Query 030248
Match_columns 180
No_of_seqs 168 out of 1539
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 10:50:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030248hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3342 Signal peptidase I [In 100.0 2.6E-41 5.7E-46 258.5 15.4 179 1-180 1-180 (180)
2 TIGR02228 sigpep_I_arch signal 100.0 1.5E-29 3.2E-34 198.0 16.7 123 38-170 21-145 (158)
3 TIGR02227 sigpep_I_bact signal 99.9 3.1E-21 6.6E-26 151.4 9.7 115 22-147 1-159 (163)
4 PRK10861 signal peptidase I; P 99.8 7.8E-18 1.7E-22 144.9 11.8 80 18-104 59-154 (324)
5 cd06530 S26_SPase_I The S26 Ty 99.7 6.1E-17 1.3E-21 113.3 8.5 78 50-143 2-85 (85)
6 TIGR02754 sod_Ni_protease nick 99.7 1.2E-16 2.6E-21 113.3 9.6 84 52-145 2-90 (90)
7 KOG0171 Mitochondrial inner me 99.7 1.8E-16 4E-21 123.4 9.3 93 51-147 36-155 (176)
8 KOG1568 Mitochondrial inner me 99.4 1.7E-12 3.7E-17 101.1 9.2 93 51-147 34-148 (174)
9 PF00717 Peptidase_S24: Peptid 99.4 2.3E-12 5.1E-17 86.5 7.3 60 52-118 1-60 (70)
10 cd06462 Peptidase_S24_S26 The 99.3 8.1E-12 1.8E-16 86.0 9.3 83 50-143 2-84 (84)
11 cd06529 S24_LexA-like Peptidas 99.1 7.3E-10 1.6E-14 76.0 10.1 78 51-143 3-80 (81)
12 COG0681 LepB Signal peptidase 99.1 2.1E-10 4.6E-15 88.7 5.8 78 19-104 7-89 (166)
13 PRK13838 conjugal transfer pil 99.1 1.3E-09 2.9E-14 86.7 10.2 68 74-145 48-170 (176)
14 COG2932 Predicted transcriptio 99.1 1.7E-09 3.7E-14 88.0 10.9 85 50-147 125-210 (214)
15 PRK00215 LexA repressor; Valid 98.9 3.4E-08 7.3E-13 79.7 11.5 83 50-148 120-203 (205)
16 TIGR02771 TraF_Ti conjugative 98.8 2.2E-08 4.9E-13 79.3 9.4 83 52-145 28-167 (171)
17 PRK10276 DNA polymerase V subu 98.8 9.3E-08 2E-12 73.1 11.2 83 50-148 53-136 (139)
18 PRK12423 LexA repressor; Provi 98.8 9.7E-08 2.1E-12 77.3 11.5 84 50-148 116-200 (202)
19 TIGR00498 lexA SOS regulatory 98.7 1.9E-07 4.2E-12 74.9 11.5 83 50-148 113-196 (199)
20 PRK13884 conjugal transfer pep 98.6 6.2E-07 1.3E-11 71.5 11.2 33 109-145 141-174 (178)
21 COG1974 LexA SOS-response tran 98.4 6.4E-06 1.4E-10 67.0 11.0 82 50-148 114-198 (201)
22 PF10502 Peptidase_S26: Signal 98.3 6.6E-07 1.4E-11 68.5 3.2 51 92-146 50-136 (138)
23 COG4959 TraF Type IV secretory 94.6 0.017 3.7E-07 45.2 1.5 33 109-145 134-167 (173)
24 COG0361 InfA Translation initi 79.4 2.1 4.6E-05 29.5 2.7 30 55-84 37-69 (75)
25 TIGR00008 infA translation ini 77.1 2.5 5.5E-05 28.5 2.5 22 62-83 45-66 (68)
26 PF05582 Peptidase_U57: YabG p 71.6 10 0.00022 32.5 5.4 38 77-118 1-38 (287)
27 PF01176 eIF-1a: Translation i 71.5 3.3 7.2E-05 27.3 2.0 13 76-88 41-53 (65)
28 cd05793 S1_IF1A S1_IF1A: Trans 69.3 4.5 9.7E-05 27.8 2.3 10 77-86 39-48 (77)
29 TIGR02594 conserved hypothetic 65.7 19 0.00042 27.0 5.4 38 75-118 72-109 (129)
30 smart00652 eIF1a eukaryotic tr 64.4 6.4 0.00014 27.5 2.4 10 77-86 44-53 (83)
31 PF10377 ATG11: Autophagy-rela 64.3 33 0.00071 25.8 6.4 58 75-145 41-98 (129)
32 cd04456 S1_IF1A_like S1_IF1A_l 63.3 7.1 0.00015 26.9 2.4 10 77-86 39-48 (78)
33 PRK12442 translation initiatio 62.6 8.5 0.00018 27.3 2.7 36 53-88 16-58 (87)
34 PF07423 DUF1510: Protein of u 59.9 17 0.00036 30.0 4.4 30 15-44 7-36 (217)
35 PRK04012 translation initiatio 59.9 8.4 0.00018 27.9 2.4 11 77-87 60-70 (100)
36 TIGR02855 spore_yabG sporulati 59.4 21 0.00046 30.6 5.0 37 78-118 1-37 (283)
37 KOG4146 Ubiquitin-like protein 53.9 16 0.00035 26.3 2.9 36 49-88 54-97 (101)
38 PF09285 Elong-fact-P_C: Elong 53.2 26 0.00056 22.7 3.6 38 55-97 18-56 (56)
39 smart00841 Elong-fact-P_C Elon 51.2 28 0.00061 22.5 3.5 38 55-97 18-56 (56)
40 PF10000 ACT_3: ACT domain; I 49.0 8.6 0.00019 26.1 0.9 35 56-90 12-49 (72)
41 COG3602 Uncharacterized protei 48.7 13 0.00029 27.8 1.9 17 56-72 12-28 (134)
42 PF02285 COX8: Cytochrome oxid 45.8 11 0.00023 23.4 0.9 13 2-14 31-43 (44)
43 PF04319 NifZ: NifZ domain; I 45.3 38 0.00083 23.3 3.6 29 58-86 1-35 (75)
44 cd05794 S1_EF-P_repeat_2 S1_EF 45.0 38 0.00082 21.9 3.4 38 55-97 18-56 (56)
45 COG3895 Predicted periplasmic 44.8 48 0.001 24.5 4.3 45 77-122 49-95 (112)
46 TIGR03024 arch_pef_cterm PEF-C 43.9 27 0.00058 19.2 2.2 19 161-179 5-23 (26)
47 COG5131 URM1 Ubiquitin-like pr 43.6 34 0.00073 24.5 3.2 34 51-88 51-92 (96)
48 PLN00208 translation initiatio 39.7 26 0.00055 27.2 2.3 23 62-84 71-93 (145)
49 PTZ00329 eukaryotic translatio 39.0 26 0.00057 27.4 2.3 25 62-86 71-95 (155)
50 PF05382 Amidase_5: Bacterioph 38.7 32 0.00069 26.6 2.7 38 51-88 49-87 (145)
51 PF14118 YfzA: YfzA-like prote 36.8 29 0.00062 24.9 2.0 16 52-67 29-44 (94)
52 cd05792 S1_eIF1AD_like S1_eIF1 36.4 29 0.00063 24.0 2.0 10 77-86 39-48 (78)
53 cd04714 BAH_BAHCC1 BAH, or Bro 36.0 89 0.0019 22.9 4.7 28 77-104 4-32 (121)
54 COG4393 Predicted membrane pro 35.7 3.2E+02 0.007 24.4 9.3 11 94-104 302-312 (405)
55 PF12751 Vac7: Vacuolar segreg 35.2 64 0.0014 29.0 4.4 48 24-71 304-351 (387)
56 PF15057 DUF4537: Domain of un 34.8 29 0.00064 25.8 1.9 21 52-72 46-66 (124)
57 COG0179 MhpD 2-keto-4-pentenoa 34.0 84 0.0018 26.6 4.8 38 61-99 224-263 (266)
58 PRK00276 infA translation init 32.4 46 0.001 22.2 2.4 22 76-97 46-70 (72)
59 PF08802 CytB6-F_Fe-S: Cytochr 32.2 1.2E+02 0.0025 18.2 4.9 29 13-41 5-33 (39)
60 PF12273 RCR: Chitin synthesis 31.0 33 0.00072 25.5 1.7 8 22-29 2-9 (130)
61 cd04466 S1_YloQ_GTPase S1_YloQ 30.1 95 0.0021 19.7 3.7 25 75-99 36-60 (68)
62 COG1188 Ribosome-associated he 30.0 1E+02 0.0022 22.4 4.0 30 73-104 45-74 (100)
63 cd04712 BAH_DCM_I BAH, or Brom 29.4 1.2E+02 0.0027 22.6 4.6 10 137-146 89-98 (130)
64 cd06555 ASCH_PF0470_like ASC-1 27.6 1.6E+02 0.0035 21.5 4.8 29 75-103 30-58 (109)
65 KOG0584 Serine/threonine prote 27.6 73 0.0016 30.4 3.6 77 4-103 130-209 (632)
66 TIGR00038 efp translation elon 27.3 1E+02 0.0022 24.5 4.0 38 56-98 146-184 (184)
67 CHL00010 infA translation init 27.1 67 0.0015 21.9 2.6 22 77-98 47-71 (78)
68 TIGR01416 Rieske_proteo ubiqui 26.7 2.1E+02 0.0044 22.5 5.6 28 67-96 41-68 (174)
69 TIGR01000 bacteriocin_acc bact 26.6 2.3E+02 0.005 25.5 6.6 38 4-42 5-42 (457)
70 cd04451 S1_IF1 S1_IF1: Transla 25.5 58 0.0013 20.9 2.0 22 76-97 40-64 (64)
71 TIGR00523 eIF-1A eukaryotic/ar 24.8 74 0.0016 22.9 2.5 10 77-86 58-67 (99)
72 PF06459 RR_TM4-6: Ryanodine R 24.7 1.8E+02 0.0039 24.8 5.2 15 28-42 176-190 (274)
73 PRK14578 elongation factor P; 24.6 1.3E+02 0.0028 24.2 4.2 37 57-98 150-187 (187)
74 PF02362 B3: B3 DNA binding do 24.5 84 0.0018 21.4 2.7 16 74-89 71-86 (100)
75 PF12961 DUF3850: Domain of Un 24.2 2.4E+02 0.0052 19.2 5.3 36 64-100 15-51 (72)
76 PF00278 Orn_DAP_Arg_deC: Pyri 24.2 86 0.0019 22.1 2.8 30 60-89 65-95 (116)
77 PRK12426 elongation factor P; 23.4 1.4E+02 0.0029 24.1 4.0 39 55-98 146-185 (185)
78 COG0690 SecE Preprotein transl 23.2 1.6E+02 0.0036 19.8 3.9 14 2-15 22-35 (73)
79 KOG0557 Dihydrolipoamide acety 23.0 1.3E+02 0.0028 27.7 4.2 38 49-86 37-75 (470)
80 PRK04542 elongation factor P; 22.8 1.7E+02 0.0036 23.6 4.4 37 57-98 151-188 (189)
81 PRK14766 lipoprotein signal pe 22.7 1.6E+02 0.0034 24.0 4.3 32 3-34 1-32 (201)
82 PF11717 Tudor-knot: RNA bindi 22.6 2E+02 0.0044 17.9 4.7 46 77-125 1-47 (55)
83 COG4473 EcsB Predicted ABC-typ 22.5 2E+02 0.0043 25.8 5.1 65 8-72 12-90 (379)
84 TIGR02178 yeiP elongation fact 22.3 1.3E+02 0.0028 24.2 3.7 38 56-98 148-186 (186)
85 TIGR00964 secE_bact preprotein 21.6 2.1E+02 0.0045 17.9 3.9 24 2-25 3-29 (55)
86 PF01426 BAH: BAH domain; Int 21.2 1E+02 0.0022 21.6 2.7 27 78-104 4-31 (119)
87 cd04717 BAH_polybromo BAH, or 21.0 1.3E+02 0.0027 21.9 3.2 28 77-104 4-32 (121)
88 smart00439 BAH Bromo adjacent 20.8 1.6E+02 0.0036 20.5 3.8 14 133-146 70-83 (120)
89 KOG4544 Uncharacterized conser 20.4 3.7E+02 0.0081 20.7 5.6 34 4-37 32-70 (144)
No 1
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.6e-41 Score=258.45 Aligned_cols=179 Identities=59% Similarity=0.984 Sum_probs=169.8
Q ss_pred CcchHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEee-cCCCCCc
Q 030248 1 MGWIGESIESIKSLQIRQVLTQGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHM-SKDPIRA 79 (180)
Q Consensus 1 ~~~~~~~~~~~~~~~~r~~~~~i~~i~~~i~v~~li~~~l~~~~~~~~p~~~V~g~SM~Ptl~~GD~v~v~~-~~~~~~~ 79 (180)
|.|..|.+..+|+|++|+.+..++++++++..++++|..+.+.+|+++|+++|.|+||||.++.||+++... ..++.+.
