Query 017680
Match_columns 368
No_of_seqs 225 out of 665
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 02:30:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017680.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017680hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2580 Mitochondrial import i 100.0 1.4E-76 3.1E-81 585.1 17.4 339 3-368 112-459 (459)
2 TIGR00984 3a0801s03tim44 mitoc 100.0 9.3E-69 2E-73 532.3 25.5 311 3-358 43-378 (378)
3 PF04280 Tim44: Tim44-like dom 100.0 7.2E-35 1.6E-39 253.9 19.0 147 209-361 1-147 (147)
4 COG4395 Uncharacterized protei 99.9 4.3E-26 9.4E-31 218.4 12.9 149 208-362 132-280 (281)
5 PF07961 MBA1: MBA1-like prote 98.5 5.9E-06 1.3E-10 78.8 15.6 126 223-360 67-199 (235)
6 PF13355 DUF4101: Protein of u 95.9 0.18 3.9E-06 43.2 11.9 96 246-358 20-117 (117)
7 KOG4599 Putative mitochondrial 94.1 0.0034 7.3E-08 62.8 -4.3 138 210-358 150-312 (379)
8 PF12870 Lumazine_bd: Lumazine 90.8 1.6 3.4E-05 34.9 8.0 29 233-261 10-38 (111)
9 KOG2580 Mitochondrial import i 90.4 0.3 6.5E-06 50.4 4.1 58 141-198 244-301 (459)
10 PF12893 Lumazine_bd_2: Putati 88.8 5.8 0.00013 32.9 10.1 92 231-359 5-113 (116)
11 PF13474 SnoaL_3: SnoaL-like d 87.7 13 0.00028 29.8 12.7 102 233-361 2-116 (121)
12 PF08332 CaMKII_AD: Calcium/ca 85.9 16 0.00035 32.0 11.4 110 231-365 4-128 (128)
13 PF14534 DUF4440: Domain of un 82.9 9.1 0.0002 29.7 8.0 69 234-307 3-79 (107)
14 PF12883 DUF3828: Protein of u 77.4 15 0.00032 31.3 8.0 84 249-360 28-117 (120)
15 TIGR02246 conserved hypothetic 60.6 88 0.0019 25.2 10.5 29 231-259 5-33 (128)
16 PRK09635 sigI RNA polymerase s 51.5 29 0.00062 34.0 5.3 50 209-260 155-204 (290)
17 TIGR02957 SigX4 RNA polymerase 41.4 47 0.001 32.1 5.0 49 209-259 145-193 (281)
18 COG4319 Ketosteroid isomerase 41.1 2.6E+02 0.0057 24.9 12.8 100 232-358 12-126 (137)
19 PF13577 SnoaL_4: SnoaL-like d 38.0 56 0.0012 26.4 4.3 105 231-359 8-126 (127)
20 PRK10533 putative lipoprotein; 37.5 1.2E+02 0.0026 27.9 6.6 62 232-295 45-111 (171)
21 PF05223 MecA_N: NTF2-like N-t 36.6 2.5E+02 0.0054 23.4 10.2 28 232-259 3-30 (118)
22 PRK08241 RNA polymerase factor 32.9 51 0.0011 32.4 3.9 52 208-259 189-243 (339)
23 PF13026 DUF3887: Protein of u 30.7 2.3E+02 0.005 23.9 6.8 81 223-307 2-96 (101)
24 PRK09636 RNA polymerase sigma 29.6 80 0.0017 30.5 4.5 49 209-259 152-200 (293)
25 cd00781 ketosteroid_isomerase 29.4 55 0.0012 26.6 2.9 29 232-260 5-33 (122)
26 PF12642 TpcC: Conjugative tra 29.3 4.6E+02 0.01 24.2 9.6 31 230-260 140-170 (232)
27 PF08898 DUF1843: Domain of un 28.7 1.2E+02 0.0026 22.8 4.3 21 237-257 5-25 (53)
28 TIGR01567 S_layer_rel_Mac S-la 26.3 3.9E+02 0.0084 26.3 8.5 80 272-363 131-216 (256)
29 PF08447 PAS_3: PAS fold; Int 24.1 3.1E+02 0.0067 20.4 6.6 64 245-321 21-85 (91)
30 KOG2542 Uncharacterized conser 22.5 1.6E+02 0.0035 30.9 5.3 64 190-255 390-457 (500)
31 PF11454 DUF3016: Protein of u 20.1 4E+02 0.0086 23.8 6.7 72 257-337 29-118 (141)
No 1
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.4e-76 Score=585.14 Aligned_cols=339 Identities=31% Similarity=0.554 Sum_probs=301.7
Q ss_pred cchhhhhhHHHHHHHHHHHHHhhhhhhccCccccCCCCCCcccccCccCchhhhhhhccccchhhhhhcccccccCcccc
Q 017680 3 AESTVKKVSASMKEKISAATEEVKGTFRTGSTDTSAKHDDDVRDGFKASSGEEKQKQTVSSDTAETFYGKLKSSISSPKF 82 (368)
Q Consensus 3 ~e~~~~k~s~~~k~k~~~~~~~~~e~~~~~k~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (368)
+|+++.++|..+|+++++++++||.+. +|+++|+ .+ +|.+++.+|++++|+++|+.-++||+||+++.+.|.|
T Consensus 112 ~e~~t~~~s~~~kk~~~e~~e~~k~~~----~ea~eS~-~~--k~t~~~~~e~~kqA~~sae~vd~~~~kv~~T~~yk~v 184 (459)
T KOG2580|consen 112 AESETQASSEVLKKKLGELKETVKLGA----EEAWESA-LG--KKTKEAVEEAQKQASGSAEEVDTFFEKVGQTAAYKAV 184 (459)
T ss_pred HHhhhhhhhHHHHHHHHHHHHHHHHHH----HHHHhhh-hh--ccchhhHHHHHHHhhcchhhhhHhhhhhhhhhhHHHH
Confidence 689999999999999999999888877 8888777 44 6999999999999999999666666666666666666
Q ss_pred hHHHHHhhhhhHHHHHhhhhhhhhhhccCCCCcccccCCCCCCCCCCCCCccceeEEecccchhhHH-HHHhhcCCcccc
Q 017680 83 TLAFQKLKEAKVVDLAKKGYDIVKDELSGSPSKRKHLEYTPSPSWTGEKSTRTDLVVTPSKKSMWSK-LKEKMQGYPVFK 161 (368)
Q Consensus 83 ~~~~~~l~~~~~~~~~~~~~~~vk~e~~~~~~~rk~~~~~~~~~~~~e~~~~t~~~~~~~k~s~w~~-~k~~~~~~p~~~ 161 (368)
|+.+..++ +-++.++.|..+||+++...++++++.+.++++++++|+|+. +.+|++|++|+||+ |++|+++|.+++
T Consensus 185 Se~~~~vk--k~~d~s~~g~~i~k~~~r~lr~r~~~~~~~~~~~~~~E~n~~-a~~vv~h~~skw~~kwe~fkek~~~~~ 261 (459)
T KOG2580|consen 185 SEVMETVK--KEIDSSRYGLDIVKERPRKLRKRTEFLGDTFPSEKVGEPNEE-AEGVVLHKDSKWYQKWEDFKEKNVVVR 261 (459)
T ss_pred HHHHHhhc--ccchhhhhhhhchhhhhhhchhhhhhhccCCCcccccCCCcc-eeeEEeccchHHHHHHHHHHhcccchH
Confidence 66666666 456666666666666666544455555566778889999887 67778899999999 999999999999
Q ss_pred ccccccCccccccccchHHhhhhhcccccchhhhhhhc-------cccccccChHHHHHHHHHhcCCCCChhhHHHHHHH
Q 017680 162 RITGISEPVVTKGQEIAEDVRERWETSDNPIVHKIQDM-------NETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQE 234 (368)
Q Consensus 162 ~~~~~~~p~~~k~~e~~~d~r~~~eeSdnP~v~~~~di-------~d~lf~ete~a~~l~eIk~~DP~Fd~~~Fl~~ar~ 234 (368)
+|. +|+..||+|+||+|+-++|+ .+++|.+|+.++++++|+++||+||.++||+.|++
T Consensus 262 k~~---------------~lk~~ydeseN~~i~~~rdvtdki~~~~~g~fsktE~Sev~tei~~iDPsF~~~~Flr~~ee 326 (459)
T KOG2580|consen 262 KFQ---------------ELKKKYDESENPSIRASRDVTDKITDVDGGLFSKTEMSEVLTEIKKIDPSFDKEDFLRECEE 326 (459)
T ss_pred HHH---------------HHHhhccccccHHHHHHHHHHHhhhhcccccchhhHHHHHHHHHHhcCCCCCcHHHHHHHHH
Confidence 999 99999999999999755554 44799999999999999999999999999999999
