Query 043831
Match_columns 243
No_of_seqs 191 out of 592
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:43:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043831.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043831hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4685 tRNA splicing endonucl 100.0 6.3E-50 1.4E-54 351.6 9.4 229 1-236 37-271 (271)
2 PRK09297 tRNA-splicing endonuc 100.0 1.6E-44 3.4E-49 305.8 18.1 157 35-204 1-157 (169)
3 TIGR00324 endA tRNA intron end 100.0 3.2E-43 6.8E-48 298.2 17.1 157 34-204 1-160 (170)
4 PRK09300 tRNA splicing endonuc 100.0 6.1E-40 1.3E-44 302.9 17.6 151 32-201 163-316 (330)
5 COG1676 SEN2 tRNA splicing end 100.0 4.8E-34 1E-38 244.1 13.8 157 33-203 10-167 (181)
6 PRK09300 tRNA splicing endonuc 100.0 5.4E-31 1.2E-35 243.5 17.1 163 35-239 1-166 (330)
7 PF01974 tRNA_int_endo: tRNA i 99.9 2.7E-27 5.8E-32 179.0 6.3 81 118-204 1-81 (85)
8 KOG4133 tRNA splicing endonucl 99.8 2.5E-20 5.4E-25 165.0 11.3 75 119-199 194-268 (290)
9 PRK09539 tRNA-splicing endonuc 99.8 2E-20 4.4E-25 150.7 7.4 91 115-222 31-121 (124)
10 PF02778 tRNA_int_endo_N: tRNA 99.6 4.3E-16 9.2E-21 113.5 6.9 66 35-108 1-67 (67)
11 KOG4772 Predicted tRNA-splicin 97.6 5.5E-05 1.2E-09 69.9 3.6 67 71-139 106-174 (364)
12 PF12928 tRNA_int_end_N2: tRNA 94.9 0.029 6.2E-07 41.2 3.2 22 74-96 49-70 (72)
13 PF05066 HARE-HTH: HB1, ASXL, 50.9 10 0.00022 27.1 1.6 53 78-138 2-63 (72)
14 cd07153 Fur_like Ferric uptake 37.1 97 0.0021 23.5 5.3 58 99-158 14-73 (116)
15 TIGR01529 argR_whole arginine 32.3 2.7E+02 0.0058 22.9 7.5 48 99-147 14-61 (146)
16 PF08513 LisH: LisH; InterPro 32.0 26 0.00055 20.7 1.0 15 120-134 3-17 (27)
17 PF01475 FUR: Ferric uptake re 30.4 1.1E+02 0.0024 23.6 4.7 57 100-158 22-80 (120)
18 PF07597 DUF1560: Protein of u 30.2 15 0.00031 24.6 -0.3 19 2-21 14-32 (49)
19 COG0735 Fur Fe2+/Zn2+ uptake r 25.6 2.1E+02 0.0046 23.4 5.7 61 100-162 35-97 (145)
20 PF12076 Wax2_C: WAX2 C-termin 24.4 1.3E+02 0.0027 25.8 4.2 104 77-189 10-130 (164)
21 PF04471 Mrr_cat: Restriction 24.1 2.2E+02 0.0049 20.8 5.3 61 122-190 11-75 (115)
22 COG4359 Uncharacterized conser 21.1 1.2E+02 0.0026 26.8 3.6 45 59-118 48-92 (220)
23 PF12549 TOH_N: Tyrosine hydro 20.9 48 0.001 19.7 0.7 10 2-11 7-16 (25)
No 1
>KOG4685 consensus tRNA splicing endonuclease SEN2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-50 Score=351.61 Aligned_cols=229 Identities=45% Similarity=0.763 Sum_probs=213.1
Q ss_pred CCCCCCCccchhhhc--chhhhHHHHHhhhcccCcceEEEEeCCeEEEeechhhHHHHHhcccccccccC--cccCceee
Q 043831 1 MGPRWKGRASEAKSS--GRSHVQNHLRFTFLSIQSEAHAVLAGYSALLAVEAEQTELLNRACFGRHIVTA--EKDKQWYQ 76 (243)
Q Consensus 1 ~~~~~~~~~~~~~~~--p~~~~~~~l~~~~~~~~~~~~g~L~g~~V~v~~~~~~~~L~~~~~yG~~~~~~--~~~~~~L~ 76 (243)
|+|+||++.+.+++. |.|+++.||+.++ .+.+-++.++.+.+++....+++++.++.++|+....+ +...++||
T Consensus 37 ~a~~~~~~g~l~k~~~e~~s~~I~el~~~~--~~~k~e~kls~~v~~~~~eqe~ae~n~r~~~~rl~~~~~~~~i~~~Lq 114 (271)
T KOG4685|consen 37 RAPRWKWLGALRKALAEPASKIISELSGSL--QWTKDEGKLSECVVLLAVEQECAELNDRCCFNRLVEWAEAEKIKEWLQ 114 (271)
T ss_pred hhhhHHHhHHHHHhhCCchhHHHHHhcccc--ccchhhcceeccceeEEechhhccchhhhhhhhhhhcccccchhhHhh
Confidence 579999999988885 9999999999999 99999999999999998999999888899999999884 45668999
Q ss_pred ecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHHHhcCCccchhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCc
Q 043831 77 LGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKAKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVH 156 (243)
Q Consensus 77 Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~~~~~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~H 156 (243)
|||+|||||.|+++||+|+.. ..+++..++|..|....++|..-|.+|+|||++||+|++|+|||+||++|++||.++|
T Consensus 115 Ls~eEAffL~y~lkci~I~~~-k~l~~~v~~w~am~~~~~~F~~~y~~y~hlrskGWvvrsGlkyG~DfllYr~gP~f~H 193 (271)
