RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780272|ref|YP_003064685.1| ATP-dependent Clp protease
proteolytic subunit [Candidatus Liberibacter asiaticus str. psy62]
(216 letters)
>gnl|CDD|144241 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. A
putative Clp protease from Cyanophora paradoxa has lost
all of these active site residues and is therefore
inactive. A member from Chlamydomonas eugametos contains
two large insertions, a member from Chlamydomonas
reinhardtii contains one large insertion.
Length = 182
Score = 317 bits (815), Expect = 1e-87
Identities = 120/182 (65%), Positives = 151/182 (82%)
Query: 27 NRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVV 86
+ GER YDIYSRLL+ERI+F+ G+I+D +A LI AQLLFLE+E+P K+I LYINSPGG V
Sbjct: 1 SGGERWYDIYSRLLRERIIFLGGEIDDEVANLIIAQLLFLESEDPDKDIYLYINSPGGSV 60
Query: 87 TAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSG 146
TAG+AIYDTMQFIKP +ST C+G AASMGS LL+AG KG RFALPNARI++HQP GG G
Sbjct: 61 TAGLAIYDTMQFIKPDVSTICLGLAASMGSFLLAAGTKGKRFALPNARIMIHQPLGGAQG 120
Query: 147 QASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLM 206
QASDIE A++I+KI+ RLNEIY ++ G+ E++EK LDRD MSA EA ++G++D+V+
Sbjct: 121 QASDIEIQAEEILKIRERLNEIYAEHTGQPLEKIEKDLDRDTFMSAEEAKEYGLIDEVIE 180
Query: 207 SR 208
SR
Sbjct: 181 SR 182
>gnl|CDD|31083 COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases
[Posttranslational modification, protein turnover,
chaperones / Intracellular trafficking and secretion].
Length = 200
Score = 308 bits (790), Expect = 1e-84
Identities = 142/198 (71%), Positives = 169/198 (85%)
Query: 18 LVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISL 77
LVPMV+EQT+RGERSYDIYSRLLKERI+F+ G+IEDHMA LI AQLLFLEAE+P K+I L
Sbjct: 3 LVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEIEDHMANLIVAQLLFLEAEDPDKDIYL 62
Query: 78 YINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILL 137
YINSPGG VTAG+AIYDTMQFIKPP+ST CMGQAASMGS+LL AG+KG RFALPNARI++
Sbjct: 63 YINSPGGSVTAGLAIYDTMQFIKPPVSTICMGQAASMGSVLLMAGDKGKRFALPNARIMI 122
Query: 138 HQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACD 197
HQPSGG GQASDIE HA++I+KIK RLN IY ++ G+T E++EK DRD MSA EA +
Sbjct: 123 HQPSGGAQGQASDIEIHAREILKIKERLNRIYAEHTGQTLEKIEKDTDRDTWMSAEEAKE 182
Query: 198 WGVVDKVLMSRIDIEEKS 215
+G++DKV+ SR + S
Sbjct: 183 YGLIDKVIESREAAAKLS 200
>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 = 307 bits (788), Expect = 2e-84
Identities = 110/171 (64%), Positives = 143/171 (83%)
Query: 34 DIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIY 93
DIYSRLLKERI+F+ G I+D +A LI AQLL+LE+E+P+K I LYINSPGG VTAG+AIY
Sbjct: 1 DIYSRLLKERIIFLGGPIDDEVANLIIAQLLYLESEDPKKPIYLYINSPGGSVTAGLAIY 60
Query: 94 DTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIER 153
DTMQ+IKPP+ST C+G AASMG+LLL+AG KG R+ALPN+RI++HQP GG GQASDIE
Sbjct: 61 DTMQYIKPPVSTICLGLAASMGALLLAAGTKGKRYALPNSRIMIHQPLGGAGGQASDIEI 120
Query: 154 HAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV 204
A++I++++RRLNEI K+ G+ E++EK DRD MSA EA ++G++DK+
Sbjct: 121 QAKEILRLRRRLNEILAKHTGQPLEKIEKDTDRDRYMSAEEAKEYGLIDKI 171
>gnl|CDD|36058 KOG0840, KOG0840, KOG0840, ATP-dependent Clp protease, proteolytic
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 275
Score = 269 bits (690), Expect = 3e-73
Identities = 111/195 (56%), Positives = 148/195 (75%), Gaps = 1/195 (0%)
Query: 21 MVVEQTNRG-ERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYI 79
+E RG ER YDIYSRLL+ERIVF+ I+D +A L+ AQLL+L++E+P+K I LYI
Sbjct: 70 FPIESPGRGRERPYDIYSRLLRERIVFLGQPIDDDVANLVIAQLLYLDSEDPKKPIYLYI 129
Query: 80 NSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQ 139
