Query psy5332
Match_columns 287
No_of_seqs 222 out of 1023
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 23:55:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5332.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5332hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1522|consensus 100.0 4E-68 8.7E-73 459.5 18.3 222 1-224 44-270 (285)
2 cd07032 RNAP_I_II_AC40 AC40 su 100.0 1.9E-65 4.1E-70 466.7 16.6 229 1-274 39-290 (291)
3 KOG1521|consensus 100.0 6.3E-65 1.4E-69 450.4 11.7 244 1-276 84-337 (338)
4 cd07031 RNAP_II_RPB3 RPB3 subu 100.0 1.6E-58 3.5E-63 418.9 17.1 214 1-220 39-263 (265)
5 cd07028 RNAP_RPB3_like RPB3 su 100.0 1.5E-49 3.3E-54 348.9 15.4 167 1-217 39-211 (212)
6 PRK00783 DNA-directed RNA poly 100.0 6.3E-49 1.4E-53 357.1 17.7 201 1-221 39-261 (263)
7 cd07030 RNAP_D D subunit of Ar 100.0 6.6E-46 1.4E-50 336.6 17.6 198 1-218 39-258 (259)
8 smart00662 RPOLD RNA polymeras 100.0 2.4E-44 5.1E-49 319.6 15.7 191 1-215 28-224 (224)
9 PRK14979 DNA-directed RNA poly 100.0 2.3E-39 4.9E-44 279.7 15.2 148 1-221 41-188 (195)
10 PF01000 RNA_pol_A_bac: RNA po 100.0 6.3E-32 1.4E-36 215.5 9.1 110 6-133 1-112 (112)
11 PRK05182 DNA-directed RNA poly 99.9 5.4E-27 1.2E-31 217.1 13.1 202 1-261 51-273 (310)
12 COG0202 RpoA DNA-directed RNA 99.9 2.1E-26 4.5E-31 213.2 16.4 199 1-261 47-269 (317)
13 cd06928 RNAP_alpha_NTD N-termi 99.9 4.8E-25 1E-29 194.6 13.8 151 1-214 41-214 (215)
14 TIGR02027 rpoA DNA-directed RN 99.9 5.5E-24 1.2E-28 196.1 13.6 197 1-261 32-259 (297)
15 CHL00013 rpoA RNA polymerase a 99.7 5E-17 1.1E-21 151.3 16.4 192 1-261 52-287 (327)
16 cd07031 RNAP_II_RPB3 RPB3 subu 98.9 1.8E-09 3.8E-14 98.5 5.5 50 229-278 215-264 (265)
17 KOG1522|consensus 98.9 3.5E-09 7.6E-14 93.1 6.3 58 229-286 218-275 (285)
18 cd00460 RNAP_RPB11_RPB3 RPB11 98.4 4.8E-07 1E-11 68.7 6.1 53 133-214 33-85 (86)
19 cd07032 RNAP_I_II_AC40 AC40 su 98.4 4.7E-07 1E-11 83.4 5.3 44 174-217 247-290 (291)
20 PRK00783 DNA-directed RNA poly 98.3 9E-07 2E-11 80.6 5.5 50 230-279 213-262 (263)
21 cd07030 RNAP_D D subunit of Ar 98.1 2.4E-06 5.2E-11 77.7 4.8 47 230-276 213-259 (259)
22 KOG1521|consensus 97.9 1.2E-05 2.7E-10 72.8 4.5 45 174-218 292-336 (338)
23 cd00460 RNAP_RPB11_RPB3 RPB11 97.8 3.3E-05 7.1E-10 58.6 5.1 36 237-272 51-86 (86)
24 cd07028 RNAP_RPB3_like RPB3 su 97.8 3E-05 6.6E-10 68.5 5.2 38 237-274 174-211 (212)
25 PF01193 RNA_pol_L: RNA polyme 97.8 2.2E-05 4.8E-10 56.5 3.5 33 181-213 34-66 (66)
26 PF01193 RNA_pol_L: RNA polyme 97.7 5.7E-05 1.2E-09 54.3 4.0 34 237-270 33-66 (66)
27 PRK14979 DNA-directed RNA poly 97.6 0.00014 3E-09 63.4 6.2 45 238-282 148-193 (195)
28 COG0202 RpoA DNA-directed RNA 97.5 0.00035 7.6E-09 65.3 8.1 135 55-277 91-225 (317)
29 smart00662 RPOLD RNA polymeras 97.5 0.00012 2.6E-09 65.3 4.6 35 238-272 190-224 (224)
30 TIGR02027 rpoA DNA-directed RN 96.2 0.0089 1.9E-07 55.6 5.5 38 237-274 171-208 (297)
31 PRK05182 DNA-directed RNA poly 93.5 0.11 2.5E-06 48.5 4.9 36 239-274 190-225 (310)
32 PF13656 RNA_pol_L_2: RNA poly 93.0 0.3 6.5E-06 36.1 5.5 37 182-218 40-76 (77)
33 PF13656 RNA_pol_L_2: RNA poly 91.0 0.88 1.9E-05 33.6 6.1 40 237-276 38-77 (77)
34 cd07029 RNAP_I_III_AC19 AC19 s 90.1 0.7 1.5E-05 34.9 4.9 36 182-217 48-83 (85)
35 cd06927 RNAP_L L subunit of Ar 89.8 0.69 1.5E-05 34.8 4.7 35 182-216 48-82 (83)
36 PRK01146 DNA-directed RNA poly 89.8 0.67 1.5E-05 35.0 4.6 35 182-216 50-84 (85)
37 cd06928 RNAP_alpha_NTD N-termi 89.3 0.48 1E-05 42.0 4.1 34 237-270 180-213 (215)
38 cd06926 RNAP_II_RPB11 RPB11 su 88.6 1.1 2.4E-05 34.4 5.1 36 182-217 56-91 (93)
39 cd07027 RNAP_RPB11_like RPB11 88.2 0.94 2E-05 34.0 4.4 35 182-216 48-82 (83)
40 cd06926 RNAP_II_RPB11 RPB11 su 83.1 3 6.6E-05 31.9 5.1 38 238-275 55-92 (93)
41 COG1761 RPB11 DNA-directed RNA 81.5 6.2 0.00014 30.7 6.3 38 182-219 54-91 (99)
42 cd07029 RNAP_I_III_AC19 AC19 s 81.4 3.6 7.8E-05 31.0 4.8 39 237-275 46-84 (85)
43 PRK01146 DNA-directed RNA poly 80.0 3.7 8.1E-05 30.9 4.5 36 238-273 49-84 (85)
44 cd06927 RNAP_L L subunit of Ar 80.0 3.9 8.4E-05 30.7 4.6 37 237-273 46-82 (83)
45 KOG3438|consensus 77.5 6.2 0.00013 30.7 5.0 44 237-280 53-96 (105)
46 cd07027 RNAP_RPB11_like RPB11 74.9 6.9 0.00015 29.3 4.7 36 238-273 47-82 (83)
47 COG1761 RPB11 DNA-directed RNA 69.0 15 0.00033 28.5 5.5 40 237-276 52-91 (99)
48 CHL00013 rpoA RNA polymerase a 66.3 11 0.00023 35.7 4.9 35 239-273 188-222 (327)
49 KOG3307|consensus 62.8 3 6.6E-05 33.6 0.5 12 20-31 83-94 (150)
50 KOG3438|consensus 61.9 14 0.00031 28.8 4.0 42 181-222 54-95 (105)
51 KOG4392|consensus 48.3 49 0.0011 26.3 5.1 42 181-222 67-108 (117)
52 KOG4392|consensus 37.6 1.1E+02 0.0025 24.3 5.7 43 237-279 66-108 (117)
53 PRK15329 chaperone protein Sic 33.2 18 0.0004 29.7 0.7 13 20-33 11-23 (138)
54 PF04775 Bile_Hydr_Trans: Acyl 26.7 95 0.0021 24.9 3.8 38 103-145 6-43 (126)
55 PF10633 NPCBM_assoc: NPCBM-as 24.5 2.6E+02 0.0057 19.8 6.3 28 106-133 43-70 (78)
56 PF04225 OapA: Opacity-associa 20.9 28 0.0006 26.1 -0.4 18 103-120 37-54 (85)
57 PHA02148 hypothetical protein 20.8 1.2E+02 0.0025 23.3 2.9 35 251-285 25-69 (110)
No 1
>KOG1522|consensus
Probab=100.00 E-value=4e-68 Score=459.53 Aligned_cols=222 Identities=61% Similarity=1.030 Sum_probs=202.5
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD 80 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d 80 (287)
+|||+|+|.-|||||+|||||||||||||.|+..+ .|+|.+||.|+++|++|||+|+|+++|++++.+.|||+||++.+
T Consensus 44 iAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~-~l~ytrdC~C~~~C~eCSVef~L~~kc~~d~T~~VtsrDL~s~~ 122 (285)
T KOG1522|consen 44 IAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIV-ELQYTRDCECDEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLD 122 (285)
T ss_pred eEEEEEEEecccccccHHHHHhhhcceeccchhhh-hhhhcccCchhccCCcceEEEEEeeeecccceeeeehHhhhccC
Confidence 69999999999999999999999999999999854 59999999999999999999999999999999999999999999
Q ss_pred CeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCCCCC---
Q psy5332 81 ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPD--- 157 (287)
Q Consensus 81 ~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~~~~--- 157 (287)
+.|.|+.+. .........-+++|+|+|||+||+|+|+|+|+||+||+||||||+++++|.|+|.+.++|+.+|..+
T Consensus 123 ~~v~pv~~~-~~~~~~~~~e~~gilI~KLRkgQELkLra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e~~~~ 201 (285)
T KOG1522|consen 123 PTVTPVDSN-RGSEIDDDSESKGILIVKLRKGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDL 201 (285)
T ss_pred CcccccccC-CCCccccccccCCcEEEEeecCCceeeeeeecccccccccccCCcceEEEEECccHhhhccCCCccccch
Confidence 999999972 2333334455789999999999999999999999999999999999999999999999999999766
Q ss_pred -CCCCCccCccccc-ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q psy5332 158 -EWPKSEYSELDET-QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRV 224 (287)
Q Consensus 158 -~~~~~~~~~~~~~-~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~~ 224 (287)
+||++-..++++. ....+|+....+|+|+|+|||+|+++|..+|.+|+++|++|++.+...++.+.+
T Consensus 202 ~Ewp~sk~~e~~~~~~e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~~l~~~~q 270 (285)
T KOG1522|consen 202 IEWPKSKNSELEEDPEEGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRLALSTEDQ 270 (285)
T ss_pred hhCCcccccCCCCCccccCCCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHhhhcccch
Confidence 9999988777665 456788888899999999999999999999999999999999999988876544
No 2
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=100.00 E-value=1.9e-65 Score=466.66 Aligned_cols=229 Identities=29% Similarity=0.436 Sum_probs=182.8
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCC------------
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQT------------ 68 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~------------ 68 (287)
||||+|+|++|||||+|||||||||||||.+++ +.|.|+++| |+++|++|+|+|+|+|+|++++.
