RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5205
(113 letters)
>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 = 152 bits (386), Expect = 2e-45
Identities = 68/150 (45%), Positives = 84/150 (56%), Gaps = 40/150 (26%)
Query: 4 EEINITFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLL-------------- 49
E+ +TFKDV G+DEAK+EL EIV+FLKNP KF+ LG K+PKGVLL
Sbjct: 48 EKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKA 107
Query: 50 ------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSV 85
GA RVRDLF+ AK PC++FIDEID+VG +R +
Sbjct: 108 VAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGL 167
Query: 86 LHPY--ANQTINQLLAEMDGFHQNEGVVVL 113
QT+NQLL EMDGF N GV+V+
Sbjct: 168 GGGNDEREQTLNQLLVEMDGFGTNTGVIVI 197
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 137 bits (348), Expect = 2e-39
Identities = 66/152 (43%), Positives = 85/152 (55%), Gaps = 40/152 (26%)
Query: 2 DPEEINITFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLL------------ 49
+++ +TF DV GVDEAK+EL E+V+FLKNP+K+ LG K+PKGVLL
Sbjct: 141 LEDQVKVTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLA 200
Query: 50 --------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKR-- 81
GA RVRDLF+ AK PC++FIDEID+VG +R
Sbjct: 201 KAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGA 260
Query: 82 TNSVLHPYANQTINQLLAEMDGFHQNEGVVVL 113
+ QT+NQLL EMDGF NEGV+V+
Sbjct: 261 GLGGGNDEREQTLNQLLVEMDGFGGNEGVIVI 292
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 134 bits (339), Expect = 4e-38
Identities = 63/146 (43%), Positives = 85/146 (58%), Gaps = 40/146 (27%)
Query: 8 ITFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLL------------------ 49
ITF+D+ G++EAK+E +E+V FLK PE+F+ +G K+PKGVLL
Sbjct: 180 ITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE 239
Query: 50 --------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSV--LH 87
GA RVRDLFK AK+ +PC+VFIDEID+VG +R + +
Sbjct: 240 AEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGN 299
Query: 88 PYANQTINQLLAEMDGFHQNEGVVVL 113
QT+NQLL EMDGF N+GV+V+
Sbjct: 300 DEREQTLNQLLTEMDGFKGNKGVIVI 325
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 113 bits (285), Expect = 8e-31
Identities = 61/150 (40%), Positives = 83/150 (55%), Gaps = 40/150 (26%)
Query: 4 EEINITFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLL-------------- 49
++I TF DV G DEAK+E+ E+VE+L+ P +F LGGK+PKGVL+
Sbjct: 145 DQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKA 204
Query: 50 ------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSV 85
GA RVRD+F+ AK PC++FIDEID+VG +R +
Sbjct: 205 IAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGL 264
Query: 86 --LHPYANQTINQLLAEMDGFHQNEGVVVL 113
H QT+NQ+L EMDGF NEG++V+
Sbjct: 265 GGGHDEREQTLNQMLVEMDGFEGNEGIIVI 294
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 107 bits (270), Expect = 3e-29
Identities = 52/144 (36%), Positives = 75/144 (52%), Gaps = 51/144 (35%)
Query: 7 NITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL---------------- 49
N+T++D+ G++E +E++E VE LK PE F +G + PKGVLL
Sbjct: 127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVA 186
Query: 50 ----------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNS--- 84
GAR VR+LF+ A+++ P ++FIDEID++ AKRT+S
Sbjct: 187 HETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS 246
Query: 85 ----VLHPYANQTINQLLAEMDGF 104
V +T+ QLLAEMDGF
Sbjct: 247 GDREV-----QRTLMQLLAEMDGF 265
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 104 bits (261), Expect = 9e-28
Identities = 54/156 (34%), Positives = 80/156 (51%), Gaps = 51/156 (32%)
Query: 4 EEINITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL------------- 49
E+ ++T++D+ G+DE QE++E+VE LKNPE F LG PKGVLL
Sbjct: 144 EKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAK 203