Q ss_pred HHHH-HHHHHHcCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCcccceEEEecceeEEEEEEeCCeeEEEEEEEEeEEEEE
Q 017680 235 AIRP-VLSAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQIYCV 313 (368)
Q Consensus 235 ~~~p-IleA~~~GDle~Lk~~cse~~y~~~~~~i~~r~~~G~~~d~kiL~I~~veL~~ak~~~~~pvitV~F~aQqI~~v 313 (368)
+|+| ||+||.+||+++||+||++++|++|++++++++++|+.+|++||||++|+|++++||+++|+|+|+|++|+|||+
T Consensus 327 ~IiPnVLeAyvkGD~evLK~wcsea~~~~~aa~~keykk~gv~~d~kILdI~~Vdia~~KmM~d~PVlIitFqaQeI~~v 406 (459)
T KOG2580|consen 327 YIIPNVLEAYVKGDLEVLKKWCSEAPFSQLAAPIKEYKKHGVYFDSKILDIRGVDIASGKMMEDGPVLIITFQAQEIMCV 406 (459)
T ss_pred hhhHHHHHHHHhccHHHHHHHHhhhHHHHHHHHHHHHHhcCeeecceeeeeccchhHHhhhhccCCEEEEEEeeEEEEEE
Confidence 9999 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeeeeccccccCC
Q 017680 314 RDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREMQQLGVQALI 368 (368)
Q Consensus 314 RDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~eiqq~g~~a~~ 368 (368)
||.+|+|||||||+|++++|+|+|+ +|++||||+. +++|||++|.++|.+++|
T Consensus 407 Rd~~GevveGd~d~i~~v~y~wvl~-rd~~El~~d~-~~~WRLlE~~r~~~~~~~ 459 (459)
T KOG2580|consen 407 RDAKGEVVEGDPDKILRVYYAWVLC-RDQDELNPDE-YAAWRLLEFSRAGTEQFL 459 (459)
T ss_pred EcCCCceecCCCCceeeEEeeeeee-ccHhhcCcch-hhhHHHHHHHhccchhcC
Confidence 9999999999999999999999995 4999998755 899999999999999876
No 2
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=100.00 E-value=9.3e-69 Score=532.31 Aligned_cols=311 Identities=23% Similarity=0.409 Sum_probs=273.2
Q ss_pred cchhhhhhHHHHHHHHHHHHHhhhhhhc-cCccccCCCCCCcccccCccCchhhhhhhccccchhhhhhcccccccCccc
Q 017680 3 AESTVKKVSASMKEKISAATEEVKGTFR-TGSTDTSAKHDDDVRDGFKASSGEEKQKQTVSSDTAETFYGKLKSSISSPK 81 (368)
Q Consensus 3 ~e~~~~k~s~~~k~k~~~~~~~~~e~~~-~~k~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (368)
+|++|.++|+.+++.|....+.|.+.+. +.++|+. |+ ..+...++|+++++ +
T Consensus 43 ~~~~~~~~s~~~~~~l~~~~~~v~~~~~~~~~s~~~--------k~---~~~~~~~ta~~~~~----------------~ 95 (378)
T TIGR00984 43 AESGTLKSSEVVGKTLGKLGDTMKKMAHKAWESELG--------KK---MKKAGAETAKTAAE----------------H 95 (378)
T ss_pred HhcccchhhHHHHHHHHHHHHHHHHHHHHHhhcHHH--------HH---HHHHHHHHhhhhhh----------------h
Confidence 4788999999999999999999999995 4444444 33 45677788888888 9
Q ss_pred chHHHHHhhhhhHHHHHhhhhhhhhhhccCCC-----------CcccccCCCCC-CCCCCCCCccceeEEecccchhhHH
Q 017680 82 FTLAFQKLKEAKVVDLAKKGYDIVKDELSGSP-----------SKRKHLEYTPS-PSWTGEKSTRTDLVVTPSKKSMWSK 149 (368)
Q Consensus 82 ~~~~~~~l~~~~~~~~~~~~~~~vk~e~~~~~-----------~~rk~~~~~~~-~~~~~e~~~~t~~~~~~~k~s~w~~ 149 (368)
|+++++.||+|++|+.+|++++.+|+|++... .||+|.+..+. ..+..+.|+. +.+|++||+|+|++
T Consensus 96 ~~~~~~~v~~T~~yk~vs~~~~~~k~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~n~~-a~~v~~~k~s~~~~ 174 (378)
T TIGR00984 96 VDKSAEPVRDTAVYKHVSQSMKDGKDSSRYGFIADKEQRRRPRELTKRTDGRDFAKSRVVEANES-VTDVVLHSDSSWYS 174 (378)
T ss_pred HHHhcccccccHHHHHHHHHHHhhhcccccccccchhhhhhHHHhhhhhcccccccccccccCCc-ccceEEecccHHHH
Confidence 99999999999999999999999999999732 24555444322 2344444433 34457799999999
Q ss_pred -HHHhhcCCccccccccccCccccccccchHHhhhhhcccccchhhhhhhccc-------cccccChHHHHHHHHHhcCC
Q 017680 150 -LKEKMQGYPVFKRITGISEPVVTKGQEIAEDVRERWETSDNPIVHKIQDMNE-------TIFQETDAAASIKEIRRRDP 221 (368)
Q Consensus 150 -~k~~~~~~p~~~~~~~~~~p~~~k~~e~~~d~r~~~eeSdnP~v~~~~di~d-------~lf~ete~a~~l~eIk~~DP 221 (368)
|.+|+++||++++|+ +||++||+||||+|+.+|+|+| +||++|+++++|++|+++||
T Consensus 175 ~w~~fk~~~~~~~~~~---------------~lk~~~~eSeNp~i~~~r~itdkv~~~~~~lF~ete~a~~l~eIk~~DP 239 (378)
T TIGR00984 175 KVEDFKESNVVYRKIQ---------------ELKKKYDESENPLVRMMRGVTDKIGGVFSGMFSETEVSEVLTEFKKIDP 239 (378)
T ss_pred HHHHHHhhCHHHHHHH---------------HHHHHhhcccChhhhHhHHhhhhhhhhhhcccCCCHHHHHHHHHHHhCC
Confidence 999999999999999 9999999999999997777666 59999999999999999999
Q ss_pred CCChhhHHHHHHHHHHH-HHHHHHcCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCcccceEEEecceeEEEEEEeC--Ce
Q 017680 222 SFSLPDFVSEVQEAIRP-VLSAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMG--SS 298 (368)
Q Consensus 222 ~Fd~~~Fl~~ar~~~~p-IleA~~~GDle~Lk~~cse~~y~~~~~~i~~r~~~G~~~d~kiL~I~~veL~~ak~~~--~~ 298 (368)
+||+.+|+.+|+.+|.| ||+||++||++.|++||++++|+.|+++|++|.++|++++++||+|++++|+++++++ +.
T Consensus 240 sFd~~~Fl~gar~aI~p~ILeAf~kGD~e~LK~~lse~vy~~f~a~I~qr~~~G~~~d~~iL~I~~veI~~ak~~e~~~~ 319 (378)
T TIGR00984 240 TFDKEHFLRFLREYIVPEILEAYVKGDLEVLKSWCSEAPFSVYATVVKEYKKMGVSTKGRILDIRGVEIASGKLLEPGDI 319 (378)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhCHHHHHHHHHHHHHHHHCCCeeeeEEeeecCeEEEEEEecCCCCe
Confidence 99999999999999655 9999999999999999999999999999999999999999999999999999999986 46
Q ss_pred eEEEEEEEEeEEEEEEcCC-CCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEee
Q 017680 299 PIIIVAFQTQQIYCVRDKH-GTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLRE 358 (368)
Q Consensus 299 pvitV~F~aQqI~~vRDk~-GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~e 358 (368)
|+|+|+|++|||+|+||++ |+||+|+|++|+++.|+|+|+| ++++++ ++.+++|||++
T Consensus 320 pviiV~F~aQqI~~vRd~~tGeVVeGd~d~I~~v~yvWtF~R-d~~~~~-~~~~~~Wrl~e 378 (378)
T TIGR00984 320 PVLIVTFRAQEINVTKNAKSGEVVAGDPDNIQRINYAWVFTR-DVEELD-NPETLGWKILE 378 (378)
T ss_pred EEEEEEEEEEEEEEEEcCCCCceeeCCCCceeEEEEEEEEEE-cccccC-CCCCCceeecC
Confidence 9999999999999999987 9999999999999999999966 788887 56799999985
No 3
>PF04280 Tim44: Tim44-like domain; InterPro: IPR007379 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane []. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005744 mitochondrial inner membrane presequence translocase complex; PDB: 2CW9_A 2FXT_A 3QK9_A.
