Query 006477
Match_columns 643
No_of_seqs 191 out of 282
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 23:50:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006477.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006477hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2402 Paf1/RNA polymerase II 100.0 3.9E-82 8.5E-87 687.0 26.4 462 80-594 62-525 (525)
2 COG5296 Transcription factor i 100.0 1.1E-74 2.4E-79 602.0 31.2 458 1-521 1-470 (521)
3 smart00719 Plus3 Short conserv 100.0 3.1E-34 6.7E-39 259.8 12.0 108 257-368 1-109 (109)
4 PF03126 Plus-3: Plus-3 domain 100.0 2.4E-32 5.3E-37 246.7 8.6 105 261-369 1-107 (108)
5 KOG2402 Paf1/RNA polymerase II 83.6 1.5 3.3E-05 50.1 5.0 38 96-133 49-86 (525)
6 PF08858 IDEAL: IDEAL domain; 68.5 12 0.00027 27.9 4.7 30 418-447 8-37 (37)
7 PRK03057 hypothetical protein; 68.1 10 0.00022 38.0 5.5 35 419-453 144-178 (180)
8 PRK03636 hypothetical protein; 65.7 11 0.00024 37.8 5.2 34 419-452 145-178 (179)
9 PF06476 DUF1090: Protein of u 53.9 74 0.0016 29.7 8.1 57 417-475 22-78 (115)
10 PF02151 UVR: UvrB/uvrC motif; 53.0 27 0.00058 25.8 4.1 31 422-452 5-35 (36)
11 PF14812 PBP1_TM: Transmembran 44.5 7.4 0.00016 34.3 0.0 15 12-26 9-23 (81)
12 PF06476 DUF1090: Protein of u 41.1 1.9E+02 0.0042 26.9 8.8 33 420-452 78-110 (115)
13 PRK11020 hypothetical protein; 39.3 1.2E+02 0.0026 28.4 7.0 32 422-453 15-46 (118)
14 PF09312 SurA_N: SurA N-termin 39.1 2.9E+02 0.0064 25.2 9.7 62 347-408 5-80 (118)
15 smart00784 SPT2 SPT2 chromatin 37.5 1.1E+02 0.0023 28.7 6.4 32 97-128 62-93 (111)
16 COG5582 Uncharacterized conser 31.2 3.7E+02 0.0081 27.0 9.3 128 281-453 45-180 (182)
17 PF08243 SPT2: SPT2 chromatin 30.0 1.7E+02 0.0037 27.4 6.5 36 98-133 66-103 (116)
18 PF08621 RPAP1_N: RPAP1-like, 27.0 94 0.002 24.8 3.7 37 97-136 4-42 (49)
19 PRK05629 hypothetical protein; 25.2 8.4E+02 0.018 25.9 13.4 89 349-450 120-222 (318)
20 PF03902 Gal4_dimer: Gal4-like 25.1 1E+02 0.0023 25.5 3.6 30 378-407 6-35 (57)
21 cd01248 PH_PLC Phospholipase C 24.7 2.4E+02 0.0053 25.5 6.6 62 302-368 46-113 (115)
22 COG3880 Modulator of heat shoc 24.3 1.3E+02 0.0027 30.2 4.7 59 395-453 101-170 (176)
23 PF04380 BMFP: Membrane fusoge 21.2 3E+02 0.0065 23.8 6.0 73 375-452 6-78 (79)
24 KOG2609 Cyclin D-interacting p 20.9 1E+02 0.0022 32.0 3.5 16 466-481 193-208 (228)
No 1
>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription]
Probab=100.00 E-value=3.9e-82 Score=686.98 Aligned_cols=462 Identities=36% Similarity=0.517 Sum_probs=346.1
Q ss_pred CCCCCCCCCCCCCCCCCCChhhhHhhccCChhHHHHHHhhhHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCchhhhh
Q 006477 80 QEEGDYDGGASEHEGDSSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKFRSRREERSTRSTKETPPLPSSRSARL 159 (643)
Q Consensus 80 ~~~~~~~~~~~p~EgkykDe~DR~~L~~MtElERE~iLaeR~ee~e~~~~r~~l~~~~~k~k~~~rk~~~~~~ssr~~Rs 159 (643)
+++++.-.+||++| +|++++||.+|+.|+|++||+|||+|. .++.+.- +.+... +...+..+++.|+
T Consensus 62 ~e~e~e~e~~~r~E-~yk~~~~R~ki~~~~e~~re~~~~er~-~~q~e~~-rk~~~~----------e~Q~~~~~~~~rs 128 (525)
T KOG2402|consen 62 DEEEDEQENPTRLE-KYKDEADREKIALMLELERETILFERS-KKQKEKR-RKSDVR----------EMQQLSDSRKERS 128 (525)
T ss_pred chhhhhhccccHHH-HHHHHHHHHHHhhhHHHHHHHHHHHHH-HHHHHHH-Hhccch----------hhhcccchhhhhh
Confidence 44455568899999 999999999999999999999999999 2222211 112111 1112234677888
Q ss_pred hhhcccccchhHHHHHHHHHHHhhcCCHHHHHhhhcccCCCCCCcccCccccccCCCCCCCCCCccccccCCCCCCCCCC
Q 006477 160 AARSADRAAAKDDALNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLSSSSQSESESRSHSDDEGST 239 (643)
Q Consensus 160 S~R~~~~~~~K~~AL~eLK~kRekk~~r~~~rr~~d~s~~~s~s~~~sp~~r~~~~s~~~ss~s~~d~e~rs~sdee~~~ 239 (643)
+.|+..+.+.+++||+.|+++|++......+....+.. .+-+.++.+ ..-++++++++.+...++..+.+..
