RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1242
(540 letters)
>gnl|CDD|214982 smart01026, Beach, Beige/BEACH domain. The BEACH domain was
described in the BEIGE protein (D1035670) and in the
highly homologous CHS protein. The BEACH domain is
usually followed by a series of WD repeats. The function
of the BEACH domain is unknown.
Length = 280
Score = 158 bits (402), Expect = 1e-44
Identities = 55/97 (56%), Positives = 70/97 (72%)
Query: 15 FFYFIVICLITGRTYNDLNQYPVFPWVLTNYDSKELDLSLSTNYRDLSKPIGALNPSRMA 74
F Y + + + GR+YNDL QYPVFPWVL +Y S+ LDLS + +RDLSKPIGALNP R+
Sbjct: 12 FEYLMHLNTLAGRSYNDLTQYPVFPWVLADYTSETLDLSNPSTFRDLSKPIGALNPERLE 71
Query: 75 YFEERYNSWEHENIKPFHYGTHYSTGVYVLNWLVRVP 111
+F ERY E +I PFHYGTHYS+ VL +L+R+
Sbjct: 72 FFYERYEELEDPDIPPFHYGTHYSSAGIVLYYLIRLE 108
>gnl|CDD|100117 cd06071, Beach, BEACH (Beige and Chediak-Higashi) domains,
implicated in membrane trafficking, are present in a
family of proteins conserved throughout eukaryotes. This
group contains human lysosomal trafficking regulator
(LYST), LPS-responsive and beige-like anchor (LRBA) and
neurobeachin. Disruption of LYST leads to
Chediak-Higashi syndrome, characterized by severe
immunodeficiency, albinism, poor blood coagulation and
neurologic problems. Neurobeachin is a candidate gene
linked to autism. LBRA seems to be upregulated in
several cancer types. It has been shown that the BEACH
domain itself is important for the function of these
proteins.
Length = 275
Score = 144 bits (365), Expect = 2e-39
Identities = 50/97 (51%), Positives = 70/97 (72%)
Query: 15 FFYFIVICLITGRTYNDLNQYPVFPWVLTNYDSKELDLSLSTNYRDLSKPIGALNPSRMA 74
F Y + + + GR++NDL+QYP+FPWV+++Y S+ELDL+ + YRDLSKPIGALN R+
Sbjct: 12 FEYLMYLNTLAGRSFNDLSQYPIFPWVISDYTSEELDLNDPSTYRDLSKPIGALNKERLQ 71
Query: 75 YFEERYNSWEHENIKPFHYGTHYSTGVYVLNWLVRVP 111
+ERY S ++ PFHYG+HYS VL +LVR+
Sbjct: 72 LLKERYESDSDDSDPPFHYGSHYSNPAIVLYYLVRLE 108
>gnl|CDD|216896 pfam02138, Beach, Beige/BEACH domain.
