Citrus Sinensis ID: 040730

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140----
Protein Sequence
ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEcccccccccccccccEEEEEcccccHHHHHHHccccccHHHHHHHcccccccccccEEEEccccccccccccccEEEEEEEEEEccccHHHHHHHHcccHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEEEEEEEcccccccEEEccEEEEEcccccHHHHHHHHcccccHHHHHHHcccccccccccEEEEEccccccccccccccEEEEEEEEcccccHHHHHHHHcccHHHHHHHcccccccEccc
Coil and Loop (DISEMBL)
ilvsnsispmspslgnqilgtkslvkvpiscpcidgirhsksttnnvrpadtidsILNGFGGLVsaeqinstselshpvndwTKLMImlpctcfnngnngvtSIYKSYVVqwgespssvgskFGVTMAELVATNGLSQSVVETF
Flexible Loop (DISEMBL)
ilvsnsispmspslgnqilgTKSLVKVPISCPCIdgirhsksttnnvrpADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVatnglsqsvvetf
Low Complexity Region (SEG)
ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF
Disordered region (IsUnstruct)
*****************ILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESP*SVGSKFGVTMAELVA************
Disordered Region (DISOPRED)
ILVSNS*SPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIML***************YKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQS**ETF
Disordered Region (DISEMBL)
ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF
Disordered Region (DISPRO)
ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVV**F
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	144	2.2.26 [Sep-21-2011]
Q93ZH0	416	LysM domain-containing GP	no	no	0.944	0.326	0.388	8e-23
Q6NPN4	423	LysM domain-containing GP	no	no	0.937	0.319	0.4	3e-21
O23006	350	LysM domain-containing GP	no	no	0.826	0.34	0.296	3e-07
Q8H8C7	356	Chitin elicitor-binding p	no	no	0.847	0.342	0.289	8e-07

>sp|Q93ZH0|LYM1_ARATH LysM domain-containing GPI-anchored protein 1 OS=Arabidopsis thaliana GN=LYM1 PE=1 SV=1

 Score =  105 bits (262), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 87/139 (62%), Gaps = 3/139 (2%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
           IL++N+I    P + N IL +K  +K+PI+C C+DGIR S ST    RP+D + SI +  
Sbjct: 68  ILLANAIDISYPDVENHILPSKLFLKIPITCSCVDGIRKSVSTHYKTRPSDNLGSIADSV 127

Query: 60  FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
           +GGLVSAEQI   + ++ P  ++  T L+I LPC CFN  +N + ++Y SYVV+  ++  
Sbjct: 128 YGGLVSAEQIQEANSVNDPSLLDVGTSLVIPLPCACFNGTDNSLPAVYLSYVVKEIDTLV 187

Query: 118 SVGSKFGVTMAELVATNGL 136
            +  ++  T+ +L+  N +
Sbjct: 188 GIARRYSTTITDLMNVNAM 206

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NPN4|LYM3_ARATH LysM domain-containing GPI-anchored protein 2 OS=Arabidopsis thaliana GN=LYM3 PE=1 SV=1

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 56/140 (40%), Positives = 87/140 (62%), Gaps = 5/140 (3%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
           +L+SNSI    P + N +L  K  +K+PI+C C+DGIR S ST    R +DT+ SI +  
Sbjct: 65  MLLSNSIDISYPDVENHVLPAKLFLKIPITCSCVDGIRKSLSTHYKTRTSDTLGSIADSV 124

Query: 60  FGGLVSAEQI---NSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESP 116
           +GGLVS EQI   NS ++LS  ++  TKL+I LPC CFN  +  + ++Y SYVV+  ++ 
Sbjct: 125 YGGLVSPEQIQVANSETDLSV-LDVGTKLVIPLPCACFNGTDESLPALYLSYVVRGIDTM 183

Query: 117 SSVGSKFGVTMAELVATNGL 136
           + +  +F  ++ +L   N +
Sbjct: 184 AGIAKRFSTSVTDLTNVNAM 203

Arabidopsis thaliana (taxid: 3702)

>sp|O23006|LYM2_ARATH LysM domain-containing GPI-anchored protein 2 OS=Arabidopsis thaliana GN=LYM2 PE=1 SV=1

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 16  NQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG--FGGLVSAEQINSTS 73
           +Q +    +V+VPI C C +G   S          D I S +    FGGLV+ E+I+  +
Sbjct: 80  DQRVNPNQVVRVPIHCSCSNGTGVSNRDIEYTIKKDDILSFVATEIFGGLVTYEKISEVN 139

Query: 74  ELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELV 131
           ++  P  +    K  I LPC+C  +  NG   ++ ++VV+ G S   + ++FG     L 
Sbjct: 140 KIPDPNKIEIGQKFWIPLPCSC--DKLNGEDVVHYAHVVKLGSSLGEIAAQFGTDNTTLA 197

Query: 132 ATNGL 136
             NG+
Sbjct: 198 QLNGI 202

Arabidopsis thaliana (taxid: 3702)

>sp|Q8H8C7|CEBIP_ORYSJ Chitin elicitor-binding protein OS=Oryza sativa subsp. japonica GN=CEBIP PE=1 SV=1

 Score = 52.4 bits (124), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 66/128 (51%), Gaps = 6/128 (4%)

Query: 13  SLGNQILGTKSLVKVPISCPCIDGIRHS-KSTTNNVRPADTIDSIL-NGFGGLVSAEQIN 70
           +L +  +   S VK+P  C C   +  S +     V+P D +D+I  N F   V+ ++I 
Sbjct: 80  TLSSAPVAANSTVKIPFRCRCNGDVGQSDRLPIYVVQPQDGLDAIARNVFNAFVTYQEIA 139

Query: 71  STSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMA 128
           + + +  P  +N    L I LPC+C  +   G   ++ +Y V  GE+ S++ +K+GVT +
Sbjct: 140 AANNIPDPNKINVSQTLWIPLPCSC--DKEEGSNVMHLAYSVGKGENTSAIAAKYGVTES 197

Query: 129 ELVATNGL 136
            L+  N +
Sbjct: 198 TLLTRNKI 205

Chitin elicitor-binding protein involved in the perception and transduction of chitin oligosaccharide elicitor signal for defense responses.

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	144
225455922	408	PREDICTED: lysM domain-containing GPI-an	0.972	0.343	0.539	3e-33
255585434	405	LysM domain GPI-anchored protein 1 precu	0.986	0.350	0.524	3e-32
388500350	226	unknown [Lotus japonicus]	0.958	0.610	0.5	5e-32
356527809	328	PREDICTED: lysM domain-containing GPI-an	0.986	0.432	0.513	1e-31
147767409	211	hypothetical protein VITISV_014762 [Viti	0.902	0.616	0.492	5e-28
388515603	412	unknown [Medicago truncatula]	0.944	0.330	0.395	3e-22
357461525	412	LysM domain-containing GPI-anchored prot	0.944	0.330	0.395	4e-22
449458099	432	PREDICTED: lysM domain-containing GPI-an	0.986	0.328	0.372	1e-21
188509929	453	peptidoglycan-binding LysM domain-contai	0.986	0.313	0.379	2e-21
356515884	418	PREDICTED: lysM domain-containing GPI-an	0.979	0.337	0.368	3e-21

>gi|225455922|ref|XP_002276124.1| PREDICTED: lysM domain-containing GPI-anchored protein 1-like [Vitis vinifera]

 Score =  146 bits (369), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 76/141 (53%), Positives = 96/141 (68%), Gaps = 1/141 (0%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGF 60
           IL +NS+ P  PS  +QI+  KSLVKVPI CPC+DGIR S STT  V+ ADT+D I  G+
Sbjct: 71  ILATNSMDPTRPSSASQIIPAKSLVKVPILCPCVDGIRRSLSTTYTVKAADTMDLISEGY 130

Query: 61  GGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVG 120
           GGLVSA+QI S +           L+I LPCTCF N NNG T++Y SYVVQ GES  S+G
Sbjct: 131 GGLVSADQIRSVNG-GKGAGYGQSLVIPLPCTCFGNTNNGATAVYMSYVVQRGESLGSIG 189

Query: 121 SKFGVTMAELVATNGLSQSVV 141
           +++  T+ +L A NGL Q V+
Sbjct: 190 ARYHTTVTDLAAVNGLGQPVI 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585434|ref|XP_002533411.1| LysM domain GPI-anchored protein 1 precursor, putative [Ricinus communis] gi|223526740|gb|EEF28969.1| LysM domain GPI-anchored protein 1 precursor, putative [Ricinus communis]

 Score =  143 bits (360), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 76/145 (52%), Positives = 101/145 (69%), Gaps = 3/145 (2%)

Query: 1   ILVSNSISPMS-PSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG 59
           IL +NSI P + PS+ NQIL   SLVK+PISCPC++GIR   ST+  V+PADT+DSI  G
Sbjct: 66  ILATNSIDPEALPSINNQILHANSLVKIPISCPCVEGIRRLMSTSYTVKPADTVDSISLG 125

Query: 60  FGGLVSAEQINSTSEL--SHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
           FGGLVS EQI ST+ +  ++P+    KL+I LPC+CF+N +NGV ++Y SYVVQ GES  
Sbjct: 126 FGGLVSGEQITSTNGINANNPLMIGQKLVIPLPCSCFDNNDNGVAAVYMSYVVQNGESLE 185

Query: 118 SVGSKFGVTMAELVATNGLSQSVVE 142
            +  +F  T+ +L   NG  Q  V+
Sbjct: 186 KIAMEFDTTVLDLENVNGFGQPQVD 210

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388500350|gb|AFK38241.1| unknown [Lotus japonicus]

 Score =  142 bits (358), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 70/140 (50%), Positives = 100/140 (71%), Gaps = 2/140 (1%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGF 60
           IL +NS+ P++PS G+QIL  KS+VK+P SCPC+DGIR S ST  NV  +DT+ SI  G+
Sbjct: 67  ILAANSVFPITPSSGHQILSAKSIVKIPFSCPCVDGIRRSISTIYNVEASDTLASISEGY 126

Query: 61  GGLVSAEQINSTSEL--SHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSS 118
           GGLV AEQI + + +  ++P+   + ++I LPC C NN NNG T++Y SYVVQ G+S  S
Sbjct: 127 GGLVGAEQIKTMNSINETNPLTYGSSIVIPLPCKCLNNVNNGDTTVYMSYVVQKGQSLGS 186

Query: 119 VGSKFGVTMAELVATNGLSQ 138
           + + +G T+++L + NGL Q
Sbjct: 187 IATMYGTTVSDLESVNGLGQ 206

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356527809|ref|XP_003532499.1| PREDICTED: lysM domain-containing GPI-anchored protein 2-like [Glycine max]

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 74/144 (51%), Positives = 98/144 (68%), Gaps = 2/144 (1%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGF 60
           IL SNS+ P++PS  +QIL  KS VK+PISC C+DGIR S ST   V  ADT+ SI  G+
Sbjct: 69  ILASNSLFPITPSSAHQILSAKSQVKIPISCSCVDGIRRSMSTIYTVHAADTLASISEGY 128

Query: 61  GGLVSAEQINSTSEL--SHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSS 118
           GGLVSAEQI   + +  ++P+     L+I LPCTCF+N NNG  +IY SYVVQ  ES  S
Sbjct: 129 GGLVSAEQIKIVNAINATNPLTYRGTLVIPLPCTCFDNVNNGGNAIYMSYVVQRRESLGS 188

Query: 119 VGSKFGVTMAELVATNGLSQSVVE 142
           + +KFG T+++L   NG  ++ V+
Sbjct: 189 IATKFGTTVSDLETVNGFGEATVD 212

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147767409|emb|CAN77911.1| hypothetical protein VITISV_014762 [Vitis vinifera]

 Score =  129 bits (323), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 70/142 (49%), Positives = 88/142 (61%), Gaps = 12/142 (8%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGF 60
           IL  NS+ P  PS  +QI+  KSLVKVPI CPC+DGIR S STT              G+
Sbjct: 71  ILAXNSMDPTRPSSASQIIPAKSLVKVPILCPCVDGIRRSLSTTYT-----------RGY 119

Query: 61  GGLVSAEQINSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVG 120
           GGLVSA+QI S +           L+I LPCTCF N NNG T++Y SYVVQ GES  S+G
Sbjct: 120 GGLVSADQIRSVNG-GKGAGYGQSLVIPLPCTCFGNTNNGATAVYMSYVVQRGESLGSIG 178

Query: 121 SKFGVTMAELVATNGLSQSVVE 142
           +++  T+ +L A NGL Q V++
Sbjct: 179 ARYRTTVTDLAAVNGLGQLVID 200

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388515603|gb|AFK45863.1| unknown [Medicago truncatula]

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 55/139 (39%), Positives = 91/139 (65%), Gaps = 3/139 (2%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
           +L +NSI    P + + IL +K  +K+PI C CIDGIR S ST   +RP+DT+ SI +  
Sbjct: 62  LLTANSIDISYPDVEHHILPSKLYLKIPIQCSCIDGIRKSVSTNYKIRPSDTLSSIADSI 121

Query: 60  FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
           +GGLVS++Q+   + ++ P  ++    L++ LPCTCFN  +NG+ +IY SYVVQ  +S +
Sbjct: 122 YGGLVSSDQLREANSVTDPNVLDVGQNLVVPLPCTCFNGSDNGLPAIYMSYVVQPLDSLN 181

Query: 118 SVGSKFGVTMAELVATNGL 136
           ++ +++  T+ +L+  N +
Sbjct: 182 NIAARYFTTLTDLMNVNAM 200

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461525|ref|XP_003601044.1| LysM domain-containing GPI-anchored protein [Medicago truncatula] gi|355490092|gb|AES71295.1| LysM domain-containing GPI-anchored protein [Medicago truncatula]

 Score =  109 bits (272), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 55/139 (39%), Positives = 91/139 (65%), Gaps = 3/139 (2%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
           +L +NSI    P + + IL +K  +K+PI C CIDGIR S ST   +RP+DT+ SI +  
Sbjct: 62  LLTANSIDISYPDVEHHILPSKLYLKIPIQCSCIDGIRKSVSTNYKIRPSDTLSSIADSI 121

