Psyllid ID: psy7583

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-
MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVV
ccccccccccccccccccccccccccccccHHHHHcccccccccccEEEEEEccccccccHHHHHHcccccccEEEEccccccccccccEEEEEEEccccccHHHHHHHHccccccccccEEEEEEEEEEEEccccccEEEEEcccccccccccccccccccccccccccEEEccccEEEEEEcccccccccccccccEEEcEEccEEccccccEEEEEEEEEEcccccEEEEEEEcccccccccHHHHcccccccEEEEEEEEEEEEccccccccccccccccHHHHHHHHHHccccccccEEEEEcccccEEEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcHHHHHHHHHccccccEEEEEcccccccEEEcccccccccccccccccEEEEEccHHHHHHHHHHHHcccccEEEEc
cccccccHHHEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHccEcccccccHHHHHHcccccccccHcccHHcccccccccccEEEEEEEcccccHcHEEEEcHHHHHcccEEEEEEEEHHHHHHccccccEEEEEccccccccccccHHHHHccccccEcccEEEccccEEEEEcccccccHccccccccccEEEcccEEcccccccEEEEEEEEEcccccEEEEEEEEEEEEcccccccccccccccEEEEEEcHHHHHHcccccccccccccccHHHHHHHHHHccccccccEEEEccccccccccEEEEcHHHHHHHHHHHHcHHHccccccEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccEEEEEEEEccccEEEEcccccccccccccHHHHHHHHHHHHHHcccccEEEEc
MGVYITNFHVRMDTLAHVlyyphkplvttrsmeYLRFRELPAGINSIVAILCYtgynqedsVILNASAVERGYFRSMEYlrfrelpagINSIVAILCYtgynqedsVILNASAVERGYFRSVFFRSYkdaeskrigdqeeqfekpnrqtcQGMRNAIydkldddgiiapglrvsgddvvigktitlpenedelegttkrfskrdgstflrnsetgivDQVMLTLnvdgykfckirvrsvripqigdkfasrhgqkgtcgiqyrqevssnkgeigdatpfndavNVQKISTLLQEYGyqlrgnevmfnghtgrkinaqvflgpTYYQRLKHMvddkihsrargpvqilvrqpmegrardgglrfgemerdcqISHGAAQFLRERLfevsdpyrihvCNFCGLIAIANMRnntfeckgcknktqisQVRLPYAAKLLFQELMSmniaprlmvv
MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDaeskrigdqeeqfekpnrqtcQGMRNAIYDKLDDDGIIApglrvsgddvvigktitlpenedelegttkrfskrdgstflrnsetgivdqvMLTLNVDGYKFCKIRVRsvripqigdkfasrhgqkgtcGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKihsrargpvqilvrqpmegrardGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELmsmniaprlmvv
MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVV
**VYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSY*************************MRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITL*********************FLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQ********IGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR**********GLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIA******
MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKD***********************MRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPE****************GSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVV
MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKD*****************RQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVV
MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPEN*********RFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVV
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVV
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 ?
Query451 2.2.26 [Sep-21-2011]
P082661176 DNA-directed RNA polymera yes N/A 0.900 0.345 0.778 0.0
P308761174 DNA-directed RNA polymera yes N/A 0.900 0.345 0.700 0.0
Q8CFI71174 DNA-directed RNA polymera yes N/A 0.900 0.345 0.698 0.0
Q105781193 DNA-directed RNA polymera yes N/A 0.898 0.339 0.646 0.0
Q54J751170 DNA-directed RNA polymera yes N/A 0.891 0.343 0.592 1e-170
Q428771191 DNA-directed RNA polymera N/A N/A 0.891 0.337 0.559 1e-156
P384201188 DNA-directed RNA polymera yes N/A 0.891 0.338 0.563 1e-156
Q020611210 DNA-directed RNA polymera yes N/A 0.891 0.332 0.557 1e-153
P085181224 DNA-directed RNA polymera yes N/A 0.891 0.328 0.548 1e-151
A5DHT21236 DNA-directed RNA polymera N/A N/A 0.891 0.325 0.538 1e-151
>sp|P08266|RPB2_DROME DNA-directed RNA polymerase II subunit RPB2 OS=Drosophila melanogaster GN=RpII140 PE=2 SV=2 Back     alignment and function desciption
 Score =  767 bits (1980), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/487 (77%), Positives = 394/487 (80%), Gaps = 81/487 (16%)

Query: 1    MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
            MGVYITNFHVRMDTLAHVLYYP KPLVTTR                              
Sbjct: 735  MGVYITNFHVRMDTLAHVLYYPMKPLVTTR------------------------------ 764

Query: 61   SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
                           SMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERG+FR
Sbjct: 765  ---------------SMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFR 809

Query: 121  SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
            SVF+RSYKD+E+KR+GDQEE FEKP+R TCQGMRNA YDKLDDDGIIAPG+RVSGDDVVI
Sbjct: 810  SVFYRSYKDSENKRVGDQEENFEKPHRGTCQGMRNAHYDKLDDDGIIAPGIRVSGDDVVI 869

Query: 181  GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
            GKTITLPEN+DEL+  TKRFSKRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVR
Sbjct: 870  GKTITLPENDDELDSNTKRFSKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVR 929

Query: 241  IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
            IPQIGDKFASRHGQKGTCGIQYRQE                                   
Sbjct: 930  IPQIGDKFASRHGQKGTCGIQYRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQG 989

Query: 266  -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
             + SNKGEIGDATPFNDAVNVQKIST LQEYGY LRGNEVM+NGHTGRKINAQVFLGPTY
Sbjct: 990  KLGSNKGEIGDATPFNDAVNVQKISTFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTY 1049

Query: 325  YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
            YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL
Sbjct: 1050 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 1109

Query: 385  FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
            FEVSDPYR+H+CNFCGLIAIAN+RNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI
Sbjct: 1110 FEVSDPYRVHICNFCGLIAIANLRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 1169

