Query 024896
Match_columns 261
No_of_seqs 116 out of 212
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 08:17:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024896.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024896hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2905 Transcription initiati 100.0 2.9E-71 6.4E-76 484.8 16.4 240 11-260 7-252 (254)
2 PF02270 TFIIF_beta: Transcrip 100.0 1E-69 2.2E-74 494.5 10.4 230 12-253 1-275 (275)
3 COG5090 TFG2 Transcription ini 100.0 1.3E-61 2.9E-66 422.2 16.7 242 2-256 11-257 (297)
4 PF09734 Tau95: RNA polymerase 95.2 0.022 4.7E-07 52.9 4.2 57 190-246 231-289 (310)
5 PF12157 DUF3591: Protein of u 94.9 0.049 1.1E-06 53.5 5.9 70 186-255 234-306 (457)
6 KOG0008 Transcription initiati 92.5 0.13 2.9E-06 55.8 4.1 73 185-257 688-765 (1563)
7 PF04801 Sin_N: Sin-like prote 90.8 0.35 7.6E-06 46.8 4.8 55 194-251 337-391 (421)
8 PF04004 Leo1: Leo1-like prote 90.6 2.9 6.2E-05 35.8 9.7 39 94-132 99-138 (171)
9 KOG2473 RNA polymerase III tra 87.9 0.86 1.9E-05 44.9 5.0 56 191-246 229-285 (484)
10 COG5179 TAF1 Transcription ini 87.7 0.68 1.5E-05 47.1 4.3 70 185-255 592-664 (968)
11 PF05132 RNA_pol_Rpc4: RNA pol 74.7 13 0.00027 30.3 6.6 20 102-121 111-130 (131)
12 KOG2428 Uncharacterized conser 66.8 19 0.00042 35.3 6.9 45 96-141 243-287 (443)
13 PF13817 DDE_Tnp_IS66_C: IS66 61.3 6 0.00013 25.7 1.6 15 220-234 12-26 (39)
14 KOG3122 DNA-directed RNA polym 58.1 21 0.00045 33.6 5.2 62 45-121 243-309 (310)
15 PRK10857 DNA-binding transcrip 54.9 23 0.00051 29.9 4.7 55 193-248 9-68 (164)
16 TIGR02010 IscR iron-sulfur clu 51.1 31 0.00067 27.8 4.7 55 194-249 10-69 (135)
17 PF02082 Rrf2: Transcriptional 50.5 39 0.00084 24.8 4.8 41 208-249 25-69 (83)
18 PF13565 HTH_32: Homeodomain-l 45.7 21 0.00045 25.5 2.6 29 192-220 32-60 (77)
19 PF09339 HTH_IclR: IclR helix- 45.6 44 0.00096 22.2 4.0 37 198-234 7-44 (52)
20 smart00550 Zalpha Z-DNA-bindin 43.9 78 0.0017 22.5 5.4 59 191-249 3-66 (68)
21 PF05595 DUF771: Domain of unk 42.7 36 0.00078 25.9 3.6 39 191-230 7-46 (91)
22 PF10826 DUF2551: Protein of u 38.7 68 0.0015 24.4 4.4 64 191-254 8-82 (83)
23 PF08208 RNA_polI_A34: DNA-dir 36.1 12 0.00026 32.4 0.0 15 20-34 3-17 (198)
24 cd00092 HTH_CRP helix_turn_hel 35.7 1.3E+02 0.0027 20.3 5.3 43 206-249 23-67 (67)
25 smart00346 HTH_ICLR helix_turn 32.3 1.3E+02 0.0028 21.8 5.1 55 198-252 9-66 (91)
26 smart00076 IFabd Interferon al 28.5 79 0.0017 25.4 3.6 44 193-236 24-73 (117)
27 PF10390 ELL: RNA polymerase I 27.6 24 0.00052 32.6 0.5 141 103-253 97-258 (284)
28 PRK14741 spoVM stage V sporula 27.1 49 0.0011 19.5 1.5 14 24-37 3-16 (26)
29 PF13412 HTH_24: Winged helix- 25.4 1.9E+02 0.0041 18.5 5.1 38 196-233 5-42 (48)
30 PF14493 HTH_40: Helix-turn-he 25.2 76 0.0016 23.7 2.8 34 190-224 50-83 (91)
31 PHA02571 a-gt.4 hypothetical p 24.2 46 0.001 26.6 1.4 36 194-231 52-87 (109)
32 PRK10219 DNA-binding transcrip 23.8 2.3E+02 0.0049 21.3 5.4 41 192-232 3-45 (107)
33 TIGR03879 near_KaiC_dom probab 23.1 1.6E+02 0.0035 21.7 4.1 38 193-230 17-54 (73)
34 KOG0661 MAPK related serine/th 22.2 1.3E+02 0.0028 30.3 4.4 43 199-251 96-140 (538)
35 cd00095 IFab Interferon alpha, 20.7 1.3E+02 0.0028 25.2 3.6 44 193-236 56-105 (152)
No 1
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=100.00 E-value=2.9e-71 Score=484.85 Aligned_cols=240 Identities=42% Similarity=0.661 Sum_probs=207.6
Q ss_pred CCCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEE-----ecccCCCCCCCCccee
Q 024896 11 GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTME-----TTAVSNDSLNRPKSYS 85 (261)
Q Consensus 11 ~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~-----l~~~~~~~~~iPkey~ 85 (261)
+.++||.++++.+|||||||+||+++|..++.+. ++|++++.+.++. .++.|.+. .....++.+.+|..|.
T Consensus 7 ~~~dl~l~~~~~~vWLvKvP~fLa~kw~~~~~~~---e~g~l~i~k~~~d-aki~l~L~e~~p~~~~~~a~~g~~p~~~~ 82 (254)
T KOG2905|consen 7 ESLDLDLENSGRGVWLVKVPKFLAEKWRKIPNSH---ESGKLRINKTPSD-AKIVLLLNEAIPEKQEREADVGKFPQQYK 82 (254)
T ss_pred hhhhhccccccceEEEEeccHHHHHHHHhccccc---ccccccccCCCCc-ceEEEEeccccccchhhhhhcccCchhhh
Confidence 6789999999999999999999999999866432 7999999876543 44444443 0011134578999999
Q ss_pred eccccCCceeeeeeecC-CcceeEEEEeeeeeEEeeCCCChHHHHHHHHHHhHHhhccccceEEeecCCCcccccCCCcc
Q 024896 86 LNMFKDFVPMSVFSESN-QGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMV 164 (261)
Q Consensus 86 l~~~~~~~~~~VFse~~-~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~~~R~~~a~~pkr~v~~ld~~~~~~~~p~~~~~ 164 (261)
+++..++.|+||||+++ +++++++|+|+|+|+|+|+. |++|++++++|+.+++.|+|+||+||++.|++|+|++||.