T KOG4685|consen 115 LSPEEAFFLSYALKCIKISLN-KCLLNEVDLWTAMRSLQPNFGKLYKAYHHLRSKGWVVRSGLKYGVDFLLYRHGPSFVH 193 (271)
T ss_pred cCHHHHHHHHhhhceeEEehh-hccccHHHHHHHHhhcchhhHHHHHHHHHHHHcCcEecccccccceEEEEecCCccce
Confidence 999999999999999999864 7789999999999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEeeCCCcCCCCcCCChHHHHhhhhhcccccCcEEEEEEec--CCCCCCccccccceEEEEEEEeeecCCCCCCC
Q 043831 157 SEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVAKTLLILTINK--NGQGTATPSCLEQYAVEERTISRWSPEQCRED 234 (243)
Q Consensus 157 S~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~sVkK~llla~v~~--~~~~~~~p~~l~~~~V~E~~~~Rw~p~~~r~~ 234 (243)
|+|.|.+.+.+.+ +..+|.++.+..|++.+|+|++++||++. .+.++++|.|+..|+|.|++++||+|.++|+|
T Consensus 194 Sey~VLi~~g~~d----r~~t~~~i~~~~Rl~~sv~Kslv~cyvd~~a~d~~mn~~~~~e~~~v~eq~~~Rwsp~~er~d 269 (271)
T KOG4685|consen 194 SEYGVLIQDGRRD----RLLTWSDIHCKVRLSGSVAKSLVLCYVDGNALDVKMNSPKCMELFTVGEQTLSRWSPGRERED 269 (271)
T ss_pred eeeeEEEecCccc----chhhHHHHhHHHHhhhhccceEEEEEEeccccccccchHHHHHHhhhhHHHHhhhCCcccccC
Confidence 9999999884332 45789999999999999999999999999 56789999999999999999999999999999
Q ss_pred cc
Q 043831 235 PA 236 (243)
Q Consensus 235 ~~ 236 (243)
++
T Consensus 270 ~d 271 (271)
T KOG4685|consen 270 QD 271 (271)
T ss_pred CC
Confidence 74
No 2
>PRK09297 tRNA-splicing endonuclease subunit alpha; Reviewed
Probab=100.00 E-value=1.6e-44 Score=305.84 Aligned_cols=157 Identities=29% Similarity=0.502 Sum_probs=145.4
Q ss_pred eEEEEeCCeEEEeechhhHHHHHhcccccccccCcccCceeeecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHHHhc
Q 043831 35 AHAVLAGYSALLAVEAEQTELLNRACFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKAK 114 (243)
Q Consensus 35 ~~g~L~g~~V~v~~~~~~~~L~~~~~yG~~~~~~~~~~~~L~Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~~~~ 114 (243)
|+|.|.|++|+|....+..+||++++||++.++ +|+|||+||+||+ .+|+|+|.+.+++++|++|+|+.+...
T Consensus 1 ~~g~l~~~~V~v~~~~~~~~Ly~~~~yG~~~~~------~L~Ls~~Ea~yL~-~~g~L~v~~~~~~~~s~~el~~~~~~~ 73 (169)
T PRK09297 1 IKGVLSGDRVVIKDVEGIRRLYNKGFYGKLLGN------PLELSLIEALYLV-EKGWLEVVDKDGELLSFEELYELAREI 73 (169)
T ss_pred CceEEeCCEEEEechHHHHHHHhCCCcCCccCC------cEEEcHHHHHHHH-HCCCEEEEcCCCcccCHHHHHHHHHhc
Confidence 689999999999333445569999999999998 8999999999999 799999998777889999999999999
Q ss_pred CCccchhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhcccccCc
Q 043831 115 KETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVAKT 194 (243)
Q Consensus 115 ~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~sVkK~ 194 (243)
+++|..+|.||+|||+|||+|+||+|||+||+||+++|...||+|+|+++++++.++ |.+|++.+|+|++|+|+
T Consensus 74 ~~~F~~~y~VY~dLr~rG~~vk~G~kfG~df~vY~~gp~~~Hs~~lV~v~~e~~~~~------~~~l~~~~Rla~~v~K~ 147 (169)
T PRK09297 74 IEKFDIKYLVYKDLRDRGYIVKSGLKYGSDFRVYERGPGIDHSPYLVKVLSEDEEIS------PNEITSFVRVSHSVRKK 147 (169)
T ss_pred cccHHHHhHHHHHHHHCCCccCCCCcCCeeEEEECCCCCCCcccEEEEEecCCCcCC------HHHHHHhhhheeecccE
Confidence 999999999999999999999999999999999999999999999999999887765 99999999999999999
Q ss_pred EEEEEEecCC
Q 043831 195 LLILTINKNG 204 (243)
Q Consensus 195 llla~v~~~~ 204 (243)
+|+|+|+.++
T Consensus 148 ~ila~vd~~~ 157 (169)
T PRK09297 148 LVLAIVDDDG 157 (169)
T ss_pred EEEEEEeCCC
Confidence 9999998544
No 3
>TIGR00324 endA tRNA intron endonuclease. The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied (PubMed:97344075) and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs.
Probab=100.00 E-value=3.2e-43 Score=298.19 Aligned_cols=157 Identities=27% Similarity=0.445 Sum_probs=145.2
Q ss_pred ceEEEEeCCeEEEeechh-hHHHHHhcccccccccCcccCceeeecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHHH
Q 043831 34 EAHAVLAGYSALLAVEAE-QTELLNRACFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMK 112 (243)
Q Consensus 34 ~~~g~L~g~~V~v~~~~~-~~~L~~~~~yG~~~~~~~~~~~~L~Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~~ 112 (243)
+.+|.|.||+|+| .+.+ ..+||++++||++.++ .|+|||+||+||+ ..|+|+|.+.++.++|++++|+.+.