Query: 445  APRLMVV 451
            APRLMV 
Sbjct: 1170 APRLMVT 1176
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 OS=Homo sapiens GN=POLR2B PE=1 SV=1 Back     alignment and function description
>sp|Q8CFI7|RPB2_MOUSE DNA-directed RNA polymerase II subunit RPB2 OS=Mus musculus GN=Polr2b PE=2 SV=2 Back     alignment and function description
>sp|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II subunit RPB2 OS=Caenorhabditis elegans GN=rpb-2 PE=2 SV=2 Back     alignment and function description
>sp|Q54J75|RPB2_DICDI DNA-directed RNA polymerase II subunit rpb2 OS=Dictyostelium discoideum GN=polr2b PE=3 SV=1 Back     alignment and function description
>sp|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 PE=2 SV=1 Back     alignment and function description
>sp|P38420|RPB2_ARATH DNA-directed RNA polymerase II subunit RPB2 OS=Arabidopsis thaliana GN=RPB135 PE=2 SV=2 Back     alignment and function description
>sp|Q02061|RPB2_SCHPO DNA-directed RNA polymerase II subunit RPB2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb2 PE=1 SV=2 Back     alignment and function description
>sp|P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB2 PE=1 SV=2 Back     alignment and function description
>sp|A5DHT2|RPB2_PICGU DNA-directed RNA polymerase II subunit RPB2 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=RPB2 PE=3 SV=3 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 ?
Query451
324120652 1176 RNA polymerase II second largest subunit 0.900 0.345 0.804 0.0
324120638 1175 RNA polymerase II second largest subunit 0.900 0.345 0.800 0.0
324120628 1174 RNA polymerase II second largest subunit 0.900 0.345 0.798 0.0
324120650 1175 RNA polymerase II second largest subunit 0.900 0.345 0.802 0.0
324120632 1174 RNA polymerase II second largest subunit 0.900 0.345 0.798 0.0
324120662 1175 RNA polymerase II second largest subunit 0.900 0.345 0.800 0.0
324120626 1175 RNA polymerase II second largest subunit 0.900 0.345 0.800 0.0
324120624 1173 RNA polymerase II second largest subunit 0.900 0.346 0.794 0.0
324120630 1175 RNA polymerase II second largest subunit 0.900 0.345 0.798 0.0
324120648 1175 RNA polymerase II second largest subunit 0.900 0.345 0.796 0.0
>gi|324120652|dbj|BAJ78717.1| RNA polymerase II second largest subunit [Bemisia tabaci] Back     alignment and taxonomy information
 Score =  791 bits (2042), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/487 (80%), Positives = 403/487 (82%), Gaps = 81/487 (16%)

Query: 1    MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
            MGVYITN+HVRMDTLAHVLYYPHKPLVTTR                              
Sbjct: 734  MGVYITNYHVRMDTLAHVLYYPHKPLVTTR------------------------------ 763

Query: 61   SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
                           SMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERG+FR
Sbjct: 764  ---------------SMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFR 808

Query: 121  SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
            SVFFRSYKD+ESKRIGDQEEQFEKPNR TCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI
Sbjct: 809  SVFFRSYKDSESKRIGDQEEQFEKPNRSTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 868

Query: 181  GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
            GKTITLPEN+DELEGTTKR+SKRD STFLRNSETGIVDQVMLTLN +GYKFCKIRVRSVR
Sbjct: 869  GKTITLPENDDELEGTTKRYSKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVR 928

Query: 241  IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
            IPQIGDKFASRHGQKGTCGIQYRQE                                   
Sbjct: 929  IPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLAPDIIINPHAIPSRMTIGHLIECLQG 988

Query: 266  -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
             VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVM+NGH+GRKINAQVFLGPTY
Sbjct: 989  KVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHSGRKINAQVFLGPTY 1048

Query: 325  YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
            YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL
Sbjct: 1049 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 1108

Query: 385  FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
            FEVSDPYRIHVCN+CGLIAIAN+RNNTFECKGCKNKTQISQVRLPYAAKLLFQELM+MNI
Sbjct: 1109 FEVSDPYRIHVCNYCGLIAIANLRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMAMNI 1168

Query: 445  APRLMVV 451
            APRLMVV
Sbjct: 1169 APRLMVV 1175

Source: Bemisia tabaci

Species: Bemisia tabaci

Genus: Bemisia

Family: Aleyrodidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|324120638|dbj|BAJ78710.1| RNA polymerase II second largest subunit [Tenodera aridifolia] Back     alignment and taxonomy information
>gi|324120628|dbj|BAJ78705.1| RNA polymerase II second largest subunit [Teleogryllus emma] Back     alignment and taxonomy information
>gi|324120650|dbj|BAJ78716.1| RNA polymerase II second largest subunit [Anacanthocoris striicornis] Back     alignment and taxonomy information
>gi|324120632|dbj|BAJ78707.1| RNA polymerase II second largest subunit [Euborellia plebeja] Back     alignment and taxonomy information
>gi|324120662|dbj|BAJ78722.1| RNA polymerase II second largest subunit [Protohermes grandis] Back     alignment and taxonomy information
>gi|324120626|dbj|BAJ78704.1| RNA polymerase II second largest subunit [Euconocephalus varius] Back     alignment and taxonomy information
>gi|324120624|dbj|BAJ78703.1| RNA polymerase II second largest subunit [Nomadacris japonica] Back     alignment and taxonomy information
>gi|324120630|dbj|BAJ78706.1| RNA polymerase II second largest subunit [Oyamia lugubris] Back     alignment and taxonomy information
>gi|324120648|dbj|BAJ78715.1| RNA polymerase II second largest subunit [Cryptotympana facialis] 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 ?
Query451
FB|FBgn02629551176 RpII140 "RNA polymerase II 140 0.412 0.158 0.951 5e-190
UNIPROTKB|A5PJW81174 POLR2B "DNA-directed RNA polym 0.423 0.162 0.848 1.1e-172
UNIPROTKB|E2RNN51174 POLR2B "DNA-directed RNA polym 0.423 0.162 0.848 1.1e-172
UNIPROTKB|I3LGP41167 POLR2B "DNA-directed RNA polym 0.423 0.163 0.848 1.1e-172
UNIPROTKB|F1NCB01174 POLR2B "DNA-directed RNA polym 0.423 0.162 0.848 2.3e-172
UNIPROTKB|F1P4F21176 POLR2B "DNA-directed RNA polym 0.423 0.162 0.848 2.3e-172
UNIPROTKB|C9J2Y91167 POLR2B "DNA-directed RNA polym 0.423 0.163 0.842 4.7e-172
UNIPROTKB|C9J4M61099 POLR2B "DNA-directed RNA polym 0.423 0.173 0.842 4.7e-172
UNIPROTKB|P308761174 POLR2B "DNA-directed RNA polym 0.423 0.162 0.842 4.7e-172
RGD|13094771174 Polr2b "polymerase (RNA) II (D 0.423 0.162 0.842 4.7e-172
FB|FBgn0262955 RpII140 "RNA polymerase II 140kD subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 948 (338.8 bits), Expect = 5.0e-190, Sum P(2) = 5.0e-190
 Identities = 177/186 (95%), Positives = 183/186 (98%)

