RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 000525
(1443 letters)
>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 = 409 bits (1053), Expect = e-131
Identities = 163/399 (40%), Positives = 221/399 (55%), Gaps = 27/399 (6%)
Query: 871 QPVGSLSACAISEAAYSALDQPISLLETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLG 930
+PVGSL+A AISE AY AL P LE+SPL LK VLEC SK + + + LS L
Sbjct: 2 EPVGSLAATAISEPAYKALLDPPQSLESSPLELLKEVLECRSKSKSKENDRRVILSLHLC 61
Query: 931 KRRHGFEY--GALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMK 988
K HGFEY ALEVKNHLE + L D+ +TSMI YSPQ +K K
Sbjct: 62 KCDHGFEYERAALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKK 121
Query: 989 RTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIV-E 1047
I T+ V + + + +D C+T + E
Sbjct: 122 AIFSTSLKI------------TKFSPWVCHFHLDKECQ-------KLSDGPCLTFSVSKE 162
Query: 1048 NFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASK---SHDDSFGELYL 1104
K + L+ ++ ++PFLL+TV+KG IK V+ILW+D S S GEL L
Sbjct: 163 VSKSSEELLDVLRDRIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVL 222
Query: 1105 RVSMSGQCHITS--LWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNL 1162
V++ C T W+ +M+ C +MD+IDW RS P +I+ GIDA + F+ L
Sbjct: 223 EVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRL 282
Query: 1163 ESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGA 1222
ESA+S TGK++L EHLL+VA++++ +GEFVGLNAKG QR+ +S+PF +A FS+P
Sbjct: 283 ESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKISAPFTEACFSSPIK 342
Query: 1223 SFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIY 1261
F+KAAK GA D+L G +DA WGK VGTG F+I++
Sbjct: 343 CFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 246 bits (628), Expect = 5e-66
Identities = 231/955 (24%), Positives = 369/955 (38%), Gaps = 175/955 (18%)
Query: 13 PSGILTGISLGISTDTEKEKLSVMEIGAVSE-----------VTNPRLGLPNPTNECSSC 61
+ GI G+ + + K+ EI A + + RLG P +C +C
Sbjct: 5 AVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTC 64
Query: 62 GAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKC-------------KTIRKE 108
G C GHFG I+ ++H F+ +I LLNS C KC K I +
Sbjct: 65 G-NLAANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEA 123
Query: 109 RQKGAGSSRKEQPRVCKYCVRNPAQWYPRMRFKLSSKDLSGKTAIIVEIDE--------- 159
K VR+ + Y + + G +E +E
Sbjct: 124 HAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPH---CGAPQHELEFEEPTIFIEKTE 180
Query: 160 ---------KLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSI 210
++ +K+ DD I FD + +P VL V L PSI
Sbjct: 181 IEEHRLLPIEIRDIFEKIIDDDLELIGFDPK----KARPEWAVLQAFLVPPL--TARPSI 234
Query: 211 -REEFILSKDAPFLKCFPVTPNNHRVTEVPHA-------------FSHEKKLFFDNWTRH 256
E S+D + N ++ E A + FFDN T
Sbjct: 235 ILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAG 294
Query: 257 LKKMVDYRGRDIELSHLVQDCLKISKLHLDKSSRKDSAEVRQKKNIDISNSSGLRWIKDV 316
+ + ++G L L Q R E R + N+
Sbjct: 295 IPQAH-HKGSGRPLKSLFQ--------------RLKGKEGRFRGNL-------------- 325
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEK 376
+GKR D R V++ DP I + E+G+P +A +L I E +N N E++ + ++
Sbjct: 326 -IGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELV-INGPDE 383
Query: 377 --GELYVCRKGGLVRIR--------------RIDALELGDIIYRPLTDGDIVLINRPPSI 420
G + RKG +IR + LE+GDI+ R L DGDIV+ NR PS+
Sbjct: 384 FPGANAI-RKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSL 442
Query: 421 HPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDK 480
H S++A VKVLP + ++P C P++ DFDGD ++ ++PQ AR E EL+ +
Sbjct: 443 HKLSILAHRVKVLP-GATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKD 501
Query: 481 QLINQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMFCPHRFLSPDIFKISKDS 540
LI+ ++G ++ QD +TAA+L+ +D L + + M P+ +KD
Sbjct: 502 NLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPAIKTKDG 561
Query: 541 -VWSGKQLFSMLLPPDFEYTFPSK------------------DVYISGGKLISA--EGSS 579
W+GKQLFS+ LP DF + +K V I G+LIS + +
Sbjct: 562 PAWTGKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNI 621
Query: 580 WLRDYEG--NLFQYLIKRYRDKV-LDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSR 636
E +L + K Y + V ++FL + + + G + DL + + +
Sbjct: 622 IGALVEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEA-KQ 680
Query: 637 KILMDEIFYGLREAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALS 696
+I + G M D + + K + +G+ +
Sbjct: 681 EIE--DDIQG-------------MKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEAL 725
Query: 697 QASVDAFKHVFWD-IQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPL 755
+A + D + A DN+ M K G++G++ L Q + LG Q +
Sbjct: 726 EADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRI 785
Query: 756 SFRFPHELSCAAWNRLRAGDNTECAKSY-----IPSA--VVENSFLTGLNPLECFIHSVT 808
F RL G + P A V+N++ GLN E F H++
Sbjct: 786 GFVLTG-------GRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMG 838
