RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4539
(84 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 46.7 bits (111), Expect = 1e-07
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 13 ELEPELEDERYKGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPD 72
E ED+ + + KV+ R + VT DDI GL AK+ ++E I P+ RP+
Sbjct: 210 EYIGVTEDDFEEALKKVLPSRGVLFEDE---DVTLDDIGGLEEAKEELKEAIETPLKRPE 266
Query: 73 IFTGL-RRPPK 82
+F L RPPK
Sbjct: 267 LFRKLGLRPPK 277
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 38.7 bits (90), Expect = 7e-05
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 37 EIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
E++ + V W DI GL KQ ++E + WP+ P+IF + RPPK
Sbjct: 442 EVLVEVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPK 488
Score = 37.2 bits (86), Expect = 3e-04
Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 5/52 (9%)
Query: 32 ERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
E IE ++ VT++DI GL AK+ I+E++ PM P++F L PPK
Sbjct: 166 EEIERKVPK----VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPK 213
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 35.3 bits (82), Expect = 0.001
Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
VT++DI GL Q I+EV+ P+ P++F L PPK
Sbjct: 148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPK 186
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 32.4 bits (74), Expect = 0.015
Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 26 IDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
+ + +E+ ++++ VT+ DI GL + I++ + P L P+++ +PPK
Sbjct: 160 FEAIPRTEVEDLVLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPK 217
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 29.8 bits (68), Expect = 0.099
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIF 74
VT++DI GL + ++E + P+ +P++F
Sbjct: 128 VTYEDIGGLEEQIREVREAVELPLKKPELF 157
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 28.6 bits (64), Expect = 0.26
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
V+++DI GL + I+E + P+ P++F + PPK
Sbjct: 119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPK 157
>gnl|CDD|227679 COG5389, COG5389, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 181
Score = 27.9 bits (62), Expect = 0.46
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 7 SGPRGKELEPELEDERYKGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVW 66
S + + D +D V+ +R +W++IAG T A +T E I+W
Sbjct: 17 SERTPQRGPVPIADVANGILDPVLRKRAGINTALLQ---SWEEIAGDTLADRTRPERIIW 73
Query: 67 P 67
P
Sbjct: 74 P 74
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 27.4 bits (61), Expect = 0.83
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 39 MDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIF 74
M + VT+ DI GL KQ I+E + P+ P+++
Sbjct: 136 MSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELY 171
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 26.7 bits (59), Expect = 1.6
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 46 TWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
++ DI GL Q I+E + P+ P+++ + +PPK
Sbjct: 181 SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPK 218
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 26.2 bits (58), Expect = 2.3
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 31 IERIENEI-MDQGKPVTWDDIAGLTFAKQTIQEVI 64
+ + M+ +T+ DIAG+ AK+ +EV+
Sbjct: 165 FGKSKARFQMEADTGITFRDIAGIEEAKEEFEEVV 199
>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen. The core
antigen of hepatitis viruses possesses a carboxyl
terminus rich in arginine. On this basis it was
predicted that the core antigen would bind DNA. There is
some experimental evidence to support this.
Length = 182
Score = 25.9 bits (57), Expect = 2.4
Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 9/67 (13%)
Query: 16 PELEDERYKGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFT 75
P LED + + ++ + + + + + W I+ LTF ++T+ E +V
Sbjct: 73 PNLEDPVSRDL---VVSYVNENMGLKARQLLWFHISCLTFGRETVTEYLV------SFGV 123
Query: 76 GLRRPPK 82
+R PP
Sbjct: 124 WIRTPPA 130
>gnl|CDD|237689 PRK14359, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 430
Score = 26.1 bits (58), Expect = 2.6
Identities = 10/43 (23%), Positives = 23/43 (53%), Gaps = 10/43 (23%)
Query: 10 RGKELEP-ELEDERYKGI---------DKVMIERIENEIMDQG 42
+G+ ++ +++E + G+ +++M ERI+ M QG
Sbjct: 203 KGETIKAVFVDEENFMGVNSKFELAKAEEIMQERIKKNAMKQG 245
>gnl|CDD|225718 COG3177, COG3177, Fic family protein [Function unknown].
Length = 348
Score = 25.5 bits (56), Expect = 3.3
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 11 GKELEPELEDERYKGIDKVMIERIENEIMDQGKPVTWDDI 50
G + D+ + ++ + E +D G+P +W DI
Sbjct: 78 GITGAGKPTDDIKEVLNYERADFYGLEHLDAGEPFSWLDI 117
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for
correct cell division in bacteria. It has ATP-dependent
zinc metalloprotease activity. It was formerly
designated cell division protein FtsH [Cellular
processes, Cell division, Protein fate, Degradation of
proteins, peptides, and glycopeptides].
Length = 495
Score = 25.3 bits (56), Expect = 3.8
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 39 MDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLR-PDIFTGL-RRPPK 82
++ VT+ D+AG+ AK+ + E++ + L+ P FT L + PK
Sbjct: 46 NEEKPKVTFKDVAGIDEAKEELMEIVDF--LKNPSKFTKLGAKIPK 89
>gnl|CDD|237733 PRK14499, PRK14499, molybdenum cofactor biosynthesis protein
MoaC/MOSC-domain-containing protein; Provisional.