NSPGG VTAG+AIYDTMQ+IKP +ST C+G AASM +LLL+AG KG R+ALPN+RI++HQ
Sbjct: 130 NSPGGSVTAGLAIYDTMQYIKPDVSTICVGLAASMAALLLAAGAKGKRYALPNSRIMIHQ 189
Query: 140 PSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWG 199
PSGG GQA+DI A+++++IK LNEIY K+ G+ E +EK +DRD MSA EA ++G
Sbjct: 190 PSGGAGGQATDIVIQAKELMRIKEYLNEIYAKHTGQPLEVIEKDMDRDRFMSAEEAKEYG 249
Query: 200 VVDKVLMSRIDIEEK 214
++DKV+ +
Sbjct: 250 LIDKVIDHPPETRVD 264
>gnl|CDD|176969 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit.
Length = 200
Score = 230 bits (589), Expect = 2e-61
Identities = 71/175 (40%), Positives = 120/175 (68%), Gaps = 1/175 (0%)
Query: 34 DIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIY 93
D+Y+RL +ER++F+ +++D +A + +++L E+ K++ L+INSPGG V +G+AIY
Sbjct: 22 DLYNRLYRERLLFLGQEVDDEIANQLIGLMVYLSIEDDTKDLYLFINSPGGSVISGLAIY 81
Query: 94 DTMQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFS-GQASDIE 152
DTMQF+KP + T C+G AASM S +L+ GE R A P+AR+++HQP+ F GQAS+
Sbjct: 82 DTMQFVKPDVHTICLGLAASMASFILAGGEITKRLAFPHARVMIHQPASSFYEGQASEFV 141
Query: 153 RHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMS 207
A++++K++ + +Y + GK + + ++RD MSA+EA +G+VD V ++
Sbjct: 142 LEAEELLKLRETITRVYAQRTGKPLWVISEDMERDVFMSATEAKAYGIVDLVAVN 196
>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 = 209 bits (532), Expect = 7e-55
Identities = 79/162 (48%), Positives = 108/162 (66%)
Query: 43 RIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPP 102
R + +TG++ED A AQLLFL A NP+K+I LYINSPGG V AGMAIYDT++FIK
Sbjct: 1 REIMLTGEVEDISANQFAAQLLFLGAVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIKAD 60
Query: 103 ISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERHAQDIVKIK 162
+ T G AASMGS++ AG KG RF LPNA +++HQP GG G A+D+ +A ++K++
Sbjct: 61 VVTIIDGLAASMGSVIAMAGAKGKRFILPNAMMMIHQPWGGTLGDATDMRIYADLLLKVE 120
Query: 163 RRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV 204
L Y G++ EE+ L+RD +SA EA ++G D +
Sbjct: 121 GNLVSAYAHKTGQSEEELHADLERDTWLSAREAVEYGFADTI 162
>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 = 155 bits (393), Expect = 1e-38
Identities = 57/163 (34%), Positives = 92/163 (56%), Gaps = 4/163 (2%)
Query: 44 IVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPI 103
++F+ G IED A + AQ+ F EA+N K I L +N+PGG V AGM I D +Q + P+
Sbjct: 1 VIFINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQASRKPV 60
Query: 104 STFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQAS--DIERHAQDIVKI 161
+ GQAAS G + +A K P R+ H P GG+ G + E + I+
Sbjct: 61 IAYVGGQAASAGYYIATAANK--IVMAPGTRVGSHGPIGGYGGNGNPTAQEADQRIILYF 118
Query: 162 KRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV 204
R + +N G+T E++E+ +++D +++A EA ++G+VD +
Sbjct: 119 IARFISLVAENRGQTTEKLEEDIEKDLVLTAQEALEYGLVDAL 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 = 109 bits (276), Expect = 4e-25
Identities = 47/141 (33%), Positives = 79/141 (56%), Gaps = 4/141 (2%)
Query: 65 FLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEK 124
L+A +I++ INSPGG V AG+AIY+ ++ K ++ G AAS S++ AG++
Sbjct: 23 ALDALGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIAMAGDE 82
Query: 125 -GMRFALPNARILLHQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKT 183
M PNA +++H PS G +G A D+ + A + KI + Y + G + EE+
Sbjct: 83 VEMP---PNAMLMIHNPSTGAAGNADDLRKAADLLDKIDESIANAYAEKTGLSEEEISAL 139
Query: 184 LDRDHIMSASEACDWGVVDKV 204
+D + ++A EA + G D++
Sbjct: 140 MDAETWLTAQEAVELGFADEI 160
>gnl|CDD|30961 COG0616, SppA, Periplasmic serine proteases (ClpP class)
[Posttranslational modification, protein turnover,
chaperones / Intracellular trafficking and secretion].
