Query 022189
Match_columns 301
No_of_seqs 180 out of 699
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:42:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022189.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022189hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4599 Putative mitochondrial 100.0 1.8E-39 3.9E-44 305.3 1.5 248 34-300 39-315 (379)
2 PF04280 Tim44: Tim44-like dom 100.0 3.5E-31 7.6E-36 224.0 18.2 144 148-300 2-147 (147)
3 TIGR00984 3a0801s03tim44 mitoc 99.9 1.3E-23 2.7E-28 203.3 17.8 147 141-296 221-377 (378)
4 COG4395 Uncharacterized protei 99.9 5.3E-23 1.1E-27 191.0 12.5 144 147-299 133-278 (281)
5 PF07961 MBA1: MBA1-like prote 99.9 1.9E-21 4.1E-26 177.9 18.8 187 102-299 8-199 (235)
6 KOG2580 Mitochondrial import i 99.8 1.9E-19 4.1E-24 174.0 12.0 149 139-296 293-448 (459)
7 KOG4599 Putative mitochondrial 97.1 0.00012 2.6E-09 70.5 0.2 198 33-301 182-379 (379)
8 PF13355 DUF4101: Protein of u 95.6 0.35 7.5E-06 40.0 12.1 98 181-297 19-117 (117)
9 PF12893 Lumazine_bd_2: Putati 94.2 0.57 1.2E-05 37.7 9.8 93 167-299 5-114 (116)
10 PF12870 Lumazine_bd: Lumazine 87.5 10 0.00022 29.1 10.3 31 167-197 8-38 (111)
11 PF14534 DUF4440: Domain of un 74.6 29 0.00062 25.9 8.3 27 169-195 2-28 (107)
12 PF13474 SnoaL_3: SnoaL-like d 64.5 63 0.0014 24.8 10.7 26 169-194 2-27 (121)
13 PF08898 DUF1843: Domain of un 54.6 38 0.00083 24.4 4.9 21 173-193 5-25 (53)
14 PF13211 DUF4019: Protein of u 45.6 1.6E+02 0.0035 23.7 10.6 79 186-297 25-104 (105)
15 PF11444 DUF2895: Protein of u 42.9 42 0.00091 30.6 4.6 49 163-211 62-116 (199)
16 PRK09635 sigI RNA polymerase s 38.5 74 0.0016 30.1 5.8 45 150-196 158-204 (290)
17 PRK06342 transcription elongat 37.4 1.1E+02 0.0023 26.8 6.1 47 113-186 15-61 (160)
18 PF05223 MecA_N: NTF2-like N-t 36.4 2.3E+02 0.0049 22.8 8.8 29 167-195 2-30 (118)
19 cd00781 ketosteroid_isomerase 36.2 36 0.00079 26.7 2.9 30 167-196 4-33 (122)
20 PRK10533 putative lipoprotein; 35.1 2.3E+02 0.0049 25.2 7.7 37 168-206 45-82 (171)
21 TIGR02960 SigX5 RNA polymerase 33.0 53 0.0012 30.8 3.9 33 163-195 201-233 (324)
22 PF07729 FCD: FCD domain; Int 31.5 1.3E+02 0.0028 22.8 5.3 37 159-195 87-123 (125)
23 TIGR02096 conserved hypothetic 31.4 29 0.00064 27.4 1.6 27 170-196 2-28 (129)
24 PF08858 IDEAL: IDEAL domain; 29.0 95 0.0021 20.4 3.4 24 169-192 12-35 (37)
25 PRK09636 RNA polymerase sigma 28.6 1E+02 0.0022 28.7 5.0 45 149-195 154-200 (293)
26 TIGR02957 SigX4 RNA polymerase 27.6 1.3E+02 0.0027 28.1 5.4 44 150-195 148-193 (281)
27 PF08332 CaMKII_AD: Calcium/ca 27.1 58 0.0013 27.4 2.7 29 166-194 3-31 (128)
28 TIGR03746 conj_TIGR03746 integ 26.0 86 0.0019 28.6 3.7 46 166-211 66-117 (202)
29 TIGR02246 conserved hypothetic 25.1 74 0.0016 24.8 2.9 29 167-195 5-33 (128)
30 PF09322 DUF1979: Domain of un 24.5 55 0.0012 23.8 1.7 37 251-289 2-38 (58)
31 PRK08241 RNA polymerase factor 22.7 1E+02 0.0022 29.2 3.8 47 149-195 192-243 (339)
32 PF01963 TraB: TraB family; I 22.3 89 0.0019 28.1 3.2 27 167-193 171-197 (259)
No 1
>KOG4599 consensus Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-39 Score=305.35 Aligned_cols=248 Identities=18% Similarity=0.257 Sum_probs=218.4
Q ss_pred cccccccccccccccccc---cccCCCCCCccCccceeeceeccccccccccc-----ccCccCCCC--chhhhhcccee
Q 022189 34 SGVSIVPEIYSQNISSCL---CKDHGALPWTRGSTMTLRSSLAPKSLLYLNEK-----RFATAQPKA--PAQARQMGALK 103 (301)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~~~~~--~~~~r~~~~~~ 103 (301)
-++++.++.-.-. .++| ||..+| .|+...++|+..... +.++.+.++ ..+||.|+++|
T Consensus 39 qn~Ip~~~~d~l~-t~~~f~~f~~l~~-----------~kfe~~d~p~~~~k~~~i~kek~k~~~~a~~v~~Pr~~ne~~ 106 (379)
T KOG4599|consen 39 QNFIPDPENDSLN-TKEWFPSFKNLSG-----------AKFESGDDPDPILKRTIISKEKMKSANKAGLVIPPRKWNERP 106 (379)
T ss_pred hhhCcchhccCCC-ChhhhhhhhccCc-----------ccccccCCccccccccchhhhhhccccccccccCCccccccc
Confidence 4555555433322 5666 888888 889999999887633 344444443 46689999999
Q ss_pred eEeeccCcccccCCCCCCCCcccccccccchhhhHHHHHHHHhHHHHHHHHHh----CCCChHHHHHHHHHHHHHHHHHH
Q 022189 104 VSISSPGFIYEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRK----SGYSKQKFYTEAVDLYKEINTLM 179 (301)
Q Consensus 104 i~~~s~g~I~epyvPp~~~~~~~~~~t~~g~~~~~~~l~~~~ks~~~i~~irk----~~Fd~~~F~~~Ak~iy~~I~~A~ 179 (301)
|+++|+|+|||+||||+|++. .+.++..|+.+..+.+.+..++.++++.+++ ..|+.++|-+.|+++|+++|.++
T Consensus 107 i~f~~~~gIfD~yVPPegdg~-~~~l~skg~~~~~~~~~k~~~~q~sir~i~~k~~~~~F~ik~f~~kakDifIqaH~~l 185 (379)
T KOG4599|consen 107 IHFSCTGGIFDAYVPPEGDGK-KSILSSKGLIQKTEILEKTVASQMSIRRIRDKDEIENFEIKDFGAKAKDIFIQAHLCL 185 (379)
T ss_pred eEEEeecccccccCCCCCCcc-cchhcCcchhHHHHHHHHHHHHHhhhhhhccCCcccceeccccchHhHHHHHHHHHHH
Confidence 999999999999999999999 7779999999999999999999999999997 58999999999999999999999