T Consensus 1 ~~~~~~~~~~~k~mn~Rq~l~Q~ln~~mivssA~MiwK~l~vvt~seSPiVVVLSgSMePaF~RGDlLfL~N~~~~p~~v 80 (180)
T KOG3342|consen 1 MLVSLEMFDDLKRMNIRQLLYQVLNFAMIVSSAYMIWKGLMVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNRNEDPIRV 80 (180)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhheeeeCCCCCEEEEEcCCcCcccccccEEEEecCCCCccee
Confidence 679999999999999999999999999999999999999999999999999999999999999999999875 5677899
Q ss_pred CcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhccCCccccceeEeeEEEEEecCcceeeeeccc
Q 030248 80 GEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQGQLWLKRQHIMGRAVGFLPYVGWVTIIMTE 159 (180)
Q Consensus 80 GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~~~~~~v~~~~IiG~v~~~iP~~G~v~~~~~~ 159 (180)
|||++|+.++.+.+++|||+.+.+. ++++..+.||||||...|..+|++++-++++++|+|++.+.+||+|++++|+++
T Consensus 81 GdivVf~vegR~IPiVHRviK~he~-~~~~~~~LTKGDNN~~dD~~Ly~~gq~~L~r~~Ivg~~~G~~Py~G~itI~mnd 159 (180)
T KOG3342|consen 81 GDIVVFKVEGREIPIVHRVIKQHEK-SNGHIKFLTKGDNNAVDDRGLYAQGQNWLERKDIVGRVRGYLPYVGMITIWMND 159 (180)
T ss_pred ccEEEEEECCccCchhHHHHHHhcc-cCCcEEEEecCCCCcccchhcccccccceeccceeeEEeeccccceEEEEEecC
Confidence 9999999999999999999998764 256778999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHhhhhcCC
Q 030248 160 KPIIKYILIGALGLLVITSKD 180 (180)
Q Consensus 160 ~p~~~~~~~~~~~~~~~~~~~ 180 (180)
.|.++|+++|.+|+.+|.+||
T Consensus 160 ~p~~KyalL~~lGl~vL~~rE 180 (180)
T KOG3342|consen 160 YPKLKYALLGGLGLSVLLHRE 180 (180)
T ss_pred CcchHHHHHHHHHHheeeccC
Confidence 999999999999999999997
No 2
>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=99.97 E-value=1.5e-29 Score=198.03 Aligned_cols=123 Identities=31% Similarity=0.568 Sum_probs=101.5
Q ss_pred HHHHHhhCCCCCeEEEeCCCccccccCCCEEEEee-cCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEec
Q 030248 38 KALMCITGSESPVVVVLSGSMEPGFKRGDILFLHM-SKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKG 116 (180)
Q Consensus 38 ~~l~~~~~~~~p~~~V~g~SM~Ptl~~GD~v~v~~-~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~G 116 (180)
..+....+++.|.+.|.|+||+|++++||++++++ ..+++++||||+|+.++++.+++|||+++.++ +++..|+|||
T Consensus 21 ~~l~~~~~~~~p~v~V~g~SM~Ptl~~GD~vlv~~~~~~~~~~GDIVvf~~~~~~~~iihRVi~v~~~--~g~~~~~tkG 98 (158)
T TIGR02228 21 YGLVSKASGPDPVVVVLSGSMEPTFNTGDLILVTGADPNDIQVGDVITYKSPGFNTPVTHRVIEINNS--GGELGFITKG 98 (158)
T ss_pred HHheeeccCCCcEEEEcCCCCcCCccCCCEEEEEecccCCCCCCCEEEEEECCCCccEEEEEEEEECC--CCcEEEEEEe
Confidence 33344456677877899999999999999999998 45789999999999887656899999999865 2456799999
Q ss_pred CCCCCCCchhhccCCccccceeEeeEEE-EEecCcceeeeecccchhHHHHHHHH
Q 030248 117 DNNYGDDRLLYAQGQLWLKRQHIMGRAV-GFLPYVGWVTIIMTEKPIIKYILIGA 170 (180)
Q Consensus 117 Dnn~~~D~~~y~~~~~~v~~~~IiG~v~-~~iP~~G~v~~~~~~~p~~~~~~~~~ 170 (180)
|||+.+|+. ++++++++|++. +++||+|++..++++... ..+++++
T Consensus 99 DnN~~~D~~-------~v~~~~IiG~v~~~~iP~~G~~~~~~~~~~~-~~~~~~~ 145 (158)
T TIGR02228 99 DNNPAPDGE-------PVPSENVIGKYLGFTIPFAGYVLVFAPQAIG-AAALLII 145 (158)
T ss_pred cCCCCCCcc-------cCCHHHEEEEEEEeccCcccEEEEEeecCch-hhhhHHh
Confidence 999999964 479999999999 789999999999999654 4444443
No 3
>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=99.85 E-value=3.1e-21 Score=151.41 Aligned_cols=115 Identities=25% Similarity=0.326 Sum_probs=93.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEeec---CCCCCcCcEEEEEeCCC-CcCEEEE
Q 030248 22 QGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---KDPIRAGEIVVFNVDGR-EIPIVHR 97 (180)
Q Consensus 22 ~i~~i~~~i~v~~li~~~l~~~~~~~~p~~~V~g~SM~Ptl~~GD~v~v~~~---~~~~~~GDIVvf~~~~~-~~~~ihR 97 (180)
|+..++++++++++++.|++.. +.|+|+||+|||++||++++++. ..++++||+|+|+.++. ...++||
T Consensus 1 ~~~~~~~~~~~~~~i~~~~~~~-------~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKR 73 (163)
T TIGR02227 1 LILSLLIAILLALLIRTFVFFP-------YKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKR 73 (163)
T ss_pred CHHHHHHHHHHHHHHHhhEEEE-------EEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEE
Confidence 3455666777777777777653 99999999999999999999983 37899999999998642 3579999
Q ss_pred EEEeCCCC----C-----------------------------------CCeeEEEEecCC-CCCCCchhhccCCccccce
Q 030248 98 VIKVHERQ----D-----------------------------------TGEVEVLTKGDN-NYGDDRLLYAQGQLWLKRQ 137 (180)
Q Consensus 98 Vi~~~~~~----~-----------------------------------~g~~~~~t~GDn-n~~~D~~~y~~~~~~v~~~ 137 (180)
|++++||. + .++++|+++||| +.|.|||.+ ++|+++
T Consensus 74 Vig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~----G~V~~~ 149 (163)
T TIGR02227 74 VIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYF----GFVPID 149 (163)
T ss_pred EEecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCc----CcCCHH
Confidence 99999872 0 025579999999 578999975 689999
Q ss_pred eEeeEEEEEe
Q 030248 138 HIMGRAVGFL 147 (180)
Q Consensus 138 ~IiG~v~~~i 147 (180)
+|+||+..++
T Consensus 150 ~I~Gk~~~~~ 159 (163)
T TIGR02227 150 DIIGKVSFVF 159 (163)
T ss_pred HeEEEEEEEE
Confidence 9999999985
No 4
>PRK10861 signal peptidase I; Provisional
Probab=99.75 E-value=7.8e-18 Score=144.90 Aligned_cols=80 Identities=24% Similarity=0.347 Sum_probs=67.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEeec---------------CCCCCcCcE
Q 030248 18 QVLTQGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---------------KDPIRAGEI 82 (180)
Q Consensus 18 ~~~~~i~~i~~~i~v~~li~~~l~~~~~~~~p~~~V~g~SM~Ptl~~GD~v~v~~~---------------~~~~~~GDI 82 (180)
.++.++..++.+++++++++.|++.. +.|+|+||+|||..||.++++|. ..++++|||
T Consensus 59 ~~~~~~~~~~~~l~i~~~ir~fv~~~-------~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDI 131 (324)
T PRK10861 59 GWLETGASVFPVLAIVLIVRSFIYEP-------FQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDI 131 (324)
T ss_pred hHHHHHHHHHHHHhHHHHHHhhEEEE-------EEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCE
Confidence 36778888888888888888888863 99999999999999999999992 146899999
Q ss_pred EEEEeCCC-CcCEEEEEEEeCCC
Q 030248 83 VVFNVDGR-EIPIVHRVIKVHER 104 (180)
Q Consensus 83 Vvf~~~~~-~~~~ihRVi~~~~~ 104 (180)
|+|+.|.+ ...+||||+++|||
T Consensus 132 VVF~~P~~~~~~yIKRVIGlPGD 154 (324)
T PRK10861 132 VVFKYPEDPKLDYIKRVVGLPGD 154 (324)
T ss_pred EEEecCCCCCCcEEEEeeecCCc
Confidence 99997753 35799999999987
No 5
>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=99.70 E-value=6.1e-17 Score=113.32 Aligned_cols=78 Identities=36% Similarity=0.557 Sum_probs=64.3
Q ss_pred eEEEeCCCccccccCCCEEEEeecCC---CCCcCcEEEEEeCCC-CcCEEEEEEEeCCCCCCCeeEEEEecCC--CCCCC
Q 030248 50 VVVVLSGSMEPGFKRGDILFLHMSKD---PIRAGEIVVFNVDGR-EIPIVHRVIKVHERQDTGEVEVLTKGDN--NYGDD 123 (180)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~v~v~~~~~---~~~~GDIVvf~~~~~-~~~~ihRVi~~~~~~~~g~~~~~t~GDn--n~~~D 123 (180)
.+.|.|+||+|++++||++++++... +++.||+|+|+.++. ..+++||+++ |+++||| |+..|
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~-----------~~~~gDn~~ns~d~ 70 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG-----------YFVLGDNRNNSLDS 70 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE-----------EEEeeCCCCCCCcc
Confidence 38999999999999999999998433 699999999999874 3589999988 7899999 55444
Q ss_pred chhhccCCccccceeEeeEE
Q 030248 124 RLLYAQGQLWLKRQHIMGRA 143 (180)
Q Consensus 124 ~~~y~~~~~~v~~~~IiG~v 143 (180)
+.. ++++.++|+|++
T Consensus 71 ~~~-----g~~~~~~i~G~~ 85 (85)
T cd06530 71 RYW-----GPVPEDDIVGKV 85 (85)
T ss_pred CCc-----CCCcHHHeEEeC
Confidence 433 457899999975
No 6
>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=99.70 E-value=1.2e-16 Score=113.28 Aligned_cols=84 Identities=21% Similarity=0.211 Sum_probs=68.5
Q ss_pred EEeCCCccccccCCCEEEEee---cCCCCCcCcEEEEEeCCC-CcCEEEEEEEeCCCCCCCeeEEEEecCCCC-CCCchh
Q 030248 52 VVLSGSMEPGFKRGDILFLHM---SKDPIRAGEIVVFNVDGR-EIPIVHRVIKVHERQDTGEVEVLTKGDNNY-GDDRLL 126 (180)
Q Consensus 52 ~V~g~SM~Ptl~~GD~v~v~~---~~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~-~~D~~~ 126 (180)
.|.|+||+|+|++||.+++++ ....++.||+++|+.+++ ...++||+++.+++ .+++.|||+. +.|++.
