Query 018907
Match_columns 349
No_of_seqs 133 out of 218
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 05:02:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018907.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018907hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5157 CDC73 RNA polymerase I 100.0 2.8E-63 6.2E-68 463.8 21.4 296 2-348 3-314 (362)
2 KOG3786 RNA polymerase II asse 100.0 2.5E-61 5.3E-66 466.9 17.2 305 1-349 2-345 (395)
3 PF05179 CDC73: RNA pol II acc 100.0 2.6E-51 5.7E-56 391.5 9.3 117 231-349 113-229 (273)
4 KOG3786 RNA polymerase II asse 97.8 7.8E-06 1.7E-10 81.0 0.9 45 51-95 1-45 (395)
5 PF14504 CAP_assoc_N: CAP-asso 43.9 21 0.00045 31.2 2.7 29 312-340 45-74 (141)
6 smart00481 POLIIIAc DNA polyme 40.4 18 0.00039 26.7 1.6 29 61-89 12-40 (67)
7 PRK07313 phosphopantothenoylcy 28.3 42 0.00091 30.5 2.2 35 233-267 112-151 (182)
8 PF14869 DUF4488: Domain of un 21.7 38 0.00082 29.7 0.6 77 235-315 39-122 (133)
9 PRK06029 3-octaprenyl-4-hydrox 21.3 74 0.0016 29.1 2.4 35 233-267 114-150 (185)
10 PF03852 Vsr: DNA mismatch end 21.0 74 0.0016 25.2 2.0 17 314-330 57-73 (75)
11 PRK05920 aromatic acid decarbo 20.9 79 0.0017 29.4 2.5 36 233-268 129-166 (204)
No 1
>COG5157 CDC73 RNA polymerase II assessory factor [Transcription]
Probab=100.00 E-value=2.8e-63 Score=463.76 Aligned_cols=296 Identities=24% Similarity=0.339 Sum_probs=221.7
Q ss_pred ChhHHHHHHHhcCCC-----------CcceecCCEEEecC----CccccCCCcceeeecCCceeeHHHHHHHHHhCCCCh
Q 018907 2 DPLSALRDFTIRSEL-----------DKVTQTGDEILFGS----DYTFPSSIETAYRSKQGNLYTLQTVVYFIKHYNLKH 66 (349)
Q Consensus 2 DpL~lLR~~~~~~~~-----------~~i~~~~~~i~Fg~----~~~~pk~~~T~f~~~~~~~ytL~si~f~~~~~d~~~ 66 (349)
..|.+||.++.+++. .+++.....+.|.. .++|+.+..|.... +..+.|++|||||+|||.++
T Consensus 3 n~ldllk~~l~~~d~~~l~~~E~~s~~~kv~~~q~~~f~~~~S~~~~fe~ne~~eiE~--DS~~qLR~v~f~wlnrD~s~ 80 (362)
T COG5157 3 NSLDLLKKALRDPDACQLSPEEIVSGGKKVPPKQMVKFKGTESKEYTFEQNEETEIEI--DSLVQLRIVLFYWLNRDKSY 80 (362)
T ss_pred cHHHHHHHHhcCccceecchhhccccCcccCceeEEEecCCCCceeecCcccceeecc--cchhhhhhhhhhhhhccchH
Confidence 568899999998851 11222345788853 24788888887764 58999999999999999999
Q ss_pred HHHHHHHHhCCCCceecCchhhHHHhhcCCCCCccccccccccccccCCCCccccCCCCCCcchhhHHHHHhccccCCch
Q 018907 67 TDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPLKDR 146 (349)
