Query 030254
Match_columns 180
No_of_seqs 142 out of 1414
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 10:56:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030254hhsearch_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 1.2E-41 2.6E-46 262.1 14.6 179 1-180 1-180 (180)
2 TIGR02228 sigpep_I_arch signal 100.0 9.8E-30 2.1E-34 199.9 17.0 143 23-175 6-150 (158)
3 TIGR02227 sigpep_I_bact signal 99.8 1E-20 2.3E-25 149.0 11.6 97 48-149 21-162 (163)
4 PRK10861 signal peptidase I; P 99.7 3E-17 6.4E-22 142.0 13.3 60 45-105 80-155 (324)
5 cd06530 S26_SPase_I The S26 Ty 99.7 1E-16 2.3E-21 112.5 8.4 79 50-143 2-85 (85)
6 TIGR02754 sod_Ni_protease nick 99.7 2.7E-16 5.9E-21 111.9 9.8 83 52-144 2-89 (90)
7 KOG0171 Mitochondrial inner me 99.7 1.6E-16 3.5E-21 124.4 9.2 96 51-150 36-159 (176)
8 KOG1568 Mitochondrial inner me 99.5 4.5E-14 9.8E-19 110.5 8.9 97 51-151 34-153 (174)
9 PF00717 Peptidase_S24: Peptid 99.4 2.3E-12 4.9E-17 86.9 7.3 60 52-118 1-60 (70)
10 cd06462 Peptidase_S24_S26 The 99.3 1.1E-11 2.4E-16 85.5 9.4 64 51-120 3-66 (84)
11 PRK13838 conjugal transfer pil 99.2 2.7E-10 5.9E-15 91.1 12.2 68 74-145 48-170 (176)
12 cd06529 S24_LexA-like Peptidas 99.1 9.1E-10 2E-14 75.8 9.6 63 51-122 3-65 (81)
13 TIGR02771 TraF_Ti conjugative 99.0 3.6E-09 7.8E-14 84.3 11.4 84 51-145 27-167 (171)
14 COG2932 Predicted transcriptio 99.0 5.1E-09 1.1E-13 85.5 10.3 85 50-147 125-210 (214)
15 COG0681 LepB Signal peptidase 98.9 4.1E-09 8.9E-14 81.7 7.9 56 49-105 32-90 (166)
16 PRK13884 conjugal transfer pep 98.8 8.3E-08 1.8E-12 76.9 12.3 66 75-144 49-173 (178)
17 PRK00215 LexA repressor; Valid 98.7 1.2E-07 2.6E-12 76.7 11.1 83 50-148 120-203 (205)
18 PRK10276 DNA polymerase V subu 98.7 2.6E-07 5.6E-12 70.9 10.8 83 50-148 53-136 (139)
19 PRK12423 LexA repressor; Provi 98.6 3.2E-07 7E-12 74.5 10.6 84 50-148 116-200 (202)
20 TIGR00498 lexA SOS regulatory 98.6 7E-07 1.5E-11 71.9 11.2 83 50-148 113-196 (199)
21 PF10502 Peptidase_S26: Signal 98.6 5.2E-08 1.1E-12 75.0 3.8 67 77-147 22-137 (138)
22 COG1974 LexA SOS-response tran 98.1 4.5E-05 9.8E-10 62.3 10.7 81 50-147 114-197 (201)
23 COG4959 TraF Type IV secretory 95.5 0.0081 1.8E-07 47.3 1.9 35 109-147 134-169 (173)
24 PF05582 Peptidase_U57: YabG p 81.8 3.5 7.6E-05 35.5 5.4 38 77-118 1-38 (287)
25 COG0361 InfA Translation initi 80.1 1.9 4.2E-05 29.9 2.7 31 54-84 36-69 (75)
26 TIGR00008 infA translation ini 75.8 3 6.4E-05 28.4 2.6 22 62-83 45-66 (68)
27 TIGR02855 spore_yabG sporulati 72.6 7.9 0.00017 33.3 5.0 37 78-118 1-37 (283)
28 PF01176 eIF-1a: Translation i 71.1 3.7 8E-05 27.3 2.2 15 74-88 39-53 (65)
29 cd05793 S1_IF1A S1_IF1A: Trans 68.7 4.8 0.0001 27.8 2.4 11 77-87 39-49 (77)
30 COG3602 Uncharacterized protei 63.1 5.7 0.00012 29.9 2.0 42 56-97 12-56 (134)
31 smart00652 eIF1a eukaryotic tr 62.6 7.5 0.00016 27.3 2.5 11 77-87 44-54 (83)
32 PF10377 ATG11: Autophagy-rela 62.1 37 0.0008 25.7 6.4 58 75-145 41-98 (129)
33 cd04456 S1_IF1A_like S1_IF1A_l 61.1 8.4 0.00018 26.7 2.5 11 77-87 39-49 (78)
34 COG3895 Predicted periplasmic 58.8 21 0.00045 26.6 4.3 46 77-123 49-96 (112)
35 PRK12442 translation initiatio 58.7 11 0.00024 26.9 2.7 37 52-88 15-58 (87)
36 TIGR02594 conserved hypothetic 58.4 37 0.0008 25.6 5.8 39 75-119 72-110 (129)
37 PRK04012 translation initiatio 57.5 10 0.00022 27.7 2.5 11 77-87 60-70 (100)
38 PF04319 NifZ: NifZ domain; I 52.8 26 0.00056 24.3 3.7 29 58-86 1-35 (75)
39 PF10000 ACT_3: ACT domain; I 52.5 6.5 0.00014 26.9 0.7 35 56-90 12-49 (72)
40 COG0179 MhpD 2-keto-4-pentenoa 50.4 31 0.00067 29.4 4.7 39 61-100 224-264 (266)
41 smart00841 Elong-fact-P_C Elon 45.4 38 0.00082 22.1 3.5 38 55-97 18-56 (56)
42 cd04714 BAH_BAHCC1 BAH, or Bro 43.2 42 0.00092 24.8 4.0 28 77-104 4-32 (121)
43 PF15057 DUF4537: Domain of un 42.8 22 0.00047 26.7 2.4 20 53-72 47-66 (124)
44 TIGR02228 sigpep_I_arch signal 42.5 1.2E+02 0.0025 23.7 6.5 57 15-72 2-71 (158)
45 cd06555 ASCH_PF0470_like ASC-1 41.8 62 0.0013 23.9 4.6 29 75-103 30-58 (109)
46 COG1188 Ribosome-associated he 40.9 51 0.0011 24.1 3.9 30 73-104 45-74 (100)
47 cd04712 BAH_DCM_I BAH, or Brom 39.8 68 0.0015 24.2 4.7 10 137-146 89-98 (130)
48 cd04720 BAH_Orc1p_Yeast BAH, o 39.6 1.1E+02 0.0024 24.3 6.1 38 67-104 41-80 (179)
49 COG5131 URM1 Ubiquitin-like pr 38.8 43 0.00092 24.1 3.1 34 51-88 51-92 (96)
50 TIGR03024 arch_pef_cterm PEF-C 38.0 38 0.00081 18.7 2.2 20 160-179 4-23 (26)
51 PTZ00329 eukaryotic translatio 37.6 29 0.00063 27.3 2.4 24 62-85 71-94 (155)
52 PLN00208 translation initiatio 37.6 30 0.00064 27.0 2.4 10 77-86 71-80 (145)
53 KOG4146 Ubiquitin-like protein 37.5 49 0.0011 24.0 3.3 35 50-88 55-97 (101)
54 cd04466 S1_YloQ_GTPase S1_YloQ 37.0 62 0.0013 20.7 3.6 25 75-99 36-60 (68)
55 cd05792 S1_eIF1AD_like S1_eIF1 36.5 29 0.00063 24.1 2.0 11 77-87 39-49 (78)
56 cd04451 S1_IF1 S1_IF1: Transla 36.4 34 0.00074 22.2 2.3 22 76-97 40-64 (64)
57 PRK11372 lysozyme inhibitor; P 36.2 68 0.0015 23.6 4.0 40 80-120 50-90 (109)
58 PF05382 Amidase_5: Bacterioph 36.0 26 0.00057 27.2 1.9 38 52-89 50-88 (145)
59 PF11717 Tudor-knot: RNA bindi 35.8 1.1E+02 0.0025 19.2 5.0 52 77-139 1-53 (55)
60 PF12961 DUF3850: Domain of Un 35.2 1.5E+02 0.0032 20.3 5.5 31 70-101 22-52 (72)
61 PF07423 DUF1510: Protein of u 34.7 52 0.0011 27.3 3.6 29 16-44 8-36 (217)
62 PF09285 Elong-fact-P_C: Elong 31.9 88 0.0019 20.3 3.6 38 55-97 18-56 (56)
63 PRK00276 infA translation init 31.8 50 0.0011 22.2 2.6 22 76-97 46-70 (72)
64 TIGR00523 eIF-1A eukaryotic/ar 31.1 51 0.0011 23.9 2.6 25 62-86 38-67 (99)
65 TIGR01416 Rieske_proteo ubiqui 30.2 1.5E+02 0.0032 23.5 5.4 28 67-96 41-68 (174)
66 cd04717 BAH_polybromo BAH, or 30.0 88 0.0019 22.8 3.8 28 77-104 4-32 (121)
67 COG3655 Predicted transcriptio 28.3 40 0.00087 23.2 1.6 17 74-90 54-70 (73)
68 COG1935 Uncharacterized conser 27.7 32 0.0007 25.9 1.1 33 61-103 38-71 (122)
69 CHL00010 infA translation init 26.1 78 0.0017 21.7 2.8 23 76-98 46-71 (78)
70 PF00278 Orn_DAP_Arg_deC: Pyri 25.9 67 0.0015 22.7 2.5 30 60-89 65-95 (116)
71 cd04721 BAH_plant_1 BAH, or Br 25.2 98 0.0021 23.3 3.4 29 75-104 6-34 (130)
72 PF02362 B3: B3 DNA binding do 25.0 79 0.0017 21.6 2.7 16 74-89 71-86 (100)
73 PF10399 UCR_Fe-S_N: Ubiquitin 24.9 1.6E+02 0.0036 17.8 3.7 24 14-37 9-32 (41)
74 PF12666 PrgI: PrgI family pro 24.6 1E+02 0.0022 21.3 3.2 27 5-31 3-34 (93)
75 TIGR02303 HpaG-C-term 4-hydrox 24.2 1.3E+02 0.0028 25.1 4.2 37 61-98 204-242 (245)
76 TIGR00038 efp translation elon 24.2 1.2E+02 0.0027 24.2 4.0 38 56-98 146-184 (184)
77 PRK11507 ribosome-associated p 24.0 33 0.00071 23.5 0.5 15 73-87 49-63 (70)
78 cd05794 S1_EF-P_repeat_2 S1_EF 23.5 1E+02 0.0023 20.0 2.8 38 55-97 18-56 (56)
79 cd05790 S1_Rrp40 S1_Rrp40: Rrp 23.1 67 0.0014 22.6 2.0 17 56-72 44-60 (86)
80 PF14118 YfzA: YfzA-like prote 23.0 59 0.0013 23.5 1.7 16 52-67 29-44 (94)
81 COG5471 Uncharacterized conser 22.8 1.1E+02 0.0024 22.4 3.1 28 58-86 2-29 (107)
82 PHA02756 hypothetical protein; 22.8 3.6E+02 0.0078 20.8 7.3 70 33-103 16-90 (164)
83 cd04497 hPOT1_OB1_like hPOT1_O 22.6 1.9E+02 0.0042 21.6 4.6 35 51-87 41-79 (138)
84 PRK14578 elongation factor P; 22.4 1.5E+02 0.0032 24.0 4.1 37 57-98 150-187 (187)
85 TIGR02219 phage_NlpC_fam putat 22.4 1.9E+02 0.0041 21.6 4.5 15 74-88 74-88 (134)
86 PRK15203 4-hydroxyphenylacetat 22.4 1.3E+02 0.0029 27.3 4.2 30 61-90 165-196 (429)
87 PRK12426 elongation factor P; 22.2 1.4E+02 0.0031 24.0 4.0 39 55-98 146-185 (185)
88 PF09956 DUF2190: Uncharacteri 22.1 1.2E+02 0.0027 22.1 3.3 28 58-86 1-28 (106)
89 smart00439 BAH Bromo adjacent 21.9 1.6E+02 0.0035 20.7 3.9 13 133-145 70-82 (120)
90 KOG1535 Predicted fumarylaceto 21.9 94 0.002 25.8 2.8 29 61-89 176-206 (217)
91 PF01426 BAH: BAH domain; Int 21.7 1E+02 0.0022 21.7 2.8 28 77-104 3-31 (119)
92 PF13550 Phage-tail_3: Putativ 21.3 1.5E+02 0.0032 22.1 3.8 26 75-102 138-163 (164)
93 PRK04542 elongation factor P; 20.9 1.9E+02 0.004 23.5 4.4 37 57-98 151-188 (189)
94 PRK05573 rplU 50S ribosomal pr 20.7 1.6E+02 0.0034 21.4 3.6 34 51-86 3-36 (103)
95 PF12791 RsgI_N: Anti-sigma fa 20.6 1.6E+02 0.0034 18.4 3.2 25 63-88 13-37 (56)