Length = 317
Score = 46.6 bits (110), Expect = 6e-06
Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 4/98 (4%)
Query: 40 LKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFI 99
++ IV G + I L A+ K + L INSPGG V A I ++ +
Sbjct: 66 VEGAIVAGGGPLRFIGGDDIEEILRAARADPSVKAVVLRINSPGGSVVASELIARALKRL 125
Query: 100 --KPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARI 135
K P+ G AAS G + A +K A P++
Sbjct: 126 RAKKPVVVSVGGYAASGGYYIALAADK--IVADPSSIT 161
>gnl|CDD|132934 cd07023, S49_Sppa_N_C, Signal peptide peptidase A (SppA), a serine
protease, has catalytic Ser-Lys dyad. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppA is
found in all three domains of life and is involved in
the cleavage of signal peptides after their removal from
the precursor proteins by signal peptidases. This
subfamily contains members with either a single domain
(sometimes referred to as 36K type), such as sohB
peptidase, protein C and archaeal signal peptide
peptidase, or an amino-terminal domain in addition to
the carboxyl-terminal protease domain that is conserved
in all the S49 family members (sometimes referred to as
67K type), similar to E. coli and Arabidopsis thaliana
SppA peptidases. Site-directed mutagenesis and sequence
analysis have shown these SppAs to be serine proteases.
The predicted active site serine for members in this
family occurs in a transmembrane domain. Mutagenesis
studies also suggest that the catalytic center comprises
a Ser-Lys dyad and not the usual Ser-His-Asp catalytic
triad found in the majority of serine proteases.
Interestingly, the single membrane spanning E. coli SppA
carries out catalysis using a Ser-Lys dyad with the
serine located in the conserved carboxy-terminal
protease domain and the lysine in the non-conserved
amino-terminal domain.
Length = 208
Score = 40.5 bits (96), Expect = 3e-04
Identities = 45/196 (22%), Positives = 80/196 (40%), Gaps = 37/196 (18%)
Query: 44 IVFVTGQIED---HMATLICAQLLFLEAENPQ-KEISLYINSPGGVVTAGMAIYDTMQFI 99
++ + G I D A + QL E+ K + L INSPGG V A IY ++ +
Sbjct: 4 VIDIEGTISDGGGIGADSLIEQLRKA-REDDSVKAVVLRINSPGGSVVASEEIYREIRRL 62
Query: 100 K---PPISTFCMGQAASMGSLLLSAGEK------------GMRFALPNARILLHQP---- 140
+ P+ AAS G + +A +K G+ PN LL +
Sbjct: 63 RKAKKPVVASMGDVAASGGYYIAAAADKIVANPTTITGSIGVIGQGPNLEELLDKLGIER 122
Query: 141 ----SGGFSGQAS-DIERHAQDIVKIKRRLNEIY-------VKNCGKTYEEVEKTLDRDH 188
SG + S D ++ ++ +++IY + G + E ++K L
Sbjct: 123 DTIKSGPGKDKGSPDRPLTEEERAILQALVDDIYDQFVDVVAEGRGMSGERLDK-LADGR 181
Query: 189 IMSASEACDWGVVDKV 204
+ + +A + G+VD++
Sbjct: 182 VWTGRQALELGLVDEL 197
>gnl|CDD|132932 cd07021, Clp_protease_NfeD_like, Nodulation formation efficiency D
(NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin operon
partner protein, STOPP; DUF107) is a member of
membrane-anchored ClpP-class proteases. Currently, more
than 300 NfeD homologs have been identified - all of
which are bacterial or archaeal in origin. Majority of
these genomes have been shown to possess operons
containing a homologous NfeD/stomatin gene pair, causing
NfeD to be previously named STOPP (stomatin operon
partner protein). 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
(1510-N or PH1510-N) from Pyrococcus horikoshii has been
shown to possess serine protease activity and has a
Ser-Lys catalytic dyad, preferentially cleaving
hydrophobic substrates. Difference in oligomeric form
and catalytic residues between 1510-N (forming a dimer)
and ClpP (forming a tetradecamer) shows a possible
functional difference: 1510-N is likely to have a
regulatory function while ClpP is involved in protein
quality control.