T Consensus 83 ~~~~~~~~~~~~~sd~~~~~k~a~eG~V~~e~~~~P~~--ne~Y~Rl~r~r~~k~~~k~r~vQ~iD~~~g~~~~p~~~~~ 160 (254)
T KOG2905|consen 83 LNMKRRFFNMFVESDSSGPKKTAVEGTVVHECDVRPSA--NEEYMRLKRERIVKASKKKRQVQVIDKVVGVHMKPVPGHL 160 (254)
T ss_pred hccCccccceeeeecCCCCccceeeeeeeeeeeccccc--CHHHHHHHHHHHHHhcCcccccccchhhcccccccCCCcc
Confidence 99998999999999987 78999999999999999996 5999999999999999999999999999999999999986
Q ss_pred cccccCcccccccCcccchhhhcccCChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcc
Q 024896 165 GLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGT 244 (261)
Q Consensus 165 ~~~~~~~~~~kk~~~~kk~~~K~~Rm~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~ 244 (261)
..++..+..++ +++.++|++|+|++||+|+||+|||+|+||+||+|+++|+||++||||||++||+||++|||+|+
T Consensus 161 ~~~~~~~~~rk----K~k~e~Kr~R~dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~NkKg~~k~t 236 (254)
T KOG2905|consen 161 RSSSNIAYERK----KAKEEGKRTRRDKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNKKGPYKNT 236 (254)
T ss_pred cccchhHHHHH----hhhhccccccccHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhccCcccCc
Confidence 43333333332 14789999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhhhccccCCCC
Q 024896 245 YELKPEYKKSVEDGGA 260 (261)
Q Consensus 245 weLKpEYk~~~~~~~~ 260 (261)
||||||||++.+++..
T Consensus 237 yeLKPEYK~~~~ee~~ 252 (254)
T KOG2905|consen 237 YELKPEYKKYKEEEKK 252 (254)
T ss_pred eecCHHHhhhhhhhhc
Confidence 9999999999988653
No 2
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=100.00 E-value=1e-69 Score=494.52 Aligned_cols=230 Identities=43% Similarity=0.672 Sum_probs=122.6
Q ss_pred CCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEEecccCCCCCCCCcceeeccccC
Q 024896 12 KGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKD 91 (261)
Q Consensus 12 ~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~l~~~~~~~~~iPkey~l~~~~~ 91 (261)
+++||+++|+++|||||||+|||++|.+..+ +++++||+|+|+.++++ ..+++|.|+.....+..||++|+|+|++.
T Consensus 1 ~~~LD~s~a~~~vWLvKVPk~l~e~W~~~~~-~~~~~iG~lri~~~~~~--~~~v~l~L~~~~~~~~~iPkey~L~~~~~ 77 (275)
T PF02270_consen 1 DGDLDTSKADRSVWLVKVPKFLSEKWSKAPD-DDEIEIGKLRISKDPNG--KPKVSLTLNDSLANHGNIPKEYDLDMSKD 77 (275)
T ss_dssp -TBEE-HHHHTEEEEEEEEHHHHHHHTTSBT-T--TEEEEEEEEEE-TT--EEEEEEEE-HHHHT-T-S--EEEEEEE--
T ss_pred Ccccccccccccccccccccccccccccccc-ccccccccccccccccc--ccccccccccccccccccccccccccccc
Confidence 4799999999999999999999999997654 46789999999987443 33455555544345569999999999999
Q ss_pred C-ceeeeeeecCC-------------------------------------------cceeEEEEeeeeeEEeeCCCChHH
Q 024896 92 F-VPMSVFSESNQ-------------------------------------------GKVAMEGKVEHKFDMKPHEKNMEE 127 (261)
Q Consensus 92 ~-~~~~VFse~~~-------------------------------------------~~~~l~G~V~~e~~~~P~~~~~~~ 127 (261)
. +|+|||||.+. ++++|+|+|+|+|+|+|+. +++
T Consensus 78 ~~~n~~VFse~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~G~I~~~~~~~P~~--~~~ 155 (275)
T PF02270_consen 78 NVQNMYVFSESDQPGFKAKNKERAGAPNAGIPASLLREKKKKDRKRKYQPYVKTIPKKTALEGRIVHECDCRPVL--NDE 155 (275)
T ss_dssp TTEEEEEEEEETT----------------------------------------ETT--EEEEEEEEEEEEE---------
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCceEEEEEEEEEEEeEECC--CHH
Confidence 6 69999998753 4789999999999999996 579
Q ss_pred HHHHHHHHhHHhhccccceEEeecCCCcccccCCCcccccccCcc-cccccCcccchhhhcccCChhHHHHHHHHHhhhC
Q 024896 128 YGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSK-DKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQ 206 (261)
Q Consensus 128 Y~~l~~~R~~~a~~pkr~v~~ld~~~~~~~~p~~~~~~~~~~~~~-~~kk~~~~kk~~~K~~Rm~k~eLld~LF~~Fe~~ 206 (261)
|++++++|+.++++|+|++++|+......+.|++.+. .+.. +. .++|++++|++|||+++|+|+||+|||+|
T Consensus 156 Y~~~~~~r~~~a~~~kr~~~~i~~~~~~~~~~~~~~~----~~~~~~~---~~~k~~~~K~~R~~~~eL~d~lF~~Fe~~ 228 (275)
T PF02270_consen 156 YRRLKRERIEKANKPKRTVQQIDEDVSQSYKPVSFHS----ANSKFFI---KKKKKQEEKRARMDKNELLDLLFKLFEKH 228 (275)
T ss_dssp -------------------------------------------------------------THHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHhcCCCCeeEEeccccccCCCCccccc----ccchhcc---cccccccccceeCCHHHHHHHHHHHHHhC
Confidence 9999999999999999999999986555666643322 1111 11 22467899999999999999999999999
Q ss_pred CCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcccccchhhhc
Q 024896 207 PNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKK 253 (261)
Q Consensus 207 ~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~ 253 (261)
+||+||+|+++|+||++||||||++||+|||+|||+|+|+||||||+
T Consensus 229 ~ywslK~L~~~t~QP~~yLKeiL~eIa~~~k~g~~~~~w~LKpeyk~ 275 (275)
T PF02270_consen 229 QYWSLKDLRQRTQQPEAYLKEILEEIAVLNKRGPHKNMWELKPEYKH 275 (275)
T ss_dssp S-B-HHHHHHH--S-HHHHHHHHHHH--EE--TT---EE----SS--
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHhccCCcCCcEecchHHcC
Confidence 99999999999999999999999999999999999999999999986
No 3
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=100.00 E-value=1.3e-61 Score=422.17 Aligned_cols=242 Identities=32% Similarity=0.487 Sum_probs=203.5
Q ss_pred CCCCCcCCCCCCCcccCCCCCcEEEEeccHHHHHHHhhhcCCCCCCcceEEEEEeCCCCCCCceeEEEecccCCCCCCCC
Q 024896 2 EDDQSNHGNGKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRP 81 (261)
Q Consensus 2 ~~~~~~~~~~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~iGkir~~~~~~~~~~~~~~~~l~~~~~~~~~iP 81 (261)
+.|+-||+.- |||+.+.+.+|||||||.||+++|.+.+ .+.|..+|++|+..+|. .++|.|.. .++++++|
T Consensus 11 ~e~~~yed~~--dLdl~~~~~kVWLvkvP~FLaekw~sr~-~~~g~~lg~~r~~~d~a-----~isLlL~n-e~~n~~~P 81 (297)
T COG5090 11 EEDDRYEDDA--DLDLNNRHTKVWLVKVPLFLAEKWLSRE-AEIGELLGTKRTSTDPA-----VISLLLSN-EFCNGGFP 81 (297)
T ss_pred cccccccccc--cccccccCceEEEEeccHHHHHHHhcch-hhhhhhhceeeecCCcc-----eEEEEecc-CCccCCCC
Confidence 4566777755 8999999999999999999999999654 34567799999986643 45555532 36788999
Q ss_pred cceeeccccCCc-eeeeeeec----CCcceeEEEEeeeeeEEeeCCCChHHHHHHHHHHhHHhhccccceEEeecCCCcc
Q 024896 82 KSYSLNMFKDFV-PMSVFSES----NQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVH 156 (261)
Q Consensus 82 key~l~~~~~~~-~~~VFse~----~~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~~~R~~~a~~pkr~v~~ld~~~~~~ 156 (261)
++|+|.+.++.+ +-|||.|+ ..+.|+|+|+|.|||++.|.. |++|+++++.|..++..+++.||+||...|+.
T Consensus 82 ~~ydl~i~~k~v~n~yVfre~et~t~~k~tavvGtV~hEC~V~P~v--Nd~Y~r~~q~r~~~~~~~K~~vq~iD~~~g~~ 159 (297)
T COG5090 82 SSYDLKIKPKDVNNYYVFRESETSTHEKNTAVVGTVNHECYVTPEV--NDEYLRYKQDRGFKSDSKKSDVQVIDYLKGGK 159 (297)
T ss_pred cceeeeeccccccceEEEecccccccccccceeeeeccceeecccc--cHHHHHHHHHhhhhhcCccccceeeecccCce
Confidence 999999999877 57899654 357899999999999999986 68999999999999999999999999988877
Q ss_pred cccCCCcccccccCcccccccCcccchhhhcccCChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhh
Q 024896 157 MRPMPGMVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYN 236 (261)
Q Consensus 157 ~~p~~~~~~~~~~~~~~~kk~~~~kk~~~K~~Rm~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~ln 236 (261)
..+ +..++.+++..+++...++.+...|+.|||++||+|+||+||++|+||++|+|+++++||++||||||++||+||
T Consensus 160 ~~~--~~~s~Rs~~~~fl~~~r~k~~~~~K~~RlpknEvlD~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~iavLn 237 (297)
T COG5090 160 RGE--KFGSLRSSTLEFLARKRKKMLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLN 237 (297)
T ss_pred ecc--CccccccchHHHHHhcchhhhcchhhcccchhHHHHHHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHHhhh
Confidence 765 222223334455544444456788999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCcccccchhhhcccc
Q 024896 237 KRGTNQGTYELKPEYKKSVE 256 (261)
Q Consensus 237 k~Gp~~~~weLKpEYk~~~~ 256 (261)
|+|||+++|+|+|||+...+
T Consensus 238 Kkgpya~kY~LrPEYK~~~d 257 (297)
T COG5090 238 KKGPYANKYELRPEYKQTMD 257 (297)
T ss_pred ccCcccceeecCHHHHhHHH
Confidence 99999999999999998754
No 4
>PF09734 Tau95: RNA polymerase III transcription factor (TF)IIIC subunit; InterPro: IPR019136 Transcription factor IIIC (TFIIIC) is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents subunit 5 (also known as the tau 95 subunit) which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable []. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.
Probab=95.24 E-value=0.022 Score=52.90 Aligned_cols=57 Identities=26% Similarity=0.362 Sum_probs=52.7
Q ss_pred CChhHHHHHHHHHhhhCCCcchHHHHHHcCC--cHHHHHHHHHHhhhhhccCCCCcccc
Q 024896 190 RDRGELEDIMFKLFERQPNWALKQLVQETDQ--PAQFLKEILNELCVYNKRGTNQGTYE 246 (261)
Q Consensus 190 m~k~eLld~LF~~Fe~~~yWslK~L~~~t~Q--Pe~yLKevL~eIa~lnk~Gp~~~~we 246 (261)
-...+++..|=.|||+.+-|+-+.|...+.. -...||.+|--+|=+=++||++..|-
T Consensus 231 ~~~~~~~~~l~~lFeeRPIW~r~~L~~~~~~~~~~~~~k~~l~~v~Y~f~~GPwr~~~v 289 (310)
T PF09734_consen 231 PVLQELIQELKKLFEERPIWTRRALLNHLPKSGSQSKLKRALPYVAYYFKNGPWRDCWV 289 (310)
T ss_pred hhHHHHHHHHHHHHhcCCccCHHHHHHhhhhcccHHHHHHHHHhhEEEEecCcccceeE
Confidence 3447889999999999999999999999999 58899999999999999999999994
No 5
>PF12157 DUF3591: Protein of unknown function (DUF3591); InterPro: IPR022591 This functionally uncharacterised domain is found centrally in the eukaryotic transcription initiation factor TFIID subunit 1.
Probab=94.95 E-value=0.049 Score=53.52 Aligned_cols=70 Identities=21% Similarity=0.445 Sum_probs=60.6
Q ss_pred hcccCChhHHHHHHHHHhh--hCCCcchHHHHHHc-CCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccc
Q 024896 186 KRTRRDRGELEDIMFKLFE--RQPNWALKQLVQET-DQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSV 255 (261)
Q Consensus 186 K~~Rm~k~eLld~LF~~Fe--~~~yWslK~L~~~t-~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~ 255 (261)
|..-.-++-|.-.+|.+|. ...--++.+|.... .|.+.=+++-|++.|.|.|.|...+.|.|||.|+--.