T Consensus 39 ~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~d~--~~~~~~~~~-~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~ 115 (291)
T cd07032 39 MAIEKVYIYNNTSVIQDEVLAHRLGLIPIKADP--RLFEYREDS-DDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELY 115 (291)
T ss_pred eeEEEEEEEECCccchhHHHHHhhcCceeecCH--HHccccccc-ccCCCCCcEEEEEEEEEccCCcccccccccccccc
Confidence 899999999999999999999999999999996 789999999 78899999999999999987652
Q ss_pred --ceeEeCCceeCCCeeeeccCCCcccCC-CCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCC
Q psy5332 69 --RHVTTADLKSTDARVVPVTSRNRDADM-NEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPD 145 (287)
Q Consensus 69 --~~V~s~Dl~s~d~~v~P~~~~~~~~~~-~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~ 145 (287)
..|||+||+ |.|.+.|...+.. +..++++||+|+||+|||+|+|+|+|+||+||+|||||||++|+|||+|.
T Consensus 116 ~~~~VyS~dl~-----~~p~g~q~~~~~~~~v~~v~~dI~I~kL~~gQ~l~le~~a~kG~Gk~HAKwsPv~ta~yr~~P~ 190 (291)
T cd07032 116 INHKVYSGDLK-----WVPIGSQEKRFADNPIRPVHPDILIAKLRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPE 190 (291)
T ss_pred cccEEECCCCE-----ecCCCccccccCCCCcEEeCCCcEEEEECCCCEEEEEEEEEcCcccccceecCceeEEEEecce
Confidence 456666665 9999987654433 34467999999999999999999999999999999999999999999999
Q ss_pred CCcccccCCC-----CCCCCCCccCcccccccCCCCCcccCCCcEEEEeec---CCccCHHHHHHHHHHHHHHHHHHHHH
Q psy5332 146 NSMRHTLFPK-----PDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVES---AGALKPENIVIMGVTVLKQKLSNLQT 217 (287)
Q Consensus 146 i~i~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs---~G~l~p~~iv~~A~~iLk~Kl~~l~~ 217 (287)
|++++.+.+. .+.||..+| .++. .|.+...+. +++
T Consensus 191 I~i~~~~~~~~~~~~~~~cP~~Vf-----------------------~i~~~~~~~~~~V~~~--~~c------------ 233 (291)
T cd07032 191 ITLLKPITGEDAEKLQKCFPPGVI-----------------------DIEEVKGKKKAVVANP--RKD------------ 233 (291)
T ss_pred EEEcCcCCHHHHHHHHhhCCCccE-----------------------EecccCCCceEEEccc--ccC------------
Confidence 9998775421 234555544 2221 111111111 122
Q ss_pred hhhcccccccccCCCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHH
Q psy5332 218 QLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 274 (287)
Q Consensus 218 ~l~~e~~~e~~~~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~ 274 (287)
.++++|.+.++..+.|.+.+.+|||+|+|||+|+|+|++|+.+|+++|++|++.|++
T Consensus 234 t~crec~~~~~~~~~V~v~~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~ 290 (291)
T cd07032 234 TLSREVLRHEEFKDKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291)
T ss_pred cccHhHhhhhccCCceeEEEeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 223333332334456888999999999999999999999999999999999999875
No 3
>KOG1521|consensus
Probab=100.00 E-value=6.3e-65 Score=450.41 Aligned_cols=244 Identities=30% Similarity=0.396 Sum_probs=197.7
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCC-----
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTAD----- 75 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~D----- 75 (287)
||||+|+|++||||++|||||||||||||.+|| +.|.|..+-++++.-. +|++|+|+|+|+++....+.+.|
T Consensus 84 mAiEkVyi~nNTSViqDEvLaHRlGLvPl~aDP--rlFe~~~e~d~~~e~~-ntlvF~L~VkC~~n~~a~~~~sdpk~Ly 160 (338)
T KOG1521|consen 84 MAIEKVYIYNNTSVIQDEVLAHRLGLVPLRADP--RLFEYRSENDEDDEKE-NTLVFKLNVKCTKNPNAKKDSSDPKELY 160 (338)
T ss_pred hheeeeEEecCccccHHHHHHHhhcCcccccCc--chhhccccCCCccCcc-ceEEEEEEeeccCCCCcccCCCChhHhc
Confidence 899999999999999999999999999999999 6788887754443222 89999999999998655555556
Q ss_pred ----ceeCCCeeeeccCCCcccCCCC-CCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCccc
Q psy5332 76 ----LKSTDARVVPVTSRNRDADMNE-YGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRH 150 (287)
Q Consensus 76 ----l~s~d~~v~P~~~~~~~~~~~~-~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~ 150 (287)
++|.|..|.|.++|...|.+++ .++++||+|+||+|||+|+++|||.|||||+|||||||+||+||++|.|.|+.
T Consensus 161 ~ns~vyS~~~~w~P~g~Q~~~f~e~~i~~~~~DILiAkLrPGQEI~le~havkGIGkdHAKfSPVaTAsYRLlP~I~l~~ 240 (338)
T KOG1521|consen 161 NNSEVYSRDLTWKPKGYQAEIFAENPIRPVHDDILIAKLRPGQEIELEAHAVKGIGKDHAKFSPVATASYRLLPTIVLLA 240 (338)
T ss_pred cCcEEecCcceeccccchhhhcccCCccccCcceEEEecCCCCEeeeeeeeecccCcccccccCcccceeeccceeEecC
Confidence 6778888999999988776654 46699999999999999999999999999999999999999999999999998
Q ss_pred ccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcccccccccC
Q psy5332 151 TLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDRVFYVINE 230 (287)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e~~~e~~~~ 230 (287)
++.++.++-..+||++ -+|.||..|. .-...|..+ -.+.+++++.+.++..
T Consensus 241 ei~ge~A~~lqkcfs~------------------gVi~iee~~~-kk~A~Vad~----------R~dT~sRe~~R~ee~~ 291 (338)
T KOG1521|consen 241 EIEGEDAERLQKCFSP------------------GVIDIEEMGG-KKRAYVADP----------RKDTCSREVLRHEELK 291 (338)
T ss_pred cccchhHHHHHhhCCC------------------CeEeeecCCC-ceEEEecCc----------ccchhhHHHhccHHhh
Confidence 8877655544555532 1345555554 111111111 1234455666666677
Q ss_pred CCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHH
Q psy5332 231 APYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 276 (287)
Q Consensus 231 ~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l 276 (287)
+.|.+.+..|||+|+|||+|+|+|+.++.+|+++|+.||+.++..+
T Consensus 292 d~V~LgrvrdHfIFsvestgal~p~~lf~eavkvle~Kc~al~~~~ 337 (338)
T KOG1521|consen 292 DKVQLGRVRDHFIFSVESTGALKPEVLFEEAVKVLEEKCRALRDEI 337 (338)
T ss_pred hheeeccccceEEEEeecccCCCchhhHHHHHHHHHHHHHHHhhcc
Confidence 7899999999999999999999999999999999999999998765
No 4
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=100.00 E-value=1.6e-58 Score=418.95 Aligned_cols=214 Identities=60% Similarity=1.023 Sum_probs=175.3
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceec-cCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYS-RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKST 79 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~-~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~ 79 (287)
||||.|+|++|||||+||||||||||||+.+++ +..|.+. ++|.|++.|+.|+++|+|+|+|++++++.|||+||.+.
T Consensus 39 ~AI~~V~I~~NtSvl~DE~iaHRlglIPl~~e~-~~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~~ 117 (265)
T cd07031 39 LAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDD-VDEFLYYSRDCDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSS 117 (265)
T ss_pred ceEEEEEEecCCcccccceeeeecccCCCccCc-HHHHhhhhhhccccCCCCCCeEEEEEEEEeccCCCceEEHHHcccc
Confidence 799999999999999999999999999999986 3455555 78999889999999999999999999999999999975
Q ss_pred -----CCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCC
Q psy5332 80 -----DARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFP 154 (287)
Q Consensus 80 -----d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~ 154 (287)
++.+.|+.... ....+++||+|+||+|||+|+|+|+|+||+||+|||||||++++|||+|.|+|++..++
T Consensus 118 ~~~~~~~~~~pi~~~~-----~~~~~~~~i~I~kL~~gq~i~le~~a~kG~Gk~HAKwsPv~~~~y~~~p~i~i~~~~~~ 192 (265)
T cd07031 118 GPKVNDVVPVPIRNDS-----EDNGEEDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYW 192 (265)
T ss_pred cccccccCCccccccc-----ccccCCCCeEEEEECCCCEEEEEEEEECCEeccCCEeccceEEEEEEccceEEcccccc
Confidence 22233333210 00145799999999999999999999999999999999999999999999999988765
Q ss_pred CCC----CCCCCccCccccc-ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5332 155 KPD----EWPKSEYSELDET-QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLA 220 (287)
Q Consensus 155 ~~~----~~~~~~~~~~~~~-~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~ 220 (287)
..+ .+...|..-+... .....+.+++++|+|+|+|||+|+++|+++|.+|+++|++|++.|.+.|+
T Consensus 193 ~~~~~~~~~c~~c~~c~~~~~~~~~~v~i~~~~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~ 263 (265)
T cd07031 193 YLEDEDKEWPKSENACIEEPPEKDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLS 263 (265)
T ss_pred chhhcccccCchhHHHhhcccccCCceEEEeeCCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 422 2222222111111 12345777889999999999999999999999999999999999998765
No 5
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=100.00 E-value=1.5e-49 Score=348.87 Aligned_cols=167 Identities=42% Similarity=0.706 Sum_probs=147.7
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCC-CCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDC-TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKST 79 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c-~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~ 79 (287)
||||.|+|++|||+|+||||||||||||+.+++.++.+...++| .|...|..|++.|+|+++++++.+..|||+||.+.
