RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16159
(175 letters)
>gnl|CDD|146145 pfam03357, Snf7, Snf7. This family of proteins are involved in
protein sorting and transport from the endosome to the
vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes
play an important role in the degradation of both lipids
and cellular proteins. In order to perform this
degradative function, vacuoles/lysosomes contain
numerous hydrolases which have been transported in the
form of inactive precursors via the biosynthetic pathway
and are proteolytically activated upon delivery to the
vacuole/lysosome. The delivery of transmembrane
proteins, such as activated cell surface receptors to
the lumen of the vacuole/lysosome, either for
degradation/downregulation, or in the case of
hydrolases, for proper localisation, requires the
formation of multivesicular bodies (MVBs). These late
endosomal structures are formed by invaginating and
budding of the limiting membrane into the lumen of the
compartment. During this process, a subset of the
endosomal membrane proteins is sorted into the forming
vesicles. Mature MVBs fuse with the vacuole/lysosome,
thereby releasing cargo containing vesicles into its
hydrolytic lumen for degradation. Endosomal proteins
that are not sorted into the intralumenal MVB vesicles
are either recycled back to the plasma membrane or Golgi
complex, or remain in the limiting membrane of the MVB
and are thereby transported to the limiting membrane of
the vacuole/lysosome as a consequence of fusion.
Therefore, the MVB sorting pathway plays a critical role
in the decision between recycling and degradation of
membrane proteins. A few archaeal sequences are also
present within this family.
Length = 169
Score = 97.7 bits (244), Expect = 3e-26
Identities = 45/144 (31%), Positives = 74/144 (51%), Gaps = 2/144 (1%)
Query: 2 ELEIKKAAKEGDKIAATILAKQLIQIRKQKTRTYAAQGKVHSIGIQNKTMGSNIKMAEAM 61
E EIKK AK+G+K AA IL KQ + KQ + + + + + +N ++ AM
Sbjct: 28 EAEIKKLAKKGNKDAALILLKQKKRYEKQLDQLDGQLANLEQVRMAIENAKTNQEVLNAM 87
Query: 62 KNTADTMKNMNSIMKPEQIAASAQEFQQGITRMNMTDEMIDEALDDMLEGSDDEQESNKI 121
K A MK MN M ++I E + + + + EM+ + LDD +DE+E +
Sbjct: 88 KGGAKAMKAMNKNMDIDKIDDLMDEIEDQMEKADEISEMLSDTLDDA--DEEDEEELDAE 145
Query: 122 IDQVLGEIGIEISGKMANAPTVSG 145
+D +L EIG E ++ +AP+ +
Sbjct: 146 LDALLDEIGDEELVELPSAPSGAL 169
>gnl|CDD|227778 COG5491, VPS24, Conserved protein implicated in secretion [Cell
motility and secretion].
Length = 204
Score = 34.8 bits (80), Expect = 0.012
Identities = 32/172 (18%), Positives = 68/172 (39%), Gaps = 13/172 (7%)
Query: 3 LEIKKAAKEGDKIAATILAKQLIQIRKQKTRTYAAQGKVHSIGIQNKTMGSNIKMAEAMK 62
++ LA++L ++RK ++R A+ ++ S+ M +
Sbjct: 23 GQVLLNEIAKKAPNRRRLAEELYKLRKARSRLDASISRLQSLDTMLFEKVV---MRQVSG 79
Query: 63 NTADTMKNMNSIMKPEQIAASAQEFQQGITRMNMTDEMIDEALDDM-----LEGSDDEQE 117
+ A MN + E I Q F+ + + ++ + M +D +E
Sbjct: 80 DMAKAAMYMNEL---ESIRRIMQLFETQFLALELVQLRLETMDELMDVVVGDPVLEDLEE 136
Query: 118 SNKIIDQVLGEIGIEI--SGKMANAPTVSGKVGEGSKSSSKTQVPSDAEIEA 167
++++++VL EIG+E+ S + A V + S ++ +AE A
Sbjct: 137 LDELVNKVLPEIGLELDESEQSLPANVVENGSVPAAVSPEARKILEEAEKIA 188
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 31.4 bits (72), Expect = 0.22
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 47 QNKTMGS-NIKMAEAMKNTADTMKNMNSIMKPEQIAASAQEFQQGITRMNMTDEMIDEA 104
Q KTMG I ++ + + + + N I+ P+ IA F I +N D EA
Sbjct: 370 QPKTMGCYGIGVSRLVAALLEQIHDENGIIWPKAIA----PFDVHIVPVNTKDFKQAEA 424
>gnl|CDD|226806 COG4367, COG4367, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 97
Score = 28.4 bits (63), Expect = 0.79
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 75 MKPEQIAASAQEFQQGITRMNMTDEMIDEAL 105
+ PEQ + QE Q ++DE I AL
Sbjct: 3 LNPEQKQRTKQELQANFELCPLSDEEIATAL 33
>gnl|CDD|200380 TIGR04129, CxxH_BA5709, CxxH/CxxC protein, BA_5709 family. Members
of this protein family occur exclusively in the
Firmicutes, in at least 50 different species. Members
average about 55 residues in length, and four of the
five invariant or nearly invariant residues occur in
motifs CxxH and CxxC. The function is unknown.
Length = 49
Score = 25.3 bits (56), Expect = 3.5
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 4/31 (12%)
Query: 98 DEMIDEALDDMLEGSDDEQESNKIIDQVLGE 128
E I+ A+DD + DE E+ ++++
Sbjct: 5 KEHIELAIDDYV----DEYETAPDLEKLEEV 31
>gnl|CDD|219974 pfam08696, Dna2, DNA replication factor Dna2. Dna2 is a DNA
replication factor with single-stranded DNA-dependent
ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease)
and helicase activities. It is required for Okazaki
fragment processing and is involved in DNA repair
pathways.
Length = 209
Score = 26.8 bits (60), Expect = 6.1
Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 9/82 (10%)
Query: 87 FQQGITRMNMTDEMIDEALDDMLEGSDDE-QESNKIIDQVLGEIGIEISGKMANAPTVSG 145
FQ+ + + E ++E LD +LE +E + D+V E+ M + P + G
Sbjct: 101 FQEALRANDFDLEFLEELLDAVLEKYLEELYLLGESQDEVREEV-------MEHLPAIEG 153
Query: 146 KVGEG-SKSSSKTQVPSDAEIE 166
+ KS S + E
Sbjct: 154 WAEQYVKKSPSSESISVSGTGE 175
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
0.306 0.122 0.308
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,409,621
Number of extensions: 757411
Number of successful extensions: 836
Number of sequences better than 10.0: 1
Number of HSP's gapped: 830
Number of HSP's successfully gapped: 64
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 56 (25.3 bits)