T Consensus 234 ~~t~~~knrL~~~iyRlf~~~~~~ri~~~di~~~Fp~~se~~iRkrLKe~~~~~R~g~~~~~W~lk~~~~lp~ 306 (457)
T PF12157_consen 234 KVTNFSKNRLKMIIYRLFNKSQPRRIKVDDIKKHFPDQSESQIRKRLKEFADFQRTGDDSGWWVLKPGFRLPD 306 (457)
T ss_pred hHHHHHHHHHHHHHHHHHhhccCCccCHHHHHHhCCCCcHHHHHHHHHHHHhccCCCCCCCeEEECCCCCCCC
Confidence 4555778889999999998 44469999999985 7899999999999999999999999999999877443
No 6
>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=92.48 E-value=0.13 Score=55.79 Aligned_cols=73 Identities=22% Similarity=0.391 Sum_probs=65.6
Q ss_pred hhcccCChhHHHHHHHHHhhhCCC----cchHHHHHHc-CCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccccC
Q 024896 185 VKRTRRDRGELEDIMFKLFERQPN----WALKQLVQET-DQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSVED 257 (261)
Q Consensus 185 ~K~~Rm~k~eLld~LF~~Fe~~~y----WslK~L~~~t-~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~~~ 257 (261)
.|..-+-+|=|+-.||.+|-+..- -.|.+|.... .|-++-+|.-|++.|.|.|.|+-.|.|.|||.|+-..++
T Consensus 688 Kk~tt~~~nrLkv~IYRlF~~s~~g~r~I~id~lsk~Fp~~se~siRKrLKecad~kR~G~~~~~W~LK~df~lp~ee 765 (1563)
T KOG0008|consen 688 KKLTTFLRNRLKVFIYRLFWKSDSGPRRIRIDDLSKAFPDQSESSIRKRLKECADFKRDGMGKNYWVLKPDFRLPDEE 765 (1563)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcCCCCcceehhHHHhhCcccchHHHHHHHHHHHHHhhcCCCCCeeEecccccCCCHH
Confidence 466678889999999999988887 8899998876 889999999999999999999999999999999977655
No 7
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=90.82 E-value=0.35 Score=46.80 Aligned_cols=55 Identities=27% Similarity=0.387 Sum_probs=48.8
Q ss_pred HHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCCCcccccchhh
Q 024896 194 ELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEY 251 (261)
Q Consensus 194 eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEY 251 (261)
-..|.|--+|.++.+-+-++|...|+-|..=+||||++||+++ |....|+||=.+
T Consensus 337 ~aRD~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~---~~~~~W~lk~~~ 391 (421)
T PF04801_consen 337 RARDYILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAVLR---PSNRGWKLKLPP 391 (421)
T ss_pred hhHHHHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhhcc---CCCCceEEccCc
Confidence 4568888999999999999999999999999999999999988 567889997543
No 8
>PF04004 Leo1: Leo1-like protein; InterPro: IPR007149 Members of this family are part of the Paf1/RNA polymerase II complex [, ]. The Paf1 complex probably functions during the elongation phase of transcription [].
Probab=90.57 E-value=2.9 Score=35.77 Aligned_cols=39 Identities=18% Similarity=0.354 Sum_probs=28.1
Q ss_pred eeeeeeecC-CcceeEEEEeeeeeEEeeCCCChHHHHHHH
Q 024896 94 PMSVFSESN-QGKVAMEGKVEHKFDMKPHEKNMEEYGRLC 132 (261)
Q Consensus 94 ~~~VFse~~-~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~ 132 (261)
..|+|.... .+-+...|.|.+++.++|...++...+++.
T Consensus 99 ~~~L~~~~~~~~~l~~~~~i~~~l~~rP~s~~s~thr~l~ 138 (171)
T PF04004_consen 99 HNYLFVRHGSSGVLQGQGHITKKLTFRPASTDSATHRRLT 138 (171)
T ss_pred cceEEEEcCCcceEEEEEEecccEEEecCCccCHHHHHHH
Confidence 477887654 356889999999999999764344445444
No 9
>KOG2473 consensus RNA polymerase III transcription factor (TF)IIIC subunit [Transcription]
Probab=87.89 E-value=0.86 Score=44.86 Aligned_cols=56 Identities=23% Similarity=0.334 Sum_probs=49.5
Q ss_pred ChhHHHHHHHHHhhhCCCcchHHHHH-HcCCcHHHHHHHHHHhhhhhccCCCCcccc
Q 024896 191 DRGELEDIMFKLFERQPNWALKQLVQ-ETDQPAQFLKEILNELCVYNKRGTNQGTYE 246 (261)
Q Consensus 191 ~k~eLld~LF~~Fe~~~yWslK~L~~-~t~QPe~yLKevL~eIa~lnk~Gp~~~~we 246 (261)
.-+|++-.|=.+|++.+-|+-+.|.. .++==.-+||-+|--||-|-.+||++++|-
T Consensus 229 ~~~e~~~~l~eLF~~RPIWtR~al~~~~~~~~~h~LK~~Lp~~AYyfssGPwr~~wi 285 (484)
T KOG2473|consen 229 SLEEVLRSLRELFEERPIWTRRALLYKELGCTHHKLKRFLPLIAYYFSSGPWRRLWI 285 (484)
T ss_pred hhHHHHHHHHHHHHhCchhhHHhHhhcccCccHHHHHHHHHHHHHHhccCchhceee
Confidence 44677778888999999999999999 566667899999999999999999999994
No 10
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=87.70 E-value=0.68 Score=47.10 Aligned_cols=70 Identities=27% Similarity=0.324 Sum_probs=58.3
Q ss_pred hhcccCChhHHHHHHHHHhhhCCC--cchHHHHHHc-CCcHHHHHHHHHHhhhhhccCCCCcccccchhhhccc
Q 024896 185 VKRTRRDRGELEDIMFKLFERQPN--WALKQLVQET-DQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSV 255 (261)
Q Consensus 185 ~K~~Rm~k~eLld~LF~~Fe~~~y--WslK~L~~~t-~QPe~yLKevL~eIa~lnk~Gp~~~~weLKpEYk~~~ 255 (261)
.|-+-|-++-|.-++|.+|...+- -.|.+|.... .|-+.-.++-|+|-+.|.|.||- |.|.|||.=.-..
