Query 025014
Match_columns 259
No_of_seqs 152 out of 221
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 09:16:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025014.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025014hhsearch_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 1.2E-29 2.5E-34 237.5 7.7 161 92-259 95-274 (379)
2 PF04280 Tim44: Tim44-like dom 99.8 3.2E-18 6.9E-23 140.8 10.5 103 148-259 2-106 (147)
3 TIGR00984 3a0801s03tim44 mitoc 99.7 2.7E-17 5.9E-22 157.2 14.0 108 145-259 225-335 (378)
4 PF07961 MBA1: MBA1-like prote 99.6 5.1E-15 1.1E-19 133.9 14.3 151 101-257 7-162 (235)
5 COG4395 Uncharacterized protei 99.5 1.2E-13 2.6E-18 127.5 8.7 105 146-259 132-238 (281)
6 KOG2580 Mitochondrial import i 97.7 0.00011 2.4E-09 71.9 8.5 103 147-258 301-406 (459)
7 KOG4599 Putative mitochondrial 96.6 0.0011 2.3E-08 63.7 1.8 159 33-257 182-340 (379)
8 TIGR02957 SigX4 RNA polymerase 74.9 59 0.0013 29.7 11.7 45 149-195 147-193 (281)
9 PRK09635 sigI RNA polymerase s 67.1 14 0.00031 34.2 5.9 46 149-196 157-204 (290)
10 PRK09636 RNA polymerase sigma 57.4 21 0.00046 32.6 5.2 45 149-195 154-200 (293)
11 TIGR02960 SigX5 RNA polymerase 56.5 16 0.00034 33.5 4.2 47 149-195 181-233 (324)
12 PF07729 FCD: FCD domain; Int 53.2 41 0.00088 25.0 5.4 37 159-195 87-123 (125)
13 PF08858 IDEAL: IDEAL domain; 53.2 26 0.00057 23.1 3.7 26 168-193 11-36 (37)
14 PRK08241 RNA polymerase factor 48.0 25 0.00054 32.6 4.1 48 148-195 191-243 (339)
15 PF05223 MecA_N: NTF2-like N-t 44.7 1.6E+02 0.0034 23.4 8.0 29 167-195 2-30 (118)
16 PF12870 Lumazine_bd: Lumazine 44.6 19 0.00042 26.9 2.3 31 167-197 8-38 (111)
17 PF08898 DUF1843: Domain of un 42.2 75 0.0016 23.1 4.8 35 173-207 5-51 (53)
18 PRK06342 transcription elongat 41.8 1E+02 0.0023 26.5 6.7 47 113-186 15-61 (160)
19 PF11444 DUF2895: Protein of u 41.2 32 0.00069 31.1 3.5 45 167-211 66-116 (199)
20 cd00781 ketosteroid_isomerase 41.0 26 0.00057 26.9 2.7 31 166-196 3-33 (122)
21 PF12893 Lumazine_bd_2: Putati 40.1 97 0.0021 24.1 5.8 50 168-217 6-72 (116)
22 PF13474 SnoaL_3: SnoaL-like d 37.9 14 0.00029 27.9 0.6 26 169-194 2-27 (121)
23 PRK13683 hypothetical protein; 33.8 44 0.00096 26.5 2.8 21 165-185 22-42 (87)
24 PF14534 DUF4440: Domain of un 33.0 12 0.00025 27.4 -0.5 27 169-195 2-28 (107)
25 cd01886 EF-G Elongation factor 31.7 1.3E+02 0.0027 27.7 5.9 46 161-206 189-240 (270)
26 TIGR03746 conj_TIGR03746 integ 23.1 78 0.0017 28.7 2.9 44 168-211 68-117 (202)
27 TIGR02096 conserved hypothetic 22.9 50 0.0011 25.4 1.4 27 170-196 2-28 (129)
28 TIGR02246 conserved hypothetic 21.0 99 0.0022 23.5 2.8 29 167-195 5-33 (128)
29 cd04170 EF-G_bact Elongation f 20.3 2.9E+02 0.0063 24.7 6.0 46 161-206 187-238 (268)
No 1
>KOG4599 consensus Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.2e-29 Score=237.49 Aligned_cols=161 Identities=17% Similarity=0.303 Sum_probs=153.1
Q ss_pred CchhhhcccceeEEEecCCcccccCCCCCCCCccccccccchhhhhHHHHHHhhhhHHHHHHHHc----CCCChhhhHHH
Q 025014 92 APAQARQMGALKVSISSPGFIYEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRK----SGYSKQKFYTE 167 (259)
Q Consensus 92 ~~~~ar~~~~~~i~i~s~G~I~dpYvPpe~~~~~~s~~t~~Gwk~~~e~l~~~~ks~~al~kIrk----~~F~~~~Fl~g 167 (259)
...+.|+|..+||+++|+|+|||+||||+|++. .+.++..|.++..+.+.+.+++.+++++|++ ..|+.++|.+.