96 TIGR02178 yeiP elongation fact 20.6 1.4E+02 0.0031 24.1 3.7 38 56-98 148-186 (186)
97 PF04322 DUF473: Protein of un 20.3 56 0.0012 24.6 1.2 21 61-81 38-59 (119)
98 cd04092 mtEFG2_II_like mtEFG2_ 20.2 1.3E+02 0.0028 20.2 2.9 13 74-86 58-70 (83)
99 PRK08564 5'-methylthioadenosin 20.1 86 0.0019 26.6 2.4 19 54-72 92-110 (267)
100 PRK07432 5'-methylthioadenosin 20.0 92 0.002 26.9 2.6 28 45-72 79-106 (290)
No 1
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-41 Score=262.11 Aligned_cols=179 Identities=58% Similarity=0.994 Sum_probs=170.3
Q ss_pred CcchHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccCeEEEcCCCccccCcCCCEEEEEe-cCCCCCc
Q 030254 1 MGWIGESIESVKSMKIRDSLFQFITLGMIVSSALIIWKGLMCITGSESPVVVVLSESMEPGFQRGDILFLQM-SKDPIRT 79 (180)
Q Consensus 1 ~~~~~~~~~~~~~~~~r~~~~~i~~~~~~i~i~~~i~~~l~~~~~~~~p~~~V~~~SM~P~l~~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 689999999999999999999999999999999999999999999999999999999999999999999986 5577899
Q ss_pred CcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhccCCceeccceEeeEEEEEEcCcceeeeeccc
Q 030254 80 GEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYAQGQFWLKQEHIMGRAVGFLPYVGWATIIMTE 159 (180)
Q Consensus 80 GDIVvf~~~~~~~~~ihRVi~~~~d~~~g~~~~~t~GDnn~~~D~~~y~~~~~~V~~~~IiG~v~~~iP~~G~~~~~~~~ 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 9999999999999999999999875 357778999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHhhhhcCC
Q 030254 160 KPIIKYILIGALGLLVITSKD 180 (180)
Q Consensus 160 ~~~~~~~l~~~~~~~~~~~~~ 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=9.8e-30 Score=199.92 Aligned_cols=143 Identities=29% Similarity=0.545 Sum_probs=110.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhccccCeEEEcCCCccccCcCCCEEEEEe-cCCCCCcCcEEEEEeCCCCcCEEEEEEEe
Q 030254 23 FITLGMIVSSALIIWKGLMCITGSESPVVVVLSESMEPGFQRGDILFLQM-SKDPIRTGEIVVFNIQGRDIPIVHRVIEV 101 (180)
Q Consensus 23 i~~~~~~i~i~~~i~~~l~~~~~~~~p~~~V~~~SM~P~l~~GD~v~v~~-~~~~~~~GDIVvf~~~~~~~~~ihRVi~~ 101 (180)
++.+++.+++.++++..+....++..|.++|.|+||+|++++||++++++ ..+++++||||+|+.++++.+++|||+++
T Consensus 6 ii~~~~~~~l~~~~~~~l~~~~~~~~p~v~V~g~SM~Ptl~~GD~vlv~~~~~~~~~~GDIVvf~~~~~~~~iihRVi~v 85 (158)
T TIGR02228 6 VIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFNTGDLILVTGADPNDIQVGDVITYKSPGFNTPVTHRVIEI 85 (158)
T ss_pred HHHHHHHHHHHHHHHHHheeeccCCCcEEEEcCCCCcCCccCCCEEEEEecccCCCCCCCEEEEEECCCCccEEEEEEEE
Confidence 33344333333333333444455567867799999999999999999997 56789999999999987656899999999
Q ss_pred cccccCCeeEEEEeccCCCCcchhhhccCCceeccceEeeEEE-EEEcCcceeeeecccchhHHHHHHHHHHHhh
Q 030254 102 HEQRQSGEVRILTKGDNNDVDDRMLYAQGQFWLKQEHIMGRAV-GFLPYVGWATIIMTEKPIIKYILIGALGLLV 175 (180)
Q Consensus 102 ~~d~~~g~~~~~t~GDnn~~~D~~~y~~~~~~V~~~~IiG~v~-~~iP~~G~~~~~~~~~~~~~~~l~~~~~~~~ 175 (180)
.++ +++..|+||||||..+|+. ++++++|+|++. +.+|++|+...++++... ..+++++.+++.
T Consensus 86 ~~~--~g~~~~~tkGDnN~~~D~~-------~v~~~~IiG~v~~~~iP~~G~~~~~~~~~~~-~~~~~~~p~~~~ 150 (158)
T TIGR02228 86 NNS--GGELGFITKGDNNPAPDGE-------PVPSENVIGKYLGFTIPFAGYVLVFAPQAIG-AAALLIIPGIGL 150 (158)
T ss_pred ECC--CCcEEEEEEecCCCCCCcc-------cCCHHHEEEEEEEeccCcccEEEEEeecCch-hhhhHHhHHHHH
Confidence 865 3556799999999998854 589999999999 789999999999999554 555555444443
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=1e-20 Score=148.96 Aligned_cols=97 Identities=25% Similarity=0.408 Sum_probs=81.0
Q ss_pred cCeEEEcCCCccccCcCCCEEEEEec---CCCCCcCcEEEEEeCCC-CcCEEEEEEEecccc----c-----C-------
Q 030254 48 SPVVVVLSESMEPGFQRGDILFLQMS---KDPIRTGEIVVFNIQGR-DIPIVHRVIEVHEQR----Q-----S------- 107 (180)
Q Consensus 48 ~p~~~V~~~SM~P~l~~GD~v~v~~~---~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~d~----~-----~------- 107 (180)
.+ +.|.|+||+|||++||++++++. ..++++||||+|+.+++ +..++|||++++||+ + |
T Consensus 21 ~~-~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~vNg~~~~~~ 99 (163)
T TIGR02227 21 FP-YKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYINGKKIDEP 99 (163)
T ss_pred EE-EEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEECCEECccc
Confidence 45 89999999999999999999982 37899999999998743 357999999999885 0 0
Q ss_pred -----------------------CeeEEEEeccCC-CCcchhhhccCCceeccceEeeEEEE-EEcC
Q 030254 108 -----------------------GEVRILTKGDNN-DVDDRMLYAQGQFWLKQEHIMGRAVG-FLPY 149 (180)
Q Consensus 108 -----------------------g~~~~~t~GDnn-~~~D~~~y~~~~~~V~~~~IiG~v~~-~iP~ 149 (180)
++++|+++|||+ .+.|||.| |+|++++|+||+.. .||.
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~----G~V~~~~I~Gk~~~~~~p~ 162 (163)
T TIGR02227 100 YLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYF----GFVPIDDIIGKVSFVFYPF 162 (163)
T ss_pred ccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCc----CcCCHHHeEEEEEEEECCC
Confidence 356899999996 46899975 68999999999986 4664
No 4
>PRK10861 signal peptidase I; Provisional
Probab=99.74 E-value=3e-17 Score=142.00 Aligned_cols=60 Identities=23% Similarity=0.405 Sum_probs=50.4
Q ss_pred ccccCeEEEcCCCccccCcCCCEEEEEe-c--------------CCCCCcCcEEEEEeCCC-CcCEEEEEEEecccc
Q 030254 45 GSESPVVVVLSESMEPGFQRGDILFLQM-S--------------KDPIRTGEIVVFNIQGR-DIPIVHRVIEVHEQR 105 (180)
Q Consensus 45 ~~~~p~~~V~~~SM~P~l~~GD~v~v~~-~--------------~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~d~ 105 (180)
+...| +.|+|+||+|||..||.++++| . ..++++||||+|+.|.+ +..++|||++++||+
T Consensus 80 fv~~~-~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~~~~~yIKRVIGlPGD~ 155 (324)
T PRK10861 80 FIYEP-FQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDPKLDYIKRVVGLPGDK 155 (324)
T ss_pred hEEEE-EEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCCCCCcEEEEeeecCCcE
Confidence 33466 9999999999999999999998 1 15689999999998754 357999999999875
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=99.69 E-value=1e-16 Score=112.55 Aligned_cols=79 Identities=33% Similarity=0.529 Sum_probs=64.2
Q ss_pred eEEEcCCCccccCcCCCEEEEEecCC---CCCcCcEEEEEeCCC-CcCEEEEEEEecccccCCeeEEEEeccCCC-Ccch
Q 030254 50 VVVVLSESMEPGFQRGDILFLQMSKD---PIRTGEIVVFNIQGR-DIPIVHRVIEVHEQRQSGEVRILTKGDNND-VDDR 124 (180)
Q Consensus 50 ~~~V~~~SM~P~l~~GD~v~v~~~~~---~~~~GDIVvf~~~~~-~~~~ihRVi~~~~d~~~g~~~~~t~GDnn~-~~D~ 124 (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 37899999999999999999997333 799999999999874 4589999998 789999933 2444
Q ss_pred hhhccCCceeccceEeeEE
Q 030254 125 MLYAQGQFWLKQEHIMGRA 143 (180)
Q Consensus 125 ~~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 432 468899999974
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=99.68 E-value=2.7e-16 Score=111.85 Aligned_cols=83 Identities=20% Similarity=0.242 Sum_probs=68.4
Q ss_pred EEcCCCccccCcCCCEEEEEe---cCCCCCcCcEEEEEeCCC-CcCEEEEEEEecccccCCeeEEEEeccCCCC-cchhh
Q 030254 52 VVLSESMEPGFQRGDILFLQM---SKDPIRTGEIVVFNIQGR-DIPIVHRVIEVHEQRQSGEVRILTKGDNNDV-DDRML 126 (180)
Q Consensus 52 ~V~~~SM~P~l~~GD~v~v~~---~~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~d~~~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 588999999999999999996 234456899999998753 36899999999865 68999999764 67765
Q ss_pred hccCCceeccceEeeEEE
Q 030254 127 YAQGQFWLKQEHIMGRAV 144 (180)
Q Consensus 127 y~~~~~~V~~~~IiG~v~ 144 (180)
+ ++++..+|+|+++
T Consensus 76 ~----g~v~~~~I~G~v~ 89 (90)
T TIGR02754 76 L----GPVPRSLLLGKVL 89 (90)
T ss_pred c----CCCcHHHEEEEEE
Confidence 4 5789999999985
No 7
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.68 E-value=1.6e-16 Score=124.44 Aligned_cols=96 Identities=26% Similarity=0.328 Sum_probs=78.0
Q ss_pred EEEcCCCccccCcCC-CEEEEEe---cCCCCCcCcEEEEEeCCC-CcCEEEEEEEecccc----------c---------
Q 030254 51 VVVLSESMEPGFQRG-DILFLQM---SKDPIRTGEIVVFNIQGR-DIPIVHRVIEVHEQR----------Q--------- 106 (180)
Q Consensus 51 ~~V~~~SM~P~l~~G-D~v~v~~---~~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~d~----------~--------- 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 778999999988777 5555466 467789999999998844 367999999999992 1
Q ss_pred --CCeeEEEEeccCCC-CcchhhhccCCceeccceEeeEEEE-EEcCc
Q 030254 107 --SGEVRILTKGDNND-VDDRMLYAQGQFWLKQEHIMGRAVG-FLPYV 150 (180)
Q Consensus 107 --~g~~~~~t~GDnn~-~~D~~~y~~~~~~V~~~~IiG~v~~-~iP~~ 150 (180)
-|+++.|+.|||.+ +.||+.| |+++...|.||+++ .||..
