Query 031410
Match_columns 160
No_of_seqs 189 out of 1145
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 13:42:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031410.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031410hhsearch_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 8E-42 1.7E-46 249.9 16.0 138 15-154 2-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 7.7E-39 1.7E-43 227.8 11.7 143 15-158 15-163 (176)
3 PRK10861 signal peptidase I; P 100.0 8.8E-37 1.9E-41 242.5 17.3 142 11-154 60-305 (324)
4 KOG1568 Mitochondrial inner me 100.0 4.2E-34 9E-39 203.3 9.4 130 26-160 24-158 (174)
5 PRK13838 conjugal transfer pil 99.9 1E-26 2.2E-31 171.5 14.8 96 55-151 40-174 (176)
6 PRK13884 conjugal transfer pep 99.9 2.9E-26 6.3E-31 169.5 15.7 129 8-148 5-175 (178)
7 TIGR02771 TraF_Ti conjugative 99.9 2.9E-26 6.3E-31 168.5 13.9 109 29-148 20-168 (171)
8 PF10502 Peptidase_S26: Signal 99.9 1.9E-25 4.1E-30 159.1 3.2 84 65-148 21-136 (138)
9 TIGR02754 sod_Ni_protease nick 99.9 2.2E-23 4.7E-28 138.2 9.8 89 37-147 2-90 (90)
10 cd06530 S26_SPase_I The S26 Ty 99.9 1.4E-21 2.9E-26 128.1 9.3 84 35-145 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.8 4.1E-19 9E-24 129.0 13.1 115 7-146 2-119 (158)
12 COG4959 TraF Type IV secretory 99.7 1.5E-17 3.3E-22 117.7 8.2 107 34-148 30-168 (173)
13 COG0681 LepB Signal peptidase 99.7 6.9E-16 1.5E-20 112.3 11.2 130 11-146 7-145 (166)
14 PF00717 Peptidase_S24: Peptid 99.3 1.2E-11 2.6E-16 77.6 8.3 57 37-99 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 99.3 5.6E-11 1.2E-15 76.8 9.4 83 35-145 2-84 (84)
16 KOG3342 Signal peptidase I [In 99.1 1E-09 2.2E-14 78.0 9.8 95 34-152 49-148 (180)
17 cd06529 S24_LexA-like Peptidas 99.0 9.8E-09 2.1E-13 65.9 9.8 52 35-94 2-53 (81)
18 COG2932 Predicted transcriptio 99.0 7.5E-09 1.6E-13 78.7 10.7 86 34-148 124-209 (214)
19 PRK10276 DNA polymerase V subu 98.6 1.5E-06 3.2E-11 61.9 11.0 83 33-148 51-134 (139)
20 PRK12423 LexA repressor; Provi 98.5 2.1E-06 4.7E-11 64.8 11.1 83 34-148 115-198 (202)
21 PRK00215 LexA repressor; Valid 98.5 3.3E-06 7.2E-11 63.6 11.4 83 33-148 118-201 (205)
22 TIGR00498 lexA SOS regulatory 98.5 4.9E-06 1.1E-10 62.4 11.8 86 33-152 111-197 (199)
23 COG1974 LexA SOS-response tran 98.0 0.00016 3.4E-09 54.6 11.2 88 33-153 112-200 (201)
24 COG0681 LepB Signal peptidase 85.4 1.1 2.5E-05 31.8 3.5 14 64-77 83-96 (166)
25 PF05257 CHAP: CHAP domain; I 81.0 5.8 0.00013 27.0 5.4 37 64-100 61-98 (124)
26 PF00238 Ribosomal_L14: Riboso 79.4 12 0.00026 26.0 6.5 85 34-139 20-105 (122)
27 smart00439 BAH Bromo adjacent 72.0 26 0.00056 23.2 7.6 73 66-148 2-83 (120)
28 TIGR02594 conserved hypothetic 71.2 28 0.0006 24.3 6.7 55 64-143 72-126 (129)
29 COG0093 RplN Ribosomal protein 70.6 32 0.0007 23.8 8.4 26 114-140 81-106 (122)
30 PF07039 DUF1325: SGF29 tudor- 70.3 29 0.00063 24.3 6.7 56 67-122 1-60 (130)
31 TIGR01067 rplN_bact ribosomal 68.2 37 0.00081 23.5 8.3 86 34-140 20-106 (122)
32 COG0361 InfA Translation initi 62.8 9.5 0.00021 24.2 2.7 20 50-72 49-68 (75)
33 PF10030 DUF2272: Uncharacteri 59.0 43 0.00093 25.0 6.0 38 64-101 92-144 (183)
34 TIGR00008 infA translation ini 58.9 12 0.00025 23.3 2.6 11 66-76 45-55 (68)
35 CHL00057 rpl14 ribosomal prote 58.5 59 0.0013 22.6 8.5 30 110-140 77-106 (122)
36 PF06890 Phage_Mu_Gp45: Bacter 58.4 45 0.00097 24.3 5.9 38 61-100 70-110 (162)
37 cd04712 BAH_DCM_I BAH, or Brom 55.5 68 0.0015 22.3 8.4 29 64-92 4-42 (130)
38 PF10000 ACT_3: ACT domain; I 55.0 8.1 0.00018 24.2 1.4 17 41-58 12-28 (72)
39 COG3602 Uncharacterized protei 54.4 15 0.00032 25.3 2.7 37 41-78 12-48 (134)
40 cd04714 BAH_BAHCC1 BAH, or Bro 54.2 19 0.0004 24.7 3.2 28 65-92 3-30 (121)
41 cd04721 BAH_plant_1 BAH, or Br 53.9 33 0.00071 24.0 4.5 27 65-93 7-33 (130)
42 PRK05483 rplN 50S ribosomal pr 53.0 75 0.0016 22.0 8.0 28 112-140 79-106 (122)
43 PF01176 eIF-1a: Translation i 52.8 13 0.00027 22.6 2.0 28 50-77 24-53 (65)
44 cd04456 S1_IF1A_like S1_IF1A_l 52.3 16 0.00034 23.3 2.4 11 66-76 39-49 (78)
45 PRK13884 conjugal transfer pep 52.2 93 0.002 22.9 7.2 53 1-58 1-61 (178)
46 PF14085 DUF4265: Domain of un 52.0 73 0.0016 21.7 6.5 47 51-99 11-58 (117)
47 PF01426 BAH: BAH domain; Int 50.7 19 0.00042 23.9 2.9 26 66-91 3-28 (119)
48 cd05793 S1_IF1A S1_IF1A: Trans 50.5 15 0.00033 23.3 2.2 12 65-76 38-49 (77)
49 smart00652 eIF1a eukaryotic tr 49.2 16 0.00036 23.4 2.2 11 66-76 44-54 (83)
50 PF10377 ATG11: Autophagy-rela 48.7 90 0.002 21.7 6.3 16 63-78 40-55 (129)
51 PF12273 RCR: Chitin synthesis 48.4 6.4 0.00014 27.4 0.2 6 51-56 36-41 (130)
52 TIGR03170 flgA_cterm flagella 47.1 86 0.0019 21.1 5.9 59 42-103 44-106 (122)
53 PF13144 SAF_2: SAF-like 46.7 1.1E+02 0.0025 22.3 7.7 57 44-103 120-180 (196)
54 cd03695 CysN_NodQ_II CysN_NodQ 44.9 62 0.0013 20.3 4.4 34 64-99 25-66 (81)
55 PRK04012 translation initiatio 43.3 23 0.0005 23.7 2.3 12 65-76 59-70 (100)
56 cd04717 BAH_polybromo BAH, or 41.1 37 0.0008 23.0 3.1 27 65-91 3-29 (121)
57 PF07423 DUF1510: Protein of u 39.9 48 0.001 25.4 3.8 18 8-25 12-29 (217)
58 cd05792 S1_eIF1AD_like S1_eIF1 38.9 25 0.00054 22.4 1.8 38 38-76 9-49 (78)
59 PRK12442 translation initiatio 38.4 40 0.00088 22.0 2.7 11 66-76 47-57 (87)
60 PRK00364 groES co-chaperonin G 38.1 1.2E+02 0.0025 19.9 7.7 90 47-145 3-94 (95)
61 cd03698 eRF3_II_like eRF3_II_l 37.9 84 0.0018 19.6 4.2 34 64-99 25-66 (83)
62 COG5131 URM1 Ubiquitin-like pr 37.5 52 0.0011 21.6 3.1 30 46-76 57-91 (96)
63 PRK14533 groES co-chaperonin G 37.1 1.2E+02 0.0026 19.8 6.9 83 48-145 4-89 (91)
64 smart00002 PLP Myelin proteoli 37.0 11 0.00024 22.8 -0.0 20 126-145 22-41 (60)
65 PF12911 OppC_N: N-terminal TM 36.9 43 0.00094 19.2 2.6 7 4-10 9-15 (56)
66 cd04089 eRF3_II eRF3_II: domai 35.7 95 0.0021 19.3 4.2 34 64-99 24-65 (82)
67 PTZ00054 60S ribosomal protein 33.6 1.8E+02 0.0038 20.7 7.5 30 110-140 95-124 (139)
68 PF12459 DUF3687: D-Ala-teicho 32.8 94 0.002 17.4 3.6 27 1-27 1-27 (42)
69 PF05382 Amidase_5: Bacterioph 31.5 71 0.0015 22.9 3.4 38 37-77 50-87 (145)
70 PF00166 Cpn10: Chaperonin 10 31.3 1.5E+02 0.0032 19.2 5.2 88 49-145 4-93 (93)
71 cd04710 BAH_fungalPHD BAH, or 31.2 80 0.0017 22.2 3.5 28 64-91 10-37 (135)
72 TIGR03673 rpl14p_arch 50S ribo 31.1 49 0.0011 23.3 2.4 31 109-140 86-116 (131)
73 PF13759 2OG-FeII_Oxy_5: Putat 31.0 60 0.0013 21.1 2.8 28 65-98 69-98 (101)
74 KOG0901 60S ribosomal protein 30.8 1.9E+02 0.0041 20.8 5.3 18 123-140 113-130 (145)
75 TIGR00523 eIF-1A eukaryotic/ar 30.7 53 0.0012 21.9 2.5 11 65-75 57-67 (99)
76 PF10913 DUF2706: Protein of u 30.3 85 0.0018 18.4 2.9 44 14-58 4-47 (60)
77 cd06555 ASCH_PF0470_like ASC-1 30.1 1.2E+02 0.0027 20.5 4.2 27 63-90 29-55 (109)
78 cd04709 BAH_MTA BAH, or Bromo 29.9 78 0.0017 23.1 3.4 26 65-91 3-28 (164)
79 PF14801 GCD14_N: tRNA methylt 29.8 75 0.0016 18.8 2.7 15 64-78 4-18 (54)
80 PRK06005 flgA flagellar basal 29.3 2.2E+02 0.0048 20.5 6.5 54 65-119 100-157 (160)
81 COG1188 Ribosome-associated he 28.4 1.2E+02 0.0027 20.2 3.9 29 63-94 46-74 (100)
82 KOG3858 Ephrin, ligand for Eph 28.3 1E+02 0.0023 23.9 4.0 33 35-77 26-58 (233)
83 PF10222 DUF2152: Uncharacteri 27.9 57 0.0012 29.0 2.8 67 52-133 52-118 (604)
84 cd03694 GTPBP_II Domain II of 27.7 1.6E+02 0.0034 18.6 4.3 36 64-99 25-70 (87)
85 PRK10507 bifunctional glutathi 27.6 3.1E+02 0.0068 24.5 7.2 58 63-120 109-177 (619)
86 cd00320 cpn10 Chaperonin 10 Kd 27.2 1.8E+02 0.0039 18.9 6.9 87 49-144 4-92 (93)
87 PF01568 Molydop_binding: Moly 26.9 1.8E+02 0.0039 18.7 4.8 27 52-78 30-56 (110)
88 PRK08515 flgA flagellar basal 26.8 2.8E+02 0.006 21.1 6.1 51 65-117 165-219 (222)
89 PTZ00320 ribosomal protein L14 26.8 1.1E+02 0.0024 22.8 3.7 32 108-140 141-172 (188)
90 KOG4146 Ubiquitin-like protein 26.8 1.1E+02 0.0024 20.2 3.3 36 36-76 56-96 (101)
91 COG0234 GroS Co-chaperonin Gro 26.8 2E+02 0.0043 19.1 6.5 28 49-76 5-45 (96)
92 PRK11578 macrolide transporter 26.7 1.7E+02 0.0037 23.8 5.3 14 84-97 71-84 (370)
93 PF14118 YfzA: YfzA-like prote 26.2 60 0.0013 21.5 2.0 16 37-53 29-44 (94)
94 TIGR02219 phage_NlpC_fam putat 25.9 1.2E+02 0.0026 21.0 3.7 13 64-76 75-87 (134)
95 PF02736 Myosin_N: Myosin N-te 25.8 94 0.002 17.0 2.6 22 78-99 8-29 (42)
96 PRK00276 infA translation init 25.8 1E+02 0.0022 18.9 3.0 12 65-76 46-57 (72)
97 PF09285 Elong-fact-P_C: Elong 25.7 1.5E+02 0.0033 17.5 3.9 36 42-87 20-56 (56)
98 PRK06804 flgA flagellar basal 25.3 3.4E+02 0.0074 21.4 6.6 51 65-116 202-256 (261)
99 cd04370 BAH BAH, or Bromo Adja 25.1 93 0.002 20.3 3.0 74 65-148 3-86 (123)
100 PF13856 Gifsy-2: ATP-binding 23.9 2E+02 0.0043 18.6 4.3 27 63-93 63-89 (95)
101 CHL00010 infA translation init 23.8 1.2E+02 0.0025 19.1 3.0 12 65-76 46-57 (78)
102 PRK12786 flgA flagellar basal 23.5 3.5E+02 0.0076 22.1 6.5 55 65-120 258-316 (338)
103 PRK08571 rpl14p 50S ribosomal 23.2 77 0.0017 22.3 2.3 31 109-140 87-117 (132)
104 COG1096 Predicted RNA-binding 22.9 2.9E+02 0.0063 20.7 5.3 32 64-95 60-91 (188)