Query: 60  FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
           +GGLVS++Q+   + ++ P  ++    L++ LPCTCFN  +NG+ +IY SYVVQ  +S +
Sbjct: 122 YGGLVSSDQLREANSVTDPNVLDVGQNLVVPLPCTCFNGSDNGLPAIYMSYVVQPLDSLN 181

Query: 118 SVGSKFGVTMAELVATNGL 136
           ++ +++  T+ +L+  N +
Sbjct: 182 NIAARYFTTLTDLMNVNAM 200

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458099|ref|XP_004146785.1| PREDICTED: lysM domain-containing GPI-anchored protein 1-like [Cucumis sativus] gi|449528597|ref|XP_004171290.1| PREDICTED: lysM domain-containing GPI-anchored protein 1-like [Cucumis sativus]

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 54/145 (37%), Positives = 89/145 (61%), Gaps = 3/145 (2%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
           IL +N+I    P + N IL ++  +K+PISC C+DGIR S ST    RP+DT+ SI +  
Sbjct: 74  ILTANAIDVSYPDVENHILPSQLFIKIPISCSCVDGIRKSVSTRYKTRPSDTLSSIADSI 133

Query: 60  FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
           + GLVS++QI   + +S P  ++    L++ LPCTCFN  +N + +IY SYVVQ  ++ +
Sbjct: 134 YAGLVSSDQIREANSISDPSLLDVGQTLVVPLPCTCFNGTDNSLPAIYLSYVVQPEDTLT 193

Query: 118 SVGSKFGVTMAELVATNGLSQSVVE 142
            +  ++  T+ +L+  N +    ++
Sbjct: 194 GIAFRYSTTITDLMDVNAMGNPAIK 218

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|188509929|gb|ACD56618.1| peptidoglycan-binding LysM domain-containing related protein [Gossypioides kirkii]

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 55/145 (37%), Positives = 89/145 (61%), Gaps = 3/145 (2%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
           IL +N+I    P + N IL +K  +K+PI C C+DGIR S ST    RP DT+ SI +  
Sbjct: 69  ILTANAIDISYPDVENHILPSKLFLKIPILCSCVDGIRKSVSTKYKTRPQDTLSSIADSI 128

Query: 60  FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
           + GLVSA+QI   + +S P  ++    L++ LPCTCFN  +NG+ +IY SYVV+  ++ +
Sbjct: 129 YAGLVSADQIREANSISDPSVLDVGENLVVPLPCTCFNGTDNGLPAIYLSYVVKAVDTLA 188

Query: 118 SVGSKFGVTMAELVATNGLSQSVVE 142
            + + +  T+ +L+  N +  + ++
Sbjct: 189 GIAASYSTTITDLMNVNAMGSTSIK 213

Source: Gossypioides kirkii

Species: Gossypioides kirkii

Genus: Gossypioides

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356515884|ref|XP_003526627.1| PREDICTED: lysM domain-containing GPI-anchored protein 1-like [Glycine max]

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 53/144 (36%), Positives = 91/144 (63%), Gaps = 3/144 (2%)

Query: 1   ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
           +L +N+I    P + + IL +K  +KVPISC C+DGIR S +T    RP+DT+ SI +  
Sbjct: 65  LLTANAIDISYPDVEHHILPSKLFLKVPISCSCVDGIRKSVATHYKTRPSDTLSSIADAV 124

Query: 60  FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
           + GLVS++Q+   + LS P  ++    L++ LPCTCFN  +N + +IY SYVV+  ++ +
Sbjct: 125 YAGLVSSDQLREANSLSDPSVLDVGQNLVVPLPCTCFNGSDNSLPAIYLSYVVRPVDTLA 184

Query: 118 SVGSKFGVTMAELVATNGLSQSVV 141
           +V +++  T+ +L+  N +  + +
Sbjct: 185 AVAARYFTTLTDLMNVNAMGSTAI 208

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	144
TAIR|locus:2201143	416	LYP2 "LysM-containing receptor	0.944	0.326	0.388	4.6e-23
TAIR|locus:2204720	423	LYM3 "lysin-motif (LysM) domai	0.937	0.319	0.4	3.4e-22
TAIR|locus:2827686	350	LYP1 "LysM-containing receptor	0.916	0.377	0.285	8.8e-10
UNIPROTKB|Q8H8C7	356	CEBIP "Chitin elicitor-binding	0.833	0.337	0.293	4.2e-09
TAIR|locus:2082359	654	LYK2 "LysM-containing receptor	0.902	0.198	0.268	8.4e-05

TAIR|locus:2201143 LYP2 "LysM-containing receptor protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 268 (99.4 bits), Expect = 4.6e-23, P = 4.6e-23
 Identities = 54/139 (38%), Positives = 87/139 (62%)

Query:     1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
             IL++N+I    P + N IL +K  +K+PI+C C+DGIR S ST    RP+D + SI +  
Sbjct:    68 ILLANAIDISYPDVENHILPSKLFLKIPITCSCVDGIRKSVSTHYKTRPSDNLGSIADSV 127

Query:    60 FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPS 117
             +GGLVSAEQI   + ++ P  ++  T L+I LPC CFN  +N + ++Y SYVV+  ++  
Sbjct:   128 YGGLVSAEQIQEANSVNDPSLLDVGTSLVIPLPCACFNGTDNSLPAVYLSYVVKEIDTLV 187

Query:   118 SVGSKFGVTMAELVATNGL 136
              +  ++  T+ +L+  N +
Sbjct:   188 GIARRYSTTITDLMNVNAM 206

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0016998 "cell wall macromolecule catabolic process" evidence=IEA;ISS

GO:0031225 "anchored to membrane" evidence=TAS

GO:0046658 "anchored to plasma membrane" evidence=IDA

GO:0006955 "immune response" evidence=IMP

GO:0042834 "peptidoglycan binding" evidence=IDA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0016570 "histone modification" evidence=RCA

GO:0048449 "floral organ formation" evidence=RCA

TAIR|locus:2204720 LYM3 "lysin-motif (LysM) domain protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 261 (96.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 56/140 (40%), Positives = 87/140 (62%)

Query:     1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNG- 59
             +L+SNSI    P + N +L  K  +K+PI+C C+DGIR S ST    R +DT+ SI +  
Sbjct:    65 MLLSNSIDISYPDVENHVLPAKLFLKIPITCSCVDGIRKSLSTHYKTRTSDTLGSIADSV 124

Query:    60 FGGLVSAEQI---NSTSELSHPVNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESP 116
             +GGLVS EQI   NS ++LS  ++  TKL+I LPC CFN  +  + ++Y SYVV+  ++ 
Sbjct:   125 YGGLVSPEQIQVANSETDLS-VLDVGTKLVIPLPCACFNGTDESLPALYLSYVVRGIDTM 183

Query:   117 SSVGSKFGVTMAELVATNGL 136
             + +  +F  ++ +L   N +
Sbjct:   184 AGIAKRFSTSVTDLTNVNAM 203

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0016998 "cell wall macromolecule catabolic process" evidence=IEA;ISS

GO:0031225 "anchored to membrane" evidence=TAS

GO:0046658 "anchored to plasma membrane" evidence=IDA

GO:0006955 "immune response" evidence=IMP

GO:0042834 "peptidoglycan binding" evidence=IDA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0042545 "cell wall modification" evidence=RCA

TAIR|locus:2827686 LYP1 "LysM-containing receptor protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 147 (56.8 bits), Expect = 8.8e-10, P = 8.8e-10
 Identities = 40/140 (28%), Positives = 73/140 (52%)

Query:     1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHS-KSTTNNVRPADTIDSILNG 59
             IL +N++ P++ S  +Q +    +V+VPI C C +G   S +     ++  D +  +   
Sbjct:    67 ILGANNL-PLNTSR-DQRVNPNQVVRVPIHCSCSNGTGVSNRDIEYTIKKDDILSFVATE 124

Query:    60 -FGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESP 116
              FGGLV+ E+I+  +++  P  +    K  I LPC+C  +  NG   ++ ++VV+ G S 
Sbjct:   125 IFGGLVTYEKISEVNKIPDPNKIEIGQKFWIPLPCSC--DKLNGEDVVHYAHVVKLGSSL 182

Query:   117 SSVGSKFGVTMAELVATNGL 136
               + ++FG     L   NG+
Sbjct:   183 GEIAAQFGTDNTTLAQLNGI 202

GO:0016998 "cell wall macromolecule catabolic process" evidence=IEA;ISS

GO:0031225 "anchored to membrane" evidence=TAS

GO:0046658 "anchored to plasma membrane" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0008061 "chitin binding" evidence=IDA

UNIPROTKB|Q8H8C7 CEBIP "Chitin elicitor-binding protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 141 (54.7 bits), Expect = 4.2e-09, P = 4.2e-09
 Identities = 37/126 (29%), Positives = 65/126 (51%)

Query:    13 SLGNQILGTKSLVKVPISCPCIDGIRHS-KSTTNNVRPADTIDSIL-NGFGGLVSAEQIN 70
             +L +  +   S VK+P  C C   +  S +     V+P D +D+I  N F   V+ ++I 
Sbjct:    80 TLSSAPVAANSTVKIPFRCRCNGDVGQSDRLPIYVVQPQDGLDAIARNVFNAFVTYQEIA 139

Query:    71 STSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMA 128
             + + +  P  +N    L I LPC+C  +   G   ++ +Y V  GE+ S++ +K+GVT +
Sbjct:   140 AANNIPDPNKINVSQTLWIPLPCSC--DKEEGSNVMHLAYSVGKGENTSAIAAKYGVTES 197

Query:   129 ELVATN 134
              L+  N
Sbjct:   198 TLLTRN 203

GO:0005515 "protein binding" evidence=IPI

GO:0043621 "protein self-association" evidence=IDA

TAIR|locus:2082359 LYK2 "LysM-containing receptor-like kinase 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 105 (42.0 bits), Expect = 8.4e-05, P = 8.4e-05
 Identities = 37/138 (26%), Positives = 61/138 (44%)

Query:     6 SISPMSPSLG----NQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFG 61
             S+S +S  LG    ++ +    L+ +PI C C +G  +  S   N    DT  S+     
Sbjct:    71 SLSDLSRHLGLDADDEYVPKGQLLLIPIECRC-NGSIYEASLIKNCVKGDTFRSVSQSLQ 129

Query:    62 GLVSAEQINSTS-ELSHP-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSV 119
             GL +   I   +  +S   + D  KL + + C+C   G +   S   +Y V   +S SS+
Sbjct:   130 GLTTCLSIREKNPHISEDKLGDNIKLRLAIRCSCPQEGVSNA-SFLVTYPVGVRDSVSSL 188

Query:   120 GSKFGVTMAELVATNGLS 137
               +F  T   +V+ N  S
Sbjct:   189 AVRFNTTEDAIVSANNKS 206


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.313   0.129   0.380    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      144       144   0.00091  102 3  11 23  0.37    32
                                                     30  0.48    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  575 (61 KB)
  Total size of DFA:  133 KB (2083 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.58u 0.14s 12.72t   Elapsed:  00:00:01
  Total cpu time:  12.58u 0.14s 12.72t   Elapsed:  00:00:01
  Start:  Sat May 11 09:07:26 2013   End:  Sat May 11 09:07:27 2013

GO:0004672 "protein kinase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0016301 "kinase activity" evidence=ISS

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00017669001 SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (260 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	144
cd00118	45	cd00118, LysM, Lysine Motif is a small domain invo	4e-04

>gnl|CDD|212030 cd00118, LysM, Lysine Motif is a small domain involved in binding peptidoglycan

 Score = 35.9 bits (84), Expect = 4e-04
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 106 KSYVVQWGESPSSVGSKFGVTMAELVATNGLS 137
           K+Y V+ G++  S+  K+GVT+ EL A N L 
Sbjct: 1   KTYTVKPGDTLWSIAKKYGVTVEELAAANPLI 32

LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes. Length = 45

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	144
PRK06347	592	autolysin; Reviewed	99.93
PRK06347	592	autolysin; Reviewed	99.89
PRK10783	456	mltD membrane-bound lytic murein transglycosylase	99.87
PRK13914	481	invasion associated secreted endopeptidase; Provis	99.7
PRK10783	456	mltD membrane-bound lytic murein transglycosylase	99.48
PF01476	44	LysM: LysM domain; InterPro: IPR018392 This domain	99.37
COG1388	124	LytE FOG: LysM repeat [Cell envelope biogenesis, o	99.34
PF01476	44	LysM: LysM domain; InterPro: IPR018392 This domain	99.28
PRK14125	103	cell division suppressor protein YneA; Provisional	99.13
COG1388	124	LytE FOG: LysM repeat [Cell envelope biogenesis, o	99.02
TIGR02899	44	spore_safA spore coat assembly protein SafA. in wh	98.97
cd00118	46	LysM Lysin domain, found in a variety of enzymes i	98.96
PRK14125	103	cell division suppressor protein YneA; Provisional	98.94
COG3858	423	Predicted glycosyl hydrolase [General function pre	98.9
PRK10871	319	nlpD lipoprotein NlpD; Provisional	98.88
TIGR02907	338	spore_VI_D stage VI sporulation protein D. SpoVID,	98.84
cd00118	46	LysM Lysin domain, found in a variety of enzymes i	98.77
TIGR02899	44	spore_safA spore coat assembly protein SafA. in wh	98.71
TIGR02907	338	spore_VI_D stage VI sporulation protein D. SpoVID,	98.67
smart00257	44	LysM Lysin motif.	98.64
smart00257	44	LysM Lysin motif.	98.62
PRK13914	481	invasion associated secreted endopeptidase; Provis	98.59
PRK10871	319	nlpD lipoprotein NlpD; Provisional	98.56
PRK11198	147	LysM domain/BON superfamily protein; Provisional	98.55
COG3858	423	Predicted glycosyl hydrolase [General function pre	98.02
PRK11198	147	LysM domain/BON superfamily protein; Provisional	98.01
COG1652	269	XkdP Uncharacterized protein containing LysM domai	97.56
PRK10190	310	L,D-transpeptidase; Provisional	97.54
PRK10260	306	L,D-transpeptidase; Provisional	97.52
PF04225	85	OapA: Opacity-associated protein A LysM-like domai	97.36
TIGR03505	74	FimV_core FimV N-terminal domain. This region is f	97.04
PF04225	85	OapA: Opacity-associated protein A LysM-like domai	96.98
PF05489	60	Phage_tail_X: Phage Tail Protein X; InterPro: IPR0	96.73
COG3061	242	OapA Cell envelope opacity-associated protein A [C	95.93
PRK11649	439	putative peptidase; Provisional	95.8
PRK10260	306	L,D-transpeptidase; Provisional	95.06
PRK10190	310	L,D-transpeptidase; Provisional	94.96
COG3170	755	FimV Tfp pilus assembly protein FimV [Cell motilit	94.3
COG1652	269	XkdP Uncharacterized protein containing LysM domai	94.15
TIGR03505	74	FimV_core FimV N-terminal domain. This region is f	93.76
PRK11649	439	putative peptidase; Provisional	92.78
PF05489	60	Phage_tail_X: Phage Tail Protein X; InterPro: IPR0	90.56
PF13518	52	HTH_28: Helix-turn-helix domain	89.57
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	88.45
COG4784	479	Putative Zn-dependent protease [General function p	87.03
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	85.87
COG5004	70	P2-like prophage tail protein X [General function	85.16
COG4254	339	Uncharacterized protein conserved in bacteria [Fun	84.68
KOG2850	186	consensus Predicted peptidoglycan-binding protein,	82.5
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	80.57
COG3170	755	FimV Tfp pilus assembly protein FimV [Cell motilit	80.01