Probab=100.00 E-value=7.2e-35 Score=253.89 Aligned_cols=147 Identities=37% Similarity=0.581 Sum_probs=132.3
Q ss_pred HHHHHHHHHhcCCCCChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCcccceEEEeccee
Q 017680 209 AAASIKEIRRRDPSFSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVE 288 (368)
Q Consensus 209 ~a~~l~eIk~~DP~Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~y~~~~~~i~~r~~~G~~~d~kiL~I~~ve 288 (368)
.+.+++.|+++||+||...|+.+|+++|.+|++||.+||++.|++|||+++|+.|..+|+++...|..++.++++|.+++
T Consensus 1 ~a~a~~~i~~~dp~Fd~~~F~~~ak~~f~~i~~A~~~~D~~~l~~~~t~~~~~~~~~~i~~~~~~g~~~~~~~v~i~~~~ 80 (147)
T PF04280_consen 1 LASAIKQIKQRDPGFDPAAFLEEAKEAFLPIQEAWAKGDLEALRPLLTEELYERLQAEIKARRSRGEVNDPEIVRIDNAE 80 (147)
T ss_dssp -HHHHCCHHHH-TT--HHHHHHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEE
T ss_pred CchHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHhCHHHHHHHHHHHHHHHHcCCcccceEEEEEEEE
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEeCCeeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeeeec
Q 017680 289 VRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREMQQ 361 (368)
Q Consensus 289 L~~ak~~~~~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~eiqq 361 (368)
|+++...++.++|+|+|.++|++|++|++|+||+|+++.+..+.|+|+|+|+ + +..+++|+|++|+|
T Consensus 81 i~~~~~~~~~~~vtv~f~~~~~~~~~d~~G~ii~G~~~~~~~~~e~W~f~r~----~--~~~~~~W~L~~i~q 147 (147)
T PF04280_consen 81 IVEAEQEGNFDQVTVRFRSQQIDYVDDKDGEIIEGDPDKIQEFTEYWTFERD----L--GSPNPNWRLAGIQQ 147 (147)
T ss_dssp EEEEEEETTEEEEEEEEEEEEEEEEETTTCTCCCCSTTS-EEEEEEEEEEE--------TTCCCTEEEEEEE-
T ss_pred eeeceeeCCEEEEEEEEEEEEEEEEECCCCcEeeCCCCCceEEEEEEEEEEe----C--CCCCCCEEEEEEeC
Confidence 9999999999999999999999999999999999999999999999999885 2 22368999999987
No 4
>COG4395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.93 E-value=4.3e-26 Score=218.40 Aligned_cols=149 Identities=26% Similarity=0.423 Sum_probs=142.8
Q ss_pred hHHHHHHHHHhcCCCCChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCcccceEEEecce
Q 017680 208 DAAASIKEIRRRDPSFSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEV 287 (368)
Q Consensus 208 e~a~~l~eIk~~DP~Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~y~~~~~~i~~r~~~G~~~d~kiL~I~~v 287 (368)
..+.+++.+...||+|++..||.+++.+|.+||+||..||+++|+.|+++++|..|.+++.+|...|.+++.+.|+|..+
T Consensus 132 ~~~ag~~~v~~~~~~f~p~~fl~~a~~a~~~Iq~a~~~~D~~tL~~L~tpev~~~~~~e~~e~~~~G~~~~ssfv~~~~~ 211 (281)
T COG4395 132 PLAAGARAVHNADPSFDPARFLNGARAAYEMIQQAYGAGDRKTLRELLTPEVMEYLEAEIAERESKGETNQSSFVTILQA 211 (281)
T ss_pred ccccchhhhhcCCcccchhHHHHHHHHHHHHHHHHhhhccHHHHHHhcCHHHHHHHHHHHhhhhhcCccccceecchhhh
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEeCCeeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeeeecc
Q 017680 288 EVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREMQQL 362 (368)
Q Consensus 288 eL~~ak~~~~~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~eiqq~ 362 (368)
+|.++++.++..++||+|..|.|.+.||++|+||+|||+.+.++.|+|+|+|.. +..+|||+|+.||+.
T Consensus 212 di~~a~~~~~~~~atv~~~~~~i~~~~dr~G~vVdGd~~~~~e~~ElWTFtR~~------~s~~p~W~LaaIq~~ 280 (281)
T COG4395 212 DIARADVEGDEDYATVAIRYQGIDVTRDRSGKVVDGDPDKPEEFAELWTFTRDT------GSRDPNWKLAAIQQA 280 (281)
T ss_pred hhhhccccCCceEEEEEEEeeeeeeeccccCceecCCCCcchhhhhheeeeccC------CCCCCCceEEeeecc
Confidence 999999999999999999999999999999999999999999999999998852 344789999999984
No 5
>PF07961 MBA1: MBA1-like protein; InterPro: IPR024621 Mba1 is an inner membrane protein that is part of the mitochondrial protein export machinery [, ]. It binds to the large subunit of mitochondrial ribosomes and cooperates with the C-terminal ribosome-binding domain of Oxa1, which is a central component of the insertion machinery of the inner membrane. In the absence of both Mba1 and the C terminus of Oxa1, mitochondrial translation products fail to be properly inserted into the inner membrane and serve as substrates of the matrix chaperone Hsp70 []. It is proposed that Mba1 functions as a ribosome receptor that cooperates with Oxa1 in the positioning of the ribosome exit site to the insertion machinery of the inner membrane [].
Probab=98.47 E-value=5.9e-06 Score=78.83 Aligned_cols=126 Identities=19% Similarity=0.176 Sum_probs=100.8
Q ss_pred CChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCcccceEEEe-cceeEEEEEEe--CC--
Q 017680 223 FSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNRILHV-SEVEVRETKMM--GS-- 297 (368)
Q Consensus 223 Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~y~~~~~~i~~r~~~G~~~d~kiL~I-~~veL~~ak~~--~~-- 297 (368)
+....|...|.+.|+.+..||++||++.|+..|+..+|+.|.+-++++-. +..++.+++.+ +.-.|+....+ .+
T Consensus 67 ~~f~~wk~~AiE~yv~~NkaFA~~~~~~L~~~c~~~v~~sL~~R~~~~P~-~~kl~W~L~k~~~~PKvvs~~~~~~p~~~ 145 (235)
T PF07961_consen 67 PRFNEWKNKAIELYVQMNKAFAAGDLDKLRKICSSWVYESLAARIKQRPK-NSKLDWKLVKYNKNPKVVSFQAIPIPGGP 145 (235)
T ss_pred CchhHHHHHHHHHHHHHHHHHHhccHHHHHHHhhHHHHHHHHHHHHhCCC-CCeeeEEEEEecCCCeEEEEeeeecCCCC
Confidence 34568999999999999999999999999999999999999999999884 56788888876 44566665543 22
Q ss_pred --eeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeeee
Q 017680 298 --SPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREMQ 360 (368)
Q Consensus 298 --~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~eiq 360 (368)
.-+++|+|.+.|-....|+.++.+++.+ +.+.|+.+|+|. +- +..|+|.|-.
