Citrus Sinensis ID: 011172

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-------490--

MWRNLARQSSTRNFKFSPSKVSQTTNFLKKITSLETQTLLDSSCPLLGFRRTSFLSSQKSNLGQSNFTQSIYPFGVLTSRSYASAAEAIASESELSGSEEVQELIDQFNEKGVSILDSSSMLDKQPKKKGTGMGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGISS

cHHHHHHHHHccccccccccccccccccccccHHHHHHcccccccccccccccccHHHHHHccccccccccccccccccccHHHHHHHHcccccccccHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEEHHHHHHccccEEEEEEccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHcccccEEcHHHHHHHHHHHHcccccccc

cHHHHHHHHHHcccccccccccccccHccccccccccccccccccccccccccEEcccccccccccccccccccccccccccEEHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHEEEEEHHcccccEEEEEEccHHHHHHHHcccccccccccccccccccccccccccEEEcccEEEEEcccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc

mwrnlarqsstrnfkfspskvsqtTNFLKKITSLETQtlldsscpllgfrrtsflssqksnlgqsnftqsiypfgvltsrsYASAAEAIAseselsgsEEVQELIDQFNEKGvsildsssmldkqpkkkgtgmgtaKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEqklapnlpyvkslflgwFEPLRDAIAKDQATAQDkwkhmtyapyfnnlpaDMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKStkkknatdnnlegdsepltndpeKLIKEQEKLKKRVTSLIKKQKLQQVRGIVkghvdskpwgqdALVKVGCRLIQLLMEtayiqppvdqlgdsppdirpAFVHTLKSFTKEAlkgrrygviecdplVRKGLEktgrhmiipympmlvpplnwrgynrgghfflpsyvmrthgarqqretikmtprsqlepvfQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGISS

mwrnlarqsstrnfkfspskvsqttNFLKKITSLETQTLLDSSCPLLGFRRTSFLssqksnlgqsnfTQSIYPFGVLTSRSYASAAEAIASESELSGSEEVQELIDQFNEKGVSildsssmldkqpkkkgtgmgtakyyMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFkstkkknatdnnlegdsepltndpekLIKEQEKLKKRVtslikkqklqqvrgivkghvdskpwgqdALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSftkealkgrrygviecdplVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETikmtprsqlepvFQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGISS

MWRNLARQSSTRNFKFSPSKVSQTTNFLKKITSLETQTLLDSSCPLLGFRRTSFLSSQKSNLGQSNFTQSIYPFGVLTsrsyasaaeaiaseselsgseeVQELIDQFNEKGVSILDSSSMLDKQPKKKGTGMGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPeklikeqeklkkRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGISS

**************************FLKKITSLETQTLLDSSCPLLGFRRTSFL**********NFTQSIYPFGVLTSR******************************************************TAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSF*****************************************LIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLG****DIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHG***************LEPVFQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGI**

MWRN***QSS*********************TSLETQ**************************************VLTSRSYASA*********************************************************RRQIKIETEAWEQAAKEY********************SLFLGWFEPLRDAIA*************TYAPYFNNLPADMMAVITMHKLV*************QAACQIGEAIENEARIQSF***************GDSEPLTNDPEKLIKEQEKLKKRVTSLIKKQKL************SKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ***SPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGI**

************NFKFSPSKVSQTTNFLKKITSLETQTLLDSSCPLLGFRRTSFLSSQKSNLGQSNFTQSIYPFGVLTSRSYASAA**************VQELIDQFNEKGVSILDSSSM***********MGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGISS

*W*****QSSTR************TN*L*KITSLETQTLLDSSCPLLGFRRTSFLSSQKSNLGQSNFTQSIYPFGVLTSRSYASAAEAIASESELSGSEEVQELIDQFNEKGVSILDSSSMLDKQPKKKGTGMGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLMCSFCGIS*

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		492	2.2.26 [Sep-21-2011]
Q93Y94		1002	DNA-directed RNA polymera	N/A	no	0.888	0.436	0.578	1e-139
Q8L6J5		1002	DNA-directed RNA polymera	N/A	no	0.908	0.446	0.535	1e-136
P92969		976	DNA-directed RNA polymera	yes	no	0.916	0.462	0.517	1e-130
Q8L6J3		1021	DNA-directed RNA polymera	N/A	no	0.928	0.447	0.506	1e-127
Q8VWF8		1020	DNA-directed RNA polymera	N/A	no	0.896	0.432	0.513	1e-127
Q9LFV6		1011	DNA-directed RNA polymera	no	no	0.906	0.441	0.491	1e-113
P69242		977	DNA-directed RNA polymera	N/A	no	0.636	0.320	0.519	2e-93
P69243		977	DNA-directed RNA polymera	N/A	no	0.636	0.320	0.519	2e-93
Q8L6J1		977	DNA-directed RNA polymera	N/A	no	0.636	0.320	0.522	8e-93
O24600		993	DNA-directed RNA polymera	no	no	0.666	0.330	0.477	3e-90

>sp\|Q93Y94\|RPOT1_NICSY DNA-directed RNA polymerase 1, mitochondrial OS=Nicotiana sylvestris GN=RPOT1 PE=2 SV=1	Back alignment and function desciption

 Score =  494 bits (1272), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 264/456 (57%), Positives = 320/456 (70%), Gaps = 19/456 (4%)

Query: 8   QSSTRNFKFSPSKVSQTTNFLKKITSLETQTLLDSSCPLLGFRRTSFLSSQKSNLGQSNF 67
           + ST N     S+ S  +   +K+  LE      S  P LG  + S  SS K +      
Sbjct: 43  EESTTNPNLGLSQNSIFSRISRKVRHLEGICEESSKNPHLGLSQNSLFSSVKGDFRVCGK 102

Query: 68  TQSIYPFGVLTSRSYASAAEAIASESELSGSEEVQELIDQFNEKGVSILDSSSMLDKQPK 127
             S    G L  RSY SAAEAIAS SE    +E+QELI++ N++  ++   +++  KQPK
Sbjct: 103 RGS-GSLGFL--RSYGSAAEAIASTSE-EDIDEIQELIEEMNKENEAL--KTNLQPKQPK 156

Query: 128 KKGTGMGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWF 187
             G GMG  KY +L+RRQIK+ETEAWE+AAKEYQ+LL DMCEQKLAPNLPY+KSLFLGWF
Sbjct: 157 TIG-GMGVGKYNLLRRRQIKVETEAWEEAAKEYQELLMDMCEQKLAPNLPYMKSLFLGWF 215

Query: 188 EPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHK--LVGLLMTNAGEVRVVQ 245
           EPLRDAIA +Q    +      YAP+F+ LPA+MMAVITMHK   + +     G  RVVQ
Sbjct: 216 EPLRDAIAAEQKLCDEGKNRGAYAPFFDQLPAEMMAVITMHKLMGLLMTGGGTGSARVVQ 275