>PRK06347 autolysin; Reviewed

Probab=99.93  E-value=4.7e-25  Score=184.80  Aligned_cols=135  Identities=19%  Similarity=0.207  Sum_probs=104.1

Q ss_pred             CcccCCCCCCCCCCCcceecCCCEEEEccCCCCCCC---------------CcccCceeeEeCCCCCHHHHHHHhCCCCC
Q 040730            1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDG---------------IRHSKSTTNNVRPADTIDSILNGFGGLVS   65 (144)
Q Consensus         1 l~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~~---------------~~~~~~~~y~V~~GdTl~~IA~~y~~~~~   65 (144)
                      |+++|+|.       .+.|.+||.|+||....-...               ........|+|++|||||.||++|+  ++
T Consensus       430 L~~~N~l~-------s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sIAkkyg--VS  500 (592)
T PRK06347        430 LKSWNNLK-------SDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNK--VT  500 (592)
T ss_pred             HHHHhCCC-------cceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHHHHHHC--CC
Confidence            46788886       457999999999974321000               0011235799999999999999999  99


Q ss_pred             HHHHHhhcCCCCC-CCCCcEEEEecccccCCCC------CCCcccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCC
Q 040730           66 AEQINSTSELSHP-VNDWTKLMIMLPCTCFNNG------NNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQ  138 (144)
Q Consensus        66 ~~~l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~~------~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~  138 (144)
                      +++|+++|++... |++||.|.||.........      ..........|+|++|||||+||++||+++++|++||+|.+
T Consensus       501 v~~L~~~N~l~s~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~L~~  580 (592)
T PRK06347        501 IANLKSWNNLKSDFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTS  580 (592)
T ss_pred             HHHHHHhcCCCcccccCCcEEEEecCcccccccccCCccCCccCccceeeecCCCCcHHHHHHHhCCCHHHHHHhcCCCc
Confidence            9999999998876 9999999999754321100      00011235689999999999999999999999999999998


Q ss_pred             CCcccC
Q 040730          139 SVVETF  144 (144)
Q Consensus       139 ~~i~~~  144 (144)
                      ..|+||
T Consensus       581 ~~L~~G  586 (592)
T PRK06347        581 NMIHVG  586 (592)
T ss_pred             ccCCCC
Confidence            889987

>PRK06347 autolysin; Reviewed

Probab=99.89  E-value=7.7e-23  Score=171.51  Aligned_cols=135  Identities=19%  Similarity=0.170  Sum_probs=103.0

Q ss_pred             CcccCCCCCCCCCCCcceecCCCEEEEccCCCCCC-----C-----------CcccCceeeEeCCCCCHHHHHHHhCCCC
Q 040730            1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCID-----G-----------IRHSKSTTNNVRPADTIDSILNGFGGLV   64 (144)
Q Consensus         1 l~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~-----~-----------~~~~~~~~y~V~~GdTl~~IA~~y~~~~   64 (144)
                      |++||+|.       .+.|.+||.|+||.......     .           ........|+|++||||+.||++|+  +
T Consensus       355 L~~~N~l~-------~d~L~~Gq~L~VP~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~ytVk~GDTL~sIA~kyg--V  425 (592)
T PRK06347        355 LKAWNNLK-------SDFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGTSTNAKVYTVVKGDSLWRIANNNK--V  425 (592)
T ss_pred             HHHHhCCC-------ccccccCcEEEEeccccccccccccccccccccccccccccCceeEEecCCCCHHHHHHHhC--C
Confidence            57889986       46799999999997421100     0           0011225899999999999999999  9


Q ss_pred             CHHHHHhhcCCCCC-CCCCcEEEEecccccCCC----C--------CCCcccceEEEEeccCCcHHHHHHHhCCCHHHHH
Q 040730           65 SAEQINSTSELSHP-VNDWTKLMIMLPCTCFNN----G--------NNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELV  131 (144)
Q Consensus        65 ~~~~l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~----~--------~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~  131 (144)
                      ++++|+++|++... |.+||.|.||........    .        ..........|+|++|||||+||++||+++++|+
T Consensus       426 Sv~~L~~~N~l~s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sIAkkygVSv~~L~  505 (592)
T PRK06347        426 TIANLKSWNNLKSDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLK  505 (592)
T ss_pred             CHHHHHHHhCCCcceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHHHHHHCCCHHHHH
Confidence            99999999998766 999999999964211000    0        0001123457999999999999999999999999


Q ss_pred             HHcCCCCCCcccC
Q 040730          132 ATNGLSQSVVETF  144 (144)
Q Consensus       132 ~~N~l~~~~i~~~  144 (144)
                      +||++.+..|++|
T Consensus       506 ~~N~l~s~~L~~G  518 (592)
T PRK06347        506 SWNNLKSDFIYPG  518 (592)
T ss_pred             HhcCCCcccccCC
Confidence            9999988888886

>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional

Probab=99.87  E-value=1e-21  Score=161.23  Aligned_cols=131  Identities=18%  Similarity=0.182  Sum_probs=99.9

Q ss_pred             CCCCCCCcceecC-C-CEEEEccCCCCC------C-C------C----c-ccCceeeEeCCCCCHHHHHHHhCCCCCHHH
Q 040730            9 PMSPSLGNQILGT-K-SLVKVPISCPCI------D-G------I----R-HSKSTTNNVRPADTIDSILNGFGGLVSAEQ   68 (144)
Q Consensus         9 ~~~p~~~~~~l~~-G-q~l~IP~~~~~~------~-~------~----~-~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~   68 (144)
                      .+||++....+.+ | +.|+||......      . .      .    . ......|+|++|||+++||++|+  ++.++
T Consensus       290 ~LNP~~kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p~~~~~~~~~~~~~y~Vk~GDTL~sIA~r~g--vs~~~  367 (456)
T PRK10783        290 TFNAGYKRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQSTLVADNTPLNSRSYKVRSGDTLSGIASRLN--VSTKD  367 (456)
T ss_pred             HhCccccCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhcccccccccCcCCceEEEECCCCcHHHHHHHHC--cCHHH
Confidence            4677776554433 3 788899854310      0 0      0    0 01235799999999999999999  99999


Q ss_pred             HHhhcCCCCC-CCCCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730           69 INSTSELSHP-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF  144 (144)
Q Consensus        69 l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~~  144 (144)
                      |.++|++... |.+||.|.||..+.+....   ......+|+|++||||++||++||+++++|++||++..+.|+||
T Consensus       368 L~~~N~l~~~~L~~Gq~L~Ip~~~~~~~~~---~~~~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~~L~pG  441 (456)
T PRK10783        368 LQQWNNLRGSKLKVGQTLTIGAGSSAQRLA---NNSDSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAKNLQPG  441 (456)
T ss_pred             HHHHcCCCcccCCCCCEEEecCCccccccc---ccccceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCCcCCCC
Confidence            9999998766 9999999999876543211   12235689999999999999999999999999999866688887

>PRK13914 invasion associated secreted endopeptidase; Provisional

Probab=99.70  E-value=1.2e-16  Score=130.58  Aligned_cols=46  Identities=22%  Similarity=0.228  Sum_probs=42.5

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEecc
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIMLP   90 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~~   90 (144)
                      ..|+|++|||||.||++|+  +++++|+++|++... |.+||.|.||..
T Consensus        28 ~tytVq~GDTLw~IA~~yg--vtv~~I~~~N~l~~~~I~~Gq~L~Ip~~   74 (481)
T PRK13914         28 STVVVEAGDTLWGIAQSKG--TTVDAIKKANNLTTDKIVPGQKLQVNEV   74 (481)
T ss_pred             ceEEECCCCCHHHHHHHHC--CCHHHHHHHhCCCcccccCCCEEEeCCC
Confidence            6799999999999999999  999999999998766 999999999843

>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional

Probab=99.48  E-value=1.1e-13  Score=113.94  Aligned_cols=81  Identities=19%  Similarity=0.215  Sum_probs=67.2

Q ss_pred             CcccCCCCCCCCCCCcceecCCCEEEEccCCCCCCCCcccCceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-C
Q 040730            1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-V   79 (144)
Q Consensus         1 l~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l   79 (144)
                      |+++|++.      . ..|.+||.|.||..+.|...........|+|++||||++||++|+  +++++|+++|++... |
T Consensus       368 L~~~N~l~------~-~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vr~GDTL~sIA~kyg--Vtv~~L~~~N~l~~~~L  438 (456)
T PRK10783        368 LQQWNNLR------G-SKLKVGQTLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAKRHG--VNIKDVMRWNSDTAKNL  438 (456)
T ss_pred             HHHHcCCC------c-ccCCCCCEEEecCCcccccccccccceeEEeCCCCCHHHHHHHhC--CCHHHHHHhcCCCCCcC
Confidence            45788886      3 679999999999877664322223347899999999999999999  999999999998765 9


Q ss_pred             CCCcEEEEecc
Q 040730           80 NDWTKLMIMLP   90 (144)
Q Consensus        80 ~~Gq~l~IP~~   90 (144)
                      ++||+|.|+..
T Consensus       439 ~pGq~L~l~v~  449 (456)
T PRK10783        439 QPGDKLTLFVK  449 (456)
T ss_pred             CCCCEEEEecC
Confidence            99999999875

>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []

Probab=99.37  E-value=5.3e-13  Score=75.74  Aligned_cols=42  Identities=26%  Similarity=0.419  Sum_probs=34.5

Q ss_pred             eEeCCCCCHHHHHHHhCCCCCHHHHHhhc-CCCCC-CCCCcEEEEe
Q 040730           45 NNVRPADTIDSILNGFGGLVSAEQINSTS-ELSHP-VNDWTKLMIM   88 (144)
Q Consensus        45 y~V~~GdTl~~IA~~y~~~~~~~~l~~~N-~~~~~-l~~Gq~l~IP   88 (144)
                      |+|++|||++.||++|+  ++.++|+++| .+... |.+||.|+||
T Consensus         1 y~V~~gDtl~~IA~~~~--~~~~~l~~~N~~~~~~~l~~G~~l~iP   44 (44)
T PF01476_consen    1 YTVQPGDTLWSIAKRYG--ISVDELMELNPNIDSDNLQPGQKLCIP   44 (44)
T ss_dssp             EEE-TT--HHHHHHHTT--S-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred             CEECcCCcHHHHHhhhh--hhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence            89999999999999998  9999999999 44444 9999999998

This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.

>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]

Probab=99.34  E-value=3.2e-12  Score=87.91  Aligned_cols=87  Identities=24%  Similarity=0.318  Sum_probs=66.9

Q ss_pred             HHHHhCCCCCHHHHHhhcCCC--CC-CCCCcEEEEecccccCC--CC-CCCccc------------ceEEEEeccCCcHH
Q 040730           56 ILNGFGGLVSAEQINSTSELS--HP-VNDWTKLMIMLPCTCFN--NG-NNGVTS------------IYKSYVVQWGESPS  117 (144)
Q Consensus        56 IA~~y~~~~~~~~l~~~N~~~--~~-l~~Gq~l~IP~~~~~~~--~~-~~~~~~------------~~~~y~V~~GdTl~  117 (144)
                      ||.+|+  +++++|+++|.+.  .. +.+||+|.++.......  .. ......            ...+|+|+.||||+
T Consensus         1 ia~~~~--~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~   78 (124)
T COG1388           1 IASKYG--VSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLS   78 (124)
T ss_pred             Cccccc--ccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHH
Confidence            466788  8999999999988  55 99999999996311110  00 000111            13589999999999


Q ss_pred             HHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730          118 SVGSKFGVTMAELVATNGLSQSVVETF  144 (144)
Q Consensus       118 ~IA~~~~~s~~~l~~~N~l~~~~i~~~  144 (144)
                      .||++|++++.+|+++|.+.++.+++|
T Consensus        79 ~Ia~~~~~tv~~l~~~n~l~~~~i~~g  105 (124)
T COG1388          79 KIARKYGVTVAELKQLNNLSSDKIKVG  105 (124)
T ss_pred             HHHHHhCCCHHHHHHHhccCCCceecC
Confidence            999999999999999999998888775

>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []

Probab=99.28  E-value=3.3e-12  Score=72.42  Aligned_cols=37  Identities=24%  Similarity=0.475  Sum_probs=30.4

Q ss_pred             EEeccCCcHHHHHHHhCCCHHHHHHHc-CCCCCCcccC
Q 040730          108 YVVQWGESPSSVGSKFGVTMAELVATN-GLSQSVVETF  144 (144)
Q Consensus       108 y~V~~GdTl~~IA~~~~~s~~~l~~~N-~l~~~~i~~~  144 (144)
                      |+|++|||+++||++|++++++|+++| ++.++.|++|
T Consensus         1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G   38 (44)
T PF01476_consen    1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPG   38 (44)
T ss_dssp             EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTT
T ss_pred             CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCC
Confidence            899999999999999999999999999 8877668876

This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.