T Consensus 95 ~v~~Pr~~ne~~i~f~~~~gIfD~yVPPegdg~-~~~l~skg~~~~~~~~~k~~~~q~sir~i~~k~~~~~F~ik~f~~k 173 (379)
T KOG4599|consen 95 LVIPPRKWNERPIHFSCTGGIFDAYVPPEGDGK-KSILSSKGLIQKTEILEKTVASQMSIRRIRDKDEIENFEIKDFGAK 173 (379)
T ss_pred cccCCccccccceEEEeecccccccCCCCCCcc-cchhcCcchhHHHHHHHHHHHHHhhhhhhccCCcccceeccccchH
Confidence 456678899999999999999999999999999 8899999999999999999999999999998 58999999999
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHhhhH---------------HHHHHHHHHHHhhhccCCeEEEEEecccccceEEEEEEe
Q 025014 168 AVDLYKEINTLMANGDKTSLRKAVTE---------------KMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLI 232 (259)
Q Consensus 168 A~~aY~~I~~AfA~GDr~~Lr~LvTe---------------~vy~~f~~~Ik~Re~~~etv~w~fVesIe~~rVV~ARl~ 232 (259)
|+++|+++|.++++.|+..+..+||| .+|+.|...+|.. +++|+||..+||.+||++||.
T Consensus 174 akDifIqaH~~l~~~de~kays~l~e~~fvhl~~~~~t~~~~flp~m~~k~K~~-----~vR~~~vs~leP~~vv~~rc~ 248 (379)
T KOG4599|consen 174 AKDIFIQAHLCLNNSDEMKAYSFLTESEFVHLKCPSITNLLHFLPVMQEKVKKG-----TVRWSFVSVLEPSRVVYVRCD 248 (379)
T ss_pred hHHHHHHHHHHHhcChHHHHHHHhhccccccccCCCccchhhhccccchhhccC-----ceeEEEEeecccceeEEEEec
Confidence 99999999999999999999999999 9999999998884 999999999999999999999
Q ss_pred ecccCCCCCeEEEEEEEEEeeEeeccC
Q 025014 233 GVDRNDLNKVFVQLTLEFLAKQVNCPY 259 (259)
Q Consensus 233 ~~~~kd~~n~~AQVTVRf~S~Q~~AiY 259 (259)
+++++ .+|.+||||||+|++|.+|+|
T Consensus 249 d~~~~-s~n~~aqitvRkh~~q~Lavy 274 (379)
T KOG4599|consen 249 DDNDK-SGNFIAQITVRKHTRQCLAVY 274 (379)
T ss_pred CCccc-ccccceeeehHHHHHHHHHHH
Confidence 87766 589999999999999999998
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=99.76 E-value=3.2e-18 Score=140.83 Aligned_cols=103 Identities=29% Similarity=0.405 Sum_probs=91.3
Q ss_pred HHHHHHHHc--CCCChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHHHHHHHHHHHhhhccCCeEEEEEecccccce
Q 025014 148 AYAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMR 225 (259)
Q Consensus 148 ~~al~kIrk--~~F~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~vy~~f~~~Ik~Re~~~etv~w~fVesIe~~r 225 (259)
+.|++.|++ |+|++..|+++|+++|.+|++|+++||.+.|+++||+++|..|..+|+.|+..|.+.+-+.| .|..++
T Consensus 2 a~a~~~i~~~dp~Fd~~~F~~~ak~~f~~i~~A~~~~D~~~l~~~~t~~~~~~~~~~i~~~~~~g~~~~~~~v-~i~~~~ 80 (147)
T PF04280_consen 2 ASAIKQIKQRDPGFDPAAFLEEAKEAFLPIQEAWAKGDLEALRPLLTEELYERLQAEIKARRSRGEVNDPEIV-RIDNAE 80 (147)
T ss_dssp HHHHCCHHHH-TT--HHHHHHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHHHHTTEEEEEEEE-EEEEEE
T ss_pred chHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHhCHHHHHHHHHHHHHHHHcCCcccceEE-EEEEEE
Confidence 467888998 99999999999999999999999999999999999999999999999999999999999987 788888
Q ss_pred EEEEEEeecccCCCCCeEEEEEEEEEeeEeeccC
Q 025014 226 TLRARLIGVDRNDLNKVFVQLTLEFLAKQVNCPY 259 (259)
Q Consensus 226 VV~ARl~~~~~kd~~n~~AQVTVRf~S~Q~~AiY 259 (259)
++++... +.+++|||||+++|+.++|
T Consensus 81 i~~~~~~--------~~~~~vtv~f~~~~~~~~~ 106 (147)
T PF04280_consen 81 IVEAEQE--------GNFDQVTVRFRSQQIDYVD 106 (147)
T ss_dssp EEEEEEE--------TTEEEEEEEEEEEEEEEEE
T ss_pred eeeceee--------CCEEEEEEEEEEEEEEEEE
Confidence 8888864 5899999999999998854