Query: 246 AACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKLKKRVTSL 305
           AA  IGEAIE+EARI  F + TKK NA   +LE       + P  ++KE+E+++K+V  L
Sbjct: 276 AASHIGEAIEHEARIHRFLEKTKKSNALSGDLE-------DTPGDIMKERERVRKKVKIL 328

Query: 306 IKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRP 365
           +KKQKLQQVR IVK   D KPWGQD LVKVGCRLIQ+LMETAYIQPP DQL D PPDIRP
Sbjct: 329 MKKQKLQQVRKIVKQQDDEKPWGQDNLVKVGCRLIQILMETAYIQPPNDQLDDCPPDIRP 388

Query: 366 AFVHTLKSFTKEALKG-RRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRG 424
           AFVHTLK  T E +KG RRYGVI+CDPLVRKGL+KT RHM+IPYMPMLVPP +W GY++G
Sbjct: 389 AFVHTLK--TVETMKGSRRYGVIQCDPLVRKGLDKTARHMVIPYMPMLVPPQSWLGYDKG 446

Query: 425 GHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQV 460
            + FLPSY+MRTHGA+QQRE +K  P+ QLEPVFQ 
Sbjct: 447 AYLFLPSYIMRTHGAKQQREAVKRVPKKQLEPVFQA 482

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Nicotiana sylvestris (taxid: 4096)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp\|Q8L6J5\|RPO1B_TOBAC DNA-directed RNA polymerase 1B, mitochondrial OS=Nicotiana tabacum GN=RPOT1-TOM PE=2 SV=2	Back alignment and function description

>sp\|P92969\|RPOT1_ARATH DNA-directed RNA polymerase 1, mitochondrial OS=Arabidopsis thaliana GN=RPOT1 PE=2 SV=1	Back alignment and function description

>sp\|Q8L6J3\|RPO2B_TOBAC DNA-directed RNA polymerase 2B, chloroplastic/mitochondrial OS=Nicotiana tabacum GN=RPOT2-TOM PE=2 SV=2	Back alignment and function description

>sp\|Q8VWF8\|RPOT2_NICSY DNA-directed RNA polymerase 2, chloroplastic/mitochondrial OS=Nicotiana sylvestris GN=RPOT2 PE=2 SV=2	Back alignment and function description

>sp\|Q9LFV6\|RPOT2_ARATH DNA-directed RNA polymerase 2, chloroplastic/mitochondrial OS=Arabidopsis thaliana GN=RPOT2 PE=1 SV=1	Back alignment and function description

>sp\|P69242\|RPOT3_NICSY DNA-directed RNA polymerase 3, chloroplastic OS=Nicotiana sylvestris GN=RPOT3 PE=2 SV=1	Back alignment and function description

>sp\|P69243\|RPO3A_TOBAC DNA-directed RNA polymerase 3A, chloroplastic OS=Nicotiana tabacum GN=RPOT3-SYL PE=3 SV=1	Back alignment and function description

>sp\|Q8L6J1\|RPO3B_TOBAC DNA-directed RNA polymerase 3B, chloroplastic OS=Nicotiana tabacum GN=RPOT3-TOM PE=2 SV=2	Back alignment and function description

>sp\|O24600\|RPOT3_ARATH DNA-directed RNA polymerase 3, chloroplastic OS=Arabidopsis thaliana GN=RPOT3 PE=2 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		492
255547027		997	DNA-directed RNA polymerase 2, chloropla	0.943	0.465	0.598	1e-154
225425009		978	PREDICTED: DNA-directed RNA polymerase 1	0.910	0.458	0.606	1e-151
449435282		968	PREDICTED: DNA-directed RNA polymerase 2	0.904	0.459	0.556	1e-142
15823750		1002	T7 bacteriophage-type single subunit RNA	0.888	0.436	0.587	1e-141
225451858		1035	PREDICTED: DNA-directed RNA polymerase 2	0.924	0.439	0.541	1e-138
21425663		1002	mitochondrial RNA polymerase [Nicotiana	0.888	0.436	0.581	1e-137
34925359		1002	RecName: Full=DNA-directed RNA polymeras	0.888	0.436	0.578	1e-137
88933965		1002	RecName: Full=DNA-directed RNA polymeras	0.908	0.446	0.535	1e-135
21425637		1002	phage-type RNA polymerase [Nicotiana tab	0.908	0.446	0.535	1e-135
224099265		877	predicted protein [Populus trichocarpa]	0.680	0.381	0.671	1e-133

>gi\|255547027\|ref\|XP_002514571.1\| DNA-directed RNA polymerase 2, chloroplast/mitochondrial precursor, putative [Ricinus communis] gi\|223546175\|gb\|EEF47677.1\| DNA-directed RNA polymerase 2, chloroplast/mitochondrial precursor, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  551 bits (1419), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 288/481 (59%), Positives = 353/481 (73%), Gaps = 17/481 (3%)

Query: 1   MWRNLARQSSTR----NFKFSPSKVSQTTNFLKKITSLETQTLLDSSCPLLGFRRTSFLS 56
           MWRN AR++S      NF    ++++Q  + L+K+   E QTLL S    LG RR S LS
Sbjct: 1   MWRNFARRTSLSSKKLNFSSDCTQLNQDLDILQKVRHPEAQTLLCSPYSFLGSRRISGLS 60

Query: 57  SQKSNLGQSNFTQSIYPFGV--LTSRSYASAA-EAIAS--ESELSGSEEVQELIDQFNE- 110
           SQ     + +FT    PFG      + YA+AA + IAS  ES+ SG +E+QE I++ N+ 
Sbjct: 61  SQNHEFIKPSFTNLTNPFGFSHFLFKGYATAAAQVIASTDESDFSGCDELQEQIEEINKH 120

Query: 111 -KGVSILDSSSMLDKQPKKKGTGMGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCE 169
            K +          +Q KK   GMG  KY +LK+RQIK+ETEAWE+AA+EYQ+LL DMCE
Sbjct: 121 HKKMDAHFRQQQQQQQRKKTIAGMGIGKYTILKKRQIKMETEAWEEAAREYQELLTDMCE 180

Query: 170 QKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHK 229
           QKLAPNLPY+KSLFLGWFEPLRDAIAK+Q  +++K   +++ PYF+ LPADMMAVITMHK
Sbjct: 181 QKLAPNLPYIKSLFLGWFEPLRDAIAKEQELSREKNNKLSHGPYFDALPADMMAVITMHK 240

Query: 230 LVGLLMT---NAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNL--EGDSEPL 284
           L+GLLMT     G VRVVQAAC +GEAIE+EARI  F + TKKK  +  N   EG  EP+
Sbjct: 241 LMGLLMTTNGGNGSVRVVQAACAVGEAIEHEARIHRFLEKTKKKKKSTKNEEPEGKLEPV 300

Query: 285 TNDPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLM 344
           T+D EKL KEQEKL+K+VT L+KKQK+QQVRG+ KGH DS PWGQ+A VKVGCRLIQLL+
Sbjct: 301 TSDAEKLAKEQEKLRKKVTELMKKQKVQQVRGLTKGHDDSMPWGQEAQVKVGCRLIQLLI 360