105 cd03697 EFTU_II EFTU_II: Elong 22.6 2.1E+02 0.0045 18.0 5.4 36 64-99 25-68 (87)
106 KOG2915 tRNA(1-methyladenosine 22.4 1.4E+02 0.0031 24.0 3.8 15 132-146 42-56 (314)
107 PF00278 Orn_DAP_Arg_deC: Pyri 22.4 1.4E+02 0.0031 19.5 3.5 25 50-76 69-93 (116)
108 COG3764 SrtA Sortase (surface 22.3 2.6E+02 0.0056 21.3 5.1 36 63-98 132-167 (210)
109 PLN00208 translation initiatio 21.8 78 0.0017 22.7 2.1 12 66-77 71-82 (145)
110 cd04451 S1_IF1 S1_IF1: Transla 21.6 1.1E+02 0.0024 18.1 2.5 12 65-76 40-51 (64)
111 PLN02289 ribulose-bisphosphate 21.4 89 0.0019 23.1 2.3 28 106-133 95-122 (176)
112 PF14900 DUF4493: Domain of un 21.3 2.4E+02 0.0053 21.3 5.0 27 107-133 57-86 (235)
113 PF11302 DUF3104: Protein of u 21.3 2.3E+02 0.005 17.9 4.1 30 65-94 5-39 (75)
114 PTZ00329 eukaryotic translatio 21.2 82 0.0018 22.9 2.1 11 66-76 71-81 (155)
115 COG4127 Uncharacterized conser 21.1 95 0.0021 24.9 2.6 26 64-90 71-96 (318)
116 COG5547 Small integral membran 20.4 1.6E+02 0.0034 17.7 2.8 14 1-14 1-14 (62)
117 cd03693 EF1_alpha_II EF1_alpha 20.3 2.4E+02 0.0053 17.8 4.5 34 64-99 29-70 (91)
118 PF15428 Imm14: Immunity prote 20.0 1.7E+02 0.0038 19.8 3.6 22 67-90 1-22 (129)
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=8e-42 Score=249.91 Aligned_cols=138 Identities=34% Similarity=0.511 Sum_probs=122.1
Q ss_pred HHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC
Q 031410 15 TLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD 94 (160)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd 94 (160)
+..++++++++++++.|+++.+.|+|+||+|||+ +||++++++..+...++++||+|+|+.|.++++.++|||+|+|||
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~-~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd 80 (163)
T TIGR02227 2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLK-EGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGD 80 (163)
T ss_pred HHHHHHHHHHHHHHHhhEEEEEEECCcccccchh-CCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEEEEecCCC
Confidence 4556667777888999999999999999999999 999999999877678999999999999877788999999999999
Q ss_pred EEEEecCC----------C---C-----------CCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEe
Q 031410 95 RVTYFKPR----------N---G-----------DSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQV 150 (160)
Q Consensus 95 ~v~~~~~~----------~---~-----------~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~ 150 (160)
+|+++++. . . ....+.+||+|+|||+|||+++|.||||||+|++++|+|||.++ +
T Consensus 81 ~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~-~ 159 (163)
T TIGR02227 81 KVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFV-F 159 (163)
T ss_pred EEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEE-E
Confidence 99998632 0 0 11245789999999999999999999999999999999999999 9
Q ss_pred cCCC
Q 031410 151 WPPN 154 (160)
Q Consensus 151 ~p~~ 154 (160)
||++
T Consensus 160 ~p~~ 163 (163)
T TIGR02227 160 YPFD 163 (163)
T ss_pred CCCC
Confidence 9985
No 2
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.7e-39 Score=227.84 Aligned_cols=143 Identities=42% Similarity=0.701 Sum_probs=124.6
Q ss_pred HHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC
Q 031410 15 TLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD 94 (160)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd 94 (160)
.......+++++....|+.++..++|.||+||+...||+++..+++++++.+++||+|++..|.++++.++|||+|+|||
T Consensus 15 ~~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD 94 (176)
T KOG0171|consen 15 FCSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGD 94 (176)
T ss_pred hHHHHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhheeeccCCc
Confidence 33445556777777789999999999999999986677777799999999999999999999999999999999999999
Q ss_pred EEEEecCCC------CCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCCcc
Q 031410 95 RVTYFKPRN------GDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGS 158 (160)
Q Consensus 95 ~v~~~~~~~------~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~~~ 158 (160)
-+++.++.. .....+..||+||+||+|||+++|.|||+|||+|...|+||++++ +||.++.+.
T Consensus 95 ~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r-~Wp~s~~~~ 163 (176)
T KOG0171|consen 95 LVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFR-IWPPSRVSG 163 (176)
T ss_pred eEEEecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEE-ecCchhcce
Confidence 888875432 222356899999999999999999999999999999999999999 999998764
No 3
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=8.8e-37 Score=242.51 Aligned_cols=142 Identities=34% Similarity=0.473 Sum_probs=122.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCC------------CCCCCCcEEEEeeCC
Q 031410 11 ALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRV------------GRLGPGDIVFVRSPV 78 (160)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~------------~~~~~GDiVvf~~p~ 78 (160)
++.++..++++++++++++.|+++++.|+|+||+|||. .||+++++|+++.. .+++|||+|+|+.|.
T Consensus 60 ~~~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~-~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~ 138 (324)
T PRK10861 60 WLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPE 138 (324)
T ss_pred HHHHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCccc-CCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCC
Confidence 56667777778888899999999999999999999999 99999999988642 579999999999999
Q ss_pred CCCceEEEEEEeeCCCEEEEe--c------CCC-----------------------------------------------
Q 031410 79 DPNKIVTKRIVGVEGDRVTYF--K------PRN----------------------------------------------- 103 (160)
Q Consensus 79 ~~~~~~iKRVv~~~Gd~v~~~--~------~~~----------------------------------------------- 103 (160)
+++..+||||+|+|||+|+++ + +..
T Consensus 139 ~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 (324)
T PRK10861 139 DPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETK 218 (324)
T ss_pred CCCCcEEEEeeecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 888899999999999999996 2 100
Q ss_pred ------C-----------------C--------------CcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEE
Q 031410 104 ------G-----------------D--------------SCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAF 146 (160)
Q Consensus 104 ------~-----------------~--------------~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~ 146 (160)
. . ...+++||+|+||++|||+++|+||||||+||+++|+|+|.
T Consensus 219 ~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~ 298 (324)
T PRK10861 219 ENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKAT 298 (324)
T ss_pred cccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEE
Confidence 0 0 01356899999999999999999999999999999999999
Q ss_pred EEEecCCC
Q 031410 147 FRQVWPPN 154 (160)
Q Consensus 147 ~~~~~p~~ 154 (160)
.+ +|+++
T Consensus 299 ~i-~~s~d 305 (324)
T PRK10861 299 AI-WMSFE 305 (324)
T ss_pred EE-EEEcC
Confidence 98 77765
No 4
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.2e-34 Score=203.30 Aligned_cols=130 Identities=39% Similarity=0.690 Sum_probs=114.2
Q ss_pred HHHhhceEEeEEEeCCCCccccCC-----CCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEec
Q 031410 26 HVTNHYLWSPTLVFGPSMLPTLNL-----TGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFK 100 (160)
Q Consensus 26 ~~~~~~~~~~~~v~g~SM~Ptl~~-----~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~ 100 (160)
..+...+.....+.|.||.|+++| ..|+|++.++.-....+.+||+|+|.+|.++++++||||+|+|||.+...+
T Consensus 24 ~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~ 103 (174)
T KOG1568|consen 24 LTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTED 103 (174)
T ss_pred eeeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeecccccEeccCC
Confidence 334455678899999999999996 238999999875556689999999999999999999999999999987633
Q ss_pred CCCCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCCccCC
Q 031410 101 PRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG 160 (160)
Q Consensus 101 ~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~~~~~ 160 (160)
.....+.+|+|||||.|||...|+|||.||||+...|+|+|+++ +||+.|++.++
T Consensus 104 ----~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~i-lwpP~R~~~~~ 158 (174)
T KOG1568|consen 104 ----EKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYI-LWPPVRWQRLD 158 (174)
T ss_pred ----CCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEE-EcChHHhhhhc
Confidence 23577899999999999999999999999999999999999999 99999988764
No 5
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.95 E-value=1e-26 Score=171.50 Aligned_cols=96 Identities=27% Similarity=0.311 Sum_probs=73.7
Q ss_pred EEEecccCCCCCCCCcEEEEeeCCCC-------------------CceEEEEEEeeCCCEEEEec-----CCC-------
Q 031410 55 LAEYVSHRVGRLGPGDIVFVRSPVDP-------------------NKIVTKRIVGVEGDRVTYFK-----PRN------- 103 (160)
Q Consensus 55 lv~~~~~~~~~~~~GDiVvf~~p~~~-------------------~~~~iKRVv~~~Gd~v~~~~-----~~~------- 103 (160)
.+.++.+..+++++||+|+|+.|.+. ...++|||+|+|||+|++++ +..
