RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 000291
(1714 letters)
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 240 bits (614), Expect = 4e-71
Identities = 106/307 (34%), Positives = 152/307 (49%), Gaps = 25/307 (8%)
Query: 141 DGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRS-GTPNFESQ 199
+ IL LPVPP CL P + + D +L+ ++K+ ++ G P+ +
Sbjct: 1 EWMILTVLPVPPPCLR-PSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIR 59
Query: 200 EVESNDLQLAVGQYLEV----RGTAKSSRDVDARFGVSQDPNSTTKAWLEK----MRTLF 251
+ LQ AV ++ R KS R P + L+ R
Sbjct: 60 NEKRL-LQEAVDTLIDNEGLPRANQKSGR-----------PLKSLSQRLKGKEGRFRQNL 107
Query: 252 IRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKL-CLT 310
+ K FS+RSVIT D ++NE+GVP EIA +TF E V NI+ L++LV N
Sbjct: 108 LGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGPNGAK 167
Query: 311 YSDGSSSYSLR--EGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHD 368
Y +L+ + SK L+ G +V R ++DGD V NR PT H+ S+QA V V +
Sbjct: 168 YIIRGKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLE 227
Query: 369 DHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLA 428
T+++NPL+C P +ADFDGD ++L PQSL A+AE EL V +LS NG +
Sbjct: 228 GKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPI 287
Query: 429 TDALLSL 435
D LL L
Sbjct: 288 QDMLLGL 294
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, 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.
Length = 867
Score = 195 bits (498), Expect = 6e-51
Identities = 196/710 (27%), Positives = 310/710 (43%), Gaps = 118/710 (16%)
Query: 116 EVKEMLKRIPEETRKKLAGKGYFPQDG----YILEYLPVPPNCLSV-PDISDGVSTMSSD 170
E++E L++IP+E + L G P+ +L LPVPP ++V P I+ S D
Sbjct: 177 EIRERLEKIPDEDAELL---GINPKVARPEWMVLTVLPVPP--VTVRPSITLETGERSED 231
Query: 171 LSIAMLKKVLKQVEIIRSSRS-GTPNFESQEVESN--DLQLAVGQYL--EVRGTAKSSRD 225
L +++ + ++ + G P +E LQ V Y E+ G
Sbjct: 232 DLTHKLVDIIRINQRLKENIEAGAPQLI---IEDLWELLQYHVATYFDNELPGIPP---- 284
Query: 226 VDARFGVSQDPNSTTKAWLEKMRTLFIRKGSG----FSSRSVITGDAYKRVNEIGVPFEI 281
AR S P T L+ F SG FS+R+VI+ D +NE+GVP +I
Sbjct: 285 --ARHR-SGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQI 341
Query: 282 AQRITFEERVNVHNINYLQELVDN-------KLCLTYSDGSSSYSLREGSKGHTF--LRP 332
A+ +T ERV NI+ L+E V N + DG +R+ +K L P
Sbjct: 342 AKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRR-IKIRDENKEELAERLEP 400
Query: 333 GQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIH 392
G VV R ++DGD V NR P+ H+ S+ V V T ++N +C P +ADFDGD ++
Sbjct: 401 GWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMN 460
Query: 393 LFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDA-----LLSLKVMFKKYFLDKA 447
L PQ+ A+AE EL VE+ +L+ G + D LL+ K + ++
Sbjct: 461 LHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTL--FTKEEV 518
Query: 448 FTQQLAMFALSPLPRPALSKARCSARWTALQILQSVLPPGF-----------DSC----- 491
T P PA+ K + WT QI + LP D+C
Sbjct: 519 QTILGVAGYFGDPPEPAIEKPK--EYWTGKQIFSAFLPEDLNFEGRAKICSSDACKKEEC 576
Query: 492 -GDRYL-IKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFA 549
D Y+ IK ++LKG D+ I + +I+ I E GPE F DS+ L + +
Sbjct: 577 PHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITL 636
Query: 550 DGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMSTQN--EL-------VDLQIENHI- 599
GF+ ++D + K A I++ I+ + + + EL V+ +E I
Sbjct: 637 RGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIM 696
Query: 600 ---------------RHVKMLVAKFIL-KSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLS 643
+++ I+ ++ G L++ + Q A +G Q S
Sbjct: 697 EVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLN---------ITQMAAMVG-QQS 746
Query: 644 DRGK-----FYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSIS 698
RG + ++TL HF++ D+ A+ G ++ F GLDP E H+
Sbjct: 747 VRGGRIRRGYRNRTL-----PHFKK---GDIG-AKAR-GFVRSSFKKGLDPTEYFFHAAG 796
Query: 699 TREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDY 748
RE +V ++ S+ G + + L+ L+D+ + YDGTVR+ N +IQF Y
Sbjct: 797 GREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGN-LIQFKY 845
Score = 46.6 bits (111), Expect = 1e-04
Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 12/88 (13%)
Query: 14 IVGIRFGLATQKEICTASISDCSISHASQ---------LANPFLGLPLEFG-KCESCGTS 63
I I+FGL + +EI S+ + + L +P LG+ +E G +C++CG
