Query 029367
Match_columns 194
No_of_seqs 201 out of 1477
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 11:47:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029367.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029367hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02227 sigpep_I_bact signal 100.0 8.8E-44 1.9E-48 278.1 18.5 151 37-192 5-163 (163)
2 PRK10861 signal peptidase I; P 100.0 1.7E-38 3.7E-43 270.4 18.4 151 37-192 67-305 (324)
3 KOG0171 Mitochondrial inner me 100.0 4.1E-34 8.8E-39 218.4 11.9 144 35-193 16-160 (176)
4 PRK13838 conjugal transfer pil 100.0 3.1E-30 6.7E-35 203.6 17.1 117 71-189 38-173 (176)
5 PRK13884 conjugal transfer pep 100.0 3.7E-29 8.1E-34 197.9 16.4 128 52-189 29-177 (178)
6 TIGR02771 TraF_Ti conjugative 100.0 3E-29 6.5E-34 197.3 15.7 127 53-189 25-170 (171)
7 PF10502 Peptidase_S26: Signal 100.0 1.8E-30 3.9E-35 197.8 2.6 108 82-189 20-138 (138)
8 KOG1568 Mitochondrial inner me 100.0 7.7E-28 1.7E-32 183.7 11.6 118 50-192 29-152 (174)
9 COG4959 TraF Type IV secretory 99.9 1.1E-21 2.3E-26 148.6 9.7 108 82-189 52-170 (173)
10 TIGR02754 sod_Ni_protease nick 99.9 3E-21 6.6E-26 136.4 10.1 89 56-186 2-90 (90)
11 cd06530 S26_SPase_I The S26 Ty 99.8 5.9E-20 1.3E-24 128.3 9.7 84 54-184 2-85 (85)
12 TIGR02228 sigpep_I_arch signal 99.7 2.9E-16 6.2E-21 122.1 12.2 85 56-185 35-119 (158)
13 COG0681 LepB Signal peptidase 99.6 1.3E-14 2.9E-19 112.4 11.4 126 40-184 17-144 (166)
14 PF00717 Peptidase_S24: Peptid 99.3 3.2E-12 7E-17 85.5 7.1 57 56-122 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 99.2 3.4E-10 7.4E-15 77.7 9.7 83 54-184 2-84 (84)
16 COG2932 Predicted transcriptio 98.8 4.1E-08 8.8E-13 79.7 10.4 56 53-119 124-179 (214)
17 cd06529 S24_LexA-like Peptidas 98.7 5.5E-08 1.2E-12 66.4 7.7 56 54-121 2-57 (81)
18 KOG3342 Signal peptidase I [In 98.7 1.6E-08 3.4E-13 77.1 5.3 92 53-186 49-145 (180)
19 PRK10276 DNA polymerase V subu 98.5 1.4E-06 2.9E-11 66.3 10.6 49 53-113 52-101 (139)
20 PRK00215 LexA repressor; Valid 98.4 5.4E-06 1.2E-10 66.7 11.1 50 52-113 118-168 (205)
21 PRK12423 LexA repressor; Provi 98.3 6.7E-06 1.4E-10 66.3 10.9 49 53-113 115-164 (202)
22 TIGR00498 lexA SOS regulatory 98.3 8.4E-06 1.8E-10 65.3 11.4 50 52-113 111-161 (199)
23 COG1974 LexA SOS-response tran 97.3 0.0054 1.2E-07 49.6 11.0 49 53-112 113-162 (201)
24 COG0681 LepB Signal peptidase 92.9 0.16 3.4E-06 38.8 4.1 29 104-132 137-165 (166)
25 COG1097 RRP4 RNA-binding prote 75.6 4.6 0.0001 33.5 4.2 77 57-133 104-194 (239)
26 cd04712 BAH_DCM_I BAH, or Brom 71.2 40 0.00088 25.1 8.2 96 82-193 4-104 (130)
27 PF05257 CHAP: CHAP domain; I 68.1 16 0.00036 26.4 5.4 37 82-123 61-98 (124)
28 cd04456 S1_IF1A_like S1_IF1A_l 67.0 6.4 0.00014 26.9 2.7 11 84-94 39-49 (78)
29 PHA02580 8 baseplate wedge sub 65.5 25 0.00055 29.8 6.4 83 50-134 74-162 (331)
30 COG0361 InfA Translation initi 64.3 7.3 0.00016 26.5 2.5 21 67-90 48-68 (75)
31 TIGR00008 infA translation ini 63.6 8.2 0.00018 25.7 2.6 21 67-90 46-66 (68)
32 COG0093 RplN Ribosomal protein 61.4 43 0.00094 24.8 6.3 24 154-178 82-105 (122)
33 PF10000 ACT_3: ACT domain; I 60.4 5.6 0.00012 26.7 1.4 18 60-77 12-29 (72)
34 COG4079 Uncharacterized protei 58.8 14 0.0003 30.9 3.7 33 102-134 247-283 (293)
35 PF12273 RCR: Chitin synthesis 58.6 8 0.00017 28.7 2.2 22 31-52 1-22 (130)
36 PF01176 eIF-1a: Translation i 58.5 8.9 0.00019 25.0 2.1 12 84-95 42-53 (65)
37 COG3602 Uncharacterized protei 57.2 9.8 0.00021 28.1 2.3 18 60-77 12-29 (134)
38 cd05793 S1_IF1A S1_IF1A: Trans 56.3 12 0.00027 25.3 2.6 11 84-94 39-49 (77)
39 smart00652 eIF1a eukaryotic tr 54.0 14 0.00031 25.4 2.6 11 84-94 44-54 (83)
40 PF14085 DUF4265: Domain of un 53.7 84 0.0018 22.8 6.9 47 68-121 10-57 (117)
41 PRK09919 anti-adapter protein 51.8 15 0.00034 26.9 2.6 23 113-135 39-61 (114)
42 PF00238 Ribosomal_L14: Riboso 51.1 68 0.0015 23.7 6.1 28 150-178 78-105 (122)
43 PRK04012 translation initiatio 49.6 17 0.00037 26.0 2.6 11 84-94 60-70 (100)
44 cd04717 BAH_polybromo BAH, or 48.6 50 0.0011 23.9 5.0 79 84-185 4-82 (121)
45 cd05792 S1_eIF1AD_like S1_eIF1 47.8 17 0.00038 24.8 2.2 26 68-94 21-49 (78)
46 PF11101 DUF2884: Protein of u 47.6 24 0.00053 28.9 3.5 25 110-134 17-42 (229)
47 TIGR01067 rplN_bact ribosomal 47.0 78 0.0017 23.5 5.8 27 152-179 80-106 (122)
48 TIGR02594 conserved hypothetic 45.5 66 0.0014 23.9 5.3 13 82-94 72-84 (129)
49 PRK12442 translation initiatio 44.7 25 0.00055 24.5 2.7 10 85-94 48-57 (87)
50 PF11302 DUF3104: Protein of u 42.5 63 0.0014 21.9 4.3 30 84-113 6-35 (75)
51 PF04319 NifZ: NifZ domain; I 42.5 52 0.0011 22.3 3.9 19 62-80 1-19 (75)
52 cd03695 CysN_NodQ_II CysN_NodQ 39.8 74 0.0016 21.3 4.4 33 82-121 25-65 (81)
53 TIGR00523 eIF-1A eukaryotic/ar 37.8 37 0.00079 24.3 2.7 10 84-93 58-67 (99)
54 CHL00057 rpl14 ribosomal prote 37.6 83 0.0018 23.3 4.7 28 151-179 79-106 (122)
55 PF06890 Phage_Mu_Gp45: Bacter 35.8 1.2E+02 0.0027 23.5 5.6 37 79-122 70-109 (162)
56 PRK05483 rplN 50S ribosomal pr 35.7 1.3E+02 0.0028 22.3 5.5 27 152-179 80-106 (122)
57 smart00439 BAH Bromo adjacent 35.6 1.5E+02 0.0033 20.6 7.6 17 174-190 70-86 (120)
58 PF00278 Orn_DAP_Arg_deC: Pyri 35.5 74 0.0016 22.3 4.2 31 64-96 65-95 (116)
59 cd04370 BAH BAH, or Bromo Adja 34.1 97 0.0021 21.6 4.6 86 84-190 4-89 (123)
60 PF01479 S4: S4 domain; Inter 33.3 16 0.00036 21.7 0.3 14 122-135 24-37 (48)
61 cd03698 eRF3_II_like eRF3_II_l 33.0 1.5E+02 0.0032 19.7 5.7 41 72-121 17-65 (83)
62 PF15057 DUF4537: Domain of un 33.0 36 0.00077 25.2 2.1 17 59-75 49-65 (124)
63 TIGR03673 rpl14p_arch 50S ribo 31.5 1.7E+02 0.0037 22.0 5.6 30 149-179 87-116 (131)
64 PF02836 Glyco_hydro_2_C: Glyc 31.2 46 0.001 27.9 2.8 15 119-133 1-15 (298)
65 PRK06789 flagellar motor switc 31.1 79 0.0017 21.4 3.4 10 125-134 45-54 (74)
66 COG0234 GroS Co-chaperonin Gro 30.8 2E+02 0.0043 20.5 6.3 27 68-94 6-45 (96)
67 PRK00364 groES co-chaperonin G 30.7 1.9E+02 0.0041 20.2 6.9 23 67-91 5-27 (95)
68 cd04089 eRF3_II eRF3_II: domai 30.4 1.7E+02 0.0036 19.5 6.0 41 72-121 16-64 (82)
69 PRK10626 hypothetical protein; 29.7 61 0.0013 27.0 3.1 24 110-134 40-64 (239)
70 PLN02289 ribulose-bisphosphate 29.3 46 0.001 26.2 2.2 25 148-172 98-122 (176)
71 smart00002 PLP Myelin proteoli 28.8 15 0.00032 23.9 -0.5 20 165-184 22-41 (60)
72 PF11012 DUF2850: Protein of u 27.9 49 0.0011 22.7 2.0 25 116-140 16-40 (79)
73 PTZ00054 60S ribosomal protein 27.7 2.8E+02 0.006 21.1 6.9 29 150-179 96-124 (139)
74 PRK14533 groES co-chaperonin G 27.6 2.2E+02 0.0047 19.9 6.9 22 68-91 6-27 (91)
75 PF05382 Amidase_5: Bacterioph 27.6 64 0.0014 24.7 2.7 40 56-97 50-89 (145)
76 cd00604 IPT_CGTD IPT domain (d 27.5 79 0.0017 21.4 3.0 22 112-133 10-38 (81)
77 cd04721 BAH_plant_1 BAH, or Br 27.4 2.6E+02 0.0056 20.7 6.1 79 83-185 7-85 (130)
78 PF13144 SAF_2: SAF-like 27.0 2.1E+02 0.0045 22.3 5.8 52 65-123 122-177 (196)
79 COG5131 URM1 Ubiquitin-like pr 26.8 64 0.0014 22.7 2.3 30 65-94 57-91 (96)
80 PLN00208 translation initiatio 26.6 62 0.0013 24.8 2.5 11 84-94 71-81 (145)
81 PRK08571 rpl14p 50S ribosomal 26.4 2.7E+02 0.0058 21.0 5.9 29 150-179 89-117 (132)
82 COG4013 Uncharacterized protei 26.3 73 0.0016 22.1 2.5 12 114-125 36-47 (91)
83 KOG0860 Synaptobrevin/VAMP-lik 25.2 54 0.0012 24.2 1.9 25 27-51 89-113 (116)
84 KOG4146 Ubiquitin-like protein 24.9 80 0.0017 22.4 2.6 36 55-94 56-96 (101)
85 PRK15095 FKBP-type peptidyl-pr 23.9 2.6E+02 0.0055 21.4 5.6 34 83-123 92-125 (156)
86 PF01426 BAH: BAH domain; Int 23.8 96 0.0021 21.7 3.0 26 84-114 3-28 (119)
87 COG2421 Predicted acetamidase/ 23.7 2E+02 0.0042 24.9 5.2 55 59-122 14-79 (305)
88 PTZ00329 eukaryotic translatio 23.5 75 0.0016 24.7 2.4 11 84-94 71-81 (155)
89 PTZ00320 ribosomal protein L14 23.5 2.6E+02 0.0056 22.3 5.4 29 149-178 143-171 (188)
90 PF14118 YfzA: YfzA-like prote 22.5 1.4E+02 0.003 21.2 3.4 14 58-71 31-44 (94)
91 PF06394 Pepsin-I3: Pepsin inh 22.3 78 0.0017 21.5 2.1 14 121-134 25-38 (76)
92 COG1126 GlnQ ABC-type polar am 22.3 24 0.00053 29.2 -0.5 45 82-134 23-67 (240)
93 PTZ00414 10 kDa heat shock pro 22.2 3E+02 0.0065 19.6 7.0 23 67-91 14-36 (100)
94 cd04714 BAH_BAHCC1 BAH, or Bro 22.0 1.2E+02 0.0026 22.0 3.3 40 84-132 4-43 (121)
95 PF08194 DIM: DIM protein; In 21.9 66 0.0014 18.7 1.4 9 123-131 23-31 (36)
96 PF00498 FHA: FHA domain; Int 21.8 2.1E+02 0.0046 17.7 5.7 33 118-160 32-68 (68)
97 cd01287 FabA FabA, beta-hydrox 21.8 3.6E+02 0.0077 20.4 6.0 42 82-135 97-139 (150)
98 PRK05933 type III secretion sy 21.8 1.3E+02 0.0028 26.4 3.7 30 115-162 329-364 (372)
99 KOG0245 Kinesin-like protein [ 21.2 1.6E+02 0.0035 29.9 4.6 37 122-162 521-557 (1221)
100 PRK04163 exosome complex RNA-b 21.0 1E+02 0.0022 25.3 2.9 20 58-77 104-123 (235)
101 TIGR03170 flgA_cterm flagella 20.3 1.9E+02 0.0041 20.6 4.0 56 61-123 44-103 (122)
102 COG5547 Small integral membran 20.3 1E+02 0.0022 19.9 2.1 23 29-51 6-28 (62)
No 1
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=100.00 E-value=8.8e-44 Score=278.15 Aligned_cols=151 Identities=36% Similarity=0.590 Sum_probs=133.6
Q ss_pred HHHHHHHHHHHHHhcceEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCC
Q 029367 37 GSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAG 116 (194)
Q Consensus 37 ~~~~l~~~~li~~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpG 116 (194)
.+++++++++++.++++.+.|+|+||+|||++||+++++|..+...++++||+|+|+.|. ..++.++|||+|+||
T Consensus 5 ~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~-----~~~~~~iKRVig~pG 79 (163)
T TIGR02227 5 LLIAILLALLIRTFVFFPYKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPD-----DNKNIYVKRVIGLPG 79 (163)
T ss_pred HHHHHHHHHHHHhhEEEEEEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCC-----CCCceeEEEEEecCC
Confidence 344556667888899999999999999999999999999998777899999999999876 356789999999999
Q ss_pred CeEEEeCCEEEECCEEcccchhccCCC--------CCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEE
Q 029367 117 DLVQVRDGSLYVNGIAQNEDFIAEHPK--------YTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRC 188 (194)
Q Consensus 117 D~V~i~~~~v~vnG~~~~~~~~~~~~~--------~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 188 (194)
|+|++++++++|||+.++++|...... ....+.+||+|+||++|||+++|+||||||+|++++|+|||.+++
T Consensus 80 d~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~~ 159 (163)
T TIGR02227 80 DKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVF 159 (163)
T ss_pred CEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEEE
Confidence 999999999999999999987654311 224467999999999999999999999999999999999999999
Q ss_pred eCCC
Q 029367 189 YRPS 192 (194)
Q Consensus 189 ~p~~ 192 (194)
||.+
T Consensus 160 ~p~~ 163 (163)
T TIGR02227 160 YPFD 163 (163)
T ss_pred CCCC
Confidence 9975
No 2
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=1.7e-38 Score=270.40 Aligned_cols=151 Identities=33% Similarity=0.425 Sum_probs=125.9
Q ss_pred HHHHHHHHHHHHHhcceEEEecCCCcccccCCCCEEEEEeeeecc------------CCCCcceEEEEecCCCCCCCCCC
Q 029367 37 GSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYF------------RNPSIHDIVTFRAPFQYPGLGEE 104 (194)
Q Consensus 37 ~~~~l~~~~li~~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~------------~~~~rGDiVvf~~p~~~~~~~~~ 104 (194)
.+++++++++++.|+++.+.|+|.||+|||..||+++++|++|.. ++|+|||||+|+.|. +++
