Citrus Sinensis ID: 040221

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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
MQSPEDSVPTPRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEEEEHHHHHHHHcccHHHHHHHccccccccccccEEEEccccccccccccccccccccccccccccccccccEEEEEccccHHHHHHHHcccHHHHHHHHcccccccccccEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccEEEEEccHHHEEEccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccHHHHHHHHccccHHHHHHHccccccEEEEccEEEcc
Coil and Loop (DISEMBL)
mqspedsvptprvpaendgsgdgrEAAVAKTAGFVVFSGIAISILKAlnplnknrnettqpqpiaestqpiqpppqqpivtkpsicteksepepascrtveiVRGDTLWGLSRKYGVSIDAIKeanglsgdtiyagkkliip
Flexible Loop (DISEMBL)
mqspedsvptprvpaendgsgdGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPiaestqpiqpppqqPIVTKPSICTEksepepascrtveivrgdtlwgLSRKYGVSIDAIkeanglsgdtiyagkkliip
Low Complexity Region (SEG)
MQSPEDSVPTPRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTqpiqpppqqpiVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP
Disordered region (IsUnstruct)
***************************VAKTAGFVVFSGIAISILKALN***********************************************CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLI**
Disordered Region (DISOPRED)
***************************VAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQP************************************VEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP
Disordered Region (DISEMBL)
*************************AAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSIC***********RTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP
Disordered Region (DISPRO)
**********************GREAAVAKTAGFVVFSGIAISILKALNPLN********************************************CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQSPEDSVPTPRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP
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	142	2.2.26 [Sep-21-2011]
P37710	737	Autolysin OS=Enterococcus	yes	no	0.457	0.088	0.462	4e-09
P0C2T5	437	Probable N-acetylmuramida	N/A	no	0.345	0.112	0.530	1e-07
A2RHZ5	437	Probable N-acetylmuramida	yes	no	0.345	0.112	0.530	2e-07
Q01836	467	Probable endopeptidase p6	yes	no	0.612	0.186	0.382	2e-07
Q9CIT4	439	Probable N-acetylmuramida	yes	no	0.345	0.111	0.489	2e-07
O34669	287	Cell wall-binding protein	yes	no	0.316	0.156	0.488	1e-06
P21171	484	Probable endopeptidase p6	yes	no	0.619	0.181	0.366	1e-06
Q01837	524	Probable endopeptidase p6	no	no	0.380	0.103	0.446	2e-06
Q01839	524	Probable endopeptidase p6	no	no	0.366	0.099	0.428	3e-06
P54421	334	Probable peptidoglycan en	no	no	0.338	0.143	0.479	5e-06

>sp|P37710|ALYS_ENTFA Autolysin OS=Enterococcus faecalis (strain ATCC 700802 / V583) GN=EF_0799 PE=3 SV=2

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 31/67 (46%), Positives = 40/67 (59%), Gaps = 2/67 (2%)

Query: 77  QPIVTK--PSICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIY 134
           Q I+ K   S     S    AS +   +  GD+LWGLS +YG+SI  IK+ NGLSGDTIY
Sbjct: 670 QTIIVKKGASAGGNASSTNSASGKRHTVKSGDSLWGLSMQYGISIQKIKQLNGLSGDTIY 729

Query: 135 AGKKLII 141
            G+ L +
Sbjct: 730 IGQTLKV 736

Hydrolyzes the cell wall of E.faecalis and M.lysodeikticus. May play an important role in cell wall growth and cell separation.
Enterococcus faecalis (strain ATCC 700802 / V583) (taxid: 226185)
EC: 3EC: .EC: 2EC: .EC: 1EC: .EC: -

>sp|P0C2T5|ACMA_LACLC Probable N-acetylmuramidase OS=Lactococcus lactis subsp. cremoris GN=acmA PE=3 SV=1

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 33/49 (67%)

Query: 93  EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
           +PAS  +V++  GDTLW LS KY  SI  +K  N LS DTIY G+ LI+
Sbjct: 314 KPASQTSVKVKSGDTLWALSVKYKTSIAQLKSWNHLSSDTIYIGQNLIV 362

Hydrolyzes the cell wall of L.lactis and M.lysodeikticus. Required for cell separation during growth.

Lactococcus lactis subsp. cremoris (taxid: 1359)

EC: 3

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: 7

>sp|A2RHZ5|ACMA_LACLM Probable N-acetylmuramidase OS=Lactococcus lactis subsp. cremoris (strain MG1363) GN=acmA PE=3 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 32/49 (65%)

Query: 93  EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
           +P S  TV++  GDTLW LS KY  SI  +K  N LS DTIY G+ LI+
Sbjct: 314 KPTSQTTVKVKSGDTLWALSVKYKTSIAQLKSWNHLSSDTIYIGQNLIV 362

Hydrolyzes the cell wall of L.lactis and M.lysodeikticus. Required for cell separation during growth.

Lactococcus lactis subsp. cremoris (strain MG1363) (taxid: 416870)

EC: 3

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: 7

>sp|Q01836|P60_LISIN Probable endopeptidase p60 OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=iap PE=3 SV=2

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 44/89 (49%), Gaps = 2/89 (2%)

Query: 55  RNETTQP-QPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIVR-GDTLWGLS 112
           + ETTQ  +P  E+   ++ P  Q     P     K  P      T   V+ GDT+W LS
Sbjct: 154 KKETTQQVKPATEAKTEVKQPTTQQTAPAPKAAETKEAPVVDQNATTHNVKSGDTIWALS 213

Query: 113 RKYGVSIDAIKEANGLSGDTIYAGKKLII 141
            KYGVS+  I   N LS  +IY G+KL I
Sbjct: 214 VKYGVSVQDIMSWNNLSSSSIYVGQKLAI 242

This major extracellular protein may be involved in the invasion of non-professional phagocytic cells by Listeria.

Listeria innocua serovar 6a (strain CLIP 11262) (taxid: 272626)

EC: 3

EC: .

EC: 4

EC: .

EC: -

EC: .

EC: -

>sp|Q9CIT4|ACMA_LACLA Probable N-acetylmuramidase OS=Lactococcus lactis subsp. lactis (strain IL1403) GN=acmA PE=3 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 34/49 (69%)

Query: 93  EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
           +PAS  T+++  GDTLWGLS KY  +I  +K  N L+ DTI+ G+ LI+
Sbjct: 316 KPASQTTIKVKSGDTLWGLSVKYKTTIAQLKSWNHLNSDTIFIGQNLIV 364

Required for cell separation during growth.

Lactococcus lactis subsp. lactis (strain IL1403) (taxid: 272623)

EC: 3

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: 7

>sp|O34669|YOCH_BACSU Cell wall-binding protein YocH OS=Bacillus subtilis (strain 168) GN=yocH PE=1 SV=1

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 33/45 (73%)

Query: 95  ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKL 139
           AS + + + +GDTLWG+S+K GV++  +KE N L+ D I AG+KL
Sbjct: 23  ASAKEITVQKGDTLWGISQKNGVNLKDLKEWNKLTSDKIIAGEKL 67

Bacillus subtilis (strain 168) (taxid: 224308)

>sp|P21171|P60_LISMO Probable endopeptidase p60 OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) GN=iap PE=1 SV=2

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 53  KNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIVR-GDTLWGL 111
           K    T Q  P AE+   ++   Q      P +   K  P      T   V+ GDT+W L
Sbjct: 156 KKETTTQQAAPAAETKTEVKQTTQ-ATTPAPKVAETKETPVVDQNATTHAVKSGDTIWAL 214

Query: 112 SRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
           S KYGVS+  I   N LS  +IY G+KL I
Sbjct: 215 SVKYGVSVQDIMSWNNLSSSSIYVGQKLAI 244

This major extracellular protein may be involved in the invasion of non-professional phagocytic cells by Listeria.

Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (taxid: 169963)

EC: 3

EC: .

EC: 4

EC: .

EC: -

EC: .

EC: -

>sp|Q01837|P60_LISIV Probable endopeptidase p60 OS=Listeria ivanovii GN=iap PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 36/56 (64%)

Query: 86  CTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
            T  + P  AS  TV +  GDTLWG+++  G ++DA+K+AN L+ D I  G+KL I
Sbjct: 16  VTAFAAPTIASASTVVVEAGDTLWGIAQDKGTTVDALKKANNLTSDKIVPGQKLQI 71

This major extracellular protein may be involved in the invasion of non-professional phagocytic cells by Listeria.

Listeria ivanovii (taxid: 1638)

EC: 3

EC: .

EC: 4

EC: .

EC: -

EC: .

EC: -

>sp|Q01839|P60_LISWE Probable endopeptidase p60 OS=Listeria welshimeri GN=iap PE=3 SV=1

 Score = 50.8 bits (120), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 86  CTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
            T  + P  AS  TV +  GDTLWG+++  G ++DA+K+AN L+ D I  G+KL +
Sbjct: 16  VTAFAAPTIASASTVVVEAGDTLWGIAQSKGTTVDALKKANNLTSDKIVPGQKLQV 71

This major extracellular protein may be involved in the invasion of non-professional phagocytic cells by Listeria.

Listeria welshimeri (taxid: 1643)

EC: 3

EC: .

EC: 4

EC: .

EC: -

EC: .

EC: -

>sp|P54421|LYTE_BACSU Probable peptidoglycan endopeptidase LytE OS=Bacillus subtilis (strain 168) GN=lytE PE=1 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 31/48 (64%)

Query: 94  PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
            AS +++++ +GDTLW LSRKY  +I  IK  N L  D IY G+ L I
Sbjct: 22  AASAQSIKVKKGDTLWDLSRKYDTTISKIKSENHLRSDIIYVGQTLSI 69

Cell wall hydrolase that cleaves gamma-D-glutamate-meso-diaminopimelate bonds in peptidoglycan (By similarity). Seems to play a role in cell separation during vegetative growth.

Bacillus subtilis (strain 168) (taxid: 224308)

EC: 3

EC: .

EC: 4

EC: .

EC: -

EC: .

EC: -

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	142
225446672	133	PREDICTED: probable endopeptidase p60-li	0.823	0.879	0.579	2e-31
42565395	132	cell wall hydrolase, partial [Hyacinthus	0.838	0.901	0.475	3e-21
116778927	148	unknown [Picea sitchensis] gi|148908768|	0.922	0.885	0.420	4e-21
116791072	152	unknown [Picea sitchensis]	0.922	0.861	0.416	8e-21
302143455	94	unnamed protein product [Vitis vinifera]	0.654	0.989	0.539	3e-20
116783392	150	unknown [Picea sitchensis]	0.816	0.773	0.410	9e-17
302758198	161	hypothetical protein SELMODRAFT_438219 [	0.823	0.726	0.330	8e-09
302758692	161	hypothetical protein SELMODRAFT_438100 [	0.823	0.726	0.314	1e-08
313122909	366	cell wall-associated hydrolase [Lactobac	0.288	0.112	0.634	7e-08
116513351	379	cell wall-associated hydrolase [Lactobac	0.338	0.126	0.562	7e-08

>gi|225446672|ref|XP_002281964.1| PREDICTED: probable endopeptidase p60-like [Vitis vinifera]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 73/126 (57%), Positives = 91/126 (72%), Gaps = 9/126 (7%)

Query: 18  DGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPP-Q 76
           +G G  +EAAVAKTAGF VFSGIA+SILKALN  N N N       + E +QP  P   +
Sbjct: 16  NGEGHSKEAAVAKTAGFFVFSGIAMSILKALNSCN-NDNNKLLTHSVTEPSQPTDPSHSR 74

Query: 77  QPIVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAG 136
           +PI        ++ E   ++ +T++IV+GDTLWGLSRK+GVSIDAIKEANGL+GDTIYAG
Sbjct: 75  EPIF-------KEKEVRESTQKTIDIVKGDTLWGLSRKHGVSIDAIKEANGLTGDTIYAG 127

Query: 137 KKLIIP 142
           KKL+IP
Sbjct: 128 KKLVIP 133

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42565395|gb|AAS20972.1| cell wall hydrolase, partial [Hyacinthus orientalis]

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 58/122 (47%), Positives = 79/122 (64%), Gaps = 3/122 (2%)

Query: 24  REAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKP 83
           + A VAK AGF+ FSGIA+SI+KAL           Q +P   +   + PP  Q    + 
Sbjct: 11  KHAIVAKAAGFLAFSGIALSIIKALTSKTHQPQPQPQQKPSPSAPPSVPPPNIQSTSKQK 70

Query: 84  SICTEKS---EPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLI 140
            +  E++       ++ RT+EI +GDTLWG+SRKYGV+IDAI+EANG++GD I+AGKKLI
Sbjct: 71  QVAAEQAGCGSSSLSASRTIEIAKGDTLWGISRKYGVTIDAIREANGITGDMIFAGKKLI 130

Query: 141 IP 142
           IP
Sbjct: 131 IP 132

Source: Hyacinthus orientalis

Species: Hyacinthus orientalis

Genus: Hyacinthus

Family: Hyacinthaceae

Order: Asparagales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116778927|gb|ABK21059.1| unknown [Picea sitchensis] gi|148908768|gb|ABR17490.1| unknown [Picea sitchensis]

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 61/145 (42%), Positives = 86/145 (59%), Gaps = 14/145 (9%)

Query: 9   PTPRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP--------LNKNRNETTQ 60
           P+ +   ++DG    ++A VA +AGFVVF+GIA+S+ KAL P        +++    TT 
Sbjct: 7   PSGKSGGKDDGK---KDAVVATSAGFVVFTGIALSLFKALWPKKPVEESFISEEAVSTTS 63

Query: 61  PQPIAESTQPIQ---PPPQQPIVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGV 117
            + I E  +      P     +        +K   +  S +T+EI +GDTLWGLSRKYGV
Sbjct: 64  TENIFEDLKEKASEVPKAANGVAYDVGKKFQKGGGKKKSNQTIEIFKGDTLWGLSRKYGV 123

Query: 118 SIDAIKEANGLSGDTIYAGKKLIIP 142
           S++AIK ANG S DTIYAG+KLI+P
Sbjct: 124 SVEAIKAANGFSDDTIYAGEKLILP 148

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116791072|gb|ABK25848.1| unknown [Picea sitchensis]

 Score =  105 bits (261), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 62/149 (41%), Positives = 86/149 (57%), Gaps = 18/149 (12%)

Query: 9   PTPRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP--------LNKNRNETTQ 60
           P+ +   ++DG    ++A VA +AGFVVF+GIA+S+ KAL P        +++    TT 
Sbjct: 7   PSGKSGGKDDGK---KDAVVATSAGFVVFTGIALSLFKALWPKKPVEESFISEEAVSTTS 63

Query: 61  PQPI-------AESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSR 113
            + I       AE      P     +        +K   +  S +T+EI +GDTLWGLSR
Sbjct: 64  TENIFEDLKVDAEEKASEVPKAANGVAYDVGKKFQKGGGKKKSNQTIEIFKGDTLWGLSR 123

Query: 114 KYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           KYGVS++AIK ANG S DTIYAG+KLI+P
Sbjct: 124 KYGVSVEAIKAANGFSDDTIYAGEKLILP 152

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143455|emb|CBI22016.3| unnamed protein product [Vitis vinifera]

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 55/102 (53%), Positives = 71/102 (69%), Gaps = 9/102 (8%)

Query: 42  ISILKALNPLNKNRNETTQPQPIAESTQPIQPPP-QQPIVTKPSICTEKSEPEPASCRTV 100
           +SILKALN  N N N       + E +QP  P   ++PI        ++ E   ++ +T+
Sbjct: 1   MSILKALNSCN-NDNNKLLTHSVTEPSQPTDPSHSREPIF-------KEKEVRESTQKTI 52

