RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18232
(486 letters)
>gnl|CDD|178955 PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 200
Score = 297 bits (763), Expect = e-100
Identities = 106/227 (46%), Positives = 136/227 (59%), Gaps = 58/227 (25%)
Query: 43 RPLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPI 102
LVP+VIEQT RGER+YDIYSRLL+ERII + G ++D +++++VAQLLFL++E K I
Sbjct: 5 MNLVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEVEDHMANLIVAQLLFLEAEDPDKDI 64
Query: 103 HMYINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRI 162
++YINSPGGSVT+GL IYDTMQ++ P ++T C+GQA SM + LLAAG KG R +LPNSRI
Sbjct: 65 YLYINSPGGSVTAGLAIYDTMQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFALPNSRI 124
Query: 163 MIHQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMI 222
MIHQP GG Q GQA
Sbjct: 125 MIHQPLGGFQ---------------------GQA-------------------------- 137
Query: 223 HQPSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKST 269
TDI+I A EI+ LKK++N + +HTG +EKI K T
Sbjct: 138 -----------TDIEIHAREILKLKKRLNEILAEHTGQPLEKIEKDT 173
Score = 75.6 bits (187), Expect = 8e-16
Identities = 26/36 (72%), Positives = 30/36 (83%)
Query: 379 RPLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPV 414
LVP+VIEQT RGER+YDIYSRLL+ERII + G V
Sbjct: 5 MNLVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEV 40
>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 = 246 bits (631), Expect = 4e-80
Identities = 95/216 (43%), Positives = 127/216 (58%), Gaps = 58/216 (26%)
Query: 54 GRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHMYINSPGGSV 113
GER YDIYSRLL+ERII + G IDD ++++++AQLLFL++E K I++YINSPGGSV
Sbjct: 1 SGGERWYDIYSRLLKERIIFLGGEIDDEVANLIIAQLLFLEAEDPDKDIYLYINSPGGSV 60
Query: 114 TSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQV 173
T+GL IYDTMQ++ P ++T C+G A SM S +LAAG KG R +LPN+RIMIHQPSGG Q
Sbjct: 61 TAGLAIYDTMQFIKPDVSTICLGLAASMGSFILAAGTKGKRFALPNARIMIHQPSGGAQ- 119
Query: 174 GLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQGQA 233
GQA
Sbjct: 120 --------------------GQA------------------------------------- 122
Query: 234 TDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKST 269
+DI+IQAEEI+ +++++N +Y +HTG +EKI K
Sbjct: 123 SDIEIQAEEILKIRERLNEIYAEHTGQPLEKIEKDL 158
Score = 46.8 bits (112), Expect = 4e-06
Identities = 16/25 (64%), Positives = 19/25 (76%)
Query: 390 GRGERAYDIYSRLLRERIICVMGPV 414
GER YDIYSRLL+ERII + G +
Sbjct: 1 SGGERWYDIYSRLLKERIIFLGGEI 25
>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 = 242 bits (621), Expect = 1e-78
Identities = 96/207 (46%), Positives = 126/207 (60%), Gaps = 58/207 (28%)
Query: 61 DIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHMYINSPGGSVTSGLGIY 120
DIYSRLL+ERII + GPIDD ++++++AQLL+L+SE KKPI++YINSPGGSVT+GL IY
Sbjct: 1 DIYSRLLKERIIFLGGPIDDEVANLIIAQLLYLESEDPKKPIYLYINSPGGSVTAGLAIY 60
Query: 121 DTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQVGLGIYDT 180
DTMQY+ PP++T C+G A SM +LLLAAG KG R++LPNSRIMIHQP GG
Sbjct: 61 DTMQYIKPPVSTICLGLAASMGALLLAAGTKGKRYALPNSRIMIHQPLGGAG-------- 112
Query: 181 MQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQGQATDIQIQA 240
GQA +DI+IQA
Sbjct: 113 -------------GQA-------------------------------------SDIEIQA 122
Query: 241 EEIINLKKQINGLYVKHTGLSIEKIGK 267
+EI+ L++++N + KHTG +EKI K
Sbjct: 123 KEILRLRRRLNEILAKHTGQPLEKIEK 149
Score = 37.4 bits (88), Expect = 0.005
Identities = 13/18 (72%), Positives = 16/18 (88%)
Query: 397 DIYSRLLRERIICVMGPV 414
DIYSRLL+ERII + GP+
Sbjct: 1 DIYSRLLKERIIFLGGPI 18
>gnl|CDD|223811 COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases
[Posttranslational modification, protein turnover,
chaperones / Intracellular trafficking and secretion].