Q Consensus 67 ~~Yv~~a~~~~i~~Vs~~DRkdLl~yL~G~~dts~~I~~~~p~~~~~~~~~~~~~~~~~d~~~~d~~~~I~~~Er~l~dr 146 (349)
++||++|++.||++|+|+||+||++||+|.+|++.+|....|..++..+. +..+........+.+-+.+.+||.+.+|
T Consensus 81 a~Y~~~C~e~gi~ni~fl~rtdlI~wlegnteSsq~l~~~~~k~EtSs~t--s~s~~~D~~~sd~~V~~~~k~eR~l~~h 158 (362)
T COG5157 81 AVYMTLCRESGIGNIYFLDRTDLIEWLEGNTESSQYLKAPGQKKETSSTT--SISARIDSEVSDPVVVETMKHERILVGH 158 (362)
T ss_pred HHHHHHHHHcCcccEEEeeHHHHHHHHhCCcchhhhhcCCCCCCCCcccc--cceeecccccccHHHhhhhhcceeecCC
Confidence 99999999999999999999999999999999999997532222111111 1112222222335899999999999999
Q ss_pred hhhhh-hcCCchHHHHhhhhHHHHHHHHHHhhhhcccccccccccCcccCCcccCCCCCCCCCCCCCCCccCCCChhhhh
Q 018907 147 EALLE-CKGIDFYSVLVSSTRREEERQRIESQQRKDGLVAKNRLMGVDERGIGYGGGGGGGGGGAGDEAYEANPKPKLLQ 225 (349)
Q Consensus 147 nsvLr-~k~~dF~~vl~~~~~~e~~~~~~~~~~~k~~~~~~~r~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~p~~~~~~ 225 (349)
|++|+ .||.+|.+++.++.. ++ ++++.+. .++.+.+| .|
T Consensus 159 ns~l~G~kpi~f~~l~kd~ed-----~l---~qs~~~s------------------~~Hk~ah~--------Rp------ 198 (362)
T COG5157 159 NSRLIGLKPISFLGLLKDKED-----KL---VQSEGGS------------------LGHKGAHG--------RP------ 198 (362)
T ss_pred CceeecccccchhhhhhhHHH-----Hh---hhhcccc------------------cccccccc--------Cc------
Confidence 99999 599999999876632 11 2222110 00001111 11
Q ss_pred cccCCCCCCCcEEEecCCcccccchhhHHHHhhcCcccCChhhhhccCCCCCceEEEEeeecCCCCCeeeEEEEEcCCCC
Q 018907 226 LKSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPST 305 (349)
Q Consensus 226 ~~~~k~~~~~PIIivPs~~tslitl~Nik~fLe~g~fv~~~~~~~~~~~~~~~~v~i~r~~~~~~~~~~~~f~vvd~~~~ 305 (349)
+|...++||||||++++|++||+|||+|||+|+||+|.+......+ -..+.+.+...+ -..+++|.+||++.+
T Consensus 199 ---~k~~~kDPIIlvp~saSS~lt~~NIK~FleEgkyV~P~n~~~~~~G--~~i~~~eK~~~~--~~g~~rfIiVd~t~~ 271 (362)
T COG5157 199 ---TKYYAKDPIILVPQSASSPLTLSNIKEFLEEGKYVNPRNLPSCSDG--IRISEVEKVELD--LDGPFRFIIVDDTGG 271 (362)
T ss_pred ---cccccCCceEEeccccccceeHHHHHHHHHhcCccCccccccCCCC--ceEEeeeehhhc--ccCceEEEEEcCCCC
Confidence 1224679999999999999999999999999999998664322111 123444444432 256799999999999
Q ss_pred CCCCCCCeEEEEEeeCCccccCCCCCCCHHHhhccccEEEEee
Q 018907 306 MKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKRIVTWGSM 348 (349)
Q Consensus 306 ~~~~~W~RVVaVf~~G~~WQFk~w~~~~p~~lF~~v~gf~~~~ 348 (349)
|+||||||||||||||++|||.+|+|++|.+||++|+||||+|