T Consensus 592 RKvt~~~knRLKm~~fRl~n~~~~g~l~I~ql~khFpdq~egq~Rq~lKEfm~y~kdGp~-g~W~Lk~~e~lld 664 (968)
T COG5179 592 RKVTVFCKNRLKMAAFRLFNSKEGGSLRISQLDKHFPDQSEGQKRQWLKEFMDYVKDGPD-GVWVLKPSEALLD 664 (968)
T ss_pred hhhHHHHhhhHHHHHHHHhhcCCCCceeeehhhhhCCCcchhHHHHHHHHHHHHhhcCCC-ceEEeccccccCC
Confidence 466778889999999999988775 7788887775 78888888888899999999997 9999999654443
No 11
>PF05132 RNA_pol_Rpc4: RNA polymerase III RPC4; InterPro: IPR007811 This family comprises a specific subunit for Pol III, the tRNA specific polymerase.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006383 transcription from RNA polymerase III promoter, 0005666 DNA-directed RNA polymerase III complex
Probab=74.69 E-value=13 Score=30.27 Aligned_cols=20 Identities=30% Similarity=0.572 Sum_probs=17.8
Q ss_pred CCcceeEEEEeeeeeEEeeC
Q 024896 102 NQGKVAMEGKVEHKFDMKPH 121 (261)
Q Consensus 102 ~~~~~~l~G~V~~e~~~~P~ 121 (261)
..+.....|.|.+++.|.|.
T Consensus 111 ~~~~~~~LG~v~~k~v~tPd 130 (131)
T PF05132_consen 111 EEGECYFLGQVSGKFVVTPD 130 (131)
T ss_pred CCCeEEEeccccceEEEccC
Confidence 55788999999999999995
No 12
>KOG2428 consensus Uncharacterized conserved protein [Function unknown]
Probab=66.82 E-value=19 Score=35.27 Aligned_cols=45 Identities=16% Similarity=0.343 Sum_probs=31.8
Q ss_pred eeeeecCCcceeEEEEeeeeeEEeeCCCChHHHHHHHHHHhHHhhc
Q 024896 96 SVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMI 141 (261)
Q Consensus 96 ~VFse~~~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~~~R~~~a~~ 141 (261)
+.|..... -+.-.|.|.+++..+|+..+...+++|...++....+
T Consensus 243 hl~vrq~t-~l~~Q~~ik~kltFrP~S~~S~tHrklt~~~a~r~~k 287 (443)
T KOG2428|consen 243 HLFVRQGT-GLQGQAVIKKKLTFRPHSTDSATHRKLTLNRADRSQK 287 (443)
T ss_pred eeEEeccc-ccchhheeeceeEeeccccchHHHHHHHHHHhhcccc
Confidence 44544332 2455779999999999987667788888888775443
No 13
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=61.32 E-value=6 Score=25.72 Aligned_cols=15 Identities=20% Similarity=0.527 Sum_probs=14.1
Q ss_pred CcHHHHHHHHHHhhh
Q 024896 220 QPAQFLKEILNELCV 234 (261)
Q Consensus 220 QPe~yLKevL~eIa~ 234 (261)
.|++||+.||+.|+.
T Consensus 12 ~P~~yL~~vL~~i~~ 26 (39)
T PF13817_consen 12 NPYAYLTDVLERIPN 26 (39)
T ss_pred CHHHHHHHHHHHHcc
Confidence 499999999999998
No 14
>KOG3122 consensus DNA-directed RNA polymerase III subunit [Transcription]
Probab=58.08 E-value=21 Score=33.57 Aligned_cols=62 Identities=21% Similarity=0.303 Sum_probs=40.0
Q ss_pred CCCcceEEEEEeCCCCCCCceeEEEecccCCCCCCCCcceeeccccC---Cc-eeeeeeec-CCcceeEEEEeeeeeEEe
Q 024896 45 DSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKD---FV-PMSVFSES-NQGKVAMEGKVEHKFDMK 119 (261)
Q Consensus 45 ~~~~iGkir~~~~~~~~~~~~~~~~l~~~~~~~~~iPkey~l~~~~~---~~-~~~VFse~-~~~~~~l~G~V~~e~~~~ 119 (261)
.+++||+|++.+. | +++|.|-+. -|++.|.-+ .+ .++|=... +.+...+.|.|.|++.|.
T Consensus 243 ~eGqvGkllV~KS--G----rVkLklG~V---------~fDV~~G~~~~FLQEl~sV~l~d~rs~nm~~LG~v~~klvvT 307 (310)
T KOG3122|consen 243 PEGQVGKLLVYKS--G----RVKLKLGDV---------LFDVSMGLDCSFLQELMSVGLGDSRSGNMTLLGSVKKKLVVT 307 (310)
T ss_pred CcCcceeEEEEec--C----ceEEEecCE---------EEEeccCchhHhhhhhheeecccccCCceEEeccccceeeeC
Confidence 3568999999863 2 455555331 155555433 12 23442222 578899999999999999
Q ss_pred eC
Q 024896 120 PH 121 (261)
Q Consensus 120 P~ 121 (261)
|.
T Consensus 308 PD 309 (310)
T KOG3122|consen 308 PD 309 (310)
T ss_pred CC
Confidence 95
No 15
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=54.90 E-value=23 Score=29.93 Aligned_cols=55 Identities=15% Similarity=0.227 Sum_probs=40.8
Q ss_pred hHHHHHHHHHhhh-CCCcchHHHHHHcCCcHHHHHHHHHHhhh--hh--ccCCCCcccccc
Q 024896 193 GELEDIMFKLFER-QPNWALKQLVQETDQPAQFLKEILNELCV--YN--KRGTNQGTYELK 248 (261)
Q Consensus 193 ~eLld~LF~~Fe~-~~yWslK~L~~~t~QPe~yLKevL~eIa~--ln--k~Gp~~~~weLK 248 (261)
=.|.-+++=+|.. .+.|++++|.++++-|..||.+||..... |. .+|+ .+-|.|.
T Consensus 9 yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~-~GGy~La 68 (164)
T PRK10857 9 YAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGP-GGGYLLG 68 (164)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCC-CCCeecc
Confidence 3466677777754 46899999999999999999999987653 22 2465 4457774
No 16
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=51.11 E-value=31 Score=27.83 Aligned_cols=55 Identities=15% Similarity=0.291 Sum_probs=39.6
Q ss_pred HHHHHHHHHhhh-CCCcchHHHHHHcCCcHHHHHHHHHHhhh---hhc-cCCCCcccccch
Q 024896 194 ELEDIMFKLFER-QPNWALKQLVQETDQPAQFLKEILNELCV---YNK-RGTNQGTYELKP 249 (261)
Q Consensus 194 eLld~LF~~Fe~-~~yWslK~L~~~t~QPe~yLKevL~eIa~---lnk-~Gp~~~~weLKp 249 (261)
.|.-+++=++.. .+.|+.++|.++++-|..||..||..... ++. +|+ .+-|.|..