T Consensus 39 ~AI~~V~I~~NtS~~~DE~iaHrlglIP~~~e~~~~~~~n~k~~~~~~~~~~~~~v~~~l~~~g~~~~~~~V~s~DL~~~ 118 (212)
T cd07028 39 MAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLYRSPEEDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIV 118 (212)
T ss_pred eEEEEEEEEcCCCcccceeeeeeeeecccccCcHHHhhhcccccccccccccceeEEEEEEccCCCCCcceEEHHHcccC
Confidence 69999999999999999999999999999998754444433444 57788999999999999977655678999999976
Q ss_pred C-----CeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCC
Q psy5332 80 D-----ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFP 154 (287)
Q Consensus 80 d-----~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~ 154 (287)
+ +.+.| +++||+|+||++||+|+|+|+|++|+||+|||||||++++|+++|.
T Consensus 119 ~~~~~~~~v~p--------------v~~di~I~kL~~gq~i~le~~~~~G~G~~hAk~sPV~~v~y~~~~~--------- 175 (212)
T cd07028 119 SNLMGRNIGHP--------------IIQDILICKLRKGQEIKLTCVAKKGIGKEHAKFGPVAAIEFRYDPV--------- 175 (212)
T ss_pred CccccCCCeEE--------------eCCCcEEEEECCCCEEEEEEEEECCCcCCCCEeCCceEEEEEEEcc---------
Confidence 5 34454 4599999999999999999999999999999999999999999871
Q ss_pred CCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHH
Q psy5332 155 KPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 217 (287)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~ 217 (287)
+|+|+|+|||+|+++|++++.+|+++|++|++.|.+
T Consensus 176 ---------------------------~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~ 211 (212)
T cd07028 176 ---------------------------ADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL 211 (212)
T ss_pred ---------------------------CCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence 589999999999999999999999999999998874
No 6
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=6.3e-49 Score=357.09 Aligned_cols=201 Identities=37% Similarity=0.611 Sum_probs=168.8
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCC-CCCCCceEEEEEEEEeeCCCCceeEeCCceeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCV-DFCSECSVEFTLDVKCVDDQTRHVTTADLKST 79 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~-~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~ 79 (287)
|||+.|+|++|||+|+||||||||||||+.++. +.|+|..+|+|+ +.|++|+++|+|+++ +|..|||+||.+.
T Consensus 39 ~Ai~~v~i~~n~s~~~de~i~hrl~lip~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~----~~~~V~a~dl~~~ 112 (263)
T PRK00783 39 MAIDDVRFYENTSVLFDEILAHRLGLIPLTTDL--DKYKPPEECTCEGEGCPDCTVTLSLEVE----GPKTVYSGDLKSS 112 (263)
T ss_pred eeEEEEEEEECCcchhHHHHHHhhcCcccccCH--HHCCCcccccccCCCCCCcEEEEEEEec----CCCcEEccccccC
Confidence 799999999999999999999999999999984 789999999865 689999999999997 7889999999874
Q ss_pred CCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCC---CC
Q psy5332 80 DARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFP---KP 156 (287)
Q Consensus 80 d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~---~~ 156 (287)
+..+.| ++||++|+||++||+|+|+|+++||+||+||||+|+++++|++.|.+.+.+.+.. +.
T Consensus 113 ~~~v~~--------------v~~~~~I~~L~~~~~l~~e~~~~~G~G~~HAKw~p~~~~~yr~~p~I~i~~~C~~C~~C~ 178 (263)
T PRK00783 113 DPDVKP--------------VDPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPGSACGYKYYPRIEVSEDCDECEKCV 178 (263)
T ss_pred CCCcee--------------cCCCcEEEEeCCCCEEEEEEEEEcCcccccCccCcceEeeecccccccccccCCchHHHH
Confidence 444554 4599999999999999999999999999999999999999999999988433322 23
Q ss_pred CCCCCCccCccc------c-c-----------ccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHh
Q psy5332 157 DEWPKSEYSELD------E-T-----------QHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQ 218 (287)
Q Consensus 157 ~~~~~~~~~~~~------~-~-----------~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~ 218 (287)
..||..++..-. . . .....+.....+++|+|++||+|+++|++++.+|+++|++|++.|.+.
T Consensus 179 ~~CP~~vi~~~~~~~~v~~~~~C~~C~~Ci~~CP~~AI~i~~~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~ 258 (263)
T PRK00783 179 EACPRGVLELKEGKLVVTDLLNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGSLPVEEILLEALKILKRKADELIEA 258 (263)
T ss_pred HhCCccccEecCCeEEEeChhhCCCchHHHHhCCCCceEEEEcCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 456665543110 0 0 012235567789999999999999999999999999999999999988
Q ss_pred hhc
Q psy5332 219 LAH 221 (287)
Q Consensus 219 l~~ 221 (287)
++.
T Consensus 259 ~~~ 261 (263)
T PRK00783 259 LEE 261 (263)
T ss_pred Hhh
Confidence 753
No 7
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=100.00 E-value=6.6e-46 Score=336.56 Aligned_cols=198 Identities=37% Similarity=0.599 Sum_probs=164.2
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCC-CCCCCCceEEEEEEEEeeCCCCceeEeCCceeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKST 79 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~-~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~ 79 (287)
|||+.|+|++|||+|+||||||||||||+.+++.++. +.++|.| ...|+.|++.|+|+++ +++.|||+||.+.
T Consensus 39 ~Ai~~V~i~~n~s~~~de~i~hrl~~ip~~~e~~~~~--~~~~~~~~~~~~~~~~~~~~l~~~----~~~~v~s~dl~~~ 112 (259)
T cd07030 39 LAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYK--YRSECSCGGAGCPLCTVTLTLSVE----GPGTVYSGDLKSS 112 (259)
T ss_pred eeEEEEEEEeCCchhhHHHHHHhhcCcccccCHHHhc--ccccccccCCCCCCcEEEEEEEcc----CCceEEccccccC
Confidence 6999999999999999999999999999999974332 3347765 4678999999999997 6789999999975
Q ss_pred CCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCC---CC
Q psy5332 80 DARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFP---KP 156 (287)
Q Consensus 80 d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~---~~ 156 (287)
+..+.| ++++|+|+||++||+|+|+++|+||+||+||||+|+++++||++|.+.+.+.+.. +.
T Consensus 113 ~~~v~~--------------~~~~~~I~~l~~~~~l~~~~~~~kg~g~~hakw~p~~~~~yr~~P~i~i~~~C~~C~~C~ 178 (259)
T cd07030 113 DPDVKP--------------VYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYKYYPVIEIDEDCDGCGKCV 178 (259)
T ss_pred CCCccc--------------cCCCcEEEEeCCCCEEEEEEEEecCccCCCCCCCCccEEEEEeecceechhhCCChHHHH
Confidence 554554 4599999999999999999999999999999999999999999999988766543 24
Q ss_pred CCCCCCccCcccc-------c----------cc-CCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHh
Q psy5332 157 DEWPKSEYSELDE-------T----------QH-EAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQ 218 (287)
Q Consensus 157 ~~~~~~~~~~~~~-------~----------~~-~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~ 218 (287)
+.||...+..-.. . .+ ...+....++++|+|+|||+|+++|++++.+|+++|++|++.|.+.
T Consensus 179 ~~CP~~vi~~d~~~~~v~~~~~C~~C~~C~~~Cp~~AI~~~~~~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~ 258 (259)
T cd07030 179 EECPRGVLELEEGKVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA 258 (259)
T ss_pred HhCCccceEccCCeeEEeChhhCcCchHHHHhCCCCcEEEEecCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 5677666531100 0 01 1235566789999999999999999999999999999999998764
No 8
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=100.00 E-value=2.4e-44 Score=319.63 Aligned_cols=191 Identities=42% Similarity=0.634 Sum_probs=155.6
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeC-
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKST- 79 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~- 79 (287)
+||+.|.|++|+|+++||||||||||+||.++. +.+.|.++|.|+..|+.|++.++|+++ +|+.|||+||.+.
T Consensus 28 ~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~~--~~~~~~~~~~~~~~~~~~~~~~~L~~~----gp~~V~a~Dl~~~~ 101 (224)
T smart00662 28 MAVTEVEIEGNTSGVQDEVLAHRLGLKPLASDP--DGDEYQRDCECEEGCEKCSVTLTLDVK----GPGEVTAGDLKSDS 101 (224)
T ss_pred ceEEEEEEecCCcchhHHHHHHHhCCeeEEEec--hhccccccccccccCCCceEEEEEEEE----cCCcEEHHHcccCC
Confidence 699999999999999999999999999999985 567788899999999999999999998 6678999999976
Q ss_pred CCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCCC----
Q psy5332 80 DARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPK---- 155 (287)
Q Consensus 80 d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~~---- 155 (287)
|+.+.|+ +|+++|+||++||+|+|+++|++|+||+||||+|+++++|++.|.|.++....+.
