Citrus Sinensis ID: 011395

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-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------

MASNIYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKAM

ccccccccccccccccccccccccccccHHHHHHHHccEEccccccccEEEcccccccccccEEEEcccccccccccHHHHHHcccEEEEEEccccccccccEEEEcccccHHHHHHHHHHHHHHHHccccccEEEEcccccHHHHHHHHHHHHHcccccEEEcccccccccHHHHHHccccccccEEEEEEccccccHHHHHHccccccEEEEEHHHHHHHcccccHHHHHHHHHHHHcccccccEEEEEcccHHHHHHcccccccEEEEEccccccEEEEEEEEEccccEEEEEEEEccEEEEEEccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccccccEEEEEEcccEEEEcccccccHHHHHHHHHHHHcccccccEEEEEcccccccHHHHHHHHHHHHHHHHccccEEEEEcHHHHHHHHHHcccccccEEEcccHHHHHHHHHHHcccccEEEEEccccccHHHHHHHHHcc

ccccccccEEEEcccccccccccccHccHHHHHHHHcccEccccEEEEEEEcccEEccccccEEEEEccccccHHHHHHHHHHcccEEEEEEccccccccccEEEEEEEEEccHHHHHHHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHHccccEEEccccccccccccEEEEEccccccEEEEEEccccccHHHHHHHHccccEEEEEccHHHHHHHcccHHHHHHHHHHHHHccccccEEEEccccHHHHHHHHHccccEEEEEccccccEEEEEEEEEccccEEEEEEEcccccEEEEEccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHcccccccEEEEEccccEEEEEccccccHHHHHHHHHHHHHccccccEEEEEEcHHHHcHHHHHHHHHHHHHHHHccccEEEEEcHHHHHHHHHHHHcccccEEEcccHHHHHHHHHHHcccccEEEEEccccHHHHHHHHHHHcc

masniyphtlactskttfrcpsnspiwtINEIAEsvngkilkwgppgiictdtrilapnknqwFFAItgqhfdahefispelygkgcvgvignqvcnnwdkgfvqvegngnvntlnSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGdshleslgSLEDVARAKgeifqesklgdvcvlnaddplvanltvprgvrkvFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVkfvipspglhLAINACAAAAVATLFGVSLAQVGislsnfspvqmRSELLVSRsgikivndaynanpiSTRAAIDLLKDIACNGKRVVILGDMlelgstereSHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKAM

masniyphtlactskttfrcpsnsPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIfqesklgdvCVLNADdplvanltvprgVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQkivkrlksndvvlvkgsramqmekVVDVIKAM

MASNIYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFsgvlvgvtgsvgksttksMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLainacaaaavaTLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKAM

****IYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRA*************

***NIYP**L**************PIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKAM

**SNIYPHTLACTSKTTFRCPSNSPIWTINEIAESVNGKILKWGPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKA*

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SSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		487	2.2.26 [Sep-21-2011]
P96613		457	UDP-N-acetylmuramoyl-trip	yes	no	0.903	0.962	0.330	3e-52
Q9AKP1		449	Probable UDP-N-acetylmura	yes	no	0.804	0.873	0.291	2e-44
Q92H60		449	Probable UDP-N-acetylmura	yes	no	0.802	0.870	0.294	2e-44
O33804		446	Probable UDP-N-acetylmura	N/A	no	0.876	0.957	0.355	2e-41
O05953		449	Probable UDP-N-acetylmura	yes	no	0.825	0.895	0.283	2e-40
O83401		459	UDP-N-acetylmuramoyl-trip	yes	no	0.856	0.908	0.281	2e-35
P11880		452	UDP-N-acetylmuramoyl-trip	N/A	no	0.856	0.922	0.299	6e-35
P45061		457	UDP-N-acetylmuramoyl-trip	yes	no	0.860	0.916	0.288	7e-34
P45450		454	UDP-N-acetylmuramoyl-trip	N/A	no	0.845	0.907	0.294	8e-34
Q89AQ1		460	UDP-N-acetylmuramoyl-trip	yes	no	0.843	0.893	0.266	9e-34

>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 =  206 bits (525), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 155/469 (33%), Positives = 239/469 (50%), Gaps = 29/469 (6%)

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

Query: 260 LTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINA 319
                  +   +G     D +L    V+    G    ++       F IP  G H  +NA
Sbjct: 233 ---AYSCQTKTYGTGTHNDYQL--QDVSQSEEGTHFTIKGIENT--FFIPILGKHNVMNA 285

Query: 320 CAAAAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDL 379
            AA A    FG++       LS      MR EL+ + SG+ I+NDAYNA+P S +AAI L
Sbjct: 286 MAAIAAGAYFGIAPEDAAKGLSGLKVTGMRLELIKTDSGLSIINDAYNASPTSMKAAIQL 345

Query: 380 LKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAEN-MNL 438
            + +   GK++++LGDMLELG  E   H++  +      ID +   G      AE  +  
Sbjct: 346 TESLEGYGKKMLVLGDMLELGDLEETFHKECGAVISPDKIDRVFTYGKLGAFIAEGALKH 405

Query: 439 IKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVV-DVIKA 486
            + D +    + + L Q + +     D++L K SR M++E++V D+I++
Sbjct: 406 FEKDRVSHYTEKKDLLQAVKENASKGDLILFKASRGMKLEEIVKDLIES 454

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\|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\|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\|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\|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\|O83401\|MURF_TREPA UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Treponema pallidum (strain Nichols) 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\|P45061\|MURF_HAEIN UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=murF PE=3 SV=1	Back alignment and function description

>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\|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

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		487
297742739		510	unnamed protein product [Vitis vinifera]	0.934	0.892	0.663	1e-164
225463627		771	PREDICTED: UDP-N-acetylmuramoyl-tripepti	0.934	0.590	0.663	1e-164
302819065		515	hypothetical protein SELMODRAFT_133115 [	0.921	0.871	0.463	1e-106
302819192		515	hypothetical protein SELMODRAFT_185918 [	0.921	0.871	0.463	1e-106
76880174		606	MurF synthetase [Physcomitrella patens s	0.921	0.740	0.451	1e-100
168029598		606	predicted protein [Physcomitrella patens	0.921	0.740	0.451	1e-99
125973492		457	UDP-N-acetylmuramoyl-tripeptide--D-alany	0.866	0.923	0.360	5e-66
296133663		458	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,	0.913	0.971	0.358	1e-63
220927933		459	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,	0.913	0.969	0.337	3e-63
354582289		461	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,	0.866	0.915	0.361	7e-62

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

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 308/464 (66%), Positives = 362/464 (78%), Gaps = 9/464 (1%)

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 RGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAA 323
            GV+KV FG R  CDVR  A +V +GG GV+VVLE+  E V+FVIPSPGLHLA NACA A
Sbjct: 281 HGVKKVLFGQRLECDVRFAAEKV-HGGHGVRVVLERNHEKVEFVIPSPGLHLAQNACATA 339

Query: 324 AVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDI 383
           AVA   GVSL QVGISLS F PV MRSEL V+++GIKI+ND YNANP+ST+AAI+LLK+I
Sbjct: 340 AVAVALGVSLPQVGISLSRFIPVSMRSELEVAKTGIKIINDVYNANPVSTKAAIELLKNI 399

Query: 384 ACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNLIKTDY 443
            C GKRV ILGDMLELG  E  SHE +LS CCD+  DLI LVG RF  AAEN+NL+    
Sbjct: 400 DCKGKRVAILGDMLELGQAETVSHEMMLSLCCDSHFDLIALVGKRFLRAAENLNLVGERN 459

Query: 444 IVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKAM 487
           ++ + DAE L+ +IV+RL  NDV+LVKGSR MQMEKVV  IKAM
Sbjct: 460 LLYSPDAESLAFEIVQRLNRNDVILVKGSRGMQMEKVVAAIKAM 503