Length = 200
Score = 242 bits (620), Expect = 2e-78
Identities = 106/227 (46%), Positives = 141/227 (62%), Gaps = 58/227 (25%)
Query: 43 RPLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPI 102
LVP+VIEQT RGER+YDIYSRLL+ERII + G I+D +++++VAQLLFL++E K I
Sbjct: 1 MALVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEIEDHMANLIVAQLLFLEAEDPDKDI 60
Query: 103 HMYINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRI 162
++YINSPGGSVT+GL IYDTMQ++ PP++T C+GQA SM S+LL AG+KG R +LPN+RI
Sbjct: 61 YLYINSPGGSVTAGLAIYDTMQFIKPPVSTICMGQAASMGSVLLMAGDKGKRFALPNARI 120
Query: 163 MIHQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMI 222
MIHQPSGG Q GQA
Sbjct: 121 MIHQPSGGAQ---------------------GQA-------------------------- 133
Query: 223 HQPSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKST 269
+DI+I A EI+ +K+++N +Y +HTG ++EKI K T
Sbjct: 134 -----------SDIEIHAREILKIKERLNRIYAEHTGQTLEKIEKDT 169
Score = 60.3 bits (147), Expect = 1e-10
Identities = 25/36 (69%), Positives = 30/36 (83%)
Query: 379 RPLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPV 414
LVP+VIEQT RGER+YDIYSRLL+ERII + G +
Sbjct: 1 MALVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEI 36
>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 = 230 bits (589), Expect = 8e-74
Identities = 104/225 (46%), Positives = 137/225 (60%), Gaps = 58/225 (25%)
Query: 45 LVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHM 104
L+P VIEQTGRGER++DIYSRLL+ERII + G ++D++++ +VAQLLFL++E +K I++
Sbjct: 3 LIPTVIEQTGRGERSFDIYSRLLKERIIFLSGEVNDNVANSIVAQLLFLEAEDPEKDIYL 62
Query: 105 YINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMI 164
YINSPGGS+T+GL IYDTMQ++ P ++T C+GQA SM + LLAAG KG R SLPNSRIMI
Sbjct: 63 YINSPGGSITAGLAIYDTMQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFSLPNSRIMI 122
Query: 165 HQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQ 224
HQP GG Q GQA
Sbjct: 123 HQPLGGAQ---------------------GQA---------------------------- 133
Query: 225 PSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKST 269
TDI+IQA EI+ LK +N + +HTG S+E+I + T
Sbjct: 134 ---------TDIEIQANEILRLKGLLNDILAEHTGQSLEQIERDT 169
Score = 64.8 bits (158), Expect = 4e-12
Identities = 25/34 (73%), Positives = 30/34 (88%)
Query: 381 LVPIVIEQTGRGERAYDIYSRLLRERIICVMGPV 414
L+P VIEQTGRGER++DIYSRLL+ERII + G V
Sbjct: 3 LIPTVIEQTGRGERSFDIYSRLLKERIIFLSGEV 36
>gnl|CDD|237133 PRK12553, PRK12553, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 207
Score = 215 bits (550), Expect = 1e-67
Identities = 85/230 (36%), Positives = 124/230 (53%), Gaps = 60/230 (26%)
Query: 42 SRPLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKP 101
SR ++P IE+T G + D Y++L ERII + G +DD+ ++ V+AQLL L+S +
Sbjct: 8 SRYILPSFIERTSYGVKESDPYNKLFEERIIFLGGQVDDASANDVMAQLLVLESIDPDRD 67
Query: 102 IHMYINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSR 161
I +YINSPGGSVT+G IYDT+Q++ P + T C GQA S ++LLAAG G R +LPN+R
Sbjct: 68 ITLYINSPGGSVTAGDAIYDTIQFIRPDVQTVCTGQAASAGAVLLAAGTPGKRFALPNAR 127
Query: 162 IMIHQPS--GGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSR 219
I+IHQPS GG++ GQA
Sbjct: 128 ILIHQPSLGGGIR---------------------GQA----------------------- 143
Query: 220 IMIHQPSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKST 269
+D++IQA EI+ +++++ + +HTG S+EKI K T
Sbjct: 144 --------------SDLEIQAREILRMRERLERILAEHTGQSVEKIRKDT 179
Score = 39.2 bits (92), Expect = 0.002
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 378 SRPLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPV 414
SR ++P IE+T G + D Y++L ERII + G V
Sbjct: 8 SRYILPSFIERTSYGVKESDPYNKLFEERIIFLGGQV 44
>gnl|CDD|139060 PRK12551, PRK12551, ATP-dependent Clp protease proteolytic subunit;
Reviewed.
