RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13739
(89 letters)
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 32.3 bits (74), Expect = 0.014
Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 3/58 (5%)
Query: 17 PHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTTHPVPTHYPSGPYP 74
P +P + PT+ P P P + LST P P + P P
Sbjct: 216 PSSFQSDTPPPSPESPTNPSPPPGP---AAPPPPPVQQVPPLSTAKPTPPSASATPAP 270
Score = 31.6 bits (72), Expect = 0.032
Identities = 17/71 (23%), Positives = 23/71 (32%), Gaps = 1/71 (1%)
Query: 15 SSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTTHPVPTHYPSGPYP 74
SSP SP P+ P P +P P P + + P P P
Sbjct: 190 SSPGVPSFPSPPEDPSSPSDSSLPPAPSS-FQSDTPPPSPESPTNPSPPPGPAAPPPPPV 248
Query: 75 VPIHYLSSPHP 85
+ LS+ P
Sbjct: 249 QQVPPLSTAKP 259
Score = 30.8 bits (70), Expect = 0.048
Identities = 13/70 (18%), Positives = 22/70 (31%)
Query: 1 MSHTSPYPVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLST 60
+ P +P P P + + P P P + LS+ P P + +T
Sbjct: 208 SDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPPSASAT 267
Query: 61 THPVPTHYPS 70
P+
Sbjct: 268 PAPIGGITLD 277
Score = 28.1 bits (63), Expect = 0.47
Identities = 15/84 (17%), Positives = 19/84 (22%), Gaps = 3/84 (3%)
Query: 2 SHTSPYPVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTT 61
S P P P + P P + S P
Sbjct: 190 SSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNP-SPPPGPAAPPPPPV 248
Query: 62 HPVPTHYPSGPYPVPIHYLSSPHP 85
VP S P P ++P P
Sbjct: 249 QQVP--PLSTAKPTPPSASATPAP 270
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 28.1 bits (63), Expect = 0.49
Identities = 16/46 (34%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 12 HYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQS 57
HYLS P I P + +P PT Y L PLP S
Sbjct: 214 HYLSIRLPAEITLPCSDYPQPTIYSPP--------LFIDRPLPKLS 251
>gnl|CDD|218827 pfam05960, DUF885, Bacterial protein of unknown function (DUF885).
This family consists of several hypothetical bacterial
proteins several of which are putative membrane
proteins.
Length = 539
Score = 26.9 bits (60), Expect = 1.2
Identities = 9/34 (26%), Positives = 11/34 (32%)
Query: 33 THYPSSPYPVPIHYLSSPHPLPIQSLSTTHPVPT 66
Y P++ LS H LS P T
Sbjct: 69 EELRYWYYRYPLNQLSGAHSGLPSLLSDQAPFET 102
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 27.0 bits (60), Expect = 1.4
Identities = 16/65 (24%), Positives = 19/65 (29%), Gaps = 6/65 (9%)
Query: 18 HPLPIQSPSTTHPVPTHYPS-----SPYPVPIHYLSSP-HPLPIQSLSTTHPVPTHYPSG 71
P P T P PS SP P + P P + T P + P
Sbjct: 374 GPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPA 433
Query: 72 PYPVP 76
PV
Sbjct: 434 AVPVN 438
>gnl|CDD|145556 pfam02478, Pneumo_phosprot, Pneumovirus phosphoprotein. This
family represents the phosphoprotein of
Paramyxoviridae, a putative RNA polymerase alpha
subunit that may function in template binding.
