Query 026572
Match_columns 236
No_of_seqs 194 out of 718
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 09:45:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026572.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026572hhsearch_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 3E-37 6.5E-42 274.3 -0.6 198 31-235 99-315 (379)
2 PF04280 Tim44: Tim44-like dom 100.0 1.5E-31 3.4E-36 215.7 17.7 143 84-235 3-147 (147)
3 PF07961 MBA1: MBA1-like prote 100.0 1.2E-27 2.7E-32 206.6 19.3 188 36-234 7-199 (235)
4 TIGR00984 3a0801s03tim44 mitoc 99.9 3.1E-24 6.8E-29 196.3 19.6 144 79-231 224-377 (378)
5 COG4395 Uncharacterized protei 99.9 3E-23 6.4E-28 182.0 12.7 140 85-233 136-277 (281)
6 KOG2580 Mitochondrial import i 99.8 4E-20 8.7E-25 168.8 12.3 144 79-231 298-448 (459)
7 KOG4599 Putative mitochondrial 97.7 1E-05 2.2E-10 73.4 0.4 172 3-236 208-379 (379)
8 PF13355 DUF4101: Protein of u 95.8 0.4 8.6E-06 37.4 12.7 96 117-231 20-116 (117)
9 PF12893 Lumazine_bd_2: Putati 94.5 0.69 1.5E-05 35.3 10.4 93 102-234 5-114 (116)
10 PF12870 Lumazine_bd: Lumazine 91.4 3 6.6E-05 30.5 9.5 31 102-132 8-38 (111)
11 PF08898 DUF1843: Domain of un 69.5 13 0.00029 25.0 4.5 21 108-128 5-25 (53)
12 PF13474 SnoaL_3: SnoaL-like d 56.8 74 0.0016 23.1 11.2 26 104-129 2-27 (121)
13 PF11444 DUF2895: Protein of u 52.6 26 0.00056 30.0 4.5 48 99-146 63-116 (199)
14 PRK09635 sigI RNA polymerase s 49.4 46 0.00099 29.8 5.9 44 86-131 159-204 (290)
15 PF13211 DUF4019: Protein of u 47.3 1.2E+02 0.0027 22.9 10.7 79 121-232 25-104 (105)
16 TIGR02960 SigX5 RNA polymerase 47.2 25 0.00055 31.3 3.9 32 99-130 202-233 (324)
17 cd00781 ketosteroid_isomerase 40.7 29 0.00063 25.8 2.8 30 102-131 4-33 (122)
18 TIGR02957 SigX4 RNA polymerase 40.3 67 0.0015 28.3 5.5 30 101-130 164-193 (281)
19 PF12690 BsuPI: Intracellular 39.5 17 0.00038 26.3 1.3 26 177-202 12-39 (82)
20 PRK09636 RNA polymerase sigma 39.4 61 0.0013 28.7 5.1 32 99-130 169-200 (293)
21 PF08858 IDEAL: IDEAL domain; 38.7 61 0.0013 19.9 3.5 25 104-128 12-36 (37)
22 PF07729 FCD: FCD domain; Int 38.4 95 0.0021 22.3 5.4 37 94-130 87-123 (125)
23 PF14534 DUF4440: Domain of un 35.7 23 0.00049 25.1 1.5 27 104-130 2-28 (107)
24 TIGR02096 conserved hypothetic 34.5 25 0.00054 26.4 1.6 27 105-131 2-28 (129)
25 PF10115 HlyU: Transcriptional 33.9 66 0.0014 24.1 3.6 27 208-235 21-47 (91)
26 PRK10533 putative lipoprotein; 33.7 2.7E+02 0.0058 23.2 7.5 27 115-141 56-82 (171)
27 TIGR03746 conj_TIGR03746 integ 33.7 56 0.0012 28.0 3.7 44 103-146 68-117 (202)
28 PF08332 CaMKII_AD: Calcium/ca 32.9 43 0.00092 26.5 2.7 29 101-129 3-31 (128)
29 PRK06342 transcription elongat 30.8 2.4E+02 0.0052 23.1 6.9 63 48-142 15-77 (160)
30 TIGR02246 conserved hypothetic 29.5 58 0.0013 24.1 2.9 29 102-130 5-33 (128)
31 PF09322 DUF1979: Domain of un 28.8 42 0.00092 22.6 1.7 36 186-223 2-37 (58)
32 PRK08241 RNA polymerase factor 28.1 78 0.0017 28.5 3.9 33 98-130 211-243 (339)
33 PF13026 DUF3887: Protein of u 27.1 1.6E+02 0.0034 22.4 4.8 38 94-135 2-39 (101)
34 PRK13683 hypothetical protein; 25.9 81 0.0018 23.4 2.9 34 159-199 41-74 (87)
35 PF01963 TraB: TraB family; I 25.7 75 0.0016 27.1 3.3 27 102-128 171-197 (259)
36 PF08969 USP8_dimer: USP8 dime 25.0 1.4E+02 0.003 22.7 4.3 30 92-121 27-56 (115)
37 PF05223 MecA_N: NTF2-like N-t 22.1 3.5E+02 0.0076 20.4 9.0 29 102-130 2-30 (118)
38 PF01627 Hpt: Hpt domain; Int 20.6 1.5E+02 0.0033 20.2 3.6 30 97-126 4-36 (90)
39 PRK09925 leu operon leader pep 20.3 1.1E+02 0.0023 17.5 2.0 22 182-203 4-25 (28)
No 1
>KOG4599 consensus Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-37 Score=274.27 Aligned_cols=198 Identities=19% Similarity=0.334 Sum_probs=183.7
Q ss_pred HhhcCceeEeecccccccccccCCCCCCcccccccchhhHhhHHHHHHHHhhHHHHHHHHh----CCCChHhHHHHHHHH
Q 026572 31 ARQMGALKVSISSPGFIYEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRK----SGYSKQKFYTEAVDL 106 (236)
Q Consensus 31 ~~~~~~~~~~~~s~g~i~e~yvpp~~~~~~~~~~t~~g~~~~~~~l~~~~~s~~~l~~ir~----~~F~~~~F~~~A~~~ 106 (236)
.|+-..++|+++|+|+|||+||||++++. .+.+++.|++++.+.+.+...+.++++.+++ .+|+.++|-+.|+++
T Consensus 99 Pr~~ne~~i~f~~~~gIfD~yVPPegdg~-~~~l~skg~~~~~~~~~k~~~~q~sir~i~~k~~~~~F~ik~f~~kakDi 177 (379)
T KOG4599|consen 99 PRKWNERPIHFSCTGGIFDAYVPPEGDGK-KSILSSKGLIQKTEILEKTVASQMSIRRIRDKDEIENFEIKDFGAKAKDI 177 (379)
T ss_pred CccccccceEEEeecccccccCCCCCCcc-cchhcCcchhHHHHHHHHHHHHHhhhhhhccCCcccceeccccchHhHHH
Confidence 34455568999999999999999999998 7889999999999999999999999999998 489999999999999
Q ss_pred HHHHHHHHHcCCHHHHHHhhhH---------------HHHHHHHHHHHHhhcCCCceeeeeecccccceEEEEEEeeeec
Q 026572 107 YKEINTLMANGDKTSLRKAVTE---------------KMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDR 171 (236)
Q Consensus 107 y~~i~~A~a~gD~~~L~~l~Te---------------~~y~~l~~~ik~r~~~g~~~~W~lv~~~~~~rvv~~r~i~i~~ 171 (236)
|+++|.|+++.|...+..+++| .||+.|....+. .+++|+|+.+++++++|++||.+...