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~~------~~~l~~dN~~~~~d~~~ 75 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDDN------GLFLLGDNPKASTDSRQ 75 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcCC------eEEEeCCCCCCCCcccc
Confidence 589999999999999999997 234456799999998753 36899999999764 6899999954 577765
Q ss_pred hccCCccccceeEeeEEEE
Q 030248 127 YAQGQLWLKRQHIMGRAVG 145 (180)
Q Consensus 127 y~~~~~~v~~~~IiG~v~~ 145 (180)
+ ++++..+|+|+|++
T Consensus 76 ~----g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 76 L----GPVPRSLLLGKVLW 90 (90)
T ss_pred c----CCCcHHHEEEEEEC
Confidence 4 57899999999864
No 7
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.68 E-value=1.8e-16 Score=123.36 Aligned_cols=93 Identities=27% Similarity=0.295 Sum_probs=77.1
Q ss_pred EEEeCCCccccccCCCEEEE-ee---cCCCCCcCcEEEEEeCCC-CcCEEEEEEEeCCCC----------C---------
Q 030248 51 VVVLSGSMEPGFKRGDILFL-HM---SKDPIRAGEIVVFNVDGR-EIPIVHRVIKVHERQ----------D--------- 106 (180)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~v~v-~~---~~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~~~----------~--------- 106 (180)
....|.||+||+.+++.+++ ++ .+..+++||||+++.|.+ .+.++|||++.+||- +
T Consensus 36 ~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v~v~~~~~~~n~~~e~~~~~ 115 (176)
T KOG0171|consen 36 VMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDLVEVHDGPLVVNDLVEKFSTP 115 (176)
T ss_pred eeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhheeeccCCceEEEecCCcccchhhhhccce
Confidence 78899999998887755554 66 356679999999998743 367999999999981 1
Q ss_pred --CCeeEEEEecCC-CCCCCchhhccCCccccceeEeeEEEEEe
Q 030248 107 --TGEVEVLTKGDN-NYGDDRLLYAQGQLWLKRQHIMGRAVGFL 147 (180)
Q Consensus 107 --~g~~~~~t~GDn-n~~~D~~~y~~~~~~v~~~~IiG~v~~~i 147 (180)
.+++++++.||| |.+.|++.| +|++...|.||+++++
T Consensus 116 i~VP~GhVfv~GDN~~nS~DSr~y----GplP~glI~gRvv~r~ 155 (176)
T KOG0171|consen 116 IRVPEGHVFVEGDNRNNSLDSRNY----GPLPMGLIQGRVVFRI 155 (176)
T ss_pred eeccCceEEEecCCCCCccccccc----CCCchhheeeeEEEEe
Confidence 267789999999 889999987 5899999999999985
No 8
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.40 E-value=1.7e-12 Score=101.08 Aligned_cols=93 Identities=24% Similarity=0.321 Sum_probs=78.0
Q ss_pred EEEeCCCccccccCC------CEEEEee---cCCCCCcCcEEEEEeCCC-CcCEEEEEEEeCCCC-----------CCCe
Q 030248 51 VVVLSGSMEPGFKRG------DILFLHM---SKDPIRAGEIVVFNVDGR-EIPIVHRVIKVHERQ-----------DTGE 109 (180)
Q Consensus 51 ~~V~g~SM~Ptl~~G------D~v~v~~---~~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~~~-----------~~g~ 109 (180)
..|.|.||.|++.++ |.|++.+ ....+.+||||+|.+|.+ ++++||||.+++++. ..++
T Consensus 34 a~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpk 113 (174)
T KOG1568|consen 34 AQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPK 113 (174)
T ss_pred eEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeecccccEeccCCCCCCceecCC
Confidence 589999999999876 8999988 234588999999998843 478999999999982 0367
Q ss_pred eEEEEecCCC-CCCCchhhccCCccccceeEeeEEEEEe
Q 030248 110 VEVLTKGDNN-YGDDRLLYAQGQLWLKRQHIMGRAVGFL 147 (180)
Q Consensus 110 ~~~~t~GDnn-~~~D~~~y~~~~~~v~~~~IiG~v~~~i 147 (180)
+++++.|||. .+.||+.+ |||+-..|.|+++..+
T Consensus 114 ghcWVegDn~~hs~DSntF----GPVS~gli~grai~il 148 (174)
T KOG1568|consen 114 GHCWVEGDNQKHSYDSNTF----GPVSTGLIVGRAIYIL 148 (174)
T ss_pred CcEEEecCCcccccccCcc----CCcchhheeeeEEEEE
Confidence 8999999994 57999754 7899999999999874
No 9
>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=99.37 E-value=2.3e-12 Score=86.53 Aligned_cols=60 Identities=35% Similarity=0.516 Sum_probs=48.0
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCC
Q 030248 52 VVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 118 (180)
Q Consensus 52 ~V~g~SM~Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDn 118 (180)
.|.|+||+|+|++||++++++. .+++.||+|+|+.++....++||+.+.+++ .+.+..+|
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~-~~~~~gdivv~~~~~~~~~~iKrv~~~~~~------~~~~~~~n 60 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPS-SEPKDGDIVVVKIDGDEELYIKRVVGEPGG------IILISSNN 60 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEET-S---TTSEEEEEETTEESEEEEEEEEETTE------EEEE-SST
T ss_pred CeECcCcccCeeCCCEEEEEEc-CCCccCeEEEEEECCceeeEEEEEEEeCCC------EEEEeccC
Confidence 4899999999999999999984 588999999999987634799999998864 57777655
No 10
>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=99.35 E-value=8.1e-12 Score=85.96 Aligned_cols=83 Identities=30% Similarity=0.409 Sum_probs=62.4
Q ss_pred eEEEeCCCccccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhcc
Q 030248 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQ 129 (180)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~~ 129 (180)
.+.|.|+||+|++.+||++++++....++.||+++++.++ ...++||+...++. ..+.+++||....+....
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~i~~~~~~~~~G~iv~~~~~~-~~~~ikrl~~~~~~-----~~~~l~~~N~~~~~~~~~-- 73 (84)
T cd06462 2 ALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPG-GELTVKRVIGLPGE-----GHYFLLGDNPNSPDSRID-- 73 (84)
T ss_pred eeEEcCCCccCcccCCCEEEEEecCCCCcCCEEEEEEcCC-CcEEEEEEEEECCC-----CEEEEECCCCCCCccccc--
Confidence 3789999999999999999999854458999999999887 34799999998751 279999998333332221
Q ss_pred CCccccceeEeeEE
Q 030248 130 GQLWLKRQHIMGRA 143 (180)
Q Consensus 130 ~~~~v~~~~IiG~v 143 (180)
. -++.+++|++
T Consensus 74 ~---~~~~~i~g~v 84 (84)
T cd06462 74 G---PPELDIVGVV 84 (84)
T ss_pred C---CCHHHEEEeC
Confidence 0 1456677753
No 11
>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=99.14 E-value=7.3e-10 Score=76.02 Aligned_cols=78 Identities=28% Similarity=0.323 Sum_probs=60.3
Q ss_pred EEEeCCCccccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhccC
Q 030248 51 VVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQG 130 (180)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~~~ 130 (180)
+.|.|+||+|++++||.+++++. ..++.||++++..++ ..++||+...+++ .+.+++||+...+.. .+
T Consensus 3 ~~v~g~sM~p~i~~gd~lii~~~-~~~~~g~i~~~~~~~--~~~ikr~~~~~~~------~~~L~s~N~~~~~~~-~~-- 70 (81)
T cd06529 3 LRVKGDSMEPTIPDGDLVLVDPS-DTPRDGDIVVARLDG--ELTVKRLQRRGGG------RLRLISDNPAYPPIE-ID-- 70 (81)
T ss_pred EEEECCCcCCccCCCCEEEEcCC-CCCCCCCEEEEEECC--EEEEEEEEECCCC------cEEEEeCCCCCCCEe-eC--
Confidence 78999999999999999999984 448999999999987 4699999988743 688999986443322 11
Q ss_pred CccccceeEeeEE
Q 030248 131 QLWLKRQHIMGRA 143 (180)
Q Consensus 131 ~~~v~~~~IiG~v 143 (180)
-+.-+++|++
T Consensus 71 ---~~~~~~ig~v 80 (81)
T cd06529 71 ---EEELEIVGVV 80 (81)
T ss_pred ---hhhEEEEEEE
Confidence 1246666654
No 12
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.07 E-value=2.1e-10 Score=88.66 Aligned_cols=78 Identities=31% Similarity=0.346 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHHHHHHH--HHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEeec---CCCCCcCcEEEEEeCCCCcC
Q 030248 19 VLTQGVSLGMIVTSALII--WKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---KDPIRAGEIVVFNVDGREIP 93 (180)
Q Consensus 19 ~~~~i~~i~~~i~v~~li--~~~l~~~~~~~~p~~~V~g~SM~Ptl~~GD~v~v~~~---~~~~~~GDIVvf~~~~~~~~ 93 (180)
...++..++.++++++++ +.+.+. .+.|+|+||+||++.||++++++. ...+..+|++.+-... ...
T Consensus 7 ~~~~~~~~~~~~~~~~~i~~~~~~~~-------~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~~~~-~~~ 78 (166)
T COG0681 7 FLELISSLLIAIILALIIGVRTFVFE-------PVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPAVV-EGD 78 (166)
T ss_pred HHHHHHHHHHHHHHhheeeeEEEEEE-------EEEECCCccccccccCCEEEEEeccccccCCccceeeecCCCC-Ccc
Confidence 456666777777777776 444443 499999999999999999999993 2235666665332222 245
Q ss_pred EEEEEEEeCCC
Q 030248 94 IVHRVIKVHER 104 (180)
Q Consensus 94 ~ihRVi~~~~~ 104 (180)
+++|+++.+||
T Consensus 79 ~~kr~~~~~GD 89 (166)
T COG0681 79 LIKRVIGLRGD 89 (166)
T ss_pred eEEEeccCCCC
Confidence 88888888776
No 13
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.06 E-value=1.3e-09 Score=86.74 Aligned_cols=68 Identities=12% Similarity=0.177 Sum_probs=55.0
Q ss_pred CCCCCcCcEEEEEeCCCC--------------------cCEEEEEEEeCCCC----C-----------------------
Q 030248 74 KDPIRAGEIVVFNVDGRE--------------------IPIVHRVIKVHERQ----D----------------------- 106 (180)
Q Consensus 74 ~~~~~~GDIVvf~~~~~~--------------------~~~ihRVi~~~~~~----~----------------------- 106 (180)
..++++||+|+|+.+... .+++|||++++||. +
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 467899999999865421 25999999999983 0
Q ss_pred --------CCeeEEEEecCCCCCCCchhhccCCccccceeEeeEEEE
Q 030248 107 --------TGEVEVLTKGDNNYGDDRLLYAQGQLWLKRQHIMGRAVG 145 (180)
Q Consensus 107 --------~g~~~~~t~GDnn~~~D~~~y~~~~~~v~~~~IiG~v~~ 145 (180)
.++++|+++|||+.|.|+|.+ ++|++++|+|++.-
T Consensus 128 l~~~~~~~vp~g~~fvlgd~~~S~DSRy~----G~V~~~~I~G~a~p 170 (176)
T PRK13838 128 LTPFPGGVVPPGHLFLHSSFAGSYDSRYF----GPVPASGLLGLARP 170 (176)
T ss_pred CCCCCccCcCCCeEEEECCCCCCCccccc----CcccHHHeEEEEEE
Confidence 145679999999889999975 68999999999864
No 14
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=99.06 E-value=1.7e-09 Score=87.97 Aligned_cols=85 Identities=22% Similarity=0.242 Sum_probs=63.0
Q ss_pred eEEEeCCCccccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhcc
Q 030248 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQ 129 (180)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~~ 129 (180)
.+.|.|+||+|++++||.++|++. .+...||.+++...++ ..++||+...++. .+.+..+|...++...+.
T Consensus 125 ~i~V~GDSMeP~~~~Gd~ilVd~~-~~~~~gd~v~v~~~g~-~~~VK~l~~~~~~------~~~l~S~N~~~~~~~~~~- 195 (214)
T COG2932 125 ALRVTGDSMEPTYEDGDTLLVDPG-VNTRRGDRVYVETDGG-ELYVKKLQREPGG------LLRLVSLNPDYYPDEIFS- 195 (214)
T ss_pred EEEEeCCcccccccCCCEEEECCC-CceeeCCEEEEEEeCC-eEEEEEEEEecCC------eEEEEeCCCCCCcccccC-
Confidence 379999999999999999999984 5567888777666653 4799999999864 566889875542322221
Q ss_pred CCccccc-eeEeeEEEEEe
Q 030248 130 GQLWLKR-QHIMGRAVGFL 147 (180)
Q Consensus 130 ~~~~v~~-~~IiG~v~~~i 147 (180)
-.. -+++|+|++..
T Consensus 196 ----~~~~v~iIgrVv~~~ 210 (214)
T COG2932 196 ----EDDDVEIIGRVVWVS 210 (214)
T ss_pred ----ccceEEEEEEEEEEe
Confidence 112 56899999864
No 15
>PRK00215 LexA repressor; Validated
Probab=98.87 E-value=3.4e-08 Score=79.67 Aligned_cols=83 Identities=24% Similarity=0.378 Sum_probs=63.5
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhc
Q 030248 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYA 128 (180)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~ 128 (180)
.+.|.|+||. |++++||++++++. ..++.||++++..++ ..++||+....+ .+.+..||.. +++..+.
T Consensus 120 ~~~V~GdSM~~~~i~~Gd~v~v~~~-~~~~~G~ivv~~~~~--~~~vKrl~~~~~-------~~~L~s~Np~-y~~~~~~ 188 (205)
T PRK00215 120 LLRVRGDSMIDAGILDGDLVIVRKQ-QTARNGQIVVALIDD--EATVKRFRREGG-------HIRLEPENPA-YEPIIVD 188 (205)
T ss_pred EEEEccCCCCCCCcCCCCEEEEeCC-CCCCCCCEEEEEECC--EEEEEEEEEeCC-------EEEEEcCCCC-CCCEEeC
Confidence 4789999995 79999999999984 567899999999876 479999987532 5889998644 4443321
Q ss_pred cCCccccceeEeeEEEEEec
Q 030248 129 QGQLWLKRQHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~v~~~~IiG~v~~~iP 148 (180)
. +.-.|+|+|++.+.
T Consensus 189 ~-----~~~~IiG~Vv~~~r 203 (205)
T PRK00215 189 P-----DRVTIEGKVVGLIR 203 (205)
T ss_pred C-----CcEEEEEEEEEEEE
Confidence 1 15789999998764
No 16
>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=98.84 E-value=2.2e-08 Score=79.34 Aligned_cols=83 Identities=18% Similarity=0.283 Sum_probs=60.4
Q ss_pred EEeCCCccccccCCCEEEEeecCCCCCcCcEEEEEeCCCCc--------------------CEEEEEEEeCCCC----C-
Q 030248 52 VVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREI--------------------PIVHRVIKVHERQ----D- 106 (180)
Q Consensus 52 ~V~g~SM~Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~--------------------~~ihRVi~~~~~~----~- 106 (180)
.=.++||-..+- . ..+ ..++++||+|+|+.++... .++|||++++||. +
T Consensus 28 ~N~T~S~P~g~Y----~-~~~-~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~ 101 (171)
T TIGR02771 28 INTTKSLPLGLY----W-TTS-SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRAD 101 (171)
T ss_pred EECCCCCcceEE----E-eCC-CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECC
Confidence 345567766553 2 222 4679999999999765321 6999999999983 0
Q ss_pred ----C---------------------------CeeEEEEecCC-CCCCCchhhccCCccccceeEeeEEEE
Q 030248 107 ----T---------------------------GEVEVLTKGDN-NYGDDRLLYAQGQLWLKRQHIMGRAVG 145 (180)
Q Consensus 107 ----~---------------------------g~~~~~t~GDn-n~~~D~~~y~~~~~~v~~~~IiG~v~~ 145 (180)
| +++ |++.||| +.|.|||.+ ++|++++|+||+.-
T Consensus 102 ~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~----G~V~~~~IiGk~~p 167 (171)
T TIGR02771 102 VVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYF----GPISREQVIGRVKP 167 (171)
T ss_pred EEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCccccc----ceecHHHeEEEEEE
Confidence 0 233 8888998 458999975 68999999999873
No 17
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.80 E-value=9.3e-08 Score=73.07 Aligned_cols=83 Identities=20% Similarity=0.211 Sum_probs=60.6
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhc
Q 030248 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYA 128 (180)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~ 128 (180)
.+.|.|+||. |++++||++++++. ..++.||+++...++ ...+||+... + .++++.+|.. +.+..+.
T Consensus 53 ~l~V~GdSM~~~~I~~GD~liVd~~-~~~~~Gdivv~~~~g--~~~vKrl~~~-~-------~~~L~s~N~~-y~~i~i~ 120 (139)
T PRK10276 53 FVKASGDSMIDAGISDGDLLIVDSA-ITASHGDIVIAAVDG--EFTVKKLQLR-P-------TVQLIPMNSA-YSPITIS 120 (139)
T ss_pred EEEEecCCCCCCCCCCCCEEEEECC-CCCCCCCEEEEEECC--EEEEEEEEEC-C-------cEEEEcCCCC-CCCEEcC
Confidence 4799999998 68999999999984 457899999998865 3689998752 2 3778888643 3333221
Q ss_pred cCCccccceeEeeEEEEEec
Q 030248 129 QGQLWLKRQHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~v~~~~IiG~v~~~iP 148 (180)
.-+.-+|+|+|++.+.
T Consensus 121 ----~~~~~~IiG~V~~~~~ 136 (139)
T PRK10276 121 ----SEDTLDVFGVVTHIVK 136 (139)
T ss_pred ----CCCcEEEEEEEEEEEE
Confidence 0124589999998763
No 18
>PRK12423 LexA repressor; Provisional
Probab=98.78 E-value=9.7e-08 Score=77.29 Aligned_cols=84 Identities=25% Similarity=0.296 Sum_probs=63.9
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhc
Q 030248 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYA 128 (180)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~ 128 (180)
.+.|.|+||. |+|.+||.+++++. .+++.||++++..++ ..++||+.... + .+.++.+| +.+++..+.
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~-~~~~~Gdivv~~~~~--~~~vKrl~~~~-~------~~~L~s~N-~~y~~i~~~ 184 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS-PEARDGQIVVARLDG--EVTIKRLERSG-D------RIRLLPRN-PAYAPIVVA 184 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC-CcCCCCCEEEEEECC--EEEEEEEEEeC-C------EEEEEcCC-CCCCCEEcC
Confidence 4799999997 79999999999984 678899999998865 36899997653 2 58889985 444444321
Q ss_pred cCCccccceeEeeEEEEEec
Q 030248 129 QGQLWLKRQHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~v~~~~IiG~v~~~iP 148 (180)
. -+.-.|+|+|++.+.
T Consensus 185 ~----~~~~~I~Gvv~g~~r 200 (202)
T PRK12423 185 P----DQDFAIEGVFCGLIR 200 (202)
T ss_pred C----CCcEEEEEEEEEEEE
Confidence 1 135689999998764
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=98.72 E-value=1.9e-07 Score=74.91 Aligned_cols=83 Identities=30% Similarity=0.426 Sum_probs=62.9
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhc
Q 030248 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYA 128 (180)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~ 128 (180)
.+.|.|+||. |.+.+||++++++. .+++.||++++..++ ..++||+....+ .+++..||.. +.+....
T Consensus 113 ~~~V~GdSM~~~~i~~Gd~v~v~~~-~~~~~G~ivvv~~~~--~~~vKrl~~~~~-------~i~L~s~N~~-y~~i~~~ 181 (199)
T TIGR00498 113 LLKVMGDSMVDAGICDGDLLIVRSQ-KDARNGEIVAAMIDG--EVTVKRFYKDGT-------KVELKPENPE-FDPIVLN 181 (199)
T ss_pred EEEecCCCCCCCCCCCCCEEEEecC-CCCCCCCEEEEEECC--EEEEEEEEEECC-------EEEEEcCCCC-CcCCcCC
Confidence 4799999996 68999999999984 678999999999854 479999876422 5788898644 3333221
Q ss_pred cCCccccceeEeeEEEEEec
Q 030248 129 QGQLWLKRQHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~v~~~~IiG~v~~~iP 148 (180)
-+.-+|+|+|++.+.
T Consensus 182 -----~~~~~IiG~Vv~~~r 196 (199)
T TIGR00498 182 -----AEDVTILGKVVGVIR 196 (199)
T ss_pred -----CCcEEEEEEEEEEEE
Confidence 125789999998764
No 20
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=98.61 E-value=6.2e-07 Score=71.54 Aligned_cols=33 Identities=21% Similarity=0.082 Sum_probs=27.9
Q ss_pred eeEEEEecCC-CCCCCchhhccCCccccceeEeeEEEE
Q 030248 109 EVEVLTKGDN-NYGDDRLLYAQGQLWLKRQHIMGRAVG 145 (180)
Q Consensus 109 ~~~~~t~GDn-n~~~D~~~y~~~~~~v~~~~IiG~v~~ 145 (180)
+++|++.||| +.+.|+|.+ ++|++++|+|++.-
T Consensus 141 ~g~~fvlgd~~~~S~DSRYf----G~V~~~~I~G~~~P 174 (178)
T PRK13884 141 ESELLLMSDVSATSFDGRYF----GPINRSQIKTVIRP 174 (178)
T ss_pred CCEEEEECCCCCCCCccccc----CcccHHHEEEEEEE
Confidence 5689999998 568999975 68999999999863
No 21
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=98.35 E-value=6.4e-06 Score=66.97 Aligned_cols=82 Identities=27% Similarity=0.427 Sum_probs=65.3
Q ss_pred eEEEeCCCcc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhc
Q 030248 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYA 128 (180)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~ 128 (180)
.+.|.|+||. +.+.+||+|+|++ ..+.+.||+|+-..++ +...+||...-.+ .+.++-- |+.+.+..
T Consensus 114 ~L~V~GdSM~~~gi~dGDlvvV~~-~~~a~~GdiVvA~i~g-~e~TvKrl~~~g~-------~i~L~p~-Np~~~~i~-- 181 (201)
T COG1974 114 FLRVSGDSMIDAGILDGDLVVVDP-TEDAENGDIVVALIDG-EEATVKRLYRDGN-------QILLKPE-NPAYPPIP-- 181 (201)
T ss_pred EEEecCCccccCcCCCCCEEEEcC-CCCCCCCCEEEEEcCC-CcEEEEEEEEeCC-------EEEEEeC-CCCCCCcc--
Confidence 4799999998 7899999999998 4778999999999998 4589999988643 4677764 55565543
Q ss_pred cCCcccc--ceeEeeEEEEEec
Q 030248 129 QGQLWLK--RQHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~v~--~~~IiG~v~~~iP 148 (180)
++ .-.|+|++++.+.
T Consensus 182 -----~~~~~~~I~G~vvgv~r 198 (201)
T COG1974 182 -----VDADSVTILGKVVGVIR 198 (201)
T ss_pred -----cCccceEEEEEEEEEEe
Confidence 23 5789999998763
No 22
>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=98.26 E-value=6.6e-07 Score=68.50 Aligned_cols=51 Identities=29% Similarity=0.372 Sum_probs=24.8
Q ss_pred cCEEEEEEEeCCCC----C-------------------------------CCeeEEEEecCC-CCCCCchhhccCCcccc
Q 030248 92 IPIVHRVIKVHERQ----D-------------------------------TGEVEVLTKGDN-NYGDDRLLYAQGQLWLK 135 (180)
Q Consensus 92 ~~~ihRVi~~~~~~----~-------------------------------~g~~~~~t~GDn-n~~~D~~~y~~~~~~v~ 135 (180)
..++|||++++||. + .++++|++.||| ..|.|||.| ++|+
T Consensus 50 ~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~vp~g~~~v~gd~~~~S~DSRy~----G~V~ 125 (138)
T PF10502_consen 50 QPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTVPEGEYFVLGDNRPNSFDSRYF----GPVP 125 (138)
T ss_dssp ---------------------------------------S-T----TEEE--TTEEEEE-SBTTS--SHHHH------EE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccCCceEeCCCEEEEecCCCCCccccCEe----cccC
Confidence 37999999999983 0 146789999988 457999986 6899
Q ss_pred ceeEeeEEEEE
Q 030248 136 RQHIMGRAVGF 146 (180)
Q Consensus 136 ~~~IiG~v~~~ 146 (180)
.++|+|++.-.
T Consensus 126 ~~~I~g~~~pl 136 (138)
T PF10502_consen 126 RSQIIGKARPL 136 (138)
T ss_dssp GGGEEEEEEEE
T ss_pred HHHEEEEEEEE
Confidence 99999999754
No 23
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=94.65 E-value=0.017 Score=45.21 Aligned_cols=33 Identities=18% Similarity=0.136 Sum_probs=26.2
Q ss_pred eeEEEEecCC-CCCCCchhhccCCccccceeEeeEEEE
Q 030248 109 EVEVLTKGDN-NYGDDRLLYAQGQLWLKRQHIMGRAVG 145 (180)
Q Consensus 109 ~~~~~t~GDn-n~~~D~~~y~~~~~~v~~~~IiG~v~~ 145 (180)
+.++++++|. +.|.|++.+ ++++.++|+|.+.=
T Consensus 134 ~~el~lL~~~~~~SfDsRYf----Gpipas~vig~aRP 167 (173)
T COG4959 134 PSELLLLTDRSSTSFDSRYF----GPIPASQVIGVARP 167 (173)
T ss_pred CCeEEEEeccCCccccccee----cccCHHHcceeeee
Confidence 4567888886 568999975 68999999998763
No 24
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=79.36 E-value=2.1 Score=29.51 Aligned_cols=30 Identities=30% Similarity=0.521 Sum_probs=21.3
Q ss_pred CCCccc---cccCCCEEEEeecCCCCCcCcEEE
Q 030248 55 SGSMEP---GFKRGDILFLHMSKDPIRAGEIVV 84 (180)
Q Consensus 55 g~SM~P---tl~~GD~v~v~~~~~~~~~GDIVv 84 (180)
++.|.= -+.+||.|+|+..+.++++|||+-
T Consensus 37 ~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~ 69 (75)
T COG0361 37 SGKMRKNRIRILPGDVVLVELSPYDLTKGRIVY 69 (75)
T ss_pred cCcchheeEEeCCCCEEEEEecccccccccEEE
Confidence 455554 567888888888667778888753
No 25
>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=77.10 E-value=2.5 Score=28.54 Aligned_cols=22 Identities=23% Similarity=0.332 Sum_probs=14.5
Q ss_pred ccCCCEEEEeecCCCCCcCcEE
Q 030248 62 FKRGDILFLHMSKDPIRAGEIV 83 (180)
Q Consensus 62 l~~GD~v~v~~~~~~~~~GDIV 83 (180)
+.+||.|.|..++.++.+|+|+
T Consensus 45 I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 45 ILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred ECCCCEEEEEECcccCCcEeEE
Confidence 4667777777655566667665
No 26
>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].
Probab=71.59 E-value=10 Score=32.53 Aligned_cols=38 Identities=29% Similarity=0.581 Sum_probs=32.2
Q ss_pred CCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCC
Q 030248 77 IRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 118 (180)
Q Consensus 77 ~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDn 118 (180)
++.||+|+=++.+.+ ++-||+.+..+ +|+..++++|-+
T Consensus 1 mkiGDIV~RKSYg~D--I~FrIidI~~~--~g~~~aiLkG~d 38 (287)
T PF05582_consen 1 MKIGDIVARKSYGKD--ILFRIIDIKEE--NGKKIAILKGLD 38 (287)
T ss_pred CCCCCEEEeeecCCc--eEEEEEEEEcC--CCceEEEEeCCc
Confidence 478999999999877 99999999875 477788999976
No 27
>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=71.55 E-value=3.3 Score=27.32 Aligned_cols=13 Identities=23% Similarity=0.419 Sum_probs=5.8
Q ss_pred CCCcCcEEEEEeC
Q 030248 76 PIRAGEIVVFNVD 88 (180)
Q Consensus 76 ~~~~GDIVvf~~~ 88 (180)
.+++||.|+....
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 3566666666543
No 28
>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=69.26 E-value=4.5 Score=27.84 Aligned_cols=10 Identities=40% Similarity=0.753 Sum_probs=4.9
Q ss_pred CCcCcEEEEE
Q 030248 77 IRAGEIVVFN 86 (180)
Q Consensus 77 ~~~GDIVvf~ 86 (180)
+++||.|...
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 3445555554
No 29
>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=65.69 E-value=19 Score=27.03 Aligned_cols=38 Identities=21% Similarity=0.175 Sum_probs=23.5
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCC
Q 030248 75 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 118 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDn 118 (180)
+++++||+|+|+..+.. .+.=+++...+ .+.+.+.|=|
T Consensus 72 ~~p~~GDiv~f~~~~~~--HVGi~~g~~~~----~g~i~~lgGN 109 (129)
T TIGR02594 72 SKPAYGCIAVKRRGGGG--HVGFVVGKDKQ----TGTIIVLGGN 109 (129)
T ss_pred CCCCccEEEEEECCCCC--EEEEEEeEcCC----CCEEEEeeCC
Confidence 35799999999865432 45545554432 2367777754
No 30
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=64.39 E-value=6.4 Score=27.46 Aligned_cols=10 Identities=50% Similarity=0.963 Sum_probs=5.1
Q ss_pred CCcCcEEEEE
Q 030248 77 IRAGEIVVFN 86 (180)
Q Consensus 77 ~~~GDIVvf~ 86 (180)
+++||.|+..
T Consensus 44 I~~GD~VlVe 53 (83)
T smart00652 44 IRRGDIVLVD 53 (83)
T ss_pred EcCCCEEEEE
Confidence 4445555554
No 31
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=64.29 E-value=33 Score=25.82 Aligned_cols=58 Identities=17% Similarity=0.253 Sum_probs=27.9
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCCCCCCCchhhccCCccccceeEeeEEEE
Q 030248 75 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQGQLWLKRQHIMGRAVG 145 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDnn~~~D~~~y~~~~~~v~~~~IiG~v~~ 145 (180)
.+++.||.++|-..... .-.+|....-.. +...|+++.|.....+. -+++.++|+++.
T Consensus 41 ~~f~~GDlvLflpt~~~-~~~~~~~~af~~---~~~~YFL~~~s~~~~~~---------~~~~w~vgrI~~ 98 (129)
T PF10377_consen 41 RNFQVGDLVLFLPTRNH-NNKKQPWAAFNV---GCPHYFLHEDSIAANEL---------KRREWIVGRIVS 98 (129)
T ss_pred ecCCCCCEEEEEecCCC-CccccceEEeeC---CCceEEEecccchhccC---------CCCCEEEEEEEE
Confidence 44677777777654322 111222222211 22367777665443221 135667777765
No 32
>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=63.28 E-value=7.1 Score=26.93 Aligned_cols=10 Identities=20% Similarity=0.787 Sum_probs=5.1
Q ss_pred CCcCcEEEEE
Q 030248 77 IRAGEIVVFN 86 (180)
Q Consensus 77 ~~~GDIVvf~ 86 (180)
+++||.|+..
T Consensus 39 I~~GD~VlV~ 48 (78)
T cd04456 39 IKRGDFLIVD 48 (78)
T ss_pred EcCCCEEEEE
Confidence 4455555554
No 33
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=62.65 E-value=8.5 Score=27.28 Aligned_cols=36 Identities=25% Similarity=0.182 Sum_probs=16.6
Q ss_pred EeCCCccc-cccCCCEEEEeec------CCCCCcCcEEEEEeC
Q 030248 53 VLSGSMEP-GFKRGDILFLHMS------KDPIRAGEIVVFNVD 88 (180)
Q Consensus 53 V~g~SM~P-tl~~GD~v~v~~~------~~~~~~GDIVvf~~~ 88 (180)
+.++.|.= .+.+|..++..-+ .-.+..||.|.....
T Consensus 16 ~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~s 58 (87)
T PRK12442 16 VLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELS 58 (87)
T ss_pred ECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEEC
Confidence 33344443 4455555554321 123455666665543
No 34
>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=59.89 E-value=17 Score=30.02 Aligned_cols=30 Identities=23% Similarity=0.186 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 030248 15 QIRQVLTQGVSLGMIVTSALIIWKALMCIT 44 (180)
Q Consensus 15 ~~r~~~~~i~~i~~~i~v~~li~~~l~~~~ 44 (180)
.+|+-...++++++++++++++....++++
T Consensus 7 ~KrRK~N~iLNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 7 QKRRKTNKILNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred HHhhhhhhhHHHHHHHHHHHHHHHhhhhee
Confidence 345555667777766666665555555444
No 35
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=59.87 E-value=8.4 Score=27.90 Aligned_cols=11 Identities=36% Similarity=0.776 Sum_probs=5.7
Q ss_pred CCcCcEEEEEe
Q 030248 77 IRAGEIVVFNV 87 (180)
Q Consensus 77 ~~~GDIVvf~~ 87 (180)
+.+||.|+...
T Consensus 60 I~~GD~VlVe~ 70 (100)
T PRK04012 60 IREGDVVIVAP 70 (100)
T ss_pred ecCCCEEEEEe
Confidence 44555555543
No 36
>TIGR02855 spore_yabG sporulation peptidase YabG. Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K.
Probab=59.37 E-value=21 Score=30.56 Aligned_cols=37 Identities=27% Similarity=0.497 Sum_probs=29.3
Q ss_pred CcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCC
Q 030248 78 RAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 118 (180)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDn 118 (180)
+.||||+=++.+.+ ++=||+.+..+ +|...++++|.+
T Consensus 1 ~iGDIV~RKSYg~D--I~FkIidI~~~--~G~~~aiLkGid 37 (283)
T TIGR02855 1 KIGDIVARKSYGCD--ILFRIIDIIEN--KGGDIAILHGEE 37 (283)
T ss_pred CCCCEEEeeecCCc--cEEEEEEEEcc--CCceEEEEeccc
Confidence 47999999999877 89999999432 355678888876
No 37
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=53.95 E-value=16 Score=26.28 Aligned_cols=36 Identities=25% Similarity=0.523 Sum_probs=26.7
Q ss_pred CeEEEeCCCccccccCCCEEEEee--------cCCCCCcCcEEEEEeC
Q 030248 49 PVVVVLSGSMEPGFKRGDILFLHM--------SKDPIRAGEIVVFNVD 88 (180)
Q Consensus 49 p~~~V~g~SM~Ptl~~GD~v~v~~--------~~~~~~~GDIVvf~~~ 88 (180)
+-+.+.++|.+|. -+++++. ...+++.||.|+|-+.
T Consensus 54 ~~lFi~~gsvrpG----ii~lINd~DWEllekedy~ledgD~ivfiST 97 (101)
T KOG4146|consen 54 DSLFIHHGSVRPG----IIVLINDMDWELLEKEDYPLEDGDHIVFIST 97 (101)
T ss_pred cceEeeCCcCcCc----EEEEEeccchhhhcccccCcccCCEEEEEEe
Confidence 4488999998874 4566654 3577999999999753
No 38
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=53.23 E-value=26 Score=22.70 Aligned_cols=38 Identities=21% Similarity=0.360 Sum_probs=22.7
Q ss_pred CCCccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEE
Q 030248 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (180)
Q Consensus 55 g~SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihR 97 (180)
+.++.| +++.|-.+.|-. -++.||.|.....+.. |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP~---FI~~Gd~I~VdT~~g~--Yv~R 56 (56)
T PF09285_consen 18 SSSYKPATLETGAEIQVPL---FIEEGDKIKVDTRDGS--YVER 56 (56)
T ss_dssp STTEEEEEETTS-EEEEET---T--TT-EEEEETTTTE--EEEE
T ss_pred CCCccEEEEcCCCEEEccc---eecCCCEEEEECCCCe--EeCC
Confidence 445666 456666666633 3789999999877654 7766
No 39
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=51.17 E-value=28 Score=22.54 Aligned_cols=38 Identities=24% Similarity=0.391 Sum_probs=24.9
Q ss_pred CCCccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEE
Q 030248 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (180)
Q Consensus 55 g~SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihR 97 (180)
++|+.| +++.|-.+.|- .=++.||.|..+....+ |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP---~FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T smart00841 18 SGGTKPATLETGAVVQVP---LFINEGDKIKVDTRTGE--YVSR 56 (56)
T ss_pred CCCcceEEECCCCEEEcC---CcccCCCEEEEECCCCc--EEcC
Confidence 345555 56777776663 34788999988876544 6554
No 40
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=49.01 E-value=8.6 Score=26.12 Aligned_cols=35 Identities=23% Similarity=0.407 Sum_probs=18.3
Q ss_pred CCccccccCCCEEEEeec-C-C-CCCcCcEEEEEeCCC
Q 030248 56 GSMEPGFKRGDILFLHMS-K-D-PIRAGEIVVFNVDGR 90 (180)
Q Consensus 56 ~SM~Ptl~~GD~v~v~~~-~-~-~~~~GDIVvf~~~~~ 90 (180)
.||+|.+.+|+.||..-. . . .....=+.+|+.+.+
T Consensus 12 ~~m~P~L~~~~yVF~t~~~~~~~~~~l~pi~~frE~EG 49 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVPGDLADPPGLEPIATFREAEG 49 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-S-GGGGGGG--SEEEEETTE
T ss_pred hhCCcEeCCCCEEEEEecCcccCccCCcceEEEEecCc
Confidence 489999999999998653 1 1 112223466766543
No 41
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.66 E-value=13 Score=27.79 Aligned_cols=17 Identities=35% Similarity=0.638 Sum_probs=14.7
Q ss_pred CCccccccCCCEEEEee
Q 030248 56 GSMEPGFKRGDILFLHM 72 (180)
Q Consensus 56 ~SM~Ptl~~GD~v~v~~ 72 (180)
.||.|.+.+||.|+-..
T Consensus 12 ~smtPeL~~G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELLDGDYVFCTV 28 (134)
T ss_pred HhcCccccCCceEEEEe
Confidence 38999999999999654
No 42
>PF02285 COX8: Cytochrome oxidase c subunit VIII; InterPro: IPR003205 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits.This family is composed of cytochrome c oxidase subunit VIII. ; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG3_Z 3ABM_M 1OCC_Z 3ASO_Z 3AG2_Z 3ABL_M 3AG4_M 3AG1_M 3ASN_M 1OCZ_M ....
Probab=45.82 E-value=11 Score=23.37 Aligned_cols=13 Identities=38% Similarity=0.731 Sum_probs=11.3
Q ss_pred cchHHHHHHHHhh
Q 030248 2 GWIGESIESIKSL 14 (180)
Q Consensus 2 ~~~~~~~~~~~~~ 14 (180)
+|++-++|+||+.
T Consensus 31 gWVLshL~~YKk~ 43 (44)
T PF02285_consen 31 GWVLSHLESYKKR 43 (44)
T ss_dssp HHHHHTHHHHHT-
T ss_pred HHHHHHHHHhhcc
Confidence 7999999999974
No 43
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=45.33 E-value=38 Score=23.29 Aligned_cols=29 Identities=28% Similarity=0.358 Sum_probs=21.4
Q ss_pred ccccccCCCEEEEeec------CCCCCcCcEEEEE
Q 030248 58 MEPGFKRGDILFLHMS------KDPIRAGEIVVFN 86 (180)
Q Consensus 58 M~Ptl~~GD~v~v~~~------~~~~~~GDIVvf~ 86 (180)
|+|.++.||.|.+.+. .-....|++.+-+
T Consensus 1 ~~p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv~~ 35 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDGTFPGKEIGELLVRK 35 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCCCCCCCCCCCEEEcC
Confidence 8999999999998771 2235667777644
No 44
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=45.02 E-value=38 Score=21.94 Aligned_cols=38 Identities=24% Similarity=0.324 Sum_probs=23.4
Q ss_pred CCCccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEE
Q 030248 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (180)
Q Consensus 55 g~SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihR 97 (180)
++++.| +++.|-.+.| +.=++.||.|..+....+ |+.|
T Consensus 18 ~~~~K~A~letG~~i~V---P~FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T cd05794 18 SSGTKPATLETGAEVQV---PLFIKEGEKIKVDTRTGE--YVER 56 (56)
T ss_pred CCCcceEEECCCCEEEc---CCeecCCCEEEEECCCCc--EecC
Confidence 446666 4566655444 233788999888876544 5554
No 45
>COG3895 Predicted periplasmic protein [General function prediction only]
Probab=44.77 E-value=48 Score=24.55 Aligned_cols=45 Identities=29% Similarity=0.376 Sum_probs=33.9
Q ss_pred CCcCcE-EEEEeCCCCcCEEEEEEEeCCCC-CCCeeEEEEecCCCCCC
Q 030248 77 IRAGEI-VVFNVDGREIPIVHRVIKVHERQ-DTGEVEVLTKGDNNYGD 122 (180)
Q Consensus 77 ~~~GDI-Vvf~~~~~~~~~ihRVi~~~~~~-~~g~~~~~t~GDnn~~~ 122 (180)
...||+ +.|-.+++ ..+...++.-.|.+ .+|...+++|||.-.-+
T Consensus 49 ~n~gd~sv~~v~Dg~-tlv~~nviSaSGAkYa~G~YvwWsKG~~A~ly 95 (112)
T COG3895 49 NNAGDISVSFVLDGK-TLVLSNVISASGAKYADGIYVWWSKGDEATLY 95 (112)
T ss_pred ecCCCceEEEEecCC-EEEEeeeeeccCccccCcEEEEEeCCCceEEE
Confidence 577999 99998886 47888998877753 24677789999864444
No 46
>TIGR03024 arch_pef_cterm PEF-C-terminal archaeal protein sorting domain. This domain, distantly related to the PEP-Cterm domain described in model TIGR02595, is found in Methanosarcina mazei in four different proteins, as well as in other archaea such as Methanococcoides burtonii. Several proteins with this domain have their genes only a short distance from a distant homology of EpsH, a proposed integral membrane transpeptidase.
Probab=43.88 E-value=27 Score=19.16 Aligned_cols=19 Identities=26% Similarity=0.450 Sum_probs=13.7
Q ss_pred hhHHHHHHHHHHHhhhhcC
Q 030248 161 PIIKYILIGALGLLVITSK 179 (180)
Q Consensus 161 p~~~~~~~~~~~~~~~~~~ 179 (180)
|.+...+++++|++++++|
T Consensus 5 ~~i~l~I~all~i~~i~~r 23 (26)
T TIGR03024 5 STIALPIIALLAIIVILRR 23 (26)
T ss_pred cchHHHHHHHHHHHHHHhh
Confidence 4445677788888888776
No 47
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=43.62 E-value=34 Score=24.48 Aligned_cols=34 Identities=26% Similarity=0.616 Sum_probs=23.3
Q ss_pred EEEeCCCccccccCCCEEEEee--------cCCCCCcCcEEEEEeC
Q 030248 51 VVVLSGSMEPGFKRGDILFLHM--------SKDPIRAGEIVVFNVD 88 (180)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~v~v~~--------~~~~~~~GDIVvf~~~ 88 (180)
+.+..++..| |-+++++. ...+++.||+|+|-+.
T Consensus 51 ifie~g~lrp----GiI~LINd~DWeLleke~y~ledgDiIvfist 92 (96)
T COG5131 51 IFIEHGELRP----GIICLINDMDWELLEKERYPLEDGDIIVFIST 92 (96)
T ss_pred eeecCCCCcc----cEEEEEcCccHhhhhcccccCCCCCEEEEEec
Confidence 5666666554 55666654 2467999999999753
No 48
>PLN00208 translation initiation factor (eIF); Provisional
Probab=39.70 E-value=26 Score=27.20 Aligned_cols=23 Identities=13% Similarity=0.397 Sum_probs=12.1
Q ss_pred ccCCCEEEEeecCCCCCcCcEEE
Q 030248 62 FKRGDILFLHMSKDPIRAGEIVV 84 (180)
Q Consensus 62 l~~GD~v~v~~~~~~~~~GDIVv 84 (180)
+.+||+|+|.....+..+|||+-
T Consensus 71 I~~GD~VlVel~~~d~~KgdIv~ 93 (145)
T PLN00208 71 IAAGDIILVGLRDYQDDKADVIL 93 (145)
T ss_pred ecCCCEEEEEccCCCCCEEEEEE
Confidence 45566666655334455555544
No 49
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=38.97 E-value=26 Score=27.41 Aligned_cols=25 Identities=12% Similarity=0.290 Sum_probs=15.9
Q ss_pred ccCCCEEEEeecCCCCCcCcEEEEE
Q 030248 62 FKRGDILFLHMSKDPIRAGEIVVFN 86 (180)
Q Consensus 62 l~~GD~v~v~~~~~~~~~GDIVvf~ 86 (180)
+.+||+|+|.....+..+|||+--.
T Consensus 71 I~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 71 INIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred ecCCCEEEEeccCCCCCEEEEEEEc
Confidence 4677777777655556667765533
No 50
>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=38.66 E-value=32 Score=26.56 Aligned_cols=38 Identities=8% Similarity=0.136 Sum_probs=26.4
Q ss_pred EEEeCCCccccccCCCEEEEeec-CCCCCcCcEEEEEeC
Q 030248 51 VVVLSGSMEPGFKRGDILFLHMS-KDPIRAGEIVVFNVD 88 (180)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~v~v~~~-~~~~~~GDIVvf~~~ 88 (180)
....++||...|...=.-.+... ..++++|||+++...
T Consensus 49 ~~~nT~tl~~~L~~~G~~~I~~~~~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 49 SAGNTETLHDWLKKNGFKKISENVDWNLQRGDIFIWGRR 87 (145)
T ss_pred CccCHHHHHHHHhhCCcEEeccCCcccccCCCEEEEcCC
Confidence 35677899987766555555442 247899999998654
No 51
>PF14118 YfzA: YfzA-like protein
Probab=36.82 E-value=29 Score=24.94 Aligned_cols=16 Identities=25% Similarity=0.534 Sum_probs=12.9
Q ss_pred EEeCCCccccccCCCE
Q 030248 52 VVLSGSMEPGFKRGDI 67 (180)
Q Consensus 52 ~V~g~SM~Ptl~~GD~ 67 (180)
.+++.|+.|.+++||.
T Consensus 29 ~~d~t~w~pnf~~g~~ 44 (94)
T PF14118_consen 29 IFDGTGWGPNFNEGDF 44 (94)
T ss_pred HhhccccccccCCCch
Confidence 4568899999998864
No 52
>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=36.37 E-value=29 Score=23.99 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=5.1
Q ss_pred CCcCcEEEEE
Q 030248 77 IRAGEIVVFN 86 (180)
Q Consensus 77 ~~~GDIVvf~ 86 (180)
+++||+|+..
T Consensus 39 IkrGd~VlV~ 48 (78)
T cd05792 39 IKRGDFVLVE 48 (78)
T ss_pred EEeCCEEEEE
Confidence 4455555554
No 53
>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=36.03 E-value=89 Score=22.93 Aligned_cols=28 Identities=39% Similarity=0.733 Sum_probs=16.9
Q ss_pred CCcCcEEEEEeCCC-CcCEEEEEEEeCCC
Q 030248 77 IRAGEIVVFNVDGR-EIPIVHRVIKVHER 104 (180)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ihRVi~~~~~ 104 (180)
++.||-|.++.++. ..++|.||..+-.+
T Consensus 4 ~~vGD~V~v~~~~~~~~pyIgrI~~i~e~ 32 (121)
T cd04714 4 IRVGDCVLFKSPGRPSLPYVARIESLWED 32 (121)
T ss_pred EEcCCEEEEeCCCCCCCCEEEEEEEEEEc
Confidence 45666666665543 34677777776544
No 54
>COG4393 Predicted membrane protein [Function unknown]
Probab=35.73 E-value=3.2e+02 Score=24.36 Aligned_cols=11 Identities=18% Similarity=0.492 Sum_probs=7.5
Q ss_pred EEEEEEEeCCC
Q 030248 94 IVHRVIKVHER 104 (180)
Q Consensus 94 ~ihRVi~~~~~ 104 (180)
-.||...+..|
T Consensus 302 kLHRF~yIA~d 312 (405)
T COG4393 302 KLHRFVYIADD 312 (405)
T ss_pred ceEEEEEEccC
Confidence 56777777665
No 55
>PF12751 Vac7: Vacuolar segregation subunit 7; InterPro: IPR024260 Vac7 is localised at the vacuole membrane, a location which is consistent with its involvement in vacuole morphology and inheritance []. Vac7 has been shown to function as an upstream regulator of the Fab1 lipid kinase pathway []. The Fab1 lipid pathway is important for correct regulation of membrane trafficking events.
Probab=35.19 E-value=64 Score=28.97 Aligned_cols=48 Identities=15% Similarity=0.127 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCCCEEEEe
Q 030248 24 VSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLH 71 (180)
Q Consensus 24 ~~i~~~i~v~~li~~~l~~~~~~~~p~~~V~g~SM~Ptl~~GD~v~v~ 71 (180)
..+++++++++++-..+.+++++.+|+.-|.=-+|.-.|-.-|.++++
T Consensus 304 ~c~~~~i~~lL~ig~~~gFv~AttKpL~~v~v~~I~NVlaS~qELmfd 351 (387)
T PF12751_consen 304 SCIYLSILLLLVIGFAIGFVFATTKPLTDVQVVSIQNVLASEQELMFD 351 (387)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhcCcccccceEEEeeeeeeccceEEEe
Confidence 333334444444444444445666776555555666555555555543
No 56
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=34.75 E-value=29 Score=25.83 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=16.2
Q ss_pred EEeCCCccccccCCCEEEEee
Q 030248 52 VVLSGSMEPGFKRGDILFLHM 72 (180)
Q Consensus 52 ~V~g~SM~Ptl~~GD~v~v~~ 72 (180)
.-.+++|.|.|+.||.|++.-
T Consensus 46 I~~~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 46 IALSDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred EEccCcccCcCCCCCEEEEec
Confidence 344578899999999999864
No 57
>COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=34.03 E-value=84 Score=26.63 Aligned_cols=38 Identities=16% Similarity=0.439 Sum_probs=26.9
Q ss_pred cccCCCEEEEeec--CCCCCcCcEEEEEeCCCCcCEEEEEE
Q 030248 61 GFKRGDILFLHMS--KDPIRAGEIVVFNVDGREIPIVHRVI 99 (180)
Q Consensus 61 tl~~GD~v~v~~~--~~~~~~GDIVvf~~~~~~~~~ihRVi 99 (180)
||++||+++.-.+ ...++.||++....++-. .+-.+|.
T Consensus 224 tL~pGDvI~TGTP~Gvg~l~~GD~v~~~iegiG-~l~n~v~ 263 (266)
T COG0179 224 TLEPGDVILTGTPSGVGFLKPGDVVEVEIEGIG-ELENTVV 263 (266)
T ss_pred ccCCCCEEEeCCCCCcccCCCCCEEEEEeccee-EEEEEEe
Confidence 7899999997542 356899999888887642 3444444
No 58
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=32.41 E-value=46 Score=22.22 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=13.8
Q ss_pred CCCcCcEEEEEe--CCC-CcCEEEE
Q 030248 76 PIRAGEIVVFNV--DGR-EIPIVHR 97 (180)
Q Consensus 76 ~~~~GDIVvf~~--~~~-~~~~ihR 97 (180)
.+.+||.|.|.. .+. ...+++|
T Consensus 46 ~i~vGD~V~ve~~~~~~~~g~Iv~r 70 (72)
T PRK00276 46 RILPGDKVTVELSPYDLTKGRITYR 70 (72)
T ss_pred ccCCCCEEEEEEcccCCCeEEEEEE
Confidence 367899999983 221 2356665
No 59
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=32.17 E-value=1.2e+02 Score=18.24 Aligned_cols=29 Identities=10% Similarity=0.167 Sum_probs=20.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030248 13 SLQIRQVLTQGVSLGMIVTSALIIWKALM 41 (180)
Q Consensus 13 ~~~~r~~~~~i~~i~~~i~v~~li~~~l~ 41 (180)
.|.+|+++.+++.-.+++.++.+++-++.
T Consensus 5 dm~RR~lmN~ll~Gava~~a~~~lyP~~~ 33 (39)
T PF08802_consen 5 DMSRRQLMNLLLGGAVAVPAGGMLYPYVK 33 (39)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHhhHHHHHHHHhhhhee
Confidence 48899999998887777766666654444
No 60
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=30.95 E-value=33 Score=25.48 Aligned_cols=8 Identities=13% Similarity=-0.255 Sum_probs=3.2
Q ss_pred HHHHHHHH
Q 030248 22 QGVSLGMI 29 (180)
Q Consensus 22 ~i~~i~~~ 29 (180)
|++.++++
T Consensus 2 W~l~~iii 9 (130)
T PF12273_consen 2 WVLFAIII 9 (130)
T ss_pred eeeHHHHH
Confidence 44443333
No 61
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=30.11 E-value=95 Score=19.65 Aligned_cols=25 Identities=16% Similarity=0.421 Sum_probs=16.2
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEE
Q 030248 75 DPIRAGEIVVFNVDGREIPIVHRVI 99 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi 99 (180)
..+-.||-|.+..++.+..+|+++.
T Consensus 36 ~~~~VGD~V~~~~~~~~~~~I~~vl 60 (68)
T cd04466 36 NPPAVGDRVEFEPEDDGEGVIEEIL 60 (68)
T ss_pred CCCCCCcEEEEEECCCCcEEEEEEe
Confidence 3478899999976543334555554
No 62
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=29.98 E-value=1e+02 Score=22.37 Aligned_cols=30 Identities=17% Similarity=0.475 Sum_probs=23.9
Q ss_pred cCCCCCcCcEEEEEeCCCCcCEEEEEEEeCCC
Q 030248 73 SKDPIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (180)
Q Consensus 73 ~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~~ 104 (180)
+..+++.||++..+..+.. +.=+|.+++..
T Consensus 45 pS~~VK~GD~l~i~~~~~~--~~v~Vl~~~~~ 74 (100)
T COG1188 45 PSKEVKVGDILTIRFGNKE--FTVKVLALGEQ 74 (100)
T ss_pred cccccCCCCEEEEEeCCcE--EEEEEEecccc
Confidence 4578999999999988754 78888887653
No 63
>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=29.41 E-value=1.2e+02 Score=22.65 Aligned_cols=10 Identities=20% Similarity=-0.087 Sum_probs=7.6
Q ss_pred eeEeeEEEEE
Q 030248 137 QHIMGRAVGF 146 (180)
Q Consensus 137 ~~IiG~v~~~ 146 (180)
.+|.|++...
T Consensus 89 ~~I~~k~~V~ 98 (130)
T cd04712 89 TEIKGVHKVD 98 (130)
T ss_pred ceeEEEEEEE
Confidence 4888988765
No 64
>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=27.57 E-value=1.6e+02 Score=21.53 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=20.6
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEeCC
Q 030248 75 DPIRAGEIVVFNVDGREIPIVHRVIKVHE 103 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi~~~~ 103 (180)
..+++||.++|+.-.....+.-+|..+..
T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V~~i~~ 58 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKVVDIRK 58 (109)
T ss_pred hcCCCCCEEEEEEcCCCcEEEEEEEEEEe
Confidence 36999999999864333357777777753
No 65
>KOG0584 consensus Serine/threonine protein kinase [General function prediction only]
Probab=27.56 E-value=73 Score=30.37 Aligned_cols=77 Identities=16% Similarity=0.227 Sum_probs=53.0
Q ss_pred hHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccccCC---CEEEEeecCCCCCcC
Q 030248 4 IGESIESIKSLQIRQVLTQGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRG---DILFLHMSKDPIRAG 80 (180)
Q Consensus 4 ~~~~~~~~~~~~~r~~~~~i~~i~~~i~v~~li~~~l~~~~~~~~p~~~V~g~SM~Ptl~~G---D~v~v~~~~~~~~~G 80 (180)
|.+-...+++++.|-+..|...|+--+ . ++.++.| |.|+.. |.||++-...++|.|
T Consensus 130 Lr~Y~kk~~~vn~kaik~W~RQILkGL----------~-yLHs~~P----------PIIHRDLKCDNIFinG~~G~VKIG 188 (632)
T KOG0584|consen 130 LREYRKKHRRVNIKAIKSWCRQILKGL----------V-YLHSQDP----------PIIHRDLKCDNIFVNGNLGEVKIG 188 (632)
T ss_pred HHHHHHHhccCCHHHHHHHHHHHHHHh----------h-hhhcCCC----------CccccccccceEEEcCCcCceeec
Confidence 444455667788888999998865322 1 1244566 777766 999999877899999
Q ss_pred cEEEEEeCCCCcCEEEEEEEeCC
Q 030248 81 EIVVFNVDGREIPIVHRVIKVHE 103 (180)
Q Consensus 81 DIVvf~~~~~~~~~ihRVi~~~~ 103 (180)
|.=+-..-.. ...+.|||.|.
T Consensus 189 DLGLAtl~r~--s~aksvIGTPE 209 (632)
T KOG0584|consen 189 DLGLATLLRK--SHAKSVIGTPE 209 (632)
T ss_pred chhHHHHhhc--cccceeccCcc
Confidence 9866543332 25566999885
No 66
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=27.30 E-value=1e+02 Score=24.51 Aligned_cols=38 Identities=24% Similarity=0.391 Sum_probs=25.9
Q ss_pred CCccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030248 56 GSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (180)
Q Consensus 56 ~SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRV 98 (180)
+|+.| +|+.|=.|-| +.=++.||.|..+....+ |+.|+
T Consensus 146 ~~~K~A~letG~~v~V---P~fi~~Gd~I~v~T~~g~--y~~R~ 184 (184)
T TIGR00038 146 GGTKPATLETGAVVQV---PLFIEEGEKIKVDTRTGE--YVERA 184 (184)
T ss_pred CCcccEEEcCCCEEEe---CCcccCCCEEEEECCCCc--EEecC
Confidence 35666 4566655555 234889999999887655 88774
No 67
>CHL00010 infA translation initiation factor 1
Probab=27.14 E-value=67 Score=21.89 Aligned_cols=22 Identities=23% Similarity=0.241 Sum_probs=13.5
Q ss_pred CCcCcEEEEEe--CCC-CcCEEEEE
Q 030248 77 IRAGEIVVFNV--DGR-EIPIVHRV 98 (180)
Q Consensus 77 ~~~GDIVvf~~--~~~-~~~~ihRV 98 (180)
+.+||.|.|.. .+. ...++||-
T Consensus 47 ~~vGD~V~ve~~~~~~~~g~Ii~r~ 71 (78)
T CHL00010 47 ILPGDRVKVELSPYDLTKGRIIYRL 71 (78)
T ss_pred cCCCCEEEEEEcccCCCeEEEEEEe
Confidence 67799999983 221 23466654
No 68
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.
Probab=26.70 E-value=2.1e+02 Score=22.53 Aligned_cols=28 Identities=14% Similarity=0.185 Sum_probs=17.2
Q ss_pred EEEEeecCCCCCcCcEEEEEeCCCCcCEEE
Q 030248 67 ILFLHMSKDPIRAGEIVVFNVDGREIPIVH 96 (180)
Q Consensus 67 ~v~v~~~~~~~~~GDIVvf~~~~~~~~~ih 96 (180)
.+-+. .++++.|.-..+..++....+.|
T Consensus 41 ~~~v~--l~eL~pG~~~~v~~~GkpI~I~~ 68 (174)
T TIGR01416 41 PTEVD--VSKIQPGQQLTVEWRGKPVFIRR 68 (174)
T ss_pred cEEEE--HHHCCCCCeEEEEECCeEEEEEe
Confidence 34452 36678888888887776433333
No 69
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=26.55 E-value=2.3e+02 Score=25.46 Aligned_cols=38 Identities=13% Similarity=-0.012 Sum_probs=18.2
Q ss_pred hHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030248 4 IGESIESIKSLQIRQVLTQGVSLGMIVTSALIIWKALMC 42 (180)
Q Consensus 4 ~~~~~~~~~~~~~r~~~~~i~~i~~~i~v~~li~~~l~~ 42 (180)
+.++=|-|.+...+.. .+++.+++++++++++|.++.-
T Consensus 5 ~~~s~~~~~~~~~~~~-~~~~~~~~~~~~~~~~WA~~~~ 42 (457)
T TIGR01000 5 FLESSEFYQKRYHNFS-TLVIVPIFLLLVFLVLFSLFAK 42 (457)
T ss_pred hhhHHHHHHhcCCCcc-hhHHHHHHHHHHHHHHHHHhEe
Confidence 3455555555333333 3343344445555666665553
No 70
>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=25.54 E-value=58 Score=20.93 Aligned_cols=22 Identities=27% Similarity=0.255 Sum_probs=14.3
Q ss_pred CCCcCcEEEEEeC--CC-CcCEEEE
Q 030248 76 PIRAGEIVVFNVD--GR-EIPIVHR 97 (180)
Q Consensus 76 ~~~~GDIVvf~~~--~~-~~~~ihR 97 (180)
.+..||.|.|+.. ++ ...++||
T Consensus 40 ~~~vGD~V~~~~~~~~~~~g~I~~~ 64 (64)
T cd04451 40 RILPGDRVKVELSPYDLTKGRIVYR 64 (64)
T ss_pred ccCCCCEEEEEEeecCCCEEEEEEC
Confidence 4788999999843 32 2356665
No 71
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=24.79 E-value=74 Score=22.90 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=6.2
Q ss_pred CCcCcEEEEE
Q 030248 77 IRAGEIVVFN 86 (180)
Q Consensus 77 ~~~GDIVvf~ 86 (180)
+++||.|+..
T Consensus 58 I~~GD~VlVs 67 (99)
T TIGR00523 58 IREGDVVIVK 67 (99)
T ss_pred ecCCCEEEEE
Confidence 5666666663
No 72
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=24.67 E-value=1.8e+02 Score=24.82 Aligned_cols=15 Identities=20% Similarity=0.122 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHHHH
Q 030248 28 MIVTSALIIWKALMC 42 (180)
Q Consensus 28 ~~i~v~~li~~~l~~ 42 (180)
+++++++.|++.|.+
T Consensus 176 lALflAFaINFILLF 190 (274)
T PF06459_consen 176 LALFLAFAINFILLF 190 (274)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456666677554443
No 73
>PRK14578 elongation factor P; Provisional
Probab=24.62 E-value=1.3e+02 Score=24.15 Aligned_cols=37 Identities=14% Similarity=0.209 Sum_probs=24.1
Q ss_pred Cccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030248 57 SMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (180)
Q Consensus 57 SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRV 98 (180)
+..| +++.|=.|-| +.=++.||.|..+....+ |+.|+
T Consensus 150 ~~KpA~leTG~~v~V---P~FI~~Gd~I~VdT~~g~--Y~~R~ 187 (187)
T PRK14578 150 QTKEAVLETGLRLQV---PPYLESGEKIKVDTRDGR--FISRA 187 (187)
T ss_pred CcceEEEcCCCEEEe---CCcccCCCEEEEECCCCc--EEeeC
Confidence 4444 4566655555 234788999988877654 88774
No 74
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=24.45 E-value=84 Score=21.41 Aligned_cols=16 Identities=25% Similarity=0.727 Sum_probs=10.1
Q ss_pred CCCCCcCcEEEEEeCC
Q 030248 74 KDPIRAGEIVVFNVDG 89 (180)
Q Consensus 74 ~~~~~~GDIVvf~~~~ 89 (180)
...++.||+++|+..+
T Consensus 71 ~n~L~~GD~~~F~~~~ 86 (100)
T PF02362_consen 71 DNGLKEGDVCVFELIG 86 (100)
T ss_dssp HCT--TT-EEEEEE-S
T ss_pred HcCCCCCCEEEEEEec
Confidence 4679999999999764
No 75
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=24.24 E-value=2.4e+02 Score=19.21 Aligned_cols=36 Identities=19% Similarity=0.311 Sum_probs=21.3
Q ss_pred CCCEEE-EeecCCCCCcCcEEEEEeCCCCcCEEEEEEE
Q 030248 64 RGDILF-LHMSKDPIRAGEIVVFNVDGREIPIVHRVIK 100 (180)
Q Consensus 64 ~GD~v~-v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~ 100 (180)
.|..-+ ++++..++++||+...+.-++. -++.|.+.
T Consensus 15 ~G~KtfEiRkNDRdf~VGD~L~L~E~~~~-~YTGr~~~ 51 (72)
T PF12961_consen 15 SGRKTFEIRKNDRDFQVGDILVLREWDNG-EYTGREIE 51 (72)
T ss_pred CCCceEEEEecCCCCCCCCEEEEEEecCC-CccccEEE
Confidence 343333 4556678999999998753321 24444443
No 76
>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=24.24 E-value=86 Score=22.06 Aligned_cols=30 Identities=23% Similarity=0.482 Sum_probs=17.7
Q ss_pred ccccCCCEEEEee-cCCCCCcCcEEEEEeCC
Q 030248 60 PGFKRGDILFLHM-SKDPIRAGEIVVFNVDG 89 (180)
Q Consensus 60 Ptl~~GD~v~v~~-~~~~~~~GDIVvf~~~~ 89 (180)
||-..+|.+.-+. .+.+++.||.++|..-|
T Consensus 65 ptC~~~D~i~~~~~lP~~l~~GD~l~f~~~G 95 (116)
T PF00278_consen 65 PTCDSGDVIARDVMLPKELEVGDWLVFENMG 95 (116)
T ss_dssp SSSSTTSEEEEEEEEESTTTTT-EEEESS-S
T ss_pred CCcCCCceEeeeccCCCCCCCCCEEEEecCc
Confidence 4556667776433 23478888888887544
No 77
>PRK12426 elongation factor P; Provisional
Probab=23.40 E-value=1.4e+02 Score=24.06 Aligned_cols=39 Identities=18% Similarity=0.341 Sum_probs=25.7
Q ss_pred CCCccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030248 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (180)
Q Consensus 55 g~SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRV 98 (180)
+++..| +++.|=.|-| +.=++.||.|.......+ |+.|+
T Consensus 146 t~~~KpAtLeTG~~V~V---P~FI~~Gd~IkVdT~~ge--Y~~R~ 185 (185)
T PRK12426 146 SGGAKKALLETGVEVLV---PPFVEIGDVIKVDTRTCE--YIQRV 185 (185)
T ss_pred CCCcccEEEcCCCEEEe---CCcccCCCEEEEECCCCe--EEeeC
Confidence 345565 5666755555 234788999988877654 77774
No 78
>COG0690 SecE Preprotein translocase subunit SecE [Intracellular trafficking and secretion]
Probab=23.20 E-value=1.6e+02 Score=19.76 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=9.4
Q ss_pred cchHHHHHHHHhhh
Q 030248 2 GWIGESIESIKSLQ 15 (180)
Q Consensus 2 ~~~~~~~~~~~~~~ 15 (180)
+++.+..+|.++-.
T Consensus 22 ~f~~~~~~E~~KV~ 35 (73)
T COG0690 22 NFFKEVRKELKKVV 35 (73)
T ss_pred HHHHHHHHHHHhcc
Confidence 45667777777764
No 79
>KOG0557 consensus Dihydrolipoamide acetyltransferase [Energy production and conversion]
Probab=23.02 E-value=1.3e+02 Score=27.74 Aligned_cols=38 Identities=16% Similarity=0.298 Sum_probs=30.6
Q ss_pred CeEEEeCCCccccccCCCEEEEee-cCCCCCcCcEEEEE
Q 030248 49 PVVVVLSGSMEPGFKRGDILFLHM-SKDPIRAGEIVVFN 86 (180)
Q Consensus 49 p~~~V~g~SM~Ptl~~GD~v~v~~-~~~~~~~GDIVvf~ 86 (180)
+...+.=.+|.||++.|.++--.+ .-+.++.||++.=-
T Consensus 37 ~h~~i~MPALSPTMeeGnIvsW~kKeGdkls~GDvl~EV 75 (470)
T KOG0557|consen 37 AHKTFSMPALSPTMEEGNIVSWKKKEGDKLSAGDVLLEV 75 (470)
T ss_pred cceEeecCCCCccccCCceeeEeeccCCccCCCceEEEE
Confidence 346677779999999999998776 55779999998743
No 80
>PRK04542 elongation factor P; Provisional
Probab=22.79 E-value=1.7e+02 Score=23.63 Aligned_cols=37 Identities=22% Similarity=0.431 Sum_probs=24.9
Q ss_pred Cccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030248 57 SMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (180)
Q Consensus 57 SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRV 98 (180)
+..| +++.|=.|-| +.=++.||.|..+....+ |+.|+
T Consensus 151 ~~KpAtLetG~~v~V---P~FI~~Gd~I~VdT~tge--Yv~R~ 188 (189)
T PRK04542 151 RTKPATLSTGLVIQV---PEYISTGEKIRINTEERK--FMGRA 188 (189)
T ss_pred CCccEEEcCCCEEEe---CCcccCCCEEEEECCCCc--EEeec
Confidence 4454 4566655555 234789999998877654 88875
No 81
>PRK14766 lipoprotein signal peptidase; Provisional
Probab=22.69 E-value=1.6e+02 Score=24.00 Aligned_cols=32 Identities=13% Similarity=0.203 Sum_probs=25.6
Q ss_pred chHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Q 030248 3 WIGESIESIKSLQIRQVLTQGVSLGMIVTSAL 34 (180)
Q Consensus 3 ~~~~~~~~~~~~~~r~~~~~i~~i~~~i~v~~ 34 (180)
||++.+-|.|---+.+-.+|...+++++.+++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 32 (201)
T PRK14766 1 WIKDKLVELKVFLKNHNYLWKFKLIVCLPIFI 32 (201)
T ss_pred ChHHHHHHHHHHHhccchhhHHHHHHHHHHHH
Confidence 89999999998888888888887776655543
No 82
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=22.60 E-value=2e+02 Score=17.86 Aligned_cols=46 Identities=20% Similarity=0.240 Sum_probs=25.8
Q ss_pred CCcCcEEEEEeCCCCcCEEEEEEEeCCCCCCCeeEEEEecCC-CCCCCch
Q 030248 77 IRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN-NYGDDRL 125 (180)
Q Consensus 77 ~~~GDIVvf~~~~~~~~~ihRVi~~~~~~~~g~~~~~t~GDn-n~~~D~~ 125 (180)
++.|+.+.....+ +..+--+|+.+..++ +...|.+.=.+ |...|.+
T Consensus 1 ~~vG~~v~~~~~~-~~~y~A~I~~~r~~~--~~~~YyVHY~g~nkR~DeW 47 (55)
T PF11717_consen 1 FEVGEKVLCKYKD-GQWYEAKILDIREKN--GEPEYYVHYQGWNKRLDEW 47 (55)
T ss_dssp --TTEEEEEEETT-TEEEEEEEEEEEECT--TCEEEEEEETTSTGCC-EE
T ss_pred CCcCCEEEEEECC-CcEEEEEEEEEEecC--CCEEEEEEcCCCCCCceee
Confidence 3567777776622 246888888876542 33345444333 7777865
No 83
>COG4473 EcsB Predicted ABC-type exoprotein transport system, permease component [Intracellular trafficking and secretion]
Probab=22.54 E-value=2e+02 Score=25.82 Aligned_cols=65 Identities=20% Similarity=0.212 Sum_probs=38.9
Q ss_pred HHHHHhhhH--HHHHHHHHHHHHHHHHHHHHHHHHHHhhCC---CCC---------eEEEeCCCccccccCCCEEEEee
Q 030248 8 IESIKSLQI--RQVLTQGVSLGMIVTSALIIWKALMCITGS---ESP---------VVVVLSGSMEPGFKRGDILFLHM 72 (180)
Q Consensus 8 ~~~~~~~~~--r~~~~~i~~i~~~i~v~~li~~~l~~~~~~---~~p---------~~~V~g~SM~Ptl~~GD~v~v~~ 72 (180)
-+++|...+ |-++++-..+.+.+++++.++.+....-+. +.| +.....+||++.++++|.|+.-+
T Consensus 12 ~~~~Ke~~~YLryv~Ndhfvl~L~ilLg~~i~qY~~llk~~p~~~~p~~~l~~iv~~lll~~g~vrT~LkeaDkVFLL~ 90 (379)
T COG4473 12 QAYYKEQNKYLRYVFNDHFVLFLLILLGFGIYQYSQLLKHIPLNHFPIFPLLAIVIVLLLSIGSVRTFLKEADKVFLLP 90 (379)
T ss_pred HHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHHHHHhhHHHHHhCCCEEEEec
Confidence 344444332 556666666666666666665544433111 112 12345789999999999999755
No 84
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=22.34 E-value=1.3e+02 Score=24.21 Aligned_cols=38 Identities=21% Similarity=0.363 Sum_probs=25.0
Q ss_pred CCccc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030248 56 GSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (180)
Q Consensus 56 ~SM~P-tl~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRV 98 (180)
+++.| +++.|=.|-| +.=++.||.|.......+ |+.|+
T Consensus 148 ~~~KpA~LeTG~~v~V---P~FI~~Gd~IkVdTrtg~--Y~~R~ 186 (186)
T TIGR02178 148 KRPKPAKLITGLVVQV---PEYITTGERILINTTERA--FMGRA 186 (186)
T ss_pred CCcccEEEcCCCEEEe---CCeecCCCEEEEECCCCc--EEccC
Confidence 34555 4566655555 234788999998877654 77774
No 85
>TIGR00964 secE_bact preprotein translocase, SecE subunit, bacterial. This model represents exclusively the bacterial (and some organellar) SecE protein. SecE is part of the core heterotrimer, SecYEG, of the Sec preprotein translocase system. Other components are the ATPase SecA, a cytosolic chaperone SecB, and an accessory complex of SecDF and YajC.
Probab=21.59 E-value=2.1e+02 Score=17.93 Aligned_cols=24 Identities=13% Similarity=0.250 Sum_probs=14.8
Q ss_pred cchHHHHHHHHhhh---HHHHHHHHHH
Q 030248 2 GWIGESIESIKSLQ---IRQVLTQGVS 25 (180)
Q Consensus 2 ~~~~~~~~~~~~~~---~r~~~~~i~~ 25 (180)
+++.+..+|.|+-. ++++.+....
T Consensus 3 ~f~~~~~~ElkkV~WPt~~e~~~~t~~ 29 (55)
T TIGR00964 3 KFFKEVKAELKKVVWPSRKELITYTIV 29 (55)
T ss_pred hHHHHHHHHHhcCcCcCHHHHHhHHHH
Confidence 46778888888764 3455444433
No 86
>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=21.22 E-value=1e+02 Score=21.62 Aligned_cols=27 Identities=30% Similarity=0.505 Sum_probs=15.4
Q ss_pred CcCcEEEEEeCC-CCcCEEEEEEEeCCC
Q 030248 78 RAGEIVVFNVDG-REIPIVHRVIKVHER 104 (180)
Q Consensus 78 ~~GDIVvf~~~~-~~~~~ihRVi~~~~~ 104 (180)
+.||.|..+.++ ...+++.||..+..+
T Consensus 4 ~vGD~V~v~~~~~~~~~~v~~I~~i~~~ 31 (119)
T PF01426_consen 4 KVGDFVYVKPDDPPEPPYVARIEEIWED 31 (119)
T ss_dssp ETTSEEEEECTSTTSEEEEEEEEEEEEE
T ss_pred eCCCEEEEeCCCCCCCCEEEEEEEEEcC
Confidence 455555555544 234677777766644
No 87
>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=20.99 E-value=1.3e+02 Score=21.87 Aligned_cols=28 Identities=21% Similarity=0.392 Sum_probs=18.2
Q ss_pred CCcCcEEEEEeCCC-CcCEEEEEEEeCCC
Q 030248 77 IRAGEIVVFNVDGR-EIPIVHRVIKVHER 104 (180)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ihRVi~~~~~ 104 (180)
++.||-|.+++++. ..+++-||..+-.+
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 32 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERLWKD 32 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEEEEC
Confidence 45677777766543 45677888776654
No 88
>smart00439 BAH Bromo adjacent homology domain.
Probab=20.76 E-value=1.6e+02 Score=20.50 Aligned_cols=14 Identities=14% Similarity=0.214 Sum_probs=10.4
Q ss_pred cccceeEeeEEEEE
Q 030248 133 WLKRQHIMGRAVGF 146 (180)
Q Consensus 133 ~v~~~~IiG~v~~~ 146 (180)
.++.+.|.|++.-.
T Consensus 70 ~i~~~~I~~kc~V~ 83 (120)
T smart00439 70 TVPLSDIIGKCNVL 83 (120)
T ss_pred cCChHHeeeEEEEE
Confidence 46778888888764
No 89
>KOG4544 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.43 E-value=3.7e+02 Score=20.69 Aligned_cols=34 Identities=12% Similarity=0.126 Sum_probs=22.6
Q ss_pred hHHHHHHHHhhh-----HHHHHHHHHHHHHHHHHHHHHH
Q 030248 4 IGESIESIKSLQ-----IRQVLTQGVSLGMIVTSALIIW 37 (180)
Q Consensus 4 ~~~~~~~~~~~~-----~r~~~~~i~~i~~~i~v~~li~ 37 (180)
+|.++.|=+++. -|+.++|+..+....+++++..
T Consensus 32 im~~l~~~rq~A~~Ia~~RE~f~w~~~f~~~avv~laa~ 70 (144)
T KOG4544|consen 32 IMAHLQERRQIAFKIAEEREKFNWIACFGSLAVVLLAAS 70 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466777766664 3788999988876555554443
Done!