T Consensus 1 ~~~~~l~~d~v~v-~~~~~~~~l~~~~~yG~~~~~------~l~LsliEa~yL~-~~g~l~v~~~~~~~ls~~el~~~~~ 72 (170)
T TIGR00324 1 EIQGKLKGDEVIV-KKKTIISDLTTREEYGNLDGD------SLNLSLIESLYLI-DLGKLRLIRSDSEPLSREELSDLAR 72 (170)
T ss_pred CeeEEEeCCEEEE-CCcchhhHHHhcccCCCCcCC------ccEEeHHHHHHHH-hCCcEEEEcCCCCcCCHHHHHHHHH
Confidence 3579999999999 6655 4569999999999988 7999999999999 7999999877888999999999999
Q ss_pred hcCCccchhhhhchhhhhcCeEeccCCcCCccEEEeeCCC--CCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhccc
Q 043831 113 AKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHP--SLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGG 190 (243)
Q Consensus 113 ~~~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P--~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~s 190 (243)
..+++|..+|.||+|||+|||+|+||+|||+||+||+++| .+.||+|+|+|+++++.++ |.+|++.+|+|++
T Consensus 73 ~~~~~f~~~y~VY~dLR~rG~~vk~G~kFG~dF~vY~~~p~~~~~Hs~~~V~v~~~~~~~~------~~~l~~~~Rla~~ 146 (170)
T TIGR00324 73 KVERGFMRKYLVYKDLRDRGYVVKTGFKFGADFRLYERGPLRDHSHSEYLVAIDDHDESID------LIDLSSGVRVAHG 146 (170)
T ss_pred hccccHHHhhHHHHHHHHCCCEecCCcccCceEEEECCCCCCCccCceEEEEEecCCCccC------HHHHHhhhhheec
Confidence 9999999999999999999999999999999999999999 8889999999999887765 9999999999999
Q ss_pred ccCcEEEEEEecCC
Q 043831 191 VAKTLLILTINKNG 204 (243)
Q Consensus 191 VkK~llla~v~~~~ 204 (243)
|||++|+|+|+.++
T Consensus 147 VkK~lvla~v~~~~ 160 (170)
T TIGR00324 147 VKKKLVIAYVDEEK 160 (170)
T ss_pred cccEEEEEEEecCC
Confidence 99999999998653
No 4
>PRK09300 tRNA splicing endonuclease; Reviewed
Probab=100.00 E-value=6.1e-40 Score=302.94 Aligned_cols=151 Identities=25% Similarity=0.414 Sum_probs=140.5
Q ss_pred CcceEEEEeCCeEEEeechhhHHHHHhcccccccccCcccCceeeecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHH
Q 043831 32 QSEAHAVLAGYSALLAVEAEQTELLNRACFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYM 111 (243)
Q Consensus 32 ~~~~~g~L~g~~V~v~~~~~~~~L~~~~~yG~~~~~~~~~~~~L~Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~ 111 (243)
..+|+|+|.|++|+| +++ ..+||+++|||++.++ ++|||||+||+||+ .+|+|+| ..++++++++.+
T Consensus 163 ~~~~~g~l~g~~V~v-~~~-~~~l~~~~~YG~~~~~-----~~L~LslvEA~yL~-~~g~L~v-----~~~~~~el~~~~ 229 (330)
T PRK09300 163 PDKVSGTLLGDRVVV-WDP-PGELYERGFYGKPLDG-----RRLQLSLVEAAYLL-ERGVLSV-----EILDADEFVERA 229 (330)
T ss_pred CCCceEEEeCCEEEE-cCc-hHHHHhcCCCCCCCCC-----CceeECHHHHHHHH-hCCCEEE-----eeCCHHHHHHHH
Confidence 467999999999999 666 5569999999999877 58999999999999 7999999 359999999999
Q ss_pred HhcCCccchhhhhchhhhhcCeEeccCCcCCccEEEeeCCC---CCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhc
Q 043831 112 KAKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHP---SLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLC 188 (243)
Q Consensus 112 ~~~~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P---~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla 188 (243)
+..+++|..+|.||+|||+|||+|+||+||||||+||+++| ..+||+|+|+|+++++.++ +.+|++.+|||
T Consensus 230 ~~~~~~F~~~y~VY~dLR~rG~~vk~G~KFG~DF~vY~~~~~~~~~~Hs~~lV~v~~~~~~~~------~~~l~~~~Rla 303 (330)
T PRK09300 230 REVEGEFDRKLAVYRDLRERGFVPKTGFKFGSDFRVYEGVESVEKLPHSEYLVRVIPDDHEFS------PRDLSRAVRLA 303 (330)
T ss_pred hhcccchHhhhHHHHHHHHCCCEecCCcccCceEEEECCCCCCCCCCcceEEEEEccCCCccC------HHHHHhhheee
Confidence 99999999999999999999999999999999999999986 7999999999999887765 99999999999
Q ss_pred ccccCcEEEEEEe
Q 043831 189 GGVAKTLLILTIN 201 (243)
Q Consensus 189 ~sVkK~llla~v~ 201 (243)
++|||++|+|+|+
T Consensus 304 ~sVrK~~vla~v~ 316 (330)
T PRK09300 304 HSVRKKMVFALID 316 (330)
T ss_pred eccceEEEEEEEE
Confidence 9999999999998
No 5
>COG1676 SEN2 tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.8e-34 Score=244.11 Aligned_cols=157 Identities=31% Similarity=0.460 Sum_probs=142.8
Q ss_pred cceEEEEeCCeEEEeechh-hHHHHHhcccccccccCcccCceeeecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHH
Q 043831 33 SEAHAVLAGYSALLAVEAE-QTELLNRACFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYM 111 (243)
Q Consensus 33 ~~~~g~L~g~~V~v~~~~~-~~~L~~~~~yG~~~~~~~~~~~~L~Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~ 111 (243)
....+.+.++.|.+ .+.+ +..+|++..+|+..+. +|+||++||+||. ++|.|++.+.++.+++++|+....
