RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5228
(114 letters)
>gnl|CDD|178955 PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 200
Score = 228 bits (584), Expect = 3e-78
Identities = 86/114 (75%), Positives = 101/114 (88%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
MQFIKP+VST+CIG AASMGAFLLA+G KGKRF+LPNSRIMIHQPLGG QGQA+DIEI A
Sbjct: 85 MQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFALPNSRIMIHQPLGGFQGQATDIEIHA 144
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQRK 114
REIL L++RLNEIL+E TG ++KI +DTDRDNFMSA+ A EY LID++L +RK
Sbjct: 145 REILKLKKRLNEILAEHTGQPLEKIEKDTDRDNFMSAEEAKEYGLIDEVLTKRK 198
>gnl|CDD|201316 pfam00574, CLP_protease, Clp protease. The Clp protease has an
active site catalytic triad. In E. coli Clp protease,
ser-111, his-136 and asp-185 form the catalytic triad.
Cyanophora parodoxa clpP-B has lost all of these active
site residues and is therefore inactive. Some members
contain one or two large insertions.
Length = 182
Score = 201 bits (513), Expect = 9e-68
Identities = 80/113 (70%), Positives = 99/113 (87%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
MQFIKP+VST+C+GLAASMG+F+LA+GTKGKRF+LPN+RIMIHQP GGAQGQASDIEIQA
Sbjct: 70 MQFIKPDVSTICLGLAASMGSFILAAGTKGKRFALPNARIMIHQPSGGAQGQASDIEIQA 129
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQR 113
EIL +R+RLNEI +E TG ++KI +D DRD FMSA+ A EY LID++++ R
Sbjct: 130 EEILKIRERLNEIYAEHTGQPLEKIEKDLDRDTFMSAEEAKEYGLIDEVIESR 182
>gnl|CDD|132928 cd07017, S14_ClpP_2, Caseinolytic protease (ClpP) is an
ATP-dependent, highly conserved serine protease. Clp
protease (caseinolytic protease; ClpP; Peptidase S14) is
a highly conserved serine protease present throughout in
bacteria and eukaryota, but seems to be absent in
archaea, mollicutes and some fungi. Clp proteases are
involved in a number of cellular processes such as
degradation of misfolded proteins, regulation of
short-lived proteins and housekeeping removal of
dysfunctional proteins. They are also implicated in the
control of cell growth, targeting DNA-binding protein
from starved cells. ClpP has also been linked to the
tight regulation of virulence genes in the pathogens
Listeria monocytogenes and Salmonella typhimurium. This
enzyme belong to the family of ATP-dependent proteases;
the functional Clp protease is comprised of two
components: a proteolytic component and one of several
regulatory ATPase components, both of which are required
for effective levels of protease activity in the
presence of ATP, although the proteolytic subunit alone
does possess some catalytic activity. Active site
consists of the triad Ser, His and Asp; some members
have lost all of these active site residues and are
therefore inactive, while others may have one or two
large insertions. ClpP seems to prefer hydrophobic or
non-polar residues at P1 or P1' positions in its
substrate. The protease exists as a tetradecamer made up
of two heptameric rings stacked back-to-back such that
the catalytic triad of each subunit is located at the
interface between three monomers, thus making
oligomerization essential for function.