Length = 196
Score = 197 bits (503), Expect = 6e-61
Identities = 98/225 (43%), Positives = 131/225 (58%), Gaps = 58/225 (25%)
Query: 45 LVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHM 104
++PIVIE++GRGERA+DIYSRLLRERII + P+ ++ +VAQLLFL++E +K I++
Sbjct: 1 MIPIVIEESGRGERAFDIYSRLLRERIIFLGEPVTSDSANRIVAQLLFLEAEDPEKDIYL 60
Query: 105 YINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMI 164
YINSPGGS +YD
Sbjct: 61 YINSPGGS------VYD------------------------------------------- 71
Query: 165 HQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQ 224
GLGI+DTMQ+V P + T CVG A SM + LL AG KG R SL +SRIMIHQ
Sbjct: 72 ---------GLGIFDTMQHVKPDVHTVCVGLAASMGAFLLCAGAKGKRSSLQHSRIMIHQ 122
Query: 225 PSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKST 269
P GG +GQA+DI+IQA+EI+ LK+++N + TG +E+I + T
Sbjct: 123 PLGGARGQASDIRIQADEILFLKERLNTELSERTGQPLERIQEDT 167
Score = 62.5 bits (152), Expect = 2e-11
Identities = 25/35 (71%), Positives = 32/35 (91%)
Query: 381 LVPIVIEQTGRGERAYDIYSRLLRERIICVMGPVS 415
++PIVIE++GRGERA+DIYSRLLRERII + PV+
Sbjct: 1 MIPIVIEESGRGERAFDIYSRLLRERIIFLGEPVT 35
>gnl|CDD|237742 PRK14513, PRK14513, ATP-dependent Clp protease proteolytic subunit;
Provisional.
Length = 201
Score = 190 bits (483), Expect = 5e-58
Identities = 90/222 (40%), Positives = 123/222 (55%), Gaps = 58/222 (26%)
Query: 44 PLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIH 103
++P VIEQTGRGER YDIYSRLL++RII V PI+ +++ +VAQLL L S++ ++ I
Sbjct: 2 SVIPYVIEQTGRGERMYDIYSRLLKDRIIFVGTPIESQMANTIVAQLLLLDSQNPEQEIQ 61
Query: 104 MYINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIM 163
MYIN PGG V +GL IYDTM+Y+ P++T CVG A SM S+LL AG+KG R +LPNSRIM
Sbjct: 62 MYINCPGGEVYAGLAIYDTMRYIKAPVSTICVGIAMSMGSVLLMAGDKGKRMALPNSRIM 121
Query: 164 IHQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIH 223
IHQ G G R + P
Sbjct: 122 IHQ----------------------------------------GSAGFRGNTP------- 134
Query: 224 QPSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKI 265
D+++QA+E++ L+ + +Y +HT L EK+
Sbjct: 135 -----------DLEVQAKEVLFLRDTLVDIYHRHTDLPHEKL 165
Score = 62.3 bits (151), Expect = 3e-11
Identities = 24/35 (68%), Positives = 29/35 (82%)
Query: 380 PLVPIVIEQTGRGERAYDIYSRLLRERIICVMGPV 414
++P VIEQTGRGER YDIYSRLL++RII V P+
Sbjct: 2 SVIPYVIEQTGRGERMYDIYSRLLKDRIIFVGTPI 36
>gnl|CDD|214340 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit.