T Consensus 146 ~~~vQ~Vvk~~TkQ~li~~~k~~~~~~~~e---~dvveyiV~~~d-~~-------t~e~~l~Gsv 199 (235)
T PF07961_consen 146 LEIVQFVVKFDTKQRLIKVDKGSEKVEKKE---RDVVEYIVFQCD-PW-------TNEWVLWGSV 199 (235)
T ss_pred CeEEEEEEEEeeeEEEEEeccccccCCccc---cceeeeEEEEEe-CC-------CCcEEEEEEe
Confidence 6789999999998877887776665543 478999999883 11 3479999854
No 6
>PF13355 DUF4101: Protein of unknown function (DUF4101)
Probab=95.90 E-value=0.18 Score=43.17 Aligned_cols=96 Identities=17% Similarity=0.291 Sum_probs=66.2
Q ss_pred CCHHHHHhhcCHHHHHHHHHHHHHHHhCCCcccce-EEEecceeEEEEEEeCCeeEEEEEEEEeEEEEEEcCCCCeecC-
Q 017680 246 GDVETLKKYCSPEVIERCKAEHTAYQSHGIFFDNR-ILHVSEVEVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITEG- 323 (368)
Q Consensus 246 GDle~Lk~~cse~~y~~~~~~i~~r~~~G~~~d~k-iL~I~~veL~~ak~~~~~pvitV~F~aQqI~~vRDk~GeVVeG- 323 (368)
.+.+.|...+++.+++.+......-.++|....-. -+.|..|++..-. ++.+. |.-.-.+...+.+ .|++..+
T Consensus 20 ~~~~~L~~vl~g~ll~~w~~~a~~~~~~g~y~~y~~~~~I~sv~~~~~~--~~ra~--v~a~v~E~~~l~~-~g~~~~~~ 94 (117)
T PF13355_consen 20 HDIDSLSEVLTGPLLSQWQDRAQWLKANGWYWEYDHKLKIDSVEVFSDS--PNRAT--VEATVTESAQLYD-NGQPDNNP 94 (117)
T ss_pred cchhHHHHHhhHHHHHHHHHHHHHHHHcCCeEEEeeeeEEEEEEEcCCC--CCeEE--EEEEEEEEEEEEe-CCccccCC
Confidence 46778999999999999999999999999875544 4445444444211 33444 3334455566888 8998886
Q ss_pred CCCceeEEEEEEEEEEecccccCCCCCCCCeEEee
Q 017680 324 GKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLRE 358 (368)
Q Consensus 324 d~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~e 358 (368)
+.....++.|..... +..|+|.+
T Consensus 95 s~~~~~~vrY~L~r~------------~~~WkI~d 117 (117)
T PF13355_consen 95 SYDSTLRVRYELVRQ------------NGQWKITD 117 (117)
T ss_pred CCCCcEEEEEEEEEc------------CCEEEecC
Confidence 666667888865551 35699975
No 7
>KOG4599 consensus Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis]
Probab=94.09 E-value=0.0034 Score=62.83 Aligned_cols=138 Identities=17% Similarity=0.249 Sum_probs=104.6
Q ss_pred HHHHHHHHhcC--CCCChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCH---------------HHHHHHHHHHHHHHh
Q 017680 210 AASIKEIRRRD--PSFSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSP---------------EVIERCKAEHTAYQS 272 (368)
Q Consensus 210 a~~l~eIk~~D--P~Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse---------------~~y~~~~~~i~~r~~ 272 (368)
-..++.|+..| -+|+.++|-..|+..|+.+.-+....|...+..|+++ .+|..+... .+
T Consensus 150 q~sir~i~~k~~~~~F~ik~f~~kakDifIqaH~~l~~~de~kays~l~e~~fvhl~~~~~t~~~~flp~m~~k----~K 225 (379)
T KOG4599|consen 150 QMSIRRIRDKDEIENFEIKDFGAKAKDIFIQAHLCLNNSDEMKAYSFLTESEFVHLKCPSITNLLHFLPVMQEK----VK 225 (379)
T ss_pred HhhhhhhccCCcccceeccccchHhHHHHHHHHHHHhcChHHHHHHHhhccccccccCCCccchhhhccccchh----hc
Confidence 45789999999 8999999999999999999999999999998888888 555444443 22
Q ss_pred CCCcccceEEE-ecceeEEEEEEeC------C-eeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccc
Q 017680 273 HGIFFDNRILH-VSEVEVRETKMMG------S-SPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEE 344 (368)
Q Consensus 273 ~G~~~d~kiL~-I~~veL~~ak~~~------~-~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~ee 344 (368)
.| .+...+|. +.-..++-++-.+ + .++|+||++++|...++|..|+.--|+++.-..|.++-+|..+.+..
T Consensus 226 ~~-~vR~~~vs~leP~~vv~~rc~d~~~~s~n~~aqitvRkh~~q~Lavydrfg~lm~g~E~i~KDv~eyvvfe~hi~~~ 304 (379)
T KOG4599|consen 226 KG-TVRWSFVSVLEPSRVVYVRCDDDNDKSGNFIAQITVRKHTRQCLAVYDRFGRLMFGSEDIKKDVLEYVVFENHIQNA 304 (379)
T ss_pred cC-ceeEEEEeecccceeEEEEecCCcccccccceeeehHHHHHHHHHHHHHHHHHhccCcccccchhHHHHHHHhhhhh
Confidence 33 23444443 2233344444332 2 68999999999999999999999999998888899999997664433
Q ss_pred cCCCCCCCCeEEee
Q 017680 345 LGEDVLYPIWKLRE 358 (368)
Q Consensus 345 l~~~~~~~~WrL~e 358 (368)
++.|||..
T Consensus 305 ------~g~wr~h~ 312 (379)
T KOG4599|consen 305 ------YGRWRLHK 312 (379)
T ss_pred ------hhhhhhcc
Confidence 57798543
No 8
>PF12870 Lumazine_bd: Lumazine-binding domain; InterPro: IPR024267 This entry represents a lumazine-binding domain found in a family of putative lipoproteins from bacteria. Lumazine is a fluorescent accessory protein having 6,7-dimethyl-8-(1'-D-ribityl) lumazine (DMRL) as its authentic chromophore; it modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength.; PDB: 3K7C_C.
Probab=90.76 E-value=1.6 Score=34.92 Aligned_cols=29 Identities=34% Similarity=0.516 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHcCCHHHHHhhcCHHHHH
Q 017680 233 QEAIRPVLSAYMKGDVETLKKYCSPEVIE 261 (368)
Q Consensus 233 r~~~~pIleA~~~GDle~Lk~~cse~~y~ 261 (368)
+++....+.|+.+||.+....||++....
T Consensus 10 ~~~v~~f~~al~~gd~~~a~~~~~~~~~~ 38 (111)
T PF12870_consen 10 EEVVKNFFDALKNGDYEKAYAYLSPESRE 38 (111)
T ss_dssp HHHHHHHHHHHCTT-HHHHHHTB--TT--
T ss_pred HHHHHHHHHHHHcCCHHHHHHhhCccccc
Confidence 44555578899999999999999998884
No 9
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.41 E-value=0.3 Score=50.39 Aligned_cols=58 Identities=16% Similarity=0.193 Sum_probs=43.0
Q ss_pred cccchhhHHHHHhhcCCccccccccccCccccccccchHHhhhhhcccccchhhhhhh
Q 017680 141 PSKKSMWSKLKEKMQGYPVFKRITGISEPVVTKGQEIAEDVRERWETSDNPIVHKIQD 198 (368)
Q Consensus 141 ~~k~s~w~~~k~~~~~~p~~~~~~~~~~p~~~k~~e~~~d~r~~~eeSdnP~v~~~~d 198 (368)
.....+|..||++....|.++++-+...|..++..++.+|++++|..++||+++++..
T Consensus 244 skw~~kwe~fkek~~~~~k~~~lk~~ydeseN~~i~~~rdvtdki~~~~~g~fsktE~ 301 (459)
T KOG2580|consen 244 SKWYQKWEDFKEKNVVVRKFQELKKKYDESENPSIRASRDVTDKITDVDGGLFSKTEM 301 (459)
T ss_pred hHHHHHHHHHHhcccchHHHHHHHhhccccccHHHHHHHHHHHhhhhcccccchhhHH
Confidence 4567777777777777777777777777777777777777777777777777765543
No 10
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=88.84 E-value=5.8 Score=32.93 Aligned_cols=92 Identities=16% Similarity=0.237 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHhhcCHHH--------------HHHHHHHHHHH---HhCCCcccceEEEecceeEEEEE
Q 017680 231 EVQEAIRPVLSAYMKGDVETLKKYCSPEV--------------IERCKAEHTAY---QSHGIFFDNRILHVSEVEVRETK 293 (368)
Q Consensus 231 ~ar~~~~pIleA~~~GDle~Lk~~cse~~--------------y~~~~~~i~~r---~~~G~~~d~kiL~I~~veL~~ak 293 (368)
..+..+..-.+++..||.+.|+..++|++ ...|.+-++.+ ...+.....+|+ .+.
T Consensus 5 ~I~~~v~~Y~dg~~~gD~~~l~~~f~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~--------~i~ 76 (116)
T PF12893_consen 5 AIEATVQDYFDGLYNGDSEKLRSAFHPDARLQGVRKGKLRTMPIEEFIARVKSRVSPKPPGQERKESIL--------SID 76 (116)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHGGGEEEEEEEEEEETTEEEEEETHHHHHHHHHC---H-SSTT-EEEEE--------EEE
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHhhCCCcEEEEEcCCceEEeCHHHHHHHHHhhccccCCCCCceeEEE--------EEE
Confidence 34445555678888999999999998876 46677777765 233433333333 334
Q ss_pred EeCCeeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeee
Q 017680 294 MMGSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREM 359 (368)
Q Consensus 294 ~~~~~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~ei 359 (368)
+.++.+.+.|.+.-. + ....++++|-+. +..|+|+.-
T Consensus 77 i~g~~A~a~v~~~~~------~-------------~~~~d~~~L~K~----------dg~WkIv~k 113 (116)
T PF12893_consen 77 IDGDVASAKVEYEFP------G-------------FWFVDYFTLVKT----------DGGWKIVSK 113 (116)
T ss_dssp EETTEEEEEEEEEEE------T-------------EEEEEEEEEEEE----------TTEEEEEEE
T ss_pred EECCEEEEEEEEEEC------C-------------CceEEEEEEEEE----------CCEEEEEEE
Confidence 457777777776543 1 156888999774 368999863
No 11
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=87.71 E-value=13 Score=29.82 Aligned_cols=102 Identities=15% Similarity=0.225 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHcCCHHHHHhhcCHHH-------------HHHHHHHHHHHHhCCCcccceEEEecceeEEEEEEeCCee
Q 017680 233 QEAIRPVLSAYMKGDVETLKKYCSPEV-------------IERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSSP 299 (368)
Q Consensus 233 r~~~~pIleA~~~GDle~Lk~~cse~~-------------y~~~~~~i~~r~~~G~~~d~kiL~I~~veL~~ak~~~~~p 299 (368)
+..+....+||.+||.+.|..+|+|++ ++.+.+-.+..-... ..--+.+.++.+ ...++..