Sbjct: 4 IGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGV-IEPGLRCKTCGGK 62
Query: 64 EPGKCEGHFGYIELPIPIYHPSHISELK 91
G+C GHFG+IEL P+ H E+
Sbjct: 63 V-GECPGHFGHIELARPVVHVGFAKEIY 89
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 193 bits (493), Expect = 3e-50
Identities = 158/592 (26%), Positives = 254/592 (42%), Gaps = 126/592 (21%)
Query: 258 FSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDN------------ 305
FS+R+VI+ D +NE+GVP IA+ +T ERV NI L+E V N
Sbjct: 322 FSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVI 381
Query: 306 -----KLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQ 360
++ LT + E ++ L PG +V R ++DGD V NR P+ H+ S+
Sbjct: 382 RPDGRRIKLTDKN------KEELAEK---LEPGWIVERHLIDGDIVLFNRQPSLHRMSIM 432
Query: 361 ALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHN 420
A V V T ++N +C P +ADFDGD ++L PQ+ A+AE L V++ +LS
Sbjct: 433 AHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRY 492
Query: 421 GNLNLQLATDA-----LLSLKVMFKKYFLDKAFTQQLAMFALS-------PLPRPALSKA 468
G + D LL+ K FT++ A+ L P P PA+
Sbjct: 493 GGPIIGGIQDHISGAYLLTRK--------STLFTKEEALDLLRAAGIDELPEPEPAIENG 544
Query: 469 RCSARWTALQILQSVLPPGF------------DSCGDRY-------LIKKSEVLKGDFDR 509
+ WT QI LP D C +IK ++L+G D+
Sbjct: 545 K--PYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDK 602
Query: 510 DTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNI 569
I + I+ I E GPE F DS+ L + + GF+ ++D + + A I
Sbjct: 603 KAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEI 662
Query: 570 QKEIQALYSLLYHRMST--QNEL-------VDLQIENHI----------------RHVKM 604
+ I+ + + EL ++ +E I +++ +
Sbjct: 663 DEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGL 722
Query: 605 LVAKFIL-KSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGK-----FYSKTLVEDIA 658
I+ ++ G +++ + Q A +G Q S RG+ + +TL
Sbjct: 723 DNPAVIMARTGARGSMLN---------LTQMAACVG-QQSVRGERIRRGYRDRTL----- 767
Query: 659 SHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFK 718
HF+ P DL A+ G ++ + GL P E H++ RE +V ++ S+ G + +
Sbjct: 768 PHFK---PGDLG-AEAR-GFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQR 822
Query: 719 NLMAVLRDVVICYDGTVRNVCSNSIIQFDY---AVNARKSHSLFPAGEPVGV 767
L+ L+D+ + YDGTVR+ +I+QF Y V+ KS G+PV V
Sbjct: 823 RLINALQDLKVEYDGTVRDT-RGNIVQFKYGEDGVDPMKSDH----GKPVDV 869
Score = 44.5 bits (106), Expect = 6e-04
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 56 KCESCGTSEPGKCEGHFGYIELPIPIYHP 84
+C++CG G+C GHFG+IEL P+ H
Sbjct: 60 RCKTCG-GRAGECPGHFGHIELARPVIHV 87
>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 = 180 bits (459), Expect = 2e-49
Identities = 79/213 (37%), Positives = 100/213 (46%), Gaps = 26/213 (12%)
Query: 762 GEPVGVLAATAMSNPAYKAVLDSSPSSNNS-WELMKEILLCRVSFNNDPIDRRVILYLND 820
GEPVG LAATA+S PAYKA+LD S +S EL+KE+L CR + DRRVIL L+
Sbjct: 1 GEPVGSLAATAISEPAYKALLDPPQSLESSPLELLKEVLECRSKSKSKENDRRVILSLHL 60
Query: 821 CGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLE 880
C C + ERAA VKN L+RV+L+D A +I+Y P+ G +G K
Sbjct: 61 CKCDHGFEYERAALEVKNHLERVTLEDLATTSMIKY-SPQATEAIVGEIGDQLNTKK--- 116
Query: 881 DLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCL 940
K KK K T S C K S+ PCL
Sbjct: 117 ---------------------KGKKKAIFSTSLKITKFSPWVCHFHLDKECQKLSDGPCL 155
Query: 941 MFVLRGASDSYLDKLSGVLANMIYPVLLETIIK 973
F + ++L VL + I P LLET+IK
Sbjct: 156 TFSVSKEVSKSSEELLDVLRDRIIPFLLETVIK 188
Score = 166 bits (421), Expect = 2e-44
Identities = 57/102 (55%), Positives = 76/102 (74%)
Query: 980 QRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFM 1039
QRL ++V+M K VL+EHL+L+A+SMT +G+ VG N+ GYKA RSL + PFTEA
Sbjct: 280 QRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSS 339
Query: 1040 PRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLW 1081
P KCF KAA+K +D+LS V+ AC+WGK VGTGS+F++LW
Sbjct: 340 PIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 192 bits (490), Expect = 3e-49
Identities = 188/737 (25%), Positives = 314/737 (42%), Gaps = 110/737 (14%)
Query: 116 EVKEMLKRIPEETRKKLAGKGYFPQDG----YILEYLPVPPNCLSV-PDISDGVSTMSSD 170
E++++ ++I ++ + + G+ P+ +L+ VPP L+ P I S D
Sbjct: 190 EIRDIFEKIIDDDLELI---GFDPKKARPEWAVLQAFLVPP--LTARPSIILETGERSED 244
Query: 171 LSIAMLKKVLKQVEIIRSSR-SGTPNFESQEVESNDLQLAVGQYL--EVRGTAKSSRDVD 227
