Citrus Sinensis ID: 040436

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-
Protein Sequence
MASNKTSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEcccccHHHHHHHccccHHHHHHHcccccccccccccEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEccccHHHHHHHccccHHHHHHHcccccccHEEEEEEEEEcccc
Coil and Loop (DISEMBL)
MASNKTSLFRNLALVLAVLLIVSMAEsrtfaggletspptcdsvygaqegdtcsnvteefnlSTDVFlainpnincdaIFVGQWLCVAGSA
Flexible Loop (DISEMBL)
masnktslFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA
Low Complexity Region (SEG)
MASNKTSLFRNlalvlavllIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA
Disordered region (IsUnstruct)
*******LFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA***
Disordered Region (DISOPRED)
*****TS**RNLALVLAVLLIVSMAES************TCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS*
Disordered Region (DISEMBL)
MASNKTSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA
Disordered Region (DISPRO)
****KTSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS*
Transmembrane Helix (TMHMM)
iiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASNKTSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA
Positional Conservation
no confident homologs detected

---

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	91	2.2.26 [Sep-21-2011]
Q37896	263	Lysozyme OS=Bacillus phag	yes	no	0.615	0.212	0.372	0.0006

>sp|Q37896|LYS_BPB03 Lysozyme OS=Bacillus phage B103 GN=15 PE=3 SV=1

 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 35  ETSPPTCDSV--YGAQEGDTCSNVTEEFNLSTDVFLAINPNI-NCDAIFVGQWLCVAGS 90
           ETS P       +  ++GDT S + ++   ST   L +NP I N + I+VGQ + V GS
Sbjct: 153 ETSKPKTSKTNTHVVKKGDTLSEIAKKIKTSTKTLLELNPTIKNPNKIYVGQRINVGGS 211

Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
Bacillus subtilis (taxid: 1423)
EC: 3EC: .EC: 2EC: .EC: 1EC: .EC: 1EC: 7

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	91
147801606	95	hypothetical protein VITISV_011096 [Viti	0.989	0.947	0.560	8e-21
255569295	96	conserved hypothetical protein [Ricinus	0.967	0.916	0.527	2e-20
255553907	95	conserved hypothetical protein [Ricinus	0.978	0.936	0.505	2e-20
224082814	94	predicted protein [Populus trichocarpa]	0.989	0.957	0.533	2e-20
255569299	96	conserved hypothetical protein [Ricinus	0.956	0.906	0.5	6e-20
255569293	104	conserved hypothetical protein [Ricinus	0.978	0.855	0.48	6e-20
255569301	104	conserved hypothetical protein [Ricinus	0.967	0.846	0.464	2e-19
147801607	95	hypothetical protein VITISV_011097 [Viti	0.945	0.905	0.528	1e-18
224093388	95	predicted protein [Populus trichocarpa]	0.846	0.810	0.607	2e-18
147801608	89	hypothetical protein VITISV_011098 [Viti	0.923	0.943	0.494	7e-18

>gi|147801606|emb|CAN74546.1| hypothetical protein VITISV_011096 [Vitis vinifera]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 51/91 (56%), Positives = 65/91 (71%), Gaps = 1/91 (1%)

Query: 2  ASNKTSLFRNLALVLAVLLIVSMAESRTF-AGGLETSPPTCDSVYGAQEGDTCSNVTEEF 60
          A+N T++F NL L+L+ LLIVSMAE R     G   S P CDSV G + GDTC  +++  
Sbjct: 4  ANNMTTMFLNLVLMLSFLLIVSMAEGRFLPVFGKAKSTPQCDSVVGVRSGDTCFAISQMS 63

Query: 61 NLSTDVFLAINPNINCDAIFVGQWLCVAGSA 91
          N++   F AINPN+NCDA+FVGQWLCVAG+A
Sbjct: 64 NMTAKAFSAINPNLNCDALFVGQWLCVAGTA 94

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569295|ref|XP_002525615.1| conserved hypothetical protein [Ricinus communis] gi|223535051|gb|EEF36733.1| conserved hypothetical protein [Ricinus communis]

 Score =  103 bits (256), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/91 (52%), Positives = 66/91 (72%), Gaps = 3/91 (3%)

Query: 4  NKTSLFRNLALVLAVLLIVSMAESRTFA---GGLETSPPTCDSVYGAQEGDTCSNVTEEF 60
          NK S+F   A+VL++ L++S A+ R  +    G   S P CDSVYGAQ+GDTC++V  +F
Sbjct: 6  NKASVFLKFAIVLSLSLMISTAQCRQISIGSSGDAKSTPECDSVYGAQDGDTCTSVATQF 65

Query: 61 NLSTDVFLAINPNINCDAIFVGQWLCVAGSA 91
          +L+ + F +INPN+NCDAIFVGQWLC  G+A
Sbjct: 66 DLTLEFFSSINPNLNCDAIFVGQWLCADGTA 96

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553907|ref|XP_002517994.1| conserved hypothetical protein [Ricinus communis] gi|223542976|gb|EEF44512.1| conserved hypothetical protein [Ricinus communis]

 Score =  103 bits (256), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 46/91 (50%), Positives = 65/91 (71%), Gaps = 2/91 (2%)

Query: 3  SNKTSLFRNLALVLAVLLIVSMAESRTFAGGL--ETSPPTCDSVYGAQEGDTCSNVTEEF 60
          +N  S+F  LA+VL++ L++S A+ +    G     S P CDSVYGAQ+GDTC++V  +F
Sbjct: 5  NNNASMFLKLAIVLSLFLMISTAQGKKLGIGFGDAKSTPECDSVYGAQDGDTCTSVANQF 64

Query: 61 NLSTDVFLAINPNINCDAIFVGQWLCVAGSA 91
          NL+ + F +INPN+NCD  FVGQWLC+ G+A
Sbjct: 65 NLTLEFFSSINPNLNCDDFFVGQWLCINGTA 95

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224082814|ref|XP_002306850.1| predicted protein [Populus trichocarpa] gi|222856299|gb|EEE93846.1| predicted protein [Populus trichocarpa]

 Score =  102 bits (255), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/90 (53%), Positives = 66/90 (73%)

Query: 2  ASNKTSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFN 61
          +SNKT+L  NLAL+L+ LLI S+ ESR+  G    S P C SV+G   GDTC+ V ++F+
Sbjct: 4  SSNKTTLLFNLALMLSFLLIASVVESRSVLGRAAASTPECVSVHGVVTGDTCTAVEKQFD 63

Query: 62 LSTDVFLAINPNINCDAIFVGQWLCVAGSA 91
          L+ + F AINPN++CD +FVGQWLCV G++
Sbjct: 64 LTANDFKAINPNLDCDKLFVGQWLCVEGTS 93

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569299|ref|XP_002525617.1| conserved hypothetical protein [Ricinus communis] gi|223535053|gb|EEF36735.1| conserved hypothetical protein [Ricinus communis]

 Score =  101 bits (252), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 45/90 (50%), Positives = 65/90 (72%), Gaps = 3/90 (3%)

Query: 4  NKTSLFRNLALVLAVLLIVSMAESRTFAGGLE---TSPPTCDSVYGAQEGDTCSNVTEEF 60
          +K S+F   A+VL++ L++S A+ R  + G      S P CDSVYGAQ+GDTC+++  +F
Sbjct: 6  DKASVFLKFAIVLSLFLMISTAQCRKISNGSSGDANSTPECDSVYGAQDGDTCTSIATQF 65

Query: 61 NLSTDVFLAINPNINCDAIFVGQWLCVAGS 90
          +L+ + F +INPN+NCDAIFVGQWLC  G+
Sbjct: 66 DLTLEFFSSINPNLNCDAIFVGQWLCTDGT 95

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569293|ref|XP_002525614.1| conserved hypothetical protein [Ricinus communis] gi|223535050|gb|EEF36732.1| conserved hypothetical protein [Ricinus communis]

 Score =  101 bits (251), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 48/100 (48%), Positives = 68/100 (68%), Gaps = 11/100 (11%)

Query: 3   SNKTSLFRNLALVLAVLLIVSMAESRTFAG-----------GLETSPPTCDSVYGAQEGD 51
           +NK S+   LA+VL++ L++S A+SR  +            G   S P CDSVYGAQ+GD
Sbjct: 5   NNKPSMLLKLAIVLSLFLMISTAQSRKISSFLFYIVNVVGFGNAKSTPECDSVYGAQDGD 64

