RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780747|ref|YP_003065160.1| putative protease IV
transmembrane protein [Candidatus Liberibacter asiaticus str. psy62]
         (293 letters)



>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 =  220 bits (562), Expect = 4e-58
 Identities = 77/202 (38%), Positives = 127/202 (62%), Gaps = 6/202 (2%)

Query: 37  HVARIAIRGQIED-----SQELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQ 91
            +A I I G I D     +  LIE++ +   DDS  A+++ ++SPGGS  A E I+R I+
Sbjct: 1   KIAVIDIEGTISDGGGIGADSLIEQLRKAREDDSVKAVVLRINSPGGSVVASEEIYREIR 60

Query: 92  KVKNR-KPVITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGV 150
           +++   KPV+  + ++AAS GY I+ A++ IVA  T++ GSIGV+ Q P ++  LDKLG+
Sbjct: 61  RLRKAKKPVVASMGDVAASGGYYIAAAADKIVANPTTITGSIGVIGQGPNLEELLDKLGI 120

Query: 151 SIKSVKSSPMKAEPSPFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSDG 210
              ++KS P K + SP   +  +   ++Q +VD  Y  FV +V+E R +  ++   L+DG
Sbjct: 121 ERDTIKSGPGKDKGSPDRPLTEEERAILQALVDDIYDQFVDVVAEGRGMSGERLDKLADG 180

Query: 211 RIWTGAEAKKVGLIDVVGGQEE 232
           R+WTG +A ++GL+D +GG ++
Sbjct: 181 RVWTGRQALELGLVDELGGLDD 202


>gnl|CDD|30961 COG0616, SppA, Periplasmic serine proteases (ClpP class)
           [Posttranslational modification, protein turnover,
           chaperones / Intracellular trafficking and secretion].
          Length = 317

 Score =  183 bits (465), Expect = 6e-47
 Identities = 70/234 (29%), Positives = 122/234 (52%), Gaps = 9/234 (3%)

Query: 32  EDNSPHVARIAIRGQIEDS---------QELIERIERISRDDSATALIVSLSSPGGSAYA 82
           +  S  +A I + G I             ++ E +     D S  A+++ ++SPGGS  A
Sbjct: 55  KRGSKVIAVIHVEGAIVAGGGPLRFIGGDDIEEILRAARADPSVKAVVLRINSPGGSVVA 114

Query: 83  GEAIFRAIQKVKNRKPVITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVK 142
            E I RA+++++ +KPV+  V   AAS GY I+ A++ IVA  +S+ GSIGV+   P  +
Sbjct: 115 SELIARALKRLRAKKPVVVSVGGYAASGGYYIALAADKIVADPSSITGSIGVISGAPNFE 174

Query: 143 PFLDKLGVSIKSVKSSPMKAEPSPFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYD 202
             L+KLGV  + + +   K   SPF  +  +  +++Q  +D +Y  FV  V+E R +  +
Sbjct: 175 ELLEKLGVEKEVITAGEYKDILSPFRPLTEEEREILQKEIDETYDEFVDKVAEGRGLSDE 234

Query: 203 KTLVLSDGRIWTGAEAKKVGLIDVVGGQEEVWQSLYALGVDQSIRKIKDWNPPK 256
               L+ GR+WTG +A ++GL+D +GG ++  +    L   + +  +       
Sbjct: 235 AVDKLATGRVWTGQQALELGLVDELGGLDDAVKDAAELAGVKDVPVVYYLEEKS 288


>gnl|CDD|144805 pfam01343, Peptidase_S49, Peptidase family S49. 
          Length = 154

 Score =  130 bits (330), Expect = 3e-31
 Identities = 51/141 (36%), Positives = 87/141 (61%)

Query: 97  KPVITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVK 156
           KPV+      AAS GY ++ A++ IVA  T++VGSIGV+ Q    +  LDKLGV I +++
Sbjct: 7   KPVVAYAGNYAASGGYYLASAADKIVANPTTIVGSIGVIMQGLNYEGLLDKLGVKIDTIR 66

Query: 157 SSPMKAEPSPFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSDGRIWTGA 216
           +   K   S F  + P+  + +Q ++D +Y  FV+ V+++RN+  D+   +++GR+WTG 
Sbjct: 67  AGEYKDAGSLFRPLTPEEREALQRMLDETYQMFVQKVAKNRNLTVDQVDKIAEGRVWTGQ 126

Query: 217 EAKKVGLIDVVGGQEEVWQSL 237
           +A + GL+D +G  ++    L
Sbjct: 127 QAVEAGLVDELGTLDDAIARL 147


>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 =  116 bits (293), Expect = 8e-27
 Identities = 54/193 (27%), Positives = 93/193 (48%), Gaps = 11/193 (5%)