+L ++K + ++ S+ +G P ++ E + LQ + G ++
Sbjct: 245 DLTHILVDIIKANQKLKESKDAGAPPLIVED-EVDHLQYHTSTFFDNATAGIPQAHHKGS 303
Query: 228 ARFGVSQDPNSTTKAWLE----KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQ 283
R P + L+ + R I K FS+R+VI+ D ++E+GVP IA
Sbjct: 304 GR------PLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAM 357
Query: 284 RITFEERVNVHNINYLQELVDN-----------------KLCLTYSDGSSSYSLREGSKG 326
++T E VN +NI ++ELV N K+ L + + +LRE ++
Sbjct: 358 KLTIPEIVNENNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQ 417
Query: 327 HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADF 386
L G +V R + DGD V NR P+ HK S+ A V V T +++P +C P +ADF
Sbjct: 418 ---LEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADF 474
Query: 387 DGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFKK-YFLD 445
DGD ++L PQ A+AE +EL V+ L+S G + D + + ++ K D
Sbjct: 475 DGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFD 534
Query: 446 KAFTQQLAMFA--LSPLPRPALSKARCSARWTALQILQSVLPPGFD-------------- 489
K +AM A PLP PA+ K + WT Q+ LP F+
Sbjct: 535 KNEASNIAMLAGITDPLPEPAI-KTKDGPAWTGKQLFSLFLPKDFNFEGIAKWSAGKAGE 593
Query: 490 ----SC-GDRY-LIKKSEVLKGDFDRDTIPSVINE---IVTSIFFEKGPEEVLEFFDSLQ 540
SC GD Y LIK+ E++ G D + I +++ E ++ I + G +EF + +
Sbjct: 594 AKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNKIL 653
Query: 541 PLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYS----LLYHRMSTQNELVDLQIE 596
+ + + GFS D + A I+ +IQ + L+ R T+ + E
Sbjct: 654 IIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKGKE 713
Query: 597 NHIRHVK---MLVAKFILK--------SSTLGYLIDSKSDSAV----------SKVVQQA 635
+R +K L A + + S+ ID+ + + + + Q A
Sbjct: 714 ELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIA 773
Query: 636 GFLGLQ-------LSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLD 688
G LG Q G + + SHF+ D N P A G +K + GL+
Sbjct: 774 GALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQE---GDDN-PDAH-GFVKNNYREGLN 828
Query: 689 PYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDY 748
E H++ RE ++ +R + G + L L D+ + YD TVR+ + IIQF +
Sbjct: 829 AAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGH-IIQFKF 887
Query: 749 AVNARKSHSLFPAGEPV 765
+ L GE
Sbjct: 888 GEDGIDPQKLD-HGEAF 903
Score = 42.7 bits (100), Expect = 0.002
Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 10/87 (11%)
Query: 14 IVGIRFGLATQKEICTASISDCSISHASQ---------LANPFLGLPLEFGKCESCGTSE 64
I GI FGL + + ++ + A L + LG KC +CG
Sbjct: 9 IDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNL- 67
Query: 65 PGKCEGHFGYIELPIPIYHPSHISELK 91
C GHFG+IEL P+ H + I +K
Sbjct: 68 AANCPGHFGHIELAEPVIHIAFIDNIK 94
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2. 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 2, contains the active site. The
invariant motif -NADFDGD- binds the active site
magnesium ion.
Length = 165
Score = 140 bits (356), Expect = 2e-38
Identities = 61/160 (38%), Positives = 86/160 (53%), Gaps = 6/160 (3%)
Query: 258 FSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDN------KLCLTY 311
FS RSVIT D +++E+GVP E+A +T E V NI L++LV N
Sbjct: 6 FSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPGAKYIK 65
Query: 312 SDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHT 371
+ L + L G +V R ++DGD V +NR PT H+ S+ A V + T
Sbjct: 66 RIKGAKRDLEYKKRIAIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRVLEGKT 125
Query: 372 VKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSV 411
+++NP +C P +ADFDGD ++L PQS A+AE EL V
Sbjct: 126 IRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEARELMLV 165
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 137 bits (347), Expect = 1e-32
Identities = 173/860 (20%), Positives = 291/860 (33%), Gaps = 203/860 (23%)
Query: 14 IVGIRFGLATQKEICTASISDCSISHASQLA-NP----FLGLPLEFG------------- 55
I I+FGLA+ +EI S P + P G
Sbjct: 4 IFDIKFGLASPEEI----------RSWSGEVKKPETINYRTKPERGGLFDERIFGPDKDY 53
Query: 56 KCESCGTSEPGKCEGHFGYIELPIPIYHP--------------SHISELKLTMYAFQLQ- 100
+C +CG + C G FG+IEL P+ H + L
Sbjct: 54 EC-TCGKYK-RICPGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCERVLYFEAYVVLGT 111
Query: 101 ----IKNDGVAQRLLSSCC-----------------------------EVKEMLKRIPEE 127