Query: 101 EIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           +IV+GDTLWGLSRK+GVSIDAIKEANGL+GDTIYAGKKL+IP
Sbjct: 53  DIVKGDTLWGLSRKHGVSIDAIKEANGLTGDTIYAGKKLVIP 94

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116783392|gb|ABK22923.1| unknown [Picea sitchensis]

 Score = 91.7 bits (226), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 55/134 (41%), Positives = 75/134 (55%), Gaps = 18/134 (13%)

Query: 25  EAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQP-QPIAESTQPIQPPPQ------- 76
           +  +A TAG VVF+GI +S+ KA    +K   E   P QP  E+   ++  PQ       
Sbjct: 19  DTFIATTAGVVVFTGIGLSLFKAFK--SKRLAEEVSPLQPSYEAVGDVRDQPQTEATEKN 76

Query: 77  -------QPIVTKPSIC-TEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGL 128
                    +V + +I    K   +  S +T+EI +GD+LW LSRKYGVS+D IK AN  
Sbjct: 77  NDVVKEVNDVVKEVNIFGFHKGGNKKRSSQTIEIFKGDSLWSLSRKYGVSVDQIKAANKY 136

Query: 129 SGDTIYAGKKLIIP 142
           + DTIYAG+KLIIP
Sbjct: 137 TDDTIYAGEKLIIP 150

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302758198|ref|XP_002962522.1| hypothetical protein SELMODRAFT_438219 [Selaginella moellendorffii] gi|300169383|gb|EFJ35985.1| hypothetical protein SELMODRAFT_438219 [Selaginella moellendorffii]

 Score = 65.1 bits (157), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 42/127 (33%), Positives = 66/127 (51%), Gaps = 10/127 (7%)

Query: 22  DGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQP--- 78
           D  +  +AK AG V+ +GIA ++ K   P  K  +E  + +  +E     +   Q+    
Sbjct: 37  DKTDYTIAKAAGAVIATGIAWTVFKTFWP--KKADE--EYERYSEGVSSFESEAQEKTEG 92

Query: 79  IVTKPSICTEKSEPEPASCR---TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYA 135
           +  + +    K  P+ +        E+  GDTL+GLSRKYGV++++IK ANG+  D I  
Sbjct: 93  LADRAASTISKKFPKFSRKHKSGAYEVCPGDTLYGLSRKYGVTVESIKAANGIHNDIIVV 152

Query: 136 GKKLIIP 142
           G KL IP
Sbjct: 153 GDKLDIP 159

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302758692|ref|XP_002962769.1| hypothetical protein SELMODRAFT_438100 [Selaginella moellendorffii] gi|300169630|gb|EFJ36232.1| hypothetical protein SELMODRAFT_438100 [Selaginella moellendorffii]

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/127 (31%), Positives = 63/127 (49%), Gaps = 10/127 (7%)

Query: 22  DGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQP--- 78
           D  +  +AK AG V+ +GIA ++ K   P    +    + +  +E     +   Q+    
Sbjct: 37  DKTDYTIAKAAGAVIATGIAWTVFKTFWP----KKADEEYERYSEGVSSFESEAQEKTEG 92

Query: 79  IVTKPSICTEKSEPEPASCR---TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYA 135
              + +    K  P+ +        E+  GDTL+GLSRKYGV++++IK ANG+  D I  
Sbjct: 93  FADRAASTISKKFPKFSRKHKSGAYEVCPGDTLYGLSRKYGVTVESIKAANGIHNDIIVV 152

Query: 136 GKKLIIP 142
           G KL IP
Sbjct: 153 GDKLDIP 159

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313122909|ref|YP_004033168.1| cell wall-associated hydrolase [Lactobacillus delbrueckii subsp. bulgaricus ND02] gi|312279472|gb|ADQ60191.1| Cell wall-associated hydrolase [Lactobacillus delbrueckii subsp. bulgaricus ND02]

 Score = 62.0 bits (149), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 34/41 (82%)

Query: 102 IVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           +V+ DTLWGLS+KYGVS+  +K+ANG+SG  IY G+KL IP
Sbjct: 34  VVKNDTLWGLSKKYGVSVSDLKKANGVSGHLIYVGQKLQIP 74

Source: Lactobacillus delbrueckii subsp. bulgaricus ND02

Species: Lactobacillus delbrueckii

Genus: Lactobacillus

Family: Lactobacillaceae

Order: Lactobacillales

Class: Bacilli

Phylum: Firmicutes

Superkingdom: Bacteria

>gi|116513351|ref|YP_812257.1| cell wall-associated hydrolase [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365] gi|116092666|gb|ABJ57819.1| Cell wall-associated hydrolase [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365]

 Score = 62.0 bits (149), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/48 (56%), Positives = 36/48 (75%)

Query: 95  ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           A   +  +V+ DTLWGLS+KYGVS+  +K+ANG+SG  IY G+KL IP
Sbjct: 27  ALADSYTVVKNDTLWGLSKKYGVSVSDLKKANGVSGHLIYVGQKLQIP 74

Source: Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365

Species: Lactobacillus delbrueckii

Genus: Lactobacillus

Family: Lactobacillaceae

Order: Lactobacillales

Class: Bacilli

Phylum: Firmicutes

Superkingdom: Bacteria

---

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	142
UNIPROTKB|Q722W8	477	iap "Protein P60" [Listeria mo	0.640	0.190	0.368	1.3e-09
UNIPROTKB|Q81WS5	265	BAS3606 "Putative cell wall hy	0.387	0.207	0.431	1.2e-07
TIGR_CMR|BA_3893	265	BA_3893 "cell wall hydrolase,	0.387	0.207	0.431	1.2e-07
TIGR_CMR|CHY_0674	274	CHY_0674 "putative cell-wall a	0.309	0.160	0.431	2.2e-06
ZFIN|ZDB-GENE-060929-1094	211	lysmd1 "LysM, putative peptido	0.373	0.251	0.446	5.4e-05
UNIPROTKB|Q1JQA8	215	LYSMD2 "LysM and putative pept	0.267	0.176	0.538	7e-05
UNIPROTKB|F1MNB9	225	LYSMD1 "LysM and putative pept	0.295	0.186	0.488	0.00014
UNIPROTKB|E2RD13	227	LYSMD1 "Uncharacterized protei	0.295	0.185	0.488	0.00014
UNIPROTKB|F1SSY1	227	LYSMD1 "Uncharacterized protei	0.295	0.185	0.488	0.00014
UNIPROTKB|Q9KV14	581	VC_0344 "N-acetylmuramoyl-L-al	0.295	0.072	0.428	0.00041

UNIPROTKB|Q722W8 iap "Protein P60" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)]

 Score = 133 (51.9 bits), Expect = 1.3e-09, Sum P(2) = 1.3e-09
 Identities = 35/95 (36%), Positives = 43/95 (45%)

Query:    50 PLNKNRNETT--QPQPIAESTXXXXXXXXXXXVTKPSICTEKSEPEPASCRTVEIVR-GD 106
             P  + + ETT  Q  P AE T              P +   K  P      T   V+ GD
Sbjct:   150 PTQEVKKETTIQQAAPAAE-TKTEVKQTTQATTPAPKVAETKETPVVDQNATTHAVKSGD 208

Query:   107 TLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
             T+W LS KYGVS+  I   N LS  +IY G+KL I
Sbjct:   209 TIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAI 243

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|Q81WS5 BAS3606 "Putative cell wall hydrolase" [Bacillus anthracis (taxid:1392)]

 Score = 125 (49.1 bits), Expect = 1.2e-07, P = 1.2e-07
 Identities = 25/58 (43%), Positives = 40/58 (68%)

Query:    85 ICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
             +C++ S  E ++  TV+  + DTLWG+S++YGVSI +IK+AN    D  + G++L IP
Sbjct:    20 VCSQ-STAEASTIHTVQ--KNDTLWGISKQYGVSIQSIKQANHKGNDQTFIGEQLHIP 74

GO:0016787 "hydrolase activity" evidence=ISS

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

TIGR_CMR|BA_3893 BA_3893 "cell wall hydrolase, putative" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 125 (49.1 bits), Expect = 1.2e-07, P = 1.2e-07
 Identities = 25/58 (43%), Positives = 40/58 (68%)

Query:    85 ICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
             +C++ S  E ++  TV+  + DTLWG+S++YGVSI +IK+AN    D  + G++L IP
Sbjct:    20 VCSQ-STAEASTIHTVQ--KNDTLWGISKQYGVSIQSIKQANHKGNDQTFIGEQLHIP 74

GO:0016787 "hydrolase activity" evidence=ISS

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

TIGR_CMR|CHY_0674 CHY_0674 "putative cell-wall associated endopeptidase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 114 (45.2 bits), Expect = 2.2e-06, P = 2.2e-06
 Identities = 19/44 (43%), Positives = 31/44 (70%)

Query:    99 TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
             T+ +  GD LW L+R+Y  +++AIK+AN L  + +  G+KL+IP
Sbjct:    27 TITVKSGDNLWLLARRYNTTVEAIKKANNLKSEALKPGQKLVIP 70

GO:0004175 "endopeptidase activity" evidence=ISS

GO:0009253 "peptidoglycan catabolic process" evidence=ISS

GO:0009405 "pathogenesis" evidence=ISS

GO:0042834 "peptidoglycan binding" evidence=ISS

ZFIN|ZDB-GENE-060929-1094 lysmd1 "LysM, putative peptidoglycan-binding, domain containing 1" [Danio rerio (taxid:7955)]

 Score = 99 (39.9 bits), Expect = 5.4e-05, P = 5.4e-05
 Identities = 25/56 (44%), Positives = 36/56 (64%)

Query:    90 SEPEPASCRTVE-IVR-GDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLIIP 142
             S   P   R +E IV+ G+TL GLS KYGVS++ IK AN L + ++I+  + L +P
Sbjct:    30 SSQSPVRQRRIEHIVQPGETLQGLSLKYGVSMEQIKRANRLYTNESIFLKESLFVP 85

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

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q1JQA8 LYSMD2 "LysM and putative peptidoglycan-binding domain-containing protein 2" [Bos taurus (taxid:9913)]

 Score = 92 (37.4 bits), Expect = 7.0e-05, Sum P(2) = 7.0e-05
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query:   105 GDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLIIP 142
             GDTL G++ KYGVS++ IK AN L + D I+  K L IP
Sbjct:    79 GDTLQGIALKYGVSMEQIKRANKLFTNDCIFLKKTLNIP 117

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

UNIPROTKB|F1MNB9 LYSMD1 "LysM and putative peptidoglycan-binding domain-containing protein 1" [Bos taurus (taxid:9913)]

 Score = 96 (38.9 bits), Expect = 0.00014, P = 0.00014
 Identities = 21/43 (48%), Positives = 30/43 (69%)

Query:   101 EIVRGDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLIIP 142
             ++  GDTL GL+ KYGV+++ IK AN L + D+I+  K L IP
Sbjct:    43 QLAPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIP 85

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

UNIPROTKB|E2RD13 LYSMD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 96 (38.9 bits), Expect = 0.00014, P = 0.00014
 Identities = 21/43 (48%), Positives = 30/43 (69%)

Query:   101 EIVRGDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLIIP 142
             ++  GDTL GL+ KYGV+++ IK AN L + D+I+  K L IP
Sbjct:    43 QLAPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIP 85

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

UNIPROTKB|F1SSY1 LYSMD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 96 (38.9 bits), Expect = 0.00014, P = 0.00014
 Identities = 21/43 (48%), Positives = 30/43 (69%)

Query:   101 EIVRGDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLIIP 142
             ++  GDTL GL+ KYGV+++ IK AN L + D+I+  K L IP
Sbjct:    43 QLAPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIP 85

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

UNIPROTKB|Q9KV14 VC_0344 "N-acetylmuramoyl-L-alanine amidase" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 98 (39.6 bits), Expect = 0.00041, P = 0.00041
 Identities = 18/42 (42%), Positives = 30/42 (71%)

Query:   101 EIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
             ++ RG+++  ++ +YGVS+DA+K+AN L   TI  G+ L IP
Sbjct:   419 KVQRGESIGLIANQYGVSVDALKKANNLKSSTISVGQLLTIP 460

GO:0008745 "N-acetylmuramoyl-L-alanine amidase activity" evidence=ISS

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

---

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: GSVIVG00018780001 SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (128 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	142
pfam01476	43	pfam01476, LysM, LysM domain	4e-15
cd00118	45	cd00118, LysM, Lysine Motif is a small domain invo	5e-13
smart00257	44	smart00257, LysM, Lysin motif	5e-11
PRK13914	481	PRK13914, PRK13914, invasion associated secreted e	5e-09
COG1388	124	COG1388, LytE, FOG: LysM repeat [Cell envelope bio	2e-08
PRK06347	592	PRK06347, PRK06347, autolysin; Reviewed	3e-07
PRK13914	481	PRK13914, PRK13914, invasion associated secreted e	5e-07
TIGR02899	44	TIGR02899, spore_safA, spore coat assembly protein	6e-06
PRK06347	592	PRK06347, PRK06347, autolysin; Reviewed	1e-05
PRK14125	103	PRK14125, PRK14125, cell division suppressor prote	2e-05
PRK06347	592	PRK06347, PRK06347, autolysin; Reviewed	3e-05
PRK06347	592	PRK06347, PRK06347, autolysin; Reviewed	1e-04
PRK11198	147	PRK11198, PRK11198, LysM domain/BON superfamily pr	6e-04

>gnl|CDD|144899 pfam01476, LysM, LysM domain

 Score = 64.3 bits (158), Expect = 4e-15
 Identities = 17/41 (41%), Positives = 30/41 (73%)

Query: 102 IVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           + +GDTL  ++++YG++++ + E NGLS   +Y G+KL IP
Sbjct: 3   VKKGDTLSSIAKRYGITVEELAELNGLSSPNLYVGQKLKIP 43

The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known. Length = 43

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

 Score = 59.0 bits (144), Expect = 5e-13
 Identities = 20/45 (44%), Positives = 31/45 (68%), Gaps = 1/45 (2%)

Query: 98  RTVEIVRGDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLII 141
           +T  +  GDTLW +++KYGV+++ +  AN L + D IY G+KL I
Sbjct: 1   KTYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 45

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

>gnl|CDD|197609 smart00257, LysM, Lysin motif

 Score = 54.0 bits (131), Expect = 5e-11
 Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 99  TVEIVRGDTLWGLSRKYGVSIDAIKEANG-LSGDTIYAGKKLII 141
           T  + +GDTL  ++R+YG+S+  + E N  L  D +  G+KL I
Sbjct: 1   TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44

Length = 44

>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase; Provisional

 Score = 53.3 bits (127), Expect = 5e-09
 Identities = 36/103 (34%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 41  AISILKALNPLNKNRNETTQPQPIAES-TQPIQPPPQQPIVTKPSICTEKSEPEPASCRT 99
             S   A     K    T Q  P AE+ T+  Q          P +   K  P      T
Sbjct: 143 VTSTPVAPTQEVKKETTTQQAAPAAETKTEVKQTTQATT--PAPKVAETKETPVVDQNAT 200

Query: 100 VEIVR-GDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
              V+ GDT+W LS KYGVS+  I   N LS  +IY G+KL I
Sbjct: 201 THAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAI 243

Length = 481

>gnl|CDD|224306 COG1388, LytE, FOG: LysM repeat [Cell envelope biogenesis, outer membrane]

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 29/106 (27%), Positives = 46/106 (43%), Gaps = 2/106 (1%)

Query: 39  GIAISILKALNPLNKNRN--ETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPAS 96
           G+++  LK  N L    +  +  Q   I           Q        +    S  +   
Sbjct: 6   GVSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPP 65

