BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy12829
(181 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|Q3T0Q3|RPB3_BOVIN DNA-directed RNA polymerase II subunit RPB3 OS=Bos taurus GN=POLR2C
PE=2 SV=1
Length = 275
Score = 302 bits (773), Expect = 1e-81, Method: Compositional matrix adjust.
Identities = 140/181 (77%), Positives = 162/181 (89%)
Query: 1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL
Sbjct: 1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct: 61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
S RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
Query: 181 G 181
G
Sbjct: 181 G 181
>sp|P19387|RPB3_HUMAN DNA-directed RNA polymerase II subunit RPB3 OS=Homo sapiens
GN=POLR2C PE=1 SV=2
Length = 275
Score = 300 bits (768), Expect = 4e-81, Method: Compositional matrix adjust.
Identities = 139/181 (76%), Positives = 161/181 (88%)
Query: 1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL
Sbjct: 1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
DEFIA R+GLIPL SD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct: 61 DEFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
S RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
Query: 181 G 181
G
Sbjct: 181 G 181
>sp|P97760|RPB3_MOUSE DNA-directed RNA polymerase II subunit RPB3 OS=Mus musculus
GN=Polr2c PE=2 SV=1
Length = 275
Score = 291 bits (744), Expect = 2e-78, Method: Compositional matrix adjust.
Identities = 135/181 (74%), Positives = 158/181 (87%)
Query: 1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
MPYANQP+V IT+LT+ENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ NS+VL
Sbjct: 1 MPYANQPTVRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDGNSSVLH 60
Query: 61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct: 61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
S RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAY KK GKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYVKKRSGKEHAKWNPTA 180
Query: 181 G 181
G
Sbjct: 181 G 181
>sp|Q54DH7|RPB3_DICDI DNA-directed RNA polymerase II subunit rpb3 OS=Dictyostelium
discoideum GN=polr2c PE=3 SV=1
Length = 302
Score = 189 bits (480), Expect = 9e-48, Method: Compositional matrix adjust.
Identities = 89/175 (50%), Positives = 131/175 (74%), Gaps = 6/175 (3%)
Query: 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
QP + I ++ ++++ F + +T++SVAN+LRRV IAE PTM ID V+ E+N++VL DEFIA
Sbjct: 11 QPELEILEIKNDSIIFILSNTDISVANALRRVMIAEVPTMCIDLVEFESNNSVLCDEFIA 70
Query: 66 SRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
R+GLIPL SD +D+ Y+RDC+C D C +CSVE L+VKC +++ R VT++DL S ++
Sbjct: 71 HRLGLIPLVSDN-IDKFCYTRDCSCSDRCDQCSVELRLNVKCTENRPRDVTSSDLLSQNS 129
Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
V+PV+S+ ++ + +I IVKLR+GQE++LRA AKKG GKEHAKW+P+
Sbjct: 130 AVIPVSSQVTSSNSEQ-----EIPIVKLRRGQEIKLRAIAKKGVGKEHAKWSPSC 179
>sp|Q39211|RPB3A_ARATH DNA-directed RNA polymerase II subunit RPB3-A OS=Arabidopsis
thaliana GN=RPB36A PE=2 SV=1
Length = 319
Score = 180 bits (457), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 94/181 (51%), Positives = 126/181 (69%), Gaps = 5/181 (2%)
Query: 3 YANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDE 62
Y P + I +L D+ KF++ +T++S+AN+LRRV I+E PT+AID V++E NS+VL+DE
Sbjct: 6 YQRFPKIKIRELKDDYAKFELRETDVSMANALRRVMISEVPTVAIDLVEIEVNSSVLNDE 65
Query: 63 FIASRIGLIPLTSDEVVDRILYSRDCTCVDF---CSECSVEFTLDVKCVDDQTRHVTTAD 119
FIA R+GLIPLTS+ + + +SRDC D C CSVEF L KCV DQT VT+ D
Sbjct: 66 FIAHRLGLIPLTSERAM-SMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDVTSRD 124
Query: 120 LKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
L S D V PV D+ +++ E I+IVKLR+GQEL+LRA A+KG GK+HAKW+P
Sbjct: 125 LYSADPTVTPV-DFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKWSPA 183
Query: 180 A 180
A
Sbjct: 184 A 184
>sp|Q39212|RPB3B_ARATH DNA-directed RNA polymerase II subunit RPB3-B OS=Arabidopsis
thaliana GN=RPB36B PE=1 SV=2
Length = 319
Score = 166 bits (421), Expect = 7e-41, Method: Compositional matrix adjust.
