RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6965
(1764 letters)
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA
polymerase II (RNAP II), C-terminal domain. RNA
polymerase II (RNAP II) is a large multi-subunit complex
responsible for the synthesis of mRNA. RNAP II consists
of a 10-subunit core enzyme and a peripheral heterodimer
of two subunits. The largest core subunit (Rpb1) of yeast
RNAP II is the best characterized member of this family.
Structure studies suggest that RNAP complexes from
different organisms share a crab-claw-shape structure. In
yeast, Rpb1 and Rpb2, the largest and the second largest
subunits, each makes up one clamp, one jaw, and part of
the cleft. Rpb1 interacts with Rpb2 to form the DNA entry
and RNA exit channels in addition to the catalytic center
of RNA synthesis. The C-terminal domain of Rpb1 makes up
part of the foot and jaw structures.
Length = 410
Score = 342 bits (880), Expect = e-105
Identities = 137/218 (62%), Positives = 168/218 (77%), Gaps = 11/218 (5%)
Query: 1460 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKK 1519
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+GIE I + ++KK
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGI---RKVFIREENKK 253
Query: 1520 RIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSV 1579
++ I E+GEFK +W+LETDG +L +VLS VDP RT SNDI EIF+VLGIEA RK++
Sbjct: 254 KVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKAL 312
Query: 1580 EKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDV 1639
KE+ V+ F G YVNYRHLALLCDVMT +GHLMAITRHGINRQDTG LMRCSFEETVD+
Sbjct: 313 LKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDI 372
Query: 1640 LMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1677
L++AAA E D ++GVSENI++GQL +GTGCFDLLLD
Sbjct: 373 LLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLLLD 410
Score = 94.6 bits (236), Expect = 4e-20
Identities = 48/105 (45%), Positives = 64/105 (60%), Gaps = 12/105 (11%)
Query: 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRC 60
ME I++KI F DDLN IF+DDNAEKLV+RIRI+N D+ K +D EDD+FL+
Sbjct: 173 MEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKK 225
Query: 61 IEANMLSDMTLQ-----FIRIMNSDDSKMQDEEDAVDKMEDDMFL 100
IE+NMLSDMTL+ + ++ K D E K ++ L
Sbjct: 226 IESNMLSDMTLKGIEGIRKVFIREENKKKVDIETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 158 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 212
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 213 EEDAVDKMEDDMFL 226
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 200 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 254
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 255 EEDAVDKMEDDMFL 268
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 242 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 296
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 297 EEDAVDKMEDDMFL 310
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 284 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 338
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 339 EEDAVDKMEDDMFL 352
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 326 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 380
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 381 EEDAVDKMEDDMFL 394
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 368 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 422
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 423 EEDAVDKMEDDMFL 436
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 410 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 464
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 465 EEDAVDKMEDDMFL 478
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 452 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 506
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 507 EEDAVDKMEDDMFL 520
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 494 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 548
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 549 EEDAVDKMEDDMFL 562
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 536 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 590
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 591 EEDAVDKMEDDMFL 604
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 578 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 632
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 633 EEDAVDKMEDDMFL 646
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 620 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 674
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 675 EEDAVDKMEDDMFL 688
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 662 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 716
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 717 EEDAVDKMEDDMFL 730
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 704 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 758
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 759 EEDAVDKMEDDMFL 772
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 746 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 800
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 801 EEDAVDKMEDDMFL 814
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 788 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 842
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 843 EEDAVDKMEDDMFL 856
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 830 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 884
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 885 EEDAVDKMEDDMFL 898
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 872 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 926
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 927 EEDAVDKMEDDMFL 940
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 914 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 968
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 969 EEDAVDKMEDDMFL 982
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 956 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1010
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1011 EEDAVDKMEDDMFL 1024
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 998 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1052
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1053 EEDAVDKMEDDMFL 1066
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1040 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1094
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1095 EEDAVDKMEDDMFL 1108
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1082 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1136
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1137 EEDAVDKMEDDMFL 1150
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1124 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1178
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1179 EEDAVDKMEDDMFL 1192
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1166 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1220
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1221 EEDAVDKMEDDMFL 1234
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1208 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1262
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1263 EEDAVDKMEDDMFL 1276
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1250 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1304
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1305 EEDAVDKMEDDMFL 1318
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1292 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1346
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1347 EEDAVDKMEDDMFL 1360
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1334 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1388
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1389 EEDAVDKMEDDMFL 1402
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
Score = 46.8 bits (112), Expect = 7e-05
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 1376 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ-----FIRIMNSDDSKMQD 1430
IRI+N D+ K +D EDD+FL+ IE+NMLSDMTL+ + ++ K D
Sbjct: 204 IRIINDDEEKEED-------SEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVD 256
Query: 1431 EEDAVDKMEDDMFL 1444
E K ++ L
Sbjct: 257 IETGEFKKREEWVL 270
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein
[Transcription, DNA-dependent RNA polymerase].