I+ + + S C +VK++LKR+
Sbjct: 112 DLEKIQLLNETEYVYDSFCAHCGAEAIKILLEKPDLETEREEETLSPTKVKKLLKRLKVV 171
Query: 128 --TRKKLAGKGYFPQDGYILEYLPVPPNCLSVPDIS-DGVSTMSSDLSIAMLKKVLKQVE 184
P + IL LPVPP L P I DG SDL+ + ++V+ +
Sbjct: 172 DAFLLSGNR----P-EWMILTVLPVPPPDLR-PSIQLDGGRFAESDLND-LYRRVINRNN 224
Query: 185 IIRSSRSGTPNFESQEVESNDLQLAVGQY--LEVRGTAKSSRDVDARFGVSQDPNSTTKA 242
++ E LQ AV R P +
Sbjct: 225 RLKRLLELAAP-IIVRNEKRMLQEAVDALFDNRRPRAVTGGR-----------PLKSLSQ 272
Query: 243 WLEKMRTLF----IRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINY 298
L+ + F + K +S RSVI+ ++N+ GVP ++A + V NI
Sbjct: 273 RLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEG 332
Query: 299 LQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHS 358
L+ + + E L V R ++DGD V +NR PT H+ S
Sbjct: 333 LRT-----------GAKYAKRMVERR-----LPEVWDVLREVIDGDPVLLNRAPTLHRLS 376
Query: 359 LQALSVYVH-DDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLS 417
+ V + ++++PL+C +ADFDGD + + P S A AE L + +L+
Sbjct: 377 IMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILT 436
Query: 418 SHNGN-----LNLQLATDALLSLKVMFKKYFLDKAFTQQLAM-FALSPLPRPALSKARCS 471
H G + + LL++ K L +A A+ A+
Sbjct: 437 PHYGGPIVAPIQDTVGGPYLLTIV--DAKLPSTPVGEIYLKDEYADDREKAEAI--AKKI 492
Query: 472 ARWTALQILQSVLPPG--------------FDSC----GDRY-LIKKSEVLKGDFDRDTI 512
T I+ ++ P F+ D I +++KG
Sbjct: 493 ELTTGKVIVSTISPDLAELSIIVTTDGRRIFNRGLPEDKDVLVKIVNGKLIKG------- 545
Query: 513 PSVINEIVTSIFFEKGPEE-VLEFFDSLQPLLMENLFADGF--------SVSLEDFSLSK 563
VI++ + +I+ E GPE L++ L G + +D
Sbjct: 546 --VIDKKIVTIYREYGPEVASKALVK-----LLDKLKNLGIKGIGGFGIGIGRKDIEAED 598
Query: 564 -------AALWNIQKEIQALYSLLYHRMSTQNELVDLQIE--NHIRHVKMLVAKFILKSS 614
A ++ K I R N + +++ +R+ + K L+
Sbjct: 599 EKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQ 658
Query: 615 TLGYLI-----DSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDL 669
L ++ S + +S++VQ G G+ G+ S + FE +
Sbjct: 659 GLDFVDIRHMGLSGARMNISQIVQLIGQQGV----MGEKIS----VLARAAFEV----TV 706
Query: 670 NYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVI 729
+ A+ G + F GL E H I R +V ++ ++ G L + L+ V +D+++
Sbjct: 707 KHLEAE-GPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQDLIV 765
Query: 730 CYDGTVRNVCSNSIIQFDYA 749
D V + +IQF+Y
Sbjct: 766 QEDDCVTDGI-GVVIQFEYG 784
>gnl|CDD|221127 pfam11523, DUF3223, Protein of unknown function (DUF3223). This
family of proteins has no known function.
Length = 76
Score = 106 bits (268), Expect = 2e-27
Identities = 40/78 (51%), Positives = 54/78 (69%), Gaps = 2/78 (2%)
Query: 1592 IRRIMHQSGYNDGDRLSADDKSFIFDNVFNYHPDKAMKMGAGIDHFKVDKHGSFQDSRCL 1651
+ I+H+ Y+DGDRLS +D+ + + + YHPD K+GAGIDHF+V H SRC
Sbjct: 1 FKAILHR--YDDGDRLSDEDEKTLLEALLEYHPDAEEKIGAGIDHFEVRTHPEGGKSRCF 58
Query: 1652 FVVSTDGSQQDFSYRKCL 1669
FVV TDG+ +DFSYRKC+
Sbjct: 59 FVVRTDGTSEDFSYRKCI 76
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. 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 3, represents the pore domain. The 3' end
of RNA is positioned close to this domain. The pore
delimited by this domain is thought to act as a channel
through which nucleotides enter the active site and/or
where the 3' end of the RNA may be extruded during
back-tracking.
Length = 158
Score = 60.7 bits (148), Expect = 2e-10
Identities = 39/143 (27%), Positives = 61/143 (42%), Gaps = 16/143 (11%)
Query: 430 DALLSLKVMFKKY-FLDKAFTQQLAMFALSPLPRPALSKARCSARWTALQILQSVLPPGF 488
D +L L ++ ++ F D+ QL M+ LP PA+ WT Q +LP
Sbjct: 17 DMVLGLYLLTRRDTFFDREEVMQLLMY-GIVLPHPAI-LKPIKPLWTGKQTFSRLLPNEI 74
Query: 489 DSCG-------------DRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEF 535
+ G LI E++ G D+ + ++ I+ E GPEE ++F
Sbjct: 75 NPKGKPKTNEETLCENDSYVLINNGELISGVIDKKLGGKSLGSLIHIIYKEYGPEETVKF 134
Query: 536 FDSLQPLLMENLFADGFSVSLED 558
D LQ L L GFS+ ++D
Sbjct: 135 LDRLQKLGFRYLTKSGFSIGIDD 157
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit.
The RNA polymerase gamma subunit, encoded by the rpoC1
gene, is found in cyanobacteria and corresponds to the
N-terminal region the beta' subunit, encoded by rpoC, in
other bacteria. The equivalent subunit in plastids and
chloroplasts is designated beta', while the product of
the rpoC2 gene is designated beta''.