Length = 171
Score = 196 bits (501), Expect = 5e-66
Identities = 82/109 (75%), Positives = 97/109 (88%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
MQ+IKP VST+C+GLAASMGA LLA+GTKGKR++LPNSRIMIHQPLGGA GQASDIEIQA
Sbjct: 63 MQYIKPPVSTICLGLAASMGALLLAAGTKGKRYALPNSRIMIHQPLGGAGGQASDIEIQA 122
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKI 109
+EIL LR+RLNEIL++ TG ++KI +DTDRD +MSA+ A EY LIDKI
Sbjct: 123 KEILRLRRRLNEILAKHTGQPLEKIEKDTDRDRYMSAEEAKEYGLIDKI 171
>gnl|CDD|188055 TIGR00493, clpP, ATP-dependent Clp endopeptidase, proteolytic
subunit ClpP. This model for the proteolytic subunit
ClpP has been rebuilt to a higher stringency. In every
bacterial genome with the ClpXP machine, a ClpP protein
will be found that scores at least 370 by This model. In
general, this ClpP member will be encoded adjacent to
the clpX gene, as were all examples used in the seed
alignment. A large fraction of genomes have one or more
additional ClpP paralogs, sometimes encoded nearby and
sometimes elsewhere. The stringency of the trusted
cutoff used here excludes the more divergent ClpP
paralogs from being called authentic ClpP by this model
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 192
Score = 193 bits (493), Expect = 1e-64
Identities = 83/110 (75%), Positives = 97/110 (88%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
MQFIKP+VST+CIG AASMGAFLLA+G KGKRFSLPNSRIMIHQPLGGAQGQA+DIEIQA
Sbjct: 81 MQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFSLPNSRIMIHQPLGGAQGQATDIEIQA 140
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKIL 110
EIL L+ LN+IL+E TG S+++I +DT+RD FMSA+ A EY LIDK+L
Sbjct: 141 NEILRLKGLLNDILAEHTGQSLEQIERDTERDFFMSAEEAKEYGLIDKVL 190
>gnl|CDD|223811 COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases
[Posttranslational modification, protein turnover,
chaperones / Intracellular trafficking and secretion].
Length = 200
Score = 190 bits (486), Expect = 2e-63
Identities = 76/114 (66%), Positives = 96/114 (84%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
MQFIKP VST+C+G AASMG+ LL +G KGKRF+LPN+RIMIHQP GGAQGQASDIEI A
Sbjct: 81 MQFIKPPVSTICMGQAASMGSVLLMAGDKGKRFALPNARIMIHQPSGGAQGQASDIEIHA 140
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQRK 114
REIL +++RLN I +E TG +++KI +DTDRD +MSA+ A EY LIDK+++ R+
Sbjct: 141 REILKIKERLNRIYAEHTGQTLEKIEKDTDRDTWMSAEEAKEYGLIDKVIESRE 194
>gnl|CDD|237133 PRK12553, PRK12553, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 207
Score = 180 bits (459), Expect = 3e-59
Identities = 69/116 (59%), Positives = 93/116 (80%), Gaps = 2/116 (1%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPL--GGAQGQASDIEI 58
+QFI+P+V T+C G AAS GA LLA+GT GKRF+LPN+RI+IHQP GG +GQASD+EI
Sbjct: 89 IQFIRPDVQTVCTGQAASAGAVLLAAGTPGKRFALPNARILIHQPSLGGGIRGQASDLEI 148
Query: 59 QAREILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQRK 114
QAREIL +R+RL IL+E TG SV+KI +DTDRD +++A+ A +Y L+D+I+ +
Sbjct: 149 QAREILRMRERLERILAEHTGQSVEKIRKDTDRDKWLTAEEAKDYGLVDQIITSYR 204
>gnl|CDD|139060 PRK12551, PRK12551, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 196
Score = 178 bits (453), Expect = 2e-58
Identities = 74/113 (65%), Positives = 93/113 (82%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
MQ +KP+V T+C+GLAASMGAFLL +G KGKR SL +SRIMIHQPLGGA+GQASDI IQA
Sbjct: 79 MQHVKPDVHTVCVGLAASMGAFLLCAGAKGKRSSLQHSRIMIHQPLGGARGQASDIRIQA 138
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQR 113
EIL+L++RLN LSE+TG +++I +DTDRD FMS A+EY LID ++ +R
Sbjct: 139 DEILFLKERLNTELSERTGQPLERIQEDTDRDFFMSPSEAVEYGLIDLVIDKR 191
>gnl|CDD|214340 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit.