Identities = 88/180 (48%), Positives = 119/180 (66%), Gaps = 3/180 (1%)
Query: 3 YANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDE 62
Y P+V I +L D+ KF++ +T++S+AN+LRRV I+E PTMAI V++E NS+VL+DE
Sbjct: 6 YQRFPTVKIRELKDDYAKFELRETDVSMANALRRVMISEVPTMAIHLVKIEVNSSVLNDE 65
Query: 63 FIASRIGLIPLTSDEVVDRILYS--RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
FIA R+ LIPLTS+ + DC + C CSVEF L KCV DQT VT+ DL
Sbjct: 66 FIAQRLSLIPLTSERAMSMRFCQDCEDCNGDEHCEFCSVEFPLSAKCVTDQTLDVTSRDL 125
Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
S D V PV ++ ++ E I+I KLR+GQEL+L+A A+KG GK+HAKW+P A
Sbjct: 126 YSADPTVTPV-DFTSNSSTSDSSEHKGIIIAKLRRGQELKLKALARKGIGKDHAKWSPAA 184
>sp|P16370|RPB3_YEAST DNA-directed RNA polymerase II subunit RPB3 OS=Saccharomyces
cerevisiae (strain ATCC 204508 / S288c) GN=RPB3 PE=1
SV=2
Length = 318
Score = 155 bits (393), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA
Sbjct: 6 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 67 RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
R+GLIPL S + ++++ YSRDC C D C +CSV TL + T +V + DL
Sbjct: 66 RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
V + RN + + E + +LI KLRKGQEL+L AKKG KEHAKW P A
Sbjct: 121 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 174
>sp|P37382|RPB3_SCHPO DNA-directed RNA polymerase II subunit RPB3 OS=Schizosaccharomyces
pombe (strain 972 / ATCC 24843) GN=rpb3 PE=1 SV=2
Length = 297
Score = 137 bits (344), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 77/180 (42%), Positives = 109/180 (60%), Gaps = 17/180 (9%)
Query: 10 HIT--DLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
HIT +++ +V F + +T L+VANSLRRV +AE PT+AID V++ N++V+ DEF+A R
Sbjct: 6 HITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHR 65
Query: 68 IGLIPLTSDEVVDR----ILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL--K 121
+G+IPL S + + + Y+R+C C +C +CSVE L+ KC + T + DL
Sbjct: 66 LGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVS 125
Query: 122 STDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
S + P+ AD G LI KLRK QE+ LR AKKG KEHAKW+PT+
Sbjct: 126 SNSSLGHPIL-----ADPKSRGP----LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA 176
>sp|P16925|CNJC_TETTH Conjugation stage-specific protein OS=Tetrahymena thermophila
GN=CNJC PE=2 SV=1
Length = 310
Score = 120 bits (300), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 72/179 (40%), Positives = 104/179 (58%), Gaps = 14/179 (7%)
Query: 11 ITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGL 70
+T+L + +F +E+ ++S+ANSLRR+ +AE T+AI V++ N++ L DE+IA R+GL
Sbjct: 8 LTNLEEFKCEFTLENCDISLANSLRRILLAEIETIAIHNVKVYENTSSLPDEYIAHRLGL 67
Query: 71 IPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKS----TD-- 124
IPL S + VD Y +C C C C++ F L V ++ VT+ DLK TD
Sbjct: 68 IPLNSAK-VDDYNYIWNCNCQGECDRCTIHFDLRVSNFTNEVLEVTSLDLKQRQDHTDED 126
Query: 125 -ARVVPVTSRNRDADMNEYGETDD--ILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
R + V S RD EYG + I I+KL KGQ++ A+KG GK H+KWNP
Sbjct: 127 AVRPIKVYSILRD----EYGNKREVGIPIIKLSKGQQIHFECEAQKGIGKMHSKWNPVC 181
>sp|Q2NFZ6|RPOD_METST DNA-directed RNA polymerase subunit D OS=Methanosphaera stadtmanae
(strain DSM 3091) GN=rpoD PE=3 SV=1
Length = 270
Score = 106 bits (265), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 63/173 (36%), Positives = 93/173 (53%), Gaps = 17/173 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
++ I + DE F VE + + N++RR+ + E PT+AI+ V + N + DE +A R
Sbjct: 2 NIEIREKDDERAVFVVEGVDDTFINTIRRICLVEIPTLAIEDVNIYKNDAKMFDEVLAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVD-DQTRHVTTADLKSTDAR 126
+GLIP+ +D +D + +C C C C V F L KC + + ++ V + DLKS D
Sbjct: 62 LGLIPIVTD--LDSYVMPSECDCESGCQHCRVSFLLKEKCEEGNDSKIVYSKDLKSDDPA 119
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
V PV D I IV+LR+G+E+ L A A+ G G EHAKW T
Sbjct: 120 VKPV--------------YDTIPIVRLREGEEVELEAIAELGLGSEHAKWQAT 158
>sp|A1RSE3|RPOD_PYRIL DNA-directed RNA polymerase subunit D OS=Pyrobaculum islandicum
(strain DSM 4184 / JCM 9189) GN=rpoD PE=3 SV=1
Length = 262
Score = 101 bits (251), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 68/173 (39%), Positives = 92/173 (53%), Gaps = 19/173 (10%)
Query: 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
P I + T +K +E S+ NS+RRV I+E P MAID+V + +N++V+ DE +A
Sbjct: 1 MPKATIVEKTPLFLKAVIEGAYPSLVNSIRRVIISELPVMAIDYVVIVSNTSVMYDEMLA 60
Query: 66 SRIGLIPLTSDEVVDRILYSRDC-TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD 124
R+GL+PLT+ + + DC T + SEC+V L + D+ V + DL S
Sbjct: 61 HRLGLVPLTTP--LQALPPIEDCETGLVDPSECTVRLMLQINAESDKI--VYSGDLVSER 116
Query: 125 ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
VVPV DI IVKL KGQ + L AYAK G KEHAKW
Sbjct: 117 PDVVPVYK--------------DIPIVKLVKGQSIILEAYAKLGRAKEHAKWQ 155
>sp|B1YC30|RPOD_PYRNV DNA-directed RNA polymerase subunit D OS=Pyrobaculum neutrophilum
(strain DSM 2338 / JCM 9278 / V24Sta) GN=rpoD PE=3 SV=1
Length = 262
Score = 100 bits (250), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 71/173 (41%), Positives = 93/173 (53%), Gaps = 19/173 (10%)
Query: 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
P+V + + T +K VE S+ NSLRRV I+E P MAID V + N++V+ DE +A
Sbjct: 1 MPAVKVVERTPLFLKAVVEGAYPSLVNSLRRVIISELPVMAIDTVIVVNNTSVMYDEMLA 60
Query: 66 SRIGLIPLTSDEVVDRILYSRDC-TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD 124