T Consensus 67 ~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~-----~~~ 141 (324)
T PRK10861 67 VFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPE-----DPK 141 (324)
T ss_pred HHHHHhHHHHHHhhEEEEEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCC-----CCC
Confidence 344556678888999999999999999999999999999998753 578999999999987 367
Q ss_pred ceEEEEEEEeCCCeEEEe--CCEEEECCEEcccch-----------------hc--------------------------
Q 029367 105 DVFIKRIVAKAGDLVQVR--DGSLYVNGIAQNEDF-----------------IA-------------------------- 139 (194)
Q Consensus 105 ~~~vKRVvglpGD~V~i~--~~~v~vnG~~~~~~~-----------------~~-------------------------- 139 (194)
..+||||+|+|||+|+++ ++++||||+.+...+ ..
T Consensus 142 ~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (324)
T PRK10861 142 LDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENG 221 (324)
T ss_pred CcEEEEeeecCCcEEEEEeCCCEEEEcCcccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 889999999999999997 899999997421110 00
Q ss_pred ---c---------------CCC-------------CCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEE
Q 029367 140 ---E---------------HPK-------------YTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRC 188 (194)
Q Consensus 140 ---~---------------~~~-------------~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~ 188 (194)
. .+. ....+++||+|+||++|||+++|+||||||+||+++|+|||.++|
T Consensus 222 ~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~~i~ 301 (324)
T PRK10861 222 IRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKATAIW 301 (324)
T ss_pred ccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEEEEE
Confidence 0 000 012467999999999999999999999999999999999999999
Q ss_pred eCCC
Q 029367 189 YRPS 192 (194)
Q Consensus 189 ~p~~ 192 (194)
++.+
T Consensus 302 ~s~d 305 (324)
T PRK10861 302 MSFE 305 (324)
T ss_pred EEcC
Confidence 9875
No 3
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.1e-34 Score=218.43 Aligned_cols=144 Identities=42% Similarity=0.622 Sum_probs=122.3
Q ss_pred hhHHHHHHHHHHHHHhcceEEEecCCCcccccCCC-CEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367 35 LDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIG-DRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA 113 (194)
Q Consensus 35 ~~~~~~l~~~~li~~~~~~~~~V~~~SM~Ptl~~G-d~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg 113 (194)
......+.++.+...++.+....+|.||+||++++ |+++..|+.+.++++++||+|++..|. .+.+.++|||+|
T Consensus 16 ~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~-----~~~~~~cKRIva 90 (176)
T KOG0171|consen 16 CSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPP-----DPKEHICKRIVA 90 (176)
T ss_pred HHHHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCC-----Cchhhhhheeec
Confidence 33444455556666788899999999999988764 566569999999999999999999988 477889999999
Q ss_pred eCCCeEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCCC
Q 029367 114 KAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSD 193 (194)
Q Consensus 114 lpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~ 193 (194)
+|||.+++.++.+.+|+.. |.+ ..++.||+||+|++|||+++|+|||+|||+|.+.|+||+++++||++.
T Consensus 91 ~eGD~v~v~~~~~~~n~~~--e~~--------~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~ 160 (176)
T KOG0171|consen 91 MEGDLVEVHDGPLVVNDLV--EKF--------STPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSR 160 (176)
T ss_pred cCCceEEEecCCcccchhh--hhc--------cceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchh
Confidence 9999999988888777543 221 156899999999999999999999999999999999999999999975
No 4
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.97 E-value=3.1e-30 Score=203.59 Aligned_cols=117 Identities=20% Similarity=0.218 Sum_probs=93.1
Q ss_pred EEEEEeeeeccCCCCcceEEEEecCCCC--------CCCCC------CceEEEEEEEeCCCeEEEeCCEEEECCEEcccc
Q 029367 71 RIIVEKASYYFRNPSIHDIVTFRAPFQY--------PGLGE------EDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNED 136 (194)
Q Consensus 71 ~vlv~k~~~~~~~~~rGDiVvf~~p~~~--------~~~~~------~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~ 136 (194)
-+.+.+..+..+++++||+|+|+.|.+. .++.. ...++|||+|+|||+|++++ +++|||+.++++
T Consensus 38 pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~-~v~iNg~~~~~~ 116 (176)
T PRK13838 38 PLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGG-SVSIDGRPLPSS 116 (176)
T ss_pred EEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECC-EEEECCEEcccc
Confidence 3566666554578999999999987642 11111 24699999999999999985 899999999998
Q ss_pred hhccCCCC-----CCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367 137 FIAEHPKY-----TSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY 189 (194)
Q Consensus 137 ~~~~~~~~-----~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 189 (194)
|....... .....+||+|+|||+|||. +|+||||||+|++++|+|+|.++|.
T Consensus 117 ~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi~t 173 (176)
T PRK13838 117 SVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPVLT 173 (176)
T ss_pred ccccccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEEEe
Confidence 76543221 1234689999999999985 8999999999999999999999875
No 5
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.97 E-value=3.7e-29 Score=197.90 Aligned_cols=128 Identities=21% Similarity=0.244 Sum_probs=97.0
Q ss_pred ceEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCC--------CCCC----CCC--ceEEEEEEEeCCC
Q 029367 52 SEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQ--------YPGL----GEE--DVFIKRIVAKAGD 117 (194)
Q Consensus 52 ~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~--------~~~~----~~~--~~~vKRVvglpGD 117 (194)
.......++||. .|=+.+ .. ..+++||+|+|++|.. +.+. +++ .+++|||+|+|||
T Consensus 29 ~~~~~N~T~S~P----~glY~~-~~-----~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD 98 (178)
T PRK13884 29 AGARVNTTKSIP----VGLYWT-SS-----APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGD 98 (178)
T ss_pred CcEEEECCCCCc----ceEEEE-eC-----CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCc
Confidence 344555677764 333333 21 5789999999998773 2222 222 4799999999999
Q ss_pred eEEEeCCEEEECCEEcccchh--ccC-----CCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367 118 LVQVRDGSLYVNGIAQNEDFI--AEH-----PKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY 189 (194)
Q Consensus 118 ~V~i~~~~v~vnG~~~~~~~~--~~~-----~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 189 (194)
+|+++++.++|||+.+++... .+. +......++||+|+||++|||+++|+||||||+|++++|+|+|.++++
T Consensus 99 ~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~t 177 (178)
T PRK13884 99 AVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVIT 177 (178)
T ss_pred EEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeEe
Confidence 999999999999999865432 221 122233469999999999999999999999999999999999999874
No 6
>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=99.97 E-value=3e-29 Score=197.29 Aligned_cols=127 Identities=24% Similarity=0.267 Sum_probs=97.6
Q ss_pred eEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCC--------CCCCCC------ceEEEEEEEeCCCe
Q 029367 53 EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQY--------PGLGEE------DVFIKRIVAKAGDL 118 (194)
Q Consensus 53 ~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~--------~~~~~~------~~~vKRVvglpGD~ 118 (194)
......++||.. |-+. +.+. ++++|||+|+|+.|.+. .++..+ ..++|||+|+|||+
T Consensus 25 ~~~~N~T~S~P~----g~Y~-~~~~----~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~ 95 (171)
T TIGR02771 25 GARINTTKSLPL----GLYW-TTSS----KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDR 95 (171)
T ss_pred eEEEECCCCCcc----eEEE-eCCC----CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCE
Confidence 344566777754 4344 3222 68999999999987631 112222 38999999999999
Q ss_pred EEEeCCEEEECCEEcccchhccCC-----CCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367 119 VQVRDGSLYVNGIAQNEDFIAEHP-----KYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY 189 (194)
Q Consensus 119 V~i~~~~v~vnG~~~~~~~~~~~~-----~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 189 (194)
|+++++.++|||+.+++.+..... .....+.+||+| ||++|||+++|+||||||+|++++|+|||.++|.
T Consensus 96 V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl~~ 170 (171)
T TIGR02771 96 VTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPLFT 170 (171)
T ss_pred EEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEeEe
Confidence 999999999999999876543211 112347899999 9999999999999999999999999999999874
No 7
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=99.96 E-value=1.8e-30 Score=197.78 Aligned_cols=108 Identities=37% Similarity=0.540 Sum_probs=34.4
Q ss_pred CCCCcceEEEEecCCC-------CCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCC----Cceee
Q 029367 82 RNPSIHDIVTFRAPFQ-------YPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYT----SDLTY 150 (194)
Q Consensus 82 ~~~~rGDiVvf~~p~~-------~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~----~~~~~ 150 (194)
..+++||+|+|+.|.. +.+...+..++|||+|+|||+|++++++++|||+.+.+.+..+..+.. ..+.+
T Consensus 20 ~~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~ 99 (138)
T PF10502_consen 20 DKIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGT 99 (138)
T ss_dssp ---------------------------------------------------------------------S-T----TEEE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceE
Confidence 3489999999999873 334556789999999999999999999999999998887765443322 25789
Q ss_pred ecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY 189 (194)
Q Consensus 151 vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 189 (194)
||+|+||++|||+++|+||||||+|++++|+|||.++|+
T Consensus 100 vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~t 138 (138)
T PF10502_consen 100 VPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLWT 138 (138)
T ss_dssp --TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEEE
T ss_pred eCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEEC
Confidence 999999999999999999999999999999999999985
No 8
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=7.7e-28 Score=183.71 Aligned_cols=118 Identities=32% Similarity=0.497 Sum_probs=103.7
Q ss_pred hcceEEEecCCCcccccCCC------CEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeC
Q 029367 50 TFSEIRFIPSSSMYPTLRIG------DRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRD 123 (194)
Q Consensus 50 ~~~~~~~V~~~SM~Ptl~~G------d~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~ 123 (194)
.+.....|.|+||.||++++ |+|++.|+.-....+.+||+|+|..|. ++++++||||+|+|||++...+
T Consensus 29 rV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~-----~p~~~~iKRv~alegd~~~t~~ 103 (174)
T KOG1568|consen 29 RVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPN-----DPDKVIIKRVAALEGDIMVTED 103 (174)
T ss_pred eEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCC-----ChhheeeeeeecccccEeccCC
Confidence 34566788999999999875 899999987554568999999999998 5899999999999999987632
Q ss_pred CEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCC
Q 029367 124 GSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192 (194)
Q Consensus 124 ~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~ 192 (194)
.....+.+|+||+||.|||...|+|||.||||+...|.|||+.++|||.