Length = 266
Score = 26.8 bits (59), Expect = 1.5
Identities = 12/57 (21%), Positives = 19/57 (33%)
Query: 32 PTHYPSSPYPVPIHYLSSPHPLPIQSLSTTHPVPTHYPSGPYPVPIHYLSSPHPHSV 88
P+H S ++ +S LP S TT P + + S + V
Sbjct: 27 PSHKRQSISGEKVNTISEKFELPTISKPTTPKGPCIKDEIISVNKVKDIESIYEKPV 83
Score = 26.0 bits (57), Expect = 2.4
Identities = 10/52 (19%), Positives = 17/52 (32%)
Query: 10 PIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTT 61
++ +S LP S TT P + + S + P+ S
Sbjct: 38 KVNTISEKFELPTISKPTTPKGPCIKDEIISVNKVKDIESIYEKPVTPTSDG 89
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 26.7 bits (59), Expect = 1.5
Identities = 17/71 (23%), Positives = 24/71 (33%), Gaps = 8/71 (11%)
Query: 1 MSHTSPYPVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLST 60
S + H SP P PI S T + + + SS P+P P+P+Q L
Sbjct: 3 RIAQSDLSLGFHSHPSPSPAPIADDSITLQIDSSFRSSSNPMP--------PIPLQLLEQ 54
Query: 61 THPVPTHYPSG 71
Sbjct: 55 KEEKEEDAGEE 65
>gnl|CDD|226175 COG3649, COG3649, CRISPR system related protein [Defense
mechanisms].
Length = 283
Score = 26.5 bits (58), Expect = 1.8
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 41 PVPIHYLSSPHPLPIQSLSTTHPVPT 66
PV I Y +S HP+ I S+ T T
Sbjct: 125 PVSIRYATSLHPIKIMSIQITASFNT 150
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 26.6 bits (58), Expect = 2.1
Identities = 15/80 (18%), Positives = 24/80 (30%), Gaps = 1/80 (1%)
Query: 2 SHTSPYPVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPH-PLPIQSLST 60
P P ++ + ST P T+ Y P P P++
Sbjct: 430 QQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPV 489
Query: 61 THPVPTHYPSGPYPVPIHYL 80
P P + P P++Y
Sbjct: 490 VEPEPVVEETKPARPPLYYF 509
Score = 24.7 bits (53), Expect = 8.5
Identities = 14/73 (19%), Positives = 19/73 (26%), Gaps = 1/73 (1%)
Query: 6 PYPVPIHYLSSPHPLPIQSPS-TTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTTHPV 64
P Y + P Q P P P P ++ + ST P
Sbjct: 400 PVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQ 459
Query: 65 PTHYPSGPYPVPI 77
T+ Y P
Sbjct: 460 STYQTEQTYQQPA 472
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 26.2 bits (58), Expect = 2.3
Identities = 17/84 (20%), Positives = 21/84 (25%)
Query: 2 SHTSPYPVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTT 61
H + P P H P+ P P P P P P
Sbjct: 80 EHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPE 139
Query: 62 HPVPTHYPSGPYPVPIHYLSSPHP 85
P+ P P S+P P
Sbjct: 140 QPLQQPVSPQVAPAPQPVHSAPQP 163
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 25.8 bits (57), Expect = 3.6
Identities = 10/68 (14%), Positives = 12/68 (17%)
Query: 18 HPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTTHPVPTHYPSGPYPVPI 77
P + + S P P S P P P P
Sbjct: 3 SSNPTSRSQSHASSSSSSSSQSSPPSSTSPRPRRRKPSASSLLHTPSILPLPKLSSPSPP 62
Query: 78 HYLSSPHP 85
P
Sbjct: 63 SVTLPPAA 70
Score = 24.7 bits (54), Expect = 7.6
Identities = 14/75 (18%), Positives = 21/75 (28%)
Query: 4 TSPYPVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTTHP 63
+S P + S S+ + P P L +P LP+ LS+ P
Sbjct: 2 SSSNPTSRSQSHASSSSSSSSQSSPPSSTSPRPRRRKPSASSLLHTPSILPLPKLSSPSP 61
Query: 64 VPTHYPSGPYPVPIH 78
P
Sbjct: 62 PSVTLPPAATTQTPQ 76
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 25.5 bits (56), Expect = 3.9
Identities = 15/87 (17%), Positives = 21/87 (24%), Gaps = 6/87 (6%)
Query: 8 PVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSPHPLPIQSLSTTHPVPTH 67
P + P + P P P P Q + P P
Sbjct: 205 QPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQ 264
Query: 68 YPSGP-----YPVPIHYLSSPHPHSVE 89
P P P + +PHP +
Sbjct: 265 QQQQPPQPQAQPPPQNQP-TPHPGLPQ 290
>gnl|CDD|233466 TIGR01553, formate-DH-alph, formate dehydrogenase, alpha subunit,
proteobacterial-type. This model describes a subset of
formate dehydrogenase alpha chains found mainly in
proteobacteria but also in Aquifex. The alpha chain
contains domains for molybdopterin dinucleotide binding
and molybdopterin oxidoreductase (pfam01568 and
pfam00384, respectively). The holo-enzyme also contains
beta and gamma subunits of 32 and 20 kDa. The enzyme
catalyzes the oxidation of formate (produced from
pyruvate during anaerobic growth) to carbon dioxide with
the concomitant release of two electrons and two
protons. The electrons are utilized mainly in the
nitrate respiration by nitrate reductase. In E. coli and
Salmonella, there are two forms of the formate
dehydrogenase, one induced by nitrate which is strictly
anaerobic (fdn), and one incuced during the transition
from aerobic to anaerobic growth (fdo). This subunit is
one of only three proteins in E. coli which contain
selenocysteine. This model is well-defined, with a
large, unpopulated trusted/noise gap [Energy metabolism,
Anaerobic, Energy metabolism, Electron transport].