T Consensus 178 fIqaH~~l~~~de~kays~l~e~~fvhl~~~~~t~~~~flp~m~~k~K~-----~~vR~~~vs~leP~~vv~~rc~d~~~ 252 (379)
T KOG4599|consen 178 FIQAHLCLNNSDEMKAYSFLTESEFVHLKCPSITNLLHFLPVMQEKVKK-----GTVRWSFVSVLEPSRVVYVRCDDDND 252 (379)
T ss_pred HHHHHHHHhcChHHHHHHHhhccccccccCCCccchhhhccccchhhcc-----CceeEEEEeecccceeEEEEecCCcc
Confidence 9999999999999999999999 999999988653 68999999999999999999987654
Q ss_pred ccCCCceEEEEEEEEEEEEEEEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEee
Q 026572 172 NDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRIK 235 (236)
Q Consensus 172 ~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~~~~~~WrL~g~i~ 235 (236)
. ..+.++|||||+|++|.+++||++|+++.|+++..+||+||+||+.|+.+.++.||++++|.
T Consensus 253 ~-s~n~~aqitvRkh~~q~Lavydrfg~lm~g~E~i~KDv~eyvvfe~hi~~~~g~wr~h~kiv 315 (379)
T KOG4599|consen 253 K-SGNFIAQITVRKHTRQCLAVYDRFGRLMFGSEDIKKDVLEYVVFENHIQNAYGRWRLHKKIV 315 (379)
T ss_pred c-ccccceeeehHHHHHHHHHHHHHHHHHhccCcccccchhHHHHHHHhhhhhhhhhhhccccc
Confidence 3 25799999999999999999999999999999999999999999999999999999999984
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=100.00 E-value=1.5e-31 Score=215.70 Aligned_cols=143 Identities=29% Similarity=0.457 Sum_probs=121.5
Q ss_pred HHHHHHHh--CCCChHhHHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecccccceE
Q 026572 84 YAIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRT 161 (236)
Q Consensus 84 ~~l~~ir~--~~F~~~~F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~~~~~rv 161 (236)
-+++.|++ |+|++..|+++|+++|..|++||++||++.|+++||+.+|+.|..+++.+...|.+ +..+.+.+
T Consensus 3 ~a~~~i~~~dp~Fd~~~F~~~ak~~f~~i~~A~~~~D~~~l~~~~t~~~~~~~~~~i~~~~~~g~~------~~~~~v~i 76 (147)
T PF04280_consen 3 SAIKQIKQRDPGFDPAAFLEEAKEAFLPIQEAWAKGDLEALRPLLTEELYERLQAEIKARRSRGEV------NDPEIVRI 76 (147)
T ss_dssp HHHCCHHHH-TT--HHHHHHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHHHHTTEE------EEEEEEEE
T ss_pred hHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHhCHHHHHHHHHHHHHHHHcCCc------ccceEEEE
Confidence 35667776 99999999999999999999999999999999999999999999999999877653 44566777
Q ss_pred EEEEEeeeecccCCCceEEEEEEEEEEEEEEEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEee
Q 026572 162 LRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRIK 235 (236)
Q Consensus 162 v~~r~i~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~~~~~~WrL~g~i~ 235 (236)
++++++++... +.+++|||+|+++|+++++|++|++++|+++.++.+.|||+|+|++++++++|+|+|+.+
T Consensus 77 ~~~~i~~~~~~---~~~~~vtv~f~~~~~~~~~d~~G~ii~G~~~~~~~~~e~W~f~r~~~~~~~~W~L~~i~q 147 (147)
T PF04280_consen 77 DNAEIVEAEQE---GNFDQVTVRFRSQQIDYVDDKDGEIIEGDPDKIQEFTEYWTFERDLGSPNPNWRLAGIQQ 147 (147)
T ss_dssp EEEEEEEEEEE---TTEEEEEEEEEEEEEEEEETTTCTCCCCSTTS-EEEEEEEEEEE--TTCCCTEEEEEEE-
T ss_pred EEEEeeeceee---CCEEEEEEEEEEEEEEEEECCCCcEeeCCCCCceEEEEEEEEEEeCCCCCCCEEEEEEeC
Confidence 77887776543 699999999999999999999999999999999999999999999999999999999853
No 3
>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=99.96 E-value=1.2e-27 Score=206.63 Aligned_cols=188 Identities=25% Similarity=0.385 Sum_probs=161.7
Q ss_pred ceeEeecccccccccccCCCCCCccccccc--chhhHhhHHHHHHHHhhHHHHHHHHh-CCCCh--HhHHHHHHHHHHHH
Q 026572 36 ALKVSISSPGFIYEPYAPREAIPFWRRWFT--RDGWRRTKDDIILELKSAYAIAKLRK-SGYSK--QKFYTEAVDLYKEI 110 (236)
Q Consensus 36 ~~~~~~~s~g~i~e~yvpp~~~~~~~~~~t--~~g~~~~~~~l~~~~~s~~~l~~ir~-~~F~~--~~F~~~A~~~y~~i 110 (236)
+.+|.+.+.|...|+||||.. ++++|+ +..|+..+.++.....|++.|.++|. ++..+ ..|.+.|.|.|+.+
T Consensus 7 ~~~~~~~~iGv~~~~yipps~---~ps~~~~P~~~~~~l~rr~~~~~~Nt~~i~~fr~~~g~k~~f~~wk~~AiE~yv~~ 83 (235)
T PF07961_consen 7 ISQFPIRHIGVMADTYIPPSF---LPSPFTSPKVWWKLLIRRLYMFALNTVSIAKFRRQTGKKPRFNEWKNKAIELYVQM 83 (235)
T ss_pred cccCCcccceeccccccChhh---ccCcccChhHHHHHHHHHHHHHhhhhheeeehhhhcCCCCchhHHHHHHHHHHHHH
Confidence 347999999999999999996 234443 34577788888888899999998887 54443 57999999999999
Q ss_pred HHHHHcCCHHHHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecccccceEEEEEEeeeecccCCCceEEEEEEEEEEEE
Q 026572 111 NTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQK 190 (236)
Q Consensus 111 ~~A~a~gD~~~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~~~~~rvv~~r~i~i~~~~~~~~~~qvtVrf~s~Q~ 190 (236)
++|||+||.+.|++.|+.++++.|.+++++++.. .+++|+|++..+.|++++.+.++++... ..+.|++|+|+|+|+
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 NKAFAAGDLDKLRKICSSWVYESLAARIKQRPKN-SKLDWKLVKYNKNPKVVSFQAIPIPGGP--LEIVQFVVKFDTKQR 160 (235)
T ss_pred HHHHHhccHHHHHHHhhHHHHHHHHHHHHhCCCC-CeeeEEEEEecCCCeEEEEeeeecCCCC--CeEEEEEEEEeeeEE
Confidence 9999999999999999999999999999999964 6899999999999999999999887653 469999999999999
Q ss_pred EEEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEe
Q 026572 191 FEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRI 234 (236)
Q Consensus 191 l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~~~~~~WrL~g~i 234 (236)
+...|+.+..+++ ..+||+||+||.++.. .+.|+|+|++
T Consensus 161 li~~~k~~~~~~~---~e~dvveyiV~~~d~~--t~e~~l~Gsv 199 (235)
T PF07961_consen 161 LIKVDKGSEKVEK---KERDVVEYIVFQCDPW--TNEWVLWGSV 199 (235)
T ss_pred EEEeccccccCCc---cccceeeeEEEEEeCC--CCcEEEEEEe
Confidence 9989987776553 3579999999999865 4499999987
No 4
>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=99.93 E-value=3.1e-24 Score=196.32 Aligned_cols=144 Identities=22% Similarity=0.297 Sum_probs=123.3
Q ss_pred HHhhHHHHHHHHh--CCCChHhHHHHHHHH-HHHHHHHHHcCCHHHHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecc
Q 026572 79 ELKSAYAIAKLRK--SGYSKQKFYTEAVDL-YKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEP 155 (236)
Q Consensus 79 ~~~s~~~l~~ir~--~~F~~~~F~~~A~~~-y~~i~~A~a~gD~~~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~ 155 (236)
+...+.+|++|+. |+|++..|+.+|++. |++|.+||++||.+.|++||++.+|+.|...|++|..+|.+++-
T Consensus 224 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 224 ETEVSEVLTEFKKIDPTFDKEHFLRFLREYIVPEILEAYVKGDLEVLKSWCSEAPFSVYATVVKEYKKMGVSTKG----- 298 (378)
T ss_pred CCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhCHHHHHHHHHHHHHHHHCCCeeee-----
Confidence 4455677888887 999999999999998 89999999999999999999999999999999999999886543
Q ss_pred cccceEEEEEEeeeecccCC--CceEEEEEEEEEEEEEEEEcCC-CceecCCCCCeeeeeEEEEEEEeCCC----CCCCe
Q 026572 156 IIKMRTLRARLIGVDRNDLN--KVFVQLTLEFLAKQKFEAYDSK-GVTVAGDKTKEVLVRDIWVFEKSLFH----PGAYW 228 (236)
Q Consensus 156 ~~~~rvv~~r~i~i~~~~~~--~~~~qvtVrf~s~Q~l~v~Dk~-G~lv~G~~~~~~dv~EywvFeR~l~~----~~~~W 228 (236)
++|+++-++|..+.+. ++.+.|+|+|.++|+.|++|++ |++|+|+++.++.+.|.|+|+|++.. +++.|
T Consensus 299 ----~iL~I~~veI~~ak~~e~~~~pviiV~F~aQqI~~vRd~~tGeVVeGd~d~I~~v~yvWtF~Rd~~~~~~~~~~~W 374 (378)
T TIGR00984 299 ----RILDIRGVEIASGKLLEPGDIPVLIVTFRAQEINVTKNAKSGEVVAGDPDNIQRINYAWVFTRDVEELDNPETLGW 374 (378)
T ss_pred ----EEeeecCeEEEEEEecCCCCeEEEEEEEEEEEEEEEEcCCCCceeeCCCCceeEEEEEEEEEEcccccCCCCCCce
Confidence 3444444444433331 4689999999999999999998 99999999999999999999999863 67889
Q ss_pred EEE
Q 026572 229 RLC 231 (236)
Q Consensus 229 rL~ 231 (236)
||.
T Consensus 375 rl~ 377 (378)
T TIGR00984 375 KIL 377 (378)
T ss_pred eec
Confidence 985
No 5
>COG4395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.90 E-value=3e-23 Score=182.02 Aligned_cols=140 Identities=20% Similarity=0.281 Sum_probs=121.7
Q ss_pred HHHHHHh--CCCChHhHHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecccccceEE
Q 026572 85 AIAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTL 162 (236)
Q Consensus 85 ~l~~ir~--~~F~~~~F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~~~~~rvv 162 (236)
+++.+.+ |.|++..|++.|+.+|.+|++||.++|.++|++|+|+++|+.|++++.++...|.+..= . .|
T Consensus 136 g~~~v~~~~~~f~p~~fl~~a~~a~~~Iq~a~~~~D~~tL~~L~tpev~~~~~~e~~e~~~~G~~~~s------s---fv 206 (281)
T COG4395 136 GARAVHNADPSFDPARFLNGARAAYEMIQQAYGAGDRKTLRELLTPEVMEYLEAEIAERESKGETNQS------S---FV 206 (281)
T ss_pred chhhhhcCCcccchhHHHHHHHHHHHHHHHHhhhccHHHHHHhcCHHHHHHHHHHHhhhhhcCccccc------e---ec
Confidence 3455555 99999999999999999999999999999999999999999999999999888775332 2 22
Q ss_pred EEEEeeeecccCCCceEEEEEEEEEEEEEEEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEE
Q 026572 163 RARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGR 233 (236)
Q Consensus 163 ~~r~i~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~~~~~~WrL~g~ 233 (236)
..-..+|...+..++..++||+|.++-+...+|+.|++|+||++.+.++.|.|+|+|+.++.+++|.|.+.
T Consensus 207 ~~~~~di~~a~~~~~~~~atv~~~~~~i~~~~dr~G~vVdGd~~~~~e~~ElWTFtR~~~s~~p~W~LaaI 277 (281)
T COG4395 207 TILQADIARADVEGDEDYATVAIRYQGIDVTRDRSGKVVDGDPDKPEEFAELWTFTRDTGSRDPNWKLAAI 277 (281)
T ss_pred chhhhhhhhccccCCceEEEEEEEeeeeeeeccccCceecCCCCcchhhhhheeeeccCCCCCCCceEEee
Confidence 22234445555567899999999999999999999999999999999999999999999999999999986
No 6
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.83 E-value=4e-20 Score=168.79 Aligned_cols=144 Identities=23% Similarity=0.331 Sum_probs=124.1
Q ss_pred HHhhHHHHHHHHh--CCCChHhHHHHHHHHH-HHHHHHHHcCCHHHHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecc
Q 026572 79 ELKSAYAIAKLRK--SGYSKQKFYTEAVDLY-KEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEP 155 (236)
Q Consensus 79 ~~~s~~~l~~ir~--~~F~~~~F~~~A~~~y-~~i~~A~a~gD~~~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~ 155 (236)
+....-.+.+|++ |+||..+|+..+++.. ++|.+||-+||++.|+.||++..|+.+.+.+++++..|-
T Consensus 298 ktE~Sev~tei~~iDPsF~~~~Flr~~ee~IiPnVLeAyvkGD~evLK~wcsea~~~~~aa~~keykk~gv--------- 368 (459)
T KOG2580|consen 298 KTEMSEVLTEIKKIDPSFDKEDFLRECEEYIIPNVLEAYVKGDLEVLKKWCSEAPFSQLAAPIKEYKKHGV--------- 368 (459)
T ss_pred hhHHHHHHHHHHhcCCCCCcHHHHHHHHHhhhHHHHHHHHhccHHHHHHHHhhhHHHHHHHHHHHHHhcCe---------
Confidence 4444456777887 9999999999998765 679999999999999999999999999999999998765
Q ss_pred cccceEEEEEEeeeecccCCCceEEEEEEEEEEEEEEEEcCCCceecCCCCCeeeeeEEEEEEEeCC--CC--CCCeEEE
Q 026572 156 IIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLF--HP--GAYWRLC 231 (236)
Q Consensus 156 ~~~~rvv~~r~i~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~--~~--~~~WrL~ 231 (236)
.-+-++++++-++|....+-.+.+.++|.|.+++++|++|.+|++++|++|.+..|.+.|||+|+.. +| ++.|||.
T Consensus 369 ~~d~kILdI~~Vdia~~KmM~d~PVlIitFqaQeI~~vRd~~GevveGd~d~i~~v~y~wvl~rd~~El~~d~~~~WRLl 448 (459)
T KOG2580|consen 369 YFDSKILDIRGVDIASGKMMEDGPVLIITFQAQEIMCVRDAKGEVVEGDPDKILRVYYAWVLCRDQDELNPDEYAAWRLL 448 (459)
T ss_pred eecceeeeeccchhHHhhhhccCCEEEEEEeeEEEEEEEcCCCceecCCCCceeeEEeeeeeeccHhhcCcchhhhHHHH
Confidence 2356777777777766555568999999999999999999999999999999999999999999764 45 7789974
No 7
>KOG4599 consensus Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis]
Probab=97.69 E-value=1e-05 Score=73.41 Aligned_cols=172 Identities=22% Similarity=0.250 Sum_probs=124.3
Q ss_pred ccccccchhhhhccccccccCCCCchHHHhhcCceeEeecccccccccccCCCCCCcccccccchhhHhhHHHHHHHHhh
Q 026572 3 LRSSLAPKSLLYLNEKRFATAQPKAPAQARQMGALKVSISSPGFIYEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKS 82 (236)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~g~i~e~yvpp~~~~~~~~~~t~~g~~~~~~~l~~~~~s 82 (236)
.++||.+++.-+|+++ -+.|.++..+-| ..|||.-. +.+.+. .-.++.|
T Consensus 208 ~~~t~~~~flp~m~~k-------------~K~~~vR~~~vs---~leP~~vv-----~~rc~d----------~~~~s~n 256 (379)
T KOG4599|consen 208 PSITNLLHFLPVMQEK-------------VKKGTVRWSFVS---VLEPSRVV-----YVRCDD----------DNDKSGN 256 (379)
T ss_pred CCccchhhhccccchh-------------hccCceeEEEEe---ecccceeE-----EEEecC----------Ccccccc
Confidence 5789999999999998 456777877666 44554321 111110 0112255
Q ss_pred HHHHHHHHhCCCChHhHHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecccccceEE
Q 026572 83 AYAIAKLRKSGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTL 162 (236)
Q Consensus 83 ~~~l~~ir~~~F~~~~F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~~~~~rvv 162 (236)
++|+...|.- +. ++.++|..++.++..+. .+++=++| |..|..+|+++..+|. ++|+++++..+++
T Consensus 257 ~~aqitvRkh------~~-q~Lavydrfg~lm~g~E--~i~KDv~e--yvvfe~hi~~~~g~wr-~h~kivp~wi~~k-- 322 (379)
T KOG4599|consen 257 FIAQITVRKH------TR-QCLAVYDRFGRLMFGSE--DIKKDVLE--YVVFENHIQNAYGRWR-LHKKIVPPWIPAK-- 322 (379)
T ss_pred cceeeehHHH------HH-HHHHHHHHHHHHhccCc--ccccchhH--HHHHHHhhhhhhhhhh-hcccccCcccccc--
Confidence 6666665541 11 88899999999999988 66777777 9999999999998885 8998876643333
Q ss_pred EEEEeeeecccCCCceEEEEEEEEEEEEEEEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEeeC
Q 026572 163 RARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRIKI 236 (236)
Q Consensus 163 ~~r~i~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~~~~~~WrL~g~i~~ 236 (236)
...+.++++-+.+.+....|+..+.+..|+. ..|..++|.++......|+|++.+.+
T Consensus 323 ------------qk~~~tl~l~~lt~~~~~~~~~~~~~~~tek-----~ke~~~~e~~~~~t~~~~~lk~~~kI 379 (379)
T KOG4599|consen 323 ------------QKAYKTLMLFILTMEKSEAYPAGPKEAVTEK-----FKECILKENDVEITILKGILKPQLKI 379 (379)
T ss_pred ------------ccchheEEeehhccCchhhcccCCccchhhh-----hhhhhhhcccccccchhcccchhhcC
Confidence 2578999999999999999998887776653 45555688888878889999987754
No 8
>PF13355 DUF4101: Protein of unknown function (DUF4101)
Probab=95.84 E-value=0.4 Score=37.37 Aligned_cols=96 Identities=17% Similarity=0.213 Sum_probs=57.9
Q ss_pred CCHHHHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecccccceEEEEEEeeeecccCCCceEEEEEEEEEEEEEEEEcC
Q 026572 117 GDKTSLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDS 196 (236)
Q Consensus 117 gD~~~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~~~~~rvv~~r~i~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk 196 (236)
.+.+.|.+++++.|++........-...| .+|++. +.+++..|.... ..-.+++|.-.-.-....||
T Consensus 20 ~~~~~L~~vl~g~ll~~w~~~a~~~~~~g--~y~~y~--------~~~~I~sv~~~~--~~~~ra~v~a~v~E~~~l~~- 86 (117)
T PF13355_consen 20 HDIDSLSEVLTGPLLSQWQDRAQWLKANG--WYWEYD--------HKLKIDSVEVFS--DSPNRATVEATVTESAQLYD- 86 (117)
T ss_pred cchhHHHHHhhHHHHHHHHHHHHHHHHcC--CeEEEe--------eeeEEEEEEEcC--CCCCeEEEEEEEEEEEEEEe-
Confidence 45779999999999999998887776654 456652 122222222111 12334444444445566788
Q ss_pred CCceecC-CCCCeeeeeEEEEEEEeCCCCCCCeEEE
Q 026572 197 KGVTVAG-DKTKEVLVRDIWVFEKSLFHPGAYWRLC 231 (236)
Q Consensus 197 ~G~lv~G-~~~~~~dv~EywvFeR~l~~~~~~WrL~ 231 (236)
.|++..+ +......|.+. |.|. ++.|+|+
T Consensus 87 ~g~~~~~~s~~~~~~vrY~--L~r~----~~~WkI~ 116 (117)
T PF13355_consen 87 NGQPDNNPSYDSTLRVRYE--LVRQ----NGQWKIT 116 (117)
T ss_pred CCccccCCCCCCcEEEEEE--EEEc----CCEEEec
Confidence 8888876 44444455543 3444 5779996
No 9
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=94.53 E-value=0.69 Score=35.27 Aligned_cols=93 Identities=16% Similarity=0.210 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhhHHH--------------HHHHHHHHHHhh---cCCCceeeeeecccccceEEEE
Q 026572 102 EAVDLYKEINTLMANGDKTSLRKAVTEKM--------------YSALKNEIKQRE---SMWSSVNWELIEPIIKMRTLRA 164 (236)
Q Consensus 102 ~A~~~y~~i~~A~a~gD~~~L~~l~Te~~--------------y~~l~~~ik~r~---~~g~~~~W~lv~~~~~~rvv~~ 164 (236)
..++....-.+++.+||.+.|++.+.+++ .+++...++.+. ..+. ++....
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 34555666778889999999999998887 356667777652 1211 112222
Q ss_pred EEeeeecccCCCceEEEEEEEEEEEEEEEEcCCCceecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEEEe
Q 026572 165 RLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCGRI 234 (236)
Q Consensus 165 r~i~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~~~~~~WrL~g~i 234 (236)
..+++. ++.+.+.|.+... .....||++|.|. ++.|+|..|+
T Consensus 73 ~~i~i~-----g~~A~a~v~~~~~-------------------~~~~~d~~~L~K~----dg~WkIv~k~ 114 (116)
T PF12893_consen 73 LSIDID-----GDVASAKVEYEFP-------------------GFWFVDYFTLVKT----DGGWKIVSKV 114 (116)
T ss_dssp EEEEEE-----TTEEEEEEEEEEE-------------------TEEEEEEEEEEEE----TTEEEEEEEE
T ss_pred EEEEEE-----CCEEEEEEEEEEC-------------------CCceEEEEEEEEE----CCEEEEEEEe
Confidence 223333 4677777776531 1257999999997 8999999986
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=91.35 E-value=3 Score=30.51 Aligned_cols=31 Identities=13% Similarity=0.145 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhhHHHHH
Q 026572 102 EAVDLYKEINTLMANGDKTSLRKAVTEKMYS 132 (236)
Q Consensus 102 ~A~~~y~~i~~A~a~gD~~~L~~l~Te~~y~ 132 (236)
..+++-.....|+.+||.+....++++..-.
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
>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=69.45 E-value=13 Score=24.95 Aligned_cols=21 Identities=19% Similarity=0.381 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCHHHHHHhhhH
Q 026572 108 KEINTLMANGDKTSLRKAVTE 128 (236)
Q Consensus 108 ~~i~~A~a~gD~~~L~~l~Te 128 (236)
..|++|.+.||+..++.+.+.
T Consensus 5 vaiq~AiasGDLa~MK~l~~~ 25 (53)
T PF08898_consen 5 VAIQQAIASGDLAQMKALAAQ 25 (53)
T ss_pred HHHHHHHHcCcHHHHHHHHHH
Confidence 579999999999999988764
No 12
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=56.76 E-value=74 Score=23.10 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHcCCHHHHHHhhhHH
Q 026572 104 VDLYKEINTLMANGDKTSLRKAVTEK 129 (236)
Q Consensus 104 ~~~y~~i~~A~a~gD~~~L~~l~Te~ 129 (236)
++++.+.++||.++|.+.+..+++++
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
>PF11444 DUF2895: Protein of unknown function (DUF2895); InterPro: IPR021548 This is a bacterial family of uncharacterised proteins.
Probab=52.64 E-value=26 Score=30.00 Aligned_cols=48 Identities=19% Similarity=0.288 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHcCC------HHHHHHhhhHHHHHHHHHHHHHhhcCCC
Q 026572 99 FYTEAVDLYKEINTLMANGD------KTSLRKAVTEKMYSALKNEIKQRESMWS 146 (236)
Q Consensus 99 F~~~A~~~y~~i~~A~a~gD------~~~L~~l~Te~~y~~l~~~ik~r~~~g~ 146 (236)
-...|--+|.++|.--.+|+ ...|+.++||.|...|.+..+.|...|+
T Consensus 63 VYaFa~yIfQQlN~W~~dG~~DY~~ni~~l~~YlTP~c~~~L~~d~~~r~~~ge 116 (199)
T PF11444_consen 63 VYAFAFYIFQQLNRWPTDGEEDYPNNIHRLSAYLTPSCQAFLEQDYEQRRNNGE 116 (199)
T ss_pred HHHHHHHHHHHHcccccCChHHHHHHHHhhhhhcCHHHHHHHHHHHHHHHhccc
Confidence 33445556777777666665 4489999999999999999998887775
No 14
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=49.37 E-value=46 Score=29.77 Aligned_cols=44 Identities=14% Similarity=0.063 Sum_probs=32.4
Q ss_pred HHHHHh--CCCChHhHHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHHH
Q 026572 86 IAKLRK--SGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMY 131 (236)
Q Consensus 86 l~~ir~--~~F~~~~F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~y 131 (236)
..++++ |.|.+ -.+...++-....+|+..||.+.|..|+++++-
T Consensus 159 r~~Lr~~~~~~~~--~~~~~~~~~~~f~~a~~~gd~~~l~~ll~~d~~ 204 (290)
T PRK09635 159 RRKINESRIAASV--EPAQHRVVTRAFIEACSNGDLDTLLEVLDPGVA 204 (290)
T ss_pred HHHHHhhCCCCCC--ChHHHHHHHHHHHHHHHhCCHHHHHHHhhhhhc
Confidence 344554 54442 233456778889999999999999999999983
No 15
>PF13211 DUF4019: Protein of unknown function (DUF4019)
Probab=47.27 E-value=1.2e+02 Score=22.92 Aligned_cols=79 Identities=13% Similarity=0.197 Sum_probs=45.3
Q ss_pred HHHHhhhHHHHHHHHHHHHHhhcCCCceeeeeecccccceEEEEEEe-eeecccCCCceEEEEEEEEEEEEEEEEcCCCc
Q 026572 121 SLRKAVTEKMYSALKNEIKQRESMWSSVNWELIEPIIKMRTLRARLI-GVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGV 199 (236)
Q Consensus 121 ~L~~l~Te~~y~~l~~~ik~r~~~g~~~~W~lv~~~~~~rvv~~r~i-~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~ 199 (236)
.++.-+++..+......++.. -|. +..=..+..... ..+. ..+-..+.|.|.|.-.
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--LGA---------VVSRELVSRQRYTSLPG---APDGEYVVVQFQTTFA--------- 81 (105)
T ss_pred HHhccCCHHHHHHHHHHHHHh--ccc---------cchhhheeeeeecCCCC---CCCceEEEEEEEeEeC---------
Confidence 457777887777776666443 232 110022222221 1211 1355588888987552
Q ss_pred eecCCCCCeeeeeEEEEEEEeCCCCCCCeEEEE
Q 026572 200 TVAGDKTKEVLVRDIWVFEKSLFHPGAYWRLCG 232 (236)
Q Consensus 200 lv~G~~~~~~dv~EywvFeR~l~~~~~~WrL~g 232 (236)
.-..+.|-++|-+.- ++.||+.|
T Consensus 82 -------~~~~~~Etvt~~~e~---dg~Wr~~G 104 (105)
T PF13211_consen 82 -------NKKQATETVTFRLEE---DGRWRVVG 104 (105)
T ss_pred -------CCCceEEEEEEEEcC---CCcEEeCC
Confidence 112389999987763 78999987
No 16
>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=47.20 E-value=25 Score=31.28 Aligned_cols=32 Identities=19% Similarity=0.127 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 99 FYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 99 F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
....-+++-....+||++||.+.|..+++|.+
T Consensus 202 ~~~~~~~~v~~~~~a~~~gD~~~l~~Lla~Dv 233 (324)
T TIGR02960 202 PSPEEQDLLERYIAAFESYDLDALTALLHEDA 233 (324)
T ss_pred CCHHHHHHHHHHHHHHHcCCHHHHHHHhcCCe
Confidence 44455677888899999999999999999876
No 17
>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=40.69 E-value=29 Score=25.80 Aligned_cols=30 Identities=10% Similarity=0.100 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhhHHHH
Q 026572 102 EAVDLYKEINTLMANGDKTSLRKAVTEKMY 131 (236)
Q Consensus 102 ~A~~~y~~i~~A~a~gD~~~L~~l~Te~~y 131 (236)
..+++.....+||+++|.+.|..+.+|.+.
T Consensus 4 ~~~~~v~~~~~a~~~~D~~~~~~l~aed~~ 33 (122)
T cd00781 4 EMKAAVQRYVEAVNAGDPEGIVALFADDAT 33 (122)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHcCCCeE
Confidence 445667778899999999999999998875
No 18
>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=40.26 E-value=67 Score=28.31 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 101 TEAVDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 101 ~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
+...++-....+|+..||.+.|..++++++
T Consensus 164 ~~~~~~~~~f~~a~~~gD~~~l~~lL~~dv 193 (281)
T TIGR02957 164 EESRQLLERFVEAAQTGDLDGLLELLAEDV 193 (281)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHhhce
Confidence 345567788899999999999999999987
No 19
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=39.54 E-value=17 Score=26.34 Aligned_cols=26 Identities=27% Similarity=0.313 Sum_probs=15.9
Q ss_pred ceEEEEEEEEEEEEE--EEEcCCCceec
Q 026572 177 VFVQLTLEFLAKQKF--EAYDSKGVTVA 202 (236)
Q Consensus 177 ~~~qvtVrf~s~Q~l--~v~Dk~G~lv~ 202 (236)
.-.-++++|.+.|+. .++|+.|+.|-
T Consensus 12 s~~~v~l~f~sgq~~D~~v~d~~g~~vw 39 (82)
T PF12690_consen 12 SDEPVTLQFPSGQRYDFVVKDKEGKEVW 39 (82)
T ss_dssp SSS-EEEEESSS--EEEEEE-TT--EEE
T ss_pred CCCeEEEEeCCCCEEEEEEECCCCCEEE
Confidence 456799999999994 67899999873
No 20
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=39.40 E-value=61 Score=28.66 Aligned_cols=32 Identities=19% Similarity=0.246 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 99 FYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 99 F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
-.+...++-....+|+.+||.+.|..+++|.+
T Consensus 169 ~~~~~~~~v~~f~~A~~~gD~~~l~~Lla~Dv 200 (293)
T PRK09636 169 SDEEGAELVEAFFAALASGDLDALVALLAPDV 200 (293)
T ss_pred CchHHHHHHHHHHHHHHhCCHHHHHHHHhhCe
Confidence 34456678889999999999999999998876
No 21
>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=38.72 E-value=61 Score=19.91 Aligned_cols=25 Identities=24% Similarity=0.252 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHcCCHHHHHHhhhH
Q 026572 104 VDLYKEINTLMANGDKTSLRKAVTE 128 (236)
Q Consensus 104 ~~~y~~i~~A~a~gD~~~L~~l~Te 128 (236)
+.++..|-.|+.+||++.-..++.+
T Consensus 12 ~~L~~~ID~ALd~~D~e~F~~Ls~e 36 (37)
T PF08858_consen 12 EQLLELIDEALDNRDKEWFYELSEE 36 (37)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHhh
Confidence 4688999999999999987777653
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=38.40 E-value=95 Score=22.32 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=29.8
Q ss_pred CChHhHHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 94 YSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 94 F~~~~F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
+..........+.+..|.+|+.+||.+.....+...+
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 3366777788888999999999999999998887654
No 23
>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=35.69 E-value=23 Score=25.12 Aligned_cols=27 Identities=15% Similarity=0.234 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 104 VDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 104 ~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
++++....+||.++|.+.+..+.++++
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 467889999999999999999988765
No 24
>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=34.51 E-value=25 Score=26.37 Aligned_cols=27 Identities=15% Similarity=0.239 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHcCCHHHHHHhhhHHHH
Q 026572 105 DLYKEINTLMANGDKTSLRKAVTEKMY 131 (236)
Q Consensus 105 ~~y~~i~~A~a~gD~~~L~~l~Te~~y 131 (236)
++.....+||+++|.+.+..++++++.
T Consensus 2 ~iv~~~~~a~~~~d~~~~~~~~~~d~~ 28 (129)
T TIGR02096 2 ELAQHWIEAFNRGDMDAVLALLAEDVL 28 (129)
T ss_pred HHHHHHHHHHHCCCHHHHHHhcCCCeE
Confidence 455667779999999999999988854
No 25
>PF10115 HlyU: Transcriptional activator HlyU; InterPro: IPR018772 This is a family of hypothetical prokaryotic proteins, with no known function. One of the proteins in this entry corresponds to the transcriptional activator HlyU, indicating a possible similar role in other members.
Probab=33.93 E-value=66 Score=24.11 Aligned_cols=27 Identities=22% Similarity=0.537 Sum_probs=19.1
Q ss_pred eeeeeEEEEEEEeCCCCCCCeEEEEEee
Q 026572 208 EVLVRDIWVFEKSLFHPGAYWRLCGRIK 235 (236)
Q Consensus 208 ~~dv~EywvFeR~l~~~~~~WrL~g~i~ 235 (236)
+.+-..|-...-.+. .++.||++|+|.
T Consensus 21 p~eYkgf~I~~~P~~-egGQfRvag~I~ 47 (91)
T PF10115_consen 21 PVEYKGFLIYPEPMS-EGGQFRVAGRIE 47 (91)
T ss_pred CeEeCCEEEEeCccc-cCCceeEEEEEE
Confidence 444555666655554 689999999995
No 26
>PRK10533 putative lipoprotein; Provisional
Probab=33.73 E-value=2.7e+02 Score=23.17 Aligned_cols=27 Identities=19% Similarity=0.364 Sum_probs=22.4
Q ss_pred HcCCHHHHHHhhhHHHHHHHHHHHHHh
Q 026572 115 ANGDKTSLRKAVTEKMYSALKNEIKQR 141 (236)
Q Consensus 115 a~gD~~~L~~l~Te~~y~~l~~~ik~r 141 (236)
.+.+...||+++|..+|..|...-++.
T Consensus 56 d~~~la~lRPyLSd~Ly~~L~~A~r~~ 82 (171)
T PRK10533 56 RSNDIAALRPYLSDKLATLLSDASRDN 82 (171)
T ss_pred chhhHHHhcccccHHHHHHHHHHhhcc
Confidence 556788999999999999999776644
No 27
>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=33.68 E-value=56 Score=28.00 Aligned_cols=44 Identities=18% Similarity=0.235 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHcCC------HHHHHHhhhHHHHHHHHHHHHHhhcCCC
Q 026572 103 AVDLYKEINTLMANGD------KTSLRKAVTEKMYSALKNEIKQRESMWS 146 (236)
Q Consensus 103 A~~~y~~i~~A~a~gD------~~~L~~l~Te~~y~~l~~~ik~r~~~g~ 146 (236)
|--+|.++|.=-.+|. ...|+.++||.|...|.+..+.|...|+
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 3445566654434443 5589999999999999999999976664
No 28
>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=32.90 E-value=43 Score=26.53 Aligned_cols=29 Identities=21% Similarity=0.337 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHcCCHHHHHHhhhHH
Q 026572 101 TEAVDLYKEINTLMANGDKTSLRKAVTEK 129 (236)
Q Consensus 101 ~~A~~~y~~i~~A~a~gD~~~L~~l~Te~ 129 (236)
++..+++...++|++.||.++..++|.++
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 45567899999999999999999999998
No 29
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=30.84 E-value=2.4e+02 Score=23.10 Aligned_cols=63 Identities=14% Similarity=0.161 Sum_probs=36.9
Q ss_pred cccccCCCCCCcccccccchhhHhhHHHHHHHHhhHHHHHHHHhCCCChHhHHHHHHHHHHHHHHHHHcCCHHHHHHhhh
Q 026572 48 YEPYAPREAIPFWRRWFTRDGWRRTKDDIILELKSAYAIAKLRKSGYSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVT 127 (236)
Q Consensus 48 ~e~yvpp~~~~~~~~~~t~~g~~~~~~~l~~~~~s~~~l~~ir~~~F~~~~F~~~A~~~y~~i~~A~a~gD~~~L~~l~T 127 (236)
.+|+.||.|.+.-..++|++|++...+.|.. ++ ..+.+|-+.||... -
T Consensus 15 ~~~~~~~r~~~~~~~~lT~~G~~~L~~El~~----------L~-----------------~~i~~Ar~~GDlsE-----a 62 (160)
T PRK06342 15 AETLLPDRPISPHPNLVTEAGLKALEDQLAQ----------AR-----------------AAYEAAQAIEDVNE-----R 62 (160)
T ss_pred ccccCCCCCCCCCCceECHHHHHHHHHHHHH----------HH-----------------HHHHHHHHCCChhH-----H
Confidence 4566776663222456899998866655542 11 25777888899877 2
Q ss_pred HHHHHHHHHHHHHhh
Q 026572 128 EKMYSALKNEIKQRE 142 (236)
Q Consensus 128 e~~y~~l~~~ik~r~ 142 (236)
.+-...+.++|+...
T Consensus 63 k~~~~~~e~rI~~L~ 77 (160)
T PRK06342 63 RRQMARPLRDLRYLA 77 (160)
T ss_pred HHHHHHHHHHHHHHH
Confidence 333334445555443
No 30
>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=29.48 E-value=58 Score=24.07 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 102 EAVDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 102 ~A~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
+.++++....+||.++|.+.+..+.++.+
T Consensus 5 ~i~~l~~~~~~a~~~~D~~~~~~~~~~Da 33 (128)
T TIGR02246 5 AIRALVATWEAAWAAGDAEGFADLFTPDG 33 (128)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhCCCc
Confidence 45678888999999999999999888874
No 31
>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=28.80 E-value=42 Score=22.65 Aligned_cols=36 Identities=19% Similarity=0.261 Sum_probs=30.2
Q ss_pred EEEEEEEEEcCCCceecCCCCCeeeeeEEEEEEEeCCC
Q 026572 186 LAKQKFEAYDSKGVTVAGDKTKEVLVRDIWVFEKSLFH 223 (236)
Q Consensus 186 ~s~Q~l~v~Dk~G~lv~G~~~~~~dv~EywvFeR~l~~ 223 (236)
.++|++-+|-..|++-.|.. -.|..|+.+.+|.+.-
T Consensus 2 s~K~~F~~~hg~GNvR~Gp~--GvdLs~Fi~~~rGIdr 37 (58)
T PF09322_consen 2 SSKVIFQIYHGEGNVRYGPT--GVDLSEFIVTSRGIDR 37 (58)
T ss_pred CCceeEEEEEcCCceeECCC--ccchhHeeeeccccCc
Confidence 46788889999999999963 4689999999998864
No 32
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=28.09 E-value=78 Score=28.46 Aligned_cols=33 Identities=18% Similarity=0.038 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 98 KFYTEAVDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 98 ~F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
.+.+.-+++-....+||.+||.+.|..+++|.+
T Consensus 211 ~~~~~~~~~v~~~~~A~~~gD~~~l~~lla~Dv 243 (339)
T PRK08241 211 PDDPEERALLARYVAAFEAYDVDALVALLTEDA 243 (339)
T ss_pred CCChHHHHHHHHHHHHHhcCCHHHHHHHhcCCE
Confidence 467777888889999999999999999999976
No 33
>PF13026 DUF3887: Protein of unknown function (DUF3887)
Probab=27.13 E-value=1.6e+02 Score=22.39 Aligned_cols=38 Identities=24% Similarity=0.376 Sum_probs=28.4
Q ss_pred CChHhHHHHHHHHHHHHHHHHHcCCHHHHHHhhhHHHHHHHH
Q 026572 94 YSKQKFYTEAVDLYKEINTLMANGDKTSLRKAVTEKMYSALK 135 (236)
Q Consensus 94 F~~~~F~~~A~~~y~~i~~A~a~gD~~~L~~l~Te~~y~~l~ 135 (236)
|+.....+.|+++. .-+..+|.+.++..|++.|=+.|.