T Consensus 272 FkpeyWdRVVciFttG~~WQf~~y~w~~p~elF~~~kgfyf~~ 314 (362)
T COG5157 272 FKPEYWDRVVCIFTTGSKWQFGRYNWRDPGELFNTIKGFYFAR 314 (362)
T ss_pred cChhhhceEEEEEecCCeeeecCcccCCHHHHHhhCCceEEEE
Confidence 9999999999999999999999999999999999999999998
No 2
>KOG3786 consensus RNA polymerase II assessory factor Cdc73p [Transcription]
Probab=100.00 E-value=2.5e-61 Score=466.87 Aligned_cols=305 Identities=33% Similarity=0.487 Sum_probs=230.3
Q ss_pred CChhHHHHHHHhcCCCCcceecC--------------CEEEecCC---ccccCCCcceeeecCCceeeHHHHHHHHHhCC
Q 018907 1 MDPLSALRDFTIRSELDKVTQTG--------------DEILFGSD---YTFPSSIETAYRSKQGNLYTLQTVVYFIKHYN 63 (349)
Q Consensus 1 ~DpL~lLR~~~~~~~~~~i~~~~--------------~~i~Fg~~---~~~pk~~~T~f~~~~~~~ytL~si~f~~~~~d 63 (349)
||.|.+|+.++..+ +.+.+.. .++.|..+ -++|+...|.-.+ +.-.+|+.+++||..++
T Consensus 2 l~sll~l~kn~~~~--h~v~l~~~~~~s~~~v~~~drk~lL~~~ng~~~~~~~~e~~~~~~--d~~~~~~i~~l~~amsd 77 (395)
T KOG3786|consen 2 LDSLLLLLKNVALK--HDVYLRASAEESIPVVTRPDRKELLFYLNGPIAKKPRTEETELEN--DSVFDLRIKSLSEAMSD 77 (395)
T ss_pred hhHHHHHHHHHhhc--CCeeeecccccCCCccccccHHHHHhhcCChhhccCCccceeeee--cccccHHHHHHHHHhcc
Confidence 68999999999999 5554421 35555322 2455555555543 44799999999999999
Q ss_pred CChHHHHHHHHhCCCCceecCchhhHHHhhcCCCCCccccccccccccccCCCCccccCCCCCCcchhhHHHHHhccccC
Q 018907 64 LKHTDYIQRARSNKLPAVTLPDRKPLYEYLTGVTDSADQIETVIANDHVLNDGKIVETDGGGDDLELDDISLIRACERPL 143 (349)
Q Consensus 64 ~~~~~Yv~~a~~~~i~~Vs~~DRkdLl~yL~G~~dts~~I~~~~p~~~~~~~~~~~~~~~~~d~~~~d~~~~I~~~Er~l 143 (349)
.++++|.++|.+.+..+++|.+|.|++.||.|-+++. .|.++.|+++||++
T Consensus 78 ~~ia~ykak~~~~~~~~~k~~~~~d~i~~~~g~~~~d-----------------------------~d~~~~i~k~Er~~ 128 (395)
T KOG3786|consen 78 ESIAEYKAKCLAKKRTNIKFLVRTDLIVWLKGNTESD-----------------------------VDLIRDILKRERPW 128 (395)
T ss_pred HHHHHHhHHHHHhcccchhcccchHHHHHhhCCcccc-----------------------------HHHHhhhhccCCcc
Confidence 9999999999999999999999999999999932210 15788999999999
Q ss_pred CchhhhhhhcCCch----HHHHhhhhHHHHHHHHHHhhhh----------ccc--ccccccccCcccCCcccCCCCCCCC
Q 018907 144 KDREALLECKGIDF----YSVLVSSTRREEERQRIESQQR----------KDG--LVAKNRLMGVDERGIGYGGGGGGGG 207 (349)
Q Consensus 144 ~drnsvLr~k~~dF----~~vl~~~~~~e~~~~~~~~~~~----------k~~--~~~~~r~~~~~~~~i~~~~~~~~~~ 207 (349)
++|.++|++.+++| .+++...+.+++.++..+.++. ..+ +..|+||.+.. ..+|++++.|.
