RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8504
(150 letters)
>gnl|CDD|233185 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter
(EST) Family.
Length = 1145
Score = 173 bits (441), Expect = 4e-51
Identities = 78/142 (54%), Positives = 107/142 (75%), Gaps = 1/142 (0%)
Query: 7 WDPVKSQAGVGILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLIT 66
WD KSQ VG+ G L++ S+ AGLG C++LGI FNA+TTQ++PFLALG+ VDD+FL+
Sbjct: 420 WDCAKSQGSVGLAGVLLVALSVAAGLGLCALLGISFNAATTQVLPFLALGVGVDDVFLLA 479
Query: 67 KTFAKYTSKNQFDSECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAIL 126
F++ T +N E TG L++TG S++L+S+ AFF A+LIPIPALR F+LQ AI+
Sbjct: 480 HAFSE-TGQNIPFEERTGECLKRTGASVVLTSISNVTAFFMAALIPIPALRAFSLQAAIV 538
Query: 127 ILFNMFVLLLVYPAIVSLDLRR 148
++FN +LLV+PAI+SLDLRR
Sbjct: 539 VVFNFAAVLLVFPAILSLDLRR 560
>gnl|CDD|192997 pfam12349, Sterol-sensing, Sterol-sensing domain of SREBP
cleavage-activation. Sterol regulatory element-binding
proteins (SREBPs) are membrane-bound transcription
factors that promote lipid synthesis in animal cells.
They are embedded in the membranes of the endoplasmic
reticulum (ER) in a helical hairpin orientation and are
released from the ER by a two-step proteolytic process.
Proteolysis begins when the SREBPs are cleaved at
Site-1, which is located at a leucine residue in the
middle of the hydrophobic loop in the lumen of the ER.
Upon proteolytic processing SREBP can activate the
expression of genes involved in cholesterol biosynthesis
and uptake. SCAP stimulates cleavage of SREBPs via
fusion of the their two C-termini. This domain is the
transmembrane region that traverses the membrane eight
times and is the sterol-sensing domain of the cleavage
protein. WD40 domains are found towards the C-terminus.
Length = 153
Score = 106 bits (266), Expect = 5e-30
Identities = 46/139 (33%), Positives = 81/139 (58%), Gaps = 1/139 (0%)
Query: 10 VKSQAGVGILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTF 69
VKS+ G+ + G + S+ + G C+ LG+PF +++PFL L + VD+MFL+
Sbjct: 2 VKSKFGLALAGVVQVLMSVASSFGLCAYLGLPFTLIPGEVIPFLVLAVGVDNMFLLVHAV 61
Query: 70 AKYTSKNQFDSECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILF 129
+ T ++ E L + G SI L+S+ + +AF +L P+PA++ F L A+ +LF
Sbjct: 62 -QRTPRSLDVEERIAEALGEVGPSITLTSLTELLAFLIGALTPMPAVQEFCLFAAVAVLF 120
Query: 130 NMFVLLLVYPAIVSLDLRR 148
+ + + + A++SLD+RR
Sbjct: 121 DFLLQITFFVAVLSLDIRR 139
>gnl|CDD|233184 TIGR00917, 2A060601, Niemann-Pick C type protein family. The model
describes Niemann-Pick C type protein in eukaryotes. The
defective protein has been associated with Niemann-Pick
disease which is described in humans as autosomal
recessive lipidosis. It is characterized by the
lysosomal accumulation of unestrified cholesterol. It is
an integral membrane protein, which indicates that this
protein is most likely involved in cholesterol transport
or acts as some component of cholesterol homeostasis
[Transport and binding proteins, Other].