Length = 274
Score = 142 bits (360), Expect = 1e-38
Identities = 51/97 (52%), Positives = 71/97 (73%), Gaps = 1/97 (1%)
Query: 15 FFYFIVICLITGRTYNDLNQYPVFPWVLTNYDSKELDLSLSTNYRDLSKPIGALNPSRMA 74
F Y +++ + GR++NDL+QYPVFPWVL +Y S+ LDL+ + YRDLSKPIGALN R+
Sbjct: 12 FEYLMLLNTLAGRSFNDLSQYPVFPWVLADYTSETLDLNDPSTYRDLSKPIGALNEERLK 71
Query: 75 YFEERYNSWEHENIKPFHYGTHYSTGVYVLNWLVRVP 111
F+ERY + E PFHYG+HYS+ VL++L+R+
Sbjct: 72 KFKERYEELD-EVGPPFHYGSHYSSPGSVLHYLIRLE 107
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 64.3 bits (157), Expect = 3e-11
Identities = 33/135 (24%), Positives = 53/135 (39%), Gaps = 33/135 (24%)
Query: 339 HNCFVTTVD---SRFLLACGFWDNSFRVFSTDNARIVQIIFGHYGVVTSRIVQIIFGHYG 395
H +V++V +L+ D + +V+ + T + + + GH
Sbjct: 92 HTSYVSSVAFSPDGRILSSSSRDKTIKVWDVE---------------TGKCLTTLRGHTD 136
Query: 396 VVTCLSRSECNITADCFIASGSADCTVLLWHWNARTQSIVGETDTPTPRATLTGHEQPVT 455
V ++ S F+AS S D T+ LW + T ATLTGH V
Sbjct: 137 WVNSVAFSPDGT----FVASSSQDGTIKLW-----------DLRTGKCVATLTGHTGEVN 181
Query: 456 SVAISAELGLVVSGS 470
SVA S + ++S S
Sbjct: 182 SVAFSPDGEKLLSSS 196
Score = 63.5 bits (155), Expect = 4e-11
Identities = 35/163 (21%), Positives = 56/163 (34%), Gaps = 45/163 (27%)
Query: 339 HNCFVTTVD---SRFLLACGFWDNSFRVFSTDNARIVQIIFGHYGVVTS----------- 384
H +V +V +A D + +++ + V + GH G V S
Sbjct: 134 HTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLL 193
Query: 385 ----------------RIVQIIFGHYGVVTCLSRSECNITADCFIASGSADCTVLLWHWN 428
+ + + GH V ++ S +ASGS D T+ +W
Sbjct: 194 SSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGY----LLASGSEDGTIRVWDL- 248
Query: 429 ARTQSIVGETDTPTPRATLTGHEQPVTSVAISAELGLVVSGSQ 471
T TL+GH VTS+A S + + SGS
Sbjct: 249 ----------RTGECVQTLSGHTNSVTSLAWSPDGKRLASGSA 281
Score = 55.8 bits (135), Expect = 1e-08
Identities = 31/130 (23%), Positives = 46/130 (35%), Gaps = 32/130 (24%)
Query: 343 VTTVDSRFLLACGFWDNSFRVFSTDNARIVQIIFGHYGVVTSRIVQIIFGHYGVVTCLSR 402
V LA G D + R++ + V+ + GH V+S
Sbjct: 57 VAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSS------------------ 98
Query: 403 SECNITADC-FIASGSADCTVLLWHWNARTQSIVGETDTPTPRATLTGHEQPVTSVAISA 461
+ D ++S S D T+ +W + +T TL GH V SVA S
Sbjct: 99 --VAFSPDGRILSSSSRDKTIKVW-----------DVETGKCLTTLRGHTDWVNSVAFSP 145
Query: 462 ELGLVVSGSQ 471
+ V S SQ
Sbjct: 146 DGTFVASSSQ 155
Score = 50.4 bits (121), Expect = 8e-07
Identities = 43/177 (24%), Positives = 70/177 (39%), Gaps = 38/177 (21%)
Query: 339 HNCFVTTV----DSRFLLACGFWDNSFRVFSTDNARIVQIIFGHYGVVTSRIVQIIFGHY 394
H VT V D + L D + +V+ + +++ + GH G V
Sbjct: 8 HTGGVTCVAFSPDGKLLATGS-GDGTIKVWDLETGELLRTLKGHTGPVRD---------- 56