Length = 200
Score = 171 bits (436), Expect = 7e-51
Identities = 51/110 (46%), Positives = 78/110 (70%)
Query: 61 DIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHMYINSPGGSVTSGLGIY 120
D+Y+RL RER++ + +DD +++ ++ +++L E K ++++INSPGGSV SGL IY
Sbjct: 22 DLYNRLYRERLLFLGQEVDDEIANQLIGLMVYLSIEDDTKDLYLFINSPGGSVISGLAIY 81
Query: 121 DTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGG 170
DTMQ+V P + T C+G A SMAS +LA GE R + P++R+MIHQP+
Sbjct: 82 DTMQFVKPDVHTICLGLAASMASFILAGGEITKRLAFPHARVMIHQPASS 131
Score = 137 bits (348), Expect = 3e-38
Identities = 46/105 (43%), Positives = 69/105 (65%), Gaps = 1/105 (0%)
Query: 164 IHQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIH 223
I+ P G V GL IYDTMQ+V P + T C+G A SMAS +LA GE R + P++R+MIH
Sbjct: 67 INSPGGSVISGLAIYDTMQFVKPDVHTICLGLAASMASFILAGGEITKRLAFPHARVMIH 126
Query: 224 QPSGG-VQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGK 267
QP+ +GQA++ ++AEE++ L++ I +Y + TG + I +
Sbjct: 127 QPASSFYEGQASEFVLEAEELLKLRETITRVYAQRTGKPLWVISE 171
Score = 28.7 bits (65), Expect = 5.1
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 397 DIYSRLLRERIICVMGPV 414
D+Y+RL RER++ + V
Sbjct: 22 DLYNRLYRERLLFLGQEV 39
>gnl|CDD|184722 PRK14514, PRK14514, ATP-dependent Clp protease proteolytic subunit;
Provisional.
Length = 221
Score = 152 bits (385), Expect = 2e-43
Identities = 82/223 (36%), Positives = 111/223 (49%), Gaps = 58/223 (26%)
Query: 45 LVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHM 104
L P ++E+ D++SRL+ +RII + IDD ++ + AQLL+L S K I +
Sbjct: 30 LNPYILEERQLNVTQMDVFSRLMMDRIIFLGTQIDDYTANTIQAQLLYLDSVDPGKDISI 89
Query: 105 YINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMI 164
YINSPGGSV +GLGIYDTMQ++ +AT C G A SMAS+LL AG KG R +LP+SR+MI
Sbjct: 90 YINSPGGSVYAGLGIYDTMQFISSDVATICTGMAASMASVLLVAGTKGKRSALPHSRVMI 149
Query: 165 HQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQ 224
HQP GG Q GQA
Sbjct: 150 HQPLGGAQ---------------------GQA---------------------------- 160
Query: 225 PSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGK 267
+DI+I A EI LKK++ + H+G +K+
Sbjct: 161 ---------SDIEITAREIQKLKKELYTIIADHSGTPFDKVWA 194
>gnl|CDD|183588 PRK12552, PRK12552, ATP-dependent Clp protease-like protein;
Reviewed.