Length = 178
Score = 35.3 bits (82), Expect = 0.012
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 44 IVFVTGQIEDHMATLICAQLLFLEA-ENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPP 102
++ + G+I+ +A + L EA E + L I++PGG V + + I D + P
Sbjct: 3 VIPIEGEIDPGLAAFVERALK--EAKEEGADAVVLDIDTPGGRVDSALEIVDLILNSPIP 60
Query: 103 ISTFCMGQAASMGSLL-LSAGEKGMRFALPNARI 135
+ +AAS G+L+ L+A E M P A I
Sbjct: 61 TIAYVNDRAASAGALIALAADEIYMA---PGATI 91
>gnl|CDD|31233 COG1030, NfeD, Membrane-bound serine protease (ClpP class)
[Posttranslational modification, protein turnover,
chaperones].
Length = 436
Score = 34.9 bits (80), Expect = 0.018
Identities = 36/172 (20%), Positives = 69/172 (40%), Gaps = 13/172 (7%)
Query: 44 IVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPI 103
++ + G I+ A + L E EN + L +++PGG++ + I + P+
Sbjct: 30 VIEIDGAIDPASADYLQRALQSAEEENAAA-VVLELDTPGGLLDSMRQIVRAILNSPVPV 88
Query: 104 STFCM---GQAASMGS-LLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERHAQDIV 159
+ + +AAS G+ +L++ M P I P G G ++ V
Sbjct: 89 IGYVVPDGARAASAGTYILMATHIAAMA---PGTNIGAATPIAG-GGTSAKEANTTNAAV 144
Query: 160 KIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMSRIDI 211
R L E G+ E+ + + ++A EA GV+D + ++
Sbjct: 145 AYIRSLAEER----GRNPTWAERFVTENLSLTAEEALRQGVIDLIARDLNEL 192
>gnl|CDD|132926 cd07015, Clp_protease_NfeD, Nodulation formation efficiency D
(NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin operon
partner protein, STOPP; DUF107) is a member of
membrane-anchored ClpP-class proteases. Currently, more
than 300 NfeD homologs have been identified - all of
which are bacterial or archaeal in origin. Majority of
these genomes have been shown to possess operons
containing a homologous NfeD/stomatin gene pair, causing
NfeD to be previously named STOPP (stomatin operon
partner protein). 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
(1510-N or PH1510-N) from Pyrococcus horikoshii has been
shown to possess serine protease activity and has a
Ser-Lys catalytic dyad, preferentially cleaving
hydrophobic substrates. Difference in oligomeric form
and catalytic residues between 1510-N (forming a dimer)
and ClpP (forming a tetradecamer) shows a possible
functional difference: 1510-N is likely to have a
regulatory function while ClpP is involved in protein
quality control.