Query: 809 SRDSSFSDNA---DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEG 860
R+ D A + G RRL + D+ YD TVR+ +G+ I+QF + +G
Sbjct: 839 GRE-GLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGH-IIQFKFGEDG 891
Score = 52.7 bits (126), Expect = 2e-06
Identities = 74/392 (18%), Positives = 142/392 (36%), Gaps = 69/392 (17%)
Query: 871 QPVGSLSACAISEAAYSALDQPI---SLLETSPLLNLKNVLE-CGSKKSNADQTMSLFLS 926
Q +G +SA +I+E + + L+ +E ++ + TM ++L
Sbjct: 979 QAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLD 1038
Query: 927 NKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEI 986
++ + A+E+ +L+ L + +++ S I + K I
Sbjct: 1039 DECKEDIEK----AIEIARNLKELKVRALIADSAIDN----------------ANEIKLI 1078
Query: 987 MKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIV 1046
E+ I E + L K + E D + + +V
Sbjct: 1079 KPDKRALENGCIP----------MERFAEIEAALAKGK-----KFEMELEDDL-IILDLV 1122
Query: 1047 ENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKK--VDILWKDKQKASKSHDDSFGELYL 1104
E R L T+ +L VKG +I++ V+++ KD + E +
Sbjct: 1123 EAADRDK-PLATLIAIRNK-ILDKPVKGVPDIERAWVELVEKDGRD----------EWII 1170
Query: 1105 RVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLES 1164
+ S S + M ID + ++ GI+A L S
Sbjct: 1171 QTSGSNLAAVLE------------MKCIDIANTITNDCFEIAGTLGIEAARNAIFNELAS 1218
Query: 1165 AISDTGKNILPEHLLIVANTLSATG--EFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGA 1222
+ D G + ++++VA+ + + G E +GL A G+ SP +A F
Sbjct: 1219 ILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVR-HGFAGEKDSPLAKAAFEITTH 1277
Query: 1223 SFIKAAKAGAVDNLQGSVDALGWGKVPSVGTG 1254
+ AA G ++ ++G +DAL G+ +G+G
Sbjct: 1278 TIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
>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 = 225 bits (576), Expect = 8e-61
Identities = 236/963 (24%), Positives = 373/963 (38%), Gaps = 234/963 (24%)
Query: 16 ILTGISLGISTDTEKEKLSVMEIGAVSEV------------TNPRLGLPNPTNECSSCGA 63
+ I G+ + E K+SV+E+ ++ +PRLG+ P C +CG
Sbjct: 3 KIGSIKFGLLSPEEIRKMSVVEV-VTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGG 61
Query: 64 KDRKACEGHF------------GFIKFPFTILHP----------------YFLSDIAKLL 95
K C GHF GF K + IL +L I KL
Sbjct: 62 K-VGECPGHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLK 120
Query: 96 NS----ICPKCKTIRKERQKGAGSSRKEQPRVCKYC------VRNPAQWYPRMRFKLSSK 145
+ I KE K C +C ++ Y K
Sbjct: 121 EEGGDLASTLIEKIVKEAAKR---------MKCPHCGEEQKKIKFEKPTYFYEEGKEGDV 171
Query: 146 DLSGKTAIIVEIDEKLSKKNKKLPDD---YWGFIPFDAQQEENSVKPNRKVLSCKQVSYL 202
L+ EI E+L K +PD+ G P A +P VL+ V +
Sbjct: 172 KLTPS-----EIRERLEK----IPDEDAELLGINPKVA-------RPEWMVLTVLPVPPV 215
Query: 203 LKDVDPSIR-EEFILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKL------------- 248
V PSI E S+D K + N R+ E A + + +
Sbjct: 216 --TVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVAT 273
Query: 249 FFDNWTRHLKKMVDYRGRDIELSHLVQDCLKISKLHLDKSSRKDSAEVRQKKNIDISNSS 308
+FDN + GR L L Q R E R + N+
Sbjct: 274 YFDNELPGIPPARHRSGR--PLKTLAQ--------------RLKGKEGRFRGNLS----- 312
Query: 309 GLRWIKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVC 368
GKR + R V++ DPNI + E+G+P Q+A+ L + ER+ WN + L
Sbjct: 313 ----------GKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELR-- 360
Query: 369 ISFRLLEKGE------LYVCRKGGLVRIRRID-----------ALELGDIIYRPLTDGDI 411
+ G YV R G RRI LE G ++ R L DGDI
Sbjct: 361 ---EYVLNGPDSWPGANYVIRPDG----RRIKIRDENKEELAERLEPGWVVERHLIDGDI 413
Query: 412 VLINRPPSIHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVE 471
VL NR PS+H S++ VKVLP +N C P++ DFDGD ++ ++PQ AR E
Sbjct: 414 VLFNRQPSLHRMSMMGHKVKVLP-GKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAE 472
Query: 472 LTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMFCPHRFLSP 531
EL+ +++ ++ + G ++ D ++ A+LL S L + ++Q + + P
Sbjct: 473 ARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPP 532
Query: 532 DIFKISKDSVWSGKQLFSMLLPPDFEYTFPSK--------------DVY--ISGGKLIS- 574
+ W+GKQ+FS LP D + +K D Y I GKL+
Sbjct: 533 EPAIEKPKEYWTGKQIFSAFLPEDLNFEGRAKICSSDACKKEECPHDAYVVIKNGKLLKG 592
Query: 575 -----AEGSSWLRDYEGNLFQYLIKRY-RDKVLDFLYAAQEVLCEWLSVRGMTVSLSDLY 628
A G+ +G + +++ Y + FL + + ++++RG T + D+
Sbjct: 593 VIDKKAIGA-----EKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDID 647
Query: 629 LASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHL--S 686
+ + K ++E+ + +A+ VD+ L+ + L G + +
Sbjct: 648 IPKEA---KEEIEEL---IEKAEKR-------VDN----LIERYRNGELEPLPGRTVEET 690
Query: 687 YEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCL 746
E + L +A +A +A KY +N + M + G++G+LL + Q + +
Sbjct: 691 LEMKIMEVLGKARDEA--------GEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMV 742
Query: 747 GLQHSLAPLSFR------FPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPL 800
G Q R PH + GD A+ + V +SF GL+P
Sbjct: 743 GQQSVRGGRIRRGYRNRTLPH---------FKKGDIGAKARGF-----VRSSFKKGLDPT 788