T Consensus 10 Al~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~-~Ggy~l~~ 69 (135)
T TIGR02010 10 AVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGP-GGGYQLGR 69 (135)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCC-CCCEeccC
Confidence 355666666643 35899999999999999999999987743 222 354 45677653
No 17
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=50.52 E-value=39 Score=24.81 Aligned_cols=41 Identities=24% Similarity=0.415 Sum_probs=29.7
Q ss_pred CcchHHHHHHcCCcHHHHHHHHHHhhhh----hccCCCCcccccch
Q 024896 208 NWALKQLVQETDQPAQFLKEILNELCVY----NKRGTNQGTYELKP 249 (261)
Q Consensus 208 yWslK~L~~~t~QPe~yLKevL~eIa~l----nk~Gp~~~~weLKp 249 (261)
.+++++|.++++-|..||..+|.....- ..+|+ .+-|.|..
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~-~GGy~L~~ 69 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGR-GGGYRLAR 69 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETST-TSEEEESS
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCC-CCceeecC
Confidence 4999999999999999999999887542 23554 45555544
No 18
>PF13565 HTH_32: Homeodomain-like domain
Probab=45.74 E-value=21 Score=25.48 Aligned_cols=29 Identities=17% Similarity=0.505 Sum_probs=25.1
Q ss_pred hhHHHHHHHHHhhhCCCcchHHHHHHcCC
Q 024896 192 RGELEDIMFKLFERQPNWALKQLVQETDQ 220 (261)
Q Consensus 192 k~eLld~LF~~Fe~~~yWslK~L~~~t~Q 220 (261)
..++.+.|..++.+++.|+.+.|.+.+.+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~ 60 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEE 60 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 57788999999999999999999886543
No 19
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=45.58 E-value=44 Score=22.24 Aligned_cols=37 Identities=11% Similarity=0.257 Sum_probs=29.4
Q ss_pred HHHHHhhhCCC-cchHHHHHHcCCcHHHHHHHHHHhhh
Q 024896 198 IMFKLFERQPN-WALKQLVQETDQPAQFLKEILNELCV 234 (261)
Q Consensus 198 ~LF~~Fe~~~y-WslK~L~~~t~QPe~yLKevL~eIa~ 234 (261)
.|+.+|.+++- |++.+|.++++=|-+-+--+|...+.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47788877776 99999999999999988777766543
No 20
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=43.90 E-value=78 Score=22.52 Aligned_cols=59 Identities=19% Similarity=0.291 Sum_probs=43.8
Q ss_pred ChhHHHHHHHHHhhhCCC--cchHHHHHHcCCcHHHHHHHHHHhh---hhhccCCCCcccccch
Q 024896 191 DRGELEDIMFKLFERQPN--WALKQLVQETDQPAQFLKEILNELC---VYNKRGTNQGTYELKP 249 (261)
Q Consensus 191 ~k~eLld~LF~~Fe~~~y--WslK~L~~~t~QPe~yLKevL~eIa---~lnk~Gp~~~~weLKp 249 (261)
+.+.+.+.|..++.++.- .+.++|...++.|..=+..+|...- -..+.+.....|.|..
T Consensus 3 ~~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 3 TQDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred CchHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEeec
Confidence 456788999999999987 9999999999999987777765432 2233333337888754
No 21
>PF05595 DUF771: Domain of unknown function (DUF771) ; InterPro: IPR008489 This entry is represented by Bacteriophage bIL285, Orf7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis.
Probab=42.65 E-value=36 Score=25.92 Aligned_cols=39 Identities=31% Similarity=0.482 Sum_probs=26.4
Q ss_pred ChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHH-HHH
Q 024896 191 DRGELEDIMFKLFERQPNWALKQLVQETDQPAQFLKE-ILN 230 (261)
Q Consensus 191 ~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKe-vL~ 230 (261)
++.++..++-.. ....+|+|++|+.+|+--..+|++ ||.
T Consensus 7 ~k~ey~el~~~~-~~~~~W~~~dl~k~~~~s~~wi~~~il~ 46 (91)
T PF05595_consen 7 DKEEYEELKKKD-LEGKWWDMKDLRKRTGKSREWIKENILY 46 (91)
T ss_pred eHHHHHHHHHHh-hccceeeHHHHHHHHCCCHHHHHHHccc
Confidence 344444443333 455679999999999988889874 444
No 22
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=38.72 E-value=68 Score=24.44 Aligned_cols=64 Identities=17% Similarity=0.333 Sum_probs=41.0
Q ss_pred ChhHHHHHHHHHhhhCCCcchHHHHHHcCCc--------HHHHHHHHHHhhhhhc---cCCCCcccccchhhhcc
Q 024896 191 DRGELEDIMFKLFERQPNWALKQLVQETDQP--------AQFLKEILNELCVYNK---RGTNQGTYELKPEYKKS 254 (261)
Q Consensus 191 ~k~eLld~LF~~Fe~~~yWslK~L~~~t~QP--------e~yLKevL~eIa~lnk---~Gp~~~~weLKpEYk~~ 254 (261)
|++-+.-.+.++|=+..-.+..+|-+....- .+-+==+=..+++|+- +---.+.|+||++|+..
T Consensus 8 D~~GiRr~vL~~fl~~~~~T~~di~e~L~~~f~vs~~~VasMVG~i~SrlGIL~~~k~~~g~~~~Y~LKe~Y~~l 82 (83)
T PF10826_consen 8 DKDGIRRAVLKLFLKGKKFTTDDIYERLKEKFDVSYRGVASMVGLIHSRLGILSIHKDSYGDHNVYSLKEKYADL 82 (83)
T ss_pred CCccHHHHHHHHHHhCCCeeHHHHHHHHHHHcCchHHHHHHHHHHHHHhhhheeecccccCCccEEEecHHhhcc
Confidence 5556667778888888888888887765431 1223333345555554 21136899999999864
No 23
>PF08208 RNA_polI_A34: DNA-directed RNA polymerase I subunit RPA34.5; InterPro: IPR013240 This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription [].; PDB: 3NFG_N.