Length = 367
Score = 158 bits (402), Expect = 5e-42
Identities = 72/187 (38%), Positives = 110/187 (58%), Gaps = 18/187 (9%)
Query: 1491 ANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSE 1550
+ ++ ++GI+ I KR++I + G+ ++++ T+G++L +VL
Sbjct: 199 KEKIKNLHIKGIKGI-------------KRVVIRKEGD-----EYVIYTEGSNLKEVLKL 240
Query: 1551 RDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKG 1610
VD RT +NDI EI +VLGIEA R ++ +E+ L+ GL V+ RHL L+ D+MT G
Sbjct: 241 EGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDG 300
Query: 1611 HLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
+ I RHGI+ + L R +FE TV L+DAA E D + GV ENII+GQ +GTG
Sbjct: 301 EVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTG 360
Query: 1671 CFDLLLD 1677
DL++D
Sbjct: 361 DVDLVMD 367
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a
large multi-subunit complex responsible for the synthesis
of all RNAs in the cell. The relative positioning of the
RNAP core is highly conserved between archaeal RNAP and
the three classes of eukaryotic RNAPs. In archaea, the
largest subunit is split into two polypeptides, A' and
A'', which are encoded by separate genes in an operon.
Sequence alignments reveal that the archaeal A'' subunit
corresponds to the C-terminal one-third of the RNAPII
largest subunit (Rpb1). In subunit A'', several loops in
the jaw domain are shorter. The RNAPII Rpb1 interacts
with the second-largest subunit (Rpb2) to form the DNA
entry and RNA exit channels in addition to the catalytic
center of RNA synthesis.
Length = 363
Score = 154 bits (391), Expect = 1e-40
Identities = 72/188 (38%), Positives = 105/188 (55%), Gaps = 18/188 (9%)
Query: 1491 ANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSE 1550
A + + ++GI+ I +V I+ E E +++ T+G++L VL
Sbjct: 194 AEKILNTKIKGIKGIKRV------------IVRKEEDE------YVIYTEGSNLKAVLKV 235
Query: 1551 RDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKG 1610
VDP RT +N+I EI +VLGIEA R ++ E+ L+ GL V+ RH+ L+ D+MT G
Sbjct: 236 EGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDG 295
Query: 1611 HLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
+ I RHGI + L R +FE TV L+DAA E D +RGV ENII+GQ +GTG
Sbjct: 296 EVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
Query: 1671 CFDLLLDA 1678
+L +D
Sbjct: 356 DVELTMDP 363
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 151 bits (385), Expect = 1e-39
Identities = 70/190 (36%), Positives = 109/190 (57%), Gaps = 18/190 (9%)
Query: 1491 ANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSE 1550
A + ++ ++GI+ I +V II E E +++ T+G++L +VL
Sbjct: 211 AEKIRNIKIKGIKGIKRV------------IIRKEGDE------YVIYTEGSNLKEVLKV 252
Query: 1551 RDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKG 1610
VD RT +N+I EI +VLGIEA R ++ +E+ L+ GL V+ RH+ L+ D+MT G
Sbjct: 253 EGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDG 312
Query: 1611 HLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
+ I RHG++ + L R +FE TV L+DAA E D ++GV+ENII+GQ +GTG
Sbjct: 313 EVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
Query: 1671 CFDLLLDAEK 1680
+L +D
Sbjct: 373 DVELTMDPPL 382
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA
polymerase III (RNAP III), C-terminal domain. Eukaryotic
RNA polymerase III (RNAP III) is a large multi-subunit
complex responsible for the synthesis of tRNAs, 5SrRNA,
Alu-RNA, U6 snRNA, among others. Rpc1 is also known as
C160 in yeast. Structure studies suggest that different
RNA polymerase complexes share a similar crab-claw-shape
structure. The C-terminal domain of Rpb1, the largest
subunit of RNAP II, makes up part of the foot and jaw
structures of RNAP II. The similarity between this domain
and the C-terminal domain of Rpb1, its counterpart in
RNAP II, suggests a similar functional and structural
role.