T Consensus 129 s~R~~~~s~~~~~a~s~lk~kR~~~~~~~k~~~e~~~e--~~~sev~~k----~~~~se~~~~~~s~e~s~~~~~~~~-- 200 (525)
T KOG2402|consen 129 SVRSSVRSDKKKSAMSLLKAKRERLEEVKKRNAEKDLE--RSLSEVTYK----RSPSSELGSEDESKEFSRRSSYDQS-- 200 (525)
T ss_pred hhccccccccchhhhHhhhcccchHHHHHHHhhhccch--hchhhhccC----CCCCCCccccccccccchhhccccc--
Confidence 88854455789999999999999543211111111100 111222222 2111222222111111111111111
Q ss_pred CCCCCCCCCCCCCCCCCCCCHhhhhcceechHHHHHhhcCccccccccccEEEEeecCCCCCCceEEEEEEEeecCCCCC
Q 006477 240 GDGGMADSDDDGAPGSGRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNVDATEPDR 319 (643)
Q Consensus 240 ~~~~~~d~~de~~~~~~~atledl~~irLsRs~L~k~~~~P~Fee~V~GCFVRV~IG~~~~g~vYRm~qI~gV~~~e~~K 319 (643)
......+++.+..+.++++||+.|||+|++|++|||+|||+++|+||||||+||.+.++|+||||+|+||. ++.|
T Consensus 201 ---~s~~~~~e~~p~~~v~~~~dln~~rlsR~~vak~~~~P~Fe~~V~gCfvRv~ig~~~~~p~YRv~~I~gV~--es~k 275 (525)
T KOG2402|consen 201 ---SSEEEDEEKDPDARVPSISDLNALRLSRHKVAKWLFSPFFESTVTGCFVRVGIGGEGSKPVYRVAEIVGVL--ESDK 275 (525)
T ss_pred ---cCcchhcccCcccCCCCHHHHHHHHhhHHHHHHHHhhhHHHHHhhhheEEeeecCcCCCCceeEEEEeeec--ccCc
Confidence 11111222234568899999999999999999999999999999999999999998667999999999997 5999
Q ss_pred ccccCCceeeeEEEEEeCCCccceeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhcCCCCHHH
Q 006477 320 SYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAAT 399 (643)
Q Consensus 320 ~Y~l~~~~Tnk~L~L~~G~~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~~~~~~lPT~~~v~~K~~~I~ka~n~~~Teed 399 (643)
||.|+++.||+||.|.||.. .++|+|++|||++||+.||++|+.+|...++.+||++.|..|+.+|.++++|+|++.+
T Consensus 276 ~Y~l~~~~Tnk~l~~~~G~s--~r~f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~sd~~ 353 (525)
T KOG2402|consen 276 PYKLEGVKTNKYLRVRHGRS--ERVFRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRLSDKE 353 (525)
T ss_pred cccccceeecceeeeecCcc--hhhcchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCccCccc
Confidence 99999999999999999986 4899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCCCchhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccc--ccchHHHHHHHHHHHhhHHHH
Q 006477 400 VKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDS--KVKDAKAIRLAEMNRKNRVEN 477 (643)
Q Consensus 400 I~~ml~~K~~~~~~~~N~a~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~~~~~--~~~~~~~~~la~IN~RNRk~N 477 (643)
|.+||++|..+...|.|+||||++|++++++|...||...|+.|+.||.+||+.+.. ....+.+..|++||+|||++
T Consensus 354 v~~~v~~k~~~~~~p~N~ameK~~l~k~r~~A~~~~d~~~a~~~~~qi~elE~~a~~~~~~~~s~i~~~~~lN~rNR~~- 432 (525)
T KOG2402|consen 354 VDQMVAEKFEASPRPRNVAMEKTGLRKERDLAQLLGDAKSAEEIQRQINELEARAEELDKARASPILKLAELNRRNRRR- 432 (525)
T ss_pred HHHHHHhhhhcCcCcchHHHHHHhHHHHHHHHHhcccHhHHHHHHHHHHHHHHHHhhhccccccccccccccchhHHHH-
Confidence 999999999999999999999999999999999999999999999999999998732 22345578899999999999
Q ss_pred HHHHHHHHHHhhhhhcCCCCCCCCcccccccceeccCCCCCccccccCCCCCCCCCCCCCCCCCccccchhhhHHHHHHH
Q 006477 478 FKNASELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVTAEANGDKNGVPGGANGEEGATGEVGMAATEAALEAA 557 (643)
Q Consensus 478 ~~~a~e~k~~~~~~k~ge~~~DPFsRrkTr~k~~y~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~ 557 (643)
++.+. ....+.++.+..+ |||||+||++++||+++++.+++-++.+.. ++.++.++.++..++
T Consensus 433 ~~~a~--~~~~~~~~~~~~~-dpfTRr~~~~~v~~~s~~k~~~~ls~~~~~--------------~~~~~~~~~~~~~~~ 495 (525)
T KOG2402|consen 433 IAKAE--LSGGAVAKNLSAP-DPFTRRKTRTSVLYGSKYKPEGALSAEIAR--------------AGKKLEASEAAEKAA 495 (525)
T ss_pred hhhhh--hhhhhhhhcCCCC-CCccccccccceeecccCCCCchhhccccc--------------cccccCccccccccc
Confidence 54542 1122223344444 999999999999999999998655433221 122222222222221
Q ss_pred hhcCCCcCCCCCCCCCcccccccccccccchhhhhhc
Q 006477 558 AGAGKLVDTNAPLDLGTESNMLHDFELDISLNALKKF 594 (643)
Q Consensus 558 a~~gk~~~~~~~~~~~~~~~~~h~f~l~i~l~~l~~~ 594 (643)
+..+++|++++++.||+|+++|||.+|++|
T Consensus 496 -------~~~s~~~~~~~l~~lh~f~~~ldl~~~~~~ 525 (525)
T KOG2402|consen 496 -------EKRSLIDQSQDLMSLHDFDLDLDLKVLQKF 525 (525)
T ss_pred -------ccccchhhhhhhhhhcccceeecccccCCC
Confidence 234788999999999999999999999876
No 2
>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
Probab=100.00 E-value=1.1e-74 Score=602.00 Aligned_cols=458 Identities=24% Similarity=0.299 Sum_probs=338.3
Q ss_pred CcchHHHHHHHcCCCCCCCCCCCCCCcccccc-CCCCC-CCCCCCCCCcccCCCCCCCCCCCCCcccccCCCCCCCCCCC
Q 006477 1 MADLENLLLEAAGRTNSAGRNRHSASSSKRRR-EGSYS-GSDSRDDDSDDNRGYGSRKPSGSQVPLKKRLDPAERDDDQG 78 (643)
Q Consensus 1 ~~~~~~~ll~~ag~~~~~~~~~~~~~~s~~~~-~~~~~-~sd~~~~~sd~~~~~~~~~~~~~~~~~~kr~~~~~~~~~~~ 78 (643)
||||+++||++||.++|-. +.|++|. .--.+ .|.++|.|.++...|.. .||-. .+.+
T Consensus 1 MaD~~deLLALAG~DdSd~------as~~KRA~dd~~~v~~~~S~EDnnE~~DY~~--~S~G~-------------~n~~ 59 (521)