Query:   265 EVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
             ++ SNKGEIGDATPFNDAVNVQKIST LQEYGY LRGNEVM+NGHTGRKINAQVFLGPTY
Sbjct:   990 KLGSNKGEIGDATPFNDAVNVQKISTFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTY 1049

Query:   325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
             YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL
Sbjct:  1050 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 1109

Query:   385 FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
             FEVSDPYR+H+CNFCGLIAIAN+RNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI
Sbjct:  1110 FEVSDPYRVHICNFCGLIAIANLRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 1169

Query:   445 APRLMV 450
             APRLMV
Sbjct:  1170 APRLMV 1175
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;NAS;IDA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS;NAS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS
GO:0003677 "DNA binding" evidence=IEA
GO:0032549 "ribonucleoside binding" evidence=IEA
UNIPROTKB|A5PJW8 POLR2B "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RNN5 POLR2B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|I3LGP4 POLR2B "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|F1NCB0 POLR2B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1P4F2 POLR2B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|C9J2Y9 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|C9J4M6 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P30876 POLR2B "DNA-directed RNA polymerase II subunit RPB2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
RGD|1309477 Polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Rattus norvegicus (taxid:10116)] 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) ?
Q8SR75RPB2_ENCCU2, ., 7, ., 7, ., 60.52270.88240.3488yesN/A
B0R8D5RPOB1_HALS32, ., 7, ., 7, ., 60.36340.88690.6578yesN/A
Q8CFI7RPB2_MOUSE2, ., 7, ., 7, ., 60.69810.90020.3458yesN/A
P08518RPB2_YEAST2, ., 7, ., 7, ., 60.54840.89130.3284yesN/A
P08266RPB2_DROME2, ., 7, ., 7, ., 60.77820.90020.3452yesN/A
P30876RPB2_HUMAN2, ., 7, ., 7, ., 60.70020.90020.3458yesN/A
P38420RPB2_ARATH2, ., 7, ., 7, ., 60.56370.89130.3383yesN/A
Q10578RPB2_CAEEL2, ., 7, ., 7, ., 60.64600.89800.3394yesN/A
Q54J75RPB2_DICDI2, ., 7, ., 7, ., 60.59290.89130.3435yesN/A
O27124RPOB1_METTH2, ., 7, ., 7, ., 60.39260.88690.6633yesN/A
Q6FLD5RPB2_CANGA2, ., 7, ., 7, ., 60.54020.89130.3286yesN/A
Q02061RPB2_SCHPO2, ., 7, ., 7, ., 60.55780.89130.3322yesN/A
P0CX03RPOB1_HALSA2, ., 7, ., 7, ., 60.36340.88690.6578yesN/A
O28392RPOB1_ARCFU2, ., 7, ., 7, ., 60.38390.89350.6672yesN/A
Q60181RPOB1_METJA2, ., 7, ., 7, ., 60.37110.89350.6336yesN/A
P41557RPOB1_METVS2, ., 7, ., 7, ., 60.36710.88470.6530yesN/A
Q753Q4RPB2_ASHGO2, ., 7, ., 7, ., 60.54730.88910.3281yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.766
4th Layer2.7.7.60.824

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query451
cd00653866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 0.0
PRK085651103 PRK08565, PRK08565, DNA-directed RNA polymerase su 1e-161
TIGR03670599 TIGR03670, rpoB_arch, DNA-directed RNA polymerase 1e-157
PRK07225605 PRK07225, PRK07225, DNA-directed RNA polymerase su 1e-148
COG00851060 COG0085, RpoB, DNA-directed RNA polymerase, beta s 1e-133
pfam00562373 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do 1e-119
pfam0456078 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, do 1e-35
TIGR020131065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 6e-33
CHL002071077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 9e-33
PRK004051112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 2e-24
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 4e-17
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 5e-16
CHL000011070 CHL00001, rpoB, RNA polymerase beta subunit 6e-13
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 4e-06
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 6e-04
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information 
 Score =  551 bits (1423), Expect = 0.0
 Identities = 194/488 (39%), Positives = 242/488 (49%), Gaps = 95/488 (19%)

Query: 1   MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
           +G    N   RMDT  ++L YP KPLV T   EY+ F ELP G N+IVA++ Y+GYN ED
Sbjct: 435 VGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFED 494

Query: 61  SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
           ++I+N S+V+RG+FRS                                            
Sbjct: 495 AIIINKSSVDRGFFRS-------------------------------------------- 510

Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
            + ++ Y+    K     EE      R     +       LD+DGII PG RV   D+++
Sbjct: 511 -IHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565

Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLT---LNVDGYKFCKIRVR 237
           GK     E E       K    RD S      E GIVD V +    LN  G K  K+ +R
Sbjct: 566 GKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIR 625

Query: 238 SVRIPQIGDKFASRHGQKGTCGIQYRQE-------------------------------- 265
             R PQIGDKFASRHGQKG       QE                                
Sbjct: 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLES 685

Query: 266 ----VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLG 321
                 +  G+ GDATPF D    + IS LL E G    G EV+++G TG  + A +F+G
Sbjct: 686 LLGKAGALLGKFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVG 744

Query: 322 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 381
           P YYQRLKHMVDDKIH+R+ GP  +L RQP++GR+R GG RFGEMERD  I+HGAA  L+
Sbjct: 745 PVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQ 804

Query: 382 ERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMS 441
           ERL   SD     VC  CG+I  AN+      C+ CK  T IS+V +PYA KLLFQEL S
Sbjct: 805 ERLTIKSDDVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQS 858

Query: 442 MNIAPRLM 449
           MNI PRL 
Sbjct: 859 MNIDPRLK 866

RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation. Length = 866
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B Back     alignment and domain information
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6 Back     alignment and domain information
>gnl|CDD|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7 Back     alignment and domain information
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional Back     alignment and domain information
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 451
PRK07225605 DNA-directed RNA polymerase subunit B'; Validated 100.0
TIGR03670599 rpoB_arch DNA-directed RNA polymerase subunit B. T 100.0
PRK085651103 DNA-directed RNA polymerase subunit B; Provisional 100.0
KOG0215|consensus1153 100.0
cd00653866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 100.0
COG00851060 RpoB DNA-directed RNA polymerase, beta subunit/140 100.0
KOG0214|consensus1141 100.0
KOG0216|consensus1111 100.0
PRK004051112 rpoB DNA-directed RNA polymerase subunit beta; Rev 100.0
TIGR020131065 rpoB DNA-directed RNA polymerase, beta subunit. Th 100.0
CHL002071077 rpoB RNA polymerase beta subunit; Provisional 100.0
CHL000011070 rpoB RNA polymerase beta subunit 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PF00562386 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int 100.0
PF0456081 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; Int 99.97
KOG0214|consensus1141 98.64
CHL002071077 rpoB RNA polymerase beta subunit; Provisional 98.31
CHL000011070 rpoB RNA polymerase beta subunit 98.08
PRK07225605 DNA-directed RNA polymerase subunit B'; Validated 93.79
TIGR03670599 rpoB_arch DNA-directed RNA polymerase subunit B. T 92.95
PF00562386 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int 91.82
cd00653866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 89.77
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 89.2
PRK085651103 DNA-directed RNA polymerase subunit B; Provisional 89.01
TIGR020131065 rpoB DNA-directed RNA polymerase, beta subunit. Th 87.81
PRK004051112 rpoB DNA-directed RNA polymerase subunit beta; Rev 87.8
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information 
Probab=100.00  E-value=2.2e-127  Score=1030.05  Aligned_cols=402  Identities=47%  Similarity=0.804  Sum_probs=372.4

Q ss_pred             CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583           1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL   80 (451)
Q Consensus         1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~   80 (451)
                      ||+|++|++.|+|+++|+|+|||+|||+|+++++++++++|+|+||+|||                              
T Consensus       162 ~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAv------------------------------  211 (605)
T PRK07225        162 LGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAV------------------------------  211 (605)
T ss_pred             cCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCeeEEEEE------------------------------
Confidence            89999999999999999999999999999999999999999999999999                              


Q ss_pred             cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCc-hhhhh
Q psy7583          81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMR-NAIYD  159 (451)
Q Consensus        81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~-~~~~~  159 (451)
                                     |||+||||||||||||+|+|||||||+||++|+.++++...+.++.|++|+.+. .+.+ ...|+
T Consensus       212 ---------------msy~GYn~EDAiIiNkssidRGlf~s~~~k~~~~~~~~~~~~~~~~~~~p~~~~-~~~~~~~~~~  275 (605)
T PRK07225        212 ---------------MSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDV-RGYRGEEAYR  275 (605)
T ss_pred             ---------------ECcCCCChhHeeeeehhhhhcCceEEEEEEEEEEEeeecCCCcceEEecCCchh-ccccChHHhh
Confidence                           999999999999999999999999999999999998887777778999987531 1222 35799


Q ss_pred             ccCcCCCcccCcEEeCCCEEEEEeeecCCCCcc-ccccccccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEee
Q psy7583         160 KLDDDGIIAPGLRVSGDDVVIGKTITLPENEDE-LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRS  238 (451)
Q Consensus       160 ~LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~-~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~  238 (451)
                      +||+||||+||++|++|||||||++|....++. ..+ ......+|+|++++.+|+|+||+|.++.+.+|.+.+||++|+
T Consensus       276 ~LD~dGi~~~G~~v~~gdiligk~sp~~~~~~~~~~~-~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~  354 (605)
T PRK07225        276 HLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFG-ISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRD  354 (605)
T ss_pred             cCCCCCCccCCCEECCCCEEEEEecCCCCccchhhhc-ccccCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEE
Confidence            999999999999999999999999986532111 001 111247899999999999999999999999999999999999


Q ss_pred             cCCCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCc
Q psy7583         239 VRIPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDA  282 (451)
Q Consensus       239 ~R~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~  282 (451)
                      .|+|+||||||||||||||||+|||||                                    ++++.|.+.|+|||...
T Consensus       355 ~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~d~t~F~~~  434 (605)
T PRK07225        355 LRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGE  434 (605)
T ss_pred             EEeccccchhhhcccCceeEEeEeccccCCcCCCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceEeecCCCCc
Confidence            999999999999999999999999999                                    57889999999999987