Length = 1204
Score = 72.2 bits (177), Expect = 1e-15
Identities = 39/149 (26%), Positives = 79/149 (53%), Gaps = 10/149 (6%)
Query: 10 VKSQAGVGILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTF 69
+ S+ +GI G ++ S++ +G S +G+ +++PFL L + VD++F++ +T+
Sbjct: 601 IDSKVLLGISGVLIVLASVVGSVGVFSYIGLKATLIIMEVIPFLVLAVGVDNIFILVQTY 660
Query: 70 AK-----YTSKNQFDSECT-----GIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVF 119
+ + E T G L + G SI L+S+ +S+AFF +L +PA+R F
Sbjct: 661 QRLERFYREVGVDNEQELTLEQQLGRALGEVGPSITLASLSESLAFFLGALSKMPAVRAF 720
Query: 120 NLQLAILILFNMFVLLLVYPAIVSLDLRR 148
+L + + + + + + A++ LD +R
Sbjct: 721 SLFAGLAVFIDFLLQITAFVALLVLDFKR 749
>gnl|CDD|217050 pfam02460, Patched, Patched family. The transmembrane protein
Patched is a receptor for the morphogene Sonic Hedgehog.
This protein associates with the smoothened protein to
transduce hedgehog signals.
Length = 801
Score = 62.0 bits (151), Expect = 5e-12
Identities = 40/141 (28%), Positives = 71/141 (50%), Gaps = 10/141 (7%)
Query: 8 DPVKSQAGVGILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLIT- 66
D V+S+ + ILGC + ++ G G PFN+ + PFL L + VDDMFL+
Sbjct: 244 DWVRSKPILAILGCLTPLMATVSAFGLLFWFGFPFNSIVC-VTPFLVLAIGVDDMFLMVH 302
Query: 67 ---KTFAKYTSKNQFDSECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQL 123
+T + K + G L + G SI ++S+ ++F + P PA+++F L
Sbjct: 303 AWQRTTKTLSVKKRM-----GETLSEAGPSITITSLTNVLSFGIGTYTPTPAIQLFCLYT 357
Query: 124 AILILFNMFVLLLVYPAIVSL 144
A+ I F+ + + A++++
Sbjct: 358 AVAIFFDFIYQITFFAAVMAI 378
>gnl|CDD|223964 COG1033, COG1033, Predicted exporters of the RND superfamily
[General function prediction only].
Length = 727
Score = 47.3 bits (113), Expect = 6e-07
Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 1/119 (0%)
Query: 26 FSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKNQFDSECTGI 85
S+L LG +LGIP TT VP L +G+ +D + + K + E
Sbjct: 232 VSVLWTLGAMGLLGIPLTI-TTSAVPPLLIGIGIDYGVHFHNRYEEERRKGRTVEEAVVE 290
Query: 86 VLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYPAIVSL 144
++ TG +++++++ + F S IPA++ F + L+I I+ L V PA++ L
Sbjct: 291 AIKHTGPAVLIAALTTAAGFLSLLTSSIPAIKEFGILLSIGIILAFLSSLTVLPALLIL 349
Score = 44.6 bits (106), Expect = 5e-06
Identities = 35/128 (27%), Positives = 59/128 (46%), Gaps = 3/128 (2%)
Query: 24 ISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKNQFDSECT 83
I+ + G +LGIP T + + LG+ VD IT+ + + K
Sbjct: 602 IAIVVGWNFGLMGLLGIPLTP-ATATLGAIILGIGVDYSIHITERYREERKKGGPKEAIE 660
Query: 84 GIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYPA-IV 142
+ +TG +I+ S++ ++ F + P P + F L I IL ++ L++ PA +V
Sbjct: 661 -TTVERTGKAILASALTTAIGFLALIFSPFPIISNFGLLTVIGILLSLLASLVLLPALLV 719
Query: 143 SLDLRRSR 150
LD RR R
Sbjct: 720 LLDGRRKR 727
>gnl|CDD|233187 TIGR00921, 2A067, The (Largely Archaeal Putative)
Hydrophobe/Amphiphile Efflux-3 (HAE3) Family.
Characterized members of the RND superfamily all
probably catalyze substrate efflux via an H+ antiport
mechanism. These proteins are found ubiquitously in
bacteria, archaea and eukaryotes. They fall into seven
phylogenetic families, this family (2.A.6.7) consists of
uncharacterised putative transporters, largely in the
Archaea [Transport and binding proteins, Unknown
substrate].