T COG5296 1 MADFQDELLALAGIDDSDV------ASNRKRAHDDLDDVLSSSSDEDNNENVDYAE--ESGGE-------------GNEK 59 (521)
T ss_pred CcchHHHHHHHcCCChhhh------hhhhhhhccchhhHhhcCCcccccccccccc--ccCCC-------------CCcc
Confidence 9999999999999997653 3344441 00001 11122223333333322 22111 1111
Q ss_pred CCCCCCCCCCCCCCCCCCCChhhhHhhccCChhHHHHHHhhhHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCchhhh
Q 006477 79 SQEEGDYDGGASEHEGDSSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKFRSRREERSTRSTKETPPLPSSRSAR 158 (643)
Q Consensus 79 ~~~~~~~~~~~~p~EgkykDe~DR~~L~~MtElERE~iLaeR~ee~e~~~~r~~l~~~~~k~k~~~rk~~~~~~ssr~~R 158 (643)
+ + .+..-+||||||||+||+||++||+|||||||.|||||.|+|+++++|+.|+.+.++.... +.. .+ +|
T Consensus 60 S-E-EE~~~NP~~LEGK~KDEaDR~~i~am~EiEREsiLFER~e~i~K~~ERr~~~~R~eqq~r~--~~~----~d--tr 129 (521)
T COG5296 60 S-E-EEKFKNPYRLEGKFKDEADRAKIMAMTEIERESILFEREEEISKLMERRELAIRMEQQHRS--SGC----TD--TR 129 (521)
T ss_pred c-h-hhhhcCCccccccccchhhHHHHhhhhhhhHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhh--ccC----cc--cc
Confidence 1 1 2234799999999999999999999999999999999999999999999998876532211 111 11 67
Q ss_pred hhhhcc--c-ccchhHHHHHHHHHHHhhcCCHHHHHhhhcccCCCCCCcccCccccccCCCCCCCCCCccccccCCCCCC
Q 006477 159 LAARSA--D-RAAAKDDALNELRAKRLKQQDPEAHRRLRDASRGGSGSRVLSPVKRKAFTPAGLSSSSQSESESRSHSDD 235 (643)
Q Consensus 159 sS~R~~--~-~~~~K~~AL~eLK~kRekk~~r~~~rr~~d~s~~~s~s~~~sp~~r~~~~s~~~ss~s~~d~e~rs~sde 235 (643)
.|+|.+ + +...|.++|.+||++|+.+.. -++++ . ..+.+ .+|=.++.++. .+++
T Consensus 130 rstr~~~~T~~a~~k~~kL~eLkk~R~R~~r--------~ysEr---~-----~e~~r------~~Dyke~eese-~g~~ 186 (521)
T COG5296 130 RSTRYEPLTSAAEEKKKKLLELKKTREREER--------LYSER---H-----IELQR------FKDYKELEESE-QGLQ 186 (521)
T ss_pred hhhhcccccchhhhhHHHHHHhHHHHHhhhc--------ccchh---h-----hhhcc------hhhhhhhhhhh-hccc
Confidence 788877 2 347799999999999964321 01100 0 00000 00000000011 0111
Q ss_pred CCCCCCCCCCCCCCCC--C-CCCCCCCHhhhhcceechHHHHHhhcCccccccccccEEEEeecCCCCCCceEEEEEEEe
Q 006477 236 EGSTGDGGMADSDDDG--A-PGSGRPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNGPIYRLCMVRNV 312 (643)
Q Consensus 236 e~~~~~~~~~d~~de~--~-~~~~~atledl~~irLsRs~L~k~~~~P~Fee~V~GCFVRV~IG~~~~g~vYRm~qI~gV 312 (643)
+.+.. ++..+.. + ....-+.|-|||.|+|+|+++++|||+|.|+++|+||||||+||...+..+||||+|.+|
T Consensus 187 eeYtP----s~~~E~vE~is~~d~~a~l~Dfn~~rvgR~~VA~~~f~P~Fed~v~Gcf~Rv~Ig~R~g~~vyRiv~V~~~ 262 (521)
T COG5296 187 EEYTP----SYAEEAVEDISRTDDFAELYDFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVGKG 262 (521)
T ss_pred cccCc----hhHHHHHHhhhhcchhhhhhhhhhhhhhHHHHHHHhcccchhhhhcceeeEEEecccCCeeEEEEEEeccc
Confidence 11111 0011111 1 224566799999999999999999999999999999999999994333399999999999
Q ss_pred ecCCCCCccccCCceeeeEEEEEeCCCccceeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhc
Q 006477 313 DATEPDRSYKLENRTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINT 392 (643)
Q Consensus 313 ~~~e~~K~Y~l~~~~Tnk~L~L~~G~~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~~~~~~lPT~~~v~~K~~~I~ka~n 392 (643)
. ...|||.++.+.||+||.|.||+. .++|+|++|||+||.+.||++|+..|....+.+|++..|..|+.+|..+++
T Consensus 263 ~--~~~kpy~~~~v~Tn~yl~v~~Gr~--~kvF~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d~~~ 338 (521)
T COG5296 263 S--TYSKPYGRKEVKTNRYLDVSTGRT--YKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMG 338 (521)
T ss_pred e--eccccccccceeeeeeEeeecCcc--eeeeEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHhC
Confidence 6 369999999999999999999975 589999999999999999999999999999999999999999999999999
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCchhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccc--cccchHHHHHHHHHH
Q 006477 393 FVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRD--SKVKDAKAIRLAEMN 470 (643)
Q Consensus 393 ~~~TeedI~~ml~~K~~~~~~~~N~a~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~~~~--~~~~~~~~~~la~IN 470 (643)
+++|+.+|.+||..|..+.+.+.|++++|++|++.++.|...||...|.+|+.||.+||...- ++..++....|+++|
T Consensus 339 ~~LSdkeis~~V~~k~e~~~k~sNvi~eKt~Lrqkrq~A~e~~n~k~~~ey~~qL~~~E~~~~~~~hN~ns~~~~L~~v~ 418 (521)
T COG5296 339 RRLSDKEISKMVACKDEVHPKRSNVIHEKTELRQKRQRAIELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVN 418 (521)
T ss_pred CcCchhHHHHHHHHHHhcCccchhHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhhhccccccccchHHHHHhh
Confidence 999999999999999999999999999999999999999999999999999999999999753 222245678899999
Q ss_pred HhhHHHHHHHHH--HHHHHhhhhhcCCCCCCCCcccccccceeccCCCCCccc
Q 006477 471 RKNRVENFKNAS--ELKRVNTSLKAGEAGYDPFSRRWTRSRNYYISKPGEEVT 521 (643)
Q Consensus 471 ~RNRk~N~~~a~--e~k~~~~~~k~ge~~~DPFsRrkTr~k~~y~~~~~~e~~ 521 (643)
+|||++|+.+++ |.+..+.+ ..-....|||||++|++..||+++....|.