Length = 300
Score = 146 bits (372), Expect = 1e-38
Identities = 67/184 (36%), Positives = 98/184 (53%), Gaps = 22/184 (11%)
Query: 1492 NMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITES---GEFKAIADWLLETDGTSLMKVL 1548
L D+ + GI + KR +I + G++K L +G L V+
Sbjct: 136 RKLPDVVVSGIPEV-------------KRAVINKDKKKGKYK------LLVEGYGLRAVM 176
Query: 1549 SERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTA 1608
+ V RT SN I E+ +VLGIEA R ++ E+ ++ +G+ ++ RH+ LL D+MT
Sbjct: 177 NTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTF 236
Query: 1609 KGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMG 1668
KG ++ ITR GI + LM SFE+T D L +AA H D + GVSE IIMG+ +G
Sbjct: 237 KGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIG 296
Query: 1669 TGCF 1672
TG F
Sbjct: 297 TGLF 300
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase
(RNAP), C-terminal domain. RNA polymerase (RNAP) is a
large multi-subunit complex responsible for the synthesis
of RNA. It is the principal enzyme of the transcription
process, and is the final target in many regulatory
pathways that control gene expression in all living
cells. At least three distinct RNAP complexes are found
in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for
the synthesis of ribosomal RNA precursor, mRNA precursor,
and 5S and tRNA, respectively. A single distinct RNAP
complex is found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. Structure
studies revealed that prokaryotic and eukaryotic RNAPs
share a conserved crab-claw-shape structure. The largest
and the second largest subunits each make up one clamp,
one jaw, and part of the cleft. The largest RNAP subunit
(Rpb1) interacts with the second-largest RNAP subunit
(Rpb2) to form the DNA entry and RNA exit channels in
addition to the catalytic center of RNA synthesis. The
region covered by this domain makes up part of the foot
and jaw structures. In archaea, some photosynthetic
organisms, and some organelles, this domain exists as a
separate subunit, while it forms the C-terminal region of
the RNAP largest subunit in eukaryotes and bacteria.
Length = 158
Score = 133 bits (337), Expect = 7e-36
Identities = 51/110 (46%), Positives = 69/110 (62%)
Query: 1562 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 1621
I E+ + LGIEA R+++ +E+ VL G+ V+ RH+ L+ DVMT G L +TR G
Sbjct: 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFR 108
Query: 1622 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1671
T LMR SFE+T L+DAAA E D + GVSENII+G+ +GTG
Sbjct: 109 ASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase compared
to three in eukaryotes (not including mitochondrial. and
chloroplast polymerases). This domain, domain 5,
represents the discontinuous cleft domain that is
required to from the central cleft or channel where the
DNA is bound.
Length = 447
Score = 135 bits (342), Expect = 2e-33
Identities = 57/196 (29%), Positives = 86/196 (43%), Gaps = 9/196 (4%)
Query: 1436 DKMEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLS 1495
+ I + ++ L I I K K +
Sbjct: 259 KDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSRK-------RKKNNLGVAKDEKGLEEEE 311
Query: 1496 DMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSER-DVD 1554
+ L I + + + K +WLL+T+G +L V+ + +D
Sbjct: 312 LLLLNKILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVID 371
Query: 1555 PVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMA 1614
+T+SNDI E+ + LGIEA R S+ E+ V +F G+YVN RHLALL D+MT KG L+
Sbjct: 372 NDKTYSNDIREMLKKLGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLG 431
Query: 1615 ITRHGINRQDT-GALM 1629
ITR G+NR+ + LM
Sbjct: 432 ITRAGLNREKSSFILM 447
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 134 bits (338), Expect = 1e-31
Identities = 73/186 (39%), Positives = 108/186 (58%), Gaps = 14/186 (7%)
Query: 1494 LSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDV 1553