T Consensus 116 i~VP~GhVfv~GDN~~nS~DSr~y----GplP~glI~gRvv~r~Wp~s 159 (176)
T KOG0171|consen 116 IRVPEGHVFVEGDNRNNSLDSRNY----GPLPMGLIQGRVVFRIWPPS 159 (176)
T ss_pred eeccCceEEEecCCCCCccccccc----CCCchhheeeeEEEEecCch
Confidence 26789999999954 6899987 57999999999996 57753
No 8
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.53 E-value=4.5e-14 Score=110.55 Aligned_cols=97 Identities=25% Similarity=0.336 Sum_probs=81.4
Q ss_pred EEEcCCCccccCcCC------CEEEEEe---cCCCCCcCcEEEEEeCCC-CcCEEEEEEEecccc-----------cCCe
Q 030254 51 VVVLSESMEPGFQRG------DILFLQM---SKDPIRTGEIVVFNIQGR-DIPIVHRVIEVHEQR-----------QSGE 109 (180)
Q Consensus 51 ~~V~~~SM~P~l~~G------D~v~v~~---~~~~~~~GDIVvf~~~~~-~~~~ihRVi~~~~d~-----------~~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 679999999999887 8999988 335699999999998854 578999999999985 1378
Q ss_pred eEEEEeccCCC-CcchhhhccCCceeccceEeeEEEE-EEcCcc
Q 030254 110 VRILTKGDNND-VDDRMLYAQGQFWLKQEHIMGRAVG-FLPYVG 151 (180)
Q Consensus 110 ~~~~t~GDnn~-~~D~~~y~~~~~~V~~~~IiG~v~~-~iP~~G 151 (180)
+++|+.|||.. +.||+.| |||+-..|.||++. .||...
T Consensus 114 ghcWVegDn~~hs~DSntF----GPVS~gli~grai~ilwpP~R 153 (174)
T KOG1568|consen 114 GHCWVEGDNQKHSYDSNTF----GPVSTGLIVGRAIYILWPPVR 153 (174)
T ss_pred CcEEEecCCcccccccCcc----CCcchhheeeeEEEEEcChHH
Confidence 89999999975 5798865 68999999999995 688554
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=86.89 Aligned_cols=60 Identities=32% Similarity=0.501 Sum_probs=48.7
Q ss_pred EEcCCCccccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccC
Q 030254 52 VVLSESMEPGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDN 118 (180)
Q Consensus 52 ~V~~~SM~P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~g~~~~~t~GDn 118 (180)
.|.|+||+|+|++||+|++++ ..+++.||+|+|+.++.+..++||+.+.+++ .+.+..||
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~-~~~~~~gdivv~~~~~~~~~~iKrv~~~~~~------~~~~~~~n 60 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDP-SSEPKDGDIVVVKIDGDEELYIKRVVGEPGG------IILISSNN 60 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEE-TS---TTSEEEEEETTEESEEEEEEEEETTE------EEEE-SST
T ss_pred CeECcCcccCeeCCCEEEEEE-cCCCccCeEEEEEECCceeeEEEEEEEeCCC------EEEEeccC
Confidence 488999999999999999998 5699999999999987744799999998876 67777666
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=99.34 E-value=1.1e-11 Score=85.54 Aligned_cols=64 Identities=33% Similarity=0.513 Sum_probs=54.4
Q ss_pred EEEcCCCccccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCC
Q 030254 51 VVVLSESMEPGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNND 120 (180)
Q Consensus 51 ~~V~~~SM~P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~g~~~~~t~GDnn~ 120 (180)
+.|.|+||+|++.+||++++++....++.||+++++.++ +..++||+...++. +.+.+++||..
T Consensus 3 ~~v~g~SM~P~i~~gd~v~i~~~~~~~~~G~iv~~~~~~-~~~~ikrl~~~~~~-----~~~~l~~~N~~ 66 (84)
T cd06462 3 LRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPG-GELTVKRVIGLPGE-----GHYFLLGDNPN 66 (84)
T ss_pred eEEcCCCccCcccCCCEEEEEecCCCCcCCEEEEEEcCC-CcEEEEEEEEECCC-----CEEEEECCCCC
Confidence 789999999999999999999843459999999999987 35799999998752 27999999943
No 11
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.21 E-value=2.7e-10 Score=91.11 Aligned_cols=68 Identities=15% Similarity=0.216 Sum_probs=55.6
Q ss_pred CCCCCcCcEEEEEeCCCC--------------------cCEEEEEEEecccc---------c------------------
Q 030254 74 KDPIRTGEIVVFNIQGRD--------------------IPIVHRVIEVHEQR---------Q------------------ 106 (180)
Q Consensus 74 ~~~~~~GDIVvf~~~~~~--------------------~~~ihRVi~~~~d~---------~------------------ 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 578999999999865331 36999999999985 0
Q ss_pred --------CCeeEEEEeccCCCCcchhhhccCCceeccceEeeEEEE
Q 030254 107 --------SGEVRILTKGDNNDVDDRMLYAQGQFWLKQEHIMGRAVG 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 046689999999888999975 68999999999863
No 12
>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=99.11 E-value=9.1e-10 Score=75.78 Aligned_cols=63 Identities=30% Similarity=0.429 Sum_probs=54.1
Q ss_pred EEEcCCCccccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCc
Q 030254 51 VVVLSESMEPGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVD 122 (180)
Q Consensus 51 ~~V~~~SM~P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~g~~~~~t~GDnn~~~ 122 (180)
+.+.|+||+|.+++||.+++++ ...++.||++++..++ ..++||+...+++ .+.++.||....
T Consensus 3 ~~v~g~sM~p~i~~gd~lii~~-~~~~~~g~i~~~~~~~--~~~ikr~~~~~~~------~~~L~s~N~~~~ 65 (81)
T cd06529 3 LRVKGDSMEPTIPDGDLVLVDP-SDTPRDGDIVVARLDG--ELTVKRLQRRGGG------RLRLISDNPAYP 65 (81)
T ss_pred EEEECCCcCCccCCCCEEEEcC-CCCCCCCCEEEEEECC--EEEEEEEEECCCC------cEEEEeCCCCCC
Confidence 7899999999999999999998 4559999999999986 4699999987644 688999997433
No 13
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.03 E-value=3.6e-09 Score=84.27 Aligned_cols=84 Identities=20% Similarity=0.319 Sum_probs=62.9
Q ss_pred EEEcCCCccccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCc--------------------CEEEEEEEecccc----c
Q 030254 51 VVVLSESMEPGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDI--------------------PIVHRVIEVHEQR----Q 106 (180)
Q Consensus 51 ~~V~~~SM~P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~--------------------~~ihRVi~~~~d~----~ 106 (180)
..-.|.||-+.+.. .. ...++++||+|+|+.|.+.. .++|||++++||+ +
T Consensus 27 ~~N~T~S~P~g~Y~-----~~-~~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~ 100 (171)
T TIGR02771 27 RINTTKSLPLGLYW-----TT-SSKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRA 100 (171)
T ss_pred EEECCCCCcceEEE-----eC-CCCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEEC
Confidence 45667788766532 22 35789999999999775321 7999999999985 0
Q ss_pred -----C---------------------------CeeEEEEeccCCC-CcchhhhccCCceeccceEeeEEEE
Q 030254 107 -----S---------------------------GEVRILTKGDNND-VDDRMLYAQGQFWLKQEHIMGRAVG 145 (180)
Q Consensus 107 -----~---------------------------g~~~~~t~GDnn~-~~D~~~y~~~~~~V~~~~IiG~v~~ 145 (180)
| +++ |+++|||++ +.|||.| |+|+.++|+||+.-
T Consensus 101 ~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~----G~V~~~~IiGk~~p 167 (171)
T TIGR02771 101 DVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYF----GPISREQVIGRVKP 167 (171)
T ss_pred CEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCccccc----ceecHHHeEEEEEE
Confidence 1 344 889999976 5799875 68999999999873
No 14
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.97 E-value=5.1e-09 Score=85.51 Aligned_cols=85 Identities=22% Similarity=0.279 Sum_probs=64.1
Q ss_pred eEEEcCCCccccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhcc
Q 030254 50 VVVVLSESMEPGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYAQ 129 (180)
Q Consensus 50 ~~~V~~~SM~P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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 ALRVTGDSMEPTYEDGDTLLVDP-GVNTRRGDRVYVETDGG-ELYVKKLQREPGG------LLRLVSLNPDYYPDEIFS- 195 (214)
T ss_pred EEEEeCCcccccccCCCEEEECC-CCceeeCCEEEEEEeCC-eEEEEEEEEecCC------eEEEEeCCCCCCcccccC-
Confidence 47899999999999999999998 67788899777776664 4799999999865 566889887653333221
Q ss_pred CCceecc-ceEeeEEEEEE
Q 030254 130 GQFWLKQ-EHIMGRAVGFL 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 111 46899998643
No 15
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=98.93 E-value=4.1e-09 Score=81.66 Aligned_cols=56 Identities=27% Similarity=0.379 Sum_probs=39.9
Q ss_pred CeEEEcCCCccccCcCCCEEEEEe---cCCCCCcCcEEEEEeCCCCcCEEEEEEEecccc
Q 030254 49 PVVVVLSESMEPGFQRGDILFLQM---SKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQR 105 (180)
Q Consensus 49 p~~~V~~~SM~P~l~~GD~v~v~~---~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~ 105 (180)
+.+.|+|+||+||++.||++++++ ....++.+|++.+.... ...+++|+++.+||.
T Consensus 32 ~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~~~~-~~~~~kr~~~~~GD~ 90 (166)
T COG0681 32 EPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPAVV-EGDLIKRVIGLRGDI 90 (166)
T ss_pred EEEEECCCccccccccCCEEEEEeccccccCCccceeeecCCCC-CcceEEEeccCCCCE
Confidence 349999999999999999999998 22346666666332222 235777777777773
No 16
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=98.82 E-value=8.3e-08 Score=76.90 Aligned_cols=66 Identities=20% Similarity=0.240 Sum_probs=49.9
Q ss_pred CCCCcCcEEEEEeCCC--------------------CcCEEEEEEEecccc----c-----C------------------
Q 030254 75 DPIRTGEIVVFNIQGR--------------------DIPIVHRVIEVHEQR----Q-----S------------------ 107 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~--------------------~~~~ihRVi~~~~d~----~-----~------------------ 107 (180)
.++++||+|+|..|.. ..+++|||++++||+ + |
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~ 128 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP 128 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence 4567777777765431 137999999999985 0 0
Q ss_pred -----------CeeEEEEeccCCC-CcchhhhccCCceeccceEeeEEE
Q 030254 108 -----------GEVRILTKGDNND-VDDRMLYAQGQFWLKQEHIMGRAV 144 (180)
Q Consensus 108 -----------g~~~~~t~GDnn~-~~D~~~y~~~~~~V~~~~IiG~v~ 144 (180)
++++|+++|||++ +.|||+| |+|++++|+|++.
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYf----G~V~~~~I~G~~~ 173 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYF----GPINRSQIKTVIR 173 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCccccc----CcccHHHEEEEEE
Confidence 3568999999865 6899875 6899999999986
No 17
>PRK00215 LexA repressor; Validated
Probab=98.75 E-value=1.2e-07 Score=76.66 Aligned_cols=83 Identities=24% Similarity=0.378 Sum_probs=62.2
Q ss_pred eEEEcCCCcc-ccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhc
Q 030254 50 VVVVLSESME-PGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYA 128 (180)
Q Consensus 50 ~~~V~~~SM~-P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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 LLRVRGDSMIDAGILDGDLVIVRK-QQTARNGQIVVALIDD--EATVKRFRRE-GG------HIRLEPENPAYE-PIIVD 188 (205)
T ss_pred EEEEccCCCCCCCcCCCCEEEEeC-CCCCCCCCEEEEEECC--EEEEEEEEEe-CC------EEEEEcCCCCCC-CEEeC
Confidence 4789999995 7999999999997 5678999999999876 4799999864 22 578999875433 22111
Q ss_pred cCCceeccceEeeEEEEEEc
Q 030254 129 QGQFWLKQEHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~V~~~~IiG~v~~~iP 148 (180)
-..-.|+|+|+..+.