T Consensus 40 g~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~~~~~ 119 (176)
T PRK13838 40 GLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPSSSVR 119 (176)
T ss_pred EEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccccccc
Confidence 33444333478999999999987542 13699999999999999874 110
Q ss_pred --------CCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEec
Q 031410 104 --------GDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVW 151 (160)
Q Consensus 104 --------~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~ 151 (160)
.......+||+|+|||+|||. +|+||||||+|++++|+|+|...|.|
T Consensus 120 ~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi~t~ 174 (176)
T PRK13838 120 RRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPVLTF 174 (176)
T ss_pred cccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEEEec
Confidence 001224579999999999984 89999999999999999999885444
No 6
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.95 E-value=2.9e-26 Score=169.50 Aligned_cols=129 Identities=17% Similarity=0.156 Sum_probs=89.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCC-------
Q 031410 8 AKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDP------- 80 (160)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~------- 80 (160)
+|++..+++.+.++++++..+. + +..++++.+...| .|-+.+. . ..+++||+|+|+.|+..
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~N~T~S~P----~glY~~~-~-----~~~~~Gd~V~f~~p~~~~~~~a~~ 72 (178)
T PRK13884 5 LKRITAGVAVAGLAALLLAALG-Y-AAGARVNTTKSIP----VGLYWTS-S-----APVEKGAYVLFCPPQRGVFDDAKE 72 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-H-hCcEEEECCCCCc----ceEEEEe-C-----CCCCCCCEEEEeCCchHHHHHHHh
Confidence 4455555444444433333322 2 2444555444434 5666543 2 47999999999977521
Q ss_pred ------------CceEEEEEEeeCCCEEEEecCC--------------CC---------CCcceEEccCCcEEEEcCCCC
Q 031410 81 ------------NKIVTKRIVGVEGDRVTYFKPR--------------NG---------DSCHTVVVPKGHVWIQGDNLY 125 (160)
Q Consensus 81 ------------~~~~iKRVv~~~Gd~v~~~~~~--------------~~---------~~~~~~~vp~~~~~v~gdn~~ 125 (160)
..+++|||+|+|||+|+++++. .. .....+++|+|+||++|||++
T Consensus 73 rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~ 152 (178)
T PRK13884 73 RGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSA 152 (178)
T ss_pred CCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCC
Confidence 1379999999999999998631 00 011235899999999999999
Q ss_pred CCCCCCcccceeCCCeEEEEEEE
Q 031410 126 ASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 126 ~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
+|+||||||+|++++|+|++...
T Consensus 153 ~S~DSRYfG~V~~~~I~G~~~Pl 175 (178)
T PRK13884 153 TSFDGRYFGPINRSQIKTVIRPV 175 (178)
T ss_pred CCCcccccCcccHHHEEEEEEEe
Confidence 99999999999999999999875
No 7
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.94 E-value=2.9e-26 Score=168.50 Aligned_cols=109 Identities=26% Similarity=0.305 Sum_probs=81.5
Q ss_pred hhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCC-------------------ceEEEEEE
Q 031410 29 NHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPN-------------------KIVTKRIV 89 (160)
Q Consensus 29 ~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~-------------------~~~iKRVv 89 (160)
..|........++||- .|-+. ..+ ..+++|||+|+|+.|.++. ..++|||+
T Consensus 20 ~~~~~~~~~N~T~S~P-----~g~Y~-~~~----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVi 89 (171)
T TIGR02771 20 GLYCVGARINTTKSLP-----LGLYW-TTS----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVL 89 (171)
T ss_pred hcceeeEEEECCCCCc-----ceEEE-eCC----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEE
Confidence 3344334445556652 45555 322 2589999999999876432 27999999
Q ss_pred eeCCCEEEEecCC--------C-------------CCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410 90 GVEGDRVTYFKPR--------N-------------GDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 90 ~~~Gd~v~~~~~~--------~-------------~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
|+|||+|+++++. . .....+.+||+| ||++|||+++|+||||||+|++++|+||+...
T Consensus 90 glpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl 168 (171)
T TIGR02771 90 GLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPL 168 (171)
T ss_pred EeCCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEe
Confidence 9999999998631 0 011236889999 99999999999999999999999999999875
No 8
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=99.91 E-value=1.9e-25 Score=159.10 Aligned_cols=84 Identities=35% Similarity=0.474 Sum_probs=32.2
Q ss_pred CCCCCcEEEEeeCCC------------CCceEEEEEEeeCCCEEEEecCC--------------------CCCCcceEEc
Q 031410 65 RLGPGDIVFVRSPVD------------PNKIVTKRIVGVEGDRVTYFKPR--------------------NGDSCHTVVV 112 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~------------~~~~~iKRVv~~~Gd~v~~~~~~--------------------~~~~~~~~~v 112 (160)
.+++||+|+|+.|.. .+..++|||+|+|||+|+++++. ......+.+|
T Consensus 21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~v 100 (138)
T PF10502_consen 21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTV 100 (138)
T ss_dssp --------------------------------------------------------------------S-T----TEEE-
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceEe
Confidence 489999999999862 24589999999999999998642 0111258999
Q ss_pred cCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410 113 PKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
|+|+||++|||+.+|+||||||+|++++|+|+|...
T Consensus 101 p~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl 136 (138)
T PF10502_consen 101 PEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPL 136 (138)
T ss_dssp -TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEE
T ss_pred CCCEEEEecCCCCCccccCEecccCHHHEEEEEEEE
Confidence 999999999999999999999999999999999884
No 9
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.90 E-value=2.2e-23 Score=138.23 Aligned_cols=89 Identities=39% Similarity=0.595 Sum_probs=78.1
Q ss_pred EEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCc
Q 031410 37 LVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGH 116 (160)
Q Consensus 37 ~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~ 116 (160)
.|.|+||+|+|+ +||++++++.......+++||+|+|+.|.++++.++||++++++ ++
T Consensus 2 ~V~g~SM~P~l~-~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~---------------------~~ 59 (90)
T TIGR02754 2 KVTGVSMSPTLP-PGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD---------------------NG 59 (90)
T ss_pred EeeCCCccCccC-CCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC---------------------Ce
Confidence 689999999999 99999999854333456789999999987667899999999764 47
Q ss_pred EEEEcCCCCCCCCCCcccceeCCCeEEEEEE
Q 031410 117 VWIQGDNLYASRDSRQFGPVPYGLIEGKAFF 147 (160)
Q Consensus 117 ~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~ 147 (160)
+|++|||+..|.|||++|+|+..+|+|+|+|
T Consensus 60 ~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 60 LFLLGDNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred EEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence 9999999999999999999999999999864
No 10
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.87 E-value=1.4e-21 Score=128.12 Aligned_cols=84 Identities=44% Similarity=0.678 Sum_probs=75.5
Q ss_pred eEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccC
Q 031410 35 PTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPK 114 (160)
Q Consensus 35 ~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~ 114 (160)
.+.+.|+||+|++. .||++++++......++++||+|+|+.+.+++..++|||++
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~------------------------ 56 (85)
T cd06530 2 PVVVPGGSMEPTLQ-PGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG------------------------ 56 (85)
T ss_pred eeEEcCCCCcCccc-CCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE------------------------
Confidence 57899999999999 99999999865433479999999999987556899999997
Q ss_pred CcEEEEcCCCCCCCCCCcccceeCCCeEEEE
Q 031410 115 GHVWIQGDNLYASRDSRQFGPVPYGLIEGKA 145 (160)
Q Consensus 115 ~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v 145 (160)
||+.|||+.+|.|||+||+++.++|+|++
T Consensus 57 --~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 --YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred --EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 99999999899999999999999999985
No 11
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.82 E-value=4.1e-19 Score=128.95 Aligned_cols=115 Identities=25% Similarity=0.270 Sum_probs=84.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhceE---EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCce
Q 031410 7 LAKEALTQTLTFARFFCLFHVTNHYLW---SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKI 83 (160)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~ 83 (160)
+.+.++.+++.+++.++++..+....+ ..+.|.|+||+||++ .||++++++.. ..++++||+|+|+.|+++ ..
T Consensus 2 ~~~~ii~~~~~~~l~~~~~~~l~~~~~~~~p~v~V~g~SM~Ptl~-~GD~vlv~~~~--~~~~~~GDIVvf~~~~~~-~~ 77 (158)
T TIGR02228 2 KISNVIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFN-TGDLILVTGAD--PNDIQVGDVITYKSPGFN-TP 77 (158)
T ss_pred hhHHHHHHHHHHHHHHHHHHHheeeccCCCcEEEEcCCCCcCCcc-CCCEEEEEecc--cCCCCCCCEEEEEECCCC-cc
Confidence 355667666666555555544433332 233499999999999 99999999843 358999999999988643 78
Q ss_pred EEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEE
Q 031410 84 VTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAF 146 (160)
Q Consensus 84 ~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~ 146 (160)
++|||+++.++. .+..|++.|||+ ...| .++|+.++|+|++.
T Consensus 78 iihRVi~v~~~~-----------------g~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~ 119 (158)
T TIGR02228 78 VTHRVIEINNSG-----------------GELGFITKGDNN-PAPD---GEPVPSENVIGKYL 119 (158)
T ss_pred EEEEEEEEECCC-----------------CcEEEEEEecCC-CCCC---cccCCHHHEEEEEE
Confidence 999999987530 012488889997 4556 68999999999998
No 12
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.73 E-value=1.5e-17 Score=117.65 Aligned_cols=107 Identities=24% Similarity=0.251 Sum_probs=80.6
Q ss_pred EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCC------------CCceEEEEEEeeCCCEEEEecC
Q 031410 34 SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVD------------PNKIVTKRIVGVEGDRVTYFKP 101 (160)
Q Consensus 34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~------------~~~~~iKRVv~~~Gd~v~~~~~ 101 (160)
..++++.+...| -|= .-+.|.+ ..+.+||+|+++.|.. ...+++|||.|+|||+|++.++
T Consensus 30 p~l~~N~S~S~p----lGl-yrv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~ 101 (173)
T COG4959 30 PGLRVNASASAP----LGL-YRVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQ 101 (173)
T ss_pred cceEeccCCCcc----eeE-EEecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecc
Confidence 456666555555 333 3344432 3569999999999863 3567999999999999999862
Q ss_pred C--------------------CCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410 102 R--------------------NGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 102 ~--------------------~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
. ......+-.+.++++|+++|..+.|+|||||||||.++|+|.+...