Probab=36.15 E-value=12 Score=32.36 Aligned_cols=15 Identities=27% Similarity=0.771 Sum_probs=12.0
Q ss_pred CCCcEEEEeccHHHH
Q 024896 20 ADRSVWLMKCPLVVA 34 (261)
Q Consensus 20 a~~~vWLvKVPk~L~ 34 (261)
.+.+|||+++|..|-
T Consensus 3 ~~kelWlI~~P~~~~ 17 (198)
T PF08208_consen 3 DGKELWLIKAPASFP 17 (198)
T ss_dssp TTEEEEEEEEETTS-
T ss_pred CCCEEEEEeCCCCCC
Confidence 466899999998775
No 24
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=35.73 E-value=1.3e+02 Score=20.34 Aligned_cols=43 Identities=19% Similarity=0.261 Sum_probs=30.7
Q ss_pred CCCcchHHHHHHcCCcHHHHHHHHHHhhh--hhccCCCCcccccch
Q 024896 206 QPNWALKQLVQETDQPAQFLKEILNELCV--YNKRGTNQGTYELKP 249 (261)
Q Consensus 206 ~~yWslK~L~~~t~QPe~yLKevL~eIa~--lnk~Gp~~~~weLKp 249 (261)
...++..+|.+.++=+...+..+|..... +...-+ .+.|.|.|
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~-~~~~~l~~ 67 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG-RGKYRVNP 67 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC-CCeEEeCC
Confidence 34699999999999999988888876654 222222 46677654
No 25
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=32.26 E-value=1.3e+02 Score=21.76 Aligned_cols=55 Identities=18% Similarity=0.338 Sum_probs=39.2
Q ss_pred HHHHHhhhC-CCcchHHHHHHcCCcHHHHHHHHHHhhh--hhccCCCCcccccchhhh
Q 024896 198 IMFKLFERQ-PNWALKQLVQETDQPAQFLKEILNELCV--YNKRGTNQGTYELKPEYK 252 (261)
Q Consensus 198 ~LF~~Fe~~-~yWslK~L~~~t~QPe~yLKevL~eIa~--lnk~Gp~~~~weLKpEYk 252 (261)
.|+.+|.++ ...++.+|.+.++=|.+-+...|...+. |-.+.+..+.|.|-+..-
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~ 66 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVL 66 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeecHHHH
Confidence 355666666 6899999999999999988888876643 223333456788877543
No 26
>smart00076 IFabd Interferon alpha, beta and delta. Interferons produce antiviral and antiproliferative responses in cells. They are classified into five groups, all of them related but gamma-interferon.
Probab=28.48 E-value=79 Score=25.38 Aligned_cols=44 Identities=20% Similarity=0.357 Sum_probs=33.6
Q ss_pred hHHHHHHHHHhhhCC---CcchH---HHHHHcCCcHHHHHHHHHHhhhhh
Q 024896 193 GELEDIMFKLFERQP---NWALK---QLVQETDQPAQFLKEILNELCVYN 236 (261)
Q Consensus 193 ~eLld~LF~~Fe~~~---yWslK---~L~~~t~QPe~yLKevL~eIa~ln 236 (261)
-+++..||.+|..+. .|+-. .|...+.|=..+|+++|.+...-.
T Consensus 24 ~emlqqif~lF~~~~ssa~W~~t~le~~l~~L~~Ql~~Le~Cl~~~~~~~ 73 (117)
T smart00076 24 HEMLQQIFNIFSSPSSSAAWNETLLESLLNELHQQLNHLEACLKQEMEEE 73 (117)
T ss_pred HHHHHHHHHHHcCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 689999999998774 48754 555556777889999998866443
No 27
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=27.56 E-value=24 Score=32.58 Aligned_cols=141 Identities=20% Similarity=0.370 Sum_probs=39.8
Q ss_pred CcceeEEEEeeeeeEEeeCCCChHHHHHHHHHHhHHhhcc--ccceEEeecC---CC--ccc-ccCCCcccccccCcccc
Q 024896 103 QGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIK--NRQIQVIDND---HG--VHM-RPMPGMVGLISSNSKDK 174 (261)
Q Consensus 103 ~~~~~l~G~V~~e~~~~P~~~~~~~Y~~l~~~R~~~a~~p--kr~v~~ld~~---~~--~~~-~p~~~~~~~~~~~~~~~ 174 (261)
.+.+.-.|.|.++..+-.. ++.|.. -++|...+..- .|.+.+|... .+ +.+ ++ +..+......+...
T Consensus 97 ~~~L~~lG~iq~KitV~At---dDSy~~-Tr~rmaq~Eee~k~~~t~~ik~~~~~~~~~~~~~~~-~~~~~~~~p~a~~~ 171 (284)
T PF10390_consen 97 PSQLSCLGSIQDKITVCAT---DDSYQA-TRERMAQAEEETKSRCTKVIKPGSSYVGKKVQIRKP-PSSISDSDPLASSR 171 (284)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCccceeeeccceeEEecc---cchhHh-HHHHHHHHhhhccccccccccCCCcCcCcccccccC-CccCCCCCcccccc
Confidence 4678899999999998776 477876 66666655543 3444454421 11 111 11 10000000000001
Q ss_pred cccCcc------cchhh-hcccCChhHHHHHHHHHhhhCCCcchHHHHHHcCC------cHHHHHHHHHHhhhhhccCCC
Q 024896 175 KKAQPV------KQTEV-KRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQ------PAQFLKEILNELCVYNKRGTN 241 (261)
Q Consensus 175 kk~~~~------kk~~~-K~~Rm~k~eLld~LF~~Fe~~~yWslK~L~~~t~Q------Pe~yLKevL~eIa~lnk~Gp~ 241 (261)
+...|. ++... ...-..+..|.+.|-.|-.=.+| +=-+|..+++. --.=|..+|.+||.++ +
T Consensus 172 ~~s~P~~~~~~~r~~~~~~~~~v~~rplReRvIHLLALkpy-kK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~-~--- 246 (284)
T PF10390_consen 172 KQSSPSNSASSSRKQNHRSNSAVSKRPLRERVIHLLALKPY-KKPELLLRLQKDGLSPKDKDELDSILQEVANLN-K--- 246 (284)
T ss_dssp ----------------------STTS-HHHHHHHHHHHS-E-EHHHHHHHHHHH---HHHHHHHHHHHHHCCEEE-T---
T ss_pred CCCCCCcccccccccccCCccccccccccccchhhhhcCcc-ccHHHHHHHHhcCCChHHHHHHHHHHHHHhccC-c---
Confidence 111111 01111 13445667788888888777777 22245444433 2367999999999999 4
Q ss_pred Ccccccchhhhc
Q 024896 242 QGTYELKPEYKK 253 (261)
Q Consensus 242 ~~~weLKpEYk~ 253 (261)
-+.|.||+.+=.