Length = 719
Score = 46.7 bits (111), Expect = 9e-07
Identities = 32/128 (25%), Positives = 58/128 (45%), Gaps = 1/128 (0%)
Query: 17 GILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKN 76
+L +I F + LG LGIP A+T VP L +G+ +D + +
Sbjct: 220 PLLPLVIILFGVAWVLGIMGWLGIPLYATTLLAVPML-IGVGIDYGIQTLNRYEEERDIG 278
Query: 77 QFDSECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLL 136
+ E +R+TG +++++ + S F + +L P + F L L ++ + LL
Sbjct: 279 RAKGEAIVTAVRRTGRAVLIALLTTSAGFAALALSEFPMVSEFGLGLVAGLITAYLLTLL 338
Query: 137 VYPAIVSL 144
V PA++
Sbjct: 339 VLPALLQS 346
Score = 45.6 bits (108), Expect = 2e-06
Identities = 34/144 (23%), Positives = 61/144 (42%), Gaps = 11/144 (7%)
Query: 3 LIKYWDPVKSQAGVGILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDM 62
L + +P+K+ + I IL +G + GIP + LGL +D
Sbjct: 585 LAVFRNPIKA-----VFPLIAIGSGILWAIGLMGLRGIPSFL-AMATTISIILGLGMDYS 638
Query: 63 FLITKTFAKYTSKNQFDSECTGIV--LRKTGLSIILSSVCKSVAFFSASLIPIPALRVFN 120
+ + +Y + + I + +TG I+ S + + F S L P +R F
Sbjct: 639 IHLAE---RYFEERKEHGPKEAITHTMERTGPGILFSGLTTAGGFLSLLLSHFPIMRNFG 695
Query: 121 LQLAILILFNMFVLLLVYPAIVSL 144
L I +L ++ L+V+PA++ L
Sbjct: 696 LVQGIGVLSSLTAALVVFPALLVL 719
>gnl|CDD|225272 COG2409, COG2409, Predicted drug exporters of the RND superfamily
[General function prediction only].
Length = 937
Score = 42.8 bits (101), Expect = 2e-05
Identities = 27/128 (21%), Positives = 54/128 (42%), Gaps = 6/128 (4%)
Query: 26 FSILAGLGFCSILGIPFNAS----TTQIVPFLALGLSVD-DMFLITKTFAKYTSKNQFDS 80
S+L G ++L F ++ L +G D +FL+++ + + + Q
Sbjct: 220 LSLLVAQGIVALLAYAFGLGVSTFALSLLVALGIGAGTDYALFLVSR-YREELREGQDRE 278
Query: 81 ECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYPA 140
G R G ++ S + ++A S +P L+ + AI + + L + PA
Sbjct: 279 AAVGTAYRTAGKTVAFSGLTVAIALLGLSFARLPFLKTLGIAAAIGVAVAVLAALTLLPA 338
Query: 141 IVSLDLRR 148
+++L RR
Sbjct: 339 LLALLGRR 346
>gnl|CDD|129913 TIGR00833, actII, Transport protein. The
Resistance-Nodulation-Cell Division (RND) Superfamily-
MmpL sub family (TC 2.A.6.5)Characterized members of the
RND superfamily all probably catalyze substrate efflux
via an H+ antiport mechanism. These proteins are found
ubiquitously in bacteria, archaea and eukaryotes. This
sub-family includes the S. coelicolor ActII3 protein,
which may play a role in drug resistance, and the M.
tuberculosis MmpL7 protein, which catalyzes export of an
outer membrane lipid, phthiocerol dimycocerosate
[Transport and binding proteins, Unknown substrate].
