RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14016
(71 letters)
>gnl|CDD|218787 pfam05871, ESCRT-II, ESCRT-II complex subunit. This family of
conserved eukaryotic proteins are subunits of the
endosome associated complex ESCRT-II which recruits
transport machinery for protein sorting at the
multivesicular body (MVB). This protein complex
transiently associates with the endosomal membrane and
thereby initiates the formation of ESCRT-III, a
membrane-associated protein complex that functions
immediately downstream of ESCRT-II during sorting of
MVB cargo. ESCRT-II in turn functions downstream of
ESCRT-I, a protein complex that binds to ubiquitinated
endosomal cargo.
Length = 139
Score = 80.8 bits (200), Expect = 1e-21
Identities = 29/57 (50%), Positives = 39/57 (68%)
Query: 8 WQYNFPPFFTLQPNEETRKKQLEAWRDLVLEYHKKTKTCIIDIQEADNTALFFNPAI 64
Y+FPPFFTLQPN ETRK+QL+AW L+L+Y + K + + EA ++ LF N I
Sbjct: 1 PIYSFPPFFTLQPNSETRKQQLQAWSSLILDYCRHHKIFSLSVLEAQDSPLFNNKKI 57
>gnl|CDD|131024 TIGR01969, minD_arch, cell division ATPase MinD, archaeal. This
model represents the archaeal branch of the MinD family.
MinD, a weak ATPase, works in bacteria with MinC as a
generalized cell division inhibitor and, through
interaction with MinE, prevents septum placement
inappropriate sites. Often several members of this
family are found in archaeal genomes, and the function
is uncharacterized. More distantly related proteins
include flagellar biosynthesis proteins and ParA
chromosome partitioning proteins. The exact roles of the
various archaeal MinD homologs are unknown.
Length = 251
Score = 26.6 bits (59), Expect = 1.1
Identities = 17/58 (29%), Positives = 22/58 (37%), Gaps = 12/58 (20%)
Query: 22 EETRKKQLEAWRDLVLEYHKKTKTCIID------------IQEADNTALFFNPAISSI 67
E RK + D++ E T +ID + AD L NP ISSI
Sbjct: 88 EGLRKADPDKLEDVLKEIIDDTDFLLIDAPAGLERDAVTALAAADELLLVVNPEISSI 145
>gnl|CDD|213558 TIGR00762, DegV, EDD domain protein, DegV family. This family of
proteins is related to DegV of Bacillus subtilis and
includes paralogous sets in several species (B.
subtilis, Deinococcus radiodurans, Mycoplasma
pneumoniae) that are closer in percent identity to each
than to most homologs from other species. This suggests
both recent paralogy and diversity of function. DegV
itself is encoded immediately downstream of DegU, a
transcriptional regulator of degradation, but is itself
uncharacterized. Crystallography suggested a
lipid-binding site, while comparison of the crystal
structure to dihydroxyacetone kinase and to a mannose
transporter EIIA domain suggests a conserved domain,
EDD, with phosphotransferase activity [Unknown function,
General].
Length = 275
Score = 25.5 bits (57), Expect = 2.1
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 24 TRKKQLEAWRDLVLEYHKKTKTCIIDIQEADN 55
RKK ++ +LV E K K + I AD
Sbjct: 202 GRKKAIKKLVELVKEDIKDGKPKRVAIIHADA 233
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 25.7 bits (57), Expect = 2.3
Identities = 11/24 (45%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 33 RDLVLEYHKKTKTCIIDIQEADNT 56
RDL + KK CII I E D
Sbjct: 232 RDLFEQA-KKNAPCIIFIDEIDAV 254
>gnl|CDD|223859 COG0788, PurU, Formyltetrahydrofolate hydrolase [Nucleotide
transport and metabolism].
Length = 287
Score = 25.6 bits (57), Expect = 2.4
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 14 PFFTLQPNEETRKKQLEAWRDLVLEY 39
PF + +E + + +L+ EY
Sbjct: 140 PFHHIPVTKENKAEAEARLLELLEEY 165
>gnl|CDD|204831 pfam12137, RapA_C, RNA polymerase recycling family C-terminal.
This domain is found in bacteria. This domain is about
360 amino acids in length. This domain is found
associated with pfam00271, pfam00176. The function of
this domain is not known, but structurally it forms an
alpha-beta fold in nature with a central beta-sheet
flanked by helices and loops, the beta-sheet being
mainly antiparallel and flanked by four alpha helices,
among which the two longer helices exhibit a coiled-coil
arrangement.