T Consensus 102 ~~~v~~v--------------np~~~I~~L~~gq~l~~e~~~~~G~G~~hak~~p~~~~~~~~~~~i~id~~~~pv~~v~ 167 (224)
T smart00662 102 DPDVEIV--------------NPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRVA 167 (224)
T ss_pred CCCcEEe--------------CCCcEEEEECCCCEEEEEEEEECCcccccCccccccCCCcCcCCEEEECCCCChhhhee
Confidence 5556654 4999999999999999999999999999999999999999999988776543221
Q ss_pred -CCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHH
Q psy5332 156 -PDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL 215 (287)
Q Consensus 156 -~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l 215 (287)
..+++..++..- .+. .......+|+|+|+|||+|+++|++++.+|+++|++|++.|
T Consensus 168 ~~~~~~~~~~~~~---~~~-~c~~~~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~~ 224 (224)
T smart00662 168 YQVECPRVVQRTD---CCR-ECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 224 (224)
T ss_pred eeccCCccceecc---cch-hhhccCCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhhC
Confidence 111222111100 000 00001237999999999999999999999999999998653
No 9
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=2.3e-39 Score=279.68 Aligned_cols=148 Identities=34% Similarity=0.492 Sum_probs=130.3
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD 80 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d 80 (287)
+||+.|.|++|||+|+|||+|||+|||||++.+ +. . .+++.|+|+++ +|+.|||+||.+.+
T Consensus 41 ~AI~~V~I~~Nts~~~DEivaHe~~lIpLK~~~-~~---~-----------~~~~~l~L~~~----gp~~Vta~Di~~~~ 101 (195)
T PRK14979 41 YAIENVYFYENSSSMYDEILAHRLGLIPIKGKP-VS---G-----------DEVITFTLSKE----GPCTVYSSDLKSEN 101 (195)
T ss_pred eeEEEEEEecCcccccchheeeeeeeeeeeeee-cc---C-----------CCcEEEEEEEe----CCceEEHHHcCCCC
Confidence 699999999999999999999999999999875 21 0 24789999986 78899999998755
Q ss_pred CeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCCCCcccccCCCCCCCC
Q psy5332 81 ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWP 160 (287)
Q Consensus 81 ~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~i~i~~~~~~~~~~~~ 160 (287)
. . +++||++|++|++||+|+|+|+|++|+||+||||+|+ .+.|++.+
T Consensus 102 ~--~--------------ivnpdi~I~tL~~g~~l~~e~~~~~G~Gy~hAk~~pv-da~y~~~~---------------- 148 (195)
T PRK14979 102 G--E--------------VAFKNIPIVKLAEGQKLEIECEALVGTGKIHAKWQPC-NAVYKQIS---------------- 148 (195)
T ss_pred C--c--------------ccCCCcEEEEECCCCEEEEEEEEECCCccccccccce-eeEEecCC----------------
Confidence 4 2 4569999999999999999999999999999999995 56675432
Q ss_pred CCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy5332 161 KSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221 (287)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~ 221 (287)
+|+++|+|||+|+++|++++.+|+++|+++++.|.+.++.
T Consensus 149 ---------------------~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~~ 188 (195)
T PRK14979 149 ---------------------NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEG 188 (195)
T ss_pred ---------------------CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5899999999999999999999999999999999988764
No 10
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....
Probab=99.97 E-value=6.3e-32 Score=215.50 Aligned_cols=110 Identities=40% Similarity=0.655 Sum_probs=97.0
Q ss_pred EEEeeCCCcchhhHhhhhcCccccccccccccceeccCC--CCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCCCee
Q psy5332 6 VQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDC--TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARV 83 (287)
Q Consensus 6 V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c--~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d~~v 83 (287)
|+|++|||+|+||++|||+|+||+.+++.++-+.+.++| .+...|+.|++++.|+++ +|+.|||+||.+.+..+
T Consensus 1 v~i~~n~s~~~dE~v~He~~~Ipgv~Edv~~iilnlk~i~~~~~~~~~~~~~~~~L~~~----g~~~V~a~di~~~~~~i 76 (112)
T PF01000_consen 1 VYIYENTSVLPDEGVAHEFGLIPGVSEDVLEIILNLKKIVIDCEEGCDDCSVTFSLKVK----GPGEVTAGDIKLEPSGI 76 (112)
T ss_dssp EEEEEETSSS-HHHHHCHHHBSTCBSSCHHHHHHHHHTT-ESSSSSTTTSEEEEEEEEE----SSSCEEGGGSEESBTTE
T ss_pred CEEEECCCeeccceeEeccccCCccccchhhhhhcchhhccccccCCCCceEEEEEEec----CCCccccceeEecCCce
Confidence 799999999999999999999999998755556677888 567899999999999998 66779999999865556
Q ss_pred eeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceec
Q psy5332 84 VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 133 (287)
Q Consensus 84 ~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKws 133 (287)
+|+ +|+++|++|++||+|+|++++++|+||+|||||
T Consensus 77 ~iv--------------n~d~~I~tl~~~~~l~~e~~i~~G~Gy~~ak~~ 112 (112)
T PF01000_consen 77 EIV--------------NPDIYIATLSEGQKLEMELYIEKGRGYVHAKWS 112 (112)
T ss_dssp EES--------------STTSEEEEEESSTEEEEEEEEEEEESEECCTS-
T ss_pred EEe--------------cCCeEEEEECCCCEEEEEEEEECCCcccccccC
Confidence 654 499999999999999999999999999999997
No 11
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=99.94 E-value=5.4e-27 Score=217.06 Aligned_cols=202 Identities=21% Similarity=0.269 Sum_probs=149.7
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeCCceeCC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD 80 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~Dl~s~d 80 (287)
+||+.|.| |.++||+++||.......+-+...+++.+...|. |++.++|+++ ||+.|||+||.+..
T Consensus 51 ~aI~~VkI---------~gv~hEf~~Ipgv~Edv~eIllNlk~i~~~~~~~-~~~~~~l~~~----gp~~VtA~Di~~~~ 116 (310)
T PRK05182 51 AAVTSVKI---------DGVLHEFSTIPGVREDVTEIILNLKGLRLKLHGD-EPVTLTLSKK----GPGEVTAGDIETDG 116 (310)
T ss_pred eEEEEEEE---------cceeeeccccCCcccchhHhhhhhccceeecCCC-ceEEEEEEec----CCeEEEHHHcCCCC
Confidence 59999999 4589999999998864322222223333333333 7899999996 88899999998632
Q ss_pred CeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccce----------------ecccceeeeeecC
Q psy5332 81 ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAK----------------WNPTAGVCFEYDP 144 (287)
Q Consensus 81 ~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAK----------------wsPV~~~~y~~~P 144 (287)
.+.| ++|+++|++|++||.|+|+++|++|+|+.+|+ |+||..+.|...+
T Consensus 117 -~v~i--------------vn~d~~IatL~~~~~l~ie~~~~kG~Gy~~~~~~~~~~~~g~i~iDa~f~PV~~vny~ve~ 181 (310)
T PRK05182 117 -DVEI--------------VNPDLVIATLNEGAKLEMELTVERGRGYVPAEENKEDAPIGRIPVDAIFSPVKKVNYTVEN 181 (310)
T ss_pred -CcEE--------------eCCCeEEEEECCCCEEEEEEEEECcCCCcccccccccCCcccEEecCCcCCccceEEEecc
Confidence 2443 45999999999999999999999999997765 7888777777654
Q ss_pred CCCcccccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcc--
Q psy5332 145 DNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD-- 222 (287)
Q Consensus 145 ~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e-- 222 (287)
. +++...++++++|+|||+|+++|.+++.+|+++|+.++..|.+. ...
T Consensus 182 ~-----------------------------~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~~-~~~~~ 231 (310)
T PRK05182 182 T-----------------------------RVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDL-EEAEE 231 (310)
T ss_pred c-----------------------------ccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhCc-ccccc
Confidence 2 12334457899999999999999999999999999999998752 211
Q ss_pred cccccc-cCCC--CCcccCCCeEEEEEeecCCCChhhHHHHH
Q psy5332 223 RVFYVI-NEAP--YNWEAKPNKYFFNVESAGALKPENIVIMG 261 (287)
Q Consensus 223 ~~~e~~-~~~~--i~~~~~~d~f~f~veS~g~l~~~~i~~~a 261 (287)
...... .... -......+.+.|||+|.+||+..+|...+
T Consensus 232 ~~~~~~~~~~~~~~~l~~~I~~L~LS~R~~n~Lk~~~I~ti~ 273 (310)
T PRK05182 232 AEEEVEEEEPEFDPILLRPIEELELSVRSYNCLKRAGINTIG 273 (310)
T ss_pred cccccccccccccccccccHHHhccchHHHHHHHHcCCcCHH
Confidence 000000 0001 11335678899999999999999988776
No 12
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=99.94 E-value=2.1e-26 Score=213.20 Aligned_cols=199 Identities=21% Similarity=0.233 Sum_probs=149.0
Q ss_pred CeeeEEEEee------CCCcchhhHhhhhcCccccccccccc---cceeccCCCCCCCCCCceEEEEEEEEeeCCC----
Q psy5332 1 MAIDWVQLEA------NSTVLSDEFIASRIGLIPLTSDEVVD---RILYSRDCTCVDFCSECSVEFTLDVKCVDDQ---- 67 (287)
Q Consensus 1 lAId~V~i~~------NtSvl~DE~lAHRLGLIPl~s~~~~~---~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~---- 67 (287)
+||+.|+|+. |.+.++|||+||||||+||.++.... .|.+...|.|..+|..|++.+.|+|.|++..