Query: 801 ECFIHSVTSRDSSFSDNA---DLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYN 857
E F H+ R+ D A G + RRL+ ++DL YDGTVR+ GN ++QF Y
Sbjct: 789 EYFFHAAGGRE-GLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGN-LIQFKYG 846
Query: 858 IEG 860
+G
Sbjct: 847 EDG 849
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 218 bits (558), Expect = 2e-58
Identities = 171/604 (28%), Positives = 267/604 (44%), Gaps = 123/604 (20%)
Query: 319 GKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEK-- 376
GKR + R V++ DPN+ + E+G+P +A+ L + ER+ WN E L + EK
Sbjct: 317 GKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVL-NGPEKHP 375
Query: 377 GELYVCRKGGLVRIRRID-----------ALELGDIIYRPLTDGDIVLINRPPSIHPHSL 425
G YV R G RRI LE G I+ R L DGDIVL NR PS+H S+
Sbjct: 376 GANYVIRPDG----RRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSI 431
Query: 426 IALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQ 485
+A V+VLP +N C P++ DFDGD ++ ++PQ AR E L+ + + +++
Sbjct: 432 MAHRVRVLP-GKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSP 490
Query: 486 QSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMFC-PHRFLSPDIFKISKDSVWSG 544
+ G ++ QD ++ A+LL S L + + L P+ + W+G
Sbjct: 491 RYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGKPYWTG 550
Query: 545 KQLFSMLLPPDFEYTFPSK-----------------DVYISGGKLIS------AEGSSWL 581
KQ+FS+ LP D F +K V I GKL+ A G+
Sbjct: 551 KQIFSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGA--- 607
Query: 582 RDYEGNLFQYLIKRY-RDKVLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILM 640
+G++ ++K Y ++ FL + + ++ +RG T + D + +I
Sbjct: 608 --EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDI-PEEAKEEI-- 662
Query: 641 DEIFYGLREAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHL--SYEKQRSAALSQA 698
DEI + EA+ V+ L+ A ++ L G L + E + L +A
Sbjct: 663 DEI---IEEAEKR-------VEE----LIEAYENGELEPLPGRTLEETLEMKIMQVLGKA 708
Query: 699 SVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPLSFR 758
+A +A KY DN + M + G++G++L L Q + C+G Q S R
Sbjct: 709 RDEA--------GEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQ------SVR 754
Query: 759 ------------FPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHS 806
PH + GD A+ + V +S+ +GL P E F H+
Sbjct: 755 GERIRRGYRDRTLPH---------FKPGDLGAEARGF-----VRSSYKSGLTPTEFFFHA 800
Query: 807 VTSRD--------SSFSDNADLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNI 858
+ R+ +S S G + RRL+ ++DL YDGTVR+ GN IVQF Y
Sbjct: 801 MGGREGLVDTAVRTSQS------GYMQRRLINALQDLKVEYDGTVRDTRGN-IVQFKYGE 853
Query: 859 EGTS 862
+G
Sbjct: 854 DGVD 857
Score = 60.6 bits (148), Expect = 5e-09
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 14/99 (14%)
Query: 16 ILTGISLGISTDTEKEKLSVMEIGAVSE------------VTNPRLGLPNPTNECSSCGA 63
+ I G+ + E K+SV +I ++ + +PRLG+ +P C +CG
Sbjct: 8 RIGSIKFGLLSPEEIRKMSVTKI-ITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGG 66
Query: 64 KDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKC 102
+ C GHFG I+ ++H F I KLL + C +C
Sbjct: 67 R-AGECPGHFGHIELARPVIHVGFAKLIYKLLRATCREC 104
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 155 bits (395), Expect = 7e-42
Identities = 68/191 (35%), Positives = 111/191 (58%), Gaps = 8/191 (4%)
Query: 318 LGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEKG 377
LGKR D R V+T DPN+KL E+G+P ++A L E + N ++L + R G
Sbjct: 108 LGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV--RNGPNG 165
Query: 378 ELYVCR----KGGLVRIRRIDA-LELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKV 432
Y+ R L + +I L++GDI+ R + DGD+VL NR P++H S+ A V+V
Sbjct: 166 AKYIIRGKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRV 225
Query: 433 LPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLL 492
L + +NPL CSP++ DFDGD ++ ++PQ++ AR E EL+ + +++ ++G+ ++
Sbjct: 226 LE-GKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPII 284
Query: 493 SLGQDSLTAAH 503
QD L +
Sbjct: 285 GPIQDMLLGLY 295
>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 = 127 bits (321), Expect = 1e-33
Identities = 60/163 (36%), Positives = 88/163 (53%), Gaps = 7/163 (4%)
Query: 319 GKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEKGE 378
GKR D R V+T DPN+KL E+G+P ++A L E + N ++L +S
Sbjct: 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPG 60
Query: 379 LYVC-RKGGLVRI-----RRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKV 432
R G R R L GDI+ R + DGD+VL+NR P++H S++A +V
Sbjct: 61 AKYIKRIKGAKRDLEYKKRIAIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRV 120
Query: 433 LPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTEL 475
L + +NP CSP++ DFDGD ++ ++PQ+ AR E EL
Sbjct: 121 LE-GKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEAREL 162
>gnl|CDD|221127 pfam11523, DUF3223, Protein of unknown function (DUF3223). This
family of proteins has no known function.