+ ++ L+GI I +V + + ++ E+ +L T G++L +V V
Sbjct: 680 IKNIVLKGIPGIERVLVKKEEHEND--------EEY------VLYTQGSNLREVFKIEGV 725
Query: 1554 DPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLM 1613
D RT +N+I EI +VLGIEA R ++ EM L+ GL V+ RHL L+ D+MTA G +
Sbjct: 726 DTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVK 785
Query: 1614 AITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFD 1673
I RHG+ + L R +FEETV L DAA H E D ++GV EN+I+G+ ++GTGC D
Sbjct: 786 PIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVD 845
Query: 1674 LLLDAE 1679
L +D E
Sbjct: 846 LRIDRE 851
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 131 bits (330), Expect = 2e-31
Identities = 70/179 (39%), Positives = 101/179 (56%), Gaps = 16/179 (8%)
Query: 1497 MTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPV 1556
+T++GI+ I + I E+ E + W++ T G++L VL +VDP
Sbjct: 339 LTIKGIKGIKRA------------IARKENDERR----WVIYTQGSNLKDVLEIDEVDPT 382
Query: 1557 RTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAIT 1616
RT++NDI EI VLGIEA R ++ E LQ GL V+ RH+ L+ D+MT G + AI
Sbjct: 383 RTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIG 442
Query: 1617 RHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLL 1675
RHGI+ + + L R +FE T L+ A E D + GV+ENII+GQ +GTG L+
Sbjct: 443 RHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLV 501
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA
polymerase I (RNAP I), C-terminal domain. RNA polymerase
I (RNAP I) is a multi-subunit protein complex responsible
for the synthesis of rRNA precursor. It consists of at
least 14 different subunits, and the largest one is
homologous to subunit Rpb1 of yeast RNAP II and subunit
beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in
yeast. Structure studies suggest that different RNAP
complexes share a similar crab-claw-shape structure. The
C-terminal domain of Rpb1, the largest subunit of RNAP
II, makes up part of the foot and jaw structures of RNAP
II. The similarity between this domain and the C-terminal
domain of Rpb1, its counterpart in RNAP II, suggests a
similar functional and structural role.
Length = 309
Score = 114 bits (287), Expect = 2e-27
Identities = 43/123 (34%), Positives = 69/123 (56%), Gaps = 1/123 (0%)
Query: 1553 VDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL 1612
+D R ++NDI + GIEA R+++ KE++ V + YG+ V+ RHL+L+ D MT +G
Sbjct: 188 LDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGY 247
Query: 1613 MAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCF 1672
R G+ + L + SFE T+ L A + + D + S +++G+ GTG F
Sbjct: 248 RPFNRIGMESSTSP-LQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLF 306
Query: 1673 DLL 1675
DLL
Sbjct: 307 DLL 309
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 118 bits (298), Expect = 1e-26
Identities = 62/216 (28%), Positives = 110/216 (50%), Gaps = 22/216 (10%)
Query: 1475 DAVDKMEDDMFLRCIEA--NMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAI 1532
D V+ + D L + A N + D ++G+ I + ++ L + D +
Sbjct: 1120 DLVEAADRDKPLATLIAIRNKILDKPVKGVPDIERAWVELVEKDGRD------------- 1166
Query: 1533 ADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGL 1592
+W+++T G++L VL + +D T +ND EI LGIEA R ++ E+ ++L+ GL
Sbjct: 1167 -EWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGL 1225
Query: 1593 YVNYRHLALLCDVMTAKGHLMAI------TRHGINRQDTGALMRCSFEETVDVLMDAAAH 1646
V+ R++ L+ D+M ++G + AI RHG + L + +FE T + AA
Sbjct: 1226 EVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALG 1285
Query: 1647 AEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK 1682
E + ++G+ + +IMGQ +G+G DLL+D
Sbjct: 1286 GEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
>gnl|CDD|218366 pfam04990, RNA_pol_Rpb1_7, RNA polymerase Rpb1, domain 7. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 7, represents a mobile module of the RNA
polymerase. Domain 7 forms a substantial interaction
with the lobe domain of Rpb2 (pfam04561).