R+GLIPLT+ + + DC + + SEC+V FTL V + T V + DL S
Sbjct: 61 HRLGLIPLTTP--LQSLPPIEDCESGLADPSECTVRFTLQVNADGEVT--VYSGDLVSER 116
Query: 125 ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
VVPV DI IVKL KGQ + L AYAK G + HAKW
Sbjct: 117 PDVVPVHK--------------DIPIVKLVKGQSIVLEAYAKLGRARGHAKWQ 155
>sp|O26144|RPOD_METTH DNA-directed RNA polymerase subunit D OS=Methanothermobacter
thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM
10044 / NBRC 100330 / Delta H) GN=rpoD PE=3 SV=1
Length = 264
Score = 100 bits (249), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 60/172 (34%), Positives = 87/172 (50%), Gaps = 19/172 (11%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
+ + + TD + F V + N++RR+ + E P +AI++V + N + DE +A R+
Sbjct: 3 IALKEKTDTEMVFVVSGVTVPFINAIRRICMMEVPKLAIEYVNMYRNDAKMFDEVLAHRL 62
Query: 69 GLIPLTSD-EVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARV 127
GL+PL +D E + + +C C ++CSECSV TL K V + DL S V
Sbjct: 63 GLVPLAADPEFAESLKMPEECDCEEYCSECSVSLTLRKK----GPGVVYSGDLVSETPAV 118
Query: 128 VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
PV DI +VKL EL L A A+ G G+EHAKW PT
Sbjct: 119 KPVYP--------------DIPLVKLGDDDELELEAVAQLGVGREHAKWEPT 156
>sp|Q8U0E4|RPOD_PYRFU DNA-directed RNA polymerase subunit D OS=Pyrococcus furiosus
(strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=rpoD
PE=3 SV=1
Length = 261
Score = 97.4 bits (241), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 62/170 (36%), Positives = 89/170 (52%), Gaps = 25/170 (14%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V I + ++++KF ++ +S AN+LRR + E PT A+D V+ N + L DE IA R+
Sbjct: 6 VQILEKKEDSIKFVLKGVHVSFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 65
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
+IPLT+ VDR + D +D ++T+ + + V + DLKS D V
Sbjct: 66 AMIPLTTP--VDR--FELDALELD-------DYTVTLSLEAEGPGIVYSGDLKSDDPDVK 114
Query: 129 PVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
PV +I IVKL +GQ L AYAK G GK+HAKW P
Sbjct: 115 PVNP--------------NIPIVKLAEGQRLVFNAYAKLGRGKDHAKWQP 150
>sp|O28002|RPOD_ARCFU DNA-directed RNA polymerase subunit D OS=Archaeoglobus fulgidus
(strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC
100126) GN=rpoD PE=3 SV=1
Length = 264
Score = 97.4 bits (241), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 56/175 (32%), Positives = 92/175 (52%), Gaps = 21/175 (12%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P + I + D +KF +++ ++ANS RR AE P MA+D+V + NS+ DE IA
Sbjct: 3 PEIEILEEKDFKIKFILKNASPALANSFRRAMKAEVPAMAVDYVDIYLNSSYFYDEVIAH 62
Query: 67 RIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
R+ ++P+ + +DR +C+C + C C + F L+V + + V + D S D
Sbjct: 63 RLAMLPIKT--YLDRFNMQSECSCGGEGCPNCQISFRLNV----EGPKVVYSGDFISDDP 116
Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
VV D+I +++L +GQ+L L A A+ G G+EHAK+ P +
Sbjct: 117 DVV--------------FAIDNIPVLELFEGQQLMLEAVARLGTGREHAKFQPVS 157
>sp|O59303|RPOD_PYRHO DNA-directed RNA polymerase subunit D OS=Pyrococcus horikoshii
(strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139
/ OT-3) GN=rpoD PE=3 SV=2
Length = 259
Score = 96.3 bits (238), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 62/171 (36%), Positives = 87/171 (50%), Gaps = 25/171 (14%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
+ I T++++ F +E ++ AN+LRR + E PT A+D V+ N + L DE IA R
Sbjct: 3 KIKILKKTEDSITFILEGVSVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHR 62
Query: 68 IGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARV 127
+ +IPL + DR + D +D ++T+ + + V + DLKS D V
Sbjct: 63 LAMIPLKTP--TDR--FELDALELD-------DYTVTLSLEAEGPGIVYSGDLKSDDPDV 111
Query: 128 VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
PVT DI IVKL KGQ L AYAK G GK+HAKW P
Sbjct: 112 KPVTP--------------DIPIVKLAKGQRLVFNAYAKLGRGKDHAKWQP 148
>sp|Q9V198|RPOD_PYRAB DNA-directed RNA polymerase subunit D OS=Pyrococcus abyssi (strain
GE5 / Orsay) GN=rpoD PE=3 SV=1
Length = 259
Score = 95.5 bits (236), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 61/170 (35%), Positives = 87/170 (51%), Gaps = 25/170 (14%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
+ I TD+++ F +E +++ AN+LRR + E PT A+D V+ N + L DE IA R+
Sbjct: 4 IKILKKTDDSITFILEGVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEIIAHRL 63
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
+IPL + VDR + D +D ++T+ + + V + DLKS D V
Sbjct: 64 AMIPLKTP--VDR--FELDALELD-------DYTVTLSLEAEGPGIVYSGDLKSDDPDVK 112
Query: 129 PVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
P DI IVKL KGQ L A+AK G GK+HAKW P
Sbjct: 113 PANP--------------DIPIVKLAKGQRLVFNAFAKLGRGKDHAKWQP 148
>sp|Q96YW0|RPOD_SULTO DNA-directed RNA polymerase subunit D OS=Sulfolobus tokodaii
(strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=rpoD
PE=3 SV=1
Length = 264
Score = 95.5 bits (236), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 58/173 (33%), Positives = 89/173 (51%), Gaps = 17/173 (9%)
Query: 11 ITDLTDEN--VKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
I+ L+ EN +K V + L + NS+RR I P MA+D V N++ L DE +A R+
Sbjct: 3 ISLLSKENNSLKLIVGNYPLELVNSIRRASILYVPVMAVDEVYFIENNSPLYDEILAHRL 62
Query: 69 GLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARV 127
+IP +SDE +D +C C + C C LDV + +T V + DLK+ D +