T Consensus 129 rt~~~il~~~~~~~~k~~~s~l~~~~~~~e~~~~v~~~~~~~~~v~~~~~~~~p~~~~y~ryi~~r--f~~~~~~~~Gs- 205 (395)
T KOG3786|consen 129 RTRTTILQSTGREFVKNIFSKLQEVKAREEDRKTVEEHNPNFMPVDPAIRIDGPKPIDYNRYIQER--FLSFGIDTYGS- 205 (395)
T ss_pred chHHHHHhhcchhhhhhHHHHhhccceeeecCcccccccccccCCCHHHhcCCccchhhhhhhhhh--hhccccccccc-
Confidence 99999999988988 2455555666655555443332 112 23578886432 22344555444
Q ss_pred CCCCCCCccCCCChhhh----hc--ccCCCCCCCcEEEecCCcccccchhhHHHHhhcCcccCChhhhhccCCCCCceEE
Q 018907 208 GGAGDEAYEANPKPKLL----QL--KSGKIGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVT 281 (349)
Q Consensus 208 ~~~~~~~~~~~p~~~~~----~~--~~~k~~~~~PIIivPs~~tslitl~Nik~fLe~g~fv~~~~~~~~~~~~~~~~v~ 281 (349)
.|..+ +|..+.. .+ .+....+++||||||+|+||||||+|||+|||||+|||...++.+++. ++++|.
T Consensus 206 -~g~~l----~~~~e~~~~~~~~~~~~~~~prr~PIIlvPsA~sSlITm~NiK~fLeEgkyvp~~~k~~~g~~-~~~~v~ 279 (395)
T KOG3786|consen 206 -HGMKL----KPVHEGARKRRKKQPGASGGPRRDPIILVPSAASSLITMLNIKEFLEEGKYVPEAAKKNQGCR-RPEEVL 279 (395)
T ss_pred -ccccC----CccchhhhhccccCCCCCCCCccCcEEEechhhcchhhHHhHHHHHHhcccCccchhhcCCCC-CCceee
Confidence 22222 1111100 00 011224589999999999999999999999999999996655555554 899999
Q ss_pred EEeeecCCCCCeeeEEEEEcCCCCCCCCCCCeEEEEEeeCCccccCCCCCCCHHHhhccccEEEEeeC
Q 018907 282 VQKKFSRDRDQVVKAYEVRDKPSTMKSEDWDRVVAVFVLGKEWQFKEWPFKDHVEIFNKRIVTWGSME 349 (349)
Q Consensus 282 i~r~~~~~~~~~~~~f~vvd~~~~~~~~~W~RVVaVf~~G~~WQFk~w~~~~p~~lF~~v~gf~~~~~ 349 (349)
|+|++++. ..+++|+|||||.+|+|+||||||||||+|++||||||||.||++||++||||||+|.
T Consensus 280 ve~kf~~~--~~~v~y~VVDn~~~ltPedWDRVVaVF~~G~~WQFk~wpw~dp~eIF~ki~gF~l~f~ 345 (395)
T KOG3786|consen 280 VEKKFDNF--KVTVRYRVVDNPTKLTPEDWDRVVAVFVTGPKWQFKGWPWRDPVEIFNKIKGFHLHFR 345 (395)
T ss_pred eeeccccc--ccceEEEEecCCCcCChhhhceEEEEEeecCccccCCCCCCCHHHHHhhcceeEEEec
Confidence 99999753 3689999999999999999999999999999999999999999999999999999994
No 3
>PF05179 CDC73: RNA pol II accessory factor, Cdc73 family; InterPro: IPR007852 Paf1 is an RNA polymerase II-associated protein in yeast, which defines a complex that is distinct from the Srb/Mediator holoenzyme. The Paf1 complex, which also contains Cdc73, Ctr9, Hpr1, Ccr4, Rtf1 and Leo1, is required for full expression of a subset of yeast genes, particularly those responsive to signals from the Pkc1/MAP kinase cascade. The complex appears to play an essential role in RNA elongation []. ; PDB: 3V46_A.
