RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13383
(105 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 = 43.8 bits (104), Expect = 1e-06
Identities = 17/40 (42%), Positives = 31/40 (77%)
Query: 17 KNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQM 56
+ +L KA+R+LD++++ +E++ KKL A+IKK+AK+G
Sbjct: 1 EAILSLRKAIRELDKKQESLEKKIKKLEAEIKKLAKKGNK 40
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 28.2 bits (64), Expect = 0.64
Identities = 10/45 (22%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 12 EEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIA---DIKKMAKE 53
E+ L + + L++ + L++ ++ +E++EK+L +++K +E
Sbjct: 88 EKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEE 132
Score = 25.1 bits (56), Expect = 9.9
Identities = 12/42 (28%), Positives = 28/42 (66%)
Query: 12 EEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKE 53
E+L K + L K ++L++++Q +E++E++L I++ +E
Sbjct: 102 LELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQE 143
>gnl|CDD|220767 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 28.3 bits (64), Expect = 0.66
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 17 KNQRALNKAMRDLD-REKQHMEQQEKKLIADIKKMAKEGQ 55
KN + + ++DLD ++ + +E L A +KK G
Sbjct: 309 KNSIGMLEGLKDLDLLARK--QAREAALRAWVKKDPARGA 346
>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869). This
bacterial family of proteins has no known function.
Length = 131
Score = 27.6 bits (62), Expect = 0.87
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 16 RKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQ 55
+ Q L + + L++E Q +E Q +K I +I+K + +
Sbjct: 19 EELQAELQEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQI 58
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 27.9 bits (62), Expect = 0.90
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 7 RKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLI-ADIKKMAKEG 54
+K TP+ + K+ AL K + LD+E E+ +KL A + +
Sbjct: 1146 KKTTPKSLWLKDLDALEKELDKLDKEDAKAEEAREKLQRAAARGESGAA 1194
>gnl|CDD|216284 pfam01074, Glyco_hydro_38, Glycosyl hydrolases family 38
N-terminal domain. Glycosyl hydrolases are key enzymes
of carbohydrate metabolism.
Length = 269
Score = 27.6 bits (62), Expect = 1.0
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 16/67 (23%)
Query: 1 MEWLFGRKITPEEMLRKNQRALNKAMRDLDREK------------QHMEQQEKKLIADIK 48
+ WL+ T +E RK QR + ++ LDR + + + +L IK
Sbjct: 12 VGWLW----TVDETRRKVQRTFSNVLKLLDRYPEFRFIQSEAQFYEWWWEDQPELFKKIK 67
Query: 49 KMAKEGQ 55
K+ EG+
Sbjct: 68 KLVAEGR 74
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 27.7 bits (62), Expect = 1.2
Identities = 11/58 (18%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 7 RKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMTLSTERHV 64
+ P+ L + + + + E +H+ ++ ++ IKK A+E + L V
Sbjct: 285 TDVIPDAALAVAVSSKLRHVEENKNELEHLNEE---ILPKIKKAAEEDKEILGIRDKV 339
>gnl|CDD|236536 PRK09479, glpX, fructose 1,6-bisphosphatase II; Reviewed.
Length = 319
Score = 27.4 bits (62), Expect = 1.3
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 10 TPEEMLRKNQRALNKAMRD-----LDREKQHMEQQEKKLIADIKKM 50
E LR +AL K + D LDR + H ++LIA+I++
Sbjct: 140 PVAENLRAVAKALGKDVSDLTVVVLDRPR-H-----EELIAEIREA 179
>gnl|CDD|217535 pfam03401, TctC, Tripartite tricarboxylate transporter family
receptor. These probable extra-cytoplasmic solute
receptors are strongly overrepresented in several
beta-proteobacteria. This family, formerly known as Bug
- Bordetella uptake gene (bug) product - is a family of
bacterial tripartite tricarboxylate receptors of the
extracytoplasmic solute binding receptor-dependent
transporter group of families, distinct from the ABC and
TRAP-T families. The TctABC system has been
characterized in S. typhimurium, and TctC is the
extracytoplasmic tricarboxylate-binding receptor which
binds the transporters TctA and TctB, two integral
membrane proteins. Complete three-component systems are
found only in bacteria.