T Consensus 102 ~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPv 168 (173)
T COG4959 102 GIAIDGKPVAASLPVDRVGRALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPV 168 (173)
T ss_pred eEEECCEEeeeeccccccCCcCCcccCCceecCCeEEEEeccCCcccccceecccCHHHcceeeeee
Confidence 1 1112234448899999999999999999999999999999999884
No 13
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.67 E-value=6.9e-16 Score=112.33 Aligned_cols=130 Identities=25% Similarity=0.321 Sum_probs=98.3
Q ss_pred HHHHHHHHHHHHHHHHHH--hhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEE
Q 031410 11 ALTQTLTFARFFCLFHVT--NHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRI 88 (160)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRV 88 (160)
...++..++.++++++++ +.++++.+.|+|+||+||++ .||++++++.++...++..+|.+ ..|......++||+
T Consensus 7 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~-~GD~v~v~k~~~~~~~~~~~~~~--~~~~~~~~~~~kr~ 83 (166)
T COG0681 7 FLELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLN-VGDRVLVKKFSYGFGKLKVPDII--VLPAVVEGDLIKRV 83 (166)
T ss_pred HHHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccc-cCCEEEEEeccccccCCccceee--ecCCCCCcceEEEe
Confidence 445555566666666666 89999999999999999999 99999999999888889999998 44555678899999
Q ss_pred EeeCCCEEEEecCCCCCCcceEEccCCcEEEE-------cCCCCCCCCCCcccceeCCCeEEEEE
Q 031410 89 VGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQ-------GDNLYASRDSRQFGPVPYGLIEGKAF 146 (160)
Q Consensus 89 v~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~-------gdn~~~s~DSR~~G~V~~~~I~G~v~ 146 (160)
++++||.+.++++.... ...+|++..++. .+....+.+++.++.......+.++.
T Consensus 84 ~~~~GD~i~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (166)
T COG0681 84 IGLRGDIVVFKDDRLYV---VPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRVI 145 (166)
T ss_pred ccCCCCEEEEECCEEEe---ecccCcchhhhhcccccccccccccccCccccccccccccccceE
Confidence 99999999998754211 223444555444 34445677777787777777777773
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=99.33 E-value=1.2e-11 Score=77.62 Aligned_cols=57 Identities=35% Similarity=0.494 Sum_probs=45.9
Q ss_pred EEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEe
Q 031410 37 LVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYF 99 (160)
Q Consensus 37 ~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~ 99 (160)
+|.|+||+|+++ .||++++++. .+++.||+|++..+.+. ..++||+.+.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~-~Gd~v~v~~~----~~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIK-DGDIVLVDPS----SEPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSS-TTEEEEEEET----S---TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCee-CCCEEEEEEc----CCCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEe
Confidence 589999999999 9999999984 48999999999986532 389999999999877665
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=99.27 E-value=5.6e-11 Score=76.76 Aligned_cols=83 Identities=41% Similarity=0.584 Sum_probs=63.5
Q ss_pred eEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccC
Q 031410 35 PTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPK 114 (160)
Q Consensus 35 ~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~ 114 (160)
.+.+.|+||+|++. .||++++++.. ..++.||++++..+. +..++||+...++ +
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~i~~~~---~~~~~G~iv~~~~~~--~~~~ikrl~~~~~--------------------~ 55 (84)
T cd06462 2 ALRVEGDSMEPTIP-DGDLVLVDKSS---YEPKRGDIVVFRLPG--GELTVKRVIGLPG--------------------E 55 (84)
T ss_pred eeEEcCCCccCccc-CCCEEEEEecC---CCCcCCEEEEEEcCC--CcEEEEEEEEECC--------------------C
Confidence 46899999999998 99999999832 248999999999854 4799999999775 2
Q ss_pred CcEEEEcCCCCCCCCCCcccceeCCCeEEEE
Q 031410 115 GHVWIQGDNLYASRDSRQFGPVPYGLIEGKA 145 (160)
Q Consensus 115 ~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v 145 (160)
+++++.+||+ +..+.+..+. ....++|++
T Consensus 56 ~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~v 84 (84)
T cd06462 56 GHYFLLGDNP-NSPDSRIDGP-PELDIVGVV 84 (84)
T ss_pred CEEEEECCCC-CCCcccccCC-CHHHEEEeC
Confidence 4889999994 5555544333 456666653
No 16
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.11 E-value=1e-09 Score=77.98 Aligned_cols=95 Identities=20% Similarity=0.249 Sum_probs=69.8
Q ss_pred EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEcc
Q 031410 34 SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVP 113 (160)
Q Consensus 34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp 113 (160)
..+.|-++||+|.++ .||.++..... ....+.||+|+|+.+. .+.+.+|||+.+-+. .-.
T Consensus 49 PiVVVLSgSMePaF~-RGDlLfL~N~~--~~p~~vGdivVf~veg-R~IPiVHRviK~he~----------------~~~ 108 (180)
T KOG3342|consen 49 PIVVVLSGSMEPAFH-RGDLLFLTNRN--EDPIRVGDIVVFKVEG-REIPIVHRVIKQHEK----------------SNG 108 (180)
T ss_pred CEEEEEcCCcCcccc-cccEEEEecCC--CCcceeccEEEEEECC-ccCchhHHHHHHhcc----------------cCC
Confidence 678899999999999 99999986422 2457999999999864 678899999986541 001
Q ss_pred CCcEEEEcCCCCCCCCCCc-c----cceeCCCeEEEEEEEEecC
Q 031410 114 KGHVWIQGDNLYASRDSRQ-F----GPVPYGLIEGKAFFRQVWP 152 (160)
Q Consensus 114 ~~~~~v~gdn~~~s~DSR~-~----G~V~~~~I~G~v~~~~~~p 152 (160)
+-+++..|||+ ..|.|- | -...+++|+|+|.- +.|
T Consensus 109 ~~~~LTKGDNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~G--~~P 148 (180)
T KOG3342|consen 109 HIKFLTKGDNN--AVDDRGLYAQGQNWLERKDIVGRVRG--YLP 148 (180)
T ss_pred cEEEEecCCCC--cccchhcccccccceeccceeeEEee--ccc
Confidence 12477889995 344442 2 35888999999976 444
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=98.98 E-value=9.8e-09 Score=65.89 Aligned_cols=52 Identities=33% Similarity=0.430 Sum_probs=44.6
Q ss_pred eEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC
Q 031410 35 PTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD 94 (160)
Q Consensus 35 ~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd 94 (160)
.+.+.|+||+|+++ .||++++++. ..++.||++++..++ ..++||+...+++
T Consensus 2 ~~~v~g~sM~p~i~-~gd~lii~~~----~~~~~g~i~~~~~~~---~~~ikr~~~~~~~ 53 (81)
T cd06529 2 ALRVKGDSMEPTIP-DGDLVLVDPS----DTPRDGDIVVARLDG---ELTVKRLQRRGGG 53 (81)
T ss_pred EEEEECCCcCCccC-CCCEEEEcCC----CCCCCCCEEEEEECC---EEEEEEEEECCCC
Confidence 36899999999998 9999999873 359999999999843 7899999997754
No 18
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.97 E-value=7.5e-09 Score=78.70 Aligned_cols=86 Identities=26% Similarity=0.272 Sum_probs=62.3
Q ss_pred EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEcc
Q 031410 34 SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVP 113 (160)
Q Consensus 34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp 113 (160)
...+|.|+||+|++. +||.++|++ .....+||.+++.. ..++.++||+...+|
T Consensus 124 ~~i~V~GDSMeP~~~-~Gd~ilVd~----~~~~~~gd~v~v~~--~g~~~~VK~l~~~~~-------------------- 176 (214)
T COG2932 124 FALRVTGDSMEPTYE-DGDTLLVDP----GVNTRRGDRVYVET--DGGELYVKKLQREPG-------------------- 176 (214)
T ss_pred EEEEEeCCccccccc-CCCEEEECC----CCceeeCCEEEEEE--eCCeEEEEEEEEecC--------------------
Confidence 457999999999999 999999987 24778899666665 246899999999776
Q ss_pred CCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410 114 KGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 114 ~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
+.+.+.++|+....|- .+..-..=+|+|+|++.
T Consensus 177 -~~~~l~S~N~~~~~~~-~~~~~~~v~iIgrVv~~ 209 (214)
T COG2932 177 -GLLRLVSLNPDYYPDE-IFSEDDDVEIIGRVVWV 209 (214)
T ss_pred -CeEEEEeCCCCCCccc-ccCccceEEEEEEEEEE
Confidence 4566888887443332 22111113589999886
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.57 E-value=1.5e-06 Score=61.90 Aligned_cols=83 Identities=16% Similarity=0.072 Sum_probs=57.8
Q ss_pred EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410 33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV 111 (160)
Q Consensus 33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~ 111 (160)
....++.|+||. |++. +||++++++- .+++.||+|++.. .++..+||+.-.
T Consensus 51 ~f~l~V~GdSM~~~~I~-~GD~liVd~~----~~~~~Gdivv~~~---~g~~~vKrl~~~-------------------- 102 (139)
T PRK10276 51 TYFVKASGDSMIDAGIS-DGDLLIVDSA----ITASHGDIVIAAV---DGEFTVKKLQLR-------------------- 102 (139)
T ss_pred EEEEEEecCCCCCCCCC-CCCEEEEECC----CCCCCCCEEEEEE---CCEEEEEEEEEC--------------------
Confidence 345899999997 6898 9999999872 3678999999986 346789998742
Q ss_pred ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410 112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
+++++..+|+.. .....-.-+.-.|+|+|.+.
T Consensus 103 ---~~~~L~s~N~~y--~~i~i~~~~~~~IiG~V~~~ 134 (139)
T PRK10276 103 ---PTVQLIPMNSAY--SPITISSEDTLDVFGVVTHI 134 (139)
T ss_pred ---CcEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEE
Confidence 146677787532 11111111123699999885
No 20
>PRK12423 LexA repressor; Provisional
Probab=98.51 E-value=2.1e-06 Score=64.75 Aligned_cols=83 Identities=20% Similarity=0.131 Sum_probs=60.2
Q ss_pred EeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410 34 SPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV 112 (160)
Q Consensus 34 ~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v 112 (160)
....|.|+||. |+|. +||++++++ ..+++.||+|++.. .++..+||+.-..
T Consensus 115 f~l~V~GdSM~~~~i~-~Gd~viv~~----~~~~~~Gdivv~~~---~~~~~vKrl~~~~-------------------- 166 (202)
T PRK12423 115 YLLQVQGDSMIDDGIL-DGDLVGVHR----SPEARDGQIVVARL---DGEVTIKRLERSG-------------------- 166 (202)
T ss_pred EEEEEecCcCCCCCcC-CCCEEEEeC----CCcCCCCCEEEEEE---CCEEEEEEEEEeC--------------------
Confidence 35799999997 7998 999999987 24788999999987 3468999987643
Q ss_pred cCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410 113 PKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
+.+++..+|+.. +...+-+-..-.|+|++...
T Consensus 167 --~~~~L~s~N~~y--~~i~~~~~~~~~I~Gvv~g~ 198 (202)
T PRK12423 167 --DRIRLLPRNPAY--APIVVAPDQDFAIEGVFCGL 198 (202)
T ss_pred --CEEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEE
Confidence 367788888632 22222221234799999875
No 21
>PRK00215 LexA repressor; Validated
Probab=98.48 E-value=3.3e-06 Score=63.64 Aligned_cols=83 Identities=23% Similarity=0.222 Sum_probs=60.5
Q ss_pred EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410 33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV 111 (160)
Q Consensus 33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~ 111 (160)
....+|.|+||. |++. +||++++++- .+++.||+|++... ++..+||+.-..
T Consensus 118 ~~~~~V~GdSM~~~~i~-~Gd~v~v~~~----~~~~~G~ivv~~~~---~~~~vKrl~~~~------------------- 170 (205)
T PRK00215 118 DFLLRVRGDSMIDAGIL-DGDLVIVRKQ----QTARNGQIVVALID---DEATVKRFRREG------------------- 170 (205)
T ss_pred eEEEEEccCCCCCCCcC-CCCEEEEeCC----CCCCCCCEEEEEEC---CEEEEEEEEEeC-------------------
Confidence 456889999995 7998 9999999872 46789999999873 378999998642
Q ss_pred ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410 112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR 148 (160)
Q Consensus 112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~ 148 (160)
|.+++..+|+.. +.....+ ..-.|+|+|...
T Consensus 171 ---~~~~L~s~Np~y--~~~~~~~-~~~~IiG~Vv~~ 201 (205)
T PRK00215 171 ---GHIRLEPENPAY--EPIIVDP-DRVTIEGKVVGL 201 (205)
T ss_pred ---CEEEEEcCCCCC--CCEEeCC-CcEEEEEEEEEE
Confidence 367788888642 2221111 035799999875
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=98.45 E-value=4.9e-06 Score=62.43 Aligned_cols=86 Identities=20% Similarity=0.164 Sum_probs=62.5
Q ss_pred EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410 33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV 111 (160)
Q Consensus 33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~ 111 (160)
...+++.|+||. |.+. +||++++++. ..++.||+|++.. .++..+||+.-. |
T Consensus 111 ~f~~~V~GdSM~~~~i~-~Gd~v~v~~~----~~~~~G~ivvv~~---~~~~~vKrl~~~-~------------------ 163 (199)
T TIGR00498 111 VFLLKVMGDSMVDAGIC-DGDLLIVRSQ----KDARNGEIVAAMI---DGEVTVKRFYKD-G------------------ 163 (199)
T ss_pred EEEEEecCCCCCCCCCC-CCCEEEEecC----CCCCCCCEEEEEE---CCEEEEEEEEEE-C------------------
Confidence 456899999996 5898 9999999862 4889999999997 457899998754 2
Q ss_pred ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecC
Q 031410 112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWP 152 (160)
Q Consensus 112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p 152 (160)
+.+++..+|+... ...... ..-.|+|+|... +..
T Consensus 164 ---~~i~L~s~N~~y~--~i~~~~-~~~~IiG~Vv~~-~r~ 197 (199)
T TIGR00498 164 ---TKVELKPENPEFD--PIVLNA-EDVTILGKVVGV-IRN 197 (199)
T ss_pred ---CEEEEEcCCCCCc--CCcCCC-CcEEEEEEEEEE-EEe
Confidence 3677888886432 111111 135799999887 543
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.99 E-value=0.00016 Score=54.62 Aligned_cols=88 Identities=18% Similarity=0.113 Sum_probs=65.4
Q ss_pred EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410 33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV 111 (160)
Q Consensus 33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~ 111 (160)
....+|.|+||. +.+. +||+++|++ ..+.+.||+|+....+ ++.-+||..--.
T Consensus 112 ~f~L~V~GdSM~~~gi~-dGDlvvV~~----~~~a~~GdiVvA~i~g--~e~TvKrl~~~g------------------- 165 (201)
T COG1974 112 TFFLRVSGDSMIDAGIL-DGDLVVVDP----TEDAENGDIVVALIDG--EEATVKRLYRDG------------------- 165 (201)
T ss_pred eEEEEecCCccccCcCC-CCCEEEEcC----CCCCCCCCEEEEEcCC--CcEEEEEEEEeC-------------------
Confidence 345799999995 6776 999999987 4689999999999854 568899987633
Q ss_pred ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCC
Q 031410 112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP 153 (160)
Q Consensus 112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~ 153 (160)
+.+++.--|+. +.+..+..- .-.|+|++... +|+.
T Consensus 166 ---~~i~L~p~Np~--~~~i~~~~~-~~~I~G~vvgv-~r~~ 200 (201)
T COG1974 166 ---NQILLKPENPA--YPPIPVDAD-SVTILGKVVGV-IRDI 200 (201)
T ss_pred ---CEEEEEeCCCC--CCCcccCcc-ceEEEEEEEEE-EecC
Confidence 36778777753 233323222 56799999998 8764
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=85.44 E-value=1.1 Score=31.84 Aligned_cols=14 Identities=29% Similarity=0.145 Sum_probs=11.5
Q ss_pred CCCCCCcEEEEeeC
Q 031410 64 GRLGPGDIVFVRSP 77 (160)
Q Consensus 64 ~~~~~GDiVvf~~p 77 (160)
....+||+|+|+.+
T Consensus 83 ~~~~~GD~i~~~~~ 96 (166)
T COG0681 83 VIGLRGDIVVFKDD 96 (166)
T ss_pred eccCCCCEEEEECC
Confidence 36789999999973
No 25
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=80.97 E-value=5.8 Score=27.02 Aligned_cols=37 Identities=24% Similarity=0.258 Sum_probs=24.2
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEEee-CCCEEEEec
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIVGV-EGDRVTYFK 100 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv~~-~Gd~v~~~~ 100 (160)
..|+.||+++|.......--.+--|.++ .+++|.+.+
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e 98 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIE 98 (124)
T ss_dssp S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEE
T ss_pred cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEE
Confidence 5899999999964333444577888888 888887754
No 26
>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=79.44 E-value=12 Score=25.98 Aligned_cols=85 Identities=20% Similarity=0.262 Sum_probs=48.1
Q ss_pred EeEEEeCCCCccccCCCCcEEEEEe-cccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410 34 SPTLVFGPSMLPTLNLTGDVILAEY-VSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV 112 (160)
Q Consensus 34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~-~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v 112 (160)
....+.+.+-.+.-. -||.+++.- -.....++++||+.-.-.=.. . +..-...|..+.+
T Consensus 20 ~cI~v~~~~~~~~a~-vGD~I~vsVkk~~~~~~vkkg~v~~avIVrt--k---~~~~r~dg~~i~F-------------- 79 (122)
T PF00238_consen 20 KCIKVLGGKRRKYAS-VGDIIVVSVKKGRPKSKVKKGQVYKAVIVRT--K---KPIRRKDGSFIKF-------------- 79 (122)
T ss_dssp EEEEETSSTTTSEE--TTSEEEEEEEEE-SSSSSTTTEEEEEEEEEC--S---SEEETTTSEEEEE--------------
T ss_pred EEEEEeCCcCccccc-cceEEEEEEeecccCccccccceEEEEEEEE--e---EEEEEeCCcEEEe--------------
Confidence 445555555556566 788887632 111135677777753322100 0 1122233444443
Q ss_pred cCCcEEEEcCCCCCCCCCCcccceeCC
Q 031410 113 PKGHVWIQGDNLYASRDSRQFGPVPYG 139 (160)
Q Consensus 113 p~~~~~v~gdn~~~s~DSR~~G~V~~~ 139 (160)
.+|.+-++.++. +...+|-+|||+.|
T Consensus 80 ~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 80 DDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp SSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred CCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 556787888874 78899999999875
No 27
>smart00439 BAH Bromo adjacent homology domain.
Probab=72.04 E-value=26 Score=23.23 Aligned_cols=73 Identities=19% Similarity=0.224 Sum_probs=35.4
Q ss_pred CCCCcEEEEeeCCCCCceEEEEEEee---CCCE-EEEec-----CCCCCCcceEEccCCcEEEEcCCCCCCCCCCcccce
Q 031410 66 LGPGDIVFVRSPVDPNKIVTKRIVGV---EGDR-VTYFK-----PRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPV 136 (160)
Q Consensus 66 ~~~GDiVvf~~p~~~~~~~iKRVv~~---~Gd~-v~~~~-----~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V 136 (160)
++.||.|.+..+.....+++-||..+ +++. ..+.- +........-..-++++|...+. --+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~~----------~~i 71 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEY----------DTV 71 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccccCCCcceEEEccC----------ccC
Confidence 45677777766543344566666554 2221 22211 10000001112345666654332 268
Q ss_pred eCCCeEEEEEEE
Q 031410 137 PYGLIEGKAFFR 148 (160)
Q Consensus 137 ~~~~I~G~v~~~ 148 (160)
+.+.|.|++.-.
T Consensus 72 ~~~~I~~kc~V~ 83 (120)
T smart00439 72 PLSDIIGKCNVL 83 (120)
T ss_pred ChHHeeeEEEEE
Confidence 889999998654
No 28
>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=71.15 E-value=28 Score=24.27 Aligned_cols=55 Identities=16% Similarity=0.065 Sum_probs=30.7
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEE
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEG 143 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G 143 (160)
.+++.||+|+|+... ...+--+++... ..|++.++|-|..+.- ..-..++++|+|
T Consensus 72 ~~p~~GDiv~f~~~~---~~HVGi~~g~~~-------------------~~g~i~~lgGNq~~~V---~~~~~~~~~~~~ 126 (129)
T TIGR02594 72 SKPAYGCIAVKRRGG---GGHVGFVVGKDK-------------------QTGTIIVLGGNQGDRV---REALYSRSRIVA 126 (129)
T ss_pred CCCCccEEEEEECCC---CCEEEEEEeEcC-------------------CCCEEEEeeCCCCCeE---EEEEEecccEEE
Confidence 478999999998522 223444444322 1247788888754322 222345555555
No 29
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=70.57 E-value=32 Score=23.76 Aligned_cols=26 Identities=31% Similarity=0.429 Sum_probs=18.0
Q ss_pred CCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 114 KGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 114 ~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
+|..-++.++ .+..-+|-||||.+|.
T Consensus 81 dNA~Viin~~-g~P~GtrI~GPVaREl 106 (122)
T COG0093 81 DNAAVIINPD-GEPRGTRIFGPVAREL 106 (122)
T ss_pred CceEEEECCC-CCcccceEecchhHHH
Confidence 3455555544 4778899999998863
No 30
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=70.28 E-value=29 Score=24.26 Aligned_cols=56 Identities=14% Similarity=0.204 Sum_probs=40.0
Q ss_pred CCCcEEEEeeC--CCCCceEEEEEEeeCCC--EEEEecCCCCCCcceEEccCCcEEEEcC
Q 031410 67 GPGDIVFVRSP--VDPNKIVTKRIVGVEGD--RVTYFKPRNGDSCHTVVVPKGHVWIQGD 122 (160)
Q Consensus 67 ~~GDiVvf~~p--~~~~~~~iKRVv~~~Gd--~v~~~~~~~~~~~~~~~vp~~~~~v~gd 122 (160)
+.||-|+++.+ ++.+..++-+|+...++ +.++.|.........++++..++.-+=.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~ 60 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPK 60 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-S
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCC
Confidence 47999999886 44678899999998777 5888865544333478888888888855
No 31
>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=68.23 E-value=37 Score=23.54 Aligned_cols=86 Identities=24% Similarity=0.276 Sum_probs=45.0
Q ss_pred EeEEEeCCCCccccCCCCcEEEEEec-ccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410 34 SPTLVFGPSMLPTLNLTGDVILAEYV-SHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV 112 (160)
Q Consensus 34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~~-~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v 112 (160)
....+.+.+..+.-. -||.+++.-. .......++|+++-.-.-.. ..-++ ...|-.+ ..
T Consensus 20 ~cI~v~~~~~~~~a~-iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrt--kk~~~---r~dG~~i--------------~F 79 (122)
T TIGR01067 20 QCIKVLGGSRRRYAT-VGDVIVVVVKDAIPNGKVKKGDVVKAVIVRT--KKGVR---RKDGSYI--------------RF 79 (122)
T ss_pred EEEEEeCCCCCCccc-cCCEEEEEEEEcCCCCccccccEEEEEEEEe--ecceE---eCCCCEE--------------EC
Confidence 445555666666665 6887776321 11112356666652211000 00111 1223333 34
Q ss_pred cCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 113 PKGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
.+|.+-++.++. +..-+|-+|||++|.
T Consensus 80 ~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 80 DDNACVLINKNK-EPRGTRIFGPVAREL 106 (122)
T ss_pred CCceEEEECCCC-CEeeeEEEccchHHH
Confidence 556677776664 677899999999875
No 32
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=62.83 E-value=9.5 Score=24.18 Aligned_cols=20 Identities=45% Similarity=0.642 Sum_probs=9.4
Q ss_pred CCcEEEEEecccCCCCCCCCcEE
Q 031410 50 TGDVILAEYVSHRVGRLGPGDIV 72 (160)
Q Consensus 50 ~Gd~vlv~~~~~~~~~~~~GDiV 72 (160)
.||.|++..+.+ +.++|||+
T Consensus 49 ~GD~V~Ve~~~~---d~~kg~I~ 68 (75)
T COG0361 49 PGDVVLVELSPY---DLTKGRIV 68 (75)
T ss_pred CCCEEEEEeccc---ccccccEE
Confidence 455555554332 34555543
No 33
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=58.98 E-value=43 Score=24.96 Aligned_cols=38 Identities=21% Similarity=0.218 Sum_probs=21.1
Q ss_pred CCCCCCcEEEEeeCCC------------CCceEEEEEEe---eCCCEEEEecC
Q 031410 64 GRLGPGDIVFVRSPVD------------PNKIVTKRIVG---VEGDRVTYFKP 101 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~------------~~~~~iKRVv~---~~Gd~v~~~~~ 101 (160)
..|+.||+|.+..... .-...+--|++ ..++++++..+
T Consensus 92 y~P~~GDlIc~~R~~~~~~~~~~~~~~~~~~~HcdIVVa~~~~d~~~v~~IGG 144 (183)
T PF10030_consen 92 YKPRPGDLICYDRGRSKTYDFASLPTSGGFPSHCDIVVAVNVVDGRTVTTIGG 144 (183)
T ss_pred CCCCCCCEEEecCCCCcccchhhhccCCCCCCceeEEEeeccCCCCEEEEEcC
Confidence 3567777777665331 12235555666 55566666543
No 34
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=58.93 E-value=12 Score=23.30 Aligned_cols=11 Identities=45% Similarity=0.516 Sum_probs=5.5
Q ss_pred CCCCcEEEEee
Q 031410 66 LGPGDIVFVRS 76 (160)
Q Consensus 66 ~~~GDiVvf~~ 76 (160)
+..||.|.+..
T Consensus 45 I~~GD~V~Ve~ 55 (68)
T TIGR00008 45 ILPGDKVKVEL 55 (68)
T ss_pred ECCCCEEEEEE
Confidence 44555555553
No 35
>CHL00057 rpl14 ribosomal protein L14
Probab=58.47 E-value=59 Score=22.55 Aligned_cols=30 Identities=17% Similarity=0.339 Sum_probs=22.0
Q ss_pred EEccCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 110 VVVPKGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 110 ~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
...-+|..-++.++. +..-+|-+|||++|.
T Consensus 77 i~F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T CHL00057 77 IRFDDNAAVVIDQEG-NPKGTRVFGPIAREL 106 (122)
T ss_pred EEcCCceEEEECCCC-CEeEeEEEccchHHH
Confidence 334556777777664 678899999999875
No 36
>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=58.42 E-value=45 Score=24.35 Aligned_cols=38 Identities=32% Similarity=0.400 Sum_probs=28.8
Q ss_pred cCCCCCCCCcEEEEeeCCCCCceEEEE---EEeeCCCEEEEec
Q 031410 61 HRVGRLGPGDIVFVRSPVDPNKIVTKR---IVGVEGDRVTYFK 100 (160)
Q Consensus 61 ~~~~~~~~GDiVvf~~p~~~~~~~iKR---Vv~~~Gd~v~~~~ 100 (160)
++.+.++.|++.+|.. ......+|| ++.+.++++++..
T Consensus 70 yR~~~L~~GEvalY~~--~G~~I~L~~~G~ii~~~~~~~~v~a 110 (162)
T PF06890_consen 70 YRPKGLKPGEVALYDD--EGQKIHLKRDGRIIEVTCKTVTVNA 110 (162)
T ss_pred ccccCCCCCcEEEEcC--CCCEEEEEecceEEeccCceEEEec
Confidence 4556799999999996 344566665 7778889888874
No 37
>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=55.54 E-value=68 Score=22.33 Aligned_cols=29 Identities=14% Similarity=0.016 Sum_probs=19.1
Q ss_pred CCCCCCcEEEEeeCCCC----------CceEEEEEEeeC
Q 031410 64 GRLGPGDIVFVRSPVDP----------NKIVTKRIVGVE 92 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~----------~~~~iKRVv~~~ 92 (160)
..++.||+|+++.++.. ...+|-||..+.
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~ 42 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMK 42 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEee
Confidence 35778888888865533 245777777654
No 38
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=55.05 E-value=8.1 Score=24.21 Aligned_cols=17 Identities=35% Similarity=0.641 Sum_probs=12.1
Q ss_pred CCCccccCCCCcEEEEEe
Q 031410 41 PSMLPTLNLTGDVILAEY 58 (160)
Q Consensus 41 ~SM~Ptl~~~Gd~vlv~~ 58 (160)
.||+|.+. .|++|+..-
T Consensus 12 ~~m~P~L~-~~~yVF~t~ 28 (72)
T PF10000_consen 12 ASMSPELN-PGEYVFCTV 28 (72)
T ss_dssp ST-EEEE--SS-EEEEEE
T ss_pred hhCCcEeC-CCCEEEEEe
Confidence 58999999 999999854
No 39
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.45 E-value=15 Score=25.34 Aligned_cols=37 Identities=19% Similarity=0.222 Sum_probs=22.0
Q ss_pred CCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCC
Q 031410 41 PSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPV 78 (160)
Q Consensus 41 ~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~ 78 (160)
.||.|.+. +||+|+..--........---+-.|+.++
T Consensus 12 ~smtPeL~-~G~yVfcT~~~ga~~~~~lePla~FRE~E 48 (134)
T COG3602 12 ASMTPELL-DGDYVFCTVAPGALQPKNLEPLATFRERE 48 (134)
T ss_pred HhcCcccc-CCceEEEEecCCcCCCcCCChHhhhcccc
Confidence 48999999 99999975322111222333455565543
No 40
>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=54.17 E-value=19 Score=24.75 Aligned_cols=28 Identities=29% Similarity=0.349 Sum_probs=21.7
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEeeC
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVGVE 92 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~~~ 92 (160)
.++.||-|.++.+++++..+|.||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~ 30 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLW 30 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 4578999999987655678899987753
No 41
>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=53.92 E-value=33 Score=23.95 Aligned_cols=27 Identities=19% Similarity=0.140 Sum_probs=18.3
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEeeCC
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVGVEG 93 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~~~G 93 (160)
.++.||.|.+..++ +..++.+|-.+-.
T Consensus 7 ~i~vGD~V~v~~~~--~~~~va~Ie~i~e 33 (130)
T cd04721 7 TISVHDFVYVLSEE--EDRYVAYIEDLYE 33 (130)
T ss_pred EEECCCEEEEeCCC--CCcEEEEEEEEEE
Confidence 57889999998654 3456666666543
No 42
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=53.04 E-value=75 Score=22.05 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=20.6
Q ss_pred ccCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 112 VPKGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
..+|.+-++.++. +..-+|-+|||++|.
T Consensus 79 F~dNavVLin~~~-~p~GTrI~Gpv~~el 106 (122)
T PRK05483 79 FDDNAAVLLNNDG-EPRGTRIFGPVAREL 106 (122)
T ss_pred cCCCEEEEECCCC-CEeEeEEeccchHHH
Confidence 3456676776653 678899999999765
No 43
>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=52.83 E-value=13 Score=22.63 Aligned_cols=28 Identities=25% Similarity=0.335 Sum_probs=13.6
Q ss_pred CCcEEEEEecc--cCCCCCCCCcEEEEeeC
Q 031410 50 TGDVILAEYVS--HRVGRLGPGDIVFVRSP 77 (160)
Q Consensus 50 ~Gd~vlv~~~~--~~~~~~~~GDiVvf~~p 77 (160)
+|..++..--. .+.--+++||+|+....
T Consensus 24 dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 24 DGEERLARIPGKFRKRIWIKRGDFVLVEPS 53 (65)
T ss_dssp TSEEEEEEE-HHHHTCC---TTEEEEEEES
T ss_pred CCCEEEEEeccceeeeEecCCCCEEEEEec
Confidence 56655553211 11234788888888854
No 44
>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=52.26 E-value=16 Score=23.25 Aligned_cols=11 Identities=27% Similarity=0.588 Sum_probs=8.1
Q ss_pred CCCCcEEEEee
Q 031410 66 LGPGDIVFVRS 76 (160)
Q Consensus 66 ~~~GDiVvf~~ 76 (160)
+++||+|+...
T Consensus 39 I~~GD~VlV~~ 49 (78)
T cd04456 39 IKRGDFLIVDP 49 (78)
T ss_pred EcCCCEEEEEe
Confidence 67777777765
No 45
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=52.22 E-value=93 Score=22.89 Aligned_cols=53 Identities=11% Similarity=-0.055 Sum_probs=28.2
Q ss_pred ChhhhHHHHHHHHHHHHHHHHHHHHHHHhhceE--------EeEEEeCCCCccccCCCCcEEEEEe
Q 031410 1 MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLW--------SPTLVFGPSMLPTLNLTGDVILAEY 58 (160)
Q Consensus 1 m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~v~g~SM~Ptl~~~Gd~vlv~~ 58 (160)
|+...|.....+..+.+.+++++.+++...+.+ ..|.+. ..| ++ .||+|.+..
T Consensus 1 m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~T~S~P~glY~~~---~~~-~~-~Gd~V~f~~ 61 (178)
T PRK13884 1 MSRILKRITAGVAVAGLAALLLAALGYAAGARVNTTKSIPVGLYWTS---SAP-VE-KGAYVLFCP 61 (178)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHhCcEEEECCCCCcceEEEEe---CCC-CC-CCCEEEEeC
Confidence 644444444444344444444444444555554 345653 445 66 899999963
No 46
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=52.01 E-value=73 Score=21.66 Aligned_cols=47 Identities=15% Similarity=0.225 Sum_probs=28.4
Q ss_pred CcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC-EEEEe
Q 031410 51 GDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD-RVTYF 99 (160)
Q Consensus 51 Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd-~v~~~ 99 (160)
++...+...+.....+..||+|.+...+ +...+.+++.-.|. ++.+-
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~--g~~~~~~~v~~sGnsTiRv~ 58 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDD--GELWFQKVVESSGNSTIRVI 58 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCC--CeEEEEEEEecCCCEEEEEE
Confidence 4444444444445689999999999754 45555555544443 55553
No 47
>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=50.74 E-value=19 Score=23.86 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=20.3
Q ss_pred CCCCcEEEEeeCCCCCceEEEEEEee
Q 031410 66 LGPGDIVFVRSPVDPNKIVTKRIVGV 91 (160)
Q Consensus 66 ~~~GDiVvf~~p~~~~~~~iKRVv~~ 91 (160)
++.||.|.+..+..+..+++.||..+
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i 28 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEI 28 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEE
Confidence 46788888887665678888888876
No 48
>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=50.53 E-value=15 Score=23.25 Aligned_cols=12 Identities=42% Similarity=0.695 Sum_probs=8.3
Q ss_pred CCCCCcEEEEee
Q 031410 65 RLGPGDIVFVRS 76 (160)
Q Consensus 65 ~~~~GDiVvf~~ 76 (160)
-+++||+|....
T Consensus 38 wI~~GD~V~Ve~ 49 (77)
T cd05793 38 WINEGDIVLVAP 49 (77)
T ss_pred EEcCCCEEEEEe
Confidence 367777777764
No 49
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=49.17 E-value=16 Score=23.45 Aligned_cols=11 Identities=45% Similarity=0.761 Sum_probs=8.3
Q ss_pred CCCCcEEEEee
Q 031410 66 LGPGDIVFVRS 76 (160)
Q Consensus 66 ~~~GDiVvf~~ 76 (160)
+++||+|++..
T Consensus 44 I~~GD~VlVe~ 54 (83)
T smart00652 44 IRRGDIVLVDP 54 (83)
T ss_pred EcCCCEEEEEe
Confidence 67888888874
No 50
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=48.71 E-value=90 Score=21.74 Aligned_cols=16 Identities=19% Similarity=0.304 Sum_probs=12.4
Q ss_pred CCCCCCCcEEEEeeCC
Q 031410 63 VGRLGPGDIVFVRSPV 78 (160)
Q Consensus 63 ~~~~~~GDiVvf~~p~ 78 (160)
++.++.||+|+|-...
T Consensus 40 ~~~f~~GDlvLflpt~ 55 (129)
T PF10377_consen 40 FRNFQVGDLVLFLPTR 55 (129)
T ss_pred EecCCCCCEEEEEecC
Confidence 3688999999998643
No 51
>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=48.40 E-value=6.4 Score=27.37 Aligned_cols=6 Identities=33% Similarity=0.446 Sum_probs=2.3
Q ss_pred CcEEEE
Q 031410 51 GDVILA 56 (160)
Q Consensus 51 Gd~vlv 56 (160)
|...+.
T Consensus 36 gt~w~~ 41 (130)
T PF12273_consen 36 GTRWMA 41 (130)
T ss_pred CceecC
Confidence 333333
No 52
>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=47.07 E-value=86 Score=21.06 Aligned_cols=59 Identities=19% Similarity=0.108 Sum_probs=33.2
Q ss_pred CCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEee----CCCEEEEecCCC
Q 031410 42 SMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGV----EGDRVTYFKPRN 103 (160)
Q Consensus 42 SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~----~Gd~v~~~~~~~ 103 (160)
...-.+. .|+.+.-+.+.. ..-+++||.|...... ++-.+--.-.|+ -||.|.++|...
T Consensus 44 ~a~r~i~-~G~~i~~~~l~~-~~~V~~G~~V~i~~~~-~~~~i~~~g~Al~~g~~G~~I~V~N~~s 106 (122)
T TIGR03170 44 VAKRPLR-AGQPLTANMLRP-PWLVKRGDTVTVIARG-GGLSVTTEGKALEDGAVGDQIRVRNLSS 106 (122)
T ss_pred heecccC-CCCeeChHhcCC-ccEEcCCCEEEEEEec-CCEEEEEEEEEccccCCCCEEEEEECCC
Confidence 3334455 566664433321 2357899999887643 233333334443 488998887543
No 53
>PF13144 SAF_2: SAF-like
Probab=46.69 E-value=1.1e+02 Score=22.34 Aligned_cols=57 Identities=16% Similarity=0.126 Sum_probs=34.1
Q ss_pred ccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEee----CCCEEEEecCCC
Q 031410 44 LPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGV----EGDRVTYFKPRN 103 (160)
Q Consensus 44 ~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~----~Gd~v~~~~~~~ 103 (160)
.-.+. .|+.+..+.+.. ..-+++||.|...... ++-.+.-...|+ .||.|.++|...
T Consensus 120 ~r~i~-~G~~i~~~~l~~-~~~V~~G~~V~v~~~~-g~i~i~~~g~Al~~G~~G~~I~V~N~~S 180 (196)
T PF13144_consen 120 KRNIR-AGQPITPSDLEP-PPLVKRGDIVTVIARS-GGISISTEGKALEDGALGDTIRVKNLSS 180 (196)
T ss_pred EEEcC-CCCEeeeccccc-ceecCCCCEEEEEEEe-CCEEEEEEEEEccCCCCCCEEEEEECCC
Confidence 34455 677666655432 2467899999887643 233333334444 488999887543
No 54
>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=44.92 E-value=62 Score=20.30 Aligned_cols=34 Identities=29% Similarity=0.306 Sum_probs=23.8
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEE--------eeCCCEEEEe
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIV--------GVEGDRVTYF 99 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv--------~~~Gd~v~~~ 99 (160)
..++.||-+.+.+. +...-+|.+- |.+||++.+.
T Consensus 25 G~v~~Gd~v~~~P~--~~~~~V~si~~~~~~~~~a~aGd~v~l~ 66 (81)
T cd03695 25 GSIRVGDEVVVLPS--GKTSRVKSIETFDGELDEAGAGESVTLT 66 (81)
T ss_pred ceEECCCEEEEcCC--CCeEEEEEEEECCcEeCEEcCCCEEEEE
Confidence 57788888888743 2355667766 7788888764
No 55
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=43.35 E-value=23 Score=23.69 Aligned_cols=12 Identities=33% Similarity=0.603 Sum_probs=8.5
Q ss_pred CCCCCcEEEEee
Q 031410 65 RLGPGDIVFVRS 76 (160)
Q Consensus 65 ~~~~GDiVvf~~ 76 (160)
-+++||+|++..
T Consensus 59 wI~~GD~VlVe~ 70 (100)
T PRK04012 59 WIREGDVVIVAP 70 (100)
T ss_pred EecCCCEEEEEe
Confidence 367788777775
No 56
>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=41.12 E-value=37 Score=23.05 Aligned_cols=27 Identities=37% Similarity=0.586 Sum_probs=19.6
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEee
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVGV 91 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~~ 91 (160)
.++.||.|.+..++++...+|-||..+
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i 29 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERL 29 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEE
Confidence 457788888887765566777777764
No 57
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=39.95 E-value=48 Score=25.41 Aligned_cols=18 Identities=6% Similarity=0.266 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 031410 8 AKEALTQTLTFARFFCLF 25 (160)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~ 25 (160)
...+|-+++.++++++++
T Consensus 12 ~N~iLNiaI~IV~lLIii 29 (217)
T PF07423_consen 12 TNKILNIAIGIVSLLIII 29 (217)
T ss_pred hhhhHHHHHHHHHHHHHH
Confidence 444554444444433333
No 58
>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=38.90 E-value=25 Score=22.43 Aligned_cols=38 Identities=18% Similarity=0.303 Sum_probs=19.8
Q ss_pred EeCCCCccccCCCCcEEEEEecccCCCC---CCCCcEEEEee
Q 031410 38 VFGPSMLPTLNLTGDVILAEYVSHRVGR---LGPGDIVFVRS 76 (160)
Q Consensus 38 v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~---~~~GDiVvf~~ 76 (160)
..|++..-...++|...++.- +.+++. +++||+|+..+
T Consensus 9 ~~G~n~~~V~~~dG~~~l~~i-P~KfRk~iWIkrGd~VlV~p 49 (78)
T cd05792 9 SKGNNLHEVETPNGSRYLVSM-PTKFRKNIWIKRGDFVLVEP 49 (78)
T ss_pred cCCCcEEEEEcCCCCEEEEEe-chhhcccEEEEeCCEEEEEe
Confidence 334443322223666666532 222222 68888888875
No 59
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=38.37 E-value=40 Score=21.97 Aligned_cols=11 Identities=27% Similarity=0.271 Sum_probs=6.7
Q ss_pred CCCCcEEEEee
Q 031410 66 LGPGDIVFVRS 76 (160)
Q Consensus 66 ~~~GDiVvf~~ 76 (160)
+..||.|.+..
T Consensus 47 Il~GD~V~VE~ 57 (87)
T PRK12442 47 ILAGDRVTLEL 57 (87)
T ss_pred ecCCCEEEEEE
Confidence 45666666664
No 60
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=38.09 E-value=1.2e+02 Score=19.94 Aligned_cols=90 Identities=19% Similarity=0.120 Sum_probs=44.4
Q ss_pred cCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEEcCCCC-
Q 031410 47 LNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLY- 125 (160)
Q Consensus 47 l~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~- 125 (160)
|.|-||+|++.+... .+-..|-+++=.. ..+......|+|+.-.... .++ ...+..+..|..-+..+...
T Consensus 3 i~Pl~drVLV~~~~~--e~~T~gGI~Lp~~--a~~k~~~G~VvaVG~G~~~-~~G----~~~~~~vk~GD~Vlf~~~~g~ 73 (95)
T PRK00364 3 LKPLGDRVLVKRLEE--EEKTAGGIVLPDS--AKEKPQEGEVVAVGPGRRL-DNG----ERVPLDVKVGDKVLFGKYAGT 73 (95)
T ss_pred ceEcCCEEEEEEccc--CccccceEEcCcc--ccCCcceEEEEEECCCeEC-CCC----CEeecccCCCCEEEEcCCCCe
Confidence 345799999987532 3455666665322 2344556677776532211 010 11222344444333333221
Q ss_pred -CCCCCCcccceeCCCeEEEE
Q 031410 126 -ASRDSRQFGPVPYGLIEGKA 145 (160)
Q Consensus 126 -~s~DSR~~G~V~~~~I~G~v 145 (160)
-..|...|=.++.++|+|++
T Consensus 74 ev~~~~~~y~iv~~~DIlavi 94 (95)
T PRK00364 74 EVKIDGEEYLILRESDILAIV 94 (95)
T ss_pred EEEECCEEEEEEEHHHEEEEe
Confidence 12344445577777887764
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=37.94 E-value=84 Score=19.61 Aligned_cols=34 Identities=26% Similarity=0.447 Sum_probs=23.2
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEE--------eeCCCEEEEe
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIV--------GVEGDRVTYF 99 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv--------~~~Gd~v~~~ 99 (160)
+.++.||-|.+.+. ....-+|.+. |.+||.+.+.
T Consensus 25 G~i~~Gd~v~i~P~--~~~~~V~si~~~~~~~~~a~aGd~v~~~ 66 (83)
T cd03698 25 GSIQKGDTLLVMPS--KESVEVKSIYVDDEEVDYAVAGENVRLK 66 (83)
T ss_pred eEEeCCCEEEEeCC--CcEEEEEEEEECCeECCEECCCCEEEEE
Confidence 56788888888642 2345666665 7788888764
No 62
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=37.54 E-value=52 Score=21.61 Aligned_cols=30 Identities=27% Similarity=0.292 Sum_probs=20.3
Q ss_pred ccCCCCcEEEEEecccC-----CCCCCCCcEEEEee
Q 031410 46 TLNLTGDVILAEYVSHR-----VGRLGPGDIVFVRS 76 (160)
Q Consensus 46 tl~~~Gd~vlv~~~~~~-----~~~~~~GDiVvf~~ 76 (160)
++. .|-.++++...+. ...++.||+|+|-+
T Consensus 57 ~lr-pGiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 57 ELR-PGIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred CCc-ccEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 355 5778888764432 23578899999875
No 63
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=37.09 E-value=1.2e+02 Score=19.82 Aligned_cols=83 Identities=18% Similarity=0.136 Sum_probs=42.6
Q ss_pred CCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeC-CCEEEEecCCCCCCcceEEccCCcEEEEcCCCCC
Q 031410 48 NLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVE-GDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYA 126 (160)
Q Consensus 48 ~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~-Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~~ 126 (160)
.|-||+|++.+... .+-..|-|++=.. .........|+|+. |.. ..+..+..|..-+.++....