Query: 52  TCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA 91
           TC+++  +F+L+ + F +INPN+NCDAIFVGQWLC  G+A
Sbjct: 65  TCTSLAAQFDLTLEFFSSINPNLNCDAIFVGQWLCTDGTA 104

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255569301|ref|XP_002525618.1| conserved hypothetical protein [Ricinus communis] gi|223535054|gb|EEF36736.1| conserved hypothetical protein [Ricinus communis]

 Score = 99.8 bits (247), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 67/99 (67%), Gaps = 11/99 (11%)

Query: 4   NKTSLFRNLALVLAVLLIVSMAESRTFAG-----------GLETSPPTCDSVYGAQEGDT 52
           NK S+   LA++L++ +++S A+SR  +            G   S P CDSVYGAQ+GDT
Sbjct: 6   NKASMLLKLAIMLSLFVMISTAQSRKISSFLFYIVNVVGFGNAKSTPECDSVYGAQDGDT 65

Query: 53  CSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA 91
           C+++  +F+L+ + F +INPN+NCDAIFVGQWLC  G+A
Sbjct: 66  CTSLAAQFDLTLEFFSSINPNLNCDAIFVGQWLCTDGTA 104

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147801607|emb|CAN74547.1| hypothetical protein VITISV_011097 [Vitis vinifera]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/87 (52%), Positives = 61/87 (70%), Gaps = 1/87 (1%)

Query: 6  TSLFRNLALVLAVLLIVSMAESRTF-AGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLST 64
          T++  NL L+L+ LLI+SMAE R     G   S P CDSV G + GDTC  +++  N++ 
Sbjct: 8  TTMLLNLFLMLSFLLIISMAEGRFLPVFGKAKSTPQCDSVVGVRSGDTCFAISQMSNMTA 67

Query: 65 DVFLAINPNINCDAIFVGQWLCVAGSA 91
            F AINPN+NCDA+F+GQWLCVAG+A
Sbjct: 68 KAFSAINPNLNCDALFIGQWLCVAGTA 94

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224093388|ref|XP_002309907.1| predicted protein [Populus trichocarpa] gi|222852810|gb|EEE90357.1| predicted protein [Populus trichocarpa]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 55/79 (69%), Gaps = 2/79 (2%)

Query: 14 LVLAVLLIVSMAESRTF--AGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAIN 71
          LVL+ LLI+SMAESR    AG    S P CD V GA  GDTC  + + FNL+   F AIN
Sbjct: 16 LVLSFLLIISMAESRILGTAGFFAKSTPECDEVVGAASGDTCFTIAQSFNLTAASFDAIN 75

Query: 72 PNINCDAIFVGQWLCVAGS 90
          PN+NC A+FVGQWLCVAGS
Sbjct: 76 PNLNCTALFVGQWLCVAGS 94

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147801608|emb|CAN74548.1| hypothetical protein VITISV_011098 [Vitis vinifera]

 Score = 94.7 bits (234), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 44/89 (49%), Positives = 66/89 (74%), Gaps = 5/89 (5%)

Query: 2  ASNKTSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFN 61
          A+NK+    N+  +L++L++VSMAESR    G + S P CD+V G + GDTC ++ ++F 
Sbjct: 4  ANNKS---LNMIFMLSLLILVSMAESRFL--GAKKSTPECDAVVGVESGDTCFDIADKFQ 58

Query: 62 LSTDVFLAINPNINCDAIFVGQWLCVAGS 90
          L+T+ F +INPN+NCDA+FVGQW+CV G+
Sbjct: 59 LTTEFFDSINPNLNCDALFVGQWVCVDGT 87

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	91
ASPGD|ASPL0000060683	589	AN9389 [Emericella nidulans (t	0.538	0.083	0.433	9.5e-05
WB|WBGene00017233	2011	F07G11.9 [Caenorhabditis elega	0.747	0.033	0.304	0.0005

ASPGD|ASPL0000060683 AN9389 [Emericella nidulans (taxid:162425)]

 Score = 104 (41.7 bits), Expect = 9.5e-05, P = 9.5e-05
 Identities = 23/53 (43%), Positives = 30/53 (56%)

Query:    38 PPTCDSVYGAQEGDTCSNVTEEFN-LSTDVFLAINPNIN--CDAIFVGQWLCV 87
             PP CD  Y  Q GDTC N+  +F+ +S    +A NP IN  C  + VG  +CV
Sbjct:   290 PPECDD-YVVQSGDTCINIAAKFSGISYQQIVAWNPTINPYCTNLLVGHNICV 341

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

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

WB|WBGene00017233 F07G11.9 [Caenorhabditis elegans (taxid:6239)]

 Score = 103 (41.3 bits), Expect = 0.00050, P = 0.00050
 Identities = 21/69 (30%), Positives = 36/69 (52%)

Query:    22 VSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFV 81
             V  A+ +  AG   TS   C      + GDTC ++     ++   F+ INP ++CD + +
Sbjct:   313 VGRAKHKREAGAA-TSEVDCSKKITVKPGDTCFSIWTSQKMTQQQFMDINPELDCDKLEI 371

Query:    82 GQWLCVAGS 90
             G+ +CV G+
Sbjct:   372 GKEVCVTGN 380


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.129   0.391    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       91        82   0.00091  102 3  11 22  0.43    29
                                                     29  0.43    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  530 (56 KB)
  Total size of DFA:  102 KB (2071 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.12u 0.12s 8.24t   Elapsed:  00:00:00
  Total cpu time:  8.12u 0.12s 8.24t   Elapsed:  00:00:00
  Start:  Fri May 10 19:23:21 2013   End:  Fri May 10 19:23:21 2013

GO:0008061 "chitin binding" evidence=IEA

GO:0004553 "hydrolase activity, hydrolyzing O-glycosyl compounds" evidence=IEA

GO:0005975 "carbohydrate metabolic process" evidence=IEA

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

GO:0004568 "chitinase activity" evidence=IEA

GO:0006032 "chitin catabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00051310 hypothetical protein (94 aa) (Populus trichocarpa)

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	91
smart00257	44	smart00257, LysM, Lysin motif	1e-08
cd00118	45	cd00118, LysM, Lysine Motif is a small domain invo	5e-08
pfam01476	43	pfam01476, LysM, LysM domain	3e-06

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

 Score = 46.3 bits (111), Expect = 1e-08
 Identities = 12/40 (30%), Positives = 23/40 (57%)

Query: 48 QEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCV 87
          ++GDT S++   + +S    L +N  ++ D + VGQ L +
Sbjct: 5  KKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44

Length = 44

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

 Score = 44.8 bits (107), Expect = 5e-08
 Identities = 14/44 (31%), Positives = 25/44 (56%)

Query: 44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCV 87
           Y  + GDT  ++ +++ ++ +   A NP IN D I+ GQ L +
Sbjct: 2  TYTVKPGDTLWSIAKKYGVTVEELAAANPLINPDCIYPGQKLKI 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|144899 pfam01476, LysM, LysM domain

 Score = 40.1 bits (95), Expect = 3e-06
 Identities = 9/40 (22%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 48 QEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCV 87
          ++GDT S++ + + ++ +    +N  ++   ++VGQ L +
Sbjct: 4  KKGDTLSSIAKRYGITVEELAELN-GLSSPNLYVGQKLKI 42