Length = 274
Score = 27.3 bits (61), Expect = 1.3
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 4 LFGRKITPEEMLRKNQRALNKAMRD 28
L K TP ++ K A+ KA++D
Sbjct: 208 LVAPKGTPPAVVEKLNDAIKKALKD 232
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 27.1 bits (60), Expect = 1.6
Identities = 10/47 (21%), Positives = 21/47 (44%)
Query: 7 RKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKE 53
R + E L K L+ + +L EK+ +E +E + + + +
Sbjct: 81 RLLDELEELEKEDDDLDGELVELQEEKEQLENEELQYLREYNLFDRN 127
>gnl|CDD|217491 pfam03320, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase,
glpX-encoded.
Length = 308
Score = 27.0 bits (61), Expect = 1.8
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 11/46 (23%)
Query: 10 TPEEMLRKNQRALNKAMRD-----LDREKQHMEQQEKKLIADIKKM 50
EE L+ +AL K + D LDR + H +LI +I++
Sbjct: 136 PVEENLKAVAKALGKDVEDLTVVVLDRPR-H-----AELIEEIREA 175
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 26.7 bits (59), Expect = 2.4
Identities = 6/39 (15%), Positives = 22/39 (56%)
Query: 15 LRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKE 53
++K + + + L++++ +++ +KL D +A++
Sbjct: 81 MQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ 119
>gnl|CDD|220506 pfam09989, DUF2229, CoA enzyme activase uncharacterized domain
(DUF2229). Members of this family include various
bacterial hypothetical proteins, as well as CoA enzyme
activases. The exact function of this domain has not, as
yet, been defined.
Length = 218
Score = 26.4 bits (59), Expect = 2.4
Identities = 11/54 (20%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 1 MEWLFGRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEG 54
E I+ EE+ ++A+ KA+ + + K+ + ++ ++ +A +++ K+G
Sbjct: 133 YELGKKLGISKEEI----KKAVEKALEEQEAFKKDLRKKGEEALAYLEEEGKKG 182
>gnl|CDD|220065 pfam08902, DUF1848, Domain of unknown function (DUF1848). This
family of proteins are functionally uncharacterized. The
C-terminus contains a cluster of cysteines that are
similar to the iron-sulfur cluster found at the
N-terminus of pfam04055.
Length = 264
Score = 26.4 bits (59), Expect = 2.8
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 7/49 (14%)
Query: 13 EMLRKNQRALNKA-MRDLDREKQHMEQQEKKLIADIKKMAKEGQMTLST 60
++ RK +R L K R+ E E++E L A + ++AK+ +TLST
Sbjct: 156 DLYRKVRRNLRKLGAREPSEE----EKRE--LAARLAEIAKKHGITLST 198
>gnl|CDD|225352 COG2747, FlgM, Negative regulator of flagellin synthesis
(anti-sigma28 factor) [Transcription / Cell motility
and secretion / Intracellular trafficking and
secretion].
Length = 93
Score = 25.8 bits (57), Expect = 2.9
Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 17 KNQRALNKAMRDLDREKQHMEQQEK----KLIADIKKMAKEGQMTLSTERHVALLLEFV 71
K + N + ++ + M+ + + ++K+ + G+ + TE+ LL+F
Sbjct: 32 KKTDSSNVEVSLSAQQAKLMQPGSSDIREEKVEELKQAIENGEYKVDTEKIADKLLDFA 90
>gnl|CDD|219971 pfam08690, GET2, GET complex subunit GET2. This family corresponds
to the GET complex subunit GET2. The GET complex is
involved in the retrieval of ER resident proteins from
the Golgi.