Sbjct: 63 AMIPFSSDEALDHYRPPEECAECKENCDGCYARVYLDVGANEGETVMVYSRDLKTDDPAI 122
Query: 128 VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
VP++ +I IV L Q++ L A + G+GKEH K++P +
Sbjct: 123 VPISG--------------NIPIVLLGPKQKVTLEARLRLGYGKEHIKFSPVS 161
>sp|Q8ZYQ3|RPOD_PYRAE DNA-directed RNA polymerase subunit D OS=Pyrobaculum aerophilum
(strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC
100827) GN=rpoD PE=3 SV=1
Length = 260
Score = 95.5 bits (236), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 68/160 (42%), Positives = 86/160 (53%), Gaps = 19/160 (11%)
Query: 19 VKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV 78
+K VE S+ NSLRRV I+E P MAID V + N++V+ DE +A R+GLIPLT+
Sbjct: 14 LKAVVEGVPPSLVNSLRRVIISELPVMAIDNVVVVNNTSVMYDEMLAHRLGLIPLTTP-- 71
Query: 79 VDRILYSRDC-TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDA 137
+ + DC + + SECS TL V D T + + DL S VVPV
Sbjct: 72 LQSLPPYEDCVSGLADPSECSTRLTLQVTAEGDTT--IYSGDLASDRPDVVPVYK----- 124
Query: 138 DMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
DI IVKL KGQ + L AYAK G K+HAKW
Sbjct: 125 ---------DIPIVKLVKGQSIVLEAYAKLGVAKDHAKWQ 155
>sp|Q9YB53|RPOD_AERPE DNA-directed RNA polymerase subunit D OS=Aeropyrum pernix (strain
ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
GN=rpoD PE=3 SV=2
Length = 286
Score = 95.1 bits (235), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 55/176 (31%), Positives = 94/176 (53%), Gaps = 17/176 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
SV + +L V+ ++ + N++RR +++ PTMA+D+ + N+T + DE +A R
Sbjct: 8 SVEVVELDSLRVRLRIRGYPVVFVNAIRRTVLSDVPTMAVDYAYIFDNTTAVYDEMVAHR 67
Query: 68 IGLIPLTSDEVVDRILYSRDCTCVDFCSE-CSVEFTL--DVKCVDDQTRHVTTADLKSTD 124
+GL+ L S+E V++ +C + E C VE +L +V + R++T DL +D
Sbjct: 68 LGLVVLDSNEAVEKYRRPEECAGKEPSEEDCFVEVSLEAEVDAEGETGRYITAGDLSISD 127
Query: 125 ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+V PV Y ET I + GQ + ++A+A+ G GKEH KW+P +
Sbjct: 128 PQVKPV-----------YPETPLIYVA---PGQRIHVQAFARLGRGKEHTKWSPAS 169
>sp|O94616|RPAC1_SCHPO DNA-directed RNA polymerases I and III subunit RPAC1
OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843)
GN=rpc40 PE=3 SV=1
Length = 348
Score = 95.1 bits (235), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 61/186 (32%), Positives = 101/186 (54%), Gaps = 17/186 (9%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V IT L E + F++ + S+AN+ RR+ IAE PT+A ++V + N++++ DE ++ RI
Sbjct: 48 VSITSLDQETMVFEISGIDASIANAFRRILIAEIPTLAFEFVYIINNTSIIQDEVLSHRI 107
Query: 69 GLIPLTSD----EVVDRILYSRDCTCVDFCSECSVEFTLDVKC---------VDDQTRHV 115
GL+P+++D + L ++ T D+ +V F+L+ KC D R
Sbjct: 108 GLVPISADPDMFKWFQHPLPGQEATHTDY---DTVVFSLNKKCEFNKNAATDEKDPKRLY 164
Query: 116 TTADLKSTDARVVPVTSR-NRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHA 174
+++ S D P + R AD DI++ KLR GQE+ L A+A G G++HA
Sbjct: 165 VNSEVYSGDLIWKPQGRQEERFADNPIRVVNPDIVVAKLRPGQEIDLEAHAILGIGQDHA 224
Query: 175 KWNPTA 180
K++P A
Sbjct: 225 KFSPVA 230
>sp|Q8PV16|RPOD_METMA DNA-directed RNA polymerase subunit D OS=Methanosarcina mazei
(strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833
/ OCM 88) GN=rpoD PE=3 SV=1
Length = 266
Score = 94.7 bits (234), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 60/171 (35%), Positives = 92/171 (53%), Gaps = 22/171 (12%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V I +L+D + KF + ++ AN +RR IA+ PT+AI++V L N++VL DE +A R+
Sbjct: 5 VDILELSDRSAKFVLSRVSMAFANGVRRAMIADVPTLAIEYVNLYDNTSVLYDEQLALRL 64
Query: 69 GLIPLTSDEVVDRILYSRDCTCV--DFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
LIPL +D ++ + +C + C C V TL + V + DL S+D +
Sbjct: 65 SLIPLVTD--IETYMPQAECEVCGGEGCPACEVSLTLSA----EGPGTVYSRDLISSDPK 118
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
+ P AD N I IV+L+KGQ+L L A A G+G++ KW
Sbjct: 119 IQP-------ADPN-------IPIVELKKGQKLVLEAIAHMGYGRDSVKWQ 155
>sp|A4WNA4|RPOD_PYRAR DNA-directed RNA polymerase subunit D OS=Pyrobaculum arsenaticum
(strain DSM 13514 / JCM 11321) GN=rpoD PE=3 SV=1
Length = 259
Score = 94.4 bits (233), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 70/172 (40%), Positives = 88/172 (51%), Gaps = 17/172 (9%)
Query: 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
P V I + + +K VE S+ NSLRRV I+E P MAID V + N++V+ DEF+A
Sbjct: 1 MPRVSIVEKSQLFLKAIVEGVPPSLVNSLRRVIISELPVMAIDTVVVVNNTSVMYDEFLA 60
Query: 66 SRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
R+GLIPLT+ + Y T V +EC L V D T V + DL S
Sbjct: 61 QRLGLIPLTTP-LHSLPTYEECATGVADPTECGTRLVLQVTADGDVT--VYSGDLTSERP 117
Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
VVPV DI IVKL KGQ + + AYAK G K+HAKW
Sbjct: 118 DVVPVYK--------------DIPIVKLVKGQSIVIEAYAKLGIAKDHAKWQ 155
>sp|P0CG28|RPOD_METAC DNA-directed RNA polymerase subunit D OS=Methanosarcina acetivorans
(strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) GN=rpoD
PE=3 SV=1
Length = 266
Score = 94.4 bits (233), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 59/171 (34%), Positives = 92/171 (53%), Gaps = 22/171 (12%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V I +L+D + KF + + + AN +RR +A+ PT+AI++V L N++VL DE +A R+
Sbjct: 5 VDILELSDRSAKFVLSNVSTAFANGIRRAMVADVPTLAIEYVNLYDNTSVLYDEQLALRL 64
Query: 69 GLIPLTSDEVVDRILYSRDCTCV--DFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
LIPL +D ++ L +C + C C V TL + V + DL S+D +