Query: 97  CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
             T  + +GDTL  ++RKYGV++  +K+ N LS D I  G+KL +P
Sbjct: 66  VVTYTVKKGDTLSKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLP 111

Length = 124

>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed

 Score = 47.8 bits (113), Expect = 3e-07
 Identities = 19/55 (34%), Positives = 35/55 (63%)

Query: 87  TEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLII 141
              ++P  ++ +T  + +GD+LW +SR+Y  ++D IK  N L+ + I+ G+KL I
Sbjct: 537 PSTNKPSNSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTI 591

Length = 592

>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase; Provisional

 Score = 47.5 bits (112), Expect = 5e-07
 Identities = 25/53 (47%), Positives = 35/53 (66%)

Query: 87  TEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKL 139
           T  + P  AS  TV +  GDTLWG+++  G ++DAIK+AN L+ D I  G+KL
Sbjct: 17  TAFAAPTIASASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKIVPGQKL 69

Length = 481

>gnl|CDD|131945 TIGR02899, spore_safA, spore coat assembly protein SafA

 Score = 40.6 bits (95), Expect = 6e-06
 Identities = 20/43 (46%), Positives = 29/43 (67%), Gaps = 2/43 (4%)

Query: 102 IVRGDTLWGLSRKYGVSIDAIKEANG-LSG-DTIYAGKKLIIP 142
           + +GDTLW +++KYGV  D + +AN  LS  + IY G K+ IP
Sbjct: 1   VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIP 43

SafA (YrbB) (SafA) of Bacillus subtilis is a protein found at the interface of the spore cortex and spore coat, and is dependent on SpoVID for its localization. This model is based on the N-terminal LysM (lysin motif) domain (see pfam01476) of SafA and, from several other spore-forming species, the protein with the most similar N-terminal region. However, this set of proteins differs greatly in C-terminal of the LysM domaim; blocks of 12-residue and 13-residue repeats are found in the Bacillus cereus group, tandem LysM domains in Thermoanaerobacter tengcongensis MB4, etc. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins [Cellular processes, Sporulation and germination]. Length = 44

>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 81  TKPSICTEKSEPEPAS---CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGK 137
           +KPS  T  S+P   +    +   +V+GD+LW ++    V+I  +K  N L  D IY G+
Sbjct: 386 SKPSTGTSTSKPSTGTSTNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQ 445

Query: 138 KL 139
           KL
Sbjct: 446 KL 447

Length = 592

>gnl|CDD|184523 PRK14125, PRK14125, cell division suppressor protein YneA; Provisional

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 10/67 (14%)

Query: 84  SICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVS--------IDAIKEANGLSGDTIYA 135
              T   +        + +  GDTLW L+ +Y           I+ +++ N L    I A
Sbjct: 25  VYATVPVDKNQYV--EITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKA 82

Query: 136 GKKLIIP 142
           G KL+IP
Sbjct: 83  GDKLVIP 89

Length = 103

>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)

Query: 81  TKPSICTEKSEPEPA---SCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGK 137
           +KPS  T  S+P      + +   + +GD+LW ++    V+I  +K  N L  D IY G+
Sbjct: 460 SKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQ 519

Query: 138 KL 139
           KL
Sbjct: 520 KL 521

Length = 592

>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 15/45 (33%), Positives = 28/45 (62%)

Query: 95  ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKL 139
           ++ +   +V+GD+LW ++  + V++  +K  N L  D IY G+KL
Sbjct: 328 SNAKIYTVVKGDSLWRIANNHKVTVANLKAWNNLKSDFIYPGQKL 372

Length = 592

>gnl|CDD|236880 PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 90  SEPEPASCRTVEIVRGDTLWGLSRK-YGVSID--AIKEANG--LSG-DTIYAGKKLIIP 142
           + P P S +   +  GDTL  +++K YG +     I EAN   L   D IY G+ L IP
Sbjct: 89  ATPAPES-QFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146

Length = 147

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	142
PRK06347	592	autolysin; Reviewed	99.88
PRK10783	456	mltD membrane-bound lytic murein transglycosylase	99.84
PRK06347	592	autolysin; Reviewed	99.83
PRK13914	481	invasion associated secreted endopeptidase; Provis	99.74
COG1388	124	LytE FOG: LysM repeat [Cell envelope biogenesis, o	99.59
PF01476	44	LysM: LysM domain; InterPro: IPR018392 This domain	99.58
PRK10783	456	mltD membrane-bound lytic murein transglycosylase	99.52
PRK14125	103	cell division suppressor protein YneA; Provisional	99.35
TIGR02899	44	spore_safA spore coat assembly protein SafA. in wh	99.27
cd00118	46	LysM Lysin domain, found in a variety of enzymes i	99.27
TIGR02907	338	spore_VI_D stage VI sporulation protein D. SpoVID,	99.26
PRK10871	319	nlpD lipoprotein NlpD; Provisional	99.19
PRK13914	481	invasion associated secreted endopeptidase; Provis	99.1
smart00257	44	LysM Lysin motif.	98.97
PF01476	44	LysM: LysM domain; InterPro: IPR018392 This domain	98.97
PRK11198	147	LysM domain/BON superfamily protein; Provisional	98.88
COG3858	423	Predicted glycosyl hydrolase [General function pre	98.64
PRK14125	103	cell division suppressor protein YneA; Provisional	98.52
TIGR02899	44	spore_safA spore coat assembly protein SafA. in wh	98.46
cd00118	46	LysM Lysin domain, found in a variety of enzymes i	98.46
TIGR02907	338	spore_VI_D stage VI sporulation protein D. SpoVID,	98.25
PRK10871	319	nlpD lipoprotein NlpD; Provisional	98.24
PF04225	85	OapA: Opacity-associated protein A LysM-like domai	98.09
smart00257	44	LysM Lysin motif.	97.97
COG1388	124	LytE FOG: LysM repeat [Cell envelope biogenesis, o	97.96
COG1652	269	XkdP Uncharacterized protein containing LysM domai	97.91
TIGR03505	74	FimV_core FimV N-terminal domain. This region is f	97.84
PRK11198	147	LysM domain/BON superfamily protein; Provisional	97.59
PRK10190	310	L,D-transpeptidase; Provisional	97.48
PRK10260	306	L,D-transpeptidase; Provisional	97.48
PF05489	60	Phage_tail_X: Phage Tail Protein X; InterPro: IPR0	96.82
PRK11649	439	putative peptidase; Provisional	96.74
COG3170	755	FimV Tfp pilus assembly protein FimV [Cell motilit	96.69
TIGR03505	74	FimV_core FimV N-terminal domain. This region is f	95.9
COG3061	242	OapA Cell envelope opacity-associated protein A [C	95.86
PRK10190	310	L,D-transpeptidase; Provisional	95.7
PRK10260	306	L,D-transpeptidase; Provisional	95.4
PRK11649	439	putative peptidase; Provisional	93.93
PF04225	85	OapA: Opacity-associated protein A LysM-like domai	93.81
COG4784	479	Putative Zn-dependent protease [General function p	93.36
COG1652	269	XkdP Uncharacterized protein containing LysM domai	92.71
KOG2850	186	consensus Predicted peptidoglycan-binding protein,	92.58
PF13518	52	HTH_28: Helix-turn-helix domain	91.72
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	90.34
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	89.1
PF05489	60	Phage_tail_X: Phage Tail Protein X; InterPro: IPR0	87.93
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	85.89
COG4254	339	Uncharacterized protein conserved in bacteria [Fun	85.48
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	83.77
PRK09413	121	IS2 repressor TnpA; Reviewed	83.07
COG2963	116	Transposase and inactivated derivatives [DNA repli	81.21
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	80.33
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	80.16
COG5004	70	P2-like prophage tail protein X [General function	80.16

>PRK06347 autolysin; Reviewed

Probab=99.88  E-value=3e-22  Score=166.44  Aligned_cols=115  Identities=23%  Similarity=0.340  Sum_probs=92.8

Q ss_pred             CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCC
Q 040221           13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEP   92 (142)
Q Consensus        13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (142)
                      ....|.+..||+++.||++|      ||++++|++||++..+.|++||.|+||...........  .       ......
T Consensus       478 ~~~~YtVk~GDTL~sIAkky------gVSv~~L~~~N~l~s~~L~~GQ~L~Ip~~~~~s~~~t~--~-------~s~~~~  542 (592)
T PRK06347        478 NAKVYTVAKGDSLWRIANNN------KVTIANLKSWNNLKSDFIYPGQKLKVSAGSTTNNTNTA--K-------PSTNKP  542 (592)
T ss_pred             cceeeeecCCCCHHHHHHHH------CCCHHHHHHhcCCCcccccCCcEEEEecCccccccccc--C-------CccCCc
Confidence            34578999999999999999      99999999999998888999999999976422110000  0       000111


Q ss_pred             CCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           93 EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        93 ~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      ......+|+|++|||||.||++||+++++|++||+|..+.|++||.|.|+
T Consensus       543 ~~~~~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~L~~~~L~~GQ~L~I~  592 (592)
T PRK06347        543 SNSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK  592 (592)
T ss_pred             cCccceeeecCCCCcHHHHHHHhCCCHHHHHHhcCCCcccCCCCCEEecC
Confidence            12346789999999999999999999999999999998889999999986

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

Probab=99.84  E-value=2.7e-20  Score=151.51  Aligned_cols=106  Identities=16%  Similarity=0.224  Sum_probs=89.7

Q ss_pred             CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCC
Q 040221           13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEP   92 (142)
Q Consensus        13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (142)
                      ....|.++.||+++.||++|      |+++.+|++||++..+.|.+||.|+||..+....                  ..
T Consensus       342 ~~~~y~Vk~GDTL~sIA~r~------gvs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~~~~~------------------~~  397 (456)
T PRK10783        342 NSRSYKVRSGDTLSGIASRL------NVSTKDLQQWNNLRGSKLKVGQTLTIGAGSSAQR------------------LA  397 (456)
T ss_pred             CceEEEECCCCcHHHHHHHH------CcCHHHHHHHcCCCcccCCCCCEEEecCCccccc------------------cc
Confidence            34568899999999999999      9999999999999778899999999997542200                  01


Q ss_pred             CCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           93 EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        93 ~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      ......+|+|++||||++||++|||++++|++||++..+.|++||+|.|+
T Consensus       398 ~~~~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~~L~pGq~L~l~  447 (456)
T PRK10783        398 NNSDSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAKNLQPGDKLTLF  447 (456)
T ss_pred             ccccceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCCcCCCCCEEEEe
Confidence            12345689999999999999999999999999999866699999999874

>PRK06347 autolysin; Reviewed

Probab=99.83  E-value=7.2e-20  Score=152.33  Aligned_cols=120  Identities=20%  Similarity=0.307  Sum_probs=91.2

Q ss_pred             CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCCC
Q 040221           14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPE   93 (142)
Q Consensus        14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (142)
                      ...|.+..||+++.||++|      ||++.+|++||++..+.|.+|+.|+||....... ......... . ........
T Consensus       405 ~~~ytVk~GDTL~sIA~ky------gVSv~~L~~~N~l~s~~L~~Gq~L~IP~~~~~~~-~t~~~s~~~-~-~~k~~s~~  475 (592)
T PRK06347        405 AKVYTVVKGDSLWRIANNN------KVTIANLKSWNNLKSDFIYPGQKLKVSAGSTSNT-NTSKPSTNT-N-TSKPSTNT  475 (592)
T ss_pred             ceeEEecCCCCHHHHHHHh------CCCHHHHHHHhCCCcceeccCcEEEEecCCcccc-ccccccccc-c-cccccccc
Confidence            4578899999999999999      9999999999999878899999999997532100 000000000 0 00000011


Q ss_pred             CCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           94 PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        94 ~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      ......|+|++|||||+||++||+++++|++||++..+.|++||.|.||
T Consensus       476 ~~~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s~~L~~GQ~L~Ip  524 (592)
T PRK06347        476 NTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQKLKVS  524 (592)
T ss_pred             cccceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCcccccCCcEEEEe
Confidence            2335689999999999999999999999999999988889999999997

>PRK13914 invasion associated secreted endopeptidase; Provisional

Probab=99.74  E-value=2.7e-17  Score=133.25  Aligned_cols=122  Identities=25%  Similarity=0.343  Sum_probs=89.9

Q ss_pred             ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCC---------------CC-----
Q 040221           15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQ---------------PP-----   74 (142)
Q Consensus        15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~---------------~~-----   74 (142)
                      .++.++.||+++.||++|      |+++++|+++|++..+.|.+||.|.||.......               .+     
T Consensus        28 ~tytVq~GDTLw~IA~~y------gvtv~~I~~~N~l~~~~I~~Gq~L~Ip~~~~~~~~~~~Vta~~LNVRsgps~s~~I  101 (481)
T PRK13914         28 STVVVEAGDTLWGIAQSK------GTTVDAIKKANNLTTDKIVPGQKLQVNEVAAAEKTEKSVSATWLNVRSGAGVDNSI  101 (481)
T ss_pred             ceEEECCCCCHHHHHHHH------CCCHHHHHHHhCCCcccccCCCEEEeCCCCcccccceeEecceEEEecCCCCCcce
Confidence            357899999999999999      9999999999999888999999999994321000               00     


Q ss_pred             --------------------------------------------CCCCc---cC-----CCC----ccc-----------
Q 040221           75 --------------------------------------------PQQPI---VT-----KPS----ICT-----------   87 (142)
Q Consensus        75 --------------------------------------------~~~~~---~~-----~~~----~~~-----------   87 (142)
                                                                  .++..   ..     ++.    +..           
T Consensus       102 Igsl~~G~~V~Vl~~~~ngW~kI~~~~GktGwV~~~YLs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (481)
T PRK13914        102 ITSIKGGTKVTVETTESNGWHKITYNDGKTGFVNGKYLTDKVTSTPVAPTQEVKKETTTQQAAPAAETKTEVKQTTQATT  181 (481)
T ss_pred             eeeecCCCEEEEeecccCCeEEEEcCCCCEEEEecccccCCCccCccccchhhhhccccccccchhcccchhccCCcccC
Confidence                                                        00000   00     000    000           


Q ss_pred             -C----CCC---CCCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           88 -E----KSE---PEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        88 -~----~~~---~~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                       +    ...   ........|+|++|||||.||++|++++++|++||++....|++||.|.||
T Consensus       182 ~~~~~~~~~~~~~~~~~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s~~L~pGQ~L~Ip  244 (481)
T PRK13914        182 PAPKVAETKETPVVDQNATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAIK  244 (481)
T ss_pred             CcccccccccCccccCCCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCccccCCCCEEEec
Confidence             0    000   012346789999999999999999999999999999988889999999997

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

Probab=99.59  E-value=9.6e-15  Score=99.70  Aligned_cols=107  Identities=29%  Similarity=0.427  Sum_probs=77.6

Q ss_pred             HHHHhcccccCCCCHHHHHHhCCCC--CCCCCCCCcEEecCCCCCCCCCC--CCCccCCCCcccCCCCCCCCCceEEEec
Q 040221           28 VAKTAGFVVFSGIAISILKALNPLN--KNRNETTQPQPIAESTQPIQPPP--QQPIVTKPSICTEKSEPEPASCRTVEIV  103 (142)
Q Consensus        28 iA~~~~~~~~~gvs~~~L~~~N~l~--~~~l~~Gq~l~vp~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~y~V~  103 (142)
                      ||.+|      ++++..|+++|.+.  .+.+.+|+.+.++..........  ......+..  ............+|+|+
T Consensus         1 ia~~~------~~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~V~   72 (124)
T COG1388           1 IASKY------GVSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVS--DSSSASKAPPVVTYTVK   72 (124)
T ss_pred             Ccccc------cccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceee--ccccccccCCCceEEEe
Confidence            56788      99999999999998  67899999999997421100000  000000000  00001112345789999


Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221          104 RGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus       104 ~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      +||+|+.||++|++++.+|+++|.+..+.+++||.|.+|
T Consensus        73 ~gdtL~~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~  111 (124)
T COG1388          73 KGDTLSKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLP  111 (124)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHhccCCCceecCcEEEEe
Confidence            999999999999999999999999999999999999875

>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=99.58  E-value=1.3e-15  Score=85.93  Aligned_cols=43  Identities=40%  Similarity=0.874  Sum_probs=37.2

Q ss_pred             EEecCCCcHHHHHHHhCCCHHHHHHHh-CCCCCCCCCCCEEecC
Q 040221          100 VEIVRGDTLWGLSRKYGVSIDAIKEAN-GLSGDTIYAGKKLIIP  142 (142)
Q Consensus       100 y~V~~GDTl~~IA~rygvs~~~L~~~N-~l~~~~l~~Gq~L~IP  142 (142)
                      |+|++||||++||++|++++++|++|| ++....|.+||.|+||
T Consensus         1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G~~l~iP   44 (44)
T PF01476_consen    1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPGQKLCIP   44 (44)
T ss_dssp             EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred             CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence            899999999999999999999999999 8888669999999998

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.

