0.85
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 145 TCDFPKPNTKVVVNIGLREINFRIRSSEGEIREGTFKVTRMRCWKITINK 194
T PK K N I F IRSSE E+++ + K T + WK+ +K
Sbjct: 25 TQSSPKTQGKENNNDDG--IKFDIRSSEKEMKQASHKFTELDLWKMLKDK 72
>gnl|CDD|189007 cd09600, M1_APN_1, Peptidase M1 family containing Aminopeptidase N.
This family contains aminopeptidase N (APN; CD13;
Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral
membrane protease belonging to the M1 gluzincin family.
It includes bacterial-type alanyl aminopeptidases as
well as PfA-M1 aminopeptidase (Plasmodium
falciparum-type). 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 = 861
Score = 30.3 bits (69), Expect = 1.2
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 5/25 (20%)
Query: 47 WD-----LEYDLELMCYVALISFNM 66
WD LEYDL+L VA+ FNM
Sbjct: 228 WDEDRFGLEYDLDLFNIVAVDDFNM 252
>gnl|CDD|132766 cd07305, Porin3_Tom40, Translocase of outer mitochondrial membrane
40 (Tom40). Tom40 forms a channel in the mitochondrial
outer membrane with a pore about 1.5 to 2.5 nanometers
wide. It functions as a transport channel for unfolded
protein chains and forms a complex with Tom5, Tom6,
Tom7, and Tom22. The primary receptors Tom20 and Tom70
recruit the unfolded precursor protein from the
mitochondrial-import stimulating factor (MSF) or
cytosolic Hsc70. The precursor passes through the Tom40
channel and through another channel in the inner
membrane, formed by Tim23, to be finally translocated
into the mitochondrial matrix. The process depends on a
proton motive force across the inner membrane and
requires a contact site where the outer and inner
membranes come close. Tom40 is also involved in
inserting outer membrane proteins into the membrane,
most likely not via a lateral opening in the pore, but
by transfering precursor proteins to an outer membrane
sorting and assembly machinery.
Length = 279
Score = 27.6 bits (62), Expect = 6.4
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 208 SQANQTQLSFEYLLAKN----KLQWITIQSNQAILMSNLLQSIIDELVL 252
S+ N +QL +Y KL I + I +++ LQS+ +L L
Sbjct: 103 SKFNMSQLELDYRGDDFTASLKLANPDILNETGIYVASYLQSVTPKLAL 151
>gnl|CDD|235050 PRK02546, PRK02546, NAD(P)H-quinone oxidoreductase subunit 4;
Provisional.
Length = 525
Score = 27.7 bits (62), Expect = 7.8
Identities = 18/73 (24%), Positives = 24/73 (32%), Gaps = 29/73 (39%)
Query: 5 MRFYPEVTPFQYVDLARKLKYYGFIEFEPCTCDFPKPNISSYWDLEYDLELMCYVA-LIS 63
M FY + F LA K DF +L+CY LI+
Sbjct: 188 MAFYGDTPTFDMTALAAK--------------DFGL-----------GFQLLCYAGLLIA 222
Query: 64 FNMS---SPLHYW 73
+ + PLH W
Sbjct: 223 YGVKLPIVPLHTW 235
>gnl|CDD|220914 pfam10950, DUF2775, Protein of unknown function (DUF2775). This
eukaryotic family of proteins has no known function.
Length = 108
Score = 26.2 bits (57), Expect = 9.1
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 6/44 (13%)
Query: 9 PEVTPFQYVDLARKLKYYGFIEFEPCTCDFPKPNISSYWDLEYD 52
P ++ + D+ K K +FEP PNIS+Y D E D
Sbjct: 50 PNISAYDDNDIDNKEKKKAIEDFEPK------PNISAYGDNEID 87
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
0.320 0.135 0.410
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,339,075
Number of extensions: 1244525
Number of successful extensions: 906
Number of sequences better than 10.0: 1
Number of HSP's gapped: 903
Number of HSP's successfully gapped: 20
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.1 bits)