T Consensus 104 --------------------~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~ 152 (174)
T KOG1568|consen 104 --------------------EKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPV 152 (174)
T ss_pred --------------------CCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChH
Confidence 2245678999999999999999999999999999999999999999985
No 9
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.86 E-value=1.1e-21 Score=148.64 Aligned_cols=108 Identities=20% Similarity=0.283 Sum_probs=94.6
Q ss_pred CCCCcceEEEEecCCC-------CCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCC----Cceee
Q 029367 82 RNPSIHDIVTFRAPFQ-------YPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYT----SDLTY 150 (194)
Q Consensus 82 ~~~~rGDiVvf~~p~~-------~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~----~~~~~ 150 (194)
..+.+||+|++++|.. +.+++...+++|||.|+|||+|++..+.+.|||+.++.....+..+.. .++..
T Consensus 52 ~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~ 131 (173)
T COG4959 52 APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRY 131 (173)
T ss_pred CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCce
Confidence 3459999999999983 667888999999999999999999999999999999877666554443 33456
Q ss_pred ecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY 189 (194)
Q Consensus 151 vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~ 189 (194)
+.++++|+|+|..+.||||||||||+.++|+|.+.++|+
T Consensus 132 l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPvwt 170 (173)
T COG4959 132 LAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPVWT 170 (173)
T ss_pred ecCCeEEEEeccCCcccccceecccCHHHcceeeeeeec
Confidence 899999999999999999999999999999999999886
No 10
>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=99.86 E-value=3e-21 Score=136.41 Aligned_cols=89 Identities=38% Similarity=0.534 Sum_probs=76.2
Q ss_pred EecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEccc
Q 029367 56 FIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNE 135 (194)
Q Consensus 56 ~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~ 135 (194)
.|.|+||+|||++||.+++++.......+++||+|+++.|. .++..++||+++++
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~-----~~~~~~vkRv~~~~-------------------- 56 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPL-----QPYGLIIKRLAAVD-------------------- 56 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCC-----CCcceEEEEeeEEc--------------------
Confidence 58999999999999999999854333556789999999875 25689999999863
Q ss_pred chhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEE
Q 029367 136 DFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLT 186 (194)
Q Consensus 136 ~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~ 186 (194)
++++|++|||+..|.|||++|+|+..+|+|||++
T Consensus 57 -----------------~~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 57 -----------------DNGLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred -----------------CCeEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence 3578999999999999999999999999999964
No 11
>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=99.82 E-value=5.9e-20 Score=128.26 Aligned_cols=84 Identities=46% Similarity=0.834 Sum_probs=74.7
Q ss_pred EEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEc
Q 029367 54 IRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQ 133 (194)
Q Consensus 54 ~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~ 133 (194)
.+.|.|+||+|++.+||++++++......++++||+|+|+.+.. ++..++|||++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~-----~~~~~vkRv~~-------------------- 56 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGD-----PGKPIIKRVIG-------------------- 56 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCC-----CCCEEEEEEEE--------------------
Confidence 57899999999999999999998764334799999999999752 46899999996
Q ss_pred ccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEE
Q 029367 134 NEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRY 184 (194)
Q Consensus 134 ~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv 184 (194)
||+.|||+.+|.|||+||+++.++|+|++
T Consensus 57 ----------------------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 ----------------------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred ----------------------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 89999999899999999999999999985
No 12
>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=99.70 E-value=2.9e-16 Score=122.07 Aligned_cols=85 Identities=29% Similarity=0.464 Sum_probs=69.1
Q ss_pred EecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEccc
Q 029367 56 FIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNE 135 (194)
Q Consensus 56 ~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~ 135 (194)
.|.|+||+||+++||.+++++... .++++||+|+|+.|. ....++|||+++.++ ++
T Consensus 35 ~V~g~SM~Ptl~~GD~vlv~~~~~--~~~~~GDIVvf~~~~------~~~~iihRVi~v~~~-----~g----------- 90 (158)
T TIGR02228 35 VVLSGSMEPTFNTGDLILVTGADP--NDIQVGDVITYKSPG------FNTPVTHRVIEINNS-----GG----------- 90 (158)
T ss_pred EEcCCCCcCCccCCCEEEEEeccc--CCCCCCCEEEEEECC------CCccEEEEEEEEECC-----CC-----------
Confidence 389999999999999999998543 689999999999875 237899999997543 00
Q ss_pred chhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEE
Q 029367 136 DFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYL 185 (194)
Q Consensus 136 ~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~ 185 (194)
+..|.+.|||+ ...| .++|+.+||+||+.
T Consensus 91 -----------------~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~ 119 (158)
T TIGR02228 91 -----------------ELGFITKGDNN-PAPD---GEPVPSENVIGKYL 119 (158)
T ss_pred -----------------cEEEEEEecCC-CCCC---cccCCHHHEEEEEE
Confidence 12477889997 5556 68999999999997
No 13
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.59 E-value=1.3e-14 Score=112.44 Aligned_cols=126 Identities=33% Similarity=0.428 Sum_probs=89.9
Q ss_pred HHHHHHHH--HHhcceEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCC
Q 029367 40 KILIGLLL--WSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGD 117 (194)
Q Consensus 40 ~l~~~~li--~~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD 117 (194)
++++++++ ..++++.+.|+|+||+||++.||+++++|..+....+..+|++.+ |. .....++||+++++||
T Consensus 17 ~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~--~~-----~~~~~~~kr~~~~~GD 89 (166)
T COG0681 17 AIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVL--PA-----VVEGDLIKRVIGLRGD 89 (166)
T ss_pred HHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceeeec--CC-----CCCcceEEEeccCCCC
Confidence 33344444 688899999999999999999999999999988888999998832 32 4678899999999999
Q ss_pred eEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEE
Q 029367 118 LVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRY 184 (194)
Q Consensus 118 ~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv 184 (194)
++.++++..++ +..+++.+.. +..++.++.++....+.+++.++.......+.++
T Consensus 90 ~i~~~~~~~~~-~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 90 IVVFKDDRLYV-VPIIPRVYGL-----------VEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred EEEEECCEEEe-ecccCcchhh-----------hhcccccccccccccccCccccccccccccccce
Confidence 99999999887 3323322211 1111111444555566666766666666666665
No 14
>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=99.35 E-value=3.2e-12 Score=85.54 Aligned_cols=57 Identities=30% Similarity=0.579 Sum_probs=47.1
Q ss_pred EecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEe
Q 029367 56 FIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVR 122 (194)
Q Consensus 56 ~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~ 122 (194)
+|.|+||+|++++||++++++. .+++.||+|++..+. .+..++||+.+.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~----~~~~~gdivv~~~~~------~~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPS----SEPKDGDIVVVKIDG------DEELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEET----S---TTSEEEEEETT------EESEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCeeCCCEEEEEEc----CCCccCeEEEEEECC------ceeeEEEEEEEeCCCEEEEe
Confidence 5789999999999999999986 589999999999854 11389999999999999986
No 15
>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=99.17 E-value=3.4e-10 Score=77.71 Aligned_cols=83 Identities=40% Similarity=0.623 Sum_probs=62.8
Q ss_pred EEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEc
Q 029367 54 IRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQ 133 (194)
Q Consensus 54 ~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~ 133 (194)
.+.+.|+||+|++.+||.+++++.. ..++.||+|++..+ .+..++||+...++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~-------~~~~~ikrl~~~~~----------------- 54 (84)
T cd06462 2 ALRVEGDSMEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP-------GGELTVKRVIGLPG----------------- 54 (84)
T ss_pred eeEEcCCCccCcccCCCEEEEEecC---CCCcCCEEEEEEcC-------CCcEEEEEEEEECC-----------------
Confidence 4678999999999999999999863 24899999999984 24899999998654
Q ss_pred ccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEE
Q 029367 134 NEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRY 184 (194)
Q Consensus 134 ~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv 184 (194)
++++++.+||+ ++.+.+..+. ...+++|++
T Consensus 55 -------------------~~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~v 84 (84)
T cd06462 55 -------------------EGHYFLLGDNP-NSPDSRIDGP-PELDIVGVV 84 (84)
T ss_pred -------------------CCEEEEECCCC-CCCcccccCC-CHHHEEEeC
Confidence 25677888884 5555554433 556666653
No 16
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.82 E-value=4.1e-08 Score=79.74 Aligned_cols=56 Identities=23% Similarity=0.369 Sum_probs=45.3
Q ss_pred eEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeE
Q 029367 53 EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLV 119 (194)
Q Consensus 53 ~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V 119 (194)
....|.|+||+|++.+||.++|++- .+..+||.|++.. ..+..++||+...+|-.+
T Consensus 124 ~~i~V~GDSMeP~~~~Gd~ilVd~~----~~~~~gd~v~v~~-------~g~~~~VK~l~~~~~~~~ 179 (214)
T COG2932 124 FALRVTGDSMEPTYEDGDTLLVDPG----VNTRRGDRVYVET-------DGGELYVKKLQREPGGLL 179 (214)
T ss_pred EEEEEeCCcccccccCCCEEEECCC----CceeeCCEEEEEE-------eCCeEEEEEEEEecCCeE
Confidence 4568999999999999999999886 5678899666665 256899999997666544
No 17
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=98.74 E-value=5.5e-08 Score=66.42 Aligned_cols=56 Identities=27% Similarity=0.428 Sum_probs=47.1
Q ss_pred EEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEE
Q 029367 54 IRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQV 121 (194)
Q Consensus 54 ~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i 121 (194)
...+.|+||+|++++||.+++++. ..++.||++++..+ +..++||+...+++.+.+
T Consensus 2 ~~~v~g~sM~p~i~~gd~lii~~~----~~~~~g~i~~~~~~--------~~~~ikr~~~~~~~~~~L 57 (81)
T cd06529 2 ALRVKGDSMEPTIPDGDLVLVDPS----DTPRDGDIVVARLD--------GELTVKRLQRRGGGRLRL 57 (81)
T ss_pred EEEEECCCcCCccCCCCEEEEcCC----CCCCCCCEEEEEEC--------CEEEEEEEEECCCCcEEE
Confidence 467899999999999999999986 45999999999983 378999999877655444
No 18
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.74 E-value=1.6e-08 Score=77.10 Aligned_cols=92 Identities=25% Similarity=0.333 Sum_probs=65.7
Q ss_pred eEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEE
Q 029367 53 EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIA 132 (194)
Q Consensus 53 ~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~ 132 (194)
.+..|-|.||||.++.||.++..... ....+.||+|+|+.++ ++.++++||+.+-+. +++
T Consensus 49 PiVVVLSgSMePaF~RGDlLfL~N~~--~~p~~vGdivVf~veg------R~IPiVHRviK~he~----~~~-------- 108 (180)
T KOG3342|consen 49 PIVVVLSGSMEPAFHRGDLLFLTNRN--EDPIRVGDIVVFKVEG------REIPIVHRVIKQHEK----SNG-------- 108 (180)
T ss_pred CEEEEEcCCcCcccccccEEEEecCC--CCcceeccEEEEEECC------ccCchhHHHHHHhcc----cCC--------
Confidence 46788899999999999999987442 2457899999999975 779999999964221 011
Q ss_pred cccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCc-c----ccccCCCeeEEEEE
Q 029367 133 QNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHV-W----GPLPVKNIAGRYLT 186 (194)
Q Consensus 133 ~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~-~----G~V~~~~I~Gkv~~ 186 (194)
+-.+...|||+ -.|-|- | -...+++|.|+|.-
T Consensus 109 --------------------~~~~LTKGDNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~G 145 (180)
T KOG3342|consen 109 --------------------HIKFLTKGDNN--AVDDRGLYAQGQNWLERKDIVGRVRG 145 (180)
T ss_pred --------------------cEEEEecCCCC--cccchhcccccccceeccceeeEEee
Confidence 11366678884 334442 1 25778999999863
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.53 E-value=1.4e-06 Score=66.32 Aligned_cols=49 Identities=24% Similarity=0.268 Sum_probs=40.5
Q ss_pred eEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367 53 EIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA 113 (194)
Q Consensus 53 ~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg 113 (194)
...+|.|+||+ |++++||.+++++- .+++.||+|++.. .+...+||+.-
T Consensus 52 f~l~V~GdSM~~~~I~~GD~liVd~~----~~~~~Gdivv~~~--------~g~~~vKrl~~ 101 (139)
T PRK10276 52 YFVKASGDSMIDAGISDGDLLIVDSA----ITASHGDIVIAAV--------DGEFTVKKLQL 101 (139)
T ss_pred EEEEEecCCCCCCCCCCCCEEEEECC----CCCCCCCEEEEEE--------CCEEEEEEEEE
Confidence 45789999998 68999999999975 4678999999876 34678999874
No 20
>PRK00215 LexA repressor; Validated
Probab=98.38 E-value=5.4e-06 Score=66.73 Aligned_cols=50 Identities=22% Similarity=0.256 Sum_probs=41.6
Q ss_pred ceEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367 52 SEIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA 113 (194)
Q Consensus 52 ~~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg 113 (194)
.....|.|+||. |++.+||++++++. ..++.||+|++.. .+...+||+.-
T Consensus 118 ~~~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~--------~~~~~vKrl~~ 168 (205)
T PRK00215 118 DFLLRVRGDSMIDAGILDGDLVIVRKQ----QTARNGQIVVALI--------DDEATVKRFRR 168 (205)
T ss_pred eEEEEEccCCCCCCCcCCCCEEEEeCC----CCCCCCCEEEEEE--------CCEEEEEEEEE
Confidence 456789999995 79999999999874 4678999999987 34789999874
No 21
>PRK12423 LexA repressor; Provisional
Probab=98.34 E-value=6.7e-06 Score=66.33 Aligned_cols=49 Identities=24% Similarity=0.257 Sum_probs=41.1
Q ss_pred eEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367 53 EIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA 113 (194)
Q Consensus 53 ~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg 113 (194)
....|.|+||. |++.+||+++|++- ..++.||+|++.. .+...+||+.-
T Consensus 115 f~l~V~GdSM~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~--------~~~~~vKrl~~ 164 (202)
T PRK12423 115 YLLQVQGDSMIDDGILDGDLVGVHRS----PEARDGQIVVARL--------DGEVTIKRLER 164 (202)
T ss_pred EEEEEecCcCCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE--------CCEEEEEEEEE
Confidence 35789999997 79999999999874 5788999999987 34688999874
No 22
>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=98.34 E-value=8.4e-06 Score=65.28 Aligned_cols=50 Identities=22% Similarity=0.255 Sum_probs=42.0
Q ss_pred ceEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367 52 SEIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA 113 (194)
Q Consensus 52 ~~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg 113 (194)
...+.|.|+||. |++.+||++++++. ..++.||+|++.. .+...+||+.-
T Consensus 111 ~f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~--------~~~~~vKrl~~ 161 (199)
T TIGR00498 111 VFLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI--------DGEVTVKRFYK 161 (199)
T ss_pred EEEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE--------CCEEEEEEEEE
Confidence 457799999996 68999999999865 5789999999987 45789999764
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.25 E-value=0.0054 Score=49.55 Aligned_cols=49 Identities=22% Similarity=0.270 Sum_probs=40.3
Q ss_pred eEEEecCCCccc-ccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEE
Q 029367 53 EIRFIPSSSMYP-TLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIV 112 (194)
Q Consensus 53 ~~~~V~~~SM~P-tl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVv 112 (194)
...+|.|+||.. .+.+||.++|++. ...+.||+|+...+ .+..-+||..