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

Probab=99.52  E-value=1e-13  Score=113.22  Aligned_cols=117  Identities=23%  Similarity=0.302  Sum_probs=79.9

Q ss_pred             CCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCC-CC-CcEEecCCCCCC-CCCCC-CCccCCCCcccCCCCC
Q 040221           18 DGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNE-TT-QPQPIAESTQPI-QPPPQ-QPIVTKPSICTEKSEP   92 (142)
Q Consensus        18 ~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~-~G-q~l~vp~~~~~~-~~~~~-~~~~~~~~~~~~~~~~   92 (142)
                      ...++.++..||+++      |+++++|.++|+... ..+. .| +.|+||...... ..... ........  ......
T Consensus       267 ~v~~~i~L~~iA~~~------gvs~~eL~~LNP~~kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p--~~~~~~  338 (456)
T PRK10783        267 DLGQQIELAQAAEMA------GMSLTKLKTFNAGYKRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQS--TLVADN  338 (456)
T ss_pred             ecCCCcCHHHHHHHc------CCCHHHHHHhCccccCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhccc--cccccc
Confidence            344566899999999      999999999998533 3222 33 677888753210 00000 00000000  000001


Q ss_pred             CCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           93 EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        93 ~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      ......+|+|++||||++||++||+++.+|++||++..+.|++||.|+||
T Consensus       339 ~~~~~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~~~L~~Gq~L~Ip  388 (456)
T PRK10783        339 TPLNSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTIG  388 (456)
T ss_pred             CcCCceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCcccCCCCCEEEec
Confidence            12346789999999999999999999999999999888889999999987

>PRK14125 cell division suppressor protein YneA; Provisional

Probab=99.35  E-value=2.8e-12  Score=85.06  Aligned_cols=48  Identities=35%  Similarity=0.684  Sum_probs=43.2

Q ss_pred             CCceEEEecCCCcHHHHHHHhCCC--------HHHHHHHhCCCCCCCCCCCEEecC
Q 040221           95 ASCRTVEIVRGDTLWGLSRKYGVS--------IDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        95 ~~~~~y~V~~GDTl~~IA~rygvs--------~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      ..+..|+|++|||||+||++|+++        +..|++.|++.++.|++||.|+||
T Consensus        34 ~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP   89 (103)
T PRK14125         34 NQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIP   89 (103)
T ss_pred             CCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEe
Confidence            467789999999999999999765        577888899999889999999998

>TIGR02899 spore_safA spore coat assembly protein SafA

Probab=99.27  E-value=9.4e-12  Score=69.45  Aligned_cols=41  Identities=49%  Similarity=0.945  Sum_probs=37.6

Q ss_pred             ecCCCcHHHHHHHhCCCHHHHHHHhC-CCC-CCCCCCCEEecC
Q 040221          102 IVRGDTLWGLSRKYGVSIDAIKEANG-LSG-DTIYAGKKLIIP  142 (142)
Q Consensus       102 V~~GDTl~~IA~rygvs~~~L~~~N~-l~~-~~l~~Gq~L~IP  142 (142)
                      |++|||||+||++|++++.+|+++|+ +.+ ..+.+||.|.||
T Consensus         1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip   43 (44)
T TIGR02899         1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIP   43 (44)
T ss_pred             CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecC
Confidence            58999999999999999999999996 655 789999999998

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=99.27  E-value=1.9e-11  Score=67.62  Aligned_cols=44  Identities=41%  Similarity=0.776  Sum_probs=41.5

Q ss_pred             EEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221           99 TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP  142 (142)
Q Consensus        99 ~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP  142 (142)
                      +|+|++|||+++||++|+++..+|+++|+... ..+.+|+.|.||
T Consensus         2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip   46 (46)
T cd00118           2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP   46 (46)
T ss_pred             EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence            69999999999999999999999999999855 889999999998

This domain may have a general peptidoglycan binding function.

>TIGR02907 spore_VI_D stage VI sporulation protein D

Probab=99.26  E-value=1.2e-11  Score=96.10  Aligned_cols=49  Identities=24%  Similarity=0.396  Sum_probs=46.6

Q ss_pred             CCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           94 PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        94 ~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      ...|.+|+|++|||||.||+|||+++.+|++||++..+.|++||.|+||
T Consensus       290 ~~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~GQ~L~IP  338 (338)
T TIGR02907       290 FTKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEGQILYIP  338 (338)
T ss_pred             ccccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence            3678999999999999999999999999999999988899999999998

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.

>PRK10871 nlpD lipoprotein NlpD; Provisional

Probab=99.19  E-value=2.7e-11  Score=94.52  Aligned_cols=46  Identities=20%  Similarity=0.345  Sum_probs=43.7

Q ss_pred             ceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221           97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP  142 (142)
Q Consensus        97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP  142 (142)
                      ..+|+|++|||||.||.+||+++.+|.+||+|.+ ..|++||+|+||
T Consensus        60 ~~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~  106 (319)
T PRK10871         60 GSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVG  106 (319)
T ss_pred             CCceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeC
Confidence            4689999999999999999999999999999988 899999999986

>PRK13914 invasion associated secreted endopeptidase; Provisional

Probab=99.10  E-value=1.6e-10  Score=94.10  Aligned_cols=47  Identities=47%  Similarity=0.783  Sum_probs=44.3

Q ss_pred             CceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           96 SCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        96 ~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      .+..|+|++|||||.||++||+++++|+++|+|..+.|++||.|+||
T Consensus        26 sa~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~~~I~~Gq~L~Ip   72 (481)
T PRK13914         26 SASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKIVPGQKLQVN   72 (481)
T ss_pred             cCceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCcccccCCCEEEeC
Confidence            44579999999999999999999999999999988899999999997

>smart00257 LysM Lysin motif

Probab=98.97  E-value=2e-09  Score=58.56  Aligned_cols=43  Identities=37%  Similarity=0.669  Sum_probs=38.9

Q ss_pred             EEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEec
Q 040221           99 TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLII  141 (142)
Q Consensus        99 ~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~I  141 (142)
                      +|+|++|||+++||++|+++..+|.++|+... ..+++|+.|.|
T Consensus         1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i   44 (44)
T smart00257        1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI   44 (44)
T ss_pred             CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence            48899999999999999999999999998544 88999999875

>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=98.97  E-value=2.7e-10  Score=63.86  Aligned_cols=43  Identities=21%  Similarity=0.188  Sum_probs=34.9

Q ss_pred             CCCCCCCCHHHHHHHhcccccCCCCHHHHHHhC-CCCCCCCCCCCcEEec
Q 040221           17 NDGSGDGREAAVAKTAGFVVFSGIAISILKALN-PLNKNRNETTQPQPIA   65 (142)
Q Consensus        17 ~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N-~l~~~~l~~Gq~l~vp   65 (142)
                      |++..|||++.||++|      |+++++|+++| ++....|.+||.|+||
T Consensus         1 y~V~~gDtl~~IA~~~------~~~~~~l~~~N~~~~~~~l~~G~~l~iP   44 (44)
T PF01476_consen    1 YTVQPGDTLWSIAKRY------GISVDELMELNPNIDSDNLQPGQKLCIP   44 (44)
T ss_dssp             EEE-TT--HHHHHHHT------TS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred             CEECcCCcHHHHHhhh------hhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence            4567899999999999      99999999999 6766569999999998

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.

>PRK11198 LysM domain/BON superfamily protein; Provisional

Probab=98.88  E-value=4.6e-09  Score=73.92  Aligned_cols=47  Identities=36%  Similarity=0.488  Sum_probs=41.8

Q ss_pred             CceEEEecCCCcHHHHHHHhC---CCHHHHHHHhC--CCC-CCCCCCCEEecC
Q 040221           96 SCRTVEIVRGDTLWGLSRKYG---VSIDAIKEANG--LSG-DTIYAGKKLIIP  142 (142)
Q Consensus        96 ~~~~y~V~~GDTl~~IA~ryg---vs~~~L~~~N~--l~~-~~l~~Gq~L~IP  142 (142)
                      ...+|+|++|||||+||++|+   ..+.+|+++|+  +.+ +.|++||+|.||
T Consensus        94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP  146 (147)
T PRK11198         94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP  146 (147)
T ss_pred             CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence            567899999999999999985   45789999997  777 889999999998

>COG3858 Predicted glycosyl hydrolase [General function prediction only]

Probab=98.64  E-value=2.8e-08  Score=79.43  Aligned_cols=89  Identities=19%  Similarity=0.121  Sum_probs=77.3

Q ss_pred             CCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCCCCCCce
Q 040221           19 GSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCR   98 (142)
Q Consensus        19 ~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (142)
                      +..|+....|+++|      +.+...|...|.+.++.+-.||.++||..                             ..
T Consensus         6 ~~pg~~~~~i~~~~------~~~~~~i~~~~~~~~d~~~~~q~~~v~~~-----------------------------~~   50 (423)
T COG3858           6 VGPGDSRLIIAVYF------PYTNNRIVNGNDYTNDDLVDGQTFVVPPS-----------------------------GH   50 (423)
T ss_pred             ccCCceeeeehhhc------cccccccccccccccccccCceeEEECCc-----------------------------ce
Confidence            45688899999999      99999997777776678999999999952                             45


Q ss_pred             EEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221           99 TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP  142 (142)
Q Consensus        99 ~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP  142 (142)
                      +|.|++||++++||++++++.+.+..+|.+.. ..+.+|-.|.+|
T Consensus        51 ~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P   95 (423)
T COG3858          51 FYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIP   95 (423)
T ss_pred             EEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEecc
Confidence            89999999999999999999999999996554 788888888877

>PRK14125 cell division suppressor protein YneA; Provisional

Probab=98.52  E-value=3e-07  Score=60.98  Aligned_cols=52  Identities=13%  Similarity=-0.027  Sum_probs=45.5

Q ss_pred             CCCCccCCCCCCCCHHHHHHHhcccccCCCC--------HHHHHHhCCCCCCCCCCCCcEEecCCC
Q 040221           11 PRVPAENDGSGDGREAAVAKTAGFVVFSGIA--------ISILKALNPLNKNRNETTQPQPIAEST   68 (142)
Q Consensus        11 ~~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs--------~~~L~~~N~l~~~~l~~Gq~l~vp~~~   68 (142)
                      ......++++.|||++.||++|      +.+        +..|++.|++.++.|.+||.|+||...
T Consensus        33 ~~~~~~~tV~~GDTLW~IA~~y------~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~   92 (103)
T PRK14125         33 KNQYVEITVQEGDTLWALADQY------AGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLK   92 (103)
T ss_pred             CCCcEEEEECCCCCHHHHHHHh------CCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCC
Confidence            4567788999999999999999      765        678889999988889999999999764

>TIGR02899 spore_safA spore coat assembly protein SafA

Probab=98.46  E-value=4.5e-07  Score=50.09  Aligned_cols=41  Identities=22%  Similarity=0.166  Sum_probs=35.9

Q ss_pred             CCCCCHHHHHHHhcccccCCCCHHHHHHhCC-CCC-CCCCCCCcEEecC
Q 040221           20 SGDGREAAVAKTAGFVVFSGIAISILKALNP-LNK-NRNETTQPQPIAE   66 (142)
Q Consensus        20 ~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~-l~~-~~l~~Gq~l~vp~   66 (142)
                      ..||+++.||++|      |+++.+|.++|+ +.+ ..+.+|+.|.||.
T Consensus         2 ~~gdtl~~IA~~~------~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~   44 (44)
T TIGR02899         2 QKGDTLWKIAKKY------GVDFDELIQANPQLSNPNLIYPGMKIKIPS   44 (44)
T ss_pred             CCCCCHHHHHHHH------CcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence            4689999999999      999999999997 433 5799999999983

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=98.46  E-value=3.5e-07  Score=49.97  Aligned_cols=44  Identities=20%  Similarity=0.205  Sum_probs=39.0

Q ss_pred             cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCC-CCCCCCCCcEEec
Q 040221           16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLN-KNRNETTQPQPIA   65 (142)
Q Consensus        16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~-~~~l~~Gq~l~vp   65 (142)
                      ++....||+++.||++|      +++..+|.++|+.. ...+.+|+.++||
T Consensus         2 ~~~v~~gdt~~~ia~~~------~~~~~~~~~~N~~~~~~~~~~g~~l~ip   46 (46)
T cd00118           2 TYTVKKGDTLSSIAQRY------GISVEELLKLNGLSDPDNLQVGQKLKIP   46 (46)
T ss_pred             EEEECCCCCHHHHHHHH------CcCHHHHHHHcCCCCccccCCCCEEecC
Confidence            35667899999999999      99999999999984 4789999999886

This domain may have a general peptidoglycan binding function.

>TIGR02907 spore_VI_D stage VI sporulation protein D

Probab=98.25  E-value=1.1e-06  Score=68.63  Aligned_cols=45  Identities=18%  Similarity=0.008  Sum_probs=41.7

Q ss_pred             ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEec
Q 040221           15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIA   65 (142)
Q Consensus        15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp   65 (142)
                      ..+.++.|||++.||+||      |+++..|+++|++..+.|.+|+.|+||
T Consensus       294 ~~YiVq~GDTL~sIAkRY------GVSV~~L~r~N~L~~~~L~~GQ~L~IP  338 (338)
T TIGR02907       294 RMCIVQEGDTIETIAERY------EISVSQLIRHNQLEDFEVNEGQILYIP  338 (338)
T ss_pred             EEEEECCCCCHHHHHHHH------CcCHHHHHHHhCCCccccCCCCEEEeC
Confidence            356789999999999999      999999999999987899999999997

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.

>PRK10871 nlpD lipoprotein NlpD; Provisional

Probab=98.24  E-value=1.4e-06  Score=68.24  Aligned_cols=48  Identities=10%  Similarity=-0.012  Sum_probs=44.0

Q ss_pred             CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCC
Q 040221           14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAES   67 (142)
Q Consensus        14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~   67 (142)
                      +.+|++..|||++.||.+|      |+++.+|.+||+|.+ +.|.+||.|.||..
T Consensus        60 ~~~y~Vk~GDTL~~IA~~~------g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~  108 (319)
T PRK10871         60 GSTYTVKKGDTLFYIAWIT------GNDFRDLAQRNNIQAPYSLNVGQTLQVGNA  108 (319)
T ss_pred             CCceEECCCCHHHHHHHHH------CcCHHHHHHhcCCCCCccccCCCEEEeCCC
Confidence            5679999999999999999      999999999999966 78999999999754

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

Probab=98.09  E-value=4.4e-06  Score=53.52  Aligned_cols=45  Identities=20%  Similarity=0.258  Sum_probs=26.6

Q ss_pred             ceEEEecCCCcHHHHHHHhCCCHHHHHHHh----CCCC-CCCCCCCEEec
Q 040221           97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEAN----GLSG-DTIYAGKKLII  141 (142)
Q Consensus        97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N----~l~~-~~l~~Gq~L~I  141 (142)
                      |..|+|++||||..|-+++|++..++.++=    .-.. ..|+|||.|.+
T Consensus         2 W~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f   51 (85)
T PF04225_consen    2 WQEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEF   51 (85)
T ss_dssp             --EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEE
T ss_pred             CcEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEE
Confidence            789999999999999999999988877763    2234 78999999863

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.

>smart00257 LysM Lysin motif

Probab=97.97  E-value=1.9e-05  Score=42.26  Aligned_cols=42  Identities=21%  Similarity=0.239  Sum_probs=35.7

Q ss_pred             CCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCC-CCCCCCCCCcEEe
Q 040221           17 NDGSGDGREAAVAKTAGFVVFSGIAISILKALNPL-NKNRNETTQPQPI   64 (142)
Q Consensus        17 ~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l-~~~~l~~Gq~l~v   64 (142)
                      +....||+++.||++|      +++..+|.++|+. ....+.+|+.++|
T Consensus         2 ~~v~~gdt~~~ia~~~------~~~~~~~~~~N~~~~~~~~~~g~~l~i   44 (44)
T smart00257        2 YTVKKGDTLSSIARRY------GISVSDLLELNNILDPDNLQVGQKLKI   44 (44)
T ss_pred             eEeCCCCCHHHHHHHh------CCCHHHHHHHcCCCCccccCCCCEEeC
Confidence            4567899999999999      9999999999995 3467889988764

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

Probab=97.96  E-value=1.1e-05  Score=54.68  Aligned_cols=48  Identities=19%  Similarity=0.229  Sum_probs=44.7

Q ss_pred             CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCC
Q 040221           14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAES   67 (142)
Q Consensus        14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~   67 (142)
                      ...|.+..||+++.||++|      ++++.+|+++|.+.++.+.+||.|.++..
T Consensus        66 ~~~~~V~~gdtL~~Ia~~~------~~tv~~l~~~n~l~~~~i~~gq~l~~~~~  113 (124)
T COG1388          66 VVTYTVKKGDTLSKIARKY------GVTVAELKQLNNLSSDKIKVGQKLKLPVS  113 (124)
T ss_pred             CceEEEecCCCHHHHHHHh------CCCHHHHHHHhccCCCceecCcEEEEecc
Confidence            4578899999999999999      99999999999999889999999999963

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

Probab=97.91  E-value=3.9e-06  Score=64.41  Aligned_cols=45  Identities=49%  Similarity=0.737  Sum_probs=39.9

Q ss_pred             eEEEecCCCcHHHHHHHh-C--CCHHHHHHHhC---CCC-CCCCCCCEEecC
Q 040221           98 RTVEIVRGDTLWGLSRKY-G--VSIDAIKEANG---LSG-DTIYAGKKLIIP  142 (142)
Q Consensus        98 ~~y~V~~GDTl~~IA~ry-g--vs~~~L~~~N~---l~~-~~l~~Gq~L~IP  142 (142)
                      .+|+|++|||||.||+++ |  +.+..|...|+   +.+ +.|++||+|.||
T Consensus       211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP  262 (269)
T COG1652         211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIP  262 (269)
T ss_pred             eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCC
Confidence            489999999999999775 4  56788999998   777 999999999998

>TIGR03505 FimV_core FimV N-terminal domain

Probab=97.84  E-value=3.6e-05  Score=48.04  Aligned_cols=37  Identities=38%  Similarity=0.644  Sum_probs=30.3

Q ss_pred             CcHHHHHHHh---C-CCHH----HHHHHhC----CCC-CCCCCCCEEecC
Q 040221          106 DTLWGLSRKY---G-VSID----AIKEANG----LSG-DTIYAGKKLIIP  142 (142)
Q Consensus       106 DTl~~IA~ry---g-vs~~----~L~~~N~----l~~-~~l~~Gq~L~IP  142 (142)
                      ||||+||++|   + +++.    .|.+.|.    -.+ +.|++|+.|.||
T Consensus         1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP   50 (74)
T TIGR03505         1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIP   50 (74)
T ss_pred             CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCC
Confidence            8999999999   3 6765    6778883    234 889999999998

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.

>PRK11198 LysM domain/BON superfamily protein; Provisional

Probab=97.59  E-value=0.00011  Score=51.62  Aligned_cols=51  Identities=16%  Similarity=0.008  Sum_probs=41.0

Q ss_pred             CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCC--CCC-CCCCCCCcEEecC
Q 040221           13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP--LNK-NRNETTQPQPIAE   66 (142)
Q Consensus        13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~--l~~-~~l~~Gq~l~vp~   66 (142)
                      ...+|....||+++.||++|   +..+..+..|.++|+  +.+ +.|.+||.|.||.
T Consensus        94 ~~~~y~Vk~GDTL~~IA~~~---~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP~  147 (147)
T PRK11198         94 ESQFYTVKSGDTLSAIAKKV---YGNANKYNKIFEANKPMLKSPDKIYPGQVLRIPE  147 (147)
T ss_pred             CCeEEEECCCCCHHHHHHHH---cCChhhHHHHHHhhhhcCCCcCCcCcCCEEecCC
Confidence            34678899999999999998   112256889999998  655 6899999999983

>PRK10190 L,D-transpeptidase; Provisional

Probab=97.48  E-value=0.00034  Score=54.68  Aligned_cols=48  Identities=25%  Similarity=0.304  Sum_probs=40.8

Q ss_pred             CCceEEEecCCC--cHHHHHHHhCCCHHHHHHHhC-CCCCCCCCCCEEecC
Q 040221           95 ASCRTVEIVRGD--TLWGLSRKYGVSIDAIKEANG-LSGDTIYAGKKLIIP  142 (142)
Q Consensus        95 ~~~~~y~V~~GD--Tl~~IA~rygvs~~~L~~~N~-l~~~~l~~Gq~L~IP  142 (142)
                      .....|+|+.+|  +|.+||++|++....|.++|. +.....++|++|.||
T Consensus        35 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP   85 (310)
T PRK10190         35 GQSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIP   85 (310)
T ss_pred             cceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEec
Confidence            456789999966  699999999999999999995 444567899999998

>PRK10260 L,D-transpeptidase; Provisional

Probab=97.48  E-value=0.00037  Score=54.40  Aligned_cols=48  Identities=23%  Similarity=0.310  Sum_probs=40.8

Q ss_pred             CCceEEEecCCC--cHHHHHHHhCCCHHHHHHHhC-CCCCCCCCCCEEecC
Q 040221           95 ASCRTVEIVRGD--TLWGLSRKYGVSIDAIKEANG-LSGDTIYAGKKLIIP  142 (142)
Q Consensus        95 ~~~~~y~V~~GD--Tl~~IA~rygvs~~~L~~~N~-l~~~~l~~Gq~L~IP  142 (142)
                      .....|+|++|+  +|..||++|++....|+++|. +.....++|++|.||
T Consensus        38 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP   88 (306)
T PRK10260         38 GQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIP   88 (306)
T ss_pred             cccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeC
Confidence            456689999966  599999999999999999995 444667899999997

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

Probab=96.82  E-value=0.0038  Score=37.31  Aligned_cols=40  Identities=40%  Similarity=0.677  Sum_probs=32.1

Q ss_pred             cCCCcHHHHHHH-hCCC---HHHHHHHh-CCCC--CCCCCCCEEecC
Q 040221          103 VRGDTLWGLSRK-YGVS---IDAIKEAN-GLSG--DTIYAGKKLIIP  142 (142)
Q Consensus       103 ~~GDTl~~IA~r-ygvs---~~~L~~~N-~l~~--~~l~~Gq~L~IP  142 (142)
                      +.||+|..|+.| ||-.   ++++.+.| +|..  ..|..|..|.||
T Consensus         6 ~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP   52 (60)
T PF05489_consen    6 TQGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILP   52 (60)
T ss_pred             eCcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECC
Confidence            499999999955 5654   37889999 6665  468899999998

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.

>PRK11649 putative peptidase; Provisional

Probab=96.74  E-value=0.0035  Score=51.53  Aligned_cols=48  Identities=21%  Similarity=0.338  Sum_probs=40.4

Q ss_pred             CCCceEEEecCCCcHHHHHHHhCCCHHHHHHHh-CCCC-CCCCCCCEEec
Q 040221           94 PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEAN-GLSG-DTIYAGKKLII  141 (142)
Q Consensus        94 ~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N-~l~~-~~l~~Gq~L~I  141 (142)
                      ...|..|+|++||||.+|=+++|++..++.++- ...+ ..|++||.|.+
T Consensus        92 ~~~~~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~  141 (439)
T PRK11649         92 EAGVHEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSW  141 (439)
T ss_pred             CCceEEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEE
Confidence            356789999999999999999999999988873 3344 78999999864

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

Probab=96.69  E-value=0.0019  Score=55.28  Aligned_cols=49  Identities=31%  Similarity=0.520  Sum_probs=39.1

Q ss_pred             CCCceEEEecCCCcHHHHHHHh----CCCH----HHHHHHhC--C--CC-CCCCCCCEEecC
Q 040221           94 PASCRTVEIVRGDTLWGLSRKY----GVSI----DAIKEANG--L--SG-DTIYAGKKLIIP  142 (142)
Q Consensus        94 ~~~~~~y~V~~GDTl~~IA~ry----gvs~----~~L~~~N~--l--~~-~~l~~Gq~L~IP  142 (142)
                      .....+|+|++|||||+||.+.    ++++    ..|++.|.  +  .+ ++|+.|++|.||
T Consensus       185 ~a~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP  246 (755)
T COG3170         185 AAPGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIP  246 (755)
T ss_pred             CCCCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeecc
Confidence            3667899999999999999887    3554    45788883  2  23 689999999998

>TIGR03505 FimV_core FimV N-terminal domain

Probab=95.90  E-value=0.019  Score=35.69  Aligned_cols=43  Identities=19%  Similarity=0.117  Sum_probs=32.9

Q ss_pred             CCHHHHHHHhcccccCCCCHH----HHHHhCCC---C-C-CCCCCCCcEEecCC
Q 040221           23 GREAAVAKTAGFVVFSGIAIS----ILKALNPL---N-K-NRNETTQPQPIAES   67 (142)
Q Consensus        23 ~~~~~iA~~~~~~~~~gvs~~----~L~~~N~l---~-~-~~l~~Gq~l~vp~~   67 (142)
                      ||++.||+++  .....+++.    .|.+.|+-   . + +.|+.|+.|.||..
T Consensus         1 DTLw~IA~~~--~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~   52 (74)
T TIGR03505         1 DTLWGIAQRV--RPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE   52 (74)
T ss_pred             CcHHHHHHHH--ccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence            7999999999  233337777    66788873   2 2 68999999999974

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.

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

Probab=95.86  E-value=0.039  Score=41.13  Aligned_cols=47  Identities=21%  Similarity=0.337  Sum_probs=40.4

Q ss_pred             CCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCC---CC--CCCCCCCEEec
Q 040221           95 ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGL---SG--DTIYAGKKLII  141 (142)
Q Consensus        95 ~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l---~~--~~l~~Gq~L~I  141 (142)
                      ..|.+|+|..|+||..+=+.+++.+.++..+-..   ..  +.|+.||.+.|
T Consensus       157 g~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki  208 (242)
T COG3061         157 GNWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKI  208 (242)
T ss_pred             ccceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEE
Confidence            4899999999999999999999999998888743   22  67999999876

>PRK10190 L,D-transpeptidase; Provisional

Probab=95.70  E-value=0.019  Score=45.10  Aligned_cols=47  Identities=13%  Similarity=0.041  Sum_probs=38.4

Q ss_pred             ccCCCCCCC--CHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCC
Q 040221           15 AENDGSGDG--REAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAES   67 (142)
Q Consensus        15 ~~~~~~~~~--~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~   67 (142)
                      .++...++|  .+..||++|      ++...+|+++|+-.+ ...++|+.|.||..
T Consensus        38 ~~~~v~~~~~~~le~iA~~f------~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~   87 (310)
T PRK10190         38 LTVTVPDHNTQPLETFAAQY------GQGLSNMLEANPGADVFLPKSGSQLTIPQQ   87 (310)
T ss_pred             EEEEecCCCCccHHHHHHHh------CCCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence            345566655  599999999      999999999999755 45679999999974

>PRK10260 L,D-transpeptidase; Provisional

Probab=95.40  E-value=0.03  Score=43.90  Aligned_cols=47  Identities=11%  Similarity=-0.075  Sum_probs=38.5

Q ss_pred             ccCCCCCCC--CHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCC
Q 040221           15 AENDGSGDG--REAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAES   67 (142)
Q Consensus        15 ~~~~~~~~~--~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~   67 (142)
                      .+++..+++  ++..||++|      ++....|+++|+..+ ...+.|+.|.||..
T Consensus        41 ~~~~v~~~~~~~le~iA~~f------~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~   90 (306)
T PRK10260         41 QVITIPEGNTQPLEYFAAEY------QMGLSNMMEANPGVDTFLPKGGTVLNIPQQ   90 (306)
T ss_pred             EEEEeCCCCCchHHHHHHHh------CCCHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence            455666655  599999999      999999999999655 45679999999974

>PRK11649 putative peptidase; Provisional

Probab=93.93  E-value=0.47  Score=39.14  Aligned_cols=120  Identities=13%  Similarity=0.076  Sum_probs=70.5

Q ss_pred             cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCC-CC-CCCCCCCcEEecCCCCC-CC-CCCCCCccC------CCCc
Q 040221           16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPL-NK-NRNETTQPQPIAESTQP-IQ-PPPQQPIVT------KPSI   85 (142)
Q Consensus        16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l-~~-~~l~~Gq~l~vp~~~~~-~~-~~~~~~~~~------~~~~   85 (142)
                      ++..+.|||++.|=+++      |++..++.++-.. .+ ..|++||.+.+-..... .. ..+......      ....
T Consensus        97 ~~~Vk~GDTl~~iL~r~------Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg~  170 (439)
T PRK11649         97 EYVVSTGDTLSSILNQY------GIDMSDISQLAAQDKELRNLKIGQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGNG  170 (439)
T ss_pred             EEEeCCCCCHHHHHHHc------CCCHHHHHHHHHcChHhhcCCCCCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCCc
Confidence            67889999999999999      9999999877332 22 58999999988644321 10 001100000      0000


Q ss_pred             ccCCCCCCCCCceEE--EecCCCcHHHHHHHhCCCHHHHHHHhC-----CCCCCCCCCCEEec
Q 040221           86 CTEKSEPEPASCRTV--EIVRGDTLWGLSRKYGVSIDAIKEANG-----LSGDTIYAGKKLII  141 (142)
Q Consensus        86 ~~~~~~~~~~~~~~y--~V~~GDTl~~IA~rygvs~~~L~~~N~-----l~~~~l~~Gq~L~I  141 (142)
                      +..........+...  ...-..+|+.-|.+-|++...+.++..     +.-..|+.|++..|
T Consensus       171 F~~~~~~~~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~~~~~~idf~~lr~GD~f~v  233 (439)
T PRK11649        171 FKETSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSV  233 (439)
T ss_pred             EEEEEeecccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHHHhccCcChhhCCCCCEEEE
Confidence            110001111111111  112247999999999999877776653     22255899988654

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

Probab=93.81  E-value=0.057  Score=34.44  Aligned_cols=47  Identities=17%  Similarity=0.076  Sum_probs=28.1

Q ss_pred             cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCC---C--CCCCCCCCCcEEecCCC
Q 040221           16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP---L--NKNRNETTQPQPIAEST   68 (142)
Q Consensus        16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~---l--~~~~l~~Gq~l~vp~~~   68 (142)
                      +++++.||+++.|-+++      |++..++.++=.   .  .-..|++||.|.+-...
T Consensus         4 ~~~V~~GDtLs~iF~~~------gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~   55 (85)
T PF04225_consen    4 EYTVKSGDTLSTIFRRA------GLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDE   55 (85)
T ss_dssp             EEE--TT--HHHHHHHT------T--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-T
T ss_pred             EEEECCCCcHHHHHHHc------CCCHHHHHHHHhccCccchHhhCCCCCEEEEEECC
Confidence            56788999999999999      999998865432   2  22689999999988653

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.

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

Probab=93.36  E-value=0.16  Score=40.62  Aligned_cols=48  Identities=29%  Similarity=0.479  Sum_probs=39.3

Q ss_pred             CCCceEEEecCCCcHHHHHHHh-CCC--HHHHHHHhCCCC-CCCCCCCEEec
Q 040221           94 PASCRTVEIVRGDTLWGLSRKY-GVS--IDAIKEANGLSG-DTIYAGKKLII  141 (142)
Q Consensus        94 ~~~~~~y~V~~GDTl~~IA~ry-gvs--~~~L~~~N~l~~-~~l~~Gq~L~I  141 (142)
                      +-.....+|++|||+.++|.+. |++  ++-++-+|.+.. ..+++|+.++|
T Consensus       425 PlrirvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi  476 (479)
T COG4784         425 PLRIRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI  476 (479)
T ss_pred             ceEEEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence            4455667899999999999776 544  667888899988 89999999986

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

Probab=92.71  E-value=0.033  Score=42.75  Aligned_cols=50  Identities=14%  Similarity=0.131  Sum_probs=44.5

Q ss_pred             cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCC---CCC-CCCCCCCcEEecCCC
Q 040221           16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP---LNK-NRNETTQPQPIAEST   68 (142)
Q Consensus        16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~---l~~-~~l~~Gq~l~vp~~~   68 (142)
                      .|++..|||++.|++++   |..++-+..|..+|+   +.+ +.|.+||.+.||...
T Consensus       212 ~~~v~rgDTl~~is~~~---Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~~  265 (269)
T COG1652         212 TNTVKRGDTLWQISKKV---YGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQL  265 (269)
T ss_pred             EEEeccCCcccccchhh---cCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCcc
Confidence            68899999999999999   888999999999999   544 799999999999753

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

Probab=92.58  E-value=0.08  Score=38.63  Aligned_cols=46  Identities=28%  Similarity=0.357  Sum_probs=35.9

Q ss_pred             ceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221           97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP  142 (142)
Q Consensus        97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP  142 (142)
                      ...-+++.||||..||-+|...+.+|++.|++.. ..+.+-+.+.+|
T Consensus         9 ~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~p   55 (186)
T KOG2850|consen    9 ELEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIP   55 (186)
T ss_pred             heeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecc
Confidence            3457899999999999999999999999997655 555544444443

>PF13518 HTH_28: Helix-turn-helix domain

Probab=91.72  E-value=0.2  Score=28.10  Aligned_cols=24  Identities=17%  Similarity=0.458  Sum_probs=21.5

Q ss_pred             cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          103 VRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       103 ~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      ..|.|+..+|++||++...+..|-
T Consensus        10 ~~g~s~~~~a~~~gis~~tv~~w~   33 (52)
T PF13518_consen   10 LEGESVREIAREFGISRSTVYRWI   33 (52)
T ss_pred             HcCCCHHHHHHHHCCCHhHHHHHH
Confidence            368899999999999999999885

>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=90.34  E-value=0.36  Score=26.74  Aligned_cols=23  Identities=17%  Similarity=0.397  Sum_probs=18.1

Q ss_pred             cCCCcHHHHHHHhCCCHHHHHHH
Q 040221          103 VRGDTLWGLSRKYGVSIDAIKEA  125 (142)
Q Consensus       103 ~~GDTl~~IA~rygvs~~~L~~~  125 (142)
                      ..|-+..+||+.||++...|+++
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            57889999999999999999875

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 ....

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

Probab=89.10  E-value=0.24  Score=30.17  Aligned_cols=25  Identities=20%  Similarity=0.461  Sum_probs=21.7

Q ss_pred             ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          102 IVRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       102 V~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      ...|.|+..||++||++...|..|=
T Consensus        20 ~~~g~sv~~va~~~gi~~~~l~~W~   44 (76)
T PF01527_consen   20 LESGESVSEVAREYGISPSTLYNWR   44 (76)
T ss_dssp             HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred             HHCCCceEeeecccccccccccHHH
Confidence            3678999999999999999999994

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.

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

Probab=87.93  E-value=1.1  Score=26.52  Aligned_cols=44  Identities=9%  Similarity=0.002  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHHhcccccCCCC--HHHHHHhCCC-CC--CCCCCCCcEEecCCC
Q 040221           21 GDGREAAVAKTAGFVVFSGIA--ISILKALNPL-NK--NRNETTQPQPIAEST   68 (142)
Q Consensus        21 ~~~~~~~iA~~~~~~~~~gvs--~~~L~~~N~l-~~--~~l~~Gq~l~vp~~~   68 (142)
                      +|||+..||-|+    ++...  ++.+.++|+- ..  ..|..|..|.+|...
T Consensus         7 ~GDtlD~I~~r~----yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i~   55 (60)
T PF05489_consen    7 QGDTLDLIAYRH----YGREDGAVEALLEANPGLADTGPVLPAGTVIILPDIP   55 (60)
T ss_pred             CcCcHHHHHHHH----hCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCCC
Confidence            799999999998    33332  3788999984 22  478999999999654

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.

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

Probab=85.89  E-value=1.1  Score=24.93  Aligned_cols=24  Identities=17%  Similarity=0.237  Sum_probs=18.6

Q ss_pred             cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          103 VRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       103 ~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      ..|.|...||+.+|++...+.+|=
T Consensus        15 ~~G~s~~~ia~~lgvs~~Tv~~w~   38 (50)
T PF13384_consen   15 REGWSIREIAKRLGVSRSTVYRWI   38 (50)
T ss_dssp             HHT--HHHHHHHHTS-HHHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHH
Confidence            349999999999999999999884

>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.48  E-value=0.93  Score=35.50  Aligned_cols=45  Identities=31%  Similarity=0.235  Sum_probs=38.3

Q ss_pred             eEEEecCCCcHHHHHHHhC---CCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221           98 RTVEIVRGDTLWGLSRKYG---VSIDAIKEANGLSG-DTIYAGKKLIIP  142 (142)
Q Consensus        98 ~~y~V~~GDTl~~IA~ryg---vs~~~L~~~N~l~~-~~l~~Gq~L~IP  142 (142)
                      .+|+|+.||||-.++..|=   -.+..++..|.+.+ ..+++|..|.||
T Consensus         6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip   54 (339)
T COG4254           6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIP   54 (339)
T ss_pred             ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCC
Confidence            6899999999999999994   33566778898888 889999999887

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=83.77  E-value=0.52  Score=27.16  Aligned_cols=24  Identities=21%  Similarity=0.509  Sum_probs=17.6

Q ss_pred             ecCCCcHHHHHHHhCCCHHHHHHH
Q 040221          102 IVRGDTLWGLSRKYGVSIDAIKEA  125 (142)
Q Consensus       102 V~~GDTl~~IA~rygvs~~~L~~~  125 (142)
                      +..|.+..+||+.||++..++..|
T Consensus        19 ~e~g~s~~~ia~~fgv~~sTv~~I   42 (53)
T PF04218_consen   19 LEEGESKRDIAREFGVSRSTVSTI   42 (53)
T ss_dssp             HHCTT-HHHHHHHHT--CCHHHHH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHH
Confidence            467889999999999998887765

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=83.07  E-value=1.5  Score=29.48  Aligned_cols=25  Identities=20%  Similarity=0.126  Sum_probs=22.9

Q ss_pred             ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          102 IVRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       102 V~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      +..|.++..||++||++...|..|=
T Consensus        26 ~~~g~sv~evA~e~gIs~~tl~~W~   50 (121)
T PRK09413         26 FEPGMTVSLVARQHGVAASQLFLWR   50 (121)
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            5678999999999999999999994

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=81.21  E-value=1.8  Score=28.59  Aligned_cols=25  Identities=24%  Similarity=0.464  Sum_probs=21.5

Q ss_pred             ecCCCcHHHHHHHhCC-CHHHHHHHh
Q 040221          102 IVRGDTLWGLSRKYGV-SIDAIKEAN  126 (142)
Q Consensus       102 V~~GDTl~~IA~rygv-s~~~L~~~N  126 (142)
                      .+.|.|+..||++||+ +...|..|=
T Consensus        21 ~~~g~sv~~vAr~~gv~~~~~l~~W~   46 (116)
T COG2963          21 LRGGDTVSEVAREFGIVSATQLYKWR   46 (116)
T ss_pred             HhcCccHHHHHHHhCCCChHHHHHHH
Confidence            4678999999999995 999999773

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=80.33  E-value=3.1  Score=20.19  Aligned_cols=23  Identities=22%  Similarity=0.419  Sum_probs=19.9

Q ss_pred             cCCCcHHHHHHHhCCCHHHHHHH
Q 040221          103 VRGDTLWGLSRKYGVSIDAIKEA  125 (142)
Q Consensus       103 ~~GDTl~~IA~rygvs~~~L~~~  125 (142)
                      ..|.++..||+.||++...+..|
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHh
Confidence            46789999999999999988765

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=80.16  E-value=2.6  Score=23.13  Aligned_cols=24  Identities=13%  Similarity=0.367  Sum_probs=15.8

Q ss_pred             ecCCCcHHHHHHHhCCCHHHHHHH
Q 040221          102 IVRGDTLWGLSRKYGVSIDAIKEA  125 (142)
Q Consensus       102 V~~GDTl~~IA~rygvs~~~L~~~  125 (142)
                      .+.|-++..||+++|.+...+.++
T Consensus        17 ~~~G~s~~~IA~~lg~s~sTV~re   40 (44)
T PF13936_consen   17 LEQGMSIREIAKRLGRSRSTVSRE   40 (44)
T ss_dssp             HCS---HHHHHHHTT--HHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCcHHHHHH
Confidence            368999999999999999887653

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

Probab=80.16  E-value=6.5  Score=23.72  Aligned_cols=45  Identities=31%  Similarity=0.471  Sum_probs=32.8

Q ss_pred             eEEEecCCCcHHHHHHHh-CCC---HHHHHHHh-CCCC--CCCCCCCEEecC
Q 040221           98 RTVEIVRGDTLWGLSRKY-GVS---IDAIKEAN-GLSG--DTIYAGKKLIIP  142 (142)
Q Consensus        98 ~~y~V~~GDTl~~IA~ry-gvs---~~~L~~~N-~l~~--~~l~~Gq~L~IP  142 (142)
                      ..++...|||+..|+.|+ |-+   .+++.+.| +|.+  ..|..|-.|.+|
T Consensus         3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lP   54 (70)
T COG5004           3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLP   54 (70)
T ss_pred             eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecC
Confidence            356677899999999665 533   46777888 7776  557777777665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	142
2djp_A	77	The Solution Structure Of The Lysm Domain Of Human		1e-04

>pdb|2DJP|A Chain A, The Solution Structure Of The Lysm Domain Of Human Hypothetical Protein Sb145 Length = 77

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 28/39 (71%), Gaps = 1/39 (2%)
Query: 105 GDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLIIP 142
           GDTL GL+ KYGV+++ IK AN L + D+I+  K L IP
Sbjct: 23  GDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIP 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	142
2djp_A	77	Hypothetical protein SB145; LYSM, structural genom	4e-14
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	3e-12
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	3e-07
1e0g_A	48	Membrane-bound lytic murein transglycosylase D; ce	1e-10
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	1e-07
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	4e-05
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	6e-04
1y7m_A	164	Hypothetical protein BSU14040; surface mutagenesis	6e-05

>2djp_A Hypothetical protein SB145; LYSM, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 77

 Score = 62.1 bits (151), Expect = 4e-14
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 90  SEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGL-SGDTIYAGKKLIIP 142
             P        ++  GDTL GL+ KYGV+++ IK AN L + D+I+  K L IP
Sbjct: 8   CSPVRERRLEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIP 61

>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} Length = 167

 Score = 59.6 bits (144), Expect = 3e-12
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 94  PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP 142
                TV + +GDTL  + R++      I   N +   D IY G+ L +P
Sbjct: 59  GGGTATVTVQQGDTLRDIGRRFDCDFHEIARRNNIQNEDLIYPGQVLQVP 108

>2l9y_A CVNH-LYSM lectin; carbohydrate, sugar binding protein; NMR {Magnaporthe oryzae 70-15} Length = 167

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 5/64 (7%)

Query: 76  QQPIVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEA-----NGLSG 130
           Q   V         +     S R V +V G  +     +Y    +  +          +G
Sbjct: 103 QVLQVPTKGGSGGGAGNFWDSARDVRLVDGGKVLEAELRYSGGWNRSRIYLDEHIGNRNG 162

Query: 131 DTIY 134
           + I+
Sbjct: 163 ELIH 166

>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 Length = 48

 Score = 52.2 bits (126), Expect = 1e-10
 Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 104 RGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           +GD+L  +++++GV+I  +   N  +   +  G KL + 
Sbjct: 9   KGDSLSSIAKRHGVNIKDVMRWNSDT-ANLQPGDKLTLF 46

>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 = 47.8 bits (113), Expect = 1e-07
 Identities = 18/99 (18%), Positives = 31/99 (31%), Gaps = 18/99 (18%)

Query: 45  LKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEP-EPASCRTVEIV 103
           L+A NP                      P      V     C ++S   +     T  + 
Sbjct: 106 LQARNPFPATNI----------------PLSATLNVLVNCSCGDESVSKDFGLFVTYPLR 149

Query: 104 RGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
             D+L  ++R  GVS D ++  N    +       + +P
Sbjct: 150 PEDSLSSIARSSGVSADILQRYNPGV-NFNSGNGIVYVP 187

>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 = 40.5 bits (94), Expect = 4e-05
 Identities = 9/92 (9%), Positives = 27/92 (29%), Gaps = 6/92 (6%)

Query: 54  NRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIVRGDTLWGLSR 113
           N +   +     +    I       ++  P  C  +         +  + + DT   ++ 
Sbjct: 38  NFDPILRYNSNIKDKDRI--QMGSRVLV-PFPCECQPGDFLGHNFSYSVRQEDTYERVAI 94

Query: 114 KY---GVSIDAIKEANGLSGDTIYAGKKLIIP 142
                  ++++++  N      I     L + 
Sbjct: 95  SNYANLTTMESLQARNPFPATNIPLSATLNVL 126

>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 = 37.4 bits (86), Expect = 6e-04
 Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 10/49 (20%)

Query: 104 RGDTLWGLSRKYGVSIDAIKEANGL----------SGDTIYAGKKLIIP 142
            G TL  +++    SI    + N              D I  G ++++P
Sbjct: 16  NGTTLSVINQNLNSSIAPYDQINFDPILRYNSNIKDKDRIQMGSRVLVP 64

>1y7m_A Hypothetical protein BSU14040; surface mutagenesis, cysteine proteases, cell WALL catabolism, structural genomics, PSI; 2.05A {Bacillus subtilis subsp} SCOP: b.160.1.1 d.7.1.1 Length = 164