Sbjct: 65 SLIPLATD--IETYLPQAECDVCGGEGCPACEVSLTLSA----EGPGTVYSRDLISSDPK 118
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
+ P AD N + IV+L+KGQ+L L A A G+G++ KW
Sbjct: 119 IQP-------ADPN-------VPIVELKKGQKLVLEAIAHMGYGRDSVKWQ 155
>sp|Q5JJF4|RPOD_PYRKO DNA-directed RNA polymerase subunit D OS=Pyrococcus kodakaraensis
(strain ATCC BAA-918 / JCM 12380 / KOD1) GN=rpoD PE=3
SV=1
Length = 259
Score = 91.7 bits (226), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 57/162 (35%), Positives = 85/162 (52%), Gaps = 25/162 (15%)
Query: 17 ENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSD 76
+++KF V ++ AN+LRR ++E PT A+D V+ N + L DE IA R+ +IPLT+
Sbjct: 12 DSIKFIVSGVDVPFANALRRTILSEVPTFAVDEVEFLENDSALFDEIIAHRLAMIPLTTP 71
Query: 77 EVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRD 136
+R +S D +D ++T+ + + V + DLKS+D V P
Sbjct: 72 H--ER--FSLDALELD-------DYTVTLSLEAEGPGMVYSGDLKSSDGDVKPANP---- 116
Query: 137 ADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
+I IVKL +GQ L AYA+ G GK+HAKW P
Sbjct: 117 ----------NIPIVKLAEGQRLTFNAYARLGRGKDHAKWQP 148
>sp|Q32L22|RPAC1_BOVIN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Bos taurus
GN=POLR1C PE=2 SV=1
Length = 346
Score = 90.5 bits (223), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 59/187 (31%), Positives = 99/187 (52%), Gaps = 23/187 (12%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V + + + +++F + + ++AN+ RR+ +AE PTMA++ V + N++++ DE +A R+
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
GLIP+ +D R+ R+ +++F L V+C TR+ A S+D +
Sbjct: 111 GLIPIHADP---RLFEYRNQGDEGGTEIDTLQFRLQVRC----TRNPHAAK-DSSDPNEL 162
Query: 129 PVTSR-----------NRDADMNEYGET----DDILIVKLRKGQELRLRAYAKKGFGKEH 173
V R AD+ G DDILI +LR GQE+ L + KG GK+H
Sbjct: 163 YVNHRVYTRHMTWVPLGNQADLFPEGAIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDH 222
Query: 174 AKWNPTA 180
AK++P A
Sbjct: 223 AKFSPVA 229
>sp|C3MZ05|RPOD_SULIM DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain M.14.25 / Kamchatka #1) GN=rpoD PE=3 SV=1
Length = 265
Score = 90.5 bits (223), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D+ + E L N++RR + P M+ID V N++ L DE +A R
Sbjct: 2 SINLLHKDDKRIDLVFEGYPLEFVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP TS+E +D + +C C + C +C + ++ + + ++ + + + D+KS D
Sbjct: 62 LALIPFTSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+VP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160
>sp|C4KJ93|RPOD_SULIK DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain M.16.4 / Kamchatka #3) GN=rpoD PE=3 SV=1
Length = 265
Score = 90.5 bits (223), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D+ + E L N++RR + P M+ID V N++ L DE +A R
Sbjct: 2 SINLLHKDDKRIDLVFEGYPLEFVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP TS+E +D + +C C + C +C + ++ + + ++ + + + D+KS D
Sbjct: 62 LALIPFTSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+VP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160
>sp|C3N054|RPOD_SULIA DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain M.16.27) GN=rpoD PE=3 SV=1
Length = 265
Score = 90.5 bits (223), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D+ + E L N++RR + P M+ID V N++ L DE +A R
Sbjct: 2 SINLLHKDDKRIDLVFEGYPLEFVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP TS+E +D + +C C + C +C + ++ + + ++ + + + D+KS D
Sbjct: 62 LALIPFTSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+VP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160
>sp|C3N8R8|RPOD_SULIY DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain Y.G.57.14 / Yellowstone #1) GN=rpoD PE=3 SV=1
Length = 265
Score = 90.1 bits (222), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D+ + E L N++RR + P M+ID V N++ L DE +A R
Sbjct: 2 SINLLHKDDKRIDLVFEGYPLEFVNAIRRATMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP TS+E +D + +C C + C +C + ++ + + ++ + + + D+KS D
Sbjct: 62 LALIPFTSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+VP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160
>sp|C3NMQ0|RPOD_SULIN DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain Y.N.15.51 / Yellowstone #2) GN=rpoD PE=3 SV=1
Length = 265
Score = 90.1 bits (222), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D+ + E L N++RR + P M+ID V N++ L DE +A R
Sbjct: 2 SINLLHKDDKRIDLVFEGYPLEFVNAIRRATMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP TS+E +D + +C C + C +C + ++ + + ++ + + + D+KS D
Sbjct: 62 LALIPFTSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+VP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160
>sp|C3MJP7|RPOD_SULIL DNA-directed RNA polymerase subunit D OS=Sulfolobus islandicus
(strain L.S.2.15 / Lassen #1) GN=rpoD PE=3 SV=1
Length = 265
Score = 90.1 bits (222), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D+ + E L N++RR + P M+ID V N++ L DE +A R
Sbjct: 2 SINLLHKDDKRIDLVFEGYPLEFVNAIRRATMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP TS+E +D + +C C + C +C + ++ + + ++ + + + D+KS D
Sbjct: 62 LALIPFTSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+VP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160
>sp|P52432|RPAC1_MOUSE DNA-directed RNA polymerases I and III subunit RPAC1 OS=Mus
musculus GN=Polr1c PE=1 SV=3
Length = 346
Score = 90.1 bits (222), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 58/187 (31%), Positives = 100/187 (53%), Gaps = 23/187 (12%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V + + ++ ++F + + ++AN+ RR+ +AE PTMA++ V + N++++ DE +A R+