Query: 395 GVVTCLSRSECNITADCFIASGSADCTVLLWHWNARTQSIVGETDTPTPRATLTGHEQPV 454
V + ++ASGS+D T+ LW + +T TLTGH V
Sbjct: 57 --VAASADGT-------YLASGSSDKTIRLW-----------DLETGECVRTLTGHTSYV 96
Query: 455 TSVAISAELGLVVSGSQLGPVLVHTTF-GDLLRSLDPPSGFASPESVVMSREGVIVV 510
+SVA S + ++ S S+ + V G L +L + + + SV S +G V
Sbjct: 97 SSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVN--SVAFSPDGTFVA 151
Score = 43.5 bits (103), Expect = 1e-04
Identities = 27/90 (30%), Positives = 37/90 (41%), Gaps = 22/90 (24%)
Query: 339 HNCFVTTVD---SRFLLACGFWDNSFRVFSTDNARIVQIIFGHYGVVTSRIVQIIFGHYG 395
H V +V +LLA G D + RV+ VQ + GH T+
Sbjct: 218 HENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGH----TNS---------- 263
Query: 396 VVTCLSRSECNITADCFIASGSADCTVLLW 425
VT L+ S +ASGSAD T+ +W
Sbjct: 264 -VTSLAWSPDG----KRLASGSADGTIRIW 288
Score = 36.2 bits (84), Expect = 0.033
Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 443 PRATLTGHEQPVTSVAISAELGLVVSGSQLGPVLV-HTTFGDLLRSL 488
R TL GH VT VA S + L+ +GS G + V G+LLR+L
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTL 47
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 40.8 bits (94), Expect = 0.002
Identities = 40/185 (21%), Positives = 64/185 (34%), Gaps = 46/185 (24%)
Query: 347 DSRFLLACGFWDNSFRVFSTDNARIVQIIFGHYGVVTS---------------------- 384
D + L + D + +++ + + + GH V+S
Sbjct: 166 DGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRL 225
Query: 385 -------RIVQIIFGHY-GVVTCLSRSECNITADCFIASGSADCTVLLWHWNARTQSIVG 436
+ + GH VV+ S +ASGS+D T+ LW + + +
Sbjct: 226 WDLSTGKLLRSTLSGHSDSVVSSFSPD------GSLLASGSSDGTIRLWDLRSSSSLL-- 277
Query: 437 ETDTPTPRATLTGHEQPVTSVAISAELGLVVSGSQLGPVLVHTTFGDLLRSLDPPSGFAS 496
TL+GH V SVA S + L+ SGS G V + L S G
Sbjct: 278 --------RTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEG 329
Query: 497 PESVV 501
P S +
Sbjct: 330 PVSSL 334
Score = 32.4 bits (72), Expect = 0.58
Identities = 41/171 (23%), Positives = 65/171 (38%), Gaps = 31/171 (18%)
Query: 329 DNFSQKLRVRHNCFVTTV----DSRFLLACGFWDNSFRVFSTDNARIVQIIFGHYGVVTS 384
+ S L H +T++ D LL+ D + +++ DN +
Sbjct: 54 PDLSSLLLRGHEDSITSIAFSPDGELLLSGS-SDGTIKLWDLDNGEKL------------ 100
Query: 385 RIVQIIFGHYGVVTCLSRSECNITADCFIASGSADCTVLLWHWNARTQSIVGETDTPTPR 444
I + H V+ L+ S + +AS S D TV LW + + I
Sbjct: 101 -IKSLEGLHDSSVSKLALSSPDGN-SILLASSSLDGTVKLWDLSTPGKLI---------- 148
Query: 445 ATLTGHEQPVTSVAISAELGLVVSGSQLGPVLV--HTTFGDLLRSLDPPSG 493
TL GH + VTS+A S + L+ SGS L + G L +L +
Sbjct: 149 RTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTD 199
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats (blades)
of the beta propeller domain.