T Consensus 10 ~~~~~~~~~~~v~~-~~~~g~~~~~~~~~~~~~~~~------~l~ls~~ea~yl~-e~g~l~~~~~~~~~~s~eel~~~~ 81 (181)
T COG1676 10 VPVEGVLEDDRVYV-KDKEGQNLIYSKEKIGTTERD------PLQLSLIEALYLA-ERGFLKVESRDGKILSFEELMDLG 81 (181)
T ss_pred ceEEEEecCcEEEE-EccCCcceeeehhhccccccc------cceecHHHHHHHh-hcceEeeccCCCccccHHHHHHHH
Confidence 34567788888888 5544 4558888888888886 7999999999999 899999998899999999999999
Q ss_pred HhcCCccchhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhcccc
Q 043831 112 KAKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGV 191 (243)
Q Consensus 112 ~~~~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~sV 191 (243)
....+.|..+|.||+|||++||+|+||+||||||++|+++|...||.|+|.++++++.++ ..+|++.+||||+|
T Consensus 82 ~~~~~~f~~~y~VY~dLr~rG~vvktG~KfG~~FrvY~~~~~~~Hs~ylV~v~~~~~~~~------~~~i~~~~Rla~sV 155 (181)
T COG1676 82 AEKEESFDERYLVYRDLRDRGYVVKTGLKFGSDFRVYRGGPDREHSEYLVLVLDENEEIS------LGDIVRKVRLAHSV 155 (181)
T ss_pred hhcccccceeeeehhhHHhCceEECccceeeeEEEEecCCCCcccceEEEEEEcCCCccc------HHHHhhhhhhhccc
Confidence 888889999999999999999999999999999999999999999999999999988765 89999999999999
Q ss_pred cCcEEEEEEecC
Q 043831 192 AKTLLILTINKN 203 (243)
Q Consensus 192 kK~llla~v~~~ 203 (243)
+|+|++|+|+.+
T Consensus 156 rK~~v~a~Vd~~ 167 (181)
T COG1676 156 RKELVLAIVDRE 167 (181)
T ss_pred eeEEEEEEEecC
Confidence 999999999973
No 6
>PRK09300 tRNA splicing endonuclease; Reviewed
Probab=99.97 E-value=5.4e-31 Score=243.51 Aligned_cols=163 Identities=23% Similarity=0.347 Sum_probs=140.5
Q ss_pred eEEEEeCCeEEEeechhhHHHHHhcccccccccCcccCceeeecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHHHhc
Q 043831 35 AHAVLAGYSALLAVEAEQTELLNRACFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKAK 114 (243)
Q Consensus 35 ~~g~L~g~~V~v~~~~~~~~L~~~~~yG~~~~~~~~~~~~L~Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~~~~ 114 (243)
|+|.|.||+|+| .+.+..++|++++||++.++ .|+|||+||+||+ .+|.|+|.+ .++++||++.+...
T Consensus 1 m~g~L~g~~V~v-~~~~~~~ly~~~~YG~~~g~------~L~LslvEalYL~-~~g~l~v~~----~~~~eel~~~~~~~ 68 (330)
T PRK09300 1 MKGELEGGVVFV-GKDARSRLYDSRGYGRPKGD------GLELAPVEAAYLL-FRGKIEIVD----GLGFRDLFARASLR 68 (330)
T ss_pred CceEEECCEEEE-CchhhhhHHhcCCCCcCCCC------eeEEcHHHHHHHH-HcCCEEEec----CCCHHHHHHHhhhc
Confidence 689999999999 66555569999999999887 7999999999999 789999972 39999999999887
Q ss_pred CCccchhhhhchhhhhcCeEeccCCcCCccEEEeeC--CCCCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhccccc
Q 043831 115 KETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRH--HPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVA 192 (243)
Q Consensus 115 ~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~--~P~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~sVk 192 (243)
++|..+|.||+|||+|||+|+|| |+||+||++ +|+..||+|+|+++.+++.++ +.+|++ |
T Consensus 69 -~~f~~~y~VY~dLR~rGy~vk~g---g~dF~vY~rG~~p~~~hs~~lV~v~~e~~~i~------~~~l~~--------r 130 (330)
T PRK09300 69 -PNFELRYLVYKDLRERGYYVQPG---DADFRVYPRGSGPGDGESKYRVRVVSERDPLP------FSDLIE--------R 130 (330)
T ss_pred -ccchheehHHHHHHHCCceeccC---CccEEEEcCCCCCCcCcccEEEEEcCCCCccC------HHHHhc--------c
Confidence 99999999999999999999999 999999996 599999999999999988765 888877 9
Q ss_pred CcEEEEEEecCCCCCCccccccceEEEEEEEeeecCCCCCCC-ccccc
Q 043831 193 KTLLILTINKNGQGTATPSCLEQYAVEERTISRWSPEQCRED-PATVA 239 (243)
Q Consensus 193 K~llla~v~~~~~~~~~p~~l~~~~V~E~~~~Rw~p~~~r~~-~~~~~ 239 (243)
|++|+|+|+.++ .|+=..+++|.|+.+.+. .+.+.
T Consensus 131 K~~vla~Vd~e~------------~vtyy~v~~~~~~g~~~~~~~~~~ 166 (330)
T PRK09300 131 KQLVLAVVDEES------------EITYYEVKRIDPKGRMEEDPPDKV 166 (330)
T ss_pred CceEEEEEcCCC------------CEEEEEEEEecCCCCCCCCCCCCc
Confidence 999999999554 233345678888888777 33433
No 7
>PF01974 tRNA_int_endo: tRNA intron endonuclease, catalytic C-terminal domain; InterPro: IPR006677 This entry represents a 3-layer alpha/beta/alpha domain found as the catalytic domain at the C-terminal in homotetrameric tRNA-intron endonucleases [], and as domains 2 and 4 (C-terminal) in the homodimeric enzymes []. tRNA-intron endonucleases (3.1.27.9 from EC) remove tRNA introns by cleaving pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-hydroxyl termini []. These enzymes recognise a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp []. Although homotetrameric enzymes contain four active sites, only two participate in the cleavage, and should therefore, be considered as a dimer of dimers.; GO: 0000213 tRNA-intron endonuclease activity, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 3IEY_B 3IF0_X 2CV8_A 3P1Z_B 3AJV_B 2GJW_D 1R0V_A 3P1Y_C 1R11_B 1RLV_A ....