Length = 619
Score = 60.0 bits (145), Expect = 8e-09
Identities = 49/180 (27%), Positives = 83/180 (46%), Gaps = 24/180 (13%)
Query: 246 KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDN 305
+ R + K +S RSVI ++++ G+P E+A + F+ V +H + Q +V+N
Sbjct: 338 RFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIEL-FQPFV-IHRL-IRQGIVNN 394
Query: 306 ----KLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQA 361
K + +D L+E ++ G V +NR PT H+ +QA
Sbjct: 395 IKAAKKLIQRADDEIWSVLQE-----------------VITGHPVMLNRAPTLHRLGIQA 437
Query: 362 LSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNG 421
+ D ++++PL+C +ADFDGD + + P SL A+ E L +LS G
Sbjct: 438 FEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATG 497
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 59.5 bits (145), Expect = 1e-08
Identities = 32/85 (37%), Positives = 48/85 (56%), Gaps = 2/85 (2%)
Query: 338 RRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQ 397
+ +M G V +NR PT H+ +QA + + + ++PL+C +ADFDGD + + P
Sbjct: 442 QEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPL 501
Query: 398 SLAAKAEV-LELFSVEKQLLSSHNG 421
SL A+AE L +FS LLS G
Sbjct: 502 SLEAQAEARLLMFS-HMNLLSPAIG 525
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 59.6 bits (144), Expect = 2e-08
Identities = 50/187 (26%), Positives = 77/187 (41%), Gaps = 46/187 (24%)
Query: 246 KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRI-------TFEERVNVHNINY 298
+ R + K FS RSVI +++E G+P +A + EER +
Sbjct: 1726 RFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQ 1785
Query: 299 LQELVDNKL-----CLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPT 353
+ +++ K CL + I +G V +NR PT
Sbjct: 1786 AKRMIEQKSNEVWECL----------------------------QEITEGYPVLLNRAPT 1817
Query: 354 THKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEK 413
HK S+QA + D ++++PL+C +ADFDGD + + P S A AE L
Sbjct: 1818 LHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVL----- 1872
Query: 414 QLLSSHN 420
+LSS N
Sbjct: 1873 -MLSSMN 1878
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 58.2 bits (141), Expect = 3e-08
Identities = 47/167 (28%), Positives = 82/167 (49%), Gaps = 30/167 (17%)
Query: 258 FSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDN----KLCLTYSD 313
+S RSVI ++++ G+P E+A + F+ V +H + Q +V+N K + +D
Sbjct: 357 YSGRSVIVVGPKLKMHQCGLPKEMAIEL-FQPFV-IHRL-IRQGIVNNIKAAKKLIQRAD 413
Query: 314 GSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVK 373
L E +++G V +NR PT H+ +QA + + ++
Sbjct: 414 PEVWQVLEE-----------------VIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQ 456
Query: 374 INPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHN 420
++PL+C +ADFDGD + + P SL A+AE L +L+S+N
Sbjct: 457 LHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLL------MLASNN 497
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 58.3 bits (141), Expect = 4e-08
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 340 IMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSL 399
++ V +NR PT H+ +QA + + +K++PL+C +ADFDGD + + P S
Sbjct: 493 VIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLST 552
Query: 400 AAKAEVLELFSVEKQLLSSHN 420
A+AE L +LSS+N
Sbjct: 553 QAQAEARVL------MLSSNN 567
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 56.2 bits (135), Expect = 2e-07
Identities = 29/90 (32%), Positives = 48/90 (53%)
Query: 346 VFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEV 405
V +NR PT H+ +QA + + ++++PL+C +ADFDGD + + P SL A+ E
Sbjct: 1854 VLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEA 1913
Query: 406 LELFSVEKQLLSSHNGNLNLQLATDALLSL 435
L +LS NG + + D +L +
Sbjct: 1914 RVLMMSTNNVLSPSNGRPIIVPSKDIVLGI 1943
>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 = 50.5 bits (121), Expect = 6e-07
Identities = 31/109 (28%), Positives = 45/109 (41%), Gaps = 16/109 (14%)
Query: 969 ETIIKENWWVRQRLSASVTMVAKG--VLKEHLILLANSMTCAGDLVGFNSGGYKALSRSL 1026
ETII+E + ++G V + H+ L+A+ MT +G L G G++A S
Sbjct: 64 ETIIRE---------IQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTS- 113
Query: 1027 NVQVPFTEATLFMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGS 1075
P A+ K AA D L V G+ +GTGS
Sbjct: 114 ----PLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
Score = 35.9 bits (83), Expect = 0.069
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 762 GEPVGVLAATAMSNPAYKAVLDS 784
GE VGVLAA ++ P + L +
Sbjct: 1 GEAVGVLAAQSIGEPGTQMTLRT 23
>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 = 52.4 bits (126), Expect = 2e-06
Identities = 42/163 (25%), Positives = 78/163 (47%), Gaps = 22/163 (13%)
Query: 258 FSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSS 317
+S RSVI ++ + G+P ++A + F+ + ++ L+D +L S+
Sbjct: 331 YSGRSVIVVGPELKMYQCGLPKKMALEL-FKPFI-------IKRLIDRELAANIK---SA 379
Query: 318 YSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPL 377
+ E + V+ I + V +NR PT H+ +QA + + ++++PL
Sbjct: 380 KKMIEQEDPEVW----DVLEDVIKE-HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPL 434
Query: 378 ICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHN 420
+C +ADFDGD + + P S A+AE L +L+S+N
Sbjct: 435 VCTAFNADFDGDQMAVHVPLSPEAQAEARAL------MLASNN 471
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 46.6 bits (112), Expect = 1e-04
Identities = 30/78 (38%), Positives = 46/78 (58%), Gaps = 12/78 (15%)
Query: 346 VFINRPPTTHKHSLQALS-VYVHDDHTVKINPLICGPLSADFDGD--CIHLFYPQSLAAK 402
V +NR PT H+ +QA V + + ++++PL+C +ADFDGD +H+ P SL A+
Sbjct: 411 VLLNRAPTLHRLGIQAFEPVLI-EGKAIQLHPLVCTAFNADFDGDQMAVHV--PLSLEAQ 467
Query: 403 AEVLELFSVEKQLLSSHN 420
AE L +LSS+N
Sbjct: 468 AEARVL------MLSSNN 479
>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 = 45.3 bits (108), Expect = 2e-04
Identities = 57/258 (22%), Positives = 102/258 (39%), Gaps = 45/258 (17%)
Query: 830 ERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDI 889
E++A +VK ++++ L + V IE E+ S D+ + I L+K ++E L++S ++
Sbjct: 75 EKSARIVKGRIEKTYLGE--VASYIE----EVYSPDDCYIL-IKLDKKIIEKLQLSKSNL 127
Query: 890 LPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGASD 949
Q K+K VV ++ + + + + LR +
Sbjct: 128 YFLLQ-----SLKRKLPDVVVSGIPEVKRAV-----INKDKKKGKYKLLVEGYGLRAVMN 177
Query: 950 SYLDKLSGVLAN---MIYPVL-----LETIIKENWWVRQRLSASVTMVAKG--VLKEHLI 999
+ + +N + VL TII E TM + G + H++
Sbjct: 178 TPGVIGTRTTSNHIMEVEKVLGIEAARSTIINE---------IQYTMKSHGMSIDPRHIM 228
Query: 1000 LLANSMTCAGDLVGFNSGGYKALSRSLNVQVPF--TEATLFMPRKCFEKAAEKRHTDNLS 1057
LLA+ MT G+++G G + S+ + F T LF AA D++
Sbjct: 229 LLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLF-------NAALHGRKDSIE 281
Query: 1058 SVVAACSWGKHVAVGTGS 1075
V GK + +GTG
Sbjct: 282 GVSECIIMGKPMPIGTGL 299
>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1. 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 1, represents the clamp domain, which a
mobile domain involved in positioning the DNA,
maintenance of the transcription bubble and positioning
of the nascent RNA strand.