Length = 172
Score = 34.7 bits (79), Expect = 0.019
Identities = 41/176 (23%), Positives = 71/176 (40%), Gaps = 17/176 (9%)
Query: 47 VTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPISTF 106
+ GQI + + E +N + I + +++PGG A I +Q K P+ +
Sbjct: 6 IKGQITSYTYDQFDRYITIAEQDNAE-AIIIELDTPGGRADAAGNIVQRIQQSKIPVIIY 64
Query: 107 CM---GQAASMGSLL-LSAGEKGMRFALPNARILLHQPSGGFSGQASDIE--RHAQD--I 158
AAS G+ + L + M P I +P G+S S IE + I
Sbjct: 65 VYPPGASAASAGTYIALGSHLIAMA---PGTSIGACRPILGYSQNGSIIEAPPKITNYFI 121
Query: 159 VKIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKVLMSRIDIEEK 214
IK E G+ E+ + +D ++ EA +GV++ V ++ +K
Sbjct: 122 AYIKSLAQE-----SGRNATIAEEFITKDLSLTPEEALKYGVIEVVARDINELLKK 172
>gnl|CDD|132930 cd07019, S49_SppA_1, Signal peptide peptidase A (SppA), a serine
protease, has catalytic Ser-Lys dyad. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppAs in
this subfamily are found in all three domains of life
and are involved in the cleavage of signal peptides
after their removal from the precursor proteins by
signal peptidases. Site-directed mutagenesis and
sequence analysis have shown these bacterial, archaeal
and thylakoid SppAs to be serine proteases. The
predicted active site serine for members in this family
occurs in a transmembrane domain. Mutagenesis studies
also suggest that the catalytic center comprises a
Ser-Lys dyad (both residues absolutely conserved within
bacteria, chloroplast and mitochondrial signal peptidase
family members) 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, similar to
Arabidopsis thaliana SppA1 peptidase. Others, including
sohB peptidase, protein C and archaeal signal peptide
peptidase, do not contain the amino-terminal domain.
Interestingly, the single membrane spanning E. coli SppA
carries out catalysis using a Ser-Lys dyad with the
serine located in the conserved carboxy-terminal
protease domain and the lysine in the non-conserved
amino-terminal domain.
Length = 211
Score = 30.0 bits (67), Expect = 0.51
Identities = 25/89 (28%), Positives = 32/89 (35%), Gaps = 17/89 (19%)
Query: 44 IVFVTGQIEDHMAT-------LICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTM 96
+VF G I D T AQ+ + K I L +NSPGG VTA I +
Sbjct: 4 VVFANGAIVDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAEL 63
Query: 97 QFIKP---PISTFCMGQAASMGSLLLSAG 122
+ P+ S G S G
Sbjct: 64 AAARAAGKPV-------VVSAGGAAASGG 85
>gnl|CDD|132933 cd07022, S49_Sppa_36K_type, Signal peptide peptidase A (SppA) 36K
type, a serine protease, has catalytic Ser-Lys dyad.
Signal peptide peptidase A (SppA; Peptidase S49;
Protease IV) 36K type: SppA is found in all three
domains of life and is involved in the cleavage of
signal peptides after their removal from the precursor
proteins by signal peptidases. Members in this subfamily
are all bacterial and include sohB peptidase and protein
C. These are sometimes referred to as 36K type since
they contain only one domain, unlike E. coli SppA that
also contains an amino-terminal domain. Site-directed
mutagenesis and sequence analysis have shown these SppAs
to be serine proteases. The predicted active site serine
for members in this family occurs in a transmembrane
domain. Mutagenesis studies also suggest that the
catalytic center comprises a Ser-Lys dyad and not the
usual Ser-His-Asp catalytic triad found in the majority
of serine proteases.
Length = 214
Score = 29.8 bits (68), Expect = 0.63
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 73 KEISLYINSPGGVVTAGMAIYDTMQFI-----KPPISTFCMGQAASMGSLLLSA 121
+ I L I+SPGG V +++ I PI F G AAS + SA
Sbjct: 44 RAIVLDIDSPGGEVA---GVFELADAIRAARAGKPIVAFVNGLAASAAYWIASA 94
>gnl|CDD|132931 cd07020, Clp_protease_NfeD_1, Nodulation formation efficiency D
(NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin operon
partner protein, STOPP; DUF107) is a member of
membrane-anchored ClpP-class proteases. Currently, more
than 300 NfeD homologs have been identified - all of
which are bacterial or archaeal in origin. Majority of
these genomes have been shown to possess operons
containing a homologous NfeD/stomatin gene pair, causing
NfeD to be previously named STOPP (stomatin operon
partner protein). 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
(1510-N or PH1510-N) from Pyrococcus horikoshii has been
shown to possess serine protease activity and has a
Ser-Lys catalytic dyad, preferentially cleaving
hydrophobic substrates. Difference in oligomeric form
and catalytic residues between 1510-N (forming a dimer)
and ClpP (forming a tetradecamer) shows a possible
functional difference: 1510-N is likely to have a
regulatory function while ClpP is involved in protein
quality control.