T Consensus 2 ~~~~~~~~~a~~~~D~~~~~~~~~~d~~~~~~~~~~~~~g~~~~~~~~~~~~~~~---~~~~~~~~~~~v---~~~~~~a 75 (121)
T PF13474_consen 2 EALLEEWIEAFERGDIDALLSLFSDDFVFFGTGPGEIWRGREAIRAYFERDFESF---RPISIEFEDVQV---SVSGDVA 75 (121)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHEEEEEEEEETTSSSEEESHHHHHHHHHHHHHTH---SEEEEEEEEEEE---EEETTEE
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhCCCEEEEcCCCCceECCHHHHHHHHHHHhhhC---ceEEEEEEEEEE---EECCCEE
Confidence 345566889999999999999887643 344444444433322 111222233343 2345666
Q ss_pred EEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeeeec
Q 017680 300 IIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREMQQ 361 (368)
Q Consensus 300 vitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~eiqq 361 (368)
+++..+..+ .+ .+|+-. ..+....++|++. +..|+++-++.
T Consensus 76 ~~~~~~~~~----~~-~~~~~~------~~~~r~t~v~~k~----------~~~Wki~h~H~ 116 (121)
T PF13474_consen 76 VVTGEFRLR----FR-NDGEEI------EMRGRATFVFRKE----------DGGWKIVHIHW 116 (121)
T ss_dssp EEEEEEEEE----EE-CTTCEE------EEEEEEEEEEEEE----------TTEEEEEEEEE
T ss_pred EEEEEEEEE----Ee-cCCccc------eeeEEEEEEEEEE----------CCEEEEEEEEe
Confidence 666655544 33 333322 3455666777654 35899998765
No 12
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus []. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. ; GO: 0004683 calmodulin-dependent protein kinase activity, 0005516 calmodulin binding, 0006468 protein phosphorylation; PDB: 2W2C_F 3H51_B 3SOA_A 2UX0_A 1HKX_M 2F86_B.
Probab=85.93 E-value=16 Score=31.96 Aligned_cols=110 Identities=20% Similarity=0.200 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHhhcCHHH------HH-HH---HHHHHHHHh-----CCCcccceEEEecceeEEEEEEe
Q 017680 231 EVQEAIRPVLSAYMKGDVETLKKYCSPEV------IE-RC---KAEHTAYQS-----HGIFFDNRILHVSEVEVRETKMM 295 (368)
Q Consensus 231 ~ar~~~~pIleA~~~GDle~Lk~~cse~~------y~-~~---~~~i~~r~~-----~G~~~d~kiL~I~~veL~~ak~~ 295 (368)
+.-..+...++|...||.+....+|+|++ .. .+ -..++-|=. .+....+.|+. +.|.++ -
T Consensus 4 eI~~l~~~w~~ai~tgD~~~~~~ly~~d~av~~Pt~s~~~~~g~~~~~~YF~~~l~~~~~~~~~tI~~-p~V~~l----g 78 (128)
T PF08332_consen 4 EIAALFDRWNDAIQTGDPETYAKLYAPDVAVFEPTVSNQLREGLEFHKFYFDHFLAKKPQGVNTTILN-PHVRLL----G 78 (128)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHEEEEEEEEEGGGTTSEEESCHHHHHHHHHTGTTTSSCEEEEEEE-EEEEEE----S
T ss_pred HHHHHHHHHHHHHHcCCHHHHhhhcCCCeeEeccccCCceecChHHHHHHHhcccccCCCceeeEecC-CeEEEc----C
Confidence 45567778999999999999999999981 11 11 011222222 11111222333 233332 2
Q ss_pred CCeeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeeeeccccc
Q 017680 296 GSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREMQQLGVQ 365 (368)
Q Consensus 296 ~~~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~eiqq~g~~ 365 (368)
++.++++=.+..| +-|++|.... .+..|..+.++. +..|+++...+.+|+
T Consensus 79 ~~~Ai~~gvy~f~----~~d~~G~~~~------~~areT~v~~~~----------~g~W~ivhhHsS~mP 128 (128)
T PF08332_consen 79 DNAAIDAGVYTFQ----FVDKDGVPRT------VQARETRVWQKR----------DGKWKIVHHHSSAMP 128 (128)
T ss_dssp TTEEEEEEEEEEE----EESTTSSEEE------EEEEEEEEEEEE----------TTEEEEEEEEEEESS
T ss_pred CCEEEEeeEEEEE----eecCCCCeee------EEEeEEEEEEEe----------CCeEEEEEEecCCCC
Confidence 3477777777666 6666663211 233444444443 357999999887663
No 13
>PF14534 DUF4440: Domain of unknown function (DUF4440); PDB: 3HX8_A 3SOY_A 3ROB_B 3GZR_A 3B7C_A 3CU3_A 3FSD_A 2R4I_C 1TP6_A.
Probab=82.88 E-value=9.1 Score=29.72 Aligned_cols=69 Identities=14% Similarity=0.186 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHcCCHHHHHhhcCHHHH--------HHHHHHHHHHHhCCCcccceEEEecceeEEEEEEeCCeeEEEEEE
Q 017680 234 EAIRPVLSAYMKGDVETLKKYCSPEVI--------ERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMGSSPIIIVAF 305 (368)
Q Consensus 234 ~~~~pIleA~~~GDle~Lk~~cse~~y--------~~~~~~i~~r~~~G~~~d~kiL~I~~veL~~ak~~~~~pvitV~F 305 (368)
..+....+||.++|.+.|..+++|++. -...+.++.+.... ....-+.+ +...+...++.++++.++
T Consensus 3 a~~~~~~~A~~~~D~~~~~~~~~~d~~~~~~~g~~~~~~~~l~~~~~~~--~~~~~~~~---~~~~v~~~gd~a~~~~~~ 77 (107)
T PF14534_consen 3 ALEEQYEDAFNAGDIDALASLYADDFVFVGPGGTILGKEAILAAFKSGF--ARFSSIKF---EDVEVRVLGDTAVVRGRW 77 (107)
T ss_dssp HHHHHHHHHHHTTHHHHHHTTEEEEEEEEETTSEEEEHHHHHHHHHHHC--EEEEEEEE---EEEEEEEETTEEEEEEEE
T ss_pred HHHHHHHHHHHhCCHHHHHhhhCCCEEEECCCCCEeCHHHHHHHHhhcc--CCCceEEE---EEEEEEEECCEEEEEEEE
Confidence 455668899999999999999887641 12344455554422 12222333 334455667777776665
Q ss_pred EE
Q 017680 306 QT 307 (368)
Q Consensus 306 ~a 307 (368)
..
T Consensus 78 ~~ 79 (107)
T PF14534_consen 78 TF 79 (107)
T ss_dssp EE
T ss_pred EE
Confidence 44
No 14
>PF12883 DUF3828: Protein of unknown function (DUF3828); InterPro: IPR024289 This domain currently has no known function.; PDB: 3KZT_A.
Probab=77.41 E-value=15 Score=31.34 Aligned_cols=84 Identities=20% Similarity=0.299 Sum_probs=51.7
Q ss_pred HHHHhhcCHHHHHHHHHHHHH-HHhCCCc--ccceEE---EecceeEEEEEEeCCeeEEEEEEEEeEEEEEEcCCCCeec
Q 017680 249 ETLKKYCSPEVIERCKAEHTA-YQSHGIF--FDNRIL---HVSEVEVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTITE 322 (368)
Q Consensus 249 e~Lk~~cse~~y~~~~~~i~~-r~~~G~~--~d~kiL---~I~~veL~~ak~~~~~pvitV~F~aQqI~~vRDk~GeVVe 322 (368)
+.+++||+.++.+.+....+. ..-.+.- ..+.-. -+.++.+..+.+.++.+.+.|+|
T Consensus 28 ~~~~~yvsk~~~~~l~~~~~~~~~~~D~D~f~~aQD~~~~w~~~i~v~~~~~~~~~a~v~v~~----------------- 90 (120)
T PF12883_consen 28 ELMERYVSKETIAKLKKIYQLEQGILDFDYFIKAQDYDPDWVSNIKVGPAKMDGDCAVVYVTF----------------- 90 (120)
T ss_dssp HHHHHHB-HHHHHHHHHHH----HHSSSBTTTTBSS--TTSGGG-EEEEEETTEEEEEEEETT-----------------
T ss_pred HHHHHHHHHHHHHHHHhhhhcccCCcCCCCceecccCChhhHhhEEEeeccccCCeEEEEEEE-----------------
Confidence 468999999999999987763 2222211 111111 15788888888888888888887
Q ss_pred CCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeeee
Q 017680 323 GGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREMQ 360 (368)
Q Consensus 323 Gd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~eiq 360 (368)
|. ..-......+.|.+. +..|+|..|.