Query: 50 -------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNS 84
GAR VR+LF+ A+++ P ++FIDEID++GAKR +S
Sbjct: 204 AVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDS 263
Query: 85 -------VLHPYANQTINQLLAEMDGFHQNEGVVVL 113
V +T+ +LL ++DGF V V+
Sbjct: 264 GTSGDREV-----QRTMLELLNQLDGFDPRGNVKVI 294
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 88.7 bits (220), Expect = 3e-22
Identities = 52/151 (34%), Positives = 79/151 (52%), Gaps = 41/151 (27%)
Query: 4 EEINITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL------------- 49
E N++++D+ G++E +E++E VE LK+PE F +G + PKGVLL
Sbjct: 115 ERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAK 174
Query: 50 -------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNS 84
GAR VR++F+ AK++ P ++FIDEID++ AKRT+S
Sbjct: 175 AVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDS 234
Query: 85 VL--HPYANQTINQLLAEMDGFHQNEGVVVL 113
+T+ QLLAE+DGF V V+
Sbjct: 235 GTSGDREVQRTLMQLLAELDGFDPRGNVKVI 265
>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 = 84.6 bits (209), Expect = 2e-20
Identities = 46/146 (31%), Positives = 71/146 (48%), Gaps = 39/146 (26%)
Query: 7 NITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL---------------- 49
N+ + D+ G++E KQEL+E VE+ LK+PE F +G + PKGVLL
Sbjct: 449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVA 508
Query: 50 ---GA-------------------RRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSVLH 87
GA + +R++F+ A+ P ++F DEID++ R
Sbjct: 509 TESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDT 568
Query: 88 PYANQTINQLLAEMDGFHQNEGVVVL 113
++ +NQLL EMDG + VVV+
Sbjct: 569 SVTDRIVNQLLTEMDGIQELSNVVVI 594
Score = 65.3 bits (159), Expect = 1e-13
Identities = 46/146 (31%), Positives = 72/146 (49%), Gaps = 40/146 (27%)
Query: 7 NITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL---------------- 49
+T++D+ G+ EAK++++E+VE +K+PE F LG + PKGVLL
Sbjct: 174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVA 233
Query: 50 ---GA-------------------RRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSVLH 87
GA R+R++FK A++ P ++FIDEID++ KR V
Sbjct: 234 NEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKR-EEVTG 292
Query: 88 PYANQTINQLLAEMDGFHQNEGVVVL 113
+ + QLL MDG V+V+
Sbjct: 293 EVEKRVVAQLLTLMDGLKGRGRVIVI 318
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 82.6 bits (204), Expect = 6e-20
Identities = 50/150 (33%), Positives = 73/150 (48%), Gaps = 42/150 (28%)
Query: 1 VDPEEI-NITFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLL---------- 49
D E I +IT DV G +EAK++ + I+E+L+NPE+F G PK VL
Sbjct: 110 EDREIISDITLDDVIGQEEAKRKCRLIMEYLENPERF---GDWAPKNVLFYGPPGTGKTM 166
Query: 50 ----------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKR 81
GARR+ +L++ A+ PC+VFIDE+D++ R
Sbjct: 167 MAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDR 226
Query: 82 TNSVLHPYANQTINQLLAEMDGFHQNEGVV 111
L ++ +N LL E+DG +NEGVV
Sbjct: 227 RYQELRGDVSEIVNALLTELDGIKENEGVV 256
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 80.6 bits (199), Expect = 4e-19
Identities = 50/152 (32%), Positives = 74/152 (48%), Gaps = 40/152 (26%)
Query: 1 VDPEEINITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL---------- 49
V E+ ++T D+ G++EAK+ELKE +E LK PE F LG + PKGVLL
Sbjct: 232 VLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTL 291
Query: 50 ----------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKR 81
+ +R+LF+ A+ P ++FIDEIDS+ + R
Sbjct: 292 LAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGR 351
Query: 82 TNSVLHPYANQTINQLLAEMDGFHQNEGVVVL 113
S + + QLL E+DG + EGV+V+
Sbjct: 352 GPSE-DGSGRRVVGQLLTELDGIEKAEGVLVI 382
Score = 39.0 bits (91), Expect = 2e-04
Identities = 23/60 (38%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 52 RRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSVLHPYANQTINQLLAEMDGFHQNEGVV 111