Length = 200
Score = 161 bits (409), Expect = 1e-51
Identities = 50/110 (45%), Positives = 77/110 (70%), Gaps = 1/110 (0%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGA-QGQASDIEIQ 59
MQF+KP+V T+C+GLAASM +F+LA G KR + P++R+MIHQP +GQAS+ ++
Sbjct: 84 MQFVKPDVHTICLGLAASMASFILAGGEITKRLAFPHARVMIHQPASSFYEGQASEFVLE 143
Query: 60 AREILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKI 109
A E+L LR+ + + +++TG + IS+D +RD FMSA A Y ++D +
Sbjct: 144 AEELLKLRETITRVYAQRTGKPLWVISEDMERDVFMSATEAKAYGIVDLV 193
>gnl|CDD|183588 PRK12552, PRK12552, ATP-dependent Clp protease-like protein;
Reviewed.
Length = 222
Score = 151 bits (382), Expect = 2e-47
Identities = 57/114 (50%), Positives = 89/114 (78%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
M++IKP V T+CIG A A +L++GTKG+R SLP++ I++HQP GA+GQA+DI+I+A
Sbjct: 103 MRYIKPPVHTICIGQAMGTAAMILSAGTKGQRASLPHATIVLHQPRSGARGQATDIQIRA 162
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQRK 114
+E+L+ ++ + EILS TG +V+K+S+DTDR +++ + A EY LID++L+ RK
Sbjct: 163 KEVLHNKRTMLEILSRNTGQTVEKLSKDTDRMFYLTPQEAKEYGLIDRVLESRK 216
>gnl|CDD|184722 PRK14514, PRK14514, ATP-dependent Clp protease proteolytic subunit;
Provisional.
Length = 221
Score = 150 bits (381), Expect = 2e-47
Identities = 63/114 (55%), Positives = 88/114 (77%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
MQFI +V+T+C G+AASM + LL +GTKGKR +LP+SR+MIHQPLGGAQGQASDIEI A
Sbjct: 108 MQFISSDVATICTGMAASMASVLLVAGTKGKRSALPHSRVMIHQPLGGAQGQASDIEITA 167
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQRK 114
REI L++ L I+++ +G K+ D+DRD +M+A+ A EY +ID++L ++
Sbjct: 168 REIQKLKKELYTIIADHSGTPFDKVWADSDRDYWMTAQEAKEYGMIDEVLIKKP 221
>gnl|CDD|132924 cd07013, S14_ClpP, Caseinolytic protease (ClpP) is an
ATP-dependent, highly conserved serine protease. Clp
protease (caseinolytic protease; ClpP; Peptidase S14) is
a highly conserved serine protease present throughout in
bacteria and eukaryota, but seems to be absent in
archaea, mollicutes and some fungi. Clp proteases are
involved in a number of cellular processes such as
degradation of misfolded proteins, regulation of
short-lived proteins and housekeeping removal of
dysfunctional proteins. Additionally, they are
implicated in the control of cell growth, targeting
DNA-binding protein from starved cells. ClpP has also
been linked to the tight regulation of virulence genes
in the pathogens Listeria monocytogenes and Salmonella
typhimurium. This enzyme belong to the family of
ATP-dependent proteases; the functional Clp protease is
comprised of two components: a proteolytic component and
one of several regulatory ATPase components, both of
which are required for effective levels of protease
activity in the presence of ATP, although the
proteolytic subunit alone does possess some catalytic
activity. Active site consists of the triad Ser, His and
Asp; some members have lost all of these active site
residues and are therefore inactive, while others may
have one or two large insertions. ClpP seems to prefer
hydrophobic or non-polar residues at P1 or P1' positions
in its substrate. The protease exists as a tetradecamer
made up of two heptameric rings stacked back-to-back
such that the catalytic triad of each subunit is located
at the interface between three monomers, thus making
oligomerization essential for function.