Length = 76
Score = 97.7 bits (244), Expect = 2e-24
Identities = 37/76 (48%), Positives = 48/76 (63%), Gaps = 1/76 (1%)
Query: 1344 LKKILHKYSIGQRLSEKDKTTVI-RALYFHPRRNEKLGIEPPDIEVTYHPEHQNSRCFSL 1402
K ILH+Y G RLS++D+ T++ L +HP EK+G EV HPE SRCF +
Sbjct: 1 FKAILHRYDDGDRLSDEDEKTLLEALLEYHPDAEEKIGAGIDHFEVRTHPEGGKSRCFFV 60
Query: 1403 VREDGSIEDFSYHKCV 1418
VR DG+ EDFSY KC+
Sbjct: 61 VRTDGTSEDFSYRKCI 76
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 98.1 bits (245), Expect = 1e-20
Identities = 64/244 (26%), Positives = 105/244 (43%), Gaps = 21/244 (8%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEK 376
+LGKR D R V++ PN+KL + G+P ++A L + N E L
Sbjct: 285 LLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGL---------RT 335
Query: 377 GELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPIS 436
G Y R RR L + R + DGD VL+NR P++H S++ VLP
Sbjct: 336 GAKYAKRM----VERR---LPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEG 388
Query: 437 SVVTINPLCCSPFHGDFDGD--CLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSL 494
+ ++PL C ++ DFDGD +H P + A E L+ ++ G +++
Sbjct: 389 KAIRLHPLVCEAYNADFDGDEMAVHV--PASGEAAAEARGLMGTQMNILTPHYGGPIVAP 446
Query: 495 GQDSLTAAHLLMEDSVLLSHLQMQQLQMFCPHRFLSPDIFKISKDSV-WSGKQLFSMLLP 553
QD++ +LL L + ++ + + I+K +GK + S + P
Sbjct: 447 IQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTISP 506
Query: 554 PDFE 557
E
Sbjct: 507 DLAE 510
Score = 56.1 bits (136), Expect = 1e-07
Identities = 25/74 (33%), Positives = 32/74 (43%), Gaps = 11/74 (14%)
Query: 789 VENSFLTGLNPLECFIHSVTSRDSSFSDNADL------PGTLTRRLMFFMRDLCTAYDGT 842
E+SFL GL E F H + R D G LTRRL+ +DL D
Sbjct: 715 GESSFLEGLTENEYFGHPIGGRTGL----VDTALKTADSGYLTRRLVDVAQDLIVQEDDC 770
Query: 843 VRNAYGNQIVQFSY 856
V + G ++QF Y
Sbjct: 771 VTDGIGV-VIQFEY 783
Score = 50.7 bits (122), Expect = 6e-06
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 47 PRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIR 106
R+ P+ EC+ CG K ++ C G FG I+ + H +F I LL+ C C+ +
Sbjct: 44 ERIFGPDKDYECT-CG-KYKRICPGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCERVL 101
>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 = 83.4 bits (207), Expect = 2e-18
Identities = 39/160 (24%), Positives = 68/160 (42%), Gaps = 15/160 (9%)
Query: 481 QLINQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQMQQLQMFCPHRFLSPDIFKISKDS 540
+++ Q+G+ ++ QD + +LL ++ QL M+ P I K K
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYGI-VLPHPAILKPIKPL 59
Query: 541 VWSGKQLFSMLLPPDFEYTFPSKD-----------VYISGGKLISA-EGSSWLRDYEGNL 588
W+GKQ FS LLP + K V I+ G+LIS G+L
Sbjct: 60 -WTGKQTFSRLLPNEINPKGKPKTNEETLCENDSYVLINNGELISGVIDKKLGGKSLGSL 118
Query: 589 FQYLIKRYR-DKVLDFLYAAQEVLCEWLSVRGMTVSLSDL 627
+ K Y ++ + FL Q++ +L+ G ++ + D+
Sbjct: 119 IHIIYKEYGPEETVKFLDRLQKLGFRYLTKSGFSIGIDDI 158
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 64.5 bits (157), Expect = 4e-10
Identities = 50/189 (26%), Positives = 82/189 (43%), Gaps = 17/189 (8%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEK 376
+LGKR D R V+ P++KL + G+P +A E + RL+E
Sbjct: 420 LLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMA-------------LELFKPFVMKRLVEL 466
Query: 377 GELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPIS 436
Y R A + D++ + D VL+NR P++H + A VL
Sbjct: 467 E--YAANIKAAKRAVDRGASYVWDVLEEVIQD-HPVLLNRAPTLHRLGIQAFE-PVLVEG 522
Query: 437 SVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQ 496
+ ++PL C+ F+ DFDGD + ++P + A+ E L+ + + GR L Q
Sbjct: 523 KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQ 582
Query: 497 DSLTAAHLL 505
D + + L
Sbjct: 583 DMIIGVYYL 591
>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 = 61.1 bits (148), Expect = 3e-09
Identities = 49/224 (21%), Positives = 103/224 (45%), Gaps = 28/224 (12%)
Query: 297 RQKKNIDISNSSGLRWIKDVV-----------LGKRNDDCFRMVVTGDPNIKLKEIGIPC 345
R+ + + +N+ L+ + D++ LGKR D R V+ P +K+ + G+P
Sbjct: 312 RRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPK 371
Query: 346 QVAERLQISERLNSWNWERLSVCISFRLLEKGELYVCRKGGLVRIRRIDALELGDIIYRP 405
++A L + RL+ +G + K I+R D E+ ++ +
Sbjct: 372 EMAIEL-------------FQPFVIHRLIRQG-IVNNIKAAKKLIQRADD-EIWSVL-QE 415
Query: 406 LTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQA 465
+ G V++NR P++H + A ++ + ++PL C F+ DFDGD + ++P +
Sbjct: 416 VITGHPVMLNRAPTLHRLGIQAFEPILVD-GRAIQLHPLVCPAFNADFDGDQMAVHVPLS 474
Query: 466 IGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDS 509
+ A+ E L+ +++ +G +++ QD + + L +
Sbjct: 475 LEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALN 518
>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 = 56.3 bits (136), Expect = 6e-09
Identities = 27/114 (23%), Positives = 55/114 (48%), Gaps = 5/114 (4%)
Query: 1141 NIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLA 1200
+I A GI+A + + ++ ++ G ++ H+ ++A+ ++ +G G+ G
Sbjct: 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFR 108
Query: 1201 LQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTG 1254
+S +SP ++A F + AA AG D L+G + + G+ +GTG