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	91
PF01476	44	LysM: LysM domain; InterPro: IPR018392 This domain	99.76
PRK14125	103	cell division suppressor protein YneA; Provisional	99.6
cd00118	46	LysM Lysin domain, found in a variety of enzymes i	99.49
smart00257	44	LysM Lysin motif.	99.33
TIGR02899	44	spore_safA spore coat assembly protein SafA. in wh	99.31
PRK06347	592	autolysin; Reviewed	99.2
PRK10783	456	mltD membrane-bound lytic murein transglycosylase	99.19
PRK06347	592	autolysin; Reviewed	99.13
PRK13914	481	invasion associated secreted endopeptidase; Provis	99.07
PRK10871	319	nlpD lipoprotein NlpD; Provisional	99.06
TIGR02907	338	spore_VI_D stage VI sporulation protein D. SpoVID,	98.9
PRK10783	456	mltD membrane-bound lytic murein transglycosylase	98.82
PRK13914	481	invasion associated secreted endopeptidase; Provis	98.82
PRK11198	147	LysM domain/BON superfamily protein; Provisional	98.72
COG1388	124	LytE FOG: LysM repeat [Cell envelope biogenesis, o	98.71
PRK10260	306	L,D-transpeptidase; Provisional	98.49
PRK10190	310	L,D-transpeptidase; Provisional	98.38
TIGR03505	74	FimV_core FimV N-terminal domain. This region is f	98.2
PF04225	85	OapA: Opacity-associated protein A LysM-like domai	97.48
COG1652	269	XkdP Uncharacterized protein containing LysM domai	97.28
PF05489	60	Phage_tail_X: Phage Tail Protein X; InterPro: IPR0	97.1
COG3170	755	FimV Tfp pilus assembly protein FimV [Cell motilit	97.08
COG3858	423	Predicted glycosyl hydrolase [General function pre	97.04
PRK11649	439	putative peptidase; Provisional	96.13
COG3858	423	Predicted glycosyl hydrolase [General function pre	93.96
COG1388	124	LytE FOG: LysM repeat [Cell envelope biogenesis, o	92.89
PF13518	52	HTH_28: Helix-turn-helix domain	90.39
COG3061	242	OapA Cell envelope opacity-associated protein A [C	89.24
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	87.82
KOG2850	186	consensus Predicted peptidoglycan-binding protein,	87.69
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	85.82
COG0739	277	NlpD Membrane proteins related to metalloendopepti	83.62
PRK09413	121	IS2 repressor TnpA; Reviewed	83.02
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	82.29
PF15145	128	DUF4577: Domain of unknown function (DUF4577)	81.58
COG4784	479	Putative Zn-dependent protease [General function p	80.29
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	80.18

>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=99.76  E-value=6.5e-19  Score=93.94  Aligned_cols=44  Identities=36%  Similarity=0.713  Sum_probs=38.7

Q ss_pred             EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436           45 YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA   88 (91)
Q Consensus        45 y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp   88 (91)
                      |+|++|||||+||++|+++.++|+++||+++|+.|++||.||||
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            89999999999999999999999999999988889999999998

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

>PRK14125 cell division suppressor protein YneA; Provisional

Probab=99.60  E-value=1.7e-14  Score=90.30  Aligned_cols=48  Identities=21%  Similarity=0.212  Sum_probs=40.7

Q ss_pred             CceEEecCCCCHHHHHHHcCCC--------HHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           42 DSVYGAQEGDTCSNVTEEFNLS--------TDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        42 ~~~y~v~~GdTc~~Ia~~~~i~--------~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ...|+|++|||||+||++|+.+        ++++.+.| +++++.|++||+|+||..
T Consensus        36 ~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N-~l~~~~I~~Gq~L~IP~~   91 (103)
T PRK14125         36 YVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVN-NLPSGHIKAGDKLVIPVL   91 (103)
T ss_pred             cEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhc-CCCCCcCCCCCEEEEecC
Confidence            3469999999999999999765        45677778 688889999999999964

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

Probab=99.49  E-value=1.1e-13  Score=71.65  Aligned_cols=45  Identities=29%  Similarity=0.485  Sum_probs=42.9

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA   88 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp   88 (91)
                      +|+|++|||||+|+++|+++.+++.++|+..+|..+.+|+.||+|
T Consensus         2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip   46 (46)
T cd00118           2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP   46 (46)
T ss_pred             EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence            699999999999999999999999999987689999999999997

This domain may have a general peptidoglycan binding function.

>smart00257 LysM Lysin motif

Probab=99.33  E-value=4.9e-12  Score=64.58  Aligned_cols=44  Identities=30%  Similarity=0.504  Sum_probs=41.2

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEE
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCV   87 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcv   87 (91)
                      +|+|++|||||+|+++|+++.+++.++|+..+|..+.+|+.+++
T Consensus         1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i   44 (44)
T smart00257        1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI   44 (44)
T ss_pred             CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence            48999999999999999999999999999778999999999985

>TIGR02899 spore_safA spore coat assembly protein SafA

Probab=99.31  E-value=4.4e-12  Score=66.50  Aligned_cols=43  Identities=23%  Similarity=0.481  Sum_probs=39.3

Q ss_pred             ecCCCCHHHHHHHcCCCHHHHHHhCCCC-CCCCCCCCCEEEEcC
Q 040436           47 AQEGDTCSNVTEEFNLSTDVFLAINPNI-NCDAIFVGQWLCVAG   89 (91)
Q Consensus        47 v~~GdTc~~Ia~~~~i~~~~l~~~Np~v-~c~~l~~G~~lcvp~   89 (91)
                      |++|||+|+||++|+++.+++.++|+.+ +...+.+|+.+.+|.
T Consensus         1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~   44 (44)
T TIGR02899         1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS   44 (44)
T ss_pred             CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence            6899999999999999999999999876 567899999999984

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

>PRK06347 autolysin; Reviewed

Probab=99.20  E-value=3.4e-11  Score=93.94  Aligned_cols=49  Identities=22%  Similarity=0.387  Sum_probs=44.1

Q ss_pred             CCCCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436           39 PTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA   88 (91)
Q Consensus        39 ~~c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp   88 (91)
                      ..|..+|+|++|||||+||++||+++++|++||+ +..+.|++||.|+|+
T Consensus       544 ~~~~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~-L~~~~L~~GQ~L~I~  592 (592)
T PRK06347        544 NSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNK-LTSNMIHVGQKLTIK  592 (592)
T ss_pred             CccceeeecCCCCcHHHHHHHhCCCHHHHHHhcC-CCcccCCCCCEEecC
Confidence            4567789999999999999999999999999996 555789999999985

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

Probab=99.19  E-value=5.4e-11  Score=90.43  Aligned_cols=51  Identities=14%  Similarity=0.195  Sum_probs=45.2

Q ss_pred             CCCCCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           38 PPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        38 ~~~c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      ...+...|+|++|||||+||++||+++++|++||+.... .|++||.|+|..
T Consensus       398 ~~~~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~-~L~pGq~L~l~v  448 (456)
T PRK10783        398 NNSDSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAK-NLQPGDKLTLFV  448 (456)
T ss_pred             ccccceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCC-cCCCCCEEEEec
Confidence            345677899999999999999999999999999986544 899999999965

>PRK06347 autolysin; Reviewed

Probab=99.13  E-value=1.1e-10  Score=91.06  Aligned_cols=51  Identities=24%  Similarity=0.331  Sum_probs=45.9

Q ss_pred             CCCCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           39 PTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        39 ~~c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ..|..+|+|++|||||+||++||+++++|++||+ +..+.|++||.|+||..
T Consensus       476 ~~~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~-l~s~~L~~GQ~L~Ip~~  526 (592)
T PRK06347        476 NTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNN-LKSDFIYPGQKLKVSAG  526 (592)
T ss_pred             cccceeeeecCCCCHHHHHHHHCCCHHHHHHhcC-CCcccccCCcEEEEecC
Confidence            4567789999999999999999999999999997 65568999999999863

>PRK13914 invasion associated secreted endopeptidase; Provisional

Probab=99.07  E-value=1.1e-09  Score=83.54  Aligned_cols=47  Identities=28%  Similarity=0.286  Sum_probs=43.5

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ..|+|++|||+|+||++||+++++|+++| +++.+.|++||.|.||..
T Consensus        28 ~tytVq~GDTLw~IA~~ygvtv~~I~~~N-~l~~~~I~~Gq~L~Ip~~   74 (481)
T PRK13914         28 STVVVEAGDTLWGIAQSKGTTVDAIKKAN-NLTTDKIVPGQKLQVNEV   74 (481)
T ss_pred             ceEEECCCCCHHHHHHHHCCCHHHHHHHh-CCCcccccCCCEEEeCCC
Confidence            46999999999999999999999999999 587788999999999864

>PRK10871 nlpD lipoprotein NlpD; Provisional

Probab=99.06  E-value=1.3e-09  Score=79.78  Aligned_cols=48  Identities=23%  Similarity=0.093  Sum_probs=43.1

Q ss_pred             CceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           42 DSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        42 ~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      ...|+|++|||+|.||.+||+++.+|.+||..-+...|++||.|.||.
T Consensus        60 ~~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~  107 (319)
T PRK10871         60 GSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGN  107 (319)
T ss_pred             CCceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCC
Confidence            357999999999999999999999999999433788999999999964

>TIGR02907 spore_VI_D stage VI sporulation protein D

Probab=98.90  E-value=2.9e-09  Score=78.01  Aligned_cols=45  Identities=24%  Similarity=0.357  Sum_probs=41.5

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA   88 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp   88 (91)
                      ..|+|++|||+|+||++||+++++|.++|+ +..+.|.+|+.|.||
T Consensus       294 ~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~-L~~~~L~~GQ~L~IP  338 (338)
T TIGR02907       294 RMCIVQEGDTIETIAERYEISVSQLIRHNQ-LEDFEVNEGQILYIP  338 (338)
T ss_pred             EEEEECCCCCHHHHHHHHCcCHHHHHHHhC-CCccccCCCCEEEeC
Confidence            469999999999999999999999999995 656789999999997

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.