Length = 910
Score = 41.9 bits (98), Expect = 4e-05
Identities = 36/129 (27%), Positives = 66/129 (51%), Gaps = 4/129 (3%)
Query: 24 ISFSILAGLGFCSILGIP----FNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKNQFD 79
+ FS++ G S+LGIP NA TT ++ L +G D +T + + K +
Sbjct: 207 VGFSVVVAQGIVSLLGIPGLIGVNAQTTVLLTALVIGAGTDYAVFLTGRYHEERRKGESL 266
Query: 80 SECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYP 139
E LR TG +I+ S++ +VAF + SL +P+ + + A+ +L + + + P
Sbjct: 267 EEAAAEALRGTGKAILGSALTVAVAFLALSLARLPSFKTLGVSCAVGVLVALLNAVTLTP 326
Query: 140 AIVSLDLRR 148
A+++L+ R
Sbjct: 327 ALLTLEGRE 335
Score = 32.2 bits (73), Expect = 0.093
Identities = 34/141 (24%), Positives = 64/141 (45%), Gaps = 11/141 (7%)
Query: 14 AGVGILGCCLISFSI---LAGLGFCSILGIPFNASTTQIVPFLALGLSVD-DMFLITKTF 69
A + ++G +S+ L+ L F ILG + S V L + L VD +M L+++
Sbjct: 770 APIVLIGSVALSYLWALGLSVLAFQHILGAELHWSVLAGVFVLLVALGVDYNMLLVSRIK 829
Query: 70 AKYTSKNQFDSECTGIV--LRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILI 127
+ + N+ TGI+ L TG I + + + + + + A+ F + + I
Sbjct: 830 EESPAGNR-----TGIIRALGSTGGVITAAGLVFAGTMAALASAQLTAIAQFGFTVGVGI 884
Query: 128 LFNMFVLLLVYPAIVSLDLRR 148
L + F++ V ++L L R
Sbjct: 885 LLDTFIVRSVTVPALTLLLGR 905
>gnl|CDD|169981 PRK09577, PRK09577, multidrug efflux protein; Reviewed.
Length = 1032
Score = 35.6 bits (82), Expect = 0.007
Identities = 34/132 (25%), Positives = 64/132 (48%), Gaps = 21/132 (15%)
Query: 25 SFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKT---------FAKYTSK 75
+F ++ GF SI T LA+G+ VDD ++ + + Y +
Sbjct: 378 TFGVMLAAGF-SI------NVLTMFGMVLAIGILVDDAIVVVENVERLMVEEGLSPYDAT 430
Query: 76 NQFDSECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLL 135
+ + +G ++ G++++L+SV +AFF ++ I R F L LA+ I F+ F+ L
Sbjct: 431 VKAMKQISGAIV---GITVVLTSVFVPMAFFGGAVGNI--YRQFALSLAVSIGFSAFLAL 485
Query: 136 LVYPAIVSLDLR 147
+ PA+ + L+
Sbjct: 486 SLTPALCATLLK 497
>gnl|CDD|233182 TIGR00915, 2A0602, The (Largely Gram-negative Bacterial)
Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. Proteins
scoring above the trusted cutoff (1000) form a tight
clade within the RND (Resistance-Nodulation-Cell
Division) superfamily. Proteins scoring greater than the
noise cutoff (100) appear to form a larger clade,
cleanly separated from more distant homologs that
include cadmium/zinc/cobalt resistance transporters.
This family is one of several subfamilies within the
scope of Pfam model pfam00873 [Cellular processes, Toxin
production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 1044
Score = 33.9 bits (78), Expect = 0.022
Identities = 28/130 (21%), Positives = 58/130 (44%), Gaps = 15/130 (11%)
Query: 27 SILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKNQFD------- 79
+L + G N + T LA+GL VDD ++ + + ++
Sbjct: 375 VLLGTFAVLAAFGFSIN-TLTMFAMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRK 433
Query: 80 --SECTGIVLRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLLV 137
+ G ++ G++++LS+V +AFF S I R F++ + + ++ V L++
Sbjct: 434 SMGQIQGALV---GIAMVLSAVFVPMAFFGGSTGAI--YRQFSITIVSAMALSVLVALIL 488
Query: 138 YPAIVSLDLR 147
PA+ + L+
Sbjct: 489 TPALCATMLK 498
>gnl|CDD|217407 pfam03176, MMPL, MMPL family. Members of this family are putative
integral membrane proteins from bacteria. Several of the
members are mycobacterial proteins. Many of the proteins
contain two copies of this aligned region. The function
of these proteins is not known, although it has been
suggested that they may be involved in lipid transport.