Length = 162
Score = 140 bits (355), Expect = 3e-44
Identities = 49/109 (44%), Positives = 71/109 (65%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
++FIK +V T+ GLAASMG+ + +G KGKRF LPN+ +MIHQP GG G A+D+ I A
Sbjct: 54 IKFIKADVVTIIDGLAASMGSVIAMAGAKGKRFILPNAMMMIHQPWGGTLGDATDMRIYA 113
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKI 109
+L + L + KTG S +++ D +RD ++SA+ A+EY D I
Sbjct: 114 DLLLKVEGNLVSAYAHKTGQSEEELHADLERDTWLSAREAVEYGFADTI 162
>gnl|CDD|237741 PRK14512, PRK14512, ATP-dependent Clp protease proteolytic subunit;
Provisional.
Length = 197
Score = 126 bits (317), Expect = 7e-38
Identities = 46/114 (40%), Positives = 79/114 (69%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
++F+KP V T+ +GL AS A + + K RFSLPN+R ++HQPL G +G A+DIEI A
Sbjct: 77 IRFVKPKVFTIGVGLVASAAALIFLAAKKESRFSLPNARYLLHQPLSGFKGVATDIEIYA 136
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQRK 114
E+ ++ LN+I++++TG + K+ +DTDRD ++ + A++Y L+ ++++ R
Sbjct: 137 NELNKVKSELNDIIAKETGQELDKVEKDTDRDFWLDSSSAVKYGLVFEVVETRL 190
>gnl|CDD|237742 PRK14513, PRK14513, ATP-dependent Clp protease proteolytic subunit;
Provisional.
Length = 201
Score = 123 bits (310), Expect = 8e-37
Identities = 54/114 (47%), Positives = 78/114 (68%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQA 60
M++IK VST+C+G+A SMG+ LL +G KGKR +LPNSRIMIHQ G +G D+E+QA
Sbjct: 81 MRYIKAPVSTICVGIAMSMGSVLLMAGDKGKRMALPNSRIMIHQGSAGFRGNTPDLEVQA 140
Query: 61 REILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKILKQRK 114
+E+L+LR L +I T +K+ +D +RD FMS + A Y LID +++ +
Sbjct: 141 KEVLFLRDTLVDIYHRHTDLPHEKLLRDMERDYFMSPEEAKAYGLIDSVIEPTR 194
>gnl|CDD|132923 cd00394, Clp_protease_like, Caseinolytic protease (ClpP) is an
ATP-dependent protease. Clp protease (caseinolytic
protease; ClpP; endopeptidase Clp; Peptidase S14;
ATP-dependent protease, ClpAP)-like enzymes are highly
conserved serine proteases and belong to the
ClpP/Crotonase superfamily. Included in this family are
Clp proteases that are involved in a number of cellular
processes such as degradation of misfolded proteins,
regulation of short-lived proteins and housekeeping
removal of dysfunctional proteins. They are also
implicated in the control of cell growth, targeting
DNA-binding protein from starved cells. The functional
Clp protease is comprised of two components: a
proteolytic component and one of several regulatory
ATPase components, both of which are required for
effective levels of protease activity in the presence of
ATP. Active site consists of the triad Ser, His and Asp,
preferring hydrophobic or non-polar residues at P1 or
P1' positions. The protease exists as a tetradecamer
made up of two heptameric rings stacked back-to-back
such that the catalytic triad of each subunit is located
at the interface between three monomers, thus making
oligomerization essential for function. Another family
included in this class of enzymes is the signal peptide
peptidase A (SppA; S49) which is involved in the
cleavage of signal peptides after their removal from the
precursor proteins by signal peptidases. Mutagenesis
studies suggest that the catalytic center of SppA
comprises a Ser-Lys dyad and not the usual Ser-His-Asp
catalytic triad found in the majority of serine
proteases. In addition to the carboxyl-terminal protease
domain that is conserved in all the S49 family members,
the E. coli SppA contains an amino-terminal domain.
Others, including sohB peptidase, protein C, protein
1510-N and archaeal signal peptide peptidase, do not
contain the amino-terminal domain. The third family
included in this hierarchy is nodulation formation
efficiency D (NfeD) which is a membrane-bound Clp-class
protease and only found in bacteria and archaea.