Sbjct: 109 -----ASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 56.1 bits (135), Expect = 2e-07
Identities = 50/181 (27%), Positives = 88/181 (48%), Gaps = 17/181 (9%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEK 376
+LGKR D R V+ PN+K+ E G+P +A L L+ +L E+
Sbjct: 1731 LLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLS-------------KLEER 1777
Query: 377 GELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPIS 436
G ++ R+ + E+ + + + +T+G VL+NR P++H S+ A K++
Sbjct: 1778 GYATTLKQA--KRMIEQKSNEVWECL-QEITEGYPVLLNRAPTLHKQSIQAFHPKLID-G 1833
Query: 437 SVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQ 496
+ ++PL CS F+ DFDGD + ++P + A E L+ ++ SG+ + Q
Sbjct: 1834 KAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQ 1893
Query: 497 D 497
D
Sbjct: 1894 D 1894
>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 = 54.6 bits (132), Expect = 3e-07
Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 15/69 (21%)
Query: 796 GLNPLECFIHSV--------TSRDSSFSDNADLPGTLTRRLMFFMRDLCTAYDGTVRNAY 847
GL P E F H++ T+ ++ + G L RRL+ + DL YD TVRN+
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAET------GYLQRRLVKALEDLVVQYDDTVRNS- 53
Query: 848 GNQIVQFSY 856
G +IVQF Y
Sbjct: 54 GGEIVQFLY 62
Score = 33.0 bits (76), Expect = 1.2
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 1149 YGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSV 1208
GI+A L + + G + HL ++A+ ++ GE +G+ GL
Sbjct: 387 LGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGLN------RE 440
Query: 1209 SSPFVQA 1215
S F+
Sbjct: 441 KSSFILM 447
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 54.2 bits (130), Expect = 6e-07
Identities = 48/211 (22%), Positives = 96/211 (45%), Gaps = 28/211 (13%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQ---ISERLNSWNWERLSVCISFRL 373
+LGKR D R V+ P +KL + G+P ++A L + +L + ++ I F
Sbjct: 1775 LLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYG---MAPTIKFA- 1830
Query: 374 LEKGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVL 433
++ R + E+ D++ + + VL+NR P++H + A +L
Sbjct: 1831 --------------SKLIRAEKPEVWDMLEEVIKEHP-VLLNRAPTLHRLGIQAFE-PIL 1874
Query: 434 PISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLS 493
+ ++PL C+ F+ DFDGD + ++P ++ A++E L+ +++ +GR ++
Sbjct: 1875 IEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIV 1934
Query: 494 LGQDSLTAAHLLMEDSVLLSHLQMQQLQMFC 524
+D + + L L + L F
Sbjct: 1935 PSKDIVLGIYYLT-----LQEPKEDDLPSFG 1960
>gnl|CDD|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4. 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 4, represents the funnel domain. The
funnel contain the binding site for some elongation
factors.
Length = 108
Score = 48.9 bits (117), Expect = 7e-07
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 709 DIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQ 749
N+A K +NS+ M +G+KG+++ + Q + C G Q
Sbjct: 36 PAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQ 76
>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 = 50.7 bits (122), Expect = 3e-06
Identities = 42/188 (22%), Positives = 80/188 (42%), Gaps = 29/188 (15%)
Query: 1067 LLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCH 1126
+L T +KG + IK+V + +K E + S +L + L
Sbjct: 197 ILNTKIKGIKGIKRVIV-----RKEE-------DEYVIYTEGS------NLKAVLK---- 234
Query: 1127 QIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLS 1186
++ +D TR+ +NI GI+A + ++ + + G ++ H+++VA+ ++
Sbjct: 235 --VEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMT 292
Query: 1187 ATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWG 1246
GE + G+A S +A F + AA G VD L+G ++ + G
Sbjct: 293 YDGEVRQIGRHGIA-----GEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVG 347
Query: 1247 KVPSVGTG 1254
+ +GTG
Sbjct: 348 QPIPLGTG 355
>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 = 51.2 bits (123), Expect = 4e-06
Identities = 48/188 (25%), Positives = 86/188 (45%), Gaps = 33/188 (17%)
Query: 318 LGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERL---QISERLNSWNWERLSVCISFRLL 374
LGKR D R V+ P +K+ + G+P ++A L I +RL + + +
Sbjct: 325 LGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRL-----IDRELAANIKSA 379
Query: 375 EKGELYVCRKGGLVRIRRIDALELGDIIY-----RPLTDGDIVLINRPPSIHPHSLIALT 429
+K I + D E+ D++ P VL+NR P++H + A
Sbjct: 380 KK------------MIEQEDP-EVWDVLEDVIKEHP------VLLNRAPTLHRLGIQAFE 420
Query: 430 VKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGR 489
VL + ++PL C+ F+ DFDGD + ++P + A+ E L+ ++N + G+
Sbjct: 421 -PVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGK 479
Query: 490 NLLSLGQD 497
+++ QD
Sbjct: 480 PIVTPSQD 487
>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 = 49.3 bits (118), Expect = 9e-06
Identities = 41/188 (21%), Positives = 78/188 (41%), Gaps = 29/188 (15%)
Query: 1067 LLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCH 1126
+ +KG + IK+V I + D E + S +L L
Sbjct: 202 IKNLHIKGIKGIKRVVI---------RKEGD---EYVIYTEGS------NLKEVLK---- 239
Query: 1127 QIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLS 1186
++ +D TR+ ++I GI+A + ++ + + G ++ HL++VA+ ++