Query: 345 ETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEALK-GRRYGVIECDPLVRKGLEKTGRH 403
           ETAYIQPPV+QLGD  PDIRPAF+HTLK+  K+  K  RRYGVIECDP+VR GLEK+ RH
Sbjct: 361 ETAYIQPPVNQLGDGLPDIRPAFMHTLKNVMKDTQKTSRRYGVIECDPIVRNGLEKSARH 420

Query: 404 MIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQVSRV 463
           M+IPYMPMLVPPLNW GY++G + FLPSYVMRTHGA+QQR  +K TP  QLEPV++    
Sbjct: 421 MVIPYMPMLVPPLNWEGYDQGAYLFLPSYVMRTHGAKQQRNAVKRTPWKQLEPVYEALNT 480

Query: 464 L 464
           L
Sbjct: 481 L 481

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225425009\|ref\|XP_002267464.1\| PREDICTED: DNA-directed RNA polymerase 1, mitochondrial [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449435282\|ref\|XP_004135424.1\| PREDICTED: DNA-directed RNA polymerase 2, chloroplastic/mitochondrial-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|15823750\|dbj\|BAB69063.1\| T7 bacteriophage-type single subunit RNA polymerase [Nicotiana sylvestris]	Back alignment and taxonomy information

>gi\|225451858\|ref\|XP_002278535.1\| PREDICTED: DNA-directed RNA polymerase 2, chloroplastic/mitochondrial [Vitis vinifera] gi\|298204431\|emb\|CBI16911.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|21425663\|emb\|CAC95019.1\| mitochondrial RNA polymerase [Nicotiana sylvestris]	Back alignment and taxonomy information

>gi\|34925359\|sp\|Q93Y94.1\|RPOT1_NICSY RecName: Full=DNA-directed RNA polymerase 1, mitochondrial; AltName: Full=NsRpoT-A; AltName: Full=T7 bacteriophage-type single subunit RNA polymerase 1; Flags: Precursor gi\|15824083\|dbj\|BAB69431.1\| T7 bacteriophage-type single subunit RNA polymerase [Nicotiana sylvestris]	Back alignment and taxonomy information

>gi\|88933965\|sp\|Q8L6J5.2\|RPO1B_TOBAC RecName: Full=DNA-directed RNA polymerase 1B, mitochondrial; AltName: Full=NictaRpoT1-tom; AltName: Full=T7 bacteriophage-type single subunit RNA polymerase 1B; Flags: Precursor	Back alignment and taxonomy information

>gi\|21425637\|emb\|CAC82574.2\| phage-type RNA polymerase [Nicotiana tabacum]	Back alignment and taxonomy information

>gi\|224099265\|ref\|XP_002311418.1\| predicted protein [Populus trichocarpa] gi\|222851238\|gb\|EEE88785.1\| predicted protein [Populus trichocarpa]	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		492
UNIPROTKB\|Q93Y94		1002	RPOT1 "DNA-directed RNA polyme	0.886	0.435	0.558	2.7e-124
UNIPROTKB\|Q8VWF8		1020	RPOT2 "DNA-directed RNA polyme	0.918	0.443	0.487	7.2e-107
UNIPROTKB\|P69242		977	RPOT3 "DNA-directed RNA polyme	0.652	0.328	0.510	6e-87
TAIR\|locus:2047515		993	SCA3 "SCABRA 3" [Arabidopsis t	0.664	0.329	0.469	9.7e-80
POMBASE\|SPAC26H5.12		1154	rpo41 "mitochondrial RNA polym	0.609	0.259	0.238	4.3e-08
CGD\|CAL0005126		1300	RPO41 [Candida albicans (taxid	0.304	0.115	0.270	1.2e-06
UNIPROTKB\|F1PCF7		1221	POLRMT "DNA-directed RNA polym	0.252	0.101	0.283	7.4e-05
UNIPROTKB\|J9P8Y8		1414	POLRMT "DNA-directed RNA polym	0.252	0.087	0.283	0.0001
ASPGD\|ASPL0000068622		1391	AN7609 [Emericella nidulans (t	0.245	0.086	0.264	0.00048

UNIPROTKB\|Q93Y94 RPOT1 "DNA-directed RNA polymerase 1, mitochondrial" [Nicotiana sylvestris (taxid:4096)]	Back alignment and assigned GO terms

 Score = 1192 (424.7 bits), Expect = 2.7e-124, Sum P(2) = 2.7e-124
 Identities = 254/455 (55%), Positives = 301/455 (66%)

Query:     8 QSSTRNFKFSPSKVSQTTNFLKKITSLETQTLLDSSCPLLGFRRTSFLSSQKSNLGQSNF 67
             + ST N     S+ S  +   +K+  LE      S  P LG  + S  SS K +      
Sbjct:    43 EESTTNPNLGLSQNSIFSRISRKVRHLEGICEESSKNPHLGLSQNSLFSSVKGDFRVCGK 102

Query:    68 TQSIYPFGVLTXXXXXXXXXXXXXXXXXXXXXXVQELIDQFNEKGVSILDSSSMLDKQPK 127
               S    G L                       +QELI++ N++  ++   +++  KQPK
Sbjct:   103 RGS----GSLGFLRSYGSAAEAIASTSEEDIDEIQELIEEMNKENEAL--KTNLQPKQPK 156

Query:   128 KKGTGMGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWF 187
               G GMG  KY +L+RRQIK+ETEAWE+AAKEYQ+LL DMCEQKLAPNLPY+KSLFLGWF
Sbjct:   157 TIG-GMGVGKYNLLRRRQIKVETEAWEEAAKEYQELLMDMCEQKLAPNLPYMKSLFLGWF 215

Query:   188 EPLRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAG--EVRVVQ 245
             EPLRDAIA +Q    +      YAP+F+ LPA+MMAVITMHKL+GLLMT  G    RVVQ
Sbjct:   216 EPLRDAIAAEQKLCDEGKNRGAYAPFFDQLPAEMMAVITMHKLMGLLMTGGGTGSARVVQ 275

Query:   246 AACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSL 305
             AA  IGEAIE+EARI  F + TKK NA    L GD E   + P            +V  L
Sbjct:   276 AASHIGEAIEHEARIHRFLEKTKKSNA----LSGDLE---DTPGDIMKERERVRKKVKIL 328

Query:   306 IKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRP 365
             +KKQKLQQVR IVK   D KPWGQD LVKVGCRLIQ+LMETAYIQPP DQL D PPDIRP
Sbjct:   329 MKKQKLQQVRKIVKQQDDEKPWGQDNLVKVGCRLIQILMETAYIQPPNDQLDDCPPDIRP 388

Query:   366 AFVHTLKSFTKEALKG-RRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRG 424
             AFVHTLK  T E +KG RRYGVI+CDPLVRKGL+KT RHM+IPYMPMLVPP +W GY++G
Sbjct:   389 AFVHTLK--TVETMKGSRRYGVIQCDPLVRKGLDKTARHMVIPYMPMLVPPQSWLGYDKG 446