Length = 332
Score = 31.9 bits (73), Expect = 0.10
Identities = 26/124 (20%), Positives = 56/124 (45%), Gaps = 6/124 (4%)
Query: 23 LISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVD-DMFLITKTFAKYTSKNQFDSE 81
+ ++A L ILGI + ++ L + + D +FL+++ + + D E
Sbjct: 181 GAAQGLVAILAH--ILGIGLSTFALNLLVVLLIAVGTDYALFLVSRY--REELRAGEDRE 236
Query: 82 CTGIV-LRKTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYPA 140
I +R TG + + + ++A + S +P +AI +L ++ L + PA
Sbjct: 237 EAVIRAVRGTGKVVTAAGLTVAIAMLALSFARLPVFAQVGPTIAIGVLVDVLAALTLLPA 296
Query: 141 IVSL 144
+++L
Sbjct: 297 LLAL 300
>gnl|CDD|185081 PRK15127, PRK15127, multidrug efflux system protein AcrB;
Provisional.
Length = 1049
Score = 30.3 bits (68), Expect = 0.37
Identities = 34/131 (25%), Positives = 64/131 (48%), Gaps = 15/131 (11%)
Query: 23 LISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKNQFD-SE 81
L +F++LA GF SI + T LA+GL VDD ++ + + ++ E
Sbjct: 377 LGTFAVLAAFGF-SI------NTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKE 429
Query: 82 CTGIVLRK-----TGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLL 136
T + + G++++LS+V +AFF S I R F++ + + ++ V L+
Sbjct: 430 ATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAI--YRQFSITIVSAMALSVLVALI 487
Query: 137 VYPAIVSLDLR 147
+ PA+ + L+
Sbjct: 488 LTPALCATMLK 498
>gnl|CDD|234225 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of this
biological process. The proteins appear to be related to
the RND family of export proteins, particularly the
hydrophobe/amphiphile efflux-3 (HAE3) family represented
by TIGR00921.
Length = 862
Score = 29.2 bits (66), Expect = 0.92
Identities = 28/117 (23%), Positives = 52/117 (44%), Gaps = 10/117 (8%)
Query: 27 SILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKNQFDSECTGIV 86
+ L + +LGIPFN + +P L LGL VD F Y + +G +
Sbjct: 749 AGLLTVAAMVLLGIPFNFANIIALPLL-LGLGVD--------FGIYMVHRWRNGVDSGNL 799
Query: 87 LR-KTGLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYPAIV 142
L+ T ++ S++ + AF S ++ P + L++ + + L+ PA++
Sbjct: 800 LQSSTARAVFFSALTTATAFGSLAVSSHPGTASMGILLSLGLGLTLLCTLIFLPALL 856
>gnl|CDD|182544 PRK10555, PRK10555, aminoglycoside/multidrug efflux system;
Provisional.
Length = 1037
Score = 29.0 bits (65), Expect = 1.1
Identities = 33/133 (24%), Positives = 64/133 (48%), Gaps = 23/133 (17%)
Query: 25 SFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSKNQFD-SECT 83
+FS+L G+ SI + T LA+GL VDD ++ + + S+ E T
Sbjct: 379 TFSVLYAFGY-SI------NTLTMFAMVLAIGLLVDDAIVVVENVERIMSEEGLTPREAT 431
Query: 84 GIVLRKT---------GLSIILSSVCKSVAFFSASLIPIPALRVFNLQLAILILFNMFVL 134
RK+ G++++LS+V +AFF + I R F++ + ++ ++ V
Sbjct: 432 ----RKSMGQIQGALVGIAMVLSAVFVPMAFFGGTTGAI--YRQFSITIVSAMVLSVLVA 485
Query: 135 LLVYPAIVSLDLR 147
+++ PA+ + L+
Sbjct: 486 MILTPALCATLLK 498
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 28.1 bits (63), Expect = 2.0
Identities = 10/39 (25%), Positives = 19/39 (48%)
Query: 103 VAFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYPAI 141
V + L F++ LA+L+ + +LLL+ P +
Sbjct: 140 VVALVLIAVVTIGLSFFSIPLALLLGLILLLLLLIIPTL 178
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 26.4 bits (59), Expect = 2.2
Identities = 8/28 (28%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 39 GIPFNASTTQIVPFLA-LGLSVDDMFLI 65
G+PF+A+ I F + L + D + ++
Sbjct: 6 GLPFSATEEDIRDFFSGLDIPPDGIHIV 33
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 27.8 bits (62), Expect = 2.8
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 64 LITKTFAKYTSKNQFDSECT 83
L+ +Y SKN F + T
Sbjct: 566 LVDSESKQYASKNDFSALAT 585
>gnl|CDD|227904 COG5617, COG5617, Predicted integral membrane protein [Function
unknown].