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

Probab=98.82  E-value=9.7e-09  Score=78.24  Aligned_cols=49  Identities=27%  Similarity=0.329  Sum_probs=44.1

Q ss_pred             CCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           41 CDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        41 c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ....|+|++|||||+||++||++.++|.+||+..+ +.|.+||.|+||..
T Consensus       342 ~~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~-~~L~~Gq~L~Ip~~  390 (456)
T PRK10783        342 NSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRG-SKLKVGQTLTIGAG  390 (456)
T ss_pred             CceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCc-ccCCCCCEEEecCC
Confidence            45679999999999999999999999999997545 78999999999863

>PRK13914 invasion associated secreted endopeptidase; Provisional

Probab=98.82  E-value=9.4e-09  Score=78.57  Aligned_cols=47  Identities=21%  Similarity=0.414  Sum_probs=43.3

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ..|+|++|||+|.||++|++++++|.+||+ +....|++||.|.||.+
T Consensus       200 ~tytVq~GDTL~sIAkrYgVtv~eI~~~N~-l~s~~L~pGQ~L~Ip~s  246 (481)
T PRK13914        200 TTHAVKSGDTIWALSVKYGVSVQDIMSWNN-LSSSSIYVGQKLAIKQT  246 (481)
T ss_pred             eEEEECCCCCHHHHHHHHCCCHHHHHHhcC-CCccccCCCCEEEecCC
Confidence            579999999999999999999999999995 65568999999999986

>PRK11198 LysM domain/BON superfamily protein; Provisional

Probab=98.72  E-value=3.7e-08  Score=64.92  Aligned_cols=49  Identities=22%  Similarity=0.333  Sum_probs=41.3

Q ss_pred             CCceEEecCCCCHHHHHHHcC---CCHHHHHHhCCC-C-CCCCCCCCCEEEEcC
Q 040436           41 CDSVYGAQEGDTCSNVTEEFN---LSTDVFLAINPN-I-NCDAIFVGQWLCVAG   89 (91)
Q Consensus        41 c~~~y~v~~GdTc~~Ia~~~~---i~~~~l~~~Np~-v-~c~~l~~G~~lcvp~   89 (91)
                      -...|+|++|||+|+||++|.   ...++|.++|+. + +.+.|++||.|.+|+
T Consensus        94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP~  147 (147)
T PRK11198         94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIPE  147 (147)
T ss_pred             CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecCC
Confidence            345799999999999999984   457799999973 4 667899999999985

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

Probab=98.71  E-value=3.3e-08  Score=62.64  Aligned_cols=46  Identities=26%  Similarity=0.429  Sum_probs=41.7

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      ..|+|+.|||++.||++|++++.+++++|. +..+.+++||.+.++.
T Consensus        67 ~~~~V~~gdtL~~Ia~~~~~tv~~l~~~n~-l~~~~i~~gq~l~~~~  112 (124)
T COG1388          67 VTYTVKKGDTLSKIARKYGVTVAELKQLNN-LSSDKIKVGQKLKLPV  112 (124)
T ss_pred             ceEEEecCCCHHHHHHHhCCCHHHHHHHhc-cCCCceecCcEEEEec
Confidence            469999999999999999999999999996 5445999999999975

>PRK10260 L,D-transpeptidase; Provisional

Probab=98.49  E-value=1.1e-06  Score=64.07  Aligned_cols=49  Identities=16%  Similarity=0.255  Sum_probs=43.8

Q ss_pred             CceEEecCCC--CHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           42 DSVYGAQEGD--TCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        42 ~~~y~v~~Gd--Tc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ..+|+|+.|+  ++.+||++|++..++|.+.||++|.-...+|+.+.||..
T Consensus        40 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~   90 (306)
T PRK10260         40 NQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQ   90 (306)
T ss_pred             cEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence            4689999966  599999999999999999999999777789999999863

>PRK10190 L,D-transpeptidase; Provisional

Probab=98.38  E-value=2.5e-06  Score=62.34  Aligned_cols=49  Identities=10%  Similarity=0.126  Sum_probs=43.9

Q ss_pred             CceEEecCCC--CHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           42 DSVYGAQEGD--TCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        42 ~~~y~v~~Gd--Tc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ..+|+|+.+|  ++.+||++|++..++|.+.||++|.-...+|+.+.||..
T Consensus        37 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~   87 (310)
T PRK10190         37 SLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQ   87 (310)
T ss_pred             eEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence            4679999966  599999999999999999999999877789999999863

>TIGR03505 FimV_core FimV N-terminal domain

Probab=98.20  E-value=1.8e-06  Score=51.11  Aligned_cols=40  Identities=28%  Similarity=0.388  Sum_probs=34.2

Q ss_pred             CCHHHHHHHc---C-CCHH----HHHHhCCCC----CCCCCCCCCEEEEcCC
Q 040436           51 DTCSNVTEEF---N-LSTD----VFLAINPNI----NCDAIFVGQWLCVAGS   90 (91)
Q Consensus        51 dTc~~Ia~~~---~-i~~~----~l~~~Np~v----~c~~l~~G~~lcvp~~   90 (91)
                      ||+|+||+++   + ++++    .|++.||..    |-+.|++|++|+||..
T Consensus         1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~   52 (74)
T TIGR03505         1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE   52 (74)
T ss_pred             CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence            8999999999   3 7776    588999977    4568999999999974

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

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

Probab=97.48  E-value=0.00015  Score=43.76  Aligned_cols=45  Identities=24%  Similarity=0.267  Sum_probs=25.9

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHh---CCCC-CCCCCCCCCEEEE
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAI---NPNI-NCDAIFVGQWLCV   87 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~---Np~v-~c~~l~~G~~lcv   87 (91)
                      ..|+|++|||+..|-+++|++..+++++   +..- .-..|.|||.+-+
T Consensus         3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f   51 (85)
T PF04225_consen    3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEF   51 (85)
T ss_dssp             -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEE
T ss_pred             cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEE
Confidence            4599999999999999999999886654   3211 3457999999865

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.

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

Probab=97.28  E-value=8.5e-05  Score=52.88  Aligned_cols=47  Identities=21%  Similarity=0.254  Sum_probs=40.6

Q ss_pred             eEEecCCCCHHHHHHHc-C--CCHHHHHHhCCC--C-CCCCCCCCCEEEEcCC
Q 040436           44 VYGAQEGDTCSNVTEEF-N--LSTDVFLAINPN--I-NCDAIFVGQWLCVAGS   90 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~-~--i~~~~l~~~Np~--v-~c~~l~~G~~lcvp~~   90 (91)
                      +|+|+.|||+|.|+.++ |  .....|+..|..  + +.+.|++||++-||..
T Consensus       212 ~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~  264 (269)
T COG1652         212 TNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ  264 (269)
T ss_pred             EEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence            79999999999999985 3  556679999984  5 7889999999999864

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

Probab=97.10  E-value=0.00095  Score=37.88  Aligned_cols=43  Identities=16%  Similarity=0.331  Sum_probs=35.3

Q ss_pred             ecCCCCHHHHHHHc-CCC---HHHHHHhCCCC-CC-CCCCCCCEEEEcC
Q 040436           47 AQEGDTCSNVTEEF-NLS---TDVFLAINPNI-NC-DAIFVGQWLCVAG   89 (91)
Q Consensus        47 v~~GdTc~~Ia~~~-~i~---~~~l~~~Np~v-~c-~~l~~G~~lcvp~   89 (91)
                      .+.|||+..|+-++ |-.   .+.+++.||++ +. .-+..|..+.+|.
T Consensus         5 t~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~   53 (60)
T PF05489_consen    5 TTQGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPD   53 (60)
T ss_pred             EeCcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCC
Confidence            34999999999885 543   37899999999 55 6788999999985

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.