Sbjct: 240 --LEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMT 297
Query: 1187 ATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWG 1246
GE + G++ K +S +A F + AA G VD L G ++ + G
Sbjct: 298 WDGEVRQIGRHGIS-GEK----ASVLARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVG 352
Query: 1247 KVPSVGTG 1254
+ +GTG
Sbjct: 353 QPIPLGTG 360
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 49.7 bits (119), Expect = 9e-06
Identities = 48/195 (24%), Positives = 92/195 (47%), Gaps = 29/195 (14%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVA-ERLQ---ISE--RLNSWNWERLSVCIS 370
+LGKR D R V+ P +K+ + G+P ++A E Q I R N ++ +
Sbjct: 350 LLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVN----NIKAA 405
Query: 371 FRLLEKGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTV 430
+L+++ + V LE ++I +G VL+NR P++H + A
Sbjct: 406 KKLIQRADPEV-----------WQVLE--EVI-----EGHPVLLNRAPTLHRLGIQAFE- 446
Query: 431 KVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRN 490
+L + ++PL C F+ DFDGD + ++P ++ A+ E L+ +++ +G
Sbjct: 447 PILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEP 506
Query: 491 LLSLGQDSLTAAHLL 505
+++ QD + + L
Sbjct: 507 IVTPSQDMVLGCYYL 521
>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 = 46.8 bits (112), Expect = 4e-05
Identities = 34/139 (24%), Positives = 56/139 (40%), Gaps = 24/139 (17%)
Query: 1122 MNDCHQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIV 1181
ND H +++ YGI+A + + + + G + P HL ++
Sbjct: 195 TNDIHAMLNT-----------------YGIEAARRAIVKEISNVFKVYGIAVDPRHLSLI 237
Query: 1182 ANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVD 1241
A+ ++ G + N G+ S +SP + F A KA G +DNL
Sbjct: 238 ADYMTFEGGYRPFNRIGM------ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSS 291
Query: 1242 ALGWGKVPSVGTGGHFDII 1260
L GK + GTG FD++
Sbjct: 292 RLVVGKPVNGGTGL-FDLL 309
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 44.4 bits (105), Expect = 3e-04
Identities = 33/138 (23%), Positives = 64/138 (46%), Gaps = 6/138 (4%)
Query: 1130 DMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATG 1189
D +D TR++ ++I GI+A + + + + G N+ H+++VA+ ++ G
Sbjct: 377 DEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDG 436
Query: 1190 EFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVP 1249
+ G++ K SS +A F G ++A G VD L G + + G+
Sbjct: 437 SVKAIGRHGIS-GEK----SSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPI 491
Query: 1250 SVGTGGHFDIIYSGEGRT 1267
++GTG ++Y G +
Sbjct: 492 TLGTGA-VSLVYKGRKKV 508
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 43.3 bits (103), Expect = 7e-04
Identities = 45/198 (22%), Positives = 80/198 (40%), Gaps = 49/198 (24%)
Query: 1067 LLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCH 1126
+ +KG + IK+V I+ K+ E + T S L
Sbjct: 214 IRNIKIKGIKGIKRV-IIRKEG-----------DEYVI---------YTE-GSNL----K 247
Query: 1127 QIMDM--IDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPE-------- 1176
+++ + +D TR+ +NI GI+A AI + KN L E
Sbjct: 248 EVLKVEGVDATRTTTNNIHEIEEVLGIEAARN--------AIIEEIKNTLEEQGLDVDIR 299
Query: 1177 HLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNL 1236
H+++VA+ ++ GE + G++ ++ +S +A F + AA G VD L
Sbjct: 300 HIMLVADMMTWDGEVRQIGRHGVSGEK-----ASVLARAAFEVTVKHLLDAAVRGEVDEL 354
Query: 1237 QGSVDALGWGKVPSVGTG 1254
+G + + G+ +GTG
Sbjct: 355 KGVTENIIVGQPIPLGTG 372
>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 = 39.5 bits (93), Expect = 0.009
Identities = 44/188 (23%), Positives = 78/188 (41%), Gaps = 27/188 (14%)
Query: 1067 LLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCH 1126
L VV G E+K+ I + D G+ L V G A+MN
Sbjct: 138 LPDVVVSGIPEVKRAVI----------NKDKKKGKYKLLVEGYG-------LRAVMN--- 177
Query: 1127 QIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLS 1186
+ TR+ ++I GI+A + ++ + G +I P H++++A+ ++
Sbjct: 178 --TPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMT 235
Query: 1187 ATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWG 1246
GE +G+ G+A ++ S + A F AA G D+++G + + G
Sbjct: 236 FKGEVLGITRFGIAKMKE-----SVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMG 290
Query: 1247 KVPSVGTG 1254
K +GTG
Sbjct: 291 KPMPIGTG 298
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 39.1 bits (91), Expect = 0.018
Identities = 32/126 (25%), Positives = 58/126 (46%), Gaps = 5/126 (3%)
Query: 1129 MDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSAT 1188
++ +D +R+ +NI GI+A + + + + G + HL++VA+ ++A
Sbjct: 722 IEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTAD 781
Query: 1189 GEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKV 1248
GE + G+A S +A F AA+ G VD L+G ++ + GK
Sbjct: 782 GEVKPIGRHGVA-----GEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKP 836
Query: 1249 PSVGTG 1254
+GTG
Sbjct: 837 IKLGTG 842
>gnl|CDD|114219 pfam05483, SCP-1, Synaptonemal complex protein 1 (SCP-1).
Synaptonemal complex protein 1 (SCP-1) is the major
component of the transverse filaments of the
synaptonemal complex. Synaptonemal complexes are
structures that are formed between homologous
chromosomes during meiotic prophase.