Majority of the NfeD genomes have been shown to possess
operons containing a homologous NfeD/stomatin gene pair,
causing NfeD to be previously named stomatin operon
partner protein (STOPP). NfeD homologs can be divided
into two groups: long and short forms. Long-form
homologs have a putative ClpP-class serine protease
domain while the short form homologs do not. Downstream
from the ClpP-class domain is the so-called NfeD or
DUF107 domain. N-terminal region of the NfeD homolog
PH1510 from Pyrococcus horikoshii has been shown to
possess serine protease activity having a Ser-Lys
catalytic dyad.
Length = 161
Score = 93.6 bits (233), Expect = 1e-25
Identities = 32/111 (28%), Positives = 56/111 (50%), Gaps = 4/111 (3%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQAS--DIEI 58
+Q + V G AAS G ++ + K P +R+ H P+GG G + E
Sbjct: 53 LQASRKPVIAYVGGQAASAGYYIATAANK--IVMAPGTRVGSHGPIGGYGGNGNPTAQEA 110
Query: 59 QAREILYLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKI 109
R ILY R +++E G + +K+ +D ++D ++A+ A+EY L+D +
Sbjct: 111 DQRIILYFIARFISLVAENRGQTTEKLEEDIEKDLVLTAQEALEYGLVDAL 161
>gnl|CDD|132927 cd07016, S14_ClpP_1, Caseinolytic protease (ClpP) is an
ATP-dependent, highly conserved serine protease. Clp
protease (caseinolytic protease; ClpP; Peptidase S14) is
a highly conserved serine protease present throughout in
bacteria and eukaryota, but seems to be absent in
archaea, mollicutes and some fungi. This subfamily only
contains bacterial sequences. Clp proteases are involved
in a number of cellular processes such as degradation of
misfolded proteins, regulation of short-lived proteins
and housekeeping removal of dysfunctional proteins. They
are also implicated in the control of cell growth,
targeting DNA-binding protein from starved cells. ClpP
has also been linked to the tight regulation of
virulence genes in the pathogens Listeria monocytogenes
and Salmonella typhimurium. This enzyme belong to the
family of ATP-dependent proteases; the functional Clp
protease is comprised of two components: a proteolytic
component and one of several regulatory ATPase
components, both of which are required for effective
levels of protease activity in the presence of ATP,
although the proteolytic subunit alone does possess some
catalytic activity. Active site consists of the triad
Ser, His and Asp; some members have lost all of these
active site residues and are therefore inactive, while
others may have one or two large insertions. ClpP seems
to prefer hydrophobic or non-polar residues at P1 or P1'
positions in its substrate. The protease exists as a
tetradecamer made up of two heptameric rings stacked
back-to-back such that the catalytic triad of each
subunit is located at the interface between three
monomers, thus making oligomerization essential for
function.
Length = 160
Score = 68.7 bits (169), Expect = 6e-16
Identities = 33/105 (31%), Positives = 55/105 (52%), Gaps = 2/105 (1%)
Query: 5 KPNVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMIHQPLGGAQGQASDIEIQAREIL 64
K V+ GLAAS + + +G + PN+ +MIH P GA G A D+ A +
Sbjct: 58 KGKVTVKIDGLAASAASVIAMAGDE--VEMPPNAMLMIHNPSTGAAGNADDLRKAADLLD 115
Query: 65 YLRQRLNEILSEKTGHSVKKISQDTDRDNFMSAKMAMEYCLIDKI 109
+ + + +EKTG S ++IS D + +++A+ A+E D+I
Sbjct: 116 KIDESIANAYAEKTGLSEEEISALMDAETWLTAQEAVELGFADEI 160
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are all
experimentally characterized. The copper P-type ATPases
have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of this
sequence does not hit anything else annotated in this
way. This error may come from the characterization paper
published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can be
found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 27.2 bits (61), Expect = 1.9
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 46 LGGAQGQASDIEIQAREILYLRQRLNEI-----LSEKTGHSVK 83
+G A G +D+ I+A +++ LR LN++ LS KT +K
Sbjct: 497 VGIAIGAGTDVAIEAADVVLLRNDLNDVATAIDLSRKTLRRIK 539
>gnl|CDD|219550 pfam07745, Glyco_hydro_53, Glycosyl hydrolase family 53. This
domain belongs to family 53 of the glycosyl hydrolase
classification. These enzymes are enzymes are endo-1,4-
beta-galactanases (EC:3.2.1.89). The structure of this
domain is known and has a TIM barrel fold.
Length = 332
Score = 26.9 bits (60), Expect = 2.8
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 23 LLASGTKGKRFSLPNSRIMIH 43
LL SG + P ++MIH
Sbjct: 155 LLNSGYWAVKDVNPTIKVMIH 175
>gnl|CDD|235744 PRK06213, PRK06213, enoyl-CoA hydratase; Provisional.
Length = 229
Score = 26.5 bits (59), Expect = 3.2
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 8 VSTLCIGLAASMGAFLLASG 27
V C G A + GAFLL S
Sbjct: 94 VIVACTGHAIAKGAFLLLSA 113
>gnl|CDD|151587 pfam11143, DUF2919, Protein of unknown function (DUF2919). This
bacterial family of proteins has no known function.
Some members are annotated as YfeZ however this cannot
be confirmed.
Length = 149
Score = 25.6 bits (57), Expect = 5.4
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 1 MQFIKPNVSTLCIGLAASMGAFLL 24
+ P+ S +GLAA + A LL
Sbjct: 46 LSLFYPDKSDFYLGLAAGVPALLL 69
>gnl|CDD|235937 PRK07111, PRK07111, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 735
Score = 25.7 bits (57), Expect = 7.0
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 63 ILYLRQRLNEILSEKTG--HSVKKISQDTDRDN 93
ILY +R I K+ ++++I DTDR+N
Sbjct: 85 ILYRAER-TRIREIKSDLMKAIEEIGNDTDREN 116
>gnl|CDD|222512 pfam14048, MBD_C, C-terminal domain of methyl-CpG binding protein
2 and 3. CpG-methylation is a frequently occurring
epigenetic modification of vertebrate genomes resulting
in transcriptional repression. This domain was found at
the C-terminus of the methyl-CpG-binding domain (MBD)
containing proteins MBD2 and MBD3, the latter was shown
to not bind directly to methyl-CpG DNA but rather
interact with components of the NuRD/Mi2 complex, an
abundant deacetylase complex. The domain is subject to
structure determination by the Joint Center of
Structural Genomics.
Length = 96
Score = 24.9 bits (55), Expect = 7.7
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 55 DIEIQAREILYLRQRLNEIL 74
DI Q R + R+RL E L
Sbjct: 77 DIRRQERRVKDARKRLAEAL 96
>gnl|CDD|237022 PRK11915, PRK11915, glycerol-3-phosphate acyltransferase; Reviewed.
Length = 621
Score = 25.3 bits (55), Expect = 8.8
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 62 EILYLRQRLNEILSEK--TGHSVKKISQDTD 90
E L LR+RL E+ ++K TG +++I+ D +
Sbjct: 289 EPLPLRKRLQELRADKSGTGSEIERIALDVE 319
>gnl|CDD|182611 PRK10642, PRK10642, proline/glycine betaine transporter;
Provisional.
Length = 490
Score = 25.4 bits (56), Expect = 9.3
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 20/74 (27%)
Query: 7 NVSTLCIGLAASMGAFLLASGTKGKRFSLPNSRIMI----------------HQPLGGAQ 50
N+S L GL ++ A+L+ S + +P +M+ ++PL GA
Sbjct: 385 NISVLVAGLTPTLAAWLVEST---QNLMMPAYYLMVVAVIGLITGVTMKETANRPLKGAT 441
Query: 51 GQASDIEIQAREIL 64
ASDI+ +A+EIL
Sbjct: 442 PAASDIQ-EAKEIL 454
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 0.371
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,605,589
Number of extensions: 477659
Number of successful extensions: 491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 485
Number of HSP's successfully gapped: 32
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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 (24.2 bits)