Q ss_pred             ccHHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccc
Q psy7583         283 VNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLR  362 (451)
Q Consensus       283 ~~~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r  362 (451)
                       +.+++++.|.++||+++|+|.||||+||++|+++||+|++|||||+|||+||+|||++||++.|||||++||+++||||
T Consensus       435 -~~~~~~~~L~~~g~~~~G~e~my~G~TG~~~~~~if~G~~yYqrL~HmV~DK~haR~~Gp~~~lTrQP~~GR~r~GG~R  513 (605)
T PRK07225        435 -DEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLR  513 (605)
T ss_pred             -hHHHHHHHHHHhCcCCCCeEEEEcCCCCCEecccEEEeehheeechhhhcchhhhccCCCCcccccCCccccccCCCee
Confidence             8999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhC
Q psy7583         363 FGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSM  442 (451)
Q Consensus       363 ~GEME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm  442 (451)
                      |||||+|||+||||+++|+|||+++||.++++||.+||++++.+.+.+.+.|+.|+++..+.++.+|||||||+|||+||
T Consensus       514 fGEMErd~lia~Gas~~L~Erl~~~SD~~~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPya~kll~~EL~sm  593 (605)
T PRK07225        514 FGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSL  593 (605)
T ss_pred             eeeeehhhhhhhhhHHHHHHHHhccCcceeEEeecCcCcceehhcccCceeecccCCCCceeeccCChhHHHHHHHHHHC
Confidence            99999999999999999999999999999999999999999877666778899999888999999999999999999999


Q ss_pred             CcccEEEE
Q psy7583         443 NIAPRLMV  450 (451)
Q Consensus       443 ~I~~r~~~  450 (451)
                      ||++||.+
T Consensus       594 ~i~~~l~~  601 (605)
T PRK07225        594 GIAPRLEL  601 (605)
T ss_pred             CceeEEEe
Confidence            99999976

>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B Back     alignment and domain information
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>KOG0215|consensus Back     alignment and domain information
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>KOG0214|consensus Back     alignment and domain information
>KOG0216|consensus Back     alignment and domain information
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>CHL00207 rpoB RNA polymerase beta subunit; Provisional Back     alignment and domain information
>CHL00001 rpoB RNA polymerase beta subunit Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PF04560 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; InterPro: IPR007641 RNA polymerases catalyse the DNA-dependent polymerisation of RNA Back     alignment and domain information
>KOG0214|consensus Back     alignment and domain information
>CHL00207 rpoB RNA polymerase beta subunit; Provisional Back     alignment and domain information
>CHL00001 rpoB RNA polymerase beta subunit Back     alignment and domain information
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B Back     alignment and domain information
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 Back     alignment and domain information
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed 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 ?
Query451
3h0g_B1210 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 1e-154
1i3q_B1224 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-152
2waq_B1131 The Complete Structure Of The Archaeal 13-Subunit D 2e-94
2pmz_B1124 Archaeal Rna Polymerase From Sulfolobus Solfataricu 5e-94
1iw7_C1119 Crystal Structure Of The Rna Polymerase Holoenzyme 2e-15
3lu0_C1342 Molecular Model Of Escherichia Coli Core Rna Polyme 1e-14
3iyd_C1342 Three-Dimensional Em Structure Of An Intact Activat 1e-14
1l9u_C1118 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 4e-14
1hqm_C1119 Crystal Structure Of Thermus Aquaticus Core Rna Pol 4e-14
1ynj_C1119 Taq Rna Polymerase-Sorangicin Complex Length = 1119 4e-14
1i6v_C1118 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 4e-14
3qqc_A 436 Crystal Structure Of Archaeal Spt45 BOUND TO THE RN 7e-06
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 Back     alignment and structure 
Iteration: 1

 Score =  541 bits (1395), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 270/484 (55%), Positives = 335/484 (69%), Gaps = 82/484 (16%)
Query: 1    MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
            MGVY+TN+ VRMDT+A++LYYP KPL TTR                              
Sbjct: 767  MGVYLTNYQVRMDTMANILYYPQKPLATTR------------------------------ 796
Query: 61   SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
                           SMEYL+FRELPAG N+IVAILCY+GYNQEDS+I+N ++++RG FR
Sbjct: 797  ---------------SMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFR 841
Query: 121  SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
            S+F+R+Y D E K      E+FE+P R T   M++  YDKL+DDG+IAPG RVSG+D++I
Sbjct: 842  SIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIII 901
Query: 181  GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
            GKT  +P + +EL   T+  +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS R
Sbjct: 902  GKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTR 961
Query: 241  IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
            IPQIGDKFASRHGQKGT G+ YR E                                   
Sbjct: 962  IPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLS 1021
Query: 266  -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
             VS+  G  GDATPF D V V+ +S LL+ +G+Q RG EVM++GHTGRK+ AQVFLGPTY
Sbjct: 1022 KVSALSGFEGDATPFTD-VTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTY 1080
Query: 325  YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
            YQRLKH+VDDKIH+RARGPVQIL RQP+EGR+RDGGLRFGEMERDCQISHG +  LRERL
Sbjct: 1081 YQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERL 1140
Query: 385  FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
            F+ SD YR+ VC+ CGLIAIA+ + +++EC+ C+N+T+ SQV LPYAAKLLFQELMSMNI
Sbjct: 1141 FDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200
Query: 445  APRL 448
            APRL
Sbjct: 1201 APRL 1204
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 Back     alignment and structure
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131 Back     alignment and structure
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 Back     alignment and structure
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1119 Back     alignment and structure
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 Back     alignment and structure
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1342 Back     alignment and structure
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 Back     alignment and structure
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1119 Back     alignment and structure
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex Length = 1119 Back     alignment and structure
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 Back     alignment and structure
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436 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 ?
Query451
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 0.0
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 0.0
4ayb_B1131 DNA-directed RNA polymerase; transferase, multi-su 0.0
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 6e-15
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 3e-10
3lu0_C1342 DNA-directed RNA polymerase subunit beta; E. coli 2e-13
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 2e-08
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210 Back     alignment and structure
 Score =  600 bits (1549), Expect = 0.0
 Identities = 270/486 (55%), Positives = 335/486 (68%), Gaps = 82/486 (16%)

