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)