T Consensus 419 ~rNRr~N~t~IR~AE~~~~Eea-~~~~~~S~P~S~L~~~s~~~~~~I~~~~N~ 470 (521)
T COG5296 419 ERNRRRNHTEIRLAEQRMNEEA-ATATPMSAPTSVLTQPSPSLSTSIMPKLNP 470 (521)
T ss_pred hhhhhccchhhhhHHHHhhhhh-ccCCccCCcchhhcCCCcchHhhhccccCc
Confidence 999999988764 22222211 112234799999999999999999877753
No 3
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=100.00 E-value=3.1e-34 Score=259.79 Aligned_cols=108 Identities=36% Similarity=0.653 Sum_probs=102.2
Q ss_pred CCCHhhhhcceechHHHHHhhcCccccccccccEEEEeecCCCCC-CceEEEEEEEeecCCCCCccccCCceeeeEEEEE
Q 006477 257 RPTYDDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNG-PIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVT 335 (643)
Q Consensus 257 ~atledl~~irLsRs~L~k~~~~P~Fee~V~GCFVRV~IG~~~~g-~vYRm~qI~gV~~~e~~K~Y~l~~~~Tnk~L~L~ 335 (643)
.++|++|++|+|+|++|++||++|+|+++|+||||||+||+++.+ ++||||+|+||. +++++|+++++.||+||.|+
T Consensus 1 ~~~l~~l~~i~L~R~~l~~~~~~p~Fe~~v~GcFVRv~ig~~~~~~~~Yrl~qI~gv~--~~~k~Y~~~~~~t~~~L~v~ 78 (109)
T smart00719 1 AIVFDNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKQPIYRLVQVTGVK--EADKPYELGGKTTNVLLEVL 78 (109)
T ss_pred CCChHHhheEEEEHHHHHHHhcCCchhHhceEeEEEEEECCCCCCCCeEEEEEEeeEE--ecCcceecCCceeeEEEEEe
Confidence 368999999999999999999999999999999999999999865 999999999997 47999999999999999999
Q ss_pred eCCCccceeeeeeeccCCcCCHHHHHHHHHHHH
Q 006477 336 WGNESSAARWQMAMVSDSPPLEEEFKQWLREVE 368 (643)
Q Consensus 336 ~G~~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~ 368 (643)
||+. .+.|+|++|||+|||++||++|+++|.
T Consensus 79 ~g~~--~~~~~i~~iSn~~fte~E~~~w~~~~~ 109 (109)
T smart00719 79 NGDS--EKVVQINFISNQDFTEEEFQRWKQAIK 109 (109)
T ss_pred cCCc--eEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence 9987 478999999999999999999999873
No 4
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=99.97 E-value=2.4e-32 Score=246.69 Aligned_cols=105 Identities=46% Similarity=0.904 Sum_probs=90.8
Q ss_pred hhhhcceechHHHHHhhcCccccccccccEEEEeecCCCCC--CceEEEEEEEeecCCCCCccccCCceeeeEEEEEeCC
Q 006477 261 DDIKEITIRRSKLAKWFMEPFFEELIVGCFVRVGIGRSKNG--PIYRLCMVRNVDATEPDRSYKLENRTTCKYLNVTWGN 338 (643)
Q Consensus 261 edl~~irLsRs~L~k~~~~P~Fee~V~GCFVRV~IG~~~~g--~vYRm~qI~gV~~~e~~K~Y~l~~~~Tnk~L~L~~G~ 338 (643)
++|++|+|+|++|++||++|+|+++|+||||||+||++..+ ++||||+|+||.. ..++|+|+++.||++|.|+||+
T Consensus 1 e~i~~i~l~Rs~l~~~~~~P~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~v~~--~~k~Y~~~~~~t~~~L~l~~g~ 78 (108)
T PF03126_consen 1 EDIKRIRLSRSQLEKWLFKPFFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVGVKE--GKKPYKLGSKKTNKYLVLRHGN 78 (108)
T ss_dssp HHHHHTBE-HHHHHHHTTSTTHHHHHTT-EEEEEEETTSSS-E--EEEEEEEEEEE--EEEEEEETTEEEEEEEEEEETT
T ss_pred CchHeEEEEHHHHHHHHcCCChhHheeEEEEEEEecCCCCCCceeEEEEEEEEEec--ccccEecCCeEEEEEEEEEECC
Confidence 68999999999999999999999999999999999998864 5799999999984 4589999999999999999999
Q ss_pred CccceeeeeeeccCCcCCHHHHHHHHHHHHh
Q 006477 339 ESSAARWQMAMVSDSPPLEEEFKQWLREVER 369 (643)
Q Consensus 339 ~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~~ 369 (643)
. .+.|+|++|||+|||++||.+|+++|++
T Consensus 79 ~--~r~~~i~~vSn~~~te~E~~~w~~~~~~ 107 (108)
T PF03126_consen 79 S--ERDFPIDMVSNSPFTEEEFERWKQSCEK 107 (108)
T ss_dssp E--EEEEEGGGBBSS---HHHHHHHHHHH--
T ss_pred c--eeEEEeEeeECCCCCHHHHHHHHHHhcc
Confidence 6 5899999999999999999999999986
No 5
>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription]
Probab=83.61 E-value=1.5 Score=50.13 Aligned_cols=38 Identities=24% Similarity=0.209 Sum_probs=30.2
Q ss_pred CCChhhhHhhccCChhHHHHHHhhhHHHHHHHHHHHHH
Q 006477 96 SSNESDDDNHGQMTELEREMMIFERDDKKVDKNLRDKF 133 (643)
Q Consensus 96 ykDe~DR~~L~~MtElERE~iLaeR~ee~e~~~~r~~l 133 (643)
.-+.+|+.+|..|+|.|+|+.+|.|+|+......|..|
T Consensus 49 ~~~~e~~~~~~~~~e~e~e~e~~~r~E~yk~~~~R~ki 86 (525)
T KOG2402|consen 49 AADNEDRARLNLLDEEEDEQENPTRLEKYKDEADREKI 86 (525)
T ss_pred hccccccccccccchhhhhhccccHHHHHHHHHHHHHH
Confidence 44778899999999999999999999976654444444
No 6