Q ss_pred HcCCHHHHHHhhcH---------------HHHHHHHHHHHHhhccCCceeeeeecccccceEEEEEEeeecccccCCCEE
Q 022189 180 ANGDKTSLRKAVTE---------------KMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFV 244 (301)
Q Consensus 180 a~gD~~~Lr~lvTe---------------~~y~~l~~~Ik~R~~~g~~v~W~lv~~le~~rvv~~rli~I~~~d~~~~~~ 244 (301)
++.|...+..++|| .||+.|...++. .+++|+++.+++|+++|++||.+..+. ..+.++
T Consensus 186 ~~~de~kays~l~e~~fvhl~~~~~t~~~~flp~m~~k~K~-----~~vR~~~vs~leP~~vv~~rc~d~~~~-s~n~~a 259 (379)
T KOG4599|consen 186 NNSDEMKAYSFLTESEFVHLKCPSITNLLHFLPVMQEKVKK-----GTVRWSFVSVLEPSRVVYVRCDDDNDK-SGNFIA 259 (379)
T ss_pred hcChHHHHHHHhhccccccccCCCccchhhhccccchhhcc-----CceeEEEEeecccceeEEEEecCCccc-ccccce
Confidence 99999999999999 999999988654 389999999999999999999887665 368999
Q ss_pred EEEEEEEeEEeeeEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEee
Q 022189 245 QLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRIK 300 (301)
Q Consensus 245 QVTVRf~s~Q~~~iyD~~GrlV~Gs~d~~~dV~EyWVFeR~l~~~~~~WrL~gki~ 300 (301)
|||||+|++|.+++||++|+++.|+++..+||+||+||+.|+.+.++.||++++|.
T Consensus 260 qitvRkh~~q~Lavydrfg~lm~g~E~i~KDv~eyvvfe~hi~~~~g~wr~h~kiv 315 (379)
T KOG4599|consen 260 QITVRKHTRQCLAVYDRFGRLMFGSEDIKKDVLEYVVFENHIQNAYGRWRLHKKIV 315 (379)
T ss_pred eeehHHHHHHHHHHHHHHHHHhccCcccccchhHHHHHHHhhhhhhhhhhhccccc
Confidence 99999999999999999999999999999999999999999999999999999885
No 2
>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=99.98 E-value=3.5e-31 Score=224.01 Aligned_cols=144 Identities=30% Similarity=0.460 Sum_probs=124.0
Q ss_pred HHHHHHHHh--CCCChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHHHHHHHHHHHHhhccCCceeeeeecccccce
Q 022189 148 AYAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMR 225 (301)
Q Consensus 148 ~~~i~~irk--~~Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~~v~W~lv~~le~~r 225 (301)
+.+++.|++ |+||+..|+++|+++|..|++||++||++.|+++||+++|+.|..+++.+...|.+ +..+.+.
T Consensus 2 a~a~~~i~~~dp~Fd~~~F~~~ak~~f~~i~~A~~~~D~~~l~~~~t~~~~~~~~~~i~~~~~~g~~------~~~~~v~ 75 (147)
T PF04280_consen 2 ASAIKQIKQRDPGFDPAAFLEEAKEAFLPIQEAWAKGDLEALRPLLTEELYERLQAEIKARRSRGEV------NDPEIVR 75 (147)
T ss_dssp HHHHCCHHHH-TT--HHHHHHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHHHHTTEE------EEEEEEE
T ss_pred chHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHhCHHHHHHHHHHHHHHHHcCCc------ccceEEE
Confidence 457788886 99999999999999999999999999999999999999999999999999877754 5566777
Q ss_pred EEEEEEeeecccccCCCEEEEEEEEEeEEeeeEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEee
Q 022189 226 TLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRIK 300 (301)
Q Consensus 226 vv~~rli~I~~~d~~~~~~QVTVRf~s~Q~~~iyD~~GrlV~Gs~d~~~dV~EyWVFeR~l~~~~~~WrL~gki~ 300 (301)
+++++++++... +.+++|||+|+++|++|++|++|++++|+++++..+.|||+|+|++++++++|+|+|+.+
T Consensus 76 i~~~~i~~~~~~---~~~~~vtv~f~~~~~~~~~d~~G~ii~G~~~~~~~~~e~W~f~r~~~~~~~~W~L~~i~q 147 (147)
T PF04280_consen 76 IDNAEIVEAEQE---GNFDQVTVRFRSQQIDYVDDKDGEIIEGDPDKIQEFTEYWTFERDLGSPNPNWRLAGIQQ 147 (147)
T ss_dssp EEEEEEEEEEEE---TTEEEEEEEEEEEEEEEEETTTCTCCCCSTTS-EEEEEEEEEEE--TTCCCTEEEEEEE-
T ss_pred EEEEEeeeceee---CCEEEEEEEEEEEEEEEEECCCCcEeeCCCCCceEEEEEEEEEEeCCCCCCCEEEEEEeC
Confidence 888888776654 799999999999999999999999999999999999999999999999999999999864
No 3
>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=99.91 E-value=1.3e-23 Score=203.28 Aligned_cols=147 Identities=21% Similarity=0.303 Sum_probs=126.5
Q ss_pred HHHHHhHHHHHHHHHh--CCCChHHHHHHHHHH-HHHHHHHHHcCCHHHHHHhhcHHHHHHHHHHHHHhhccCCceeeee
Q 022189 141 IILELKSAYAIAKLRK--SGYSKQKFYTEAVDL-YKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWEL 217 (301)
Q Consensus 141 l~~~~ks~~~i~~irk--~~Fd~~~F~~~Ak~i-y~~I~~A~a~gD~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~~v~W~l 217 (301)
+..+...+.+|++|+. |+||+..|+.+|+.+ |++|.+||++||.+.|++||++.+|+.|...|++|...|.+++-
T Consensus 221 lF~ete~a~~l~eIk~~DPsFd~~~Fl~gar~aI~p~ILeAf~kGD~e~LK~~lse~vy~~f~a~I~qr~~~G~~~d~-- 298 (378)
T TIGR00984 221 MFSETEVSEVLTEFKKIDPTFDKEHFLRFLREYIVPEILEAYVKGDLEVLKSWCSEAPFSVYATVVKEYKKMGVSTKG-- 298 (378)
T ss_pred ccCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhCHHHHHHHHHHHHHHHHCCCeeee--
Confidence 4556777889999996 999999999999988 89999999999999999999999999999999999999986543
Q ss_pred ecccccceEEEEEEeeeccccc-C-CCEEEEEEEEEeEEeeeEEcCC-CceecCCCCCeeeeeEEEEEEEeCCC----CC
Q 022189 218 IEPIIKMRTLRARLIGVDRNDL-N-KVFVQLTLEFLAKQKFEAYDSK-GVTVAGDKTKEVLVRDIWVFEKSLFH----PG 290 (301)
Q Consensus 218 v~~le~~rvv~~rli~I~~~d~-~-~~~~QVTVRf~s~Q~~~iyD~~-GrlV~Gs~d~~~dV~EyWVFeR~l~~----~~ 290 (301)
++|+++-++|..+.+ + ++.+.|+|+|.++|+.|++|++ |+||+|+++++..+.+.|+|+|+++. +.
