RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy682
(330 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 = 110 bits (276), Expect = 4e-28
Identities = 51/154 (33%), Positives = 72/154 (46%), Gaps = 61/154 (39%)
Query: 178 REPFTTMYLALQEGKFDHPNRLFSSISLAWKNCQRDTSDVKVHTTFGDLLRSLDPPSGFA 237
EPFTT++L LQ G+FDH +RLF S++ W++ A
Sbjct: 107 LEPFTTLFLQLQGGRFDHADRLFHSVAATWRS---------------------------A 139
Query: 238 SPESVVMSREGVIVVNYERGHIAAFTMNGNRLRHESHNDNLQELIPELFFLPEMLVNSNG 297
S ES M+ ++ELIPE F+LPE LVN NG
Sbjct: 140 SLES--MTD-------------------------------VKELIPEFFYLPEFLVNING 166
Query: 298 YCLGKTEDNVNINNVELPPWA-SSPEQFVRINRM 330
+ G +D ++++VELPPWA SPE+F+R +R
Sbjct: 167 FDFGTRQDGEDVDDVELPPWAKGSPEEFIRKHRE 200
>gnl|CDD|216896 pfam02138, Beach, Beige/BEACH domain.
Length = 274
Score = 82.3 bits (204), Expect = 5e-18
Identities = 30/58 (51%), Positives = 40/58 (68%), Gaps = 1/58 (1%)
Query: 273 SHNDNLQELIPELFFLPEMLVNSNGYCLGKTEDNVNINNVELPPWASSPEQFVRINRM 330
++++ELIPE F+LPE L N N + LGK D +++VELPPWA SPE+FV NR
Sbjct: 140 ESMNDVKELIPEFFYLPEFLKNINNFDLGKR-DGEKVDDVELPPWAKSPEEFVYKNRK 196
Score = 65.7 bits (161), Expect = 3e-12
Identities = 24/40 (60%), Positives = 30/40 (75%)
Query: 179 EPFTTMYLALQEGKFDHPNRLFSSISLAWKNCQRDTSDVK 218
EPFTT+++ LQ GKFDH +RLFSSI AWK+ +DVK
Sbjct: 107 EPFTTLHIELQGGKFDHADRLFSSIEEAWKSVSESMNDVK 146
>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 = 81.5 bits (202), Expect = 9e-18
Identities = 27/51 (52%), Positives = 37/51 (72%), Gaps = 1/51 (1%)
Query: 280 ELIPELFFLPEMLVNSNGYCLGKTEDNVNINNVELPPWASSPEQFVRINRM 330
ELIPE ++LPE +N N + GK +D +N+VELPPWA SPE+F+R +R
Sbjct: 148 ELIPEFYYLPEFFLNINKFDFGK-QDGEKVNDVELPPWAKSPEEFIRKHRE 197
Score = 63.0 bits (154), Expect = 2e-11
Identities = 21/40 (52%), Positives = 30/40 (75%)
Query: 179 EPFTTMYLALQEGKFDHPNRLFSSISLAWKNCQRDTSDVK 218
EPFTT++L+LQ G FD +RLF+SI +W++ + SDVK
Sbjct: 108 EPFTTLHLSLQGGHFDAADRLFNSIPSSWRSASENPSDVK 147
>gnl|CDD|172668 PRK14180, PRK14180, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 31.5 bits (71), Expect = 0.53
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 210 CQRDTSDVKVHTTFGDLLRSLDPPSGFASPESVVMSREGVIVVNYERGHI 259
C R T+D+K HTT D+L F + + M +EG +V++ H+
Sbjct: 188 CHRFTTDLKSHTTKADILIVAVGKPNFITAD---MVKEGAVVIDVGINHV 234
>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 = 0.90
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 243 VMSREGVIVVNYERGHIAAFTMNGNR 268
V ++ ++VVN GH A ++ R
Sbjct: 161 VSAKNPILVVNIGNGHTLAALVDDGR 186
>gnl|CDD|218287 pfam04841, Vps16_N, Vps16, N-terminal region. This protein forms
part of the Class C vacuolar protein sorting (Vps)
complex. Vps16 is essential for vacuolar protein
sorting, which is essential for viability in plants, but
not yeast. The Class C Vps complex is required for
SNARE-mediated membrane fusion at the lysosome-like
yeast vacuole. It is thought to play essential roles in
membrane docking and fusion at the Golgi-to-endosome and
endosome-to-vacuole stages of transport. The role of
VPS16 in this complex is not known.