R+R+LF+ A+ P ++FIDEID++ KR +S + + QLLA MDG + + +V
Sbjct: 63 LRLRELFEEAEKLAPSIIFIDEIDALAPKR-SSDQGEVERRVVAQLLALMDGLKRGQVIV 121
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 72.2 bits (178), Expect = 1e-17
Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 39 LGGKLPKGVLLGARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSVLHPYANQTINQLL 98
+ K V +R+R+LF+AAK PCV+FIDEID++ R S + + +NQLL
Sbjct: 31 GSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSR-GSGGDSESRRVVNQLL 89
Query: 99 AEMDGFHQNEGVVVL 113
E+DGF + V++
Sbjct: 90 TELDGFTSSLSKVIV 104
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 72.1 bits (177), Expect = 3e-16
Identities = 47/158 (29%), Positives = 72/158 (45%), Gaps = 55/158 (34%)
Query: 4 EEINITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL------------- 49
E+ ++T+ D+ G+D KQE++E VE L PE + +G P+GVLL
Sbjct: 138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAK 197
Query: 50 -------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNS 84
G R VRD+F+ A++ P ++FIDE+DS+ KR ++
Sbjct: 198 AVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDA 257
Query: 85 VLHPYANQT---------INQLLAEMDGFHQNEGVVVL 113
QT + +LL +MDGF Q V V+
Sbjct: 258 -------QTGADREVQRILLELLNQMDGFDQTTNVKVI 288
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 69.8 bits (171), Expect = 2e-15
Identities = 46/152 (30%), Positives = 71/152 (46%), Gaps = 44/152 (28%)
Query: 3 PEEINITFKDVRGVDEAKQELKEIVEF-LKNPEKFSTLGGKLPKGVLL------------ 49
P E ++ D+ G+++ QE+KE VE L +PE + +G K PKGV+L
Sbjct: 178 PLE---SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLA 234
Query: 50 --------------------------GARRVRDLFKAAKDRTPCVVFIDEIDSVGAKR-- 81
G + VR+LF+ A++ P +VFIDEID++G KR
Sbjct: 235 KAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYD 294
Query: 82 TNSVLHPYANQTINQLLAEMDGFHQNEGVVVL 113
S +T+ +LL ++DGF V V+
Sbjct: 295 ATSGGEKEIQRTMLELLNQLDGFDSRGDVKVI 326
>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 = 43.2 bits (102), Expect = 6e-06
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 52 RRVRDLF----KAAKDRTPCVVFIDEIDSVGAKRTNSVLHPYANQTINQLLAEMDGFHQN 107
R++R +F + A + P +VF DE+DS+ R + V + QLLAE+DG
Sbjct: 272 RQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGSGVSSDVETTVVPQLLAEIDGVESL 331
Query: 108 EGVVVL 113
+ V+V+
Sbjct: 332 DNVIVI 337
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 35.6 bits (82), Expect = 0.002
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 48 LLGARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSVLHPYANQTINQLLAEMDGFHQN 107
L G VR LF+ A+ P V+FIDEIDS+ N++L L D
Sbjct: 67 LFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALL--------RVLETLNDLRIDR 118
Query: 108 EGVVVL 113
E V V+
Sbjct: 119 ENVRVI 124
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only
detects a fraction of this vast family. The poorly
conserved N-terminal helix is missing from the
alignment.
Length = 148
Score = 34.7 bits (79), Expect = 0.003
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 45 KGVLLGARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSVL 86
K G R+R A+ P V+ +DEI S+ ++L
Sbjct: 58 KASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALL 99
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 30.8 bits (70), Expect = 0.13
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 53 RVRDLFKAAKDRTPCVVFIDEID 75
R+R + + A+ +PC+++IDEID
Sbjct: 306 RMRQMIRIAEALSPCILWIDEID 328
>gnl|CDD|132035 TIGR02990, ectoine_eutA, ectoine utilization protein EutA. Members
of this protein family are EutA, a predicted
arylmalonate decarboxylase found in a conserved ectoine
utilization operon of species that include Sinorhizobium
meliloti 1021 (where it is known to be induced by
ectoine), Mesorhizobium loti and Silicibacter pomeroyi.