T Consensus 299 -------~iL~I~~veI~~ak~~e~~~~pviiV~F~aQqI~~vRd~~tGeVVeGd~d~I~~v~yvWtF~Rd~~~~~~~~~ 371 (378)
T TIGR00984 299 -------RILDIRGVEIASGKLLEPGDIPVLIVTFRAQEINVTKNAKSGEVVAGDPDNIQRINYAWVFTRDVEELDNPET 371 (378)
T ss_pred -------EEeeecCeEEEEEEecCCCCeEEEEEEEEEEEEEEEEcCCCCceeeCCCCceeEEEEEEEEEEcccccCCCCC
Confidence 344444444444333 2 4689999999999999999999 99999999999999999999999863 56
Q ss_pred CCeEEE
Q 022189 291 AYWRLC 296 (301)
Q Consensus 291 ~~WrL~ 296 (301)
+.|||.
T Consensus 372 ~~Wrl~ 377 (378)
T TIGR00984 372 LGWKIL 377 (378)
T ss_pred Cceeec
Confidence 789985
No 4
>COG4395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.89 E-value=5.3e-23 Score=190.98 Aligned_cols=144 Identities=20% Similarity=0.272 Sum_probs=125.9
Q ss_pred HHHHHHHHHh--CCCChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHHHHHHHHHHHHhhccCCceeeeeecccccc
Q 022189 147 SAYAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKM 224 (301)
Q Consensus 147 s~~~i~~irk--~~Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~~v~W~lv~~le~~ 224 (301)
...+++.+.+ |.|++..|+..|+.+|.+|++||+.+|.++|++|+|+++|+.|++++.++..+|.++. .
T Consensus 133 ~~ag~~~v~~~~~~f~p~~fl~~a~~a~~~Iq~a~~~~D~~tL~~L~tpev~~~~~~e~~e~~~~G~~~~---------s 203 (281)
T COG4395 133 LAAGARAVHNADPSFDPARFLNGARAAYEMIQQAYGAGDRKTLRELLTPEVMEYLEAEIAERESKGETNQ---------S 203 (281)
T ss_pred cccchhhhhcCCcccchhHHHHHHHHHHHHHHHHhhhccHHHHHHhcCHHHHHHHHHHHhhhhhcCcccc---------c
Confidence 3445666775 9999999999999999999999999999999999999999999999999988887633 2
Q ss_pred eEEEEEEeeecccccCCCEEEEEEEEEeEEeeeEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEe
Q 022189 225 RTLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRI 299 (301)
Q Consensus 225 rvv~~rli~I~~~d~~~~~~QVTVRf~s~Q~~~iyD~~GrlV~Gs~d~~~dV~EyWVFeR~l~~~~~~WrL~gki 299 (301)
.-|..-..+|...+..++.+++||+|..+-+..++|+.|++|+||++++.++.|+|+|+|..++.+++|.|.++=
T Consensus 204 sfv~~~~~di~~a~~~~~~~~atv~~~~~~i~~~~dr~G~vVdGd~~~~~e~~ElWTFtR~~~s~~p~W~LaaIq 278 (281)
T COG4395 204 SFVTILQADIARADVEGDEDYATVAIRYQGIDVTRDRSGKVVDGDPDKPEEFAELWTFTRDTGSRDPNWKLAAIQ 278 (281)
T ss_pred eecchhhhhhhhccccCCceEEEEEEEeeeeeeeccccCceecCCCCcchhhhhheeeeccCCCCCCCceEEeee
Confidence 223333345566666789999999999999999999999999999999999999999999999999999999864
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=99.88 E-value=1.9e-21 Score=177.89 Aligned_cols=187 Identities=24% Similarity=0.354 Sum_probs=157.7
Q ss_pred eeeEeeccCcccccCCCCCCCCccccccc-c-cchhhhHHHHHHHHhHHHHHHHHHh-C--CCChHHHHHHHHHHHHHHH
Q 022189 102 LKVSISSPGFIYEPYAPREAIPFWRRWFT-R-DGWRRTKDDIILELKSAYAIAKLRK-S--GYSKQKFYTEAVDLYKEIN 176 (301)
Q Consensus 102 ~~i~~~s~g~I~epyvPp~~~~~~~~~~t-~-~g~~~~~~~l~~~~ks~~~i~~irk-~--~Fd~~~F~~~Ak~iy~~I~ 176 (301)
.+|.+...|...|+||||.- +.++|+ | ..|+..+.++...+.+.+.+...|. . .+.-..+.+.|.+.|..++
T Consensus 8 ~~~~~~~iGv~~~~yipps~---~ps~~~~P~~~~~~l~rr~~~~~~Nt~~i~~fr~~~g~k~~f~~wk~~AiE~yv~~N 84 (235)
T PF07961_consen 8 SQFPIRHIGVMADTYIPPSF---LPSPFTSPKVWWKLLIRRLYMFALNTVSIAKFRRQTGKKPRFNEWKNKAIELYVQMN 84 (235)
T ss_pred ccCCcccceeccccccChhh---ccCcccChhHHHHHHHHHHHHHhhhhheeeehhhhcCCCCchhHHHHHHHHHHHHHH
Confidence 36788889999999999965 344443 3 3477778888888888888888775 3 3556789999999999999
Q ss_pred HHHHcCCHHHHHHhhcHHHHHHHHHHHHHhhccCCceeeeeecccccceEEEEEEeeecccccCCCEEEEEEEEEeEEee
Q 022189 177 TLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQKF 256 (301)
Q Consensus 177 ~A~a~gD~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~~v~W~lv~~le~~rvv~~rli~I~~~d~~~~~~QVTVRf~s~Q~~ 256 (301)
+|||+||.+.|++.|+..+++.|.+.+++++. +.+++|+|+...+.|++|+.+.+.++.. ...+.|++|+|+|+|++
T Consensus 85 kaFA~~~~~~L~~~c~~~v~~sL~~R~~~~P~-~~kl~W~L~k~~~~PKvvs~~~~~~p~~--~~~~vQ~Vvk~~TkQ~l 161 (235)
T PF07961_consen 85 KAFAAGDLDKLRKICSSWVYESLAARIKQRPK-NSKLDWKLVKYNKNPKVVSFQAIPIPGG--PLEIVQFVVKFDTKQRL 161 (235)
T ss_pred HHHHhccHHHHHHHhhHHHHHHHHHHHHhCCC-CCeeeEEEEEecCCCeEEEEeeeecCCC--CCeEEEEEEEEeeeEEE
Confidence 99999999999999999999999999999985 4589999999999999999999888765 34699999999999999
Q ss_pred eEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEe
Q 022189 257 EAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRI 299 (301)
Q Consensus 257 ~iyD~~GrlV~Gs~d~~~dV~EyWVFeR~l~~~~~~WrL~gki 299 (301)
..+|+.+..+++. .+||+||.||.++.. .+.|+|+|++