Length = 40
Score = 34.6 bits (80), Expect = 0.005
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 383 TSRIVQIIFGHYGVVTCLSRSECNITADCFIASGSADCTVLLWH 426
+ +++ + GH G VT ++ S ++ASGS D T+ LW
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDG----KYLASGSDDGTIKLWD 40
Score = 33.4 bits (77), Expect = 0.014
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 440 TPTPRATLTGHEQPVTSVAISAELGLVVSGS 470
+ TL GH PVTSVA S + + SGS
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGS 31
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 33.5 bits (77), Expect = 0.013
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 385 RIVQIIFGHYGVVTCLSRSECNITADCFIASGSADCTVLLWH 426
++++ + GH G VT ++ S +ASGS D TV +W
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDG----NLLASGSDDGTVRVWD 39
Score = 32.3 bits (74), Expect = 0.037
Identities = 15/29 (51%), Positives = 17/29 (58%)
Query: 442 TPRATLTGHEQPVTSVAISAELGLVVSGS 470
TL GH PVTSVA S + L+ SGS
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGS 30
>gnl|CDD|233552 TIGR01736, FGAM_synth_II, phosphoribosylformylglycinamidine
synthase II. Phosphoribosylformylglycinamidine synthase
is a single, long polypeptide in most Proteobacteria and
eukarotes. Three proteins are required in Bacillus
subtilis and many other species. This is the longest of
the three and is designated PurL,
phosphoribosylformylglycinamidine synthase II, or FGAM
synthase II [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 715
Score = 31.9 bits (73), Expect = 0.88
Identities = 14/68 (20%), Positives = 23/68 (33%), Gaps = 10/68 (14%)
Query: 99 TGVYVLNW----LVRVPIGALNPSPSIQSPSYAETPGS------PPGNLPLTLDPILTHP 148
G L + + +PI L +P + PS PP +L +L+ P
Sbjct: 333 EGRIRLYYKGEVVADLPIELLADAPEYERPSEPPKYPEEEKEPEPPADLEDAFLKVLSSP 392
Query: 149 TSNNNAPV 156
+ V
Sbjct: 393 NIASKEWV 400
>gnl|CDD|215467 PLN02866, PLN02866, phospholipase D.
Length = 1068
Score = 31.3 bits (71), Expect = 1.5
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 85 HENIKPFHYGTHYSTGVY 102
HEN+K Y H+S+GVY
Sbjct: 426 HENVKVLRYPDHFSSGVY 443
>gnl|CDD|219994 pfam08735, DUF1786, Putative pyruvate format-lyase activating
enzyme (DUF1786). This family is annotated as pyruvate
formate-lyase activating enzyme (EC:1.97.1.4) in
UniProt. It is not clear where this annotation comes
from.
Length = 252
Score = 30.7 bits (70), Expect = 1.5
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 492 SGFAS-------PESVVMSREGVIVVNYERGHIAAFTMNGNR 526
+G A+ P+ V ++ ++VVN GH A ++ R
Sbjct: 147 TGPAAVLGALEDPK--VSAKNPILVVNIGNGHTLAALVDDGR 186
>gnl|CDD|213357 cd12823, Mrs2_Mfm1p-like, Saccharomyces cerevisiae inner
mitochondrial membrane Mg2+ transporters Mfm1p and
Mrs2p-like family. A eukaryotic subfamily belonging to
the Escherichia coli CorA-Salmonella typhimurium
ZntB_like family (EcCorA_ZntB-like) family of the MIT
superfamily of essential membrane proteins involved in
transporting divalent cations (uptake or efflux) across
membranes. This functionally diverse subfamily includes
the inner mitochondrial membrane Mg2+ transporters
Saccharomyces cerevisiae Mfm1p/Lpe10p, Mrs2p, and human
MRS2/ MRS2L. It also includes a family of Arabidopsis
thaliana proteins (AtMGTs) some of which are localized
to distinct tissues, and not all of which can transport
Mg2+. Structures of the intracellular domain of two
EcCorA_ZntB-like family transporters: Vibrio
parahaemolyticus and Salmonella typhimurium ZntB form
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 through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, as in some
ZntB family proteins, may be associated with the
transport of different divalent cations, such as zinc
and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 323
Score = 30.3 bits (69), Expect = 2.6
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 485 LRSLDPPSGFASPESVVMSREGVIVVNYERGHIAA 519
LR LDP S ++ RE I+VN E HI A
Sbjct: 31 LRLLDPT--LTSYPPSILVRENAILVNLE--HIRA 61
>gnl|CDD|236243 PRK08327, PRK08327, acetolactate synthase catalytic subunit;
Validated.