Length = 308
Score = 25.2 bits (55), Expect = 4.2
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 28 KVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGL 77
K +IE IE ++ +G + IA + AK+T E+I P+ +G+
Sbjct: 37 KEVIEAIEERLLPKGDVFSVAKIAAIMAAKKT-SELI--PLCHNIFLSGV 83
>gnl|CDD|215689 pfam00067, p450, Cytochrome P450. Cytochrome P450s are
haem-thiolate proteins involved in the oxidative
degradation of various compounds. They are particularly
well known for their role in the degradation of
environmental toxins and mutagens. They can be divided
into 4 classes, according to the method by which
electrons from NAD(P)H are delivered to the catalytic
site. Sequence conservation is relatively low within the
family - there are only 3 absolutely conserved residues
- but their general topography and structural fold are
highly conserved. The conserved core is composed of a
coil termed the 'meander', a four-helix bundle, helices
J and K, and two sets of beta-sheets. These constitute
the haem-binding loop (with an absolutely conserved
cysteine that serves as the 5th ligand for the haem
iron), the proton-transfer groove and the absolutely
conserved EXXR motif in helix K. While prokaryotic P450s
are soluble proteins, most eukaryotic P450s are
associated with microsomal membranes. their general
enzymatic function is to catalyze regiospecific and
stereospecific oxidation of non-activated hydrocarbons
at physiological temperatures.
Length = 461
Score = 24.9 bits (55), Expect = 5.8
Identities = 10/48 (20%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 16 PELEDERYKGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEV 63
PE++++ + ID E++ + T+DD+ + + I+E
Sbjct: 292 PEVQEKLREEID---------EVIGDKRSPTYDDLQNMPYLDAVIKET 330
>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 753
Score = 24.6 bits (54), Expect = 7.0
Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 3/63 (4%)
Query: 2 DVDMPSGPRGKELEPELEDERY---KGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQ 58
+V++ +G G ++ GI KV++ ++ EI+ + V I
Sbjct: 618 EVEVITGEPGAVVKIIAGILEALVQSGILKVIVSHLDLEIIKEEPKVKVKGIEAPGLDSN 677
Query: 59 TIQ 61
+
Sbjct: 678 RLD 680
>gnl|CDD|213356 cd12822, TmCorA-like, Thermotoga maritima CorA-like family. This
family belongs to the MIT superfamily of essential
membrane proteins involved in transporting divalent
cations (uptake or efflux) across membranes. Members of
the Thermotoga maritima CorA_like family are found in
all three kingdoms of life. It is a functionally diverse
family, in addition to the CorA Co2+ transporter from
the hyperthermophilic Thermotoga maritima, it includes
three Saccharomyces cerevisiae members: two plasma
membrane proteins, the Mg2+ transporter Alr1p/Swc3p and
the putative Mg2+ transporter, Alr2p, and the vacuole
membrane protein Mnr2p, a putative Mg2+ transporter.
Thermotoga maritima CorA forms funnel-shaped
homopentamers, the tip of the funnel is formed from two
C-terminal transmembrane (TM) helices from each monomer,
and the large opening of the funnel from the N-terminal
cytoplasmic domains. The GMN signature motif of the MIT
superfamily occurs just after TM1, mutation within this
motif is known to abolish Mg2+ transport by Alr1p.
Natural variants in this signature sequence may be
associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 289
Score = 24.5 bits (54), Expect = 7.2
Identities = 8/55 (14%), Positives = 26/55 (47%), Gaps = 7/55 (12%)
Query: 31 IERIENEIMDQGKPVTWDDIAGLTFAKQTIQEV--IVWPMLRPDIFTGLRRPPKD 83
++ +E+EI+++ + ++ L ++ + + I+ P ++ L R +
Sbjct: 130 LDELEDEILEEPRREVLRELFAL---RRELLRLRRILSPQ--REVLNRLLRRENE 179
>gnl|CDD|213362 cd12828, TmCorA-like_1, Thermotoga maritima CorA_like subfamily.
This subfamily belongs to the Thermotoga maritima CorA
(TmCorA)-family of the MIT superfamily of essential
membrane proteins involved in transporting divalent
cations (uptake or efflux) across membranes. Members of
this subfamily are found in all three kingdoms of life.
It is functionally diverse subfamily, in addition to the
CorA Co2+ transporter from the hyperthermophilic
Thermotoga maritima, it includes Methanosarcina mazei
CorA which may be involved in transport of copper and/or
other divalent metal ions. Thermotoga maritima CorA
forms funnel-shaped homopentamers, the tip of the funnel
is formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by a related protein, Saccharomyces cerevisiae
Alr1p. Natural variants in this signature sequence may
be associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 294
Score = 24.3 bits (54), Expect = 9.0
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 31 IERIENEIMDQGKPVTWDDIAGLTFAKQTIQEV--IVWPMLRPDIFTGLRR 79
IE +E E+++ P T + I L K+ + + +WP LR ++ L R
Sbjct: 135 IEDLEEELLENPTPETLERIHKL---KRELLFLRRSIWP-LR-EVINRLLR 180
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
0.317 0.140 0.426
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,713,404
Number of extensions: 400332
Number of successful extensions: 453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 453
Number of HSP's successfully gapped: 33
Length of query: 84
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 32
Effective length of database: 8,631,194
Effective search space: 276198208
Effective search space used: 276198208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.3 bits)