Length = 1009
Score = 25.6 bits (56), Expect = 4.2
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 12/80 (15%)
Query: 8 PVPIHYLSSPHPLPIQSPSTTHPVPTHYPSSP----YPVPIHYLSSPHPLPIQSLSTTHP 63
P+P HY P++SP T+P + +P Y + P P ++TT+
Sbjct: 840 PLPEHYE------PMESPVITNPFHPNVLHNPTALHYKTDEKAVGDPKRYPF--VATTYR 891
Query: 64 VPTHYPSGPYPVPIHYLSSP 83
+ H+ + P + P
Sbjct: 892 LTEHWHTWTRNTPWLLEAEP 911
>gnl|CDD|219355 pfam07267, Nucleo_P87, Nucleopolyhedrovirus capsid protein P87.
This family consists of several Nucleopolyhedrovirus
capsid protein P87 sequences. P87 is expressed late in
infection and concentrated in infected cell nuclei.
Length = 606
Score = 25.6 bits (56), Expect = 4.3
Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 7/72 (9%)
Query: 4 TSPYPVPIHYLSSPHPLPIQSPSTTHPVPTHYPS--SPYPVPIHYLS---SPHPLPIQSL 58
+P P+ S P + + P+ S +P P Y S +P P PI +
Sbjct: 265 NTPAQTPMPERSWQTPAQTPARRISTPMTEEIKSWQTPLQTPAMYSSDYQAPKPEPIYTW 324
Query: 59 STTHPVPTHYPS 70
+ +PS
Sbjct: 325 EE--LLRERFPS 334
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 25.3 bits (55), Expect = 4.8
Identities = 21/78 (26%), Positives = 26/78 (33%), Gaps = 3/78 (3%)
Query: 1 MSHTSPYPVPIHYLSSPHPLPIQSPSTTHPV---PTHYPSSPYPVPIHYLSSPHPLPIQS 57
MS SP P S P P PS P P P P + SP P QS
Sbjct: 411 MSSPSPVPQVQTNQSMPQPPQPSVPSPGGPGSQPPQSVSGGMIPSPPALMPSPSPQMSQS 470
Query: 58 LSTTHPVPTHYPSGPYPV 75
++ + S P+
Sbjct: 471 PASQRTIQQDMVSPGGPL 488
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 25.2 bits (55), Expect = 5.3
Identities = 14/64 (21%), Positives = 19/64 (29%), Gaps = 8/64 (12%)
Query: 17 PHPLPIQSPSTTHPVPTHYPSSPYPVPIHYLSSP--------HPLPIQSLSTTHPVPTHY 68
P P + + + PT PS+ P P P+ PVP
Sbjct: 366 PQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTP 425
Query: 69 PSGP 72
S P
Sbjct: 426 ESAP 429
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
0.313 0.134 0.450
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,728,914
Number of extensions: 375569
Number of successful extensions: 723
Number of sequences better than 10.0: 1
Number of HSP's gapped: 605
Number of HSP's successfully gapped: 168
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.4 bits)