Length = 298
Score = 25.5 bits (56), Expect = 5.4
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 62 RHVALLLEFV---IIVGPENRENFENSDL----RPQSNFFAVFTIGEV 102
R A+LL F+ G + + S L P SNFF +FT EV
Sbjct: 173 RWAAVLLPFIYHITRPGDFHSSHLYVSALLEVFMPPSNFFTIFTTFEV 220
>gnl|CDD|202504 pfam02996, Prefoldin, Prefoldin subunit. This family comprises of
several prefoldin subunits. The biogenesis of the
cytoskeletal proteins actin and tubulin involves
interaction of nascent chains of each of the two
proteins with the oligomeric protein prefoldin (PFD) and
their subsequent transfer to the cytosolic chaperonin
CCT (chaperonin containing TCP-1). Electron microscopy
shows that eukaryotic PFD, which has a similar structure
to its archaeal counterpart, interacts with unfolded
actin along the tips of its projecting arms. In its
PFD-bound state, actin seems to acquire a conformation
similar to that adopted when it is bound to CCT.
Length = 120
Score = 24.9 bits (55), Expect = 6.5
Identities = 9/44 (20%), Positives = 23/44 (52%)
Query: 22 LNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMTLSTERHVA 65
L +A+ L + + +E+Q +KL +++K+ + + + V
Sbjct: 75 LEEAIEFLKKRIEELEKQLEKLEEELEKLKDQITTLEANLQQVQ 118
>gnl|CDD|236949 PRK11655, ubiC, chorismate pyruvate lyase; Provisional.
Length = 169
Score = 25.0 bits (55), Expect = 7.5
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 3 WLFGRKITPEEMLRKNQRAL 22
WL GR + PE L + AL
Sbjct: 88 WLAGRTVVPESTLSGPELAL 107
>gnl|CDD|119069 pfam10549, ORF11CD3, ORF11CD3 domain. This domain was identified
by Iyer and colleagues.
Length = 57
Score = 23.9 bits (52), Expect = 7.6
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 10/50 (20%)
Query: 19 QRALNKAMRDLDREKQHM--------EQQEKK--LIADIKKMAKEGQMTL 58
+ N+A + EK + KK L A I+++ + Q+TL
Sbjct: 5 MQEYNQACAEYKDEKDIASLCGKGLARWKIKKPVLEARIEELEDQLQITL 54
>gnl|CDD|200138 TIGR01879, hydantase, amidase, hydantoinase/carbamoylase family.
Enzymes in this subfamily hydrolize the amide bonds of
compounds containing carbamoyl groups or hydantoin
rings. These enzymes are members of the broader family
of amidases represented by pfam01546.
Length = 400
Score = 25.2 bits (55), Expect = 7.8
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 26 MRDLDREKQHMEQQEKKLIADIKKMAKEGQMTLSTER 62
+R D + ++L DIK ++ E + + ER
Sbjct: 280 LRHTDAAV--LRDFTQQLENDIKAISDERDIGIDIER 314
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 25.2 bits (56), Expect = 8.1
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 13 EMLRKNQRALNKAMRDLDREKQHMEQQE 40
E LR+ Q ++ RDL +E+ + ++ E
Sbjct: 595 ETLREQQGLSDETFRDL-QEQFNAQRGE 621
>gnl|CDD|172947 PRK14472, PRK14472, F0F1 ATP synthase subunit B; Provisional.
Length = 175
Score = 24.8 bits (54), Expect = 8.5
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 12 EEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKE 53
E +LRKN+ L KA + D+ + ++ +KL A+I + A
Sbjct: 69 EAILRKNRELLAKADAEADKIIREGKEYAEKLRAEITEKAHT 110
>gnl|CDD|216134 pfam00816, Histone_HNS, H-NS histone family.
Length = 92
Score = 24.5 bits (54), Expect = 8.5
Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 22 LNKAMRDLDREKQHMEQQEKK-LIADIKKMAKEGQMTLS 59
L + L++E + + E+ +A+I+++A E +TL
Sbjct: 3 LEALIEKLEKEIEAARKAERAAALAEIRELAAEYGLTLE 41
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 0.368
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,446,705
Number of extensions: 464982
Number of successful extensions: 1023
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1006
Number of HSP's successfully gapped: 143
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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: 53 (24.3 bits)