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

Probab=97.08  E-value=0.00048  Score=55.18  Aligned_cols=49  Identities=18%  Similarity=0.402  Sum_probs=40.5

Q ss_pred             CCceEEecCCCCHHHHHHHc----CCCHHH----HHHhCCCC----CCCCCCCCCEEEEcC
Q 040436           41 CDSVYGAQEGDTCSNVTEEF----NLSTDV----FLAINPNI----NCDAIFVGQWLCVAG   89 (91)
Q Consensus        41 c~~~y~v~~GdTc~~Ia~~~----~i~~~~----l~~~Np~v----~c~~l~~G~~lcvp~   89 (91)
                      -...|++++|||+|+||...    ++|+++    |++.||+.    |-+.|..|.+|-||.
T Consensus       187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~  247 (755)
T COG3170         187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPS  247 (755)
T ss_pred             CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccc
Confidence            34689999999999999987    456554    99999987    445799999999985

>COG3858 Predicted glycosyl hydrolase [General function prediction only]

Probab=97.04  E-value=0.00079  Score=51.07  Aligned_cols=49  Identities=18%  Similarity=0.237  Sum_probs=43.2

Q ss_pred             CceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           42 DSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        42 ~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ...|.|++|||+++||.+++++.+++..+|..+....+.+|-.+.+|..
T Consensus        49 ~~~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~   97 (423)
T COG3858          49 GHFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSA   97 (423)
T ss_pred             ceEEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEeccCC
Confidence            3679999999999999999999999999997655567889998888864

>PRK11649 putative peptidase; Provisional

Probab=96.13  E-value=0.011  Score=45.28  Aligned_cols=44  Identities=18%  Similarity=0.277  Sum_probs=36.7

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCC-CCCCCCCCCEEEE
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNI-NCDAIFVGQWLCV   87 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v-~c~~l~~G~~lcv   87 (91)
                      .|+|++|||+.+|-+++|++..++.++-... +-.+|.+||.|-+
T Consensus        97 ~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~  141 (439)
T PRK11649         97 EYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSW  141 (439)
T ss_pred             EEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEE
Confidence            6999999999999999999999887763222 4458999999876

>COG3858 Predicted glycosyl hydrolase [General function prediction only]

Probab=93.96  E-value=0.031  Score=42.62  Aligned_cols=46  Identities=22%  Similarity=0.202  Sum_probs=40.1

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      .|.|++||+...|++.|+.+..++..-|.-.+ +.+.+||.+.||..
T Consensus         3 i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~-d~~~~~q~~~v~~~   48 (423)
T COG3858           3 IHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTN-DDLVDGQTFVVPPS   48 (423)
T ss_pred             EEEccCCceeeeehhhcccccccccccccccc-ccccCceeEEECCc
Confidence            58999999999999999999999976663336 88999999999874

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

Probab=92.89  E-value=0.083  Score=33.06  Aligned_cols=33  Identities=27%  Similarity=0.459  Sum_probs=29.1

Q ss_pred             HHHHcCCCHHHHHHhCCCCC--CCCCCCCCEEEEcC
Q 040436           56 VTEEFNLSTDVFLAINPNIN--CDAIFVGQWLCVAG   89 (91)
Q Consensus        56 Ia~~~~i~~~~l~~~Np~v~--c~~l~~G~~lcvp~   89 (91)
                      ||.+|++++++++++|. ++  .+.+.+|+.+.+++
T Consensus         1 ia~~~~~~v~~l~~~n~-~~~~s~~i~~gq~l~~~~   35 (124)
T COG1388           1 IASKYGVSVKALKKANA-LTGKSDAIKPGQVLKIPG   35 (124)
T ss_pred             CcccccccHHHHHHHhc-ccCCCCccccCceEEccC
Confidence            57899999999999994 54  78899999999986

>PF13518 HTH_28: Helix-turn-helix domain

Probab=90.39  E-value=0.31  Score=25.56  Aligned_cols=24  Identities=21%  Similarity=0.401  Sum_probs=21.2

Q ss_pred             cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436           48 QEGDTCSNVTEEFNLSTDVFLAIN   71 (91)
Q Consensus        48 ~~GdTc~~Ia~~~~i~~~~l~~~N   71 (91)
                      ..|.|..++|+++||+...+.+|-
T Consensus        10 ~~g~s~~~~a~~~gis~~tv~~w~   33 (52)
T PF13518_consen   10 LEGESVREIAREFGISRSTVYRWI   33 (52)
T ss_pred             HcCCCHHHHHHHHCCCHhHHHHHH
Confidence            368899999999999999988875

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

Probab=89.24  E-value=0.83  Score=32.40  Aligned_cols=47  Identities=17%  Similarity=0.193  Sum_probs=39.1

Q ss_pred             CCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCC----C-CCCCCCCCEEEEc
Q 040436           41 CDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNI----N-CDAIFVGQWLCVA   88 (91)
Q Consensus        41 c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v----~-c~~l~~G~~lcvp   88 (91)
                      -.+.|+|+.|+|+--+=+.+++.+.|...+=. +    + -++|+.||.+.|.
T Consensus       158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMak-veGagkpLSnlkaGq~Vki~  209 (242)
T COG3061         158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAK-VEGAGKPLSNLKAGQKVKIS  209 (242)
T ss_pred             cceeEEecCCccHHHHHhccCCChHHhHHHHh-hccCCCchhhccCCCEEEEE
Confidence            34569999999999999999999999888763 3    1 3479999999884

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

Probab=87.82  E-value=0.24  Score=28.12  Aligned_cols=25  Identities=20%  Similarity=0.453  Sum_probs=21.2

Q ss_pred             ecCCCCHHHHHHHcCCCHHHHHHhC
Q 040436           47 AQEGDTCSNVTEEFNLSTDVFLAIN   71 (91)
Q Consensus        47 v~~GdTc~~Ia~~~~i~~~~l~~~N   71 (91)
                      .++|.|..++|++|||+...|..|=
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            3678999999999999999999884

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.

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

Probab=87.69  E-value=0.45  Score=32.76  Aligned_cols=46  Identities=13%  Similarity=0.087  Sum_probs=33.6

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      ..++|+|||+..||=+|..+..++.+.|....-.....-..+|+|.
T Consensus        11 ~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv   56 (186)
T KOG2850|consen   11 EVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPV   56 (186)
T ss_pred             eeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceeccc
Confidence            4789999999999999999999999999322112344444555544

>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=85.82  E-value=1.1  Score=23.43  Aligned_cols=24  Identities=17%  Similarity=0.339  Sum_probs=18.3

Q ss_pred             ecCCCCHHHHHHHcCCCHHHHHHh
Q 040436           47 AQEGDTCSNVTEEFNLSTDVFLAI   70 (91)
Q Consensus        47 v~~GdTc~~Ia~~~~i~~~~l~~~   70 (91)
                      .+.|-|..+||+.+|++...+++.
T Consensus        18 ~~~G~si~~IA~~~gvsr~TvyR~   41 (45)
T PF02796_consen   18 YAEGMSIAEIAKQFGVSRSTVYRY   41 (45)
T ss_dssp             HHTT--HHHHHHHTTS-HHHHHHH
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHH
Confidence            357899999999999999999875

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 ....

