Citrus Sinensis ID: 022062

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300---

MASNIYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREM

ccccccccccccccccccccccccccccHHHHHHHHccEEccccccccEEccccccccccccEEEEcccccccccccHHHHHHcccEEEEEEccccccccccEEEEEccccHHHHHHHHHHHHHHHHHcccccEEEEcccccHHHHHHHHHHHHHcccccEEEcccccccccHHHHHHccccccccEEEEEEccccccHHHHHHccccccEEEEEcHHHHHHcccccHHHHHHHHHHHHHccccccEEEEEcccHHHHHHcccccccEEEEEccccccEEEEEEEEEcccEEEEEEEcccccc

ccccccccEEEEEcccccccccccHHHcHHHHHHHHcccEccccEEcEEEEcccEEccccccEEEEEccccccHHHHHHHHHHcccEEEEEEccccccccccEEEEEEEEEHHHHHHHHHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHHccccEEEccccccccccccEEEEcccccccEEEEEEccccccHHHHHHHHccccEEEEEccHHHHHHccccHHHHHHHHHHHHHccccccEEEEEcccHHHHHHHHHccccEEEEcccccccEEEEEEEEccccEEEEEEccccccc

masniyphtlactskttfrcpsnspiwtINEIAEsvngkilkwgppgiictdtrilapnknqwFFAItgqhfdahefispelygkgcvgvignqvcnnwdkgfvqvegngnvntlnSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGdshleslgSLEDVARAKgeifqesklgdvcvlnaddplvanltvprgvrkvFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREM

masniyphtlactskttfrcpsnsPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIfqesklgdvCVLNADdplvanltvprgVRKVFFGWRRGCDVRLVAAqvangglgvqvvlekerem

MASNIYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFsgvlvgvtgsvgksttksMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREM

****IYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVL******

***********CTSKT**RCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEK****

**SNIYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEK****

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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	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		303	2.2.26 [Sep-21-2011]
P96613		457	UDP-N-acetylmuramoyl-trip	yes	no	0.726	0.481	0.362	8e-29
P45450		454	UDP-N-acetylmuramoyl-trip	N/A	no	0.656	0.438	0.369	4e-27
O33804		446	Probable UDP-N-acetylmura	N/A	no	0.788	0.535	0.365	1e-25
Q9AKP1		449	Probable UDP-N-acetylmura	yes	no	0.613	0.414	0.335	1e-23
O05953		449	Probable UDP-N-acetylmura	yes	no	0.735	0.496	0.307	2e-23
Q92H60		449	Probable UDP-N-acetylmura	yes	no	0.610	0.412	0.333	3e-23
P11880		452	UDP-N-acetylmuramoyl-trip	N/A	no	0.699	0.469	0.331	2e-20
Q89AQ1		460	UDP-N-acetylmuramoyl-trip	yes	no	0.640	0.421	0.311	1e-19
P0A5L4		510	UDP-N-acetylmuramoyl-trip	yes	no	0.782	0.464	0.305	2e-18
P0A5L5		510	UDP-N-acetylmuramoyl-trip	yes	no	0.782	0.464	0.305	2e-18

>sp\|P96613\|MURF_BACSU UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Bacillus subtilis (strain 168) GN=murF PE=3 SV=1	Back alignment and function desciption

 Score =  127 bits (320), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 87/240 (36%), Positives = 130/240 (54%), Gaps = 20/240 (8%)

Query: 28  TINEIAESVNGKIL--KWGPPGI--ICTDTRILAPNKNQWFFAITGQHFDAHEFISPELY 83
           T+  IAE V G +   ++    I  + TDTR L   ++Q F  + G+ FD H F+  + +
Sbjct: 5   TVKNIAEMVKGTLANPQYEQTVIHGVATDTRKL--EQHQLFIPLKGERFDGHSFVE-QAF 61

Query: 84  GKGCVGVIGNQVCNNWDKGFVQVEGNGNV----NTLNSLVNMACYARNSRFSGVLVGVTG 139
             G   V+       WD+       N  V    +TL +L  +A  A        ++GVTG
Sbjct: 62  EAGVAAVL-------WDRSVPNPPENHAVILVDDTLTALQQLAK-AYLQELGTRVIGVTG 113

Query: 140 SVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGE 199
           S GK+TTK MI   L +    V ++ GN+NN +G+ L+++ +    +IAVLEMGMS KGE
Sbjct: 114 SNGKTTTKDMIHAVLGT-QYRVHKTGGNFNNHIGLPLTVLAMPENTEIAVLEMGMSAKGE 172

Query: 200 ILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVAN 259
           I  L+R+A P+  V+ N+G+SH++ LGS E +A AK EI    K   V +   D+PL+ N
Sbjct: 173 IDLLSRLANPDAAVITNIGESHMQDLGSREGIAEAKLEIINGLKEDGVLIYIGDEPLLQN 232

Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.
Bacillus subtilis (strain 168) (taxid: 224308)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: 1EC: 0

>sp\|P45450\|MURF_SYNY3 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=murF PE=3 SV=1	Back alignment and function description

>sp\|O33804\|MURF_STRTO Probable UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Streptomyces toyocaensis GN=murF PE=3 SV=2	Back alignment and function description

>sp\|Q9AKP1\|MURF_RICMO Probable UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Rickettsia montana GN=murF PE=3 SV=1	Back alignment and function description

>sp\|O05953\|MURF_RICPR Probable UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Rickettsia prowazekii (strain Madrid E) GN=murF PE=3 SV=2	Back alignment and function description

>sp\|Q92H60\|MURF_RICCN Probable UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Rickettsia conorii (strain ATCC VR-613 / Malish 7) GN=murF PE=3 SV=1	Back alignment and function description

>sp\|P11880\|MURF_ECOLI UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Escherichia coli (strain K12) GN=murF PE=1 SV=2	Back alignment and function description

>sp\|Q89AQ1\|MURF_BUCBP UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=murF PE=3 SV=1	Back alignment and function description

>sp\|P0A5L4\|MURF_MYCTU UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Mycobacterium tuberculosis GN=murF PE=3 SV=1	Back alignment and function description

>sp\|P0A5L5\|MURF_MYCBO UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) GN=murF PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		303
297742739		510	unnamed protein product [Vitis vinifera]	0.891	0.529	0.655	7e-95
225463627		771	PREDICTED: UDP-N-acetylmuramoyl-tripepti	0.891	0.350	0.655	2e-94
168029598		606	predicted protein [Physcomitrella patens	0.877	0.438	0.487	3e-65
76880174		606	MurF synthetase [Physcomitrella patens s	0.877	0.438	0.487	4e-65
302819065		515	hypothetical protein SELMODRAFT_133115 [	0.874	0.514	0.469	6e-62
302819192		515	hypothetical protein SELMODRAFT_185918 [	0.874	0.514	0.469	7e-62
303290893		624	predicted protein [Micromonas pusilla CC	0.785	0.381	0.446	2e-38
220927933		459	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,	0.821	0.542	0.365	2e-36
332982163		464	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,	0.834	0.545	0.364	3e-36
118581693		469	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,	0.785	0.507	0.416	3e-36

>gi\|297742739\|emb\|CBI35373.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  353 bits (905), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 183/279 (65%), Positives = 217/279 (77%), Gaps = 9/279 (3%)

Query: 24  SPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELY 83
           SP+WT++EIAE+VNG I++ GPPG ICTDTR L P   QWFFAI G++FDAHEFI+PEL 
Sbjct: 49  SPLWTVDEIAEAVNGTIVQRGPPGPICTDTRTLEPG--QWFFAIRGENFDAHEFITPELG 106

Query: 84  GKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGK 143
            KGCVGVIGN VC NWDKGFV++ G     TL SL  MA YARN +F G LVGVTGS GK
Sbjct: 107 HKGCVGVIGNWVCPNWDKGFVEMGGE----TLTSLEKMANYARN-KFHGCLVGVTGSAGK 161

Query: 144 STTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILEL 203
           +TT++MIAL LESLG+ V Q++GN NNR+GV LSLIGI + V   VLE+GM  +GEI+EL
Sbjct: 162 TTTRTMIALTLESLGL-VHQTHGNENNRIGVCLSLIGIPQNVGFVVLELGMDRRGEIMEL 220

Query: 204 ARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVP 263
           AR ARP IRV+LNVG +HLE+  SLE+VA AKGEI  E+K GDVCVLNADDPLV +L VP
Sbjct: 221 ARKARPSIRVILNVGCAHLENFASLEEVAMAKGEILAEAKPGDVCVLNADDPLVMSLPVP 280

Query: 264 RGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKERE 302
            GV+KV FG R  CDVR  A +V +GG GV+VVLE+  E
Sbjct: 281 HGVKKVLFGQRLECDVRFAAEKV-HGGHGVRVVLERNHE 318

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225463627\|ref\|XP_002271742.1\| PREDICTED: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|168029598\|ref\|XP_001767312.1\| predicted protein [Physcomitrella patens subsp. patens] gi\|162681376\|gb\|EDQ67803.1\| predicted protein [Physcomitrella patens subsp. patens]	Back alignment and taxonomy information