It is missing from two other species with the other
ectoine transport and utilization genes: Pseudomonas
putida and Agrobacterium tumefaciens.
Length = 239
Score = 29.9 bits (67), Expect = 0.19
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 47 VLLGARRVRDLFKAAKDRTPCVV----FIDEIDSVGAKRTNSVLHPYANQT 93
V++G V AAK TP V +D + ++G +R S+L PY +T
Sbjct: 84 VVIGDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGVRRI-SLLTPYTPET 133
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 29.4 bits (66), Expect = 0.40
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 68 VVFIDEIDSVGAKRTNSVLHPYANQTINQLLAEMDGFHQNEGVVV 112
V+F+DE ++ P+ + I+ LLA M+ ++ VV+
Sbjct: 378 VLFLDEAYTLVETG-YGQKDPFGLEAIDTLLARMEN-DRDRLVVI 420
>gnl|CDD|213250 cd03283, ABC_MutS-like, ATP-binding cassette domain of MutS-like
homolog. The MutS protein initiates DNA mismatch repair
by recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 199
Score = 28.8 bits (65), Expect = 0.42
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 51 ARRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNS 84
RR++++ + AK P + +DEI K TNS
Sbjct: 91 LRRLKEIVEKAKKGEPVLFLLDEI----FKGTNS 120
>gnl|CDD|222266 pfam13616, Rotamase_3, PPIC-type PPIASE domain. Rotamases
increase the rate of protein folding by catalyzing the
interconversion of cis-proline and trans-proline.
Length = 114
Score = 28.0 bits (63), Expect = 0.58
Identities = 9/34 (26%), Positives = 13/34 (38%)
Query: 6 INITFKDVRGVDEAKQELKEIVEFLKNPEKFSTL 39
I + + + EAK I LK F+ L
Sbjct: 21 ILVAYAGAQRKAEAKALADSIYNALKGGADFAAL 54
>gnl|CDD|226459 COG3950, COG3950, Predicted ATP-binding protein involved in
virulence [General function prediction only].
Length = 440
Score = 28.4 bits (63), Expect = 0.75
Identities = 22/56 (39%), Positives = 23/56 (41%), Gaps = 12/56 (21%)
Query: 47 VLLGARRVRDLFKAAKDR----TPCVVFIDEIDSVGAKRTNSVLHPYANQTINQLL 98
V ARR L D TP +V IDEID LHP Q INQ L
Sbjct: 273 VADIARRCVVLNPYLSDALAKLTPGIVLIDEIDLF--------LHPKWQQQINQKL 320
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 27.2 bits (61), Expect = 1.4
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 57 LFKAAKDRTPCVVFIDEID 75
L +A + + +V IDEI+
Sbjct: 67 LTEAVRRKPYSIVLIDEIE 85
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 27.2 bits (61), Expect = 1.7
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 8/41 (19%)
Query: 9 TFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLL 49
T DV G ++AK++L+E +E S L GK K +LL
Sbjct: 12 TLSDVVGNEKAKEQLREWIE--------SWLKGKPKKALLL 44
>gnl|CDD|215702 pfam00083, Sugar_tr, Sugar (and other) transporter.
Length = 449
Score = 27.3 bits (61), Expect = 2.0
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 9 TFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLLGARRVR 55
+RGV + QE++E + L + S K L + VR
Sbjct: 209 VLAKLRGVSDVDQEIQEEKDSL----ERSVEAEKASWLELFRGKTVR 251
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 27.2 bits (61), Expect = 2.1
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 53 RVRDLFKAAKDRTPCVVFIDEIDS-VGA 79
R++ + K + ++FIDEI + VGA
Sbjct: 250 RLKAVLKEVEKSKNVILFIDEIHTIVGA 277
>gnl|CDD|187857 cd09726, RAMP_I_III, CRISPR/Cas system-associated RAMP superfamily
protein. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily proteins.
Length = 177
Score = 26.6 bits (58), Expect = 2.6
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 5 EINITFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKG 46
+T + G E ++ LKE+++ L + LG K +G
Sbjct: 134 TFELTLDNGAGKAEDEELLKELLKALLDLLTDLGLGAKRTRG 175
>gnl|CDD|193495 cd03873, Zinc_peptidase_like, Zinc peptidases M18, M20, M28, and
M42. Zinc peptidases play vital roles in metabolic and
signaling pathways throughout all kingdoms of life.