Length = 135
Score = 86.9 bits (216), Expect = 8e-20
Identities = 36/72 (50%), Positives = 54/72 (75%), Gaps = 3/72 (4%)
Query: 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRC 60
M+ I++KI FGDDL+ I++DDNAEKLV+RIR+ + + K E+ D+ EDD+FL+
Sbjct: 67 MKDIAQKIKQEFGDDLHVIYSDDNAEKLVIRIRVKDDEGEK---EDSVGDEDEDDVFLKR 123
Query: 61 IEANMLSDMTLQ 72
+E+NMLS +TL+
Sbjct: 124 LESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 116 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 156
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 158 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 198
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 200 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 240
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 242 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 282
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 284 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 324
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 326 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 366
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 368 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 408
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 410 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 450
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 452 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 492
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 494 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 534
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 536 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 576
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 578 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 618
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 620 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 660
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 662 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 702
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 704 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 744
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 746 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 786
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 788 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 828
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 830 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 870
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 872 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 912
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 914 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 954
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 956 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 996
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 998 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1038
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1040 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1080
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1082 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1122
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1124 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1164
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1166 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1206
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1208 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1248
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1250 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1290
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1292 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1332
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1334 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1374
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1376 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1416
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1418 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1458
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
Score = 43.0 bits (102), Expect = 2e-04
Identities = 17/41 (41%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 1460 IRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1500
IR+ + + K E+ D+ EDD+FL+ +E+NMLS +TL+
Sbjct: 98 IRVKDDEGEK---EDSVGDEDEDDVFLKRLESNMLSSLTLR 135
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 75.0 bits (185), Expect = 2e-13
Identities = 57/282 (20%), Positives = 109/282 (38%), Gaps = 17/282 (6%)
Query: 1397 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 1456
+D I + + ++ D +++ + +F R +
Sbjct: 480 DDREKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDGRR---IFNRGLP---EDKDV 533
Query: 1457 LQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTD 1516
L I + K+ + +DK ++ + S ++ ++ + + +
Sbjct: 534 LVKIV-----NGKL--IKGVIDKKIVTIYREY-GPEVASKALVKLLDKLKNLGIKG-IGG 584
Query: 1517 SKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVR 1576
I + + ++E +G+ L +L + D RT N+I EI +VLGIEA+R
Sbjct: 585 FGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALR 644
Query: 1577 KSVEKEMNTVLQFYGLYVN-YRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 1635
++ +E+ L+ GL RH+ L M + I + G+ + L R +FE
Sbjct: 645 NAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAFEV 704
Query: 1636 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1677
TV L +A E+ + G++EN G TG D L
Sbjct: 705 TVKHL-EAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALK 745
>gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial
DNA-dependent RNA polymerase (RNAP), C-terminal domain.
Bacterial RNA polymerase (RNAP) is a large multi-subunit
complex responsible for the synthesis of all RNAs in the
cell. This family also includes the eukaryotic
plastid-encoded RNAP beta" subunit. Structure studies
suggest that RNAP complexes from different organisms
share a crab-claw-shape structure with two pincers
defining a central cleft. Beta' and beta, the largest and
the second largest subunits of bacterial RNAP, each makes
up one pincer and part of the base of the cleft. The
C-terminal domain includes a G loop that forms part of
the floor of the downstream DNA-binding cavity. The
position of the G loop may determine the switch of the
bridge helix between flipped-out and normal alpha-helical
conformations.
Length = 204
Score = 48.3 bits (116), Expect = 8e-06
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 1594 VNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR 1653
N R L L + L+ IT+ +N + + SF+ET VL +AA + D +R
Sbjct: 129 ENKRLLLLGKKPAKYEPVLLGITKASLNTE--SFISAASFQETTKVLTEAAIEGKIDWLR 186
Query: 1654 GVSENIIMGQLPRMGTGC 1671
G+ EN+I+G+L GTG
Sbjct: 187 GLKENVILGRLIPAGTGL 204
>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA
polymerase IV, C-terminal domain. Higher plants have
five multi-subunit nuclear RNA polymerases: RNAP I, RNAP
II and RNAP III, which are essential for viability; plus
the two isoforms of the non-essential polymerase RNAP IV
(IVa and IVb), which specialize in small RNA-mediated
gene silencing pathways. RNAP IVa and/or RNAP IVb might
be involved in RNA-directed DNA methylation of endogenous
repetitive elements, silencing of transgenes, regulation
of flowering-time genes, inducible regulation of adjacent
gene pairs, and spreading of mobile silencing signals.
NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b
is the largest subunit of RNAP IVb. The full subunit
compositions of RNAP IVa and RNAP IVb are not known, nor
are their templates or enzymatic products. However, it
has been shown that RNAP IVa and, to a lesser extent,
RNAP IVb are crucial for several RNA-mediated gene
silencing phenomena.