Sbjct: 51 VDVVQMDEDTLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
GLIP+ +D R+ R+ + +++F L V+C TR+ A S+D +
Sbjct: 111 GLIPILADP---RLFEYRNQGEEEGTEIDTLQFRLQVRC----TRNPNAAK-DSSDPNEL 162
Query: 129 PVTSR-----------NRDADMNEYGET----DDILIVKLRKGQELRLRAYAKKGFGKEH 173
V + AD+ G DDILI +LR GQE+ L + KG GK+H
Sbjct: 163 YVNHKVYTRHMTWVPLGNQADVFPEGTIRPVHDDILIAQLRPGQEIDLMMHCVKGIGKDH 222
Query: 174 AKWNPTA 180
AK++P A
Sbjct: 223 AKFSPVA 229
>sp|P95989|RPOD_SULSO DNA-directed RNA polymerase subunit D OS=Sulfolobus solfataricus
(strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) GN=rpoD
PE=1 SV=1
Length = 265
Score = 89.7 bits (221), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 52/174 (29%), Positives = 87/174 (50%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D + E L N++RR + P MA+D V N++ L DE +A R
Sbjct: 2 SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP S+E +D + +C C + C +C + ++ + ++ R + + D+KS D
Sbjct: 62 LALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAE-APNEPRMIYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
VVP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 VVPISG--------------DIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVS 160
>sp|O15160|RPAC1_HUMAN DNA-directed RNA polymerases I and III subunit RPAC1 OS=Homo
sapiens GN=POLR1C PE=1 SV=1
Length = 346
Score = 89.4 bits (220), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 58/187 (31%), Positives = 100/187 (53%), Gaps = 23/187 (12%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V + + + +++F + + ++AN+ RR+ +AE PTMA++ V + N++++ DE +A R+
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
GLIP+ +D R+ R+ + +++F L V+C TR+ A S+D +
Sbjct: 111 GLIPIHADP---RLFEYRNQGDEEGTEIDTLQFRLQVRC----TRNPHAAK-DSSDPNEL 162
Query: 129 PVTSR-----------NRDADMNEYGET----DDILIVKLRKGQELRLRAYAKKGFGKEH 173
V + AD+ G DDILI +LR GQE+ L + KG GK+H
Sbjct: 163 YVNHKVYTRHMTWIPLGNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDH 222
Query: 174 AKWNPTA 180
AK++P A
Sbjct: 223 AKFSPVA 229
>sp|A5UN55|RPOD_METS3 DNA-directed RNA polymerase subunit D OS=Methanobrevibacter smithii
(strain PS / ATCC 35061 / DSM 861) GN=rpoD PE=3 SV=1
Length = 274
Score = 89.0 bits (219), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 57/173 (32%), Positives = 91/173 (52%), Gaps = 24/173 (13%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
+ + TD+ + F V D E+ N++RR + P +AI+ V + N + + +E +A R+
Sbjct: 3 IEVKSQTDDEIVFIVRDAEVPFINAIRRCAMVNVPKIAIEDVNIMRNDSAMFNEVLAHRL 62
Query: 69 GLIPLTS--DEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
GL PL S D + L D D+ SV F+L ++ + V + DL S+D++
Sbjct: 63 GLTPLVSNMDAIEGLPLPGDD----DYEENNSVMFSLK----EEGPKVVYSKDLISSDSK 114
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
+ PV D I +VKL++G++L + A AK G+GKEHAKW PT
Sbjct: 115 IKPV--------------YDTIPLVKLKEGEKLNIEAVAKVGYGKEHAKWMPT 153
>sp|Q54SN4|RPAC1_DICDI DNA-directed RNA polymerases I and III subunit rpac1
OS=Dictyostelium discoideum GN=polr1c PE=3 SV=1
Length = 345
Score = 87.8 bits (216), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 56/163 (34%), Positives = 88/163 (53%), Gaps = 10/163 (6%)
Query: 21 FQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVD 80
F++ + +AN+LRR+ I+E PTMAI+ V + N+++L DE +A R+G+IP+ VD
Sbjct: 73 FEMIGIDAPIANALRRIMISEIPTMAIEKVYIINNTSILQDEVLAHRLGMIPIK----VD 128
Query: 81 RILYSRDCTCVDFCSECSVEFTLDVKCVDDQ-TRHVTTADLKSTDARVVPVTSRNRDADM 139
++ ++ +E ++ F L VKC D T + S VP T +
Sbjct: 129 PRKFNFKLPNKEYTAEDTLIFQLKVKCEKDSVTGKIINETALSKHLIWVP-TQDQEEMFP 187
Query: 140 NEYGET----DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
NE DDI I+KLR GQ + ++ Y +K G+EH KW+P
Sbjct: 188 NEEDRPRPMEDDIPIMKLRPGQVIDIQCYCEKNIGREHIKWSP 230
>sp|P39471|RPOD_SULAC DNA-directed RNA polymerase subunit D OS=Sulfolobus acidocaldarius
(strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 /
NCIMB 11770) GN=rpoD PE=3 SV=2
Length = 264
Score = 87.8 bits (216), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 53/163 (32%), Positives = 80/163 (49%), Gaps = 16/163 (9%)
Query: 19 VKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV 78
++ +E+ L NS+RR I P MA+D V N++ L DE +A R+ L+P SDE
Sbjct: 13 LRLVLENYPLEFVNSIRRASILYVPVMAVDEVYFIENNSPLYDEILAHRLALVPFVSDEA 72
Query: 79 VDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDA 137
++ +C C + C C LDV+ DQ + + DLKS D + PV+
Sbjct: 73 LEHYRPPEECAECKENCDGCYNRVYLDVE-AKDQPLMIYSRDLKSEDQMITPVSG----- 126
Query: 138 DMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
I IV L Q++ L A + G+GKEH K++P +
Sbjct: 127 ---------AIPIVLLGSKQKISLEARLRLGYGKEHIKYSPVS 160
>sp|P07703|RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
GN=RPC40 PE=1 SV=1
Length = 335
Score = 87.4 bits (215), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 58/185 (31%), Positives = 94/185 (50%), Gaps = 16/185 (8%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V+I+ L F + + + S+AN+ RR+ I+E P++A ++V N++V+ DE +A RI
Sbjct: 42 VNISSLDAREANFDLINIDTSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHRI 101
Query: 69 GLIPLTSDEVVDRILYSRDCTCVD---FCSECSVEFTLDVKCV---------DDQTRHVT 116
GL+PL D +L D D F E ++ +L+VKC D