>gi\|76880174\|dbj\|BAE45859.1\| MurF synthetase [Physcomitrella patens subsp. patens]	Back alignment and taxonomy information

>gi\|302819065\|ref\|XP_002991204.1\| hypothetical protein SELMODRAFT_133115 [Selaginella moellendorffii] gi\|300141032\|gb\|EFJ07748.1\| hypothetical protein SELMODRAFT_133115 [Selaginella moellendorffii]	Back alignment and taxonomy information

>gi\|302819192\|ref\|XP_002991267.1\| hypothetical protein SELMODRAFT_185918 [Selaginella moellendorffii] gi\|300140978\|gb\|EFJ07695.1\| hypothetical protein SELMODRAFT_185918 [Selaginella moellendorffii]	Back alignment and taxonomy information

>gi\|303290893\|ref\|XP_003064733.1\| predicted protein [Micromonas pusilla CCMP1545] gi\|226453759\|gb\|EEH51067.1\| predicted protein [Micromonas pusilla CCMP1545]	Back alignment and taxonomy information

>gi\|220927933\|ref\|YP_002504842.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium cellulolyticum H10] gi\|219998261\|gb\|ACL74862.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium cellulolyticum H10]	Back alignment and taxonomy information

>gi\|332982163\|ref\|YP_004463604.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Mahella australiensis 50-1 BON] gi\|332699841\|gb\|AEE96782.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Mahella australiensis 50-1 BON]	Back alignment and taxonomy information

>gi\|118581693\|ref\|YP_902943.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase [Pelobacter propionicus DSM 2379] gi\|118504403\|gb\|ABL00886.1\| UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase [Pelobacter propionicus DSM 2379]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		303
TIGR_CMR\|CHY_2073		458	CHY_2073 "UDP-N-acetylmuramoyl	0.792	0.524	0.307	9.1e-26
TIGR_CMR\|SPO_1183		464	SPO_1183 "UDP-N-acetylmuramoyl	0.831	0.543	0.318	5.4e-22
TIGR_CMR\|BA_0246		458	BA_0246 "UDP-N-acetylmuramoyla	0.742	0.491	0.301	3.9e-21
TIGR_CMR\|CBU_0124		446	CBU_0124 "UDP-N-acetylmuramoyl	0.702	0.477	0.318	5.9e-21
UNIPROTKB\|Q9KPG3		453	VC_2405 "UDP-N-acetylmuramoyl-	0.706	0.472	0.283	1e-18
TIGR_CMR\|VC_2405		453	VC_2405 "UDP-N-acetylmuramoyla	0.706	0.472	0.283	1e-18
UNIPROTKB\|P11880		452	murF [Escherichia coli K-12 (t	0.402	0.269	0.388	4.4e-18
UNIPROTKB\|Q48EF4		456	murF "UDP-N-acetylmuramoyl-tri	0.650	0.432	0.276	2.2e-17
TIGR_CMR\|CPS_4469		513	CPS_4469 "UDP-N-acetylmuramoyl	0.633	0.374	0.304	3e-17
TIGR_CMR\|SO_4223		460	SO_4223 "UDP-N-acetylmuramoyla	0.458	0.302	0.338	8.6e-14

TIGR_CMR\|CHY_2073 CHY_2073 "UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

 Score = 294 (108.6 bits), Expect = 9.1e-26, P = 9.1e-26
 Identities = 78/254 (30%), Positives = 124/254 (48%)

Query:    49 ICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEG 108
             + TDTR L P     F A+ G+  D HEF+ P+   KG  GV+   V   +     Q+  
Sbjct:    27 VSTDTRTLKPYA--LFVALHGEKLDGHEFV-PDAVAKGAAGVV---VERPFSINVTQIVV 80

Query:   109 NGNVNTLNSLVNMACYARNSRFXXXXXXXXXXXXXXXXXXMIALALESLGVNVFQSYGNW 168
                 +T  +L  +A Y R                      + A+  +    NV  +  N+
Sbjct:    81 K---DTFRALQELALYNRQKEGLKVIGITGSNGKTTTKDLVKAVLRQKY--NVCATEKNF 135

Query:   169 NNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSL 228
             NN +GV L+L+  D   ++ ++EMGM G GEI  L ++ARP+I ++ N+G++HLE L S 
Sbjct:   136 NNELGVPLTLLNFDENTEVGIVEMGMRGLGEIDALCQVARPDIGIITNIGEAHLELLKSQ 195

Query:   229 EDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVAN 288
             E++ARAK E+ +      V ++N + P +  +     V+K FFG R G D+ +      +
Sbjct:   196 ENIARAKSELIKNLPGDGVAIINGESPYIKEIVANIPVKKYFFGHRAG-DLYIKKFSQED 254

Query:   289 GGLGVQV--VLEKE 300
              GL      +LE+E
Sbjct:   255 DGLRFITAGILEEE 268

GO:0009252 "peptidoglycan biosynthetic process" evidence=ISS

GO:0047480 "UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity" evidence=ISS

TIGR_CMR\|SPO_1183 SPO_1183 "UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	Back alignment and assigned GO terms

TIGR_CMR\|BA_0246 BA_0246 "UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alany l-D-alanyl ligase" [Bacillus anthracis str. Ames (taxid:198094)]	Back alignment and assigned GO terms

TIGR_CMR\|CBU_0124 CBU_0124 "UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alany l-D-alanyl ligase" [Coxiella burnetii RSA 493 (taxid:227377)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9KPG3 VC_2405 "UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]	Back alignment and assigned GO terms

TIGR_CMR\|VC_2405 VC_2405 "UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alany l-D-alanyl ligase" [Vibrio cholerae O1 biovar El Tor (taxid:686)]	Back alignment and assigned GO terms

UNIPROTKB\|P11880 murF [Escherichia coli K-12 (taxid:83333)]	Back alignment and assigned GO terms

UNIPROTKB\|Q48EF4 murF "UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase" [Pseudomonas syringae pv. phaseolicola 1448A (taxid:264730)]	Back alignment and assigned GO terms

TIGR_CMR\|CPS_4469 CPS_4469 "UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase" [Colwellia psychrerythraea 34H (taxid:167879)]	Back alignment and assigned GO terms

TIGR_CMR\|SO_4223 SO_4223 "UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alany l-D-alanyl ligase" [Shewanella oneidensis MR-1 (taxid:211586)]	Back alignment and assigned GO terms

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	0.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00003087001	SubName- Full=Chromosome undetermined scaffold_139, whole genome shotgun sequence; (510 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00000431001	SubName- Full=Chromosome chr2 scaffold_105, whole genome shotgun sequence; (510 aa)	•	•	•	•	•	•	•	•	0.996
	GSVIVG00003447001	SubName- Full=Chromosome undetermined scaffold_143, whole genome shotgun sequence; (374 aa)	•		•	•		•	•		0.988
	GSVIVG00025526001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (402 aa)	•		•	•		•	•		0.983
	GSVIVG00017740001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (320 aa)	•		•	•			•		0.970
	GSVIVG00038228001	SubName- Full=Chromosome chr14 scaffold_9, whole genome shotgun sequence; (344 aa)	•		•				•		0.964
	GSVIVG00037717001	SubName- Full=Chromosome undetermined scaffold_91, whole genome shotgun sequence; (527 aa)	•		•				•	•	0.904
	GSVIVG00027244001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (424 aa)	•						•		0.899
	GSVIVG00027807001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (471 aa)	•		•				•		0.892
	GSVIVG00021622001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (423 aa)	•						•		0.881
	GSVIVG00032399001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (228 aa)	•						•		0.850

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		303
COG0770		451	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide sy	1e-59
TIGR01143		417	TIGR01143, murF, UDP-N-acetylmuramoyl-tripeptide--	3e-55
PRK11929		958	PRK11929, PRK11929, putative bifunctional UDP-N-ac	2e-44
pfam08245		178	pfam08245, Mur_ligase_M, Mur ligase middle domain	6e-37
PRK14093		479	PRK14093, PRK14093, UDP-N-acetylmuramoylalanyl-D-g	1e-34
PRK11930		822	PRK11930, PRK11930, putative bifunctional UDP-N-ac	3e-27
PRK10773		453	PRK10773, murF, UDP-N-acetylmuramoyl-tripeptide--D	3e-26
TIGR01087		433	TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-gl	4e-20
COG0771		448	COG0771, MurD, UDP-N-acetylmuramoylalanine-D-gluta	6e-18
PRK14106		450	PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	4e-13
PRK02006		498	PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	7e-13
PRK02472		447	PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	7e-13
TIGR01085		464	TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide sy	1e-12
PRK14016		727	PRK14016, PRK14016, cyanophycin synthetase; Provis	3e-11
PRK11929		958	PRK11929, PRK11929, putative bifunctional UDP-N-ac	1e-10
PRK00141		473	PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	1e-10
TIGR02068		864	TIGR02068, cya_phycin_syn, cyanophycin synthetase	5e-10
COG0773		459	COG0773, MurC, UDP-N-acetylmuramate-alanine ligase	2e-09
PRK03803		448	PRK03803, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	9e-09
PRK01390		460	PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	2e-08
PRK03369		488	PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	6e-08
PRK04690		468	PRK04690, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	7e-08
PRK01438		480	PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	7e-08
COG0769		475	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synt	8e-08
PRK01710		458	PRK01710, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	4e-07
PRK03806		438	PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	3e-06
TIGR01082		448	TIGR01082, murC, UDP-N-acetylmuramate--alanine lig	5e-06
PRK04308		445	PRK04308, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	5e-06
PRK04663		438	PRK04663, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	4e-05
TIGR01499		398	TIGR01499, folC, folylpolyglutamate synthase/dihyd	5e-05
PRK00421		461	PRK00421, murC, UDP-N-acetylmuramate--L-alanine li	8e-05
PRK00139		460	PRK00139, murE, UDP-N-acetylmuramoylalanyl-D-gluta	8e-05
PRK01368		454	PRK01368, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	2e-04
PLN02913		510	PLN02913, PLN02913, dihydrofolate synthetase	9e-04
COG0285		427	COG0285, FolC, Folylpolyglutamate synthase [Coenzy	0.001
PRK02705		459	PRK02705, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	0.001