This family corresponds to several clans in the MEROPS
database, including the MH clan, which contains 4
families (M18, M20, M28, M42). The peptidase M20 family
includes carboxypeptidases such as the glutamate
carboxypeptidase from Pseudomonas, the thermostable
carboxypeptidase Ss1 of broad specificity from archaea
and yeast Gly-X carboxypeptidase. The dipeptidases
include bacterial dipeptidase, peptidase V (PepV), a
eukaryotic, non-specific dipeptidase, and two Xaa-His
dipeptidases (carnosinases). There is also the
bacterial aminopeptidase, peptidase T (PepT) that acts
only on tripeptide substrates and has therefore been
termed a tripeptidase. Peptidase family M28 contains
aminopeptidases and carboxypeptidases, and has
co-catalytic zinc ions. However, several enzymes in
this family utilize other first row transition metal
ions such as cobalt and manganese. Each zinc ion is
tetrahedrally co-ordinated, with three amino acid
ligands plus activated water; one aspartate residue
binds both metal ions. The aminopeptidases in this
family are also called bacterial leucyl
aminopeptidases, but are able to release a variety of
N-terminal amino acids. IAP aminopeptidase and
aminopeptidase Y preferentially release basic amino
acids while glutamate carboxypeptidase II
preferentially releases C-terminal glutamates.
Glutamate carbxypeptidase II and plasma glutamate
carboxypeptidase hydrolyze dipeptides. Peptidase
families M18 and M42 contain metalloaminopeptidases.
M18 is widely distributed in bacteria and eukaryotes.
However, only yeast aminopeptidase I and mammalian
aspartyl aminopeptidase have been characterized in
detail. Some of M42 (also known as glutamyl
aminopeptidase) enzymes exhibit aminopeptidase
specificity while others also have
acylaminoacylpeptidase activity (i.e. hydrolysis of
acylated N-terminal residues).
Length = 237
Score = 26.6 bits (59), Expect = 2.8
Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 25/92 (27%)
Query: 7 NITFKDVRGVDEAKQELKEIVEFLKNPEKFSTL----GGKLPKGVLLGARRVRDLFKAAK 62
++T ++ D +EL+E+ ++ L GG VLL A
Sbjct: 10 SVTGEEAEFADRIARELEELGIDVEVDAHIGNLIVEYGGGEKPPVLLMA----------- 58
Query: 63 DRTPCVVFIDEIDSVGAKRTNSVLHPYANQTI 94
ID V A T P+A T+
Sbjct: 59 ----------HIDVVPAGDTWWWEFPFAVDTL 80
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 26.6 bits (58), Expect = 3.1
Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 10/99 (10%)
Query: 4 EEINITFKDVRGVDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLLGARRVRDLFKAAKD 63
+ ++R + + +L ++V+ L L L KG+ G +R+ L A
Sbjct: 147 LPFSFILGNLRNLRNIELKLLDLVKRLFLESDLLRLLKLLIKGISDGTKRLLALLLALLS 206
Query: 64 --RTPCVVFIDEIDSVGAKRTNSVLHPYANQTINQLLAE 100
++ IDE + N LHP + + +LL E
Sbjct: 207 ALPKGSLLLIDEPE-------NG-LHPKLLRKLVELLKE 237
>gnl|CDD|223848 COG0777, AccD, Acetyl-CoA carboxylase beta subunit [Lipid
metabolism].
Length = 294
Score = 26.5 bits (59), Expect = 3.1
Identities = 11/35 (31%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 36 FSTLGGKLPKGVLLGARRVRDLFKAAKDRTPCVVF 70
F+ +GG + G ++G + R + +A +D+ P V+F
Sbjct: 131 FAFMGGSM--GSVVGEKITRAIERAIEDKLPLVLF 163
>gnl|CDD|227586 COG5261, IQG1, Protein involved in regulation of cellular
morphogenesis/cytokinesis [Cell division and chromosome
partitioning / Signal transduction mechanisms].