Length = 330
Score = 43.8 bits (104), Expect = 6e-04
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 17/83 (20%)
Query: 14 IVGIRFGLATQKEICTASISDCSISHASQLANPFLGLPLEFG-------------KCESC 60
I I+FG+A+ +EI S ++ L P G CE+C
Sbjct: 4 IKEIQFGIASPEEI--RKWSVGEVTKPETYNYGSL-KPEPGGLLDERMGTIKKKSICETC 60
Query: 61 GTSEPGKCEGHFGYIELPIPIYH 83
G +C GHFG+IEL P++H
Sbjct: 61 GVEVT-ECPGHFGHIELAKPVFH 82
Score = 35.4 bits (82), Expect = 0.24
Identities = 40/151 (26%), Positives = 59/151 (39%), Gaps = 34/151 (22%)
Query: 96 AFQLQIKNDGVAQ-----RLLSSCCEVKEMLKRIPEETRKKLAGKGYFPQDGY----ILE 146
A + +KN + + R L+ +V ++ K+I +E + L G+ P IL
Sbjct: 172 AIKALLKNIEIEELKEKLRKLNPE-KVLQIFKKISKEDEEIL---GFNPSGNRPEWMILT 227
Query: 147 YLPVPPNCL--SVPDISDGVSTMSSDL-----SIAMLKKVLKQVEIIRSSRSGTPNFESQ 199
LPVPP C+ SV DG DL I LK++ G P+ +
Sbjct: 228 VLPVPPPCIRPSVQ--LDGGRFAEDDLTHKLRDIIKRNNRLKKML-----EEGAPSHIIR 280
Query: 200 EVESNDLQLAVGQYL--EVRG----TAKSSR 224
E E LQ V ++ G KS R
Sbjct: 281 E-EKRLLQEHVATLFDNDIPGQPPALQKSGR 310
>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 = 43.3 bits (103), Expect = 7e-04
Identities = 31/94 (32%), Positives = 39/94 (41%), Gaps = 27/94 (28%)
Query: 997 HLILLANSMTCAGDLVGFNSGGYKALSR---SLNVQVPFTEATLFMPRKCFE-------K 1046
HL L+A+ MT F GGY+ +R + P + + FE K
Sbjct: 233 HLSLIADYMT-------F-EGGYRPFNRIGMESSTS-PLQKMS-------FETTLAFLKK 276
Query: 1047 AAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLL 1080
A DNLSS + GK V GTG FDLL
Sbjct: 277 ATLNGDIDNLSSPSSRLVVGKPVNGGTGL-FDLL 309
>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 = 41.1 bits (97), Expect = 0.004
Identities = 26/70 (37%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 686 GLDPYEEMTHSISTREVIVRSSRGL-------SEPGTLFKNLMAVLRDVVICYDGTVRNV 738
GL P E H++ RE GL +E G L + L+ L D+V+ YD TVRN
Sbjct: 1 GLTPQEFFFHTMGGRE-------GLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRN- 52
Query: 739 CSNSIIQFDY 748
I+QF Y
Sbjct: 53 SGGEIVQFLY 62
>gnl|CDD|225260 COG2386, CcmB, ABC-type transport system involved in cytochrome c
biogenesis, permease component [Posttranslational
modification, protein turnover, chaperones].
Length = 221
Score = 35.4 bits (82), Expect = 0.17
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 431 ALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALSKARCSARWTALQILQSVLPP 486
+LL L+ +F+ + D + Q + LSPLP A+ + A W + + P
Sbjct: 63 SLLGLERLFRDDYEDGSLEQLM----LSPLPLAAVVLGKVLAHWLLTGLPLVLASP 114
>gnl|CDD|227493 COG5164, SPT5, Transcription elongation factor [Transcription].