>gnl\|CDD\|223841 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

 Score =  196 bits (501), Expect = 1e-59
 Identities = 89/283 (31%), Positives = 144/283 (50%), Gaps = 19/283 (6%)

Query: 26  IWTINEIAESVNGKILKWGPPGI--ICTDTRILAPNKNQWFFAITGQHFDAHEFISPELY 83
           + T++E+A+ + G ++   P  +  +  D+R         F A+ G+ FD H+FI   L 
Sbjct: 2   LLTLDELADILGGALVGADPVVVSGVSIDSR--KVKPGDLFVALKGERFDGHDFIEQALA 59

Query: 84  GKGCVGVIGNQVCNNWDKGFVQVEGNGNV----NTLNSLVNMACYARNSRFSGVLVGVTG 139
             G   V+         +  +       V    +TL +L  +A   R  +F+  ++ +TG
Sbjct: 60  -AGAAAVL-------VARPVLPPAIPLVVLLVLDTLEALGKLAKAYR-QKFNAKVIAITG 110

Query: 140 SVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGE 199
           S GK+TTK M+A  L + G  V  + GN+NN +G+ L+L+ +    + AVLEMGM+  GE
Sbjct: 111 SNGKTTTKEMLAAILSTKG-KVHATPGNFNNEIGLPLTLLRLPADTEYAVLEMGMNHPGE 169

Query: 200 ILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVAN 259
           I EL+ +ARP+I V+ N+G++HLE  GS E +A AK EI    +   + +LNAD+PL+ N
Sbjct: 170 IAELSEIARPDIAVITNIGEAHLEGFGSREGIAEAKAEILAGLRPEGIAILNADNPLLKN 229

Query: 260 -LTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKER 301
                   + + FG   G D R     +   G    + +E   
Sbjct: 230 WAAKIGNAKVLSFGLNNGGDFRATNIHLDEEGSSFTLDIEGGE 272

Length = 451

>gnl\|CDD\|233291 TIGR01143, murF, UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase	Back alignment and domain information

>gnl\|CDD\|237025 PRK11929, PRK11929, putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D- alanine ligase; Provisional	Back alignment and domain information

>gnl\|CDD\|219763 pfam08245, Mur_ligase_M, Mur ligase middle domain	Back alignment and domain information

>gnl\|CDD\|184501 PRK14093, PRK14093, UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional	Back alignment and domain information

>gnl\|CDD\|237026 PRK11930, PRK11930, putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional	Back alignment and domain information

>gnl\|CDD\|182718 PRK10773, murF, UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed	Back alignment and domain information

>gnl\|CDD\|233266 TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase	Back alignment and domain information

>gnl\|CDD\|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>gnl\|CDD\|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|234995 PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|235041 PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|233265 TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide synthetase	Back alignment and domain information

>gnl\|CDD\|237586 PRK14016, PRK14016, cyanophycin synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|237025 PRK11929, PRK11929, putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D- alanine ligase; Provisional	Back alignment and domain information

>gnl\|CDD\|234662 PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase	Back alignment and domain information

>gnl\|CDD\|223844 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>gnl\|CDD\|235160 PRK03803, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|179571 PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|179872 PRK04690, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|179297 PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>gnl\|CDD\|179323 PRK01710, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|179651 PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|233264 TIGR01082, murC, UDP-N-acetylmuramate--alanine ligase	Back alignment and domain information

>gnl\|CDD\|167786 PRK04308, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|179871 PRK04663, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|233440 TIGR01499, folC, folylpolyglutamate synthase/dihydrofolate synthase	Back alignment and domain information

>gnl\|CDD\|234757 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase; Provisional	Back alignment and domain information

>gnl\|CDD\|234660 PRK00139, murE, UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional	Back alignment and domain information

>gnl\|CDD\|179286 PRK01368, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|178501 PLN02913, PLN02913, dihydrofolate synthetase	Back alignment and domain information

>gnl\|CDD\|223362 COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism]	Back alignment and domain information

>gnl\|CDD\|235059 PRK02705, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		303
PRK14093		479	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminop	100.0
COG0770		451	MurF UDP-N-acetylmuramyl pentapeptide synthase [Ce	100.0
PRK10773		453	murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-a	100.0
TIGR01143		417	murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-a	100.0
PRK11930		822	putative bifunctional UDP-N-acetylmuramoyl-tripept	100.0
PRK00139		460	murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-d	100.0
TIGR01085		464	murE UDP-N-acetylmuramyl-tripeptide synthetase. A	100.0
PRK11929		958	putative bifunctional UDP-N-acetylmuramoylalanyl-D	100.0
PRK11929		958	putative bifunctional UDP-N-acetylmuramoylalanyl-D	100.0
PRK14022		481	UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine l	100.0
COG0769		475	MurE UDP-N-acetylmuramyl tripeptide synthase [Cell	100.0
PF08245		188	Mur_ligase_M: Mur ligase middle domain; InterPro:	99.97
COG0773		459	MurC UDP-N-acetylmuramate-alanine ligase [Cell env	99.96
PRK00421		461	murC UDP-N-acetylmuramate--L-alanine ligase; Provi	99.95
PRK00141		473	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.95
COG0771		448	MurD UDP-N-acetylmuramoylalanine-D-glutamate ligas	99.95
TIGR01081		448	mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl	99.94
PRK01710		458	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.94
PRK03806		438	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.94
TIGR01087		433	murD UDP-N-acetylmuramoylalanine--D-glutamate liga	99.94
PRK01368		454	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.94
PRK02006		498	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.94
TIGR01082		448	murC UDP-N-acetylmuramate--alanine ligase. UDP-N-a	99.94
PRK04308		445	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.94
PRK04663		438	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.94
PRK01390		460	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.93
PRK00683		418	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.93
PRK04690		468	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.93
PRK02472		447	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.93
PRK03369		488	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.93
PRK01438		480	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.92
PRK14106		450	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.92
PRK02705		459	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.92
PRK14573		809	bifunctional D-alanyl-alanine synthetase A/UDP-N-a	99.92
PRK03803		448	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.92
PRK03815		401	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	99.92
TIGR01499		397	folC folylpolyglutamate synthase/dihydrofolate syn	99.91
PRK14016		727	cyanophycin synthetase; Provisional	99.91
TIGR02068		864	cya_phycin_syn cyanophycin synthetase. Cyanophycin	99.91
PRK10846		416	bifunctional folylpolyglutamate synthase/ dihydrof	99.88
PLN02913		510	dihydrofolate synthetase	99.83
PLN02881		530	tetrahydrofolylpolyglutamate synthase	99.78
COG0285		427	FolC Folylpolyglutamate synthase [Coenzyme metabol	99.71
PF01225		83	Mur_ligase: Mur ligase family, catalytic domain Th	99.44
KOG2525		496	consensus Folylpolyglutamate synthase [Coenzyme tr	99.3
COG1703		323	ArgK Putative periplasmic protein kinase ArgK and	93.33
PF04613		72	LpxD: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-a	93.02
TIGR03815		322	CpaE_hom_Actino helicase/secretion neighborhood Cp	91.38
COG1044		338	LpxD UDP-3-O-[3-hydroxymyristoyl]	91.26
PRK06696		223	uridine kinase; Validated	91.19
PRK15453		290	phosphoribulokinase; Provisional	91.18
PRK00652		325	lpxK tetraacyldisaccharide 4'-kinase; Reviewed	90.72
PRK00892		343	lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-ac	90.66
PHA02519		387	plasmid partition protein SopA; Reviewed	90.44
TIGR03172		232	probable selenium-dependent hydroxylase accessory	90.3
PRK13705		388	plasmid-partitioning protein SopA; Provisional	89.85
TIGR03029		274	EpsG chain length determinant protein tyrosine kin	89.74
TIGR03018		207	pepcterm_TyrKin exopolysaccharide/PEPCTERM locus t	89.59
TIGR01007		204	eps_fam capsular exopolysaccharide family. This mo	89.55
PRK13869		405	plasmid-partitioning protein RepA; Provisional	89.55
TIGR01853		324	lipid_A_lpxD UDP-3-O-[3-hydroxymyristoyl] glucosam	89.48
COG0769		475	MurE UDP-N-acetylmuramyl tripeptide synthase [Cell	87.84
PF00485		194	PRK: Phosphoribulokinase / Uridine kinase family;	87.79
PRK05439		311	pantothenate kinase; Provisional	87.78
COG1763		161	MobB Molybdopterin-guanine dinucleotide biosynthes	87.49
COG2403		449	Predicted GTPase [General function prediction only	87.42
cd02042		104	ParA ParA and ParB of Caulobacter crescentus belon	87.15
PF03205		140	MobB: Molybdopterin guanine dinucleotide synthesis	87.06
PRK10416		318	signal recognition particle-docking protein FtsY;	86.27
PRK07667		193	uridine kinase; Provisional	86.16
cd01983		99	Fer4_NifH The Fer4_NifH superfamily contains a var	86.03
COG1936		180	Predicted nucleotide kinase (related to CMP and AM	85.92
PRK14489		366	putative bifunctional molybdopterin-guanine dinucl	85.46
TIGR03453		387	partition_RepA plasmid partitioning protein RepA.	84.97
PF02606		326	LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPr	84.53
cd02040		270	NifH NifH gene encodes component II (iron protein)	84.42
COG0132		223	BioD Dethiobiotin synthetase [Coenzyme metabolism]	84.32
TIGR00554		290	panK_bact pantothenate kinase, bacterial type. Sho	84.23
COG0237		201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	84.16
PRK13232		273	nifH nitrogenase reductase; Reviewed	83.69
PRK09435		332	membrane ATPase/protein kinase; Provisional	83.62
cd02029		277	PRK_like Phosphoribulokinase-like (PRK-like) is a	83.44
PRK14494		229	putative molybdopterin-guanine dinucleotide biosyn	82.72
PRK12723		388	flagellar biosynthesis regulator FlhF; Provisional	81.74
PRK14974		336	cell division protein FtsY; Provisional	81.2
PF03308		266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	80.93
TIGR03371		246	cellulose_yhjQ cellulose synthase operon protein Y	80.88
KOG0780		483	consensus Signal recognition particle, subunit Srp	80.37