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=68.45 E-value=12 Score=27.95 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 006477 418 AAEKDRLRRELEVAQSRHDEVDMERIKKRL 447 (643)
Q Consensus 418 a~eK~rL~~ele~A~~~gD~~ev~~l~~qL 447 (643)
.++|..|..+|+.|...||.+.-.+|..+|
T Consensus 8 ~~~~~~L~~~ID~ALd~~D~e~F~~Ls~eL 37 (37)
T PF08858_consen 8 EFRKEQLLELIDEALDNRDKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHhhC
Confidence 478999999999999999999999998876
No 7
>PRK03057 hypothetical protein; Provisional
Probab=68.06 E-value=10 Score=38.04 Aligned_cols=35 Identities=31% Similarity=0.566 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhc
Q 006477 419 AEKDRLRRELEVAQSRHDEVDMERIKKRLQELEAS 453 (643)
Q Consensus 419 ~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~~ 453 (643)
.++.+|+.+|+.|.++||.+.-.+|..+|+.|+.+
T Consensus 144 ~~~~~L~~~ID~ALd~~D~e~F~~Lt~~L~~l~~~ 178 (180)
T PRK03057 144 NEVSRLRMQIDQALDRKDMEEFQRLTEKLKKLEGQ 178 (180)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhc
Confidence 78999999999999999999999999999999653
No 8
>PRK03636 hypothetical protein; Provisional
Probab=65.69 E-value=11 Score=37.77 Aligned_cols=34 Identities=21% Similarity=0.474 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHh
Q 006477 419 AEKDRLRRELEVAQSRHDEVDMERIKKRLQELEA 452 (643)
Q Consensus 419 ~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~ 452 (643)
++|.+|+.+|+.|..+||.+.-.+|..+|++|+.
T Consensus 145 ~r~~~L~~~ID~ALd~~D~e~F~~Ls~~l~~L~~ 178 (179)
T PRK03636 145 FRREKLLKQIDEALDRRDKEAFHRLSDELNQLRT 178 (179)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhc
Confidence 7899999999999999999999999999999974
No 9
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=53.94 E-value=74 Score=29.70 Aligned_cols=57 Identities=19% Similarity=0.336 Sum_probs=41.0
Q ss_pred hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHhhHH
Q 006477 417 VAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEASRDSKVKDAKAIRLAEMNRKNRV 475 (643)
Q Consensus 417 ~a~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~~~~~~~~~~~~~~la~IN~RNRk 475 (643)
=+.....|..+|++|+..||...|.-|+.-|.++...=.. ..-...+..+|...+.+
T Consensus 22 C~~K~~~Ie~qI~~Ak~~gN~~rv~GLe~AL~~v~~~Ctd--~~l~~e~q~ki~~~~~k 78 (115)
T PF06476_consen 22 CEAKEQAIEKQIEYAKAHGNQHRVAGLEKALEEVKAHCTD--EGLKAERQQKIAEKQQK 78 (115)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcCC--chhhHHHHHHHHHHHHH
Confidence 3467788999999999999999999999999999875221 01123344555555544
No 10
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=52.96 E-value=27 Score=25.77 Aligned_cols=31 Identities=19% Similarity=0.358 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHh
Q 006477 422 DRLRRELEVAQSRHDEVDMERIKKRLQELEA 452 (643)
Q Consensus 422 ~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~ 452 (643)
..|..++..|....|+++++.|..+|..|+.
T Consensus 5 ~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~ 35 (36)
T PF02151_consen 5 KELEEKMEEAVENEDFEKAARLRDQIKALKK 35 (36)
T ss_dssp HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCHHHHHHHHHHHHHHHc
Confidence 4578889999999999999999999999975
No 11
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=44.51 E-value=7.4 Score=34.25 Aligned_cols=15 Identities=20% Similarity=0.404 Sum_probs=0.0
Q ss_pred cCCCCCCCCCCCCCC
Q 006477 12 AGRTNSAGRNRHSAS 26 (643)
Q Consensus 12 ag~~~~~~~~~~~~~ 26 (643)
-||+|++.+..++++
T Consensus 9 iGRkgk~~~~~~~~~ 23 (81)
T PF14812_consen 9 IGRKGKKSRPKRKRP 23 (81)
T ss_dssp ---------------
T ss_pred cCcCCCCCCCCCCcc
Confidence 477766654433333
No 12
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=41.14 E-value=1.9e+02 Score=26.94 Aligned_cols=33 Identities=27% Similarity=0.346 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHh
Q 006477 420 EKDRLRRELEVAQSRHDEVDMERIKKRLQELEA 452 (643)
Q Consensus 420 eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~ 452 (643)
+-.....+|..|++.||.++|.+.+.+|.+-..
