Citrus Sinensis ID: 016039

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------
MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSRFCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC
cHHHHcccHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEcccccEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHccccHHHcccHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHcccccccccccccccccccHHHHHHHHHccccHHHHHHHcccccccccccc
ccHHccccHHHHHHHHHHccccccccccccHHHHcHHHHHHHHHHHHHHHHHHHHHHccccccccEEEccccEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccEEEEccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccHHHHccccHHHHHHHHHHcccEccccccccccHHHHHHHHHHHccccccHHHHHHHHccccccccc
mehildgsSYVEAAQKfheidplqkpkqdryalrtspqwlgpqaEVIRASTKSIEREInsvndnplidvsrnkalhggnfqgtpigvsmdnSRLAIASIGKLMFAQFSELVNDfysnglpsnlsggrnpcldygfkGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTmgvngelhpsrfcekdllkvvdreyvfsyaddpcsatypLMRKLRQVLVDHAltnnedlknaNASIFLKIGAFEEELKTLLPKEVESARSafesgnleipnrikecrsyplyRFVREELGAryltgekaispgeecDKVFTAICQGKIIDPLLEClkewdgsplpic
mehildgsSYVEAAQKfheidplqkpkqdRYALRtspqwlgpqaEVIRASTKSIEReinsvndnplIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMgvngelhpsrfcEKDLLKVVDREYVFSyaddpcsatyPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARsafesgnleipnrikecrsyPLYRFVREELGARYLTGekaispgeECDKVFTAICQGKIIDPLLECLkewdgsplpic
MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSRFCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC
*****************************************************************LIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQ********VNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSRFCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLP************GNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWD*******
MEHILDGSSYV**************PKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEE*****VKNTISQVAKKVLTMGVNGELHPSRFCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC
MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSRFCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC
****LDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSRFCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDL*NANASIFLKIGAFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC
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MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSRFCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC
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 ?
Query396 2.2.26 [Sep-21-2011]
O64963717 Phenylalanine ammonia-lya N/A no 1.0 0.552 0.868 0.0
P45726714 Phenylalanine ammonia-lya N/A no 1.0 0.554 0.856 0.0
Q42667722 Phenylalanine ammonia-lya N/A no 1.0 0.548 0.858 0.0
P25872715 Phenylalanine ammonia-lya N/A no 1.0 0.553 0.848 0.0
P35513712 Phenylalanine ammonia-lya N/A no 1.0 0.556 0.856 0.0
P27990725 Phenylalanine ammonia-lya N/A no 1.0 0.546 0.856 0.0
P45733712 Phenylalanine ammonia-lya N/A no 1.0 0.556 0.856 0.0
P35510725 Phenylalanine ammonia-lya yes no 1.0 0.546 0.833 0.0
P45729718 Phenylalanine ammonia-lya N/A no 1.0 0.551 0.838 0.0
O23865708 Phenylalanine ammonia-lya N/A no 1.0 0.559 0.843 0.0
>sp|O64963|PAL1_PRUAV Phenylalanine ammonia-lyase 1 OS=Prunus avium GN=PAL1 PE=2 SV=1 Back     alignment and function desciption
 Score =  734 bits (1895), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 344/396 (86%), Positives = 374/396 (94%)

Query: 1   MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINS 60
           MEHILDGSSYV+AA+K HE DPLQKPKQDRYALRTSPQWLGPQ EVIR STKSIEREI+S
Sbjct: 322 MEHILDGSSYVKAAKKLHEQDPLQKPKQDRYALRTSPQWLGPQIEVIRYSTKSIEREIDS 381

Query: 61  VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLP 120
           VNDNPLIDVSRNKALHGGNFQGTPIGVSMDN+RLAIASIGKLMFAQFSELVNDFY+NGLP
Sbjct: 382 VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNTRLAIASIGKLMFAQFSELVNDFYNNGLP 441

Query: 121 SNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARK 180
           SNLSGGRNP LDYGFKGAEIAMA+YCSELQFLANPVTNHVQSAEQHNQDVNSLGLIS+RK
Sbjct: 442 SNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRK 501

Query: 181 TAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR 240
           TAEAVDILKLMSST+L+ALCQAIDLRHLEENL++TVKNT+SQVAK+ LT GVNGELHPSR
Sbjct: 502 TAEAVDILKLMSSTFLVALCQAIDLRHLEENLRNTVKNTVSQVAKRTLTTGVNGELHPSR 561

Query: 241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIG 300
           FCEKDLLKVVDREYVF+Y DDPCSATYPLM+KLRQVLV+HALTN E+ KNA+ SIF KI 
Sbjct: 562 FCEKDLLKVVDREYVFAYIDDPCSATYPLMQKLRQVLVEHALTNGENEKNASTSIFQKIV 621

Query: 301 AFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAIS 360
           AFEEELK LLPKEV+SAR+A +SG+  +PNRI ECRSYPLY+FVREELGA YLTGEK  S
Sbjct: 622 AFEEELKVLLPKEVDSARAALDSGSAGVPNRITECRSYPLYKFVREELGAEYLTGEKVRS 681

Query: 361 PGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC 396
           PGEECDKVFTAIC+GKIIDP+L+CL+ W+G+PLPIC
Sbjct: 682 PGEECDKVFTAICEGKIIDPILDCLEGWNGAPLPIC 717
This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton.
Prunus avium (taxid: 42229)
EC: 4EC: .EC: 3EC: .EC: 1EC: .EC: 2EC: 4
>sp|P45726|PALY_CAMSI Phenylalanine ammonia-lyase OS=Camellia sinensis GN=PAL PE=2 SV=1 Back     alignment and function description
>sp|Q42667|PALY_CITLI Phenylalanine ammonia-lyase OS=Citrus limon GN=PAL6 PE=2 SV=1 Back     alignment and function description
>sp|P25872|PAL1_TOBAC Phenylalanine ammonia-lyase OS=Nicotiana tabacum GN=TPA1 PE=2 SV=1 Back     alignment and function description
>sp|P35513|PAL2_TOBAC Phenylalanine ammonia-lyase OS=Nicotiana tabacum GN=PALA PE=2 SV=2 Back     alignment and function description
>sp|P27990|PALY_MEDSA Phenylalanine ammonia-lyase OS=Medicago sativa PE=2 SV=1 Back     alignment and function description
>sp|P45733|PAL3_TOBAC Phenylalanine ammonia-lyase OS=Nicotiana tabacum PE=2 SV=1 Back     alignment and function description
>sp|P35510|PAL1_ARATH Phenylalanine ammonia-lyase 1 OS=Arabidopsis thaliana GN=PAL1 PE=1 SV=3 Back     alignment and function description
>sp|P45729|PAL3_PETCR Phenylalanine ammonia-lyase 3 OS=Petroselinum crispum GN=PAL3 PE=2 SV=1 Back     alignment and function description
>sp|O23865|PAL1_DAUCA Phenylalanine ammonia-lyase 1 OS=Daucus carota GN=PAL1 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 ?
Query396
225435357 717 PREDICTED: phenylalanine ammonia-lyase [ 1.0 0.552 0.881 0.0
387571558 706 phenylalanine ammonia-lyase [Camellia ja 1.0 0.560 0.876 0.0
251826414 706 phenylalanine ammonia-lyase [Camellia ol 1.0 0.560 0.876 0.0
124245049 720 phenylalanine ammonia lyase [Pyrus commu 1.0 0.55 0.873 0.0
295002604 719 phenylalanine ammonia-lyase 1 precursor 1.0 0.550 0.876 0.0
382929313 720 phenylalanine ammonialyase [Malus hybrid 1.0 0.55 0.873 0.0
374257940 719 phenylalanine ammonia-lyase [Pyrus x bre 1.0 0.550 0.873 0.0
399144522 717 phenylalanine ammonia lyase [Prunus sali 1.0 0.552 0.868 0.0
6647711 717 RecName: Full=Phenylalanine ammonia-lyas 1.0 0.552 0.868 0.0
7208616 730 phenylalanine ammonia-lyase 2 [Rubus ida 1.0 0.542 0.866 0.0
>gi|225435357|ref|XP_002285277.1| PREDICTED: phenylalanine ammonia-lyase [Vitis vinifera] gi|147801854|emb|CAN74850.1| hypothetical protein VITISV_000789 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  748 bits (1930), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/396 (88%), Positives = 376/396 (94%)