Length = 381
Score = 49.0 bits (117), Expect = 1e-05
Identities = 32/130 (24%), Positives = 53/130 (40%), Gaps = 6/130 (4%)
Query: 1553 VDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL 1612
+D R+ I +I VLGI+A + + + + + G V HL L+ D MT G
Sbjct: 252 IDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEF 311
Query: 1613 MAITRHGINRQDTGA-----LMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRM 1667
+ + G Q F + + AA +D + GV + G+ +
Sbjct: 312 VGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPV 371
Query: 1668 GTGC-FDLLL 1676
GTG F++L
Sbjct: 372 GTGSKFEILW 381
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 48.1 bits (114), Expect = 6e-05
Identities = 48/193 (24%), Positives = 82/193 (42%), Gaps = 60/193 (31%)
Query: 1517 SKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVR 1576
S+ + +I G+F D L+ D DP D+ +I +VLG+EA+
Sbjct: 2612 SRSKHVIVNEGDFVRKGDLLM--------------DGDP------DLHDILRVLGLEALA 2651
Query: 1577 KSVEKEMNTVLQFYGLYVNYRHLALLC--------------------------------D 1604
+ E+ V + G+ ++ +HL ++ D
Sbjct: 2652 HYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDREND 2711
Query: 1605 VMTAKG----HLMAITRHGINR---QDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSE 1657
M+ G H + I + GI R + + + SF+ET VL +AA ++DP+ G+ E
Sbjct: 2712 AMSNSGKRPAHYLPILQ-GITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKE 2770
Query: 1658 NIIMGQLPRMGTG 1670
N+I+G+L GTG
Sbjct: 2771 NVIVGRLIPAGTG 2783
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it but
also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 47.0 bits (112), Expect = 1e-04
Identities = 38/150 (25%), Positives = 64/150 (42%), Gaps = 44/150 (29%)
Query: 1562 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHG-- 1619
D ++ ++ GI+AV++ + KE+ V + G+ +N +H+ ++ M K + IT G
Sbjct: 988 DPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRK---VRITDSGDS 1044
Query: 1620 -------INRQ-------------------------------DTGA-LMRCSFEETVDVL 1640
I+ +T + L SF+ET VL
Sbjct: 1045 NLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVL 1104
Query: 1641 MDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
DAA + D + G+ EN+I+G L GTG
Sbjct: 1105 TDAAIKGKVDYLLGLKENVIIGNLIPAGTG 1134
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 45.2 bits (107), Expect = 4e-04
Identities = 38/139 (27%), Positives = 62/139 (44%), Gaps = 40/139 (28%)
Query: 1571 GIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK-------------GHL----- 1612
++ V++ + E+ V Q G+ ++ +H+ ++ MT+K G L
Sbjct: 1084 SLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQ 1143
Query: 1613 -------MAITRHGINRQDTGALM--------------RCSFEETVDVLMDAAAHAEADP 1651
MAIT G Q T L+ SF+ET VL +AA ++D
Sbjct: 1144 VEQVNEAMAIT-GGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDW 1202
Query: 1652 MRGVSENIIMGQLPRMGTG 1670
+RG+ EN+I+G+L GTG
Sbjct: 1203 LRGLKENVIIGRLIPAGTG 1221
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 43.9 bits (105), Expect = 0.001
Identities = 20/39 (51%), Positives = 28/39 (71%)
Query: 1632 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
SF+ET VL +AA + DP+RG+ EN+I+G+L GTG
Sbjct: 1098 SFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTG 1136
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 42.3 bits (100), Expect = 0.003
Identities = 19/39 (48%), Positives = 28/39 (71%)
Query: 1632 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
SF+ET VL +AA ++D +RG+ EN+I+G+L GTG
Sbjct: 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 39.1 bits (91), Expect = 0.025
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 1595 NYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRG 1654
N R +AL + A+ L+ ITR I + SF+ET VL +A+ + D +
Sbjct: 2799 NARVIALKGEPAIAEPVLLGITRAAIGSDSI--ISAASFQETTKVLTEASIAMKKDFLED 2856
Query: 1655 VSENIIMGQLPRMGTGCF 1672
+ EN+++G++ +GTG +
Sbjct: 2857 LKENVVLGRMIPVGTGMY 2874
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 38.4 bits (90), Expect = 0.041
Identities = 18/40 (45%), Positives = 24/40 (60%)
Query: 1632 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1671
SF+ET VL AA D ++G+ EN+I+G L GTG
Sbjct: 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 35.2 bits (81), Expect = 0.38
Identities = 18/39 (46%), Positives = 25/39 (64%)
Query: 1632 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
SF+ET VL DAA + D + G+ EN+I+G+ GTG
Sbjct: 1197 SFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
>gnl|CDD|215251 PLN02457, PLN02457, phenylalanine ammonia-lyase.