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=99.74 E-value=2.7e-17 Score=157.19 Aligned_cols=108 Identities=18% Similarity=0.243 Sum_probs=100.3
Q ss_pred hhhHHHHHHHHc--CCCChhhhHHHHHHH-HHHHHHHHhcCCHHHHHHhhhHHHHHHHHHHHHhhhccCCeEEEEEeccc
Q 025014 145 LKSAYAIAKLRK--SGYSKQKFYTEAVDL-YKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPI 221 (259)
Q Consensus 145 ~ks~~al~kIrk--~~F~~~~Fl~gA~~a-Y~~I~~AfA~GDr~~Lr~LvTe~vy~~f~~~Ik~Re~~~etv~w~fVesI 221 (259)
...+.+|+.|++ |+|++..|+.+|+.+ |.||++||++||++.|+++|++++|..|..+|++|+++|.+++.+|| +|
T Consensus 225 te~a~~l~eIk~~DPsFd~~~Fl~gar~aI~p~ILeAf~kGD~e~LK~~lse~vy~~f~a~I~qr~~~G~~~d~~iL-~I 303 (378)
T TIGR00984 225 TEVSEVLTEFKKIDPTFDKEHFLRFLREYIVPEILEAYVKGDLEVLKSWCSEAPFSVYATVVKEYKKMGVSTKGRIL-DI 303 (378)
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhCHHHHHHHHHHHHHHHHCCCeeeeEEe-ee
Confidence 334678999999 999999999999999 89999999999999999999999999999999999999999999998 89
Q ss_pred ccceEEEEEEeecccCCCCCeEEEEEEEEEeeEeeccC
Q 025014 222 IKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQVNCPY 259 (259)
Q Consensus 222 e~~rVV~ARl~~~~~kd~~n~~AQVTVRf~S~Q~~AiY 259 (259)
+...|+.|++.+ .+..+.|+|||+++|+.+++
T Consensus 304 ~~veI~~ak~~e------~~~~pviiV~F~aQqI~~vR 335 (378)
T TIGR00984 304 RGVEIASGKLLE------PGDIPVLIVTFRAQEINVTK 335 (378)
T ss_pred cCeEEEEEEecC------CCCeEEEEEEEEEEEEEEEE
Confidence 999999999843 35689999999999998864
No 4
>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=99.63 E-value=5.1e-15 Score=133.95 Aligned_cols=151 Identities=25% Similarity=0.393 Sum_probs=129.6
Q ss_pred ceeEEEecCCcccccCCCCCCCCccccccc--cchhhhhHHHHHHhhhhHHHHHHHHc-CCCC--hhhhHHHHHHHHHHH
Q 025014 101 ALKVSISSPGFIYEPYAPREAIPFWRRWFT--RDGWRRTKDDIILELKSAYAIAKLRK-SGYS--KQKFYTEAVDLYKEI 175 (259)
Q Consensus 101 ~~~i~i~s~G~I~dpYvPpe~~~~~~s~~t--~~Gwk~~~e~l~~~~ks~~al~kIrk-~~F~--~~~Fl~gA~~aY~~I 175 (259)
..+|.+..-|...|+|+||.-.| ++++ +..|+..+.++.-...+.+.+.+-+. .|.. -..+.+.|.+.|+.+
T Consensus 7 ~~~~~~~~iGv~~~~yipps~~p---s~~~~P~~~~~~l~rr~~~~~~Nt~~i~~fr~~~g~k~~f~~wk~~AiE~yv~~ 83 (235)
T PF07961_consen 7 ISQFPIRHIGVMADTYIPPSFLP---SPFTSPKVWWKLLIRRLYMFALNTVSIAKFRRQTGKKPRFNEWKNKAIELYVQM 83 (235)
T ss_pred cccCCcccceeccccccChhhcc---CcccChhHHHHHHHHHHHHHhhhhheeeehhhhcCCCCchhHHHHHHHHHHHHH
Confidence 34788899999999999997633 2333 35788899999888889888887777 5544 458899999999999
Q ss_pred HHHHhcCCHHHHHHhhhHHHHHHHHHHHHhhhccCCeEEEEEecccccceEEEEEEeecccCCCCCeEEEEEEEEEeeEe
Q 025014 176 NTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQV 255 (259)
Q Consensus 176 ~~AfA~GDr~~Lr~LvTe~vy~~f~~~Ik~Re~~~etv~w~fVesIe~~rVV~ARl~~~~~kd~~n~~AQVTVRf~S~Q~ 255 (259)
++|||+||.+.|+++|+..+|++|.+-++.|- .+.++.|+++.-.+.|+||..+..+++.+ .+.+.|+.|||.|+|.
T Consensus 84 NkaFA~~~~~~L~~~c~~~v~~sL~~R~~~~P-~~~kl~W~L~k~~~~PKvvs~~~~~~p~~--~~~~vQ~Vvk~~TkQ~ 160 (235)
T PF07961_consen 84 NKAFAAGDLDKLRKICSSWVYESLAARIKQRP-KNSKLDWKLVKYNKNPKVVSFQAIPIPGG--PLEIVQFVVKFDTKQR 160 (235)
T ss_pred HHHHHhccHHHHHHHhhHHHHHHHHHHHHhCC-CCCeeeEEEEEecCCCeEEEEeeeecCCC--CCeEEEEEEEEeeeEE
Confidence 99999999999999999999999999999986 45699999998899999999999887665 5669999999999999
Q ss_pred ec
Q 025014 256 NC 257 (259)
Q Consensus 256 ~A 257 (259)
+.