Query: 1    MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
            MGVY+TN+ VRMDT+A++LYYP KPL TTRSMEYL+FRELPAG N+IVAILCY+GYNQED
Sbjct: 767  MGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQED 826

Query: 61   SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
            S+I+N ++++RG FRS+                                           
Sbjct: 827  SIIMNQASIDRGLFRSI------------------------------------------- 843

Query: 121  SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
              F+R+Y D E K      E+FE+P R T   M++  YDKL+DDG+IAPG RVSG+D++I
Sbjct: 844  --FYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIII 901

Query: 181  GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
            GKT  +P + +EL   T+  +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS R
Sbjct: 902  GKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTR 961

Query: 241  IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
            IPQIGDKFASRHGQKGT G+ YR E                                   
Sbjct: 962  IPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLS 1021

Query: 266  -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
             VS+  G  GDATPF D V V+ +S LL+ +G+Q RG EVM++GHTGRK+ AQVFLGPTY
Sbjct: 1022 KVSALSGFEGDATPFTD-VTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTY 1080

Query: 325  YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
            YQRLKH+VDDKIH+RARGPVQIL RQP+EGR+RDGGLRFGEMERDCQISHG +  LRERL
Sbjct: 1081 YQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERL 1140

Query: 385  FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
            F+ SD YR+ VC+ CGLIAIA+ + +++EC+ C+N+T+ SQV LPYAAKLLFQELMSMNI
Sbjct: 1141 FDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200

Query: 445  APRLMV 450
            APRL  
Sbjct: 1201 APRLFT 1206
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Length = 1224 Back     alignment and structure
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Length = 1131 Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query451
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 100.0
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 100.0
4ayb_B1131 DNA-directed RNA polymerase; transferase, multi-su 100.0
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 100.0
3lu0_C1342 DNA-directed RNA polymerase subunit beta; E. coli 100.0
3tbi_B228 DNA-directed RNA polymerase subunit beta; transcri 99.39
3qqc_A 436 DNA-directed RNA polymerase subunit B, DNA-direct 99.37
2a6h_C1119 DNA-directed RNA polymerase beta chain; RNA polyme 98.18
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 97.81
3h0g_B1210 DNA-directed RNA polymerase II subunit RPB2; trans 88.97
1twf_B1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 86.79
1gh9_A71 8.3 kDa protein (gene MTH1184); beta+alpha complex 85.29
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Back     alignment and structure
Probab=100.00  E-value=3e-123  Score=1064.67  Aligned_cols=404  Identities=66%  Similarity=1.119  Sum_probs=360.3

Q ss_pred             CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583           1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL   80 (451)
Q Consensus         1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~   80 (451)
                      ||++.+|+..|+|+..|+|+|||+|||+|+.+++++++++|+||||+|||                              
T Consensus       778 ~g~~~~n~~~r~dt~~~~l~ypQkPlV~t~~~~~~~~~elp~G~N~iVAv------------------------------  827 (1224)
T 1twf_B          778 MGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAI------------------------------  827 (1224)
T ss_dssp             CBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCEEEEEEE------------------------------
T ss_pred             cccccceeeeecccccceeecCcCCeEEcccccccccccCCCCeeEEEEE------------------------------
Confidence            79999999999999999999999999999999999999999999999999                              


Q ss_pred             cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCchhhhhc
Q psy7583          81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDK  160 (451)
Q Consensus        81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~~~~~~~  160 (451)
                                     |||+||||||||||||+|++||+|||+||++|++++++...+.++.|++|+.+.+++.+...|++
T Consensus       828 ---------------m~y~GYN~EDAiIin~~sv~rg~~~s~~~~~y~~~~~~~~~~~~e~~~~P~~~~~~~~~~~~~~~  892 (1224)
T 1twf_B          828 ---------------ACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDK  892 (1224)
T ss_dssp             ---------------CBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGG
T ss_pred             ---------------ecccCcccchhhhhhhhHHhcCCeeEEEEEEEEEEeeeCCCCceeEecCCChhhccCccHHHHhh
Confidence                           99999999999999999999999999999999999888666778899999876677777788999


Q ss_pred             cCcCCCcccCcEEeCCCEEEEEeeecCCCCccccccccccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEeecC
Q psy7583         161 LDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR  240 (451)
Q Consensus       161 LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~R  240 (451)
                      ||+||||+||++|++|||||||++|..+.+.++....+...++|+|++++++|+|+||+|.++.+.+|.+.|||++|++|
T Consensus       893 LD~dGiv~~G~~V~~gDilvgK~~p~~~~~~~~~~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkV~ir~~R  972 (1224)
T 1twf_B          893 LDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTK  972 (1224)
T ss_dssp             CCTTSBCCTTCEECTTCEEECEECCCC-------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEE
T ss_pred             cccCCccCCccEecCCCEEEEEecCCCccccccccccccCccceeEEEeeCCCCeEEEEEEEEecCCCCEEEEEEEEecC
Confidence            99999999999999999999999998654333333334457899999999999999999999999999999999999999


Q ss_pred             CCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCccc
Q psy7583         241 IPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDAVN  284 (451)
Q Consensus       241 ~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~~~  284 (451)
                      +|+||||||||||||||||+|||||                                    +|++.|.+.|+|||++. +
T Consensus       973 ~p~iGDKfasRHGqKGvis~i~p~eDMPf~~dG~~pDiIiNPhg~PSRMtiGqllE~~lgka~~~~G~~~datpF~~~-~ 1051 (1224)
T 1twf_B          973 IPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDI-T 1051 (1224)
T ss_dssp             CCCTTCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSC-C
T ss_pred             CCCchhhhhhhccCcceeeeecccccCCcCCCCCCccEEeCCCcCccccccchhHHHHhhHHHHhcCceeecCCCCCc-c
Confidence            9999999999999999999999999                                    57889999999999987 9