T Consensus 91 G~-~~~~~~~~~~~l~ke----------~g~WkI~~V~ 117 (120)
T PF12883_consen 91 GK-NNEKKQTVIVCLVKE----------NGRWKIDDVR 117 (120)
T ss_dssp TS-TT-EEEEEEEEEEEE----------TTEEEEEEES
T ss_pred ec-CCCCCEEEEEEEEEE----------CCEEEEEEee
Confidence 22 112355666677553 4789999875
No 15
>TIGR02246 conserved hypothetical protein. This family consists of uncharacterized proteins found in a number of genera and species, including Streptomyces, Xanthomonas, Oceanobacillus iheyensis, Caulobacter crescentus CB15, and Xylella fastidiosa. The function is unknown.
Probab=60.63 E-value=88 Score=25.23 Aligned_cols=29 Identities=17% Similarity=0.355 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHhhcCHHH
Q 017680 231 EVQEAIRPVLSAYMKGDVETLKKYCSPEV 259 (368)
Q Consensus 231 ~ar~~~~pIleA~~~GDle~Lk~~cse~~ 259 (368)
..+..+....+||.+||.+.|..++++++
T Consensus 5 ~i~~l~~~~~~a~~~~D~~~~~~~~~~Da 33 (128)
T TIGR02246 5 AIRALVATWEAAWAAGDAEGFADLFTPDG 33 (128)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhCCCc
Confidence 35556666889999999999988777763
No 16
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=51.46 E-value=29 Score=34.04 Aligned_cols=50 Identities=22% Similarity=0.293 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCCCChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHHH
Q 017680 209 AAASIKEIRRRDPSFSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEVI 260 (368)
Q Consensus 209 ~a~~l~eIk~~DP~Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~y 260 (368)
..++.+.++...|.|... -..-++.....+.|+..||++.|..+++|++-
T Consensus 155 l~RAr~~Lr~~~~~~~~~--~~~~~~~~~~f~~a~~~gd~~~l~~ll~~d~~ 204 (290)
T PRK09635 155 AHRARRKINESRIAASVE--PAQHRVVTRAFIEACSNGDLDTLLEVLDPGVA 204 (290)
T ss_pred HHHHHHHHHhhCCCCCCC--hHHHHHHHHHHHHHHHhCCHHHHHHHhhhhhc
Confidence 457888898888877643 22334555569999999999999999999983
No 17
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=41.38 E-value=47 Score=32.09 Aligned_cols=49 Identities=18% Similarity=0.375 Sum_probs=37.6
Q ss_pred HHHHHHHHHhcCCCCChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHH
Q 017680 209 AAASIKEIRRRDPSFSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEV 259 (368)
Q Consensus 209 ~a~~l~eIk~~DP~Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~ 259 (368)
..++.+.|+..-|.|... -...+......+.|+..||++.|..++++++
T Consensus 145 l~RAr~~Lr~~~~~~~~~--~~~~~~~~~~f~~a~~~gD~~~l~~lL~~dv 193 (281)
T TIGR02957 145 VSRARRHLDARRPRFEVS--REESRQLLERFVEAAQTGDLDGLLELLAEDV 193 (281)
T ss_pred HHHHHHHHHhhCCCCCCC--hHHHHHHHHHHHHHHHhCCHHHHHHHHhhce
Confidence 467888888877766543 2334455666999999999999999999987
No 18
>COG4319 Ketosteroid isomerase homolog [Function unknown]
Probab=41.14 E-value=2.6e+02 Score=24.93 Aligned_cols=100 Identities=16% Similarity=0.137 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHHcCCHHHHHh---------------hcCHHHHHHHHHHHHHHHhCCCcccceEEEecceeEEEEEEeC
Q 017680 232 VQEAIRPVLSAYMKGDVETLKK---------------YCSPEVIERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMG 296 (368)
Q Consensus 232 ar~~~~pIleA~~~GDle~Lk~---------------~cse~~y~~~~~~i~~r~~~G~~~d~kiL~I~~veL~~ak~~~ 296 (368)
.+..|.+-..|+.++|.+.+-. .|+.+.|...-..+...-..++.+...-| .|.. .+
T Consensus 12 I~a~i~dw~~Av~a~D~~av~~~YtdDav~f~~~~~~~~Gk~~i~k~~~~~~~~~~~~~~f~~~el-----~v~~---~G 83 (137)
T COG4319 12 IRAAIADWAAAVRAKDADAVADFYTDDAVVFPPPGLQRKGKAAIRKAFEGIFAMGIGPLKFTLEEL-----QVHE---SG 83 (137)
T ss_pred HHHHHHHHHHHHhcccHHHHHHhcCCceEEecCCCCcccCHHHHHHHHHHHHHhccCCCcceeeee-----eeec---cC
Confidence 4455555567999999999873 45666777776666665544443332222 2221 34
Q ss_pred CeeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEee
Q 017680 297 SSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLRE 358 (368)
Q Consensus 297 ~~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~e 358 (368)
+.+.++=.+... .+.+ |++.....-...|.|++.. +.+|+|+-
T Consensus 84 D~a~~~~~~~~~----~~~~------dg~~~~~~~Rat~v~rK~~---------dg~Wk~~~ 126 (137)
T COG4319 84 DVAFVTALLLLT----GTKK------DGPPADLAGRATYVFRKEA---------DGGWKLAH 126 (137)
T ss_pred CEEEEEEeeeee----ccCC------CCcchhheeeeEEEEEEcC---------CCCEEEEE
Confidence 555554444332 1112 3344446678889997631 46899863
No 19
>PF13577 SnoaL_4: SnoaL-like domain; PDB: 3S5C_B 3EJV_A 2RFR_A 3B8L_F 2CHC_A 3A76_A 3EF8_B.
Probab=37.96 E-value=56 Score=26.38 Aligned_cols=105 Identities=13% Similarity=0.072 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHhhcCHHH--------------HHHHHHHHHHHHhCCCcccceEEEecceeEEEEEEeC
Q 017680 231 EVQEAIRPVLSAYMKGDVETLKKYCSPEV--------------IERCKAEHTAYQSHGIFFDNRILHVSEVEVRETKMMG 296 (368)
Q Consensus 231 ~ar~~~~pIleA~~~GDle~Lk~~cse~~--------------y~~~~~~i~~r~~~G~~~d~kiL~I~~veL~~ak~~~ 296 (368)
.+++.+.....++..+|.+.+..+++++. ...+...+..+.... . ...+.-..-++. +++
T Consensus 8 ~I~~l~~~~~~~~D~~~~~~~~~lft~d~~~~~~~~~~~~~~G~~~i~~~~~~~~~~~---~-~~~H~~~~~~v~--~dg 81 (127)
T PF13577_consen 8 AIRDLIARYARALDTGDWEEWADLFTEDAVFDFPGFGFGRYRGRDAIRAFLRARFDGF---A-ATRHMVTNPVVD--VDG 81 (127)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTTCEEEEESHHHHHHHHHHHHHHE---E-EEEEEEEEEEEE--EET
T ss_pred HHHHHHHHHHHHhhCCCHHHHHhccCCcEEEEEeCccccccCCHHHHHHHHHHhcccc---c-ceeEEccceEEE--EcC
Confidence 34455555678889999999988775542 122333333332211 1 222221222333 355
Q ss_pred CeeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEecccccCCCCCCCCeEEeee
Q 017680 297 SSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEELGEDVLYPIWKLREM 359 (368)
Q Consensus 297 ~~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel~~~~~~~~WrL~ei 359 (368)
+.+.++.. ......... +| .+.-..-..|.+.|.+. +..|++..+
T Consensus 82 d~A~~~~~--~~~~~~~~~-~g-----~~~~~~~g~y~~~~~r~----------~g~W~i~~~ 126 (127)
T PF13577_consen 82 DTATVRSY--VLATHRDPD-DG-----EPALWSGGRYTDELVRE----------DGGWRISSR 126 (127)
T ss_dssp TEEEEEEE--EEEEEEEET-TT-----EEEEEEEEEEEEEEEEE----------TTEEEEEEE
T ss_pred CEEEEEEE--EEEEEEEcC-CC-----ceEEEEEEEEEEEEEEE----------CCEEEEEEE
Confidence 55444444 333333333 22 23334457888888774 356999875
No 20
>PRK10533 putative lipoprotein; Provisional
Probab=37.46 E-value=1.2e+02 Score=27.87 Aligned_cols=62 Identities=15% Similarity=0.162 Sum_probs=42.4
Q ss_pred HHHHHHH-HHHHHHcCCHHHHHhhcCHHHHHHHHHHHHHHHh----CCCcccceEEEecceeEEEEEEe
Q 017680 232 VQEAIRP-VLSAYMKGDVETLKKYCSPEVIERCKAEHTAYQS----HGIFFDNRILHVSEVEVRETKMM 295 (368)
Q Consensus 232 ar~~~~p-IleA~~~GDle~Lk~~cse~~y~~~~~~i~~r~~----~G~~~d~kiL~I~~veL~~ak~~ 295 (368)
|+..|-- |+. ...++..||+|+|..+|..|....+.... .|..+.+..-+-..+++..+...