T Consensus 161 li 162 (235)
T PF07961_consen 161 LI 162 (235)
T ss_pred EE
Confidence 84
No 5
>COG4395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.47 E-value=1.2e-13 Score=127.51 Aligned_cols=105 Identities=19% Similarity=0.256 Sum_probs=95.9
Q ss_pred hhHHHHHHHHc--CCCChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHHHHHHHHHHHhhhccCCeEEEEEeccccc
Q 025014 146 KSAYAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIK 223 (259)
Q Consensus 146 ks~~al~kIrk--~~F~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~vy~~f~~~Ik~Re~~~etv~w~fVesIe~ 223 (259)
....+++.+.+ +.|+|+.|+++|+.+|+||++|++.||+++|++|+|++||+.|+.+|.+||..|++.+-+|| .|..
T Consensus 132 ~~~ag~~~v~~~~~~f~p~~fl~~a~~a~~~Iq~a~~~~D~~tL~~L~tpev~~~~~~e~~e~~~~G~~~~ssfv-~~~~ 210 (281)
T COG4395 132 PLAAGARAVHNADPSFDPARFLNGARAAYEMIQQAYGAGDRKTLRELLTPEVMEYLEAEIAERESKGETNQSSFV-TILQ 210 (281)
T ss_pred ccccchhhhhcCCcccchhHHHHHHHHHHHHHHHHhhhccHHHHHHhcCHHHHHHHHHHHhhhhhcCccccceec-chhh
Confidence 45667788887 99999999999999999999999999999999999999999999999999999999999998 8999
Q ss_pred ceEEEEEEeecccCCCCCeEEEEEEEEEeeEeeccC
Q 025014 224 MRTLRARLIGVDRNDLNKVFVQLTLEFLAKQVNCPY 259 (259)
Q Consensus 224 ~rVV~ARl~~~~~kd~~n~~AQVTVRf~S~Q~~AiY 259 (259)
..|+++-+ .+..+++||+|..+-+.++|
T Consensus 211 ~di~~a~~--------~~~~~~atv~~~~~~i~~~~ 238 (281)
T COG4395 211 ADIARADV--------EGDEDYATVAIRYQGIDVTR 238 (281)
T ss_pred hhhhhccc--------cCCceEEEEEEEeeeeeeec
Confidence 99998876 46889999999998886543
No 6
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.75 E-value=0.00011 Score=71.87 Aligned_cols=103 Identities=17% Similarity=0.279 Sum_probs=85.5
Q ss_pred hHHHHHHHHc--CCCChhhhHHHHHHHHHH-HHHHHhcCCHHHHHHhhhHHHHHHHHHHHHhhhccCCeEEEEEeccccc
Q 025014 147 SAYAIAKLRK--SGYSKQKFYTEAVDLYKE-INTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIK 223 (259)
Q Consensus 147 s~~al~kIrk--~~F~~~~Fl~gA~~aY~~-I~~AfA~GDr~~Lr~LvTe~vy~~f~~~Ik~Re~~~etv~w~fVesIe~ 223 (259)
....+..|++ |+||.++|+..-++.-+= |.+|+-.||.+.|++.|.|..|+-..+.++.-...|=-.+-+++ .|+.
T Consensus 301 ~Sev~tei~~iDPsF~~~~Flr~~ee~IiPnVLeAyvkGD~evLK~wcsea~~~~~aa~~keykk~gv~~d~kIL-dI~~ 379 (459)
T KOG2580|consen 301 MSEVLTEIKKIDPSFDKEDFLRECEEYIIPNVLEAYVKGDLEVLKKWCSEAPFSQLAAPIKEYKKHGVYFDSKIL-DIRG 379 (459)
T ss_pred HHHHHHHHHhcCCCCCcHHHHHHHHHhhhHHHHHHHHhccHHHHHHHHhhhHHHHHHHHHHHHHhcCeeecceee-eecc
Confidence 3456778888 999999999999987776 99999999999999999999999999999998877777788887 7888
Q ss_pred ceEEEEEEeecccCCCCCeEEEEEEEEEeeEeecc
Q 025014 224 MRTLRARLIGVDRNDLNKVFVQLTLEFLAKQVNCP 258 (259)
Q Consensus 224 ~rVV~ARl~~~~~kd~~n~~AQVTVRf~S~Q~~Ai 258 (259)
..|..++|-+ ..=-+-|.|.+++|+.+
T Consensus 380 Vdia~~KmM~--------d~PVlIitFqaQeI~~v 406 (459)
T KOG2580|consen 380 VDIASGKMME--------DGPVLIITFQAQEIMCV 406 (459)
T ss_pred chhHHhhhhc--------cCCEEEEEEeeEEEEEE
Confidence 7777666632 22346688889988865
No 7
>KOG4599 consensus Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis]
Probab=96.56 E-value=0.0011 Score=63.72 Aligned_cols=159 Identities=19% Similarity=0.200 Sum_probs=113.2
Q ss_pred cCccccccccccccccccccccCCCCCCccccccccccccccccccccccccccccCCCCchhhhcccceeEEEecCCcc
Q 025014 33 SSGVSIVPEIYSQNISSCLCKDHGALPWTRGSTMTLRSSLAPKSLLYLNEKRFATAQPKAPAQARQMGALKVSISSPGFI 112 (259)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ar~~~~~~i~i~s~G~I 112 (259)
+..+.|..|.. +||.++.+|+ +.+.-.++++-+.+..+|+++ -+-|.++..+-| +
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 56677777755 8999999998 889999999999999999854 344556666655 6
Q ss_pred cccCCCCCCCCccccccccchhhhhHHHHHHhhhhHHHHHHHHcCCCChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhh
Q 025014 113 YEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRKSGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVT 192 (259)
Q Consensus 113 ~dpYvPpe~~~~~~s~~t~~Gwk~~~e~l~~~~ks~~al~kIrk~~F~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvT 192 (259)
+|||.-. |.+.++. -.++++.+|+..+|+-+ . ++..+|..++.+++.+. ..++=|+
T Consensus 237 leP~~vv-----~~rc~d~----------~~~s~n~~aqitvRkh~------~-q~Lavydrfg~lm~g~E--~i~KDv~ 292 (379)
T KOG4599|consen 237 LEPSRVV-----YVRCDDD----------NDKSGNFIAQITVRKHT------R-QCLAVYDRFGRLMFGSE--DIKKDVL 292 (379)
T ss_pred cccceeE-----EEEecCC----------cccccccceeeehHHHH------H-HHHHHHHHHHHHhccCc--ccccchh
Confidence 7776531 1111110 01225566666666511 1 89999999999999997 6677777
Q ss_pred HHHHHHHHHHHHhhhccCCeEEEEEecccccceEEEEEEeecccCCCCCeEEEEEEEEEeeEeec
Q 025014 193 EKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQVNC 257 (259)
Q Consensus 193 e~vy~~f~~~Ik~Re~~~etv~w~fVesIe~~rVV~ARl~~~~~kd~~n~~AQVTVRf~S~Q~~A 257 (259)
| |..|++.|++++..|. ++|++|. .++.+++ ..+.++++-+.+.|..-
T Consensus 293 e--yvvfe~hi~~~~g~wr-~h~kivp-----~wi~~kq---------k~~~tl~l~~lt~~~~~ 340 (379)
T KOG4599|consen 293 E--YVVFENHIQNAYGRWR-LHKKIVP-----PWIPAKQ---------KAYKTLMLFILTMEKSE 340 (379)
T ss_pred H--HHHHHHhhhhhhhhhh-hcccccC-----ccccccc---------cchheEEeehhccCchh
Confidence 7 9999999999999998 9999974 3455553 36777777777666543
No 8
>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=74.94 E-value=59 Score=29.71 Aligned_cols=45 Identities=18% Similarity=0.192 Sum_probs=33.4
Q ss_pred HHHHHHHc--CCCChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 149 YAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 149 ~al~kIrk--~~F~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
.|..+|++ +.|.+ -.++.+.+=..-..|++.||.+.|..||+|+|
T Consensus 147 RAr~~Lr~~~~~~~~--~~~~~~~~~~~f~~a~~~gD~~~l~~lL~~dv 193 (281)
T TIGR02957 147 RARRHLDARRPRFEV--SREESRQLLERFVEAAQTGDLDGLLELLAEDV 193 (281)
T ss_pred HHHHHHHhhCCCCCC--ChHHHHHHHHHHHHHHHhCCHHHHHHHHhhce
Confidence 45555665 44432 23456677788889999999999999999998
No 9
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=67.11 E-value=14 Score=34.24 Aligned_cols=46 Identities=15% Similarity=0.065 Sum_probs=35.0
Q ss_pred HHHHHHHc--CCCChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHHH
Q 025014 149 YAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMY 196 (259)
Q Consensus 149 ~al~kIrk--~~F~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~vy 196 (259)
.|..+|++ +.|+ ...++.+.+-..-..|++.||.+.|..||++++-
T Consensus 157 RAr~~Lr~~~~~~~--~~~~~~~~~~~~f~~a~~~gd~~~l~~ll~~d~~ 204 (290)
T PRK09635 157 RARRKINESRIAAS--VEPAQHRVVTRAFIEACSNGDLDTLLEVLDPGVA 204 (290)
T ss_pred HHHHHHHhhCCCCC--CChHHHHHHHHHHHHHHHhCCHHHHHHHhhhhhc
Confidence 45556665 5454 3345667788888899999999999999999995
No 10
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=57.38 E-value=21 Score=32.61 Aligned_cols=45 Identities=18% Similarity=0.232 Sum_probs=34.8
Q ss_pred HHHHHHHc--CCCChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 149 YAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 149 ~al~kIrk--~~F~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
.|..+|++ +.+. ...+...++-..-..||+.||.+.|..|++|++
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 45566666 4332 345567778888899999999999999999987
No 11
>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=56.48 E-value=16 Score=33.54 Aligned_cols=47 Identities=21% Similarity=0.114 Sum_probs=34.8
Q ss_pred HHHHHHHc--CCC----ChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 149 YAIAKLRK--SGY----SKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 149 ~al~kIrk--~~F----~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
.|..+|++ ... .+....+.-+++-..-..|++.||.+.|..|++|+|
T Consensus 181 Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD~~~l~~Lla~Dv 233 (324)
T TIGR02960 181 RARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYDLDALTALLHEDA 233 (324)
T ss_pred HHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCCHHHHHHHhcCCe
Confidence 45556665 322 223466667777888889999999999999999976
No 12
>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=53.24 E-value=41 Score=25.00 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=31.0
Q ss_pred CChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 159 YSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 159 F~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
+......+...+-+..|.+|+.+||.+..+.+++.+.
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 3477788888888999999999999999999988764
No 13
>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=53.21 E-value=26 Score=23.13 Aligned_cols=26 Identities=23% Similarity=0.238 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHhhhH
Q 025014 168 AVDLYKEINTLMANGDKTSLRKAVTE 193 (259)
Q Consensus 168 A~~aY~~I~~AfA~GDr~~Lr~LvTe 193 (259)
=+.++..|-.|+.+||++.-..|..+
T Consensus 11 ~~~L~~~ID~ALd~~D~e~F~~Ls~e 36 (37)
T PF08858_consen 11 KEQLLELIDEALDNRDKEWFYELSEE 36 (37)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHhh
Confidence 35688999999999999998887654
No 14
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=48.02 E-value=25 Score=32.62 Aligned_cols=48 Identities=19% Similarity=0.068 Sum_probs=37.7
Q ss_pred HHHHHHHHc--CCC---ChhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 148 AYAIAKLRK--SGY---SKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 148 ~~al~kIrk--~~F---~~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
..|..+|++ +.+ -+..+.+.-+++-+....|+.+||.+.|..|++|+|
T Consensus 191 ~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD~~~l~~lla~Dv 243 (339)
T PRK08241 191 QRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDVDALVALLTEDA 243 (339)
T ss_pred HHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCCHHHHHHHhcCCE
Confidence 355666666 321 134688888888899999999999999999999988
No 15
>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=44.73 E-value=1.6e+02 Score=23.37 Aligned_cols=29 Identities=7% Similarity=0.113 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 167 EAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 167 gA~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
.+++....-..|+++||-...-.++++..
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 46777888899999999999999999888
No 16
>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=44.60 E-value=19 Score=26.87 Aligned_cols=31 Identities=13% Similarity=0.145 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHhhhHHHHH
Q 025014 167 EAVDLYKEINTLMANGDKTSLRKAVTEKMYS 197 (259)
Q Consensus 167 gA~~aY~~I~~AfA~GDr~~Lr~LvTe~vy~ 197 (259)
.++++-..-..|+.+||-++...++++..-.
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 3456667778899999999999999887763
No 17
>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=42.17 E-value=75 Score=23.06 Aligned_cols=35 Identities=26% Similarity=0.378 Sum_probs=26.8
Q ss_pred HHHHHHHhcCCHHHHHHhhhH------------HHHHHHHHHHHhhh
Q 025014 173 KEINTLMANGDKTSLRKAVTE------------KMYSALKNEIKQRE 207 (259)
Q Consensus 173 ~~I~~AfA~GDr~~Lr~LvTe------------~vy~~f~~~Ik~Re 207 (259)
.-|+.|.+.||...++.|++. .+++.++.+|..-|
T Consensus 5 vaiq~AiasGDLa~MK~l~~~aeq~L~~~~~i~~al~~Lk~EIaklE 51 (53)
T PF08898_consen 5 VAIQQAIASGDLAQMKALAAQAEQQLAEAGDIAAALEKLKAEIAKLE 51 (53)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHHHh
Confidence 458999999999999998874 35666677776654
No 18
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=41.80 E-value=1e+02 Score=26.54 Aligned_cols=47 Identities=17% Similarity=0.157 Sum_probs=31.0
Q ss_pred cccCCCCCCCCccccccccchhhhhHHHHHHhhhhHHHHHHHHcCCCChhhhHHHHHHHHHHHHHHHhcCCHHH
Q 025014 113 YEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRKSGYSKQKFYTEAVDLYKEINTLMANGDKTS 186 (259)
Q Consensus 113 ~dpYvPpe~~~~~~s~~t~~Gwk~~~e~l~~~~ks~~al~kIrk~~F~~~~Fl~gA~~aY~~I~~AfA~GDr~~ 186 (259)
.+|+.|+.|.+.-.-++|++|++...+.|.... ..|-.|-+.||...
T Consensus 15 ~~~~~~~r~~~~~~~~lT~~G~~~L~~El~~L~---------------------------~~i~~Ar~~GDlsE 61 (160)
T PRK06342 15 AETLLPDRPISPHPNLVTEAGLKALEDQLAQAR---------------------------AAYEAAQAIEDVNE 61 (160)
T ss_pred ccccCCCCCCCCCCceECHHHHHHHHHHHHHHH---------------------------HHHHHHHHCCChhH
Confidence 345566555333256899999988777764321 35777888999776
No 19
>PF11444 DUF2895: Protein of unknown function (DUF2895); InterPro: IPR021548 This is a bacterial family of uncharacterised proteins.
Probab=41.24 E-value=32 Score=31.09 Aligned_cols=45 Identities=18% Similarity=0.269 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhcCCH------HHHHHhhhHHHHHHHHHHHHhhhccCC
Q 025014 167 EAVDLYKEINTLMANGDK------TSLRKAVTEKMYSALKNEIKQRESMWS 211 (259)
Q Consensus 167 gA~~aY~~I~~AfA~GDr------~~Lr~LvTe~vy~~f~~~Ik~Re~~~e 211 (259)
=|--+|..+|.--.+|.. .+|+.++|++|...+.++.+.|...||
T Consensus 66 Fa~yIfQQlN~W~~dG~~DY~~ni~~l~~YlTP~c~~~L~~d~~~r~~~ge 116 (199)
T PF11444_consen 66 FAFYIFQQLNRWPTDGEEDYPNNIHRLSAYLTPSCQAFLEQDYEQRRNNGE 116 (199)
T ss_pred HHHHHHHHHcccccCChHHHHHHHHhhhhhcCHHHHHHHHHHHHHHHhccc
Confidence 356678888888888865 489999999999999999998886665
No 20
>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=40.96 E-value=26 Score=26.89 Aligned_cols=31 Identities=10% Similarity=0.097 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHhhhHHHH
Q 025014 166 TEAVDLYKEINTLMANGDKTSLRKAVTEKMY 196 (259)
Q Consensus 166 ~gA~~aY~~I~~AfA~GDr~~Lr~LvTe~vy 196 (259)
++.+++-+....|+.+||.+.|..|++|++.
T Consensus 3 ~~~~~~v~~~~~a~~~~D~~~~~~l~aed~~ 33 (122)
T cd00781 3 QEMKAAVQRYVEAVNAGDPEGIVALFADDAT 33 (122)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHcCCCeE
Confidence 3455666777889999999999999999886
No 21
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=40.05 E-value=97 Score=24.13 Aligned_cols=50 Identities=16% Similarity=0.139 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHhhhHHH--------------HHHHHHHHHhh---hccCCeEEEEE
Q 025014 168 AVDLYKEINTLMANGDKTSLRKAVTEKM--------------YSALKNEIKQR---ESMWSSVNWEL 217 (259)
Q Consensus 168 A~~aY~~I~~AfA~GDr~~Lr~LvTe~v--------------y~~f~~~Ik~R---e~~~etv~w~f 217 (259)
.+++-..-.+++.+||.+.|+.+..+++ .++|...++.| ...+....+++
T Consensus 6 I~~~v~~Y~dg~~~gD~~~l~~~f~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i 72 (116)
T PF12893_consen 6 IEATVQDYFDGLYNGDSEKLRSAFHPDARLQGVRKGKLRTMPIEEFIARVKSRVSPKPPGQERKESI 72 (116)
T ss_dssp HHHHHHHHHHHHHHT-HHHHGGGEEEEEEEEEEETTEEEEEETHHHHHHHHHC---H-SSTT-EEEE
T ss_pred HHHHHHHHHHHHHhcCHHHHHHhhCCCcEEEEEcCCceEEeCHHHHHHHHHhhccccCCCCCceeEE
Confidence 3444455668889999999999998887 46778888877 34445555554
No 22
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=37.89 E-value=14 Score=27.91 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHhcCCHHHHHHhhhHH
Q 025014 169 VDLYKEINTLMANGDKTSLRKAVTEK 194 (259)
Q Consensus 169 ~~aY~~I~~AfA~GDr~~Lr~LvTe~ 194 (259)
+++.+..++|+++||.+.|..+.+++
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 56788999999999999999988754
No 23
>PRK13683 hypothetical protein; Provisional
Probab=33.81 E-value=44 Score=26.49 Aligned_cols=21 Identities=29% Similarity=0.498 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHhcCCHH
Q 025014 165 YTEAVDLYKEINTLMANGDKT 185 (259)
Q Consensus 165 l~gA~~aY~~I~~AfA~GDr~ 185 (259)
.+.|+.+|.+|.+|+..|+-+
T Consensus 22 ~edA~alYq~I~~am~sg~P~ 42 (87)
T PRK13683 22 AEDAEALYQQIRQAMRSGNPR 42 (87)
T ss_pred HHHHHHHHHHHHHHHhcCCCc
Confidence 467889999999998877643
No 24
