RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4987
(299 letters)
>gnl|CDD|220407 pfam09794, Avl9, Transport protein Avl9. Avl9 is a protein
involved in exocytic transport from the Golgi. It has
been speculated that Avl9 could play a role in deforming
membranes for vesicle fission and/or in recruiting
cargo.
Length = 379
Score = 272 bits (699), Expect = 3e-90
Identities = 109/230 (47%), Positives = 148/230 (64%), Gaps = 23/230 (10%)
Query: 88 QVEYAFPPLIEGTSSESNECPSEWKYLPTLALPDGSHNYEEDTVYFHLP---SLTDSKKT 144
+VE+ +P L E ++ PS WK LP LALPDGSHN+EED YF L T T
Sbjct: 16 EVEFWYPGL-----DEDSDDPSLWKNLPFLALPDGSHNFEEDFSYFTLLYDEPDTRPATT 70
Query: 145 VFGISCFRQIPVEKLKNQTADLTRNTVQKSVCVLSTVPLYGHVQVKMALITHAYFEEGDF 204
+FGISC+RQI LKN+ AD+TR+TVQK+V V+S P++G ++ K+++IT+AYFE+GDF
Sbjct: 71 LFGISCYRQIKSSDLKNRPADVTRSTVQKAVVVISRQPIFGQIKDKLSIITNAYFEQGDF 130
Query: 205 SKVSLLKDTYHHLNSCLSQIEDLSNA-PQLFVGLSARELILKFRHNALLLFKLLLLERKC 263
S +L Y +LN+ + L+VGLS REL+LKFRH L+LFKLLLLE+K
Sbjct: 131 SDTDILVSLYENLNATFKSLGGEELEESDLYVGLSLRELVLKFRHKTLVLFKLLLLEKKV 190
Query: 264 VFYCSPVKPLCSTILSLLSLHPSMI--------------ETGLAKSTSIK 299
+FY SPV+ LC+ +SLLSL P ++ E+ L+K TS+K
Sbjct: 191 LFYGSPVERLCNLQMSLLSLIPGLLSNLQDSGSPSLDSYESNLSKPTSLK 240
Score = 41.1 bits (97), Expect = 5e-04
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 9 ILHVLVVGFHHKKGCQV-FFFCNFH 32
IL + VV FHHK+G +V F++
Sbjct: 1 ILGICVVDFHHKRGPEVEFWYPGLD 25
>gnl|CDD|219579 pfam07792, Afi1, Docking domain of Afi1 for Arf3 in vesicle
trafficking. This domain occurs at the N-terminal of
Afi1, a protein necessary for vesicle trafficking in
yeast. This domain is the interacting region of the
protein which binds to Arf3. Afi1 is distributed
asymmetrically at the plasma membrane and is required
for polarized distribution of Arf3 but not of an Arf3
guanine nucleotide-exchange factor, Yel1p. However, Afi1
is not required for targeting of Arf3 or Yel1p to the
plasma membrane. Afi1 functions as an Arf3
polarization-specific adapter and participates in
development of polarity. Although Arf3 is the homologue
of human Arf6 it does not function in the same way, not
being necessary for endocytosis or for mating factor
receptor internalisation. In the S phase, however, it is
concentrated at the plasma membrane of the emerging bud.
Because of its polarized localisation and its critical
function in the normal budding pattern of yeast, Arf3 is
probably a regulator of vesicle trafficking, which is
important for polarized growth.
Length = 57
Score = 48.3 bits (116), Expect = 6e-08
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 88 QVEYAFPPLIEGTSSESNECPSEWKYLPTLALPDGSHNYEEDTVYFHLP 136
VE+ +P S+ LP L+LPDG H EED YF L
Sbjct: 16 VVEWQYPK---------PLGESDLSNLPFLSLPDGIHEREEDFTYFRLR 55
Score = 28.7 bits (65), Expect = 0.46
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 9 ILHVLVVGFHHKKGCQVFFFCNFHNSGGESVKGTLPGILALP 50
I + +V F HK+G V + + GES LP L+LP
Sbjct: 1 IEAIFLVEFDHKRGPVVEW--QYPKPLGESDLSNLPF-LSLP 39
>gnl|CDD|220412 pfam09804, DUF2347, Uncharacterized conserved protein (DUF2347).
Members of this family of hypothetical proteins have no
known function.