Length = 706
Score = 33.5 bits (77), Expect = 1.1
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 11/68 (16%)
Query: 1528 EFKAIADWLLETDGTSLMKVLSER-DVDPVRTFSNDICEIF---QVLG--IEAVR---KS 1578
E AI + +L DG+S MK + + DP++ D + Q LG IE +R KS
Sbjct: 306 EAAAIMEHIL--DGSSYMKAAKKLHETDPLQKPKQDRYALRTSPQWLGPQIEVIRAATKS 363
Query: 1579 VEKEMNTV 1586
+E+E+N+V
Sbjct: 364 IEREINSV 371
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 79 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 136
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 137 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 196
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 197 LQFIRIMNSDDSKMQDEEDAVDKMEDD 223
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 163 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 220
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 221 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 280
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 281 LQFIRIMNSDDSKMQDEEDAVDKMEDD 307
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 247 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 304
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 305 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 364
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 365 LQFIRIMNSDDSKMQDEEDAVDKMEDD 391
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 331 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 388
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 389 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 448
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 449 LQFIRIMNSDDSKMQDEEDAVDKMEDD 475
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 415 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 472
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 473 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 532
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 533 LQFIRIMNSDDSKMQDEEDAVDKMEDD 559
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 499 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 556
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 557 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 616
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 617 LQFIRIMNSDDSKMQDEEDAVDKMEDD 643
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 583 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 640
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 641 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 700
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 701 LQFIRIMNSDDSKMQDEEDAVDKMEDD 727
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 667 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 724
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 725 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 784
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 785 LQFIRIMNSDDSKMQDEEDAVDKMEDD 811
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 751 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 808
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 809 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 868
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 869 LQFIRIMNSDDSKMQDEEDAVDKMEDD 895
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 835 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 892
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 893 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 952
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 953 LQFIRIMNSDDSKMQDEEDAVDKMEDD 979
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 919 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 976
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 977 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 1036
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 1037 LQFIRIMNSDDSKMQDEEDAVDKMEDD 1063
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 1003 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 1060
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 1061 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 1120
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 1121 LQFIRIMNSDDSKMQDEEDAVDKMEDD 1147
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 1087 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 1144
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 1145 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 1204
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 1205 LQFIRIMNSDDSKMQDEEDAVDKMEDD 1231
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 1171 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 1228
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 1229 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 1288
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 1289 LQFIRIMNSDDSKMQDEEDAVDKMEDD 1315
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 1255 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 1312
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 1313 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 1372
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 1373 LQFIRIMNSDDSKMQDEEDAVDKMEDD 1399
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Score = 30.6 bits (68), Expect = 9.7
Identities = 34/147 (23%), Positives = 52/147 (35%), Gaps = 23/147 (15%)
Query: 1339 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR--IMNSDDSKMQDEEDAVDKM 1396
DD K D + D +E D M + DDS + + A+D M
Sbjct: 396 PDDIKRDDSDTMADDIERDDSAAVEYYTACESMADDAANDSVAERDDSDAVECDTAIDSM 455
Query: 1397 EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMT 1456
DD + + + SD + SDD + + A+D M DD
Sbjct: 456 ADDTAIDSMADDAASD------AVAESDDGDAVENDTAIDSMADDTASN----------- 498
Query: 1457 LQFIRIMNSDDSKMQDEEDAVDKMEDD 1483
+ SDD +++ A+D M DD
Sbjct: 499 ----SMAESDDGDNVEDDTAIDSMADD 521
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.133 0.365
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 87,137,158
Number of extensions: 8736104
Number of successful extensions: 7247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7128
Number of HSP's successfully gapped: 194
Length of query: 1764
Length of database: 10,937,602
Length adjustment: 111
Effective length of query: 1653
Effective length of database: 6,014,308
Effective search space: 9941651124
Effective search space used: 9941651124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 66 (29.2 bits)