T Consensus 113 f~L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~-------g~e~TvKrl~ 162 (201)
T COG1974 113 FFLRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALID-------GEEATVKRLY 162 (201)
T ss_pred EEEEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcC-------CCcEEEEEEE
Confidence 456899999965 5678999999976 78899999999984 3468899866
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=92.89 E-value=0.16 Score=38.79 Aligned_cols=29 Identities=31% Similarity=0.542 Sum_probs=23.6
Q ss_pred CceEEEEEEEeCCCeEEEeCCEEEECCEE
Q 029367 104 EDVFIKRIVAKAGDLVQVRDGSLYVNGIA 132 (194)
Q Consensus 104 ~~~~vKRVvglpGD~V~i~~~~v~vnG~~ 132 (194)
...++||+.++|||.+...+..+.+||+.
T Consensus 137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~ 165 (166)
T COG0681 137 KKDYIKRVIGLPGDNILYTDDDLPINGKP 165 (166)
T ss_pred ccccccceEEeeccceeeccCceeecCCC
Confidence 46799999999999999886448787763
No 25
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=75.63 E-value=4.6 Score=33.47 Aligned_cols=77 Identities=17% Similarity=0.277 Sum_probs=41.8
Q ss_pred ecCCCcccccCCCCEEEEEeeee-------------ccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEE-e
Q 029367 57 IPSSSMYPTLRIGDRIIVEKASY-------------YFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQV-R 122 (194)
Q Consensus 57 V~~~SM~Ptl~~Gd~vlv~k~~~-------------~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i-~ 122 (194)
..+..|.|.|+.||++...-... .+++++.|-+|-..+-.-.+-..+...++|-+...-+=.|.+ .
T Consensus 104 ~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 104 NAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred ccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 34788999999999988654321 245667787777765321111112222222222222222222 5
Q ss_pred CCEEEECCEEc
Q 029367 123 DGSLYVNGIAQ 133 (194)
Q Consensus 123 ~~~v~vnG~~~ 133 (194)
||.++|+++..
T Consensus 184 NG~IWV~~~~~ 194 (239)
T COG1097 184 NGRIWVDGENE 194 (239)
T ss_pred CCEEEecCCCc
Confidence 77888887654
No 26
>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=71.16 E-value=40 Score=25.10 Aligned_cols=96 Identities=10% Similarity=-0.007 Sum_probs=46.0
Q ss_pred CCCCcceEEEEecCCCCCCC-----CCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeE
Q 029367 82 RNPSIHDIVTFRAPFQYPGL-----GEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYV 156 (194)
Q Consensus 82 ~~~~rGDiVvf~~p~~~~~~-----~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~y 156 (194)
..++.||+|+++++...... .....+|-||..+--+ .++..++.|+-+-.+-. ...+. .-.+.++
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~----~~g~~~~h~~W~yrp~e-----Tv~g~-~~~~~El 73 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKG----SDGSKMFHGRWLYRGCD-----TVLGN-YANEREL 73 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeec----CCCceEEEEEEEEcchh-----ccccc-cCCCceE
Confidence 34678999999876531100 0124567776553222 12333333332211100 00011 3345677
Q ss_pred EEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCCC
Q 029367 157 YVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSD 193 (194)
Q Consensus 157 fvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~ 193 (194)
|+ .|+. +...-. .+ .++|+||+..-+.+..+
T Consensus 74 FL-Sd~c-~~~~~~---~~-~~~I~~k~~V~~~~~~~ 104 (130)
T cd04712 74 FL-TNEC-TCLELD---LL-STEIKGVHKVDWSGTPW 104 (130)
T ss_pred EE-eccc-cccccc---cc-cceeEEEEEEEEecCcC
Confidence 77 4554 221111 11 55999999888777543
No 27
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=68.14 E-value=16 Score=26.39 Aligned_cols=37 Identities=19% Similarity=0.252 Sum_probs=23.5
Q ss_pred CCCCcceEEEEecCCCCCCCCCCceEEEEEEEe-CCCeEEEeC
Q 029367 82 RNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAK-AGDLVQVRD 123 (194)
Q Consensus 82 ~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvgl-pGD~V~i~~ 123 (194)
..|+.|||++|.... ....-.+--|.++ .+++|.+.+
T Consensus 61 ~~P~~Gdivv~~~~~-----~~~~GHVaIV~~v~~~~~i~v~e 98 (124)
T PF05257_consen 61 STPQPGDIVVWDSGS-----GGGYGHVAIVESVNDGGTITVIE 98 (124)
T ss_dssp S---TTEEEEEEECT-----TTTT-EEEEEEEE-TTSEEEEEE
T ss_pred cccccceEEEeccCC-----CCCCCeEEEEEEECCCCEEEEEE
Confidence 689999999996221 2334477788888 888888743
No 28
>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=67.05 E-value=6.4 Score=26.85 Aligned_cols=11 Identities=9% Similarity=0.024 Sum_probs=6.3
Q ss_pred CCcceEEEEec
Q 029367 84 PSIHDIVTFRA 94 (194)
Q Consensus 84 ~~rGDiVvf~~ 94 (194)
+++||+|++..
T Consensus 39 I~~GD~VlV~~ 49 (78)
T cd04456 39 IKRGDFLIVDP 49 (78)
T ss_pred EcCCCEEEEEe
Confidence 35666666654
No 29
>PHA02580 8 baseplate wedge subunit; Provisional
Probab=65.54 E-value=25 Score=29.80 Aligned_cols=83 Identities=13% Similarity=-0.021 Sum_probs=44.1
Q ss_pred hcceEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEE-E-----eC
Q 029367 50 TFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ-V-----RD 123 (194)
Q Consensus 50 ~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~-i-----~~ 123 (194)
......+|.++-..+-+..-|+.-..- .......-||||+...-.-++.......++-||+-+|----+ + +.
T Consensus 74 ~Mmg~vKI~~s~ld~VvpRkDWgd~ry--~np~~f~i~dIVvvNsapyNrt~~g~GwmvYRcvDvP~~G~CSI~si~~K~ 151 (331)
T PHA02580 74 HMMGAVKIPKSMLDAVIPRKDWGDTRY--PNPKTFFINDIVVVNSAPYNRTDSGAGWMVYRCVDVPDTGSCSISSITNKV 151 (331)
T ss_pred hhhhheecCHhhhhheecccccCCCCC--CCCeEEEecCEEEEcccccccCCCCCceEEEEEeccCCCceeeeeeccCcc
Confidence 334445555444444444333322111 011234789999997533222223457899999999864222 2 34
Q ss_pred CEEEECCEEcc
Q 029367 124 GSLYVNGIAQN 134 (194)
Q Consensus 124 ~~v~vnG~~~~ 134 (194)
.-+.+.|+--+
T Consensus 152 eC~~iGGkWtp 162 (331)
T PHA02580 152 ECIKLGGKWTP 162 (331)
T ss_pred ceeeeCCEECC
Confidence 55778887543
No 30
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=64.32 E-value=7.3 Score=26.47 Aligned_cols=21 Identities=33% Similarity=0.471 Sum_probs=11.0
Q ss_pred CCCCEEEEEeeeeccCCCCcceEE
Q 029367 67 RIGDRIIVEKASYYFRNPSIHDIV 90 (194)
Q Consensus 67 ~~Gd~vlv~k~~~~~~~~~rGDiV 90 (194)
.+||.|+|....| ..++|||+
T Consensus 48 ~~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 48 LPGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred CCCCEEEEEeccc---ccccccEE
Confidence 4566666655543 24555543
No 31
>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=63.57 E-value=8.2 Score=25.70 Aligned_cols=21 Identities=29% Similarity=0.409 Sum_probs=9.4
Q ss_pred CCCCEEEEEeeeeccCCCCcceEE
Q 029367 67 RIGDRIIVEKASYYFRNPSIHDIV 90 (194)
Q Consensus 67 ~~Gd~vlv~k~~~~~~~~~rGDiV 90 (194)
.+||.|.|....| ++.+|+||
T Consensus 46 ~~GD~V~Ve~spy---d~tkgrIi 66 (68)
T TIGR00008 46 LPGDKVKVELSPY---DLTRGRIT 66 (68)
T ss_pred CCCCEEEEEECcc---cCCcEeEE
Confidence 3455555544432 24444443
No 32
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=61.43 E-value=43 Score=24.77 Aligned_cols=24 Identities=8% Similarity=0.389 Sum_probs=15.4
Q ss_pred CeEEEecCCCCCCCCCCccccccCC
Q 029367 154 GYVYVLGDNRNNSFDSHVWGPLPVK 178 (194)
Q Consensus 154 g~yfvlGDn~~~S~DSR~~G~V~~~ 178 (194)
|...++.++ .+-.-+|-||||.++
T Consensus 82 NA~Viin~~-g~P~GtrI~GPVaRE 105 (122)
T COG0093 82 NAAVIINPD-GEPRGTRIFGPVARE 105 (122)
T ss_pred ceEEEECCC-CCcccceEecchhHH
Confidence 333444333 366688999999876
No 33
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=60.40 E-value=5.6 Score=26.72 Aligned_cols=18 Identities=28% Similarity=0.464 Sum_probs=12.5
Q ss_pred CCcccccCCCCEEEEEee
Q 029367 60 SSMYPTLRIGDRIIVEKA 77 (194)
Q Consensus 60 ~SM~Ptl~~Gd~vlv~k~ 77 (194)
.||+|.+++|++|++.-.
T Consensus 12 ~~m~P~L~~~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVP 29 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-
T ss_pred hhCCcEeCCCCEEEEEec
Confidence 589999999999998764
No 34
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.75 E-value=14 Score=30.86 Aligned_cols=33 Identities=24% Similarity=0.475 Sum_probs=27.7
Q ss_pred CCCceEEEEEEEe----CCCeEEEeCCEEEECCEEcc
Q 029367 102 GEEDVFIKRIVAK----AGDLVQVRDGSLYVNGIAQN 134 (194)
Q Consensus 102 ~~~~~~vKRVvgl----pGD~V~i~~~~v~vnG~~~~ 134 (194)
+|+..++++|-+- |||.|.++++.+.|+|+.+.
T Consensus 247 gPg~~v~m~v~~~g~~~pGd~vvv~dg~mki~G~d~k 283 (293)
T COG4079 247 GPGEEVVMAVEGNGEVEPGDRVVVKDGVMKIDGKDLK 283 (293)
T ss_pred CCCceEEEEEccCCccCCCCEEEEecCceEeccccce
Confidence 5677888888774 99999999999999998653
No 35
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=58.63 E-value=8 Score=28.70 Aligned_cols=22 Identities=14% Similarity=0.172 Sum_probs=12.3
Q ss_pred chhhhhHHHHHHHHHHHHHhcc
Q 029367 31 RWPGLDGSLKILIGLLLWSTFS 52 (194)
Q Consensus 31 ~~~~~~~~~~l~~~~li~~~~~ 52 (194)
||..+.+++++++++++..++.
