RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14168
(276 letters)
>gnl|CDD|216919 pfam02181, FH2, Formin Homology 2 Domain.
Length = 372
Score = 154 bits (391), Expect = 1e-44
Identities = 62/179 (34%), Positives = 93/179 (51%), Gaps = 6/179 (3%)
Query: 74 EKLLSMLPTDEEKCKILEAVSANPGVPLGSAENFLLELSNINELVARLKLWAFKLDYENL 133
E LL M PT EE K+ E LG AE FLLELS I L RL+ FK +E
Sbjct: 118 ENLLKMAPTKEELKKLKEY--KGDPSKLGRAEQFLLELSKIPRLEERLEALLFKSTFEEE 175
Query: 134 EREVAEPLMDLKQGMDILRRNPTFKAILSTLLSIGIFLNGT----EVKGFQIEYLTKVPE 189
E+ L L+ + LR + FK +L +L++G ++N KGF++ L K+ +
Sbjct: 176 VEELKPSLETLEAASEELRESRKFKKLLELILALGNYMNSGTRRGNAKGFKLSSLLKLSD 235
Query: 190 VKDTVHKHSLLHHLCDLVLHQFPQSTDLYSEIGPVTRASKVDFDELASSLRRMETECKA 248
K T +K +LLH+L ++ + P D SE+ V +A+KVD ++L ++ +E K
Sbjct: 236 TKSTDNKTTLLHYLVKIIREKLPDLLDFSSELSHVEKAAKVDLEQLEKDVKELEKGLKK 294
Score = 63.1 bits (154), Expect = 2e-11
Identities = 32/74 (43%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 1 MDSTVVNREGIEKLLSMLPTDEEKCKILEAVSANPGVPLGSAENFLLELSNINELVARLK 60
MD +V+ E +E LL M PT EE K+ E LG AE FLLELS I L RL+
Sbjct: 107 MDESVLGLELLENLLKMAPTKEELKKLKEY--KGDPSKLGRAEQFLLELSKIPRLEERLE 164
Query: 61 LWAFKLDYENLERE 74
FK +E E
Sbjct: 165 ALLFKSTFEEEVEE 178
>gnl|CDD|214697 smart00498, FH2, Formin Homology 2 Domain. FH proteins control
rearrangements of the actin cytoskeleton, especially in
the context of cytokinesis and cell polarisation.
Members of this family have been found to interact with
Rho-GTPases, profilin and other actin-assoziated
proteins. These interactions are mediated by the
proline-rich FH1 domain, usually located in front of FH2
(but not listed in SMART). Despite this cytosolic
function, vertebrate formins have been assigned
functions within the nucleus. A set of Formin-Binding
Proteins (FBPs) has been shown to bind FH1 with their WW
domain.
Length = 392
Score = 109 bits (274), Expect = 1e-27
Identities = 53/193 (27%), Positives = 92/193 (47%), Gaps = 13/193 (6%)
Query: 74 EKLLSMLPTDEEKCKILEAVSANPGVPLGSAENFLLELSNINELVARLKLWAFKLDYENL 133
E+LL PT EE K+ E +P L AE FLL +SNI L RL FK ++E
Sbjct: 117 EQLLKYAPTKEELKKLREYKEEDP-EELARAEQFLLLISNIPYLEERLNALLFKANFEEE 175
Query: 134 EREVAEPLMDLKQGMDILRRNPTFKAILSTLLSIGIFLNGT----EVKGFQIEYLTKVPE 189
++ + ++ + LR + F+ +L +L+IG ++NG + GF++ L K+ +
Sbjct: 176 VEDLKPQIEKVEAACEELRESKKFRKLLELILAIGNYMNGGSRRGQAYGFKLSSLLKLSD 235
Query: 190 VKDTVHKHSLLHHLCDLVLHQF--------PQSTDLYSEIGPVTRASKVDFDELASSLRR 241
VK +K +LLH L ++ ++ + P +A+K +D+L L
Sbjct: 236 VKSADNKTTLLHFLVKIIRKKYLGGLSDPENLDDKFIEVMKPFLKAAKEKYDKLQKDLSD 295
Query: 242 METECKASFDYLK 254
++T + +Y
Sbjct: 296 LKTRFEKLVEYYG 308
>gnl|CDD|227200 COG4863, COG4863, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 439
Score = 32.1 bits (73), Expect = 0.33
Identities = 20/87 (22%), Positives = 29/87 (33%), Gaps = 4/87 (4%)
Query: 45 FLLELSNINELVARLKLWAFKLDYENL----EREKLLSMLPTDEEKCKILEAVSANPGVP 100
LL + + LV +W F+ DY E E + + V
Sbjct: 9 VLLTVLVVMSLVLTYGIWTFQPDYAEGDNSTESEVRTKHKIEKTTQKMSETIRPRDMIVH 68
Query: 101 LGSAENFLLELSNINELVARLKLWAFK 127
AE + + NEL + LK W K
Sbjct: 69 DNDAEYKIDDNDLYNELWSDLKHWDVK 95
>gnl|CDD|182109 PRK09848, PRK09848, glucuronide transporter; Provisional.