>PRK14125 cell division suppressor protein YneA; Provisional

Probab=99.13  E-value=1.7e-10  Score=77.17  Aligned_cols=49  Identities=16%  Similarity=0.198  Sum_probs=42.2

Q ss_pred             CceeeEeCCCCCHHHHHHHhCCCCC--------HHHHHhhcCCCCC-CCCCcEEEEeccc
Q 040730           41 KSTTNNVRPADTIDSILNGFGGLVS--------AEQINSTSELSHP-VNDWTKLMIMLPC   91 (144)
Q Consensus        41 ~~~~y~V~~GdTl~~IA~~y~~~~~--------~~~l~~~N~~~~~-l~~Gq~l~IP~~~   91 (144)
                      ....|+|++|||||+||++|+  ++        +++|++.|.+.++ |++||.|.||...
T Consensus        35 ~~~~~tV~~GDTLW~IA~~y~--~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~   92 (103)
T PRK14125         35 QYVEITVQEGDTLWALADQYA--GKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLK   92 (103)
T ss_pred             CcEEEEECCCCCHHHHHHHhC--CCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCC
Confidence            347899999999999999997  43        5788889999877 9999999999753

>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]

Probab=99.02  E-value=1e-09  Score=75.44  Aligned_cols=82  Identities=18%  Similarity=0.265  Sum_probs=63.3

Q ss_pred             cccCCCCCCCCCCCcceecCCCEEEEccCCCCCCC-Cc----cc-------------CceeeEeCCCCCHHHHHHHhCCC
Q 040730            2 LVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDG-IR----HS-------------KSTTNNVRPADTIDSILNGFGGL   63 (144)
Q Consensus         2 ~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~~-~~----~~-------------~~~~y~V~~GdTl~~IA~~y~~~   63 (144)
                      .++|.+..     ..+.+.+||.|.+|....-... ..    ..             ....|+|++||||+.||++|+  
T Consensus        13 ~~~n~~~~-----~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~~Ia~~~~--   85 (124)
T COG1388          13 KKANALTG-----KSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLSKIARKYG--   85 (124)
T ss_pred             HHHhcccC-----CCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHHHHHHHhC--
Confidence            45677762     2678999999999974221110 00    00             125799999999999999999  


Q ss_pred             CCHHHHHhhcCCCCC-CCCCcEEEEecc
Q 040730           64 VSAEQINSTSELSHP-VNDWTKLMIMLP   90 (144)
Q Consensus        64 ~~~~~l~~~N~~~~~-l~~Gq~l~IP~~   90 (144)
                      +++.+|+++|.+.++ +++||.|.++..
T Consensus        86 ~tv~~l~~~n~l~~~~i~~gq~l~~~~~  113 (124)
T COG1388          86 VTVAELKQLNNLSSDKIKVGQKLKLPVS  113 (124)
T ss_pred             CCHHHHHHHhccCCCceecCcEEEEecc
Confidence            999999999999988 999999999863

>TIGR02899 spore_safA spore coat assembly protein SafA

Probab=98.97  E-value=1.1e-09  Score=61.38  Aligned_cols=40  Identities=25%  Similarity=0.360  Sum_probs=35.7

Q ss_pred             eCCCCCHHHHHHHhCCCCCHHHHHhhcCC-CCC--CCCCcEEEEe
Q 040730           47 VRPADTIDSILNGFGGLVSAEQINSTSEL-SHP--VNDWTKLMIM   88 (144)
Q Consensus        47 V~~GdTl~~IA~~y~~~~~~~~l~~~N~~-~~~--l~~Gq~l~IP   88 (144)
                      |++|||||+||++|+  ++.++|.++|+. .++  +.+||.|.||
T Consensus         1 v~~gdtl~~IA~~~~--~~~~~l~~~N~~~~~~~~~~~g~~l~ip   43 (44)
T TIGR02899         1 VQKGDTLWKIAKKYG--VDFDELIQANPQLSNPNLIYPGMKIKIP   43 (44)
T ss_pred             CCCCCCHHHHHHHHC--cCHHHHHHHhhcCCCCCCcCCCCEEecC
Confidence            589999999999999  899999999984 343  9999999998

in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.

>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation

Probab=98.96  E-value=2.1e-09  Score=59.56  Aligned_cols=43  Identities=35%  Similarity=0.474  Sum_probs=39.2

Q ss_pred             eeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEe
Q 040730           44 TNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIM   88 (144)
Q Consensus        44 ~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP   88 (144)
                      .|+|++|||++.||++|+  ++.++|.++|+....  +.+|+.|.||
T Consensus         2 ~~~v~~gdt~~~ia~~~~--~~~~~~~~~N~~~~~~~~~~g~~l~ip   46 (46)
T cd00118           2 TYTVKKGDTLSSIAQRYG--ISVEELLKLNGLSDPDNLQVGQKLKIP   46 (46)
T ss_pred             EEEECCCCCHHHHHHHHC--cCHHHHHHHcCCCCccccCCCCEEecC
Confidence            689999999999999998  999999999998543  9999999987

This domain may have a general peptidoglycan binding function.

>PRK14125 cell division suppressor protein YneA; Provisional

Probab=98.94  E-value=1.5e-09  Score=72.58  Aligned_cols=41  Identities=15%  Similarity=0.191  Sum_probs=36.3

Q ss_pred             ceEEEEeccCCcHHHHHHHhCCC--------HHHHHHHcCCCCCCcccC
Q 040730          104 IYKSYVVQWGESPSSVGSKFGVT--------MAELVATNGLSQSVVETF  144 (144)
Q Consensus       104 ~~~~y~V~~GdTl~~IA~~~~~s--------~~~l~~~N~l~~~~i~~~  144 (144)
                      ...+|+|++|||||+||++|+++        ++.|++.|+++++.|+||
T Consensus        35 ~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~G   83 (103)
T PRK14125         35 QYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAG   83 (103)
T ss_pred             CcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCC
Confidence            45789999999999999999875        577888999998899987

>COG3858 Predicted glycosyl hydrolase [General function prediction only]

Probab=98.90  E-value=1.7e-09  Score=87.03  Aligned_cols=80  Identities=19%  Similarity=0.165  Sum_probs=70.6

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHHHHH
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGS  121 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~  121 (144)
                      ..|.|++||++..|+++|.  .+..+|...|.+..+ +.+||.+.||..              ...|.|++|||+++||+
T Consensus         2 ~i~~~~pg~~~~~i~~~~~--~~~~~i~~~~~~~~d~~~~~q~~~v~~~--------------~~~y~~~~~d~~~Sia~   65 (423)
T COG3858           2 SIHLVGPGDSRLIIAVYFP--YTNNRIVNGNDYTNDDLVDGQTFVVPPS--------------GHFYDVGPGDTLTSIAR   65 (423)
T ss_pred             EEEEccCCceeeeehhhcc--ccccccccccccccccccCceeEEECCc--------------ceEEEecCCcchhhhhh
Confidence            3689999999999999999  899999777777766 999999999853              25799999999999999


Q ss_pred             HhCCCHHHHHHHcCCCC
Q 040730          122 KFGVTMAELVATNGLSQ  138 (144)
Q Consensus       122 ~~~~s~~~l~~~N~l~~  138 (144)
                      +|+++++.+..+|....
T Consensus        66 ~~~vt~~~~~~m~~~~~   82 (423)
T COG3858          66 TVGVTQDSAAIMNFVIC   82 (423)
T ss_pred             hhcCCHHHHHhhccccc
Confidence            99999999999997643

>PRK10871 nlpD lipoprotein NlpD; Provisional

Probab=98.88  E-value=2.6e-09  Score=84.20  Aligned_cols=47  Identities=19%  Similarity=0.160  Sum_probs=43.3

Q ss_pred             ceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730           42 STTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP   90 (144)
Q Consensus        42 ~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~   90 (144)
                      ...|+|++|||||.||++|+  +++.+|.++|.+.++  |++||.|.||..
T Consensus        60 ~~~y~Vk~GDTL~~IA~~~g--~~~~~La~~N~l~~p~~I~~GQ~L~i~~~  108 (319)
T PRK10871         60 GSTYTVKKGDTLFYIAWITG--NDFRDLAQRNNIQAPYSLNVGQTLQVGNA  108 (319)
T ss_pred             CCceEECCCCHHHHHHHHHC--cCHHHHHHhcCCCCCccccCCCEEEeCCC
Confidence            36899999999999999999  999999999999876  999999999754

>TIGR02907 spore_VI_D stage VI sporulation protein D

Probab=98.84  E-value=5.7e-09  Score=82.04  Aligned_cols=44  Identities=27%  Similarity=0.322  Sum_probs=41.6

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEe
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIM   88 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP   88 (144)
                      ..|+|++|||||.||++|+  ++++.|+++|++... |++||.|.||
T Consensus       294 ~~YiVq~GDTL~sIAkRYG--VSV~~L~r~N~L~~~~L~~GQ~L~IP  338 (338)
T TIGR02907       294 RMCIVQEGDTIETIAERYE--ISVSQLIRHNQLEDFEVNEGQILYIP  338 (338)
T ss_pred             EEEEECCCCCHHHHHHHHC--cCHHHHHHHhCCCccccCCCCEEEeC
Confidence            7899999999999999999  999999999998855 9999999997

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.

>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation

Probab=98.77  E-value=1.6e-08  Score=55.93  Aligned_cols=38  Identities=29%  Similarity=0.588  Sum_probs=33.5

Q ss_pred             EEEeccCCcHHHHHHHhCCCHHHHHHHcCC-CCCCcccC
Q 040730          107 SYVVQWGESPSSVGSKFGVTMAELVATNGL-SQSVVETF  144 (144)
Q Consensus       107 ~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l-~~~~i~~~  144 (144)
                      +|+|++|||+++||++|+++..+|.++|+. ....+.+|
T Consensus         2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g   40 (46)
T cd00118           2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVG   40 (46)
T ss_pred             EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCC
Confidence            589999999999999999999999999998 44556654

This domain may have a general peptidoglycan binding function.

>TIGR02899 spore_safA spore coat assembly protein SafA

Probab=98.71  E-value=1.8e-08  Score=56.32  Aligned_cols=35  Identities=31%  Similarity=0.471  Sum_probs=29.6

Q ss_pred             eccCCcHHHHHHHhCCCHHHHHHHcC-CCC-CCcccC
Q 040730          110 VQWGESPSSVGSKFGVTMAELVATNG-LSQ-SVVETF  144 (144)
Q Consensus       110 V~~GdTl~~IA~~~~~s~~~l~~~N~-l~~-~~i~~~  144 (144)
                      |++|||||+||++|++++++|.++|+ +.+ ..+++|
T Consensus         1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g   37 (44)
T TIGR02899         1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPG   37 (44)
T ss_pred             CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCC
Confidence            68899999999999999999999997 433 456665

in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.

>TIGR02907 spore_VI_D stage VI sporulation protein D

Probab=98.67  E-value=2.9e-08  Score=78.16  Aligned_cols=41  Identities=17%  Similarity=0.341  Sum_probs=37.3

Q ss_pred             ceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730          104 IYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF  144 (144)
Q Consensus       104 ~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~~  144 (144)
                      ....|+|++|||||+||+|||++++.|+++|++.+..|++|
T Consensus       292 ~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~G  332 (338)
T TIGR02907       292 KLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEG  332 (338)
T ss_pred             ccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCC
Confidence            34689999999999999999999999999999987778876

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.

>smart00257 LysM Lysin motif

Probab=98.64  E-value=9.4e-08  Score=52.11  Aligned_cols=42  Identities=26%  Similarity=0.373  Sum_probs=36.4

Q ss_pred             eeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCC-C-CCCCcEEEE
Q 040730           44 TNNVRPADTIDSILNGFGGLVSAEQINSTSELSH-P-VNDWTKLMI   87 (144)
Q Consensus        44 ~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~-~-l~~Gq~l~I   87 (144)
                      .|+|++|||++.||++|+  ++.++|.++|+... . +.+|+.|.|
T Consensus         1 ~~~v~~gdt~~~ia~~~~--~~~~~~~~~N~~~~~~~~~~g~~l~i   44 (44)
T smart00257        1 TYTVKKGDTLSSIARRYG--ISVSDLLELNNILDPDNLQVGQKLKI   44 (44)
T ss_pred             CeEeCCCCCHHHHHHHhC--CCHHHHHHHcCCCCccccCCCCEEeC
Confidence            488999999999999999  89999999999543 3 889998864

>smart00257 LysM Lysin motif

Probab=98.62  E-value=7.3e-08  Score=52.57  Aligned_cols=38  Identities=21%  Similarity=0.525  Sum_probs=32.5

Q ss_pred             EEEeccCCcHHHHHHHhCCCHHHHHHHcCC-CCCCcccC
Q 040730          107 SYVVQWGESPSSVGSKFGVTMAELVATNGL-SQSVVETF  144 (144)
Q Consensus       107 ~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l-~~~~i~~~  144 (144)
                      +|+|++|||+++||++|+++.++|.++|+. ....+++|
T Consensus         1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g   39 (44)
T smart00257        1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVG   39 (44)
T ss_pred             CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCC
Confidence            388999999999999999999999999994 44556654

>PRK13914 invasion associated secreted endopeptidase; Provisional

Probab=98.59  E-value=8.9e-08  Score=79.02  Aligned_cols=46  Identities=35%  Similarity=0.353  Sum_probs=43.4

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEecc
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIMLP   90 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~~   90 (144)
                      ..|+|++|||||.||++|+  +++++|+++|++... |++||.|.||..
T Consensus       200 ~tytVq~GDTL~sIAkrYg--Vtv~eI~~~N~l~s~~L~pGQ~L~Ip~s  246 (481)
T PRK13914        200 TTHAVKSGDTIWALSVKYG--VSVQDIMSWNNLSSSSIYVGQKLAIKQT  246 (481)
T ss_pred             eEEEECCCCCHHHHHHHHC--CCHHHHHHhcCCCccccCCCCEEEecCC
Confidence            5899999999999999999  999999999999877 999999999965

>PRK10871 nlpD lipoprotein NlpD; Provisional

Probab=98.56  E-value=6.5e-08  Score=76.36  Aligned_cols=39  Identities=15%  Similarity=0.207  Sum_probs=35.3