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\|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\|76880174\|dbj\|BAE45859.1\| MurF synthetase [Physcomitrella patens subsp. patens]	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|125973492|ref|YP_001037402.1| UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase [Clostridium thermocellum ATCC 27405] gi|256003308|ref|ZP_05428299.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum DSM 2360] gi|281417693|ref|ZP_06248713.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum JW20] gi|385778591|ref|YP_005687756.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum DSM 1313] gi|419723581|ref|ZP_14250696.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum AD2] gi|419724594|ref|ZP_14251656.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum YS] gi|125713717|gb|ABN52209.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum ATCC 27405] gi|255992598|gb|EEU02689.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum DSM 2360] gi|281409095|gb|EFB39353.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum JW20] gi|316940271|gb|ADU74305.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum DSM 1313] gi|380772141|gb|EIC05999.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum YS] gi|380780263|gb|EIC09946.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Clostridium thermocellum AD2]

Back alignment and taxonomy information

>gi\|296133663\|ref\|YP_003640910.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Thermincola potens JR] gi\|296032241\|gb\|ADG83009.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Thermincola potens JR]	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\|354582289\|ref\|ZP_09001191.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Paenibacillus lactis 154] gi\|353199688\|gb\|EHB65150.1\| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Paenibacillus lactis 154]	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		487
TIGR_CMR\|BA_0246		458	BA_0246 "UDP-N-acetylmuramoyla	0.911	0.969	0.292	2.4e-44
TIGR_CMR\|CHY_2073		458	CHY_2073 "UDP-N-acetylmuramoyl	0.854	0.908	0.290	1.9e-42
TIGR_CMR\|SPO_1183		464	SPO_1183 "UDP-N-acetylmuramoyl	0.913	0.959	0.294	3.4e-38
TIGR_CMR\|CBU_0124		446	CBU_0124 "UDP-N-acetylmuramoyl	0.887	0.968	0.288	2.7e-36
TIGR_CMR\|SO_4223		460	SO_4223 "UDP-N-acetylmuramoyla	0.671	0.710	0.300	5.7e-36
UNIPROTKB\|Q48EF4		456	murF "UDP-N-acetylmuramoyl-tri	0.856	0.914	0.253	1.1e-34
UNIPROTKB\|P11880		452	murF [Escherichia coli K-12 (t	0.907	0.977	0.270	1.2e-33
TIGR_CMR\|CPS_4469		513	CPS_4469 "UDP-N-acetylmuramoyl	0.852	0.808	0.281	3.2e-33
UNIPROTKB\|Q9KPG3		453	VC_2405 "UDP-N-acetylmuramoyl-	0.891	0.958	0.252	1.6e-31
TIGR_CMR\|VC_2405		453	VC_2405 "UDP-N-acetylmuramoyla	0.891	0.958	0.252	1.6e-31

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

 Score = 467 (169.5 bits), Expect = 2.4e-44, P = 2.4e-44
 Identities = 137/468 (29%), Positives = 220/468 (47%)

Query:    28 TINEIAESVNGKILKWGPPGI----ICTDTRILAPNKNQWFFAITGQHFDAHEFISPELY 83
             T+ ++ + +NG  L     GI    +  DTR +   K   +  I G+ FD H F+   + 
Sbjct:     5 TLKQVEQMINGTGLAEQYEGITIQGVSIDTRKI--EKGNLYVPIQGERFDGHAFVDKAVE 62

Query:    84 GKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTL-NSLVNMACYARNSRFXXXXXXXXXXXX 142
               G V  +       W K       N  V  + ++L  +   A+N R             
Sbjct:    63 N-GAVATL-------WVKDVANPPENLPVIFVEDTLSALQMLAKNYRDQLDVKVIGVTGS 114

Query:   143 XXXXXXM-IALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEIL 201
                     I  +L +    V ++ GN+NN +G+ L+++ ++   ++AVLEMGMS +GEI 
Sbjct:   115 NGKTSTKDIVTSLLATKFKVQKTEGNFNNHIGLPLTILNLEENTEVAVLEMGMSSRGEIE 174

Query:   202 ELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLT 261
              L+++ARP   ++ N+G++HL  LGS E +A AK EI    + G V V N D+PL+ N  
Sbjct:   175 FLSKLARPNAAIITNIGEAHLMDLGSREAIAEAKLEIVTGLQEGGVFVYNGDEPLLTN-R 233

Query:   262 VPRG---VRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLXXX 318
             VP        V FG  R  D       V     G    + +E E + F +P  G H    
Sbjct:   234 VPEMNLIAETVTFGDARANDY--YPTTVTLQATGTHFKMNRE-ENISFYLPVLGKHNVYN 290

Query:   319 XXXXXXXXTLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAID 378
                       FGV+  ++   L       MR E++ + SG+ I+NDAYNA+P +  AA  
Sbjct:   291 TLASMAIAKYFGVTWEEMKEGLVTLQMTGMRMEIVKTDSGLTIINDAYNASPTAMEAAFH 350

Query:   379 LLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNL 438
             L+  +    K++V+LGDMLELG  E + H ++      A I  +   G      AE   +
Sbjct:   351 LMNGLDGFSKKIVVLGDMLELGDQEVQFHYEVGKLIDPAKISYVFTYGKLGAQIAEGAKI 410

Query:   439 -IKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIK 485
                 + +   ++ E L +++   + + DVVLVK SR M++E+V+ ++K
Sbjct:   411 NFPNERVKAYDNKEELVKELQAVVDTKDVVLVKASRGMKLEEVITMLK 458

GO:0009252 "peptidoglycan biosynthetic process" evidence=ISS

GO:0016881 "acid-amino acid ligase activity" evidence=ISS

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

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\|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

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

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

UNIPROTKB\|P11880 murF [Escherichia coli K-12 (taxid:83333)]	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

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

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P96613	MURF_BACSU	6, ., 3, ., 2, ., 1, 0	0.3304	0.9034	0.9628	yes	no

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	6.3.2.10	0.824
3rd Layer	6.3.2	0.766

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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		487
COG0770		451	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide sy	1e-112
TIGR01143		417	TIGR01143, murF, UDP-N-acetylmuramoyl-tripeptide--	1e-105
PRK11929		958	PRK11929, PRK11929, putative bifunctional UDP-N-ac	1e-84
PRK14093		479	PRK14093, PRK14093, UDP-N-acetylmuramoylalanyl-D-g	2e-62
PRK11930		822	PRK11930, PRK11930, putative bifunctional UDP-N-ac	7e-47
PRK10773		453	PRK10773, murF, UDP-N-acetylmuramoyl-tripeptide--D	2e-46
pfam08245		178	pfam08245, Mur_ligase_M, Mur ligase middle domain	1e-35
COG0771		448	COG0771, MurD, UDP-N-acetylmuramoylalanine-D-gluta	2e-35
TIGR01087		433	TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-gl	2e-33
COG0773		459	COG0773, MurC, UDP-N-acetylmuramate-alanine ligase	1e-24
PRK02472		447	PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	6e-22
PRK04690		468	PRK04690, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	9e-22
PRK14106		450	PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	5e-21
TIGR01082		448	TIGR01082, murC, UDP-N-acetylmuramate--alanine lig	3e-19
PRK11929		958	PRK11929, PRK11929, putative bifunctional UDP-N-ac	4e-19
PRK02006		498	PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	6e-18
PRK00421		461	PRK00421, murC, UDP-N-acetylmuramate--L-alanine li	4e-17
PRK01390		460	PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	2e-16
TIGR01085		464	TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide sy	3e-16
PRK03803		448	PRK03803, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	9e-16
COG0769		475	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synt	1e-15
PRK00141		473	PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	1e-14
PRK01438		480	PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	2e-14
PRK03369		488	PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	9e-14
PRK00139		460	PRK00139, murE, UDP-N-acetylmuramoylalanyl-D-gluta	7e-13
PRK14016		727	PRK14016, PRK14016, cyanophycin synthetase; Provis	2e-12
TIGR02068		864	TIGR02068, cya_phycin_syn, cyanophycin synthetase	3e-12
PRK01368		454	PRK01368, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	3e-12
PRK04308		445	PRK04308, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	6e-12
PRK03806		438	PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	3e-11
PRK01710		458	PRK01710, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	4e-11
PRK04663		438	PRK04663, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	1e-09
pfam02875		88	pfam02875, Mur_ligase_C, Mur ligase family, glutam	3e-09
COG0285		427	COG0285, FolC, Folylpolyglutamate synthase [Coenzy	4e-08
PRK02705		459	PRK02705, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	4e-07
PRK14573		809	PRK14573, PRK14573, bifunctional D-alanyl-alanine	4e-07
TIGR01499		398	TIGR01499, folC, folylpolyglutamate synthase/dihyd	6e-07
PRK00683		418	PRK00683, murD, UDP-N-acetylmuramoyl-L-alanyl-D-gl	2e-04
PLN02913		510	PLN02913, PLN02913, dihydrofolate synthetase	0.003