Q ss_pred             HHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccccc
Q psy7583         285 VQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFG  364 (451)
Q Consensus       285 ~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~G  364 (451)
                      ++++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||+||+||||+||++.|||||++||+++||||||
T Consensus      1052 ~~~i~~~L~~~g~~~~G~e~ly~G~TG~~~~~~i~vG~~YyqkL~HmV~DKihaRs~GP~~~lT~QP~~Gr~r~GG~RfG 1131 (1224)
T 1twf_B         1052 VEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFG 1131 (1224)
T ss_dssp             HHHHHHHHHTTTSCTTSEECEECTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC----------------CCCCC
T ss_pred             HHHHHHHHHHcCCCCCCCEEeecCCCCCCccceEEEehhHhhcchhhcccCceEEeeCCCcccccCCCcccccCCceecc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccce-EEeecccceeEeccCCCCCccceecCchhHHHHHHHHHhCC
Q psy7583         365 EMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLI-AIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMN  443 (451)
Q Consensus       365 EME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~-~~~~~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm~  443 (451)
                      |||||||+|||||++|+|||+.+||.+.++||..||++ ++.+..++.++|+.|+++.++..+.||||||||+|||+|||
T Consensus      1132 EMErd~L~a~Gaa~~L~ErL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~~c~~c~~~~~i~~~~iPysfklL~~EL~sm~ 1211 (1224)
T 1twf_B         1132 EMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMN 1211 (1224)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEEEECCHHHHHHHHHHHHTT
T ss_pred             hhhhhhHHhccHHHHHHHHHhcCCccceeEeeccCCCeeeecccccCceECCcCCCCCccccccCCHhHHHHHHHHHHCC
Confidence            99999999999999999999999999999999999999 77666677889999988888999999999999999999999


Q ss_pred             cccEEEE
Q psy7583         444 IAPRLMV  450 (451)
Q Consensus       444 I~~r~~~  450 (451)
                      |++||.+
T Consensus      1212 i~~~l~~ 1218 (1224)
T 1twf_B         1212 ITPRLYT 1218 (1224)
T ss_dssp             BCCEEES
T ss_pred             CeeEEEe
Confidence            9999975
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Back     alignment and structure
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli} Back     alignment and structure
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Back     alignment and structure
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Back     alignment and structure
>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1 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 451
d1twfb_1207 e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c 1e-138
d1smyc_1119 e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop 1e-100
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1207 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  423 bits (1089), Expect = e-138
 Identities = 266/487 (54%), Positives = 328/487 (67%), Gaps = 83/487 (17%)

Query: 1    MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
            MGV++TN++VRMDT+A++LYYP KPL TTR+MEYL+FRELPAG N+IVAI CY+GYNQED
Sbjct: 761  MGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQED 820

Query: 61   SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
            S+I+N S+++RG FRS+                                           
Sbjct: 821  SMIMNQSSIDRGLFRSL------------------------------------------- 837

Query: 121  SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
              FFRSY D E K      E FEKP R     M++  YDKLDDDG+IAPG+RVSG+DV+I
Sbjct: 838  --FFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVII 895

Query: 181  GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
            GKT  +  +E+EL   T   SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +
Sbjct: 896  GKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTK 955

Query: 241  IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
            IPQIGDKFASRHGQKGT GI YR+E                                   
Sbjct: 956  IPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLS 1015

Query: 266  -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
             V++  G  GDA+PF D + V+ IS LL+E+GYQ RG EVM+NGHTG+K+ AQ+F GPTY
Sbjct: 1016 KVAALSGNEGDASPFTD-ITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTY 1074

Query: 325  YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
            YQRL+HMVDDKIH+RARGP+Q+L RQP+EGR+RDGGLRFGEMERDC I+HGAA FL+ERL
Sbjct: 1075 YQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERL 1134

Query: 385  FEVSDPYRIHVCNFCGLIA-IANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMN 443
             E SD +R+H+C  CGL+  IA + +N FECKGC NK  I Q+ +PYAAKLLFQELM+MN
Sbjct: 1135 MEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMN 1194

Query: 444  IAPRLMV 450
            I PRL  
Sbjct: 1195 ITPRLYT 1201
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 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 ?
Query451
d1twfb_1207 RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyc_1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 100.0
d1smyc_1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 92.64
d1twfb_1207 RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta 82.83
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.2e-117  Score=1025.08  Aligned_cols=404  Identities=65%  Similarity=1.115  Sum_probs=359.1

Q ss_pred             CcccccCcccCCccceEeccCCCccceeccccccccCCCCCCcceeeeeeeeecccCCCCcEEeccceeccceEeeeccc
Q psy7583           1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSMEYL   80 (451)
Q Consensus         1 ~G~~~~n~~~R~D~~~~~L~yPQ~Plv~T~~~~~~~~d~~p~G~NaiVAV~sytgynqed~~~~n~~~i~rG~~r~~~~~   80 (451)
                      ||+|++|++.|.|+++|+|+|||+|||+|+.+++++++++|.|+||+|||                              
T Consensus       761 ~G~~~~~~~~r~D~~~~~l~~pQ~Plv~t~~~~~~~~~e~p~G~N~iVAv------------------------------  810 (1207)
T d1twfb_         761 MGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAI------------------------------  810 (1207)
T ss_dssp             CBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCEEEEEEE------------------------------
T ss_pred             CCccccccceeccccceeEecCCCceeeccchhhhhhhcccchhceEEEE------------------------------
Confidence            79999999999999999999999999999999999999999999999999                              