Length = 408
Score = 30.2 bits (68), Expect = 1.7
Identities = 20/110 (18%), Positives = 33/110 (30%), Gaps = 13/110 (11%)
Query: 158 FVTTVDSRFLLACGFWDNSFREPFTTMYLALQEGKFDHPNRLFSSISLAWKNCQRDTSDV 217
V T R L G + + L + N S + +
Sbjct: 141 AVLTKSGRVYLLNGVEEPLLWRNKPEIPNLLTK------NHWSCSDTSIILLLVDHVYQI 194
Query: 218 KVHTTFGDLLRSLDPPSGFASPESVVMSREGVIVVNYERGHIAAFTMNGN 267
+ G+LL+ + S + I V+ R H+A +TM G
Sbjct: 195 S--LSVGELLKLITEQSSQHANTKWHK-----ISVSDNRRHLALYTMTGK 237
>gnl|CDD|182631 PRK10667, PRK10667, Hha toxicity attenuator; Provisional.
Length = 122
Score = 28.4 bits (64), Expect = 2.1
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 17/72 (23%)
Query: 258 HIAAFTMNGNRLRHESHNDNLQELIPELFFLPE--MLVNSNGYCLGKTEDNVNINNVELP 315
HIA F +N ++++ + L E I E +L + ML +S G IN+ +L
Sbjct: 54 HIATFALN-FKIKYPEDSK-LIEQIDE--YLDDTYMLFSSYG-----------INDQDLQ 98
Query: 316 PWASSPEQFVRI 327
W S + R
Sbjct: 99 KWRKSGNRLFRC 110
>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 = 29.5 bits (67), Expect = 2.1
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 227 LRSLDPPSGFASPESVVMSREGVIVVNYERGHIAA 261
LR LDP S ++ RE I+VN E HI A
Sbjct: 31 LRLLDPT--LTSYPPSILVRENAILVNLE--HIRA 61
>gnl|CDD|225745 COG3204, COG3204, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 316
Score = 28.9 bits (65), Expect = 4.0
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 221 TTFGDLLRSLDPPSGFASPESVVMSREGVIVVNYER 256
T GDL+R++ P +GF+ PE++ V+ ER
Sbjct: 114 TKEGDLIRTI-PLTGFSDPETIEYIGGNQFVIVDER 148
>gnl|CDD|220311 pfam09609, Cas_GSU0054, CRISPR-associated protein, GSU0054 family
(Cas_GSU0054). This entry represents a rare
CRISPR-associated protein. So far, members are found in
Geobacter sulfurreducens and in two unpublished genomes:
Gemmata obscuriglobus and Actinomyces naeslundii.
CRISPR-associated proteins typically are found near
CRISPR repeats and other CRISPR-associated proteins,
have low levels of sequence identify, have sequence
relationships that suggest lateral transfer, and show
some sequence similarity to DNA-active proteins such as
helicases and repair proteins.
Length = 519
Score = 28.8 bits (64), Expect = 4.9
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 9/81 (11%)
Query: 195 HPNRLFSSISLAWKNCQRDTSDVKVHTTFGDLLRSLDPPSGFASPESVVMSREGVIVV-- 252
P R+F ++ W + DV + L SL P FA P ++V V
Sbjct: 32 SPWRIFQALVATWAKVDAEDKDVL------NWLESLPEPPVFALPPALVAPNATRHYVPR 85
Query: 253 NYERGHIAAFTMNGNRLRHES 273
+ RG + + +RH
Sbjct: 86 AWGRGK-KNWHGSATLIRHRP 105
>gnl|CDD|226499 COG4012, COG4012, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 342
Score = 28.3 bits (63), Expect = 6.0
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 249 VIVVNYERGHIAAFTMNGNRLR--HESHN-----DNLQELIPEL 285
+VV+Y GH A ++ +R+ +E H + L++ I
Sbjct: 229 ALVVDYGNGHTTAALVDEDRIVGVYEHHTIRLSPEKLEDQIIRF 272
>gnl|CDD|130464 TIGR01397, fliM_switch, flagellar motor switch protein FliM.
Members of this family are the flagellar motor switch
protein FliM. The family excludes FliM homologs that
lack an N-terminal region critical to interaction with
phosphorylated CheY. One set lacking this N-terminal
region is found in Rhizobium meliloti, in which the
direction of flagellar rotation is not reversible (i.e.
the FliM homolog does not act to reverse the motor
direction), and in related species. Another is found in
Buchnera, an obligate intracellular endosymbiont with
genes for many of the components of the flagellar
apparatus, but not, apparently, for flagellin iself
[Cellular processes, Chemotaxis and motility].
Length = 320
Score = 27.7 bits (62), Expect = 7.9
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 212 RDTSDVKVHT----TFGDLLRSLDPPSGFASPESVVMSREGVIVVN 253
R +V V + T+G+ LRSL P+ + +I ++
Sbjct: 72 RRFVEVSVASVDQLTYGEFLRSLPVPTSLNVFRMEPLRGTALIEID 117
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
0.319 0.134 0.417
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: 16,719,353
Number of extensions: 1545969
Number of successful extensions: 1038
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1035
Number of HSP's successfully gapped: 21
Length of query: 330
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 233
Effective length of database: 6,635,264
Effective search space: 1546016512
Effective search space used: 1546016512
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: 59 (26.4 bits)