T Consensus 162 i~~~k~~~~~~~~---e~dvveyiV~~~d~~--t~e~~l~Gsv 199 (235)
T PF07961_consen 162 IKVDKGSEKVEKK---ERDVVEYIVFQCDPW--TNEWVLWGSV 199 (235)
T ss_pred EEeccccccCCcc---ccceeeeEEEEEeCC--CCcEEEEEEe
Confidence 8899876655433 569999999998754 4599999987
No 6
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.80 E-value=1.9e-19 Score=173.97 Aligned_cols=149 Identities=22% Similarity=0.322 Sum_probs=128.6
Q ss_pred HHHHHHHhHHHHHHHHHh--CCCChHHHHHHHHHHH-HHHHHHHHcCCHHHHHHhhcHHHHHHHHHHHHHhhccCCceee
Q 022189 139 DDIILELKSAYAIAKLRK--SGYSKQKFYTEAVDLY-KEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNW 215 (301)
Q Consensus 139 ~~l~~~~ks~~~i~~irk--~~Fd~~~F~~~Ak~iy-~~I~~A~a~gD~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~~v~W 215 (301)
..|..+......+.+|++ |+||.++|+..+++.+ ++|.+|+-.||++.|++||++..|+.+.+.+++.+..|-.
T Consensus 293 ~g~fsktE~Sev~tei~~iDPsF~~~~Flr~~ee~IiPnVLeAyvkGD~evLK~wcsea~~~~~aa~~keykk~gv~--- 369 (459)
T KOG2580|consen 293 GGLFSKTEMSEVLTEIKKIDPSFDKEDFLRECEEYIIPNVLEAYVKGDLEVLKKWCSEAPFSQLAAPIKEYKKHGVY--- 369 (459)
T ss_pred cccchhhHHHHHHHHHHhcCCCCCcHHHHHHHHHhhhHHHHHHHHhccHHHHHHHHhhhHHHHHHHHHHHHHhcCee---
Confidence 446667777778888986 9999999999998755 6799999999999999999999999999999999877642
Q ss_pred eeecccccceEEEEEEeeecccccCCCEEEEEEEEEeEEeeeEEcCCCceecCCCCCeeeeeEEEEEEEeCC--CC--CC
Q 022189 216 ELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLF--HP--GA 291 (301)
Q Consensus 216 ~lv~~le~~rvv~~rli~I~~~d~~~~~~QVTVRf~s~Q~~~iyD~~GrlV~Gs~d~~~dV~EyWVFeR~l~--~~--~~ 291 (301)
.+-++|+++=++|....+-.+.+.+.|.|++++++|++|.+|+||+|++|++..|.+.|||+|+.. ++ ++
T Consensus 370 ------~d~kILdI~~Vdia~~KmM~d~PVlIitFqaQeI~~vRd~~GevveGd~d~i~~v~y~wvl~rd~~El~~d~~~ 443 (459)
T KOG2580|consen 370 ------FDSKILDIRGVDIASGKMMEDGPVLIITFQAQEIMCVRDAKGEVVEGDPDKILRVYYAWVLCRDQDELNPDEYA 443 (459)
T ss_pred ------ecceeeeeccchhHHhhhhccCCEEEEEEeeEEEEEEEcCCCceecCCCCceeeEEeeeeeeccHhhcCcchhh
Confidence 355677777677666666679999999999999999999999999999999999999999999754 34 77
Q ss_pred CeEEE
Q 022189 292 YWRLC 296 (301)
Q Consensus 292 ~WrL~ 296 (301)
.|||.
T Consensus 444 ~WRLl 448 (459)
T KOG2580|consen 444 AWRLL 448 (459)
T ss_pred hHHHH
Confidence 89974
No 7
>KOG4599 consensus Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis]
Probab=97.12 E-value=0.00012 Score=70.54 Aligned_cols=198 Identities=20% Similarity=0.205 Sum_probs=135.4
Q ss_pred ccccccccccccccccccccccCCCCCCccCccceeeceecccccccccccccCccCCCCchhhhhccceeeEeeccCcc
Q 022189 33 SSGVSIVPEIYSQNISSCLCKDHGALPWTRGSTMTLRSSLAPKSLLYLNEKRFATAQPKAPAQARQMGALKVSISSPGFI 112 (301)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~s~g~I 112 (301)
+..+.|..|.. +++.+|..+- +.+..++.|+...+-.+|+++ -+-|.++..+-| +
T Consensus 182 H~~l~~~de~k---ays~l~e~~f------vhl~~~~~t~~~~flp~m~~k-------------~K~~~vR~~~vs---~ 236 (379)
T KOG4599|consen 182 HLCLNNSDEMK---AYSFLTESEF------VHLKCPSITNLLHFLPVMQEK-------------VKKGTVRWSFVS---V 236 (379)
T ss_pred HHHHhcChHHH---HHHHhhcccc------ccccCCCccchhhhccccchh-------------hccCceeEEEEe---e
Confidence 45666666655 5666666643 677777888888888888755 233444555555 4
Q ss_pred cccCCCCCCCCcccccccccchhhhHHHHHHHHhHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhc
Q 022189 113 YEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRKSGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVT 192 (301)
Q Consensus 113 ~epyvPp~~~~~~~~~~t~~g~~~~~~~l~~~~ks~~~i~~irk~~Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvT 192 (301)
+|||.- -+.+.+. .-.++.+.+|+..+|+- +. +|.++|..++.++..+. ..++=++
T Consensus 237 leP~~v-----v~~rc~d----------~~~~s~n~~aqitvRkh------~~-q~Lavydrfg~lm~g~E--~i~KDv~ 292 (379)
T KOG4599|consen 237 LEPSRV-----VYVRCDD----------DNDKSGNFIAQITVRKH------TR-QCLAVYDRFGRLMFGSE--DIKKDVL 292 (379)
T ss_pred ccccee-----EEEEecC----------CcccccccceeeehHHH------HH-HHHHHHHHHHHHhccCc--ccccchh
Confidence 555432 0111110 00112445555555441 11 88899999999999888 6667777
Q ss_pred HHHHHHHHHHHHHhhccCCceeeeeecccccceEEEEEEeeecccccCCCEEEEEEEEEeEEeeeEEcCCCceecCCCCC
Q 022189 193 EKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTK 272 (301)
Q Consensus 193 e~~y~~l~~~Ik~R~~~g~~v~W~lv~~le~~rvv~~rli~I~~~d~~~~~~QVTVRf~s~Q~~~iyD~~GrlV~Gs~d~ 272 (301)
+ |..|..+|+++..+|. ++|++++...+++ .+.+.++++-+.+.+....|+..|.+..|+.
T Consensus 293 e--yvvfe~hi~~~~g~wr-~h~kivp~wi~~k--------------qk~~~tl~l~~lt~~~~~~~~~~~~~~~tek-- 353 (379)
T KOG4599|consen 293 E--YVVFENHIQNAYGRWR-LHKKIVPPWIPAK--------------QKAYKTLMLFILTMEKSEAYPAGPKEAVTEK-- 353 (379)
T ss_pred H--HHHHHHhhhhhhhhhh-hcccccCcccccc--------------ccchheEEeehhccCchhhcccCCccchhhh--
Confidence 7 9999999999999884 9999876644333 2578999999999999999999888777653
Q ss_pred eeeeeEEEEEEEeCCCCCCCeEEEEEeeC
Q 022189 273 EVLVRDIWVFEKSLFHPGAYWRLCGRIKI 301 (301)
Q Consensus 273 ~~dV~EyWVFeR~l~~~~~~WrL~gki~~ 301 (301)
+.|.-++|..+......|+|++.+.+
T Consensus 354 ---~ke~~~~e~~~~~t~~~~~lk~~~kI 379 (379)
T KOG4599|consen 354 ---FKECILKENDVEITILKGILKPQLKI 379 (379)
T ss_pred ---hhhhhhhcccccccchhcccchhhcC
Confidence 45555588888777889999987754
No 8
>PF13355 DUF4101: Protein of unknown function (DUF4101)
Probab=95.59 E-value=0.35 Score=39.97 Aligned_cols=98 Identities=16% Similarity=0.206 Sum_probs=59.2
Q ss_pred cCCHHHHHHhhcHHHHHHHHHHHHHhhccCCceeeeeecccccceEEEEEEeeecccccCCCEEEEEEEEEeEEeeeEEc
Q 022189 181 NGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYD 260 (301)
Q Consensus 181 ~gD~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~~v~W~lv~~le~~rvv~~rli~I~~~d~~~~~~QVTVRf~s~Q~~~iyD 260 (301)
..+.+.|.+++++.|++........-...|. +|++. +.+++..|.... ..-.+++|.-.-.-....||
T Consensus 19 ~~~~~~L~~vl~g~ll~~w~~~a~~~~~~g~--y~~y~--------~~~~I~sv~~~~--~~~~ra~v~a~v~E~~~l~~ 86 (117)
T PF13355_consen 19 PHDIDSLSEVLTGPLLSQWQDRAQWLKANGW--YWEYD--------HKLKIDSVEVFS--DSPNRATVEATVTESAQLYD 86 (117)
T ss_pred CcchhHHHHHhhHHHHHHHHHHHHHHHHcCC--eEEEe--------eeeEEEEEEEcC--CCCCeEEEEEEEEEEEEEEe
Confidence 3567799999999999999988877666553 56653 122222222221 12334444444455667788
Q ss_pred CCCceecC-CCCCeeeeeEEEEEEEeCCCCCCCeEEEE
Q 022189 261 SKGVTVAG-DKTKEVLVRDIWVFEKSLFHPGAYWRLCG 297 (301)
Q Consensus 261 ~~GrlV~G-s~d~~~dV~EyWVFeR~l~~~~~~WrL~g 297 (301)
.|++..+ +......|.+ .|.|. ++.|+|+.
T Consensus 87 -~g~~~~~~s~~~~~~vrY--~L~r~----~~~WkI~d 117 (117)
T PF13355_consen 87 -NGQPDNNPSYDSTLRVRY--ELVRQ----NGQWKITD 117 (117)
T ss_pred -CCccccCCCCCCcEEEEE--EEEEc----CCEEEecC
Confidence 8998876 4444445544 34444 56799963
No 9
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=94.24 E-value=0.57 Score=37.75 Aligned_cols=93 Identities=15% Similarity=0.200 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhcHHH--------------HHHHHHHHHHhh---ccCCceeeeeecccccceEEEE
Q 022189 167 EAVDLYKEINTLMANGDKTSLRKAVTEKM--------------YSALKNEIKQRE---SMWSSVNWELIEPIIKMRTLRA 229 (301)
Q Consensus 167 ~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~--------------y~~l~~~Ik~R~---~~g~~v~W~lv~~le~~rvv~~ 229 (301)
..++......+++.+||.+.|++.+.|++ .+++...++.+. ..+. .+.-..
T Consensus 5 ~I~~~v~~Y~dg~~~gD~~~l~~~f~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~------------~~~~~i 72 (116)
T PF12893_consen 5 AIEATVQDYFDGLYNGDSEKLRSAFHPDARLQGVRKGKLRTMPIEEFIARVKSRVSPKPPGQ------------ERKESI 72 (116)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHGGGEEEEEEEEEEETTEEEEEETHHHHHHHHHC---H-SST------------T-EEEE
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHhhCCCcEEEEEcCCceEEeCHHHHHHHHHhhccccCCCC------------CceeEE
Confidence 34556666778899999999999999887 356667777652 1111 111111
Q ss_pred EEeeecccccCCCEEEEEEEEEeEEeeeEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEe
Q 022189 230 RLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRI 299 (301)
Q Consensus 230 rli~I~~~d~~~~~~QVTVRf~s~Q~~~iyD~~GrlV~Gs~d~~~dV~EyWVFeR~l~~~~~~WrL~gki 299 (301)
..++| .++.+.+.|.+.... ..+.||.+|.|. ++.|+|..|+
T Consensus 73 ~~i~i-----~g~~A~a~v~~~~~~-------------------~~~~d~~~L~K~----dg~WkIv~k~ 114 (116)
T PF12893_consen 73 LSIDI-----DGDVASAKVEYEFPG-------------------FWFVDYFTLVKT----DGGWKIVSKV 114 (116)
T ss_dssp EEEEE-----ETTEEEEEEEEEEET-------------------EEEEEEEEEEEE----TTEEEEEEEE
T ss_pred EEEEE-----ECCEEEEEEEEEECC-------------------CceEEEEEEEEE----CCEEEEEEEe
Confidence 22333 357888888775321 257999999997 7899999986
No 10
>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=87.52 E-value=10 Score=29.11 Aligned_cols=31 Identities=13% Similarity=0.145 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhcHHHHH
Q 022189 167 EAVDLYKEINTLMANGDKTSLRKAVTEKMYS 197 (301)
Q Consensus 167 ~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~y~ 197 (301)
..+++-.....|+.+||.+....++++..-.