Q ss_pred             cccccCCCcceEEEEeeccccccccceeeccceeccCceeEEEEEEEEeeecccCCCcceeeecCCcccccCCchhhhhc
Q psy7583          81 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDK  160 (451)
Q Consensus        81 ~~~el~~G~N~~Va~msy~GYn~EDAiIiNkssidRG~f~s~~~k~~~~~~~~~~~~~~~~f~~P~~~~~~~~~~~~~~~  160 (451)
                                     |||+||||||||||||+|++||||||+||++|++++++...+.++.+..|......+.+...|++
T Consensus       811 ---------------msy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  875 (1207)
T d1twfb_         811 ---------------ACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDK  875 (1207)
T ss_dssp             ---------------CBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGG
T ss_pred             ---------------EeccCcccccccccchhhhhhcccceeeeEEEEEEeccccccccccccccccccccccchhhhhc
Confidence                           99999999999999999999999999999999999988887778888888776666667778999


Q ss_pred             cCcCCCcccCcEEeCCCEEEEEeeecCCCCccccccccccccceeeEEecCCcceEEEEEEEEeccCCeeEEEEEEeecC
Q psy7583         161 LDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR  240 (451)
Q Consensus       161 LD~dGi~~vG~~v~~gDiligK~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~R  240 (451)
                      ||+||||++|++|++||+||||++|....++.+........++|.|+.++.+|+|+||+|.++.+.++.+.+||+||+.|
T Consensus       876 Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~~~~~~~~~~s~~~~~~~~g~V~~v~~~~~~~~~~~~kv~i~~~R  955 (1207)
T d1twfb_         876 LDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTK  955 (1207)
T ss_dssp             CCTTSBCCTTCEECTTCEEECEECCCC-------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEE
T ss_pred             ccccccccccccccCCceeeeeeeccCCchhhhhhccccccccceeEEccCCCCeEEEEEEEeecccccceeeEEEEEEe
Confidence            99999999999999999999999997654433322223346789999999999999999999999999999999999999


Q ss_pred             CCccccccccccCCccEEeeeehhh------------------------------------HhhhcCCceeecCCCCccc
Q psy7583         241 IPQIGDKFASRHGQKGTCGIQYRQE------------------------------------VSSNKGEIGDATPFNDAVN  284 (451)
Q Consensus       241 ~p~IGDKFsSRHGQKGvvs~i~~~e------------------------------------~~~~~G~~~d~tpF~~~~~  284 (451)
                      +|+||||||||||||||||+|||+|                                    +|++.|.+.|+|||++. .
T Consensus       956 ~p~iGDKfasRhGqKGv~s~i~p~eDMPf~~dG~~pDiI~NP~g~PSRMtiGql~E~~~gk~~~~~g~~~d~t~F~~~-~ 1034 (1207)
T d1twfb_         956 IPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDI-T 1034 (1207)
T ss_dssp             CCCTTCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSC-C
T ss_pred             ccchhhhhhhccCCcceeeeeechhhCCcCCCCCCccEEECCCcCcccCcHHHHHHHHHHHHHHhcCCccccCCCCCc-c
Confidence            9999999999999999999999999                                    57899999999999987 8


Q ss_pred             HHHHHHHHHHhCCCCCCcEEEEcCccCceeeeeeeeeeeeEeeeccccCceeeeeeccCeeeeeecCCCcccccCccccc
Q psy7583         285 VQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFG  364 (451)
Q Consensus       285 ~~~~~~~l~~~g~~~~g~~~~~~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G~~~~lt~Qp~~Gr~~~Gg~r~G  364 (451)
                      .+++++.|.++||+++|+|.||||+|||+|+++||+|++|||||+|||+||+|||++||++.|||||++||+++||||||
T Consensus      1035 ~~~~~~~L~~~g~~~~G~e~ly~G~tG~~~~~~i~~G~~yy~rL~HmV~DK~~~Rs~Gp~~~lT~QP~~Gr~~~GG~R~G 1114 (1207)
T d1twfb_        1035 VEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFG 1114 (1207)
T ss_dssp             HHHHHHHHHTTTSCTTSEECEECTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC----------------CCCCC
T ss_pred             HHHHHHHHHHcCCCCCCCEEEECCCCCCCccceEEEehhHhhhhhhhhccccEeeccCCCCccccCCCCccccCCCccee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHhcchhHHHHHhhcccCCceeeeeeccccceEEee-cccceeEeccCCCCCccceecCchhHHHHHHHHHhCC
Q psy7583         365 EMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIAN-MRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMN  443 (451)
Q Consensus       365 EME~~~l~~~g~~~~l~e~l~~~SD~~~~~vC~~CG~~~~~~-~~~~~~~C~~C~~~~~~~~v~iPy~~klL~~EL~sm~  443 (451)
                      |||+|||+|||||++|+|||+.+||.+.++||.+||++++.. .+...+.|+.|+++.++..+.+|||||||+|||+|||
T Consensus      1115 EME~dal~a~Gaa~~L~e~l~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~c~~c~~~~~i~~~~iPy~fk~l~~EL~sm~ 1194 (1207)
T d1twfb_        1115 EMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMN 1194 (1207)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEEEECCHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHhHHHHHHHHhhccCCccceeccccCCceEEEecccccceeecCCCCCCCccccCCCHHHHHHHHHHHHCC
Confidence            999999999999999999999999999999999999998753 4567889999999899999999999999999999999


Q ss_pred             cccEEEE
Q psy7583         444 IAPRLMV  450 (451)
Q Consensus       444 I~~r~~~  450 (451)
                      |++||.+
T Consensus      1195 i~~~l~~ 1201 (1207)
T d1twfb_        1195 ITPRLYT 1201 (1207)
T ss_dssp             BCCEEES
T ss_pred             CceEEEe
Confidence            9999986
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure