RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy946
(714 letters)
>gnl|CDD|214823 smart00799, DENN, Domain found in a variety of signalling proteins,
always encircled by uDENN and dDENN. The DENN domain is
found in a variety of signalling proteins involved in
Rab-mediated processes or regulation of MAPKs signalling
pathways. The DENN domain is always encircled on both
sides by more divergent domains, called uDENN (for
upstream DENN) and dDENN (for downstream DENN). The
function of the DENN domain remains to date unclear,
although it appears to represent a good candidate for a
GTP/GDP exchange activity.
Length = 183
Score = 168 bits (429), Expect = 9e-49
Identities = 61/186 (32%), Positives = 99/186 (53%), Gaps = 6/186 (3%)
Query: 88 SDTSMVIISLLPWHESFYKLLNCVVEITNGSSPQLLWTFLEDIYNANIPEYG--QIIYAT 145
+ + I+S LP+ E F K+LN + + SS L L + +P G ++ +
Sbjct: 1 APKCICILSRLPFFELFRKILNELYRLLPSSSNLPLE-LLISLLLYPVPPPGGSLVLVSL 59
Query: 146 SKNTEYTCQAPNQYQLPSIPENKNLTEYC-AIEPVNMLHIFASMLYERRIVITSKRLSRV 204
Q P LP I +L E + N+L +FA++L ERRI+ TS LS +
Sbjct: 60 GPGDLIELQRPLDSSLPLID--FSLHELFECLGVENILQLFAALLLERRIIFTSSNLSTL 117
Query: 205 SACVQAANSVIYPMCWQHIFIPLMPRDLLDYLTAPMPYMVGLPEILLDSVRRNELGDVVL 264
SA ++A +++YP WQHI+IP++P LLD L+AP P+++G+ + V+ DVV+
Sbjct: 118 SAVIEALLALLYPFVWQHIYIPILPASLLDVLSAPTPFIIGVHSSYFEEVKELPDEDVVV 177
Query: 265 LNADTN 270
++ DT
Sbjct: 178 VDLDTG 183
Score = 130 bits (329), Expect = 6e-35
Identities = 43/113 (38%), Positives = 70/113 (61%), Gaps = 1/113 (0%)
Query: 278 DLNTLPQDVKNLTEYC-AIEPVNMLHIFASMLYERRIVITSKRLSRVSACVQAANLVIYP 336
++LP +L E + N+L +FA++L ERRI+ TS LS +SA ++A ++YP
Sbjct: 71 LDSSLPLIDFSLHELFECLGVENILQLFAALLLERRIIFTSSNLSTLSAVIEALLALLYP 130
Query: 337 MCWQHIFIPLMPRDLLDYLTAPMPYMVGLPEILLDSVRRNELGDVVLLNADTN 389
WQHI+IP++P LLD L+AP P+++G+ + V+ DVV+++ DT
Sbjct: 131 FVWQHIYIPILPASLLDVLSAPTPFIIGVHSSYFEEVKELPDEDVVVVDLDTG 183
>gnl|CDD|216898 pfam02141, DENN, DENN (AEX-3) domain. DENN (after differentially
expressed in neoplastic vs normal cells) is a domain
which occurs in several proteins involved in Rab-
mediated processes or regulation of MAPK signalling
pathways.
Length = 185
Score = 150 bits (380), Expect = 7e-42
Identities = 60/185 (32%), Positives = 97/185 (52%), Gaps = 7/185 (3%)
Query: 90 TSMVIISLLPWHESFYKLLNCVVEITNGSSPQLLWTFL-EDIYNANIPEYG--QIIYATS 146
+ IIS LP+ E F K L+ + S P L F+ +Y P G Q++
Sbjct: 4 KAYCIISRLPFFELFKKFLDELYTRRTISPPLPLERFIANLLYEVPFPPPGRTQVLKPLG 63
Query: 147 KNTEYTCQAPNQYQLPSIPENKNLTE-YCAIEPVNMLHIFASMLYERRIVITSKRLSRVS 205
Q P+ +LP +L + + P N+L +F + L ERRI+ S RL+R++
Sbjct: 64 VTELILLQRPSDSELP--LSGVDLHLLFRCLGPENVLQLFEAALTERRIIFLSSRLARLT 121
Query: 206 ACVQAANSVIYPMCWQHIFIPLMPRDLLDYLTAPMPYMVGLPEILLDSVRRNELGDVVLL 265
+A +++YP WQHI+IP++P LLD L+AP P+++G+ D + + L DVV++
Sbjct: 122 LVAEALVALLYPFKWQHIYIPVLPASLLDVLSAPTPFIIGVHSRYFD-LLEDPLDDVVIV 180
Query: 266 NADTN 270
+ DT
Sbjct: 181 DLDTG 185
Score = 114 bits (287), Expect = 3e-29
Identities = 38/94 (40%), Positives = 61/94 (64%), Gaps = 1/94 (1%)
Query: 296 EPVNMLHIFASMLYERRIVITSKRLSRVSACVQAANLVIYPMCWQHIFIPLMPRDLLDYL 355
P N+L +F + L ERRI+ S RL+R++ +A ++YP WQHI+IP++P LLD L
Sbjct: 93 GPENVLQLFEAALTERRIIFLSSRLARLTLVAEALVALLYPFKWQHIYIPVLPASLLDVL 152
Query: 356 TAPMPYMVGLPEILLDSVRRNELGDVVLLNADTN 389
+AP P+++G+ D + + L DVV+++ DT
Sbjct: 153 SAPTPFIIGVHSRYFD-LLEDPLDDVVIVDLDTG 185
>gnl|CDD|202641 pfam03455, dDENN, dDENN domain. This region is always found
associated with pfam02141. It is predicted to form a
globular domain. This domain is predicted to be
completely alpha helical. Although not statistically
supported it has been suggested that this domain may be
similar to members of the Rho/Rac/Cdc42 GEF family.