>PRK14093 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional	Back alignment and domain information

Probab=100.00  E-value=2.3e-53  Score=418.44  Aligned_cols=264  Identities=32%  Similarity=0.454  Sum_probs=230.4

Q ss_pred             CccCHHHHHHHcCCeeccc--CCcceEEeccCccccCCCcEEEEecCCcCChhhcHHHhHhcCCceEEEEcccCCC---C
Q 022062           25 PIWTINEIAESVNGKILKW--GPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNN---W   99 (303)
Q Consensus        25 ~~~~l~~l~~~~~~~~~~~--~~i~~i~~dsr~v~~~~g~lFval~G~~~dg~~~i~~A~~~~GA~~vv~~~~~~~---~   99 (303)
                      ++|++.+|++.++|.+.+.  ..+++|++|||.++|  |+||||++|+++|||+|+++|++ +||+++|++++...   .
T Consensus         5 ~~~~~~~i~~~~~~~~~~~~~~~i~~i~~DSR~v~~--g~lFval~G~~~DGh~fi~~A~~-~GA~~~v~~~~~~~~~~~   81 (479)
T PRK14093          5 PLWTSDAMAEAMGATRSGALPRDVTGISIDSRTLAP--GDAYFAIKGDVHDGHAFVAAALK-AGAALAVVERAQRDKFAA   81 (479)
T ss_pred             CccCHHHHHHHhCCeecCCCCCceeEEEeecCCCCC--CCEEEEeccCcCChHHHHHHHHH-cCCcEEEEecccccccCC
Confidence            4689999999999987632  349999999999999  99999999999999999999999 99999999864211   2


Q ss_pred             CceEEEEcCCCcccHHHHHHHHHHHhhcCCCCCcEEEEeCCCCCcHHHHHHHHHHHhCCCCeEEecCCCcCccchhhHHh
Q 022062          100 DKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLI  179 (303)
Q Consensus       100 ~~~~i~V~~~~~~d~~~al~~la~~~~~p~~~~~vIgVTGTnGKTTt~~ml~~iL~~~g~~~~~t~g~~n~~~g~p~~l~  179 (303)
                      ++|+++|+     |++++|+.||++|+. ..++++||||||||||||++||+++|+..|. +..+.|++|+.+|.|+++.
T Consensus        82 ~~~~i~V~-----d~~~al~~la~~~~~-~~~~~vIgVTGS~GKTTT~~ml~~iL~~~g~-~~~~~g~~n~~iG~p~~l~  154 (479)
T PRK14093         82 DAPLLVVD-----DVLAALRDLGRAARA-RLEAKVIAVTGSVGKTSTKEALRGVLGAQGE-THASVASFNNHWGVPLSLA  154 (479)
T ss_pred             CCCEEEEC-----CHHHHHHHHHHHHHH-hcCCCEEEEcCCCCccHHHHHHHHHHHhcCC-ccCCCccCCCccchhHHHH
Confidence            57999999     999999999995554 4678999999999999999999999977665 4568999999999999999


Q ss_pred             cccCCCCEEEEEecCCChhhHHHhhcccCccEEEEcCCChhhhhccCCHHHHHHHHHHHhhcCCCCCEEEEeCCChhhhh
Q 022062          180 GIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVAN  259 (303)
Q Consensus       180 ~~~~~~~~~V~E~~~s~~~~~~~l~~~~~p~iaViTNi~~dHld~~gt~e~~~~aK~~l~~~~~~~g~~Vin~Dd~~~~~  259 (303)
                      ++..+++++|||+|+++.++++++...++|+++|||||++||+|+|+|+|+|+++|.+||+.+++++.+|+|.|||+...
T Consensus       155 ~~~~~~~~~V~E~g~s~~~e~~~~~~~~~PdiaViTNI~~DHLd~~gt~e~~~~aK~~l~~~~~~~g~~VlN~Dd~~~~~  234 (479)
T PRK14093        155 RCPADARFAVFEIGMNHAGEIEPLVKMVRPHVAIITTVEPVHLEFFSGIEAIADAKAEIFTGLEPGGAAVLNRDNPQFDR  234 (479)
T ss_pred             cCCCCCcEEEEEeCCCCCchHHHHhcccCCCEEEEcCCCHHHHhhcCCHHHHHHHHHHHHccCCCCCEEEEeCCcHHHHH
Confidence            88888999999999999999888888899999999999999999999999999999999998888899999999999887


Q ss_pred             hcC--CC--CCeEEEEecCCCceEEEEEEEEeeCCCeEEEEEEEC
Q 022062          260 LTV--PR--GVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKE  300 (303)
Q Consensus       260 ~~~--~~--~~~vit~g~~~~ad~~~~~i~~~~~~~g~~f~l~~~  300 (303)
                      +..  ..  ..++++||.+..+++++.+++  ....++.|.+..+
T Consensus       235 l~~~~~~~~~~~vi~~g~~~~~~~~~~~~~--~~~~~~~~~~~~~  277 (479)
T PRK14093        235 LAASARAAGIARIVSFGADEKADARLLDVA--LHADCSAVHADIL  277 (479)
T ss_pred             HHHHhhhccCCcEEEEeCCCCccEEEEEEE--EcCCceEEEEEEC
Confidence            651  10  126899998766789998888  7777777777643

>COG0770 MurF UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed	Back alignment and domain information

>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase	Back alignment and domain information

>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional	Back alignment and domain information

>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional	Back alignment and domain information

>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetase	Back alignment and domain information

>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional	Back alignment and domain information

>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional	Back alignment and domain information

>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase; Provisional	Back alignment and domain information

>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>PF08245 Mur_ligase_M: Mur ligase middle domain; InterPro: IPR013221 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment	Back alignment and domain information

>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional	Back alignment and domain information

>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>TIGR01081 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase	Back alignment and domain information

>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase	Back alignment and domain information

>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase	Back alignment and domain information

>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK14106 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK14573 bifunctional D-alanyl-alanine synthetase A/UDP-N-acetylmuramate--L-alanine ligase; Provisional	Back alignment and domain information

>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>PRK03815 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>TIGR01499 folC folylpolyglutamate synthase/dihydrofolate synthase	Back alignment and domain information

>PRK14016 cyanophycin synthetase; Provisional	Back alignment and domain information

>TIGR02068 cya_phycin_syn cyanophycin synthetase	Back alignment and domain information

>PRK10846 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional	Back alignment and domain information

>PLN02913 dihydrofolate synthetase	Back alignment and domain information

>PLN02881 tetrahydrofolylpolyglutamate synthase	Back alignment and domain information

>COG0285 FolC Folylpolyglutamate synthase [Coenzyme metabolism]	Back alignment and domain information

>PF01225 Mur_ligase: Mur ligase family, catalytic domain This Prosite entry is a subset of the Pfam family	Back alignment and domain information

>KOG2525 consensus Folylpolyglutamate synthase [Coenzyme transport and metabolism]	Back alignment and domain information