Length = 1054
Score = 26.4 bits (58), Expect = 4.0
Identities = 10/34 (29%), Positives = 12/34 (35%), Gaps = 3/34 (8%)
Query: 16 VDEAKQELKEIVEFLKNPEKFSTLGGKLPKGVLL 49
V EAK I E ++ L GV L
Sbjct: 46 VSEAK---IWIEEVIEEALPELCFEDSLRNGVFL 76
>gnl|CDD|145649 pfam02610, Arabinose_Isome, L-arabinose isomerase. This is a
family of L-arabinose isomerases, AraA, EC:5.3.1.4.
These enzymes catalyze the reaction: L-arabinose <=>
L-ribulose. This reaction is the first step in the
pathway of L-arabinose utilisation as a carbon source
after entering the cell L-arabinose is converted into
L-ribulose by the L-arabinose isomerases enzyme.
Length = 359
Score = 26.0 bits (58), Expect = 4.3
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 12/50 (24%)
Query: 24 KEIVEFLKNPEKFSTLGGKLP-----KGVLLGARRVRDLFKAAKDRTPCV 68
+EIVE L GKLP K V+ + L + A C
Sbjct: 32 QEIVEGLNA-------SGKLPVKIVLKPVVTTPDEITALCREANYDENCA 74
>gnl|CDD|234363 TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood
CpaE-like protein. Members of this protein family
belong to the MinD/ParA family of P-loop NTPases, and in
particular show homology to the CpaE family of pilus
assembly proteins (see PMID:12370432). Nearly all
members are found, not only in a gene context consistent
with pilus biogenesis or a pilus-like secretion
apparatus, but also near a DEAD/DEAH-box helicase,
suggesting an involvement in DNA transfer activity. The
model describes a clade restricted to the
Actinobacteria.
Length = 322
Score = 26.1 bits (58), Expect = 4.6
Identities = 20/76 (26%), Positives = 29/76 (38%), Gaps = 12/76 (15%)
Query: 47 VLLGARRVRDLFKAAKDRTPCVVFI----------DEIDSVGAKRTNSVLHPYANQTINQ 96
VL+ A A R VV + +VGA+ + P A + +
Sbjct: 23 VLVDADMAEACAAAGLPRRRRVVLVGGGEPGGALWRAAAAVGAEHV--AVLPEAEGWLVE 80
Query: 97 LLAEMDGFHQNEGVVV 112
LLA++D GVVV
Sbjct: 81 LLADLDQSPPARGVVV 96
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 25.8 bits (58), Expect = 6.0
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 69 VFIDEIDSVGAKRTNS 84
VFIDEID + A+ +S
Sbjct: 253 VFIDEIDKIAARGGSS 268
>gnl|CDD|225518 COG2971, COG2971, Predicted N-acetylglucosamine kinase
[Carbohydrate transport and metabolism].
Length = 301
Score = 25.7 bits (57), Expect = 6.1
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 16 VDEAKQELKEIVEFL---KNPEKFSTLGGKLPKGVLLGARRVRDLFKAAKD 63
+ EA + ++E L EK S LGG P + R L
Sbjct: 229 LKEAAAYIATLLEALSIFNGSEKLSLLGGLAPSYPYYLSLFRRALLVPPIG 279
>gnl|CDD|129606 TIGR00515, accD, acetyl-CoA carboxylase, carboxyl transferase, beta
subunit. The enzyme acetyl-CoA carboxylase contains a
biotin carboxyl carrier protein or domain, a biotin
carboxylase, and a carboxyl transferase. This model
represents the beta chain of the carboxyl transferase
for cases in which the architecture of the protein is as
in E. coli, in which the carboxyltransferase portion
consists of two non-identical subnits, alpha and beta
[Fatty acid and phospholipid metabolism, Biosynthesis].
Length = 285
Score = 25.5 bits (56), Expect = 6.9
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 36 FSTLGGKLPKGVLLGARRVRDLFKAAKDRTPCVVF 70
F+ +GG + G ++G + VR + KA +D P ++F
Sbjct: 129 FAFMGGSM--GSVVGEKFVRAIEKALEDNCPLIIF 161
>gnl|CDD|236408 PRK09200, PRK09200, preprotein translocase subunit SecA; Reviewed.