Length = 569
Score = 30.4 bits (69), Expect = 2.6
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 437 ETDTPTPRATLTGHEQPVTSVAISAELGLVVSGSQLGPVLVHTTFG 482
P P + HE VAIS G + + V+VH G
Sbjct: 45 AAGRPLPEFVICPHE----IVAISMAHGYALVTGKPQAVMVHVDVG 86
>gnl|CDD|239556 cd03474, Rieske_T4moC, Toluene-4-monooxygenase effector protein
complex (T4mo), Rieske ferredoxin subunit; The Rieske
domain is a [2Fe-2S] cluster binding domain involved in
electron transfer. T4mo is a four-protein complex that
catalyzes the NADH- and O2-dependent hydroxylation of
toluene to form p-cresol. T4mo consists of an NADH
oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a
catalytic effector protein (T4moD), and a Rieske
ferredoxin (T4moC). T4moC contains a Rieske domain and
functions as an obligate electron carrier between T4moF
and T4moH. Rieske ferredoxins are found as subunits of
membrane oxidase complexes, cis-dihydrodiol-forming
aromatic dioxygenases, bacterial assimilatory nitrite
reductases, and arsenite oxidase. Rieske ferredoxins are
also found as soluble electron carriers in bacterial
dioxygenase and monooxygenase complexes.
Length = 108
Score = 28.5 bits (64), Expect = 2.9
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 414 ASGSADCTVL-----LWHWNARTQSIVGETDTP 441
A G D VL LW ++A T + D
Sbjct: 50 AEGGFDGGVLTCRAHLWQFDADTGEGLNPRDCR 82
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 30.1 bits (67), Expect = 3.6
Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 11/88 (12%)
Query: 413 IASGSADCTVLLWHWNARTQSIVGETDTPTPRATLTGHEQPVTSVAISAELGLVVSGSQL 472
+ S S D T+ LW + I TP + GH V +S G + +GS+
Sbjct: 675 LVSSSTDNTLKLWDLSMSISGI-----NETPLHSFMGHTNVKNFVGLSVSDGYIATGSET 729
Query: 473 GPVLV-HTTF-----GDLLRSLDPPSGF 494
V V H F +++DP SG
Sbjct: 730 NEVFVYHKAFPMPVLSYKFKTIDPVSGL 757
>gnl|CDD|225745 COG3204, COG3204, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 316
Score = 28.9 bits (65), Expect = 6.0
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 447 LTGHEQPVTSVAISAELGLVVSGSQLGPVLVH-TTFGDLLRSLDPPSGFASPESVVMSRE 505
+ G V+S+ + + + + + +V T GDL+R++ P +GF+ PE++
Sbjct: 81 ILGETANVSSLTYNPDTRTLFAVTNKPAAIVELTKEGDLIRTI-PLTGFSDPETIEYIGG 139
Query: 506 GVIVVNYER 514
V+ ER
Sbjct: 140 NQFVIVDER 148
>gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain
fusion protein; Provisional.
Length = 906
Score = 29.4 bits (66), Expect = 6.5
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 35 YP-VFPWVLTNYDSKELDLSLSTNYRDL 61
YP F WV + S +L + +L
Sbjct: 615 YPEAFIWVAKSILSYSWELDYLDSSEEL 642
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 0.426
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,585,515
Number of extensions: 2649927
Number of successful extensions: 1929
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1906
Number of HSP's successfully gapped: 31
Length of query: 540
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 438
Effective length of database: 6,413,494
Effective search space: 2809110372
Effective search space used: 2809110372
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: 61 (27.2 bits)