Query:   425 GHFFLPSYVMRTHGARQQRETIKMTPRSQLEPVFQ 459
              + FLPSY+MRTHGA+QQRE +K  P+ QLEPVFQ
Sbjct:   447 AYLFLPSYIMRTHGAKQQREAVKRVPKKQLEPVFQ 481

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB\|Q8VWF8 RPOT2 "DNA-directed RNA polymerase 2, chloroplastic/mitochondrial" [Nicotiana sylvestris (taxid:4096)]	Back alignment and assigned GO terms

UNIPROTKB\|P69242 RPOT3 "DNA-directed RNA polymerase 3, chloroplastic" [Nicotiana sylvestris (taxid:4096)]	Back alignment and assigned GO terms

TAIR\|locus:2047515 SCA3 "SCABRA 3" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

POMBASE\|SPAC26H5.12 rpo41 "mitochondrial RNA polymerase Rpo41" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

CGD\|CAL0005126 RPO41 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PCF7 POLRMT "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|J9P8Y8 POLRMT "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000068622 AN7609 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!
4th Layer	2.7.7.6	LOW 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
Query		492
PHA00452		807	PHA00452, PHA00452, T3/T7-like RNA polymerase	7e-19
COG5108		1117	COG5108, RPO41, Mitochondrial DNA-directed RNA pol	2e-13

>gnl\|CDD\|222797 PHA00452, PHA00452, T3/T7-like RNA polymerase	Back alignment and domain information

 Score = 89.7 bits (223), Expect = 7e-19
 Identities = 53/290 (18%), Positives = 98/290 (33%), Gaps = 47/290 (16%)

Query: 141 LKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQAT 200
           L   Q+++E EA+ +  + ++  L    E   A + P  + L      P+ +AI   +  
Sbjct: 5   LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEE 64

Query: 201 AQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARI 260
            + + +          +  +++AVIT+   + +L+ +         A  IG AIE+E R 
Sbjct: 65  YKKRGRAAKARGLLRLVDPEVLAVITLKVTLDMLL-SKETPTAQAVATAIGRAIEDEIRF 123

Query: 261 QSFFKSTKK--KNATDNNLEGDSEPLTNDPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIV 318
                   K  K   +                          R  S+     +  V   +
Sbjct: 124 GRIEDLNPKYFKKVVEYLKR---------------------SRTGSVYHIAFMMVVEADM 162

Query: 319 KGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSFTKEA 378
               +  PW ++  + VG  L++ L+E+  +                  V          
Sbjct: 163 VLLGEWDPWPKEDYIHVGKWLLEALIESTGL---------------VELVRHTG-----G 202

Query: 379 LKGRRYGVIECDPLVRKGLEKTGRHM--IIP-YMPMLVPPLNWRGYNRGG 425
             G+ +  +E      + L+        I P Y PM+VPP  W     GG
Sbjct: 203 NGGKDHEYLELSEEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGG 252

Length = 807

>gnl\|CDD\|227439 COG5108, RPO41, Mitochondrial DNA-directed RNA polymerase [Transcription]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		492
KOG1038		1088	consensus Mitochondrial/chloroplast DNA-directed R	100.0
PF14700		318	RPOL_N: DNA-directed RNA polymerase N-terminal; PD	100.0
PHA00452		807	T3/T7-like RNA polymerase	100.0
COG5108		1117	RPO41 Mitochondrial DNA-directed RNA polymerase [T	100.0

>KOG1038 consensus Mitochondrial/chloroplast DNA-directed RNA polymerase RPO41, provides primers for DNA replication-initiation [Transcription; Replication, recombination and repair]	Back alignment and domain information

Probab=100.00  E-value=1.5e-76  Score=636.82  Aligned_cols=469  Identities=41%  Similarity=0.665  Sum_probs=381.6

Q ss_pred             Chhhhhhhh------hcccccc-CCC--------CCCccchhhhh---hcc-cccccccCCCCCCccccccccccccccc
Q 011172            1 MWRNLARQS------STRNFKF-SPS--------KVSQTTNFLKK---ITS-LETQTLLDSSCPLLGFRRTSFLSSQKSN   61 (492)
Q Consensus         1 ~~~~~~~~~------~~~~~~~-~~~--------~~~~~~~~~~~---~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   61 (492)
                      ||+|+..++      ..+.... +.+        .++--.++|+-   ... |.... ..++++..|+++..+++-.|  
T Consensus        89 ~~~~~l~~s~~~~t~~~~~~~~l~~~s~t~~l~~~~~~i~~~~S~~~~~lt~~~~~~-~~~p~~~~~~~~~~~l~~~n--  165 (1088)
T KOG1038|consen   89 MWRNLLLKSFQNETMALRRHAALNPSSTTLGLLDPVEAISGIFSSLAKVLTTLRHKL-LVSPEHVRGIRQLLGLNNIN--  165 (1088)
T ss_pred             HhhhhHHHHhhhhhHHHHhhccCCchhhcccccchhhcchhhhhhhhhhhHHHhccc-ccCchhhhhhHHhhccchhh--
Confidence            799999998      5554443 222        11222344442   222 22222 35677788888888887666  


Q ss_pred             cCCCCCccCCCCccccccccccchhhhhhc---ccccCchHHHHHHHHHHHhhcccc-----cccccccccccccccCCC
Q 011172           62 LGQSNFTQSIYPFGVLTSRSYASAAEAIAS---ESELSGSEEVQELIDQFNEKGVSI-----LDSSSMLDKQPKKKGTGM  133 (492)
Q Consensus        62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~  133 (492)
                          +|.+...+.+| ..+||+-+++..-+   +.+++..+++.+++++|.++....     .......+...+....++
T Consensus       166 ----sF~~~~~~l~G-~~~g~s~a~e~~~~~~~~~~s~~~~~~~~~~~~m~ke~~~~~~~~~~~~~~~~~~~lk~v~k~~  240 (1088)
T KOG1038|consen  166 ----SFPHSSEVLSG-LIKGSSLAGESENPTDQEGDSSNKQEINELVTKMEKEGNSLNQISSKFLEESRDLPLKAVRKGF  240 (1088)
T ss_pred             ----cccchhhhhhc-ccccchHHHHHhCcccccccccchhhHHHHHhHhhhhhhhhhHHHHHHHHHHhcccHHHHHHhc
Confidence                45566666666 67888444555444   333445779999999999987431     111222223335666677