Length = 66
Score = 80.7 bits (200), Expect = 7e-19
Identities = 31/66 (46%), Positives = 42/66 (63%)
Query: 419 GDGVARAFLRALVQLIGGYRDALKFHQGQEITFNDAAFVESRPAAMQPFLRKMLDLQIFQ 478
D V AFLR L GGYR L++ +G ITF +F++SRP + +PFL + L+ Q+F
Sbjct: 1 DDQVREAFLRFFASLFGGYRSFLRYIRGSPITFQKESFLKSRPKSHRPFLSRFLETQMFA 60
Query: 479 QFKEER 484
QF EER
Sbjct: 61 QFIEER 66
>gnl|CDD|129037 smart00801, dDENN, Domain always found downstream of DENN domain,
found in a variety of signalling proteins. The dDENN
domain is part of the tripartite DENN domain. It is
always found downstream of the DENN domain itself, which
is found in a variety of signalling proteins involved in
Rab-mediated processes or regulation of MAPKs signalling
pathways. The DENN domain is always encircled on both
sides by more divergent domains, called uDENN (for
upstream DENN) and dDENN (for downstream DENN). The
function of the DENN domain remains to date unclear,
although it appears to represent a good candidate for a
GTP/GDP exchange activity.
Length = 69
Score = 75.0 bits (185), Expect = 8e-17
Identities = 32/69 (46%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 419 GDGVARAFLRALVQLIGGYRDALKF---HQGQEITFNDAAFVESRPAAMQPFLRKMLDLQ 475
D + AFLR V L GGYR+ L+ G ITF+ +F++SRP++ +PFL K L+ Q
Sbjct: 1 NDEIREAFLRFFVNLFGGYRNFLRELRKEPGPVITFDKESFLKSRPSSERPFLSKFLETQ 60
Query: 476 IFQQFKEER 484
+F QF EER
Sbjct: 61 MFSQFIEER 69
>gnl|CDD|214824 smart00800, uDENN, Domain always found upstream of DENN domain,
found in a variety of signalling proteins. The uDENN
domain is part of the tripartite DENN domain. It is
always found upstream of the DENN domain itself, which
is found in a variety of signalling proteins involved
in Rab-mediated processes or regulation of MAPKs
signalling pathways. The DENN domain is always
encircled on both sides by more divergent domains,
called uDENN (for upstream DENN) and dDENN (for
downstream DENN). The function of the DENN domain
remains to date unclear, although it appears to
represent a good candidate for a GTP/GDP exchange
activity.
Length = 89
Score = 58.1 bits (141), Expect = 1e-10
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 13/85 (15%)
Query: 12 KHLFECFCEVARPQGKEPAW------VLQKFP-GSYKDESVLKNVPKFAYPCKLENTS-- 62
LF+ F V P +LQ++P ++D + ++P F +P L+ +
Sbjct: 2 SRLFDYFVVVGLDSDTGPLGRSYKPEILQRYPEKDFEDFPLPDSIPLFCFPEGLDFVTQT 61
Query: 63 ----VEYYSFVLTDLDSKFTFGYCR 83
+++SFVLTD+D +G+C
Sbjct: 62 SSKDPQFFSFVLTDIDGSRRYGFCL 86
>gnl|CDD|217569 pfam03456, uDENN, uDENN domain. This region is always found
associated with pfam02141. It is predicted to form an
all beta domain.