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 13/44 (29%), Positives = 26/44 (59%)

Query: 99  TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           T ++ +GDTL  ++  + +S  A+ +AN      + AG+ ++IP
Sbjct: 3   TYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIP 46

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	142
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	99.87
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	99.86
2djp_A	77	Hypothetical protein SB145; LYSM, structural genom	99.59
1e0g_A	48	Membrane-bound lytic murein transglycosylase D; ce	99.55
2gu1_A	361	Zinc peptidase; alpha/beta, beta barrel, structura	99.47
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	99.45
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	99.45
1e0g_A	48	Membrane-bound lytic murein transglycosylase D; ce	98.84
2gu1_A	361	Zinc peptidase; alpha/beta, beta barrel, structura	98.82
2djp_A	77	Hypothetical protein SB145; LYSM, structural genom	98.81
4a1k_A	165	Putative L, D-transpeptidase YKUD; transferase, pe	97.94
3slu_A	371	M23 peptidase domain protein; outer membrane, hydr	97.65
3slu_A	371	M23 peptidase domain protein; outer membrane, hydr	97.07
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	87.78
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.25
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	84.85
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	84.27
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	83.4
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	81.6

>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=99.87  E-value=5.1e-22  Score=146.32  Aligned_cols=106  Identities=16%  Similarity=0.103  Sum_probs=86.3

Q ss_pred             ccCCCCCCCCHHHHH-HHhcccccCC--CCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCC
Q 040221           15 AENDGSGDGREAAVA-KTAGFVVFSG--IAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSE   91 (142)
Q Consensus        15 ~~~~~~~~~~~~~iA-~~~~~~~~~g--vs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (142)
                      ..|+++.|||++.|| ++|      +  +++++|+++|++..+.|.+||.|.||..+.+...               ...
T Consensus        79 ~~Y~V~~GDTL~~IA~~~y------~~lvt~~~L~~~N~~~~~~l~~Gq~L~IP~~~~~~~~---------------~~~  137 (212)
T 4eby_A           79 FSYSVRQEDTYERVAISNY------ANLTTMESLQARNPFPATNIPLSATLNVLVNCSCGDE---------------SVS  137 (212)
T ss_dssp             EEEECCTTCCHHHHHHTTT------TTSSCHHHHHHHCCSCTTCCCTTCEEEEEEECCCCCT---------------TTC
T ss_pred             eEEEecCCCcHHHHHHHhc------CCCCCHHHHHHhcCCCcccCCCCCEEEEcCCCcCCCc---------------ccc
Confidence            568899999999999 799      9  9999999999977789999999999976532110               000


Q ss_pred             CCCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           92 PEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        92 ~~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      .......+|+|++|||||.||++||+++++|++||++.+..+..|+ |.||
T Consensus       138 ~~~~~~~~Y~V~~GDTL~~IA~~fgvsv~~L~~~N~~~~~~~~~g~-l~IP  187 (212)
T 4eby_A          138 KDFGLFVTYPLRPEDSLSSIARSSGVSADILQRYNPGVNFNSGNGI-VYVP  187 (212)
T ss_dssp             SSCCCEEEEECCTTCCHHHHHHHHTSCHHHHHHHSTTCCTTSCSSE-EEEE
T ss_pred             cCCCCeEEEEECCCCcHHHHHHHHCcCHHHHHHhcCCCccCCCCCE-EEec
Confidence            1123347899999999999999999999999999988766566665 8887

>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=99.86  E-value=2.3e-22  Score=148.21  Aligned_cols=103  Identities=10%  Similarity=0.075  Sum_probs=87.4

Q ss_pred             cCCCCCCCCHHHHHHHhcccccCCCCH--------HHHHHhC-CCC-CCCCCCCCcEEecCCCCCCCCCCCCCccCCCCc
Q 040221           16 ENDGSGDGREAAVAKTAGFVVFSGIAI--------SILKALN-PLN-KNRNETTQPQPIAESTQPIQPPPQQPIVTKPSI   85 (142)
Q Consensus        16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~--------~~L~~~N-~l~-~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~   85 (142)
                      .|.++.|||++.||++|      |+++        ++|+++| ++. .+.|.+||.|+||..+.+..             
T Consensus        11 ~Y~V~~GDTL~~IA~~~------~vsv~~~~~~~~~~I~~~Np~l~~~~~l~~Gq~L~IP~~~~~~~-------------   71 (212)
T 4eby_A           11 SYYLENGTTLSVINQNL------NSSIAPYDQINFDPILRYNSNIKDKDRIQMGSRVLVPFPCECQP-------------   71 (212)
T ss_dssp             EEECCTTCCHHHHHHHT------CCSSSCCCSSCCHHHHTTCTTCSCTTSCCTTCEEEEEECCEEET-------------
T ss_pred             EEEeCCCCCHHHHHHHH------CCCchhccccCHHHHHHhccCCCCcCccCCCCEEEEeccccccC-------------
Confidence            57888999999999999      9998        9999999 885 47899999999997642200             


Q ss_pred             ccCCCCCCCCCceEEEecCCCcHHHHH-HHhC--CCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           86 CTEKSEPEPASCRTVEIVRGDTLWGLS-RKYG--VSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        86 ~~~~~~~~~~~~~~y~V~~GDTl~~IA-~ryg--vs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                           ........+|+|++|||||.|| ++|+  +++++|++||++..+.|++||+|.||
T Consensus        72 -----~~~~~~~~~Y~V~~GDTL~~IA~~~y~~lvt~~~L~~~N~~~~~~l~~Gq~L~IP  126 (212)
T 4eby_A           72 -----GDFLGHNFSYSVRQEDTYERVAISNYANLTTMESLQARNPFPATNIPLSATLNVL  126 (212)
T ss_dssp             -----TTEEEEEEEEECCTTCCHHHHHHTTTTTSSCHHHHHHHCCSCTTCCCTTCEEEEE
T ss_pred             -----CccccCceEEEecCCCcHHHHHHHhcCCCCCHHHHHHhcCCCcccCCCCCEEEEc
Confidence                 0001235689999999999999 7999  99999999999777899999999997

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

Probab=99.59  E-value=7e-16  Score=96.29  Aligned_cols=47  Identities=45%  Similarity=0.647  Sum_probs=44.3

Q ss_pred             CceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221           96 SCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP  142 (142)
Q Consensus        96 ~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP  142 (142)
                      .+..|+|++|||||.||++|++++++|+++|++.. +.|++||+|+||
T Consensus        14 ~~~~y~V~~GDTL~~IA~~~~~~~~~l~~~N~l~~~~~l~~Gq~l~iP   61 (77)
T 2djp_A           14 RRLEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIP   61 (77)
T ss_dssp             EEEEECCCTTCCHHHHHHHHTCCHHHHHHHHTCCCSSCGGGSSCEEEE
T ss_pred             CcEEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEEEC
Confidence            46689999999999999999999999999999986 899999999997

>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=99.55  E-value=6.5e-15  Score=83.55  Aligned_cols=45  Identities=24%  Similarity=0.414  Sum_probs=42.2

Q ss_pred             ceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      +.+|+|++|||||+||++||+++++|+++|+ ..+.|++||.|.||
T Consensus         2 ~~~y~V~~GDtl~~Ia~~~~~~~~~l~~~N~-~~~~l~~G~~l~ip   46 (48)
T 1e0g_A            2 SITYRVRKGDSLSSIAKRHGVNIKDVMRWNS-DTANLQPGDKLTLF   46 (48)
T ss_dssp             CCEEEECTTCCHHHHHHHHTCCHHHHHHHCS-CGGGCCTTEEEECC
T ss_pred             CEEEEEcCCCcHHHHHHHHCcCHHHHHHhCC-CCCcCCcCCEEEEe
Confidence            4589999999999999999999999999999 55899999999998

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

Probab=99.47  E-value=1.5e-14  Score=113.94  Aligned_cols=122  Identities=9%  Similarity=0.011  Sum_probs=84.2

Q ss_pred             ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCC-----CCCCCCCCcEEecCCCCCCC--CCCCCCcc-------
Q 040221           15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLN-----KNRNETTQPQPIAESTQPIQ--PPPQQPIV-------   80 (142)
Q Consensus        15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~-----~~~l~~Gq~l~vp~~~~~~~--~~~~~~~~-------   80 (142)
                      ..++++.|||++.||++|      |++.++|.++|++.     .+.|++||.|.||.......  ..+.....       
T Consensus         8 ~~~~Vk~GDTL~~Ia~r~------gvs~~~l~~~n~~~~~~~~~~~L~~Gq~L~i~~~~~~~l~~l~~~~~~~~~~~~~~   81 (361)
T 2gu1_A            8 IHYMVKVGDTLSGIFAQL------GVPYSILQKILSVDLDHLQLDMIQPGEELELMMDDMGQLSRLIYHMSIVEKAIYTR   81 (361)
T ss_dssp             EEEECCTTCCHHHHHHHT------TCCHHHHHHHHHHGGGTCCGGGCCTTCEEEEEECTTSCEEEEEEEEETTEEEEEEE
T ss_pred             eEEEECCCCcHHHHHHHc------CCCHHHHHHHHhhcccccchhcCCCCCEEEEEECCCCcceEEEEEcCccceEEEEe
Confidence            467899999999999999      99999999999874     26899999999996432100  00000000       


Q ss_pred             CCCCcccCC--CCCCCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC------CCCCCCCEEecC
Q 040221           81 TKPSICTEK--SEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG------DTIYAGKKLIIP  142 (142)
Q Consensus        81 ~~~~~~~~~--~~~~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~------~~l~~Gq~L~IP  142 (142)
                      .....+...  ..........|.++.|||||.||++||++...|++||++..      ..|++||+|.|+
T Consensus        82 ~~~g~f~~~~~~~~~~~~~~~~~v~igdSL~~iA~~~Gvs~~~i~~ln~i~~~~idf~~~Lr~GD~l~V~  151 (361)
T 2gu1_A           82 ENDGSFSYDFQEISGEWREILFSGEINGSFSVSARRVGLTSSQVANITQVMKDKIDFSRSLRAGDRFDIL  151 (361)
T ss_dssp             CTTSCEEEEEEECCCEEEEEEEEEESSSCHHHHHHHTTCCHHHHHHHHHHHTTTCCTTTCCCC-CEEEEE
T ss_pred             cCCCcceeeecccCceEEEEEEEEEECCcHHHHHHHcCCCHHHHHHHHHhhcccccccccCCCCCEEEEE
Confidence            000000000  00111234578999999999999999999999999997643      469999999874

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

Probab=99.45  E-value=8.6e-14  Score=98.86  Aligned_cols=48  Identities=31%  Similarity=0.614  Sum_probs=45.5

Q ss_pred             CCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221           95 ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP  142 (142)
Q Consensus        95 ~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP  142 (142)
                      ....+|+|++|||||.||++|++++.+|++||+|.+ +.|++||+|.||
T Consensus        60 ~~~~~y~V~~GDTL~~IA~~~~~~~~~l~~~N~~~~~~~i~~Gq~L~ip  108 (167)
T 2l9y_A           60 GGTATVTVQQGDTLRDIGRRFDCDFHEIARRNNIQNEDLIYPGQVLQVP  108 (167)
T ss_dssp             CSCEEEEECTTCCHHHHHHHTTCCHHHHHHHHTCCGGGCCCTTEEEEES
T ss_pred             CCCceEEECCCCcHHHHHHHcCCCHHHHHHHcCCCCcccccCCCEEEEc
Confidence            456789999999999999999999999999999999 999999999997

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

Probab=99.45  E-value=7.9e-16  Score=109.40  Aligned_cols=95  Identities=7%  Similarity=-0.132  Sum_probs=75.5

Q ss_pred             CCCCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCC
Q 040221           11 PRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEK   89 (142)
Q Consensus        11 ~~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~   89 (142)
                      ...+..|+++.|||++.||++|      |+++.+|+++|++.+ +.|++||.|.||....... ..+             
T Consensus        59 ~~~~~~y~V~~GDTL~~IA~~~------~~~~~~l~~~N~~~~~~~i~~Gq~L~ip~~~~~~~-~~~-------------  118 (167)
T 2l9y_A           59 GGGTATVTVQQGDTLRDIGRRF------DCDFHEIARRNNIQNEDLIYPGQVLQVPTKGGSGG-GAG-------------  118 (167)
T ss_dssp             CCSCEEEEECTTCCHHHHHHHT------TCCHHHHHHHHTCCGGGCCCTTEEEEESCCCCCSS-SSC-------------
T ss_pred             CCCCceEEECCCCcHHHHHHHc------CCCHHHHHHHcCCCCcccccCCCEEEEcCCCCccc-ccc-------------
Confidence            5568899999999999999999      999999999999987 8999999999997542200 000             


Q ss_pred             CCCCCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221           90 SEPEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus        90 ~~~~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                       .........|.|++||+|+.||++||.++..+..+|
T Consensus       119 -~~~~~~~~~~~v~~GdtL~aIA~r~G~~v~s~i~Ln  154 (167)
T 2l9y_A          119 -NFWDSARDVRLVDGGKVLEAELRYSGGWNRSRIYLD  154 (167)
T ss_dssp             -CGGGGEEEEEEETTTTEEEEEEEETTEEEEEEECGG
T ss_pred             -ccccccceEEEeCCcCChHHHHHHcCCceEEEEEcc
Confidence             000122457999999999999999998877777666

>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=98.84  E-value=2.1e-09  Score=60.38  Aligned_cols=45  Identities=11%  Similarity=0.079  Sum_probs=41.1

Q ss_pred             ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecC
Q 040221           15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAE   66 (142)
Q Consensus        15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~   66 (142)
                      ..|.+..|||++.||++|      |+++.+|+++|+ ..+.|.+||.|.||.
T Consensus         3 ~~y~V~~GDtl~~Ia~~~------~~~~~~l~~~N~-~~~~l~~G~~l~ip~   47 (48)
T 1e0g_A            3 ITYRVRKGDSLSSIAKRH------GVNIKDVMRWNS-DTANLQPGDKLTLFV   47 (48)
T ss_dssp             CEEEECTTCCHHHHHHHH------TCCHHHHHHHCS-CGGGCCTTEEEECCC
T ss_pred             EEEEEcCCCcHHHHHHHH------CcCHHHHHHhCC-CCCcCCcCCEEEEec
Confidence            457788999999999999      999999999999 667899999999985

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

Probab=98.82  E-value=1.4e-09  Score=85.47  Aligned_cols=48  Identities=23%  Similarity=0.283  Sum_probs=42.4

Q ss_pred             CCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCC-----CCCCCCCCEEecC
Q 040221           95 ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLS-----GDTIYAGKKLIIP  142 (142)
Q Consensus        95 ~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~-----~~~l~~Gq~L~IP  142 (142)
                      ..|..|+|++||||+.|+++||+++++|++||++.     .+.|++||.|.||
T Consensus         5 ~~~~~~~Vk~GDTL~~Ia~r~gvs~~~l~~~n~~~~~~~~~~~L~~Gq~L~i~   57 (361)
T 2gu1_A            5 PKRIHYMVKVGDTLSGIFAQLGVPYSILQKILSVDLDHLQLDMIQPGEELELM   57 (361)
T ss_dssp             --CEEEECCTTCCHHHHHHHTTCCHHHHHHHHHHGGGTCCGGGCCTTCEEEEE
T ss_pred             CCceEEEECCCCcHHHHHHHcCCCHHHHHHHHhhcccccchhcCCCCCEEEEE
Confidence            46889999999999999999999999999999764     2689999999886

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

Probab=98.81  E-value=2.6e-09  Score=66.09  Aligned_cols=50  Identities=18%  Similarity=0.068  Sum_probs=45.2