Length = 801
Score = 26.3 bits (58), Expect = 8.1
Identities = 22/100 (22%), Positives = 33/100 (33%), Gaps = 6/100 (6%)
Query: 16 VGILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTFAKYTSK 75
V +LG G I F T + L ++ +F +T+ FA
Sbjct: 285 VSLLGIIYAIRRSTPGFVTRLI----FWLGMTSLFLPWLFKLPLNQLFWMTR-FAPIALA 339
Query: 76 NQFDSECTGIVLRKTGLSIILSSVCKSV-AFFSASLIPIP 114
F S L+ + IIL + F L+ IP
Sbjct: 340 PFFISLLNWFKLKVLIIPIILQLLLADSSRSFMFLLVAIP 379
>gnl|CDD|201483 pfam00873, ACR_tran, AcrB/AcrD/AcrF family. Members of this family
are integral membrane proteins. Some are involved in
drug resistance. AcrB cooperates with a membrane fusion
protein, AcrA, and an outer membrane channel TolC. The
structure shows the AcrB forms a homotrimer.
Length = 1021
Score = 26.1 bits (58), Expect = 8.4
Identities = 24/104 (23%), Positives = 48/104 (46%), Gaps = 14/104 (13%)
Query: 53 LALGLSVDDMFLITKTFAKYTSKNQFD---------SECTGIVLRKTGLSIILSSVCKSV 103
LA+GL VDD ++ + + ++ E G ++ ++++LS+V +
Sbjct: 393 LAIGLVVDDAIVVVENIERGLAEEGLKPLEAAYKSMGEIGGALV---AIALVLSAVFLPI 449
Query: 104 AFFSASLIPIPALRVFNLQLAILILFNMFVLLLVYPAIVSLDLR 147
AF I R F + + + IL ++ V L + PA+ + L+
Sbjct: 450 AFLGGVTGRI--FRQFAITIVLAILLSVLVALTLTPALCATLLK 491
>gnl|CDD|240373 PTZ00345, PTZ00345, glycerol-3-phosphate dehydrogenase;
Provisional.
Length = 365
Score = 26.1 bits (58), Expect = 8.5
Identities = 18/73 (24%), Positives = 26/73 (35%), Gaps = 8/73 (10%)
Query: 10 VKSQAGVGILGCCLISFSILAGLGFCSILGIPFNASTTQIVPFLALGLSVDDMFLITKTF 69
V GV + G + I GFC LG+ N + I + +++M L K F
Sbjct: 201 VPDVIGVEVCGA--LKNIIALAAGFCDGLGLGTNTKSAII------RIGLEEMKLFGKIF 252
Query: 70 AKYTSKNQFDSEC 82
F C
Sbjct: 253 FPNVMDETFFESC 265
>gnl|CDD|222531 pfam14085, DUF4265, Domain of unknown function (DUF4265). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 139 and 168 amino
acids in length.
Length = 117
Score = 25.2 bits (56), Expect = 8.7
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 50 VPFLALGLSVDDMFLITK 67
PF A GL+ D+
Sbjct: 19 SPFFAYGLARGDVVRAED 36
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
0.331 0.144 0.426
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,507,276
Number of extensions: 686304
Number of successful extensions: 1133
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1119
Number of HSP's successfully gapped: 93
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 54 (24.5 bits)