Q ss_pred             ChH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHcccCCCchh-HHHHHHHHHHHHHHHHHHHHHHHhhc--cCcc
Q 011172          134 GTA-KYYMLKRRQIKIETEAWEQAAKEYQ-DLLADMCEQKLAPNLPY-VKSLFLGWFEPLRDAIAKDQATAQDK--WKHM  208 (492)
Q Consensus       134 ~~~-~~~~l~~rQl~LE~ea~e~A~er~r-~~~e~~~~~g~a~~l~~-~k~Ll~~W~~~L~~aI~~e~~~~~~~--~~r~  208 (492)
                      +.. +|..+.+||..+|+++|+.|+++|+ +...+||+..+++++|+ +++|+++||++|+++|++|++.++..  +.|.
T Consensus       241 ~~~~d~~~l~~Rq~~~e~~~~e~a~e~~k~el~~~~c~~~l~~~lp~~lk~lf~~W~~~l~~ai~ee~n~~r~~~~~~r~  320 (1088)
T KOG1038|consen  241 GDFKDFFNLDRRQVKLETEAWERAAEEWKIELESDMCEGSLAPNLPYNLKSLFLGWFKPLRDAIKEEINLLRALVRKGRL  320 (1088)
T ss_pred             cchHhHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence            766 8999999999999999999999999 78889999999999999 99999999999999999999999886  7899


Q ss_pred             ccccccccCChhHHHHHHHHHHHHHhccCC--CCccHHHHHHHHHHHHHHHHHHHHhhhhhhccccccCCCCCCCCCCCC
Q 011172          209 TYAPYFNNLPADMMAVITMHKLVGLLMTNA--GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTN  286 (492)
Q Consensus       209 ~y~pyL~~L~~d~LA~Iti~~~l~~l~~~~--~~~~v~~la~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~  286 (492)
                      .|+|||++||++++|+|||+++|+++++|+  +|+++++++..||++||+|+++..+.++..+.+..+            
T Consensus       321 ~Y~p~L~lL~a~k~aviti~el~~ll~tg~~~~~~~v~~aa~~~G~aveqe~ri~~~lq~~~k~~~~~------------  388 (1088)
T KOG1038|consen  321 NYAPFLKLLDADKMAVITIHELMGLLMTGGETGGVRVVQAAKSLGRAVEQEFRIEQFLQRKTKNKAGD------------  388 (1088)
T ss_pred             ccchHHHhcChhhHHHHHHHHHHhhhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccch------------
Confidence            999999999999999999999999999987  899999999999999999999999987754322211            


Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCc
Q 011172          287 DPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPA  366 (492)
Q Consensus       287 d~~~~~~~~~~lrk~~~~l~k~~k~~~~~~~~~~~~~~~~W~~~~~~kVGs~Li~lLietakI~v~~~~~~~~~~~~~PA  366 (492)
                       .....++....++.+..++++.++.+.......++...+||..++++||++||++||++++|+++++++.++.++.+||
T Consensus       389 -~~~~~ke~~~~~~~v~~l~~~~k~~~~~~~~~~~~~~~pWp~~v~~kvGs~L~~lL~~~aki~~~~~~~~~~~~~~~pa  467 (1088)
T KOG1038|consen  389 -SYCELKELGKSRKEVRQLVQNLKLSQRLSGPESHLSEKPWPSAVQAKVGSRLIELLMQVAKIQVPADQPDTKLPDERPA  467 (1088)
T ss_pred             -HHHHHHHhhcccHHHHHHHHHHHHHHHhcccccccccCCccHHHHHHHHHHHHHHHHHHhcCCCcccCcCcCccccchh
Confidence             1122345556677788777777777766666666778999999999999999999999999999999999999999999


Q ss_pred             eEEEEeeccccccCCeEEEEEEeCHHHHHHHHhhcccccCCCCceeeCCCCCCCCCCccccccccchhcccCcHHHHHHH
Q 011172          367 FVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVMRTHGARQQRETI  446 (492)
Q Consensus       367 F~H~~~~~~~~~~~gkk~GvI~~hp~l~~~l~~~~~~~~~p~LPMLvPPkPWts~~~GGYL~~~s~lmR~~g~~~Q~~~l  446 (492)
                      |+|+|++ ++.++.|++||+|+|||.+.+.|++.+.|+..+++||||||+||++|++||||++|++||||||+++|+.|+
T Consensus       468 f~h~f~~-~n~~~~~~~~g~ie~~pll~r~leks~~~~~~~~vPMLvpPkpWt~~~~Ggyl~~~s~lmRt~g~~~Q~~~l  546 (1088)
T KOG1038|consen  468 FVHTFQV-TNGQKGGRKYGVIECHPLLSRGLEKSALHFVPPLVPMLVPPKPWTGYDSGGYLFLPSYLMRTHGAKEQVDYL  546 (1088)
T ss_pred             hhhheee-ecccccceeeeeeecCHHHHHHhhhhhccccccccccccCCCCCCCCCCCceEecchhhhhcCCcHHHHHHH
Confidence            9999995 455556889999999999999999999899989999999999999999999999999999999999999977


Q ss_pred             HcC-CCCCchhHHHHHHHhcCCCceecHHHHHHHHHHHh---ccCCCCCC
Q 011172          447 KMT-PRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLM---CSFCGISS  492 (492)
Q Consensus       447 ~~a-~~~qL~~Vf~aLN~LGstpWrIN~~VLdvI~~~~~---~~~l~IP~  492 (492)
                      ..+ +.++|++||||||+||+|+||||.+|||+|+.+ |   +++++||+
T Consensus       547 lkas~~~~l~~v~daL~~LG~t~WrVN~rvldvV~ri-w~~Gg~~~~~v~  595 (1088)
T KOG1038|consen  547 LKASPPGQLDPVFDALDTLGNTKWRVNRRVLDVVIRI-WQNGGCFLLIVP  595 (1088)
T ss_pred             HhcCChhhhHHHHHHHHHhcCCCeeecchHHHHHHHH-HhcCCCccCCCC
Confidence            555 789999999999999999999999999999776 6   88998885

>PF14700 RPOL_N: DNA-directed RNA polymerase N-terminal; PDB: 3SPA_A 1CEZ_A 1H38_B 1S77_D 1QLN_A 1S0V_D 3E2E_A 2PI4_A 3E3J_B 1S76_D	Back alignment and domain information

>PHA00452 T3/T7-like RNA polymerase	Back alignment and domain information

>COG5108 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]	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		492
1aro_P		883	T7 Rna Polymerase Complexed With T7 Lysozyme Length		3e-04
2pi4_A		878	T7rnap Complexed With A Phi10 Protein And Initiatin		3e-04
4rnp_A		883	Bacteriophage T7 Rna Polymerase, High Salt Crystal		3e-04
3e2e_A		889	Crystal Structure Of An Intermediate Complex Of T7		8e-04