Probab=100.00 E-value=2.6e-51 Score=391.45 Aligned_cols=117 Identities=45% Similarity=0.815 Sum_probs=80.1
Q ss_pred CCCCCcEEEecCCcccccchhhHHHHhhcCcccCChhhhhccCCCCCceEEEEeeecCCCCCeeeEEEEEcCCCCCCCCC
Q 018907 231 IGEGVPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVKNMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKPSTMKSED 310 (349)
Q Consensus 231 ~~~~~PIIivPs~~tslitl~Nik~fLe~g~fv~~~~~~~~~~~~~~~~v~i~r~~~~~~~~~~~~f~vvd~~~~~~~~~ 310 (349)
..+++||||||+++||||||+|||+|||||+||++++++..++ .++++|+|+|++.++. ..+++|+|||||.+|+|||
T Consensus 113 ~~~~~PIIiVp~s~sSlitm~NiK~FLed~~fv~~~~~~~~~~-~~~~~v~i~r~~~~~~-~~~v~f~VvD~~~~~~ped 190 (273)
T PF05179_consen 113 RRSKDPIIIVPPSASSLITMYNIKQFLEDGKFVPPDEKRKSGS-SKPNEVTIQRKFDRIK-PGPVRFRVVDNPEKFTPED 190 (273)
T ss_dssp ---S--EEE----TT-SS-TTTHHHHHHH--------GGGS----TTSEEEEEE--TTSS-S--EEEEEESSSTT--GGG
T ss_pred cCCCCCEEEECCcccchhHHHHHHHHHHcCeeecCccccccCC-CCCCEEEEEeccCCCC-CCceeEEEecChhhCCccc
Confidence 4578999999999999999999999999999999988877655 4889999999997542 2389999999999999999
Q ss_pred CCeEEEEEeeCCccccCCCCCCCHHHhhccccEEEEeeC
Q 018907 311 WDRVVAVFVLGKEWQFKEWPFKDHVEIFNKRIVTWGSME 349 (349)
Q Consensus 311 W~RVVaVf~~G~~WQFk~w~~~~p~~lF~~v~gf~~~~~ 349 (349)
|+|||||||+|++||||+|||++|++||++||||||+|+
T Consensus 191 W~RVVAVF~~G~~WQFk~w~~~~P~~LF~~v~gf~~~~~ 229 (273)
T PF05179_consen 191 WDRVVAVFVTGQAWQFKGWPWSDPVELFQKVKGFYVHYD 229 (273)
T ss_dssp GGGEEEEE--S-GGGGTTSSS-SHHHHHHHSEEEEEEET
T ss_pred CCeEEEEEeECchhhhCCCCCCCHHHHhhcCcEEEEEec
Confidence 999999999999999999999999999999999999996
No 4
>KOG3786 consensus RNA polymerase II assessory factor Cdc73p [Transcription]
Probab=97.76 E-value=7.8e-06 Score=81.01 Aligned_cols=45 Identities=40% Similarity=0.716 Sum_probs=44.4
Q ss_pred eHHHHHHHHHhCCCChHHHHHHHHhCCCCceecCchhhHHHhhcC
Q 018907 51 TLQTVVYFIKHYNLKHTDYIQRARSNKLPAVTLPDRKPLYEYLTG 95 (349)
Q Consensus 51 tL~si~f~~~~~d~~~~~Yv~~a~~~~i~~Vs~~DRkdLl~yL~G 95 (349)
||+||+|+.+|..++|..||++|.++.++.|+.+||++||.||+|
T Consensus 1 tl~sll~l~kn~~~~h~v~l~~~~~~s~~~v~~~drk~lL~~~ng 45 (395)
T KOG3786|consen 1 TLDSLLLLLKNVALKHDVYLRASAEESIPVVTRPDRKELLFYLNG 45 (395)
T ss_pred ChhHHHHHHHHHhhcCCeeeecccccCCCccccccHHHHHhhcCC
Confidence 699999999999999999999999999999999999999999999
No 5
>PF14504 CAP_assoc_N: CAP-associated N-terminal