Length = 787
Score = 35.9 bits (82), Expect = 0.21
Identities = 58/230 (25%), Positives = 95/230 (41%), Gaps = 45/230 (19%)
Query: 159 EKLSKKNKKLPDDYWGF-IPFDAQQEE--NSVKPNRKVLSCKQVSYL------LKDVDPS 209
+KL +NK+L + + QE+ N K ++L KQ+ L L+D S
Sbjct: 495 DKLLLENKELTQEASDMTLELKKHQEDIINCKKQEERML--KQIENLEEKEMNLRDELES 552
Query: 210 IREEFILSKDAPFLKC-FPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDI 268
+REEFI D +KC + N R E ++ +N +LKK ++ + ++I
Sbjct: 553 VREEFIQKGDE--VKCKLDKSEENARSIEYEVLKKEKQMKILENKCNNLKKQIENKNKNI 610
Query: 269 ELSHLVQDCL----------------KISKLHLDKSSRKDSAEV---RQKKNIDISNSSG 309
E H L K++KL L+ +S K E +K I+ S
Sbjct: 611 EELHQENKALKKKGSAENKQLNAYEIKVNKLELELASAKQKFEEIIDNYQKEIEDKKISE 670
Query: 310 LRWIKDVVLGKRNDDCFRMVVTGDPNIKL-KEIGIPCQ--VAERLQISER 356
+ +++V K D +KL KEI CQ +AE + + E+
Sbjct: 671 EKLLEEVEKAK---------AIADEAVKLQKEIDKRCQHKIAEMVALMEK 711
>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 = 34.6 bits (80), Expect = 0.36
Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 10/85 (11%)
Query: 58 CSSCGAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIRKERQKGAGSSR 117
C +CG + C GHFG I+ + H F I +L +C C ++
Sbjct: 57 CETCG-VEVTECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSL---------LLN 106
Query: 118 KEQPRVCKYCVRNPAQWYPRMRFKL 142
+ V +P + R K
Sbjct: 107 ESVKYFFLKVVIDPKGKNSKKRLKK 131
>gnl|CDD|179901 PRK04964, PRK04964, hypothetical protein; Provisional.
Length = 66
Score = 29.7 bits (67), Expect = 1.6
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 460 GYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSV 510
GY+P A+G ++ +A D+ L +S R + + AA+LL+ D V
Sbjct: 21 GYVPDALGCVLKALNEIAADEAL--PESVRE-----KAAYAAANLLVSDYV 64
>gnl|CDD|130990 TIGR01935, NOT-MenG, RraA famliy. The E. coli member of this family
has been characterized as a regulator of RNase E and its
crystal structure has been analyzed. This model was
initially classified as a "hypothetical equivalog"
expressing the tentative hypothesis that all members
might have the same function as the E. coli enzyme.
Considering the second clade of enterobacterial sequences
within this family, that appears to be less tenable. The
function of these sequences outside of the narrow RraA
equivalog model (TIGR02998) remains obscure. All of these
were initially annotated as MenG, AKA
S-adenosylmethionine: 2-demethylmenaquinone
methyltransferase (EC 2.1.-.-). See the references
characterizing this as a case of transitive annotation
error in the case of the E. coli protein [Unknown
function, General].
Length = 150
Score = 31.1 bits (71), Expect = 1.8
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 1366 IRALYFHPRRNEKLGIEPPDIEVTYH 1391
++AL HPR+ EK G D+ VT+
Sbjct: 105 VKALAAHPRKTEKRGAGEVDVPVTFA 130
>gnl|CDD|222891 PHA02585, 16, small terminase protein; Provisional.
Length = 161
Score = 31.3 bits (71), Expect = 2.0
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 4/52 (7%)
Query: 631 SHSCSRKILMDEIFYGLREAQDTCNFQ-QLMVDSHMNFLMSAKDSESTRSLQ 681
SH +RK +++ Y L + +FQ Q+++D+ L +AK+SES R ++
Sbjct: 35 SHPANRKPDLEDD-YSL--VRRNMHFQQQMLMDAAKIALENAKNSESPRHVE 83
>gnl|CDD|198274 cd10411, SH2_SH2B2, Src homology 2 (SH2) domain found in SH2B adapter
proteins (SH2B1, SH2B2, SH2B3). SH2B2 (APS), like other
members of the SH2B adapter protein family, contains a
pleckstrin homology domain, at least one dimerization
domain, and a C-terminal SH2 domain which binds to
phosphorylated tyrosines in a variety of tyrosine
kinases. SH2B1 and SH2B2 function in signaling pathways
found downstream of growth hormone receptor and receptor
tyrosine kinases, including the insulin, insulin-like
growth factor-I (IGF-I), platelet-derived growth factor
(PDGF), nerve growth factor, hepatocyte growth factor,
and fibroblast growth factor receptors. SH2B2beta, a new
isoform of SH2B2, is an endogenous inhibitor of SH2B1
and/or SH2B2 (SH2B2alpha), negatively regulating insulin
signaling and/or JAK2-mediated cellular responses. In
general SH2 domains are involved in signal transduction.
They typically bind pTyr-containing ligands via two
surface pockets, a pTyr and hydrophobic binding pocket,
allowing proteins with SH2 domains to localize to
tyrosine phosphorylated sites.
Length = 97
Score = 29.6 bits (66), Expect = 3.1
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 8/39 (20%)
Query: 1103 YLRVSM--SGQCHITSLWSALMNDCHQIMDMIDWTRSHP 1139
+LR+S+ GQCH+ LW + DM+ +HP
Sbjct: 59 HLRLSLNGHGQCHVQHLWF------QSVFDMLRHFHTHP 91
>gnl|CDD|227387 COG5054, ERV1, Mitochondrial sulfhydryl oxidase involved in the
biogenesis of cytosolic Fe/S proteins [Posttranslational
modification, protein turnover, chaperones].