Q ss_pred             EEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCC-CCcccC
Q 040730          106 KSYVVQWGESPSSVGSKFGVTMAELVATNGLSQ-SVVETF  144 (144)
Q Consensus       106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~-~~i~~~  144 (144)
                      .+|+|++|||||+||.+||+++.+|.+||+|.+ ..|++|
T Consensus        61 ~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~G  100 (319)
T PRK10871         61 STYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVG  100 (319)
T ss_pred             CceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCC
Confidence            479999999999999999999999999999965 468876

>PRK11198 LysM domain/BON superfamily protein; Provisional

Probab=98.55  E-value=1.3e-07  Score=67.12  Aligned_cols=46  Identities=22%  Similarity=0.234  Sum_probs=38.8

Q ss_pred             eeeEeCCCCCHHHHHHHhCC-CCCHHHHHhhcC--CCCC--CCCCcEEEEe
Q 040730           43 TTNNVRPADTIDSILNGFGG-LVSAEQINSTSE--LSHP--VNDWTKLMIM   88 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~-~~~~~~l~~~N~--~~~~--l~~Gq~l~IP   88 (144)
                      ..|+|++|||||.||++|.+ ...+..|.++|+  +.++  |.+||.|.||
T Consensus        96 ~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP  146 (147)
T PRK11198         96 QFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP  146 (147)
T ss_pred             eEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence            67999999999999998743 245789999998  5554  9999999998

>COG3858 Predicted glycosyl hydrolase [General function prediction only]

Probab=98.02  E-value=9.7e-06  Score=65.70  Aligned_cols=62  Identities=26%  Similarity=0.242  Sum_probs=54.9

Q ss_pred             cceecCCCEEEEccCCCCCCCCcccCceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730           16 NQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP   90 (144)
Q Consensus        16 ~~~l~~Gq~l~IP~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~   90 (144)
                      ++.|..||.+.||..           ...|.|++|||+++||++|+  ++.+.++.+|....+  ++.|-.+.+|..
T Consensus        34 ~d~~~~~q~~~v~~~-----------~~~y~~~~~d~~~Sia~~~~--vt~~~~~~m~~~~~~~~l~~~~~l~~P~~   97 (423)
T COG3858          34 NDDLVDGQTFVVPPS-----------GHFYDVGPGDTLTSIARTVG--VTQDSAAIMNFVICPGYLQYGLNLYIPSA   97 (423)
T ss_pred             cccccCceeEEECCc-----------ceEEEecCCcchhhhhhhhc--CCHHHHHhhcccccccceeeeeEEeccCC
Confidence            377899999999953           35899999999999999999  999999999988875  999999999864

>PRK11198 LysM domain/BON superfamily protein; Provisional

Probab=98.01  E-value=7.8e-06  Score=58.02  Aligned_cols=40  Identities=18%  Similarity=0.203  Sum_probs=32.7

Q ss_pred             eEEEEeccCCcHHHHHHHhC---CCHHHHHHHcC--CCC-CCcccC
Q 040730          105 YKSYVVQWGESPSSVGSKFG---VTMAELVATNG--LSQ-SVVETF  144 (144)
Q Consensus       105 ~~~y~V~~GdTl~~IA~~~~---~s~~~l~~~N~--l~~-~~i~~~  144 (144)
                      ..+|+|++|||||+||++|.   ..+.+|+++|+  +.+ ..|+||
T Consensus        95 ~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pG  140 (147)
T PRK11198         95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPG  140 (147)
T ss_pred             CeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcC
Confidence            35799999999999999985   34789999998  654 458876

>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]

Probab=97.56  E-value=2.7e-05  Score=60.23  Aligned_cols=48  Identities=29%  Similarity=0.329  Sum_probs=41.2

Q ss_pred             eeeEeCCCCCHHHHHH-HhCCCCCHHHHHhhcC---CCCC--CCCCcEEEEecc
Q 040730           43 TTNNVRPADTIDSILN-GFGGLVSAEQINSTSE---LSHP--VNDWTKLMIMLP   90 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~-~y~~~~~~~~l~~~N~---~~~~--l~~Gq~l~IP~~   90 (144)
                      .+|+|++|||||.||+ .|+....+..|..+|.   +.++  |.+||.|.||..
T Consensus       211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~  264 (269)
T COG1652         211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ  264 (269)
T ss_pred             eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence            3899999999999999 7887677789999999   3444  999999999964

>PRK10190 L,D-transpeptidase; Provisional

Probab=97.54  E-value=0.00022  Score=56.22  Aligned_cols=46  Identities=11%  Similarity=0.120  Sum_probs=41.5

Q ss_pred             eeeEeCCCC--CHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730           43 TTNNVRPAD--TIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP   90 (144)
Q Consensus        43 ~~y~V~~Gd--Tl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~   90 (144)
                      ..|+|+.+|  +|..||++|+  +...+|+++|+..++  .++|++|.||..
T Consensus        38 ~~~~v~~~~~~~le~iA~~f~--~g~~~l~~aNPgvd~~~p~~G~~i~iP~~   87 (310)
T PRK10190         38 LTVTVPDHNTQPLETFAAQYG--QGLSNMLEANPGADVFLPKSGSQLTIPQQ   87 (310)
T ss_pred             EEEEecCCCCccHHHHHHHhC--CCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence            679999866  5999999999  999999999999988  679999999964

>PRK10260 L,D-transpeptidase; Provisional

Probab=97.52  E-value=0.00024  Score=55.94  Aligned_cols=46  Identities=7%  Similarity=0.034  Sum_probs=41.3

Q ss_pred             eeeEeCCCC--CHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730           43 TTNNVRPAD--TIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP   90 (144)
Q Consensus        43 ~~y~V~~Gd--Tl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~   90 (144)
                      ..|+|++|+  +|..||++|+  +...+|+++|+..++  .++|++|.||..
T Consensus        41 ~~~~v~~~~~~~le~iA~~f~--~g~~~l~~aNPgvdp~lp~~G~~i~iP~~   90 (306)
T PRK10260         41 QVITIPEGNTQPLEYFAAEYQ--MGLSNMMEANPGVDTFLPKGGTVLNIPQQ   90 (306)
T ss_pred             EEEEeCCCCCchHHHHHHHhC--CCHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence            689999966  5999999999  999999999999987  579999999964

>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein

Probab=97.36  E-value=0.00014  Score=46.95  Aligned_cols=46  Identities=20%  Similarity=0.281  Sum_probs=26.4

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhh---cCCCC---CCCCCcEEEEecc
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINST---SELSH---PVNDWTKLMIMLP   90 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~---N~~~~---~l~~Gq~l~IP~~   90 (144)
                      ..|+|++||||..|-++++  ++..+|.++   .....   .|+|||.|.+-..
T Consensus         3 ~~~~V~~GDtLs~iF~~~g--ls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d   54 (85)
T PF04225_consen    3 QEYTVKSGDTLSTIFRRAG--LSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD   54 (85)
T ss_dssp             -EEE--TT--HHHHHHHTT----HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred             cEEEECCCCcHHHHHHHcC--CCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence            3699999999999999998  888776655   32222   2999999998764

This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.

>TIGR03505 FimV_core FimV N-terminal domain

Probab=97.04  E-value=0.00072  Score=42.52  Aligned_cols=40  Identities=18%  Similarity=-0.002  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhC--CCCCHH----HHHhhcCCC----CC--CCCCcEEEEecc
Q 040730           51 DTIDSILNGFG--GLVSAE----QINSTSELS----HP--VNDWTKLMIMLP   90 (144)
Q Consensus        51 dTl~~IA~~y~--~~~~~~----~l~~~N~~~----~~--l~~Gq~l~IP~~   90 (144)
                      ||||+||++|.  +-+++.    .|.+.|+..    +.  |++|+.|.||..
T Consensus         1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~   52 (74)
T TIGR03505         1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE   52 (74)
T ss_pred             CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence            89999999884  224554    677889854    12  999999999964

This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.

>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein

Probab=96.98  E-value=0.00092  Score=43.12  Aligned_cols=28  Identities=25%  Similarity=0.473  Sum_probs=18.0

Q ss_pred             EEEEeccCCcHHHHHHHhCCCHHHHHHH
Q 040730          106 KSYVVQWGESPSSVGSKFGVTMAELVAT  133 (144)
Q Consensus       106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~  133 (144)
                      ..|+|++||||+.|-+++|++..+|.++
T Consensus         3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v   30 (85)
T PF04225_consen    3 QEYTVKSGDTLSTIFRRAGLSASDLYAV   30 (85)
T ss_dssp             -EEE--TT--HHHHHHHTT--HHHHHHH
T ss_pred             cEEEECCCCcHHHHHHHcCCCHHHHHHH
Confidence            3699999999999999999998777554

This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.

>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX

Probab=96.73  E-value=0.0026  Score=38.33  Aligned_cols=45  Identities=20%  Similarity=0.158  Sum_probs=34.4

Q ss_pred             eEeCCCCCHHHHHH-HhCCCCCH-HHHHhhcCCCC---C-CCCCcEEEEecc
Q 040730           45 NNVRPADTIDSILN-GFGGLVSA-EQINSTSELSH---P-VNDWTKLMIMLP   90 (144)
Q Consensus        45 y~V~~GdTl~~IA~-~y~~~~~~-~~l~~~N~~~~---~-l~~Gq~l~IP~~   90 (144)
                      |+. .|||+..|+. .||..-.. +.+.++|+...   + |..|..|.+|.-
T Consensus         4 ~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i   54 (60)
T PF05489_consen    4 YTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI   54 (60)
T ss_pred             EEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence            444 9999999999 56643223 78999999752   3 999999999953

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.

>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]

Probab=95.93  E-value=0.038  Score=41.59  Aligned_cols=75  Identities=15%  Similarity=0.181  Sum_probs=48.7

Q ss_pred             CcceecCCCEEEEccCCCC-CCCCcccCceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCC---CC---CCCCcEEEE
Q 040730           15 GNQILGTKSLVKVPISCPC-IDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELS---HP---VNDWTKLMI   87 (144)
Q Consensus        15 ~~~~l~~Gq~l~IP~~~~~-~~~~~~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~---~~---l~~Gq~l~I   87 (144)
                      ....++.+|...+|..... +.......-.+|+|+.|+||..+-|..+  ....|+-.+-...   .+   |+.||.+.|
T Consensus       131 e~~p~q~~q~~~v~~~~~~~P~~~s~g~wqsy~V~~G~TLaQlFRdn~--LpitDVnAMakveGagkpLSnlkaGq~Vki  208 (242)
T COG3061         131 EPEPIQAKQEKKVPRTVDAQPFKPSSGNWQSYTVPQGKTLAQLFRDNN--LPITDVNAMAKVEGAGKPLSNLKAGQKVKI  208 (242)
T ss_pred             ccchhhccCccccCCccccCccccCcccceeEEecCCccHHHHHhccC--CChHHhHHHHhhccCCCchhhccCCCEEEE
Confidence            3445667788887743221 1111111347999999999999999776  6666665443322   22   999999999


Q ss_pred             eccc
Q 040730           88 MLPC   91 (144)
Q Consensus        88 P~~~   91 (144)
                      -...
T Consensus       209 ~~na  212 (242)
T COG3061         209 SLNA  212 (242)
T ss_pred             EEcC
Confidence            8764

>PRK11649 putative peptidase; Provisional

Probab=95.80  E-value=0.061  Score=44.66  Aligned_cols=91  Identities=20%  Similarity=0.136  Sum_probs=57.8

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcC-CC--CCCCCCcEEEEecccccCC--------CC-------CCCc---
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSE-LS--HPVNDWTKLMIMLPCTCFN--------NG-------NNGV---  101 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~-~~--~~l~~Gq~l~IP~~~~~~~--------~~-------~~~~---  101 (144)
                      ..|+|++||||..|=++++  ++..++.++-. ..  ..|++||.|.+-......-        ..       ..+.   
T Consensus        96 ~~~~Vk~GDTl~~iL~r~G--i~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg~F~~  173 (439)
T PRK11649         96 HEYVVSTGDTLSSILNQYG--IDMSDISQLAAQDKELRNLKIGQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGNGFKE  173 (439)
T ss_pred             EEEEeCCCCCHHHHHHHcC--CCHHHHHHHHHcChHhhcCCCCCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCCcEEE
Confidence            4899999999999999999  89888776622 11  2399999999864321100        00       0000   


Q ss_pred             -------ccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730          102 -------TSIYKSYVVQWGESPSSVGSKFGVTMAELVATNG  135 (144)
Q Consensus       102 -------~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~  135 (144)
                             ..........-..+|+.-|.+-|++...++++..
T Consensus       174 ~~~~~~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~  214 (439)
T PRK11649        174 TSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIK  214 (439)
T ss_pred             EEeecccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHH
Confidence                   0000011122256899999999999887776654

>PRK10260 L,D-transpeptidase; Provisional

Probab=95.06  E-value=0.044  Score=43.32  Aligned_cols=36  Identities=6%  Similarity=0.146  Sum_probs=30.7

Q ss_pred             ceEEEEeccCC--cHHHHHHHhCCCHHHHHHHcCCCCC
Q 040730          104 IYKSYVVQWGE--SPSSVGSKFGVTMAELVATNGLSQS  139 (144)
Q Consensus       104 ~~~~y~V~~Gd--Tl~~IA~~~~~s~~~l~~~N~l~~~  139 (144)
                      ....|+|+.|+  +|..||++|++...+|+++|+--++
T Consensus        39 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp   76 (306)
T PRK10260         39 QNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDT   76 (306)
T ss_pred             ccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCC
Confidence            34679999966  5999999999999999999997554

>PRK10190 L,D-transpeptidase; Provisional

Probab=94.96  E-value=0.048  Score=43.20  Aligned_cols=36  Identities=8%  Similarity=0.122  Sum_probs=30.7

Q ss_pred             ceEEEEeccCC--cHHHHHHHhCCCHHHHHHHcCCCCC
Q 040730          104 IYKSYVVQWGE--SPSSVGSKFGVTMAELVATNGLSQS  139 (144)
Q Consensus       104 ~~~~y~V~~Gd--Tl~~IA~~~~~s~~~l~~~N~l~~~  139 (144)
                      ....|+|+.+|  +|..||++|++...+|+++|+--++
T Consensus        36 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~   73 (310)
T PRK10190         36 QSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADV   73 (310)
T ss_pred             ceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCC
Confidence            34679999866  5999999999999999999997554