Probab=99.94 E-value=2.7e-27 Score=179.05 Aligned_cols=81 Identities=38% Similarity=0.696 Sum_probs=75.7
Q ss_pred cchhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhcccccCcEEE
Q 043831 118 FPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVAKTLLI 197 (243)
Q Consensus 118 F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~sVkK~lll 197 (243)
|..+|.||+|||++||+|+||+|||+||+||+++|...||+|+|+|+++++.++ |.+|++.+|+|++|+|++|+
T Consensus 1 F~~~y~vY~dLr~rG~~v~~G~kfG~df~vY~~~p~~~Hs~~~V~v~~~~~~~~------~~~l~~~~Rla~~v~K~~il 74 (85)
T PF01974_consen 1 FWRKYAVYRDLRSRGYVVKPGIKFGCDFLVYPGDPGRYHSSYLVHVLSEDDPIS------WSDLIALVRLATSVKKELIL 74 (85)
T ss_dssp HHHHHHHHHHHHHTT-EEEEEGGGTSSEEEETSCTTSSSSSEEEEEEETTSEEE------HHHHHHHHHHHHHTTSEEEE
T ss_pred CchhhHHHHHHHHCCCEECccCcCCceEEEEeCCCCCcCceEEEEEEcCCCccC------HHHHHHHHHHHhhcCcEEEE
Confidence 678999999999999999999999999999999999999999999999887765 99999999999999999999
Q ss_pred EEEecCC
Q 043831 198 LTINKNG 204 (243)
Q Consensus 198 a~v~~~~ 204 (243)
|+|+.++
T Consensus 75 a~v~~~~ 81 (85)
T PF01974_consen 75 AYVDKEG 81 (85)
T ss_dssp EEETTTS
T ss_pred EEEcCCC
Confidence 9997655
No 8
>KOG4133 consensus tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=2.5e-20 Score=165.01 Aligned_cols=75 Identities=25% Similarity=0.407 Sum_probs=71.1
Q ss_pred chhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhcccccCcEEEE
Q 043831 119 PLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVAKTLLIL 198 (243)
Q Consensus 119 ~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~sVkK~llla 198 (243)
..+|.+|+|||++||++.||-+|||||+|||+||..+||+|+|.+..+++.++ ..++++.+||.++|+|.++++
T Consensus 194 ~lrY~iyKdLwdrGfyLs~ggrFGgdFlvYPGDPLrfHahyivq~~~~~~~I~------~l~lI~~gRLgt~VkKs~vig 267 (290)
T KOG4133|consen 194 ELRYSIYKDLWDRGFYLSPGGRFGGDFLVYPGDPLRFHAHYIVQCWAPEDTIP------LLELIAGGRLGTSVKKSWVIG 267 (290)
T ss_pred hhHHHHHHHHHHcCceeCcccccCceeEecCCcchheeeheeeeeccCCCCcC------HHHHHHhhhhhhhhhhhheee
Confidence 56999999999999999999999999999999999999999999887777766 899999999999999999998
Q ss_pred E
Q 043831 199 T 199 (243)
Q Consensus 199 ~ 199 (243)
+
T Consensus 268 g 268 (290)
T KOG4133|consen 268 G 268 (290)
T ss_pred c
Confidence 8
No 9
>PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed
Probab=99.82 E-value=2e-20 Score=150.72 Aligned_cols=91 Identities=13% Similarity=0.120 Sum_probs=79.4
Q ss_pred CCccchhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhcccccCc
Q 043831 115 KETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGGVAKT 194 (243)
Q Consensus 115 ~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~sVkK~ 194 (243)
.+.|..+|+||+|||+|||+|+||+|||++|.+|++ .||.|+|+|+++++.++ +.+|...+|+||+|+|+
T Consensus 31 ~~~~~~kylVYkDLR~RGyvVk~G~kfg~~~~~~~~----~~s~ylV~Vl~E~~~is------~~eL~~~vr~a~svrK~ 100 (124)
T PRK09539 31 YLVNWDKVDVFVDLKQRGRKTIDGIDEISLIIKDKE----NKYTAMVLIVDENEKVS------FKKILDKLHFSKSMNLE 100 (124)
T ss_pred hhcccceEEEehhHHhCCCeeccCCceeEEEEecCC----CCceEEEEEecCCCccC------HHHHHHHHHHHhhccce
Confidence 578889999999999999999999999999999943 69999999999998765 99999999999999999
Q ss_pred EEEEEEecCCCCCCccccccceEEEEEE
Q 043831 195 LLILTINKNGQGTATPSCLEQYAVEERT 222 (243)
Q Consensus 195 llla~v~~~~~~~~~p~~l~~~~V~E~~ 222 (243)
+|||+||.++ .+--|.++++.
T Consensus 101 lVLAVVD~eg-------dVTYY~v~~i~ 121 (124)
T PRK09539 101 LYLAIVDKYG-------DVTYYTLSEIK 121 (124)
T ss_pred eEEEEEcCCC-------cEEEEEEEEee
Confidence 9999999666 24555555443
No 10
>PF02778 tRNA_int_endo_N: tRNA intron endonuclease, N-terminal domain; InterPro: IPR006678 This entry represents a 2-layer alpha/beta domain found at the N-terminal in homotetrameric tRNA-intron endonucleases [], and as domains 1 (N-terminal) and 3 in the homodimeric enzymes []. tRNA-intron endonucleases (3.1.27.9 from EC) remove tRNA introns by cleaving pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-hydroxyl termini []. These enzymes recognise a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp []. Although homotetrameric enzymes contain four active sites, only two participate in the cleavage, and should therefore, be considered as a dimer of dimers.; GO: 0000213 tRNA-intron endonuclease activity, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1A79_D 2CV8_A 3P1Z_B 3AJV_B 3IEY_A 2ZYZ_D 2GJW_D 1R0V_A 3P1Y_C 1R11_B ....