T Consensus 247 ~~~y~Lk~~~yk 258 (284)
T PF10390_consen 247 DNSYTLKDHFYK 258 (284)
T ss_dssp TTEEEE-STHHH
T ss_pred CCeEEehHHHHh
Confidence 579999998643
No 28
>PRK14741 spoVM stage V sporulation protein M; Provisional
Probab=27.11 E-value=49 Score=19.48 Aligned_cols=14 Identities=14% Similarity=0.228 Sum_probs=10.6
Q ss_pred EEEEeccHHHHHHH
Q 024896 24 VWLMKCPLVVAKSW 37 (261)
Q Consensus 24 vWLvKVPk~L~e~W 37 (261)
.|-+|+|+||.---
T Consensus 3 fytiklpkflgg~v 16 (26)
T PRK14741 3 FYTIKLPKFLGGIV 16 (26)
T ss_pred eEEEeccHHHHHHH
Confidence 57789999997543
No 29
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=25.43 E-value=1.9e+02 Score=18.50 Aligned_cols=38 Identities=13% Similarity=0.257 Sum_probs=29.7
Q ss_pred HHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHHhh
Q 024896 196 EDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNELC 233 (261)
Q Consensus 196 ld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~eIa 233 (261)
.-.|+.+..+++.-+.++|.+.++=+.+.+...|++..
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34566777779999999999999999999988887754
No 30
>PF14493 HTH_40: Helix-turn-helix domain
Probab=25.23 E-value=76 Score=23.74 Aligned_cols=34 Identities=9% Similarity=-0.013 Sum_probs=25.5
Q ss_pred CChhHHHHHHHHHhhhCCCcchHHHHHHcCCcHHH
Q 024896 190 RDRGELEDIMFKLFERQPNWALKQLVQETDQPAQF 224 (261)
Q Consensus 190 m~k~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~y 224 (261)
.+++ ..+.|-.+|++..+|+||.|++..+-=..|
T Consensus 50 l~~e-~~~~I~~~~~~~~~~~lk~i~e~l~~~~sy 83 (91)
T PF14493_consen 50 LSEE-EIKQIEDAIEKLGSEKLKPIKEALPGDYSY 83 (91)
T ss_pred CCHH-HHHHHHHHHHHcCcccHHHHHHHCCCCCCH
Confidence 3444 578888899999999999999887643333
No 31
>PHA02571 a-gt.4 hypothetical protein; Provisional
Probab=24.16 E-value=46 Score=26.56 Aligned_cols=36 Identities=25% Similarity=0.421 Sum_probs=24.8
Q ss_pred HHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHHH
Q 024896 194 ELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILNE 231 (261)
Q Consensus 194 eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~e 231 (261)
.-...||.+=...--|.|+-||.+++|| |-.++|+-
T Consensus 52 HAe~al~~~Nk~~Y~YAI~KLR~i~kQp--~~de~i~t 87 (109)
T PHA02571 52 HAEEALFDNNKEQYVYAIKKLRDIYKQP--YTDELIET 87 (109)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHHHHcCC--CcHHHHHH
Confidence 3445666663222228999999999999 77777753
No 32
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=23.80 E-value=2.3e+02 Score=21.33 Aligned_cols=41 Identities=2% Similarity=0.212 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHhhhCC--CcchHHHHHHcCCcHHHHHHHHHHh
Q 024896 192 RGELEDIMFKLFERQP--NWALKQLVQETDQPAQFLKEILNEL 232 (261)
Q Consensus 192 k~eLld~LF~~Fe~~~--yWslK~L~~~t~QPe~yLKevL~eI 232 (261)
.++++..+...-+.+. -|++.+|.+.+.-...||..+..+.
T Consensus 3 ~~~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 3 HQKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred hHHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4455555555555543 3999999999888888887777765
No 33
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=23.13 E-value=1.6e+02 Score=21.74 Aligned_cols=38 Identities=13% Similarity=0.199 Sum_probs=32.7
Q ss_pred hHHHHHHHHHhhhCCCcchHHHHHHcCCcHHHHHHHHH
Q 024896 193 GELEDIMFKLFERQPNWALKQLVQETDQPAQFLKEILN 230 (261)
Q Consensus 193 ~eLld~LF~~Fe~~~yWslK~L~~~t~QPe~yLKevL~ 230 (261)
.+....+|.++...+-+|.+++.++++-++.-++..+.
T Consensus 17 ~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 17 DSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 45677889888777889999999999999999988875
No 34
>KOG0661 consensus MAPK related serine/threonine protein kinase [Signal transduction mechanisms]
Probab=22.20 E-value=1.3e+02 Score=30.29 Aligned_cols=43 Identities=23% Similarity=0.454 Sum_probs=31.4
Q ss_pred HHHHhhhCC-CcchHHHHHHcCCcHHHHHHHHHHhhhhhccCCC-Ccccccchhh
Q 024896 199 MFKLFERQP-NWALKQLVQETDQPAQFLKEILNELCVYNKRGTN-QGTYELKPEY 251 (261)
Q Consensus 199 LF~~Fe~~~-yWslK~L~~~t~QPe~yLKevL~eIa~lnk~Gp~-~~~weLKpEY 251 (261)
||.++.... +.+..+++. |+-+||..+|+.|+.|=| + -||||-
T Consensus 96 LYqLmK~R~r~fse~~irn-------im~QilqGL~hiHk~GfFHR---DlKPEN 140 (538)
T KOG0661|consen 96 LYQLMKDRNRLFSESDIRN-------IMYQILQGLAHIHKHGFFHR---DLKPEN 140 (538)
T ss_pred HHHHHhhcCCcCCHHHHHH-------HHHHHHHHHHHHHhcCcccc---cCChhh
Confidence 666664333 477777764 677899999999999974 4 378874
No 35
>cd00095 IFab Interferon alpha, beta. Includes also interferon omega and tau. Different from interferon gamma family. Type I interferons(alpha, beta) belong to the larger helical cytokine superfamily, which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules. All function as regulators of cellular activty by interacting with cell-surface receptors and activating various signalling pathways. Interferons produce antiviral and antiproliferative responses in cells. Receptor specificity determines function of the various members of the family.
Probab=20.68 E-value=1.3e+02 Score=25.20 Aligned_cols=44 Identities=20% Similarity=0.346 Sum_probs=33.7
Q ss_pred hHHHHHHHHHhhhCC---CcchH---HHHHHcCCcHHHHHHHHHHhhhhh
Q 024896 193 GELEDIMFKLFERQP---NWALK---QLVQETDQPAQFLKEILNELCVYN 236 (261)
Q Consensus 193 ~eLld~LF~~Fe~~~---yWslK---~L~~~t~QPe~yLKevL~eIa~ln 236 (261)
-+++..||.+|..+. .|+-. +|.....|=..+|++++.+.+.-.
T Consensus 56 ~emlqqif~LF~~~~ssa~Wnet~le~fl~~L~~Ql~~Le~C~~~~~~~~ 105 (152)
T cd00095 56 HEMLQQIFNIFSTPSSSAAWNETLLESLLNELHQQLNHLETCLEQEMGEE 105 (152)
T ss_pred HHHHHHHHHHHcCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 689999999998774 48754 555556777889999998876443
Done!