>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.30  E-value=0.034  Score=48.30  Aligned_cols=49  Identities=18%  Similarity=0.121  Sum_probs=37.0

Q ss_pred             ceeeEeCCCCCHHHHHHHhCC--CCCH----HHHHhhcCCCC------CCCCCcEEEEecc
Q 040730           42 STTNNVRPADTIDSILNGFGG--LVSA----EQINSTSELSH------PVNDWTKLMIMLP   90 (144)
Q Consensus        42 ~~~y~V~~GdTl~~IA~~y~~--~~~~----~~l~~~N~~~~------~l~~Gq~l~IP~~   90 (144)
                      +.+|+|++|||||.||.+-.+  -+|+    ..|.++|+-..      .+++|++|.||..
T Consensus       188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~  248 (755)
T COG3170         188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA  248 (755)
T ss_pred             CcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence            478999999999999985432  2344    45677788541      2999999999964

>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]

Probab=94.15  E-value=0.016  Score=44.86  Aligned_cols=39  Identities=15%  Similarity=0.278  Sum_probs=30.2

Q ss_pred             EEEEeccCCcHHHHHHH-hCCC--HHHHHHHcC---CC-CCCcccC
Q 040730          106 KSYVVQWGESPSSVGSK-FGVT--MAELVATNG---LS-QSVVETF  144 (144)
Q Consensus       106 ~~y~V~~GdTl~~IA~~-~~~s--~~~l~~~N~---l~-~~~i~~~  144 (144)
                      .+|+|++|||||.||++ ||..  ...|..+|+   ++ .+.|+||
T Consensus       211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pG  256 (269)
T COG1652         211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPG  256 (269)
T ss_pred             eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCc
Confidence            38999999999999965 6654  578889998   54 3457775

>TIGR03505 FimV_core FimV N-terminal domain

Probab=93.76  E-value=0.065  Score=33.63  Aligned_cols=22  Identities=14%  Similarity=0.253  Sum_probs=17.2

Q ss_pred             CcHHHHHHHh---C-CCHH----HHHHHcC
Q 040730          114 ESPSSVGSKF---G-VTMA----ELVATNG  135 (144)
Q Consensus       114 dTl~~IA~~~---~-~s~~----~l~~~N~  135 (144)
                      ||||+||++|   + +++.    .|.+.|+
T Consensus         1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp   30 (74)
T TIGR03505         1 DTLWGIAQRVRPDNSVSLYQMMLALYRANP   30 (74)
T ss_pred             CcHHHHHHHHccCCCCCHHHHHHHHHHHCH
Confidence            8999999999   3 6765    5667775

This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.

>PRK11649 putative peptidase; Provisional

Probab=92.78  E-value=0.15  Score=42.42  Aligned_cols=28  Identities=29%  Similarity=0.587  Sum_probs=25.5

Q ss_pred             EEEEeccCCcHHHHHHHhCCCHHHHHHH
Q 040730          106 KSYVVQWGESPSSVGSKFGVTMAELVAT  133 (144)
Q Consensus       106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~  133 (144)
                      ..|+|++||||++|-+++|++..++.++
T Consensus        96 ~~~~Vk~GDTl~~iL~r~Gi~~~di~~l  123 (439)
T PRK11649         96 HEYVVSTGDTLSSILNQYGIDMSDISQL  123 (439)
T ss_pred             EEEEeCCCCCHHHHHHHcCCCHHHHHHH
Confidence            5899999999999999999998887766

>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX

Probab=90.56  E-value=0.39  Score=28.81  Aligned_cols=26  Identities=15%  Similarity=0.304  Sum_probs=21.0

Q ss_pred             ccCCcHHHHH-HHhCCC---HHHHHHHcCC
Q 040730          111 QWGESPSSVG-SKFGVT---MAELVATNGL  136 (144)
Q Consensus       111 ~~GdTl~~IA-~~~~~s---~~~l~~~N~l  136 (144)
                      +.||||..|+ +.||-.   ++.+.++|+-
T Consensus         6 ~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~   35 (60)
T PF05489_consen    6 TQGDTLDLIAYRHYGREDGAVEALLEANPG   35 (60)
T ss_pred             eCcCcHHHHHHHHhCcHHHHHHHHHHHChh
Confidence            4899999999 557765   4788999974

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.

>PF13518 HTH_28: Helix-turn-helix domain

Probab=89.57  E-value=0.39  Score=27.08  Aligned_cols=24  Identities=21%  Similarity=0.288  Sum_probs=20.6

Q ss_pred             ccCCcHHHHHHHhCCCHHHHHHHc
Q 040730          111 QWGESPSSVGSKFGVTMAELVATN  134 (144)
Q Consensus       111 ~~GdTl~~IA~~~~~s~~~l~~~N  134 (144)
                      ..|.|+..+|++||++...+..|=
T Consensus        10 ~~g~s~~~~a~~~gis~~tv~~w~   33 (52)
T PF13518_consen   10 LEGESVREIAREFGISRSTVYRWI   33 (52)
T ss_pred             HcCCCHHHHHHHHCCCHhHHHHHH
Confidence            468899999999999998887763

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=88.45  E-value=0.61  Score=26.02  Aligned_cols=23  Identities=22%  Similarity=0.323  Sum_probs=17.7

Q ss_pred             ccCCcHHHHHHHhCCCHHHHHHH
Q 040730          111 QWGESPSSVGSKFGVTMAELVAT  133 (144)
Q Consensus       111 ~~GdTl~~IA~~~~~s~~~l~~~  133 (144)
                      +.|-++..||+.||++...|.++
T Consensus        19 ~~G~si~~IA~~~gvsr~TvyR~   41 (45)
T PF02796_consen   19 AEGMSIAEIAKQFGVSRSTVYRY   41 (45)
T ss_dssp             HTT--HHHHHHHTTS-HHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHH
Confidence            67899999999999999988764

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>COG4784 Putative Zn-dependent protease [General function prediction only]

Probab=87.03  E-value=1  Score=36.54  Aligned_cols=45  Identities=20%  Similarity=0.214  Sum_probs=34.1

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCC-CHHHHHhhcCCCCC--CCCCcEEEE
Q 040730           43 TTNNVRPADTIDSILNGFGGLV-SAEQINSTSELSHP--VNDWTKLMI   87 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~-~~~~l~~~N~~~~~--l~~Gq~l~I   87 (144)
                      ..-+|++|||+.++|.+..|.. +++-++-+|.+...  +++|++++|
T Consensus       429 rvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi  476 (479)
T COG4784         429 RVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI  476 (479)
T ss_pred             EEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence            3467899999999999665522 34566777888754  999999987

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=85.87  E-value=0.51  Score=28.86  Aligned_cols=24  Identities=29%  Similarity=0.447  Sum_probs=20.9

Q ss_pred             eccCCcHHHHHHHhCCCHHHHHHH
Q 040730          110 VQWGESPSSVGSKFGVTMAELVAT  133 (144)
Q Consensus       110 V~~GdTl~~IA~~~~~s~~~l~~~  133 (144)
                      ...|.|+..||++||++...|..|
T Consensus        20 ~~~g~sv~~va~~~gi~~~~l~~W   43 (76)
T PF01527_consen   20 LESGESVSEVAREYGISPSTLYNW   43 (76)
T ss_dssp             HHHHCHHHHHHHHHTS-HHHHHHH
T ss_pred             HHCCCceEeeecccccccccccHH
Confidence            478999999999999999999877

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>COG5004 P2-like prophage tail protein X [General function prediction only]

Probab=85.16  E-value=1.6  Score=26.53  Aligned_cols=47  Identities=15%  Similarity=0.140  Sum_probs=35.5

Q ss_pred             eeEeCCCCCHHHHHH-HhCCCCCH-HHHHhhcCCCC---C-CCCCcEEEEecc
Q 040730           44 TNNVRPADTIDSILN-GFGGLVSA-EQINSTSELSH---P-VNDWTKLMIMLP   90 (144)
Q Consensus        44 ~y~V~~GdTl~~IA~-~y~~~~~~-~~l~~~N~~~~---~-l~~Gq~l~IP~~   90 (144)
                      +|....|||+..+.. .|+....+ +.+..+|+...   + +..|-.|.+|-.
T Consensus         4 ~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~   56 (70)
T COG5004           4 IVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDI   56 (70)
T ss_pred             EEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCC
Confidence            566789999999999 46643222 68889999764   3 888888888854

>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.68  E-value=0.91  Score=35.86  Aligned_cols=49  Identities=24%  Similarity=0.267  Sum_probs=39.3

Q ss_pred             eeeEeCCCCCHHHHHHHhCCC-CCHHHHHhhcCCCCC--CCCCcEEEEeccc
Q 040730           43 TTNNVRPADTIDSILNGFGGL-VSAEQINSTSELSHP--VNDWTKLMIMLPC   91 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~-~~~~~l~~~N~~~~~--l~~Gq~l~IP~~~   91 (144)
                      ..|.|+.||||..++..|-.+ ..+..++..|....+  +++|..|.||.+.
T Consensus         6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~   57 (339)
T COG4254           6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPA   57 (339)
T ss_pred             ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCcc
Confidence            689999999999999977522 123567788888887  9999999999764

>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]

Probab=82.50  E-value=0.76  Score=33.89  Aligned_cols=47  Identities=13%  Similarity=0.193  Sum_probs=38.4

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEeccc
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLPC   91 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~~   91 (144)
                      ..-+++.||||..||=.|.  ..+.+|.+.|.+...  +..-..+.+|...
T Consensus        10 l~~~iq~~dt~~a~al~~~--~~va~i~RvN~~~r~q~f~a~~~i~~pv~~   58 (186)
T KOG2850|consen   10 LEVTIQEGDTLQAIALNYE--SDVADIKRVNNDDREQRFNALRSISIPVTR   58 (186)
T ss_pred             eeeeeccCchhhhHHhhcc--cchhhheeeccchhhhhhccccceecccch
Confidence            4567899999999998888  788999999977653  7777788888653

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=80.57  E-value=2.1  Score=23.88  Aligned_cols=23  Identities=17%  Similarity=0.218  Sum_probs=17.3

Q ss_pred             ccCCcHHHHHHHhCCCHHHHHHH
Q 040730          111 QWGESPSSVGSKFGVTMAELVAT  133 (144)
Q Consensus       111 ~~GdTl~~IA~~~~~s~~~l~~~  133 (144)
                      ..|.|...||+.+|++...+..|
T Consensus        15 ~~G~s~~~ia~~lgvs~~Tv~~w   37 (50)
T PF13384_consen   15 REGWSIREIAKRLGVSRSTVYRW   37 (50)
T ss_dssp             HHT--HHHHHHHHTS-HHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHH
Confidence            34999999999999999888776

>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=80.01  E-value=1.1  Score=39.43  Aligned_cols=33  Identities=24%  Similarity=0.287  Sum_probs=24.3

Q ss_pred             ceEEEEeccCCcHHHHHHHhC----CCH----HHHHHHcCC
Q 040730          104 IYKSYVVQWGESPSSVGSKFG----VTM----AELVATNGL  136 (144)
Q Consensus       104 ~~~~y~V~~GdTl~~IA~~~~----~s~----~~l~~~N~l  136 (144)
                      ...+|+|++|||||+||.+--    +|+    ..|.++|+-
T Consensus       187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~  227 (755)
T COG3170         187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQ  227 (755)
T ss_pred             CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChh
Confidence            346899999999999997643    454    455666753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	144
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	2e-16

>4eby_A Chitin elicitor receptor kinase 1; pathogen-associated molecular patterns, pattern recognition receptors, LYSM, lysine chitin oligomer; HET: NAG BMA; 1.65A {Arabidopsis thaliana} PDB: 4ebz_A* Length = 212

 Score = 72.1 bits (176), Expect = 2e-16
 Identities = 25/137 (18%), Positives = 59/137 (43%), Gaps = 3/137 (2%)

Query: 4   SNSISPMSPSLGNQ-ILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSI-LNGFG 61
            + I   + ++ ++  +   S V VP  C C  G     + + +VR  DT + + ++ + 
Sbjct: 39  FDPILRYNSNIKDKDRIQMGSRVLVPFPCECQPGDFLGHNFSYSVRQEDTYERVAISNYA 98

Query: 62  GLVSAEQINSTSELSHP-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVG 120
            L + E + + +      +     L +++ C+C +   +    ++ +Y ++  +S SS+ 
Sbjct: 99  NLTTMESLQARNPFPATNIPLSATLNVLVNCSCGDESVSKDFGLFVTYPLRPEDSLSSIA 158

Query: 121 SKFGVTMAELVATNGLS 137
              GV+   L   N   
Sbjct: 159 RSSGVSADILQRYNPGV 175

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	144
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	100.0
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	99.91
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	99.75
2gu1_A	361	Zinc peptidase; alpha/beta, beta barrel, structura	99.55
2djp_A	77	Hypothetical protein SB145; LYSM, structural genom	99.44
2djp_A	77	Hypothetical protein SB145; LYSM, structural genom	99.33
1e0g_A	48	Membrane-bound lytic murein transglycosylase D; ce	99.32
1e0g_A	48	Membrane-bound lytic murein transglycosylase D; ce	99.22
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	99.03
4a1k_A	165	Putative L, D-transpeptidase YKUD; transferase, pe	98.76
2gu1_A	361	Zinc peptidase; alpha/beta, beta barrel, structura	98.32
3slu_A	371	M23 peptidase domain protein; outer membrane, hydr	97.58
3slu_A	371	M23 peptidase domain protein; outer membrane, hydr	95.34
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	85.13

>4eby_A Chitin elicitor receptor kinase 1; pathogen-associated molecular patterns, pattern recognition receptors, LYSM, lysine chitin oligomer; HET: NAG BMA; 1.65A {Arabidopsis thaliana} PDB: 4ebz_A*

Probab=100.00  E-value=4.9e-34  Score=212.46  Aligned_cols=137  Identities=20%  Similarity=0.302  Sum_probs=113.0