Length = 62
Score = 51.1 bits (123), Expect = 2e-08
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 32 VLQKFPGS-YKDESVLKNVPKFAYPCKLE-----NTSVEYYSFVLTDLDSKFTFGYCR 83
VL +FP ++D VP F +P L+ +++SFVLTD D +G+C
Sbjct: 4 VLDRFPEKDHRDPPFPDAVPMFCFPEGLDFVTSREQEPQFFSFVLTDEDGSRRYGFCL 61
>gnl|CDD|200362 TIGR04111, BcepMu_gp16, phage-associated protein, BcepMu gp16
family. Members of this protein family occur in
Burkholderia phage BcepMu, Pseudomonas phage B3, and
Burkholderia phage KS10, and many bacterial putative
prophage regions. The member from Burkholderia phage
BcepMu is named gp16. Homology suggests DNA-binding
activity [Mobile and extrachromosomal element functions,
Prophage functions].
Length = 55
Score = 31.4 bits (72), Expect = 0.12
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 579 QQYKEWLRTVGKEGRAFVKTWVRERGKDVRFVYKGLRSKLK 619
+Q K R G + W RE G R VY+ L + K
Sbjct: 3 EQAKAEFRRQGIS----IAQWARENGFSPRLVYRVLNGRRK 39
>gnl|CDD|234218 TIGR03459, crt_membr, carotene biosynthesis associated membrane
protein. This model represents a family of hydrophobic
and presumed membrane proteins found in the
Actinobacteria. The genes encoding these proteins are
syntenically associated with (found proximal to) genes
of carotene biosynthesis ususally including phytoene
synthase (crtB), phytoene dehydrogenase (crtI) and
geranylgeranyl pyrophosphate synthase (ispA).
Length = 470
Score = 32.4 bits (74), Expect = 0.80
Identities = 42/147 (28%), Positives = 60/147 (40%), Gaps = 38/147 (25%)
Query: 301 LHIFASMLYERRIVITSKRLSRVSACVQAANLVIYPMCWQHIF-IPLMPRDLLDYLTAPM 359
L I A ++ RR+++ + L V A + + I P+ +F +P+M RD+ YL
Sbjct: 56 LMILAWVILGRRVLVGAATLHTVRATIA---IWIGPL----LFAVPMMSRDVYSYLMQGA 108
Query: 360 -------PYMVGL---PEILLDSVRRNELGDVVLLNADTNVLTTPHDDLNTLPQDVIATL 409
PY VG P LLD V + D TTP+ L+ L I T+
Sbjct: 109 LLRDGFDPYTVGAAANPGPLLDEV-----------SPDWRNTTTPYGPLHLLVGQAITTV 157
Query: 410 KKQLRNKTTGDGV-ARAFLRALVQLIG 435
TGD V A L+ L G
Sbjct: 158 --------TGDNVTAGTLAFKLLSLPG 176
>gnl|CDD|222011 pfam13257, DUF4048, Domain of unknown function (DUF4048). This
presumed domain is functionally uncharacterized. This
domain family is found in eukaryotes, and is typically
between 228 and 257 amino acids in length.
Length = 242
Score = 31.3 bits (71), Expect = 1.4
Identities = 14/23 (60%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 123 LWTFLEDIYNANIPEYGQIIYAT 145
LWTFLEDI A + E G I AT
Sbjct: 97 LWTFLEDIRQATVGEEG--INAT 117
>gnl|CDD|222973 PHA03081, PHA03081, putative metalloprotease; Provisional.
Length = 595
Score = 31.5 bits (72), Expect = 1.8
Identities = 33/162 (20%), Positives = 54/162 (33%), Gaps = 50/162 (30%)
Query: 345 PLMPRDLLDYLTAPMPYMVGLPEILLDSVRRNEL-----GDVV---------LLNA-DT- 388
P + D+ DY+T + + LL S+ R+ D + + N D
Sbjct: 298 PWLSHDIFDYIT----TINDNSKSLLKSLERDIYASIRERDYIVIYPNFSKSIFNTRDRQ 353
Query: 389 -------NVLTTPHDDLNTLPQDVIATLKKQLRNKTT---GDGVARAFLRALVQLIGGYR 438
+ + N P+ I +KKQ N+ GD + + V L GY+
Sbjct: 354 RHKIVVLDCPDNNNIGRNHKPKRSIPLMKKQTSNEIFIRYGDA---SLID-YVTLALGYK 409
Query: 439 DALKFHQGQEIT-------------FNDAAFVE---SRPAAM 464
D + I F++ S+PAAM
Sbjct: 410 DNKLKRTNEGIRIRHQFSADDIKAIMESDTFLKYSKSKPAAM 451
>gnl|CDD|241513 cd13359, PH_ELMO1_CED-12, Engulfment and cell motility protein 1
pleckstrin homology (PH) domain. DOCK2 (Dedicator of
cytokinesis 2), a hematopoietic cell-specific, atypical
GEF, controls lymphocyte migration through Rac
activation. A DOCK2-ELMO1 complex s necessary for
DOCK2-mediated Rac signaling. DOCK2 contains a SH3
domain at its N-terminus, followed by a lipid binding
DHR1 domain, and a Rac-binding DHR2 domain at its
C-terminus. ELMO1, a mammalian homolog of C. elegans
CED-12, contains the N-terminal RhoG-binding region, the
ELMO domain, the PH domain, and the C-terminal sequence
with three PxxP motifs. The C-terminal region of ELMO1,
including the Pro-rich sequence, binds the
SH3-containing region of DOCK2 forming a intermolecular
five-helix bundle along with the PH domain of ELMO1.