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]	Back alignment and domain information

>PF04613 LpxD: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD ; InterPro: IPR020573 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (2	Back alignment and domain information

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein	Back alignment and domain information

>COG1044 LpxD UDP-3-O-[3-hydroxymyristoyl]	Back alignment and domain information

>PRK06696 uridine kinase; Validated	Back alignment and domain information

>PRK15453 phosphoribulokinase; Provisional	Back alignment and domain information

>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed	Back alignment and domain information

>PRK00892 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional	Back alignment and domain information

>PHA02519 plasmid partition protein SopA; Reviewed	Back alignment and domain information

>TIGR03172 probable selenium-dependent hydroxylase accessory protein YqeC	Back alignment and domain information

>PRK13705 plasmid-partitioning protein SopA; Provisional	Back alignment and domain information

>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG	Back alignment and domain information

>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase	Back alignment and domain information

>TIGR01007 eps_fam capsular exopolysaccharide family	Back alignment and domain information

>PRK13869 plasmid-partitioning protein RepA; Provisional	Back alignment and domain information

>TIGR01853 lipid_A_lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase	Back alignment and domain information

>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2	Back alignment and domain information

>PRK05439 pantothenate kinase; Provisional	Back alignment and domain information

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	Back alignment and domain information

>COG2403 Predicted GTPase [General function prediction only]	Back alignment and domain information

>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation	Back alignment and domain information

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A	Back alignment and domain information

>PRK10416 signal recognition particle-docking protein FtsY; Provisional	Back alignment and domain information

>PRK07667 uridine kinase; Provisional	Back alignment and domain information

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain	Back alignment and domain information

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]	Back alignment and domain information

>PRK14489 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional	Back alignment and domain information

>TIGR03453 partition_RepA plasmid partitioning protein RepA	Back alignment and domain information

>PF02606 LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPro: IPR003758 Tetraacyldisaccharide 4'-kinase phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability []	Back alignment and domain information

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase	Back alignment and domain information

>COG0132 BioD Dethiobiotin synthetase [Coenzyme metabolism]	Back alignment and domain information

>TIGR00554 panK_bact pantothenate kinase, bacterial type	Back alignment and domain information

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]	Back alignment and domain information

>PRK13232 nifH nitrogenase reductase; Reviewed	Back alignment and domain information

>PRK09435 membrane ATPase/protein kinase; Provisional	Back alignment and domain information

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes	Back alignment and domain information

>PRK14494 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional	Back alignment and domain information

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PRK14974 cell division protein FtsY; Provisional	Back alignment and domain information

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components	Back alignment and domain information

>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ	Back alignment and domain information

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		303
1gg4_A		452	Crystal Structure Of Escherichia Coli Udpmurnac-Tri		3e-14
2am1_A		454	Sp Protein Ligand 1 Length = 454		7e-08

>pdb|1GG4|A Chain A, Crystal Structure Of Escherichia Coli Udpmurnac-Tripeptide D-Alanyl-D-Alanine-Adding Enzyme (Murf) At 2.3 Angstrom Resolution Length = 452

Back alignment and structure

Iteration: 1

Score = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 67/226 (29%), Positives = 99/226 (43%), Gaps = 14/226 (6%) Query: 49 ICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEG 108 + TDTR L P F A+ G+ FDAH+F G ++ + + + V+ Sbjct: 27 VTTDTRKLTPGC--LFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLIVK--- 81 Query: 109 NGNVNTLNSLVNMACYARNSRFXXXXXXXXXXXXXXXXXXMIALALESLGVNVFQSYGNW 168 +T + +A + R + A L G N + GN Sbjct: 82 ----DTRLAFGELAAWVRQ-QVPARVVALTGSSGKTSVKEXTAAILSQCG-NTLYTAGNL 135 Query: 169 NNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSL 228 NN +GV +L+ + D AV+E+G + +GEI + RPE +V N+ +HLE GSL Sbjct: 136 NNDIGVPXTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSL 195 Query: 229 EDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWR 274 VA+AKGEIF + + NAD+ N G RKV WR Sbjct: 196 AGVAKAKGEIFSGLPENGIAIXNADNNDWLNWQSVIGSRKV---WR 238

PyMOL of 1gg4

>pdb|2AM1|A Chain A, Sp Protein Ligand 1 Length = 454

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		303
1gg4_A		452	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diamino	4e-74
2am1_A		454	SP protein, UDP-N-acetylmuramoylalanine-D-glutamyl	6e-72
3lk7_A		451	UDP-N-acetylmuramoylalanine--D-glutamate ligase; a	6e-20
2x5o_A		439	UDP-N-acetylmuramoylalanine--D-glutamate ligase; A	4e-17
1e8c_A		498	UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diami	2e-09
2f00_A		491	UDP-N-acetylmuramate--L-alanine ligase; amide bond	2e-09
1p3d_A		475	UDP-N-acetylmuramate--alanine ligase; alpha/beta p	4e-09
2wtz_A		535	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-di	1e-08
1j6u_A		469	UDP-N-acetylmuramate-alanine ligase MURC; structur	3e-06

>1gg4_A UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase...; alpha/beta sheet; 2.30A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1 c.72.2.1 Length = 452	Back alignment and structure

 Score =  233 bits (597), Expect = 4e-74
 Identities = 83/276 (30%), Positives = 133/276 (48%), Gaps = 20/276 (7%)

Query: 27  WTINEIAESVNGKILKWGPPGII---CTDTRILAPNKNQWFFAITGQHFDAHEFISPELY 83
            T++++ + +NG++   G    +    TDTR L P     F A+ G+ FDAH+F   +  
Sbjct: 4   VTLSQLTDILNGELQ--GADITLDAVTTDTRKLTPG--CLFVALKGERFDAHDFA-DQAK 58

Query: 84  GKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGK 143
             G   ++ ++  +  D   + V+     +T  +   +A + R  +    +V +TGS GK
Sbjct: 59  AGGAGALLVSRPLDI-DLPQLIVK-----DTRLAFGELAAWVR-QQVPARVVALTGSSGK 111

Query: 144 STTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILEL 203
           ++ K M A  L   G N   + GN NN +GV ++L+ +    D AV+E+G + +GEI   
Sbjct: 112 TSVKEMTAAILSQCG-NTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWT 170

Query: 204 ARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVP 263
             + RPE  +V N+  +HLE  GSL  VA+AKGEIF       + ++NAD+    N    
Sbjct: 171 VSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSV 230

Query: 264 RGVRKV-FFGWR-RGCDVRLVAAQVANGGLGVQVVL 297
            G RKV  F       D    A  +     G +  L
Sbjct: 231 IGSRKVWRFSPNAANSDFT--ATNIHVTSHGTEFTL 264

PyMOL of 1gg4

>2am1_A SP protein, UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-A alanine ligase, MURF protein; HET: 1LG; 2.50A {Streptococcus pneumoniae} PDB: 2am2_A* Length = 454	Back alignment and structure

>3lk7_A UDP-N-acetylmuramoylalanine--D-glutamate ligase; agalacitae, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: MSE; 1.50A {Streptococcus agalactiae} Length = 451	Back alignment and structure

>2x5o_A UDP-N-acetylmuramoylalanine--D-glutamate ligase; ATP-binding, cell cycle, cell division, cell shape, cell WAL biogenesis/degradation; HET: KCX VSV; 1.46A {Escherichia coli} PDB: 2wjp_A* 2xpc_A* 2y1o_A* 2jff_A* 2jfh_A* 2uuo_A* 2uup_A* 2vtd_A* 2vte_A* 2jfg_A* 2y66_A* 2y67_A* 2y68_A* 4uag_A* 1e0d_A* 1uag_A* 1eeh_A* 3uag_A* 2uag_A* Length = 439	Back alignment and structure

>1e8c_A UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase; peptidoglycan biosynthesis; HET: KCX UAG API; 2.00A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1 c.72.2.1 Length = 498	Back alignment and structure

>2f00_A UDP-N-acetylmuramate--L-alanine ligase; amide bond ligase, ATPase, bacterial cell WALL; 2.50A {Escherichia coli} Length = 491	Back alignment and structure

>1p3d_A UDP-N-acetylmuramate--alanine ligase; alpha/beta protein; HET: UMA ANP; 1.70A {Haemophilus influenzae} SCOP: c.5.1.1 c.59.1.1 c.72.2.1 PDB: 1gqq_A* 1p31_A* 1gqy_A* Length = 475	Back alignment and structure

>2wtz_A UDP-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-diaminopimelate ligase; nucleotide-binding, peptidoglycan synthesis, MURE, C shape; HET: KCX UAG; 3.00A {Mycobacterium tuberculosis} PDB: 2xja_A* Length = 535	Back alignment and structure