T Consensus 8 ~P~~~v~~f~~al~~gd~~~a~~~~~~~~~~ 38 (111)
T PF12870_consen 8 TPEEVVKNFFDALKNGDYEKAYAYLSPESRE 38 (111)
T ss_dssp -HHHHHHHHHHHHCTT-HHHHHHTB--TT--
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHhhCccccc
Confidence 3456677788899999999999999988774
No 11
>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=74.56 E-value=29 Score=25.90 Aligned_cols=27 Identities=15% Similarity=0.234 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 169 VDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 169 k~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
++++....+||.++|.+.+..+.+|++
T Consensus 2 ~a~~~~~~~A~~~~D~~~~~~~~~~d~ 28 (107)
T PF14534_consen 2 RALEEQYEDAFNAGDIDALASLYADDF 28 (107)
T ss_dssp HHHHHHHHHHHHTTHHHHHHTTEEEEE
T ss_pred HHHHHHHHHHHHhCCHHHHHhhhCCCE
Confidence 467888999999999999999988765
No 12
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=64.52 E-value=63 Score=24.80 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHcCCHHHHHHhhcHH
Q 022189 169 VDLYKEINTLMANGDKTSLRKAVTEK 194 (301)
Q Consensus 169 k~iy~~I~~A~a~gD~~~Lr~lvTe~ 194 (301)
++++.+..+||.+||.+.+..+++++
T Consensus 2 ~~~~~~~~~a~~~~D~~~~~~~~~~d 27 (121)
T PF13474_consen 2 EALLEEWIEAFERGDIDALLSLFSDD 27 (121)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHEEEE
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhCCC
Confidence 46788999999999999999988754
No 13
>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=54.56 E-value=38 Score=24.43 Aligned_cols=21 Identities=19% Similarity=0.381 Sum_probs=18.4
Q ss_pred HHHHHHHHcCCHHHHHHhhcH
Q 022189 173 KEINTLMANGDKTSLRKAVTE 193 (301)
Q Consensus 173 ~~I~~A~a~gD~~~Lr~lvTe 193 (301)
..||+|.+.||+..++.+.+.
T Consensus 5 vaiq~AiasGDLa~MK~l~~~ 25 (53)
T PF08898_consen 5 VAIQQAIASGDLAQMKALAAQ 25 (53)
T ss_pred HHHHHHHHcCcHHHHHHHHHH
Confidence 579999999999999988764
No 14
>PF13211 DUF4019: Protein of unknown function (DUF4019)
Probab=45.60 E-value=1.6e+02 Score=23.75 Aligned_cols=79 Identities=13% Similarity=0.200 Sum_probs=45.2
Q ss_pred HHHHhhcHHHHHHHHHHHHHhhccCCceeeeeecccccceEEEEEEe-eecccccCCCEEEEEEEEEeEEeeeEEcCCCc
Q 022189 186 SLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLI-GVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGV 264 (301)
Q Consensus 186 ~Lr~lvTe~~y~~l~~~Ik~R~~~g~~v~W~lv~~le~~rvv~~rli-~I~~~d~~~~~~QVTVRf~s~Q~~~iyD~~Gr 264 (301)
.++.-++++.+......++.. -|.- ... ..+...-. ..+. ..+..++.|.|.++--
T Consensus 25 ~fk~~~t~~~w~~~l~~~R~~--LG~v--------~~R-~~~~~~~~~~~pg---~P~G~Yv~v~f~T~F~--------- 81 (105)
T PF13211_consen 25 FFKKAITEEQWVAQLRAARAP--LGAV--------VSR-ELVSRQRYTSLPG---APDGEYVVVQFQTTFA--------- 81 (105)
T ss_pred HHhccCCHHHHHHHHHHHHHh--cccc--------chh-hheeeeeecCCCC---CCCceEEEEEEEeEeC---------
Confidence 567778888777776655433 3321 011 12222211 1111 1245588888987662
Q ss_pred eecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEE
Q 022189 265 TVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCG 297 (301)
Q Consensus 265 lV~Gs~d~~~dV~EyWVFeR~l~~~~~~WrL~g 297 (301)
+-..+.|-++|.+. .++.||+.|
T Consensus 82 -------~~~~~~Etvt~~~e---~dg~Wr~~G 104 (105)
T PF13211_consen 82 -------NKKQATETVTFRLE---EDGRWRVVG 104 (105)
T ss_pred -------CCCceEEEEEEEEc---CCCcEEeCC
Confidence 11237999998775 478999986
No 15
>PF11444 DUF2895: Protein of unknown function (DUF2895); InterPro: IPR021548 This is a bacterial family of uncharacterised proteins.
Probab=42.90 E-value=42 Score=30.56 Aligned_cols=49 Identities=18% Similarity=0.283 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHcCC------HHHHHHhhcHHHHHHHHHHHHHhhccCC
Q 022189 163 KFYTEAVDLYKEINTLMANGD------KTSLRKAVTEKMYSALKNEIKQRESMWS 211 (301)
Q Consensus 163 ~F~~~Ak~iy~~I~~A~a~gD------~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~ 211 (301)
.-...|--||.+++.--.+|+ +..|+.++||+|...|.+..+.|...|+
T Consensus 62 ~VYaFa~yIfQQlN~W~~dG~~DY~~ni~~l~~YlTP~c~~~L~~d~~~r~~~ge 116 (199)
T PF11444_consen 62 TVYAFAFYIFQQLNRWPTDGEEDYPNNIHRLSAYLTPSCQAFLEQDYEQRRNNGE 116 (199)
T ss_pred HHHHHHHHHHHHHcccccCChHHHHHHHHhhhhhcCHHHHHHHHHHHHHHHhccc
Confidence 334456667888887666666 4589999999999999999998887775
No 16
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=38.53 E-value=74 Score=30.08 Aligned_cols=45 Identities=16% Similarity=0.079 Sum_probs=33.5
Q ss_pred HHHHHHh--CCCChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHHH
Q 022189 150 AIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMY 196 (301)
Q Consensus 150 ~i~~irk--~~Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~y 196 (301)
|.++|++ |.|+. ..++.+++-....+|+..||.+.|..++++++-
T Consensus 158 Ar~~Lr~~~~~~~~--~~~~~~~~~~~f~~a~~~gd~~~l~~ll~~d~~ 204 (290)
T PRK09635 158 ARRKINESRIAASV--EPAQHRVVTRAFIEACSNGDLDTLLEVLDPGVA 204 (290)
T ss_pred HHHHHHhhCCCCCC--ChHHHHHHHHHHHHHHHhCCHHHHHHHhhhhhc
Confidence 4455554 54543 234456788889999999999999999999984
No 17
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=37.38 E-value=1.1e+02 Score=26.78 Aligned_cols=47 Identities=19% Similarity=0.206 Sum_probs=29.6
Q ss_pred cccCCCCCCCCcccccccccchhhhHHHHHHHHhHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHcCCHHH
Q 022189 113 YEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRKSGYSKQKFYTEAVDLYKEINTLMANGDKTS 186 (301)
Q Consensus 113 ~epyvPp~~~~~~~~~~t~~g~~~~~~~l~~~~ks~~~i~~irk~~Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~ 186 (301)
.+|+.||.+.+.-..++|++|.+...+.|... + ..+.+|-+.||+..