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

 Score =  340 bits (873), Expect = e-112
 Identities = 164/469 (34%), Positives = 251/469 (53%), Gaps = 26/469 (5%)

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 -LTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAIN 318
                   + + FG   G D R     +   G    + +E      +F +P PG H   N
Sbjct: 230 WAAKIGNAKVLSFGLNNGGDFRATNIHLDEEGSSFTLDIEGGE--AEFELPLPGRHNVTN 287

Query: 319 ACAAAAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAID 378
           A AAAA+A   G+ L ++   L    PV+ R E+++  +G  +++D+YNANP S RAA+D
Sbjct: 288 ALAAAALALELGLDLEEIAAGLKELKPVKGRLEVILLANGKTLIDDSYNANPDSMRAALD 347

Query: 379 LLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAENMNL 438
           LL  +    K + +LGDMLELG    E HE++  Y  +A IDL+ LVG+  +A AE    
Sbjct: 348 LLAALP-GRKGIAVLGDMLELGEESEELHEEVGEYAVEAGIDLVFLVGELSKAIAE---A 403

Query: 439 IKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKAM 487
           +    I   +  E L   +   L+  DVVLVKGSR M++EKVVD +   
Sbjct: 404 LGNKGIYFADKEE-LITSLKALLRKGDVVLVKGSRGMKLEKVVDALLGK 451

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\|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\|219763 pfam08245, Mur_ligase_M, Mur ligase middle domain	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\|233266 TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase	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\|235041 PRK02472, 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\|184511 PRK14106, 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\|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\|234995 PRK02006, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional	Back alignment and domain information

>gnl\|CDD\|234757 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase; 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\|233265 TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide synthetase	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\|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	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\|179297 PRK01438, 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\|234660 PRK00139, murE, UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional	Back alignment and domain information

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

>gnl\|CDD\|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase	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\|167786 PRK04308, 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\|179323 PRK01710, 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\|217262 pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase domain	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

>gnl\|CDD\|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase A/UDP-N-acetylmuramate--L-alanine ligase; Provisional	Back alignment and domain information

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

>gnl\|CDD\|179086 PRK00683, 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		487
COG0770		451	MurF UDP-N-acetylmuramyl pentapeptide synthase [Ce	100.0
PRK14093		479	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminop	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
PRK11929		958	putative bifunctional UDP-N-acetylmuramoylalanyl-D	100.0
TIGR01085		464	murE UDP-N-acetylmuramyl-tripeptide synthetase. A	100.0
PRK00139		460	murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-d	100.0
PRK14022		481	UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine l	100.0
PRK11929		958	putative bifunctional UDP-N-acetylmuramoylalanyl-D	100.0
COG0769		475	MurE UDP-N-acetylmuramyl tripeptide synthase [Cell	100.0
PRK01710		458	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK03806		438	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
COG0773		459	MurC UDP-N-acetylmuramate-alanine ligase [Cell env	100.0
PRK00421		461	murC UDP-N-acetylmuramate--L-alanine ligase; Provi	100.0
PRK04308		445	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK04663		438	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK02006		498	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
TIGR01087		433	murD UDP-N-acetylmuramoylalanine--D-glutamate liga	100.0
PRK03803		448	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
TIGR01081		448	mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl	100.0
PRK00141		473	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK01390		460	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
TIGR01082		448	murC UDP-N-acetylmuramate--alanine ligase. UDP-N-a	100.0
PRK14106		450	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
COG0771		448	MurD UDP-N-acetylmuramoylalanine-D-glutamate ligas	100.0
PRK02472		447	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK02705		459	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK03369		488	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK01368		454	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK00683		418	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK01438		480	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PRK04690		468	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
TIGR02068		864	cya_phycin_syn cyanophycin synthetase. Cyanophycin	100.0
TIGR01499		397	folC folylpolyglutamate synthase/dihydrofolate syn	100.0
PRK03815		401	murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate syn	100.0
PLN02913		510	dihydrofolate synthetase	100.0
PRK14573		809	bifunctional D-alanyl-alanine synthetase A/UDP-N-a	100.0
PRK10846		416	bifunctional folylpolyglutamate synthase/ dihydrof	100.0
COG0285		427	FolC Folylpolyglutamate synthase [Coenzyme metabol	100.0
PLN02881		530	tetrahydrofolylpolyglutamate synthase	100.0
PF08245		188	Mur_ligase_M: Mur ligase middle domain; InterPro:	100.0
PRK14016		727	cyanophycin synthetase; Provisional	99.98
KOG2525		496	consensus Folylpolyglutamate synthase [Coenzyme tr	99.95
PF02875		91	Mur_ligase_C: Mur ligase family, glutamate ligase	99.62
PF01225		83	Mur_ligase: Mur ligase family, catalytic domain Th	99.41
PF08353		113	DUF1727: Domain of unknown function (DUF1727); Int	97.38
COG1703		323	ArgK Putative periplasmic protein kinase ArgK and	95.5
PF03308		266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	93.55
PRK09435		332	membrane ATPase/protein kinase; Provisional	92.28
PF04613		72	LpxD: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-a	91.28
PRK00652		325	lpxK tetraacyldisaccharide 4'-kinase; Reviewed	91.18
TIGR03172		232	probable selenium-dependent hydroxylase accessory	89.37
PRK15453		290	phosphoribulokinase; Provisional	88.99
TIGR03815		322	CpaE_hom_Actino helicase/secretion neighborhood Cp	88.73
COG1044		338	LpxD UDP-3-O-[3-hydroxymyristoyl]	88.41
PHA02519		387	plasmid partition protein SopA; Reviewed	87.82
COG1763		161	MobB Molybdopterin-guanine dinucleotide biosynthes	87.61
COG1936		180	Predicted nucleotide kinase (related to CMP and AM	87.47
PRK13705		388	plasmid-partitioning protein SopA; Provisional	86.84
PRK14489		366	putative bifunctional molybdopterin-guanine dinucl	86.79
PRK00892		343	lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-ac	86.58
TIGR01007		204	eps_fam capsular exopolysaccharide family. This mo	86.19
PF03205		140	MobB: Molybdopterin guanine dinucleotide synthesis	85.63
cd01983		99	Fer4_NifH The Fer4_NifH superfamily contains a var	85.53
PRK06696		223	uridine kinase; Validated	85.15
PRK05439		311	pantothenate kinase; Provisional	84.76
PF00485		194	PRK: Phosphoribulokinase / Uridine kinase family;	84.31
PRK13869		405	plasmid-partitioning protein RepA; Provisional	84.27
COG2403		449	Predicted GTPase [General function prediction only	84.2
COG0132		223	BioD Dethiobiotin synthetase [Coenzyme metabolism]	83.73
COG0769		475	MurE UDP-N-acetylmuramyl tripeptide synthase [Cell	83.69
PRK07667		193	uridine kinase; Provisional	83.46
TIGR03029		274	EpsG chain length determinant protein tyrosine kin	83.29
TIGR03018		207	pepcterm_TyrKin exopolysaccharide/PEPCTERM locus t	82.31
COG4240		300	Predicted kinase [General function prediction only	82.2
PRK14494		229	putative molybdopterin-guanine dinucleotide biosyn	81.89
TIGR01853		324	lipid_A_lpxD UDP-3-O-[3-hydroxymyristoyl] glucosam	81.55
TIGR00554		290	panK_bact pantothenate kinase, bacterial type. Sho	81.19
cd03109		134	DTBS Dethiobiotin synthetase (DTBS) is the penulti	81.02
cd02029		277	PRK_like Phosphoribulokinase-like (PRK-like) is a	80.87