T Consensus 78 kV~ere~eL~eA~~~G~~~KI~K~~~KL~ea~~ 110 (115)
T PF06476_consen 78 KVAEREAELKEAQAKGDSDKIAKRQKKLAEAKA 110 (115)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 444557788888899999888888888876543
No 13
>PRK11020 hypothetical protein; Provisional
Probab=39.32 E-value=1.2e+02 Score=28.44 Aligned_cols=32 Identities=31% Similarity=0.413 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhc
Q 006477 422 DRLRRELEVAQSRHDEVDMERIKKRLQELEAS 453 (643)
Q Consensus 422 ~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~~ 453 (643)
..+.+++..|..+||.+.+.++..+++.|+..
T Consensus 15 D~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~ 46 (118)
T PRK11020 15 DAIRHKLAAASLRGDAEKYAQFEKEKATLEAE 46 (118)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 44678899999999999999999999999875
No 14
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=39.06 E-value=2.9e+02 Score=25.22 Aligned_cols=62 Identities=18% Similarity=0.272 Sum_probs=35.7
Q ss_pred eeeccCCcCCHHHHHHHHHHHH----hcCCCCCCHHHHHHHHH--------HHH--HHhcCCCCHHHHHHHHHHhh
Q 006477 347 MAMVSDSPPLEEEFKQWLREVE----RNSGRMPSKQDVLEKKE--------SIQ--KINTFVYSAATVKQMLQEKK 408 (643)
Q Consensus 347 m~~VSNspfTe~Ef~rw~~~~~----~~~~~lPT~~~v~~K~~--------~I~--ka~n~~~TeedI~~ml~~K~ 408 (643)
..+|-|.+||..|++.....+. ..+...|....+.++.- .++ +-.+...|+++|+..|+.-.
T Consensus 5 vAvVn~eiIt~sel~~~~~~~~~~~~~~~~~~~~~~~l~~qvLd~LI~e~L~~q~ak~~gI~vsd~evd~~i~~ia 80 (118)
T PF09312_consen 5 VAVVNDEIITQSELEQRLAQLKAQIQQQGQQIPPRNQLRKQVLDQLIDEKLQLQEAKRLGIKVSDEEVDEAIANIA 80 (118)
T ss_dssp EEEESSSEEEHHHHHHHHHHHHHHHHTTT-----HHHHHHHHHHHHHHHHHHHHHHHHCT----HHHHHHHHHHHH
T ss_pred EEEECCcCcCHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 4678899999999999988765 44667777665544331 122 23466778888888776644
No 15
>smart00784 SPT2 SPT2 chromatin protein. This entry includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation PUBMED:15563464.
Probab=37.47 E-value=1.1e+02 Score=28.68 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=26.5
Q ss_pred CChhhhHhhccCChhHHHHHHhhhHHHHHHHH
Q 006477 97 SNESDDDNHGQMTELEREMMIFERDDKKVDKN 128 (643)
Q Consensus 97 kDe~DR~~L~~MtElERE~iLaeR~ee~e~~~ 128 (643)
.|..|+..-.+..+|++|.-.+.|+-.++..+
T Consensus 62 dd~dD~dMEa~~~~i~~EE~~s~r~a~~ED~~ 93 (111)
T smart00784 62 DDDDDDDMEAGGADIQEEERRSARLARLEDRE 93 (111)
T ss_pred cccchhhhhcCHHHHHHHHHHHHHHHHHhhHH
Confidence 34467778889999999999999999888754
No 16
>COG5582 Uncharacterized conserved protein [Function unknown]
Probab=31.22 E-value=3.7e+02 Score=26.98 Aligned_cols=128 Identities=19% Similarity=0.349 Sum_probs=76.9
Q ss_pred cccccccccEEEEeecCCCC---C---CceEEEEEEEeecCCCCCcc-cc-CCceeeeEEEEEeCCCccceeeeeeeccC
Q 006477 281 FFEELIVGCFVRVGIGRSKN---G---PIYRLCMVRNVDATEPDRSY-KL-ENRTTCKYLNVTWGNESSAARWQMAMVSD 352 (643)
Q Consensus 281 ~Fee~V~GCFVRV~IG~~~~---g---~vYRm~qI~gV~~~e~~K~Y-~l-~~~~Tnk~L~L~~G~~~~~r~f~m~~VSN 352 (643)
-|-+.+.||=-=+.|..+.. + ..|++ +- ..+.|.+ .+ -+.....||.|.|-+... .
T Consensus 45 hFve~~e~c~rtL~iSt~~v~~~pf~F~k~~i---~t---~d~ekafhDir~N~~~~iyiqLHF~~a~~-~--------- 108 (182)
T COG5582 45 HFVEEAEGCPRTLIISTHGVHEVPFQFYKYNI---KT---MDPEKAFHDIRANPNEAIYIQLHFAGASK-N--------- 108 (182)
T ss_pred HhHHHHcCCcceeEeeccccCcccchhhhhhh---hc---cCHHHHHHHHhcCCccCeEEEeeeccccc-C---------
Confidence 37778888876666654331 2 22222 11 1233433 11 134466788887755421 1
Q ss_pred CcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhhhcCCCCchhHHHHHHHHHHHHHHH
Q 006477 353 SPPLEEEFKQWLREVERNSGRMPSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQ 432 (643)
Q Consensus 353 spfTe~Ef~rw~~~~~~~~~~lPT~~~v~~K~~~I~ka~n~~~TeedI~~ml~~K~~~~~~~~N~a~eK~rL~~ele~A~ 432 (643)
..|...+..+ -.+|-.-....|.+++..+ .|.+ . =.++++..|.++++.|.