>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]

Probab=83.62  E-value=2.7  Score=29.11  Aligned_cols=47  Identities=26%  Similarity=0.379  Sum_probs=39.4

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      ..+.++.|+++..+++++++...++.+.|....-..+..|+.+-++.
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   48 (277)
T COG0739           2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPR   48 (277)
T ss_pred             ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecc
Confidence            35899999999999999999999999999655333788888887765

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=83.02  E-value=1.5  Score=27.64  Aligned_cols=27  Identities=15%  Similarity=0.177  Sum_probs=23.6

Q ss_pred             EecCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436           46 GAQEGDTCSNVTEEFNLSTDVFLAINP   72 (91)
Q Consensus        46 ~v~~GdTc~~Ia~~~~i~~~~l~~~Np   72 (91)
                      ..+.|.|..+||++|||+...|++|=.
T Consensus        25 ~~~~g~sv~evA~e~gIs~~tl~~W~r   51 (121)
T PRK09413         25 SFEPGMTVSLVARQHGVAASQLFLWRK   51 (121)
T ss_pred             HHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            356799999999999999999999943

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

Probab=82.29  E-value=1.6  Score=22.73  Aligned_cols=24  Identities=13%  Similarity=0.203  Sum_probs=18.1

Q ss_pred             cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436           48 QEGDTCSNVTEEFNLSTDVFLAIN   71 (91)
Q Consensus        48 ~~GdTc~~Ia~~~~i~~~~l~~~N   71 (91)
                      ..|.|..+||+.+|++...+.+|=
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            349999999999999999988773

>PF15145 DUF4577: Domain of unknown function (DUF4577)

Probab=81.58  E-value=4.5  Score=25.85  Aligned_cols=28  Identities=21%  Similarity=0.292  Sum_probs=24.1

Q ss_pred             EEecCCCCHHHHHHHc---CCCHHHHHHhCC
Q 040436           45 YGAQEGDTCSNVTEEF---NLSTDVFLAINP   72 (91)
Q Consensus        45 y~v~~GdTc~~Ia~~~---~i~~~~l~~~Np   72 (91)
                      -.+|.|.-..+++++.   |-+.++|++.|.
T Consensus        84 LiiQTgnkMddvSrRL~aEgKdIdeLKKiN~  114 (128)
T PF15145_consen   84 LIIQTGNKMDDVSRRLTAEGKDIDELKKINS  114 (128)
T ss_pred             heeeccchHHHHHHHHHhccCCHHHHHHHHH
Confidence            5688899999999986   788999999884

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

Probab=80.29  E-value=4.2  Score=31.06  Aligned_cols=45  Identities=16%  Similarity=0.267  Sum_probs=35.1

Q ss_pred             ceEEecCCCCHHHHHHHc-CC--CHHHHHHhCCCC-CCCCCCCCCEEEEc
Q 040436           43 SVYGAQEGDTCSNVTEEF-NL--STDVFLAINPNI-NCDAIFVGQWLCVA   88 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~-~i--~~~~l~~~Np~v-~c~~l~~G~~lcvp   88 (91)
                      ...+|++|||+.++|.+- |+  +++-|.-+|- + -.....||+++.|-
T Consensus       429 rvvtVk~GqT~~~lAA~m~G~~rkldlfRllNa-m~~~a~~~pGd~vKii  477 (479)
T COG4784         429 RVVTVKPGQTMASLAARMMGTDRKLDLFRLLNA-MSPGATVRPGDKVKII  477 (479)
T ss_pred             EEEEecCCccHHHHHhhccCchhHHHHHHHHhc-cCCCCcCCCCCeeeec
Confidence            468999999999999875 43  3566888884 5 45589999999873

>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=80.18  E-value=2.8  Score=18.90  Aligned_cols=23  Identities=9%  Similarity=0.356  Sum_probs=19.4

Q ss_pred             cCCCCHHHHHHHcCCCHHHHHHh
Q 040436           48 QEGDTCSNVTEEFNLSTDVFLAI   70 (91)
Q Consensus        48 ~~GdTc~~Ia~~~~i~~~~l~~~   70 (91)
                      +.|.+..+|++.+|++...+.++
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHh
Confidence            45789999999999999888764

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	91
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	6e-04

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

 Score = 35.8 bits (82), Expect = 6e-04
 Identities = 13/55 (23%), Positives = 19/55 (34%)

Query: 37  SPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGSA 91
                 +    Q+GDT  ++   F+         N   N D I+ GQ L V    
Sbjct: 57  GGGGGTATVTVQQGDTLRDIGRRFDCDFHEIARRNNIQNEDLIYPGQVLQVPTKG 111

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	91
1e0g_A	48	Membrane-bound lytic murein transglycosylase D; ce	99.52
2djp_A	77	Hypothetical protein SB145; LYSM, structural genom	99.41
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	99.36
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	99.24
4eby_A	212	Chitin elicitor receptor kinase 1; pathogen-associ	99.16
4a1k_A	165	Putative L, D-transpeptidase YKUD; transferase, pe	98.98
2gu1_A	361	Zinc peptidase; alpha/beta, beta barrel, structura	98.56
2gu1_A	361	Zinc peptidase; alpha/beta, beta barrel, structura	97.75
3slu_A	371	M23 peptidase domain protein; outer membrane, hydr	97.24
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	87.41
2l9y_A	167	CVNH-LYSM lectin; carbohydrate, sugar binding prot	86.81
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	82.31
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	82.02
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	81.85
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	81.25
2lfc_A	160	Fumarate reductase, flavoprotein subunit; structur	80.59
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	80.4

>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=99.52  E-value=1.7e-14  Score=76.96  Aligned_cols=45  Identities=16%  Similarity=0.264  Sum_probs=42.3

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      ..|+|++|||+|+||++|+++.++|.++|+  +.+.|++||.+.||.
T Consensus         3 ~~y~V~~GDtl~~Ia~~~~~~~~~l~~~N~--~~~~l~~G~~l~ip~   47 (48)
T 1e0g_A            3 ITYRVRKGDSLSSIAKRHGVNIKDVMRWNS--DTANLQPGDKLTLFV   47 (48)
T ss_dssp             CEEEECTTCCHHHHHHHHTCCHHHHHHHCS--CGGGCCTTEEEECCC
T ss_pred             EEEEEcCCCcHHHHHHHHCcCHHHHHHhCC--CCCcCCcCCEEEEec
Confidence            469999999999999999999999999998  778999999999985

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

Probab=99.41  E-value=1.5e-13  Score=80.32  Aligned_cols=48  Identities=17%  Similarity=0.196  Sum_probs=43.5

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      ..|+|++|||+|+||++|++++++|+++|+..+.+.|++||.|.||..
T Consensus        16 ~~y~V~~GDTL~~IA~~~~~~~~~l~~~N~l~~~~~l~~Gq~l~iP~~   63 (77)
T 2djp_A           16 LEHQLEPGDTLAGLALKYGVTMEQIKRANRLYTNDSIFLKKTLYIPIL   63 (77)
T ss_dssp             EEECCCTTCCHHHHHHHHTCCHHHHHHHHTCCCSSCGGGSSCEEEEEE
T ss_pred             EEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEEECCC
Confidence            459999999999999999999999999996546789999999999853

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

Probab=99.36  E-value=6e-13  Score=88.43  Aligned_cols=50  Identities=26%  Similarity=0.272  Sum_probs=44.8

Q ss_pred             CCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436           41 CDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS   90 (91)
Q Consensus        41 c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~   90 (91)
                      -...|+|++|||||+||++|++++.+|.++|.--+.+.|++||+|.||..
T Consensus        61 ~~~~y~V~~GDTL~~IA~~~~~~~~~l~~~N~~~~~~~i~~Gq~L~ip~~  110 (167)
T 2l9y_A           61 GTATVTVQQGDTLRDIGRRFDCDFHEIARRNNIQNEDLIYPGQVLQVPTK  110 (167)
T ss_dssp             SCEEEEECTTCCHHHHHHHTTCCHHHHHHHHTCCGGGCCCTTEEEEESCC
T ss_pred             CCceEEECCCCcHHHHHHHcCCCHHHHHHHcCCCCcccccCCCEEEEcCC
Confidence            34689999999999999999999999999995337789999999999964

>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=99.24  E-value=1.2e-11  Score=84.87  Aligned_cols=51  Identities=31%  Similarity=0.432  Sum_probs=46.4