T Consensus 45 aqqfyd~riq~--d~~~la~lRPyLSd~Ly~~L~~A~r~~~~~~~~~GDiFSS~~eG~TsA~VasastI 111 (171)
T PRK10533 45 AQQFYDYRIQH--RSNDIAALRPYLSDKLATLLSDASRDNSHRQLLSGDPFSSRTTLPDSAHVASASTI 111 (171)
T ss_pred HHHHHHHHhcc--chhhHHHhcccccHHHHHHHHHHhhccccCCcccCCcccccccCCccceecccccC
Confidence 3444433 665 77889999999999999999988775432 24344444555667777777544
No 21
>PF05223 MecA_N: NTF2-like N-terminal transpeptidase domain; InterPro: IPR007887 The multiple antibiotic resistance of methicillin-resistant strains of Staphylococcus aureus (MRSA) has become a major clinical problem worldwide. Methicillin resistance in MRSA strains is due to the acquisition of the mecA gene via horizontal transfer from an unidentified species which encodes penicillin-binding protein 2a (PBP2a). The structure of the N-terminal domain from MecA is known [] Q53707 from SWISSPROT and is found to be similar to that found in NTF2 IPR002075 from INTERPRO. The length of the PBP2A N-terminal domain (which positions the transpeptidase active site more than 100A from the expected C terminus of the transmembrane anchor) suggests a possible structural role and potentially gives the transpeptidase domain substantial reach from the cell membrane. This domain seems unlikely to have an enzymatic function.; GO: 0046677 response to antibiotic; PDB: 1MWS_B 1MWT_B 1MWR_A 1MWU_A 1VQQ_A.
Probab=36.63 E-value=2.5e+02 Score=23.39 Aligned_cols=28 Identities=25% Similarity=0.337 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHcCCHHHHHhhcCHHH
Q 017680 232 VQEAIRPVLSAYMKGDVETLKKYCSPEV 259 (368)
Q Consensus 232 ar~~~~pIleA~~~GDle~Lk~~cse~~ 259 (368)
.+..+...+.||.+||.+.+-.+++...
T Consensus 3 p~~~~~~f~~aw~~~dy~~m~~~~~~~~ 30 (118)
T PF05223_consen 3 PEETAEAFLEAWEKGDYAAMYELTSDPS 30 (118)
T ss_dssp --HHHHHHHHHHHTT-HHHHHHTB-HHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHhhchhh
Confidence 4556677899999999999999999888
No 22
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=32.88 E-value=51 Score=32.40 Aligned_cols=52 Identities=15% Similarity=0.151 Sum_probs=39.2
Q ss_pred hHHHHHHHHHhcCCCCC---hhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHH
Q 017680 208 DAAASIKEIRRRDPSFS---LPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEV 259 (368)
Q Consensus 208 e~a~~l~eIk~~DP~Fd---~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~ 259 (368)
-..++.+.|++..|.+. ...+...-+......++||.+||++.|..+++|++
T Consensus 189 ~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD~~~l~~lla~Dv 243 (339)
T PRK08241 189 ALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDVDALVALLTEDA 243 (339)
T ss_pred HHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCCHHHHHHHhcCCE
Confidence 35678899998666521 22355666666777899999999999999999976
No 23
>PF13026 DUF3887: Protein of unknown function (DUF3887)
Probab=30.75 E-value=2.3e+02 Score=23.89 Aligned_cols=81 Identities=12% Similarity=0.178 Sum_probs=46.8
Q ss_pred CChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHHHHHHH-HHHHH-----HHhCCCcc---cceEEEe---c--cee
Q 017680 223 FSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEVIERCK-AEHTA-----YQSHGIFF---DNRILHV---S--EVE 288 (368)
Q Consensus 223 Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~y~~~~-~~i~~-----r~~~G~~~---d~kiL~I---~--~ve 288 (368)
|+.+.+.+.|++.+..+. .+|.+.+..-|++.|=+.|. ..+.. ..+.|.+- ....-.+ + ...
T Consensus 2 f~~Ekv~~~Aeevi~~~N----~~dy~~v~~~~d~~mk~aL~~e~~~~~~~~~l~k~G~f~~f~ki~~~~~~d~~~~~~v 77 (101)
T PF13026_consen 2 FDEEKVKQKAEEVIDLLN----EKDYDKVHEKYDEKMKNALTAEELKEKWGPVLEKAGAFESFEKITVSMIEDKDGYATV 77 (101)
T ss_pred CcHHHHHHHHHHHHHHHh----HhhHHHHHHHHhHHHHHhcCHHHHHHHHHHHHHhccccchhhhhhhhcccccCcceEE
Confidence 788888888887665544 48888888888888777776 33322 22334221 1111111 1 223
Q ss_pred EEEEEEeCCeeEEEEEEEE
Q 017680 289 VRETKMMGSSPIIIVAFQT 307 (368)
Q Consensus 289 L~~ak~~~~~pvitV~F~a 307 (368)
|+-++..++...++|+|.-
T Consensus 78 V~vakYen~~~~ftitF~~ 96 (101)
T PF13026_consen 78 VQVAKYENGKHQFTITFDN 96 (101)
T ss_pred EEEecccCccEEEEEEeCc
Confidence 4445555667777777754
No 24
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=29.58 E-value=80 Score=30.54 Aligned_cols=49 Identities=27% Similarity=0.447 Sum_probs=37.0
Q ss_pred HHHHHHHHHhcCCCCChhhHHHHHHHHHHHHHHHHHcCCHHHHHhhcCHHH
Q 017680 209 AAASIKEIRRRDPSFSLPDFVSEVQEAIRPVLSAYMKGDVETLKKYCSPEV 259 (368)
Q Consensus 209 ~a~~l~eIk~~DP~Fd~~~Fl~~ar~~~~pIleA~~~GDle~Lk~~cse~~ 259 (368)
..++.+.+++.-|.+.. .....++.....+.||.+||.+.|..+++|++
T Consensus 152 l~RAr~~Lr~~~~~~~~--~~~~~~~~v~~f~~A~~~gD~~~l~~Lla~Dv 200 (293)
T PRK09636 152 ASRARKHVRAARPRFPV--SDEEGAELVEAFFAALASGDLDALVALLAPDV 200 (293)
T ss_pred HHHHHHHHHhhCCCCCC--CchHHHHHHHHHHHHHHhCCHHHHHHHHhhCe
Confidence 46788888887776532 22344555666999999999999999998876
No 25
>cd00781 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria.
Probab=29.38 E-value=55 Score=26.56 Aligned_cols=29 Identities=17% Similarity=0.269 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHcCCHHHHHhhcCHHHH
Q 017680 232 VQEAIRPVLSAYMKGDVETLKKYCSPEVI 260 (368)
Q Consensus 232 ar~~~~pIleA~~~GDle~Lk~~cse~~y 260 (368)
.+..+....+||.+||.+.|..+++|++.
T Consensus 5 ~~~~v~~~~~a~~~~D~~~~~~l~aed~~ 33 (122)
T cd00781 5 MKAAVQRYVEAVNAGDPEGIVALFADDAT 33 (122)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHcCCCeE
Confidence 45555668899999999999999888775
No 26
>PF12642 TpcC: Conjugative transposon protein TcpC; InterPro: IPR024735 This family of bacterial proteins are annotated as conjugative transposon protein TcpC. The transfer clostridial plasmid (tcp) locus is part of some conjugative antibiotic resistance and virulence plasmids. TcpC was one of five genes whose products had low-level sequence identity to Tn916 proteins, having similarity to ORF13 homologues from Tn916, Tn5397, and CW459tet [].; PDB: 3UB1_A.