T Consensus 47 ~Av~~V~I~~v~hef~s~~gv~Edvl~~~LnLk~L~~~~~~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~ 126 (317)
T COG0202 47 AAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATL 126 (317)
T ss_pred ceEEEEEEeccccccccCcCcHHHHHHHHhcCceeeeecccccceEEEEeccCCccccHhhcccceeEEEECCCceeeec
Confidence 6999999999 33499999999999999999986322 3778888888889999999999999987643
Q ss_pred --------CceeEeCCceeCCCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecccceee
Q psy5332 68 --------TRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVC 139 (287)
Q Consensus 68 --------~~~V~s~Dl~s~d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~ 139 (287)
...|+++|+++.. ...+ ...+..-+...|+++++|+++|.+..++.|.+|+|++||||+|++
T Consensus 127 ~~~~~l~~~~~V~~G~gyv~~-----~~~~--~~~~~v~~i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T--- 196 (317)
T COG0202 127 TEDAKLEMELRVYSGDGYVPA-----EGNR--EDDPPVGPIAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPET--- 196 (317)
T ss_pred cCCcceEEEEEEEcCccEecc-----cccc--ccCCCceeeeCCCceeeeeeceEEEEeEEEeccCCceeEEEEEee---
Confidence 2467999998621 1111 011111134589999999999999999999999999999998765
Q ss_pred eeecCCCCcccccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhh
Q psy5332 140 FEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 219 (287)
Q Consensus 140 y~~~P~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l 219 (287)
+|++.|++++..|.++|.++++.|.+..
T Consensus 197 ----------------------------------------------------~gsi~~~~a~~~aa~il~e~~~~~~~~~ 224 (317)
T COG0202 197 ----------------------------------------------------NGSIRPEEALAIAAKILIEHLEVFVELC 224 (317)
T ss_pred ----------------------------------------------------ccEeehHHHHHHHHHHHHHHHHHHHhhc
Confidence 4556666778889999999998888765
Q ss_pred hcc--ccccccc-CCCCCcccCCCeEEEEEeecCCCChhhHHHHH
Q psy5332 220 AHD--RVFYVIN-EAPYNWEAKPNKYFFNVESAGALKPENIVIMG 261 (287)
Q Consensus 220 ~~e--~~~e~~~-~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a 261 (287)
... ...+..+ ...-......+.+.|+|+|.+||+..+|-..+
T Consensus 225 ~~~~~~~~e~~~~~~~~~~~~~I~~l~lsvrs~ncLk~~~i~~i~ 269 (317)
T COG0202 225 PKAVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLKREGIETIG 269 (317)
T ss_pred cccceeecccccccccccccccccccccceeeehhhcccCchhhH
Confidence 321 1111100 00122234688899999999999999998876
No 13
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=99.92 E-value=4.8e-25 Score=194.62 Aligned_cols=151 Identities=22% Similarity=0.309 Sum_probs=121.7
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccc------cccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTA 74 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~------~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~ 74 (287)
+||+.|.|+.| +||+|+||...... ++++.+..+| ..|++.++|+++ ||+.|||+
T Consensus 41 ~aI~~v~I~~~---------~He~~~Ipgv~Edv~~IllNlk~~~~~~~~------~~~~~~~~l~~~----gp~~V~a~ 101 (215)
T cd06928 41 AAITAVKIEGV---------LHEFSTIPGVREDVLEILLNLKEIVFKSDS------EDEPQVLRLKVK----GPGVVTAA 101 (215)
T ss_pred EEEEEEEEccc---------ccccccCCCccccHHHHhhccccEEEEecC------CCceEEEEEEEe----cCeEEEhH
Confidence 59999999998 89999999987543 2455555544 268999999997 88999999
Q ss_pred CceeCCCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEecccccccee-----------------cccce
Q psy5332 75 DLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKW-----------------NPTAG 137 (287)
Q Consensus 75 Dl~s~d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKw-----------------sPV~~ 137 (287)
||.+.+. +.| ++|+++|++|++||+|+|+|++++|+|+.+|+| +||-.
T Consensus 102 Di~~~~~-i~i--------------vnp~~~IatL~~~~~l~ie~~i~~G~Gy~~~~~~~~~~~~~~~~~iDa~f~PV~~ 166 (215)
T cd06928 102 DIELPSG-VEI--------------VNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFSPVRK 166 (215)
T ss_pred hcCcCCC-cEE--------------eCCCcEEEEECCCCEEEEEEEEECcCcceeccccccccCCCceEEeCCCcCCeEE
Confidence 9987553 444 459999999999999999999999999999987 44444
Q ss_pred eeeeecCCCCcccccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHH
Q psy5332 138 VCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSN 214 (287)
Q Consensus 138 ~~y~~~P~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~ 214 (287)
+.|..++ .+++.+...++++|+|||+|+++|++++.+|+++|++.+..
T Consensus 167 vny~v~~-----------------------------~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~~ 214 (215)
T cd06928 167 VNYSVES-----------------------------TRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSP 214 (215)
T ss_pred EEEEEEE-----------------------------eecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhhc
Confidence 4444332 12333566899999999999999999999999999998753
No 14
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=99.91 E-value=5.5e-24 Score=196.10 Aligned_cols=197 Identities=18% Similarity=0.265 Sum_probs=143.1
Q ss_pred CeeeEEEEeeCCCcchhhHhhhhcCccccccccc------cccceeccCCCCCCCCCCceEEEEEEEEeeCCCCceeEeC
Q psy5332 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTA 74 (287)
Q Consensus 1 lAId~V~i~~NtSvl~DE~lAHRLGLIPl~s~~~------~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~V~s~ 74 (287)
.||..|.|.. ++|+++.||-..... ++++.+..+| ..+. .++|+++ ||+.|||+
T Consensus 32 ~aI~~vkI~g---------v~HEf~~I~GV~Edv~eIllNlK~i~~~~~~------~~~~-~~~l~~~----gp~~VtA~ 91 (297)
T TIGR02027 32 AAITAVKIDG---------VLHEFSTIEGVKEDVTEIILNLKQLVVKSEG------DGER-TMTLSKK----GPGVVTAG 91 (297)
T ss_pred eEEEEEEEcc---------eecccccCCCccccHHHHHhhhhceEEeccC------CCcE-EEEEEEe----CCEEEEhh
Confidence 4888998865 899999999776432 2344444333 3333 7888886 89999999
Q ss_pred CceeCCCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccce-----------------ecccce
Q psy5332 75 DLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAK-----------------WNPTAG 137 (287)
Q Consensus 75 Dl~s~d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAK-----------------wsPV~~ 137 (287)
||.+.+..+. +++||++|++|.+||.|+|++++.+|+|+.+|. |+||-.
T Consensus 92 Di~~~p~~ie--------------ivnpd~~IatL~~~~~L~iel~i~~G~Gy~~~~~~~~~~~~~~~i~iDa~FsPV~~ 157 (297)
T TIGR02027 92 DIKAPPGDVE--------------IVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLK 157 (297)
T ss_pred hcccCCCCcE--------------EeCCCeEEEEECCCCEEEEEEEEEcccccCcccccccccCccccccccccccCeEE
Confidence 9985333344 456999999999999999999999999996553 555555
Q ss_pred eeeeecCCCCcccccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHH
Q psy5332 138 VCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 217 (287)
Q Consensus 138 ~~y~~~P~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~ 217 (287)
+.|...+ .+++.....|+++|+|||+|+++|.+++.+|+++|++++..|.+
T Consensus 158 Vny~ve~-----------------------------~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~ 208 (297)
T TIGR02027 158 VNYEVEN-----------------------------TRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN 208 (297)
T ss_pred EEEEEee-----------------------------eeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 5555432 12334456789999999999999999999999999999999875
Q ss_pred hhhcc-cc-c---cc--ccCC-CCCcccCCCeEEEEEeecCCCChhhHHHHH
Q psy5332 218 QLAHD-RV-F---YV--INEA-PYNWEAKPNKYFFNVESAGALKPENIVIMG 261 (287)
Q Consensus 218 ~l~~e-~~-~---e~--~~~~-~i~~~~~~d~f~f~veS~g~l~~~~i~~~a 261 (287)
. +.. .. . +. .... .-......+.+.|||||.+||+..+|...+
T Consensus 209 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L~LSvR~~n~Lk~~~I~ti~ 259 (297)
T TIGR02027 209 L-DEEIEAFEEEQEEEEEELEDAKLLSIKIEELDLSVRSYNCLKRAGIHTLG 259 (297)
T ss_pred c-hhccccccccccccccccccchhccccHHHhCccHHHHhHHHHcCCcCHH
Confidence 2 211 00 0 00 0000 111335688999999999999999998877
No 15
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=99.74 E-value=5e-17 Score=151.26 Aligned_cols=192 Identities=15% Similarity=0.090 Sum_probs=140.8
Q ss_pred CeeeEEEEeeCCCcch----------hhHhhhhcCccccccccccccceeccCCCCCCCCCCceEEEEEEEEeeCCCCce
Q psy5332 1 MAIDWVQLEANSTVLS----------DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRH 70 (287)
Q Consensus 1 lAId~V~i~~NtSvl~----------DE~lAHRLGLIPl~s~~~~~~~~~~~~c~~~~~c~~ctv~~~L~v~~~~~~~~~ 70 (287)
+||..|.|.... --+ .|+| ++|..|++++++ . ....+.|+++ ||+.
T Consensus 52 ~aIt~vkI~gv~-hEfs~i~GV~Edv~eIi-lNLK~I~~k~~~--~----------------~~~~~~l~~~----Gp~~ 107 (327)
T CHL00013 52 TCITRAKIEGVP-HEYSTIPGIRESVLEIL-LNLKEIVLKSNL--Y----------------GPQKASICVQ----GPKY 107 (327)
T ss_pred eEEEEEEECCcc-ccccCCCCcccCHHHHH-HhhhcCeEEccC--C----------------CcEEEEEEEe----CCeE
Confidence 588889886543 444 6666 999999998763 1 1357888886 8999
Q ss_pred eEeCCceeCCCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccc--------------eecccc
Q psy5332 71 VTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHA--------------KWNPTA 136 (287)
Q Consensus 71 V~s~Dl~s~d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HA--------------KwsPV~ 136 (287)
|||+||... +.+. +++|+.+||+|..|+.|+|++++.+|+|+..| -|+||-
T Consensus 108 vtA~Di~~p-~~ie--------------ivnpd~~Iatl~~~~~l~~el~ie~G~GY~~~~~~~~~~g~i~iDa~FsPV~ 172 (327)
T CHL00013 108 VTAQDIILP-PSVE--------------IVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKNFQDGSFPIDAVFMPVR 172 (327)
T ss_pred EEeeeeccC-CCeE--------------EeCCCeEEEEeCCCCEEEEEEEEECccCceeccccccCCCcEEeCCCCCCee
Confidence 999999854 2233 45799999999999999999999999999433 567777
Q ss_pred eeeeeecCCCCcccccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHH
Q psy5332 137 GVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 216 (287)
Q Consensus 137 ~~~y~~~P~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~ 216 (287)
.+.|...+. ..+... .++.+|+|+|+|+++|.+++.+|+++|.+.+..|.
T Consensus 173 kVny~Ve~~-----------------------------~~~~~~-~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~ 222 (327)
T CHL00013 173 NVNYSIHSY-----------------------------GNGNEK-QEILFLEIWTNGSITPKEALHEASRNLIDLFIPFL 222 (327)
T ss_pred EEEEEEEEc-----------------------------ccCCcc-cceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 777765531 112122 78999999999999999999999999999998886
Q ss_pred Hhhhccc------cc------------c-cccCC-CCCcccCCCeEEEEEeecCCCChhhHHHHH
Q psy5332 217 TQLAHDR------VF------------Y-VINEA-PYNWEAKPNKYFFNVESAGALKPENIVIMG 261 (287)
Q Consensus 217 ~~l~~e~------~~------------e-~~~~~-~i~~~~~~d~f~f~veS~g~l~~~~i~~~a 261 (287)
+.-.... .. . ..... .-......+.+.|||||.+||+..+|...+
T Consensus 223 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ie~L~LSvRs~NcLk~a~I~ti~ 287 (327)
T CHL00013 223 HAEEENLKLENNENRVTLLFTFHDRLTDLKKNKKEIALKQIFIEQLELSVRAYNCLKRANIHTLL 287 (327)
T ss_pred cchhhhcccccccccccccccccccccccccchhhhhhhceeHHhccCchhhhhhhhhcCccCHH
Confidence 4211100 00 0 00000 001234578899999999999999998888
No 16
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=98.89 E-value=1.8e-09 Score=98.46 Aligned_cols=50 Identities=52% Similarity=0.923 Sum_probs=46.5
Q ss_pred cCCCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhh
Q psy5332 229 NEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 278 (287)
Q Consensus 229 ~~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~ 278 (287)
....|++.+++|+|+|+|||+|+|+|++|+.+|+++|++|+++|++.|++
T Consensus 215 ~~~~v~i~~~~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~~ 264 (265)
T cd07031 215 KDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264 (265)
T ss_pred cCCceEEEeeCCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44578899999999999999999999999999999999999999999875
No 17
>KOG1522|consensus
Probab=98.87 E-value=3.5e-09 Score=93.06 Aligned_cols=58 Identities=52% Similarity=0.853 Sum_probs=52.4
Q ss_pred cCCCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhhhcccccc
Q psy5332 229 NEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHELSHDALA 286 (287)
Q Consensus 229 ~~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~~~~~~~~ 286 (287)
.+.++++..++|+|+|+|||+|+|+|.+|+..|+++||+|+..|+.+|+.+.+.++|+
T Consensus 218 e~~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~~l~~~~q~~~~~ 275 (285)
T KOG1522|consen 218 EGAPYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRLALSTEDQNDAQA 275 (285)
T ss_pred ccCCCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHhhhcccchhhhhh
Confidence 3456888889999999999999999999999999999999999999999988876653
No 18
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=98.44 E-value=4.8e-07 Score=68.72 Aligned_cols=53 Identities=19% Similarity=0.390 Sum_probs=44.5
Q ss_pred cccceeeeeecCCCCcccccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHH
Q psy5332 133 NPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKL 212 (287)
Q Consensus 133 sPV~~~~y~~~P~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl 212 (287)
+||..|+|+..+.. +....+.++|+|+|||+|+++|.+++.+|+++|++++
T Consensus 33 ~pV~~a~Y~v~hp~-----------------------------~~~~~~~d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~ 83 (86)
T cd00460 33 SPVEFAAYYVEHPV-----------------------------KLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKL 83 (86)
T ss_pred CCceEEEEEeCCCc-----------------------------cCCCCCCCeEEEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence 99999999986432 1224457899999999999999999999999999998
Q ss_pred HH
Q psy5332 213 SN 214 (287)
Q Consensus 213 ~~ 214 (287)
+.
T Consensus 84 ~~ 85 (86)
T cd00460 84 EH 85 (86)
T ss_pred hh
Confidence 65
No 19
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=98.36 E-value=4.7e-07 Score=83.39 Aligned_cols=44 Identities=25% Similarity=0.493 Sum_probs=40.0
Q ss_pred CCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHH
Q psy5332 174 APYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 217 (287)
Q Consensus 174 ~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~ 217 (287)
..+.+++..|||+|+|||+|+++|+++|.+|+++|++|++.|.+
T Consensus 247 ~~V~v~~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~ 290 (291)
T cd07032 247 DKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291)
T ss_pred CceeEEEeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 34667888999999999999999999999999999999998864
No 20
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=98.30 E-value=9e-07 Score=80.64 Aligned_cols=50 Identities=30% Similarity=0.447 Sum_probs=46.1
Q ss_pred CCCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhh
Q psy5332 230 EAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHE 279 (287)
Q Consensus 230 ~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~ 279 (287)
...+++...+|+|+|+|||+|+|+|++|+..|+++|++||++|.+.|++.
T Consensus 213 ~~AI~i~~~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~~~~~ 262 (263)
T PRK00783 213 GKAIRVSDDENKFIFTVESDGSLPVEEILLEALKILKRKADELIEALEEL 262 (263)
T ss_pred CCceEEEEcCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 44678888999999999999999999999999999999999999999864
No 21
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=98.14 E-value=2.4e-06 Score=77.70 Aligned_cols=47 Identities=28% Similarity=0.511 Sum_probs=43.0
Q ss_pred CCCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHH
Q psy5332 230 EAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 276 (287)
Q Consensus 230 ~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l 276 (287)
.+.+++.++.++|+|+|||+|+++|++|+.+|+++|++|++.|.+.|
T Consensus 213 ~~AI~~~~~~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~~ 259 (259)
T cd07030 213 AGAIRVGWDEDRFIFEVESDGSLPPKEILLEALRILKEKADELIEAL 259 (259)
T ss_pred CCcEEEEecCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 35678889999999999999999999999999999999999998764
No 22
>KOG1521|consensus
Probab=97.90 E-value=1.2e-05 Score=72.83 Aligned_cols=45 Identities=33% Similarity=0.495 Sum_probs=40.8
Q ss_pred CCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHh
Q psy5332 174 APYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQ 218 (287)
Q Consensus 174 ~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~ 218 (287)
+.+..++..|||+|+|||+|+++|+.++.+|+++|+.|+..+.+.
T Consensus 292 d~V~LgrvrdHfIFsvestgal~p~~lf~eavkvle~Kc~al~~~ 336 (338)
T KOG1521|consen 292 DKVQLGRVRDHFIFSVESTGALKPEVLFEEAVKVLEEKCRALRDE 336 (338)
T ss_pred hheeeccccceEEEEeecccCCCchhhHHHHHHHHHHHHHHHhhc
Confidence 356678889999999999999999999999999999999988754
No 23
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=97.82 E-value=3.3e-05 Score=58.61 Aligned_cols=36 Identities=28% Similarity=0.642 Sum_probs=33.3
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL 272 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l 272 (287)
.+.|+|+|+|||+|+++|.+++.+|+++|++|++.|
T Consensus 51 ~~~d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~~~~ 86 (86)
T cd00460 51 TDEDKFILRIETVGSIPPEEALRRAVEILRKKLEHL 86 (86)
T ss_pred CCCCeEEEEEEECCCCCHHHHHHHHHHHHHHHHhhC
Confidence 558899999999999999999999999999999753
No 24
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=97.80 E-value=3e-05 Score=68.51 Aligned_cols=38 Identities=29% Similarity=0.632 Sum_probs=35.7
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 274 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~ 274 (287)
.+.|+|+|+|||+|+++|++++.+|+++|++|++.|.+
T Consensus 174 ~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~ 211 (212)
T cd07028 174 PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL 211 (212)
T ss_pred ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence 36799999999999999999999999999999999875
No 25
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=97.79 E-value=2.2e-05 Score=56.49 Aligned_cols=33 Identities=30% Similarity=0.745 Sum_probs=29.6
Q ss_pred CCCcEEEEeecCCccCHHHHHHHHHHHHHHHHH
Q psy5332 181 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLS 213 (287)
Q Consensus 181 ~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~ 213 (287)
.+++++|+|||+|+++|++++.+|++.|+++++
T Consensus 34 ~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~~ 66 (66)
T PF01193_consen 34 NEDKFVFRIETDGSLTPKEALLKAIKILKEKLN 66 (66)
T ss_dssp EEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHHC
T ss_pred CCCEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence 468999999999999999999999999999873
No 26
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=97.66 E-value=5.7e-05 Score=54.30 Aligned_cols=34 Identities=29% Similarity=0.726 Sum_probs=30.7
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLS 270 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~ 270 (287)
...++|+|+|||+|+++|.+++..|++.|++||+
T Consensus 33 ~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~~ 66 (66)
T PF01193_consen 33 PNEDKFVFRIETDGSLTPKEALLKAIKILKEKLN 66 (66)
T ss_dssp SEEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHHC
T ss_pred CCCCEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence 4678999999999999999999999999999984
No 27
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=97.60 E-value=0.00014 Score=63.40 Aligned_cols=45 Identities=29% Similarity=0.408 Sum_probs=41.0
Q ss_pred CCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhh-hcc
Q psy5332 238 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHE-LSH 282 (287)
Q Consensus 238 ~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~-~~~ 282 (287)
+.|+|+|.|||+|+++|++++..|+++|+++++.|.+.|++. +++
T Consensus 148 ~~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~~~~~~~ 193 (195)
T PRK14979 148 SNDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEGIELSD 193 (195)
T ss_pred CCcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 368999999999999999999999999999999999999874 443
No 28
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=97.51 E-value=0.00035 Score=65.33 Aligned_cols=135 Identities=19% Similarity=0.249 Sum_probs=90.6
Q ss_pred EEEEEEEEeeCCCCceeEeCCceeCCCeeeeccCCCcccCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccccccceecc
Q psy5332 55 VEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 134 (287)
Q Consensus 55 v~~~L~v~~~~~~~~~V~s~Dl~s~d~~v~P~~~~~~~~~~~~~~~~~dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsP 134 (287)
+.|+++.. +++.||++|+..... ++ ++||+..|+.|..|.+|.|++++..|.|+ +|
T Consensus 91 ~~~~~~~~----g~g~v~a~d~~~~~~-lE--------------v~np~~~ia~~~~~~~l~~~~~V~~G~gy-----v~ 146 (317)
T COG0202 91 VTLELDKE----GPGEVTASDITVPLD-LE--------------VVNPDHVIATLTEDAKLEMELRVYSGDGY-----VP 146 (317)
T ss_pred eEEEEecc----CCccccHhhccccee-EE--------------EECCCceeeeccCCcceEEEEEEEcCccE-----ec
Confidence 67788875 788999999985421 22 46799999999999999999999999998 44
Q ss_pred cceeeeeecCCCCcccccCCCCCCCCCCccCcccccccCCCCCcccCCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHH
Q psy5332 135 TAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSN 214 (287)
Q Consensus 135 V~~~~y~~~P~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~ 214 (287)
.-... ...|.+. .. .+++.|+++.+ |++..