Length = 607
Score = 35.8 bits (82), Expect = 0.25
Identities = 25/129 (19%), Positives = 33/129 (25%), Gaps = 13/129 (10%)
Query: 1349 APA-ENPLSGWGTEAQDSGKSSDW--------SEWKDHANATASWGRNGSEENSGWDTKA 1399
PA +P WG E + K S E +W + + +
Sbjct: 466 TPALNDPGIDWGDEKDNWYKGSLIHALGKGLALEDYRDGLFMTAWKGQATSASEISFVQP 525
Query: 1400 SW--KTKALDKLDDVGSAVENSS-SVWGAREDFSTKGWEDSSKPSANEKSIVH-QIGGWN 1455
W LD + N WG STKG + N K I W
Sbjct: 526 RWNNLVCVLDGEKKGTCGILNGINGDWGGTVIRSTKGSVVHWPMNDNSKKIYDGGASAWG 585
Query: 1456 VPDAKGTDD 1464
D
Sbjct: 586 NQDDGNRSA 594
>gnl|CDD|200083 TIGR01190, ccmB, heme exporter protein CcmB. This model describes
the cyt c biogenesis protein encoded by ccmB in
bacteria. Bacterial c-type cytochromes are located on
the periplasmic side of the cytoplasmic membrane.
Several gene products encoded in a locus designated as
'ccm' are implicated in the transport and assembly of
the functional cytochrome C. This cluster includes
genes: ccmA;B;C;D;E;F;G and H. The posttranslational
pathway includes the transport of heme moiety, the
secretion of the apoprotein and the covalent attachment
of the heme with the apoprotein. The proteins ccmA and B
represent an ABC transporter; ccmC and D participate in
heme transfer to ccmE, which function as a periplasmic
heme chaperone. The presence of ccmF, G and H is
suggested to be obligatory for the final functional
assembly of cytochrome C [Protein fate, Protein and
peptide secretion and trafficking, Transport and binding
proteins, Other].
Length = 211
Score = 33.5 bits (77), Expect = 0.59
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 431 ALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALSKARCSARWTALQILQSVLPP 486
+LLSL +F+ F D + L + ALSP P A+ A W + +L P
Sbjct: 57 SLLSLDRLFRDDFEDGS----LDLLALSPTPLELTVLAKVLAHWLVTGLPLVLLSP 108
>gnl|CDD|220748 pfam10427, Ago_hook, Argonaute hook. This region has been called the
argonaute hook. It has been shown to bind to the Piwi
domain pfam02171 of Argnonaute proteins.
Length = 136
Score = 31.8 bits (72), Expect = 1.1
Identities = 30/139 (21%), Positives = 45/139 (32%), Gaps = 31/139 (22%)
Query: 1197 AWGKSSDDKLEKAGSPS-RKPSGWGTEASWGESSCDKWENVGSPAAKSFSEWGTEASWGK 1255
AWG ++ G + SGWG + VG+PA K S S
Sbjct: 23 AWGHPNNSGPWGEGRAAGAGTSGWGDD------------PVGAPALKPGS-----KSMQN 65
Query: 1256 SFGDKPENVSPAAKTSSGWGSEASWGKSSGDRQENVGGSASKPLSGWGAKASWGKSSEDK 1315
+ DK + + W E S G S+ + G + WG +S K
Sbjct: 66 GWDDKDMPLL--GSRHNSWEDEESVGGGVW------NNKQSQESASSGNSSGWGNAS-KK 116
Query: 1316 LEEVETTVAKPSSAWGTEA 1334
++ + S W A
Sbjct: 117 VDGGD----MGGSNWQDHA 131
>gnl|CDD|206639 cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide
binding). The alpha subunit of G proteins contains the
guanine nucleotide binding site. The heterotrimeric
GNP-binding proteins are signal transducers that
communicate signals from many hormones,
neurotransmitters, chemokines, and autocrine and
paracrine factors. Extracellular signals are received by
receptors, which activate the G proteins, which in turn
route the signals to several distinct intracellular
signaling pathways. The alpha subunit of G proteins is a
weak GTPase. In the resting state, heterotrimeric G
proteins are associated at the cytosolic face of the
plasma membrane and the alpha subunit binds to GDP. Upon
activation by a receptor GDP is replaced with GTP, and
the G-alpha/GTP complex dissociates from the beta and
gamma subunits. This results in activation of downstream
signaling pathways, such as cAMP synthesis by adenylyl
cyclase, which is terminated when GTP is hydrolized and
the heterotrimers reconstitute.
Length = 315
Score = 32.1 bits (74), Expect = 2.5
Identities = 10/74 (13%), Positives = 31/74 (41%), Gaps = 10/74 (13%)
Query: 1594 RIMHQSGYNDGDRLSADDKSFIFDNVFNYHPDKAMKMG-AGIDHFKVD--KHGSFQDSRC 1650
+I+H +G++D +R + I+ N+ +MK ++ + + +D++
Sbjct: 21 KILHGNGFSDEERREF--RPVIYSNILQ-----SMKALLRAMETLNIPYGDPENEKDAKK 73
Query: 1651 LFVVSTDGSQQDFS 1664
+ ++ +
Sbjct: 74 ILSLAPRAEEGPLP 87
>gnl|CDD|188057 TIGR00511, ribulose_e2b2, ribose-1,5-bisphosphate isomerase, e2b2
family. The delineation of this family was based
originally, in part, on a discussion and
neighbor-joining phylogenetic study by Kyrpides and
Woese of archaeal and other proteins homologous to the
alpha, beta, and delta subunits of eukaryotic initiation
factor 2B (eIF-2B), a five-subunit molecule that
catalyzes GTP recycling for eIF-2. Recently, Sato, et
al. assigned the function ribulose-1,5 bisphosphate
isomerase [Energy metabolism, Other].