Q ss_pred             CCCC-c--eEEecCCCCHHHHHHHcCCCH--------HHHHHhCCCC-CCCCCCCCCEEEEcC
Q 040436           39 PTCD-S--VYGAQEGDTCSNVTEEFNLST--------DVFLAINPNI-NCDAIFVGQWLCVAG   89 (91)
Q Consensus        39 ~~c~-~--~y~v~~GdTc~~Ia~~~~i~~--------~~l~~~Np~v-~c~~l~~G~~lcvp~   89 (91)
                      ..|+ .  .|+|++|||+|.||++||+++        ++|+++||++ +.+.|.+||.|.||.
T Consensus         3 ~~C~~a~~~Y~V~~GDTL~~IA~~~~vsv~~~~~~~~~~I~~~Np~l~~~~~l~~Gq~L~IP~   65 (212)
T 4eby_A            3 TSCPLALASYYLENGTTLSVINQNLNSSIAPYDQINFDPILRYNSNIKDKDRIQMGSRVLVPF   65 (212)
T ss_dssp             CCCSCEEEEEECCTTCCHHHHHHHTCCSSSCCCSSCCHHHHTTCTTCSCTTSCCTTCEEEEEE
T ss_pred             CCCccceEEEEeCCCCCHHHHHHHHCCCchhccccCHHHHHHhccCCCCcCccCCCCEEEEec
Confidence            4587 3  499999999999999999998        9999999999 688999999999994

>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=99.16  E-value=4.1e-11  Score=82.14  Aligned_cols=46  Identities=22%  Similarity=0.271  Sum_probs=43.1

Q ss_pred             ceEEecCCCCHHHHH-HHcC--CCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           43 SVYGAQEGDTCSNVT-EEFN--LSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia-~~~~--i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      ..|+|++|||+|+|| ++|+  +++++|+++|+ ++.+.|++||.|.||.
T Consensus        79 ~~Y~V~~GDTL~~IA~~~y~~lvt~~~L~~~N~-~~~~~l~~Gq~L~IP~  127 (212)
T 4eby_A           79 FSYSVRQEDTYERVAISNYANLTTMESLQARNP-FPATNIPLSATLNVLV  127 (212)
T ss_dssp             EEEECCTTCCHHHHHHTTTTTSSCHHHHHHHCC-SCTTCCCTTCEEEEEE
T ss_pred             eEEEecCCCcHHHHHHHhcCCCCCHHHHHHhcC-CCcccCCCCCEEEEcC
Confidence            469999999999999 8999  99999999998 8888999999999984

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

Probab=98.98  E-value=5.8e-10  Score=73.67  Aligned_cols=46  Identities=28%  Similarity=0.609  Sum_probs=41.9

Q ss_pred             ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      .+|+||+|||+++||++|+++.++|+++||++|.. +.+|+.+.||.
T Consensus         3 ~~y~V~~GdtL~~IA~~f~~g~~~l~~aNp~vd~~-l~~g~~i~ip~   48 (165)
T 4a1k_A            3 LTYQVKQGDTLNSIAADFRISTAALLQANPSLQAG-LTAGQSIVIPG   48 (165)
T ss_dssp             EEEECCTTCCHHHHHHHTTCCHHHHHHHCGGGGGC-CCTTCEEEETT
T ss_pred             EEEEECCCCCHHHHHHHhCCCHHHHHHhCccCCCc-cCCCccccCcc
Confidence            36999999999999999999999999999998754 68999999975

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

Probab=98.56  E-value=2.5e-08  Score=72.64  Aligned_cols=48  Identities=21%  Similarity=0.172  Sum_probs=42.1

Q ss_pred             CceEEecCCCCHHHHHHHcCCCHHHHHHhCCCC----CCCCCCCCCEEEEcC
Q 040436           42 DSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNI----NCDAIFVGQWLCVAG   89 (91)
Q Consensus        42 ~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v----~c~~l~~G~~lcvp~   89 (91)
                      ...|+|++|||+|+|+++||++.++++++|...    +.+.|.+||.|.+|.
T Consensus         7 ~~~~~Vk~GDTL~~Ia~r~gvs~~~l~~~n~~~~~~~~~~~L~~Gq~L~i~~   58 (361)
T 2gu1_A            7 RIHYMVKVGDTLSGIFAQLGVPYSILQKILSVDLDHLQLDMIQPGEELELMM   58 (361)
T ss_dssp             CEEEECCTTCCHHHHHHHTTCCHHHHHHHHHHGGGTCCGGGCCTTCEEEEEE
T ss_pred             ceEEEECCCCcHHHHHHHcCCCHHHHHHHHhhcccccchhcCCCCCEEEEEE
Confidence            346999999999999999999999999999643    257899999999974

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

Probab=97.75  E-value=1.8e-05  Score=57.56  Aligned_cols=45  Identities=9%  Similarity=0.189  Sum_probs=37.9

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCC----C-CCCCCCCEEEEc
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNIN----C-DAIFVGQWLCVA   88 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~----c-~~l~~G~~lcvp   88 (91)
                      .|.++.|||+|.||+++|++.+++++||....    - ..|.+||++.|+
T Consensus       102 ~~~v~igdSL~~iA~~~Gvs~~~i~~ln~i~~~~idf~~~Lr~GD~l~V~  151 (361)
T 2gu1_A          102 LFSGEINGSFSVSARRVGLTSSQVANITQVMKDKIDFSRSLRAGDRFDIL  151 (361)
T ss_dssp             EEEEESSSCHHHHHHHTTCCHHHHHHHHHHHTTTCCTTTCCCC-CEEEEE
T ss_pred             EEEEEECCcHHHHHHHcCCCHHHHHHHHHhhcccccccccCCCCCEEEEE
Confidence            58889999999999999999999999996332    2 569999999986

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

Probab=97.24  E-value=0.00047  Score=50.51  Aligned_cols=47  Identities=17%  Similarity=0.133  Sum_probs=39.1

Q ss_pred             CceEEecCCCCHHHHHHHcCCCHHHHHHhCCCC----CCCCCCCCCEEEEc
Q 040436           42 DSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNI----NCDAIFVGQWLCVA   88 (91)
Q Consensus        42 ~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v----~c~~l~~G~~lcvp   88 (91)
                      ...|+|++|||+.+|-+++|++..++.+++...    +-..|.+||.|.+.
T Consensus        14 W~~~~V~~GDTL~~IL~r~Gls~~di~~i~~~~~~~~~l~~LrpGq~l~i~   64 (371)
T 3slu_A           14 WVQEAVQPGDSLADVLARSGMARDEIARITEKYGGEADLRHLRADQSVHVL   64 (371)
T ss_dssp             EEEEECCTTCCHHHHHHHTTCCHHHHHHHHTTC------CCBCSSSEEEEE
T ss_pred             eEEEEECCCCcHHHHHHHcCCCHHHHHHHHHhccccCchhhCCCCCEEEEE
Confidence            445999999999999999999999988887544    45789999999873

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

Probab=87.41  E-value=0.36  Score=25.53  Aligned_cols=24  Identities=4%  Similarity=0.109  Sum_probs=20.7

Q ss_pred             cCCCC----HHHHHHHcCCCHHHHHHhC
Q 040436           48 QEGDT----CSNVTEEFNLSTDVFLAIN   71 (91)
Q Consensus        48 ~~GdT----c~~Ia~~~~i~~~~l~~~N   71 (91)
                      +.|.+    ..+||++|||+...|.+|=
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    9999999999999999884

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

Probab=86.81  E-value=0.0023  Score=42.02  Aligned_cols=34  Identities=9%  Similarity=-0.053  Sum_probs=27.6

Q ss_pred             CCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCC
Q 040436           41 CDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNI   74 (91)
Q Consensus        41 c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v   74 (91)
                      +...|.|++|||+++||+++|.+.+..+.+|..+
T Consensus       124 ~~~~~~v~~GdtL~aIA~r~G~~v~s~i~Ln~~I  157 (167)
T 2l9y_A          124 ARDVRLVDGGKVLEAELRYSGGWNRSRIYLDEHI  157 (167)
T ss_dssp             EEEEEEETTTTEEEEEEEETTEEEEEEECGGGTE
T ss_pred             cceEEEeCCcCChHHHHHHcCCceEEEEEccccc
Confidence            3457999999999999999997777766666554

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

Probab=82.31  E-value=0.92  Score=26.02  Aligned_cols=22  Identities=5%  Similarity=0.191  Sum_probs=20.3

Q ss_pred             CCCHHHHHHHcCCCHHHHHHhC
Q 040436           50 GDTCSNVTEEFNLSTDVFLAIN   71 (91)
Q Consensus        50 GdTc~~Ia~~~~i~~~~l~~~N   71 (91)
                      |.|..+||+++||+...|++|=
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            7899999999999999999884