T Consensus 147 ~~~~~-~~~~~v~--~i-------~~D~~~spv~k-----------------------vqy~v----------------- 176 (317)
T COG0202 147 AEGNR-EDDPPVG--PI-------AVDAPFSPVRK-----------------------VQYIV----------------- 176 (317)
T ss_pred ccccc-ccCCCce--ee-------eCCCceeeeee-----------------------ceEEE-----------------
Confidence 33222 2223220 00 11222221110 01100
Q ss_pred HHHhhhcccccccccCCCCCcccCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHh
Q psy5332 215 LQTQLAHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLA 277 (287)
Q Consensus 215 l~~~l~~e~~~e~~~~~~i~~~~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~ 277 (287)
....+......||..|.++|.|++.|...+..|.++|.+.+..+.+...
T Consensus 177 --------------e~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~ 225 (317)
T COG0202 177 --------------EEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCP 225 (317)
T ss_pred --------------EeEEEeccCCceeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhcc
Confidence 0001122356889999999999999999999999999999998877554
No 29
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=97.50 E-value=0.00012 Score=65.31 Aligned_cols=35 Identities=40% Similarity=0.706 Sum_probs=32.5
Q ss_pred CCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHH
Q psy5332 238 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL 272 (287)
Q Consensus 238 ~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l 272 (287)
+.|+|+|+|||+|+++|++++.+|+++|++|++.|
T Consensus 190 ~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~~ 224 (224)
T smart00662 190 EYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 224 (224)
T ss_pred CCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhhC
Confidence 47899999999999999999999999999999753
No 30
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=96.17 E-value=0.0089 Score=55.56 Aligned_cols=38 Identities=16% Similarity=0.427 Sum_probs=34.7
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 274 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~ 274 (287)
...|+|+|.|||+|+++|.+++.+|+++|++++..+.+
T Consensus 171 ~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~ 208 (297)
T TIGR02027 171 TDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN 208 (297)
T ss_pred ccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 34589999999999999999999999999999998864
No 31
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=93.50 E-value=0.11 Score=48.52 Aligned_cols=36 Identities=25% Similarity=0.500 Sum_probs=33.5
Q ss_pred CCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHH
Q psy5332 239 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 274 (287)
Q Consensus 239 ~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~ 274 (287)
-|+++|.|+|.|+++|.+.+..|+++|++.+..+.+
T Consensus 190 ~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~ 225 (310)
T PRK05182 190 YDKLILEVETDGSITPEEALALAAKILVEQLSVFVD 225 (310)
T ss_pred ceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 578999999999999999999999999999988754
No 32
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=92.95 E-value=0.3 Score=36.15 Aligned_cols=37 Identities=16% Similarity=0.287 Sum_probs=32.8
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHh
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQ 218 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~ 218 (287)
.+++.+.|.|+|..+|.+++.+|++-|.+.++.|.+.
T Consensus 40 ~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~~ 76 (77)
T PF13656_consen 40 ENKINLRIQTKGGITPIEALKKALEDLIKICEELKKE 76 (77)
T ss_dssp SSEEEEEEEESTTS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 5789999999999999999999999999999888753
No 33
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=91.04 E-value=0.88 Score=33.63 Aligned_cols=40 Identities=15% Similarity=0.267 Sum_probs=35.6
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 276 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l 276 (287)
.-.++.+|.|.+.|..+|.+++.+|++-|.+.++.+++.+
T Consensus 38 Pl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~~F 77 (77)
T PF13656_consen 38 PLENKINLRIQTKGGITPIEALKKALEDLIKICEELKKEF 77 (77)
T ss_dssp TTSSEEEEEEEESTTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 4578999999999999999999999999999999988764
No 34
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=90.13 E-value=0.7 Score=34.89 Aligned_cols=36 Identities=17% Similarity=0.286 Sum_probs=32.6
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHH
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 217 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~ 217 (287)
.++..|.|.|+|+.+|.+++.+|++-|...++.+.+
T Consensus 48 ~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~~ 83 (85)
T cd07029 48 ENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHILS 83 (85)
T ss_pred CCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 468899999999999999999999999999988765
No 35
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=89.82 E-value=0.69 Score=34.76 Aligned_cols=35 Identities=9% Similarity=0.155 Sum_probs=31.5
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHH
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 216 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~ 216 (287)
.++..+.|.|+|..+|.+++.+|++-|.+.++.|.
T Consensus 48 ~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~ 82 (83)
T cd06927 48 LSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFL 82 (83)
T ss_pred CCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46788999999999999999999999999887765
No 36
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=89.81 E-value=0.67 Score=34.98 Aligned_cols=35 Identities=6% Similarity=0.153 Sum_probs=31.5
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHH
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 216 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~ 216 (287)
.+++.|.|.|+|..+|.+++.+|++-|.+.++.|.
T Consensus 50 ~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~ 84 (85)
T PRK01146 50 ISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFL 84 (85)
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46788999999999999999999999999887765
No 37
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=89.31 E-value=0.48 Score=41.96 Aligned_cols=34 Identities=18% Similarity=0.385 Sum_probs=30.8
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLS 270 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~ 270 (287)
...|.++|.|+|.|++.|.+.+..|+++|++.+.
T Consensus 180 ~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~ 213 (215)
T cd06928 180 TDYEKLILEIWTNGSISPEEALAQAAKILINHFS 213 (215)
T ss_pred CCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhh
Confidence 3567899999999999999999999999998775
No 38
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=88.56 E-value=1.1 Score=34.35 Aligned_cols=36 Identities=22% Similarity=0.369 Sum_probs=32.5
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHH
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT 217 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~ 217 (287)
.++..+.|.|+|+.+|.+++.+|++-|...++.|.+
T Consensus 56 ~~~~~l~i~t~~~~~p~~al~~a~~~l~~~~~~~~~ 91 (93)
T cd06926 56 EHKIELRIQTDGSITPKEALKNAITDLISELSLLKE 91 (93)
T ss_pred CCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 468899999999999999999999999999988764
No 39
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=88.15 E-value=0.94 Score=34.02 Aligned_cols=35 Identities=17% Similarity=0.310 Sum_probs=31.1
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHH
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 216 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~ 216 (287)
.++..|.|.|+|..+|.+++.+|++-|.+.++.|.
T Consensus 48 ~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~~l~ 82 (83)
T cd07027 48 IDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHLG 82 (83)
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 46788999999999999999999999999887654
No 40
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=83.06 E-value=3 Score=31.94 Aligned_cols=38 Identities=21% Similarity=0.346 Sum_probs=34.7
Q ss_pred CCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHH
Q psy5332 238 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQ 275 (287)
Q Consensus 238 ~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~ 275 (287)
-.+..+|.|.+.|..+|.+.+..|++-|...++.+++.
T Consensus 55 l~~~~~l~i~t~~~~~p~~al~~a~~~l~~~~~~~~~~ 92 (93)
T cd06926 55 LEHKIELRIQTDGSITPKEALKNAITDLISELSLLKEE 92 (93)
T ss_pred CCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 36789999999999999999999999999999988764
No 41
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=81.51 E-value=6.2 Score=30.67 Aligned_cols=38 Identities=13% Similarity=0.270 Sum_probs=33.4
Q ss_pred CCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhh
Q psy5332 182 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 219 (287)
Q Consensus 182 ~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l 219 (287)
.+...+.|-+.|.++|.+++.+|++-+.+.++.|...+
T Consensus 54 ~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~~~ 91 (99)
T COG1761 54 IDNPKIRIKTKGGVDPKEALKRAARKILKDLEELLDQF 91 (99)
T ss_pred CCCceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677889999999999999999999999999998744
No 42
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=81.37 E-value=3.6 Score=31.01 Aligned_cols=39 Identities=15% Similarity=0.267 Sum_probs=35.0
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQ 275 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~ 275 (287)
.-.+...|.|.+.|..+|.+.+..|++-|.+.++.+.+.
T Consensus 46 Pl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~~~ 84 (85)
T cd07029 46 PSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHILST 84 (85)
T ss_pred CCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 346789999999999999999999999999999988764
No 43
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=80.05 E-value=3.7 Score=30.92 Aligned_cols=36 Identities=6% Similarity=0.130 Sum_probs=32.9
Q ss_pred CCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHH
Q psy5332 238 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 273 (287)
Q Consensus 238 ~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~ 273 (287)
-.++.+|.|.+.|..+|.+.+..|++-|.+.|+.+.
T Consensus 49 l~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~ 84 (85)
T PRK01146 49 LISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFL 84 (85)
T ss_pred CCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 367899999999999999999999999999998775
No 44
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=79.98 E-value=3.9 Score=30.69 Aligned_cols=37 Identities=8% Similarity=0.131 Sum_probs=33.3
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 273 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~ 273 (287)
.-.++..|.|.+.|..+|.+.+..|++-|.+.|+.+.
T Consensus 46 Pl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~ 82 (83)
T cd06927 46 PLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFL 82 (83)
T ss_pred CCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4467999999999999999999999999999998775
No 45
>KOG3438|consensus
Probab=77.52 E-value=6.2 Score=30.74 Aligned_cols=44 Identities=11% Similarity=0.230 Sum_probs=40.3
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhhh
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHEL 280 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~~ 280 (287)
...|...|.|.+.|.+++.+++..|++-|++=++.+...++++.
T Consensus 53 Pse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF~~~i 96 (105)
T KOG3438|consen 53 PSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKFEEEI 96 (105)
T ss_pred CchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66889999999999999999999999999999999998887753
No 46
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=74.87 E-value=6.9 Score=29.32 Aligned_cols=36 Identities=17% Similarity=0.286 Sum_probs=32.7
Q ss_pred CCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHH
Q psy5332 238 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 273 (287)
Q Consensus 238 ~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~ 273 (287)
-.+...|.|.+.|..+|.+.+..|++-|.+.++.|.
T Consensus 47 l~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~~l~ 82 (83)
T cd07027 47 VIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHLG 82 (83)
T ss_pred CCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 367899999999999999999999999999998764
No 47
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=69.01 E-value=15 Score=28.53 Aligned_cols=40 Identities=13% Similarity=0.242 Sum_probs=36.7
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHH
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 276 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l 276 (287)
.-.+++.+.|.+.|-..|.+.+.+|++-+-+.+..|...+
T Consensus 52 P~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~~~ 91 (99)
T COG1761 52 PLIDNPKIRIKTKGGVDPKEALKRAARKILKDLEELLDQF 91 (99)
T ss_pred CCCCCceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999999999999999999999966
No 48
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=66.30 E-value=11 Score=35.72 Aligned_cols=35 Identities=11% Similarity=0.222 Sum_probs=32.4
Q ss_pred CCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHH
Q psy5332 239 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 273 (287)
Q Consensus 239 ~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~ 273 (287)
-|.++|.|++.|++.|.+.+..|.++|.+=+..+.
T Consensus 188 ~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~ 222 (327)
T CHL00013 188 QEILFLEIWTNGSITPKEALHEASRNLIDLFIPFL 222 (327)
T ss_pred cceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 67899999999999999999999999999887765
No 49
>KOG3307|consensus
Probab=62.83 E-value=3 Score=33.64 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=10.0
Q ss_pred hhhhcCcccccc
Q psy5332 20 IASRIGLIPLTS 31 (287)
Q Consensus 20 lAHRLGLIPl~s 31 (287)
++||||++|+--
T Consensus 83 vfHRLG~VpvgE 94 (150)
T KOG3307|consen 83 VFHRLGKVPVGE 94 (150)
T ss_pred hhhhccCcccCc
Confidence 689999999753
No 50
>KOG3438|consensus
Probab=61.95 E-value=14 Score=28.76 Aligned_cols=42 Identities=10% Similarity=0.209 Sum_probs=35.3
Q ss_pred CCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcc
Q psy5332 181 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222 (287)
Q Consensus 181 ~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e 222 (287)
-.++..|.|.|.|+.++.+++.+|+.-|.+-++.....+..+
T Consensus 54 se~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF~~~ 95 (105)
T KOG3438|consen 54 SEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKFEEE 95 (105)
T ss_pred chhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 368999999999999999999999999988888776655443
No 51
>KOG4392|consensus
Probab=48.30 E-value=49 Score=26.31 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=37.0
Q ss_pred CCCcEEEEeecCCccCHHHHHHHHHHHHHHHHHHHHHhhhcc
Q psy5332 181 KPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHD 222 (287)
Q Consensus 181 ~~d~fif~VEs~G~l~p~~iv~~A~~iLk~Kl~~l~~~l~~e 222 (287)
...+|++.|-|+-..+|.+++..|+.-|...++.+...+..+
T Consensus 67 l~~~~~LRiqtt~d~~p~~al~~a~~~l~~el~~l~~~f~~~ 108 (117)
T KOG4392|consen 67 LEHKIILRVQTTEDCSPADALTNAITDLIEELSLLENRFKAE 108 (117)
T ss_pred ccccEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999999999999999888776543
No 52
>KOG4392|consensus
Probab=37.65 E-value=1.1e+02 Score=24.26 Aligned_cols=43 Identities=21% Similarity=0.317 Sum_probs=38.7
Q ss_pred cCCCeEEEEEeecCCCChhhHHHHHHHHHHHHHHHHHHHHhhh
Q psy5332 237 AKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHE 279 (287)
Q Consensus 237 ~~~d~f~f~veS~g~l~~~~i~~~a~~~l~~k~~~l~~~l~~~ 279 (287)
.-..+|++.|-++.-.+|.+.+..|+.-|..++..|...+...
T Consensus 66 Pl~~~~~LRiqtt~d~~p~~al~~a~~~l~~el~~l~~~f~~~ 108 (117)
T KOG4392|consen 66 PLEHKIILRVQTTEDCSPADALTNAITDLIEELSLLENRFKAE 108 (117)
T ss_pred cccccEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466899999999999999999999999999999998888764
No 53
>PRK15329 chaperone protein SicP; Provisional
Probab=33.23 E-value=18 Score=29.73 Aligned_cols=13 Identities=46% Similarity=0.897 Sum_probs=11.7
Q ss_pred hhhhcCcccccccc
Q psy5332 20 IASRIGLIPLTSDE 33 (287)
Q Consensus 20 lAHRLGLIPl~s~~ 33 (287)
+|||||| ||.-|.
T Consensus 11 ~~~~lGL-pL~fDd 23 (138)
T PRK15329 11 LGEALGL-PLTFDD 23 (138)
T ss_pred HHHHhCC-ceEEcC
Confidence 7899999 999885
No 54
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=26.70 E-value=95 Score=24.86 Aligned_cols=38 Identities=34% Similarity=0.541 Sum_probs=25.2
Q ss_pred CeEEEEeCCCCEEEEEEEEEeccccccceecccceeeeeecCC
Q psy5332 103 DILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPD 145 (287)
Q Consensus 103 dI~I~kL~pGQ~I~le~~a~kGiGk~HAKwsPV~~~~y~~~P~ 145 (287)
+|.|.=|.|||.+.+++...-.-| ..|+ |.|.|+-++.
T Consensus 6 ~I~v~GL~p~~~vtl~a~~~~~~g---~~w~--S~A~f~Ad~~ 43 (126)
T PF04775_consen 6 DIRVSGLPPGQEVTLRARLTDDNG---VQWQ--SYATFRADEN 43 (126)
T ss_dssp EEEEES--TT-EEEEEEEEE-TTS----EEE--EEEEEE--TT
T ss_pred EEEEeCCCCCCEEEEEEEEEeCCC---CEEE--EEEEEEcCCC
Confidence 688889999999999999997555 4788 5677887654
No 55
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=24.48 E-value=2.6e+02 Score=19.81 Aligned_cols=28 Identities=7% Similarity=0.119 Sum_probs=16.3
Q ss_pred EEEeCCCCEEEEEEEEEeccccccceec
Q psy5332 106 IVKLRKGQELRLRAYAKKGFGKEHAKWN 133 (287)
Q Consensus 106 I~kL~pGQ~I~le~~a~kGiGk~HAKws 133 (287)
+..|.||+...+.....-.-+-....|.
T Consensus 43 ~~~l~pG~s~~~~~~V~vp~~a~~G~y~ 70 (78)
T PF10633_consen 43 VPSLPPGESVTVTFTVTVPADAAPGTYT 70 (78)
T ss_dssp E--B-TTSEEEEEEEEEE-TT--SEEEE
T ss_pred cccCCCCCEEEEEEEEECCCCCCCceEE
Confidence 3389999999988888877665444444
No 56
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=20.87 E-value=28 Score=26.09 Aligned_cols=18 Identities=22% Similarity=0.372 Sum_probs=9.7
Q ss_pred CeEEEEeCCCCEEEEEEE
Q psy5332 103 DILIVKLRKGQELRLRAY 120 (287)
Q Consensus 103 dI~I~kL~pGQ~I~le~~ 120 (287)
+=.+.+|+|||+|.+.+-
T Consensus 37 ~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 37 AKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp T--GGG--TT-EEEEEE-
T ss_pred cchHhhCCCCCEEEEEEC
Confidence 345679999999998765
No 57
>PHA02148 hypothetical protein
Probab=20.85 E-value=1.2e+02 Score=23.33 Aligned_cols=35 Identities=17% Similarity=0.314 Sum_probs=24.7
Q ss_pred CCChhhHHHHHHHHHHH----------HHHHHHHHHhhhhccccc
Q psy5332 251 ALKPENIVIMGVTVLKQ----------KLSNLQTQLAHELSHDAL 285 (287)
Q Consensus 251 ~l~~~~i~~~a~~~l~~----------k~~~l~~~l~~~~~~~~~ 285 (287)
.|+.++|..+|++++|+ +|+++...-++++|+|-+
T Consensus 25 ~~~i~~~k~~A~E~FK~iE~RIA~D~~~L~~~A~~R~NEL~~HE~ 69 (110)
T PHA02148 25 PLPISDLKVEAFELFKKIEERIAHDQTRLEELAKSRENELRRHEA 69 (110)
T ss_pred CCChhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Confidence 47788999999988864 455565666667777643
Done!