Length = 301
Score = 32.0 bits (73), Expect = 2.7
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 6/34 (17%)
Query: 331 RPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSV 364
R G++ +RI DGD + TH +S ALSV
Sbjct: 104 RIGEIGAKRIRDGDVIM------THCNSEAALSV 131
>gnl|CDD|218595 pfam05460, ORC6, Origin recognition complex subunit 6 (ORC6). This
family consists of several eukaryotic origin recognition
complex subunit 6 (ORC6) proteins. Despite differences in
their structure and sequences among eukaryotic
replicators, ORC is a conserved feature of replication
initiation in all eukaryotes. ORC-related genes have been
identified in organisms ranging from S. pombe to plants
to humans. All DNA replication initiation is driven by a
single conserved eukaryotic initiator complex termed he
origin recognition complex (ORC). The ORC is a six
protein complex. The function of ORC is reviewed in.
Length = 297
Score = 31.1 bits (70), Expect = 5.1
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 1143 PVFEDLVEDQSWLENKQENANWDSEADCRKSS--EDKWEKLGTSL 1185
P+ E+ +ED+ W + ++ A+ + K E LG+ L
Sbjct: 243 PIVEEWLEDEDWFREIEIKYDYFDGAEEEQVIRKRVKLEGLGSML 287
>gnl|CDD|227845 COG5558, COG5558, Transposase [DNA replication, recombination, and
repair].
Length = 261
Score = 30.6 bits (69), Expect = 6.0
Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 15/80 (18%)
Query: 1625 DKAMK----MGAGIDHFKVDKHGS-----FQDSRCLFVV-STDGSQQDFSYRKCLESFIR 1674
+KA+ MG ++ +DK+ S F ++V+ + ++ F + + +E +
Sbjct: 144 EKALGMLKSMGVKVNSISLDKYYSSTLRLFDAETAVYVIPKRNLARIGFDWLRVIERIVE 203
Query: 1675 GKYPDLVDEFIGKYFRRPRS 1694
Y F+ +YF+R S
Sbjct: 204 APY-----RFLKRYFKRNLS 218
>gnl|CDD|181428 PRK08446, PRK08446, coproporphyrinogen III oxidase; Provisional.
Length = 350
Score = 31.1 bits (71), Expect = 6.1
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 236 PNSTTKAWLEKMRTL 250
PNS TKAWL+ M+ L
Sbjct: 93 PNSATKAWLKGMKNL 107
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 31.2 bits (71), Expect = 6.2
Identities = 20/110 (18%), Positives = 32/110 (29%), Gaps = 22/110 (20%)
Query: 441 KYFLDKAFTQQLAMFALSPLPRPALSKARCSARWTALQILQSVLPPGFDSCGDRYLIKKS 500
YF+ F Q LSPL +Q + ++ R L ++
Sbjct: 53 GYFIKGKFDQFERNIPLSPL----------------VQAFRDLMGQLLSESDTRILSWRA 96
Query: 501 EVLK--GDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLF 548
+L G+ + I VI E+ LE + F
Sbjct: 97 RLLAALGENGQVIID-VIPEL---ELIIGKRPPALELSPTAAQNRFNLAF 142
>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit. This
family consist of exodeoxyribonuclease VII, large
subunit XseA which catalyses exonucleolytic cleavage in
either the 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. Exonuclease VII consists of
one large subunit and four small subunits [DNA
metabolism, Degradation of DNA].
Length = 432
Score = 31.0 bits (70), Expect = 6.3
Identities = 25/107 (23%), Positives = 43/107 (40%), Gaps = 33/107 (30%)
Query: 79 IPIYHPSHISELKLTMYAFQLQIKNDGVAQRLLSSCCEVKEMLKRIPEETRKKLAGKGYF 138
I +Y P ++ F++Q +G+ Q E+ ++KLA +G F
Sbjct: 76 ISVYEPRGDYQI----ICFEMQPAGEGLLQLAY--------------EQLKEKLAAEGLF 117
Query: 139 PQDGYILEY---LPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQ 182
Q EY LP P + GV T + ++A + +LK+
Sbjct: 118 DQ-----EYKKPLPHFPKRV-------GVITSQTGAALADILHILKR 152
>gnl|CDD|217522 pfam03379, CcmB, CcmB protein. CcmB is the product of one of a
cluster of Ccm genes that are necessary for cytochrome c
biosynthesis in eubacteria. Expression of these proteins
is induced when the organisms are grown under anaerobic
conditions with nitrate or nitrite as the final electron
acceptor. CcmB is required for the export of haem to the
periplasm.
Length = 215
Score = 30.3 bits (69), Expect = 6.8
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 412 EKQLLSS-HNGNLNLQLATDALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALSKARC 470
E LL+ G + + +LLSL+ +F F D + L + LSP P L A+
Sbjct: 40 EPALLARIAPGIIWVAALLSSLLSLERLFAADFEDGS----LELLLLSPTPLEKLVLAKA 95
Query: 471 SARWTALQILQSVLPP 486
A W + +L P
Sbjct: 96 LAHWLLTGLPLILLSP 111
>gnl|CDD|237601 PRK14076, pnk, inorganic polyphosphate/ATP-NAD kinase; Provisional.
Length = 569
Score = 30.9 bits (70), Expect = 7.2
Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 491 CGDRYLIKKSEV---LKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENL 547
G+ + K++++ + D ++ +PS +NE+V + K P ++L F + L+E +
Sbjct: 403 SGEYEIEKRTKLSGFILKDGHQNILPSALNEVVITT---KNPAKMLHFEVYVNGELVEEV 459
Query: 548 FADGFSVS 555
ADG +S
Sbjct: 460 RADGIIIS 467
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
0.315 0.131 0.394
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 85,401,708
Number of extensions: 8331379
Number of successful extensions: 6370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6349
Number of HSP's successfully gapped: 60
Length of query: 1714
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1604
Effective length of database: 6,058,662
Effective search space: 9718093848
Effective search space used: 9718093848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 66 (29.0 bits)