Length = 448
Score = 30.9 bits (70), Expect = 0.80
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 121 LKLWAFKLDYENLEREVAEPLMDLKQGMDILRRN-PTFKAILSTLLSIGIFLNGTEVKGF 179
L FK EN+ R VA+P LK + L+RN P F + L + + F
Sbjct: 196 LYFICFKSTRENVVRIVAQP--SLKISLQTLKRNRPLFMLCIGALCVLISTFAVSASSLF 253
Query: 180 QIEYL 184
+ Y+
Sbjct: 254 YVRYV 258
>gnl|CDD|182453 PRK10429, PRK10429, melibiose:sodium symporter; Provisional.
Length = 473
Score = 30.8 bits (70), Expect = 0.85
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 132 NLEREVAEPLMDLKQGMDILRRNPTFKAILSTLLSIGIFLNGTEVKGFQIEYLTKVPEVK 191
N L LK + ++ +N +L L+ I N + GF I Y T V
Sbjct: 209 NQVSAEGSHL-TLKDIVALIYKNDQLSCLLGMALAYNIASN--IINGFAIYYFTYVIGDA 265
Query: 192 D 192
D
Sbjct: 266 D 266
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production and
conversion].
Length = 313
Score = 29.4 bits (67), Expect = 1.9
Identities = 8/28 (28%), Positives = 20/28 (71%)
Query: 4 TVVNREGIEKLLSMLPTDEEKCKILEAV 31
V+ + G+E++L +L +D+E+ K+ ++
Sbjct: 270 AVLGKNGVEEILELLLSDDEQEKLDKSA 297
>gnl|CDD|217533 pfam03398, Ist1, Regulator of Vps4 activity in the MVB pathway.
ESCRT-I, -II, and -III are endosomal sorting complexes
required for transporting proteins and carry out cargo
sorting and vesicle formation in the multivesicular
bodies, MVBs, pathway. These complexes are transiently
recruited from the cytoplasm to the endosomal membrane
where they bind transmembrane proteins previously marked
for degradation by mono-ubiquitination. Assembly of
ESCRT-III, a complex composed of at least four subunits
(Vps2, Vps24, Vps20, Snf7), is intimately linked with
MVB vesicle formation, its disassembly being an
essential step in the MVB vesicle formation, a reaction
that is carried out by Vps4, an AAA-type ATPase. The
family Ist1 is a regulator of Vps4 activity; by
interacting with Did2 and Vps4, Ist1 appears to regulate
the recruitment and oligomerisation of Vps4. Together
Ist1, Did2, and Vta1 form a network of interconnected
regulatory proteins that modulate Vps4 activity, thereby
regulating the flow of cargo through the MVB pathway.
Length = 165
Score = 28.3 bits (64), Expect = 2.8
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 4 TVVNREGIEKLLSMLPTDEEKCKILEAVSANPGVPL 39
VN + +EKL P++E K L+ ++ VP
Sbjct: 130 CGVNPKIVEKLSVKPPSEELVEKYLKEIAKEYNVPW 165
>gnl|CDD|216179 pfam00898, Orbi_VP2, Orbivirus outer capsid protein VP2. VP2 acts
as an anchor for VP1 and VP3. VP2 contains a
non-specific DNA and RNA binding domain in the
N-terminus.
Length = 946
Score = 28.9 bits (65), Expect = 3.3
Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 149 DILRRNPTFKAILSTLLSIGIFLNGTEVKGFQIEYLTKVPEVKDTVHKHSLLHHLCDLVL 208
I+RR P + L ++SI I NG F + V+ V K SLL + CD+VL
Sbjct: 874 QIVRRFPLSRKHLKGIVSISIDQNGQ----FS---VHTSGIVRHRVCKKSLLKYKCDVVL 926
Query: 209 HQFP 212
+FP
Sbjct: 927 VKFP 930
>gnl|CDD|226523 COG4036, COG4036, Predicted membrane protein [Function unknown].