T Consensus 189 -----~~~~~IiG~Vv~~~r 203 (205)
T PRK00215 189 -----PDRVTIEGKVVGLIR 203 (205)
T ss_pred -----CCcEEEEEEEEEEEE
Confidence 013689999987653
No 18
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.69 E-value=2.6e-07 Score=70.89 Aligned_cols=83 Identities=17% Similarity=0.233 Sum_probs=59.4
Q ss_pred eEEEcCCCcc-ccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhc
Q 030254 50 VVVVLSESME-PGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYA 128 (180)
Q Consensus 50 ~~~V~~~SM~-P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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 FVKASGDSMIDAGISDGDLLIVDS-AITASHGDIVIAAVDGE--FTVKKLQL-R-P------TVQLIPMNSAYSP-ITIS 120 (139)
T ss_pred EEEEecCCCCCCCCCCCCEEEEEC-CCCCCCCCEEEEEECCE--EEEEEEEE-C-C------cEEEEcCCCCCCC-EEcC
Confidence 4789999998 6899999999997 45689999999987653 68999875 2 2 3678888754322 1110
Q ss_pred cCCceeccceEeeEEEEEEc
Q 030254 129 QGQFWLKQEHIMGRAVGFLP 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 0122479999987653
No 19
>PRK12423 LexA repressor; Provisional
Probab=98.64 E-value=3.2e-07 Score=74.53 Aligned_cols=84 Identities=24% Similarity=0.279 Sum_probs=62.6
Q ss_pred eEEEcCCCcc-ccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhc
Q 030254 50 VVVVLSESME-PGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYA 128 (180)
Q Consensus 50 ~~~V~~~SM~-P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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 LLQVQGDSMIDDGILDGDLVGVHR-SPEARDGQIVVARLDG--EVTIKRLERSG-D------RIRLLPRNPAY-APIVVA 184 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeC-CCcCCCCCEEEEEECC--EEEEEEEEEeC-C------EEEEEcCCCCC-CCEEcC
Confidence 4789999997 7999999999997 5788999999998864 46899987642 2 57888987543 332211
Q ss_pred cCCceeccceEeeEEEEEEc
Q 030254 129 QGQFWLKQEHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~V~~~~IiG~v~~~iP 148 (180)
+-+.-.|+|++++.+.
T Consensus 185 ----~~~~~~I~Gvv~g~~r 200 (202)
T PRK12423 185 ----PDQDFAIEGVFCGLIR 200 (202)
T ss_pred ----CCCcEEEEEEEEEEEE
Confidence 1124589999998764
No 20
>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=98.59 E-value=7e-07 Score=71.91 Aligned_cols=83 Identities=28% Similarity=0.448 Sum_probs=62.0
Q ss_pred eEEEcCCCcc-ccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhc
Q 030254 50 VVVVLSESME-PGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYA 128 (180)
Q Consensus 50 ~~~V~~~SM~-P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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-~~- 180 (199)
T TIGR00498 113 LLKVMGDSMVDAGICDGDLLIVRS-QKDARNGEIVAAMIDG--EVTVKRFYKD-GT------KVELKPENPEFDPI-VL- 180 (199)
T ss_pred EEEecCCCCCCCCCCCCCEEEEec-CCCCCCCCEEEEEECC--EEEEEEEEEE-CC------EEEEEcCCCCCcCC-cC-
Confidence 4789999996 6899999999997 5789999999999843 4799998754 32 57888987543332 11
Q ss_pred cCCceeccceEeeEEEEEEc
Q 030254 129 QGQFWLKQEHIMGRAVGFLP 148 (180)
Q Consensus 129 ~~~~~V~~~~IiG~v~~~iP 148 (180)
.-..-.|+|+|+..+.
T Consensus 181 ----~~~~~~IiG~Vv~~~r 196 (199)
T TIGR00498 181 ----NAEDVTILGKVVGVIR 196 (199)
T ss_pred ----CCCcEEEEEEEEEEEE
Confidence 1124689999987653
No 21
>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=98.57 E-value=5.2e-08 Score=74.97 Aligned_cols=67 Identities=25% Similarity=0.366 Sum_probs=25.6
Q ss_pred CCcCcEEEEEeCC-------------CCcCEEEEEEEecccc----c-------------------------------CC
Q 030254 77 IRTGEIVVFNIQG-------------RDIPIVHRVIEVHEQR----Q-------------------------------SG 108 (180)
Q Consensus 77 ~~~GDIVvf~~~~-------------~~~~~ihRVi~~~~d~----~-------------------------------~g 108 (180)
+++||+|+|..|. ++.+++|||++++||+ + -+
T Consensus 22 ~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~vp 101 (138)
T PF10502_consen 22 IERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTVP 101 (138)
T ss_dssp -------------------------------------------------------------------S-T----TEEE--
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceEeC
Confidence 5666666666543 1247999999999995 0 05
Q ss_pred eeEEEEeccCCC-CcchhhhccCCceeccceEeeEEEEEE
Q 030254 109 EVRILTKGDNND-VDDRMLYAQGQFWLKQEHIMGRAVGFL 147 (180)
Q Consensus 109 ~~~~~t~GDnn~-~~D~~~y~~~~~~V~~~~IiG~v~~~i 147 (180)
+++|+++|||++ +.|||.| |+|+.++|+|++.-.|
T Consensus 102 ~g~~~v~gd~~~~S~DSRy~----G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 102 EGEYFVLGDNRPNSFDSRYF----GPVPRSQIIGKARPLW 137 (138)
T ss_dssp TTEEEEE-SBTTS--SHHHH------EEGGGEEEEEEEEE
T ss_pred CCEEEEecCCCCCccccCEe----cccCHHHEEEEEEEEE
Confidence 678999998866 4799986 5899999999997543
No 22
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=98.09 E-value=4.5e-05 Score=62.34 Aligned_cols=81 Identities=27% Similarity=0.436 Sum_probs=62.5
Q ss_pred eEEEcCCCcc-ccCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhc
Q 030254 50 VVVVLSESME-PGFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYA 128 (180)
Q Consensus 50 ~~~V~~~SM~-P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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-------QILLKPENPA-YPPIP-- 181 (201)
T ss_pred EEEecCCccccCcCCCCCEEEEcC-CCCCCCCCEEEEEcCC-CcEEEEEEEEeCC-------EEEEEeCCCC-CCCcc--
Confidence 4789999998 7889999999997 8899999999999998 4589999887432 4666665543 33322
Q ss_pred cCCceec--cceEeeEEEEEE
Q 030254 129 QGQFWLK--QEHIMGRAVGFL 147 (180)
Q Consensus 129 ~~~~~V~--~~~IiG~v~~~i 147 (180)
++ .-.|+|++++.+
T Consensus 182 -----~~~~~~~I~G~vvgv~ 197 (201)
T COG1974 182 -----VDADSVTILGKVVGVI 197 (201)
T ss_pred -----cCccceEEEEEEEEEE
Confidence 33 468999999865
No 23
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=95.49 E-value=0.0081 Score=47.27 Aligned_cols=35 Identities=14% Similarity=0.113 Sum_probs=27.1
Q ss_pred eeEEEEeccCCC-CcchhhhccCCceeccceEeeEEEEEE
Q 030254 109 EVRILTKGDNND-VDDRMLYAQGQFWLKQEHIMGRAVGFL 147 (180)
Q Consensus 109 ~~~~~t~GDnn~-~~D~~~y~~~~~~V~~~~IiG~v~~~i 147 (180)
+..+++++|.++ +.|+|+| |+++.++|+|.+.=.|
T Consensus 134 ~~el~lL~~~~~~SfDsRYf----Gpipas~vig~aRPvw 169 (173)
T COG4959 134 PSELLLLTDRSSTSFDSRYF----GPIPASQVIGVARPVW 169 (173)
T ss_pred CCeEEEEeccCCccccccee----cccCHHHcceeeeeee
Confidence 456888898765 5799975 6899999999876443
No 24
>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=81.77 E-value=3.5 Score=35.55 Aligned_cols=38 Identities=32% Similarity=0.632 Sum_probs=32.5
Q ss_pred CCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccC
Q 030254 77 IRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDN 118 (180)
Q Consensus 77 ~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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 478999999998886 99999999875 577788899977
No 25
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=80.12 E-value=1.9 Score=29.87 Aligned_cols=31 Identities=26% Similarity=0.479 Sum_probs=22.6
Q ss_pred cCCCccc---cCcCCCEEEEEecCCCCCcCcEEE
Q 030254 54 LSESMEP---GFQRGDILFLQMSKDPIRTGEIVV 84 (180)
Q Consensus 54 ~~~SM~P---~l~~GD~v~v~~~~~~~~~GDIVv 84 (180)
.+|.|+= -+.+||+|++.....+++.|||+-
T Consensus 36 I~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~ 69 (75)
T COG0361 36 ISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVY 69 (75)
T ss_pred ccCcchheeEEeCCCCEEEEEecccccccccEEE
Confidence 3456655 678889888888667788888763
No 26
>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=75.76 E-value=3 Score=28.40 Aligned_cols=22 Identities=23% Similarity=0.365 Sum_probs=12.9
Q ss_pred CcCCCEEEEEecCCCCCcCcEE
Q 030254 62 FQRGDILFLQMSKDPIRTGEIV 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 4566666666544456666654
No 27
>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=72.56 E-value=7.9 Score=33.29 Aligned_cols=37 Identities=30% Similarity=0.538 Sum_probs=29.9
Q ss_pred CcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccC
Q 030254 78 RTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDN 118 (180)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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 57999999998887 99999999432 366688888877
No 28
>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=71.06 E-value=3.7 Score=27.27 Aligned_cols=15 Identities=20% Similarity=0.324 Sum_probs=7.5
Q ss_pred CCCCCcCcEEEEEeC
Q 030254 74 KDPIRTGEIVVFNIQ 88 (180)
Q Consensus 74 ~~~~~~GDIVvf~~~ 88 (180)
.-.+++||.|+....
T Consensus 39 ~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 39 RIWIKRGDFVLVEPS 53 (65)
T ss_dssp CC---TTEEEEEEES
T ss_pred eEecCCCCEEEEEec
Confidence 345677777776654
No 29
>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=68.71 E-value=4.8 Score=27.84 Aligned_cols=11 Identities=36% Similarity=0.604 Sum_probs=6.0
Q ss_pred CCcCcEEEEEe
Q 030254 77 IRTGEIVVFNI 87 (180)
Q Consensus 77 ~~~GDIVvf~~ 87 (180)
+++||.|+...
T Consensus 39 I~~GD~V~Ve~ 49 (77)
T cd05793 39 INEGDIVLVAP 49 (77)
T ss_pred EcCCCEEEEEe
Confidence 45555555543
No 30
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.08 E-value=5.7 Score=29.94 Aligned_cols=42 Identities=24% Similarity=0.387 Sum_probs=24.8
Q ss_pred CCccccCcCCCEEEEEecC---CCCCcCcEEEEEeCCCCcCEEEE
Q 030254 56 ESMEPGFQRGDILFLQMSK---DPIRTGEIVVFNIQGRDIPIVHR 97 (180)
Q Consensus 56 ~SM~P~l~~GD~v~v~~~~---~~~~~GDIVvf~~~~~~~~~ihR 97 (180)
.||.|.+.+||.|+-.... .+..---+-.|+.+..-.+++.|
T Consensus 12 ~smtPeL~~G~yVfcT~~~ga~~~~~lePla~FRE~EG~tLiler 56 (134)
T COG3602 12 ASMTPELLDGDYVFCTVAPGALQPKNLEPLATFREREGLTLILER 56 (134)
T ss_pred HhcCccccCCceEEEEecCCcCCCcCCChHhhhccccCcEEEEeh
Confidence 4899999999999876411 11122234567665443334433
No 31
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=62.64 E-value=7.5 Score=27.28 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=6.2
Q ss_pred CCcCcEEEEEe
Q 030254 77 IRTGEIVVFNI 87 (180)
Q Consensus 77 ~~~GDIVvf~~ 87 (180)
+++||.|+...