Length = 222
Score = 152 bits (385), Expect = 3e-43
Identities = 70/219 (31%), Positives = 112/219 (51%), Gaps = 59/219 (26%)
Query: 61 DIYSRLLRERIICVMGPIDDS----------LSSVVVAQLLFLQSESSKKPIHMYINSPG 110
D+ S LL+ERI+ + P+ ++ +++AQLL+L+ + +KPI+ YINS G
Sbjct: 22 DLPSLLLKERIVYLGLPLFSDDDAKRQVGMDVTELIIAQLLYLEFDDPEKPIYFYINSTG 81
Query: 111 GSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGG 170
S W G A + A
Sbjct: 82 TS--------------------WYTGDAIGFETEAFA----------------------- 98
Query: 171 VQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQ 230
I DTM+Y+ PP+ T C+GQA A+++L+AG KG R SLP++ I++HQP G +
Sbjct: 99 ------ICDTMRYIKPPVHTICIGQAMGTAAMILSAGTKGQRASLPHATIVLHQPRSGAR 152
Query: 231 GQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKST 269
GQATDIQI+A+E+++ K+ + + ++TG ++EK+ K T
Sbjct: 153 GQATDIQIRAKEVLHNKRTMLEILSRNTGQTVEKLSKDT 191
>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 = 128 bits (322), Expect = 5e-35
Identities = 56/196 (28%), Positives = 85/196 (43%), Gaps = 58/196 (29%)
Query: 70 RIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHMYINSPGGSVTSGLGIYDTMQYVLPP 129
R I + G ++D ++ AQLLFL + + +K I++YINSPGG V +G+ IYDT++++
Sbjct: 1 REIMLTGEVEDISANQFAAQLLFLGAVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIKAD 60
Query: 130 IATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQVGLGIYDTMQYVLPPIA 189
+ T G A SM S++ AG KG R LPN+ +MIHQP GG
Sbjct: 61 VVTIIDGLAASMGSVIAMAGAKGKRFILPNAMMMIHQPWGGTL----------------- 103
Query: 190 TWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQGQATDIQIQAEEIINLKKQ 249
G A M I A+ ++ ++
Sbjct: 104 ----GDATDMR-------------------------------------IYADLLLKVEGN 122
Query: 250 INGLYVKHTGLSIEKI 265
+ Y TG S E++
Sbjct: 123 LVSAYAHKTGQSEEEL 138
>gnl|CDD|237741 PRK14512, PRK14512, ATP-dependent Clp protease proteolytic subunit;
Provisional.
Length = 197
Score = 105 bits (264), Expect = 2e-26
Identities = 46/117 (39%), Positives = 72/117 (61%), Gaps = 3/117 (2%)
Query: 65 RLLRERIICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHMYINSPGGSVTSGLGIYDTMQ 124
+ L+ R I + G I+ LS + ++L L++ SKKPI +YI+S GG + +G I++ ++
Sbjct: 19 KFLKSRSIVIAGEINKDLSELFQEKILLLEALDSKKPIFVYIDSEGGDIDAGFAIFNMIR 78
Query: 125 YVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQP-SG--GVQVGLGIY 178
+V P + T VG S A+L+ A +K R SLPN+R ++HQP SG GV + IY
Sbjct: 79 FVKPKVFTIGVGLVASAAALIFLAAKKESRFSLPNARYLLHQPLSGFKGVATDIEIY 135
Score = 99.5 bits (248), Expect = 3e-24
Identities = 49/149 (32%), Positives = 77/149 (51%), Gaps = 9/149 (6%)
Query: 162 IMIHQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIM 221
+ I G + G I++ +++V P + T VG S A+L+ A +K R SLPN+R +
Sbjct: 58 VYIDSEGGDIDAGFAIFNMIRFVKPKVFTIGVGLVASAAALIFLAAKKESRFSLPNARYL 117
Query: 222 IHQPSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKIGKSTVCFYVLHDPYIC 281
+HQP G +G ATDI+I A E+ +K ++N + K TG ++K+ K T D
Sbjct: 118 LHQPLSGFKGVATDIEIYANELNKVKSELNDIIAKETGQELDKVEKDTD-----RD---- 168
Query: 282 FWINGLYVKHTGLSIEKIGKSTNLTEELS 310
FW++ GL E + L E +S
Sbjct: 169 FWLDSSSAVKYGLVFEVVETRLELEEFIS 197
>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 = 92.1 bits (229), Expect = 6e-22
Identities = 32/102 (31%), Positives = 53/102 (51%), Gaps = 2/102 (1%)
Query: 71 IICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHMYINSPGGSVTSGLGIYDTMQYVLPPI 130