Q ss_pred             CcccC-CCCCCCCCCCcceecCCCEEEEccCCCCCCCCcccCceeeEeCCCCCHHHHH-HHhCCCCCHHHHHhhcCCCCC
Q 040730            1 ILVSN-SISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSIL-NGFGGLVSAEQINSTSELSHP   78 (144)
Q Consensus         1 l~~~N-~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~~~~~~~~~~y~V~~GdTl~~IA-~~y~~~~~~~~l~~~N~~~~~   78 (144)
                      |+++| +|.      ..+.|++||.|+||..|.|..+........|+|++|||||.|| ++|++++++++|+++|++...
T Consensus        42 I~~~Np~l~------~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~~~y~~lvt~~~L~~~N~~~~~  115 (212)
T 4eby_A           42 ILRYNSNIK------DKDRIQMGSRVLVPFPCECQPGDFLGHNFSYSVRQEDTYERVAISNYANLTTMESLQARNPFPAT  115 (212)
T ss_dssp             HHTTCTTCS------CTTSCCTTCEEEEEECCEEETTTEEEEEEEEECCTTCCHHHHHHTTTTTSSCHHHHHHHCCSCTT
T ss_pred             HHHhccCCC------CcCccCCCCEEEEeccccccCCccccCceEEEecCCCcHHHHHHHhcCCCCCHHHHHHhcCCCcc
Confidence            35677 775      4678999999999999998654333345789999999999999 699999999999999996554


Q ss_pred             -CCCCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCccc
Q 040730           79 -VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVET  143 (144)
Q Consensus        79 -l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~  143 (144)
                       |++||.|.||..|.|+............+|+|++|||||+||++||+++++|++||++.+..+.+
T Consensus       116 ~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~~fgvsv~~L~~~N~~~~~~~~~  181 (212)
T 4eby_A          116 NIPLSATLNVLVNCSCGDESVSKDFGLFVTYPLRPEDSLSSIARSSGVSADILQRYNPGVNFNSGN  181 (212)
T ss_dssp             CCCTTCEEEEEEECCCCCTTTCSSCCCEEEEECCTTCCHHHHHHHHTSCHHHHHHHSTTCCTTSCS
T ss_pred             cCCCCCEEEEcCCCcCCCcccccCCCCeEEEEECCCCcHHHHHHHHCcCHHHHHHhcCCCccCCCC
Confidence             99999999999988865432222334578999999999999999999999999999987655543

>4eby_A Chitin elicitor receptor kinase 1; pathogen-associated molecular patterns, pattern recognition receptors, LYSM, lysine chitin oligomer; HET: NAG BMA; 1.65A {Arabidopsis thaliana} PDB: 4ebz_A*

Probab=99.91  E-value=4.5e-24  Score=158.71  Aligned_cols=97  Identities=18%  Similarity=0.285  Sum_probs=84.4

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCH--------HHHHhhc-CCCC-C-CCCCcEEEEecccccCCCCCCCcccceEEEEec
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSA--------EQINSTS-ELSH-P-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQ  111 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~--------~~l~~~N-~~~~-~-l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~  111 (144)
                      ..|+|++|||||.||++|+  +++        ++|+++| .+.+ . |++||.|.||..|.|....   ......+|+|+
T Consensus        10 ~~Y~V~~GDTL~~IA~~~~--vsv~~~~~~~~~~I~~~Np~l~~~~~l~~Gq~L~IP~~~~~~~~~---~~~~~~~Y~V~   84 (212)
T 4eby_A           10 ASYYLENGTTLSVINQNLN--SSIAPYDQINFDPILRYNSNIKDKDRIQMGSRVLVPFPCECQPGD---FLGHNFSYSVR   84 (212)
T ss_dssp             EEEECCTTCCHHHHHHHTC--CSSSCCCSSCCHHHHTTCTTCSCTTSCCTTCEEEEEECCEEETTT---EEEEEEEEECC
T ss_pred             EEEEeCCCCCHHHHHHHHC--CCchhccccCHHHHHHhccCCCCcCccCCCCEEEEeccccccCCc---cccCceEEEec
Confidence            5899999999999999999  898        9999999 6753 3 9999999999998876321   22345789999


Q ss_pred             cCCcHHHHH-HHhC--CCHHHHHHHcCCCCCCcccC
Q 040730          112 WGESPSSVG-SKFG--VTMAELVATNGLSQSVVETF  144 (144)
Q Consensus       112 ~GdTl~~IA-~~~~--~s~~~l~~~N~l~~~~i~~~  144 (144)
                      +|||||+|| ++|+  +++++|+++|++.+..|++|
T Consensus        85 ~GDTL~~IA~~~y~~lvt~~~L~~~N~~~~~~l~~G  120 (212)
T 4eby_A           85 QEDTYERVAISNYANLTTMESLQARNPFPATNIPLS  120 (212)
T ss_dssp             TTCCHHHHHHTTTTTSSCHHHHHHHCCSCTTCCCTT
T ss_pred             CCCcHHHHHHHhcCCCCCHHHHHHhcCCCcccCCCC
Confidence            999999999 8999  99999999999888888886

>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15}

Probab=99.75  E-value=9e-20  Score=130.95  Aligned_cols=94  Identities=14%  Similarity=0.027  Sum_probs=74.5

Q ss_pred             CceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHH
Q 040730           41 KSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSS  118 (144)
Q Consensus        41 ~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~  118 (144)
                      ....|+|++|||||.||++|+  +++.+|+++|++.++  |++||+|.||...................|.|++||||++
T Consensus        61 ~~~~y~V~~GDTL~~IA~~~~--~~~~~l~~~N~~~~~~~i~~Gq~L~ip~~~~~~~~~~~~~~~~~~~~~v~~GdtL~a  138 (167)
T 2l9y_A           61 GTATVTVQQGDTLRDIGRRFD--CDFHEIARRNNIQNEDLIYPGQVLQVPTKGGSGGGAGNFWDSARDVRLVDGGKVLEA  138 (167)
T ss_dssp             SCEEEEECTTCCHHHHHHHTT--CCHHHHHHHHTCCGGGCCCTTEEEEESCCCCCSSSSCCGGGGEEEEEEETTTTEEEE
T ss_pred             CCceEEECCCCcHHHHHHHcC--CCHHHHHHHcCCCCcccccCCCEEEEcCCCCccccccccccccceEEEeCCcCChHH
Confidence            347899999999999999998  999999999999875  9999999999754321101111112346799999999999


Q ss_pred             HHHHhCCCHHHHHHHcCC
Q 040730          119 VGSKFGVTMAELVATNGL  136 (144)
Q Consensus       119 IA~~~~~s~~~l~~~N~l  136 (144)
                      ||++||.++++++.+|..
T Consensus       139 IA~r~G~~v~s~i~Ln~~  156 (167)
T 2l9y_A          139 ELRYSGGWNRSRIYLDEH  156 (167)
T ss_dssp             EEEETTEEEEEEECGGGT
T ss_pred             HHHHcCCceEEEEEcccc
Confidence            999999888777777754

>2gu1_A Zinc peptidase; alpha/beta, beta barrel, structural genomics, PSI, protein structure initiative; 1.90A {Vibrio cholerae}

Probab=99.55  E-value=7.3e-15  Score=116.74  Aligned_cols=100  Identities=13%  Similarity=0.086  Sum_probs=76.9

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCC-----C-CCCCcEEEEecccccCC--------C--------CCC-
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSH-----P-VNDWTKLMIMLPCTCFN--------N--------GNN-   99 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~-----~-l~~Gq~l~IP~~~~~~~--------~--------~~~-   99 (144)
                      ..|+|++||||+.|+++|+  ++.++|.++|.+..     . |++||.|.||.......        .        ... 
T Consensus         8 ~~~~Vk~GDTL~~Ia~r~g--vs~~~l~~~n~~~~~~~~~~~L~~Gq~L~i~~~~~~~l~~l~~~~~~~~~~~~~~~~~g   85 (361)
T 2gu1_A            8 IHYMVKVGDTLSGIFAQLG--VPYSILQKILSVDLDHLQLDMIQPGEELELMMDDMGQLSRLIYHMSIVEKAIYTRENDG   85 (361)
T ss_dssp             EEEECCTTCCHHHHHHHTT--CCHHHHHHHHHHGGGTCCGGGCCTTCEEEEEECTTSCEEEEEEEEETTEEEEEEECTTS
T ss_pred             eEEEECCCCcHHHHHHHcC--CCHHHHHHHHhhcccccchhcCCCCCEEEEEECCCCcceEEEEEcCccceEEEEecCCC
Confidence            6899999999999999999  99999999998752     2 99999999996421100        0        000 


Q ss_pred             ---------CcccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCC------CCcccC
Q 040730          100 ---------GVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQ------SVVETF  144 (144)
Q Consensus       100 ---------~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~------~~i~~~  144 (144)
                               ........|.|+.|||||+||++||+++++|++||++..      ..|++|
T Consensus        86 ~f~~~~~~~~~~~~~~~~~v~igdSL~~iA~~~Gvs~~~i~~ln~i~~~~idf~~~Lr~G  145 (361)
T 2gu1_A           86 SFSYDFQEISGEWREILFSGEINGSFSVSARRVGLTSSQVANITQVMKDKIDFSRSLRAG  145 (361)
T ss_dssp             CEEEEEEECCCEEEEEEEEEESSSCHHHHHHHTTCCHHHHHHHHHHHTTTCCTTTCCCC-
T ss_pred             cceeeecccCceEEEEEEEEEECCcHHHHHHHcCCCHHHHHHHHHhhcccccccccCCCC
Confidence                     001123468999999999999999999999999999843      346665

>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=5.1e-14  Score=88.47  Aligned_cols=60  Identities=22%  Similarity=0.277  Sum_probs=51.7

Q ss_pred             CCCEEEEccCCCCCCCCcccCceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEeccc
Q 040730           21 TKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLPC   91 (144)
Q Consensus        21 ~Gq~l~IP~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~~   91 (144)
                      .||.+.||...         ....|+|++|||||.||++|+  +++++|+++|++.++  |.+||.|.||...
T Consensus         3 ~Gq~l~ip~~~---------~~~~y~V~~GDTL~~IA~~~~--~~~~~l~~~N~l~~~~~l~~Gq~l~iP~~~   64 (77)
T 2djp_A            3 SGSSGCSPVRE---------RRLEHQLEPGDTLAGLALKYG--VTMEQIKRANRLYTNDSIFLKKTLYIPILT   64 (77)
T ss_dssp             CCCCCCCCCCE---------EEEEECCCTTCCHHHHHHHHT--CCHHHHHHHHTCCCSSCGGGSSCEEEEEEC
T ss_pred             CCcEeeccCCC---------CcEEEEECCCCcHHHHHHHHC--cCHHHHHHHcCCCCccccCCCCEEEECCCC
Confidence            58889888531         236799999999999999999  999999999999753  9999999999753

>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=7.5e-13  Score=83.08  Aligned_cols=52  Identities=15%  Similarity=0.106  Sum_probs=44.0

Q ss_pred             CCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCC-CCCcccC
Q 040730           81 DWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLS-QSVVETF  144 (144)
Q Consensus        81 ~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~-~~~i~~~  144 (144)
                      .||.+.+|..            ....+|+|++|||||+||++|++++++|+++|++. ...|++|
T Consensus         3 ~Gq~l~ip~~------------~~~~~y~V~~GDTL~~IA~~~~~~~~~l~~~N~l~~~~~l~~G   55 (77)
T 2djp_A            3 SGSSGCSPVR------------ERRLEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLK   55 (77)
T ss_dssp             CCCCCCCCCC------------EEEEEECCCTTCCHHHHHHHHTCCHHHHHHHHTCCCSSCGGGS
T ss_pred             CCcEeeccCC------------CCcEEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCCccccCCC
Confidence            5788888742            13568999999999999999999999999999997 4578876

>1e0g_A Membrane-bound lytic murein transglycosylase D; cell WALL, hydrolase, glycosidase, lipoprotein, outer membrane, multigene family; NMR {Escherichia coli} SCOP: d.7.1.1

Probab=99.32  E-value=1.9e-12  Score=73.76  Aligned_cols=44  Identities=23%  Similarity=0.339  Sum_probs=40.2

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEec
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIML   89 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~   89 (144)
                      ..|+|++|||||+||++|+  +++++|+++|+ ... |.+||.|.||.
T Consensus         3 ~~y~V~~GDtl~~Ia~~~~--~~~~~l~~~N~-~~~~l~~G~~l~ip~   47 (48)
T 1e0g_A            3 ITYRVRKGDSLSSIAKRHG--VNIKDVMRWNS-DTANLQPGDKLTLFV   47 (48)
T ss_dssp             CEEEECTTCCHHHHHHHHT--CCHHHHHHHCS-CGGGCCTTEEEECCC
T ss_pred             EEEEEcCCCcHHHHHHHHC--cCHHHHHHhCC-CCCcCCcCCEEEEec
Confidence            5799999999999999999  99999999999 433 99999999985

>1e0g_A Membrane-bound lytic murein transglycosylase D; cell WALL, hydrolase, glycosidase, lipoprotein, outer membrane, multigene family; NMR {Escherichia coli} SCOP: d.7.1.1

Probab=99.22  E-value=9.8e-12  Score=70.74  Aligned_cols=38  Identities=24%  Similarity=0.379  Sum_probs=34.8

Q ss_pred             EEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730          106 KSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF  144 (144)
Q Consensus       106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~~  144 (144)
                      .+|+|++|||||+||++|++++++|+++|+ ....|+||
T Consensus         3 ~~y~V~~GDtl~~Ia~~~~~~~~~l~~~N~-~~~~l~~G   40 (48)
T 1e0g_A            3 ITYRVRKGDSLSSIAKRHGVNIKDVMRWNS-DTANLQPG   40 (48)
T ss_dssp             CEEEECTTCCHHHHHHHHTCCHHHHHHHCS-CGGGCCTT
T ss_pred             EEEEEcCCCcHHHHHHHHCcCHHHHHHhCC-CCCcCCcC
Confidence            479999999999999999999999999999 76678876

>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15}

Probab=99.03  E-value=1.9e-10  Score=82.31  Aligned_cols=40  Identities=18%  Similarity=0.348  Sum_probs=36.5