Length = 187
Score = 29.1 bits (66), Expect = 1.1
Identities = 40/177 (22%), Positives = 69/177 (38%), Gaps = 21/177 (11%)
Query: 47 VTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDTMQFIKPPISTF 106
+ G I A + + E I + +++PGG++ + I + P+ +
Sbjct: 6 INGAITPATADYLERAIDQAEEGGADALI-IELDTPGGLLDSTREIVQAILASPVPVVVY 64
Query: 107 CM---GQAASMGSL-LLSAGEKGMRFALPNARILLHQP-SGGFSGQASDIERHA--QDIV 159
+AAS G+ LL+A M P I P + G G + + D V
Sbjct: 65 VYPSGARAASAGTYILLAAHIAAMA---PGTNIGAAHPVAIGGGGGSDPVMEKKILNDAV 121
Query: 160 KIKRRLNEIYVKNCGKTYEEVEKTLDRDHIMSASEACDWGVVDKV------LMSRID 210
R L E+ G+ E EK + ++A EA GV+D + L+ ++D
Sbjct: 122 AYIRSLAELR----GRNAEWAEKAVRESLSLTAEEALKLGVIDLIAADLNELLKKLD 174
>gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit
[Transcription].
Length = 1386
Score = 28.0 bits (62), Expect = 2.2
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 20 PMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYI 79
P V+ + G D+ +L + I+ I+ H++ L+ + + Q +++LYI
Sbjct: 262 PSVMSEDKAGTNEDDLTMKLTE--IILTNDVIKKHLSKGTPINLIMEDWDFLQLQVALYI 319
Query: 80 NS 81
NS
Sbjct: 320 NS 321
>gnl|CDD|153357 cd07673, F-BAR_FCHO2, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only 2
protein. F-BAR domains are dimerization modules that
bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
The specific function of FCH domain Only 2 (FCHO2) is
still unknown. It contains an N-terminal F-BAR domain
and a C-terminal domain of unknown function named SAFF
which is also present in FCHO1 and endophilin
interacting protein 1. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 269
Score = 27.7 bits (61), Expect = 2.4
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 150 DIERHAQDIVKIKRRLNEIYVKNCGKTYEEVEKTLDRDH-IMSASEA 195
++ R Q+++K ++ E VK+ KT EEV TL+ I S ++A
Sbjct: 85 ELVRKLQELIKEVQKYGEEQVKSHKKTKEEVAGTLEAVQNIQSITQA 131
>gnl|CDD|36327 KOG1111, KOG1111, KOG1111, N-acetylglucosaminyltransferase complex,
subunit PIG-A/SPT14, required for phosphatidylinositol
biosynthesis/Sulfolipid synthase [Cell
wall/membrane/envelope biogenesis, Posttranslational
modification, protein turnover, chaperones, Lipid
transport and metabolism].
Length = 426
Score = 27.6 bits (61), Expect = 2.8
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 15/98 (15%)
Query: 98 FIKPPIS-TFCMG--QAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERH 154
F+ ++ FCM +AAS G ++S G+ LP I L +P D+
Sbjct: 275 FLNTSLTEAFCMVIVEAASCGLPVVSTRVGGIPEVLPEDMITLGEPG------PDDLVGA 328
Query: 155 AQDIVKIKRRLNEIYVKNCGKTY------EEVEKTLDR 186
+ + R L + K Y E EK DR
Sbjct: 329 VEKAITKLRTLPLEFHDRVKKMYSWKDVAERTEKVYDR 366
>gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 26.0 bits (57), Expect = 7.9
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 116 SLLLSAGEKGMRFALPNARILLHQP 140
+LS GE+ R A AR+LLH+P
Sbjct: 513 DRVLSGGEQ-QRLAF--ARLLLHKP 534
>gnl|CDD|110924 pfam01972, SDH_sah, Serine dehydrogenase proteinase. This family
of archaebacterial proteins, formerly known as DUF114,
has been found to be a serine dehydrogenase proteinase
distantly related to ClpP proteinases that belong to the
serine proteinase superfamily. The family has a
catalytic triad of Ser, Asp, His residues, which shows
an altered residue ordering compared with the ClpP
proteinases but similar to that of the carboxypeptidase
clan.