T Consensus 1 RW~l~~iii~~i~l~~~~~~~~ 22 (130)
T PF12273_consen 1 RWVLFAIIIVAILLFLFLFYCH 22 (130)
T ss_pred CeeeHHHHHHHHHHHHHHHHHH
Confidence 4656655555555555555544
No 36
>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=58.54 E-value=8.9 Score=24.97 Aligned_cols=12 Identities=17% Similarity=0.077 Sum_probs=7.3
Q ss_pred CCcceEEEEecC
Q 029367 84 PSIHDIVTFRAP 95 (194)
Q Consensus 84 ~~rGDiVvf~~p 95 (194)
+++||+|++...
T Consensus 42 I~~GD~V~V~~~ 53 (65)
T PF01176_consen 42 IKRGDFVLVEPS 53 (65)
T ss_dssp --TTEEEEEEES
T ss_pred cCCCCEEEEEec
Confidence 577888877753
No 37
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.25 E-value=9.8 Score=28.07 Aligned_cols=18 Identities=39% Similarity=0.471 Sum_probs=15.1
Q ss_pred CCcccccCCCCEEEEEee
Q 029367 60 SSMYPTLRIGDRIIVEKA 77 (194)
Q Consensus 60 ~SM~Ptl~~Gd~vlv~k~ 77 (194)
.||+|-|.+||+|+..--
T Consensus 12 ~smtPeL~~G~yVfcT~~ 29 (134)
T COG3602 12 ASMTPELLDGDYVFCTVA 29 (134)
T ss_pred HhcCccccCCceEEEEec
Confidence 479999999999997543
No 38
>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=56.32 E-value=12 Score=25.35 Aligned_cols=11 Identities=27% Similarity=0.147 Sum_probs=6.4
Q ss_pred CCcceEEEEec
Q 029367 84 PSIHDIVTFRA 94 (194)
Q Consensus 84 ~~rGDiVvf~~ 94 (194)
+++||+|++..
T Consensus 39 I~~GD~V~Ve~ 49 (77)
T cd05793 39 INEGDIVLVAP 49 (77)
T ss_pred EcCCCEEEEEe
Confidence 35666666654
No 39
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=53.97 E-value=14 Score=25.44 Aligned_cols=11 Identities=27% Similarity=0.132 Sum_probs=6.7
Q ss_pred CCcceEEEEec
Q 029367 84 PSIHDIVTFRA 94 (194)
Q Consensus 84 ~~rGDiVvf~~ 94 (194)
+++||+|++..
T Consensus 44 I~~GD~VlVe~ 54 (83)
T smart00652 44 IRRGDIVLVDP 54 (83)
T ss_pred EcCCCEEEEEe
Confidence 35666666654
No 40
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=53.69 E-value=84 Score=22.84 Aligned_cols=47 Identities=13% Similarity=0.396 Sum_probs=31.8
Q ss_pred CCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCC-eEEE
Q 029367 68 IGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGD-LVQV 121 (194)
Q Consensus 68 ~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD-~V~i 121 (194)
.+|...+...++....+..||+|.++.. .+...+.+++.-.|- |+++
T Consensus 10 ~~~~y~l~n~Pf~a~glA~gDvV~~~~~-------~g~~~~~~~v~~sGnsTiRv 57 (117)
T PF14085_consen 10 GDDTYRLDNIPFFAYGLALGDVVRAEPD-------DGELWFQKVVESSGNSTIRV 57 (117)
T ss_pred CCCEEEEEecccccCCCCCCCEEEEEeC-------CCeEEEEEEEecCCCEEEEE
Confidence 4566667777777788999999999984 355555555544443 4544
No 41
>PRK09919 anti-adapter protein IraM; Provisional
Probab=51.83 E-value=15 Score=26.90 Aligned_cols=23 Identities=9% Similarity=0.138 Sum_probs=19.7
Q ss_pred EeCCCeEEEeCCEEEECCEEccc
Q 029367 113 AKAGDLVQVRDGSLYVNGIAQNE 135 (194)
Q Consensus 113 glpGD~V~i~~~~v~vnG~~~~~ 135 (194)
=.|||.+...+..+.+||++.+-
T Consensus 39 L~pG~~i~~~~~gvliNdk~~pI 61 (114)
T PRK09919 39 LPPGSIITPVKSGVLLNDKPYPI 61 (114)
T ss_pred eCCCCEEEEcCCeEEECCcEeEE
Confidence 35999999999999999997643
No 42
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=51.07 E-value=68 Score=23.71 Aligned_cols=28 Identities=21% Similarity=0.469 Sum_probs=20.8
Q ss_pred eecCCeEEEecCCCCCCCCCCccccccCC
Q 029367 150 YVPVGYVYVLGDNRNNSFDSHVWGPLPVK 178 (194)
Q Consensus 150 ~vp~g~yfvlGDn~~~S~DSR~~G~V~~~ 178 (194)
...+|.+.++.++. +...+|-+|||+++
T Consensus 78 ~F~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 78 KFDDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp EESSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred EeCCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 34456667777774 78999999999864
No 43
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=49.59 E-value=17 Score=26.01 Aligned_cols=11 Identities=18% Similarity=0.108 Sum_probs=6.4
Q ss_pred CCcceEEEEec
Q 029367 84 PSIHDIVTFRA 94 (194)
Q Consensus 84 ~~rGDiVvf~~ 94 (194)
+.+||+|++..
T Consensus 60 I~~GD~VlVe~ 70 (100)
T PRK04012 60 IREGDVVIVAP 70 (100)
T ss_pred ecCCCEEEEEe
Confidence 35666666654
No 44
>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=48.63 E-value=50 Score=23.91 Aligned_cols=79 Identities=20% Similarity=0.150 Sum_probs=40.6
Q ss_pred CCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCC
Q 029367 84 PSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNR 163 (194)
Q Consensus 84 ~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~ 163 (194)
++.||.|.+..+.+ ++..+|-||..+--+ .+|..++++.-.-.+--... ......-++++|+.+.
T Consensus 4 ~~vGD~V~v~~~~~-----~~~~~i~~I~~i~~~----~~g~~~~~~~Wf~rP~et~~----~~~~~~~~~Evfls~~-- 68 (121)
T cd04717 4 YRVGDCVYVANPED-----PSKPIIFRIERLWKD----EDGEKFFFGCWFYRPEETFH----EPTRKFYKNEVFKSPL-- 68 (121)
T ss_pred EECCCEEEEeCCCC-----CCCCEEEEEeEEEEC----CCCCEEEEEEEEeChHHccC----CCccccccCceEEcCc--
Confidence 46799999887652 356778887753111 23445555543322111100 0011223466666432
Q ss_pred CCCCCCCccccccCCCeeEEEE
Q 029367 164 NNSFDSHVWGPLPVKNIAGRYL 185 (194)
Q Consensus 164 ~~S~DSR~~G~V~~~~I~Gkv~ 185 (194)
+--++.+.|+||+.
T Consensus 69 --------~d~~~~~~I~~kc~ 82 (121)
T cd04717 69 --------YETVPVEEIVGKCA 82 (121)
T ss_pred --------cccccHHHhcCeeE
Confidence 23566777777774
No 45
>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=47.79 E-value=17 Score=24.80 Aligned_cols=26 Identities=27% Similarity=0.314 Sum_probs=14.0
Q ss_pred CCCEEEEEeeeeccCC---CCcceEEEEec
Q 029367 68 IGDRIIVEKASYYFRN---PSIHDIVTFRA 94 (194)
Q Consensus 68 ~Gd~vlv~k~~~~~~~---~~rGDiVvf~~ 94 (194)
+|...++..- ..+++ +++||+|++.+
T Consensus 21 dG~~~l~~iP-~KfRk~iWIkrGd~VlV~p 49 (78)
T cd05792 21 NGSRYLVSMP-TKFRKNIWIKRGDFVLVEP 49 (78)
T ss_pred CCCEEEEEec-hhhcccEEEEeCCEEEEEe
Confidence 4555554432 22222 47788887765
No 46
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=47.57 E-value=24 Score=28.90 Aligned_cols=25 Identities=28% Similarity=0.691 Sum_probs=20.2
Q ss_pred EEEEeCCCeEEE-eCCEEEECCEEcc
Q 029367 110 RIVAKAGDLVQV-RDGSLYVNGIAQN 134 (194)
Q Consensus 110 RVvglpGD~V~i-~~~~v~vnG~~~~ 134 (194)
+|.+..|+.+.| .+|.++|||+.+.
T Consensus 17 ~v~~~~~~~~~I~~~g~L~i~G~~v~ 42 (229)
T PF11101_consen 17 EVVQASGEKLRIDPDGNLFINGKKVS 42 (229)
T ss_pred EEEeCCCceEEEcCCCcEEECCEEcc
Confidence 456677788888 7899999999864
No 47
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=46.98 E-value=78 Score=23.47 Aligned_cols=27 Identities=11% Similarity=0.310 Sum_probs=17.7
Q ss_pred cCCeEEEecCCCCCCCCCCccccccCCC
Q 029367 152 PVGYVYVLGDNRNNSFDSHVWGPLPVKN 179 (194)
Q Consensus 152 p~g~yfvlGDn~~~S~DSR~~G~V~~~~ 179 (194)
.+|...++.++. +-.-+|-+|||+++-
T Consensus 80 ~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 80 DDNACVLINKNK-EPRGTRIFGPVAREL 106 (122)
T ss_pred CCceEEEECCCC-CEeeeEEEccchHHH
Confidence 345555555543 667788999998764
No 48
>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=45.46 E-value=66 Score=23.92 Aligned_cols=13 Identities=23% Similarity=0.230 Sum_probs=11.1
Q ss_pred CCCCcceEEEEec
Q 029367 82 RNPSIHDIVTFRA 94 (194)
Q Consensus 82 ~~~~rGDiVvf~~ 94 (194)
.+++.||+|+|+.
T Consensus 72 ~~p~~GDiv~f~~ 84 (129)
T TIGR02594 72 SKPAYGCIAVKRR 84 (129)
T ss_pred CCCCccEEEEEEC
Confidence 4689999999975
No 49
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=44.74 E-value=25 Score=24.53 Aligned_cols=10 Identities=30% Similarity=0.172 Sum_probs=5.1
Q ss_pred CcceEEEEec
Q 029367 85 SIHDIVTFRA 94 (194)
Q Consensus 85 ~rGDiVvf~~ 94 (194)
..||.|.+..
T Consensus 48 l~GD~V~VE~ 57 (87)
T PRK12442 48 LAGDRVTLEL 57 (87)
T ss_pred cCCCEEEEEE
Confidence 4455555544
No 50
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=42.54 E-value=63 Score=21.92 Aligned_cols=30 Identities=10% Similarity=0.138 Sum_probs=13.7
Q ss_pred CCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367 84 PSIHDIVTFRAPFQYPGLGEEDVFIKRIVA 113 (194)
Q Consensus 84 ~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg 113 (194)
++.||.|+++...+.....++...+..|+-
T Consensus 6 Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~ 35 (75)
T PF11302_consen 6 VKPGDTVIVQDEQEVGQKQDKDWWMGQVIH 35 (75)
T ss_pred cCCCCEEEEecCccccccCCCCcEEEEEEE
Confidence 455555555554422222334455554443
No 51
>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=42.47 E-value=52 Score=22.31 Aligned_cols=19 Identities=26% Similarity=0.392 Sum_probs=15.6
Q ss_pred cccccCCCCEEEEEeeeec
Q 029367 62 MYPTLRIGDRIIVEKASYY 80 (194)
Q Consensus 62 M~Ptl~~Gd~vlv~k~~~~ 80 (194)
|+|.+..||.|.+.+...+
T Consensus 1 ~~p~f~~G~~V~a~~~irN 19 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRN 19 (75)
T ss_pred CCCccCCCCEEEEEEEeEc
Confidence 7899999999998876543
No 52
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=39.77 E-value=74 Score=21.33 Aligned_cols=33 Identities=24% Similarity=0.237 Sum_probs=23.0
Q ss_pred CCCCcceEEEEecCCCCCCCCCCceEEEEEE--------EeCCCeEEE
Q 029367 82 RNPSIHDIVTFRAPFQYPGLGEEDVFIKRIV--------AKAGDLVQV 121 (194)
Q Consensus 82 ~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVv--------glpGD~V~i 121 (194)
+.++.||-|.+.+. ....-+|.+- |.+||.|.+
T Consensus 25 G~v~~Gd~v~~~P~-------~~~~~V~si~~~~~~~~~a~aGd~v~l 65 (81)
T cd03695 25 GSIRVGDEVVVLPS-------GKTSRVKSIETFDGELDEAGAGESVTL 65 (81)
T ss_pred ceEECCCEEEEcCC-------CCeEEEEEEEECCcEeCEEcCCCEEEE
Confidence 67788998888763 2345666665 777887776
No 53
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=37.81 E-value=37 Score=24.25 Aligned_cols=10 Identities=20% Similarity=0.218 Sum_probs=6.4
Q ss_pred CCcceEEEEe
Q 029367 84 PSIHDIVTFR 93 (194)
Q Consensus 84 ~~rGDiVvf~ 93 (194)
+++||+|++.