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

Probab=100.00  E-value=7.1e-89  Score=696.02  Aligned_cols=444  Identities=37%  Similarity=0.569  Sum_probs=411.1

Q ss_pred             ccCHHHHHHHhCCeeccCC--CCCeEEeeCCccccCCCCEEEEecCCcCCcccchHHhhhcCCceEEEeccccCCCCcc-
Q 011395           26 IWTINEIAESVNGKILKWG--PPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKG-  102 (487)
Q Consensus        26 ~~~l~~l~~~~~~~~~~~~--~~~~i~~dsr~v~~~~g~lFva~~G~~~dgh~~~~~A~~~~Ga~~~v~~~~~~~~~~~-  102 (487)
                      +|++.+++.++++.+.+..  .+++|++|||.+.|  |++|+|++|++||||+|+++|++ +||.+++++++...+..| 
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~Dsr~v~~--g~lF~al~G~~~Dgh~fi~~A~~-~GA~a~~v~r~~~~~~~~~   78 (451)
T COG0770           2 LLTLDELADILGGALVGADPVVVSGVSIDSRKVKP--GDLFVALKGERFDGHDFIEQALA-AGAAAVLVARPVLPPAIPL   78 (451)
T ss_pred             cccHHHHHHHhCCccccCcccceeeEEeecccCCC--CceeEEccCccccccchHHHHHh-cCCEEEEEecCcCCccccc
Confidence            5899999999999887655  38999999999999  99999999999999999999999 999999999987655556 


Q ss_pred             -EEEEcCCCCccHHHHHHHHHHHHhhcCCCCcEEEEeCCCChHhHHHHHHHHHHhCCCceEecCCCCCCcchhhhHhhcC
Q 011395          103 -FVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGI  181 (487)
Q Consensus       103 -~i~V~~~~~~d~~~aL~~la~~~~~p~~~~~vI~VTGTnGKTTT~~ml~~iL~~~g~~v~~t~g~~n~~~g~p~~l~~~  181 (487)
                       ++.|.     |+++||++|+.++++ ..+.++|+||||+|||||++|++++| +..++|++|.|||||++|+|++++++
T Consensus        79 ~~~~V~-----d~~~al~~la~~~~~-~~~~kvIaITGS~GKTTTKe~la~iL-~~~~~v~~t~gn~Nn~iGlPltll~~  151 (451)
T COG0770          79 VVLLVL-----DTLEALGKLAKAYRQ-KFNAKVIAITGSNGKTTTKEMLAAIL-STKGKVHATPGNFNNEIGLPLTLLRL  151 (451)
T ss_pred             ceEEeH-----HHHHHHHHHHHHHHH-hcCCcEEEEeCCCCcHHHHHHHHHHH-hhcCeEecCCCccCccccchhHHHhC
Confidence             89999     999999999999999 88999999999999999999999999 56789999999999999999999999


Q ss_pred             CCCCcEEEEeccCCCcchHHhhccccCCcEEEEcCCChhhhhcCCCHHHHHHHHHhhcccCCCCCeEEEcCCcHHHHhhc
Q 011395          182 DRAVDIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLT  261 (487)
Q Consensus       182 ~~~~~~~V~E~g~~~~g~i~~~~~~~~pdvaViTNI~~dHl~~~gs~e~~~~aK~~i~~~~~~~~~~vln~Dd~~~~~~~  261 (487)
                      ..++|++|+|||+++.|+|..++++++||++|||||+.+|+++|||.|+++++|.+|+.+++++|++|+|.|++....+.
T Consensus       152 ~~~~e~~VlEmG~~~~GeI~~l~~i~~P~iavItnIg~aHle~fgs~e~Ia~aK~Ei~~~~~~~g~ai~n~d~~~~~~~~  231 (451)
T COG0770         152 PADTEYAVLEMGMNHPGEIAELSEIARPDIAVITNIGEAHLEGFGSREGIAEAKAEILAGLRPEGIAILNADNPLLKNWA  231 (451)
T ss_pred             CCcccEEEEEcCCCCCCcHHHHhcccCCCEEEEcChhHHHHHhcCCHHHHHHHHHHHHhccCCCcEEEEECccHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999877666


Q ss_pred             CC-CCCcEEEEeCCCCceEEEEeceEEecCCeEEEEEeecceEEEEEeCCCchhhHHHHHHHHHHHHHcCCCHHHHHHHh
Q 011395          262 VP-RGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISL  340 (487)
Q Consensus       262 ~~-~~~~vi~~g~~~~~d~~~~~~~i~~~~~~~~~~~~~~~~~~~~~l~l~G~~nv~NalaAia~a~~lg~~~~~i~~~L  340 (487)
                      .+ ...++++||.+..+|+++.+  +.....+.+|++...+....+.+|++|+||+.|+++|+++|+.+|+++++|+++|
T Consensus       232 ~~~~~~~v~~fg~~~~~d~~~~~--i~~~~~~~~f~~~~~~~~~~~~l~~~G~hn~~NalaA~a~a~~lG~~~e~i~~~L  309 (451)
T COG0770         232 AKIGNAKVLSFGLNNGGDFRATN--IHLDEEGSSFTLDIEGGEAEFELPLPGRHNVTNALAAAALALELGLDLEEIAAGL  309 (451)
T ss_pred             hhcCCCcEEEEcCCCCCceeeEE--EEEcCCceEEEEEecCceEEEEecCCcHhHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            22 23789999987567999999  9998888999998763333899999999999999999999999999999999999


Q ss_pred             cCCCCCCCceeEEeecCCeEEEEecCCCCHHHHHHHHHHHHccccCCcEEEEEcCCCCCCcccHHHHHHHHHHHHHcCCC
Q 011395          341 SNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACID  420 (487)
Q Consensus       341 ~~~~~~~gR~e~~~~~~~~~ii~Dsya~np~s~~~~l~~l~~~~~~~~~i~Vlg~m~e~G~~~~~~~~~~~~~l~~~~~d  420 (487)
                      +.+++++||+|.+...++.++|||+||+||+||+++++.+..++ .++.|+|+|+|.|+|+.+.+.|+++++.+...++|
T Consensus       310 ~~~~~~~gR~~~~~~~~g~~iIdD~YNAnp~sm~aai~~l~~~~-~~~~i~VlGdM~ELG~~s~~~H~~v~~~~~~~~~d  388 (451)
T COG0770         310 KELKPVKGRLEVILLANGKTLIDDSYNANPDSMRAALDLLAALP-GRKGIAVLGDMLELGEESEELHEEVGEYAVEAGID  388 (451)
T ss_pred             HhcCCCCccceeEecCCCcEEEEcCCCCCHHHHHHHHHHHhhCc-cCCcEEEeCChhhhCccHHHHHHHHHHHHHhcCce
Confidence            99999999999666668999999999999999999999999988 34449999999999999999999999999998899