Probab=99.64 E-value=4.3e-16 Score=113.52 Aligned_cols=66 Identities=24% Similarity=0.434 Sum_probs=54.6
Q ss_pred eEEEEeCCeEEEeech-hhHHHHHhcccccccccCcccCceeeecHHHHHHhhhcCCceEEEcCCCCCCCHHHHH
Q 043831 35 AHAVLAGYSALLAVEA-EQTELLNRACFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELW 108 (243)
Q Consensus 35 ~~g~L~g~~V~v~~~~-~~~~L~~~~~yG~~~~~~~~~~~~L~Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~ 108 (243)
|+|.|.|++|+| .+. +..+||+++|||++..+ ++|+|||+||+||++ .|+|+|. .+|+.+|++|+|
T Consensus 1 m~g~L~g~~V~v-~d~~~~~~ly~~~~YG~~~~~-----~~L~LslvEa~YL~~-~g~l~v~-~~g~~ls~~el~ 67 (67)
T PF02778_consen 1 MKGELSGDRVVV-WDKEAARELYENGFYGKPLDD-----ERLQLSLVEALYLLE-KGKLEVY-EDGKKLSFEELW 67 (67)
T ss_dssp -EEEEETTEEEE-SSHHHHHHHHHTTT-SEECET-----SCEEEEHHHHHHHHH-TTSEEEE-TTSCEE-HHHHH
T ss_pred CcEEEeCCEEEE-CcccHHHHHHhcCCCCCCCCC-----CcEEEeHHHHHHHHh-CCcEEEe-eCCcCCCHHHhC
Confidence 789999999999 554 45569999999996544 489999999999995 6999998 689999999987
No 11
>KOG4772 consensus Predicted tRNA-splicing endonuclease subunit [Translation, ribosomal structure and biogenesis]
Probab=97.58 E-value=5.5e-05 Score=69.94 Aligned_cols=67 Identities=27% Similarity=0.392 Sum_probs=51.7
Q ss_pred cCceeeecHHHHHHhhhcCCceEEEc-CCCCCCCHHHHHHHHHhcCCccchhhhhchhhhhcCeEe-ccCC
Q 043831 71 DKQWYQLGMEEGFYLCHSLKCLKIVG-EDNSTKNDDELWQYMKAKKETFPLLYKAYSHLRKKNWVV-RSGS 139 (243)
Q Consensus 71 ~~~~L~Lsl~EA~yL~~~~g~L~V~~-~~~~~ls~~el~~~~~~~~~~F~~~y~VY~dLR~rG~vv-ksG~ 139 (243)
+...+-|-++||+||+ +.|.+.... .++-+++.++|+..+...... +.+|.||+||+..||+| +++.
T Consensus 106 dsgklyl~~eEalYL~-ErG~l~~cg~e~~I~~sl~dLys~~~s~~~s-~enYlVyahLkrlGfiv~rhn~ 174 (364)
T KOG4772|consen 106 DSGKLYLFIEEALYLS-ERGELQSCGHEDDIVISLKDLYSEIASEKYS-MENYLVYAHLKRLGFIVKRHNV 174 (364)
T ss_pred ccCceEEeHHHHHHHH-HhhhhhhhcCccchhhHHHHHHHHHhhhhcc-hhHHHHHHHHHhcceeeeccCC
Confidence 3345999999999999 677554432 356679999999887764433 77999999999999998 5554
No 12
>PF12928 tRNA_int_end_N2: tRNA-splicing endonuclease subunit sen54 N-term; InterPro: IPR024336 tRNA-splicing endonucleases (3.1.27.9 from EC) catalyse the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini [, ]. The genes encoding these proteins are homologous in eukaryotes and archea. The eukaryotic tRNA-splicing endonucleases are heterotetrameric while the archaeal endonucleases can be split into homodimeric and homotetrameric subgroups. This entry represents the N-terminal domain of Sen54, a non-catalytic subunit of the tRNA-splicing endonuclease complex. Defects in human Sen54 are a cause of pontocerebellar hypoplasia type 4 [].
Probab=94.88 E-value=0.029 Score=41.24 Aligned_cols=22 Identities=27% Similarity=0.157 Sum_probs=20.0
Q ss_pred eeeecHHHHHHhhhcCCceEEEc
Q 043831 74 WYQLGMEEGFYLCHSLKCLKIVG 96 (243)
Q Consensus 74 ~L~Lsl~EA~yL~~~~g~L~V~~ 96 (243)
.+-|.|+||+||+ ++|.|.+..
T Consensus 49 ~~~L~pEEalyLv-ErGsL~l~~ 70 (72)
T PF12928_consen 49 KLWLLPEEALYLV-ERGSLDLWW 70 (72)
T ss_pred eEEEeHHHHHHHH-hcCcEEEEe
Confidence 6889999999999 899999874
No 13
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=50.86 E-value=10 Score=27.11 Aligned_cols=53 Identities=15% Similarity=0.365 Sum_probs=32.6
Q ss_pred cHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHHHhc--------CCccchhhhhchhhh-hcCeEeccC
Q 043831 78 GMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKAK--------KETFPLLYKAYSHLR-KKNWVVRSG 138 (243)
Q Consensus 78 sl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~~~~--------~~~F~~~y~VY~dLR-~rG~vvksG 138 (243)
|..||+|-+- + +.|.||++.|+|+.+... +|.-.+.-.+|.|++ ..|-+++-|
T Consensus 2 t~~eaa~~vL-----~---~~~~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg 63 (72)
T PF05066_consen 2 TFKEAAYEVL-----E---EAGRPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIKNEDSRFVKVG 63 (72)
T ss_dssp -HHHHHHHHH-----H---HH-S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH-T-SS-EESS
T ss_pred CHHHHHHHHH-----H---hcCCCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcccCCCCEEEeC
Confidence 5678888772 1 245899999999988753 222333447899998 677677665
No 14
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=37.11 E-value=97 Score=23.54 Aligned_cols=58 Identities=14% Similarity=0.289 Sum_probs=36.0
Q ss_pred CCCCCHHHHHHHHHhcCC--ccchhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccc
Q 043831 99 NSTKNDDELWQYMKAKKE--TFPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSE 158 (243)
Q Consensus 99 ~~~ls~~el~~~~~~~~~--~F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~ 158 (243)
+.++|.+|+++.+....+ ....-|..-..|-+.|++-+- ..+.....|...+...|..