+I + G I+D + + AQ+ F ++++S K I + +N+PGG V +G+ I D +Q P+
Sbjct: 1 VIFINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQASRKPV 60
Query: 131 ATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQ 172
+ GQA S + A K P +R+ H P GG
Sbjct: 61 IAYVGGQAASAGYYIATAANK--IVMAPGTRVGSHGPIGGYG 100
Score = 65.9 bits (161), Expect = 7e-13
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 4/104 (3%)
Query: 164 IHQPSGGVQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIH 223
++ P G V G+ I D +Q P+ + GQA S + A K P +R+ H
Sbjct: 36 VNTPGGRVDAGMNIVDALQASRKPVIAYVGGQAASAGYYIATAANK--IVMAPGTRVGSH 93
Query: 224 QPSGGVQGQA--TDIQIQAEEIINLKKQINGLYVKHTGLSIEKI 265
P GG G T + I+ + L ++ G + EK+
Sbjct: 94 GPIGGYGGNGNPTAQEADQRIILYFIARFISLVAENRGQTTEKL 137
>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 = 74.5 bits (184), Expect = 7e-16
Identities = 29/81 (35%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 92 FLQSESSKKPIHMYINSPGGSVTSGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEK 151
L + I + INSPGG V +GL IY+ ++ + G A S AS++ AG++
Sbjct: 23 ALDALGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIAMAGDE 82
Query: 152 -GMRHSLPNSRIMIHQPSGGV 171
M PN+ +MIH PS G
Sbjct: 83 VEMP---PNAMLMIHNPSTGA 100
Score = 71.0 bits (175), Expect = 1e-14
Identities = 37/110 (33%), Positives = 57/110 (51%), Gaps = 6/110 (5%)
Query: 159 NSRIMIHQPSGG--VQVGLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEK-GMRHSL 215
+S I + S G V GL IY+ ++ + G A S AS++ AG++ M
Sbjct: 30 DSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIAMAGDEVEMP--- 86
Query: 216 PNSRIMIHQPSGGVQGQATDIQIQAEEIINLKKQINGLYVKHTGLSIEKI 265
PN+ +MIH PS G G A D++ A+ + + + I Y + TGLS E+I
Sbjct: 87 PNAMLMIHNPSTGAAGNADDLRKAADLLDKIDESIANAYAEKTGLSEEEI 136
>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 = 31.4 bits (72), Expect = 0.69
Identities = 28/96 (29%), Positives = 44/96 (45%), Gaps = 11/96 (11%)
Query: 71 IICVMGPIDDSLSSVVVAQLLFLQSESSK---KPIHMYINSPGGSVTSGLGIYDTMQYVL 127
+I + G ID L++ V L E+ + + + I++PGG V S L I D +
Sbjct: 3 VIPIEGEIDPGLAAFVERAL----KEAKEEGADAVVLDIDTPGGRVDSALEIVDLILNSP 58
Query: 128 PPIATWCVGQACSMASLL-LAAGEKGMRHSLPNSRI 162
P + +A S +L+ LAA E M P + I
Sbjct: 59 IPTIAYVNDRAASAGALIALAADEIYMA---PGATI 91
>gnl|CDD|213553 TIGR00706, SppA_dom, signal peptide peptidase SppA, 36K type. The
related but duplicated, double-length protein SppA
(protease IV) of E. coli was shown experimentally to
degrade signal peptides as are released by protein
processing and secretion. This protein shows stronger
homology to the C-terminal region of SppA than to the
N-terminal domain or to the related putative protease
SuhB. The member of this family from Bacillus subtilis
was shown to have properties consistent with a role in
degrading signal peptides after cleavage from precursor
proteins, although it was not demonstrated conclusively
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 208
Score = 30.4 bits (69), Expect = 1.6
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 2/89 (2%)
Query: 71 IICVMGPIDDSLSSVVVAQLLFLQSESSKKPIHMYINSPGGSVTSGLGIYDTMQYV--LP 128
++ V G I D + +L ++ + + K + + INSPGG+V + IY ++ +
Sbjct: 4 VLEVSGAIADVSPEDFLKKLERIKDDKTIKALVLRINSPGGTVVASEEIYKKLEKLKAKK 63
Query: 129 PIATWCVGQACSMASLLLAAGEKGMRHSL 157
P+ G A S + A ++ +