>1j6u_A UDP-N-acetylmuramate-alanine ligase MURC; structural genomics, TM0231, JCSG, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: c.5.1.1 c.59.1.1 c.72.2.1 Length = 469	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		303
1gg4_A		452	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diamino	100.0
2am1_A		454	SP protein, UDP-N-acetylmuramoylalanine-D-glutamyl	100.0
2wtz_A		535	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-di	100.0
1e8c_A		498	UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diami	100.0
3eag_A		326	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-ME	100.0
2f00_A		491	UDP-N-acetylmuramate--L-alanine ligase; amide bond	99.97
1p3d_A		475	UDP-N-acetylmuramate--alanine ligase; alpha/beta p	99.97
3hn7_A		524	UDP-N-acetylmuramate-L-alanine ligase; ATP-binding	99.97
4hv4_A		494	UDP-N-acetylmuramate--L-alanine ligase; MURC, yers	99.97
2x5o_A		439	UDP-N-acetylmuramoylalanine--D-glutamate ligase; A	99.96
3lk7_A		451	UDP-N-acetylmuramoylalanine--D-glutamate ligase; a	99.95
2vos_A		487	Folylpolyglutamate synthase protein FOLC; ligase,	99.95
1jbw_A		428	Folylpolyglutamate synthase; FPGS folate AMPPCP te	99.95
3nrs_A		437	Dihydrofolate:folylpolyglutamate synthetase; struc	99.95
1o5z_A		442	Folylpolyglutamate synthase/dihydrofolate synthas;	99.94
1j6u_A		469	UDP-N-acetylmuramate-alanine ligase MURC; structur	99.94
1w78_A		422	FOLC bifunctional protein; DHFS, dihydrofolate syn	99.93
3eh0_A		341	UDP-3-O-[3-hydroxymyristoyl] glucosamine N- acyltr	91.99
2g0t_A		350	Conserved hypothetical protein; structural genomic	91.54
1rz3_A		201	Hypothetical protein rbstp0775; MCSG, structural g	91.39
3bfv_A		271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	91.36
4dzz_A		206	Plasmid partitioning protein PARF; deviant walker	90.63
4e79_A		357	UDP-3-O-acylglucosamine N-acyltransferase; lipopol	90.56
3of5_A		228	Dethiobiotin synthetase; structural genomics, cent	90.37
3cio_A		299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	90.31
1xjc_A		169	MOBB protein homolog; structural genomics, midwest	89.75
3pmo_A		372	UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltr;	89.7
3la6_A		286	Tyrosine-protein kinase WZC; P-loop protein, nucle	89.44
3fwy_A		314	Light-independent protochlorophyllide reductase I	89.35
1byi_A		224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	88.5
3ea0_A		245	ATPase, para family; alpha-beta-alpha sandwich, st	87.46
1pjq_A		457	CYSG, siroheme synthase; rossman fold, nucleotide	86.88
1wcv_1		257	SOJ, segregation protein; ATPase, bacterial, chrom	85.03
3fgn_A		251	Dethiobiotin synthetase; biotin biosynthesis, BIOD	84.6
1g3q_A		237	MIND ATPase, cell division inhibitor; alpha-beta-a	84.49
3c8u_A		208	Fructokinase; YP_612366.1, putative fructose trans	84.11
2xj4_A		286	MIPZ; replication, cell division, ATPase, WACA; 1.	82.98
2oze_A		298	ORF delta'; para, walker type atpases, DNA segrega	82.59
1a7j_A		290	Phosphoribulokinase; transferase, calvin cycle; 2.	82.49
3qxc_A		242	Dethiobiotin synthetase; DTBS, structural genomics	81.88
1zu4_A		320	FTSY; GTPase, signal recognition particle, SRP, re	81.58
3k9g_A		267	PF-32 protein; ssgcid, SBRI, decode biostructures,	81.09
2z0h_A		197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	81.07
1hyq_A		263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	80.71
2ph1_A		262	Nucleotide-binding protein; alpha-beta protein, st	80.51
3end_A		307	Light-independent protochlorophyllide reductase ir	80.49
3ez2_A		398	Plasmid partition protein A; type IA, DNA binding,	80.44
3q9l_A		260	Septum site-determining protein MIND; ATPase, bact	80.23

>1gg4_A UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase...; alpha/beta sheet; 2.30A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1 c.72.2.1	Back alignment and structure

Probab=100.00  E-value=8.6e-53  Score=410.14  Aligned_cols=260  Identities=30%  Similarity=0.442  Sum_probs=223.4

Q ss_pred             cCHHHHHHHcCCeeccc-CCcceEEeccCccccCCCcEEEEecCCcCChhhcHHHhHhcCCceEEEEcccCCCCCceEEE
Q 022062           27 WTINEIAESVNGKILKW-GPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQ  105 (303)
Q Consensus        27 ~~l~~l~~~~~~~~~~~-~~i~~i~~dsr~v~~~~g~lFval~G~~~dg~~~i~~A~~~~GA~~vv~~~~~~~~~~~~i~  105 (303)
                      |++++|++.+++++..+ ..|+++++|||.++|  |++|+|++|.++|||+|+++|++ +||.+||++++.+ +++|+|.
T Consensus         4 ~~l~~i~~~~~~~~~~~~~~i~~i~~Dsr~v~~--g~lf~al~G~~~dgh~f~~~a~~-~Ga~~vv~~~~~~-~~~p~i~   79 (452)
T 1gg4_A            4 VTLSQLTDILNGELQGADITLDAVTTDTRKLTP--GCLFVALKGERFDAHDFADQAKA-GGAGALLVSRPLD-IDLPQLI   79 (452)
T ss_dssp             EEHHHHHHHTTEEEESCCCEESCEESCGGGCCT--TCEEECCBCSSCBTTTTHHHHHH-TTCCEEEESSCCS-CSSCEEE
T ss_pred             CcHHHHHHHhCCEEeCCCceEEEEEEeCCCcCC--CcEEEEeCCCCCCHHHHHHHHHH-cCCEEEEECCCcC-CCCCEEE
Confidence            68999999999987642 248999999999999  99999999999999999999999 9999999998654 2689999


Q ss_pred             EcCCCcccHHHHHHHHHHHhhcCCCCCcEEEEeCCCCCcHHHHHHHHHHHhCCCCeEEecCCCcCccchhhHHhcccCCC
Q 022062          106 VEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAV  185 (303)
Q Consensus       106 V~~~~~~d~~~al~~la~~~~~p~~~~~vIgVTGTnGKTTt~~ml~~iL~~~g~~~~~t~g~~n~~~g~p~~l~~~~~~~  185 (303)
                      |+     |++++|++|+..++. ..++++||||||||||||++||+++|++.| ++.++.|++|+.+|.|++++.++.++
T Consensus        80 v~-----~~~~~l~~la~~~~~-~~~~~vI~VTGTnGKTTT~~~l~~iL~~~g-~~~~t~g~~n~~ig~p~t~~~~~~~~  152 (452)
T 1gg4_A           80 VK-----DTRLAFGELAAWVRQ-QVPARVVALTGSSGKTSVKEMTAAILSQCG-NTLYTAGNLNNDIGVPMTLLRLTPEY  152 (452)
T ss_dssp             ES-----CHHHHHHHHHHHHHH-HSCCEEEEEECSSCHHHHHHHHHHHHTTTS-CEEECCTTCCSTTHHHHHHTTCCTTC
T ss_pred             EC-----CHHHHHHHHHHHHhc-CCCCCEEEEeCCCCcHHHHHHHHHHHHhcC-CEeeccccccCCcchhHHHHcCCCCC
Confidence            99     999999999995543 245889999999999999999999997777 67789999999999999998888889


Q ss_pred             CEEEEEecCCChhhHHHhhcccCccEEEEcCCChhhhhccCCHHHHHHHHHHHhhcCCCCCEEEEeCCChhhhhhc--CC
Q 022062          186 DIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLT--VP  263 (303)
Q Consensus       186 ~~~V~E~~~s~~~~~~~l~~~~~p~iaViTNi~~dHld~~gt~e~~~~aK~~l~~~~~~~g~~Vin~Dd~~~~~~~--~~  263 (303)
                      +++|||+|+++.+++.++.+.++|+++|||||++||+|+|||+|+|+++|++||+.+++++.+|+|.|||+...+.  ..
T Consensus       153 d~~VlE~g~~~~~~~~~~~~~~~p~vaviTNI~~DHld~~gt~e~~~~aK~~i~~~~~~~~~~V~n~dd~~~~~~~~~~~  232 (452)
T 1gg4_A          153 DYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIG  232 (452)
T ss_dssp             SEEEEECCCSSSSHHHHHHHHHCCSEEEECCCC--------CHHHHHHHHHGGGGGCCTTCEEEEETTBCCHHHHHHHHT
T ss_pred             cEEEEEeCCCCcchHHHHhCccCCCEEEECCCChHHhhhcCCHHHHHHHHHHHHhhcccCCEEEEeCCcHHHHHHHHhhc
Confidence            9999999999999999988878999999999999999999999999999999999988889999999999887763  22


Q ss_pred             CCCeEEEEecCC-CceEEEEEEEEeeCCCeEEEEEEEC
Q 022062          264 RGVRKVFFGWRR-GCDVRLVAAQVANGGLGVQVVLEKE  300 (303)
Q Consensus       264 ~~~~vit~g~~~-~ad~~~~~i~~~~~~~g~~f~l~~~  300 (303)
                       ..++++||.+. ++|+++.+++  ....+..|.+..+
T Consensus       233 -~~~~~~~g~~~~~~d~~~~~~~--~~~~g~~~~~~~~  267 (452)
T 1gg4_A          233 -SRKVWRFSPNAANSDFTATNIH--VTSHGTEFTLQTP  267 (452)
T ss_dssp             -TSEEEEECSSCTTCSBEEEEEE--ECSSSEEEEEEET
T ss_pred             -CCCEEEEeCCCCCCcEEEEEEE--EcCCceEEEEEEC
Confidence             26899999865 6789999888  7777888887654

PyMOL of 1gg4

>2am1_A SP protein, UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-A alanine ligase, MURF protein; HET: 1LG; 2.50A {Streptococcus pneumoniae} PDB: 2am2_A*	Back alignment and structure

>2wtz_A UDP-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-diaminopimelate ligase; nucleotide-binding, peptidoglycan synthesis, MURE, C shape; HET: KCX UAG; 3.00A {Mycobacterium tuberculosis} PDB: 2xja_A*	Back alignment and structure

>1e8c_A UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate ligase; peptidoglycan biosynthesis; HET: KCX UAG API; 2.00A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1 c.72.2.1	Back alignment and structure

>3eag_A UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-ME diaminopimelate ligase; UDP-N-acetylmuramate:L-alanyl-G glutamyl-MESO-diaminopimelate ligase; 2.55A {Neisseria meningitidis MC58}	Back alignment and structure

>2f00_A UDP-N-acetylmuramate--L-alanine ligase; amide bond ligase, ATPase, bacterial cell WALL; 2.50A {Escherichia coli}	Back alignment and structure

>1p3d_A UDP-N-acetylmuramate--alanine ligase; alpha/beta protein; HET: UMA ANP; 1.70A {Haemophilus influenzae} SCOP: c.5.1.1 c.59.1.1 c.72.2.1 PDB: 1gqq_A* 1p31_A* 1gqy_A*	Back alignment and structure

>3hn7_A UDP-N-acetylmuramate-L-alanine ligase; ATP-binding, nucleotide-binding, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.65A {Psychrobacter arcticus 273-4}	Back alignment and structure

>4hv4_A UDP-N-acetylmuramate--L-alanine ligase; MURC, yersinia pestis peptidoglycan synthesis; HET: AMP; 2.25A {Yersinia pestis} PDB: 2f00_A	Back alignment and structure

>2x5o_A UDP-N-acetylmuramoylalanine--D-glutamate ligase; ATP-binding, cell cycle, cell division, cell shape, cell WAL biogenesis/degradation; HET: KCX VSV; 1.46A {Escherichia coli} PDB: 2wjp_A* 2xpc_A* 2y1o_A* 2jff_A* 2jfh_A* 2uuo_A* 2uup_A* 2vtd_A* 2vte_A* 2jfg_A* 2y66_A* 2y67_A* 2y68_A* 4uag_A* 1e0d_A* 1uag_A* 1eeh_A* 3uag_A* 2uag_A*	Back alignment and structure

>3lk7_A UDP-N-acetylmuramoylalanine--D-glutamate ligase; agalacitae, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: MSE; 1.50A {Streptococcus agalactiae}	Back alignment and structure

>2vos_A Folylpolyglutamate synthase protein FOLC; ligase, peptidoglycan synthesis, cell division; HET: ADP; 2.0A {Mycobacterium tuberculosis} PDB: 2vor_A*	Back alignment and structure

>1jbw_A Folylpolyglutamate synthase; FPGS folate AMPPCP ternary complex, ligase; HET: KCX ACQ TMF; 1.85A {Lactobacillus casei} SCOP: c.59.1.2 c.72.2.2 PDB: 1fgs_A* 1jbv_A* 2gca_A 2gc5_A* 2gc6_A* 2gcb_A	Back alignment and structure

>3nrs_A Dihydrofolate:folylpolyglutamate synthetase; structural genomics, center for structural genomics of infec diseases, csgid; HET: TLA MES; 1.80A {Yersinia pestis} PDB: 3n2a_A* 3pyz_A* 3qcz_A*	Back alignment and structure

>1o5z_A Folylpolyglutamate synthase/dihydrofolate synthas; TM0166, structural genomics, JC protein structure initiative; 2.10A {Thermotoga maritima} SCOP: c.59.1.2 c.72.2.2	Back alignment and structure

>1j6u_A UDP-N-acetylmuramate-alanine ligase MURC; structural genomics, TM0231, JCSG, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: c.5.1.1 c.59.1.1 c.72.2.1	Back alignment and structure

>1w78_A FOLC bifunctional protein; DHFS, dihydrofolate synthase, synthase, ATP-binding, folate biosynthesis, ligase, multifunctional enzyme; HET: KCX PD8 ADP; 1.82A {Escherichia coli} PDB: 1w7k_A*	Back alignment and structure

>3eh0_A UDP-3-O-[3-hydroxymyristoyl] glucosamine N- acyltransferase; LPXD, LEFT-handed parallel beta helix, acyl carrier protein, antibiotic resistance; 2.60A {Escherichia coli}	Back alignment and structure

>2g0t_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.67A {Thermotoga maritima} SCOP: c.37.1.10	Back alignment and structure

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6	Back alignment and structure

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*	Back alignment and structure

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*	Back alignment and structure

>4e79_A UDP-3-O-acylglucosamine N-acyltransferase; lipopolysaccaride synthesis; 2.66A {Acinetobacter baumannii} PDB: 4e75_A	Back alignment and structure

>3of5_A Dethiobiotin synthetase; structural genomics, center for structural genomics of infec diseases, csgid, ligase; 1.52A {Francisella tularensis subsp}	Back alignment and structure

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}	Back alignment and structure

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10	Back alignment and structure

>3pmo_A UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltr; lipid A biosynthesis pathway, transferase; 1.30A {Pseudomonas aeruginosa}	Back alignment and structure

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}	Back alignment and structure

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}	Back alignment and structure

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A	Back alignment and structure

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}	Back alignment and structure

>1pjq_A CYSG, siroheme synthase; rossman fold, nucleotide binding motif, SAM, NAD, phosphoserine, transferase/oxidoreductase/lyase complex; HET: SEP PGE SAH; 2.21A {Salmonella typhimurium} SCOP: c.2.1.11 c.90.1.1 e.37.1.1 PDB: 1pjs_A* 1pjt_A*	Back alignment and structure

>1wcv_1 SOJ, segregation protein; ATPase, bacterial, chromosome segregation; 1.6A {Thermus thermophilus} PDB: 2bej_A* 2bek_A*	Back alignment and structure

>3fgn_A Dethiobiotin synthetase; biotin biosynthesis, BIOD, ATP-BIND ligase, magnesium, nucleotide-binding; 1.85A {Mycobacterium tuberculosis} PDB: 3fmf_A* 3fmi_A* 3fpa_A*	Back alignment and structure

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*	Back alignment and structure

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}	Back alignment and structure

>2xj4_A MIPZ; replication, cell division, ATPase, WACA; 1.60A {Caulobacter vibrioides} PDB: 2xj9_A* 2xit_A	Back alignment and structure

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}	Back alignment and structure

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6	Back alignment and structure

>3qxc_A Dethiobiotin synthetase; DTBS, structural genomics, ATP BIND biology, protein structure initiative, midwest center for S genomics, MCSG; HET: ATP; 1.34A {Helicobacter pylori} PDB: 3mle_A* 3qxh_A* 3qxj_A* 3qxs_A* 3qxx_A* 3qy0_A* 2qmo_A	Back alignment and structure

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A	Back alignment and structure

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A	Back alignment and structure

>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell division, cell cycle; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.10	Back alignment and structure

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*	Back alignment and structure

>3ez2_A Plasmid partition protein A; type IA, DNA binding, winged-HTH, DNA bindin; HET: ADP EPE; 2.05A {Escherichia coli} PDB: 3ez6_A* 3ez7_A	Back alignment and structure

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		303
d1p3da3		215	c.72.2.1 (A:107-321) UDP-N-acetylmuramate-alanine	5e-17
d1gg4a4		214	c.72.2.1 (A:99-312) UDP-murNac-tripeptide D-alanyl	1e-11
d1gg4a3		98	c.98.1.1 (A:1-98) UDP-murNac-tripeptide D-alanyl-D	3e-06
d1e8ca3		234	c.72.2.1 (A:104-337) UDP-N-acetylmuramyl tripeptid	2e-05
d2jfga3		204	c.72.2.1 (A:94-297) UDP-N-acetylmuramoyl-L-alanine	4e-05
d1j6ua3		207	c.72.2.1 (A:89-295) UDP-N-acetylmuramate-alanine l	1e-04
d1e8ca1		101	c.98.1.1 (A:3-103) UDP-N-acetylmuramyl tripeptide	0.002

>d1p3da3 c.72.2.1 (A:107-321) UDP-N-acetylmuramate-alanine ligase MurC {Haemophilus influenzae [TaxId: 727]} Length = 215	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: MurCDEF
domain: UDP-N-acetylmuramate-alanine ligase MurC
species: Haemophilus influenzae [TaxId: 727]

 Score = 76.0 bits (186), Expect = 5e-17
 Identities = 33/147 (22%), Positives = 55/147 (37%), Gaps = 10/147 (6%)

Query: 135 VGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGM 194
           + V G+ GK+TT +MI++      ++     G      G    L     A    + E   
Sbjct: 15  IAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGKNAHL----GASRYLIAEADE 70

Query: 195 SGKGEILELARMARPEIRVVLNVG-DSHLESLGSLEDVARAKGEIFQESKLGDVCVLNAD 253
           S     L L    +P + VV N+  D      G  E +     +         + V+ AD
Sbjct: 71  S-DASFLHL----QPMVSVVTNMEPDHMDTYEGDFEKMKATYVKFLHNLPFYGLAVMCAD 125

Query: 254 DPLVANLTVPRGVRKVFFGWRRGCDVR 280
           DP++  L    G + + +G+    D R
Sbjct: 126 DPVLMELVPKVGRQVITYGFSEQADYR 152

PyMOL of d1p3da3

>d1gg4a4 c.72.2.1 (A:99-312) UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF {Escherichia coli [TaxId: 562]} Length = 214	Back information, alignment and structure

>d1gg4a3 c.98.1.1 (A:1-98) UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF {Escherichia coli [TaxId: 562]} Length = 98	Back information, alignment and structure

>d1e8ca3 c.72.2.1 (A:104-337) UDP-N-acetylmuramyl tripeptide synthetase MurE {Escherichia coli [TaxId: 562]} Length = 234	Back information, alignment and structure

>d2jfga3 c.72.2.1 (A:94-297) UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD {Escherichia coli [TaxId: 562]} Length = 204	Back information, alignment and structure

>d1j6ua3 c.72.2.1 (A:89-295) UDP-N-acetylmuramate-alanine ligase MurC {Thermotoga maritima [TaxId: 2336]} Length = 207	Back information, alignment and structure

>d1e8ca1 c.98.1.1 (A:3-103) UDP-N-acetylmuramyl tripeptide synthetase MurE {Escherichia coli [TaxId: 562]} Length = 101	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		303
d1gg4a4		214	UDP-murNac-tripeptide D-alanyl-D-alanine-adding en	100.0
d1p3da3		215	UDP-N-acetylmuramate-alanine ligase MurC {Haemophi	99.97
d1e8ca3		234	UDP-N-acetylmuramyl tripeptide synthetase MurE {Es	99.97
d1j6ua3		207	UDP-N-acetylmuramate-alanine ligase MurC {Thermoto	99.93
d2jfga3		204	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	99.93
d1o5za2		296	Folylpolyglutamate synthetase {Thermotoga maritima	99.9
d2gc6a2		296	Folylpolyglutamate synthetase {Lactobacillus casei	99.89
d1gg4a3		98	UDP-murNac-tripeptide D-alanyl-D-alanine-adding en	99.87
d1e8ca1		101	UDP-N-acetylmuramyl tripeptide synthetase MurE {Es	99.77
d1byia_		224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.79
d1a7ja_		288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	92.99
d2p67a1		327	LAO/AO transport system kinase ArgK {Escherichia c	92.75
d1xjca_		165	Molybdopterin-guanine dinucleotide biosynthesis pr	91.9
d1nksa_		194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	91.61
d1rz3a_		198	Hypothetical protein rbstp0775 {Bacillus stearothe	91.08
d1np6a_		170	Molybdopterin-guanine dinucleotide biosynthesis pr	90.4
d2afhe1		289	Nitrogenase iron protein {Azotobacter vinelandii [	90.29
d2qm8a1		323	Metallochaperone MeaB {Methylobacterium extorquens	90.01
d1sq5a_		308	Pantothenate kinase PanK {Escherichia coli [TaxId:	89.13
d1hyqa_		232	Cell division regulator MinD {Archaeon Archaeoglob	88.84
d1ls1a2		207	GTPase domain of the signal sequence recognition p	87.63
d1khta_		190	Adenylate kinase {Archaeon Methanococcus voltae [T	86.35
d2qy9a2		211	GTPase domain of the signal recognition particle r	86.32
d1cp2a_		269	Nitrogenase iron protein {Clostridium pasteurianum	84.67
d1g3qa_		237	Cell division regulator MinD {Archaeon Pyrococcus	82.91
d1vhta_		208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	82.79
d1deka_		241	Deoxynucleoside monophosphate kinase {Bacteriophag	81.84
d1uj2a_		213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	80.91

>d1gg4a4 c.72.2.1 (A:99-312) UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribokinase-like
superfamily: MurD-like peptide ligases, catalytic domain
family: MurCDEF
domain: UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.9e-33  Score=241.54  Aligned_cols=166  Identities=33%  Similarity=0.460  Sum_probs=141.0

Q ss_pred             cEEEEeCCCCCcHHHHHHHHHHHhCCCCeEEecCCCcCccchhhHHhcccCCCCEEEEEecCCChhhHHHhhcccCccEE
Q 022062          133 VLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIR  212 (303)
Q Consensus       133 ~vIgVTGTnGKTTt~~ml~~iL~~~g~~~~~t~g~~n~~~g~p~~l~~~~~~~~~~V~E~~~s~~~~~~~l~~~~~p~ia  212 (303)
                      ++||||||||||||++||+++|++.|.. .++.|+.|+.+|.+..++....+.++.++|++++..+....+...+.|+++
T Consensus         3 kvI~VTGTnGKTTt~~mi~~iL~~~g~~-~~~~g~~n~~~g~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~p~~~   81 (214)
T d1gg4a4           3 RVVALTGSSGKTSVKEMTAAILSQCGNT-LYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAA   81 (214)
T ss_dssp             EEEEEECSSCHHHHHHHHHHHHTTTSCE-EECCTTCCSTTHHHHHHTTCCTTCSEEEEECCCSSSSHHHHHHHHHCCSEE
T ss_pred             CEEEEeCCCcHHHHHHHHHHHHHhCCCC-EEEeCcccCccccchhhhhcccccccchhhhhhhhcccccccccccCchhe
Confidence            6999999999999999999999777754 468999999999998888888889999999998888888877777899999


Q ss_pred             EEcCCChhhhhccCCHHHHHHHHHHHhhcCCCCCEEEEeCCChhhhhhc-CCCCCeEEEEecCC-CceEEEEEEEEeeCC
Q 022062          213 VVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLT-VPRGVRKVFFGWRR-GCDVRLVAAQVANGG  290 (303)
Q Consensus       213 ViTNi~~dHld~~gt~e~~~~aK~~l~~~~~~~g~~Vin~Dd~~~~~~~-~~~~~~vit~g~~~-~ad~~~~~i~~~~~~  290 (303)
                      |||||++||+|+|+++|+|+++|.++|+.+++.|.+|+|.||+....+. .....++++||.+. .+|+++.++.  ...
T Consensus        82 viTNi~~dHld~~~~~~~~~~~k~~~~~~~~~~g~~v~n~dd~~~~~~~~~~~~~~~~~~~~~~~~ad~~~~~~~--~~~  159 (214)
T d1gg4a4          82 LVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIH--VTS  159 (214)
T ss_dssp             EECCCC--------CHHHHHHHHHGGGGGCCTTCEEEEETTBCCHHHHHHHHTTSEEEEECSSCTTCSBEEEEEE--ECS
T ss_pred             eeehhccccccccccHHHHHhhhhhHhhhhccCCccccccccHHHHHHHHHhcCCceeeeccCCCCcceeeeeEE--EeC
Confidence            9999999999999999999999999999999999999999999988776 21236889999874 6999999999  999


Q ss_pred             CeEEEEEEECC
Q 022062          291 LGVQVVLEKER  301 (303)
Q Consensus       291 ~g~~f~l~~~~  301 (303)
                      +++.|++..++
T Consensus       160 ~~~~~~i~~~~  170 (214)
T d1gg4a4         160 HGTEFTLQTPT  170 (214)
T ss_dssp             SSEEEEEEETT
T ss_pred             CceEEEEEECC
Confidence            99999998765

PyMOL of d1gg4a4

>d1p3da3 c.72.2.1 (A:107-321) UDP-N-acetylmuramate-alanine ligase MurC {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1e8ca3 c.72.2.1 (A:104-337) UDP-N-acetylmuramyl tripeptide synthetase MurE {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1j6ua3 c.72.2.1 (A:89-295) UDP-N-acetylmuramate-alanine ligase MurC {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2jfga3 c.72.2.1 (A:94-297) UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2gc6a2 c.72.2.2 (A:1-296) Folylpolyglutamate synthetase {Lactobacillus casei [TaxId: 1582]}	Back information, alignment and structure

>d1gg4a3 c.98.1.1 (A:1-98) UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1e8ca1 c.98.1.1 (A:3-103) UDP-N-acetylmuramyl tripeptide synthetase MurE {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}	Back information, alignment and structure

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}	Back information, alignment and structure

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}	Back information, alignment and structure

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}	Back information, alignment and structure

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}	Back information, alignment and structure

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}	Back information, alignment and structure

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}	Back information, alignment and structure

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}	Back information, alignment and structure

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure