Query 030877
Match_columns 170
No_of_seqs 115 out of 1163
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 05:56:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02227 sigpep_I_bact signal 100.0 4E-40 8.7E-45 247.4 16.6 139 21-160 2-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 4.9E-36 1.1E-40 219.7 11.6 144 22-165 16-164 (176)
3 PRK10861 signal peptidase I; P 100.0 5.3E-35 1.2E-39 238.9 17.8 143 17-160 60-305 (324)
4 KOG1568 Mitochondrial inner me 100.0 6.3E-32 1.4E-36 197.7 10.2 131 33-168 25-160 (174)
5 TIGR02771 TraF_Ti conjugative 99.9 1.1E-25 2.4E-30 170.0 13.8 121 24-155 9-168 (171)
6 PRK13884 conjugal transfer pep 99.9 3E-25 6.4E-30 168.7 16.0 107 39-156 29-176 (178)
7 PRK13838 conjugal transfer pil 99.9 1.9E-25 4.2E-30 169.2 13.0 86 69-155 48-171 (176)
8 PF10502 Peptidase_S26: Signal 99.9 1E-24 2.2E-29 159.5 3.0 86 70-155 20-136 (138)
9 TIGR02754 sod_Ni_protease nick 99.9 1.2E-21 2.5E-26 133.3 9.9 89 43-154 2-90 (90)
10 cd06530 S26_SPase_I The S26 Ty 99.8 3.1E-20 6.7E-25 124.8 9.4 84 41-152 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.8 8.9E-18 1.9E-22 125.3 13.0 115 13-153 2-119 (158)
12 COG4959 TraF Type IV secretory 99.6 6.5E-16 1.4E-20 112.6 7.9 88 71-159 53-171 (173)
13 COG0681 LepB Signal peptidase 99.6 6.3E-15 1.4E-19 110.0 11.4 129 17-152 7-144 (166)
14 KOG3342 Signal peptidase I [In 99.3 1.6E-11 3.6E-16 89.5 8.4 124 5-154 12-145 (180)
15 PF00717 Peptidase_S24: Peptid 99.3 6E-11 1.3E-15 76.3 8.9 59 43-107 1-59 (70)
16 cd06462 Peptidase_S24_S26 The 99.2 2.4E-10 5.2E-15 75.6 9.6 82 41-151 2-83 (84)
17 cd06529 S24_LexA-like Peptidas 98.8 8.9E-08 1.9E-12 62.9 10.0 56 41-104 2-57 (81)
18 COG2932 Predicted transcriptio 98.7 1.4E-07 3.1E-12 73.5 10.8 89 40-158 124-212 (214)
19 TIGR00498 lexA SOS regulatory 98.4 6.6E-06 1.4E-10 63.3 12.0 88 38-159 110-198 (199)
20 PRK00215 LexA repressor; Valid 98.4 7.9E-06 1.7E-10 63.2 11.8 86 38-157 117-203 (205)
21 PRK10276 DNA polymerase V subu 98.4 1.1E-05 2.3E-10 59.0 11.5 50 39-96 51-101 (139)
22 PRK12423 LexA repressor; Provi 98.3 1.5E-05 3.3E-10 61.7 11.6 85 40-157 115-200 (202)
23 COG1974 LexA SOS-response tran 97.8 0.00061 1.3E-08 52.8 11.6 88 39-159 112-200 (201)
24 PF07039 DUF1325: SGF29 tudor- 84.6 6.7 0.00014 28.2 7.1 56 73-129 1-60 (130)
25 PF05257 CHAP: CHAP domain; I 83.4 3.8 8.3E-05 28.6 5.4 38 70-107 61-99 (124)
26 TIGR02594 conserved hypothetic 82.8 5.2 0.00011 28.7 5.9 55 70-150 72-126 (129)
27 COG0681 LepB Signal peptidase 80.6 2.3 5E-05 31.0 3.5 13 71-83 84-96 (166)
28 cd04712 BAH_DCM_I BAH, or Brom 59.1 64 0.0014 23.1 8.0 84 70-159 4-102 (130)
29 COG0093 RplN Ribosomal protein 55.9 62 0.0013 23.0 6.0 27 120-147 80-106 (122)
30 PF10000 ACT_3: ACT domain; I 52.8 7.9 0.00017 24.9 1.1 18 47-65 12-29 (72)
31 COG0361 InfA Translation initi 52.6 17 0.00038 23.6 2.7 20 56-78 49-68 (75)
32 smart00439 BAH Bromo adjacent 52.4 70 0.0015 21.6 7.1 15 142-156 70-84 (120)
33 cd04456 S1_IF1A_like S1_IF1A_l 51.6 15 0.00032 24.0 2.3 11 72-82 39-49 (78)
34 TIGR00008 infA translation ini 50.9 17 0.00038 23.1 2.5 11 72-82 45-55 (68)
35 PF01176 eIF-1a: Translation i 46.8 16 0.00035 22.7 1.9 13 71-83 41-53 (65)
36 COG3602 Uncharacterized protei 45.2 13 0.00029 26.3 1.4 17 47-64 12-28 (134)
37 PRK11578 macrolide transporter 45.1 77 0.0017 26.4 6.2 14 90-103 71-84 (370)
38 PF06890 Phage_Mu_Gp45: Bacter 44.5 98 0.0021 23.2 6.0 39 67-107 70-111 (162)
39 PF01426 BAH: BAH domain; Int 42.1 40 0.00087 22.8 3.5 26 72-97 3-28 (119)
40 COG3944 Capsular polysaccharid 41.7 1.4E+02 0.003 23.6 6.6 16 49-65 40-55 (226)
41 PF12459 DUF3687: D-Ala-teicho 41.6 52 0.0011 18.9 3.2 25 8-32 2-26 (42)
42 cd05793 S1_IF1A S1_IF1A: Trans 41.4 24 0.00052 23.0 2.1 11 72-82 39-49 (77)
43 PF05382 Amidase_5: Bacterioph 40.6 48 0.001 24.4 3.8 39 42-83 49-87 (145)
44 smart00652 eIF1a eukaryotic tr 40.1 26 0.00056 23.2 2.1 11 72-82 44-54 (83)
45 PRK10507 bifunctional glutathi 39.3 1.4E+02 0.0031 27.3 7.3 58 70-127 110-177 (619)
46 cd04714 BAH_BAHCC1 BAH, or Bro 38.1 50 0.0011 23.2 3.5 27 71-97 3-29 (121)
47 cd03695 CysN_NodQ_II CysN_NodQ 36.9 1.1E+02 0.0023 19.7 4.7 34 70-105 25-66 (81)
48 PF07423 DUF1510: Protein of u 36.8 59 0.0013 25.6 4.0 19 12-30 10-28 (217)
49 PRK12442 translation initiatio 36.5 42 0.00091 22.5 2.7 11 72-82 47-57 (87)
50 cd04721 BAH_plant_1 BAH, or Br 35.1 99 0.0021 22.1 4.7 25 71-97 7-31 (130)
51 PRK04012 translation initiatio 34.7 35 0.00076 23.4 2.1 11 72-82 60-70 (100)
52 PLN03148 Blue copper-like prot 34.6 2E+02 0.0043 21.7 7.1 15 70-84 44-58 (167)
53 cd05792 S1_eIF1AD_like S1_eIF1 33.9 31 0.00067 22.6 1.7 39 43-82 8-49 (78)
54 PF10030 DUF2272: Uncharacteri 33.6 1.9E+02 0.004 22.1 6.1 15 70-84 92-106 (183)
55 PRK13884 conjugal transfer pep 33.1 2.1E+02 0.0046 21.5 7.3 19 40-63 42-60 (178)
56 PRK00969 hypothetical protein; 31.5 2.5E+02 0.0053 25.1 7.2 37 117-153 440-487 (508)
57 PF13172 PepSY_TM_1: PepSY-ass 31.3 89 0.0019 16.6 3.3 25 11-35 2-26 (34)
58 PRK00276 infA translation init 30.6 78 0.0017 20.0 3.2 12 71-82 46-57 (72)
59 PF10913 DUF2706: Protein of u 30.4 74 0.0016 19.2 2.7 44 20-64 4-47 (60)
60 cd03698 eRF3_II_like eRF3_II_l 30.1 1.5E+02 0.0033 18.9 4.6 34 70-105 25-66 (83)
61 PF12911 OppC_N: N-terminal TM 30.0 74 0.0016 18.7 2.9 7 10-16 5-11 (56)
62 PF12059 DUF3540: Protein of u 29.8 2.1E+02 0.0046 22.1 6.0 26 56-82 20-45 (202)
63 PF15428 Imm14: Immunity prote 29.8 84 0.0018 21.9 3.6 22 73-96 1-22 (129)
64 CHL00010 infA translation init 29.7 82 0.0018 20.4 3.2 24 71-94 46-71 (78)
65 CHL00038 psbL photosystem II p 28.5 1.1E+02 0.0025 17.0 3.1 27 4-30 4-30 (38)
66 smart00831 Cation_ATPase_N Cat 27.3 1.4E+02 0.0031 17.8 4.5 27 7-33 34-60 (64)
67 PF13800 Sigma_reg_N: Sigma fa 27.2 1.6E+02 0.0035 19.5 4.4 7 10-16 10-16 (96)
68 cd04717 BAH_polybromo BAH, or 26.8 94 0.002 21.5 3.4 26 71-96 3-28 (121)
69 cd06555 ASCH_PF0470_like ASC-1 26.3 1.4E+02 0.003 20.8 4.0 26 70-96 30-55 (109)
70 PF14085 DUF4265: Domain of un 25.6 2.4E+02 0.0051 19.6 6.5 46 57-104 11-57 (117)
71 PF11302 DUF3104: Protein of u 24.5 1.8E+02 0.0039 18.9 4.0 29 71-99 5-38 (75)
72 PF13759 2OG-FeII_Oxy_5: Putat 24.4 69 0.0015 21.4 2.2 24 71-100 69-92 (101)
73 PF09163 Form-deh_trans: Forma 24.2 1.4E+02 0.0031 17.3 3.2 28 11-38 5-32 (44)
74 cd04451 S1_IF1 S1_IF1: Transla 24.1 94 0.002 18.9 2.6 12 71-82 40-51 (64)
75 TIGR02219 phage_NlpC_fam putat 23.7 1.2E+02 0.0027 21.4 3.6 13 70-82 75-87 (134)
76 cd03584 NTR_complement_C4 NTR/ 23.2 3.1E+02 0.0067 20.1 6.6 35 120-159 90-125 (153)
77 COG5131 URM1 Ubiquitin-like pr 22.7 1.1E+02 0.0024 20.7 2.8 31 51-82 56-91 (96)
78 smart00002 PLP Myelin proteoli 22.5 22 0.00049 22.1 -0.5 20 133-152 22-41 (60)
79 PF00238 Ribosomal_L14: Riboso 22.5 56 0.0012 23.2 1.5 28 118-146 78-105 (122)
80 COG4127 Uncharacterized conser 22.3 88 0.0019 25.8 2.7 26 70-96 71-96 (318)
81 PF14118 YfzA: YfzA-like prote 22.1 76 0.0016 21.6 2.0 15 44-59 30-44 (94)
82 COG1096 Predicted RNA-binding 22.1 2.8E+02 0.0061 21.3 5.2 33 69-101 59-91 (188)
83 PF05781 MRVI1: MRVI1 protein; 22.0 1.4E+02 0.003 26.8 4.0 26 15-40 478-503 (538)
84 PF00278 Orn_DAP_Arg_deC: Pyri 21.3 1.2E+02 0.0027 20.3 3.1 29 51-82 65-93 (116)
85 PF10222 DUF2152: Uncharacteri 20.6 1.1E+02 0.0023 28.0 3.1 68 58-141 52-119 (604)
86 CHL00057 rpl14 ribosomal prote 20.4 3.3E+02 0.0071 19.4 7.7 30 117-147 77-106 (122)
87 PLN02289 ribulose-bisphosphate 20.2 92 0.002 23.6 2.3 27 114-140 96-122 (176)
No 1
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=100.00 E-value=4e-40 Score=247.39 Aligned_cols=139 Identities=33% Similarity=0.498 Sum_probs=122.4
Q ss_pred HHHHHHHHHHHHHHhhceEEeEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCC
Q 030877 21 SLLVGKFFCCLHVVNTYVCTPALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGD 100 (170)
Q Consensus 21 ~~~l~~~~~~~~~~~~~~~~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD 100 (170)
+..++++++++++++.|+++.+.|+|+||+|||+ +||++++++..+...++++||+|+|+.|.++++.++|||+|+|||
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~-~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd 80 (163)
T TIGR02227 2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLK-EGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGD 80 (163)
T ss_pred HHHHHHHHHHHHHHHhhEEEEEEECCcccccchh-CCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEEEEecCCC
Confidence 4556677778888999999999999999999999 999999999887778999999999999877788999999999999
Q ss_pred EEEEecC-----C----C----CC----------CCcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEe
Q 030877 101 RVSYVAD-----P----K----SS----------DKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIW 157 (170)
Q Consensus 101 ~v~i~~~-----~----~----~~----------~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~ 157 (170)
+|.++++ + . .. ....+.+||+|||||+|||+++|.|||+||+|++++|+|||.+++|
T Consensus 81 ~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~~~ 160 (163)
T TIGR02227 81 KVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVFY 160 (163)
T ss_pred EEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEEEC
Confidence 9998765 1 0 00 1234679999999999999999999999999999999999999999
Q ss_pred CCC
Q 030877 158 PPK 160 (170)
Q Consensus 158 p~~ 160 (170)
|++
T Consensus 161 p~~ 163 (163)
T TIGR02227 161 PFD 163 (163)
T ss_pred CCC
Confidence 985
No 2
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.9e-36 Score=219.70 Aligned_cols=144 Identities=41% Similarity=0.703 Sum_probs=126.5
Q ss_pred HHHHHHHHHHHHHhhceEEeEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCE
Q 030877 22 LLVGKFFCCLHVVNTYVCTPALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDR 101 (170)
Q Consensus 22 ~~l~~~~~~~~~~~~~~~~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~ 101 (170)
......++++++...|+.++....|.||+||+...||+++.+++++.++.+++||+|++..|.++.+.++|||+|+|||-
T Consensus 16 ~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~ 95 (176)
T KOG0171|consen 16 CSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDL 95 (176)
T ss_pred HHHHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhheeeccCCce
Confidence 34455566777777899999999999999999867777777999999999999999999999999999999999999998
Q ss_pred EEEecCCCCC-----CCcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEeCCCCcccC
Q 030877 102 VSYVADPKSS-----DKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPPKDFGSL 165 (170)
Q Consensus 102 v~i~~~~~~~-----~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~ 165 (170)
+++.+++... .+..++.||+||+||+|||+++|.|||+|||+|...|+||+++++||..+.+..
T Consensus 96 v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~ 164 (176)
T KOG0171|consen 96 VEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGL 164 (176)
T ss_pred EEEecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhccee
Confidence 8888775432 223468999999999999999999999999999999999999999999987754
No 3
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=5.3e-35 Score=238.90 Aligned_cols=143 Identities=30% Similarity=0.464 Sum_probs=124.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhceEEeEEEeCCCCcccCCCCCcEEEEEeccCCC------------CCCCCCcEEEEEcCC
Q 030877 17 GFEKSLLVGKFFCCLHVVNTYVCTPALAYGPSMLPTINLTGDLVLAERISTRF------------NKVCPGDVVLVRSPV 84 (170)
Q Consensus 17 ~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~------------~~~~~GDiV~f~~p~ 84 (170)
++.++..++++++++++++.|+++++.|+|+||+|||. .||+++++|++|.+ .+|++||+|+|+.|.
T Consensus 60 ~~~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~-~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~ 138 (324)
T PRK10861 60 WLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPE 138 (324)
T ss_pred HHHHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCccc-CCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCC
Confidence 66677777788888899999999999999999999999 99999999998753 579999999999998
Q ss_pred CCCeeEEEEEEEeCCCEEEEe--cC-----CCC-----------------------------------------------
Q 030877 85 VPRRIVTKRVIGMEGDRVSYV--AD-----PKS----------------------------------------------- 110 (170)
Q Consensus 85 ~~~~~~vkRVva~~GD~v~i~--~~-----~~~----------------------------------------------- 110 (170)
+++..++|||+|+|||+|+++ ++ ++.
T Consensus 139 ~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 (324)
T PRK10861 139 DPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETK 218 (324)
T ss_pred CCCCcEEEEeeecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 888899999999999999986 22 100
Q ss_pred ------C-----------------C--------------CcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEE
Q 030877 111 ------S-----------------D--------------KFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVF 153 (170)
Q Consensus 111 ------~-----------------~--------------~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~ 153 (170)
. . ...+++||+|+||++|||+++|+||||||+|++++|+|+|.
T Consensus 219 ~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~ 298 (324)
T PRK10861 219 ENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKAT 298 (324)
T ss_pred cccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEE
Confidence 0 0 01355999999999999999999999999999999999999
Q ss_pred EEEeCCC
Q 030877 154 LRIWPPK 160 (170)
Q Consensus 154 ~~~~p~~ 160 (170)
+++|+++
T Consensus 299 ~i~~s~d 305 (324)
T PRK10861 299 AIWMSFE 305 (324)
T ss_pred EEEEEcC
Confidence 9999886
No 4
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=6.3e-32 Score=197.73 Aligned_cols=131 Identities=41% Similarity=0.708 Sum_probs=114.4
Q ss_pred HHhhceEEeEEEeCCCCcccCCC-----CCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecC
Q 030877 33 VVNTYVCTPALAYGPSMLPTINL-----TGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVAD 107 (170)
Q Consensus 33 ~~~~~~~~~~~v~~~SM~P~l~~-----~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~ 107 (170)
-+...+.....+.|.||.|+++| ..|++++.++.-.-..+.+||+|++..|.+++++++|||+|+|||.+.-
T Consensus 25 t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t--- 101 (174)
T KOG1568|consen 25 TFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVT--- 101 (174)
T ss_pred eeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeecccccEecc---
Confidence 34445678899999999999996 2389999998753345889999999999999999999999999998874
Q ss_pred CCCCCCcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEeCCCCcccCCCC
Q 030877 108 PKSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPPKDFGSLGRR 168 (170)
Q Consensus 108 ~~~~~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~~~~ 168 (170)
..+......+|+|||||.|||...|.|||.||||+...|+|+|++++||+.|++.+.++
T Consensus 102 --~~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~~~ 160 (174)
T KOG1568|consen 102 --EDEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLDKE 160 (174)
T ss_pred --CCCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhhhccc
Confidence 23456788999999999999999999999999999999999999999999999887653
No 5
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.94 E-value=1.1e-25 Score=170.00 Aligned_cols=121 Identities=29% Similarity=0.380 Sum_probs=88.6
Q ss_pred HHHHHHHHHHHhhceEEeEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCC----------------
Q 030877 24 VGKFFCCLHVVNTYVCTPALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPR---------------- 87 (170)
Q Consensus 24 l~~~~~~~~~~~~~~~~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~---------------- 87 (170)
+++++..+.+...|........++|| |.|-+. ... ..++++||+|+|+.|.++.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~N~T~S~-----P~g~Y~-~~~----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p 78 (171)
T TIGR02771 9 AGLALSGLTILGLYCVGARINTTKSL-----PLGLYW-TTS----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCP 78 (171)
T ss_pred HHHHHHHHHhhhcceeeEEEECCCCC-----cceEEE-eCC----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccC
Confidence 33333344444555555566777777 455555 322 2589999999999875321
Q ss_pred ---eeEEEEEEEeCCCEEEEecC-----CC---------------CCCCcceEEecCCeEEEEcCCCCCCCCCCcccccc
Q 030877 88 ---RIVTKRVIGMEGDRVSYVAD-----PK---------------SSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVP 144 (170)
Q Consensus 88 ---~~~vkRVva~~GD~v~i~~~-----~~---------------~~~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~ 144 (170)
..++|||+|+|||+|+++++ +. ......+.+||+| ||++|||+++|+||||||+|+
T Consensus 79 ~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~ 157 (171)
T TIGR02771 79 GGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPIS 157 (171)
T ss_pred cCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceec
Confidence 27999999999999998754 10 0111237899999 999999999999999999999
Q ss_pred CCCeEEEEEEE
Q 030877 145 YGLIEGRVFLR 155 (170)
Q Consensus 145 ~~~I~Gkv~~~ 155 (170)
+++|+||+..+
T Consensus 158 ~~~IiGk~~pl 168 (171)
T TIGR02771 158 REQVIGRVKPL 168 (171)
T ss_pred HHHeEEEEEEe
Confidence 99999999864
No 6
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.94 E-value=3e-25 Score=168.65 Aligned_cols=107 Identities=21% Similarity=0.207 Sum_probs=80.6
Q ss_pred EEeEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCC-------------------CeeEEEEEEEeCC
Q 030877 39 CTPALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVP-------------------RRIVTKRVIGMEG 99 (170)
Q Consensus 39 ~~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~-------------------~~~~vkRVva~~G 99 (170)
.......++|+ |.|-+.+. . .++++||+|+|+.|... ...++|||+|+||
T Consensus 29 ~~~~~N~T~S~-----P~glY~~~-~-----~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pG 97 (178)
T PRK13884 29 AGARVNTTKSI-----PVGLYWTS-S-----APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKG 97 (178)
T ss_pred CcEEEECCCCC-----cceEEEEe-C-----CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCC
Confidence 34445555665 46666653 2 57999999999977521 1379999999999
Q ss_pred CEEEEecC-----CC-----------------CCCCcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEE
Q 030877 100 DRVSYVAD-----PK-----------------SSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRI 156 (170)
Q Consensus 100 D~v~i~~~-----~~-----------------~~~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~ 156 (170)
|+|+++++ +. .......+++|+|+||++|||+++|+||||||+|++++|+|++..++
T Consensus 98 D~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~ 176 (178)
T PRK13884 98 DAVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVI 176 (178)
T ss_pred cEEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeE
Confidence 99998765 10 00112245899999999999999999999999999999999998753
No 7
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.93 E-value=1.9e-25 Score=169.24 Aligned_cols=86 Identities=29% Similarity=0.381 Sum_probs=68.7
Q ss_pred CCCCCCCcEEEEEcCCCC-------------------CeeEEEEEEEeCCCEEEEecC----CCC---------------
Q 030877 69 FNKVCPGDVVLVRSPVVP-------------------RRIVTKRVIGMEGDRVSYVAD----PKS--------------- 110 (170)
Q Consensus 69 ~~~~~~GDiV~f~~p~~~-------------------~~~~vkRVva~~GD~v~i~~~----~~~--------------- 110 (170)
.+++++||+|+|+.|.+. ...++|||+|+|||+|++++. +..
T Consensus 48 ~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~~~~~~~~~~g~~ 127 (176)
T PRK13838 48 DRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPSSSVRRRDGEGRP 127 (176)
T ss_pred CCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccccccccccccCCc
Confidence 468999999999987542 135999999999999998632 100
Q ss_pred CCCcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEE
Q 030877 111 SDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLR 155 (170)
Q Consensus 111 ~~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~ 155 (170)
.....+.+||+|+|||+|||. +|+||||||+|++++|+|+|..+
T Consensus 128 l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi 171 (176)
T PRK13838 128 LTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPV 171 (176)
T ss_pred CCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEE
Confidence 011224689999999999985 89999999999999999999875
No 8
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=99.90 E-value=1e-24 Score=159.55 Aligned_cols=86 Identities=31% Similarity=0.434 Sum_probs=32.3
Q ss_pred CCCCCCcEEEEEcCCC------------CCeeEEEEEEEeCCCEEEEecCC------------------CC-CCCcceEE
Q 030877 70 NKVCPGDVVLVRSPVV------------PRRIVTKRVIGMEGDRVSYVADP------------------KS-SDKFETVV 118 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~------------~~~~~vkRVva~~GD~v~i~~~~------------------~~-~~~~~~~~ 118 (170)
..+++||+|+|+.|.. .+..++|||+|+|||+|+++++. .. ....++.+
T Consensus 20 ~~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~ 99 (138)
T PF10502_consen 20 DKIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGT 99 (138)
T ss_dssp ---------------------------------------------------------------------S-T----TEEE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceE
Confidence 3589999999999852 24589999999999999987651 11 11125899
Q ss_pred ecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEE
Q 030877 119 VPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLR 155 (170)
Q Consensus 119 ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~ 155 (170)
||+|+||++|||+++|+||||||+|++++|+|++..+
T Consensus 100 vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl 136 (138)
T PF10502_consen 100 VPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPL 136 (138)
T ss_dssp --TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEE
T ss_pred eCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEE
Confidence 9999999999999999999999999999999999875
No 9
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.87 E-value=1.2e-21 Score=133.27 Aligned_cols=89 Identities=34% Similarity=0.547 Sum_probs=77.7
Q ss_pred EEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEEecCC
Q 030877 43 LAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQG 122 (170)
Q Consensus 43 ~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~ip~~ 122 (170)
.|.|+||+|+|+ +||++++++.......+++||+|+|+.|.+++..++||++++++ +
T Consensus 2 ~V~g~SM~P~l~-~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~----------------------~ 58 (90)
T TIGR02754 2 KVTGVSMSPTLP-PGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD----------------------N 58 (90)
T ss_pred EeeCCCccCccC-CCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC----------------------C
Confidence 689999999999 99999999854333456789999999887667899999999753 5
Q ss_pred eEEEEcCCCCCCCCCCccccccCCCeEEEEEE
Q 030877 123 HVWIEGDNIYESNDSRKFGAVPYGLIEGRVFL 154 (170)
Q Consensus 123 ~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~ 154 (170)
++|++|||+..|.|||++|+|+..+|+|+|+|
T Consensus 59 ~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 59 GLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred eEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence 79999999999999999999999999999864
No 10
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.83 E-value=3.1e-20 Score=124.78 Aligned_cols=84 Identities=45% Similarity=0.680 Sum_probs=75.2
Q ss_pred eEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEEec
Q 030877 41 PALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVP 120 (170)
Q Consensus 41 ~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~ip 120 (170)
.+.+.|+||+|+++ .||++++++....+..+++||+|+|+.+.+++..++|||++
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~------------------------ 56 (85)
T cd06530 2 PVVVPGGSMEPTLQ-PGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG------------------------ 56 (85)
T ss_pred eeEEcCCCCcCccc-CCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE------------------------
Confidence 57899999999998 99999999876333379999999999986556889999988
Q ss_pred CCeEEEEcCCCCCCCCCCccccccCCCeEEEE
Q 030877 121 QGHVWIEGDNIYESNDSRKFGAVPYGLIEGRV 152 (170)
Q Consensus 121 ~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv 152 (170)
||++|||+++|.|||++|+++.++|+|++
T Consensus 57 ---~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 ---YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred ---EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 99999999999999999999999999985
No 11
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.77 E-value=8.9e-18 Score=125.35 Aligned_cols=115 Identities=27% Similarity=0.279 Sum_probs=85.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhceE--EeE-EEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCee
Q 030877 13 FAKEGFEKSLLVGKFFCCLHVVNTYVC--TPA-LAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRI 89 (170)
Q Consensus 13 ~~~~~~~~~~~l~~~~~~~~~~~~~~~--~~~-~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~ 89 (170)
+.+++..+++++++++++...+..... .++ .|.|+||+|+++ +||++++++.. ..++++||+|+|+.|.++ ..
T Consensus 2 ~~~~ii~~~~~~~l~~~~~~~l~~~~~~~~p~v~V~g~SM~Ptl~-~GD~vlv~~~~--~~~~~~GDIVvf~~~~~~-~~ 77 (158)
T TIGR02228 2 KISNVIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFN-TGDLILVTGAD--PNDIQVGDVITYKSPGFN-TP 77 (158)
T ss_pred hhHHHHHHHHHHHHHHHHHHHheeeccCCCcEEEEcCCCCcCCcc-CCCEEEEEecc--cCCCCCCCEEEEEECCCC-cc
Confidence 355666666655555555555444333 233 499999999998 99999999854 368999999999988543 78
Q ss_pred EEEEEEEeCCCEEEEecCCCCCCCcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEE
Q 030877 90 VTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVF 153 (170)
Q Consensus 90 ~vkRVva~~GD~v~i~~~~~~~~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~ 153 (170)
++|||+++.++. .+..|++.|||.. ..| .++++.++|+|++.
T Consensus 78 iihRVi~v~~~~------------------g~~~~~tkGDnN~-~~D---~~~v~~~~IiG~v~ 119 (158)
T TIGR02228 78 VTHRVIEINNSG------------------GELGFITKGDNNP-APD---GEPVPSENVIGKYL 119 (158)
T ss_pred EEEEEEEEECCC------------------CcEEEEEEecCCC-CCC---cccCCHHHEEEEEE
Confidence 999999987530 1124888899963 345 78999999999998
No 12
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.64 E-value=6.5e-16 Score=112.58 Aligned_cols=88 Identities=26% Similarity=0.353 Sum_probs=70.7
Q ss_pred CCCCCcEEEEEcCCC------------CCeeEEEEEEEeCCCEEEEecC-----CC--------------CCCCcceEEe
Q 030877 71 KVCPGDVVLVRSPVV------------PRRIVTKRVIGMEGDRVSYVAD-----PK--------------SSDKFETVVV 119 (170)
Q Consensus 71 ~~~~GDiV~f~~p~~------------~~~~~vkRVva~~GD~v~i~~~-----~~--------------~~~~~~~~~i 119 (170)
...+||+|+++.|.. +..+++|||.|+|||+|.+.++ ++ .-.-..+..+
T Consensus 53 Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l 132 (173)
T COG4959 53 PVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRYL 132 (173)
T ss_pred CcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCcee
Confidence 459999999999852 3567999999999999998654 10 1122345558
Q ss_pred cCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEeCC
Q 030877 120 PQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPP 159 (170)
Q Consensus 120 p~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~ 159 (170)
.++|+|+++|..+.|+||||||||+.++|+|.+..+ |-.
T Consensus 133 ~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPv-wt~ 171 (173)
T COG4959 133 APSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPV-WTE 171 (173)
T ss_pred cCCeEEEEeccCCcccccceecccCHHHcceeeeee-ecc
Confidence 999999999999999999999999999999998874 533
No 13
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.62 E-value=6.3e-15 Score=109.96 Aligned_cols=129 Identities=30% Similarity=0.357 Sum_probs=98.8
Q ss_pred HHHHHHHHHHHHHHHHHH--hhceEEeEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEE
Q 030877 17 GFEKSLLVGKFFCCLHVV--NTYVCTPALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRV 94 (170)
Q Consensus 17 ~~~~~~~l~~~~~~~~~~--~~~~~~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRV 94 (170)
.+.++..++.++++++++ +.++++.+.|+|+||+||++ .||+++++++++.+..++.+|.+ ..|......++||+
T Consensus 7 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~-~GD~v~v~k~~~~~~~~~~~~~~--~~~~~~~~~~~kr~ 83 (166)
T COG0681 7 FLELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLN-VGDRVLVKKFSYGFGKLKVPDII--VLPAVVEGDLIKRV 83 (166)
T ss_pred HHHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccc-cCCEEEEEeccccccCCccceee--ecCCCCCcceEEEe
Confidence 344555566666666666 89999999999999999999 99999999999988889999988 44445578899999
Q ss_pred EEeCCCEEEEecCCCCCCCcceEEecCCeEEEE-------cCCCCCCCCCCccccccCCCeEEEE
Q 030877 95 IGMEGDRVSYVADPKSSDKFETVVVPQGHVWIE-------GDNIYESNDSRKFGAVPYGLIEGRV 152 (170)
Q Consensus 95 va~~GD~v~i~~~~~~~~~~~~~~ip~~~y~vl-------gdn~~~s~DSR~~G~V~~~~I~Gkv 152 (170)
.+++||.+.++++.... ...+|++..++. .+....+.+++.++.....+.+.++
T Consensus 84 ~~~~GD~i~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 84 IGLRGDIVVFKDDRLYV----VPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred ccCCCCEEEEECCEEEe----ecccCcchhhhhcccccccccccccccCccccccccccccccce
Confidence 99999999998652211 234455555544 4444577888888888888888887
No 14
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.29 E-value=1.6e-11 Score=89.48 Aligned_cols=124 Identities=21% Similarity=0.295 Sum_probs=87.4
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHHHH---HHHHhhceEEeEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEE
Q 030877 5 NQLSLFVTFAKEGFEKSLLVGKFFCC---LHVVNTYVCTPALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVR 81 (170)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~~~~~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~ 81 (170)
++|+. +....++++...++.-+.++ +.++...-..+..|.++||+|.++ .||.++..... ....+.||+|+|+
T Consensus 12 k~mn~-Rq~l~Q~ln~~mivssA~MiwK~l~vvt~seSPiVVVLSgSMePaF~-RGDlLfL~N~~--~~p~~vGdivVf~ 87 (180)
T KOG3342|consen 12 KRMNI-RQLLYQVLNFAMIVSSAYMIWKGLMVVTGSESPIVVVLSGSMEPAFH-RGDLLFLTNRN--EDPIRVGDIVVFK 87 (180)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHhhheeeeCCCCCEEEEEcCCcCcccc-cccEEEEecCC--CCcceeccEEEEE
Confidence 34443 66666666655555444443 333334445678999999999999 99999997533 2567999999999
Q ss_pred cCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEEecCC--eEEEEcCCCCCCCCCCc-c----ccccCCCeEEEEEE
Q 030877 82 SPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQG--HVWIEGDNIYESNDSRK-F----GAVPYGLIEGRVFL 154 (170)
Q Consensus 82 ~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~ip~~--~y~vlgdn~~~s~DSR~-~----G~V~~~~I~Gkv~~ 154 (170)
.+ ++..+++|||+.+-+. .+| ++++.||| |..|.|. | -..++++|+|+|.-
T Consensus 88 ve-gR~IPiVHRviK~he~-------------------~~~~~~~LTKGDN--N~~dD~~Ly~~gq~~L~r~~Ivg~~~G 145 (180)
T KOG3342|consen 88 VE-GREIPIVHRVIKQHEK-------------------SNGHIKFLTKGDN--NAVDDRGLYAQGQNWLERKDIVGRVRG 145 (180)
T ss_pred EC-CccCchhHHHHHHhcc-------------------cCCcEEEEecCCC--CcccchhcccccccceeccceeeEEee
Confidence 87 4578899999876542 122 47778999 5566664 2 36899999999864
No 15
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=99.26 E-value=6e-11 Score=76.34 Aligned_cols=59 Identities=32% Similarity=0.461 Sum_probs=47.4
Q ss_pred EEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecC
Q 030877 43 LAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVAD 107 (170)
Q Consensus 43 ~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~ 107 (170)
+|.|+||+|+++ +||++++++. .+++.||+|++..+.+. ..++||+.+.+|+.+.+..+
T Consensus 1 ~V~GdSM~P~i~-~Gd~v~v~~~----~~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~~~ 59 (70)
T PF00717_consen 1 RVEGDSMEPTIK-DGDIVLVDPS----SEPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILISSN 59 (70)
T ss_dssp EEESSTTGGTSS-TTEEEEEEET----S---TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-SS
T ss_pred CeECcCcccCee-CCCEEEEEEc----CCCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEecc
Confidence 589999999998 9999999985 48999999999987421 38999999999998887644
No 16
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=99.20 E-value=2.4e-10 Score=75.60 Aligned_cols=82 Identities=44% Similarity=0.595 Sum_probs=63.5
Q ss_pred eEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEEec
Q 030877 41 PALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVP 120 (170)
Q Consensus 41 ~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~ip 120 (170)
.+.+.|+||+|++. +||++++++.. ..++.||++++..+. +..++||+...++
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~i~~~~---~~~~~G~iv~~~~~~--~~~~ikrl~~~~~--------------------- 54 (84)
T cd06462 2 ALRVEGDSMEPTIP-DGDLVLVDKSS---YEPKRGDIVVFRLPG--GELTVKRVIGLPG--------------------- 54 (84)
T ss_pred eeEEcCCCccCccc-CCCEEEEEecC---CCCcCCEEEEEEcCC--CcEEEEEEEEECC---------------------
Confidence 46899999999998 99999999854 248999999999863 5899999998764
Q ss_pred CCeEEEEcCCCCCCCCCCccccccCCCeEEE
Q 030877 121 QGHVWIEGDNIYESNDSRKFGAVPYGLIEGR 151 (170)
Q Consensus 121 ~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gk 151 (170)
++++++.+||+ ++.+.+..+. ....++|+
T Consensus 55 ~~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~ 83 (84)
T cd06462 55 EGHYFLLGDNP-NSPDSRIDGP-PELDIVGV 83 (84)
T ss_pred CCEEEEECCCC-CCCcccccCC-CHHHEEEe
Confidence 36889999994 5555544433 55666665
No 17
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=98.81 E-value=8.9e-08 Score=62.93 Aligned_cols=56 Identities=34% Similarity=0.462 Sum_probs=46.6
Q ss_pred eEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEE
Q 030877 41 PALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSY 104 (170)
Q Consensus 41 ~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i 104 (170)
..++.|+||+|.++ +||++++++.. .++.||+++++.+ +..++||+...+++++.+
T Consensus 2 ~~~v~g~sM~p~i~-~gd~lii~~~~----~~~~g~i~~~~~~---~~~~ikr~~~~~~~~~~L 57 (81)
T cd06529 2 ALRVKGDSMEPTIP-DGDLVLVDPSD----TPRDGDIVVARLD---GELTVKRLQRRGGGRLRL 57 (81)
T ss_pred EEEEECCCcCCccC-CCCEEEEcCCC----CCCCCCEEEEEEC---CEEEEEEEEECCCCcEEE
Confidence 36899999999998 99999999853 5999999999976 378999999977554333
No 18
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.74 E-value=1.4e-07 Score=73.54 Aligned_cols=89 Identities=24% Similarity=0.160 Sum_probs=62.4
Q ss_pred EeEEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEEe
Q 030877 40 TPALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVV 119 (170)
Q Consensus 40 ~~~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~i 119 (170)
....|.|+||+|++. +||.++|++. .+..+||.|++.... +..++||+.-.+|
T Consensus 124 ~~i~V~GDSMeP~~~-~Gd~ilVd~~----~~~~~gd~v~v~~~g--~~~~VK~l~~~~~-------------------- 176 (214)
T COG2932 124 FALRVTGDSMEPTYE-DGDTLLVDPG----VNTRRGDRVYVETDG--GELYVKKLQREPG-------------------- 176 (214)
T ss_pred EEEEEeCCccccccc-CCCEEEECCC----CceeeCCEEEEEEeC--CeEEEEEEEEecC--------------------
Confidence 347999999999998 9999999984 467899977776532 6899999988766
Q ss_pred cCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEeC
Q 030877 120 PQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWP 158 (170)
Q Consensus 120 p~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p 158 (170)
|.+.+..+|++.. +.+.+-.=..=+|+|+|++..-+
T Consensus 177 --~~~~l~S~N~~~~-~~~~~~~~~~v~iIgrVv~~~~~ 212 (214)
T COG2932 177 --GLLRLVSLNPDYY-PDEIFSEDDDVEIIGRVVWVSRL 212 (214)
T ss_pred --CeEEEEeCCCCCC-cccccCccceEEEEEEEEEEeee
Confidence 4555777776432 22221111113589999987543
No 19
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=98.42 E-value=6.6e-06 Score=63.33 Aligned_cols=88 Identities=22% Similarity=0.171 Sum_probs=62.4
Q ss_pred eEEeEEEeCCCCc-ccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcce
Q 030877 38 VCTPALAYGPSML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFET 116 (170)
Q Consensus 38 ~~~~~~v~~~SM~-P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~ 116 (170)
-...+++.|+||. |.+. +||++++++. ..++.||+|++... +...+||+.-. |
T Consensus 110 ~~f~~~V~GdSM~~~~i~-~Gd~v~v~~~----~~~~~G~ivvv~~~---~~~~vKrl~~~-~----------------- 163 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGIC-DGDLLIVRSQ----KDARNGEIVAAMID---GEVTVKRFYKD-G----------------- 163 (199)
T ss_pred CEEEEEecCCCCCCCCCC-CCCEEEEecC----CCCCCCCEEEEEEC---CEEEEEEEEEE-C-----------------
Confidence 3456899999996 6897 9999999874 47899999999973 67899998653 2
Q ss_pred EEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEeCC
Q 030877 117 VVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPP 159 (170)
Q Consensus 117 ~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~ 159 (170)
+.+++..+|+... ...... ..-+|+|+|+..+..+
T Consensus 164 -----~~i~L~s~N~~y~--~i~~~~-~~~~IiG~Vv~~~r~~ 198 (199)
T TIGR00498 164 -----TKVELKPENPEFD--PIVLNA-EDVTILGKVVGVIRNF 198 (199)
T ss_pred -----CEEEEEcCCCCCc--CCcCCC-CcEEEEEEEEEEEEec
Confidence 4566677776321 111110 1358999999887644
No 20
>PRK00215 LexA repressor; Validated
Probab=98.38 E-value=7.9e-06 Score=63.21 Aligned_cols=86 Identities=24% Similarity=0.232 Sum_probs=60.9
Q ss_pred eEEeEEEeCCCCc-ccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcce
Q 030877 38 VCTPALAYGPSML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFET 116 (170)
Q Consensus 38 ~~~~~~v~~~SM~-P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~ 116 (170)
-....+|.|+||. |++. +||++++++. ..++.||+|++..+ +...+||+.-.
T Consensus 117 ~~~~~~V~GdSM~~~~i~-~Gd~v~v~~~----~~~~~G~ivv~~~~---~~~~vKrl~~~------------------- 169 (205)
T PRK00215 117 EDFLLRVRGDSMIDAGIL-DGDLVIVRKQ----QTARNGQIVVALID---DEATVKRFRRE------------------- 169 (205)
T ss_pred CeEEEEEccCCCCCCCcC-CCCEEEEeCC----CCCCCCCEEEEEEC---CEEEEEEEEEe-------------------
Confidence 3456889999995 7998 9999999873 36789999999875 37899999753
Q ss_pred EEecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEe
Q 030877 117 VVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIW 157 (170)
Q Consensus 117 ~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~ 157 (170)
+|.+++..+|+.. +...... ..-.|+|+|+..+-
T Consensus 170 ----~~~~~L~s~Np~y--~~~~~~~-~~~~IiG~Vv~~~r 203 (205)
T PRK00215 170 ----GGHIRLEPENPAY--EPIIVDP-DRVTIEGKVVGLIR 203 (205)
T ss_pred ----CCEEEEEcCCCCC--CCEEeCC-CcEEEEEEEEEEEE
Confidence 2456667777532 1211111 03589999988754
No 21
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.36 E-value=1.1e-05 Score=58.99 Aligned_cols=50 Identities=24% Similarity=0.334 Sum_probs=40.9
Q ss_pred EEeEEEeCCCCc-ccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEE
Q 030877 39 CTPALAYGPSML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIG 96 (170)
Q Consensus 39 ~~~~~v~~~SM~-P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva 96 (170)
....++.|+||. |++. +||++++++. .+++.||+|++... +...+||+.-
T Consensus 51 ~f~l~V~GdSM~~~~I~-~GD~liVd~~----~~~~~Gdivv~~~~---g~~~vKrl~~ 101 (139)
T PRK10276 51 TYFVKASGDSMIDAGIS-DGDLLIVDSA----ITASHGDIVIAAVD---GEFTVKKLQL 101 (139)
T ss_pred EEEEEEecCCCCCCCCC-CCCEEEEECC----CCCCCCCEEEEEEC---CEEEEEEEEE
Confidence 345899999997 6898 9999999974 35789999998863 5678999864
No 22
>PRK12423 LexA repressor; Provisional
Probab=98.30 E-value=1.5e-05 Score=61.70 Aligned_cols=85 Identities=22% Similarity=0.132 Sum_probs=59.7
Q ss_pred EeEEEeCCCCc-ccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEE
Q 030877 40 TPALAYGPSML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVV 118 (170)
Q Consensus 40 ~~~~v~~~SM~-P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~ 118 (170)
...+|.|+||. |++. +||++++++. .+++.||+|++... +...+||+.-..
T Consensus 115 f~l~V~GdSM~~~~i~-~Gd~viv~~~----~~~~~Gdivv~~~~---~~~~vKrl~~~~-------------------- 166 (202)
T PRK12423 115 YLLQVQGDSMIDDGIL-DGDLVGVHRS----PEARDGQIVVARLD---GEVTIKRLERSG-------------------- 166 (202)
T ss_pred EEEEEecCcCCCCCcC-CCCEEEEeCC----CcCCCCCEEEEEEC---CEEEEEEEEEeC--------------------
Confidence 35799999997 7998 9999999873 47889999999874 468899986532
Q ss_pred ecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEe
Q 030877 119 VPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIW 157 (170)
Q Consensus 119 ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~ 157 (170)
+.+++..+|+.. +...+-+-..-.|+|+++..+.
T Consensus 167 ---~~~~L~s~N~~y--~~i~~~~~~~~~I~Gvv~g~~r 200 (202)
T PRK12423 167 ---DRIRLLPRNPAY--APIVVAPDQDFAIEGVFCGLIR 200 (202)
T ss_pred ---CEEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEEEE
Confidence 356666777522 2222212123489999887653
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.78 E-value=0.00061 Score=52.83 Aligned_cols=88 Identities=22% Similarity=0.162 Sum_probs=64.2
Q ss_pred EEeEEEeCCCCc-ccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceE
Q 030877 39 CTPALAYGPSML-PTINLTGDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETV 117 (170)
Q Consensus 39 ~~~~~v~~~SM~-P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~ 117 (170)
....+|.|+||. +.+. +||+++|++. .+.+.||+|+...++ .+..+||..--
T Consensus 112 ~f~L~V~GdSM~~~gi~-dGDlvvV~~~----~~a~~GdiVvA~i~g--~e~TvKrl~~~-------------------- 164 (201)
T COG1974 112 TFFLRVSGDSMIDAGIL-DGDLVVVDPT----EDAENGDIVVALIDG--EEATVKRLYRD-------------------- 164 (201)
T ss_pred eEEEEecCCccccCcCC-CCCEEEEcCC----CCCCCCCEEEEEcCC--CcEEEEEEEEe--------------------
Confidence 445799999995 6665 8999999974 589999999999864 56788998652
Q ss_pred EecCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEEEEeCC
Q 030877 118 VVPQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFLRIWPP 159 (170)
Q Consensus 118 ~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~ 159 (170)
.+.+++.-.|+. +.+..+..- .-.|+|+++.++|+.
T Consensus 165 ---g~~i~L~p~Np~--~~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 165 ---GNQILLKPENPA--YPPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred ---CCEEEEEeCCCC--CCCcccCcc-ceEEEEEEEEEEecC
Confidence 245677767752 222333222 458999999998874
No 24
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=84.60 E-value=6.7 Score=28.25 Aligned_cols=56 Identities=11% Similarity=0.084 Sum_probs=41.0
Q ss_pred CCCcEEEEEcC--CCCCeeEEEEEEEeCCCE--EEEecCCCCCCCcceEEecCCeEEEEcC
Q 030877 73 CPGDVVLVRSP--VVPRRIVTKRVIGMEGDR--VSYVADPKSSDKFETVVVPQGHVWIEGD 129 (170)
Q Consensus 73 ~~GDiV~f~~p--~~~~~~~vkRVva~~GD~--v~i~~~~~~~~~~~~~~ip~~~y~vlgd 129 (170)
++||-|+++.+ ++.+.+++-+|+...+++ ..+.+..... ....++++..++..+-.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~-~~~~~~~~~~~iIPLP~ 60 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDGNRYEVEDPDPEE-EKKRYKLSRKQIIPLPK 60 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTTTEEEEEETTTCT-TTEEEEEEGGGEEEE-S
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCCCEEEEecCCCCC-CCceEEeCHHHEEECCC
Confidence 57999999876 455789999999998885 7776543332 33488999999999977
No 25
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=83.38 E-value=3.8 Score=28.64 Aligned_cols=38 Identities=18% Similarity=0.205 Sum_probs=25.4
Q ss_pred CCCCCCcEEEEEcCCCCCeeEEEEEEEe-CCCEEEEecC
Q 030877 70 NKVCPGDVVLVRSPVVPRRIVTKRVIGM-EGDRVSYVAD 107 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~~~~~~vkRVva~-~GD~v~i~~~ 107 (170)
..|++||+++|........-.|--|.++ .++++++.+.
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e~ 99 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIEQ 99 (124)
T ss_dssp S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEEC
T ss_pred cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEEC
Confidence 6899999999964333344578888888 8888887644
No 26
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=82.82 E-value=5.2 Score=28.72 Aligned_cols=55 Identities=16% Similarity=0.116 Sum_probs=31.3
Q ss_pred CCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEEecCCeEEEEcCCCCCCCCCCccccccCCCeE
Q 030877 70 NKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEGDNIYESNDSRKFGAVPYGLIE 149 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~I~ 149 (170)
.++++||+|+|+.. +.-.|.-+++..+ ..|.+.++|-|..+.. ..-..++++|+
T Consensus 72 ~~p~~GDiv~f~~~---~~~HVGi~~g~~~--------------------~~g~i~~lgGNq~~~V---~~~~~~~~~~~ 125 (129)
T TIGR02594 72 SKPAYGCIAVKRRG---GGGHVGFVVGKDK--------------------QTGTIIVLGGNQGDRV---REALYSRSRIV 125 (129)
T ss_pred CCCCccEEEEEECC---CCCEEEEEEeEcC--------------------CCCEEEEeeCCCCCeE---EEEEEecccEE
Confidence 47899999999853 2223444444322 1357888888864433 22233555555
Q ss_pred E
Q 030877 150 G 150 (170)
Q Consensus 150 G 150 (170)
|
T Consensus 126 ~ 126 (129)
T TIGR02594 126 A 126 (129)
T ss_pred E
Confidence 5
No 27
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=80.62 E-value=2.3 Score=31.01 Aligned_cols=13 Identities=23% Similarity=0.371 Sum_probs=11.1
Q ss_pred CCCCCcEEEEEcC
Q 030877 71 KVCPGDVVLVRSP 83 (170)
Q Consensus 71 ~~~~GDiV~f~~p 83 (170)
...+||+|+|+.+
T Consensus 84 ~~~~GD~i~~~~~ 96 (166)
T COG0681 84 IGLRGDIVVFKDD 96 (166)
T ss_pred ccCCCCEEEEECC
Confidence 5789999999974
No 28
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=59.08 E-value=64 Score=23.08 Aligned_cols=84 Identities=13% Similarity=-0.053 Sum_probs=42.0
Q ss_pred CCCCCCcEEEEEcCCCC----------CeeEEEEEEEeCCC-----EEEEecCCCCCCCcceEEecCCeEEEEcCCCCCC
Q 030877 70 NKVCPGDVVLVRSPVVP----------RRIVTKRVIGMEGD-----RVSYVADPKSSDKFETVVVPQGHVWIEGDNIYES 134 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~~----------~~~~vkRVva~~GD-----~v~i~~~~~~~~~~~~~~ip~~~y~vlgdn~~~s 134 (170)
..++.||+|+++.++.. ...+|-||..+.-+ .+..+=--...+..-.-.-.+.++|+.......+
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~~~~~~ElFLSd~c~~~~ 83 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGNYANERELFLTNECTCLE 83 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccccCCCceEEEeccccccc
Confidence 35778888888876433 24567777655433 1111000000011111144567777763332222
Q ss_pred CCCCccccccCCCeEEEEEEEEeCC
Q 030877 135 NDSRKFGAVPYGLIEGRVFLRIWPP 159 (170)
Q Consensus 135 ~DSR~~G~V~~~~I~Gkv~~~~~p~ 159 (170)
.++. .+.|+||+..-+.+.
T Consensus 84 ~~~~------~~~I~~k~~V~~~~~ 102 (130)
T cd04712 84 LDLL------STEIKGVHKVDWSGT 102 (130)
T ss_pred cccc------cceeEEEEEEEEecC
Confidence 2222 569999987765543
No 29
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=55.87 E-value=62 Score=22.99 Aligned_cols=27 Identities=26% Similarity=0.298 Sum_probs=18.5
Q ss_pred cCCeEEEEcCCCCCCCCCCccccccCCC
Q 030877 120 PQGHVWIEGDNIYESNDSRKFGAVPYGL 147 (170)
Q Consensus 120 p~~~y~vlgdn~~~s~DSR~~G~V~~~~ 147 (170)
.+|.+-++.++ .+..-+|-||||.+|.
T Consensus 80 ddNA~Viin~~-g~P~GtrI~GPVaREl 106 (122)
T COG0093 80 DDNAAVIINPD-GEPRGTRIFGPVAREL 106 (122)
T ss_pred CCceEEEECCC-CCcccceEecchhHHH
Confidence 34455555555 3778899999998863
No 30
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=52.84 E-value=7.9 Score=24.94 Aligned_cols=18 Identities=33% Similarity=0.545 Sum_probs=12.2
Q ss_pred CCCcccCCCCCcEEEEEec
Q 030877 47 PSMLPTINLTGDLVLAERI 65 (170)
Q Consensus 47 ~SM~P~l~~~Gd~v~v~~~ 65 (170)
.||+|.++ +|++|++.--
T Consensus 12 ~~m~P~L~-~~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELN-PGEYVFCTVP 29 (72)
T ss_dssp ST-EEEE--SS-EEEEEE-
T ss_pred hhCCcEeC-CCCEEEEEec
Confidence 58999999 9999998653
No 31
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=52.63 E-value=17 Score=23.64 Aligned_cols=20 Identities=35% Similarity=0.547 Sum_probs=9.6
Q ss_pred CCcEEEEEeccCCCCCCCCCcEE
Q 030877 56 TGDLVLAERISTRFNKVCPGDVV 78 (170)
Q Consensus 56 ~Gd~v~v~~~~~~~~~~~~GDiV 78 (170)
+||.|++...++ +..+||++
T Consensus 49 ~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 49 PGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred CCCEEEEEeccc---ccccccEE
Confidence 455555555442 34455543
No 32
>smart00439 BAH Bromo adjacent homology domain.
Probab=52.38 E-value=70 Score=21.56 Aligned_cols=15 Identities=27% Similarity=0.297 Sum_probs=11.6
Q ss_pred cccCCCeEEEEEEEE
Q 030877 142 AVPYGLIEGRVFLRI 156 (170)
Q Consensus 142 ~V~~~~I~Gkv~~~~ 156 (170)
-++.+.|+|++.-..
T Consensus 70 ~i~~~~I~~kc~V~~ 84 (120)
T smart00439 70 TVPLSDIIGKCNVLS 84 (120)
T ss_pred cCChHHeeeEEEEEE
Confidence 688889999986644
No 33
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=51.56 E-value=15 Score=24.02 Aligned_cols=11 Identities=27% Similarity=0.573 Sum_probs=7.4
Q ss_pred CCCCcEEEEEc
Q 030877 72 VCPGDVVLVRS 82 (170)
Q Consensus 72 ~~~GDiV~f~~ 82 (170)
+++||+|+.+.
T Consensus 39 I~~GD~VlV~~ 49 (78)
T cd04456 39 IKRGDFLIVDP 49 (78)
T ss_pred EcCCCEEEEEe
Confidence 56777777764
No 34
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=50.93 E-value=17 Score=23.15 Aligned_cols=11 Identities=45% Similarity=0.661 Sum_probs=5.7
Q ss_pred CCCCcEEEEEc
Q 030877 72 VCPGDVVLVRS 82 (170)
Q Consensus 72 ~~~GDiV~f~~ 82 (170)
+..||.|.++.
T Consensus 45 I~~GD~V~Ve~ 55 (68)
T TIGR00008 45 ILPGDKVKVEL 55 (68)
T ss_pred ECCCCEEEEEE
Confidence 44555555543
No 35
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=46.78 E-value=16 Score=22.75 Aligned_cols=13 Identities=38% Similarity=0.496 Sum_probs=7.5
Q ss_pred CCCCCcEEEEEcC
Q 030877 71 KVCPGDVVLVRSP 83 (170)
Q Consensus 71 ~~~~GDiV~f~~p 83 (170)
-+++||.|.+...
T Consensus 41 wI~~GD~V~V~~~ 53 (65)
T PF01176_consen 41 WIKRGDFVLVEPS 53 (65)
T ss_dssp ---TTEEEEEEES
T ss_pred ecCCCCEEEEEec
Confidence 4688888888753
No 36
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.18 E-value=13 Score=26.26 Aligned_cols=17 Identities=35% Similarity=0.548 Sum_probs=14.7
Q ss_pred CCCcccCCCCCcEEEEEe
Q 030877 47 PSMLPTINLTGDLVLAER 64 (170)
Q Consensus 47 ~SM~P~l~~~Gd~v~v~~ 64 (170)
.||+|.+. +||+|+..-
T Consensus 12 ~smtPeL~-~G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELL-DGDYVFCTV 28 (134)
T ss_pred HhcCcccc-CCceEEEEe
Confidence 37999999 999999864
No 37
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=45.07 E-value=77 Score=26.42 Aligned_cols=14 Identities=29% Similarity=0.264 Sum_probs=10.2
Q ss_pred EEEEEEEeCCCEEE
Q 030877 90 VTKRVIGMEGDRVS 103 (170)
Q Consensus 90 ~vkRVva~~GD~v~ 103 (170)
.++++...+||+|.
T Consensus 71 ~V~~v~v~~G~~V~ 84 (370)
T PRK11578 71 QLKTLSVAIGDKVK 84 (370)
T ss_pred EEEEEEcCCCCEEc
Confidence 56677777888774
No 38
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=44.46 E-value=98 Score=23.17 Aligned_cols=39 Identities=28% Similarity=0.343 Sum_probs=28.5
Q ss_pred CCCCCCCCCcEEEEEcCCCCCeeEEEE---EEEeCCCEEEEecC
Q 030877 67 TRFNKVCPGDVVLVRSPVVPRRIVTKR---VIGMEGDRVSYVAD 107 (170)
Q Consensus 67 ~~~~~~~~GDiV~f~~p~~~~~~~vkR---Vva~~GD~v~i~~~ 107 (170)
|+.+.++.||+.+|.... ....+|| ++.+.++++.+...
T Consensus 70 yR~~~L~~GEvalY~~~G--~~I~L~~~G~ii~~~~~~~~v~a~ 111 (162)
T PF06890_consen 70 YRPKGLKPGEVALYDDEG--QKIHLKRDGRIIEVTCKTVTVNAA 111 (162)
T ss_pred ccccCCCCCcEEEEcCCC--CEEEEEecceEEeccCceEEEecC
Confidence 445678999999999643 4455654 77888899888743
No 39
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=42.08 E-value=40 Score=22.83 Aligned_cols=26 Identities=23% Similarity=0.258 Sum_probs=20.1
Q ss_pred CCCCcEEEEEcCCCCCeeEEEEEEEe
Q 030877 72 VCPGDVVLVRSPVVPRRIVTKRVIGM 97 (170)
Q Consensus 72 ~~~GDiV~f~~p~~~~~~~vkRVva~ 97 (170)
++.||.|.+..+.......+.||..+
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i 28 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEI 28 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEE
Confidence 56889998888765677888888665
No 40
>COG3944 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]
Probab=41.71 E-value=1.4e+02 Score=23.59 Aligned_cols=16 Identities=19% Similarity=0.389 Sum_probs=12.1
Q ss_pred CcccCCCCCcEEEEEec
Q 030877 49 MLPTINLTGDLVLAERI 65 (170)
Q Consensus 49 M~P~l~~~Gd~v~v~~~ 65 (170)
+.|+++ ....++|+..
T Consensus 40 i~P~Yq-ssTqilV~~~ 55 (226)
T COG3944 40 IKPTYQ-SSTQILVNQS 55 (226)
T ss_pred cCcccc-cceEEEEecc
Confidence 478898 7777787663
No 41
>PF12459 DUF3687: D-Ala-teichoic acid biosynthesis protein; InterPro: IPR021008 Proteins in this family are bacterial proteins of approximately 50 amino acids in length. There are two completely conserved residues (L and Y) that may be functionally important. A number of entries are annotated as D-Ala-teichoic acid biosynthesis protein; however there is no direct evidence to support this annotation.
Probab=41.61 E-value=52 Score=18.95 Aligned_cols=25 Identities=4% Similarity=-0.229 Sum_probs=14.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Q 030877 8 SLFVTFAKEGFEKSLLVGKFFCCLH 32 (170)
Q Consensus 8 ~~~~~~~~~~~~~~~~l~~~~~~~~ 32 (170)
..+++..+-+.++++.++++++++.
T Consensus 2 ~~~~~~~~fi~~T~fYf~Ill~L~y 26 (42)
T PF12459_consen 2 IKQKPAVKFIGKTLFYFAILLALIY 26 (42)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666666666555555443
No 42
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=41.43 E-value=24 Score=22.96 Aligned_cols=11 Identities=45% Similarity=0.782 Sum_probs=7.6
Q ss_pred CCCCcEEEEEc
Q 030877 72 VCPGDVVLVRS 82 (170)
Q Consensus 72 ~~~GDiV~f~~ 82 (170)
+++||.|.++.
T Consensus 39 I~~GD~V~Ve~ 49 (77)
T cd05793 39 INEGDIVLVAP 49 (77)
T ss_pred EcCCCEEEEEe
Confidence 56777777764
No 43
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=40.58 E-value=48 Score=24.38 Aligned_cols=39 Identities=5% Similarity=-0.016 Sum_probs=28.1
Q ss_pred EEEeCCCCcccCCCCCcEEEEEeccCCCCCCCCCcEEEEEcC
Q 030877 42 ALAYGPSMLPTINLTGDLVLAERISTRFNKVCPGDVVLVRSP 83 (170)
Q Consensus 42 ~~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~p 83 (170)
....+++|...|. +.-+..+..-. ..++++|||+++...
T Consensus 49 ~~~nT~tl~~~L~-~~G~~~I~~~~--~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 49 SAGNTETLHDWLK-KNGFKKISENV--DWNLQRGDIFIWGRR 87 (145)
T ss_pred CccCHHHHHHHHh-hCCcEEeccCC--cccccCCCEEEEcCC
Confidence 3567888989887 66666665421 137899999998665
No 44
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=40.12 E-value=26 Score=23.16 Aligned_cols=11 Identities=45% Similarity=0.767 Sum_probs=8.1
Q ss_pred CCCCcEEEEEc
Q 030877 72 VCPGDVVLVRS 82 (170)
Q Consensus 72 ~~~GDiV~f~~ 82 (170)
+++||+|+++.
T Consensus 44 I~~GD~VlVe~ 54 (83)
T smart00652 44 IRRGDIVLVDP 54 (83)
T ss_pred EcCCCEEEEEe
Confidence 67788887764
No 45
>PRK10507 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional
Probab=39.30 E-value=1.4e+02 Score=27.27 Aligned_cols=58 Identities=10% Similarity=0.075 Sum_probs=37.8
Q ss_pred CCCCCCcEEEEEcC-CCCCeeEEEEEEEeCCCEEEEecCCCC---------CCCcceEEecCCeEEEE
Q 030877 70 NKVCPGDVVLVRSP-VVPRRIVTKRVIGMEGDRVSYVADPKS---------SDKFETVVVPQGHVWIE 127 (170)
Q Consensus 70 ~~~~~GDiV~f~~p-~~~~~~~vkRVva~~GD~v~i~~~~~~---------~~~~~~~~ip~~~y~vl 127 (170)
..|+.||+++|... +....=.|--|+.+..+.|.|.+.... -....+++..+|.|++.
T Consensus 110 ~~P~~gdLlI~~~~~~~~p~GHVAVVt~V~~~~V~iaeQN~~~~~w~~~~~~sR~l~l~~~~g~~~i~ 177 (619)
T PRK10507 110 RAPEAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLK 177 (619)
T ss_pred CCCCCCcEEEeCCCCCCCCCceEEEEEEEcCCeEEEEeccccccCCCCCCCeeeEEEEEEeCCEEEEE
Confidence 58999999999853 212223566778888999998654221 11224455567888886
No 46
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=38.08 E-value=50 Score=23.16 Aligned_cols=27 Identities=30% Similarity=0.401 Sum_probs=20.3
Q ss_pred CCCCCcEEEEEcCCCCCeeEEEEEEEe
Q 030877 71 KVCPGDVVLVRSPVVPRRIVTKRVIGM 97 (170)
Q Consensus 71 ~~~~GDiV~f~~p~~~~~~~vkRVva~ 97 (170)
.++.||-|.++.++.+...+|.||..+
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i 29 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESL 29 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEE
Confidence 467899999998765566788888654
No 47
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=36.88 E-value=1.1e+02 Score=19.67 Aligned_cols=34 Identities=21% Similarity=0.257 Sum_probs=24.0
Q ss_pred CCCCCCcEEEEEcCCCCCeeEEEEEE--------EeCCCEEEEe
Q 030877 70 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 105 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~~~~~~vkRVv--------a~~GD~v~i~ 105 (170)
..++.||-+.+.+.. ....+|.+- |.+||.+.+.
T Consensus 25 G~v~~Gd~v~~~P~~--~~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 25 GSIRVGDEVVVLPSG--KTSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred ceEECCCEEEEcCCC--CeEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 578888888886532 345666665 8888888775
No 48
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=36.80 E-value=59 Score=25.58 Aligned_cols=19 Identities=0% Similarity=-0.057 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 030877 12 TFAKEGFEKSLLVGKFFCC 30 (170)
Q Consensus 12 ~~~~~~~~~~~~l~~~~~~ 30 (170)
+-...+|+.++.+++++++
T Consensus 10 RK~N~iLNiaI~IV~lLIi 28 (217)
T PF07423_consen 10 RKTNKILNIAIGIVSLLII 28 (217)
T ss_pred hhhhhhHHHHHHHHHHHHH
Confidence 3444556554444443333
No 49
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=36.54 E-value=42 Score=22.50 Aligned_cols=11 Identities=27% Similarity=0.407 Sum_probs=5.7
Q ss_pred CCCCcEEEEEc
Q 030877 72 VCPGDVVLVRS 82 (170)
Q Consensus 72 ~~~GDiV~f~~ 82 (170)
+..||.|.++.
T Consensus 47 Il~GD~V~VE~ 57 (87)
T PRK12442 47 ILAGDRVTLEL 57 (87)
T ss_pred ecCCCEEEEEE
Confidence 44555555543
No 50
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=35.06 E-value=99 Score=22.08 Aligned_cols=25 Identities=16% Similarity=0.095 Sum_probs=16.1
Q ss_pred CCCCCcEEEEEcCCCCCeeEEEEEEEe
Q 030877 71 KVCPGDVVLVRSPVVPRRIVTKRVIGM 97 (170)
Q Consensus 71 ~~~~GDiV~f~~p~~~~~~~vkRVva~ 97 (170)
.++.||.|.+..++ +...+.+|-.+
T Consensus 7 ~i~vGD~V~v~~~~--~~~~va~Ie~i 31 (130)
T cd04721 7 TISVHDFVYVLSEE--EDRYVAYIEDL 31 (130)
T ss_pred EEECCCEEEEeCCC--CCcEEEEEEEE
Confidence 47889999998654 33345555443
No 51
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=34.71 E-value=35 Score=23.44 Aligned_cols=11 Identities=45% Similarity=0.742 Sum_probs=7.8
Q ss_pred CCCCcEEEEEc
Q 030877 72 VCPGDVVLVRS 82 (170)
Q Consensus 72 ~~~GDiV~f~~ 82 (170)
+++||+|++..
T Consensus 60 I~~GD~VlVe~ 70 (100)
T PRK04012 60 IREGDVVIVAP 70 (100)
T ss_pred ecCCCEEEEEe
Confidence 57777777764
No 52
>PLN03148 Blue copper-like protein; Provisional
Probab=34.64 E-value=2e+02 Score=21.67 Aligned_cols=15 Identities=20% Similarity=0.306 Sum_probs=12.8
Q ss_pred CCCCCCcEEEEEcCC
Q 030877 70 NKVCPGDVVLVRSPV 84 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~ 84 (170)
+.++.||.++|+...
T Consensus 44 k~F~VGD~LvF~Y~~ 58 (167)
T PLN03148 44 QTFYVGDLISFRYQK 58 (167)
T ss_pred CCCccCCEEEEEecC
Confidence 579999999999753
No 53
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=33.87 E-value=31 Score=22.59 Aligned_cols=39 Identities=28% Similarity=0.365 Sum_probs=20.6
Q ss_pred EEeCCCCcccCCCCCcEEEEEeccCCCCC---CCCCcEEEEEc
Q 030877 43 LAYGPSMLPTINLTGDLVLAERISTRFNK---VCPGDVVLVRS 82 (170)
Q Consensus 43 ~v~~~SM~P~l~~~Gd~v~v~~~~~~~~~---~~~GDiV~f~~ 82 (170)
...|++..-...++|...++.. +..|+. +++||+|+..+
T Consensus 8 ~~~G~n~~~V~~~dG~~~l~~i-P~KfRk~iWIkrGd~VlV~p 49 (78)
T cd05792 8 GSKGNNLHEVETPNGSRYLVSM-PTKFRKNIWIKRGDFVLVEP 49 (78)
T ss_pred EcCCCcEEEEEcCCCCEEEEEe-chhhcccEEEEeCCEEEEEe
Confidence 3344443333334666666542 222332 68888888865
No 54
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=33.56 E-value=1.9e+02 Score=22.13 Aligned_cols=15 Identities=27% Similarity=0.332 Sum_probs=10.4
Q ss_pred CCCCCCcEEEEEcCC
Q 030877 70 NKVCPGDVVLVRSPV 84 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~ 84 (170)
..|+.||+|.+....
T Consensus 92 y~P~~GDlIc~~R~~ 106 (183)
T PF10030_consen 92 YKPRPGDLICYDRGR 106 (183)
T ss_pred CCCCCCCEEEecCCC
Confidence 367888888876543
No 55
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=33.10 E-value=2.1e+02 Score=21.50 Aligned_cols=19 Identities=21% Similarity=0.176 Sum_probs=12.9
Q ss_pred EeEEEeCCCCcccCCCCCcEEEEE
Q 030877 40 TPALAYGPSMLPTINLTGDLVLAE 63 (170)
Q Consensus 40 ~~~~v~~~SM~P~l~~~Gd~v~v~ 63 (170)
..|.+. ..| ++ .||+|++.
T Consensus 42 glY~~~---~~~-~~-~Gd~V~f~ 60 (178)
T PRK13884 42 GLYWTS---SAP-VE-KGAYVLFC 60 (178)
T ss_pred eEEEEe---CCC-CC-CCCEEEEe
Confidence 356664 334 66 89999986
No 56
>PRK00969 hypothetical protein; Provisional
Probab=31.53 E-value=2.5e+02 Score=25.09 Aligned_cols=37 Identities=24% Similarity=0.258 Sum_probs=26.4
Q ss_pred EEecCCeEEEEcCCCC-------CCCCCCcccc----ccCCCeEEEEE
Q 030877 117 VVVPQGHVWIEGDNIY-------ESNDSRKFGA----VPYGLIEGRVF 153 (170)
Q Consensus 117 ~~ip~~~y~vlgdn~~-------~s~DSR~~G~----V~~~~I~Gkv~ 153 (170)
-.++.|.+=+-++.+. +.-||..||| ..-.+|+||++
T Consensus 440 ~~V~ag~IgvTN~a~k~~G~iGVR~~d~d~fGPTGE~F~gTNIIGrVv 487 (508)
T PRK00969 440 DKVKAGEIGVTNMAAKYKGMIGVRLSDNDEFGPTGEPFEGTNIIGRVV 487 (508)
T ss_pred CccccceEeeechhhhcCceEEEEccCCcccCCCCCCccCceeEEEec
Confidence 3566666666666653 3458888996 67789999976
No 57
>PF13172 PepSY_TM_1: PepSY-associated TM helix
Probab=31.26 E-value=89 Score=16.60 Aligned_cols=25 Identities=16% Similarity=0.107 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 030877 11 VTFAKEGFEKSLLVGKFFCCLHVVN 35 (170)
Q Consensus 11 ~~~~~~~~~~~~~l~~~~~~~~~~~ 35 (170)
++..+++-+++.+++.+.++++.+.
T Consensus 2 r~~~~~~H~~~g~~~~~~ll~~~lT 26 (34)
T PF13172_consen 2 RKFWRKIHRWLGLIAAIFLLLLALT 26 (34)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666555555555554443
No 58
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=30.55 E-value=78 Score=20.05 Aligned_cols=12 Identities=42% Similarity=0.703 Sum_probs=9.9
Q ss_pred CCCCCcEEEEEc
Q 030877 71 KVCPGDVVLVRS 82 (170)
Q Consensus 71 ~~~~GDiV~f~~ 82 (170)
.+..||.|.++.
T Consensus 46 ~i~vGD~V~ve~ 57 (72)
T PRK00276 46 RILPGDKVTVEL 57 (72)
T ss_pred ccCCCCEEEEEE
Confidence 378899999984
No 59
>PF10913 DUF2706: Protein of unknown function (DUF2706); InterPro: IPR024444 This family of proteins with unknown function appears to be restricted to Rickettsia spp.
Probab=30.39 E-value=74 Score=19.21 Aligned_cols=44 Identities=7% Similarity=0.060 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHhhceEEeEEEeCCCCcccCCCCCcEEEEEe
Q 030877 20 KSLLVGKFFCCLHVVNTYVCTPALAYGPSMLPTINLTGDLVLAER 64 (170)
Q Consensus 20 ~~~~l~~~~~~~~~~~~~~~~~~~v~~~SM~P~l~~~Gd~v~v~~ 64 (170)
.+.++++++++.-++...-..+|.+.+.-..|.+. ++.-+-+++
T Consensus 4 ~lkf~lv~imlaqllsctpsapyeikspcvs~did-d~s~ls~np 47 (60)
T PF10913_consen 4 SLKFLLVLIMLAQLLSCTPSAPYEIKSPCVSADID-DNSSLSVNP 47 (60)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCccccCCccccccC-CCccccccc
Confidence 34455556666666655556678888888888887 777666654
No 60
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=30.10 E-value=1.5e+02 Score=18.88 Aligned_cols=34 Identities=21% Similarity=0.379 Sum_probs=23.8
Q ss_pred CCCCCCcEEEEEcCCCCCeeEEEEEE--------EeCCCEEEEe
Q 030877 70 NKVCPGDVVLVRSPVVPRRIVTKRVI--------GMEGDRVSYV 105 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~~~~~~vkRVv--------a~~GD~v~i~ 105 (170)
..++.||-|.+.+.. ...-+|.+. |.+||.+.+.
T Consensus 25 G~i~~Gd~v~i~P~~--~~~~V~si~~~~~~~~~a~aGd~v~~~ 66 (83)
T cd03698 25 GSIQKGDTLLVMPSK--ESVEVKSIYVDDEEVDYAVAGENVRLK 66 (83)
T ss_pred eEEeCCCEEEEeCCC--cEEEEEEEEECCeECCEECCCCEEEEE
Confidence 578888888886532 345666665 8888888764
No 61
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=30.05 E-value=74 Score=18.66 Aligned_cols=7 Identities=0% Similarity=-0.040 Sum_probs=2.7
Q ss_pred HHHHHHH
Q 030877 10 FVTFAKE 16 (170)
Q Consensus 10 ~~~~~~~ 16 (170)
|+...++
T Consensus 5 ~~~~~~~ 11 (56)
T PF12911_consen 5 WKDAWRR 11 (56)
T ss_pred HHHHHHH
Confidence 3333333
No 62
>PF12059 DUF3540: Protein of unknown function (DUF3540); InterPro: IPR021927 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Probab=29.82 E-value=2.1e+02 Score=22.11 Aligned_cols=26 Identities=31% Similarity=0.399 Sum_probs=22.5
Q ss_pred CCcEEEEEeccCCCCCCCCCcEEEEEc
Q 030877 56 TGDLVLAERISTRFNKVCPGDVVLVRS 82 (170)
Q Consensus 56 ~Gd~v~v~~~~~~~~~~~~GDiV~f~~ 82 (170)
.|. +-..+...|.-.|..||.|++..
T Consensus 20 ~G~-~~arrAaSCLl~P~~GD~VLv~~ 45 (202)
T PF12059_consen 20 DGE-WRARRAASCLLEPAVGDTVLVSG 45 (202)
T ss_pred CCE-EEEEeccccccCCCCCCEEEEee
Confidence 677 78888888888999999999965
No 63
>PF15428 Imm14: Immunity protein 14
Probab=29.79 E-value=84 Score=21.93 Aligned_cols=22 Identities=32% Similarity=0.450 Sum_probs=16.9
Q ss_pred CCCcEEEEEcCCCCCeeEEEEEEE
Q 030877 73 CPGDVVLVRSPVVPRRIVTKRVIG 96 (170)
Q Consensus 73 ~~GDiV~f~~p~~~~~~~vkRVva 96 (170)
|.||+..+..+ .+.+...||++
T Consensus 1 K~GDIF~ipL~--~~~y~~G~Vi~ 22 (129)
T PF15428_consen 1 KPGDIFCIPLD--DGKYGFGRVIG 22 (129)
T ss_pred CCceEEEEEcC--CCCEEEEEEEe
Confidence 57999999876 36778888883
No 64
>CHL00010 infA translation initiation factor 1
Probab=29.72 E-value=82 Score=20.37 Aligned_cols=24 Identities=25% Similarity=0.366 Sum_probs=14.4
Q ss_pred CCCCCcEEEEEc--CCCCCeeEEEEE
Q 030877 71 KVCPGDVVLVRS--PVVPRRIVTKRV 94 (170)
Q Consensus 71 ~~~~GDiV~f~~--p~~~~~~~vkRV 94 (170)
.|..||.|.|+. .++....++.|-
T Consensus 46 ~~~vGD~V~ve~~~~~~~~g~Ii~r~ 71 (78)
T CHL00010 46 RILPGDRVKVELSPYDLTKGRIIYRL 71 (78)
T ss_pred ccCCCCEEEEEEcccCCCeEEEEEEe
Confidence 367899999984 222234455543
No 65
>CHL00038 psbL photosystem II protein L
Probab=28.54 E-value=1.1e+02 Score=16.98 Aligned_cols=27 Identities=15% Similarity=0.059 Sum_probs=14.0
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHH
Q 030877 4 RNQLSLFVTFAKEGFEKSLLVGKFFCC 30 (170)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~l~~~~~~ 30 (170)
+|+=++-..+-|.-+-|-++++.++++
T Consensus 4 ~NPN~q~VELNRTSLy~GLLlifvl~v 30 (38)
T CHL00038 4 SNPNKQNVELNRTSLYWGLLLIFVLAV 30 (38)
T ss_pred CCCCCCccchhhhhHHHHHHHHHHHHH
Confidence 444445555566656555555444444
No 66
>smart00831 Cation_ATPase_N Cation transporter/ATPase, N-terminus. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+, Na+, Ca2+, Na+/K+, and H+/K+. In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases PUBMED:12480547, PUBMED:12529322.
Probab=27.32 E-value=1.4e+02 Score=17.75 Aligned_cols=27 Identities=11% Similarity=0.047 Sum_probs=15.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 030877 7 LSLFVTFAKEGFEKSLLVGKFFCCLHV 33 (170)
Q Consensus 7 ~~~~~~~~~~~~~~~~~l~~~~~~~~~ 33 (170)
-..|+.+++.+...+.+++++++++.+
T Consensus 34 ~s~~~~~l~~~~~p~~~iL~~~a~is~ 60 (64)
T smart00831 34 RSPLLRFLRQFHNPLIYILLAAAVLSA 60 (64)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 455666666666655555555444443
No 67
>PF13800 Sigma_reg_N: Sigma factor regulator N-terminal
Probab=27.17 E-value=1.6e+02 Score=19.50 Aligned_cols=7 Identities=0% Similarity=-0.244 Sum_probs=2.7
Q ss_pred HHHHHHH
Q 030877 10 FVTFAKE 16 (170)
Q Consensus 10 ~~~~~~~ 16 (170)
|+..++.
T Consensus 10 ~k~~l~~ 16 (96)
T PF13800_consen 10 RKSRLRT 16 (96)
T ss_pred HHHHHHH
Confidence 3333433
No 68
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=26.82 E-value=94 Score=21.54 Aligned_cols=26 Identities=27% Similarity=0.365 Sum_probs=17.2
Q ss_pred CCCCCcEEEEEcCCCCCeeEEEEEEE
Q 030877 71 KVCPGDVVLVRSPVVPRRIVTKRVIG 96 (170)
Q Consensus 71 ~~~~GDiV~f~~p~~~~~~~vkRVva 96 (170)
.++.||.|.+..+.++....+.||..
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~ 28 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIER 28 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeE
Confidence 35678888888765545556666644
No 69
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=26.34 E-value=1.4e+02 Score=20.81 Aligned_cols=26 Identities=15% Similarity=0.256 Sum_probs=16.6
Q ss_pred CCCCCCcEEEEEcCCCCCeeEEEEEEE
Q 030877 70 NKVCPGDVVLVRSPVVPRRIVTKRVIG 96 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~~~~~~vkRVva 96 (170)
+.++.||.++|..-.+ +..+.-+|+.
T Consensus 30 ~~ikvGD~I~f~~~~~-~~~l~v~V~~ 55 (109)
T cd06555 30 QQIKVGDKILFNDLDT-GQQLLVKVVD 55 (109)
T ss_pred hcCCCCCEEEEEEcCC-CcEEEEEEEE
Confidence 4799999999986433 3334444443
No 70
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=25.63 E-value=2.4e+02 Score=19.63 Aligned_cols=46 Identities=17% Similarity=0.190 Sum_probs=28.3
Q ss_pred CcEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCC-EEEE
Q 030877 57 GDLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGD-RVSY 104 (170)
Q Consensus 57 Gd~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD-~v~i 104 (170)
++...+...+.-...+..||+|.++..+ +...+.+++.-.|. |+.+
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~--g~~~~~~~v~~sGnsTiRv 57 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDD--GELWFQKVVESSGNSTIRV 57 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCC--CeEEEEEEEecCCCEEEEE
Confidence 4444555444434678999999999764 55555555554444 4554
No 71
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=24.52 E-value=1.8e+02 Score=18.92 Aligned_cols=29 Identities=34% Similarity=0.462 Sum_probs=15.5
Q ss_pred CCCCCcEEEEEcCC-----CCCeeEEEEEEEeCC
Q 030877 71 KVCPGDVVLVRSPV-----VPRRIVTKRVIGMEG 99 (170)
Q Consensus 71 ~~~~GDiV~f~~p~-----~~~~~~vkRVva~~G 99 (170)
..+.||.|+++... ......+..|+...|
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~g 38 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEG 38 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEec
Confidence 45666666666542 123455555555444
No 72
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=24.41 E-value=69 Score=21.36 Aligned_cols=24 Identities=29% Similarity=0.237 Sum_probs=13.2
Q ss_pred CCCCCcEEEEEcCCCCCeeEEEEEEEeCCC
Q 030877 71 KVCPGDVVLVRSPVVPRRIVTKRVIGMEGD 100 (170)
Q Consensus 71 ~~~~GDiV~f~~p~~~~~~~vkRVva~~GD 100 (170)
+++.||+|+|.. .+.++|..-.+|
T Consensus 69 ~p~~G~lvlFPs------~l~H~v~p~~~~ 92 (101)
T PF13759_consen 69 EPEEGDLVLFPS------WLWHGVPPNNSD 92 (101)
T ss_dssp ---TTEEEEEET------TSEEEE----SS
T ss_pred CCCCCEEEEeCC------CCEEeccCcCCC
Confidence 688999999984 466777666665
No 73
>PF09163 Form-deh_trans: Formate dehydrogenase N, transmembrane; InterPro: IPR015246 The transmembrane domain of the beta subunit of formate dehydrogenase consists of a single transmembrane helix. This domain acts as a transmembrane anchor, allowing the conduction of electrons within the protein []. ; PDB: 1KQG_B 1KQF_B.
Probab=24.17 E-value=1.4e+02 Score=17.27 Aligned_cols=28 Identities=18% Similarity=-0.017 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhce
Q 030877 11 VTFAKEGFEKSLLVGKFFCCLHVVNTYV 38 (170)
Q Consensus 11 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 38 (170)
.++.|.+++.+..+++.+.++..+..|+
T Consensus 5 V~lWKg~~Kpl~~~~~~~~~~~~~~Hyi 32 (44)
T PF09163_consen 5 VTLWKGVLKPLGAAGMGATAAAGFFHYI 32 (44)
T ss_dssp HHHHHTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 3456667777777777777766666654
No 74
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=24.08 E-value=94 Score=18.93 Aligned_cols=12 Identities=42% Similarity=0.672 Sum_probs=9.9
Q ss_pred CCCCCcEEEEEc
Q 030877 71 KVCPGDVVLVRS 82 (170)
Q Consensus 71 ~~~~GDiV~f~~ 82 (170)
.+..||.|.++.
T Consensus 40 ~~~vGD~V~~~~ 51 (64)
T cd04451 40 RILPGDRVKVEL 51 (64)
T ss_pred ccCCCCEEEEEE
Confidence 478899999984
No 75
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=23.72 E-value=1.2e+02 Score=21.45 Aligned_cols=13 Identities=38% Similarity=0.690 Sum_probs=11.1
Q ss_pred CCCCCCcEEEEEc
Q 030877 70 NKVCPGDVVLVRS 82 (170)
Q Consensus 70 ~~~~~GDiV~f~~ 82 (170)
.++++||+|.|..
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 4789999999974
No 76
>cd03584 NTR_complement_C4 NTR/C345C domain, complement C4 subfamily; The NTR domain found in complement C4 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C4 is a key player in the activation of the component classical pathway. C4 is cleaved by activated C1 to yield C4a anaphylatoxin, and the larger fragment C4b, an essential component of the C3- and C5-convertase enzymes. C4b binds covalently to the surface of pathogens through a reactive thioester. The role of the NTR/C345C domain in C4 (C4b) is unclear.
Probab=23.16 E-value=3.1e+02 Score=20.10 Aligned_cols=35 Identities=17% Similarity=0.158 Sum_probs=20.6
Q ss_pred cCCeEEEEcCCCCCCCCCCccccccCCCeEEEEEE-EEeCC
Q 030877 120 PQGHVWIEGDNIYESNDSRKFGAVPYGLIEGRVFL-RIWPP 159 (170)
Q Consensus 120 p~~~y~vlgdn~~~s~DSR~~G~V~~~~I~Gkv~~-~~~p~ 159 (170)
+..+|++||.+. ...|.+ | +...++|.=.| -.||-
T Consensus 90 ~gk~YLImG~~~-~~~~~~--~--~~~Y~L~~~tWvE~wP~ 125 (153)
T cd03584 90 KGKEYLIMGKDG-ATSDSN--G--HMQYLLDSKTWVEKIPS 125 (153)
T ss_pred CCCEEEEEcCCC-CCcCcC--C--cEEEEeCCCceEEECCC
Confidence 667899999865 323332 2 23556665444 34776
No 77
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=22.69 E-value=1.1e+02 Score=20.68 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=20.3
Q ss_pred ccCCCCCcEEEEEeccCC-----CCCCCCCcEEEEEc
Q 030877 51 PTINLTGDLVLAERISTR-----FNKVCPGDVVLVRS 82 (170)
Q Consensus 51 P~l~~~Gd~v~v~~~~~~-----~~~~~~GDiV~f~~ 82 (170)
-++. +|-.++++...+. -..++.||+|+|-+
T Consensus 56 g~lr-pGiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 56 GELR-PGIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred CCCc-ccEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 4455 6777788765543 13568888888864
No 78
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=22.51 E-value=22 Score=22.10 Aligned_cols=20 Identities=30% Similarity=0.732 Sum_probs=16.0
Q ss_pred CCCCCCccccccCCCeEEEE
Q 030877 133 ESNDSRKFGAVPYGLIEGRV 152 (170)
Q Consensus 133 ~s~DSR~~G~V~~~~I~Gkv 152 (170)
-+.|-|.||.+|-++.=||+
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 37899999999877766764
No 79
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=22.49 E-value=56 Score=23.21 Aligned_cols=28 Identities=21% Similarity=0.252 Sum_probs=22.3
Q ss_pred EecCCeEEEEcCCCCCCCCCCccccccCC
Q 030877 118 VVPQGHVWIEGDNIYESNDSRKFGAVPYG 146 (170)
Q Consensus 118 ~ip~~~y~vlgdn~~~s~DSR~~G~V~~~ 146 (170)
...+|.+-++.++. +...+|-+|||+++
T Consensus 78 ~F~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 78 KFDDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp EESSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred EeCCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 34567888888885 78999999999864
No 80
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=22.30 E-value=88 Score=25.76 Aligned_cols=26 Identities=27% Similarity=0.413 Sum_probs=20.9
Q ss_pred CCCCCCcEEEEEcCCCCCeeEEEEEEE
Q 030877 70 NKVCPGDVVLVRSPVVPRRIVTKRVIG 96 (170)
Q Consensus 70 ~~~~~GDiV~f~~p~~~~~~~vkRVva 96 (170)
.++++||.|+...+ .++.+++.+|.+
T Consensus 71 neI~KGDlvi~y~k-~~r~y~IGkVts 96 (318)
T COG4127 71 NEIQKGDLVITYSK-SNRTYLIGKVTS 96 (318)
T ss_pred HHhccCcEEEeecc-cCceEEEEEecC
Confidence 37999999998776 447889999876
No 81
>PF14118 YfzA: YfzA-like protein
Probab=22.11 E-value=76 Score=21.57 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=11.5
Q ss_pred EeCCCCcccCCCCCcE
Q 030877 44 AYGPSMLPTINLTGDL 59 (170)
Q Consensus 44 v~~~SM~P~l~~~Gd~ 59 (170)
..+.|+.|.++ +|++
T Consensus 30 ~d~t~w~pnf~-~g~~ 44 (94)
T PF14118_consen 30 FDGTGWGPNFN-EGDF 44 (94)
T ss_pred hhccccccccC-CCch
Confidence 35788999998 6773
No 82
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.06 E-value=2.8e+02 Score=21.35 Aligned_cols=33 Identities=27% Similarity=0.322 Sum_probs=24.0
Q ss_pred CCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCE
Q 030877 69 FNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDR 101 (170)
Q Consensus 69 ~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~ 101 (170)
+..+++||+|.-+.-.-+....+=||+++.+-.
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~ 91 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKE 91 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEeccc
Confidence 346788888887776556677777888877743
No 83
>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].
Probab=21.99 E-value=1.4e+02 Score=26.81 Aligned_cols=26 Identities=12% Similarity=0.009 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhceEE
Q 030877 15 KEGFEKSLLVGKFFCCLHVVNTYVCT 40 (170)
Q Consensus 15 ~~~~~~~~~l~~~~~~~~~~~~~~~~ 40 (170)
|.++.++++++++++++.++...+|+
T Consensus 478 K~LWIsvAliVLLAaLlSfLtg~~fq 503 (538)
T PF05781_consen 478 KVLWISVALIVLLAALLSFLTGLFFQ 503 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccc
Confidence 44455555555555555555544443
No 84
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=21.32 E-value=1.2e+02 Score=20.32 Aligned_cols=29 Identities=21% Similarity=0.428 Sum_probs=16.8
Q ss_pred ccCCCCCcEEEEEeccCCCCCCCCCcEEEEEc
Q 030877 51 PTINLTGDLVLAERISTRFNKVCPGDVVLVRS 82 (170)
Q Consensus 51 P~l~~~Gd~v~v~~~~~~~~~~~~GDiV~f~~ 82 (170)
|+.. .+|.+.-+... ..+++.||+++|..
T Consensus 65 ptC~-~~D~i~~~~~l--P~~l~~GD~l~f~~ 93 (116)
T PF00278_consen 65 PTCD-SGDVIARDVML--PKELEVGDWLVFEN 93 (116)
T ss_dssp SSSS-TTSEEEEEEEE--ESTTTTT-EEEESS
T ss_pred CCcC-CCceEeeeccC--CCCCCCCCEEEEec
Confidence 4555 67766533222 13788888888875
No 85
>PF10222 DUF2152: Uncharacterized conserved protein (DUF2152); InterPro: IPR018795 This entry includes mainly uncharacterised proteins, though some are described as belonging to the glycoside hydrolase family 65.
Probab=20.64 E-value=1.1e+02 Score=28.01 Aligned_cols=68 Identities=18% Similarity=0.237 Sum_probs=37.4
Q ss_pred cEEEEEeccCCCCCCCCCcEEEEEcCCCCCeeEEEEEEEeCCCEEEEecCCCCCCCcceEEecCCeEEEEcCCCCCCCCC
Q 030877 58 DLVLAERISTRFNKVCPGDVVLVRSPVVPRRIVTKRVIGMEGDRVSYVADPKSSDKFETVVVPQGHVWIEGDNIYESNDS 137 (170)
Q Consensus 58 d~v~v~~~~~~~~~~~~GDiV~f~~p~~~~~~~vkRVva~~GD~v~i~~~~~~~~~~~~~~ip~~~y~vlgdn~~~s~DS 137 (170)
+.++-+++........+||.++...|.......+--| |. -.....+..|..|+.|..+.-+.+.
T Consensus 52 ~~Cl~~~l~~w~~~~~e~da~i~~~~~p~e~~~~P~V-GN---------------G~iGl~V~~d~L~I~~~~R~l~~~~ 115 (604)
T PF10222_consen 52 GKCLQDRLAPWYSQAEEGDAVILHPPKPQEKNYLPFV-GN---------------GYIGLDVDSDNLYIKGSGRALSLPV 115 (604)
T ss_pred chhHHHHHHHHHHHHhcCCEEEccCCCCCcccCCcee-cC---------------CEEEEEEcCCeEEEEecCccccccc
Confidence 4556666554445678999999885431111122111 10 1334456666777777665566666
Q ss_pred Cccc
Q 030877 138 RKFG 141 (170)
Q Consensus 138 R~~G 141 (170)
++.-
T Consensus 116 ~f~P 119 (604)
T PF10222_consen 116 PFHP 119 (604)
T ss_pred CCCc
Confidence 6653
No 86
>CHL00057 rpl14 ribosomal protein L14
Probab=20.45 E-value=3.3e+02 Score=19.36 Aligned_cols=30 Identities=13% Similarity=0.243 Sum_probs=22.3
Q ss_pred EEecCCeEEEEcCCCCCCCCCCccccccCCC
Q 030877 117 VVVPQGHVWIEGDNIYESNDSRKFGAVPYGL 147 (170)
Q Consensus 117 ~~ip~~~y~vlgdn~~~s~DSR~~G~V~~~~ 147 (170)
....+|.+-++.++. +..-+|-+|||+++-
T Consensus 77 i~F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T CHL00057 77 IRFDDNAAVVIDQEG-NPKGTRVFGPIAREL 106 (122)
T ss_pred EEcCCceEEEECCCC-CEeEeEEEccchHHH
Confidence 344567777777775 678899999999765
No 87
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=20.22 E-value=92 Score=23.60 Aligned_cols=27 Identities=19% Similarity=0.172 Sum_probs=20.7
Q ss_pred cceEEecCCeEEEEcCCCCCCCCCCcc
Q 030877 114 FETVVVPQGHVWIEGDNIYESNDSRKF 140 (170)
Q Consensus 114 ~~~~~ip~~~y~vlgdn~~~s~DSR~~ 140 (170)
.-+++.++|..+....+.+..+|.|||
T Consensus 96 clEf~~~~~~~~r~~~~s~~yyD~rYW 122 (176)
T PLN02289 96 CLEFELEHGFVYREHHRSPGYYDGRYW 122 (176)
T ss_pred eeeeccCCceeEecCCCCCCcccCcee
Confidence 356666778888877777788999997
Done!