Length = 181
Score = 30.6 bits (69), Expect = 4.2
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 963 YSPQTGSMKHFSPWICHFH 981
Y PQ S + + W C H
Sbjct: 136 YPPQVSSREAATTWACEVH 154
>gnl|CDD|218870 pfam06045, Rhamnogal_lyase, Rhamnogalacturonate lyase family.
Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the
rhamnogalacturonan I (RG-I) backbone of pectin. This
family contains mainly members from plants, but also
contains the plant pathogen Erwinia chrysanthemi.
Length = 220
Score = 30.6 bits (69), Expect = 4.8
Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 6/99 (6%)
Query: 1177 HLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNL 1236
LL++ +S + + L + +H V + VQ SNPG I + +DNL
Sbjct: 7 LLLLLVPAVSLAVPGLNGGSVSLHVDDRHVVVDNGIVQVTLSNPG-GAITGIRYNGIDNL 65
Query: 1237 QGSVDALG----WGKVPSV-GTGGHFDIIYSGEGRTLSK 1270
+ D W V + G FD+I E +++
Sbjct: 66 LEARDKEKNRGYWDVVWNFPGVKSIFDVIVGTEFEVITQ 104
>gnl|CDD|236045 PRK07534, PRK07534, methionine synthase I; Validated.
Length = 336
Score = 30.5 bits (69), Expect = 6.0
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 1134 WTRSHPDNIRSFCLAYGIDAGLQFFLTN 1161
W HPDNI + + +DAG LTN
Sbjct: 39 WNEDHPDNITALHQGF-VDAGSDIILTN 65
>gnl|CDD|227201 COG4864, COG4864, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 328
Score = 30.6 bits (69), Expect = 6.2
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 1128 IMDMIDWTRSH------PDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNI 1173
I+ I + H PD+I L G+D+G F + +++ A D GKNI
Sbjct: 178 IVSTIGSSDEHTKVLENPDSISKTVLEKGLDSGTAFEILSIDIADVDIGKNI 229
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 30.6 bits (70), Expect = 6.9
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 17/99 (17%)
Query: 409 GDIVLINRPPSIH--------PHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHG 460
G VL+NR P++H P +L + ++PL C F+ DFDGD +
Sbjct: 447 GHPVLLNRAPTLHRLGIQAFQP---------ILVEGRAICLHPLVCKGFNADFDGDQMAV 497
Query: 461 YIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSL 499
++P ++ A+ E L+ L++ G + QD L
Sbjct: 498 HVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDML 536
>gnl|CDD|237900 PRK15071, PRK15071, lipopolysaccharide ABC transporter permease;
Provisional.
Length = 356
Score = 30.6 bits (70), Expect = 7.0
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 567 ISGGKLISAEGSSWLRDYEGNLFQYLIKRYRDK 599
ISGG L+S + W +D GN F Y I R D
Sbjct: 138 ISGGSLLSTQQGVWAKD--GNDFVY-IGRVEDD 167
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 30.8 bits (71), Expect = 7.4
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 443 PLCCSPFHGDFDGD 456
PL C+ F+ DFDGD
Sbjct: 441 PLVCTAFNADFDGD 454
>gnl|CDD|182376 PRK10319, PRK10319, N-acetylmuramoyl-l-alanine amidase I;
Provisional.
Length = 287
Score = 30.1 bits (68), Expect = 8.2
Identities = 33/89 (37%), Positives = 41/89 (46%), Gaps = 30/89 (33%)
Query: 729 KAGSKGNLLK-----LVQ-----HSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTE 778
KA K +LL+ LVQ +SL LG H L + + H+L NTE
Sbjct: 177 KATDKDHLLQQVLFDLVQTDTIKNSLTLG-SHILKKI--KPVHKLHS---------RNTE 224
Query: 779 CA-----KS-YIPSAVVENSFLTGLNPLE 801
A KS IPS +VE SF+T NP E
Sbjct: 225 QAAFVVLKSPSIPSVLVETSFIT--NPEE 251
>gnl|CDD|117355 pfam08785, Ku_PK_bind, Ku C terminal domain like. The
non-homologous end joining (NHEJ) pathway is one method
by which double stranded breaks in chromosomal DNA are
repaired. Ku is a component of a multi-protein complex
that is involved in the NHEJ. Ku has affinity for DNA
ends and recruits the DNA-dependent protein kinase
catalytic subunit (DNA-PKcs). This domain is found at
the C terminal of Ku which binds to DNA-PKcs.
Length = 120
Score = 28.9 bits (65), Expect = 8.8
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 250 FDNWTRHLKKMVDYRGRDIELSHLVQDCLKISKLHLDKSSRKDSA 294
F+ + +HLK+ V R + LVQ + + + K + S
Sbjct: 66 FNEFLKHLKEKVQERQLNDFWELLVQKKITL----ISKDEAEGSD 106
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 30.4 bits (69), Expect = 8.9
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 533 IFKISKDSVWSGKQLFSMLLPPDFEYTFPSKDVYISGGKLISAEGSSWLRDYEGNLFQYL 592
+++++KD G L ++ +P T + G+LI +GS+ LR EG++ +
Sbjct: 416 VYELAKDKWCVGAALRNLRMPKW---TRIA--AVFRDGQLIHPQGSTRLR--EGDVL-CV 467
Query: 593 IKRYRDK-VLDFLYAAQEV 610
I RD L L+++
Sbjct: 468 IGSERDLRALGKLFSSAPP 486
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 0.136 0.408
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: 72,610,697
Number of extensions: 7167834
Number of successful extensions: 5471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5420
Number of HSP's successfully gapped: 61
Length of query: 1443
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1334
Effective length of database: 6,103,016
Effective search space: 8141423344
Effective search space used: 8141423344
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 (21.8 bits)
S2: 65 (28.6 bits)