Query: 1   MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINS 60
           MEHILDGS+YV+AAQ  HEIDPLQKPKQDRYALRTSPQWLGPQ EVIR STKSIEREINS
Sbjct: 322 MEHILDGSAYVKAAQMLHEIDPLQKPKQDRYALRTSPQWLGPQIEVIRTSTKSIEREINS 381

Query: 61  VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLP 120
           VNDNPLIDVSRNKALHGGNFQGTPIGVSMDN+RLAIASIGKLMFAQFSELVNDFY+NGLP
Sbjct: 382 VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNTRLAIASIGKLMFAQFSELVNDFYNNGLP 441

Query: 121 SNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARK 180
           SNLSGGRNP LDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLIS+RK
Sbjct: 442 SNLSGGRNPSLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRK 501

Query: 181 TAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR 240
           T EA+DILKLMSSTYL+ALCQAIDLRHLEENLK+TVKNT+SQVAKKVLT+G+NGELHPSR
Sbjct: 502 TEEAIDILKLMSSTYLVALCQAIDLRHLEENLKNTVKNTVSQVAKKVLTIGINGELHPSR 561

Query: 241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIG 300
           FCEKDLLKVVDRE+VF+Y DDPCSATYPLM+ LRQVLVDHAL NNEDL+N++ SIFLKIG
Sbjct: 562 FCEKDLLKVVDREHVFAYIDDPCSATYPLMQNLRQVLVDHALMNNEDLRNSSTSIFLKIG 621

Query: 301 AFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAIS 360
           AFEEELKTLLPK+VES R AF++GNL IPNRIKECRSYPLY+FVREE G  +LTGEK  S
Sbjct: 622 AFEEELKTLLPKDVESTRIAFDNGNLAIPNRIKECRSYPLYKFVREESGTEFLTGEKVTS 681

Query: 361 PGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC 396
           PGEE DKVF+AIC+GKIIDPLL+CL +WDG+PLPIC
Sbjct: 682 PGEEFDKVFSAICEGKIIDPLLKCLNDWDGTPLPIC 717

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|387571558|gb|AFJ80777.1| phenylalanine ammonia-lyase [Camellia japonica] Back     alignment and taxonomy information
>gi|251826414|gb|ACT21093.1| phenylalanine ammonia-lyase [Camellia oleifera] Back     alignment and taxonomy information
>gi|124245049|gb|ABB70117.2| phenylalanine ammonia lyase [Pyrus communis] Back     alignment and taxonomy information
>gi|295002604|gb|ADF59061.1| phenylalanine ammonia-lyase 1 precursor [Pyrus x bretschneideri] Back     alignment and taxonomy information
>gi|382929313|gb|AFG30054.1| phenylalanine ammonialyase [Malus hybrid cultivar] Back     alignment and taxonomy information
>gi|374257940|gb|AEZ01784.1| phenylalanine ammonia-lyase [Pyrus x bretschneideri] Back     alignment and taxonomy information
>gi|399144522|gb|AFP24940.1| phenylalanine ammonia lyase [Prunus salicina] Back     alignment and taxonomy information
>gi|6647711|sp|O64963.1|PAL1_PRUAV RecName: Full=Phenylalanine ammonia-lyase 1 gi|2935294|gb|AAC78457.1| phenylalanine ammonia-lyase [Prunus avium] Back     alignment and taxonomy information
>gi|7208616|gb|AAF40224.1|AF237955_1 phenylalanine ammonia-lyase 2 [Rubus idaeus] 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 ?
Query396
TAIR|locus:2057981725 PAL1 "PHE ammonia lyase 1" [Ar 1.0 0.546 0.833 1.8e-181
TAIR|locus:2101958717 PAL2 "phenylalanine ammonia-ly 1.0 0.552 0.823 1e-180
TAIR|locus:2076244707 PAL4 "phenylalanine ammonia-ly 1.0 0.560 0.818 6.1e-174
ASPGD|ASPL0000017810686 AN3897 [Emericella nidulans (t 0.510 0.294 0.441 1.6e-42
ASPGD|ASPL0000000997701 AN6075 [Emericella nidulans (t 0.919 0.519 0.312 1.5e-41
TIGR_CMR|SO_4374521 SO_4374 "histidine ammonia-lya 0.520 0.395 0.336 3.8e-29
DICTYBASE|DDB_G0273787529 DDB_G0273787 "putative histidi 0.512 0.383 0.376 8.2e-23
DICTYBASE|DDB_G0273081529 DDB_G0273081 "putative histidi 0.512 0.383 0.376 8.2e-23
UNIPROTKB|Q1LRV9533 Rmet_0231 "Tyrosine ammonia-ly 0.515 0.382 0.305 5.9e-19
UNIPROTKB|Q0VZ68531 cmdF "Tyrosine 2,3-aminomutase 0.429 0.320 0.373 5.2e-18
TAIR|locus:2057981 PAL1 "PHE ammonia lyase 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1761 (625.0 bits), Expect = 1.8e-181, P = 1.8e-181
 Identities = 330/396 (83%), Positives = 368/396 (92%)

Query:     1 MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINS 60
             MEHILDGSSY++ AQK HE+DPLQKPKQDRYALRTSPQWLGPQ EVIR +TKSIEREINS
Sbjct:   330 MEHILDGSSYMKLAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRYATKSIEREINS 389

Query:    61 VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLP 120
             VNDNPLIDVSRNKA+HGGNFQGTPIGVSMDN+RLAIA+IGKLMFAQFSELVNDFY+NGLP
Sbjct:   390 VNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLP 449

Query:   121 SNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARK 180
             SNL+  RNP LDYGFKGAEIAMA+YCSELQ+LANPVT+HVQSAEQHNQDVNSLGLIS+RK
Sbjct:   450 SNLTASRNPSLDYGFKGAEIAMASYCSELQYLANPVTSHVQSAEQHNQDVNSLGLISSRK 509

Query:   181 TAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR 240
             T+EAVDILKLMS+T+L+A+CQA+DLRHLEENL+ TVKNT+SQVAKKVLT GVNGELHPSR
Sbjct:   510 TSEAVDILKLMSTTFLVAICQAVDLRHLEENLRQTVKNTVSQVAKKVLTTGVNGELHPSR 569

Query:   241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIG 300
             FCEKDLLKVVDRE V++YADDPCSATYPL++KLRQV+VDHAL N E  KNA  SIF KIG
Sbjct:   570 FCEKDLLKVVDREQVYTYADDPCSATYPLIQKLRQVIVDHALINGESEKNAVTSIFHKIG 629

Query:   301 AFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAIS 360
             AFEEELK +LPKEVE+AR+A+++G   IPNRIKECRSYPLYRFVREELG   LTGEK  S
Sbjct:   630 AFEEELKAVLPKEVEAARAAYDNGTSAIPNRIKECRSYPLYRFVREELGTELLTGEKVTS 689

Query:   361 PGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC 396
             PGEE DKVFTAIC+GKIIDP++ECL EW+G+P+PIC
Sbjct:   690 PGEEFDKVFTAICEGKIIDPMMECLNEWNGAPIPIC 725
GO:0003824 "catalytic activity" evidence=IEA
GO:0005737 "cytoplasm" evidence=ISM;IEA
GO:0006559 "L-phenylalanine catabolic process" evidence=IEA
GO:0009058 "biosynthetic process" evidence=IEA
GO:0009699 "phenylpropanoid biosynthetic process" evidence=TAS
GO:0016841 "ammonia-lyase activity" evidence=IEA
GO:0045548 "phenylalanine ammonia-lyase activity" evidence=ISS;IDA;TAS
GO:0006979 "response to oxidative stress" evidence=IEP
GO:0080167 "response to karrikin" evidence=IEP
GO:0009555 "pollen development" evidence=IMP
GO:0009819 "drought recovery" evidence=IMP
GO:0010224 "response to UV-B" evidence=IMP
GO:0046244 "salicylic acid catabolic process" evidence=IMP
GO:0046274 "lignin catabolic process" evidence=IMP
GO:0006598 "polyamine catabolic process" evidence=RCA
GO:0009611 "response to wounding" evidence=RCA;TAS
GO:0009698 "phenylpropanoid metabolic process" evidence=RCA
GO:0009805 "coumarin biosynthetic process" evidence=RCA
GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA
GO:0042398 "cellular modified amino acid biosynthetic process" evidence=RCA
GO:0006952 "defense response" evidence=TAS
TAIR|locus:2101958 PAL2 "phenylalanine ammonia-lyase 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2076244 PAL4 "phenylalanine ammonia-lyase 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ASPGD|ASPL0000017810 AN3897 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
ASPGD|ASPL0000000997 AN6075 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
TIGR_CMR|SO_4374 SO_4374 "histidine ammonia-lyase, putative" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0273787 DDB_G0273787 "putative histidine ammonia-lyase" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0273081 DDB_G0273081 "putative histidine ammonia-lyase" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|Q1LRV9 Rmet_0231 "Tyrosine ammonia-lyase" [Cupriavidus metallidurans CH34 (taxid:266264)] Back     alignment and assigned GO terms
UNIPROTKB|Q0VZ68 cmdF "Tyrosine 2,3-aminomutase" [Chondromyces crocatus (taxid:52)] 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) ?
P45727PALY_PERAE4, ., 3, ., 1, ., 2, 40.83871.00.6387N/Ano
P45735PALY_VITVI4, ., 3, ., 1, ., 2, 40.85101.00.9519nono
P07218PAL1_PHAVU4, ., 3, ., 1, ., 2, 40.83331.00.7826N/Ano
P35510PAL1_ARATH4, ., 3, ., 1, ., 2, 40.83331.00.5462yesno
Q40910PAL4_POPKI4, ., 3, ., 1, ., 2, 40.83621.00.6935N/Ano

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer4.3.1.240.946
3rd Layer4.3.1LOW CONFIDENCE prediction!

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 ?
Query396
PLN02457706 PLN02457, PLN02457, phenylalanine ammonia-lyase 0.0
TIGR01226680 TIGR01226, phe_am_lyase, phenylalanine ammonia-lya 0.0
pfam00221477 pfam00221, Lyase_aromatic, Aromatic amino acid lya 1e-107
cd00332444 cd00332, PAL-HAL, Phenylalanine ammonia-lyase (PAL 1e-85
COG2986498 COG2986, HutH, Histidine ammonia-lyase [Amino acid 7e-34
TIGR03832507 TIGR03832, Tyr_2_3_mutase, tyrosine 2,3-aminomutas 8e-26
TIGR01225506 TIGR01225, hutH, histidine ammonia-lyase 1e-24
PRK09367500 PRK09367, PRK09367, histidine ammonia-lyase; Provi 2e-24
cd01594231 cd01594, Lyase_I_like, Lyase class I_like superfam 4e-14
>gnl|CDD|215251 PLN02457, PLN02457, phenylalanine ammonia-lyase Back     alignment and domain information 
 Score =  882 bits (2282), Expect = 0.0
 Identities = 344/396 (86%), Positives = 367/396 (92%)

Query: 1   MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINS 60
           MEHILDGSSY++AA+K HE DPLQKPKQDRYALRTSPQWLGPQ EVIRA+TKSIEREINS
Sbjct: 311 MEHILDGSSYMKAAKKLHETDPLQKPKQDRYALRTSPQWLGPQIEVIRAATKSIEREINS 370

Query: 61  VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLP 120
           VNDNPLIDV+R+KALHGGNFQGTPIGVSMDN+RLAIA+IGKLMFAQFSELVNDFY+NGLP
Sbjct: 371 VNDNPLIDVARDKALHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLP 430

Query: 121 SNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARK 180
           SNLSGGRNP LDYGFKGAEIAMA+YCSELQ+LANPVTNHVQSAEQHNQDVNSLGLISARK
Sbjct: 431 SNLSGGRNPSLDYGFKGAEIAMASYCSELQYLANPVTNHVQSAEQHNQDVNSLGLISARK 490

Query: 181 TAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR 240
           TAEAVDILKLMSSTYL+ALCQAIDLRHLEENLKS VKNT+SQVAKK LT G NGELHPSR
Sbjct: 491 TAEAVDILKLMSSTYLVALCQAIDLRHLEENLKSAVKNTVSQVAKKTLTTGANGELHPSR 550

Query: 241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIG 300
           FCEKDLLKVVDRE VFSY DDPCSATYPLM+KLRQVLV+HAL N E  KNA+ S+F KIG
Sbjct: 551 FCEKDLLKVVDREPVFSYIDDPCSATYPLMQKLRQVLVEHALANGEAEKNASTSVFRKIG 610

Query: 301 AFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAIS 360
           AFEEELK  LPKEVE+AR A+E+G   IPNRIKECRSYPLYRFVREELG   LTGEK  S
Sbjct: 611 AFEEELKAALPKEVEAAREAYENGTAPIPNRIKECRSYPLYRFVREELGTELLTGEKTRS 670

Query: 361 PGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC 396
           PGEE DKVF AICQGK+IDPLLECLKEW+G+PLPIC
Sbjct: 671 PGEEFDKVFDAICQGKLIDPLLECLKEWNGAPLPIC 706

Length = 706
>gnl|CDD|130293 TIGR01226, phe_am_lyase, phenylalanine ammonia-lyase Back     alignment and domain information
>gnl|CDD|215800 pfam00221, Lyase_aromatic, Aromatic amino acid lyase Back     alignment and domain information
>gnl|CDD|176460 cd00332, PAL-HAL, Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL) Back     alignment and domain information
>gnl|CDD|225533 COG2986, HutH, Histidine ammonia-lyase [Amino acid transport and metabolism] Back     alignment and domain information
>gnl|CDD|163544 TIGR03832, Tyr_2_3_mutase, tyrosine 2,3-aminomutase Back     alignment and domain information
>gnl|CDD|200086 TIGR01225, hutH, histidine ammonia-lyase Back     alignment and domain information
>gnl|CDD|236484 PRK09367, PRK09367, histidine ammonia-lyase; Provisional Back     alignment and domain information
>gnl|CDD|176466 cd01594, Lyase_I_like, Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 396
PLN02457706 phenylalanine ammonia-lyase 100.0
KOG0222715 consensus Phenylalanine and histidine ammonia-lyas 100.0
TIGR01226680 phe_am_lyase phenylalanine ammonia-lyase. Members 100.0
COG2986498 HutH Histidine ammonia-lyase [Amino acid transport 100.0
TIGR01225506 hutH histidine ammonia-lyase. This enzyme deaminat 100.0
TIGR03832507 Tyr_2_3_mutase tyrosine 2,3-aminomutase. Members o 100.0
PRK09367500 histidine ammonia-lyase; Provisional 100.0
PF00221473 Lyase_aromatic: Aromatic amino acid lyase; InterPr 100.0
cd00332444 PAL-HAL Phenylalanine ammonia-lyase (PAL) and hist 100.0
cd01594231 Lyase_I_like Lyase class I_like superfamily: conta 99.35
>PLN02457 phenylalanine ammonia-lyase Back     alignment and domain information 
Probab=100.00  E-value=9.9e-119  Score=948.65  Aligned_cols=396  Identities=87%  Similarity=1.317  Sum_probs=383.2

Q ss_pred             ChhhhcCCccchhhhhcccCCCCCCCCCCcccccchhhhhhHHHHHHHHHHHHHHHHhhcCCCCCeeecCCCccccCCCC
Q 016039            1 MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNF   80 (396)
Q Consensus         1 ~r~lL~GS~l~~~~~~~~~~~~~~~~~QD~ySlR~~PQv~G~~~d~l~~a~~~i~~EiNS~~DNPli~~~~~~v~~ggNF   80 (396)
                      ||++|+||++++...+.+..+|..+++||||||||+||||||++|+|++++++|++||||+||||||++++++++|||||
T Consensus       311 ir~lL~GS~l~~~~~~~~~~~~~~~~vQD~YSLRc~PQvlGp~~d~l~~a~~~ie~ElNS~tDNPLId~~~~~vl~GGNF  390 (706)
T PLN02457        311 MEHILDGSSYMKAAKKLHETDPLQKPKQDRYALRTSPQWLGPQIEVIRAATKSIEREINSVNDNPLIDVARDKALHGGNF  390 (706)
T ss_pred             HHHHhCcCccchhhhhccccccccCcCCCchhhhhhhhhHHHHHHHHHHHHHHHHHHHhccCCCCceeCCCCceeeCCCC
Confidence            68999999999876655666766789999999999999999999999999999999999999999999988899999999


Q ss_pred             CcchhHHHhHhHHHHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCccccchHHHHHHHHHHHHHhhhcCCCCccc
Q 016039           81 QGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHV  160 (396)
Q Consensus        81 ~~~~va~a~d~l~~Ala~l~~~~~~r~~~L~~p~~~~gLP~~L~~~~~~~~~~g~~~~q~~~aal~aE~~~La~P~s~~~  160 (396)
                      ||+||+++||++++||+++|++++||+++|+||.+|+|||+||+++++||++||||++||++|||++||++||||+|+|+
T Consensus       391 ~g~~va~amD~l~lAla~lg~ls~rr~~~Lvnp~~n~GLP~fL~~~~~pgl~~Gf~~~q~taAAl~sEl~~LA~PvS~~~  470 (706)
T PLN02457        391 QGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQYLANPVTNHV  470 (706)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccCCCCHhhcCCCCCCcccccHHHHHHHHHHHHHHHHhcCCCccCc
Confidence            99999999999999999999999999999999999999999999756899999999999999999999999999999999


Q ss_pred             ccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHhcCCCCCCCCCc
Q 016039          161 QSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR  240 (396)
Q Consensus       161 ~~~~~~~eD~~S~a~~aar~~~~~v~~l~~i~A~ell~a~QA~dlR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~dR  240 (396)
                      +|+++|||||||||++||||+.+++|++++|+||||+++|||+|||+++++|+++++++++++|+++++.+.++.+.+.|
T Consensus       471 ~pt~~~nED~~Smg~~sArkt~e~ve~l~~~lAieLl~a~QAlDLR~~~~~l~~~~~~~~~~vr~~v~~~~~~~~~~~~~  550 (706)
T PLN02457        471 QSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLVALCQAIDLRHLEENLKSAVKNTVSQVAKKTLTTGANGELHPSR  550 (706)
T ss_pred             ccccCCccccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHccccCCCccccccc
Confidence            99999999999999999999999999999999999999999999999888999999999999999999998899999999


Q ss_pred             cCHHHHHHHHhhhccccccCCCCCCchHHHHHHHHHHHHHHhcccccccCcchhHhhhHHHHHHHHHhhcHHHHHHHHHH
Q 016039          241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSA  320 (396)
Q Consensus       241 ~~~~dl~~~~~~~~~~~~~~d~~~~~~~l~~~l~~vl~~~~l~~~~~~~~~~~~~~~~i~~fe~el~~~L~~~~~~~R~a  320 (396)
                      ++++|+.+++++.++|+|+||||+++||+|++++++||+|++++++.+++..+++|++|..|+++++.+|+++|+++|++
T Consensus       551 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~f~~~~~~~l~~~~~~~r~~  630 (706)
T PLN02457        551 FCEKDLLKVVDREPVFSYIDDPCSATYPLMQKLRQVLVEHALANGEAEKNASTSVFRKIGAFEEELKAALPKEVEAAREA  630 (706)
T ss_pred             cCHHHHHHHHhhcceecccCCCcccchhHHHHHHHHHHHHHhhCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999998877777778999999999999999999999999999


Q ss_pred             hhcCCCCCccccccCCcchhHHHHHhhhCccccccccccCCCccHHHHHHHHhcCcchhhHHHhhccccCCCCCCC
Q 016039          321 FESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC  396 (396)
Q Consensus       321 f~~g~~~~~~~i~~~~S~pLY~FVR~eLgvp~~~G~~~~T~G~~is~IyeAIr~G~l~d~ll~cl~~~~~~p~~~~  396 (396)
                      |++|..++||+|++|||||||+|||+|||||||+|++++|||+||||||+|||+|+|++|||+||++|+|+|+|||
T Consensus       631 ~~~~~~~~~~ri~~~~s~~lY~fVR~~L~~~~~~g~~~~~~g~~~~~v~~ai~~g~~~~~l~~~~~~~~~~~~~~~  706 (706)
T PLN02457        631 YENGTAPIPNRIKECRSYPLYRFVREELGTELLTGEKTRSPGEEFDKVFDAICQGKLIDPLLECLKEWNGAPLPIC  706 (706)
T ss_pred             HhcCCccccchhhcCcchHHHHHHHHHcCCccccCCCCCCCCccHHHHHHHHHCCccHHHHHHHHHhcCCCCCCCC
Confidence            9999888999999999999999999999999999999999999999999999999999999999999999999998

>KOG0222 consensus Phenylalanine and histidine ammonia-lyase [Secondary metabolites biosynthesis, transport and catabolism] Back     alignment and domain information
>TIGR01226 phe_am_lyase phenylalanine ammonia-lyase Back     alignment and domain information
>COG2986 HutH Histidine ammonia-lyase [Amino acid transport and metabolism] Back     alignment and domain information
>TIGR01225 hutH histidine ammonia-lyase Back     alignment and domain information
>TIGR03832 Tyr_2_3_mutase tyrosine 2,3-aminomutase Back     alignment and domain information
>PRK09367 histidine ammonia-lyase; Provisional Back     alignment and domain information
>PF00221 Lyase_aromatic: Aromatic amino acid lyase; InterPro: IPR001106 This entry represents phenylalanine ammonia-lyase (PAL; 4 Back     alignment and domain information
>cd00332 PAL-HAL Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL) Back     alignment and domain information
>cd01594 Lyase_I_like Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions 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 ?
Query396
1w27_A714 Phenylalanine Ammonia-Lyase (Pal) From Petroselinum 0.0
2yii_A705 Manipulating The Regioselectivity Of Phenylalanine 3e-99
4baa_A705 Redesign Of A Phenylalanine Aminomutase Into A Beta 4e-99
3nz4_A696 Crystal Structure Of A Taxus Phenylalanine Aminomut 4e-98
1t6j_A714 Crystal Structure Of Phenylalanine Ammonia Lyase Fr 5e-49
1y2m_A716 Crystal Structure Of Phenylalanine Ammonia-Lyase Fr 6e-49
2nyf_A567 Crystal Structure Of Phenylalanine Ammonia-Lyase Fr 3e-31
2nyn_A565 Crystal Structure Of Phenylalanine Ammonia-Lyase Fr 8e-31
3czo_A539 Crystal Structure Of Double Mutant Phenylalanine Am 2e-29
3unv_A547 Pantoea Agglomerans Phenylalanine Aminomutase Lengt 4e-24
2qve_A526 Crystal Structure Of Sgtam Bound To Mechanism Based 1e-22
2rjr_A537 Substrate Mimic Bound To Sgtam Length = 537 1e-22
3kdy_A537 X-Ray Crystal Structure Of Tyrosine Aminomutase Mut 1e-22
3kdz_A537 X-Ray Crystal Structure Of A Tyrosine Aminomutase M 1e-22
2ohy_A539 X-Ray Crystal Structure Of Tyrosine Aminomutase Fro 1e-22
2o6y_A521 Tyrosine Ammonia-Lyase From Rhodobacter Sphaeroides 1e-19
2o78_A521 Tyrosine Ammonia-lyase From Rhodobacter Sphaeroides 1e-19
1gk3_A509 Histidine Ammonia-Lyase (Hal) Mutant D145a From Pse 2e-16
1gkm_A507 Histidine Ammonia-Lyase (Hal) From Pseudomonas Puti 3e-16
1gkj_A507 Histidine Ammonia-Lyase (Hal) Mutant Y280f From Pse 6e-16
1eb4_A507 Histidine Ammonia-Lyase (Hal) Mutant F329a From Pse 3e-15
1gk2_A509 Histidine Ammonia-Lyase (Hal) Mutant F329g From Pse 3e-15
>pdb|1W27|A Chain A, Phenylalanine Ammonia-Lyase (Pal) From Petroselinum Crispum Length = 714 Back     alignment and structure 
Iteration: 1

 Score =  714 bits (1843), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 330/396 (83%), Positives = 368/396 (92%)
Query: 1   MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINS 60
           MEHILDGS+YV+AAQK HE+DPLQKPKQDRYALRTSPQWLGPQ EVIR+STK IEREINS
Sbjct: 319 MEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINS 378
Query: 61  VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLP 120
           VNDNPLIDVSRNKA+HGGNFQGTPIGVSMDN+RLAIA+IGKLMFAQFSELVNDFY+NGLP
Sbjct: 379 VNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLP 438
Query: 121 SNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARK 180
           SNLSGGRNP LDYGFKGAEIAMA+YCSELQFLANPVTNHVQSAEQHNQDVNSLGLIS+RK
Sbjct: 439 SNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRK 498
Query: 181 TAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR 240
           T+EAV+ILKLMS+T+L+ LCQAIDLRHLEENLKSTVKNT+S VAK+VLTMGVNGELHPSR
Sbjct: 499 TSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSR 558
Query: 241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIG 300
           FCEKDLL+VVDREY+F+Y DDPCSATYPLM+KLRQ LV+HAL N ++ +N + SIF KI 
Sbjct: 559 FCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIA 618
Query: 301 AFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAIS 360
            FE+ELK LLPKEVESAR+A ESGN  IPNRI+ECRSYPLY+FVR+ELG  YLTGEK  S
Sbjct: 619 TFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTS 678
Query: 361 PGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC 396
           PGEE +KVF A+ +G+IIDPLLECL+ W+G+PLPIC
Sbjct: 679 PGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC 714
>pdb|2YII|A Chain A, Manipulating The Regioselectivity Of Phenylalanine Aminomutase: New Insights Into The Reaction Mechanism Of Mio-dependent Enzymes From Structure-guided Directed Evolution Length = 705 Back     alignment and structure
>pdb|4BAA|A Chain A, Redesign Of A Phenylalanine Aminomutase Into A Beta- Phenylalanine Ammonia Lyase Length = 705 Back     alignment and structure
>pdb|3NZ4|A Chain A, Crystal Structure Of A Taxus Phenylalanine Aminomutase Length = 696 Back     alignment and structure
>pdb|1T6J|A Chain A, Crystal Structure Of Phenylalanine Ammonia Lyase From Rhodosporidium Toruloides Length = 714 Back     alignment and structure
>pdb|1Y2M|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From Yeast Rhododporidium Toruloides Length = 716 Back     alignment and structure
>pdb|2NYF|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From Nostoc Punctiforme Length = 567 Back     alignment and structure
>pdb|2NYN|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From Anabaena Variabilis Length = 565 Back     alignment and structure
>pdb|3CZO|A Chain A, Crystal Structure Of Double Mutant Phenylalanine Ammonia-Lyase From Anabaena Variabilis Length = 539 Back     alignment and structure
>pdb|3UNV|A Chain A, Pantoea Agglomerans Phenylalanine Aminomutase Length = 547 Back     alignment and structure
>pdb|2QVE|A Chain A, Crystal Structure Of Sgtam Bound To Mechanism Based Inhibitor Length = 526 Back     alignment and structure
>pdb|2RJR|A Chain A, Substrate Mimic Bound To Sgtam Length = 537 Back     alignment and structure
>pdb|3KDY|A Chain A, X-Ray Crystal Structure Of Tyrosine Aminomutase Mutant Construct Length = 537 Back     alignment and structure
>pdb|3KDZ|A Chain A, X-Ray Crystal Structure Of A Tyrosine Aminomutase Mutant Construct With Bound Ligand Length = 537 Back     alignment and structure
>pdb|2OHY|A Chain A, X-Ray Crystal Structure Of Tyrosine Aminomutase From Streptomyces Globisporus Length = 539 Back     alignment and structure
>pdb|2O6Y|A Chain A, Tyrosine Ammonia-Lyase From Rhodobacter Sphaeroides Length = 521 Back     alignment and structure
>pdb|2O78|A Chain A, Tyrosine Ammonia-lyase From Rhodobacter Sphaeroides (his89phe Variant) Complexed With Cinnamic Acid Length = 521 Back     alignment and structure
>pdb|1GK3|A Chain A, Histidine Ammonia-Lyase (Hal) Mutant D145a From Pseudomonas Putida Length = 509 Back     alignment and structure
>pdb|1GKM|A Chain A, Histidine Ammonia-Lyase (Hal) From Pseudomonas Putida Inhibited With L-Cysteine Length = 507 Back     alignment and structure
>pdb|1GKJ|A Chain A, Histidine Ammonia-Lyase (Hal) Mutant Y280f From Pseudomonas Putida Length = 507 Back     alignment and structure
>pdb|1EB4|A Chain A, Histidine Ammonia-Lyase (Hal) Mutant F329a From Pseudomonas Putida Length = 507 Back     alignment and structure
>pdb|1GK2|A Chain A, Histidine Ammonia-Lyase (Hal) Mutant F329g From Pseudomonas Putida Length = 509 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 ?
Query396
1w27_A714 Phenylalanine ammonia-lyase 1; phenylpropanoid met 0.0
2yii_A705 Phenylalanine ammonia-lyase; HET: MDO; 2.18A {Taxu 0.0
1y2m_A716 Phenylalanine ammonia-lyase; alpha helices; HET: M 1e-168
2qve_A526 Tyrosine aminomutase; MIO, enediyne, transferase; 4e-99
3unv_A547 ADMH; MIO, lyase; HET: KWS SFE PHE; 1.54A {Pantoea 6e-93
2o6y_A521 Putative histidine ammonia-lyase; methylidene imid 3e-90
2nyn_A565 Phenylalanine/histidine ammonia-lyase; methylidene 1e-79
1gkm_A507 Histidase, HAL, histidine ammonia-lyase; histidine 3e-78
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-04
>1w27_A Phenylalanine ammonia-lyase 1; phenylpropanoid metabolism, MIO; HET: MDO; 1.7A {Petroselinum crispum} SCOP: a.127.1.2 Length = 714 Back     alignment and structure
 Score =  594 bits (1534), Expect = 0.0
 Identities = 330/396 (83%), Positives = 368/396 (92%)

Query: 1   MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINS 60
           MEHILDGS+YV+AAQK HE+DPLQKPKQDRYALRTSPQWLGPQ EVIR+STK IEREINS
Sbjct: 319 MEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINS 378