Sbjct: 64 PVVASMGGMAASGGYYISMAADEIFANPG 92
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 30.6 bits (69), Expect = 2.0
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 174 GLGIYDTMQYVLPPIATWCVGQACSMASLLLAAGEKGMRHSLPNSRIMIHQPSGGVQGQA 233
G G YD++ + L T VG A + LLL A + + LP I ++ + G++ Q
Sbjct: 283 GGGRYDSLIHQLGGPKTPAVGCAIGLERLLLIAKDNII---LPKQSIDVYIATQGLKAQK 339
Query: 234 TDIQI-QAEEIINLKKQIN 251
+I Q E N+K +++
Sbjct: 340 KGWEIIQFLEKQNIKFELD 358
>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 = 29.8 bits (68), Expect = 2.2
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 71 IICVMGPIDDSLSSV---VVAQLLFLQSESSKKPIHMYINSPGGSVT-SGLGIYD 121
+I + G I D ++ QL + + S K + + INSPGGSV S IY
Sbjct: 4 VIDIEGTISDGGGIGADSLIEQLRKAREDDSVKAVVLRINSPGGSVVASEE-IYR 57
>gnl|CDD|147485 pfam05323, Pox_A21, Poxvirus A21 Protein. This family consists of
several poxvirus A21 proteins.
Length = 111
Score = 28.8 bits (65), Expect = 2.4
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 381 LVPIVIEQTGRGERAYDIYSRLLRERIICVMGPVSLY 417
+VP + E+ R A+D Y L ++ ICV + Y
Sbjct: 18 IVPAISEKLRREYDAFDKYKN-LGKKFICVDDRLFSY 53
Score = 27.7 bits (62), Expect = 5.7
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 45 LVPIVIEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSS 84
+VP + E+ R A+D Y L ++ ICV DD L S
Sbjct: 18 IVPAISEKLRREYDAFDKYKN-LGKKFICV----DDRLFS 52
>gnl|CDD|218353 pfam04963, Sigma54_CBD, Sigma-54 factor, core binding domain. This
domain makes a direct interaction with the core RNA
polymerase, to form an enhancer dependent holoenzyme.
The centre of this domain contains a very weak
similarity to a helix-turn-helix motif which may
represent the other DNA binding domain.
Length = 195
Score = 29.9 bits (68), Expect = 2.4
Identities = 17/34 (50%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 450 LCEQLSLDDISCEERSITLLALILALYPYGYIQI 483
L EQL L S +R I L ALI AL GY+Q
Sbjct: 21 LLEQLELAPFSDADRLIAL-ALIDALDDTGYLQA 53
>gnl|CDD|223689 COG0616, SppA, Periplasmic serine proteases (ClpP class)
[Posttranslational modification, protein turnover,
chaperones / Intracellular trafficking and secretion].
Length = 317
Score = 29.3 bits (66), Expect = 4.6
Identities = 24/98 (24%), Positives = 37/98 (37%), Gaps = 14/98 (14%)
Query: 37 HSATLSRPLVPIVIEQTGRGERAYDIYSRLLRER------IICVMGPIDDSLSSV----- 85
+L L P + +R LLR+R +I V G I +
Sbjct: 24 WLLSLILLLAPTLKAVGLLAKRLGK-LEALLRKRGSKVIAVIHVEGAIVAGGGPLRFIGG 82
Query: 86 --VVAQLLFLQSESSKKPIHMYINSPGGSVTSGLGIYD 121
+ L +++ S K + + INSPGGSV + I
Sbjct: 83 DDIEEILRAARADPSVKAVVLRINSPGGSVVASELIAR 120
>gnl|CDD|188076 TIGR00720, sda_mono, L-serine dehydratase, iron-sulfur-dependent,
single chain form. This enzyme is also called serine
deaminase and L-serine dehydratase 1. L-serine
ammonia-lyase converts serine into pyruvate in the
gluconeogenesis pathway from serine. This enzyme is
comprised of a single chain in Escherichia coli,
Mycobacterium tuberculosis, and several other species,
but has separate alpha and beta chains in Bacillus
subtilis and related species. The beta and alpha chains
are homologous to the N-terminal and C-terminal regions,
respectively, but are rather deeply branched in a UPGMA
tree. This enzyme requires iron and dithiothreitol for
activation in vitro, and is a predicted 4Fe-4S protein.
Escherichia coli Pseudomonas aeruginosa have two copies
of this protein [Energy metabolism, Amino acids and
amines, Energy metabolism, Glycolysis/gluconeogenesis].
Length = 450
Score = 29.2 bits (66), Expect = 4.8
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 17/52 (32%)
Query: 135 VGQACSMASLLLA------------AGEKGMRHSLPNSRIMIHQPSGG-VQV 173
VG ACSMA+ LA A E M H+L + P GG VQ+
Sbjct: 342 VGVACSMAAAGLAELLGGTPEQVENAAEIAMEHNLG----LTCDPVGGLVQI 389
Score = 29.2 bits (66), Expect = 6.0
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 12/35 (34%)
Query: 193 VGQACSMASLLLA------------AGEKGMRHSL 215
VG ACSMA+ LA A E M H+L
Sbjct: 342 VGVACSMAAAGLAELLGGTPEQVENAAEIAMEHNL 376
>gnl|CDD|233097 TIGR00705, SppA_67K, signal peptide peptidase SppA, 67K type. This
model represents the signal peptide peptidase A (SppA,
protease IV) as found in E. coli, Treponema pallidum,
Mycobacterium leprae, and several other species, in
which it has a molecular mass around 67 kDa and a
duplication such that the N-terminal half shares
extensive homology with the C-terminal half. This enzyme
was shown in E. coli to form homotetramers. E. coli
SohB, which is most closely homologous to the C-terminal
duplication of SppA, is predicted to perform a similar
function of small peptide degradation, but in the
periplasm. Many prokaryotes have a single SppA/SohB
homolog that may perform the function of either or both
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 584
Score = 29.4 bits (66), Expect = 5.4
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 15/71 (21%)
Query: 60 YDIYSRLLRER--------IICVMGPIDD-------SLSSVVVAQLLFLQSESSKKPIHM 104
D Y+R +R I+ + GPI D + V A L +S+ K + +
Sbjct: 293 LDDYNRDRPQRHDVQDKIGIVHLEGPIADGRDTEGNTGGDTVAALLRVARSDPDIKAVVL 352
Query: 105 YINSPGGSVTS 115
INSPGGSV +
Sbjct: 353 RINSPGGSVFA 363
>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 = 28.9 bits (65), Expect = 5.9
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 203 LLAAGEKGMRHSLPNSRIMIHQPSGGVQGQ 232
LL +G ++ P ++MIH +G G
Sbjct: 155 LLNSGYWAVKDVNPTIKVMIHLDNGEDNGT 184
>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 = 28.3 bits (64), Expect = 6.9
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 106 INSPGGSVTSGLGIYDTMQYV-----LPPIATWCVGQACSMASLLLAA 148
I+SPGG V G+++ + PI + G A S A + +A
Sbjct: 50 IDSPGGEVA---GVFELADAIRAARAGKPIVAFVNGLAASAAYWIASA 94
>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
Putative enoyl reductase of polyketide synthase.
Polyketide synthases produce polyketides in step by step
mechanism that is similar to fatty acid synthesis. Enoyl
reductase reduces a double to single bond. Erythromycin
is one example of a polyketide generated by 3 complex
enzymes (megasynthases). 2-enoyl thioester reductase
(ETR) catalyzes the NADPH-dependent dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding.
Length = 293
Score = 28.3 bits (64), Expect = 9.7
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 216 PNSRIMIHQPSGGVQGQATDIQI 238
++IH +GGV GQA IQ+
Sbjct: 108 KGESVLIHAAAGGV-GQAA-IQL 128
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
0.324 0.139 0.423
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,414,212
Number of extensions: 2380434
Number of successful extensions: 2395
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2384
Number of HSP's successfully gapped: 57
Length of query: 486
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 385
Effective length of database: 6,457,848
Effective search space: 2486271480
Effective search space used: 2486271480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 61 (27.3 bits)