Q ss_pred             EEEEECccHHHHHHHhhhhcCCeEEEECCHHHHHHHHHhhCCCCCEEEEecCCCCcHHHHHHHHHh
Q 011395          421 LIGLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIKA  486 (487)
Q Consensus       421 ~vi~~g~~~~~i~~~~~~~~~~~~~~~~d~~~ai~~l~~~~~~~d~vLv~GSr~~~~e~~~~~l~~  486 (487)
                      .++++|+..+.+.+.+..    ...+|.+.+++++.+.+.++++|+|||||||++.||++++.|+.
T Consensus       389 ~v~~~G~~~~~i~~~~~~----~~~~f~~~~~l~~~l~~~l~~gd~vLvKgSr~~~le~vv~~l~~  450 (451)
T COG0770         389 LVFLVGELSKAIAEALGN----KGIYFADKEELITSLKALLRKGDVVLVKGSRGMKLEKVVDALLG  450 (451)
T ss_pred             EEEEEccchHHHHHhcCC----CeEecCCHHHHHHHHHHhcCCCCEEEEEcCccccHHHHHHHHhc
Confidence            999999999999988742    27789999999999999999999999999999999999999864

>PRK14093 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional	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

>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

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

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

>PRK14022 UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine 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

>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	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

>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

>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

>PRK02006 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

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

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

>PRK00141 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

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

>PRK14106 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

>PRK02472 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

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

>PRK01368 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

>PRK01438 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

>TIGR02068 cya_phycin_syn cyanophycin synthetase	Back alignment and domain information

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

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

>PLN02913 dihydrofolate synthetase	Back alignment and domain information

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

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

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

>PLN02881 tetrahydrofolylpolyglutamate synthase	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

>PRK14016 cyanophycin synthetase; Provisional	Back alignment and domain information

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

>PF02875 Mur_ligase_C: Mur ligase family, glutamate ligase domain This Prosite entry is a subset of the Pfam family	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

>PF08353 DUF1727: Domain of unknown function (DUF1727); InterPro: IPR013564 This domain of unknown function is found at the C terminus of bacterial proteins which include UDP-N-acetylmuramyl tripeptide synthase and the related Mur ligase	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

>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

>PRK09435 membrane ATPase/protein kinase; Provisional	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

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

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

>PRK15453 phosphoribulokinase; Provisional	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

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

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

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

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

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

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

>TIGR01007 eps_fam capsular exopolysaccharide family	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

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

>PRK06696 uridine kinase; Validated	Back alignment and domain information

>PRK05439 pantothenate kinase; Provisional	Back alignment and domain information

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

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

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

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

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

>PRK07667 uridine kinase; 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

>COG4240 Predicted kinase [General function prediction only]	Back alignment and domain information

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

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

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

>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms	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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		487
1gg4_A		452	Crystal Structure Of Escherichia Coli Udpmurnac-Tri		3e-27
2am1_A		454	Sp Protein Ligand 1 Length = 454		2e-20
3lk7_A		451	The Crystal Structure Of Udp-N-Acetylmuramoylalanin		9e-07

>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 = 119 bits (299), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 116/441 (26%), Positives = 186/441 (42%), Gaps = 24/441 (5%) 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 EDVARAKGEIFQESKLGDVCVLNADDPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVAN 288 VA+AKGEIF + + NAD+ N G RKV+ + A + Sbjct: 196 AGVAKAKGEIFSGLPENGIAIXNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHV 255 Query: 289 GGLGVQVVLEKEREMVKFVIPSPGLHLXXXXXXXXXXXTLFGVSLAQVGISLSNFSPVQM 348 G + L+ V ++P PG H G +L + L+N V Sbjct: 256 TSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSXSVGATLDAIKAGLANLKAVPG 315 Query: 349 RSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHE 408 R + +++D+YNAN S AA+ +L + G RV+++GD ELG+ H Sbjct: 316 RLFPIQLAENQLLLDDSYNANVGSXTAAVQVLAEXP--GYRVLVVGDXAELGAESEACHV 373 Query: 409 KILSYCCDACIDLIGLVGDRFRA--AAENMNLIKTDYIVVTNDAEIL--SQKIVKRLKSN 464 ++ A ID + VG + A A + D + ++L Q+++ Sbjct: 374 QVGEAAKAAGIDRVLSVGKQSHAISTASGVGEHFADKTALITRLKLLIAEQQVI------ 427 Query: 465 DVVLVKGSRAMQMEKVVDVIK 485 +LVKGSR+ E+VV ++ Sbjct: 428 -TILVKGSRSAAXEEVVRALQ 447

PyMOL of 1gg4

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

Back alignment and structure

>pdb|3LK7|A Chain A, The Crystal Structure Of Udp-N-Acetylmuramoylalanine-D- Glutamate (Murd) Ligase From Streptococcus Agalactiae To 1.5a Length = 451

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		487
2am1_A		454	SP protein, UDP-N-acetylmuramoylalanine-D-glutamyl	1e-138
1gg4_A		452	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diamino	1e-137
3lk7_A		451	UDP-N-acetylmuramoylalanine--D-glutamate ligase; a	9e-36
2x5o_A		439	UDP-N-acetylmuramoylalanine--D-glutamate ligase; A	2e-32
1p3d_A		475	UDP-N-acetylmuramate--alanine ligase; alpha/beta p	3e-22
2f00_A		491	UDP-N-acetylmuramate--L-alanine ligase; amide bond	5e-21
1j6u_A		469	UDP-N-acetylmuramate-alanine ligase MURC; structur	3e-19
1e8c_A		498	UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diami	2e-18
2wtz_A		535	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-di	2e-15
3hn7_A		524	UDP-N-acetylmuramate-L-alanine ligase; ATP-binding	1e-14
3eag_A		326	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-ME	9e-14
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
1o5z_A		442	Folylpolyglutamate synthase/dihydrofolate synthas;	9e-06
2vos_A		487	Folylpolyglutamate synthase protein FOLC; ligase,	9e-05
1jbw_A		428	Folylpolyglutamate synthase; FPGS folate AMPPCP te	4e-04

>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

 Score =  404 bits (1041), Expect = e-138
 Identities = 113/472 (23%), Positives = 217/472 (45%), Gaps = 34/472 (7%)

Query: 27  WTINEIAESVNGKILKWGPPGI----ICTDTRILAPNKNQWFFAITGQHFDAHEFISPEL 82
            TI+EIA+ V  K                D+R++       F  + G   D H+FI    
Sbjct: 3   LTIHEIAQVVGAKNDISIFEDTQLEKAEFDSRLIGTG--DLFVPLKGAR-DGHDFI-ETA 58

Query: 83  YGKGCVGVIGNQVCNNWDKGFVQVEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVG 142
           +  G    +  +  +  +  ++ V+     + L +  ++A Y    + +  +  VTGS G
Sbjct: 59  FENGAAVTLSEKEVS--NHPYILVD-----DVLTAFQSLASYYLE-KTTVDVFAVTGSNG 110

Query: 143 KSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILE 202
           K+TTK M+A  L +     +++ GN+NN +G+  +++ +    +  VLEMG    G+I  
Sbjct: 111 KTTTKDMLAHLLSTRY-KTYKTQGNYNNEIGLPYTVLHMPEGTEKLVLEMGQDHLGDIHL 169

Query: 203 LARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLTV 262
           L+ +ARP+  +V  VG++HL       ++A+ K +I      G + +  AD  +   L  
Sbjct: 170 LSELARPKTAIVTLVGEAHLAFFKDRSEIAKGKMQIADGMASGSLLLAPADPIVEDYL-- 227

Query: 263 PRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAA 322
           P   + V FG  +G ++ +         L  +    ++       +P  G + A NA  A
Sbjct: 228 PIDKKVVRFG--QGAELEITDLVERKDSLTFKANFLEQA----LDLPVTGKYNATNAMIA 281

Query: 323 AAVATLFGVSLAQVGISLSNFSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKD 382
           + VA   GVS  Q+ ++  +    + R+E   + +G  I++D YNANP + +  ++    
Sbjct: 282 SYVALQEGVSEEQIRLAFQHLELTRNRTEWKKAANGADILSDVYNANPTAMKLILETFSA 341

Query: 383 IACN--GKRVVILGDMLELGSTERESHEKILSYCCDACIDLIGLVGDRFRAAAE------ 434
           I  N  GK++ +L DM ELG    + H +++       +D++   G+     A+      
Sbjct: 342 IPANEGGKKIAVLADMKELGDQSVQLHNQMILSLSPDVLDIVIFYGEDIAQLAQLASQMF 401

Query: 435 -NMNLIKTDYIVVTNDAEILSQKIVKRLKSNDVVLVKGSRAMQMEKVVDVIK 485
              ++         +  E L +++ + L ++D +L+KGS +M + K+V+ ++
Sbjct: 402 PIGHVYYFKKTEDQDQFEDLVKQVKESLGAHDQILLKGSNSMNLAKLVESLE 453

PyMOL of 2am1

>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

>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

>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

>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

>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

>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

>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

>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} Length = 524	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} Length = 326	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	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 Length = 442	Back alignment and structure

>2vos_A Folylpolyglutamate synthase protein FOLC; ligase, peptidoglycan synthesis, cell division; HET: ADP; 2.0A {Mycobacterium tuberculosis} PDB: 2vor_A* Length = 487	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 Length = 428	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		487
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
3hn7_A		524	UDP-N-acetylmuramate-L-alanine ligase; ATP-binding	100.0
1p3d_A		475	UDP-N-acetylmuramate--alanine ligase; alpha/beta p	100.0
2f00_A		491	UDP-N-acetylmuramate--L-alanine ligase; amide bond	100.0
2x5o_A		439	UDP-N-acetylmuramoylalanine--D-glutamate ligase; A	100.0
4hv4_A		494	UDP-N-acetylmuramate--L-alanine ligase; MURC, yers	100.0
3lk7_A		451	UDP-N-acetylmuramoylalanine--D-glutamate ligase; a	100.0
1jbw_A		428	Folylpolyglutamate synthase; FPGS folate AMPPCP te	100.0
2vos_A		487	Folylpolyglutamate synthase protein FOLC; ligase,	100.0
1o5z_A		442	Folylpolyglutamate synthase/dihydrofolate synthas;	100.0
1j6u_A		469	UDP-N-acetylmuramate-alanine ligase MURC; structur	100.0
3nrs_A		437	Dihydrofolate:folylpolyglutamate synthetase; struc	100.0
1w78_A		422	FOLC bifunctional protein; DHFS, dihydrofolate syn	100.0
3eag_A		326	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-ME	100.0
3mvn_A		163	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamayl-M	99.85
2g0t_A		350	Conserved hypothetical protein; structural genomic	90.53
3pmo_A		372	UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltr;	89.81
3eh0_A		341	UDP-3-O-[3-hydroxymyristoyl] glucosamine N- acyltr	89.77
4e79_A		357	UDP-3-O-acylglucosamine N-acyltransferase; lipopol	89.25
1xjc_A		169	MOBB protein homolog; structural genomics, midwest	88.51
1rz3_A		201	Hypothetical protein rbstp0775; MCSG, structural g	88.41
3bl4_A		124	Uncharacterized protein; structural genomics, join	88.11
3fwy_A		314	Light-independent protochlorophyllide reductase I	87.71
3of5_A		228	Dethiobiotin synthetase; structural genomics, cent	86.69
4dzz_A		206	Plasmid partitioning protein PARF; deviant walker	86.49
3bfv_A		271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	86.37
1byi_A		224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	86.03
3cio_A		299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	84.87
3la6_A		286	Tyrosine-protein kinase WZC; P-loop protein, nucle	84.43
3fgn_A		251	Dethiobiotin synthetase; biotin biosynthesis, BIOD	82.27
3c8u_A		208	Fructokinase; YP_612366.1, putative fructose trans	81.61
3ea0_A		245	ATPase, para family; alpha-beta-alpha sandwich, st	81.12
3qxc_A		242	Dethiobiotin synthetase; DTBS, structural genomics	80.93
2oze_A		298	ORF delta'; para, walker type atpases, DNA segrega	80.89
1g3q_A		237	MIND ATPase, cell division inhibitor; alpha-beta-a	80.77
3dm5_A		443	SRP54, signal recognition 54 kDa protein; protein-	80.25
1wcv_1		257	SOJ, segregation protein; ATPase, bacterial, chrom	80.11
3kl4_A		433	SRP54, signal recognition 54 kDa protein; signal r	80.11

>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=4.8e-85  Score=682.49  Aligned_cols=438  Identities=30%  Similarity=0.420  Sum_probs=385.2

Q ss_pred             cCHHHHHHHhCCeeccC-CCCCeEEeeCCccccCCCCEEEEecCCcCCcccchHHhhhcCCceEEEeccccCCCCccEEE
Q 011395           27 WTINEIAESVNGKILKW-GPPGIICTDTRILAPNKNQWFFAITGQHFDAHEFISPELYGKGCVGVIGNQVCNNWDKGFVQ  105 (487)
Q Consensus        27 ~~l~~l~~~~~~~~~~~-~~~~~i~~dsr~v~~~~g~lFva~~G~~~dgh~~~~~A~~~~Ga~~~v~~~~~~~~~~~~i~  105 (487)
                      |++++|++.+++.+.+. ..|+++++|||.++|  |++|||++|+++|||+|+++|++ +||.++|++++.+ +++|++.
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            79999999999886542 238999999999999  99999999999999999999999 9999999998754 2689999


Q ss_pred             EcCCCCccHHHHHHHHHHHHhhcCCCCcEEEEeCCCChHhHHHHHHHHHHhCCCceEecCCCCCCcchhhhHhhcCCCCC
Q 011395          106 VEGNGNVNTLNSLVNMACYARNSRFSGVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAV  185 (487)
Q Consensus       106 V~~~~~~d~~~aL~~la~~~~~p~~~~~vI~VTGTnGKTTT~~ml~~iL~~~g~~v~~t~g~~n~~~g~p~~l~~~~~~~  185 (487)
                      |+     |++++|++|+.+++. ..+.++|+||||||||||++||+++|++.| ++..+.||+|+++|.|++++++..++
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     999999999997665 456899999999999999999999997777 67789999999999999999988889


Q ss_pred             cEEEEeccCCCcchHHhhccccCCcEEEEcCCChhhhhcCCCHHHHHHHHHhhcccCCCCCeEEEcCCcHHHHhh--cCC
Q 011395          186 DIAVLEMGMSGKGEILELARMARPEIRVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANL--TVP  263 (487)
Q Consensus       186 ~~~V~E~g~~~~g~i~~~~~~~~pdvaViTNI~~dHl~~~gs~e~~~~aK~~i~~~~~~~~~~vln~Dd~~~~~~--~~~  263 (487)
                      +++|+|+|+++.+++.+++++++|+++|||||++||+++|||+|+|+++|++||+.+++++.+|+|.|||....+  ...
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            999999999999999999888899999999999999999999999999999999998889999999999987766  322


Q ss_pred             CCCcEEEEeCCC-CceEEEEeceEEecCCeEEEEEeecceEEEEEeCCCchhhHHHHHHHHHHHHHcCCCHHHHHHHhcC
Q 011395          264 RGVRKVFFGWRR-GCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISLSN  342 (487)
Q Consensus       264 ~~~~vi~~g~~~-~~d~~~~~~~i~~~~~~~~~~~~~~~~~~~~~l~l~G~~nv~NalaAia~a~~lg~~~~~i~~~L~~  342 (487)
                       ++++++||.+. .+|+++.+  +.....+..|.+..++....+.++++|.||++|+++|++++..+|++++.|+++|++
T Consensus       233 -~~~~~~~g~~~~~~d~~~~~--~~~~~~g~~~~~~~~~~~~~~~l~l~G~hn~~NalaA~a~~~~lgi~~~~i~~~L~~  309 (452)
T 1gg4_A          233 -SRKVWRFSPNAANSDFTATN--IHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSMSVGATLDAIKAGLAN  309 (452)
T ss_dssp             -TSEEEEECSSCTTCSBEEEE--EEECSSSEEEEEEETTEEEEEEECSSSTHHHHHHHHHHHHHHHTTCCHHHHHHHHTT
T ss_pred             -CCCEEEEeCCCCCCcEEEEE--EEEcCCceEEEEEECCCEEEEEeCCCcHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence             36899999865 57888877  777666777877654222378999999999999999999999999999999999999


Q ss_pred             CCCCCCceeEEeecCCeEEEEecCCCCHHHHHHHHHHHHccccCCcEEEEEcCCCCCCcccHHHHHHHHHHHHHcCCCEE
Q 011395          343 FSPVQMRSELLVSRSGIKIVNDAYNANPISTRAAIDLLKDIACNGKRVVILGDMLELGSTERESHEKILSYCCDACIDLI  422 (487)
Q Consensus       343 ~~~~~gR~e~~~~~~~~~ii~Dsya~np~s~~~~l~~l~~~~~~~~~i~Vlg~m~e~G~~~~~~~~~~~~~l~~~~~d~v  422 (487)
                      |+++|||||++...+++++|||||||||+|++++++++++++  +|+++|||+|.|+|+++++.|++|++.+.+..+|.+
T Consensus       310 ~~~~~gR~e~~~~~~~~~vidDsyahnp~s~~~~l~~l~~~~--~~~i~V~G~~~e~g~~~~~~~~~~~~~~~~~~~d~v  387 (452)
T 1gg4_A          310 LKAVPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAEMP--GYRVLVVGDMAELGAESEACHVQVGEAAKAAGIDRV  387 (452)
T ss_dssp             CCCCTTSSEEEEEETTEEEEECCSCCCHHHHHHHHHHHHHSS--SEEEEEECCCCCCTTHHHHHHHHHHHHHHHHTCSEE
T ss_pred             CCCCCCCceEEECCCCcEEEEeCCCCCHHHHHHHHHHHHhcc--CCEEEEECCccccCChhHHHHHHHHHHHHHcCCCEE
Confidence            999999999998767899999999999999999999998764  689999999999999999999999999887559999


Q ss_pred             EEECccHHHHHHHhhhhcCCeEEEECCHHHHHHHHHhhCCC--CCEEEEecCCCCcHHHHHHHHH
Q 011395          423 GLVGDRFRAAAENMNLIKTDYIVVTNDAEILSQKIVKRLKS--NDVVLVKGSRAMQMEKVVDVIK  485 (487)
Q Consensus       423 i~~g~~~~~i~~~~~~~~~~~~~~~~d~~~ai~~l~~~~~~--~d~vLv~GSr~~~~e~~~~~l~  485 (487)
                      |++|+.++.+.+.+..     ..+++|+++|++.+.+.+++  ||+||++||+++.||++++.|.
T Consensus       388 i~~g~~~~~i~~~~~~-----~~~~~~~~~ai~~a~~~~~~~~gd~VLv~GS~~~~~e~i~~~l~  447 (452)
T 1gg4_A          388 LSVGKQSHAISTASGV-----GEHFADKTALITRLKLLIAEQQVITILVKGSRSAAMEEVVRALQ  447 (452)
T ss_dssp             EEESSSTHHHHHHTTS-----CEEESSHHHHHHHHHHHHHHCSSEEEEEECCGGGTTHHHHHHHC
T ss_pred             EEECcCHHHHHHHhhc-----CceeCCHHHHHHHHHHhhcccCCcEEEEEcCCcCCHHHHHHHHH
Confidence            9999999988886632     13679999999999999998  9999999999999999999884

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

>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

>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

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

>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

>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

>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

>2vos_A Folylpolyglutamate synthase protein FOLC; ligase, peptidoglycan synthesis, cell division; HET: ADP; 2.0A {Mycobacterium tuberculosis} PDB: 2vor_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

>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

>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

>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

>3mvn_A UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamayl-M diaminopimelate ligase; structural genomics, MCSG, PSI-2; 1.90A {Haemophilus ducreyi}	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

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

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

>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

>3bl4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, unknown function; 2.20A {Arthrobacter SP}	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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}	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

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_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		487
d1p3da3		215	c.72.2.1 (A:107-321) UDP-N-acetylmuramate-alanine	2e-26
d1gg4a4		214	c.72.2.1 (A:99-312) UDP-murNac-tripeptide D-alanyl	6e-24
d1gg4a1		135	c.59.1.1 (A:313-447) UDP-murNac-tripeptide D-alany	6e-24
d1e8ca3		234	c.72.2.1 (A:104-337) UDP-N-acetylmuramyl tripeptid	4e-12
d2jfga3		204	c.72.2.1 (A:94-297) UDP-N-acetylmuramoyl-L-alanine	5e-12
d1j6ua3		207	c.72.2.1 (A:89-295) UDP-N-acetylmuramate-alanine l	9e-11
d1gg4a3		98	c.98.1.1 (A:1-98) UDP-murNac-tripeptide D-alanyl-D	4e-05

>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 =  104 bits (259), Expect = 2e-26
 Identities = 51/210 (24%), Positives = 85/210 (40%), Gaps = 11/210 (5%)

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 DPLVANLTVPRGVRKVFFGWRRGCDVRLVAAQVANGGLGVQVVLEKEREMVKFVIPSPGL 313
           DP++  L    G + + +G+    D R +      G  G   V+    E +  ++  PG 
Sbjct: 126 DPVLMELVPKVGRQVITYGFSEQADYR-IEDYEQTGFQGHYTVICPNNERINVLLNVPGK 184

Query: 314 HLAINACAAAAVATLFGVSLAQVGISLSNF 343
           H A+NA AA AVA   G++   +  +L++F
Sbjct: 185 HNALNATAALAVAKEEGIANEAILEALADF 214

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

>d1gg4a1 c.59.1.1 (A:313-447) UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF {Escherichia coli [TaxId: 562]} Length = 135	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

>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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		487
d1gg4a4		214	UDP-murNac-tripeptide D-alanyl-D-alanine-adding en	100.0
d1p3da3		215	UDP-N-acetylmuramate-alanine ligase MurC {Haemophi	100.0
d1e8ca3		234	UDP-N-acetylmuramyl tripeptide synthetase MurE {Es	100.0
d2jfga3		204	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	100.0
d1j6ua3		207	UDP-N-acetylmuramate-alanine ligase MurC {Thermoto	100.0
d1o5za2		296	Folylpolyglutamate synthetase {Thermotoga maritima	99.98
d2gc6a2		296	Folylpolyglutamate synthetase {Lactobacillus casei	99.97
d1gg4a1		135	UDP-murNac-tripeptide D-alanyl-D-alanine-adding en	99.95
d1gg4a3		98	UDP-murNac-tripeptide D-alanyl-D-alanine-adding en	99.87
d1e8ca2		160	UDP-N-acetylmuramyl tripeptide synthetase MurE {Es	99.8
d1e8ca1		101	UDP-N-acetylmuramyl tripeptide synthetase MurE {Es	99.73
d1j6ua2		151	UDP-N-acetylmuramate-alanine ligase MurC {Thermoto	99.56
d1p3da2		152	UDP-N-acetylmuramate-alanine ligase MurC {Haemophi	99.51
d2jfga2		140	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	99.47
d1o5za1		137	Folylpolyglutamate synthetase, C-terminal domain {	99.36
d2gc6a1		129	Folylpolyglutamate synthetase, C-terminal domain {	99.23
d2p67a1		327	LAO/AO transport system kinase ArgK {Escherichia c	94.48
d2qm8a1		323	Metallochaperone MeaB {Methylobacterium extorquens	93.77
d1byia_		224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.49
d1a7ja_		288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	90.56
d1xjca_		165	Molybdopterin-guanine dinucleotide biosynthesis pr	90.3
d1np6a_		170	Molybdopterin-guanine dinucleotide biosynthesis pr	89.44
d1rz3a_		198	Hypothetical protein rbstp0775 {Bacillus stearothe	89.37
d1nksa_		194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	88.63
d2nu7b1		150	Succinyl-CoA synthetase, beta-chain, C-terminal do	87.64
d1eucb1		148	Succinyl-CoA synthetase, beta-chain, C-terminal do	86.71
d2afhe1		289	Nitrogenase iron protein {Azotobacter vinelandii [	85.8
d1ls1a2		207	GTPase domain of the signal sequence recognition p	84.64
d1khta_		190	Adenylate kinase {Archaeon Methanococcus voltae [T	83.92
d1hyqa_		232	Cell division regulator MinD {Archaeon Archaeoglob	82.32
d2qy9a2		211	GTPase domain of the signal recognition particle r	81.9
d1sq5a_		308	Pantothenate kinase PanK {Escherichia coli [TaxId:	81.55

>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=1.9e-40  Score=308.85  Aligned_cols=210  Identities=33%  Similarity=0.470  Sum_probs=181.1

Q ss_pred             CcEEEEeCCCChHhHHHHHHHHHHhCCCceEecCCCCCCcchhhhHhhcCCCCCcEEEEeccCCCcchHHhhccccCCcE
Q 011395          132 GVLVGVTGSVGKSTTKSMIALALESLGVNVFQSYGNWNNRVGVALSLIGIDRAVDIAVLEMGMSGKGEILELARMARPEI  211 (487)
Q Consensus       132 ~~vI~VTGTnGKTTT~~ml~~iL~~~g~~v~~t~g~~n~~~g~p~~l~~~~~~~~~~V~E~g~~~~g~i~~~~~~~~pdv  211 (487)
                      .++|+||||||||||++||+++|++.|.++ .+.|++|+++|.|..++....+.++.++|+++...++...+...+.|++
T Consensus         2 ~kvI~VTGTnGKTTt~~mi~~iL~~~g~~~-~~~g~~n~~~g~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~p~~   80 (214)
T d1gg4a4           2 ARVVALTGSSGKTSVKEMTAAILSQCGNTL-YTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEA   80 (214)
T ss_dssp             CEEEEEECSSCHHHHHHHHHHHHTTTSCEE-ECCTTCCSTTHHHHHHTTCCTTCSEEEEECCCSSSSHHHHHHHHHCCSE
T ss_pred             CCEEEEeCCCcHHHHHHHHHHHHHhCCCCE-EEeCcccCccccchhhhhcccccccchhhhhhhhcccccccccccCchh
Confidence            479999999999999999999998887665 5899999999999988888889999999999988888888888889999


Q ss_pred             EEEcCCChhhhhcCCCHHHHHHHHHhhcccCCCCCeEEEcCCcHHHHhhc-CCCCCcEEEEeCC-CCceEEEEeceEEec
Q 011395          212 RVVLNVGDSHLESLGSLEDVARAKGEIFQESKLGDVCVLNADDPLVANLT-VPRGVRKVFFGWR-RGCDVRLVAAQVANG  289 (487)
Q Consensus       212 aViTNI~~dHl~~~gs~e~~~~aK~~i~~~~~~~~~~vln~Dd~~~~~~~-~~~~~~vi~~g~~-~~~d~~~~~~~i~~~  289 (487)
                      +|+|||++||+|+|+++|+|+++|.++++.++++|.+|+|.||+....+. ...+.++++|+.. +.+|+++.+  +...
T Consensus        81 ~viTNi~~dHld~~~~~~~~~~~k~~~~~~~~~~g~~v~n~dd~~~~~~~~~~~~~~~~~~~~~~~~ad~~~~~--~~~~  158 (214)
T d1gg4a4          81 ALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATN--IHVT  158 (214)
T ss_dssp             EEECCCC--------CHHHHHHHHHGGGGGCCTTCEEEEETTBCCHHHHHHHHTTSEEEEECSSCTTCSBEEEE--EEEC
T ss_pred             eeeehhccccccccccHHHHHhhhhhHhhhhccCCccccccccHHHHHHHHHhcCCceeeeccCCCCcceeeee--EEEe
Confidence            99999999999999999999999999999999999999999999887765 1123678899986 468999998  8888


Q ss_pred             CCeEEEEEeecceEEEEEeCCCchhhHHHHHHHHHHHHHcCCCHHHHHHHhcCCC
Q 011395          290 GLGVQVVLEKEREMVKFVIPSPGLHLAINACAAAAVATLFGVSLAQVGISLSNFS  344 (487)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~l~l~G~~nv~NalaAia~a~~lg~~~~~i~~~L~~~~  344 (487)
                      ..+..|++..++...++++|++|.||++|+++|++++..+|++++.|+++|++|+
T Consensus       159 ~~~~~~~i~~~~~~~~~~l~l~G~hn~~NalaAia~~~~lgi~~~~i~~~l~~fk  213 (214)
T d1gg4a4         159 SHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSMSVGATLDAIKAGLANLK  213 (214)
T ss_dssp             SSSEEEEEEETTEEEEEEECSSSTHHHHHHHHHHHHHHHTTCCHHHHHHHHTTCC
T ss_pred             CCceEEEEEECCceEEEEeCCCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhcC
Confidence            8899999977643348999999999999999999999999999999999999997

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

>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

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

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

>d1gg4a1 c.59.1.1 (A:313-447) UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF {Escherichia coli [TaxId: 562]}	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

>d1e8ca2 c.59.1.1 (A:338-497) UDP-N-acetylmuramyl tripeptide synthetase MurE {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

>d1j6ua2 c.59.1.1 (A:296-446) UDP-N-acetylmuramate-alanine ligase MurC {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1p3da2 c.59.1.1 (A:322-473) UDP-N-acetylmuramate-alanine ligase MurC {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d2jfga2 c.59.1.1 (A:298-437) UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1o5za1 c.59.1.2 (A:294-430) Folylpolyglutamate synthetase, C-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2gc6a1 c.59.1.2 (A:297-425) Folylpolyglutamate synthetase, C-terminal domain {Lactobacillus casei [TaxId: 1582]}	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

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}	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

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {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

>d2nu7b1 c.23.4.1 (B:239-388) Succinyl-CoA synthetase, beta-chain, C-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1eucb1 c.23.4.1 (B:246-393) Succinyl-CoA synthetase, beta-chain, C-terminal domain {Pig (Sus scrofa) [TaxId: 9823]}	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

>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

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	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

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