Query: 51  QELIERIERISRDDSATALIVSLSSPGGSAY----AGEAIFRAIQKVKNRKPVITEVHEM 106
           + +   I     D    A+++ + SPGG         +AI  A    +  KP++  V+ +
Sbjct: 28  EGIAAAIRAALADPDVRAIVLDIDSPGGEVAGVFELADAIRAA----RAGKPIVAFVNGL 83

Query: 107 AASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPSP 166
           AASA Y I+ A++ IV   T+ VGSIGV+  +      L+K G+ +  + +   K + +P
Sbjct: 84  AASAAYWIASAADRIVVTPTAGVGSIGVVASHVDQSKALEKAGLKVTLIFAGAHKVDGNP 143

Query: 167 FSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSD-GRIWTGAEAKKVGLID 225
              ++ +A   +Q  VD+ Y  FV  V+ +R +      V +  G ++ G EA   GL D
Sbjct: 144 DEPLSDEARARLQAEVDALYAMFVAAVARNRGLSAAA--VRATEGGVFRGQEAVAAGLAD 201

Query: 226 VVGGQEEVWQSLY 238
            VG  ++   +L 
Sbjct: 202 AVGTLDDALAALA 214


>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 =  103 bits (259), Expect = 4e-23
 Identities = 58/175 (33%), Positives = 95/175 (54%), Gaps = 2/175 (1%)

Query: 55  ERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNR-KPVITEVHEMAASAGYL 113
            +I     D    A+++ ++SPGGS  A E I   +   +   KPV+      AAS GY 
Sbjct: 28  AQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSAGGAAASGGYW 87

Query: 114 ISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPSPFSEVNPK 173
           IS  +N IVA  ++L GSIG+      V+  LD +GV    V +SP+ A+ S    + P+
Sbjct: 88  ISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPL-ADVSITRALPPE 146

Query: 174 AVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSDGRIWTGAEAKKVGLIDVVG 228
           A   +Q  +++ Y  F+ LV+++R+   ++   ++ G +WTG +AK  GL+D +G
Sbjct: 147 AQLGLQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLG 201


>gnl|CDD|132929 cd07018, S49_SppA_67K_type, Signal peptide peptidase A (SppA) 67K
           type, a serine protease, has catalytic Ser-Lys dyad.
           Signal peptide peptidase A (SppA; Peptidase S49;
           Protease IV) 67K 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
           contain 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. Unlike the eukaryotic functional homologs
           that are proposed to be aspartic proteases,
           site-directed mutagenesis and sequence analysis have
           shown that members in this subfamily, mostly bacterial,
           are 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. 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 = 222

 Score = 91.4 bits (228), Expect = 2e-19
 Identities = 46/190 (24%), Positives = 93/190 (48%), Gaps = 4/190 (2%)

Query: 51  QELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKN-RKPVITEVHEMAAS 109
           ++L+E +E+ + DD    +++ L    G     E + +A+++ +   KPVI    +  + 
Sbjct: 32  RDLLEALEKAAEDDRIKGIVLDLDGLSGGLAKLEELRQALERFRASGKPVIAYA-DGYSQ 90

Query: 110 AGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPSPFSE 169
             Y ++ A++ I    +  V   G+  +  + K  LDKLGV ++  +    K+   PF+ 
Sbjct: 91  GQYYLASAADEIYLNPSGSVELTGLSAETLFFKGLLDKLGVEVQVFRVGEYKSAVEPFTR 150

Query: 170 VN--PKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSDGRIWTGAEAKKVGLIDVV 227
            +  P+A +  Q ++DS +  ++  V+ SR +  D    L D    +  EA + GL+D +
Sbjct: 151 DDMSPEAREQTQALLDSLWDQYLADVAASRGLSPDALEALIDLGGDSAEEALEAGLVDGL 210

Query: 228 GGQEEVWQSL 237
             ++E+   L
Sbjct: 211 AYRDELEARL 220


>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 = 86.3 bits (214), Expect = 1e-17
 Identities = 58/190 (30%), Positives = 84/190 (44%), Gaps = 33/190 (17%)

Query: 41  IAIRGQIED-SQELIERIERISRDD-SATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKP 98
           I I G IED S + +    R +  D S  A+++ +++PGG   AG  I  A+Q    RKP
Sbjct: 2   IFINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQAS--RKP 59

Query: 99  VITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSS 158
           VI  V   AASAGY I+ A+N IV A  + VGS G +  Y                    
Sbjct: 60  VIAYVGGQAASAGYYIATAANKIVMAPGTRVGSHGPIGGYGGNG---------------- 103

Query: 159 PMKAEPSPFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLV-LSDGRIWTGAE 217
                       NP A +  Q ++      F+ LV+E+R    +K    +    + T  E
Sbjct: 104 ------------NPTAQEADQRIILYFIARFISLVAENRGQTTEKLEEDIEKDLVLTAQE 151

Query: 218 AKKVGLIDVV 227
           A + GL+D +
Sbjct: 152 ALEYGLVDAL 161


>gnl|CDD|132925 cd07014, S49_SppA, Signal peptide peptidase A.  Signal peptide
           peptidase A (SppA; Peptidase S49; Protease IV): SppA is
           an intramembrane enzyme 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. Unlike the eukaryotic functional
           homologs that are proposed to be aspartic proteases,
           site-directed mutagenesis and sequence analysis have
           shown these bacterial, archaeal and thylakoid SppAs to
           be ClpP-like serine proteases. The predicted active site
           serine for members in this family occurs in a
           transmembrane domain, cleaving peptide bonds in the
           plane of the lipid bilayer. 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 (sometimes
           referred to as 67K type). Others, including sohB
           peptidase, protein C, protein 1510-N and archaeal signal
           peptide peptidase, do not contain the amino-terminal
           domain (sometimes referred to as 36K type).
           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. This family also contains
           homologs that either have been found experimentally to
           be without peptidase activity, or lack amino acid
           residues that are believed to be essential for the
           catalytic activity of peptidases.
          Length = 177

 Score = 64.6 bits (157), Expect = 3e-11
 Identities = 51/193 (26%), Positives = 85/193 (44%), Gaps = 40/193 (20%)

Query: 48  EDSQELIERIERISRDDSA-TALIVSLSSPGGSAYAGEAIFRAIQKVKN-RKPVITEVHE 105
             S +      R +R D    A+++ ++SPGGS  A E I   +   +   KPV+     
Sbjct: 21  NVSGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVASGGG 80

Query: 106 MAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPS 165
            AAS GY IS  +N IVA  ++LVGSIG+                               
Sbjct: 81  NAASGGYWISTPANYIVANPSTLVGSIGIF------------------------------ 110

Query: 166 PFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLV-LSDGRIWTGAEAKKVGLI 224
                   A Q+    +++ Y  F+ LV+++R+   ++ +  ++ G +WTG +AK  GL+
Sbjct: 111 ----GVQLADQLS---IENGYKRFITLVADNRHSTPEQQIDKIAQGGVWTGQDAKANGLV 163

Query: 225 DVVGGQEEVWQSL 237
           D +G  ++    L
Sbjct: 164 DSLGSFDDAVAKL 176


>gnl|CDD|31233 COG1030, NfeD, Membrane-bound serine protease (ClpP class)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 436

 Score = 53.0 bits (127), Expect = 1e-07
 Identities = 36/125 (28%), Positives = 59/125 (47%), Gaps = 8/125 (6%)

Query: 11  RYVMLSLVTLTVVYFSWSSHVEDNSPHVARIAIRGQIED-SQELIERIERISRDDSATAL 69
           R  ++ L  L +   + S  V      V  I I G I+  S + ++R  + + +++A A+
Sbjct: 3   RAGLIILALLLLALAAPS--VATAEKKVYVIEIDGAIDPASADYLQRALQSAEEENAAAV 60

Query: 70  IVSLSSPGGSAYAGEAIFRAIQKVKNRKPVITEVHE---MAASAGYLISCASNIIVAAET 126
           ++ L +PGG   +   I RAI       PVI  V      AASAG  I  A++I   A  
Sbjct: 61  VLELDTPGGLLDSMRQIVRAILNSPV--PVIGYVVPDGARAASAGTYILMATHIAAMAPG 118

Query: 127 SLVGS 131
           + +G+
Sbjct: 119 TNIGA 123


>gnl|CDD|31083 COG0740, ClpP, Protease subunit of ATP-dependent Clp proteases
           [Posttranslational modification, protein turnover,
           chaperones / Intracellular trafficking and secretion].
          Length = 200

 Score = 50.6 bits (121), Expect = 5e-07
 Identities = 45/195 (23%), Positives = 76/195 (38%), Gaps = 33/195 (16%)

Query: 41  IAIRGQIEDS--QELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKP 98
           I + G+IED     ++ ++  +  +D    + + ++SPGGS  AG AI+  +Q +K   P
Sbjct: 30  IFLGGEIEDHMANLIVAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYDTMQFIK--PP 87

Query: 99  VITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSS 158
           V T     AAS G ++  A            G  G  F  P                 + 
Sbjct: 88  VSTICMGQAASMGSVLLMA------------GDKGKRFALPN----------------AR 119

Query: 159 PMKAEPSPFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSD-GRIWTGAE 217
            M  +PS  ++     +++    +        R+ +E      +K    +D     +  E
Sbjct: 120 IMIHQPSGGAQGQASDIEIHAREILKIKERLNRIYAEHTGQTLEKIEKDTDRDTWMSAEE 179

Query: 218 AKKVGLIDVVGGQEE 232
           AK+ GLID V    E
Sbjct: 180 AKEYGLIDKVIESRE 194


>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 = 50.7 bits (122), Expect = 5e-07
 Identities = 45/200 (22%), Positives = 82/200 (41%), Gaps = 35/200 (17%)

Query: 41  IAIRGQIEDSQE-LIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKPV 99
           I I G+I+      +ER  + ++++ A A+++ + +PGG   +   I   I       P 
Sbjct: 4   IPIEGEIDPGLAAFVERALKEAKEEGADAVVLDIDTPGGRVDSALEIVDLILNS--PIPT 61

Query: 100 ITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSP 159
           I  V++ AASAG LI+ A++ I  A  + +G+   +       P         K    S 
Sbjct: 62  IAYVNDRAASAGALIALAADEIYMAPGATIGAAEPI-------PGDGNGAADEKVQ--SY 112

Query: 160 MKAEPSPFSE---VNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSDGRIWT-- 214
            +A+    +E    +P   + M              V +   +P    + +  G + T  
Sbjct: 113 WRAKMRAAAEKKGRDPDIAEAM--------------VDKDIEVP---GVGIKGGELLTLT 155

Query: 215 GAEAKKVGLID-VVGGQEEV 233
             EA KVG  + + G  +E+
Sbjct: 156 ADEALKVGYAEGIAGSLDEL 175


>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 = 49.5 bits (119), Expect = 1e-06
 Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 6/98 (6%)

Query: 38  VARIAIRGQIED-SQELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNR 96
           V  + I G I   + + +ER    + +  A ALI+ L +PGG   +   I +AI    + 
Sbjct: 1   VYVLEINGAITPATADYLERAIDQAEEGGADALIIELDTPGGLLDSTREIVQAIL--ASP 58

Query: 97  KPVITEVH---EMAASAGYLISCASNIIVAAETSLVGS 131
            PV+  V+     AASAG  I  A++I   A  + +G+
Sbjct: 59  VPVVVYVYPSGARAASAGTYILLAAHIAAMAPGTNIGA 96


>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 = 48.7 bits (117), Expect = 2e-06
 Identities = 43/209 (20%), Positives = 73/209 (34%), Gaps = 65/209 (31%)

Query: 51  QELIERIERISRDDSATALIVS--------------LSSPGGSAYAGEAIFRAIQKV--- 93
            EL   ++    D     ++++              L++   +     A  R +Q++   
Sbjct: 29  DELAAALDEAEADPDVRVVVLTGAGKAFCAGADLKELAALSDAGEEARAFIRELQELLRA 88

Query: 94  --KNRKPVITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVS 151
             +  KPVI  V+  A   G  ++ A +I +AAE +        F  P V     KLG+ 
Sbjct: 89  LLRLPKPVIAAVNGAALGGGLELALACDIRIAAEDA-------KFGLPEV-----KLGLV 136

Query: 152 IKSVKSSPMKAEPSPFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVLSDGR 211
                       P                          RLV  +R     + L+L+ GR
Sbjct: 137 ------------PGG-----------------GGTQRLPRLVGPARA----RELLLT-GR 162

Query: 212 IWTGAEAKKVGLIDVVGGQEEVWQSLYAL 240
             +  EA ++GL+D V   EE+  +   L
Sbjct: 163 RISAEEALELGLVDEVVPDEELLAAALEL 191


>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 = 47.8 bits (113), Expect = 4e-06
 Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 6/105 (5%)

Query: 38  VARIAIRGQIEDSQE-LIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNR 96
           V    I+GQI        +R   I+  D+A A+I+ L +PGG A A   I + IQ+ K  
Sbjct: 1   VYVAQIKGQITSYTYDQFDRYITIAEQDNAEAIIIELDTPGGRADAAGNIVQRIQQSK-- 58

Query: 97  KPVITEVH---EMAASAGYLISCASNIIVAAETSLVGSIGVLFQY 138
            PVI  V+     AASAG  I+  S++I  A  + +G+   +  Y
Sbjct: 59  IPVIIYVYPPGASAASAGTYIALGSHLIAMAPGTSIGACRPILGY 103


>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 = 46.8 bits (112), Expect = 7e-06
 Identities = 24/93 (25%), Positives = 47/93 (50%), Gaps = 10/93 (10%)

Query: 41  IAIRGQIEDS-----QELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKN 95
           I I G I        +E  + ++ +  D     + V ++SPGG  +AG AI+ A+++ K 
Sbjct: 3   IYIYGDIGSDWGVTAKEFKDALDALGDDSD---ITVRINSPGGDVFAGLAIYNALKRHKG 59

Query: 96  RKPVITEVHEMAASAGYLISCASNIIVAAETSL 128
           +  V  ++  +AASA  +I+ A + +     ++
Sbjct: 60  K--VTVKIDGLAASAASVIAMAGDEVEMPPNAM 90


>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 = 43.7 bits (103), Expect = 7e-05
 Identities = 42/141 (29%), Positives = 72/141 (51%), Gaps = 19/141 (13%)

Query: 47  IEDSQELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKPVITEVHEM 106
           IEDS+E++  I R++  D    LI+   +PGG A A   I +A+++ K +  VI  V   
Sbjct: 75  IEDSEEILRAI-RLTPKDMPIDLIIH--TPGGLALAATQIAKALKEHKAKTTVI--VPHY 129

Query: 107 AASAGYLISCASNIIVAAETSLVGSIG-VLFQYPYVKPFLDKLGVSIKSV--KSSPMKAE 163
           A S G LI+ A++ I+  E +++G +   + QYP           SI     K  P K +
Sbjct: 130 AMSGGTLIALAADEIIMDENAVLGPVDPQIGQYP---------AASILKAVEKKGPKKID 180

Query: 164 PSPF--SEVNPKAVQMMQDVV 182
                 ++++ KA++ M++ V
Sbjct: 181 DQTLILADISKKAIKQMEEFV 201


>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 = 39.8 bits (94), Expect = 9e-04
 Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 75  SPGGSAYAGEAIFRAIQKVKNRKPVITEVHEMAASAGYLISCA 117
           SPGGS  AG AI+  +Q +K    V T    +AAS G  +  A
Sbjct: 55  SPGGSVTAGLAIYDTMQFIKP--DVSTICLGLAASMGSFLLAA 95


>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 = 39.0 bits (92), Expect = 0.001
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 73  LSSPGGSAYAGEAIFRAIQKVKNRKPVITEVHEMAASAGYLISCA 117
           ++SPGGS  AG AI+  +Q +K   PV T    +AAS G L+  A
Sbjct: 46  INSPGGSVTAGLAIYDTMQYIKP--PVSTICLGLAASMGALLLAA 88


>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 = 38.4 bits (89), Expect = 0.002
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 4/81 (4%)

Query: 39  ARIAIRGQIED--SQELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNR 96
             I + G++ED  + +   ++  +   +    + + ++SPGG  +AG AI+  I+ +K  
Sbjct: 1   REIMLTGEVEDISANQFAAQLLFLGAVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIK-- 58

Query: 97  KPVITEVHEMAASAGYLISCA 117
             V+T +  +AAS G +I+ A
Sbjct: 59  ADVVTIIDGLAASMGSVIAMA 79


>gnl|CDD|31227 COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid
           metabolism].
          Length = 257

 Score = 37.4 bits (86), Expect = 0.005
 Identities = 24/103 (23%), Positives = 39/103 (37%), Gaps = 22/103 (21%)

Query: 48  EDSQELIERIERISRDDSATALIVSLSSPGGSAYAG---------------EAIFRAIQK 92
           E   EL E ++    D     ++  L+  G +  AG               E + +  Q 
Sbjct: 32  EMLDELAEALDEAEADPDVRVVV--LTGAGKAFSAGADLKELLSPEDGNAAENLMQPGQD 89

Query: 93  VKNR-----KPVITEVHEMAASAGYLISCASNIIVAAETSLVG 130
           +        KPVI  V+  A   G  ++ A +I +AAE +  G
Sbjct: 90  LLRALADLPKPVIAAVNGYALGGGLELALACDIRIAAEDAKFG 132


>gnl|CDD|73197 cd00347, Flavin_utilizing_monoxygenases, Flavin-utilizing
           monoxygenases.
          Length = 90

 Score = 36.9 bits (85), Expect = 0.007
 Identities = 21/91 (23%), Positives = 32/91 (35%), Gaps = 8/91 (8%)

Query: 25  FSWSSHVEDNSPHVARIAIRGQIEDSQELIERIERISRDDSATALIVSLSSPGGSAYAGE 84
           F             A   +        EL    ER+  D +  A+    SSP  +  AGE
Sbjct: 3   FGLFLPPPGGGGATAAEDLE----YLVELARLAERLGFDAAWVAIWFGGSSPPVAEQAGE 58

Query: 85  A----IFRAIQKVKNRKPVITEVHEMAASAG 111
           +    +F A +  +     +    E AA+AG
Sbjct: 59  SGDGLLFAAREPPEEVAEALARYREAAAAAG 89


>gnl|CDD|36058 KOG0840, KOG0840, KOG0840, ATP-dependent Clp protease, proteolytic
           subunit [Posttranslational modification, protein
           turnover, chaperones].
          Length = 275

 Score = 36.5 bits (84), Expect = 0.009
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 41  IAIRGQIED--SQELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKP 98
           + +   I+D  +  +I ++  +  +D    + + ++SPGGS  AG AI+  +Q +K    
Sbjct: 95  VFLGQPIDDDVANLVIAQLLYLDSEDPKKPIYLYINSPGGSVTAGLAIYDTMQYIKP--D 152

Query: 99  VITEVHEMAASAGYLISCA 117
           V T    +AAS   L+  A
Sbjct: 153 VSTICVGLAASMAALLLAA 171


>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 = 33.4 bits (77), Expect = 0.069
 Identities = 23/124 (18%), Positives = 50/124 (40%), Gaps = 25/124 (20%)

Query: 52  ELIERIERISRDDSATALIVS--------------LSSPGGSAYA-----GEAIFRAIQK 92
           ELI+ +E++ +D S  A++++              +++   +  A        ++  ++ 
Sbjct: 21  ELIQALEKLEQDPSVRAVVLTGAPGAFSAGADIKEMAAKRPAQQAQFSLEALDLWSRLED 80

Query: 93  VKNRKPVITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQ-YP--YVKPFLDK-L 148
           +   KPVI  V+  A   G  ++ A +  +AA+ +  G         P       L + +
Sbjct: 81  LP--KPVIAAVNGYALGGGLELALACDYRIAADNAKFGLPETKLGIIPGAGGTQRLPRII 138

Query: 149 GVSI 152
           G S 
Sbjct: 139 GHSA 142


>gnl|CDD|176969 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit.
          Length = 200

 Score = 33.3 bits (77), Expect = 0.084
 Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 75  SPGGSAYAGEAIFRAIQKVKNRKPVITEVHEMAASAGYLISCASNI 120
           SPGGS  +G AI+  +Q VK    V T    +AAS    I     I
Sbjct: 69  SPGGSVISGLAIYDTMQFVK--PDVHTICLGLAASMASFILAGGEI 112


>gnl|CDD|36272 KOG1054, KOG1054, KOG1054, Glutamate-gated AMPA-type ion channel
           receptor subunit GluR2 and related subunits [Inorganic
           ion transport and metabolism, Amino acid transport and
           metabolism, Signal transduction mechanisms].
          Length = 897

 Score = 33.1 bits (75), Expect = 0.10
 Identities = 53/193 (27%), Positives = 80/193 (41%), Gaps = 32/193 (16%)

Query: 111 GYLISCASNIIVAAET-SLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPSPFSE 169
           G L+   ++I VA  T +LV    + F     KPF+  LG+SI   K  P K++P  FS 
Sbjct: 489 GELVYGRADIAVAPLTITLVREEVIDFS----KPFM-SLGISIMIKK--PQKSKPGVFSF 541

Query: 170 VNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDK-TLVLSDGRIWTGAEAKKVGLIDVVG 228
           ++P A ++   +V +     V L   SR  PY+  T     GR        + G+ +   
Sbjct: 542 LDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFN--- 598

Query: 229 GQEEVWQSLYAL---GVDQSIRKIKDWNPPKNYWFCDL-------KNLSISSLLEDTIP- 277
               +W SL A    G D S R +        +WF  L        NL+    +E  +  
Sbjct: 599 ---SLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSP 655

Query: 278 ------LMKQTKV 284
                 L KQT++
Sbjct: 656 IESAEDLAKQTEI 668


>gnl|CDD|146756 pfam04286, DUF445, Protein of unknown function (DUF445).  Predicted
           to be a membrane protein.
          Length = 367

 Score = 30.7 bits (70), Expect = 0.48
 Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 3/36 (8%)

Query: 31  VEDNSPHVARIAIRGQIE--DSQELIERIERISRDD 64
           +E     + ++ I   +   D++EL E IE I   D
Sbjct: 307 LERYHLEIGQL-ISETVNRWDAEELEELIELIVGRD 341


>gnl|CDD|33682 COG3894, COG3894, Uncharacterized metal-binding protein [General
           function prediction only].
          Length = 614

 Score = 29.9 bits (67), Expect = 0.94
 Identities = 36/175 (20%), Positives = 60/175 (34%), Gaps = 26/175 (14%)

Query: 70  IVSLSSPGGSAYAGE-------AIFRAIQKVKN--RKPVITEV--HEMAASAGYLISCAS 118
           IV+ S+  G A+ G+       A   AI  V+    +     V  +EMA + G L  C S
Sbjct: 350 IVTASAAAGPAFEGQEISHGMRASPGAIDDVREFEGEEWRYTVLDNEMAKAPGVLGICGS 409

Query: 119 NIIV-AAETSLVGSIG----VLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPSPFSEVNPK 173
             I   AE    G  G    V          ++K GV   +            F+E + +
Sbjct: 410 GEIDEVAEMYANGITGTGVIVKIALAARSGLVEKPGVKFPAELLE--LGNGITFTEKDIE 467

Query: 174 AVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLVL----SDGRIWTGAEAKKVGLI 224
                +  + + +      + E   I  +    +    + G      +A  +GLI
Sbjct: 468 EAGKAKGAIRAGH----MTLIEKAGIELEDIERIYMAGAFGTYIDAKKAMVIGLI 518


>gnl|CDD|147479 pfam05311, Baculo_PP31, Baculovirus 33KDa late protein (PP31).
           Autographa californica nuclear polyhedrosis virus
           (AcMNPV) pp31 is a nuclear phosphoprotein that
           accumulates in the virogenic stroma, which is the viral
           replication centre in the infected-cell nucleus, binds
           to DNA, and serves as a late expression factor.
          Length = 267

 Score = 29.3 bits (66), Expect = 1.4
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 13/67 (19%)

Query: 142 KPFLD------KLGVSIKSVKSSPMKAEPSPFSEVNPKAVQMMQDVVDSS-------YHW 188
           KPF+D      KLG SI+   +S    E +P    N K  +     +  S       Y+ 
Sbjct: 98  KPFVDIFDFMEKLGKSIEVKSASSSSTESNPGKRRNSKRTEANVAEIKESNEKRSKLYNE 157

Query: 189 FVRLVSE 195
           F R+++E
Sbjct: 158 FYRVLNE 164


>gnl|CDD|31758 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
           recombination, and repair].
          Length = 440

 Score = 29.1 bits (65), Expect = 1.5
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 10/62 (16%)

Query: 50  SQELIERIERISRDDSATALIVSLSSPGGS-----AYAGEAIFRAIQKVKNRKPVITEV- 103
           ++E++E IER ++      LIV+    GGS     A+  E + RAI    +R PVI+ V 
Sbjct: 178 AEEIVEAIERANQRGDVDVLIVARG--GGSIEDLWAFNDEIVARAI--AASRIPVISAVG 233

Query: 104 HE 105
           HE
Sbjct: 234 HE 235


>gnl|CDD|33213 COG3407, MVD1, Mevalonate pyrophosphate decarboxylase [Lipid
           metabolism].
          Length = 329

 Score = 29.1 bits (65), Expect = 1.6
 Identities = 26/120 (21%), Positives = 47/120 (39%), Gaps = 14/120 (11%)

Query: 6   KKIKTRYVMLSLVTLTVVYFSWSSHVEDNSPHVARIAIRGQIEDSQELIERIERISRDDS 65
           KK+ +R  M      +  Y +W  H E++     + AIR   +D +++ E  E  S +  
Sbjct: 188 KKVSSREGMQLTAETSPFYDAWLEHSEEDL-EEMKEAIRE--KDFEKIGELAENDSLEMH 244

Query: 66  ATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKPVITEVHEMAASAGYLISCASNIIVAAE 125
           AT     +SS     Y  +   R I+ V        E+ +   +  + +    N+ V   
Sbjct: 245 AT----LMSSGPPFFYLTDESLRIIEFVH-------ELRKEGNAVYFTMDAGPNVKVITL 293


>gnl|CDD|145733 pfam02738, Ald_Xan_dh_C2, Molybdopterin-binding domain of aldehyde
           dehydrogenase. 
          Length = 543

 Score = 28.8 bits (65), Expect = 1.7
 Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 10/62 (16%)

Query: 38  VARIAIRGQIEDSQELIERIERISRDDSATALIVSLSSPGGSA---YAGEAIFRAIQKVK 94
           VA+IA         EL   ++ I      T  + + S   GS      G A+  A +K+K
Sbjct: 347 VAQIAAE-------ELGIPLDDIRVISGDTDKVPNGSGTYGSRGTDVNGNAVRLACEKLK 399

Query: 95  NR 96
            R
Sbjct: 400 ER 401


>gnl|CDD|144091 pfam00370, FGGY_N, FGGY family of carbohydrate kinases, N-terminal
           domain.  This domain adopts a ribonuclease H-like fold
           and is structurally related to the C-terminal domain.
          Length = 245

 Score = 28.4 bits (64), Expect = 2.1
 Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 8/62 (12%)

Query: 231 EEVWQSLYALGVDQSIRKIKDWNPPKNYWFCDLKNLSISSLLEDTIPLMKQTKVQGLWAV 290
           EE+WQ+L      Q+IRKI             +K + IS      + L K  K      +
Sbjct: 46  EEIWQALA-----QAIRKI---LQQSGISPKQIKGIGISGQGHGLVLLDKNDKPLYPAIL 97

Query: 291 WN 292
           WN
Sbjct: 98  WN 99


>gnl|CDD|143396 cd07077, ALDH-like, NAD(P)+-dependent aldehyde dehydrogenase-like
           (ALDH-like) family.  The aldehyde dehydrogenase-like
           (ALDH-like) group of the ALDH superfamily of
           NAD(P)+-dependent enzymes which, in general, oxidize a
           wide range of  endogenous and exogenous aliphatic and
           aromatic aldehydes to their corresponding carboxylic
           acids and play an  important role in detoxification.
           This group includes families ALDH18, ALDH19, and ALDH20
           and represents such proteins as gamma-glutamyl phosphate
           reductase, LuxC-like acyl-CoA reductase, and coenzyme A
           acylating aldehyde dehydrogenase.  All of these proteins
           have a conserved cysteine that aligns with the catalytic
           cysteine of the ALDH group.
          Length = 397