Sbjct: 102 GLVPLKVDP---DMLTWVDSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYN 158
Query: 117 TADLKSTDARVVPVTSRNRD-ADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAK 175
A + + D + P ++ AD DIL+ KLR GQE+ L+A+ G G +HAK
Sbjct: 159 NAHVYARDLKFEPQGRQSTTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAK 218
Query: 176 WNPTA 180
++P +
Sbjct: 219 FSPVS 223
>sp|A3MXZ5|RPOD_PYRCJ DNA-directed RNA polymerase subunit D OS=Pyrobaculum calidifontis
(strain JCM 11548 / VA1) GN=rpoD PE=3 SV=1
Length = 258
Score = 84.3 bits (207), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 65/179 (36%), Positives = 87/179 (48%), Gaps = 31/179 (17%)
Query: 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
P V I + + K VE S+ NSLRRV I+E P +AID V + N++V+ DE +A
Sbjct: 1 MPKVSIVEKSQFFAKAVVEGVPPSLINSLRRVIISELPVLAIDSVVVVNNTSVMYDEMLA 60
Query: 66 SRIGLIPLTSDEVVDRILYSRDCTCVDFC-------SECSVEFTLDVKCVDDQTRHVTTA 118
R+GLIPLT+ +D ++ C SEC+V TL V D V
Sbjct: 61 HRLGLIPLTTP--------LKDLPPIEDCESGLVDPSECTVRLTLQVNATGDVV--VYAG 110
Query: 119 DLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
DL + V PV DI IVKL +GQ + + AYAK G ++HAKW
Sbjct: 111 DLVADRPDVAPVYK--------------DIPIVKLVEGQSVVVEAYAKLGRARDHAKWQ 155
>sp|Q6KZP5|RPOD_PICTO DNA-directed RNA polymerase subunit D OS=Picrophilus torridus
(strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC
100828) GN=rpoD PE=3 SV=1
Length = 271
Score = 77.4 bits (189), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 58/184 (31%), Positives = 94/184 (51%), Gaps = 33/184 (17%)
Query: 11 ITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL--------EAN----STV 58
I +L D +KF + ++ANS+RR I + P +AI+ V E N S
Sbjct: 4 IIELKDNYIKFSISGITPAIANSIRRTLINDIPKLAIENVVFHHGEIRDSEGNVYDSSLP 63
Query: 59 LSDEFIASRIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTT 117
L DE +A R+GLIPL +D ++ + C+C + C C+V+++++ +
Sbjct: 64 LFDEVVALRLGLIPLKTDL---KMNFRDQCSCNGEGCDLCTVKYSIN---------KLGP 111
Query: 118 ADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
AD+ S+D ++P+ + D+ I IVKL+KGQ + + A G GK+HAKW
Sbjct: 112 ADVFSSD--LIPIN----NPDLKPVDPM--IPIVKLKKGQAMLVTCEAIMGRGKDHAKWQ 163
Query: 178 PTAG 181
T+G
Sbjct: 164 VTSG 167
>sp|Q8TVB8|RPOD_METKA DNA-directed RNA polymerase subunit D OS=Methanopyrus kandleri
(strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
GN=rpoD PE=3 SV=1
Length = 275
Score = 73.9 bits (180), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 52/166 (31%), Positives = 73/166 (43%), Gaps = 20/166 (12%)
Query: 17 ENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSD 76
E F +E+T N++RR PT+ I+ V + N T + DE +A R+GLIPL D
Sbjct: 17 ERATFIIEETSAEFVNTIRRALYTLVPTLRIEEVIIYENDTPMYDEMLAHRLGLIPLRVD 76
Query: 77 EVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNR 135
+ +D+ C C C +C V L+V + V DLK V P
Sbjct: 77 D-IDQFELPDLCDCGGKGCEKCQVRAELEV----EGPTKVYARDLKFDHPDVEPAFP--- 128
Query: 136 DADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
D LI ++ + Q +RL A G G EHAKW P +
Sbjct: 129 -----------DTLITEVGEDQRIRLEVIAVPGLGLEHAKWKPVSA 163
>sp|Q57648|RPOD_METJA DNA-directed RNA polymerase subunit D OS=Methanocaldococcus
jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
10045 / NBRC 100440) GN=rpoD PE=1 SV=1
Length = 191
Score = 72.8 bits (177), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 47/151 (31%), Positives = 74/151 (49%), Gaps = 35/151 (23%)
Query: 28 LSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRD 87
+S +N++RR+ I+E PT AI+ V + NS+ + DE +A R+GLIP+ +++ +
Sbjct: 24 ISFSNAIRRIMISEVPTFAIEDVYIYENSSSMDDEILAHRLGLIPIKGKPLLENEV---- 79
Query: 88 CTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDD 147
+ FTL+ + V ++DLKS + V +
Sbjct: 80 -----------ITFTLE----KEGPCTVYSSDLKSENGEVA----------------FKN 108
Query: 148 ILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
I IVKL KGQ +++ A G GK HAKW P
Sbjct: 109 IPIVKLGKGQRIQIECEAIPGIGKVHAKWQP 139
>sp|Q3IQT6|RPOD_NATPD DNA-directed RNA polymerase subunit D OS=Natronomonas pharaonis
(strain DSM 2160 / ATCC 35678) GN=rpoD PE=3 SV=1
Length = 247
Score = 72.4 bits (176), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 55/169 (32%), Positives = 82/169 (48%), Gaps = 32/169 (18%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V D + + +F V + AN LRR IA+ PT++ID +++ NS+V+ DE +A R+
Sbjct: 7 VTFIDRDERSARFLVRGVTPAFANGLRRAMIADVPTLSIDTLRVVENSSVMFDEQLALRL 66
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
GL+PLT T D+ +V +DV+ + DL S+D +V
Sbjct: 67 GLVPLT--------------TPDDYEPGETVTLAIDVEG----PATAYSGDLVSSDDKVQ 108
Query: 129 PVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
P AD N I I++L+ Q+L L A A G GK+HAK
Sbjct: 109 P-------ADEN-------IPIIELKDDQQLELEADATLGRGKDHAKHQ 143
>sp|Q9HJD9|RPOD_THEAC DNA-directed RNA polymerase subunit D OS=Thermoplasma acidophilum
(strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 /
AMRC-C165) GN=rpoD PE=3 SV=1
Length = 271
Score = 72.0 bits (175), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 58/187 (31%), Positives = 92/187 (49%), Gaps = 35/187 (18%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL--------EAN----S 56
V I L+D+ ++F+++ S AN+LRR I + P +AI+ V E N S
Sbjct: 3 VKIFKLSDKYIRFEIDGITPSQANALRRTLINDIPKLAIENVTFHHGEIRDSEGNVYDSS 62
Query: 57 TVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVD-FCSECSVEFTLDVKCVDDQTRHV 115
L DE +A R+GLIPL +D ++ + C+C CS C+V ++++ V