>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme Length = 883

Back alignment and structure

Iteration: 1

Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust. Identities = 72/327 (22%), Positives = 120/327 (36%), Gaps = 82/327 (25%) Query: 141 LKRRQIKIETEAWEQAAKEYQDL---------LADMCEQK--LAPNLPYVKSLFLGWFEP 189 L R Q+ +E E++E ++ + +AD K + LP + + WFE Sbjct: 32 LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 91 Query: 190 LRDAIAKDQATAQDKWKHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQ 249 ++ + K T + + + +A IT+ + L T+A V A Sbjct: 92 VK----------AKRGKRPTAFQFLQEIKPEAVAYITIKTTLACL-TSADNTTVQAVASA 140 Query: 250 IGEAIENEA---RIQSFFKSTKKKNATDNNLEGDSEPLTNDPXXXXXXXXXXXXRVTSLI 306 IG AIE+EA RI+ KKN + RV + Sbjct: 141 IGRAIEDEARFGRIRDLEAKHFKKNVEEQ----------------------LNKRVGHVY 178 Query: 307 KKQKLQQV------RGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQ----L 356 KK +Q V +G++ G S W ++ + VG R I++L+E+ + Q + Sbjct: 179 KKAFMQVVEADMLSKGLLGGEAWSS-WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVV 237 Query: 357 GDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPL 416 G I L EA+ R + P+ + P +VPP Sbjct: 238 GQDSETIE------LAPEYAEAIATRAGALAGISPM---------------FQPCVVPPK 276 Query: 417 NWRGYNRGGHFF---LPSYVMRTHGAR 440 W G GG++ P ++RTH + Sbjct: 277 PWTGITGGGYWANGRRPLALVRTHSKK 303

PyMOL of 1aro

>pdb|2PI4|A Chain A, T7rnap Complexed With A Phi10 Protein And Initiating Gtps. Length = 878

Back alignment and structure

>pdb|4RNP|A Chain A, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form, Low Temperature Data, Alpha-Carbons Only Length = 883

Back alignment and structure

>pdb|3E2E|A Chain A, Crystal Structure Of An Intermediate Complex Of T7 Rnap And 7nt Of Rna Length = 889

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		492
3spa_A		1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-38
1msw_D		883	DNA-directed RNA polymerase, bacteriophage T7 RNA;	9e-31
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134	Back alignment and structure

 Score =  148 bits (374), Expect = 2e-38
 Identities = 53/355 (14%), Positives = 114/355 (32%), Gaps = 36/355 (10%)

Query: 114 SILDSSSMLDKQPKKKGTGMGTAKYYMLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLA 173
            +L      D +       +       L  +Q+ +E  A        +       E K A
Sbjct: 276 KLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQLHME-LASRVCVVSVEKPTLPSKEVKHA 334

Query: 174 PNLPYVKSLFLGWFEPLRDAIAKDQATAQDKWK--HMTYAPYFNNLPADMMAVITMHKLV 231
                +K+L   W + L  A+ + +   + +      +  P+   L    +  + +  L 
Sbjct: 335 RK--TLKTLRDQWEKALCRALRETKNRLEREVYEGRFSLYPFLCLLDEREVVRMLLQVLQ 392

Query: 232 GLLMTNA--GEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPE 289
            L         +    +A      +    R+    ++ +                     
Sbjct: 393 ALPAQGESFTTLARELSARTFSRHVVQRQRVSGQVQALQN-----------------HYR 435

Query: 290 KLIKEQEKLKKRVTSLIKKQKLQQVRGIVKGHVDSKPWGQDALVKVGCRLIQLLMETAYI 349
           K +       +     + +Q  + +       +  +PW     +++G  L ++L++   +
Sbjct: 436 KYLCLLASDAEVPEPCLPRQYWEAL--GAPEALREQPWPLPVQMELGKLLAEMLVQATQM 493

Query: 350 QPPVDQLGDSPPDIRPAFVHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGRHMII--- 406
              +D+       + P   H            ++ G+++  P   + LEK     +    
Sbjct: 494 PCSLDK-PHRSSRLVPVLYHVYSFR-----NVQQIGILKPHPAYVQLLEKAAEPTLTFEA 547

Query: 407 PYMPMLVPPLNWRGYNRGGHFFLPSYVMRT-HGARQQRETIKMTPRSQLEPVFQV 460
             +PML PPL W   + G     P+ +MRT  GA Q +E ++  P + L      
Sbjct: 548 VDVPMLCPPLPWTSPHSGAFLLSPTKLMRTVEGATQHQELLETCPPTALHGALDA 602

PyMOL of 3spa

>1msw_D DNA-directed RNA polymerase, bacteriophage T7 RNA; T7RNAP elongation complex, transcription/DNA/RNA complex; 2.10A {Enterobacteria phage T7} SCOP: e.8.1.3 PDB: 1h38_A 1cez_A 1qln_A* 1s0v_A* 1s76_D* 1s77_D* 4rnp_A 3e2e_A* 3e3j_C* 1aro_P 2pi4_A* 2pi5_A Length = 883	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

>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
Query		492
1msw_D		883	DNA-directed RNA polymerase, bacteriophage T7 RNA;	100.0
3spa_A		1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	100.0

>1msw_D DNA-directed RNA polymerase, bacteriophage T7 RNA; T7RNAP elongation complex, transcription/DNA/RNA complex; 2.10A {Enterobacteria phage T7} SCOP: e.8.1.3 PDB: 1h38_A 1cez_A 1qln_A* 1s0v_A* 1s76_D* 1s77_D* 4rnp_A 3e2e_A* 3e3j_C* 1aro_P 2pi4_A* 2pi5_A	Back alignment and structure

Probab=100.00  E-value=5.8e-52  Score=466.18  Aligned_cols=311  Identities=21%  Similarity=0.319  Sum_probs=245.6

Q ss_pred             HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCchhHHHHHHHHHHHHHHHHHHHHHHHhh-ccCccccccc
Q 011172          136 AKYY-MLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQD-KWKHMTYAPY  213 (492)
Q Consensus       136 ~~~~-~l~~rQl~LE~ea~e~A~er~r~~~e~~~~~g~a~~l~~~k~Ll~~W~~~L~~aI~~e~~~~~~-~~~r~~y~py  213 (492)
                      +.|+ .|++||++||+++++.|++||++.+++++++|.++++|++++|+.+|+++|+++|+++++.... .+.++.|+||
T Consensus        26 ~~~~~~l~~rQ~~lE~e~~~~a~~r~~~~~~~~~~~g~~~~~~~~~~l~~~~~~~l~~~i~~~~~~~~~~~g~~~~~~~~  105 (883)
T 1msw_D           26 DHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQF  105 (883)
T ss_dssp             TTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCGGGSTTTHHHHHHHHHHHHHHHHHHHHHHHHSCSCCCTTTTT
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCChhhHHHHHHHHHHHHHHHHHHHHHHhcccCcchHHHHH
Confidence            3455 5689999999999999999999999999999999999999999999999999999999988763 4468999999


Q ss_pred             cccCChhHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHHHHHHhhhhhhccccccCCCCCCCCCCCCChHHHHH
Q 011172          214 FNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIK  293 (492)
Q Consensus       214 L~~L~~d~LA~Iti~~~l~~l~~~~~~~~v~~la~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~d~~~~~~  293 (492)
                      |++||+|++|+|||+++|++++++ +++++++++.+||++||+|++++++.+.+++.+.+..                  
T Consensus       106 L~~l~~e~lA~iti~~~l~~~~~~-~~~~~~~~~~~iG~ave~E~~~~~~~~~~~~~~~~~~------------------  166 (883)
T 1msw_D          106 LQEIKPEAVAYITIKTTLACLTSA-DNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNV------------------  166 (883)
T ss_dssp             TTSSCHHHHHHHHHHHHHHHHHHC-SCCBHHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHHT------------------
T ss_pred             HHhCCHHHHHHHHHHHHHHHhccc-CCccHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH------------------
Confidence            999999999999999999999873 5789999999999999999999999887765443211                  


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh-hC----CCCCCCCCHHHHHHHHHHHHHHHHHH-ccccCCCCCCCCCCCCccCce
Q 011172          294 EQEKLKKRVTSLIKKQKLQQVRGIV-KG----HVDSKPWGQDALVKVGCRLIQLLMET-AYIQPPVDQLGDSPPDIRPAF  367 (492)
Q Consensus       294 ~~~~lrk~~~~l~k~~k~~~~~~~~-~~----~~~~~~W~~~~~~kVGs~Li~lLiet-akI~v~~~~~~~~~~~~~PAF  367 (492)
                       .+.++++.+...++...+.+.... ..    .+++.+|+..++++||++|+++|+++ +.+++....            
T Consensus       167 -~~~l~~~~~~~~k~~~~~~~~~~~~~~g~~~~~~~~~W~~~~~~~vG~~Li~~l~~~~~~~~~~~~~------------  233 (883)
T 1msw_D          167 -EEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQN------------  233 (883)
T ss_dssp             -SHHHHHSCSHHHHHHHHHHHHHHSTTTTTTTTCCCCCCCTTHHHHHHHHHHHHHHHHCTTEEEECC-------------
T ss_pred             -HHHHHhcccHHHHHHHHHHHHHHhhhccccccCCCCCCCHHHHHHHHHHHHHHHHHhhCCcceeccc------------
Confidence             122333333222222223333211 11    36789999999999999999999996 565443211            


Q ss_pred             EEEEeeccccccCCeEEEEEEeCHHHHHHHHhhcc--cccCC-CCceeeCCCCCCCCCCcccccc---ccchhcccCcHH
Q 011172          368 VHTLKSFTKEALKGRRYGVIECDPLVRKGLEKTGR--HMIIP-YMPMLVPPLNWRGYNRGGHFFL---PSYVMRTHGARQ  441 (492)
Q Consensus       368 ~H~~~~~~~~~~~gkk~GvI~~hp~l~~~l~~~~~--~~~~p-~LPMLvPPkPWts~~~GGYL~~---~s~lmR~~g~~~  441 (492)
                               ...+++++|+|+|||.+++.+.+...  ..+.| +|||||||+||+++++||||..   +..+||+++   
T Consensus       234 ---------~~~~~k~~~~i~~~~~~~~~l~~~~~~~~~~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~~~ir~~~---  301 (883)
T 1msw_D          234 ---------AGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHS---  301 (883)
T ss_dssp             ----------------CCEEEECHHHHHHHHHHHHHHTTSCCCCCCBSSCCBCCSSSBSCBSSSCCSSCCBSEECSS---
T ss_pred             ---------cCCCCceeeEEEeCHHHHHHHhhcccchhhcCCCCCceeeCCccCCCCCCCCccCCCcccchhhcccC---
Confidence                     01126889999999999999987532  23455 9999999999999999999975   345667653   


Q ss_pred             HHHHHHcCCCCCchhHHHHHHHhcCCCceecHHHHHHHHHHHh----ccCCCCCC
Q 011172          442 QRETIKMTPRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLM----CSFCGISS  492 (492)
Q Consensus       442 Q~~~l~~a~~~qL~~Vf~aLN~LGstpWrIN~~VLdvI~~~~~----~~~l~IP~  492 (492)
                       +.++++.++++|+.||+|||+||+|||+||.+||++|.++ |    ++++|||+
T Consensus       302 -~~~~~~~~~~~l~~v~~aLN~L~~t~w~IN~~vL~vi~~~-~~~~g~~~~~ip~  354 (883)
T 1msw_D          302 -KKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVI-TKWKHCPVEDIPA  354 (883)
T ss_dssp             -TTHHHHTTTCCCHHHHHHHHHHHTCCEEECHHHHHHHHHH-TTCSSCSSTTCCC
T ss_pred             -HHHHHhccccchHHHHHHHHHhccCCeEecHHHHHHHHHH-HhhcCCcccCCCC
Confidence             3456656678999999999999999999999999998765 5    68899985

PyMOL of 1msw

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}	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		492
d1mswd_		882	e.8.1.3 (D:) T7 RNA polymerase {Bacteriophage T7 [	6e-59

>d1mswd_ e.8.1.3 (D:) T7 RNA polymerase {Bacteriophage T7 [TaxId: 10760]} Length = 882	Back information, alignment and structure


class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: T7 RNA polymerase
domain: T7 RNA polymerase
species: Bacteriophage T7 [TaxId: 10760]

 Score =  206 bits (525), Expect = 6e-59
 Identities = 60/326 (18%), Positives = 108/326 (33%), Gaps = 44/326 (13%)

Query: 141 LKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQAT 200
           L R Q+ +E E++E     ++ +     +     +    K L       +   I      
Sbjct: 31  LAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEE 90

Query: 201 AQDKW-KHMTYAPYFNNLPADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEAR 259
            + K  K  T   +   +  + +A IT+   +  L +      V   A  IG AIE+EAR
Sbjct: 91  VKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSA-DNTTVQAVASAIGRAIEDEAR 149

Query: 260 IQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKLKKRVTSLIKKQKLQQVRGIVK 319
                    K                   +K ++EQ  L KRV  + KK  +Q V   + 
Sbjct: 150 FGRIRDLEAKHF-----------------KKNVEEQ--LNKRVGHVYKKAFMQVVEADML 190

Query: 320 -----GHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKSF 374
                G      W ++  + VG R I++L+E+  +     Q                +  
Sbjct: 191 SKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPE-- 248

Query: 375 TKEALKGRRYGVIECDPLVRKGLEKTGRHMIIPYMPMLVPPLNWRGYNRGGHFFLPSYVM 434
             EA+  R   +    P+               + P +VPP  W G   GG++      +
Sbjct: 249 YAEAIATRAGALAGISPM---------------FQPCVVPPKPWTGITGGGYWANGRRPL 293

Query: 435 RTHGARQQRETIKMTPRSQLEPVFQV 460
                   ++ +       +  V++ 
Sbjct: 294 ALVR-THSKKALMRYEDVYMPEVYKA 318

PyMOL of d1mswd_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		492
d1mswd_		882	T7 RNA polymerase {Bacteriophage T7 [TaxId: 10760]	100.0

>d1mswd_ e.8.1.3 (D:) T7 RNA polymerase {Bacteriophage T7 [TaxId: 10760]}	Back information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: T7 RNA polymerase
domain: T7 RNA polymerase
species: Bacteriophage T7 [TaxId: 10760]