 Score = 27.6 bits (61), Expect = 4.6
 Identities = 23/115 (20%), Positives = 34/115 (29%), Gaps = 15/115 (13%)

Query: 80  AYAGEAIFRAIQKVKNRKPVI-------------TEVHEMAASAGYLISCASNIIVAAET 126
           A  G     A  K     PVI             T   E A+ + +          A+E 
Sbjct: 187 ATGGRDAVDAAVKHSPHIPVIGFGAGNSPVVVDETADEERASGSVHDSKFFDQNACASEQ 246

Query: 127 SLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPSPFSEVNPKAVQMMQDV 181
           +L     VL   P  + F  KL V    V               + +A++ M  +
Sbjct: 247 NLYVVDDVL--DPLYEEFKLKLVVEGLKVPQETKPLSKETTPSFDDEALESMTPL 299


>gnl|CDD|36895 KOG1682, KOG1682, KOG1682, Enoyl-CoA isomerase [Lipid transport and
           metabolism].
          Length = 287

 Score = 27.4 bits (60), Expect = 4.9
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 73  LSSPGGSAYAGEAIFRAIQKVKN-----RKPVITEVHEMAASAGYLISCASNIIVAAETS 127
           L++  GS    E +F+    V N       PVI +V+  AA+AG  +  + +++VA + S
Sbjct: 98  LTNEPGSDIHAE-VFQTCTDVMNDIRNLPVPVIAKVNGYAAAAGCQLVASCDMVVATKNS 156

Query: 128 LVGSIGV 134
              + G 
Sbjct: 157 KFSTPGA 163


>gnl|CDD|36892 KOG1679, KOG1679, KOG1679, Enoyl-CoA hydratase [Lipid transport and
           metabolism].
          Length = 291

 Score = 27.3 bits (60), Expect = 5.1
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 3/46 (6%)

Query: 203 KTLVLSDGRIWTGAEAKKVGLIDVVGGQEEVWQSLY--ALGVDQSI 246
           K L+ +  R+  GAEA K+GL++ V  Q E   + Y  AL + + I
Sbjct: 186 KELIFT-ARVLNGAEAAKLGLVNHVVEQNEEGDAAYQKALELAREI 230


>gnl|CDD|147546 pfam05416, Peptidase_C37, Southampton virus-type processing
           peptidase.  Corresponds to Merops family C37.
           Norwalk-like viruses (NLVs), including the Southampton
           virus, cause acute non-bacterial gastroenteritis in
           humans. The NLV genome encodes three open reading frames
           (ORFs). ORF1 encodes a polyprotein, which is processed
           by the viral protease into six proteins.
          Length = 535

 Score = 27.1 bits (60), Expect = 6.2
 Identities = 11/30 (36%), Positives = 13/30 (43%)

Query: 230 QEEVWQSLYALGVDQSIRKIKDWNPPKNYW 259
           +EE  +     G D   RK  DWNP    W
Sbjct: 321 KEERAKLGLVTGSDIRKRKPIDWNPKGPLW 350


>gnl|CDD|30807 COG0459, GroL, Chaperonin GroEL (HSP60 family) [Posttranslational
           modification, protein turnover, chaperones].
          Length = 524

 Score = 26.7 bits (59), Expect = 7.8
 Identities = 21/105 (20%), Positives = 39/105 (37%), Gaps = 4/105 (3%)

Query: 31  VEDNSPHVARIAIRGQIEDSQELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAI 90
            +  +  VA I +RG  E   EL E+  RI  +D+   +  ++         G A   A 
Sbjct: 353 RKAKAGGVATILVRGATE--VELDEKERRI--EDALNVVRAAVEEGKIVPGGGAAEIEAA 408

Query: 91  QKVKNRKPVITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVL 135
            +++     +    E      +  +  +     AE + +  I VL
Sbjct: 409 LRLREYAMTVEGGDEQLGIEAFARALEAPPRQLAENAGLDPIEVL 453


  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
   0.317    0.132    0.389 

Gapped
Lambda     K      H
   0.267   0.0619    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,481,304
Number of extensions: 173072
Number of successful extensions: 556
Number of sequences better than 10.0: 1
Number of HSP's gapped: 538
Number of HSP's successfully gapped: 52
Length of query: 293
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 200
Effective length of database: 4,254,100
Effective search space: 850820000
Effective search space used: 850820000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.0 bits)