Probab=43.91 E-value=21 Score=31.21 Aligned_cols=29 Identities=24% Similarity=0.472 Sum_probs=24.6
Q ss_pred CeEEEEEeeCCccccCCCCCCCH-HHhhcc
Q 018907 312 DRVVAVFVLGKEWQFKEWPFKDH-VEIFNK 340 (349)
Q Consensus 312 ~RVVaVf~~G~~WQFk~w~~~~p-~~lF~~ 340 (349)
++||++++.|..|...+++.+.+ .++|++
T Consensus 45 ~kV~~lyt~~~~~~~~p~kiG~s~~~v~~~ 74 (141)
T PF14504_consen 45 GKVVALYTNGNDINVSPFKIGMSKSEVFKK 74 (141)
T ss_pred CEEEEEEECCcccccCCeecCCCHHHHHHh
Confidence 99999999999999999998866 456654
No 6
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=40.43 E-value=18 Score=26.73 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=24.8
Q ss_pred hCCCChHHHHHHHHhCCCCceecCchhhH
Q 018907 61 HYNLKHTDYIQRARSNKLPAVTLPDRKPL 89 (349)
Q Consensus 61 ~~d~~~~~Yv~~a~~~~i~~Vs~~DRkdL 89 (349)
+...+..+|++.|++.|+..|.+.|...+
T Consensus 12 ~~~~~~~~~~~~a~~~g~~~v~iTDh~~~ 40 (67)
T smart00481 12 DGALSPEELVKRAKELGLKAIAITDHGNL 40 (67)
T ss_pred cccCCHHHHHHHHHHcCCCEEEEeeCCcc
Confidence 34467889999999999999999999854
No 7
>PRK07313 phosphopantothenoylcysteine decarboxylase; Validated
Probab=28.28 E-value=42 Score=30.46 Aligned_cols=35 Identities=26% Similarity=0.313 Sum_probs=27.8
Q ss_pred CCCcEEEecC----CcccccchhhHHHHhhcCcccC-Chh
Q 018907 233 EGVPIILVPS----ASQTLITIYNVKEFLEDGVYIP-TDV 267 (349)
Q Consensus 233 ~~~PIIivPs----~~tslitl~Nik~fLe~g~fv~-~~~ 267 (349)
.+.|+||+|+ ...+.++.-|+..+=+.|..|= |..
T Consensus 112 ~~~pvvi~Pamn~~m~~~p~~~~Nl~~L~~~G~~vi~p~~ 151 (182)
T PRK07313 112 ATTPKLIAPAMNTKMYENPATQRNLKTLKEDGVQEIEPKE 151 (182)
T ss_pred CCCCEEEEECCCHHHhcCHHHHHHHHHHHHCCCEEECCCC
Confidence 4689999997 3457899999999999987654 543
No 8
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=21.72 E-value=38 Score=29.66 Aligned_cols=77 Identities=19% Similarity=0.255 Sum_probs=49.3
Q ss_pred CcEEEecCCcccccchhhHHHHhhcCcccCChhhhh--ccCCCCCceEEEEeeecCCCCCeeeEEEEEcCC-----CCCC
Q 018907 235 VPIILVPSASQTLITIYNVKEFLEDGVYIPTDVKVK--NMNGMRPECVTVQKKFSRDRDQVVKAYEVRDKP-----STMK 307 (349)
Q Consensus 235 ~PIIivPs~~tslitl~Nik~fLe~g~fv~~~~~~~--~~~~~~~~~v~i~r~~~~~~~~~~~~f~vvd~~-----~~~~ 307 (349)
.=|.++|.+. |.||.+===++..|+.|+..=++.- .+...+.+++.+++..+ +--.++|.+=+.. ...-
T Consensus 39 ~Ni~~~~~~~-aiIt~~GtY~~~sD~~Y~E~IeKnv~lp~~~g~~n~l~fe~~~d---nll~iky~~~~~~~~~~~~~w~ 114 (133)
T PF14869_consen 39 VNITMIPKSG-AIITGYGTYEQPSDNIYVESIEKNVHLPFLDGKDNELEFELLHD---NLLKIKYFLPGDLNGNEINQWF 114 (133)