Sbjct: 63 LPLFDEMVAHRLGLIPLKTDLTMN---FRDQCSCGGKGCSLCTVTYSINKL----GPSTV 115
Query: 116 TTADLKS-TDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHA 174
++DL++ + ++PV +I IVKL Q + + A A G KEHA
Sbjct: 116 FSSDLQAVSHPDLIPVDG--------------EIPIVKLGPKQAILITAEAILGTAKEHA 161
Query: 175 KWNPTAG 181
KW T+G
Sbjct: 162 KWQVTSG 168
>sp|Q97B93|RPOD_THEVO DNA-directed RNA polymerase subunit D OS=Thermoplasma volcanium
(strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 /
GSS1) GN=rpoD PE=3 SV=1
Length = 271
Score = 71.6 bits (174), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 59/187 (31%), Positives = 90/187 (48%), Gaps = 35/187 (18%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL--------EAN----S 56
V I L+D+ + F+++ S AN+LRR I + P +AI+ V E N S
Sbjct: 3 VKIFKLSDKYMSFEIDGITPSQANALRRTLINDIPKLAIENVTFHHGEIRDAEGNVYDSS 62
Query: 57 TVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVD-FCSECSVEFTLDVKCVDDQTRHV 115
L DE +A R+GLIPL +D ++ + C+C CS C+V ++++ V
Sbjct: 63 LPLFDEMVAHRLGLIPLKTDLSLN---FRDQCSCGGKGCSLCTVTYSIN----KIGPASV 115
Query: 116 TTADLKS-TDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHA 174
+ D+++ + +VPV DI IVKL Q + + A A G KEHA
Sbjct: 116 MSGDIQAISHPDLVPVDP--------------DIPIVKLGAKQAILITAEAILGTAKEHA 161
Query: 175 KWNPTAG 181
KW T+G
Sbjct: 162 KWQVTSG 168
>sp|Q9HQJ4|RPOD_HALSA DNA-directed RNA polymerase subunit D OS=Halobacterium salinarum
(strain ATCC 700922 / JCM 11081 / NRC-1) GN=rpoD PE=3
SV=1
Length = 248
Score = 70.1 bits (170), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 52/169 (30%), Positives = 77/169 (45%), Gaps = 32/169 (18%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V D D +F V + + AN +RR + + PT++ID V+ NS+V+ DE + R+
Sbjct: 8 VEFVDRDDREARFVVRNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFDEQLGLRL 67
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
GL+PLT+ E D+ + +V LDV+ + DL S D V
Sbjct: 68 GLVPLTTPE--------------DYAAGEAVTLALDVEG----PGTAYSGDLVSNDPEV- 108
Query: 129 PVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
AD N I I++L+ Q L L A A G G++HAK
Sbjct: 109 ------EAADEN-------IPIIELKDDQRLELEADAVMGHGRDHAKHQ 144
>sp|B0R4Y2|RPOD_HALS3 DNA-directed RNA polymerase subunit D OS=Halobacterium salinarum
(strain ATCC 29341 / DSM 671 / R1) GN=rpoD PE=3 SV=1
Length = 248
Score = 70.1 bits (170), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 52/169 (30%), Positives = 77/169 (45%), Gaps = 32/169 (18%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
V D D +F V + + AN +RR + + PT++ID V+ NS+V+ DE + R+
Sbjct: 8 VEFVDRDDREARFVVRNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFDEQLGLRL 67
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVV 128
GL+PLT+ E D+ + +V LDV+ + DL S D V
Sbjct: 68 GLVPLTTPE--------------DYAAGEAVTLALDVEG----PGTAYSGDLVSNDPEV- 108
Query: 129 PVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
AD N I I++L+ Q L L A A G G++HAK
Sbjct: 109 ------EAADEN-------IPIIELKDDQRLELEADAVMGHGRDHAKHQ 144
>sp|Q00813|RPOD_HALMA DNA-directed RNA polymerase subunit D OS=Haloarcula marismortui
(strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
GN=rpoD PE=3 SV=1
Length = 259
Score = 62.0 bits (149), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 49/147 (33%), Positives = 73/147 (49%), Gaps = 31/147 (21%)
Query: 29 SVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDC 88
+ AN +RR +A+ PT +ID V++ N++V+ +E I R+GL+PLT+D
Sbjct: 27 AFANGIRRAMVADVPTFSIDTVRVIENTSVMFNEQIGLRLGLVPLTTD------------ 74
Query: 89 TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDI 148
DF E E TL + D ++DL S+D V AD D+I
Sbjct: 75 -LDDF--EIGDEVTLSLSV--DGPSTAYSSDLVSSDPMV-------EAAD-------DNI 115
Query: 149 LIVKLRKGQELRLRAYAKKGFGKEHAK 175
I+ L++GQ L + A A G+EHAK
Sbjct: 116 PIIDLKEGQRLEVEADAVLDTGREHAK 142
>sp|B2G8V2|RPOA_LACRJ DNA-directed RNA polymerase subunit alpha OS=Lactobacillus reuteri
(strain JCM 1112) GN=rpoA PE=3 SV=1
Length = 314
Score = 38.9 bits (89), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 48/169 (28%), Positives = 71/169 (42%), Gaps = 33/169 (19%)
Query: 6 QPSVHITDLTDENVKFQVEDTE----LSVANSLRRVFIAETPTMAIDWVQLEANSTVLSD 61
+P++H + TD KF VE E ++ NSLRRV IA P AI +Q++ +
Sbjct: 6 KPNIHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGAAITSMQIDG----VLH 61
Query: 62 EFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLK 121
EF +T D V +I+ + + SE LDVK VT +D++
Sbjct: 62 EFSTVE----GVTED--VTQIILNLKKVSLKLDSEDQKNLELDVKG----PAEVTASDIQ 111
Query: 122 STDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFG 170
+ VT N D+ I + G EL ++ A KG G
Sbjct: 112 GDN----EVTILN-----------PDLHIATVADGAELHIKLTADKGRG 145
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.318 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 64,912,968
Number of Sequences: 539616
Number of extensions: 2452948
Number of successful extensions: 6448
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 54
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 6326
Number of HSP's gapped (non-prelim): 90
length of query: 181
length of database: 191,569,459
effective HSP length: 110
effective length of query: 71
effective length of database: 132,211,699
effective search space: 9387030629
effective search space used: 9387030629
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)