Query: 61  VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLP 120
           VNDNPLIDVSRNKA+HGGNFQGTPIGVSMDN+RLAIA+IGKLMFAQFSELVNDFY+NGLP
Sbjct: 379 VNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLP 438

Query: 121 SNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARK 180
           SNLSGGRNP LDYGFKGAEIAMA+YCSELQFLANPVTNHVQSAEQHNQDVNSLGLIS+RK
Sbjct: 439 SNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRK 498

Query: 181 TAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR 240
           T+EAV+ILKLMS+T+L+ LCQAIDLRHLEENLKSTVKNT+S VAK+VLTMGVNGELHPSR
Sbjct: 499 TSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSR 558

Query: 241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIG 300
           FCEKDLL+VVDREY+F+Y DDPCSATYPLM+KLRQ LV+HAL N ++ +N + SIF KI 
Sbjct: 559 FCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIA 618

Query: 301 AFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAIS 360
            FE+ELK LLPKEVESAR+A ESGN  IPNRI+ECRSYPLY+FVR+ELG  YLTGEK  S
Sbjct: 619 TFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTS 678

Query: 361 PGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC 396
           PGEE +KVF A+ +G+IIDPLLECL+ W+G+PLPIC
Sbjct: 679 PGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC 714
>2yii_A Phenylalanine ammonia-lyase; HET: MDO; 2.18A {Taxus wallichiana var} PDB: 3nz4_A* Length = 705 Back     alignment and structure
>1y2m_A Phenylalanine ammonia-lyase; alpha helices; HET: MSE; 1.60A {Rhodosporidium toruloides} PDB: 1t6j_A* 1t6p_A* Length = 716 Back     alignment and structure
>2qve_A Tyrosine aminomutase; MIO, enediyne, transferase; HET: MDO 247; 2.00A {Streptomyces globisporus} PDB: 2rjr_A* 2rjs_A* 2ohy_A* 3kdz_A* 3kdy_A* Length = 526 Back     alignment and structure
>3unv_A ADMH; MIO, lyase; HET: KWS SFE PHE; 1.54A {Pantoea agglomerans} Length = 547 Back     alignment and structure
>2o6y_A Putative histidine ammonia-lyase; methylidene imidazolone prosthetic group; HET: MDO; 1.50A {Rhodobacter sphaeroides} PDB: 2o7b_A* 2o7d_A* 2o7e_A* 2o78_A* 2o7f_A* Length = 521 Back     alignment and structure
>2nyn_A Phenylalanine/histidine ammonia-lyase; methylidene imidazolone prosthetic group; HET: MDO; 1.90A {Anabaena variabilis} PDB: 3czo_A* 2nyf_A* Length = 565 Back     alignment and structure
>1gkm_A Histidase, HAL, histidine ammonia-lyase; histidine degradation; HET: MDO; 1.0A {Pseudomonas putida} SCOP: a.127.1.2 PDB: 1b8f_A* 1gkj_A* 1eb4_A* 1gk3_A 1gk2_A Length = 507 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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query396
1w27_A714 Phenylalanine ammonia-lyase 1; phenylpropanoid met 100.0
2yii_A705 Phenylalanine ammonia-lyase; HET: MDO; 2.18A {Taxu 100.0
1y2m_A716 Phenylalanine ammonia-lyase; alpha helices; HET: M 100.0
3unv_A547 ADMH; MIO, lyase; HET: KWS SFE PHE; 1.54A {Pantoea 100.0
2nyn_A565 Phenylalanine/histidine ammonia-lyase; methylidene 100.0
1gkm_A507 Histidase, HAL, histidine ammonia-lyase; histidine 100.0
2qve_A526 Tyrosine aminomutase; MIO, enediyne, transferase; 100.0
2o6y_A521 Putative histidine ammonia-lyase; methylidene imid 100.0
>1w27_A Phenylalanine ammonia-lyase 1; phenylpropanoid metabolism, MIO; HET: MDO; 1.7A {Petroselinum crispum} SCOP: a.127.1.2 Back     alignment and structure
Probab=100.00  E-value=1.5e-116  Score=934.12  Aligned_cols=396  Identities=83%  Similarity=1.307  Sum_probs=382.1

Q ss_pred             ChhhhcCCccchhhhhcccCCCCCCCCCCcccccchhhhhhHHHHHHHHHHHHHHHHhhcCCCCCeeecCCCccccCCCC
Q 016039            1 MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNF   80 (396)
Q Consensus         1 ~r~lL~GS~l~~~~~~~~~~~~~~~~~QD~ySlR~~PQv~G~~~d~l~~a~~~i~~EiNS~~DNPli~~~~~~v~~ggNF   80 (396)
                      ||++|+||++++...+.+..|+..+++||||||||+||||||++|+|++++++|++||||++|||+|++++|+++|||||
T Consensus       319 ir~lL~gS~l~~~~~~~~~~~~~~~rvQD~YSlRc~PQV~Ga~~d~l~~a~~~le~ElNS~tDNPlI~~~~g~v~sGGNF  398 (714)
T 1w27_A          319 MEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINSVNDNPLIDVSRNKAIHGGNF  398 (714)
T ss_dssp             HHHHHHTCSSCCCCCSSCSSCCCCSSSCCCHHHHTHHHHHHHHHHHHHHHHHHHHHHTTSCCCSSEEETTTTEEECCCTT
T ss_pred             HHHHhCccchhhhcccccccCcccCcCcCcceecchhhhhHHHHHHHHHHHHHHHHHHhcCCCCCeeeCCCCceeeCCCc
Confidence            68999999999887544555666689999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchhHHHhHhHHHHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCccccchHHHHHHHHHHHHHhhhcCCCCccc
Q 016039           81 QGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHV  160 (396)
Q Consensus        81 ~~~~va~a~d~l~~Ala~l~~~~~~r~~~L~~p~~~~gLP~~L~~~~~~~~~~g~~~~q~~~aal~aE~~~La~P~s~~~  160 (396)
                      ||+||++|||++++|++++|++++||+.+|+||.+|+|||+||+++++||+|||||++||++|||++|||+||+|+|+|+
T Consensus       399 hg~pvA~AmD~L~iAla~lg~lserR~~~Lvdp~~~~GLP~fL~~~~~~glnsGfmi~Q~taAal~sEnk~LA~PaSvds  478 (714)
T 1w27_A          399 QGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHV  478 (714)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTTSTTCCGGGCCSSCGGGCCTTHHHHHHHHHHHHHHHHHTSCSTTCC
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChhhcCCCCCCcccchHHHHHHHHHHHHHHHHhcCCCccCC
Confidence            99999999999999999999999999999999999889999999766899999999999999999999999999999999


Q ss_pred             ccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHhcCCCCCCCCCc
Q 016039          161 QSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR  240 (396)
Q Consensus       161 ~~~~~~~eD~~S~a~~aar~~~~~v~~l~~i~A~ell~a~QA~dlR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~dR  240 (396)
                      +|+++|||||||||++||||+.+++||+++|+|||||++|||+|||+++.+++++++++++++++++++++.++.+.+.|
T Consensus       479 ~pts~~qEDhvSmg~~aArk~~~~venl~~vlAiELl~a~QAiDlR~~~~~~~~~~~~~~~~~r~~v~~~~~~~~~~~~~  558 (714)
T 1w27_A          479 QSAEQHNQDVNSLGLISSRKTSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSR  558 (714)
T ss_dssp             CCBTTTTBSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCBTTTBCCSSCH
T ss_pred             ccccCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHhccCCCccccccc
Confidence            99999999999999999999999999999999999999999999999889999999999999999999999999999999


Q ss_pred             cCHHHHHHHHhhhccccccCCCCCCchHHHHHHHHHHHHHHhcccccccCcchhHhhhHHHHHHHHHhhcHHHHHHHHHH
Q 016039          241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSA  320 (396)
Q Consensus       241 ~~~~dl~~~~~~~~~~~~~~d~~~~~~~l~~~l~~vl~~~~l~~~~~~~~~~~~~~~~i~~fe~el~~~L~~~~~~~R~a  320 (396)
                      ++++++.+++++.++|.|++|||+.+||+|+|++++||+|++++++.+++..+++|++|+.|+++++.+|+++|+++|++
T Consensus       559 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~r~~  638 (714)
T 1w27_A          559 FCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIATFEDELKALLPKEVESARAA  638 (714)
T ss_dssp             HHHHHHHHHHHHSCGGGTTTSTTCTTSHHHHHHHHHHHHHHHTSGGGGGSGGGCSGGGHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHhhhHHHHhhcCcccccchHHHHHHHHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999988766766677889999999999999999999999999


Q ss_pred             hhcCCCCCccccccCCcchhHHHHHhhhCccccccccccCCCccHHHHHHHHhcCcchhhHHHhhccccCCCCCCC
Q 016039          321 FESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC  396 (396)
Q Consensus       321 f~~g~~~~~~~i~~~~S~pLY~FVR~eLgvp~~~G~~~~T~G~~is~IyeAIr~G~l~d~ll~cl~~~~~~p~~~~  396 (396)
                      |++|++++|++|++|||||||+|||+|||||||+|++++|||+||||||+|||+|+|++|||+||++|+|+|+|||
T Consensus       639 f~~g~~~~~~~i~~~~s~~lY~fVR~~Lg~~~~~g~~~~~~g~~~~~i~~ai~~g~~~~~l~~~~~~~~~~~~~~~  714 (714)
T 1w27_A          639 LESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTSPGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC  714 (714)
T ss_dssp             HHTTCCSSCCGGGGSTTHHHHHHHHTTSCCCCCCTTSSCCHHHHHHHHHHHHHTTTTHHHHHHTTTTCCSSCCCCC
T ss_pred             HhcCCcCccchhhcCCchhHHHHHHHHcCCCcccCCCCCCCchhHHHHHHHHHCCccHHHHHHHHhhhcCCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999998
>2yii_A Phenylalanine ammonia-lyase; HET: MDO; 2.18A {Taxus wallichiana var} PDB: 3nz4_A* Back     alignment and structure
>1y2m_A Phenylalanine ammonia-lyase; alpha helices; HET: MSE; 1.60A {Rhodosporidium toruloides} PDB: 1t6j_A* 1t6p_A* Back     alignment and structure
>3unv_A ADMH; MIO, lyase; HET: KWS SFE PHE; 1.54A {Pantoea agglomerans} Back     alignment and structure
>2nyn_A Phenylalanine/histidine ammonia-lyase; methylidene imidazolone prosthetic group; HET: MDO; 1.90A {Anabaena variabilis} PDB: 3czo_A* 2nyf_A* Back     alignment and structure
>1gkm_A Histidase, HAL, histidine ammonia-lyase; histidine degradation; HET: MDO; 1.0A {Pseudomonas putida} SCOP: a.127.1.2 PDB: 1b8f_A* 1gkj_A* 1eb4_A* 1gk3_A 1gk2_A Back     alignment and structure
>2qve_A Tyrosine aminomutase; MIO, enediyne, transferase; HET: MDO 247; 2.00A {Streptomyces globisporus} PDB: 2rjr_A* 2rjs_A* 2ohy_A* 3kdz_A* 3kdy_A* Back     alignment and structure
>2o6y_A Putative histidine ammonia-lyase; methylidene imidazolone prosthetic group; HET: MDO; 1.50A {Rhodobacter sphaeroides} PDB: 2o7b_A* 2o7d_A* 2o7e_A* 2o78_A* 2o7f_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 396
d1w27a_692 a.127.1.2 (A:) Phenylalanine ammonia-lyase, PAL {P 0.0
d1t6ja_678 a.127.1.2 (A:) Phenylalanine ammonia-lyase, PAL {F 1e-143
d1gkma_509 a.127.1.2 (A:) Histidine ammonia-lyase (HAL) {Pseu 7e-62
>d1w27a_ a.127.1.2 (A:) Phenylalanine ammonia-lyase, PAL {Parsley (Petroselinum crispum), PAL1 [TaxId: 4043]} Length = 692 Back     information, alignment and structure

class: All alpha proteins
fold: L-aspartase-like
superfamily: L-aspartase-like
family: HAL/PAL-like
domain: Phenylalanine ammonia-lyase, PAL
species: Parsley (Petroselinum crispum), PAL1 [TaxId: 4043]

 Score =  564 bits (1455), Expect = 0.0
 Identities = 330/396 (83%), Positives = 368/396 (92%)

Query: 1   MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINS 60
           MEHILDGS+YV+AAQK HE+DPLQKPKQDRYALRTSPQWLGPQ EVIR+STK IEREINS
Sbjct: 297 MEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINS 356

Query: 61  VNDNPLIDVSRNKALHGGNFQGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLP 120
           VNDNPLIDVSRNKA+HGGNFQGTPIGVSMDN+RLAIA+IGKLMFAQFSELVNDFY+NGLP
Sbjct: 357 VNDNPLIDVSRNKAIHGGNFQGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLP 416

Query: 121 SNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISARK 180
           SNLSGGRNP LDYGFKGAEIAMA+YCSELQFLANPVTNHVQSAEQHNQDVNSLGLIS+RK
Sbjct: 417 SNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHVQSAEQHNQDVNSLGLISSRK 476

Query: 181 TAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR 240
           T+EAV+ILKLMS+T+L+ LCQAIDLRHLEENLKSTVKNT+S VAK+VLTMGVNGELHPSR
Sbjct: 477 TSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSR 536

Query: 241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIG 300
           FCEKDLL+VVDREY+F+Y DDPCSATYPLM+KLRQ LV+HAL N ++ +N + SIF KI 
Sbjct: 537 FCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIA 596

Query: 301 AFEEELKTLLPKEVESARSAFESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAIS 360
            FE+ELK LLPKEVESAR+A ESGN  IPNRI+ECRSYPLY+FVR+ELG  YLTGEK  S
Sbjct: 597 TFEDELKALLPKEVESARAALESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTS 656

Query: 361 PGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC 396
           PGEE +KVF A+ +G+IIDPLLECL+ W+G+PLPIC
Sbjct: 657 PGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC 692
>d1t6ja_ a.127.1.2 (A:) Phenylalanine ammonia-lyase, PAL {Fungi (Rhodosporidium toruloides) [TaxId: 5286]} Length = 678 Back     information, alignment and structure
>d1gkma_ a.127.1.2 (A:) Histidine ammonia-lyase (HAL) {Pseudomonas putida [TaxId: 303]} Length = 509 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 ?
Query396
d1w27a_692 Phenylalanine ammonia-lyase, PAL {Parsley (Petrose 100.0
d1t6ja_678 Phenylalanine ammonia-lyase, PAL {Fungi (Rhodospor 100.0
d1gkma_509 Histidine ammonia-lyase (HAL) {Pseudomonas putida 100.0
>d1w27a_ a.127.1.2 (A:) Phenylalanine ammonia-lyase, PAL {Parsley (Petroselinum crispum), PAL1 [TaxId: 4043]} Back     information, alignment and structure
class: All alpha proteins
fold: L-aspartase-like
superfamily: L-aspartase-like
family: HAL/PAL-like
domain: Phenylalanine ammonia-lyase, PAL
species: Parsley (Petroselinum crispum), PAL1 [TaxId: 4043]

Probab=100.00  E-value=7.1e-120  Score=955.71  Aligned_cols=396  Identities=83%  Similarity=1.307  Sum_probs=388.3

Q ss_pred             ChhhhcCCccchhhhhcccCCCCCCCCCCcccccchhhhhhHHHHHHHHHHHHHHHHhhcCCCCCeeecCCCccccCCCC
Q 016039            1 MEHILDGSSYVEAAQKFHEIDPLQKPKQDRYALRTSPQWLGPQAEVIRASTKSIEREINSVNDNPLIDVSRNKALHGGNF   80 (396)
Q Consensus         1 ~r~lL~GS~l~~~~~~~~~~~~~~~~~QD~ySlR~~PQv~G~~~d~l~~a~~~i~~EiNS~~DNPli~~~~~~v~~ggNF   80 (396)
                      ||++|+||++++..++.+..++..+++||||||||+||||||++|+|++++++|++||||++|||+||+++++++|||||
T Consensus       297 ir~lL~gS~l~~~~~~~~~~~~~~~~vQD~YSlRc~PQv~Ga~~d~l~~a~~~ie~ElNS~tDNPlI~~~~~~v~sgGNF  376 (692)
T d1w27a_         297 MEHILDGSAYVKAAQKLHEMDPLQKPKQDRYALRTSPQWLGPQIEVIRSSTKMIEREINSVNDNPLIDVSRNKAIHGGNF  376 (692)
T ss_dssp             HHHHHHTCSSCCCCCSSCSSCCCCSSSCCCHHHHTHHHHHHHHHHHHHHHHHHHHHHTTSCCCSSEEETTTTEEECCCTT
T ss_pred             HHHHhcCChhhhhhhhhccccccccccCCccchhhHHHHHHHHHHHHHHHHHHHHHHHhccCCCceeecCCCceeecCcc
Confidence            68999999999998888888899999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchhHHHhHhHHHHHHHHHHHHHHHHHHhcccccCCCCCCCCCCCCCCCccccchHHHHHHHHHHHHHhhhcCCCCccc
Q 016039           81 QGTPIGVSMDNSRLAIASIGKLMFAQFSELVNDFYSNGLPSNLSGGRNPCLDYGFKGAEIAMAAYCSELQFLANPVTNHV  160 (396)
Q Consensus        81 ~~~~va~a~d~l~~Ala~l~~~~~~r~~~L~~p~~~~gLP~~L~~~~~~~~~~g~~~~q~~~aal~aE~~~La~P~s~~~  160 (396)
                      ||+||+++||++++||+++|++++||+.+|+||.+|+|||+||+++++||++||||++||++|||++|||+||+|+|+|+
T Consensus       377 hg~~ia~amD~l~iAla~lg~lserR~~~Lvnp~~~~GLP~fL~~~~~pgl~~Gf~~~q~taaal~sE~~~LA~P~S~~s  456 (692)
T d1w27a_         377 QGTPIGVSMDNTRLAIAAIGKLMFAQFSELVNDFYNNGLPSNLSGGRNPSLDYGFKGAEIAMASYCSELQFLANPVTNHV  456 (692)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTTSTTCCGGGCCSSCGGGCCTTHHHHHHHHHHHHHHHHHTSCSTTCC
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCChhhcCCCCCccccccHHHHHHHHHHHHHHHHhcCCcccCc
Confidence            99999999999999999999999999999999999999999999866899999999999999999999999999999999


Q ss_pred             ccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHhcCCCCCCCCCc
Q 016039          161 QSAEQHNQDVNSLGLISARKTAEAVDILKLMSSTYLIALCQAIDLRHLEENLKSTVKNTISQVAKKVLTMGVNGELHPSR  240 (396)
Q Consensus       161 ~~~~~~~eD~~S~a~~aar~~~~~v~~l~~i~A~ell~a~QA~dlR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~dR  240 (396)
                      +|+++|||||||||++||||+.+++|++++|+||||+++|||+|||+.+.+++++++++|+++|+++++.+.|+++.+||
T Consensus       457 ~~ts~~~ED~~Smg~~sArk~~~~ve~l~~ilAieLl~a~QAiDLR~~~~~~~~~~~~~~~~vr~~v~~~~~Dr~l~~d~  536 (692)
T d1w27a_         457 QSAEQHNQDVNSLGLISSRKTSEAVEILKLMSTTFLVGLCQAIDLRHLEENLKSTVKNTVSSVAKRVLTMGVNGELHPSR  536 (692)
T ss_dssp             CCBTTTTBSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCBTTTBCCSSCH
T ss_pred             ccccCccccccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccChHHHHHHHHHHHhCCcccCCCCCCcch
Confidence            99999999999999999999999999999999999999999999999989999999999999999999999999999999


Q ss_pred             cCHHHHHHHHhhhccccccCCCCCCchHHHHHHHHHHHHHHhcccccccCcchhHhhhHHHHHHHHHhhcHHHHHHHHHH
Q 016039          241 FCEKDLLKVVDREYVFSYADDPCSATYPLMRKLRQVLVDHALTNNEDLKNANASIFLKIGAFEEELKTLLPKEVESARSA  320 (396)
Q Consensus       241 ~~~~dl~~~~~~~~~~~~~~d~~~~~~~l~~~l~~vl~~~~l~~~~~~~~~~~~~~~~i~~fe~el~~~L~~~~~~~R~a  320 (396)
                      ++++|+.+++++.++|+|+||||+.+||||+|+++++++|++++.+.+++..+++|++|+.|+++++.+|+++|+++|++
T Consensus       537 ~~~~dl~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~  616 (692)
T d1w27a_         537 FCEKDLLRVVDREYIFAYIDDPCSATYPLMQKLRQTLVEHALKNGDNERNLSTSIFQKIATFEDELKALLPKEVESARAA  616 (692)
T ss_dssp             HHHHHHHHHHHHSCGGGTTTSTTCTTSHHHHHHHHHHHHHHHTSGGGGGSGGGCSGGGHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHhhhhhhhccCcccccchHHHHHHHHHHHHHhhccccccCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999888888888899999999999999999999999999


Q ss_pred             hhcCCCCCccccccCCcchhHHHHHhhhCccccccccccCCCccHHHHHHHHhcCcchhhHHHhhccccCCCCCCC
Q 016039          321 FESGNLEIPNRIKECRSYPLYRFVREELGARYLTGEKAISPGEECDKVFTAICQGKIIDPLLECLKEWDGSPLPIC  396 (396)
Q Consensus       321 f~~g~~~~~~~i~~~~S~pLY~FVR~eLgvp~~~G~~~~T~G~~is~IyeAIr~G~l~d~ll~cl~~~~~~p~~~~  396 (396)
                      |++|.+++||+|++|||||||+|||+|||||||+|++++|||+||||||+|||+|+|++|||+||++|+|+|+|||
T Consensus       617 ~~~~~~~~~~~~~~~~s~~ly~fvR~~l~~~~~~g~~~~~~g~~~~~v~~ai~~g~~~~~~~~~l~~~~~~~~~~~  692 (692)
T d1w27a_         617 LESGNPAIPNRIEECRSYPLYKFVRKELGTEYLTGEKVTSPGEEFEKVFIAMSKGEIIDPLLECLESWNGAPLPIC  692 (692)
T ss_dssp             HHTTCCSSCCGGGGSTTHHHHHHHHTTSCCCCCCTTSSCCHHHHHHHHHHHHHTTTTHHHHHHTTTTCCSSCCCCC
T ss_pred             HhcCCccchhhhcCCcchHHHHHHHHHcCCCccCCCCCCCCcccHHHHHHHHHcCCchHHHHHHHhhcCCCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999
>d1t6ja_ a.127.1.2 (A:) Phenylalanine ammonia-lyase, PAL {Fungi (Rhodosporidium toruloides) [TaxId: 5286]} Back     information, alignment and structure
>d1gkma_ a.127.1.2 (A:) Histidine ammonia-lyase (HAL) {Pseudomonas putida [TaxId: 303]} Back     information, alignment and structure