T Consensus 109 --------pqyl~vLe~n-p~~~~~~~~~~~~k~lad~------------~ie~-~-------~~~f~~~~LL~~IDeAL 159 (182)
T COG5582 109 --------PQYLAVLESN-PQLPENLSEQTKLKELADA------------LIER-S-------VHAFERKKLLQQIDEAL 159 (182)
T ss_pred --------hHHHHHHhhC-hhcccCHHHHHHHHHHHHH------------HHHH-H-------HHHHHHHHHHHHHHHHH
Confidence 2455555554 3455544555566655532 1211 1 14589999999999999
Q ss_pred HcCCHHHHHHHHHHHHHHHhc
Q 006477 433 SRHDEVDMERIKKRLQELEAS 453 (643)
Q Consensus 433 ~~gD~~ev~~l~~qL~eLe~~ 453 (643)
+..|.+.-..|..+|++|...
T Consensus 160 d~~Dk~~F~~L~q~Lq~L~~~ 180 (182)
T COG5582 160 DMRDKERFYQLVQILQQLDLV 180 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHhc
Confidence 999999999999999998754
No 17
>PF08243 SPT2: SPT2 chromatin protein; InterPro: IPR013256 This entry includes the Saccharomyces cerevisiae (Baker's yeast) protein SPT2 which is a chromatin protein involved in transcriptional regulation []. These proteins shows conservation of several domains across numerous species, including having a cluster of positively charged amino acids. This cluster probably functions in the binding properties of the proteins []. Sin1p/Spt2p probably modulates the local chromatin structure by binding two strands of double-stranded DNA at their crossover point. Sin1p/Spt2p has sequence similarity to HMG1 and serves as a negative transcriptional regulator of a small family of genes that are activated by the SWI/SNF chromatin-remodelling complex. It is also involved in maintaining the integrity of chromatin during transcription elongation. Sin1p/Spt2 is required for, and is directly involved in, the efficient recruitment of the mRNA cleavage/polyadenylation complex []. Spt2 is also involved in regulating levels of histone H3 over transcribed regions [].
Probab=30.05 E-value=1.7e+02 Score=27.41 Aligned_cols=36 Identities=17% Similarity=0.224 Sum_probs=28.0
Q ss_pred Chhh--hHhhccCChhHHHHHHhhhHHHHHHHHHHHHH
Q 006477 98 NESD--DDNHGQMTELEREMMIFERDDKKVDKNLRDKF 133 (643)
Q Consensus 98 De~D--R~~L~~MtElERE~iLaeR~ee~e~~~~r~~l 133 (643)
|+.| +..=++.-+|++|+-.+.|+-.++..+...++
T Consensus 66 D~dD~~~dMEA~~~~I~~EE~rS~r~A~~ED~~e~~~e 103 (116)
T PF08243_consen 66 DDDDDSRDMEASFADIEKEEKRSARIARLEDEREERRE 103 (116)
T ss_pred chhhhhHhhhcCHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 4455 77778889999999999999999886544443
No 18
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=27.03 E-value=94 Score=24.83 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=25.9
Q ss_pred CChhhhHhhccCChhHHHHHHhhhHHHHHHH--HHHHHHHHH
Q 006477 97 SNESDDDNHGQMTELEREMMIFERDDKKVDK--NLRDKFRSR 136 (643)
Q Consensus 97 kDe~DR~~L~~MtElERE~iLaeR~ee~e~~--~~r~~l~~~ 136 (643)
.+++-.++|.+|++ |+|+.+|.+-+... .+-++|..+
T Consensus 4 I~~EN~~rL~~MS~---eEI~~er~eL~~~LdP~li~~L~~R 42 (49)
T PF08621_consen 4 IHEENEARLASMSP---EEIEEEREELLESLDPKLIEFLKKR 42 (49)
T ss_pred HhHHHHHHHHhCCH---HHHHHHHHHHHHhCCHHHHHHHHHh
Confidence 46778899999998 55777777777654 455555443
No 19
>PRK05629 hypothetical protein; Validated
Probab=25.23 E-value=8.4e+02 Score=25.91 Aligned_cols=89 Identities=12% Similarity=0.098 Sum_probs=54.8
Q ss_pred eccCCcCCHHHHHHHHHHHHhcCCCCCCHHHH-----------HHHHHHHHHHhcC---CCCHHHHHHHHHHhhhcCCCC
Q 006477 349 MVSDSPPLEEEFKQWLREVERNSGRMPSKQDV-----------LEKKESIQKINTF---VYSAATVKQMLQEKKSASSRP 414 (643)
Q Consensus 349 ~VSNspfTe~Ef~rw~~~~~~~~~~lPT~~~v-----------~~K~~~I~ka~n~---~~TeedI~~ml~~K~~~~~~~ 414 (643)
+|-..++++.++.+|+...-.....-.+.+.+ ..=..+|.++..| ..|.++|++++.... .
T Consensus 120 ~ve~~~~~~~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~~~It~e~V~~~v~~~~-----~ 194 (318)
T PRK05629 120 VHEAAKLKPRERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQGNVTVEKVRAYYVGVA-----E 194 (318)
T ss_pred EeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCc-----c
Confidence 34445889999999998776555443444333 2222566676544 589999998876532 1
Q ss_pred chhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Q 006477 415 LNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQEL 450 (643)
Q Consensus 415 ~N~a~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eL 450 (643)
.|+ =.+--|...||...+-.+=..|...
T Consensus 195 ~~i--------F~l~dAv~~g~~~~Al~~l~~l~~~ 222 (318)
T PRK05629 195 VSG--------FDIADLACAGQVSKAVASTRRALQL 222 (318)
T ss_pred chH--------HHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 233 2345566777777776665555443
No 20
>PF03902 Gal4_dimer: Gal4-like dimerisation domain; InterPro: IPR005600 The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of alpha-helix), is essential for dimerisation []. ; PDB: 1HBW_B 1D66_A 3COQ_A.