>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=33.01 E-value=12 Score=27.37 Aligned_cols=27 Identities=15% Similarity=0.234 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 169 VDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 169 ~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
+++++...+|+.++|.+.|..++++++
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 467888999999999999999998765
No 25
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=31.71 E-value=1.3e+02 Score=27.70 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=39.4
Q ss_pred hhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhh------HHHHHHHHHHHHhh
Q 025014 161 KQKFYTEAVDLYKEINTLMANGDKTSLRKAVT------EKMYSALKNEIKQR 206 (259)
Q Consensus 161 ~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvT------e~vy~~f~~~Ik~R 206 (259)
|....+.++++..++.+++|..|-+-|..++. |+++..+..++.++
T Consensus 189 p~~~~~~~~~~r~~l~e~vae~dd~L~e~yl~~~~~~~~el~~~l~~~~~~~ 240 (270)
T cd01886 189 PEDLLEEAEEAREELIETLAEFDDELMEKYLEGEEITEEEIKAAIRKGTIAN 240 (270)
T ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHhCCCCCCHHHHHHHHHHHHHcC
Confidence 45778889999999999999999999988775 57888888888876
No 26
>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=23.09 E-value=78 Score=28.72 Aligned_cols=44 Identities=18% Similarity=0.235 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHhcCC------HHHHHHhhhHHHHHHHHHHHHhhhccCC
Q 025014 168 AVDLYKEINTLMANGD------KTSLRKAVTEKMYSALKNEIKQRESMWS 211 (259)
Q Consensus 168 A~~aY~~I~~AfA~GD------r~~Lr~LvTe~vy~~f~~~Ik~Re~~~e 211 (259)
|-.+|.++|.=-.+|. ...|+.++|++|..-|.++.+.|.+.||
T Consensus 68 a~yI~QQlNrW~~~Ge~dY~~ni~~l~~YlTP~c~~~L~~d~~~R~~~ge 117 (202)
T TIGR03746 68 AFYIFQQLNRWPKDGEQDYGANIFRLSPYLTPSCRAFLQQDYELRRSNGE 117 (202)
T ss_pred HHHHHHHHhhccccchHHHHHHHHhcccccCHHHHHHHHHHHHHHhhcch
Confidence 3445566665555554 3489999999999999999999976554
No 27
>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=22.95 E-value=50 Score=25.44 Aligned_cols=27 Identities=15% Similarity=0.239 Sum_probs=21.1
Q ss_pred HHHHHHHHHHhcCCHHHHHHhhhHHHH
Q 025014 170 DLYKEINTLMANGDKTSLRKAVTEKMY 196 (259)
Q Consensus 170 ~aY~~I~~AfA~GDr~~Lr~LvTe~vy 196 (259)
++.+...+|+++||.+.|..++++++.
T Consensus 2 ~iv~~~~~a~~~~d~~~~~~~~~~d~~ 28 (129)
T TIGR02096 2 ELAQHWIEAFNRGDMDAVLALLAEDVL 28 (129)
T ss_pred HHHHHHHHHHHCCCHHHHHHhcCCCeE
Confidence 344556678999999999999988853
No 28
>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=21.03 E-value=99 Score=23.46 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHhhhHHH
Q 025014 167 EAVDLYKEINTLMANGDKTSLRKAVTEKM 195 (259)
Q Consensus 167 gA~~aY~~I~~AfA~GDr~~Lr~LvTe~v 195 (259)
+-++++..-..|+.+||-+.|..+.++++
T Consensus 5 ~i~~l~~~~~~a~~~~D~~~~~~~~~~Da 33 (128)
T TIGR02246 5 AIRALVATWEAAWAAGDAEGFADLFTPDG 33 (128)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhCCCc
Confidence 45677788889999999999999998884
No 29
>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group
Probab=20.26 E-value=2.9e+02 Score=24.70 Aligned_cols=46 Identities=15% Similarity=0.291 Sum_probs=38.5
Q ss_pred hhhhHHHHHHHHHHHHHHHhcCCHHHHHHhhh------HHHHHHHHHHHHhh
Q 025014 161 KQKFYTEAVDLYKEINTLMANGDKTSLRKAVT------EKMYSALKNEIKQR 206 (259)
Q Consensus 161 ~~~Fl~gA~~aY~~I~~AfA~GDr~~Lr~LvT------e~vy~~f~~~Ik~R 206 (259)
|....+.++++-.++.+++|..|-+-|..++. ++.+..+..++..+
T Consensus 187 p~~~~~~~~~~~~~l~e~~a~~dd~l~e~yl~~~~~~~~~l~~~l~~~~~~~ 238 (268)
T cd04170 187 PEELKEEVAEAREELLEAVAETDDELMEKYLEGGELTEEELHAGLRRALRAG 238 (268)
T ss_pred CHHHHHHHHHHHHHHHHHHhhCCHHHHHHHhCCCCCCHHHHHHHHHHHHHhC
Confidence 45778888899999999999999998888776 56778888888875
Done!