Autoinhibition of ELMO1 and DOCK2 is accomplished by the
interactions of the EID and EAD domains and SH3 and DHR2
domains, respectively. The interaction of DOCK2 and
ELMO1 mutually relieve their autoinhibition and results
in the activation of Rac1. The PH domain of ELMO1 does
not bind phosphoinositides due to the absence of key
binding residues. It more closely resembles the FERM
domain rather than other PH domains. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 126
Score = 28.8 bits (65), Expect = 4.8
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 577 VKQQYKEWLRTVGKEGRAFVKTWVRERGKDVRFVYKGLRSKLKEDKHGEAKSHSAPSSPT 636
+KQQ +L EG F K R R KD +F Y L K +G+ + + P+
Sbjct: 3 IKQQRLNFL----VEGTLFPKYNARRR-KD-KFWYCRLSPNHKVLHYGDCEESAQPAPLE 56
Query: 637 QLRKK 641
L +K
Sbjct: 57 SLPEK 61
>gnl|CDD|163499 TIGR03787, marine_sort_RR, proteobacterial dedicated sortase system
response regulator. This model describes a family of
DNA-binding response regulator proteins, associated with
an adjacent histidine kinase (TIGR03785) to form a
two-component system. This system co-occurs with, and
often is adjacent to, a proteobacterial variant form of
the protein sorting transpeptidase called sortase
(TIGR03784), and a single target protein for the
sortase. We give this protein the gene symbol pdsR, for
Proteobacterial Dedicated Sortase system Response
regulator.
Length = 227
Score = 29.3 bits (66), Expect = 6.6
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 6/40 (15%)
Query: 437 YRDALKFHQGQEITFNDAAFVESRPAAMQPFLRKMLDLQI 476
Y DALK Q T+ D RP+AMQ F +++ DL I
Sbjct: 16 YADALKRQGYQVTTYAD------RPSAMQAFRQRLPDLAI 49
>gnl|CDD|182325 PRK10239, PRK10239,
2-amino-4-hydroxy-6-hydroxymethyldihyropteridine
pyrophosphokinase; Provisional.
Length = 159
Score = 28.6 bits (64), Expect = 7.9
Identities = 24/75 (32%), Positives = 32/75 (42%), Gaps = 21/75 (28%)
Query: 226 PLMPRDLLDYLTAPMPYMVGL-PEILLDSVRRNELG-----------------DVVLLNA 267
PL P+D DYL A + L PE LL+ +R EL D++L
Sbjct: 45 PLGPQDQPDYLNAAVALETALAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGN 104
Query: 268 D---TNVLTTPHDDL 279
+ T LT PH D+
Sbjct: 105 EVINTERLTVPHYDM 119
Score = 28.6 bits (64), Expect = 7.9
Identities = 24/75 (32%), Positives = 32/75 (42%), Gaps = 21/75 (28%)
Query: 345 PLMPRDLLDYLTAPMPYMVGL-PEILLDSVRRNELG-----------------DVVLLNA 386
PL P+D DYL A + L PE LL+ +R EL D++L
Sbjct: 45 PLGPQDQPDYLNAAVALETALAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGN 104
Query: 387 D---TNVLTTPHDDL 398
+ T LT PH D+
Sbjct: 105 EVINTERLTVPHYDM 119
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 29.1 bits (66), Expect = 10.0
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 13/66 (19%)
Query: 363 VGLPEILLDSVRR--NELGDVVL-----LNADTNVLTTPHDDLNTLPQDVIATLKKQLRN 415
+ LPE + V+ EL ++ + LN DT L ++L LP+D + L+K
Sbjct: 119 LDLPEATRERVKALKKELSELSIKFSKNLNEDTTFLWFTEEELEGLPEDYLDALEK---- 174
Query: 416 KTTGDG 421
T DG
Sbjct: 175 --TEDG 178
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 0.408
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,509,065
Number of extensions: 3586421
Number of successful extensions: 2744
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2737
Number of HSP's successfully gapped: 20
Length of query: 714
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 610
Effective length of database: 6,324,786
Effective search space: 3858119460
Effective search space used: 3858119460
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: 63 (28.0 bits)