T Consensus 58 I~~GD~VlVs 67 (99)
T TIGR00523 58 IREGDVVIVK 67 (99)
T ss_pred ecCCCEEEEE
Confidence 4667777663
No 54
>CHL00057 rpl14 ribosomal protein L14
Probab=37.59 E-value=83 Score=23.35 Aligned_cols=28 Identities=18% Similarity=0.292 Sum_probs=18.4
Q ss_pred ecCCeEEEecCCCCCCCCCCccccccCCC
Q 029367 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKN 179 (194)
Q Consensus 151 vp~g~yfvlGDn~~~S~DSR~~G~V~~~~ 179 (194)
..+|...++.++. +-.-+|-+|||+++-
T Consensus 79 F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T CHL00057 79 FDDNAAVVIDQEG-NPKGTRVFGPIAREL 106 (122)
T ss_pred cCCceEEEECCCC-CEeEeEEEccchHHH
Confidence 3445555555553 667788999998764
No 55
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=35.81 E-value=1.2e+02 Score=23.53 Aligned_cols=37 Identities=16% Similarity=0.300 Sum_probs=25.1
Q ss_pred eccCCCCcceEEEEecCCCCCCCCCCceEEEE---EEEeCCCeEEEe
Q 029367 79 YYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKR---IVAKAGDLVQVR 122 (194)
Q Consensus 79 ~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKR---VvglpGD~V~i~ 122 (194)
|..+.++.||+++|... .....+|| ++...++++++.
T Consensus 70 yR~~~L~~GEvalY~~~-------G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 70 YRPKGLKPGEVALYDDE-------GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred ccccCCCCCcEEEEcCC-------CCEEEEEecceEEeccCceEEEe
Confidence 44456789999999873 33555655 666777777764
No 56
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=35.65 E-value=1.3e+02 Score=22.27 Aligned_cols=27 Identities=11% Similarity=0.282 Sum_probs=17.3
Q ss_pred cCCeEEEecCCCCCCCCCCccccccCCC
Q 029367 152 PVGYVYVLGDNRNNSFDSHVWGPLPVKN 179 (194)
Q Consensus 152 p~g~yfvlGDn~~~S~DSR~~G~V~~~~ 179 (194)
.+|...++.++. +-.-+|-+|||+++-
T Consensus 80 ~dNavVLin~~~-~p~GTrI~Gpv~~el 106 (122)
T PRK05483 80 DDNAAVLLNNDG-EPRGTRIFGPVAREL 106 (122)
T ss_pred CCCEEEEECCCC-CEeEeEEeccchHHH
Confidence 345555555443 667788899998653
No 57
>smart00439 BAH Bromo adjacent homology domain.
Probab=35.63 E-value=1.5e+02 Score=20.62 Aligned_cols=17 Identities=18% Similarity=0.358 Sum_probs=12.8
Q ss_pred cccCCCeeEEEEEEEeC
Q 029367 174 PLPVKNIAGRYLTRCYR 190 (194)
Q Consensus 174 ~V~~~~I~Gkv~~~~~p 190 (194)
-++.+.|+||+.-....
T Consensus 70 ~i~~~~I~~kc~V~~~~ 86 (120)
T smart00439 70 TVPLSDIIGKCNVLSKS 86 (120)
T ss_pred cCChHHeeeEEEEEEcc
Confidence 68888999998765543
No 58
>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=35.47 E-value=74 Score=22.33 Aligned_cols=31 Identities=23% Similarity=0.211 Sum_probs=19.9
Q ss_pred cccCCCCEEEEEeeeeccCCCCcceEEEEecCC
Q 029367 64 PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPF 96 (194)
Q Consensus 64 Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~ 96 (194)
||...+|++.-...-. .+++.||+++|..-+
T Consensus 65 ptC~~~D~i~~~~~lP--~~l~~GD~l~f~~~G 95 (116)
T PF00278_consen 65 PTCDSGDVIARDVMLP--KELEVGDWLVFENMG 95 (116)
T ss_dssp SSSSTTSEEEEEEEEE--STTTTT-EEEESS-S
T ss_pred CCcCCCceEeeeccCC--CCCCCCCEEEEecCc
Confidence 5667888876433321 388999999998644
No 59
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=34.11 E-value=97 Score=21.62 Aligned_cols=86 Identities=15% Similarity=0.079 Sum_probs=40.5
Q ss_pred CCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCC
Q 029367 84 PSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNR 163 (194)
Q Consensus 84 ~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~ 163 (194)
++.||.|.+..+... ....+++.||..+--+ +++..++.+...-.+..... .......++++|+..+.
T Consensus 4 y~vgd~V~v~~~~~~---~~~~~~i~~I~~i~~~----~~~~~~~~v~wf~rp~e~~~----~~~~~~~~~Elf~s~~~- 71 (123)
T cd04370 4 YEVGDSVYVEPDDSI---KSDPPYIARIEELWED----TNGSKQVKVRWFYRPEETPK----GLSPFALRRELFLSDHL- 71 (123)
T ss_pred EecCCEEEEecCCcC---CCCCCEEEEEeeeeEC----CCCCEEEEEEEEEchhHhcc----ccccccccceeEEecCc-
Confidence 466887777765410 1245677777654222 12333333332211100000 00002345666664322
Q ss_pred CCCCCCCccccccCCCeeEEEEEEEeC
Q 029367 164 NNSFDSHVWGPLPVKNIAGRYLTRCYR 190 (194)
Q Consensus 164 ~~S~DSR~~G~V~~~~I~Gkv~~~~~p 190 (194)
--++.+.|.||+.-....
T Consensus 72 ---------~~i~v~~I~gkc~V~~~~ 89 (123)
T cd04370 72 ---------DEIPVESIIGKCKVLFVS 89 (123)
T ss_pred ---------cccCHHHhccccEEEech
Confidence 257777888888665544
No 60
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=33.34 E-value=16 Score=21.69 Aligned_cols=14 Identities=29% Similarity=0.560 Sum_probs=11.8
Q ss_pred eCCEEEECCEEccc
Q 029367 122 RDGSLYVNGIAQNE 135 (194)
Q Consensus 122 ~~~~v~vnG~~~~~ 135 (194)
++|.++|||+.+..
T Consensus 24 ~~g~V~VNg~~v~~ 37 (48)
T PF01479_consen 24 KQGRVKVNGKVVKD 37 (48)
T ss_dssp HTTTEEETTEEESS
T ss_pred CCCEEEECCEEEcC
Confidence 57899999998774
No 61
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=32.98 E-value=1.5e+02 Score=19.71 Aligned_cols=41 Identities=24% Similarity=0.238 Sum_probs=26.0
Q ss_pred EEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEE--------EeCCCeEEE
Q 029367 72 IIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIV--------AKAGDLVQV 121 (194)
Q Consensus 72 vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVv--------glpGD~V~i 121 (194)
++.-+... +.++.||-|.+.+.. ...-+|.+- |.+||.+.+
T Consensus 17 vv~G~v~~--G~i~~Gd~v~i~P~~-------~~~~V~si~~~~~~~~~a~aGd~v~~ 65 (83)
T cd03698 17 VVSGKVES--GSIQKGDTLLVMPSK-------ESVEVKSIYVDDEEVDYAVAGENVRL 65 (83)
T ss_pred EEEEEEee--eEEeCCCEEEEeCCC-------cEEEEEEEEECCeECCEECCCCEEEE
Confidence 34444433 677889888887632 345666665 778887775
No 62
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=32.95 E-value=36 Score=25.18 Aligned_cols=17 Identities=29% Similarity=0.683 Sum_probs=11.2
Q ss_pred CCCcccccCCCCEEEEE
Q 029367 59 SSSMYPTLRIGDRIIVE 75 (194)
Q Consensus 59 ~~SM~Ptl~~Gd~vlv~ 75 (194)
+++|.+.|+.||.||..
T Consensus 49 ~~~~~~~L~~GD~VLA~ 65 (124)
T PF15057_consen 49 SDAMRHSLQVGDKVLAP 65 (124)
T ss_pred cCcccCcCCCCCEEEEe
Confidence 45666777777777665
No 63
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=31.53 E-value=1.7e+02 Score=21.97 Aligned_cols=30 Identities=10% Similarity=0.160 Sum_probs=21.4
Q ss_pred eeecCCeEEEecCCCCCCCCCCccccccCCC
Q 029367 149 TYVPVGYVYVLGDNRNNSFDSHVWGPLPVKN 179 (194)
Q Consensus 149 ~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~ 179 (194)
+..-+|...++.++. +-.-+|-||||+++-
T Consensus 87 i~FddNa~VLin~~~-~P~GTRI~GpV~rEl 116 (131)
T TIGR03673 87 VKFEDNAVVIVTPDG-EPKGTEIKGPVAREA 116 (131)
T ss_pred EEeCCcEEEEECCCC-CEeeeEEEccchHHH
Confidence 344556666666654 677889999999875
No 64
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=31.22 E-value=46 Score=27.89 Aligned_cols=15 Identities=47% Similarity=0.915 Sum_probs=13.3
Q ss_pred EEEeCCEEEECCEEc
Q 029367 119 VQVRDGSLYVNGIAQ 133 (194)
Q Consensus 119 V~i~~~~v~vnG~~~ 133 (194)
|+++++.+++||+++
T Consensus 1 vev~~~~~~lNGk~~ 15 (298)
T PF02836_consen 1 VEVKDGGFYLNGKPI 15 (298)
T ss_dssp EEEETTEEEETTEEE
T ss_pred CEEECCEEEECCEEE
Confidence 688999999999975
No 65
>PRK06789 flagellar motor switch protein; Validated
Probab=31.11 E-value=79 Score=21.35 Aligned_cols=10 Identities=10% Similarity=0.086 Sum_probs=6.2
Q ss_pred EEEECCEEcc
Q 029367 125 SLYVNGIAQN 134 (194)
Q Consensus 125 ~v~vnG~~~~ 134 (194)
.+++||+.++
T Consensus 45 dI~vNg~lia 54 (74)
T PRK06789 45 RLMLENEEIG 54 (74)
T ss_pred EEEECCEEEe
Confidence 4677776544
No 66
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=30.77 E-value=2e+02 Score=20.47 Aligned_cols=27 Identities=22% Similarity=0.466 Sum_probs=16.6
Q ss_pred CCCEEEEEeeeec-------------cCCCCcceEEEEec
Q 029367 68 IGDRIIVEKASYY-------------FRNPSIHDIVTFRA 94 (194)
Q Consensus 68 ~Gd~vlv~k~~~~-------------~~~~~rGDiVvf~~ 94 (194)
-||+|++.+.... ..++++|.+|+.-.
T Consensus 6 L~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~ 45 (96)
T COG0234 6 LGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGP 45 (96)
T ss_pred cCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEcc
Confidence 3788888776321 23566777777654
No 67
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=30.75 E-value=1.9e+02 Score=20.22 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=13.6
Q ss_pred CCCCEEEEEeeeeccCCCCcceEEE
Q 029367 67 RIGDRIIVEKASYYFRNPSIHDIVT 91 (194)
Q Consensus 67 ~~Gd~vlv~k~~~~~~~~~rGDiVv 91 (194)
+-||+|++.+... .+-..|-+++
T Consensus 5 Pl~drVLV~~~~~--e~~T~gGI~L 27 (95)
T PRK00364 5 PLGDRVLVKRLEE--EEKTAGGIVL 27 (95)
T ss_pred EcCCEEEEEEccc--CccccceEEc
Confidence 3479999987632 2334455544
No 68
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=30.45 E-value=1.7e+02 Score=19.46 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=26.0
Q ss_pred EEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEE--------EeCCCeEEE
Q 029367 72 IIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIV--------AKAGDLVQV 121 (194)
Q Consensus 72 vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVv--------glpGD~V~i 121 (194)
++.-+... +.++.||-|.+.+. ....-+|.+- |.+||.+.+
T Consensus 16 vv~G~v~~--G~i~~G~~v~i~P~-------~~~~~V~si~~~~~~~~~a~aGd~v~l 64 (82)
T cd04089 16 VVLGKVES--GTIKKGDKLLVMPN-------KTQVEVLSIYNEDVEVRYARPGENVRL 64 (82)
T ss_pred EEEEEEee--eEEecCCEEEEeCC-------CcEEEEEEEEECCEECCEECCCCEEEE
Confidence 44445543 67888998888763 2345666665 667777665
No 69
>PRK10626 hypothetical protein; Provisional
Probab=29.75 E-value=61 Score=26.98 Aligned_cols=24 Identities=25% Similarity=0.552 Sum_probs=16.7
Q ss_pred EEEEeCCCeEEE-eCCEEEECCEEcc
Q 029367 110 RIVAKAGDLVQV-RDGSLYVNGIAQN 134 (194)
Q Consensus 110 RVvglpGD~V~i-~~~~v~vnG~~~~ 134 (194)
+|++..|+ +.| .+|.+||||+.+.
T Consensus 40 ~V~~~sg~-l~I~~dg~L~inGk~v~ 64 (239)
T PRK10626 40 QVVGASGN-LVISPDGNVMRNGKQLS 64 (239)
T ss_pred EEEecCCc-eEEcCCCCEEECCEEec
Confidence 34555666 555 4679999999864
No 70
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=29.25 E-value=46 Score=26.21 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=20.0
Q ss_pred eeeecCCeEEEecCCCCCCCCCCcc
Q 029367 148 LTYVPVGYVYVLGDNRNNSFDSHVW 172 (194)
Q Consensus 148 ~~~vp~g~yfvlGDn~~~S~DSR~~ 172 (194)
+++.++|..+-...+....+|.|||
T Consensus 98 Ef~~~~~~~~r~~~~s~~yyD~rYW 122 (176)
T PLN02289 98 EFELEHGFVYREHHRSPGYYDGRYW 122 (176)
T ss_pred eeccCCceeEecCCCCCCcccCcee
Confidence 5666778888877777788999997
No 71
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=28.82 E-value=15 Score=23.87 Aligned_cols=20 Identities=25% Similarity=0.488 Sum_probs=16.9
Q ss_pred CCCCCCccccccCCCeeEEE
Q 029367 165 NSFDSHVWGPLPVKNIAGRY 184 (194)
Q Consensus 165 ~S~DSR~~G~V~~~~I~Gkv 184 (194)
-+.|-|.||.+|-++.-|||
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 47899999999988877775
No 72
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=27.94 E-value=49 Score=22.67 Aligned_cols=25 Identities=12% Similarity=0.283 Sum_probs=20.1
Q ss_pred CCeEEEeCCEEEECCEEcccchhcc
Q 029367 116 GDLVQVRDGSLYVNGIAQNEDFIAE 140 (194)
Q Consensus 116 GD~V~i~~~~v~vnG~~~~~~~~~~ 140 (194)
-|++++....|++||+.++..|.-+
T Consensus 16 ~e~~~l~~~GV~~ngrlV~T~F~fD 40 (79)
T PF11012_consen 16 AEEFTLNESGVFRNGRLVATSFEFD 40 (79)
T ss_pred ccEEEECCCcEEECCCEEeeEEEEC
Confidence 3788888999999999988776544
No 73
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=27.69 E-value=2.8e+02 Score=21.12 Aligned_cols=29 Identities=14% Similarity=0.163 Sum_probs=20.1
Q ss_pred eecCCeEEEecCCCCCCCCCCccccccCCC
Q 029367 150 YVPVGYVYVLGDNRNNSFDSHVWGPLPVKN 179 (194)
Q Consensus 150 ~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~ 179 (194)
...+|...++.++. +-.-+|-||||++|-
T Consensus 96 ~F~dNA~VLin~~~-~p~GTRI~GpV~rEl 124 (139)
T PTZ00054 96 YFEDNAGVIVNPKG-EMKGSAITGPVAKEC 124 (139)
T ss_pred EeCCcEEEEECCCC-CEeeeEEeCchhHHH
Confidence 34456666665553 677889999999875
No 74
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=27.62 E-value=2.2e+02 Score=19.90 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=12.9
Q ss_pred CCCEEEEEeeeeccCCCCcceEEE
Q 029367 68 IGDRIIVEKASYYFRNPSIHDIVT 91 (194)
Q Consensus 68 ~Gd~vlv~k~~~~~~~~~rGDiVv 91 (194)
-||+|++.+... .+-..|-|++
T Consensus 6 l~DRVLVk~~~~--e~~T~gGI~L 27 (91)
T PRK14533 6 LGERLLIKPIKE--EKKTEGGIVL 27 (91)
T ss_pred cCCEEEEEEccc--cceecccEEe
Confidence 489999987632 2234455444
No 75
>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=27.56 E-value=64 Score=24.68 Aligned_cols=40 Identities=10% Similarity=-0.085 Sum_probs=27.4
Q ss_pred EecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCC
Q 029367 56 FIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQ 97 (194)
Q Consensus 56 ~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~ 97 (194)
.....+|...|...-+..+..-. ..++++|||+++.....
T Consensus 50 ~~nT~tl~~~L~~~G~~~I~~~~--~~~~q~GDI~I~g~~g~ 89 (145)
T PF05382_consen 50 AGNTETLHDWLKKNGFKKISENV--DWNLQRGDIFIWGRRGN 89 (145)
T ss_pred ccCHHHHHHHHhhCCcEEeccCC--cccccCCCEEEEcCCCC
Confidence 34667888877666666665431 14789999999877653
No 76
>cd00604 IPT_CGTD IPT domain (domain D) of cyclodextrin glycosyltransferase (CGTase) and similar enzymes. These enzymes are involved in the enzymatic hydrolysis of alpha-1,4 linkages of starch polymers and belong to the glycosyl hydrolase family 13. Most consist of three domains (A,B,C) but CGTase is more complex and has two additional domains (D,E). The function of the IPT/D domain is unknown.
Probab=27.52 E-value=79 Score=21.45 Aligned_cols=22 Identities=32% Similarity=0.696 Sum_probs=16.9
Q ss_pred EEeCCCeEEEe-------CCEEEECCEEc
Q 029367 112 VAKAGDLVQVR-------DGSLYVNGIAQ 133 (194)
Q Consensus 112 vglpGD~V~i~-------~~~v~vnG~~~ 133 (194)
.|.||++|.+. ++.+++++...
T Consensus 10 ~g~pG~~VtI~G~gFg~~~~~V~~g~~~a 38 (81)
T cd00604 10 MGKPGNTVTISGEGFGSTGGTVYFGGTAA 38 (81)
T ss_pred CCCCCCEEEEEEECCCCCccEEEECCEEE
Confidence 57899999986 46788888653
No 77
>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=27.41 E-value=2.6e+02 Score=20.71 Aligned_cols=79 Identities=20% Similarity=0.123 Sum_probs=38.6
Q ss_pred CCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCC
Q 029367 83 NPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDN 162 (194)
Q Consensus 83 ~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn 162 (194)
.++.||.|.+..++ +..++.+|-.+--| .++...+++.-.-.+--.... .......++++|+. ++
T Consensus 7 ~i~vGD~V~v~~~~-------~~~~va~Ie~i~ed----~~g~~~v~v~WF~~p~E~~~~---~~~~~~~~~EvFlS-~~ 71 (130)
T cd04721 7 TISVHDFVYVLSEE-------EDRYVAYIEDLYED----KKGSKMVKVRWFHTTDEVGAA---LSPDSVNPREIFLS-PN 71 (130)
T ss_pred EEECCCEEEEeCCC-------CCcEEEEEEEEEEc----CCCCEEEEEEEecCHHHhccc---cCCCCCCCCeEEEc-CC
Confidence 35789998888642 34466666553222 123444444432211000000 00111345677763 22
Q ss_pred CCCCCCCCccccccCCCeeEEEE
Q 029367 163 RNNSFDSHVWGPLPVKNIAGRYL 185 (194)
Q Consensus 163 ~~~S~DSR~~G~V~~~~I~Gkv~ 185 (194)
+--++.+.|.||+.
T Consensus 72 ---------~d~i~~~~I~gk~~ 85 (130)
T cd04721 72 ---------LQVISVECIDGLAT 85 (130)
T ss_pred ---------ccccchHHeeeeeE
Confidence 23578888888884
No 78
>PF13144 SAF_2: SAF-like
Probab=27.04 E-value=2.1e+02 Score=22.31 Aligned_cols=52 Identities=23% Similarity=0.123 Sum_probs=23.8
Q ss_pred ccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEe----CCCeEEEeC
Q 029367 65 TLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAK----AGDLVQVRD 123 (194)
Q Consensus 65 tl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvgl----pGD~V~i~~ 123 (194)
.+.+|+.+.-+.+.. ...+++||.|...... .+..+.-...|+ .||+|.+++
T Consensus 122 ~i~~G~~i~~~~l~~-~~~V~~G~~V~v~~~~------g~i~i~~~g~Al~~G~~G~~I~V~N 177 (196)
T PF13144_consen 122 NIRAGQPITPSDLEP-PPLVKRGDIVTVIARS------GGISISTEGKALEDGALGDTIRVKN 177 (196)
T ss_pred EcCCCCEeeeccccc-ceecCCCCEEEEEEEe------CCEEEEEEEEEccCCCCCCEEEEEE
Confidence 344455444443321 1234666666665532 233333333333 566666654
No 79
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=26.77 E-value=64 Score=22.72 Aligned_cols=30 Identities=20% Similarity=0.261 Sum_probs=21.2
Q ss_pred ccCCCCEEEEEeeeecc-----CCCCcceEEEEec
Q 029367 65 TLRIGDRIIVEKASYYF-----RNPSIHDIVTFRA 94 (194)
Q Consensus 65 tl~~Gd~vlv~k~~~~~-----~~~~rGDiVvf~~ 94 (194)
++.+|-.++++...+.. ..++.||+|+|-+
T Consensus 57 ~lrpGiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 57 ELRPGIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred CCcccEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 45577778888776532 3468899999875
No 80
>PLN00208 translation initiation factor (eIF); Provisional
Probab=26.59 E-value=62 Score=24.81 Aligned_cols=11 Identities=18% Similarity=0.145 Sum_probs=6.5
Q ss_pred CCcceEEEEec
Q 029367 84 PSIHDIVTFRA 94 (194)
Q Consensus 84 ~~rGDiVvf~~ 94 (194)
+++||+|++..
T Consensus 71 I~~GD~VlVel 81 (145)
T PLN00208 71 IAAGDIILVGL 81 (145)
T ss_pred ecCCCEEEEEc
Confidence 35666666654
No 81
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=26.39 E-value=2.7e+02 Score=20.97 Aligned_cols=29 Identities=7% Similarity=0.108 Sum_probs=20.6
Q ss_pred eecCCeEEEecCCCCCCCCCCccccccCCC
Q 029367 150 YVPVGYVYVLGDNRNNSFDSHVWGPLPVKN 179 (194)
Q Consensus 150 ~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~ 179 (194)
...+|...++.++. +-.-+|-+|||++|-
T Consensus 89 ~F~dNa~VLin~~~-~p~GTRI~GpV~~El 117 (132)
T PRK08571 89 KFEDNAAVIVTPEG-TPKGTEIKGPVAREA 117 (132)
T ss_pred EeCCcEEEEECCCC-CEeeeEEeccchHHH
Confidence 44456666666554 677889999999875
No 82
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.34 E-value=73 Score=22.13 Aligned_cols=12 Identities=33% Similarity=0.537 Sum_probs=6.8
Q ss_pred eCCCeEEEeCCE
Q 029367 114 KAGDLVQVRDGS 125 (194)
Q Consensus 114 lpGD~V~i~~~~ 125 (194)
+||..|...++.
T Consensus 36 IpG~vv~~n~g~ 47 (91)
T COG4013 36 IPGRVVHYNDGL 47 (91)
T ss_pred eccEEEEeeccE
Confidence 566666555554
No 83
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.20 E-value=54 Score=24.16 Aligned_cols=25 Identities=12% Similarity=0.210 Sum_probs=14.9
Q ss_pred ccccchhhhhHHHHHHHHHHHHHhc
Q 029367 27 WAFLRWPGLDGSLKILIGLLLWSTF 51 (194)
Q Consensus 27 ~~~l~~~~~~~~~~l~~~~li~~~~ 51 (194)
|++++++.+.+++++++++++..++
T Consensus 89 Wkn~Km~~il~~v~~i~l~iiii~~ 113 (116)
T KOG0860|consen 89 WKNCKMRIILGLVIIILLVVIIIYI 113 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5577777766666665555544443
No 84
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=24.87 E-value=80 Score=22.42 Aligned_cols=36 Identities=17% Similarity=0.211 Sum_probs=25.0
Q ss_pred EEecCCCcccccCCCCEEEEEeeeecc-----CCCCcceEEEEec
Q 029367 55 RFIPSSSMYPTLRIGDRIIVEKASYYF-----RNPSIHDIVTFRA 94 (194)
Q Consensus 55 ~~V~~~SM~Ptl~~Gd~vlv~k~~~~~-----~~~~rGDiVvf~~ 94 (194)
..+.++|.. +|-.+++++..+.. -.++.||.|+|-.
T Consensus 56 lFi~~gsvr----pGii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 56 LFIHHGSVR----PGIIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred eEeeCCcCc----CcEEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 567777766 56667887766532 2468899999865
No 85
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=23.88 E-value=2.6e+02 Score=21.38 Aligned_cols=34 Identities=26% Similarity=0.286 Sum_probs=23.9
Q ss_pred CCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeC
Q 029367 83 NPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRD 123 (194)
Q Consensus 83 ~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~ 123 (194)
.++.|..+.+..+ .|..+.-||..+-+++|.++-
T Consensus 92 ~~~~G~~~~~~~~-------~G~~~~~~V~~i~~~~v~vD~ 125 (156)
T PRK15095 92 EPEIGAIMLFTAM-------DGSEMPGVIREINGDSITVDF 125 (156)
T ss_pred CCCCCCEEEEECC-------CCCEEEEEEEEEcCCEEEEEC
Confidence 4677777776553 345677788888888888864
No 86
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=23.76 E-value=96 Score=21.71 Aligned_cols=26 Identities=19% Similarity=0.198 Sum_probs=19.0
Q ss_pred CCcceEEEEecCCCCCCCCCCceEEEEEEEe
Q 029367 84 PSIHDIVTFRAPFQYPGLGEEDVFIKRIVAK 114 (194)
Q Consensus 84 ~~rGDiVvf~~p~~~~~~~~~~~~vKRVvgl 114 (194)
++.||.|.+..+. ....+.+.||..+
T Consensus 3 ~~vGD~V~v~~~~-----~~~~~~v~~I~~i 28 (119)
T PF01426_consen 3 YKVGDFVYVKPDD-----PPEPPYVARIEEI 28 (119)
T ss_dssp EETTSEEEEECTS-----TTSEEEEEEEEEE
T ss_pred EeCCCEEEEeCCC-----CCCCCEEEEEEEE
Confidence 3668888888765 3567888888865
No 87
>COG2421 Predicted acetamidase/formamidase [Energy production and conversion]
Probab=23.75 E-value=2e+02 Score=24.88 Aligned_cols=55 Identities=18% Similarity=0.253 Sum_probs=31.3
Q ss_pred CCCccccc--CCCCEEEEEeeeeccC---------CCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEe
Q 029367 59 SSSMYPTL--RIGDRIIVEKASYYFR---------NPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVR 122 (194)
Q Consensus 59 ~~SM~Ptl--~~Gd~vlv~k~~~~~~---------~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~ 122 (194)
+.+|.|.. ++||.|.+......-. .+...|.-.+++ -.+-.+++ -|.|||.++++
T Consensus 14 ~~~~~pv~~v~~Gd~V~iet~d~~~gq~~~~~~~~~~~~iD~~rv~p-------~TGPi~v~--gA~pGD~L~V~ 79 (305)
T COG2421 14 DPSLPPVETVKPGDTVTIETLDALGGQIKAEETLEDIFKIDFSRVHP-------LTGPIYVE--GAEPGDALEVE 79 (305)
T ss_pred CCCCCcceecCCCCEEEEEEEeccCccccccchhhhhcccCcccccC-------CCCCeEEe--ccCCCceEEEE
Confidence 46677744 7899999887654211 223333333222 23444555 67888888775
No 88
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=23.50 E-value=75 Score=24.65 Aligned_cols=11 Identities=27% Similarity=0.308 Sum_probs=6.3
Q ss_pred CCcceEEEEec
Q 029367 84 PSIHDIVTFRA 94 (194)
Q Consensus 84 ~~rGDiVvf~~ 94 (194)
+..||+|++..