Probab=29.27 E-value=4.6e+02 Score=24.19 Aligned_cols=31 Identities=26% Similarity=0.543 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHcCCHHHHHhhcCHHHH
Q 017680 230 SEVQEAIRPVLSAYMKGDVETLKKYCSPEVI 260 (368)
Q Consensus 230 ~~ar~~~~pIleA~~~GDle~Lk~~cse~~y 260 (368)
..+.......+.||..|+.+.|.-|+.+..-
T Consensus 140 ~~i~~fl~~Ff~aY~t~~~~~L~~y~~~~~~ 170 (232)
T PF12642_consen 140 KPIEEFLEQFFKAYLTGNQGDLSYYMKPGAI 170 (232)
T ss_dssp HHHHHHHHHHHHHHHHS-HHHHHTTB-TT--
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHhcCCcc
Confidence 3444444448999999999999999997753
No 27
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=28.74 E-value=1.2e+02 Score=22.80 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=17.9
Q ss_pred HHHHHHHHcCCHHHHHhhcCH
Q 017680 237 RPVLSAYMKGDVETLKKYCSP 257 (368)
Q Consensus 237 ~pIleA~~~GDle~Lk~~cse 257 (368)
.+|+.|...||+..+|.+...
T Consensus 5 vaiq~AiasGDLa~MK~l~~~ 25 (53)
T PF08898_consen 5 VAIQQAIASGDLAQMKALAAQ 25 (53)
T ss_pred HHHHHHHHcCcHHHHHHHHHH
Confidence 469999999999999987654
No 28
>TIGR01567 S_layer_rel_Mac S-layer-related duplication domain. Members of the family show regions of local similarity to known archaeal S-layer proteins as in the family described by model TIGR01564.
Probab=26.26 E-value=3.9e+02 Score=26.31 Aligned_cols=80 Identities=19% Similarity=0.204 Sum_probs=49.6
Q ss_pred hCCCcccceEEEecc----eeEEEEEEe--CCeeEEEEEEEEeEEEEEEcCCCCeecCCCCceeEEEEEEEEEEeccccc
Q 017680 272 SHGIFFDNRILHVSE----VEVRETKMM--GSSPIIIVAFQTQQIYCVRDKHGTITEGGKDTIQTVYYAWAMQQVDAEEL 345 (368)
Q Consensus 272 ~~G~~~d~kiL~I~~----veL~~ak~~--~~~pvitV~F~aQqI~~vRDk~GeVVeGd~d~i~~v~yvW~f~r~d~eel 345 (368)
+.|..++..||.... .-.....+. ++.|++.|.+. +|-.|..+.+..+.++|.+....+-++
T Consensus 131 KdG~~Vdd~ivs~~~~~~~~~~~~~~~~~~~dv~i~~vhv~------------~vf~g~~~s~v~i~gi~~is~d~~~~I 198 (256)
T TIGR01567 131 KDGEEVDSEIISVSTVDDDDFTYTADLGDEEDVPIFIVYVD------------SVFEGEEDSAVFLKGLLLIDKDEPLEI 198 (256)
T ss_pred eCCcEeeeeEEccCcccCCceEEEeecCCCCCEEEEEEEEe------------eeeccCccceEEEEEEEEEcCCCceEe
Confidence 356777777777732 222232322 24566666553 366788899999999999964445555
Q ss_pred CCCCCCCCeEEeeeeccc
Q 017680 346 GEDVLYPIWKLREMQQLG 363 (368)
Q Consensus 346 ~~~~~~~~WrL~eiqq~g 363 (368)
+.+.....-.+.++.-.+
T Consensus 199 ~~GDefG~~ev~~is~~~ 216 (256)
T TIGR01567 199 ENGDEFGEMEVVETSESG 216 (256)
T ss_pred ecCCCcCcEEEEEecCCc
Confidence 444455667777765543
No 29
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=24.11 E-value=3.1e+02 Score=20.43 Aligned_cols=64 Identities=17% Similarity=0.198 Sum_probs=39.9
Q ss_pred cCCHHHHHhhcCHHHHHHHHHHHHH-HHhCCCcccceEEEecceeEEEEEEeCCeeEEEEEEEEeEEEEEEcCCCCee
Q 017680 245 KGDVETLKKYCSPEVIERCKAEHTA-YQSHGIFFDNRILHVSEVEVRETKMMGSSPIIIVAFQTQQIYCVRDKHGTIT 321 (368)
Q Consensus 245 ~GDle~Lk~~cse~~y~~~~~~i~~-r~~~G~~~d~kiL~I~~veL~~ak~~~~~pvitV~F~aQqI~~vRDk~GeVV 321 (368)
..+...+..+++|+=...+...+.+ ....|.. ..+ +..+. ..++-++-|+.+++ +++|.+|+++
T Consensus 21 ~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~-----~~~-e~R~~----~~~G~~~wi~~~~~---~~~d~~g~~~ 85 (91)
T PF08447_consen 21 KPDFEEWLERIHPDDRERVRQAIQQAALQNGEP-----FEI-EYRIR----RKDGEYRWIEVRGR---PIFDENGKPI 85 (91)
T ss_dssp CBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-E-----EEE-EEEEE----GTTSTEEEEEEEEE---EEETTTS-EE
T ss_pred cCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcc-----eEE-EEEEE----CCCCCEEEEEEEEE---EEECCCCCEE
Confidence 5778889999999999999999988 4444422 222 22222 23455566666665 5678888654
No 30
>KOG2542 consensus Uncharacterized conserved protein (YdiU family) [Function unknown]
Probab=22.54 E-value=1.6e+02 Score=30.91 Aligned_cols=64 Identities=19% Similarity=0.295 Sum_probs=49.6
Q ss_pred cchhhhhhhc---cccccccChHHHHHHHHHhcCCCCChhhHHHHHHHHHHH-HHHHHHcCCHHHHHhhc
Q 017680 190 NPIVHKIQDM---NETIFQETDAAASIKEIRRRDPSFSLPDFVSEVQEAIRP-VLSAYMKGDVETLKKYC 255 (368)
Q Consensus 190 nP~v~~~~di---~d~lf~ete~a~~l~eIk~~DP~Fd~~~Fl~~ar~~~~p-IleA~~~GDle~Lk~~c 255 (368)
|-++.-+|.- .+....+++.+......+++.|.|....++ .++++-. ..+|...||...++.+|
T Consensus 390 new~kw~rny~~ry~~~~~~~g~aar~~~ekkanm~fvnpkyV--Lrnyi~q~ai~aaeegDfSevkkv~ 457 (500)
T KOG2542|consen 390 NEWAKWLRNYRARYDKDLEGAGDAARWQAEKKANMHFVNPKYV--LRNYIAQNAIEAAEEGDFSEVKKVL 457 (500)
T ss_pred hHHHHHHHHHHHHHhhhccCccchHHHHHHhhccccccChHHH--HHHHHHHHHHHHHhccCHHHHHHHH
Confidence 4555444443 234577888999999999999999999987 4667766 78999999999998854
No 31
>PF11454 DUF3016: Protein of unknown function (DUF3016); InterPro: IPR021557 This is a bacterial family of uncharacterised proteins.
Probab=20.14 E-value=4e+02 Score=23.83 Aligned_cols=72 Identities=11% Similarity=0.302 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHh----CCCcccceEEEecceeEEE------------EEEeCC--eeEEEEEEEEeEEEEEEcCCC
Q 017680 257 PEVIERCKAEHTAYQS----HGIFFDNRILHVSEVEVRE------------TKMMGS--SPIIIVAFQTQQIYCVRDKHG 318 (368)
Q Consensus 257 e~~y~~~~~~i~~r~~----~G~~~d~kiL~I~~veL~~------------ak~~~~--~pvitV~F~aQqI~~vRDk~G 318 (368)
+.+++.|...+....+ .|.+++..|.+| +|++ ++++-+ -|-|.++| .++|.+|
T Consensus 29 ~~~~~~L~~~~~~la~~~Lp~gq~L~v~VtDv---DLAG~~~P~~~~~~~dvRvvkdi~pPRI~l~Y------~L~d~~G 99 (141)
T PF11454_consen 29 ERVFAQLTKHFQKLAAKYLPPGQTLEVTVTDV---DLAGDVEPFWGSGANDVRVVKDIYPPRIELSY------TLTDADG 99 (141)
T ss_pred HHHHHHHHHHHHHHHHhhCCCCCEEEEEEEec---ccCcccccCcCCCCCcEEEEccCCCCcEEEEE------EEECCCC
Confidence 3455555555554444 477666666655 3332 233333 36666666 3778999
Q ss_pred CeecCCCCceeEEEEEEEE
Q 017680 319 TITEGGKDTIQTVYYAWAM 337 (368)
Q Consensus 319 eVVeGd~d~i~~v~yvW~f 337 (368)
.||.-...++....|....
T Consensus 100 ~vi~~g~e~L~Dm~fl~~~ 118 (141)
T PF11454_consen 100 KVIKQGEEKLKDMGFLMRP 118 (141)
T ss_pred cEEEecceEEecchhhcCC
Confidence 9887666666666664444
Done!