Length = 224
Score = 28.7 bits (64), Expect = 3.3
Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 28/101 (27%)
Query: 76 LLSMLPTDEEKCKILEAVSANPGVPLGSAENFLLELSNINELVARLK--LWAFKL-DYEN 132
+L+ + TD + IL PG+ +G AE L+ S + L+AR L ++E
Sbjct: 56 ILASVGTDLAEALIL------PGLVVGLAE--LIATSEV--LIAREMRYTDEDSLPEFEP 105
Query: 133 LEREVAEPLMDLKQGMDILRRNPTFKAILSTLLSIGIFLNG 173
L+ M++LR PTF AI+ L+ G+ L G
Sbjct: 106 LD-------------MEVLRTAPTFLAII--LIVYGVLLTG 131
>gnl|CDD|129709 TIGR00622, ssl1, transcription factor ssl1. All proteins in this
family for which functions are known are components of
the TFIIH complex which is involved in the initiaiton of
transcription and nucleotide excision repair.This family
is based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 112
Score = 27.2 bits (60), Expect = 4.5
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 201 HHL------CDLVLHQFPQSTDLYSEIGPVTRASKVDFDELASSLRRMETECKASF 250
HHL ++ L ++ S + GP + FDEL S R + CK F
Sbjct: 36 HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVF 91
>gnl|CDD|239204 cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding
domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
DHPD catalyzes the first step in pyrimidine degradation:
the NADPH-dependent reduction of uracil and thymine to
the corresponding 5,6-dihydropyrimidines. DHPD contains
two FAD, two FMN and eight [4Fe-4S] clusters, arranged
in two electron transfer chains that pass its
homodimeric interface twice. Two of the Fe-S clusters
show a hitherto unobserved coordination involving a
glutamine residue.
Length = 289
Score = 28.1 bits (63), Expect = 4.5
Identities = 29/130 (22%), Positives = 47/130 (36%), Gaps = 20/130 (15%)
Query: 2 DSTVVNREGIEKLLSMLPTDEEKCKILEAVSANPGVPL-----GSAENFLLELSNINELV 56
++N G L L D I +A PG PL GS++ +EL+ +
Sbjct: 68 QLGILNSFG----LPNLGLDVWLQDIAKAKKEFPGQPLIASVGGSSKEDYVELA---RKI 120
Query: 57 ARLKLWAFKLD----YENLEREKLLSMLPTDEEKCKILEAVSANPGVPLGSAENFLLELS 112
R A +L+ R+ +L+AV A +PL + +L
Sbjct: 121 ERAGAKALELNLSCPNVGGGRQLGQDPEAVAN----LLKAVKAAVDIPLLVKLSPYFDLE 176
Query: 113 NINELVARLK 122
+I EL +
Sbjct: 177 DIVELAKAAE 186
>gnl|CDD|218569 pfam05361, PP1_inhibitor, PKC-activated protein phosphatase-1
inhibitor. Contractility of vascular smooth muscle
depends on phosphorylation of myosin light chains, and
is modulated by hormonal control of myosin phosphatase
activity. Signaling pathways activate kinases such as
PKC or Rho-dependent kinases that phosphorylate the
myosin phosphatase inhibitor protein called CPI-17.
Phosphorylation of CPI-17 at Thr-38 enhances its
inhibitory potency 1000-fold, creating a molecular
switch for regulating contraction.
Length = 145
Score = 27.5 bits (61), Expect = 4.5
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 10/50 (20%)
Query: 11 IEKLLSMLPTDEEKCKILEAVSANPGVPLGSAENFLLELSNINELVARLK 60
I++LL LP+DEE+ + L+A+ + P E F I EL+ +LK
Sbjct: 76 IDELLD-LPSDEERTRKLQAILQSCSNP---TEVF------IRELLQKLK 115
>gnl|CDD|218594 pfam05450, Nicastrin, Nicastrin. Nicastrin and presenilin are two
major components of the gamma-secretase complex, which
executes the intramembrane proteolysis of type I
integral membrane proteins such as the amyloid precursor
protein (APP) and Notch. Nicastrin is synthesised in
fibroblasts and neurons as an
endoglycosidase-H-sensitive glycosylated precursor
protein (immature nicastrin) and is then modified by
complex glycosylation in the Golgi apparatus and by
sialylation in the trans-Golgi network (mature
nicastrin). A region featured in this family has a fold
similar to human transferrin receptor (TfR) and a
bacterial aminopeptidase. It is implicated in the
pathogenesis of Alzheimer's disease.