T Consensus 14 ~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~--~~~~~~~~y~~~~~~~h~H 73 (116)
T cd07153 14 DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI--ELGDGKARYELNTDEHHHH 73 (116)
T ss_pred CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE--EeCCCceEEEeCCCCCCCc
Confidence 457999999999977544 344455555577789998763 2233345665433234443
No 15
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=32.33 E-value=2.7e+02 Score=22.88 Aligned_cols=48 Identities=15% Similarity=0.053 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHhcCCccchhhhhchhhhhcCeEeccCCcCCccEEE
Q 043831 99 NSTKNDDELWQYMKAKKETFPLLYKAYSHLRKKNWVVRSGSQYGVDFVA 147 (243)
Q Consensus 99 ~~~ls~~el~~~~~~~~~~F~~~y~VY~dLR~rG~vvksG~KFG~DF~v 147 (243)
....|-+||.+.+...... ...=.||+||++.|.+-.+.-.-+.-|.+
T Consensus 14 ~~i~tqeeL~~~L~~~G~~-vsqaTIsRdL~elglvk~~~~~g~~~Y~~ 61 (146)
T TIGR01529 14 EKISTQEELVALLKAEGIE-VTQATVSRDLRELGAVKVRDEDGSYVYSL 61 (146)
T ss_pred CCCCCHHHHHHHHHHhCCC-cCHHHHHHHHHHcCCEEEECCCCcEEEee
Confidence 3457889999999776555 55778999999999975443222334554
No 16
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=32.00 E-value=26 Score=20.70 Aligned_cols=15 Identities=20% Similarity=0.208 Sum_probs=12.0
Q ss_pred hhhhhchhhhhcCeE
Q 043831 120 LLYKAYSHLRKKNWV 134 (243)
Q Consensus 120 ~~y~VY~dLR~rG~v 134 (243)
+.+.||++|..+||.
T Consensus 3 Ln~lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 3 LNQLIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHHHHCT-H
T ss_pred HHHHHHHHHHHCCcH
Confidence 468899999999985
No 17
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=30.37 E-value=1.1e+02 Score=23.55 Aligned_cols=57 Identities=12% Similarity=0.286 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHhcCCcc--chhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccc
Q 043831 100 STKNDDELWQYMKAKKETF--PLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSE 158 (243)
Q Consensus 100 ~~ls~~el~~~~~~~~~~F--~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~ 158 (243)
..+|.+|+++.+....+.. ..-|..-..|.+.|.+.+- .++.....|.......|..
T Consensus 22 ~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~--~~~~~~~~Y~~~~~~~h~h 80 (120)
T PF01475_consen 22 EHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKI--EFGDGESRYELSTCHHHHH 80 (120)
T ss_dssp SSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE--EETTSEEEEEESSSSSCEE
T ss_pred CCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEE--EcCCCcceEeecCCCcceE
Confidence 3789999999998765543 4567777788899998874 5567778888755334433
No 18
>PF07597 DUF1560: Protein of unknown function (DUF1560); InterPro: IPR011454 This is a small family of short hypothetical proteins in Rhodopirellula baltica.
Probab=30.24 E-value=15 Score=24.58 Aligned_cols=19 Identities=37% Similarity=0.400 Sum_probs=13.5
Q ss_pred CCCCCCccchhhhcchhhhH
Q 043831 2 GPRWKGRASEAKSSGRSHVQ 21 (243)
Q Consensus 2 ~~~~~~~~~~~~~~p~~~~~ 21 (243)
+.||.+++++|| -|+|+.+
T Consensus 14 ~~rwecrrfeak-hplskni 32 (49)
T PF07597_consen 14 RSRWECRRFEAK-HPLSKNI 32 (49)
T ss_pred cchhhhhhhhhc-Cccccce
Confidence 458999999943 2776654
No 19
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=25.63 E-value=2.1e+02 Score=23.36 Aligned_cols=61 Identities=15% Similarity=0.270 Sum_probs=42.8
Q ss_pred CCCCHHHHHHHHHhcCCc--cchhhhhchhhhhcCeEeccCCcCCccEEEeeCCCCCCccceEEE
Q 043831 100 STKNDDELWQYMKAKKET--FPLLYKAYSHLRKKNWVVRSGSQYGVDFVAYRHHPSLVHSEYAVL 162 (243)
Q Consensus 100 ~~ls~~el~~~~~~~~~~--F~~~y~VY~dLR~rG~vvksG~KFG~DF~vY~~~P~~~HS~~~V~ 162 (243)
..+|.+++.+.++...+. +..-|.+-+-|.+.|.+-+- .++..+..|..-....|..++..
T Consensus 35 ~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~--~~~~~~~~y~~~~~~~H~HliC~ 97 (145)
T COG0735 35 GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRL--EFEGGKTRYELNSEPHHHHLICL 97 (145)
T ss_pred CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEE--EeCCCEEEEecCCCCcccEEEec
Confidence 459999999999876544 56677777888899988664 34667888976433355554443
No 20
>PF12076 Wax2_C: WAX2 C-terminal domain; InterPro: IPR021940 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 170 amino acids in length. This domain is found associated with PF04116 from PFAM. This domain has a conserved LEGW sequence motif. This region has similarity to short chain dehydrogenases [].