T Consensus 44 I~~GD~VlVe~ 54 (83)
T smart00652 44 IRRGDIVLVDP 54 (83)
T ss_pred EcCCCEEEEEe
Confidence 55666666543
No 32
>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=62.12 E-value=37 Score=25.67 Aligned_cols=58 Identities=17% Similarity=0.247 Sum_probs=27.4
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCCCCcchhhhccCCceeccceEeeEEEE
Q 030254 75 DPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNNDVDDRMLYAQGQFWLKQEHIMGRAVG 145 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~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 RNFQVGDLVLFLPTRNHN-NKKQPWAAFNV---GCPHYFLHEDSIAANEL---------KRREWIVGRIVS 98 (129)
T ss_pred ecCCCCCEEEEEecCCCC-ccccceEEeeC---CCceEEEecccchhccC---------CCCCEEEEEEEE
Confidence 346777777776543221 11222222211 22367776666543111 135667777653
No 33
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=61.10 E-value=8.4 Score=26.70 Aligned_cols=11 Identities=18% Similarity=0.649 Sum_probs=6.2
Q ss_pred CCcCcEEEEEe
Q 030254 77 IRTGEIVVFNI 87 (180)
Q Consensus 77 ~~~GDIVvf~~ 87 (180)
+++||.|+...
T Consensus 39 I~~GD~VlV~~ 49 (78)
T cd04456 39 IKRGDFLIVDP 49 (78)
T ss_pred EcCCCEEEEEe
Confidence 55666665543
No 34
>COG3895 Predicted periplasmic protein [General function prediction only]
Probab=58.75 E-value=21 Score=26.64 Aligned_cols=46 Identities=26% Similarity=0.449 Sum_probs=35.9
Q ss_pred CCcCcE-EEEEeCCCCcCEEEEEEEecccc-cCCeeEEEEeccCCCCcc
Q 030254 77 IRTGEI-VVFNIQGRDIPIVHRVIEVHEQR-QSGEVRILTKGDNNDVDD 123 (180)
Q Consensus 77 ~~~GDI-Vvf~~~~~~~~~ihRVi~~~~d~-~~g~~~~~t~GDnn~~~D 123 (180)
...||+ +.|-.+++ .++...++.-.|.. .+|...+|+|||.-.-+|
T Consensus 49 ~n~gd~sv~~v~Dg~-tlv~~nviSaSGAkYa~G~YvwWsKG~~A~lyd 96 (112)
T COG3895 49 NNAGDISVSFVLDGK-TLVLSNVISASGAKYADGIYVWWSKGDEATLYD 96 (112)
T ss_pred ecCCCceEEEEecCC-EEEEeeeeeccCccccCcEEEEEeCCCceEEEe
Confidence 578999 99988877 57889999877753 357788999999865443
No 35
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=58.69 E-value=11 Score=26.89 Aligned_cols=37 Identities=19% Similarity=0.161 Sum_probs=19.5
Q ss_pred EEcCCCccc-cCcCCCEEEEEe------cCCCCCcCcEEEEEeC
Q 030254 52 VVLSESMEP-GFQRGDILFLQM------SKDPIRTGEIVVFNIQ 88 (180)
Q Consensus 52 ~V~~~SM~P-~l~~GD~v~v~~------~~~~~~~GDIVvf~~~ 88 (180)
.+.++.|.- .+.+|..++..- ..-.+.+||.|.....
T Consensus 15 e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~s 58 (87)
T PRK12442 15 EVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELS 58 (87)
T ss_pred EECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEEC
Confidence 344455554 456666665542 1233566777766544
No 36
>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=58.40 E-value=37 Score=25.61 Aligned_cols=39 Identities=26% Similarity=0.193 Sum_probs=22.6
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccCC
Q 030254 75 DPIRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDNN 119 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~g~~~~~t~GDnn 119 (180)
+++++||+|+|+..+.+ -+.=+++...+ .+.+.+.|=|.
T Consensus 72 ~~p~~GDiv~f~~~~~~--HVGi~~g~~~~----~g~i~~lgGNq 110 (129)
T TIGR02594 72 SKPAYGCIAVKRRGGGG--HVGFVVGKDKQ----TGTIIVLGGNQ 110 (129)
T ss_pred CCCCccEEEEEECCCCC--EEEEEEeEcCC----CCEEEEeeCCC
Confidence 46899999999865432 22223332221 13677777664
No 37
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=57.55 E-value=10 Score=27.65 Aligned_cols=11 Identities=36% Similarity=0.749 Sum_probs=6.7
Q ss_pred CCcCcEEEEEe
Q 030254 77 IRTGEIVVFNI 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 56666666654
No 38
>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=52.80 E-value=26 Score=24.30 Aligned_cols=29 Identities=28% Similarity=0.387 Sum_probs=21.7
Q ss_pred ccccCcCCCEEEEEe------cCCCCCcCcEEEEE
Q 030254 58 MEPGFQRGDILFLQM------SKDPIRTGEIVVFN 86 (180)
Q Consensus 58 M~P~l~~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 899999999999876 12346777777733
No 39
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=52.48 E-value=6.5 Score=26.87 Aligned_cols=35 Identities=20% Similarity=0.318 Sum_probs=18.9
Q ss_pred CCccccCcCCCEEEEEec-C-CC-CCcCcEEEEEeCCC
Q 030254 56 ESMEPGFQRGDILFLQMS-K-DP-IRTGEIVVFNIQGR 90 (180)
Q Consensus 56 ~SM~P~l~~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 589999999999999752 1 11 22223467776533
No 40
>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=50.39 E-value=31 Score=29.39 Aligned_cols=39 Identities=18% Similarity=0.451 Sum_probs=28.6
Q ss_pred cCcCCCEEEEEe--cCCCCCcCcEEEEEeCCCCcCEEEEEEE
Q 030254 61 GFQRGDILFLQM--SKDPIRTGEIVVFNIQGRDIPIVHRVIE 100 (180)
Q Consensus 61 ~l~~GD~v~v~~--~~~~~~~GDIVvf~~~~~~~~~ihRVi~ 100 (180)
||++||+++.-. -...++.||++.....+-. .+..+|..
T Consensus 224 tL~pGDvI~TGTP~Gvg~l~~GD~v~~~iegiG-~l~n~v~~ 264 (266)
T COG0179 224 TLEPGDVILTGTPSGVGFLKPGDVVEVEIEGIG-ELENTVVK 264 (266)
T ss_pred ccCCCCEEEeCCCCCcccCCCCCEEEEEeccee-EEEEEEee
Confidence 789999999875 3457999999988887642 35555543
No 41
>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=45.44 E-value=38 Score=22.09 Aligned_cols=38 Identities=18% Similarity=0.337 Sum_probs=23.7
Q ss_pred CCCccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEE
Q 030254 55 SESMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHR 97 (180)
Q Consensus 55 ~~SM~P-~l~~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 smart00841 18 SGGTKPATLETGAVVQV---PLFINEGDKIKVDTRTGE--YVSR 56 (56)
T ss_pred CCCcceEEECCCCEEEc---CCcccCCCEEEEECCCCc--EEcC
Confidence 445665 5566755544 356889998888766443 5544
No 42
>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=43.22 E-value=42 Score=24.80 Aligned_cols=28 Identities=39% Similarity=0.748 Sum_probs=18.2
Q ss_pred CCcCcEEEEEeCCC-CcCEEEEEEEeccc
Q 030254 77 IRTGEIVVFNIQGR-DIPIVHRVIEVHEQ 104 (180)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ihRVi~~~~d 104 (180)
++.||-|.++.++. +.+++.||..+-.+
T Consensus 4 ~~vGD~V~v~~~~~~~~pyIgrI~~i~e~ 32 (121)
T cd04714 4 IRVGDCVLFKSPGRPSLPYVARIESLWED 32 (121)
T ss_pred EEcCCEEEEeCCCCCCCCEEEEEEEEEEc
Confidence 46677777776543 34677777777654
No 43
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=42.81 E-value=22 Score=26.66 Aligned_cols=20 Identities=30% Similarity=0.458 Sum_probs=15.3
Q ss_pred EcCCCccccCcCCCEEEEEe
Q 030254 53 VLSESMEPGFQRGDILFLQM 72 (180)
Q Consensus 53 V~~~SM~P~l~~GD~v~v~~ 72 (180)
-.+++|+|.|+.||.|++..
T Consensus 47 ~~~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 47 ALSDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred EccCcccCcCCCCCEEEEec
Confidence 34568888888888888864
No 44
>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=42.52 E-value=1.2e+02 Score=23.71 Aligned_cols=57 Identities=16% Similarity=0.323 Sum_probs=34.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhh-------hhhccccC------eEEEcCCCccccCcCCCEEEEEe
Q 030254 15 KIRDSLFQFITLGMIVSSALIIWKGLM-------CITGSESP------VVVVLSESMEPGFQRGDILFLQM 72 (180)
Q Consensus 15 ~~r~~~~~i~~~~~~i~i~~~i~~~l~-------~~~~~~~p------~~~V~~~SM~P~l~~GD~v~v~~ 72 (180)
.++++++.++.++++++++..+...+. +..++-.| .+.+...+ ...++.||++.++.
T Consensus 2 ~~~~ii~~~~~~~l~~~~~~~l~~~~~~~~p~v~V~g~SM~Ptl~~GD~vlv~~~~-~~~~~~GDIVvf~~ 71 (158)
T TIGR02228 2 KISNVIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFNTGDLILVTGAD-PNDIQVGDVITYKS 71 (158)
T ss_pred hhHHHHHHHHHHHHHHHHHHHheeeccCCCcEEEEcCCCCcCCccCCCEEEEEecc-cCCCCCCCEEEEEE
Confidence 356778888877777766655544433 33444445 22333311 23689999999986
No 45
>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=41.82 E-value=62 Score=23.89 Aligned_cols=29 Identities=17% Similarity=0.486 Sum_probs=21.6
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEecc
Q 030254 75 DPIRTGEIVVFNIQGRDIPIVHRVIEVHE 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 46999999999864333457788888764
No 46
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=40.93 E-value=51 Score=24.08 Aligned_cols=30 Identities=17% Similarity=0.444 Sum_probs=24.2
Q ss_pred cCCCCCcCcEEEEEeCCCCcCEEEEEEEeccc
Q 030254 73 SKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQ 104 (180)
Q Consensus 73 ~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d 104 (180)
+..+++.||++....+.+ .++=+|.+++..
T Consensus 45 pS~~VK~GD~l~i~~~~~--~~~v~Vl~~~~~ 74 (100)
T COG1188 45 PSKEVKVGDILTIRFGNK--EFTVKVLALGEQ 74 (100)
T ss_pred cccccCCCCEEEEEeCCc--EEEEEEEecccc
Confidence 567899999999998866 478888887653
No 47
>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=39.77 E-value=68 Score=24.18 Aligned_cols=10 Identities=20% Similarity=-0.091 Sum_probs=7.5
Q ss_pred ceEeeEEEEE
Q 030254 137 EHIMGRAVGF 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 3899988754
No 48
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. 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=39.58 E-value=1.1e+02 Score=24.31 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=26.9
Q ss_pred EEEEEe--cCCCCCcCcEEEEEeCCCCcCEEEEEEEeccc
Q 030254 67 ILFLQM--SKDPIRTGEIVVFNIQGRDIPIVHRVIEVHEQ 104 (180)
Q Consensus 67 ~v~v~~--~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d 104 (180)
.+...+ ....+++||.|+++.+....+++..|..+..+
T Consensus 41 ~i~l~R~~d~~~~~vGD~Vlik~~~~~~~~V~iI~ei~~~ 80 (179)
T cd04720 41 KIFLARDSDGLELSVGDTILVKDDVANSPSVYLIHEIRLN 80 (179)
T ss_pred cEEEEEccCCeEEeCCCEEEEeCCCCCCCEEEEEEEEEeC
Confidence 344443 45679999999999876555677777777644
No 49
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=38.81 E-value=43 Score=24.13 Aligned_cols=34 Identities=24% Similarity=0.534 Sum_probs=23.7
Q ss_pred EEEcCCCccccCcCCCEEEEEe--------cCCCCCcCcEEEEEeC
Q 030254 51 VVVLSESMEPGFQRGDILFLQM--------SKDPIRTGEIVVFNIQ 88 (180)
Q Consensus 51 ~~V~~~SM~P~l~~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 5677776555 55677764 2356999999999753
No 50
>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=38.02 E-value=38 Score=18.74 Aligned_cols=20 Identities=25% Similarity=0.373 Sum_probs=13.8
Q ss_pred chhHHHHHHHHHHHhhhhcC
Q 030254 160 KPIIKYILIGALGLLVITSK 179 (180)
Q Consensus 160 ~~~~~~~l~~~~~~~~~~~~ 179 (180)
.+..-..++++++++++++|
T Consensus 4 F~~i~l~I~all~i~~i~~r 23 (26)
T TIGR03024 4 FSTIALPIIALLAIIVILRR 23 (26)
T ss_pred CcchHHHHHHHHHHHHHHhh
Confidence 34334566678888998887
No 51
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=37.64 E-value=29 Score=27.32 Aligned_cols=24 Identities=13% Similarity=0.332 Sum_probs=14.2
Q ss_pred CcCCCEEEEEecCCCCCcCcEEEE
Q 030254 62 FQRGDILFLQMSKDPIRTGEIVVF 85 (180)
Q Consensus 62 l~~GD~v~v~~~~~~~~~GDIVvf 85 (180)
+.+||+|+|.....+...|||+--
T Consensus 71 I~~GD~VlVel~~yd~~KgdIi~R 94 (155)
T PTZ00329 71 INIGDIILVSLRDFQDSKADVILK 94 (155)
T ss_pred ecCCCEEEEeccCCCCCEEEEEEE
Confidence 466666666654445666666543
No 52
>PLN00208 translation initiation factor (eIF); Provisional
Probab=37.63 E-value=30 Score=27.00 Aligned_cols=10 Identities=30% Similarity=0.757 Sum_probs=4.9
Q ss_pred CCcCcEEEEE
Q 030254 77 IRTGEIVVFN 86 (180)
Q Consensus 77 ~~~GDIVvf~ 86 (180)
+++||+|+..
T Consensus 71 I~~GD~VlVe 80 (145)
T PLN00208 71 IAAGDIILVG 80 (145)
T ss_pred ecCCCEEEEE
Confidence 4455555544
No 53
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=37.47 E-value=49 Score=23.99 Aligned_cols=35 Identities=23% Similarity=0.465 Sum_probs=26.1
Q ss_pred eEEEcCCCccccCcCCCEEEEEe--------cCCCCCcCcEEEEEeC
Q 030254 50 VVVVLSESMEPGFQRGDILFLQM--------SKDPIRTGEIVVFNIQ 88 (180)
Q Consensus 50 ~~~V~~~SM~P~l~~GD~v~v~~--------~~~~~~~GDIVvf~~~ 88 (180)
-+.+..+|.+| |-+++++. ....++.||.|+|-+.
T Consensus 55 ~lFi~~gsvrp----Gii~lINd~DWEllekedy~ledgD~ivfiST 97 (101)
T KOG4146|consen 55 SLFIHHGSVRP----GIIVLINDMDWELLEKEDYPLEDGDHIVFIST 97 (101)
T ss_pred ceEeeCCcCcC----cEEEEEeccchhhhcccccCcccCCEEEEEEe
Confidence 47889998776 44677765 3466999999999753
No 54
>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=36.95 E-value=62 Score=20.67 Aligned_cols=25 Identities=16% Similarity=0.408 Sum_probs=16.9
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEE
Q 030254 75 DPIRTGEIVVFNIQGRDIPIVHRVI 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 4478999999986544434566554
No 55
>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=36.51 E-value=29 Score=24.13 Aligned_cols=11 Identities=27% Similarity=0.619 Sum_probs=6.8
Q ss_pred CCcCcEEEEEe
Q 030254 77 IRTGEIVVFNI 87 (180)
Q Consensus 77 ~~~GDIVvf~~ 87 (180)
+++||+|+..+
T Consensus 39 IkrGd~VlV~p 49 (78)
T cd05792 39 IKRGDFVLVEP 49 (78)
T ss_pred EEeCCEEEEEe
Confidence 56666666654
No 56
>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=36.40 E-value=34 Score=22.19 Aligned_cols=22 Identities=27% Similarity=0.252 Sum_probs=14.9
Q ss_pred CCCcCcEEEEEeC--CC-CcCEEEE
Q 030254 76 PIRTGEIVVFNIQ--GR-DIPIVHR 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 4889999999843 32 2357775
No 57
>PRK11372 lysozyme inhibitor; Provisional
Probab=36.15 E-value=68 Score=23.58 Aligned_cols=40 Identities=20% Similarity=0.270 Sum_probs=26.5
Q ss_pred CcEEEEEeCCCCcCEEEEEEEecccc-cCCeeEEEEeccCCC
Q 030254 80 GEIVVFNIQGRDIPIVHRVIEVHEQR-QSGEVRILTKGDNND 120 (180)
Q Consensus 80 GDIVvf~~~~~~~~~ihRVi~~~~d~-~~g~~~~~t~GDnn~ 120 (180)
+|-+.|..+++ .+..+++++-.|.. .++...||+|||.-.
T Consensus 50 ~~~v~l~~~~~-~~~L~~~~SASGArY~~g~~~fWtKG~eA~ 90 (109)
T PRK11372 50 RQEVSFVYDNQ-LLHLKQGISASGARYTDGIYVFWSKGDEAT 90 (109)
T ss_pred CCeEEEEECCE-EEEEEEeeccCcCcEeCCcEEEEEeCCeEE
Confidence 56666666554 46777877665542 246678999998743
No 58
>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=35.99 E-value=26 Score=27.19 Aligned_cols=38 Identities=11% Similarity=0.229 Sum_probs=25.9
Q ss_pred EEcCCCccccCcCCCEEEEEe-cCCCCCcCcEEEEEeCC
Q 030254 52 VVLSESMEPGFQRGDILFLQM-SKDPIRTGEIVVFNIQG 89 (180)
Q Consensus 52 ~V~~~SM~P~l~~GD~v~v~~-~~~~~~~GDIVvf~~~~ 89 (180)
...++||...|...=.-.+.. ...++++|||+++...+
T Consensus 50 ~~nT~tl~~~L~~~G~~~I~~~~~~~~q~GDI~I~g~~g 88 (145)
T PF05382_consen 50 AGNTETLHDWLKKNGFKKISENVDWNLQRGDIFIWGRRG 88 (145)
T ss_pred ccCHHHHHHHHhhCCcEEeccCCcccccCCCEEEEcCCC
Confidence 467789988765554555544 22479999999986553
No 59
>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=35.80 E-value=1.1e+02 Score=19.19 Aligned_cols=52 Identities=19% Similarity=0.352 Sum_probs=31.4
Q ss_pred CCcCcEEEEEeCCCCcCEEEEEEEecccccCCeeEEEEeccC-CCCcchhhhccCCceeccceE
Q 030254 77 IRTGEIVVFNIQGRDIPIVHRVIEVHEQRQSGEVRILTKGDN-NDVDDRMLYAQGQFWLKQEHI 139 (180)
Q Consensus 77 ~~~GDIVvf~~~~~~~~~ihRVi~~~~d~~~g~~~~~t~GDn-n~~~D~~~y~~~~~~V~~~~I 139 (180)
+++|+.|.... ..+..+--+|+.+..+ ++...|.+.=++ |...|. +|+.++|
T Consensus 1 ~~vG~~v~~~~-~~~~~y~A~I~~~r~~--~~~~~YyVHY~g~nkR~De--------WV~~~~i 53 (55)
T PF11717_consen 1 FEVGEKVLCKY-KDGQWYEAKILDIREK--NGEPEYYVHYQGWNKRLDE--------WVPESRI 53 (55)
T ss_dssp --TTEEEEEEE-TTTEEEEEEEEEEEEC--TTCEEEEEEETTSTGCC-E--------EEETTTE
T ss_pred CCcCCEEEEEE-CCCcEEEEEEEEEEec--CCCEEEEEEcCCCCCCcee--------eecHHHc
Confidence 35788777766 2335788889988765 244566676555 444564 4666665
No 60
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=35.23 E-value=1.5e+02 Score=20.35 Aligned_cols=31 Identities=19% Similarity=0.320 Sum_probs=19.9
Q ss_pred EEecCCCCCcCcEEEEEeCCCCcCEEEEEEEe
Q 030254 70 LQMSKDPIRTGEIVVFNIQGRDIPIVHRVIEV 101 (180)
Q Consensus 70 v~~~~~~~~~GDIVvf~~~~~~~~~ihRVi~~ 101 (180)
++++.++.++||+...+.-.++ -++.|.+..
T Consensus 22 iRkNDRdf~VGD~L~L~E~~~~-~YTGr~~~~ 52 (72)
T PF12961_consen 22 IRKNDRDFQVGDILVLREWDNG-EYTGREIEA 52 (72)
T ss_pred EEecCCCCCCCCEEEEEEecCC-CccccEEEE
Confidence 3446788999999999864322 255444443
No 61
>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=34.73 E-value=52 Score=27.26 Aligned_cols=29 Identities=17% Similarity=0.157 Sum_probs=15.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 030254 16 IRDSLFQFITLGMIVSSALIIWKGLMCIT 44 (180)
Q Consensus 16 ~r~~~~~i~~~~~~i~i~~~i~~~l~~~~ 44 (180)
+|+-...+|++++.+++++++.++..+++
T Consensus 8 KrRK~N~iLNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 8 KRRKTNKILNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred HhhhhhhhHHHHHHHHHHHHHHHhhhhee
Confidence 34555567777766666555544443333
No 62
>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=31.85 E-value=88 Score=20.34 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=21.5
Q ss_pred CCCccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEE
Q 030254 55 SESMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHR 97 (180)
Q Consensus 55 ~~SM~P-~l~~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 SSSYKPATLETGAEIQVP---LFIEEGDKIKVDTRDGS--YVER 56 (56)
T ss_dssp STTEEEEEETTS-EEEEE---TT--TT-EEEEETTTTE--EEEE
T ss_pred CCCccEEEEcCCCEEEcc---ceecCCCEEEEECCCCe--EeCC
Confidence 345666 45666555543 55889999998876543 6665
No 63
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=31.78 E-value=50 Score=22.15 Aligned_cols=22 Identities=23% Similarity=0.202 Sum_probs=14.4
Q ss_pred CCCcCcEEEEEe--CCC-CcCEEEE
Q 030254 76 PIRTGEIVVFNI--QGR-DIPIVHR 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 478899999983 221 2356666
No 64
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=31.06 E-value=51 Score=23.90 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=13.1
Q ss_pred CcCCCEEEEEe-----cCCCCCcCcEEEEE
Q 030254 62 FQRGDILFLQM-----SKDPIRTGEIVVFN 86 (180)
Q Consensus 62 l~~GD~v~v~~-----~~~~~~~GDIVvf~ 86 (180)
+.+|..+++.- ..-.+++||.|+..
T Consensus 38 ~~dG~~~la~i~GK~Rk~iwI~~GD~VlVs 67 (99)
T TIGR00523 38 CLDGKTRLGRIPGKLKKRIWIREGDVVIVK 67 (99)
T ss_pred eCCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence 34555555542 12236677777763
No 65
>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=30.22 E-value=1.5e+02 Score=23.45 Aligned_cols=28 Identities=14% Similarity=0.217 Sum_probs=18.6
Q ss_pred EEEEEecCCCCCcCcEEEEEeCCCCcCEEE
Q 030254 67 ILFLQMSKDPIRTGEIVVFNIQGRDIPIVH 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 34442 57888898888888877433333
No 66
>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=29.96 E-value=88 Score=22.81 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=18.9
Q ss_pred CCcCcEEEEEeCCC-CcCEEEEEEEeccc
Q 030254 77 IRTGEIVVFNIQGR-DIPIVHRVIEVHEQ 104 (180)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ihRVi~~~~d 104 (180)
++.||-|.++++++ ..+++-||..+-.+
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 32 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERLWKD 32 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEEEEC
Confidence 46677777776553 45678888887654
No 67
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=28.27 E-value=40 Score=23.23 Aligned_cols=17 Identities=12% Similarity=0.200 Sum_probs=13.6
Q ss_pred CCCCCcCcEEEEEeCCC
Q 030254 74 KDPIRTGEIVVFNIQGR 90 (180)
Q Consensus 74 ~~~~~~GDIVvf~~~~~ 90 (180)
.-+.++||++.|..+.+
T Consensus 54 ~LeCqpgDiley~~d~~ 70 (73)
T COG3655 54 ALECQPGDILEYVPDSD 70 (73)
T ss_pred HcCCChhheeEEecCCc
Confidence 45789999999987654
No 68
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=27.69 E-value=32 Score=25.87 Aligned_cols=33 Identities=27% Similarity=0.489 Sum_probs=19.8
Q ss_pred cCcCCCEEEEEe-cCCCCCcCcEEEEEeCCCCcCEEEEEEEecc
Q 030254 61 GFQRGDILFLQM-SKDPIRTGEIVVFNIQGRDIPIVHRVIEVHE 103 (180)
Q Consensus 61 ~l~~GD~v~v~~-~~~~~~~GDIVvf~~~~~~~~~ihRVi~~~~ 103 (180)
.+++||+||+.. ..+++..|- .=++.+|+.++-
T Consensus 38 rl~~GDlVFlT~~~~~Dl~~Gt----------sGiiAkV~~vev 71 (122)
T COG1935 38 RLHEGDLVFLTSTSLEDLTKGT----------SGIIAKVRRVEV 71 (122)
T ss_pred cCCCCCEEEEehhHhhHhhcCc----------ceeEEEEEEEEE
Confidence 467777777765 445554442 126777777653
No 69
>CHL00010 infA translation initiation factor 1
Probab=26.10 E-value=78 Score=21.68 Aligned_cols=23 Identities=22% Similarity=0.235 Sum_probs=14.2
Q ss_pred CCCcCcEEEEEe--CCC-CcCEEEEE
Q 030254 76 PIRTGEIVVFNI--QGR-DIPIVHRV 98 (180)
Q Consensus 76 ~~~~GDIVvf~~--~~~-~~~~ihRV 98 (180)
.+.+||.|.|.. .+. ...++||-
T Consensus 46 ~~~vGD~V~ve~~~~~~~~g~Ii~r~ 71 (78)
T CHL00010 46 RILPGDRVKVELSPYDLTKGRIIYRL 71 (78)
T ss_pred ccCCCCEEEEEEcccCCCeEEEEEEe
Confidence 367899999983 221 13566664
No 70
>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=25.87 E-value=67 Score=22.72 Aligned_cols=30 Identities=23% Similarity=0.506 Sum_probs=18.9
Q ss_pred ccCcCCCEEEEEe-cCCCCCcCcEEEEEeCC
Q 030254 60 PGFQRGDILFLQM-SKDPIRTGEIVVFNIQG 89 (180)
Q Consensus 60 P~l~~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 4566778876443 23488999999987654
No 71
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=25.18 E-value=98 Score=23.29 Aligned_cols=29 Identities=14% Similarity=0.057 Sum_probs=20.0
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEeccc
Q 030254 75 DPIRTGEIVVFNIQGRDIPIVHRVIEVHEQ 104 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi~~~~d 104 (180)
..+++||.|..+++++ .+++.+|..+..+
T Consensus 6 ~~i~vGD~V~v~~~~~-~~~va~Ie~i~ed 34 (130)
T cd04721 6 VTISVHDFVYVLSEEE-DRYVAYIEDLYED 34 (130)
T ss_pred EEEECCCEEEEeCCCC-CcEEEEEEEEEEc
Confidence 4477888888876653 4577777777655
No 72
>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=24.98 E-value=79 Score=21.64 Aligned_cols=16 Identities=25% Similarity=0.785 Sum_probs=10.2
Q ss_pred CCCCCcCcEEEEEeCC
Q 030254 74 KDPIRTGEIVVFNIQG 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 5789999999999764
No 73
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=24.92 E-value=1.6e+02 Score=17.79 Aligned_cols=24 Identities=25% Similarity=0.145 Sum_probs=12.3
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHH
Q 030254 14 MKIRDSLFQFITLGMIVSSALIIW 37 (180)
Q Consensus 14 ~~~r~~~~~i~~~~~~i~i~~~i~ 37 (180)
-..|+++......+..+..+.++|
T Consensus 9 ~~RRdFL~~at~~~gavG~~~~a~ 32 (41)
T PF10399_consen 9 PTRRDFLTIATSAVGAVGAAAAAW 32 (41)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHH
Confidence 456777655444444444444444
No 74
>PF12666 PrgI: PrgI family protein; InterPro: IPR024414 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Probab=24.60 E-value=1e+02 Score=21.32 Aligned_cols=27 Identities=15% Similarity=0.128 Sum_probs=14.8
Q ss_pred HHHHHHHhh-----cchHHHHHHHHHHHHHHH
Q 030254 5 GESIESVKS-----MKIRDSLFQFITLGMIVS 31 (180)
Q Consensus 5 ~~~~~~~~~-----~~~r~~~~~i~~~~~~i~ 31 (180)
.|+++.|++ +++|+++--+...++..+
T Consensus 3 pkdi~~~e~ki~~GlT~RQl~~l~~~~~~~~~ 34 (93)
T PF12666_consen 3 PKDISKYEEKIFFGLTLRQLICLAIGALVGVG 34 (93)
T ss_pred CcchhhccchhccCCCHHHHHHHHHHHHHHHH
Confidence 355555444 577777655544444433
No 75
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (TIGR02305). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=24.23 E-value=1.3e+02 Score=25.09 Aligned_cols=37 Identities=16% Similarity=0.485 Sum_probs=25.0
Q ss_pred cCcCCCEEEEEe--cCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030254 61 GFQRGDILFLQM--SKDPIRTGEIVVFNIQGRDIPIVHRV 98 (180)
Q Consensus 61 ~l~~GD~v~v~~--~~~~~~~GDIVvf~~~~~~~~~ihRV 98 (180)
+|++||+|+.-. ....++.||.+.-...+-. .+..+|
T Consensus 204 tL~pGDvIlTGTp~g~~~l~~GD~v~~~i~glG-~l~n~v 242 (245)
T TIGR02303 204 TLEPGDVILTGTPKGLSDVKPGDVVRLEIEGVG-ALENPI 242 (245)
T ss_pred CcCCCCEEEcCCCCCCeEcCCCCEEEEEEcCce-eEEEEE
Confidence 788899888865 2345888888887776442 344444
No 76
>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=24.23 E-value=1.2e+02 Score=24.16 Aligned_cols=38 Identities=18% Similarity=0.332 Sum_probs=25.2
Q ss_pred CCccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030254 56 ESMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRV 98 (180)
Q Consensus 56 ~SM~P-~l~~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 36666 4566643333 466899999998877554 77774
No 77
>PRK11507 ribosome-associated protein; Provisional
Probab=23.97 E-value=33 Score=23.46 Aligned_cols=15 Identities=27% Similarity=0.310 Sum_probs=12.4
Q ss_pred cCCCCCcCcEEEEEe
Q 030254 73 SKDPIRTGEIVVFNI 87 (180)
Q Consensus 73 ~~~~~~~GDIVvf~~ 87 (180)
..+++.+||+|.|..
T Consensus 49 RgkKl~~GD~V~~~g 63 (70)
T PRK11507 49 KRCKIVAGQTVSFAG 63 (70)
T ss_pred cCCCCCCCCEEEECC
Confidence 368899999999864
No 78
>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=23.47 E-value=1e+02 Score=19.99 Aligned_cols=38 Identities=21% Similarity=0.329 Sum_probs=22.8
Q ss_pred CCCccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEE
Q 030254 55 SESMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHR 97 (180)
Q Consensus 55 ~~SM~P-~l~~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 456676 4566643322 456788998888766443 5544
No 79
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=23.10 E-value=67 Score=22.63 Aligned_cols=17 Identities=18% Similarity=0.604 Sum_probs=13.9
Q ss_pred CCccccCcCCCEEEEEe
Q 030254 56 ESMEPGFQRGDILFLQM 72 (180)
Q Consensus 56 ~SM~P~l~~GD~v~v~~ 72 (180)
..|+|.|+.||+|..+-
T Consensus 44 k~~rp~L~~GDlV~ArV 60 (86)
T cd05790 44 KRNRPNLNVGDLVYARV 60 (86)
T ss_pred ccccccCCCCCEEEEEE
Confidence 45789999999998874
No 80
>PF14118 YfzA: YfzA-like protein
Probab=23.02 E-value=59 Score=23.49 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=12.7
Q ss_pred EEcCCCccccCcCCCE
Q 030254 52 VVLSESMEPGFQRGDI 67 (180)
Q Consensus 52 ~V~~~SM~P~l~~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 3556899999999874
No 81
>COG5471 Uncharacterized conserved protein [Function unknown]
Probab=22.83 E-value=1.1e+02 Score=22.45 Aligned_cols=28 Identities=14% Similarity=0.307 Sum_probs=20.6
Q ss_pred ccccCcCCCEEEEEecCCCCCcCcEEEEE
Q 030254 58 MEPGFQRGDILFLQMSKDPIRTGEIVVFN 86 (180)
Q Consensus 58 M~P~l~~GD~v~v~~~~~~~~~GDIVvf~ 86 (180)
|....++|+-+-+.. ...++.||.|++-
T Consensus 2 akNfv~~gktveiva-~~~i~SGd~VlvG 29 (107)
T COG5471 2 AKNFVEPGKTVEIVA-PAAIKSGDLVLVG 29 (107)
T ss_pred cccccCCCCEEEEec-ccccccCCEEEEe
Confidence 455678888887765 5778888888774
No 82
>PHA02756 hypothetical protein; Provisional
Probab=22.78 E-value=3.6e+02 Score=20.75 Aligned_cols=70 Identities=17% Similarity=0.160 Sum_probs=42.7
Q ss_pred HHHHHHhhhhhhccccCeEEEcCCCccccCcCCCEEEEEecCCCCCcCcEEEEEeCCC-----CcCEEEEEEEecc
Q 030254 33 ALIIWKGLMCITGSESPVVVVLSESMEPGFQRGDILFLQMSKDPIRTGEIVVFNIQGR-----DIPIVHRVIEVHE 103 (180)
Q Consensus 33 ~~~i~~~l~~~~~~~~p~~~V~~~SM~P~l~~GD~v~v~~~~~~~~~GDIVvf~~~~~-----~~~~ihRVi~~~~ 103 (180)
.-+.|..+.-++|..+--=.+.+.|-.|.+++=+++++.+ .++.+-=.+-.|+-+.- ..+++|..-++..
T Consensus 16 lgfswlql~wffg~~svgg~iltpsa~pyipplslii~~p-sn~c~gwav~~~~~~wlglfei~lpvvhyfa~vgp 90 (164)
T PHA02756 16 LGFSWLQLPWFFGIPSVGGFILTPSAHPYIPPLSLIITKP-SNECEGWAVKFFEGNWLGLFEIHLPVVHYFAGVGP 90 (164)
T ss_pred HhHHHHhhHHhhccCCcceEEECCCCCCCCCCeEEEEEcc-CCcccceEEEEEeeeeeeeEEEeeeeeeeeccCCc
Confidence 3356766665555433223588999999999999988886 34443333334443321 1457787776543
No 83
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=22.62 E-value=1.9e+02 Score=21.63 Aligned_cols=35 Identities=14% Similarity=0.293 Sum_probs=21.5
Q ss_pred EEEcCCCccccCcCCCEEEE-Eec---CCCCCcCcEEEEEe
Q 030254 51 VVVLSESMEPGFQRGDILFL-QMS---KDPIRTGEIVVFNI 87 (180)
Q Consensus 51 ~~V~~~SM~P~l~~GD~v~v-~~~---~~~~~~GDIVvf~~ 87 (180)
+++...|+.+ ..|=.+.+ .+. -..++.||||+++.
T Consensus 41 l~i~D~S~~~--~~~l~v~~F~~~~~~LP~v~~GDVIll~~ 79 (138)
T cd04497 41 LTITDPSLAN--SDGLTVKLFRPNEESLPIVKVGDIILLRR 79 (138)
T ss_pred EEEECCCCCC--CCcEEEEEECCChhhCCCCCCCCEEEEEE
Confidence 6788888876 33323322 221 12369999999985
No 84
>PRK14578 elongation factor P; Provisional
Probab=22.43 E-value=1.5e+02 Score=23.98 Aligned_cols=37 Identities=14% Similarity=0.222 Sum_probs=23.1
Q ss_pred Cccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030254 57 SMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRV 98 (180)
Q Consensus 57 SM~P-~l~~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 4555533332 456899999988877554 77774
No 85
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=22.39 E-value=1.9e+02 Score=21.56 Aligned_cols=15 Identities=27% Similarity=0.614 Sum_probs=11.6
Q ss_pred CCCCCcCcEEEEEeC
Q 030254 74 KDPIRTGEIVVFNIQ 88 (180)
Q Consensus 74 ~~~~~~GDIVvf~~~ 88 (180)
.+++++||+|.|+..
T Consensus 74 ~~~~qpGDlvff~~~ 88 (134)
T TIGR02219 74 CDAAQPGDVLVFRWR 88 (134)
T ss_pred hhcCCCCCEEEEeeC
Confidence 467899999988753
No 86
>PRK15203 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase; Provisional
Probab=22.35 E-value=1.3e+02 Score=27.25 Aligned_cols=30 Identities=23% Similarity=0.372 Sum_probs=22.7
Q ss_pred cCcCCCEEEEEec--CCCCCcCcEEEEEeCCC
Q 030254 61 GFQRGDILFLQMS--KDPIRTGEIVVFNIQGR 90 (180)
Q Consensus 61 ~l~~GD~v~v~~~--~~~~~~GDIVvf~~~~~ 90 (180)
||++||+++.-.+ ...+++||.+.....+-
T Consensus 165 tL~pGDvI~TGTP~g~~~l~~GD~v~~~i~gi 196 (429)
T PRK15203 165 TLNPGDAILLGTPQARVEIQPGDRVRVLAEGF 196 (429)
T ss_pred CcCCCCEEEcCCCCCceECCCCCEEEEEEeCe
Confidence 7889999988652 24588999888877654
No 87
>PRK12426 elongation factor P; Provisional
Probab=22.23 E-value=1.4e+02 Score=24.03 Aligned_cols=39 Identities=13% Similarity=0.286 Sum_probs=24.7
Q ss_pred CCCccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030254 55 SESMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRV 98 (180)
Q Consensus 55 ~~SM~P-~l~~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 4566644433 356889999988876554 77774
No 88
>PF09956 DUF2190: Uncharacterized conserved protein (DUF2190); InterPro: IPR011231 This entry is represented by Bacteriophage VT1-Sakai, H0018. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised conserved proteins.
Probab=22.11 E-value=1.2e+02 Score=22.07 Aligned_cols=28 Identities=25% Similarity=0.433 Sum_probs=21.3
Q ss_pred ccccCcCCCEEEEEecCCCCCcCcEEEEE
Q 030254 58 MEPGFQRGDILFLQMSKDPIRTGEIVVFN 86 (180)
Q Consensus 58 M~P~l~~GD~v~v~~~~~~~~~GDIVvf~ 86 (180)
|+-.+++||.+-+.. ...++.||.|+.-
T Consensus 1 mkNyvq~G~~i~~ta-~~~V~sG~~V~vG 28 (106)
T PF09956_consen 1 MKNYVQDGDTIDVTA-PAAVASGDVVVVG 28 (106)
T ss_pred CCccccCCCEEEEec-CcccccCCEEEEC
Confidence 777888998887775 4478888887763
No 89
>smart00439 BAH Bromo adjacent homology domain.
Probab=21.94 E-value=1.6e+02 Score=20.65 Aligned_cols=13 Identities=15% Similarity=0.194 Sum_probs=10.1
Q ss_pred eeccceEeeEEEE
Q 030254 133 WLKQEHIMGRAVG 145 (180)
Q Consensus 133 ~V~~~~IiG~v~~ 145 (180)
.++.+.|.|++.-
T Consensus 70 ~i~~~~I~~kc~V 82 (120)
T smart00439 70 TVPLSDIIGKCNV 82 (120)
T ss_pred cCChHHeeeEEEE
Confidence 4778899998864
No 90
>KOG1535 consensus Predicted fumarylacetoacetate hydralase [General function prediction only]
Probab=21.87 E-value=94 Score=25.75 Aligned_cols=29 Identities=10% Similarity=0.423 Sum_probs=20.6
Q ss_pred cCcCCCEEEEEe--cCCCCCcCcEEEEEeCC
Q 030254 61 GFQRGDILFLQM--SKDPIRTGEIVVFNIQG 89 (180)
Q Consensus 61 ~l~~GD~v~v~~--~~~~~~~GDIVvf~~~~ 89 (180)
|+.+||+++.-. .-.+++.||++-..-.+
T Consensus 176 tL~~GDvILTGTP~GVg~v~~Gd~i~~ei~~ 206 (217)
T KOG1535|consen 176 TLEPGDVILTGTPEGVGEVKPGDVIQCELLE 206 (217)
T ss_pred eecCCCEEEecCCCccccccCCCEEEecccc
Confidence 677788888865 23567888888776553
No 91
>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=21.65 E-value=1e+02 Score=21.71 Aligned_cols=28 Identities=25% Similarity=0.455 Sum_probs=16.6
Q ss_pred CCcCcEEEEEeCC-CCcCEEEEEEEeccc
Q 030254 77 IRTGEIVVFNIQG-RDIPIVHRVIEVHEQ 104 (180)
Q Consensus 77 ~~~GDIVvf~~~~-~~~~~ihRVi~~~~d 104 (180)
++.||.|..+.++ .+.+++.||..+..+
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~~~ 31 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIWED 31 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEEcC
Confidence 3456666655544 234677777777654
No 92
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=21.33 E-value=1.5e+02 Score=22.05 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=17.9
Q ss_pred CCCCcCcEEEEEeCCCCcCEEEEEEEec
Q 030254 75 DPIRTGEIVVFNIQGRDIPIVHRVIEVH 102 (180)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ihRVi~~~ 102 (180)
..+++||+|....++. ...=||.+++
T Consensus 138 ~~l~pGDvi~l~~~~~--~~~~RI~~i~ 163 (164)
T PF13550_consen 138 LALEPGDVIALSDDGR--DMRFRITEIE 163 (164)
T ss_pred ccCCCCCEEEEEeCCC--ceEEEEEEEe
Confidence 4478888888877744 3677777654
No 93
>PRK04542 elongation factor P; Provisional
Probab=20.92 E-value=1.9e+02 Score=23.46 Aligned_cols=37 Identities=24% Similarity=0.428 Sum_probs=24.0
Q ss_pred Cccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030254 57 SMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRV 98 (180)
Q Consensus 57 SM~P-~l~~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 4566643333 456899999988877554 77775
No 94
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=20.66 E-value=1.6e+02 Score=21.40 Aligned_cols=34 Identities=15% Similarity=0.352 Sum_probs=24.4
Q ss_pred EEEcCCCccccCcCCCEEEEEecCCCCCcCcEEEEE
Q 030254 51 VVVLSESMEPGFQRGDILFLQMSKDPIRTGEIVVFN 86 (180)
Q Consensus 51 ~~V~~~SM~P~l~~GD~v~v~~~~~~~~~GDIVvf~ 86 (180)
.+|..++.+=...+||.+.+++- +.+.||-|.|.
T Consensus 3 AIi~~gGkQykV~~Gd~i~v~~l--~~~~G~~i~l~ 36 (103)
T PRK05573 3 AIIKTGGKQYKVEEGDVIKVEKL--DAEVGDTVEFD 36 (103)
T ss_pred EEEEECCEEEEEeCCCEEEEccc--CCCCCCEEEEe
Confidence 35666777777889999999872 35677776665
No 95
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=20.61 E-value=1.6e+02 Score=18.36 Aligned_cols=25 Identities=16% Similarity=0.408 Sum_probs=19.7
Q ss_pred cCCCEEEEEecCCCCCcCcEEEEEeC
Q 030254 63 QRGDILFLQMSKDPIRTGEIVVFNIQ 88 (180)
Q Consensus 63 ~~GD~v~v~~~~~~~~~GDIVvf~~~ 88 (180)
.+|+.+-+.+ ..+++.||-|.|...
T Consensus 13 ~dGeF~~ik~-~~~~~vG~eI~~~~~ 37 (56)
T PF12791_consen 13 PDGEFIKIKR-KPGMEVGQEIEFDEK 37 (56)
T ss_pred CCCcEEEEeC-CCCCcccCEEEEech
Confidence 5788888876 445999999999865
No 96
>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=20.57 E-value=1.4e+02 Score=24.06 Aligned_cols=38 Identities=24% Similarity=0.393 Sum_probs=24.4
Q ss_pred CCccc-cCcCCCEEEEEecCCCCCcCcEEEEEeCCCCcCEEEEE
Q 030254 56 ESMEP-GFQRGDILFLQMSKDPIRTGEIVVFNIQGRDIPIVHRV 98 (180)
Q Consensus 56 ~SM~P-~l~~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 34565 4566643333 456899999988877554 77774
No 97
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=20.32 E-value=56 Score=24.61 Aligned_cols=21 Identities=29% Similarity=0.540 Sum_probs=14.1
Q ss_pred cCcCCCEEEEEe-cCCCCCcCc
Q 030254 61 GFQRGDILFLQM-SKDPIRTGE 81 (180)
Q Consensus 61 ~l~~GD~v~v~~-~~~~~~~GD 81 (180)
.+++||.||+.. +.+++.+|+
T Consensus 38 ~~~~Gd~VFlT~~~~~Dl~~Gt 59 (119)
T PF04322_consen 38 SLDPGDRVFLTSVSLEDLTPGT 59 (119)
T ss_pred cCCCCCEEEEecCCHHHCCCCC
Confidence 457888888876 556665554
No 98
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=20.25 E-value=1.3e+02 Score=20.17 Aligned_cols=13 Identities=23% Similarity=0.358 Sum_probs=9.2
Q ss_pred CCCCCcCcEEEEE
Q 030254 74 KDPIRTGEIVVFN 86 (180)
Q Consensus 74 ~~~~~~GDIVvf~ 86 (180)
.++...|||+...
T Consensus 58 v~~~~aGdI~~i~ 70 (83)
T cd04092 58 IPSLSAGNIGVIT 70 (83)
T ss_pred CCeeCCCCEEEEE
Confidence 3567888888753
No 99
>PRK08564 5'-methylthioadenosine phosphorylase II; Reviewed
Probab=20.10 E-value=86 Score=26.62 Aligned_cols=19 Identities=16% Similarity=0.359 Sum_probs=16.6
Q ss_pred cCCCccccCcCCCEEEEEe
Q 030254 54 LSESMEPGFQRGDILFLQM 72 (180)
Q Consensus 54 ~~~SM~P~l~~GD~v~v~~ 72 (180)
..+||.|.+++||+++.+.
T Consensus 92 avGsl~~~~~pGDlVv~~D 110 (267)
T PRK08564 92 AVGSLREDYKPGDFVIPDQ 110 (267)
T ss_pred cccccCCCCCCCCEEeehh
Confidence 4479999999999999875
No 100
>PRK07432 5'-methylthioadenosine phosphorylase; Provisional
Probab=20.01 E-value=92 Score=26.90 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=21.3
Q ss_pred ccccCeEEEcCCCccccCcCCCEEEEEe
Q 030254 45 GSESPVVVVLSESMEPGFQRGDILFLQM 72 (180)
Q Consensus 45 ~~~~p~~~V~~~SM~P~l~~GD~v~v~~ 72 (180)
|..+-+.+-..+|+.|.+++||+++.+.
T Consensus 79 Gv~~ii~tna~Gsln~~~~pGdlvv~~D 106 (290)
T PRK07432 79 GVEYLISASAVGSLKEEAKPLDMVVPDQ 106 (290)
T ss_pred CCCEEEEEeccccccCCCCCCCEEeecc
Confidence 4434334566689999999999999875
Done!