Length = 227
Score = 27.9 bits (62), Expect = 4.7
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 26 KILEAVSANPGVPLGSAENFLLELSNINELVARLKLWAFKLDYEN 70
K+L A ++NPG+P S ++FL N + +V L ++EN
Sbjct: 145 KVLPASTSNPGLPPSSLQSFLRANPNFSAVV----LADRPTEFEN 185
Score = 27.9 bits (62), Expect = 4.7
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 88 KILEAVSANPGVPLGSAENFLLELSNINELVARLKLWAFKLDYEN 132
K+L A ++NPG+P S ++FL N + +V L ++EN
Sbjct: 145 KVLPASTSNPGLPPSSLQSFLRANPNFSAVV----LADRPTEFEN 185
>gnl|CDD|221397 pfam12054, DUF3535, Domain of unknown function (DUF3535). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 439 to 459 amino acids in length. This domain is
found associated with pfam00271, pfam02985, pfam00176.
This domain has two completely conserved residues (P and
K) that may be functionally important.
Length = 442
Score = 28.4 bits (64), Expect = 4.7
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 232 FDELASSLRRMETECKASFDYLK 254
+DEL SL+R+ T+C+ +
Sbjct: 185 YDELVPSLKRLRTQCQQLLNTFV 207
>gnl|CDD|234207 TIGR03434, ADOP, Acidobacterial duplicated orphan permease.
Members of this protein family are found, so far, only
in three species of Acidobacteria, namely Acidobacteria
bacterium Ellin345, Acidobacterium capsulatum ATCC
51196, and Solibacter usitatus Ellin6076, where they
form large paralogous families. Each protein contains
two copies of a domain called the efflux ABC transporter
permease protein (pfam02687). However, unlike other
members of that family (including LolC, FtsX, and MacB),
genes for these proteins are essentially never found
fused or adjacent to ABC transporter ATP-binding protein
(pfam00005) genes. We name this family ADOP, for
Acidobacterial Duplicated Orphan Permease, to reflect
the restricted lineage, internal duplication, lack of
associated ATP-binding cassette proteins, and permease
homology. The function is unknown.
Length = 803
Score = 28.3 bits (64), Expect = 5.1
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 6/34 (17%)
Query: 143 DLKQGMDILRRNPTFK--AILSTLLSIG----IF 170
DL+ + LRR+P F A+L+ L IG IF
Sbjct: 4 DLRYALRTLRRSPGFTAVAVLTLALGIGANTAIF 37
>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating
C4-dicarboxylate transport system [Signal transduction
mechanisms].
Length = 603
Score = 28.4 bits (64), Expect = 5.3
Identities = 14/38 (36%), Positives = 16/38 (42%)
Query: 107 FLLELSNINELVARLKLWAFKLDYENLEREVAEPLMDL 144
LL L ARL+L + LER V E DL
Sbjct: 310 LLLALWLRRRRRARLRLAELQEARAELERRVEERTADL 347
>gnl|CDD|237743 PRK14515, PRK14515, aspartate ammonia-lyase; Provisional.
Length = 479
Score = 28.0 bits (62), Expect = 6.6
Identities = 12/51 (23%), Positives = 26/51 (50%)
Query: 213 QSTDLYSEIGPVTRASKVDFDELASSLRRMETECKASFDYLKLIIKHDGSA 263
Q+TD Y+E+ + ++ ++A+ LR M + + + L + GS+
Sbjct: 275 QNTDAYTEVSAALKVCMMNMSKIANDLRLMASGPRVGLAEIMLPARQPGSS 325
>gnl|CDD|224389 COG1472, BglX, Beta-glucosidase-related glycosidases [Carbohydrate
transport and metabolism].
Length = 397
Score = 27.4 bits (61), Expect = 9.0
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 204 CDLVLHQFPQSTDLYSEIGPVTRASKVDFDELASSLRRM 242
D+VL +LY V + L ++RR+
Sbjct: 274 VDIVLV----CNELYEAYLVVLELVGLSEARLDDAVRRI 308
>gnl|CDD|235747 PRK06222, PRK06222, ferredoxin-NADP(+) reductase subunit alpha;
Reviewed.
Length = 281
Score = 27.1 bits (61), Expect = 9.6
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 222 GPVTRASKVDFDELASSLRRMETECKASFD 251
GP VDFDEL L + E K + +
Sbjct: 240 GPEFDGHLVDFDELMRRLAMYKEEEKLALE 269
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.134 0.379
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,833,618
Number of extensions: 1318137
Number of successful extensions: 1337
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1327
Number of HSP's successfully gapped: 41
Length of query: 276
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 180
Effective length of database: 6,679,618
Effective search space: 1202331240
Effective search space used: 1202331240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.2 bits)