Probab=25.12 E-value=1e+02 Score=25.50 Aligned_cols=30 Identities=10% Similarity=0.395 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHh
Q 006477 378 QDVLEKKESIQKINTFVYSAATVKQMLQEK 407 (643)
Q Consensus 378 ~~v~~K~~~I~ka~n~~~TeedI~~ml~~K 407 (643)
-+|+.+...+..++.+-|...+|+.+|+..
T Consensus 6 TeVE~Rl~~lE~ll~~lfP~~did~lL~~~ 35 (57)
T PF03902_consen 6 TEVENRLEKLEQLLRELFPGEDIDDLLNDR 35 (57)
T ss_dssp HHHHHHHHHHHHHHCCCSSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHCCCcCHHHHHHcc
Confidence 478999999999999999999999999774
No 21
>cd01248 PH_PLC Phospholipase C (PLC) pleckstrin homology (PH) domain. Phospholipase C (PLC) pleckstrin homology (PH) domain. There are several isozymes of PLC (beta, gamma, delta, epsilon. zeta). While, PLC beta, gamma and delta all have N-terminal PH domains, lipid binding specificity is not conserved between them. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=24.75 E-value=2.4e+02 Score=25.49 Aligned_cols=62 Identities=16% Similarity=0.421 Sum_probs=43.8
Q ss_pred CceEEEEEEEeecCCCCCccccCC------ceeeeEEEEEeCCCccceeeeeeeccCCcCCHHHHHHHHHHHH
Q 006477 302 PIYRLCMVRNVDATEPDRSYKLEN------RTTCKYLNVTWGNESSAARWQMAMVSDSPPLEEEFKQWLREVE 368 (643)
Q Consensus 302 ~vYRm~qI~gV~~~e~~K~Y~l~~------~~Tnk~L~L~~G~~~~~r~f~m~~VSNspfTe~Ef~rw~~~~~ 368 (643)
..--|..|..|......+.|+... ...+.+|.|.||..-+ .-.|++|. .+.++++.|...+.
T Consensus 46 ~~l~i~~IkeIR~G~~~k~~~~~~~~~~~~~~e~~~fTIiy~~~~~--~k~L~lVA---~s~~~a~~W~~gL~ 113 (115)
T cd01248 46 KVLDISSIKEIRTGKQPKDLKLRAELNQGNSLEERCFTIVYGTDLN--LKSLDLVA---PSEEEAKTWVSGLR 113 (115)
T ss_pred cEEEehhhhhhhCCCCCcchHHhhhhhcCCCccccEEEEEECCCCC--eeEEEEEE---CCHHHHHHHHHHHh
Confidence 567889999998655556665431 3567899999998621 22377775 57899999998765
No 22
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=24.27 E-value=1.3e+02 Score=30.21 Aligned_cols=59 Identities=14% Similarity=0.220 Sum_probs=46.1
Q ss_pred CCHHHHHHHHHHhhhc-----CC------CCchhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhc
Q 006477 395 YSAATVKQMLQEKKSA-----SS------RPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEAS 453 (643)
Q Consensus 395 ~TeedI~~ml~~K~~~-----~~------~~~N~a~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~~ 453 (643)
+-...|.-+|.+=+.- ++ ...|+.++-..|...|+-+..+-|.++++.|.+||..|+..
T Consensus 101 tf~~~i~pi~~rvq~g~~~H~GK~P~~~~~~i~~~~~I~~L~e~Lq~~i~~EefEeAA~iRDqIr~Lk~k 170 (176)
T COG3880 101 TFESQISPIITRVQGGYVEHVGKVPKRIGRKINPKRKIIALKEALQDLIEREEFEEAAVIRDQIRALKAK 170 (176)
T ss_pred HHHHHhhHHHHHhhCCceeecCcCcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3566677777664432 12 24577788889999999999999999999999999999875
No 23
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=21.18 E-value=3e+02 Score=23.84 Aligned_cols=73 Identities=12% Similarity=0.199 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhhhcCCCCchhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHh
Q 006477 375 PSKQDVLEKKESIQKINTFVYSAATVKQMLQEKKSASSRPLNVAAEKDRLRRELEVAQSRHDEVDMERIKKRLQELEA 452 (643)
Q Consensus 375 PT~~~v~~K~~~I~ka~n~~~TeedI~~ml~~K~~~~~~~~N~a~eK~rL~~ele~A~~~gD~~ev~~l~~qL~eLe~ 452 (643)
+..++|.+++.++-... .-.-.||...|+..-.-.....++ +-|....-..+++ ..-.++++.|+.+|..||+
T Consensus 6 ~~~d~~~~~~~~~~~~~--~~~~~e~e~~~r~~l~~~l~kldl-VtREEFd~q~~~L--~~~r~kl~~LEarl~~LE~ 78 (79)
T PF04380_consen 6 KIFDDLAKQISEALPAA--QGPREEIEKNIRARLQSALSKLDL-VTREEFDAQKAVL--ARTREKLEALEARLAALEA 78 (79)
T ss_pred hHHHHHHHHHHHHHHhh--hhhHHHHHHHHHHHHHHHHHHCCC-CcHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhc
Confidence 45566666666555443 233456776666553323333444 2222222222111 1112356666667766664
No 24
>KOG2609 consensus Cyclin D-interacting protein GCIP [Cell cycle control, cell division, chromosome partitioning; RNA processing and modification]
Probab=20.87 E-value=1e+02 Score=31.99 Aligned_cols=16 Identities=25% Similarity=0.202 Sum_probs=13.9
Q ss_pred HHHHHHhhHHHHHHHH
Q 006477 466 LAEMNRKNRVENFKNA 481 (643)
Q Consensus 466 la~IN~RNRk~N~~~a 481 (643)
|..||.||++.|-+--
T Consensus 193 idfINerN~kFNkKl~ 208 (228)
T KOG2609|consen 193 IDFINERNKKFNKKLE 208 (228)
T ss_pred hhHHHHhHHHHHHHHH
Confidence 7999999999998654
Done!