Q ss_pred             CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCCC
Q 040221           13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAEST   68 (142)
Q Consensus        13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~~   68 (142)
                      .-..|.+..|||++.||++|      ++++.+|+++|++.. +.|.+||.|+||...
T Consensus        14 ~~~~y~V~~GDTL~~IA~~~------~~~~~~l~~~N~l~~~~~l~~Gq~l~iP~~~   64 (77)
T 2djp_A           14 RRLEHQLEPGDTLAGLALKY------GVTMEQIKRANRLYTNDSIFLKKTLYIPILT   64 (77)
T ss_dssp             EEEEECCCTTCCHHHHHHHH------TCCHHHHHHHHTCCCSSCGGGSSCEEEEEEC
T ss_pred             CcEEEEECCCCcHHHHHHHH------CcCHHHHHHHcCCCCccccCCCCEEEECCCC
Confidence            34569999999999999999      999999999999975 789999999999764

>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=97.94  E-value=5.9e-06  Score=58.17  Aligned_cols=47  Identities=15%  Similarity=0.022  Sum_probs=41.7

Q ss_pred             ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCC
Q 040221           15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAES   67 (142)
Q Consensus        15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~   67 (142)
                      ..|++++|||+..||++|      +++..+|+++|+..+..|.+|+.+.||..
T Consensus         3 ~~y~V~~GdtL~~IA~~f------~~g~~~l~~aNp~vd~~l~~g~~i~ip~~   49 (165)
T 4a1k_A            3 LTYQVKQGDTLNSIAADF------RISTAALLQANPSLQAGLTAGQSIVIPGL   49 (165)
T ss_dssp             EEEECCTTCCHHHHHHHT------TCCHHHHHHHCGGGGGCCCTTCEEEETTC
T ss_pred             EEEEECCCCCHHHHHHHh------CCCHHHHHHhCccCCCccCCCccccCccC
Confidence            357789999999999999      99999999999876666889999999853

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

Probab=97.65  E-value=9.1e-05  Score=58.37  Aligned_cols=48  Identities=17%  Similarity=0.192  Sum_probs=41.9

Q ss_pred             CCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCC----C-CCCCCCCEEec
Q 040221           94 PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLS----G-DTIYAGKKLII  141 (142)
Q Consensus        94 ~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~----~-~~l~~Gq~L~I  141 (142)
                      ...|..|+|++||||..|-+++|++..++.+++...    . ..|++||.|.+
T Consensus        11 ~~~W~~~~V~~GDTL~~IL~r~Gls~~di~~i~~~~~~~~~l~~LrpGq~l~i   63 (371)
T 3slu_A           11 TAYWVQEAVQPGDSLADVLARSGMARDEIARITEKYGGEADLRHLRADQSVHV   63 (371)
T ss_dssp             CCEEEEEECCTTCCHHHHHHHTTCCHHHHHHHHTTC------CCBCSSSEEEE
T ss_pred             CCceEEEEECCCCcHHHHHHHcCCCHHHHHHHHHhccccCchhhCCCCCEEEE
Confidence            467999999999999999999999999999997432    4 78999999875

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

Probab=97.07  E-value=0.0021  Score=50.60  Aligned_cols=120  Identities=12%  Similarity=0.046  Sum_probs=74.6

Q ss_pred             cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCC-----CCCCCCCCcEEecCCCCCC--CCCCCCCc---------
Q 040221           16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLN-----KNRNETTQPQPIAESTQPI--QPPPQQPI---------   79 (142)
Q Consensus        16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~-----~~~l~~Gq~l~vp~~~~~~--~~~~~~~~---------   79 (142)
                      +++.+.|||++.|-+++      |++..++.+++...     ...|++||.+.+.......  ...+....         
T Consensus        16 ~~~V~~GDTL~~IL~r~------Gls~~di~~i~~~~~~~~~l~~LrpGq~l~i~~~~~~~l~~l~~~~~~~~~~~~v~i   89 (371)
T 3slu_A           16 QEAVQPGDSLADVLARS------GMARDEIARITEKYGGEADLRHLRADQSVHVLVGGDGGAREVQFFTDEDGERNLVAL   89 (371)
T ss_dssp             EEECCTTCCHHHHHHHT------TCCHHHHHHHHTTC------CCBCSSSEEEEEECTTSCEEEEEEEECCTTEEEEEEE
T ss_pred             EEEECCCCcHHHHHHHc------CCCHHHHHHHHHhccccCchhhCCCCCEEEEEECCCCCeEEEEEEecCCCceeEEEE
Confidence            57889999999999999      99999999887643     2689999999997643210  00000000         


Q ss_pred             cCCCCcccCCCCCCC--CCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCC-----CCCCCCCCCEEec
Q 040221           80 VTKPSICTEKSEPEP--ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGL-----SGDTIYAGKKLII  141 (142)
Q Consensus        80 ~~~~~~~~~~~~~~~--~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l-----~~~~l~~Gq~L~I  141 (142)
                      ...............  .....+...-.++||..+.+.|++...+++++++     .-..|++|+++.|
T Consensus        90 ~~~dg~f~~~~~~~~~~~~~~~~~g~I~~Sl~~a~~~agl~~~~~~~l~~i~~~~idf~~l~~GD~f~v  158 (371)
T 3slu_A           90 EKKGGIWRRSASEADMKVLPTLRSVVVKTSARGSLARAEVPVEIRESLSGIFAGRFSLDGLKEGDAVRL  158 (371)
T ss_dssp             EEETTEEEECCCGGGEEEEEEEEEEECSSCHHHHHHHTTCCHHHHHHHHHHHTTTCCTTCCCTTCEEEE
T ss_pred             EecCCeeEEEeeecccceeeeEEEEEEeccHHHHHHHcCCCHHHHHHHHHHHccCcCHHHcCCCCEEEE
Confidence            000000000000000  0011123344789999999999999888888743     2245899999876

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

Probab=87.78  E-value=0.53  Score=26.44  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=21.2

Q ss_pred             cCCCc----HHHHHHHhCCCHHHHHHHh
Q 040221          103 VRGDT----LWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       103 ~~GDT----l~~IA~rygvs~~~L~~~N  126 (142)
                      ..|.+    +..||++|||+...|..|=
T Consensus        19 ~~g~s~~~~~~~vA~~~gIs~~tl~~W~   46 (59)
T 2glo_A           19 RNDNDCKGNQRATARKYNIHRRQIQKWL   46 (59)
T ss_dssp             HHCTTTTTCHHHHHHHTTSCHHHHHHHH
T ss_pred             HcCCCcchHHHHHHHHHCcCHHHHHHHH
Confidence            45677    9999999999999999994

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=85.25  E-value=0.82  Score=27.82  Aligned_cols=24  Identities=17%  Similarity=0.261  Sum_probs=21.6

Q ss_pred             cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          103 VRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       103 ~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      ..|.++..||++|||+...|.+|=
T Consensus        36 ~~g~s~~~iA~~~gIs~sTl~rW~   59 (87)
T 2elh_A           36 HDGESKASVARDIGVPESTLRGWC   59 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHH
Confidence            578999999999999999998883

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=84.85  E-value=1.1  Score=23.18  Aligned_cols=24  Identities=25%  Similarity=0.167  Sum_probs=21.5

Q ss_pred             cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          103 VRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       103 ~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      ..|-+...||+.+|++...+..|=
T Consensus        19 ~~g~s~~~IA~~lgis~~Tv~~~~   42 (51)
T 1tc3_C           19 LLNVSLHEMSRKISRSRHCIRVYL   42 (51)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            578899999999999999998874

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=84.27  E-value=0.77  Score=28.30  Aligned_cols=22  Identities=18%  Similarity=0.292  Sum_probs=20.7

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHh
Q 040221          105 GDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       105 GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      |.++..||+.|||+...|.+|=
T Consensus        23 g~s~~~ia~~~gIs~~tl~rW~   44 (97)
T 2jn6_A           23 GASLQQIANDLGINRVTLKNWI   44 (97)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHH
T ss_pred             CChHHHHHHHHCcCHHHHHHHH
Confidence            7899999999999999999994

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=83.40  E-value=1.1  Score=28.12  Aligned_cols=26  Identities=15%  Similarity=-0.074  Sum_probs=22.9

Q ss_pred             EecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          101 EIVRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       101 ~V~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      ....+.++.++|++|+++..+|..|-
T Consensus        45 ~~~g~~s~~e~arry~Is~s~i~~W~   70 (95)
T 2jrt_A           45 VIHGLITEREALDRYSLSEEEFALWR   70 (95)
T ss_dssp             HHTTSSCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            34567799999999999999999997

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=81.60  E-value=0.93  Score=23.87  Aligned_cols=23  Identities=13%  Similarity=0.304  Sum_probs=21.1

Q ss_pred             cCCCcHHHHHHHhCCCHHHHHHH
Q 040221          103 VRGDTLWGLSRKYGVSIDAIKEA  125 (142)
Q Consensus       103 ~~GDTl~~IA~rygvs~~~L~~~  125 (142)
                      ..|-+...||+.+|++...+.+|
T Consensus        19 ~~g~s~~~ia~~lgvs~~Tv~r~   41 (52)
T 1jko_C           19 EKGHPRQQLAIIFGIGVSTLYRY   41 (52)
T ss_dssp             HTTCCHHHHHHTTSCCHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHH
Confidence            46789999999999999999987

---

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	142
d1e0ga_	48	d.7.1.1 (A:) Membrane-bound lytic murein transclyc	2e-13
d1y7ma2	48	d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-term	5e-12

>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 = 58.5 bits (142), Expect = 2e-13
 Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 99  TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           T  + +GD+L  +++++GV+I  +   N  +   +  G KL + 
Sbjct: 4   TYRVRKGDSLSSIAKRHGVNIKDVMRWNSDT-ANLQPGDKLTLF 46

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

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]

 Score = 54.8 bits (132), Expect = 5e-12
 Identities = 13/44 (29%), Positives = 26/44 (59%)

Query: 99  TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142
           T ++ +GDTL  ++  + +S  A+ +AN      + AG+ ++IP
Sbjct: 3   TYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIP 46

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	142
d1e0ga_	48	Membrane-bound lytic murein transclycosylase D, Ml	99.7
d1y7ma2	48	Hypothetical protein YkuD, N-terminal domain {Baci	99.67
d1y7ma2	48	Hypothetical protein YkuD, N-terminal domain {Baci	99.15
d1e0ga_	48	Membrane-bound lytic murein transclycosylase D, Ml	99.14
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	93.82
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	85.57
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	81.13

>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=99.70  E-value=7.2e-18  Score=94.79  Aligned_cols=45  Identities=24%  Similarity=0.406  Sum_probs=41.9

Q ss_pred             ceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      ..+|+|++|||||.||++||+++++|++||++.+ .|++||+|.||
T Consensus         2 ~v~y~V~~GDTl~~IA~~y~vs~~~i~~~N~l~~-~l~~Gq~L~i~   46 (48)
T d1e0ga_           2 SITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTA-NLQPGDKLTLF   46 (48)
T ss_dssp             CCEEEECTTCCHHHHHHHHTCCHHHHHHHCSCGG-GCCTTEEEECC
T ss_pred             cEEEEECCCCCHHHHHHHHCCCHHHHHHHcCCcc-cCcCCCEEEEE
Confidence            3589999999999999999999999999999864 69999999997

>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=99.67  E-value=3.5e-18  Score=96.26  Aligned_cols=45  Identities=29%  Similarity=0.464  Sum_probs=43.2

Q ss_pred             eEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221           98 RTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP  142 (142)
Q Consensus        98 ~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP  142 (142)
                      .+|+|++|||||+||++|++++++|++||++.++.|++||.|+||
T Consensus         2 i~y~V~~GDTL~~IA~~y~v~~~~i~~~N~~~~~~l~~Gq~L~IP   46 (48)
T d1y7ma2           2 LTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIP   46 (48)
T ss_dssp             EEEECCTTCCHHHHHHHTTSCCCCCCCTSCTTCSSCCTTCEEEET
T ss_pred             EEEEECCCCCHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCEEEeC
Confidence            479999999999999999999999999999988889999999998

>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=99.15  E-value=2.4e-12  Score=71.85  Aligned_cols=45  Identities=16%  Similarity=0.048  Sum_probs=42.3

Q ss_pred             cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecC
Q 040221           16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAE   66 (142)
Q Consensus        16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~   66 (142)
                      .|.++.|||++.||++|      |+++++|+++|++.++.|.+||.|+||.
T Consensus         3 ~y~V~~GDTL~~IA~~y------~v~~~~i~~~N~~~~~~l~~Gq~L~IPg   47 (48)
T d1y7ma2           3 TYQVKQGDTLNSIAADF------RISTAALLQANPSLQAGLTAGQSIVIPG   47 (48)
T ss_dssp             EEECCTTCCHHHHHHHT------TSCCCCCCCTSCTTCSSCCTTCEEEETT
T ss_pred             EEEECCCCCHHHHHHHh------CCCHHHHHHHcCCCCCCCCCCCEEEeCC
Confidence            47889999999999999      9999999999999887899999999995

>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=99.14  E-value=1e-11  Score=69.08  Aligned_cols=45  Identities=11%  Similarity=0.035  Sum_probs=41.1

Q ss_pred             ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecC
Q 040221           15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAE   66 (142)
Q Consensus        15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~   66 (142)
                      ..|++..|||++.||++|      |+++++|+++|++.+ .|++||.|.||.
T Consensus         3 v~y~V~~GDTl~~IA~~y------~vs~~~i~~~N~l~~-~l~~Gq~L~i~v   47 (48)
T d1e0ga_           3 ITYRVRKGDSLSSIAKRH------GVNIKDVMRWNSDTA-NLQPGDKLTLFV   47 (48)
T ss_dssp             CEEEECTTCCHHHHHHHH------TCCHHHHHHHCSCGG-GCCTTEEEECCC
T ss_pred             EEEEECCCCCHHHHHHHH------CCCHHHHHHHcCCcc-cCcCCCEEEEEe
Confidence            457889999999999999      999999999999864 699999999985

>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=93.82  E-value=0.024  Score=30.00  Aligned_cols=24  Identities=13%  Similarity=0.331  Sum_probs=21.9

Q ss_pred             ecCCCcHHHHHHHhCCCHHHHHHH
Q 040221          102 IVRGDTLWGLSRKYGVSIDAIKEA  125 (142)
Q Consensus       102 V~~GDTl~~IA~rygvs~~~L~~~  125 (142)
                      +..|.+..+||+.|||+...|.++
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            357999999999999999999987

>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=85.57  E-value=0.29  Score=28.64  Aligned_cols=23  Identities=17%  Similarity=0.276  Sum_probs=21.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHh
Q 040221          104 RGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       104 ~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      .|-++..||++|||+...|..|=
T Consensus        22 ~g~s~~~vA~~lGIs~~tl~~W~   44 (89)
T d2jn6a1          22 DGASLQQIANDLGINRVTLKNWI   44 (89)
T ss_dssp             GGSCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHH
Confidence            47899999999999999999994

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.13  E-value=0.61  Score=25.76  Aligned_cols=25  Identities=20%  Similarity=0.186  Sum_probs=22.2

Q ss_pred             ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221          102 IVRGDTLWGLSRKYGVSIDAIKEAN  126 (142)
Q Consensus       102 V~~GDTl~~IA~rygvs~~~L~~~N  126 (142)
                      +..|.+...||++|+|+...+.+|=
T Consensus        27 ~~~G~s~r~aA~rf~VS~s~v~k~l   51 (63)
T d1k78a1          27 AHQGVRPCDISRQLRVSHGCVSKIL   51 (63)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            4689999999999999998888874