Length = 286
Score = 26.0 bits (57), Expect = 8.5
Identities = 14/52 (26%), Positives = 24/52 (46%)
Query: 73 KEISLYINSPGGVVTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAGEK 124
I L I++PGG+ A I ++ K + A S G+L+ A ++
Sbjct: 92 MPIDLIIHTPGGLALAATQIAKALKEHKAKTTVIVPHYAMSGGTLIALAADE 143
>gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette
transporter (Pat) is involved in the import of very
long-chain fatty acids (VLCFA) into the peroxisome. The
peroxisomal membrane forms a permeability barrier for a
wide variety of metabolites required for and formed
during fatty acid beta-oxidation. To communicate with
the cytoplasm and mitochondria, peroxisomes need
dedicated proteins to transport such hydrophilic
molecules across their membranes. X-linked
adrenoleukodystrophy (X-ALD) is caused by mutations in
the ALD gene, which encodes ALDP (adrenoleukodystrophy
protein ), a peroxisomal integral membrane protein that
is a member of the ATP-binding cassette (ABC)
transporter protein family. The disease is
characterized by a striking and unpredictable variation
in phenotypic expression. Phenotypes include the
rapidly progressive childhood cerebral form (CCALD), the
milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic)..
Length = 166
Score = 25.9 bits (57), Expect = 8.7
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 3/23 (13%)
Query: 119 LSAGEKGMRFALPNARILLHQPS 141
LS GE+ R A AR+LLH+P
Sbjct: 92 LSGGEQ-QRLAF--ARLLLHKPK 111
>gnl|CDD|37685 KOG2474, KOG2474, KOG2474, Zinc transporter and related ZIP
domain-containing proteins [Inorganic ion transport and
metabolism].
Length = 406
Score = 25.8 bits (56), Expect = 8.8
Identities = 8/37 (21%), Positives = 14/37 (37%)
Query: 86 VTAGMAIYDTMQFIKPPISTFCMGQAASMGSLLLSAG 122
AG +Y + I P + AS+G++
Sbjct: 357 FAAGAMLYVVLDDIIPEAQRSDNSKLASLGTICGKWC 393
>gnl|CDD|37518 KOG2307, KOG2307, KOG2307, Low density lipoprotein receptor
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 705
Score = 25.7 bits (56), Expect = 9.4
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 134 RILLHQPSGGFSGQASDIERHAQDIVKIK 162
++LL PS A+ +ER A ++ ++K
Sbjct: 151 KMLLSPPSKEQQDGATSLERIALELNQLK 179
>gnl|CDD|119339 cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase
superfamily. This superfamily contains a diverse set of
enzymes including enoyl-CoA hydratase, napthoate
synthase, methylmalonyl-CoA decarboxylase,
3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA
isomerase. Many of these play important roles in fatty
acid metabolism. In addition to a conserved structural
core and the formation of trimers (or dimers of
trimers), a common feature in this superfamily is the
stabilization of an enolate anion intermediate derived
from an acyl-CoA substrate. This is accomplished by two
conserved backbone NH groups in active sites that form
an oxyanion hole..
Length = 195
Score = 25.6 bits (57), Expect = 9.6
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 189 IMSASEACDWGVVDKVL 205
+SA EA + G+VD+V+
Sbjct: 163 RISAEEALELGLVDEVV 179
>gnl|CDD|144097 pfam00378, ECH, Enoyl-CoA hydratase/isomerase family. This family
contains a diverse set of enzymes including: Enoyl-CoA
hydratase. Napthoate synthase. Carnitate racemase.
3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA
delta-isomerase.
Length = 169
Score = 25.7 bits (57), Expect = 9.7
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 190 MSASEACDWGVVDKVL 205
+ A EA G+VDKV+
Sbjct: 153 IRAQEALKMGLVDKVV 168
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.135 0.387
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,543,184
Number of extensions: 128765
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 311
Number of HSP's successfully gapped: 28
Length of query: 216
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 126
Effective length of database: 4,318,927
Effective search space: 544184802
Effective search space used: 544184802
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 (21.8 bits)
S2: 55 (25.2 bits)