Probab=24.38 E-value=1.3e+02 Score=25.82 Aligned_cols=104 Identities=18% Similarity=0.272 Sum_probs=59.2
Q ss_pred ecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHHHh-cCCccchhhhhchhhhhcCeEeccCC--------cCCccEEE
Q 043831 77 LGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKA-KKETFPLLYKAYSHLRKKNWVVRSGS--------QYGVDFVA 147 (243)
Q Consensus 77 Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~~~-~~~~F~~~y~VY~dLR~rG~vvksG~--------KFG~DF~v 147 (243)
+.-.=|+||+ ++| +.|.- ++.++ ++.++. ..+++..+.+.-..+..+=|+|-.|+ .=|+.|.=
T Consensus 10 varaiA~~LC-~rg-v~V~m-----~~~~~-y~~lk~~~~~~~~~~Lv~~~~~~~K~WlVGd~l~~~EQ~~Ap~Gt~Fip 81 (164)
T PF12076_consen 10 VARAIALALC-RRG-VQVVM-----LSKER-YESLKSEAPEECQSNLVQSTSYQAKTWLVGDGLTEEEQKWAPKGTHFIP 81 (164)
T ss_pred HHHHHHHHHH-hcC-CEEEE-----ecHHH-HHHHHHHcCHHhhccEEeecCCCceeEEeCCCCCHHHHhcCCCCCEEee
Confidence 4455689999 677 55542 23333 343433 22333322222234445889997777 34899988
Q ss_pred eeCCC-------CCCccceEEEEeeCCCcCC-CCcCCChHHHHhhhhhcc
Q 043831 148 YRHHP-------SLVHSEYAVLVLAEGEDGE-NGRLRVWSDIHCTVRLCG 189 (243)
Q Consensus 148 Y~~~P-------~~~HS~~~V~v~~~~~~~~-~~~~~s~~~l~~~~Rla~ 189 (243)
|..-| ..||+-=...+-.+-+.+. |+..+ .+-..++-|.+.
T Consensus 82 fsqfP~~~~RkDC~Y~~tPAM~~P~~~~nl~sCEnwl-pRrVmsAwr~aG 130 (164)
T PF12076_consen 82 FSQFPPKKVRKDCTYHSTPAMKVPKSMENLHSCENWL-PRRVMSAWRAAG 130 (164)
T ss_pred ccCCCcHHHhCCCcccCcccccCChhhhhhhhhhccc-hhhHHHHHhhhh
Confidence 77543 5777776666644433333 55544 455666668764
No 21
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=24.09 E-value=2.2e+02 Score=20.77 Aligned_cols=61 Identities=13% Similarity=0.082 Sum_probs=31.5
Q ss_pred hhhchhhhhcCeE-e---ccCCcCCccEEEeeCCCCCCccceEEEEeeCCCcCCCCcCCChHHHHhhhhhccc
Q 043831 122 YKAYSHLRKKNWV-V---RSGSQYGVDFVAYRHHPSLVHSEYAVLVLAEGEDGENGRLRVWSDIHCTVRLCGG 190 (243)
Q Consensus 122 y~VY~dLR~rG~v-v---ksG~KFG~DF~vY~~~P~~~HS~~~V~v~~~~~~~~~~~~~s~~~l~~~~Rla~s 190 (243)
..+..-|+..||. + .++-..|.|++++..+.+. ..++|.+........ ...+......+..
T Consensus 11 ~l~~~ll~~~g~~~v~~~~~~~d~giDi~~~~~~~~~--~~~~vqcK~~~~~v~------~~~v~~~~~~~~~ 75 (115)
T PF04471_consen 11 ELVAELLRKLGYTDVEVTGGSGDGGIDIIAEKDDLGK--ERILVQCKRYKKKVD------VKAVRQLIGKAKK 75 (115)
T ss_dssp ---HHHHHTTT-EEEEEE-SSSEEEEEEEEEETT-----EEEEEEE---S-EE-------HHHHHHHHHHHGG
T ss_pred HHHHHHHHHcCCccEEEeccCCCCCEEEEEEEcccCc--eEEEEEEEEeccccc------hHHHHHHhhhhhc
Confidence 3455678888988 5 3444679999988854232 277888877543332 5555555554443
No 22
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=21.13 E-value=1.2e+02 Score=26.83 Aligned_cols=45 Identities=24% Similarity=0.290 Sum_probs=28.3
Q ss_pred cccccccccCcccCceeeecHHHHHHhhhcCCceEEEcCCCCCCCHHHHHHHHHhcCCcc
Q 043831 59 ACFGRHIVTAEKDKQWYQLGMEEGFYLCHSLKCLKIVGEDNSTKNDDELWQYMKAKKETF 118 (243)
Q Consensus 59 ~~yG~~~~~~~~~~~~L~Lsl~EA~yL~~~~g~L~V~~~~~~~ls~~el~~~~~~~~~~F 118 (243)
-+||++.+. +-+|+.|++=.+. ..+.|. -++.|+++++.+.+-.|
T Consensus 48 d~~g~mf~~-------i~~s~~Eile~ll--k~i~Id------p~fKef~e~ike~di~f 92 (220)
T COG4359 48 DGFGRMFGS-------IHSSLEEILEFLL--KDIKID------PGFKEFVEWIKEHDIPF 92 (220)
T ss_pred HHHHHHHHh-------cCCCHHHHHHHHH--hhcccC------ccHHHHHHHHHHcCCCE
Confidence 345555555 6777788776651 224442 26888888888776655
No 23
>PF12549 TOH_N: Tyrosine hydroxylase N terminal ; InterPro: IPR021164 This domain family is found in eukaryotes, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. Tyrosine hydroxylase converts L-tyrosine to L-DOPA in the catecholamine synthesis pathway. ; GO: 0004511 tyrosine 3-monooxygenase activity, 0055114 oxidation-reduction process
Probab=20.90 E-value=48 Score=19.70 Aligned_cols=10 Identities=30% Similarity=0.391 Sum_probs=8.5
Q ss_pred CCCCCCccch
Q 043831 2 GPRWKGRASE 11 (243)
Q Consensus 2 ~~~~~~~~~~ 11 (243)
+|+|||.+++
T Consensus 7 s~~~~G~r~a 16 (25)
T PF12549_consen 7 SPQAKGFRRA 16 (25)
T ss_pred CCCCccchhh
Confidence 7899998877
Done!