Probab=100.00  E-value=6.5e-49  Score=444.73  Aligned_cols=308  Identities=21%  Similarity=0.329  Sum_probs=240.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCchhHHHHHHHHHHHHHHHHHHHHHHHhh-ccCccccccccccCC
Q 011172          140 MLKRRQIKIETEAWEQAAKEYQDLLADMCEQKLAPNLPYVKSLFLGWFEPLRDAIAKDQATAQD-KWKHMTYAPYFNNLP  218 (492)
Q Consensus       140 ~l~~rQl~LE~ea~e~A~er~r~~~e~~~~~g~a~~l~~~k~Ll~~W~~~L~~aI~~e~~~~~~-~~~r~~y~pyL~~L~  218 (492)
                      +|++||++||+++++.|++||++.+++++++|.+++++++++++.+|+++|+++|+++++..+. .+.++.|+|||+.||
T Consensus        30 ~L~~rQ~~LE~ea~~~g~~R~r~~~e~~~~rg~~s~~~~g~~li~~~l~~l~~~I~~~~~~~~~~~G~~~~~~~yL~~l~  109 (882)
T d1mswd_          30 RLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIK  109 (882)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCGGGSTTTHHHHHHHHHHHHHHHHHHHHHHHHSCSCCCTTTTTTTSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHhcCC
Confidence            5888999999999999999999999999999999999999999999999999999999887754 345788999999999


Q ss_pred             hhHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHHHHHHhhhhhhccccccCCCCCCCCCCCCChHHHHHHHHHH
Q 011172          219 ADMMAVITMHKLVGLLMTNAGEVRVVQAACQIGEAIENEARIQSFFKSTKKKNATDNNLEGDSEPLTNDPEKLIKEQEKL  298 (492)
Q Consensus       219 ~d~LA~Iti~~~l~~l~~~~~~~~v~~la~~IG~aVe~E~~~~~~~~~~~k~~~~~~~~~~~~~~l~~d~~~~~~~~~~l  298 (492)
                      ||++|+|||+++|++++++ ++.++++++.+||+|||+|++++++.+.+++.+.+.++                   +.+
T Consensus       110 pe~lA~Itik~~ld~l~~~-~~~~~t~va~~IG~AVE~E~r~~~~~~~~~~~~~k~~~-------------------~~~  169 (882)
T d1mswd_         110 PEAVAYITIKTTLACLTSA-DNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVE-------------------EQL  169 (882)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-SCCBHHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHHTS-------------------HHH
T ss_pred             HHHHHHHHHHHHHHHhcCC-CCChHHHHHHHHHHHHHHHHHHHHHHHhChHHHHHhhH-------------------HHH
Confidence            9999999999999999875 46799999999999999999999998887765543221                   122


Q ss_pred             HHHHHHHHHHHHHHHHHH--hhh---CCCCCCCCCHHHHHHHHHHHHHHHHHHccccCCCCCCCCCCCCccCceEEEEee
Q 011172          299 KKRVTSLIKKQKLQQVRG--IVK---GHVDSKPWGQDALVKVGCRLIQLLMETAYIQPPVDQLGDSPPDIRPAFVHTLKS  373 (492)
Q Consensus       299 rk~~~~l~k~~k~~~~~~--~~~---~~~~~~~W~~~~~~kVGs~Li~lLietakI~v~~~~~~~~~~~~~PAF~H~~~~  373 (492)
                      ++......++...+.+..  ..+   ..+.|.+|+..+++|||++|+++|++++++..                 .....
T Consensus       170 ~k~~~~~~kk~~~~~~~~~~~~~~~~~~~~w~~W~~~~r~kVG~~Lle~l~e~tg~~~-----------------~~~~~  232 (882)
T d1mswd_         170 NKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVS-----------------LHRQN  232 (882)
T ss_dssp             HHSCSHHHHHHHHHHHHHHSTTTTTTTTCCCCCCCTTHHHHHHHHHHHHHHHHCTTEE-----------------EECC-
T ss_pred             HHHhhHHHHHHHHHHHHHHHHHhhhccccccCccCHHHHHHHHHHHHHHHHHHhCCce-----------------eeccc
Confidence            232222222222222221  111   13578999999999999999999999999832                 11111


Q ss_pred             ccccccCCeEEEEEEeCHHHHHHHHhhcc--cccCC-CCceeeCCCCCCCCCCccccccccc---hhcccCcHHHHHHHH
Q 011172          374 FTKEALKGRRYGVIECDPLVRKGLEKTGR--HMIIP-YMPMLVPPLNWRGYNRGGHFFLPSY---VMRTHGARQQRETIK  447 (492)
Q Consensus       374 ~~~~~~~gkk~GvI~~hp~l~~~l~~~~~--~~~~p-~LPMLvPPkPWts~~~GGYL~~~s~---lmR~~g~~~Q~~~l~  447 (492)
                      .   ..+++++++|.+||++.+.++....  ..+.| +|||||||+||+++++||||+..+.   +||++...    ++.
T Consensus       233 ~---~~~~k~~~~v~~t~~~~~~l~~~~~~~~~~~P~~lPMlvpP~pW~~~~~GGYl~~~~~~~~~~~~~~~~----~~~  305 (882)
T d1mswd_         233 A---GVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKK----ALM  305 (882)
T ss_dssp             ----------CCEEEECHHHHHHHHHHHHHHTTSCCCCCCBSSCCBCCSSSBSCBSSSCCSSCCBSEECSSTT----HHH
T ss_pred             c---ccccCcCcceeecHHHHHHHHhhHhHHHhcCcccccccCCCccCCCCCcCCeeecCCCceeccccccHh----hhh
Confidence            0   1247889999999999999987543  35778 9999999999999999999987654   44444332    233


Q ss_pred             cCCCCCchhHHHHHHHhcCCCceecHHHHHHHHHHHh----ccCCCCCC
Q 011172          448 MTPRSQLEPVFQVSRVLYSSIFYDLFNLYRLIINFLM----CSFCGISS  492 (492)
Q Consensus       448 ~a~~~qL~~Vf~aLN~LGstpWrIN~~VLdvI~~~~~----~~~l~IP~  492 (492)
                      +..+++|+.||+|||+||+|||+||.+||+++ +.+|    +.+.+||+
T Consensus       306 ~~~~~~l~~v~~aLN~LQst~wrIN~~vLdv~-~~~~~~~~~~~~~iP~  353 (882)
T d1mswd_         306 RYEDVYMPEVYKAINIAQNTAWKINKKVLAVA-NVITKWKHCPVEDIPA  353 (882)
T ss_dssp             HTTTCCCHHHHHHHHHHHTCCEEECHHHHHHH-HHHTTCSSCSSTTCCC
T ss_pred             hccccchHHHHHHHHHHhcCCeEeCHHHHHHH-HHHHhcCCCcccccCc
Confidence            44567999999999999999999999999977 5556    45667774

PyMOL of d1mswd_