Q ss_pred             eEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCC-CCcccC
Q 040730          105 YKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQ-SVVETF  144 (144)
Q Consensus       105 ~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~-~~i~~~  144 (144)
                      ..+|+|++|||||+||++|++++.+|+++|++.+ ..|+||
T Consensus        62 ~~~y~V~~GDTL~~IA~~~~~~~~~l~~~N~~~~~~~i~~G  102 (167)
T 2l9y_A           62 TATVTVQQGDTLRDIGRRFDCDFHEIARRNNIQNEDLIYPG  102 (167)
T ss_dssp             CEEEEECTTCCHHHHHHHTTCCHHHHHHHHTCCGGGCCCTT
T ss_pred             CceEEECCCCcHHHHHHHcCCCHHHHHHHcCCCCcccccCC
Confidence            4689999999999999999999999999999976 568876

>4a1k_A Putative L, D-transpeptidase YKUD; transferase, peptidoglycan synthesis; HET: CME; 1.75A {Bacillus subtilis} PDB: 4a1j_A 4a1i_A* 1y7m_A 3zqd_A 4a52_A*

Probab=98.76  E-value=5.6e-09  Score=74.42  Aligned_cols=45  Identities=20%  Similarity=0.251  Sum_probs=42.1

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEec
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIML   89 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~   89 (144)
                      .+|+|++||||+.||++|+  ++..+|+++|+..++ +.+|+.|.||.
T Consensus         3 ~~y~V~~GdtL~~IA~~f~--~g~~~l~~aNp~vd~~l~~g~~i~ip~   48 (165)
T 4a1k_A            3 LTYQVKQGDTLNSIAADFR--ISTAALLQANPSLQAGLTAGQSIVIPG   48 (165)
T ss_dssp             EEEECCTTCCHHHHHHHTT--CCHHHHHHHCGGGGGCCCTTCEEEETT
T ss_pred             EEEEECCCCCHHHHHHHhC--CCHHHHHHhCccCCCccCCCccccCcc
Confidence            5899999999999999999  999999999998877 89999999984

>2gu1_A Zinc peptidase; alpha/beta, beta barrel, structural genomics, PSI, protein structure initiative; 1.90A {Vibrio cholerae}

Probab=98.32  E-value=1.7e-07  Score=74.32  Aligned_cols=46  Identities=7%  Similarity=0.121  Sum_probs=39.6

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCC------C-CCCCcEEEEecc
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSH------P-VNDWTKLMIMLP   90 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~------~-l~~Gq~l~IP~~   90 (144)
                      ..|+++.|||||.||++|+  ++.+.|+++|.+..      . |++|++|.|+..
T Consensus       101 ~~~~v~igdSL~~iA~~~G--vs~~~i~~ln~i~~~~idf~~~Lr~GD~l~V~~~  153 (361)
T 2gu1_A          101 ILFSGEINGSFSVSARRVG--LTSSQVANITQVMKDKIDFSRSLRAGDRFDILVK  153 (361)
T ss_dssp             EEEEEESSSCHHHHHHHTT--CCHHHHHHHHHHHTTTCCTTTCCCC-CEEEEEEE
T ss_pred             EEEEEEECCcHHHHHHHcC--CCHHHHHHHHHhhcccccccccCCCCCEEEEEEE
Confidence            4688999999999999999  99999999998753      2 999999999864

>3slu_A M23 peptidase domain protein; outer membrane, hydrolase; 2.41A {Neisseria meningitidis}

Probab=97.58  E-value=0.00051  Score=54.54  Aligned_cols=92  Identities=12%  Similarity=0.127  Sum_probs=64.3

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCC----C--CCCCCcEEEEecccccCCCC-----CCCccc--------
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELS----H--PVNDWTKLMIMLPCTCFNNG-----NNGVTS--------  103 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~----~--~l~~Gq~l~IP~~~~~~~~~-----~~~~~~--------  103 (144)
                      ..|+|++||||..|-++++  ++..++.+++...    .  .|++||.|.+.......-..     ......        
T Consensus        15 ~~~~V~~GDTL~~IL~r~G--ls~~di~~i~~~~~~~~~l~~LrpGq~l~i~~~~~~~l~~l~~~~~~~~~~~~v~i~~~   92 (371)
T 3slu_A           15 VQEAVQPGDSLADVLARSG--MARDEIARITEKYGGEADLRHLRADQSVHVLVGGDGGAREVQFFTDEDGERNLVALEKK   92 (371)
T ss_dssp             EEEECCTTCCHHHHHHHTT--CCHHHHHHHHTTC------CCBCSSSEEEEEECTTSCEEEEEEEECCTTEEEEEEEEEE
T ss_pred             EEEEECCCCcHHHHHHHcC--CCHHHHHHHHHhccccCchhhCCCCCEEEEEECCCCCeEEEEEEecCCCceeEEEEEec
Confidence            6799999999999999999  9999998886654    1  29999999997642110000     000000        


Q ss_pred             ---------------ceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCC
Q 040730          104 ---------------IYKSYVVQWGESPSSVGSKFGVTMAELVATNGL  136 (144)
Q Consensus       104 ---------------~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l  136 (144)
                                     ....+.+.-.++|+..|.+.|++.+.+++++.+
T Consensus        93 dg~f~~~~~~~~~~~~~~~~~g~I~~Sl~~a~~~agl~~~~~~~l~~i  140 (371)
T 3slu_A           93 GGIWRRSASEADMKVLPTLRSVVVKTSARGSLARAEVPVEIRESLSGI  140 (371)
T ss_dssp             TTEEEECCCGGGEEEEEEEEEEECSSCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCeeEEEeeecccceeeeEEEEEEeccHHHHHHHcCCCHHHHHHHHHH
Confidence                           000122334899999999999999999888865

>3slu_A M23 peptidase domain protein; outer membrane, hydrolase; 2.41A {Neisseria meningitidis}

Probab=95.34  E-value=0.021  Score=45.23  Aligned_cols=41  Identities=17%  Similarity=0.112  Sum_probs=33.3

Q ss_pred             ceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCC-----CCCcccC
Q 040730          104 IYKSYVVQWGESPSSVGSKFGVTMAELVATNGLS-----QSVVETF  144 (144)
Q Consensus       104 ~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~-----~~~i~~~  144 (144)
                      .-..|+|++||||.+|-+++|++..++.+++...     -..|+||
T Consensus        13 ~W~~~~V~~GDTL~~IL~r~Gls~~di~~i~~~~~~~~~l~~LrpG   58 (371)
T 3slu_A           13 YWVQEAVQPGDSLADVLARSGMARDEIARITEKYGGEADLRHLRAD   58 (371)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTCCHHHHHHHHTTC------CCBCSS
T ss_pred             ceEEEEECCCCcHHHHHHHcCCCHHHHHHHHHhccccCchhhCCCC
Confidence            4567999999999999999999999999987653     3456554

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=85.13  E-value=0.57  Score=26.53  Aligned_cols=25  Identities=4%  Similarity=0.064  Sum_probs=21.4

Q ss_pred             eccCCc----HHHHHHHhCCCHHHHHHHc
Q 040730          110 VQWGES----PSSVGSKFGVTMAELVATN  134 (144)
Q Consensus       110 V~~GdT----l~~IA~~~~~s~~~l~~~N  134 (144)
                      +..|.+    +..||++||++...|..|=
T Consensus        18 ~~~g~s~~~~~~~vA~~~gIs~~tl~~W~   46 (59)
T 2glo_A           18 YRNDNDCKGNQRATARKYNIHRRQIQKWL   46 (59)
T ss_dssp             HHHCTTTTTCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHcCCCcchHHHHHHHHHCcCHHHHHHHH
Confidence            356778    9999999999999998883

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	144
d1e0ga_	48	d.7.1.1 (A:) Membrane-bound lytic murein transclyc	2e-04

>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]} Length = 48

class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]

 Score = 35.4 bits (82), Expect = 2e-04
 Identities = 9/31 (29%), Positives = 19/31 (61%)

Query: 107 SYVVQWGESPSSVGSKFGVTMAELVATNGLS 137
           +Y V+ G+S SS+  + GV + +++  N  +
Sbjct: 4   TYRVRKGDSLSSIAKRHGVNIKDVMRWNSDT 34

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	144
d1e0ga_	48	Membrane-bound lytic murein transclycosylase D, Ml	99.58
d1y7ma2	48	Hypothetical protein YkuD, N-terminal domain {Baci	99.56
d1e0ga_	48	Membrane-bound lytic murein transclycosylase D, Ml	99.48
d1y7ma2	48	Hypothetical protein YkuD, N-terminal domain {Baci	99.46
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	92.74
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	82.22
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	80.82

>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]

Probab=99.58  E-value=8.1e-16  Score=87.04  Aligned_cols=45  Identities=22%  Similarity=0.297  Sum_probs=42.2

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCCCCCCcEEEEec
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHPVNDWTKLMIML   89 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~l~~Gq~l~IP~   89 (144)
                      .+|+|++|||||.||++|+  +++++|+++|++.+.|++||.|.||.
T Consensus         3 v~y~V~~GDTl~~IA~~y~--vs~~~i~~~N~l~~~l~~Gq~L~i~v   47 (48)
T d1e0ga_           3 ITYRVRKGDSLSSIAKRHG--VNIKDVMRWNSDTANLQPGDKLTLFV   47 (48)
T ss_dssp             CEEEECTTCCHHHHHHHHT--CCHHHHHHHCSCGGGCCTTEEEECCC
T ss_pred             EEEEECCCCCHHHHHHHHC--CCHHHHHHHcCCcccCcCCCEEEEEe
Confidence            5799999999999999999  99999999999875699999999985

>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Hypothetical protein YkuD, N-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.56  E-value=5e-16  Score=88.05  Aligned_cols=45  Identities=20%  Similarity=0.251  Sum_probs=42.4

Q ss_pred             eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEec
Q 040730           43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIML   89 (144)
Q Consensus        43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~   89 (144)
                      .+|+|++|||||+||++|+  +++++|+++|++.++ |++||.|.||.
T Consensus         2 i~y~V~~GDTL~~IA~~y~--v~~~~i~~~N~~~~~~l~~Gq~L~IPg   47 (48)
T d1y7ma2           2 LTYQVKQGDTLNSIAADFR--ISTAALLQANPSLQAGLTAGQSIVIPG   47 (48)
T ss_dssp             EEEECCTTCCHHHHHHHTT--SCCCCCCCTSCTTCSSCCTTCEEEETT
T ss_pred             EEEEECCCCCHHHHHHHhC--CCHHHHHHHcCCCCCCCCCCCEEEeCC
Confidence            4799999999999999999  999999999999887 99999999983

>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]

Probab=99.48  E-value=1.3e-14  Score=82.00  Aligned_cols=38  Identities=24%  Similarity=0.342  Sum_probs=35.3

Q ss_pred             EEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730          106 KSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF  144 (144)
Q Consensus       106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~~  144 (144)
                      .+|+|++|||||+||++||+++++|++||++.+ .|+||
T Consensus         3 v~y~V~~GDTl~~IA~~y~vs~~~i~~~N~l~~-~l~~G   40 (48)
T d1e0ga_           3 ITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTA-NLQPG   40 (48)
T ss_dssp             CEEEECTTCCHHHHHHHHTCCHHHHHHHCSCGG-GCCTT
T ss_pred             EEEEECCCCCHHHHHHHHCCCHHHHHHHcCCcc-cCcCC
Confidence            579999999999999999999999999999965 58887

>d1y7ma2 d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Hypothetical protein YkuD, N-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.46  E-value=3.3e-15  Score=84.55  Aligned_cols=39  Identities=23%  Similarity=0.334  Sum_probs=37.2

Q ss_pred             EEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730          106 KSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF  144 (144)
Q Consensus       106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~~  144 (144)
                      .+|+|++|||||+||++|++++++|+++|++.++.|++|
T Consensus         2 i~y~V~~GDTL~~IA~~y~v~~~~i~~~N~~~~~~l~~G   40 (48)
T d1y7ma2           2 LTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAG   40 (48)
T ss_dssp             EEEECCTTCCHHHHHHHTTSCCCCCCCTSCTTCSSCCTT
T ss_pred             EEEEECCCCCHHHHHHHhCCCHHHHHHHcCCCCCCCCCC
Confidence            579999999999999999999999999999988889987

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=92.74  E-value=0.042  Score=29.22  Aligned_cols=24  Identities=17%  Similarity=0.333  Sum_probs=21.9

Q ss_pred             eccCCcHHHHHHHhCCCHHHHHHH
Q 040730          110 VQWGESPSSVGSKFGVTMAELVAT  133 (144)
Q Consensus       110 V~~GdTl~~IA~~~~~s~~~l~~~  133 (144)
                      +..|++...||+.|||+...|.++
T Consensus        18 ~~~G~s~~~iA~~~gVSr~TiYry   41 (47)
T d1ijwc_          18 LEKGHPRQQLAIIFGIGVSTLYRY   41 (47)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHhh
Confidence            467999999999999999999876

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=82.22  E-value=0.69  Score=24.15  Aligned_cols=24  Identities=8%  Similarity=0.173  Sum_probs=21.6

Q ss_pred             eCCCCCHHHHHHHhCCCCCHHHHHhh
Q 040730           47 VRPADTIDSILNGFGGLVSAEQINST   72 (144)
Q Consensus        47 V~~GdTl~~IA~~y~~~~~~~~l~~~   72 (144)
                      +..|.+...||+.|+  |+-.+|.++
T Consensus        18 ~~~G~s~~~iA~~~g--VSr~TiYry   41 (47)
T d1ijwc_          18 LEKGHPRQQLAIIFG--IGVSTLYRY   41 (47)
T ss_dssp             HHTTCCHHHHHHHHT--CCHHHHHHH
T ss_pred             HHCCCCHHHHHHHHC--cCHHHHHhh
Confidence            357999999999999  999999887

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=80.82  E-value=0.54  Score=27.65  Aligned_cols=22  Identities=18%  Similarity=0.240  Sum_probs=20.4

Q ss_pred             cCCcHHHHHHHhCCCHHHHHHH
Q 040730          112 WGESPSSVGSKFGVTMAELVAT  133 (144)
Q Consensus       112 ~GdTl~~IA~~~~~s~~~l~~~  133 (144)
                      .|-++..||++|||+...|..|
T Consensus        22 ~g~s~~~vA~~lGIs~~tl~~W   43 (89)
T d2jn6a1          22 DGASLQQIANDLGINRVTLKNW   43 (89)
T ss_dssp             GGSCHHHHHHHHTSCHHHHHHH
T ss_pred             CCCcHHHHHHHHCCCHHHHHHH
Confidence            4889999999999999999888