Length = 496
Score = 44.7 bits (106), Expect = 3e-05
Identities = 55/216 (25%), Positives = 76/216 (35%), Gaps = 47/216 (21%)
Query: 118 ALPDGSHNYEEDTVYFHLPSLTDSKKTVFGISCFRQIPVEKLKNQTADLTRNTVQKSVCV 177
+LP G H ED VYF K +G+S FRQ P E+ +N RN SV V
Sbjct: 35 SLPSGIHEVSEDLVYFVHE------KEYYGLSAFRQNPAEEEEND----RRNVKMYSVGV 84
Query: 178 LSTVPL-YGHV--------------------QVKMALITHAY----FEEGDFSKVSLLKD 212
L VPL G + + K ++ + + S
Sbjct: 85 L--VPLSNGFIGASWRYAEKLKELLSSWLQDEDKYEILEEYWETNKSSDLKKPSPSPDSP 142
Query: 213 TYHHLNSCLSQIEDLSNAPQLFVGLSAR-------ELILKFRHNALLLFKLLLLERKCVF 265
+ L + L LS EL+ K L+K LL ++ +
Sbjct: 143 LDSPSSLRLGAPDSLFRNRAGSDALSPFHPLSSLPELLDKLGPLIFPLYKAALLRKRILI 202
Query: 266 YCS-PVKPLCSTI--LSLLSLHPSMIETGLAKSTSI 298
+ PV LCS + LSLLSL P + L S
Sbjct: 203 FSEAPVSLLCSFVYCLSLLSLIPLSLLALLGSPASY 238
>gnl|CDD|219936 pfam08616, SPA, Stabilisation of polarity axis. Yeast AFI1
(ARF3-interaction protein 1) has been shown to interact
with the outer plaque of the spindle pole body. In
Aspergillus nidulans the protein member is necessary for
stabilisation of the polarity axes during septation. and
in S. cerevisiae it functions as a polarisation-specific
docking factor.
Length = 114
Score = 30.3 bits (69), Expect = 0.47
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 242 LILKFRHNALLLFKLLLLERKCVFYCS--PVKPLCSTILSLLSL 283
L+ KF +LL+ LL +++ +F +C+ +L+L +L
Sbjct: 7 LLGKFGPPIILLWNALLTQKRIIFLSYQPSAGEVCNFVLALCNL 50
>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 = 29.9 bits (68), Expect = 1.1
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 234 FVGLSARELILKFRH-NALLLFKLLLLERKCVFYCSPVKPLCSTILSLLSL 283
+ S EL N L LF LLLER+ +F S + L + I +LL+L
Sbjct: 77 LIDFSLHELFECLGVENILQLFAALLLERRIIFTSSNLSTLSAVIEALLAL 127
>gnl|CDD|234113 TIGR03117, cas_csf4, CRISPR type AFERR-associated DEAD/DEAH-box
helicase Csf4. Members of this family show up near
CRISPR repeats in Acidithiobacillus ferrooxidans ATCC
23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens
DSM 15236. In the latter two species, the CRISPR/cas
locus is found on a plasmid. This family is one of
several characteristic of a type of CRISPR-associated
(cas) gene cluster we designate Aferr after A.
ferrooxidans, where it is both chromosomal and the only
type of cas gene cluster found. The gene is designated
csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein
1), as it lies farthest (fourth closest) from the
repeats in the A. ferrooxidans genome [Mobile and
extrachromosomal element functions, Other].
Length = 636
Score = 30.3 bits (68), Expect = 1.4
Identities = 23/113 (20%), Positives = 31/113 (27%), Gaps = 16/113 (14%)
Query: 33 NSGGESVKGTLPGILALPYSPPLPPENCKRGHREV-------LIGLADLYQFSFNIQCYV 85
N E++ L L EN K+ V I + +
Sbjct: 283 NKELETLFADLDAALDACSVGRNRDEN-KKALSVVKDVKKARFILDNAITAIQGKASAVL 341
Query: 86 KFQVEYAFPPLIEGTSSESNECPSEWKYLP--------TLALPDGSHNYEEDT 130
+F + FP LI G WK + TL LPD D
Sbjct: 342 QFSPDRRFPSLIVGREDLGKVMGGLWKDVTHGAIIVSATLYLPDRFGQMSCDY 394
>gnl|CDD|171815 PRK12911, PRK12911, bifunctional preprotein translocase subunit
SecD/SecF; Reviewed.
Length = 1403
Score = 28.3 bits (63), Expect = 7.1
Identities = 11/37 (29%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 152 RQIPVEKLKNQTADLTRNTVQKSVCVLSTVPLYGHVQ 188
R+I +E+ Q +D + + + +LST+ L GH++
Sbjct: 44 RKI-IERFTKQVSDARNDLIPRVSKILSTLKLRGHIK 79
>gnl|CDD|218133 pfam04533, Herpes_U44, Herpes virus U44 protein. This is a family
of proteins from dsDNA beta-herpesvirinae and
gamma-herpesvirinae viruses. The function is not known,
and the proteins are named variously as U44, BSRF1,
UL71, and M71. The family BSRF1 has been merged into
this.
Length = 211
Score = 27.0 bits (60), Expect = 9.7
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 102 SESNECPSEWKYLPTLALPDG 122
E ECP W+ L LP G
Sbjct: 28 DEVEECPERWRAEIDLGLPPG 48
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
0.322 0.138 0.419
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,826,533
Number of extensions: 1376597
Number of successful extensions: 868
Number of sequences better than 10.0: 1
Number of HSP's gapped: 865
Number of HSP's successfully gapped: 16
Length of query: 299
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 203
Effective length of database: 6,679,618
Effective search space: 1355962454
Effective search space used: 1355962454
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 (21.9 bits)
S2: 59 (26.4 bits)