T Consensus 15 ~~~~~~~r~~~~~~~~lT~~G~~~L~~El~~L----------~-----------------~~i~~Ar~~GDlsE 61 (160)
T PRK06342 15 AETLLPDRPISPHPNLVTEAGLKALEDQLAQA----------R-----------------AAYEAAQAIEDVNE 61 (160)
T ss_pred ccccCCCCCCCCCCceECHHHHHHHHHHHHHH----------H-----------------HHHHHHHHCCChhH
Confidence 45666765533325579999966555444331 0 25788889999887
No 18
>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=36.37 E-value=2.3e+02 Score=22.79 Aligned_cols=29 Identities=7% Similarity=0.113 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 167 EAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 167 ~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
.+++.+....+||++||.+.+-.+++...
T Consensus 2 ~p~~~~~~f~~aw~~~dy~~m~~~~~~~~ 30 (118)
T PF05223_consen 2 SPEETAEAFLEAWEKGDYAAMYELTSDPS 30 (118)
T ss_dssp ---HHHHHHHHHHHTT-HHHHHHTB-HHH
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHhhchhh
Confidence 45677888899999999999999999888
No 19
>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=36.19 E-value=36 Score=26.69 Aligned_cols=30 Identities=10% Similarity=0.100 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhcHHHH
Q 022189 167 EAVDLYKEINTLMANGDKTSLRKAVTEKMY 196 (301)
Q Consensus 167 ~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~y 196 (301)
..+++.....+||++||.+.|..+.+|.+.
T Consensus 4 ~~~~~v~~~~~a~~~~D~~~~~~l~aed~~ 33 (122)
T cd00781 4 EMKAAVQRYVEAVNAGDPEGIVALFADDAT 33 (122)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHcCCCeE
Confidence 446677788999999999999999998876
No 20
>PRK10533 putative lipoprotein; Provisional
Probab=35.13 E-value=2.3e+02 Score=25.20 Aligned_cols=37 Identities=22% Similarity=0.395 Sum_probs=27.7
Q ss_pred HHHHH-HHHHHHHHcCCHHHHHHhhcHHHHHHHHHHHHHh
Q 022189 168 AVDLY-KEINTLMANGDKTSLRKAVTEKMYSALKNEIKQR 206 (301)
Q Consensus 168 Ak~iy-~~I~~A~a~gD~~~Lr~lvTe~~y~~l~~~Ik~R 206 (301)
|++-| ..|++ .+.+...||+++++.+|..|...-++.
T Consensus 45 aqqfyd~riq~--d~~~la~lRPyLSd~Ly~~L~~A~r~~ 82 (171)
T PRK10533 45 AQQFYDYRIQH--RSNDIAALRPYLSDKLATLLSDASRDN 82 (171)
T ss_pred HHHHHHHHhcc--chhhHHHhcccccHHHHHHHHHHhhcc
Confidence 44444 34555 667889999999999999999876654
No 21
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=33.00 E-value=53 Score=30.81 Aligned_cols=33 Identities=18% Similarity=0.117 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 163 KFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 163 ~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
.....-+++-....+||.+||.+.|..+++|.+
T Consensus 201 ~~~~~~~~~v~~~~~a~~~gD~~~l~~Lla~Dv 233 (324)
T TIGR02960 201 PPSPEEQDLLERYIAAFESYDLDALTALLHEDA 233 (324)
T ss_pred CCCHHHHHHHHHHHHHHHcCCHHHHHHHhcCCe
Confidence 344456677888999999999999999999876
No 22
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=31.49 E-value=1.3e+02 Score=22.80 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=29.7
Q ss_pred CChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 159 YSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 159 Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
+..........+.+..|.+|+.+||.+..+..+...+
T Consensus 87 ~~~~~~~~~~~~~h~~i~~ai~~~d~~~a~~~~~~h~ 123 (125)
T PF07729_consen 87 IRSKEDLERSLEEHREIIDAIRAGDPEAAREALRQHI 123 (125)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred hhhhhhhhhhHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence 3366777778888999999999999999998887654
No 23
>TIGR02096 conserved hypothetical protein, steroid delta-isomerase-related. This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes.
Probab=31.35 E-value=29 Score=27.39 Aligned_cols=27 Identities=15% Similarity=0.239 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHcCCHHHHHHhhcHHHH
Q 022189 170 DLYKEINTLMANGDKTSLRKAVTEKMY 196 (301)
Q Consensus 170 ~iy~~I~~A~a~gD~~~Lr~lvTe~~y 196 (301)
++.....+||+++|.+.+..++++++.
T Consensus 2 ~iv~~~~~a~~~~d~~~~~~~~~~d~~ 28 (129)
T TIGR02096 2 ELAQHWIEAFNRGDMDAVLALLAEDVL 28 (129)
T ss_pred HHHHHHHHHHHCCCHHHHHHhcCCCeE
Confidence 455667789999999999999998854
No 24
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=28.98 E-value=95 Score=20.44 Aligned_cols=24 Identities=21% Similarity=0.213 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHcCCHHHHHHhhc
Q 022189 169 VDLYKEINTLMANGDKTSLRKAVT 192 (301)
Q Consensus 169 k~iy~~I~~A~a~gD~~~Lr~lvT 192 (301)
+.++..|-.|+.+||++.-..++.