Length = 790
Score = 25.7 bits (57), Expect = 7.2
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 12/46 (26%)
Query: 69 VFIDEIDSV------------GAKRTNSVLHPYANQTINQLLAEMD 102
IDEIDS+ G R S L+ A + + L ++D
Sbjct: 203 AIIDEIDSILLDEAQTPLIISGKPRVQSNLYHIAAKFVKTLEEDVD 248
>gnl|CDD|178166 PLN02551, PLN02551, aspartokinase.
Length = 521
Score = 25.5 bits (56), Expect = 7.5
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 5/35 (14%)
Query: 52 RRVRDLFKAAKDRTPCVVFIDEIDSVGAKRTNSVL 86
R V DL + D P VV S K TN++L
Sbjct: 70 REVADLILSFPDERPVVVL-----SAMGKTTNNLL 99
>gnl|CDD|234367 TIGR03828, pfkB, 1-phosphofructokinase. This enzyme acts in
concert with the fructose-specific phosphotransferase
system (PTS) which imports fructose as
fructose-1-phosphate. The action of
1-phosphofructokinase results in
beta-D-fructose-1,6-bisphosphate and is an entry point
into glycolysis (GenProp0688).
Length = 304
Score = 25.2 bits (56), Expect = 7.9
Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 12/54 (22%)
Query: 6 INITFKDVRGV------------DEAKQELKEIVEFLKNPEKFSTLGGKLPKGV 47
IN+ K+ G +E + L E + + L G LP GV
Sbjct: 88 INVKIKEPSGTETKLNGPGPEISEEELEALLEKLRAQLAEGDWLVLSGSLPPGV 141
>gnl|CDD|239426 cd03310, CIMS_like, CIMS - Cobalamine-independent methonine
synthase, or MetE. Many members have been characterized
as 5-methyltetrahydropteroyltriglutamate-homocysteine
methyltransferases, EC:2.1.1.14, mostly from bacteria
and plants. This enzyme catalyses the last step in the
production of methionine by transferring a methyl group
from 5-methyltetrahydrofolate to L-homocysteine without
using an intermediate methyl carrier. The active enzyme
has a dual (beta-alpha)8-barrel structure, and this
model covers both the N-and C-terminal barrel, and some
single-barrel sequences, mostly from Archaea. It is
assumed that the homologous N-terminal barrel has
evolved from the C-terminus via gene duplication and has
subsequently lost binding sites, and it seems as if the
two barrels forming the active enzyme may sometimes
reside on different polypeptides. The C-terminal domain
incorporates the Zinc ion, which binds and activates
homocysteine. Side chains from both barrels contribute
to the binding of the folate substrate.
Length = 321
Score = 25.5 bits (56), Expect = 8.8
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 51 ARRVRDLFKAAKDRTPCVVFIDE 73
A +R+ K K+R VV IDE
Sbjct: 150 AEFLREQVKELKNRGIVVVQIDE 172
>gnl|CDD|232990 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit,
non-spirochete bacterial. Every known example of the
phenylalanyl-tRNA synthetase, except the monomeric form
of mitochondrial, is an alpha 2 beta 2 heterotetramer.
The beta subunits break into two subfamilies that are
considerably different in sequence, length, and pattern
of gaps. This model represents the subfamily that
includes the beta subunit from Bacteria other than
spirochetes, as well as a chloroplast-encoded form from
Porphyra purpurea. The chloroplast-derived sequence is
considerably shorter at the amino end, however, so This
model was built in fragment mode [Protein synthesis,
tRNA aminoacylation].
Length = 797
Score = 25.3 bits (56), Expect = 9.9
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 17 DEAKQELKEIVEFLKNPEKFSTLGGK---LPKGVLLGA 51
D K E +V K E F+TL GK L KG L+ A
Sbjct: 270 DADKIEGNIVVRSAKEGESFTTLDGKERELKKGDLVIA 307
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
0.318 0.138 0.389
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,040,255
Number of extensions: 535243
Number of successful extensions: 944
Number of sequences better than 10.0: 1
Number of HSP's gapped: 922
Number of HSP's successfully gapped: 82
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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 (21.7 bits)
S2: 53 (24.6 bits)