Length = 362
Score = 25.6 bits (57), Expect = 2.4
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 23 ETRKKQLEAWRDLVLEYH----KKTKTCIIDIQEADNTALFFN 61
E K +LE RD +LE + ++ + I I+E DN N
Sbjct: 71 EALKAELEQGRDRLLELNSCGPERAQALIEAIEEEDNDTELPN 113
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 25.2 bits (56), Expect = 3.0
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 23 ETRKKQLEAWRDLVLEYH----KKTKTCIIDIQEADN-TAL 58
E K QLE RD +LE + +K + I E D+ T L
Sbjct: 665 EALKAQLEQGRDRLLELNSCGGEKAQALAEAIAEQDDDTNL 705
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 25.2 bits (56), Expect = 3.3
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 7 PWQYNFPPFFTLQPNEETRKKQL 29
W+Y+ P FF+ Q + R +++
Sbjct: 170 SWKYSIPLFFSTQGFDTFRNREI 192
>gnl|CDD|241507 cd13353, PH-GRAM2_TBC1D8, TBC1 domain family member 8 (TBC1D8;
also called Vascular Rab-GAP/TBC-containing protein)
Pleckstrin Homology-Glucosyltransferases, Rab-like
GTPase activators and Myotubularins (PH-GRAM) domain,
repeat 2. TBC1D8 may act as a GTPase-activating
protein for Rab family protein(s). TBC1D8 contains two
N-terminal PH-GRAM domain and a C-terminal
Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This
cd contains the second repeat of the PH-GRAM domain.
The GRAM domain is found in glucosyltransferases,
myotubularins and other putative membrane-associated
proteins. The GRAM domain is part of a larger motif
with a pleckstrin homology (PH) domain fold.
Length = 132
Score = 24.7 bits (54), Expect = 4.3
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 47 IIDIQEADNTALFFNPAISSI 67
++ I++ ++T+L NP I SI
Sbjct: 74 VVSIEKMEDTSLLPNPIIVSI 94
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 24.6 bits (55), Expect = 4.4
Identities = 5/6 (83%), Positives = 6/6 (100%)
Query: 10 YNFPPF 15
YNFPP+
Sbjct: 380 YNFPPY 385
>gnl|CDD|129782 TIGR00699, GABAtrns_euk, 4-aminobutyrate aminotransferase,
eukaryotic type. This enzyme is a class III
pyridoxal-phosphate-dependent aminotransferase. This
model describes known eukaryotic examples of the enzyme.
The degree of sequence difference between this set and
known bacterial examples is greater than the distance
between either set the most similar enzyme with distinct
function, and so separate models are built for
prokaryotic and eukaryotic sets. Alternate names include
GABA transaminase, gamma-amino-N-butyrate transaminase,
and beta-alanine--oxoglutarate aminotransferase [Central
intermediary metabolism, Other].
Length = 464
Score = 24.4 bits (53), Expect = 5.6
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 6 WPWQYNFPPF-FTLQPN-EETRKKQ---LEAWRDLVLEYHKKTKTCIID-IQE--ADNTA 57
WP Q FP + L+ + +E K++ LE DL+ ++HK I++ IQ DN A
Sbjct: 211 WP-QAPFPSLKYPLEEHVKENAKEEQRCLEEVEDLIKKWHKPVAAIIVEPIQSEGGDNHA 269
>gnl|CDD|131303 TIGR02249, integrase_gron, integron integrase. Members of this
family are integrases associated with integrons (and
super-integrons), which are systems for incorporating
and expressing cassettes of laterally transferred DNA.
Incorporation occurs at an attI site. A super-integron,
as in Vibrio sp., may include over 100 cassettes. This
family belongs to the phage integrase family (pfam00589)
that also includes recombinases XerC (TIGR02224) and
XerD (TIGR02225), which are bacterial housekeeping
proteins. Within this family of integron integrases,
some are designated by class, e.g. IntI4, a class 4
integron integrase from Vibrio cholerae N16961 [DNA
metabolism, DNA replication, recombination, and repair,
Mobile and extrachromosomal element functions, Other].
Length = 315
Score = 24.3 bits (53), Expect = 6.5
Identities = 6/13 (46%), Positives = 7/13 (53%)
Query: 3 DVQWPWQYNFPPF 15
+W WQY FP
Sbjct: 209 PKEWGWQYLFPSH 221
>gnl|CDD|203727 pfam07688, KaiA, KaiA domain. The cyanobacterial clock proteins
KaiA and KaiB are proposed as regulators of the
circadian rhythm in cyanobacteria. The overall fold of
the KaiA monomer is that of a four-helix bundle, which
forms a dimer in the known structure.
Length = 283
Score = 24.5 bits (53), Expect = 6.6
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 11 NFPPFFTLQPNEETRKKQLEAWRDLVLEYHKKTKTCIIDIQEADNTALFFNPAISSILYA 70
N P+ + + + +R++VL Y I N A F + +S +L
Sbjct: 181 NLSPYEKQKLLQALQSS----YREIVLSYFSPNSNVNQSIDNFVNMAFFADVPVSQVLEI 236
Query: 71 H 71
H
Sbjct: 237 H 237
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
0.321 0.134 0.440
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,550,479
Number of extensions: 253134
Number of successful extensions: 320
Number of sequences better than 10.0: 1
Number of HSP's gapped: 320
Number of HSP's successfully gapped: 18
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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: 53 (24.0 bits)