>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=82.02  E-value=1.2  Score=21.88  Aligned_cols=25  Identities=8%  Similarity=0.178  Sum_probs=21.7

Q ss_pred             ecCCCCHHHHHHHcCCCHHHHHHhC
Q 040436           47 AQEGDTCSNVTEEFNLSTDVFLAIN   71 (91)
Q Consensus        47 v~~GdTc~~Ia~~~~i~~~~l~~~N   71 (91)
                      .+.|.|..+||+.+|++...++++=
T Consensus        18 ~~~g~s~~~ia~~lgvs~~Tv~r~l   42 (52)
T 1jko_C           18 LEKGHPRQQLAIIFGIGVSTLYRYF   42 (52)
T ss_dssp             HHTTCCHHHHHHTTSCCHHHHHHHS
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            3568899999999999999998873

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

Probab=81.85  E-value=1.5  Score=25.96  Aligned_cols=28  Identities=14%  Similarity=0.153  Sum_probs=23.4

Q ss_pred             ecCCCCHHHHHHHcCCCHHHHHHhCCCC
Q 040436           47 AQEGDTCSNVTEEFNLSTDVFLAINPNI   74 (91)
Q Consensus        47 v~~GdTc~~Ia~~~~i~~~~l~~~Np~v   74 (91)
                      ...+.|..++|++|+|+.++|.+|-...
T Consensus        46 ~~g~~s~~e~arry~Is~s~i~~W~r~~   73 (95)
T 2jrt_A           46 IHGLITEREALDRYSLSEEEFALWRSAV   73 (95)
T ss_dssp             HTTSSCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             HcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3445699999999999999999997544

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

Probab=81.25  E-value=1.3  Score=25.09  Aligned_cols=23  Identities=9%  Similarity=0.342  Sum_probs=20.8

Q ss_pred             cCCCCHHHHHHHcCCCHHHHHHh
Q 040436           48 QEGDTCSNVTEEFNLSTDVFLAI   70 (91)
Q Consensus        48 ~~GdTc~~Ia~~~~i~~~~l~~~   70 (91)
                      +.|.+..+||+++||+...|++|
T Consensus        36 ~~g~s~~~iA~~~gIs~sTl~rW   58 (87)
T 2elh_A           36 HDGESKASVARDIGVPESTLRGW   58 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHH
Confidence            46889999999999999998887

>2lfc_A Fumarate reductase, flavoprotein subunit; structural genomics, northeast structural genomics consortiu PSI-biology; NMR {Lactobacillus plantarum}

Probab=80.59  E-value=1  Score=28.55  Aligned_cols=27  Identities=7%  Similarity=-0.011  Sum_probs=21.9

Q ss_pred             EecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436           46 GAQEGDTCSNVTEEFNLSTDV----FLAINP   72 (91)
Q Consensus        46 ~v~~GdTc~~Ia~~~~i~~~~----l~~~Np   72 (91)
                      .+..+||+.++|++.|++.+.    +.++|.
T Consensus        91 ~~~kadTleeLA~~~gid~~~L~~TV~~yN~  121 (160)
T 2lfc_A           91 PVFVKGSLESAAEQAGIVVDELVQTVKNYQG  121 (160)
T ss_dssp             CSEECSSHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ceEecCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            456789999999999999875    566773

>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=80.40  E-value=1.7  Score=20.88  Aligned_cols=23  Identities=4%  Similarity=-0.015  Sum_probs=20.4

Q ss_pred             cCCCCHHHHHHHcCCCHHHHHHh
Q 040436           48 QEGDTCSNVTEEFNLSTDVFLAI   70 (91)
Q Consensus        48 ~~GdTc~~Ia~~~~i~~~~l~~~   70 (91)
                      ..|.+..+||+.+|++...+.++
T Consensus        19 ~~g~s~~~IA~~lgis~~Tv~~~   41 (51)
T 1tc3_C           19 LLNVSLHEMSRKISRSRHCIRVY   41 (51)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHH
Confidence            46889999999999999988776

---

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	91
d1y7ma2	48	d.7.1.1 (A:1-48) Hypothetical protein YkuD, N-term	1e-04
d1e0ga_	48	d.7.1.1 (A:) Membrane-bound lytic murein transclyc	6e-04

>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 = 34.0 bits (78), Expect = 1e-04
 Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89
           Y  ++GDT +++  +F +ST   L  NP++    +  GQ + + G
Sbjct: 3  TYQVKQGDTLNSIAADFRISTAALLQANPSLQ-AGLTAGQSIVIPG 47

>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 = 32.7 bits (75), Expect = 6e-04
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 42 DSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWL 85
          DS+ Y  ++GD+ S++ +   ++    +  N +     +  G  L
Sbjct: 1  DSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTA--NLQPGDKL 43

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	91
d1y7ma2	48	Hypothetical protein YkuD, N-terminal domain {Baci	99.64
d1e0ga_	48	Membrane-bound lytic murein transclycosylase D, Ml	99.54
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	91.59
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	80.53

>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=99.64  E-value=2.5e-17  Score=88.11  Aligned_cols=45  Identities=29%  Similarity=0.635  Sum_probs=41.9

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      .|+|++|||+|+||++||++.++|+++|+..+ +.|++||.++||+
T Consensus         3 ~y~V~~GDTL~~IA~~y~v~~~~i~~~N~~~~-~~l~~Gq~L~IPg   47 (48)
T d1y7ma2           3 TYQVKQGDTLNSIAADFRISTAALLQANPSLQ-AGLTAGQSIVIPG   47 (48)
T ss_dssp             EEECCTTCCHHHHHHHTTSCCCCCCCTSCTTC-SSCCTTCEEEETT
T ss_pred             EEEECCCCCHHHHHHHhCCCHHHHHHHcCCCC-CCCCCCCEEEeCC
Confidence            59999999999999999999999999998655 5799999999997

>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=99.54  E-value=2.9e-15  Score=79.93  Aligned_cols=44  Identities=16%  Similarity=0.246  Sum_probs=40.3

Q ss_pred             eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436           44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG   89 (91)
Q Consensus        44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~   89 (91)
                      .|+|++|||+|+||++||+++++|.++|+ +. +.|++||.|.||.
T Consensus         4 ~y~V~~GDTl~~IA~~y~vs~~~i~~~N~-l~-~~l~~Gq~L~i~v   47 (48)
T d1e0ga_           4 TYRVRKGDSLSSIAKRHGVNIKDVMRWNS-DT-ANLQPGDKLTLFV   47 (48)
T ss_dssp             EEEECTTCCHHHHHHHHTCCHHHHHHHCS-CG-GGCCTTEEEECCC
T ss_pred             EEEECCCCCHHHHHHHHCCCHHHHHHHcC-Cc-ccCcCCCEEEEEe
Confidence            59999999999999999999999999995 53 4799999999984

>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=91.59  E-value=0.068  Score=26.74  Aligned_cols=26  Identities=12%  Similarity=0.268  Sum_probs=23.5

Q ss_pred             ecCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436           47 AQEGDTCSNVTEEFNLSTDVFLAINP   72 (91)
Q Consensus        47 v~~GdTc~~Ia~~~~i~~~~l~~~Np   72 (91)
                      +..|++..+||+.|||+...|+++=|
T Consensus        18 ~~~G~s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_          18 LEKGHPRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHhhCC
Confidence            46799999999999999999998865

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

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

Probab=80.53  E-value=0.55  Score=25.66  Aligned_cols=22  Identities=5%  Similarity=0.274  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHcCCCHHHHHHh
Q 040436           49 EGDTCSNVTEEFNLSTDVFLAI   70 (91)
Q Consensus        49 ~GdTc~~Ia~~~~i~~~~l~~~   70 (91)
                      .|-+.-+||+++||+...|.+|
T Consensus        22 ~g~s~~~vA~~lGIs~~tl~~W   43 (89)
T d2jn6a1          22 DGASLQQIANDLGINRVTLKNW   43 (89)
T ss_dssp             GGSCHHHHHHHHTSCHHHHHHH
T ss_pred             CCCcHHHHHHHHCCCHHHHHHH
Confidence            4889999999999999999988