T Consensus 71 I~~GD~VlVel 81 (155)
T PTZ00329 71 INIGDIILVSL 81 (155)
T ss_pred ecCCCEEEEec
Confidence 35666666654
No 89
>PTZ00320 ribosomal protein L14; Provisional
Probab=23.48 E-value=2.6e+02 Score=22.34 Aligned_cols=29 Identities=14% Similarity=0.059 Sum_probs=21.3
Q ss_pred eeecCCeEEEecCCCCCCCCCCccccccCC
Q 029367 149 TYVPVGYVYVLGDNRNNSFDSHVWGPLPVK 178 (194)
Q Consensus 149 ~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~ 178 (194)
+..-+|...++.++. +-.-+|-||||+++
T Consensus 143 IrFDdNAaVLIN~qg-ePlGTRIfGPVaRE 171 (188)
T PTZ00320 143 TNFDRNTCILMNDQR-VPLGTRVMYCAGRH 171 (188)
T ss_pred EEeCCcEEEEECCCC-CEeeeEEecchhHH
Confidence 345566777777664 78889999999865
No 90
>PF14118 YfzA: YfzA-like protein
Probab=22.51 E-value=1.4e+02 Score=21.16 Aligned_cols=14 Identities=21% Similarity=0.297 Sum_probs=11.4
Q ss_pred cCCCcccccCCCCE
Q 029367 58 PSSSMYPTLRIGDR 71 (194)
Q Consensus 58 ~~~SM~Ptl~~Gd~ 71 (194)
.+.+++|.+++||+
T Consensus 31 d~t~w~pnf~~g~~ 44 (94)
T PF14118_consen 31 DGTGWGPNFNEGDF 44 (94)
T ss_pred hccccccccCCCch
Confidence 36889999998874
No 91
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=22.35 E-value=78 Score=21.51 Aligned_cols=14 Identities=43% Similarity=0.691 Sum_probs=11.3
Q ss_pred EeCCEEEECCEEcc
Q 029367 121 VRDGSLYVNGIAQN 134 (194)
Q Consensus 121 i~~~~v~vnG~~~~ 134 (194)
+.++.||+||..+.
T Consensus 25 V~~nklyvng~~~R 38 (76)
T PF06394_consen 25 VQNNKLYVNGKYAR 38 (76)
T ss_dssp EETTEEEETTCEEE
T ss_pred EECCEEEECCEeec
Confidence 46899999998654
No 92
>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]
Probab=22.27 E-value=24 Score=29.18 Aligned_cols=45 Identities=20% Similarity=0.259 Sum_probs=32.0
Q ss_pred CCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcc
Q 029367 82 RNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQN 134 (194)
Q Consensus 82 ~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~ 134 (194)
-++++|++|++.-|. +.|+.-+=||+.. .-.++.|.++|+|+.+.
T Consensus 23 l~v~~Gevv~iiGpS-----GSGKSTlLRclN~---LE~~~~G~I~i~g~~~~ 67 (240)
T COG1126 23 LSVEKGEVVVIIGPS-----GSGKSTLLRCLNG---LEEPDSGSITVDGEDVG 67 (240)
T ss_pred eeEcCCCEEEEECCC-----CCCHHHHHHHHHC---CcCCCCceEEECCEecc
Confidence 467999999999887 4666656666531 12357899999997653
No 93
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=22.24 E-value=3e+02 Score=19.64 Aligned_cols=23 Identities=13% Similarity=0.387 Sum_probs=13.5
Q ss_pred CCCCEEEEEeeeeccCCCCcceEEE
Q 029367 67 RIGDRIIVEKASYYFRNPSIHDIVT 91 (194)
Q Consensus 67 ~~Gd~vlv~k~~~~~~~~~rGDiVv 91 (194)
+-||+|++.+... .+-..|-|++
T Consensus 14 PL~dRVLVk~~~~--e~kT~gGIiL 36 (100)
T PTZ00414 14 PLGQRVLVKRTLA--AKQTKAGVLI 36 (100)
T ss_pred ecCCEEEEEEccc--ccccccCEEc
Confidence 3589999987642 2233444444
No 94
>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=22.01 E-value=1.2e+02 Score=22.04 Aligned_cols=40 Identities=20% Similarity=0.212 Sum_probs=25.5
Q ss_pred CCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEE
Q 029367 84 PSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIA 132 (194)
Q Consensus 84 ~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~ 132 (194)
++.||-|.++.+. .+..++|.||..+- +-+++..++++.-
T Consensus 4 ~~vGD~V~v~~~~-----~~~~pyIgrI~~i~----e~~~g~~~~~v~W 43 (121)
T cd04714 4 IRVGDCVLFKSPG-----RPSLPYVARIESLW----EDPEGNMVVRVKW 43 (121)
T ss_pred EEcCCEEEEeCCC-----CCCCCEEEEEEEEE----EcCCCCEEEEEEE
Confidence 4679999998865 23567899987542 1123555665553
No 95
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=21.86 E-value=66 Score=18.67 Aligned_cols=9 Identities=33% Similarity=0.715 Sum_probs=5.6
Q ss_pred CCEEEECCE
Q 029367 123 DGSLYVNGI 131 (194)
Q Consensus 123 ~~~v~vnG~ 131 (194)
.|.|+|||+
T Consensus 23 pG~ViING~ 31 (36)
T PF08194_consen 23 PGNVIINGK 31 (36)
T ss_pred CCeEEECce
Confidence 456666665
No 96
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=21.83 E-value=2.1e+02 Score=17.75 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=20.3
Q ss_pred eEEEe----CCEEEECCEEcccchhccCCCCCCceeeecCCeEEEec
Q 029367 118 LVQVR----DGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLG 160 (194)
Q Consensus 118 ~V~i~----~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlG 160 (194)
.+.++ .+.++|||+.+.. ..+..+.+|..+.+|
T Consensus 32 ~~~i~d~~s~ngt~vng~~l~~----------~~~~~L~~gd~i~~G 68 (68)
T PF00498_consen 32 QFYIEDLGSTNGTFVNGQRLGP----------GEPVPLKDGDIIRFG 68 (68)
T ss_dssp EEEEEESSSSS-EEETTEEESS----------TSEEEE-TTEEEEET
T ss_pred eEEEEeCCCCCcEEECCEEcCC----------CCEEECCCCCEEEcC
Confidence 55553 3679999988765 235667777766655
No 97
>cd01287 FabA FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA structure is a homodimer with two independent active sites located at the dimer interface. Each active site is tunnel-shaped and completely inaccessible to solvent. No metal ions or cofactors are required for ligand binding or catalysis.
Probab=21.77 E-value=3.6e+02 Score=20.41 Aligned_cols=42 Identities=26% Similarity=0.373 Sum_probs=27.3
Q ss_pred CCCCcce-EEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEccc
Q 029367 82 RNPSIHD-IVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNE 135 (194)
Q Consensus 82 ~~~~rGD-iVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~ 135 (194)
+.+..|| .+.++. -++++-..-+..+..-++.+++||+.+.+
T Consensus 97 ~~v~Pgd~~l~~e~------------~i~~~~~~~~~~~~~~~~~~~vdg~~v~~ 139 (150)
T cd01287 97 GQITPHNKKVTYEV------------HIKEVGRDGPRPYIIADASLWVDGLRIYE 139 (150)
T ss_pred ccCcCCCEEEEEEE------------EEEEEEccCCccEEEEEEEEEECCEEEEE
Confidence 5678888 788776 34444443333445567888999987654
No 98
>PRK05933 type III secretion system protein; Validated
Probab=21.75 E-value=1.3e+02 Score=26.42 Aligned_cols=30 Identities=27% Similarity=0.438 Sum_probs=21.4
Q ss_pred CCCeEEEeC------CEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCC
Q 029367 115 AGDLVQVRD------GSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDN 162 (194)
Q Consensus 115 pGD~V~i~~------~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn 162 (194)
+|..|+.+. -.++|||+.+ ..|++.+.+||
T Consensus 329 ~GSVIeLDk~a~GEpVDI~VNGrLI------------------ARGEVVVVdd~ 364 (372)
T PRK05933 329 PGSILQFDGVHPTLGVDIILNGAKV------------------GRGEIIALGDV 364 (372)
T ss_pred CCCEEEeCCcCCCCCEEEEECCEEE------------------eeeeEEEECCe
Confidence 788888842 2588999754 45778777775
No 99
>KOG0245 consensus Kinesin-like protein [Cytoskeleton]
Probab=21.23 E-value=1.6e+02 Score=29.86 Aligned_cols=37 Identities=22% Similarity=0.224 Sum_probs=26.9
Q ss_pred eCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCC
Q 029367 122 RDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDN 162 (194)
Q Consensus 122 ~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn 162 (194)
.+.+.|||||.+.++-...+ ...+.+..+|||...+.
T Consensus 521 e~aetyVNGk~v~ep~qL~~----GdRiilG~~H~frfn~P 557 (1221)
T KOG0245|consen 521 EDAETYVNGKLVTEPTQLRS----GDRIILGGNHVFRFNHP 557 (1221)
T ss_pred CccceeEccEEcCCcceecc----CCEEEEcCceeEEecCH
Confidence 46789999999988654332 24577888888887654
No 100
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=20.97 E-value=1e+02 Score=25.34 Aligned_cols=20 Identities=30% Similarity=0.414 Sum_probs=15.9
Q ss_pred cCCCcccccCCCCEEEEEee
Q 029367 58 PSSSMYPTLRIGDRIIVEKA 77 (194)
Q Consensus 58 ~~~SM~Ptl~~Gd~vlv~k~ 77 (194)
....|.+.++.||.|...-.
T Consensus 104 d~~~~~~~~~~GDlV~akV~ 123 (235)
T PRK04163 104 EGTDLRKYLDIGDYIIAKVK 123 (235)
T ss_pred chhhhHhhCCCCCEEEEEEE
Confidence 45789999999999887644
No 101
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=20.27 E-value=1.9e+02 Score=20.64 Aligned_cols=56 Identities=21% Similarity=0.059 Sum_probs=29.6
Q ss_pred CcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEe----CCCeEEEeC
Q 029367 61 SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAK----AGDLVQVRD 123 (194)
Q Consensus 61 SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvgl----pGD~V~i~~ 123 (194)
...-.+.+|+.+.-+.+.. ..-+++||.|...... .+..+--...|+ -||.|.++|
T Consensus 44 ~a~r~i~~G~~i~~~~l~~-~~~V~~G~~V~i~~~~------~~~~i~~~g~Al~~g~~G~~I~V~N 103 (122)
T TIGR03170 44 VAKRPLRAGQPLTANMLRP-PWLVKRGDTVTVIARG------GGLSVTTEGKALEDGAVGDQIRVRN 103 (122)
T ss_pred heecccCCCCeeChHhcCC-ccEEcCCCEEEEEEec------CCEEEEEEEEEccccCCCCEEEEEE
Confidence 3334555666554433321 1345788888777643 333333334433 678887763
No 102
>COG5547 Small integral membrane protein [Function unknown]
Probab=20.25 E-value=1e+02 Score=19.90 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=13.5
Q ss_pred ccchhhhhHHHHHHHHHHHHHhc
Q 029367 29 FLRWPGLDGSLKILIGLLLWSTF 51 (194)
Q Consensus 29 ~l~~~~~~~~~~l~~~~li~~~~ 51 (194)
..+|+.+..++.++++.++.++.
T Consensus 6 ~fkypIIgglvglliAili~t~G 28 (62)
T COG5547 6 KFKYPIIGGLVGLLIAILILTFG 28 (62)
T ss_pred HhccchHHHHHHHHHHHHHHHHH
Confidence 34566666666666665555543
Done!