T Consensus 12 ~~L~~~ID~ALd~~D~e~F~~Ls~ 35 (37)
T PF08858_consen 12 EQLLELIDEALDNRDKEWFYELSE 35 (37)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHh
Confidence 467889999999999998777664
No 25
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=28.57 E-value=1e+02 Score=28.72 Aligned_cols=45 Identities=18% Similarity=0.232 Sum_probs=32.8
Q ss_pred HHHHHHHh--CCCChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 149 YAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 149 ~~i~~irk--~~Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
.|.++|++ |.+. .-.+...++-....+|+.+||.+.|..+++|.+
T Consensus 154 RAr~~Lr~~~~~~~--~~~~~~~~~v~~f~~A~~~gD~~~l~~Lla~Dv 200 (293)
T PRK09636 154 RARKHVRAARPRFP--VSDEEGAELVEAFFAALASGDLDALVALLAPDV 200 (293)
T ss_pred HHHHHHHhhCCCCC--CCchHHHHHHHHHHHHHHhCCHHHHHHHHhhCe
Confidence 34555665 4332 234456778889999999999999999998876
No 26
>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=27.58 E-value=1.3e+02 Score=28.07 Aligned_cols=44 Identities=18% Similarity=0.232 Sum_probs=31.7
Q ss_pred HHHHHHh--CCCChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 150 AIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 150 ~i~~irk--~~Fd~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
|.+++++ |.|... .++..++-....+|+..||.+.|..++++++
T Consensus 148 Ar~~Lr~~~~~~~~~--~~~~~~~~~~f~~a~~~gD~~~l~~lL~~dv 193 (281)
T TIGR02957 148 ARRHLDARRPRFEVS--REESRQLLERFVEAAQTGDLDGLLELLAEDV 193 (281)
T ss_pred HHHHHHhhCCCCCCC--hHHHHHHHHHHHHHHHhCCHHHHHHHHhhce
Confidence 4444554 444322 2345667788899999999999999999987
No 27
>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=27.09 E-value=58 Score=27.42 Aligned_cols=29 Identities=21% Similarity=0.337 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHcCCHHHHHHhhcHH
Q 022189 166 TEAVDLYKEINTLMANGDKTSLRKAVTEK 194 (301)
Q Consensus 166 ~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~ 194 (301)
++..+++...++|++.||.++..++|+++
T Consensus 3 ~eI~~l~~~w~~ai~tgD~~~~~~ly~~d 31 (128)
T PF08332_consen 3 QEIAALFDRWNDAIQTGDPETYAKLYAPD 31 (128)
T ss_dssp HHHHHHHHHHHHHHHHT-HHHHHHHEEEE
T ss_pred HHHHHHHHHHHHHHHcCCHHHHhhhcCCC
Confidence 34567899999999999999999999998
No 28
>TIGR03746 conj_TIGR03746 integrating conjugative element protein, PFL_4703 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. The function is unknown.
Probab=26.01 E-value=86 Score=28.64 Aligned_cols=46 Identities=17% Similarity=0.201 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHcCC------HHHHHHhhcHHHHHHHHHHHHHhhccCC
Q 022189 166 TEAVDLYKEINTLMANGD------KTSLRKAVTEKMYSALKNEIKQRESMWS 211 (301)
Q Consensus 166 ~~Ak~iy~~I~~A~a~gD------~~~Lr~lvTe~~y~~l~~~Ik~R~~~g~ 211 (301)
..|--+|.+++.=-.+|. +..|+.++||+|...|.+..+.|...|+
T Consensus 66 aFa~yI~QQlNrW~~~Ge~dY~~ni~~l~~YlTP~c~~~L~~d~~~R~~~ge 117 (202)
T TIGR03746 66 AFAFYIFQQLNRWPKDGEQDYGANIFRLSPYLTPSCRAFLQQDYELRRSNGE 117 (202)
T ss_pred hhHHHHHHHHhhccccchHHHHHHHHhcccccCHHHHHHHHHHHHHHhhcch
Confidence 345556777765444444 5589999999999999999999976654
No 29
>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=25.14 E-value=74 Score=24.78 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 167 EAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 167 ~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
+.++++....+||.++|.+.+..+.++.+
T Consensus 5 ~i~~l~~~~~~a~~~~D~~~~~~~~~~Da 33 (128)
T TIGR02246 5 AIRALVATWEAAWAAGDAEGFADLFTPDG 33 (128)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhCCCc
Confidence 45778888999999999999999988874
No 30
>PF09322 DUF1979: Domain of unknown function (DUF1979); InterPro: IPR015401 This N-terminal domain is functionally uncharacterised and found in various Oryza sativa (Rice) mutator-like transposases.
Probab=24.46 E-value=55 Score=23.75 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=31.5
Q ss_pred EeEEeeeEEcCCCceecCCCCCeeeeeEEEEEEEeCCCC
Q 022189 251 LAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHP 289 (301)
Q Consensus 251 ~s~Q~~~iyD~~GrlV~Gs~d~~~dV~EyWVFeR~l~~~ 289 (301)
.++|++-+|-..|++-.|.. -.|..|+.+.+|.++.+
T Consensus 2 s~K~~F~~~hg~GNvR~Gp~--GvdLs~Fi~~~rGIdrp 38 (58)
T PF09322_consen 2 SSKVIFQIYHGEGNVRYGPT--GVDLSEFIVTSRGIDRP 38 (58)
T ss_pred CCceeEEEEEcCCceeECCC--ccchhHeeeeccccCch
Confidence 56788889999999999984 47899999999998753
No 31
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=22.69 E-value=1e+02 Score=29.25 Aligned_cols=47 Identities=19% Similarity=0.071 Sum_probs=35.3
Q ss_pred HHHHHHHh--CCC---ChHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhcHHH
Q 022189 149 YAIAKLRK--SGY---SKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (301)
Q Consensus 149 ~~i~~irk--~~F---d~~~F~~~Ak~iy~~I~~A~a~gD~~~Lr~lvTe~~ 195 (301)
.|.++|++ |.+ -+..+.+..+++-....+||.+||.+.|..+++|.+
T Consensus 192 RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD~~~l~~lla~Dv 243 (339)
T PRK08241 192 RARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDVDALVALLTEDA 243 (339)
T ss_pred HHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCCHHHHHHHhcCCE
Confidence 44555665 321 123566777888889999999999999999999976
No 32
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=22.31 E-value=89 Score=28.07 Aligned_cols=27 Identities=19% Similarity=0.329 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhcH
Q 022189 167 EAVDLYKEINTLMANGDKTSLRKAVTE 193 (301)
Q Consensus 167 ~Ak~iy~~I~~A~a~gD~~~Lr~lvTe 193 (301)
...+.+..+.++|.+||.+.|.++..+
T Consensus 171 ~~~~~~~~~~~~~~~gd~~~l~~~~~~ 197 (259)
T PF01963_consen 171 DGEKMLEQLIEAWKNGDLDALMELMKE 197 (259)
T ss_pred cchHHHHHHHHHHHccCHHHHHHHHHh
Confidence 345678899999999999999988755
Done!