T ss_pred EEEEEeCCCC-cEEEEeEEEEEcCCccceeeecceecCcccCCCccEEEEEecCC---CEEEEEEEcCCCccccccCCcE
Confidence 3444456554 8888887777888888886433311 11123678888887763 3345788877663 3456
Q ss_pred CCCCCeEE
Q 018907 308 SEDWDRVV 315 (349)
Q Consensus 308 ~~~W~RVV 315 (349)
-|.|.||+
T Consensus 115 ~E~W~RV~ 122 (133)
T PF14869_consen 115 HEYWKRVP 122 (133)
T ss_pred EEEEEecc
Confidence 78999986
No 9
>PRK06029 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
Probab=21.28 E-value=74 Score=29.09 Aligned_cols=35 Identities=20% Similarity=0.259 Sum_probs=28.0
Q ss_pred CCCcEEEecCCc-ccccchhhHHHHhhcCc-ccCChh
Q 018907 233 EGVPIILVPSAS-QTLITIYNVKEFLEDGV-YIPTDV 267 (349)
Q Consensus 233 ~~~PIIivPs~~-tslitl~Nik~fLe~g~-fv~~~~ 267 (349)
.+.|+||+|..+ ...++.-|+..+-+.|. ++||..
T Consensus 114 ~~~pvii~P~~M~~~p~~~~Nl~~L~~~G~~vi~P~~ 150 (185)
T PRK06029 114 ERRRLVLCVRETPLHLGHLRNMTKLAEMGAIIMPPVP 150 (185)
T ss_pred cCCCEEEEeccccCCHHHHHHHHHHHHCcCEEECCCc
Confidence 568999999764 36899999999999887 555655
No 10
>PF03852 Vsr: DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine []. GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine []. The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology []. ; GO: 0004519 endonuclease activity, 0006298 mismatch repair; PDB: 1ODG_A 1VSR_A 1CW0_A.
Probab=21.03 E-value=74 Score=25.18 Aligned_cols=17 Identities=35% Similarity=0.653 Sum_probs=11.7
Q ss_pred EEEEEeeCCccccCCCC
Q 018907 314 VVAVFVLGKEWQFKEWP 330 (349)
Q Consensus 314 VVaVf~~G~~WQFk~w~ 330 (349)
=|||||.|.=|.=-+|+
T Consensus 57 k~aIFVdGCFWHgh~c~ 73 (75)
T PF03852_consen 57 KIAIFVDGCFWHGHDCP 73 (75)
T ss_dssp TEEEEEE-TTTTT-SST
T ss_pred CEEEEEecceeCCCCCC
Confidence 39999999999754443
No 11
>PRK05920 aromatic acid decarboxylase; Validated
Probab=20.87 E-value=79 Score=29.43 Aligned_cols=36 Identities=31% Similarity=0.457 Sum_probs=28.8
Q ss_pred CCCcEEEecCC-cccccchhhHHHHhhcCc-ccCChhh
Q 018907 233 EGVPIILVPSA-SQTLITIYNVKEFLEDGV-YIPTDVK 268 (349)
Q Consensus 233 ~~~PIIivPs~-~tslitl~Nik~fLe~g~-fv~~~~~ 268 (349)
.+.|++|+|+. ..+.++.-|+..+.+.|. +++|...
T Consensus 129 ~~~pvvi~P~~m~~~~~~~~nl~~L~~~G~~ii~P~~g 166 (204)
T PRK05920 129 ERRKLILVPRETPLSLIHLENMLKLAEAGAIILPAIPA 166 (204)
T ss_pred cCCCEEEEeCCCCCCHHHHHHHHHHHHCCCEEeCCccc
Confidence 56899999984 457889999999999887 5566553
Done!