T Consensus 2 f~~Ekv~~~Aeevi----~~~N~~dy~~v~~~~d~~mk~aL~ 39 (101)
T PF13026_consen 2 FDEEKVKQKAEEVI----DLLNEKDYDKVHEKYDEKMKNALT 39 (101)
T ss_pred CcHHHHHHHHHHHH----HHHhHhhHHHHHHHHhHHHHHhcC
Confidence 66677777776554 445568999999888888877777
No 34
>PRK13683 hypothetical protein; Provisional
Probab=25.87 E-value=81 Score=23.37 Aligned_cols=34 Identities=26% Similarity=0.287 Sum_probs=17.1
Q ss_pred ceEEEEEEeeeecccCCCceEEEEEEEEEEEEEEEEcCCCc
Q 026572 159 MRTLRARLIGVDRNDLNKVFVQLTLEFLAKQKFEAYDSKGV 199 (236)
Q Consensus 159 ~rvv~~r~i~i~~~~~~~~~~qvtVrf~s~Q~l~v~Dk~G~ 199 (236)
|+++...|-.+.+. -.+.++=.+.+-| +|+|+|-
T Consensus 41 P~llELtCek~~~K----kiavlssEi~aVq---i~eKs~~ 74 (87)
T PRK13683 41 PRLLELTCEKVEDK----KIAVLSSEISAVQ---IYEKSGA 74 (87)
T ss_pred CcEEEEEecCcCCc----EEEEEeeeeEEEE---EEeccCc
Confidence 45667777554332 3444444444444 3566654
No 35
>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=25.72 E-value=75 Score=27.06 Aligned_cols=27 Identities=19% Similarity=0.329 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhhH
Q 026572 102 EAVDLYKEINTLMANGDKTSLRKAVTE 128 (236)
Q Consensus 102 ~A~~~y~~i~~A~a~gD~~~L~~l~Te 128 (236)
...+.+.++.++|.+||.+.|.++..+
T Consensus 171 ~~~~~~~~~~~~~~~gd~~~l~~~~~~ 197 (259)
T PF01963_consen 171 DGEKMLEQLIEAWKNGDLDALMELMKE 197 (259)
T ss_pred cchHHHHHHHHHHHccCHHHHHHHHHh
Confidence 345678899999999999999888754
No 36
>PF08969 USP8_dimer: USP8 dimerisation domain; InterPro: IPR015063 This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It has no known function. ; PDB: 2XZE_B 2A9U_A.
Probab=24.97 E-value=1.4e+02 Score=22.66 Aligned_cols=30 Identities=17% Similarity=0.335 Sum_probs=25.4
Q ss_pred CCCChHhHHHHHHHHHHHHHHHHHcCCHHH
Q 026572 92 SGYSKQKFYTEAVDLYKEINTLMANGDKTS 121 (236)
Q Consensus 92 ~~F~~~~F~~~A~~~y~~i~~A~a~gD~~~ 121 (236)
++-....+...|..+|.+...+...||.+.
T Consensus 27 ~~~~l~~y~rsa~~l~~~A~~~~~egd~E~ 56 (115)
T PF08969_consen 27 KNIPLKRYLRSANKLLREAEEYRQEGDEEQ 56 (115)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHHHHCT-HHH
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHCCCHHH
Confidence 566778899999999999999999999875
No 37
>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=22.11 E-value=3.5e+02 Score=20.36 Aligned_cols=29 Identities=7% Similarity=0.113 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHhhhHHH
Q 026572 102 EAVDLYKEINTLMANGDKTSLRKAVTEKM 130 (236)
Q Consensus 102 ~A~~~y~~i~~A~a~gD~~~L~~l~Te~~ 130 (236)
.+++......+||++||.+.+..+++...
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 38
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=20.58 E-value=1.5e+02 Score=20.20 Aligned_cols=30 Identities=20% Similarity=0.316 Sum_probs=24.3
Q ss_pred HhHHHHHHHHHHHHHHHH---HcCCHHHHHHhh
Q 026572 97 QKFYTEAVDLYKEINTLM---ANGDKTSLRKAV 126 (236)
Q Consensus 97 ~~F~~~A~~~y~~i~~A~---a~gD~~~L~~l~ 126 (236)
..|.+.+.+....+.+++ ..+|.+.++..+
T Consensus 4 ~~f~~~~~~~~~~l~~~~~~~~~~d~~~l~~~~ 36 (90)
T PF01627_consen 4 DIFLEEAPEDLEQLEQALQALEQEDWEELRRLA 36 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHCSSHHCHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHH
Confidence 468889999999999999 788888776554
No 39
>PRK09925 leu operon leader peptide; Provisional
Probab=20.35 E-value=1.1e+02 Score=17.54 Aligned_cols=22 Identities=23% Similarity=0.397 Sum_probs=15.9
Q ss_pred EEEEEEEEEEEEEcCCCceecC
Q 026572 182 TLEFLAKQKFEAYDSKGVTVAG 203 (236)
Q Consensus 182 tVrf~s~Q~l~v~Dk~G~lv~G 203 (236)
.|||.+-..+-...-.|++|.|
T Consensus 4 ivrf~gllllna~s~rgr~v~g 25 (28)
T PRK09925 4 IVRFIGLLLLNASSLRGRRVSG 25 (28)
T ss_pred EEEEeeeeeeehhhhcCccccc
Confidence 5788876666555567888877
Done!