T Consensus 4 ~Pl~DRVLVk~~~~--e~~T~gGI~Lp~~--a~ek~~~G~VvavG~g~~-----------~~~~~Vk~GD~Vl~~~y~g~ 68 (91)
T PRK14533 4 IPLGERLLIKPIKE--EKKTEGGIVLPDS--AKEKPMKAEVVAVGKLDD-----------EEDFDIKVGDKVIFSKYAGT 68 (91)
T ss_pred eEcCCEEEEEEccc--cceecccEEeccc--ccCCcceEEEEEECCCCc-----------cccccccCCCEEEEccCCCe
Confidence 35799999987532 2345666666332 22344555666654 210 11333444444444443211
Q ss_pred --CCCCCcccceeCCCeEEEE
Q 031410 127 --SRDSRQFGPVPYGLIEGKA 145 (160)
Q Consensus 127 --s~DSR~~G~V~~~~I~G~v 145 (160)
..|...|=.++.++|+|++
T Consensus 69 ev~~~~~~y~iv~e~DILa~i 89 (91)
T PRK14533 69 EIKIDDEDYIIIDVNDILAKI 89 (91)
T ss_pred EEEECCEEEEEEEhHhEEEEe
Confidence 2333344477777787764
No 64
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=37.04 E-value=11 Score=22.81 Aligned_cols=20 Identities=35% Similarity=0.705 Sum_probs=16.3
Q ss_pred CCCCCCcccceeCCCeEEEE
Q 031410 126 ASRDSRQFGPVPYGLIEGKA 145 (160)
Q Consensus 126 ~s~DSR~~G~V~~~~I~G~v 145 (160)
-..|-|.||.+|-.+.-||+
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 46899999999987776765
No 65
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=36.95 E-value=43 Score=19.19 Aligned_cols=7 Identities=14% Similarity=0.762 Sum_probs=2.8
Q ss_pred hhHHHHH
Q 031410 4 WGLLAKE 10 (160)
Q Consensus 4 ~~~~~~~ 10 (160)
|+++.|.
T Consensus 9 ~~~f~~n 15 (56)
T PF12911_consen 9 WRRFRRN 15 (56)
T ss_pred HHHHHhC
Confidence 3444333
No 66
>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=35.71 E-value=95 Score=19.33 Aligned_cols=34 Identities=21% Similarity=0.320 Sum_probs=23.3
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEE--------eeCCCEEEEe
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIV--------GVEGDRVTYF 99 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv--------~~~Gd~v~~~ 99 (160)
..++.||-+.+.+. +...-+|.+- |.+||.+.+.
T Consensus 24 G~i~~G~~v~i~P~--~~~~~V~si~~~~~~~~~a~aGd~v~l~ 65 (82)
T cd04089 24 GTIKKGDKLLVMPN--KTQVEVLSIYNEDVEVRYARPGENVRLR 65 (82)
T ss_pred eEEecCCEEEEeCC--CcEEEEEEEEECCEECCEECCCCEEEEE
Confidence 56788888888743 2355667766 6778877764
No 67
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=33.62 E-value=1.8e+02 Score=20.74 Aligned_cols=30 Identities=17% Similarity=0.078 Sum_probs=22.0
Q ss_pred EEccCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 110 VVVPKGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 110 ~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
+...+|.+-++.++. +..-+|-||||++|.
T Consensus 95 i~F~dNA~VLin~~~-~p~GTRI~GpV~rEl 124 (139)
T PTZ00054 95 IYFEDNAGVIVNPKG-EMKGSAITGPVAKEC 124 (139)
T ss_pred EEeCCcEEEEECCCC-CEeeeEEeCchhHHH
Confidence 344556676776653 677899999999987
No 68
>PF12459 DUF3687: D-Ala-teichoic acid biosynthesis protein; InterPro: IPR021008 Proteins in this family are bacterial proteins of approximately 50 amino acids in length. There are two completely conserved residues (L and Y) that may be functionally important. A number of entries are annotated as D-Ala-teichoic acid biosynthesis protein; however there is no direct evidence to support this annotation.
Probab=32.85 E-value=94 Score=17.36 Aligned_cols=27 Identities=19% Similarity=0.082 Sum_probs=14.7
Q ss_pred ChhhhHHHHHHHHHHHHHHHHHHHHHH
Q 031410 1 MRRWGLLAKEALTQTLTFARFFCLFHV 27 (160)
Q Consensus 1 m~~~~~~~~~~~~~~~~~~~~~~~~~~ 27 (160)
|..++...+-+.+.+...++.++++.+
T Consensus 1 ~~~~~~~~~fi~~T~fYf~Ill~L~yl 27 (42)
T PF12459_consen 1 MIKQKPAVKFIGKTLFYFAILLALIYL 27 (42)
T ss_pred CcccchHHHHHHHHHHHHHHHHHHHHH
Confidence 445555566666665555555444443
No 69
>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=31.53 E-value=71 Score=22.85 Aligned_cols=38 Identities=13% Similarity=-0.076 Sum_probs=26.6
Q ss_pred EEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeC
Q 031410 37 LVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSP 77 (160)
Q Consensus 37 ~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p 77 (160)
.....+|...|. ..-+..+..-. ..++++|||++...+
T Consensus 50 ~~nT~tl~~~L~-~~G~~~I~~~~--~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 50 AGNTETLHDWLK-KNGFKKISENV--DWNLQRGDIFIWGRR 87 (145)
T ss_pred ccCHHHHHHHHh-hCCcEEeccCC--cccccCCCEEEEcCC
Confidence 456688888787 66666665411 147899999998765
No 70
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=31.28 E-value=1.5e+02 Score=19.18 Aligned_cols=88 Identities=16% Similarity=0.069 Sum_probs=46.4
Q ss_pred CCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEEcCCCC--C
Q 031410 49 LTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLY--A 126 (160)
Q Consensus 49 ~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~--~ 126 (160)
|-||+|++.+.. ..+-..|-+++=.. .......-+|+|+...... .++. ..+..+..|..-+..+... -
T Consensus 4 Pl~drVLV~~~~--~e~~T~~GiiLp~~--~~~~~~~G~VvaVG~G~~~-~~g~----~~~~~vk~GD~Vl~~~~~g~~v 74 (93)
T PF00166_consen 4 PLGDRVLVKKIE--AEEKTASGIILPES--AKEKPNQGKVVAVGPGRYN-ENGE----EVPMDVKVGDKVLFPKYAGTEV 74 (93)
T ss_dssp ESTTEEEEEECS--CTCTCTTSCCE-CC--SSSSEEEEEEEEE-SEEET-TTSS----EEETSS-TTSEEEEETTTSEEE
T ss_pred ecCCEEEEEEcc--ccceecceEEeccc--cccccceeEEEEcCCcccc-CCCc----EeeeeeeeccEEeccccCceEE
Confidence 468999998853 24566777776632 2346677778887653322 1110 1122344444444443321 1
Q ss_pred CCCCCcccceeCCCeEEEE
Q 031410 127 SRDSRQFGPVPYGLIEGKA 145 (160)
Q Consensus 127 s~DSR~~G~V~~~~I~G~v 145 (160)
..|...|=.++.++|.|+.
T Consensus 75 ~~~~~~~~~~~~~dIlavi 93 (93)
T PF00166_consen 75 KFDGEKYLIVREDDILAVI 93 (93)
T ss_dssp EETTEEEEEEEGGGEEEEE
T ss_pred EECCEEEEEEEHHHeEEEC
Confidence 2355556678888888763
No 71
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. 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=31.16 E-value=80 Score=22.20 Aligned_cols=28 Identities=18% Similarity=0.176 Sum_probs=22.3
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEEee
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIVGV 91 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv~~ 91 (160)
..++.||-|.+.++..++.++|.||...
T Consensus 10 ~~~~vgD~Vyv~~~~~~ePyyIgrI~e~ 37 (135)
T cd04710 10 ELLKVNDHIYMSSEPPGEPYYIGRIMEF 37 (135)
T ss_pred eEEeCCCEEEEecCCCCCCCEEEEEEEE
Confidence 4689999999997655667889999874
No 72
>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=31.14 E-value=49 Score=23.31 Aligned_cols=31 Identities=19% Similarity=0.158 Sum_probs=23.3
Q ss_pred eEEccCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 109 TVVVPKGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 109 ~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
....-+|.+-++.++. +..-+|-||||++|.
T Consensus 86 ~i~FddNa~VLin~~~-~P~GTRI~GpV~rEl 116 (131)
T TIGR03673 86 RVKFEDNAVVIVTPDG-EPKGTEIKGPVAREA 116 (131)
T ss_pred EEEeCCcEEEEECCCC-CEeeeEEEccchHHH
Confidence 3445566777777764 677899999999886
No 73
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=31.03 E-value=60 Score=21.09 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=14.7
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEeeCCC--EEEE
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVGVEGD--RVTY 98 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd--~v~~ 98 (160)
+++.||+|+|.. .+.|+|..-.+| +|++
T Consensus 69 ~p~~G~lvlFPs------~l~H~v~p~~~~~~Risi 98 (101)
T PF13759_consen 69 EPEEGDLVLFPS------WLWHGVPPNNSDEERISI 98 (101)
T ss_dssp ---TTEEEEEET------TSEEEE----SSS-EEEE
T ss_pred CCCCCEEEEeCC------CCEEeccCcCCCCCEEEE
Confidence 678999999984 466777765554 4443
No 74
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=30.79 E-value=1.9e+02 Score=20.75 Aligned_cols=18 Identities=33% Similarity=0.289 Sum_probs=13.0
Q ss_pred CCCCCCCCCcccceeCCC
Q 031410 123 NLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 123 n~~~s~DSR~~G~V~~~~ 140 (160)
+...-.-||.+|||+.+.
T Consensus 113 ~~~e~~gs~i~G~v~~e~ 130 (145)
T KOG0901|consen 113 NKGEPKGSAITGPVGKEL 130 (145)
T ss_pred ccCccccceeccccChhH
Confidence 444667788899888764
No 75
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=30.74 E-value=53 Score=21.88 Aligned_cols=11 Identities=36% Similarity=0.746 Sum_probs=8.1
Q ss_pred CCCCCcEEEEe
Q 031410 65 RLGPGDIVFVR 75 (160)
Q Consensus 65 ~~~~GDiVvf~ 75 (160)
-+++||+|++.
T Consensus 57 wI~~GD~VlVs 67 (99)
T TIGR00523 57 WIREGDVVIVK 67 (99)
T ss_pred EecCCCEEEEE
Confidence 36788888884
No 76
>PF10913 DUF2706: Protein of unknown function (DUF2706); InterPro: IPR024444 This family of proteins with unknown function appears to be restricted to Rickettsia spp.
Probab=30.30 E-value=85 Score=18.42 Aligned_cols=44 Identities=7% Similarity=0.049 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEe
Q 031410 14 QTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEY 58 (160)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~ 58 (160)
.+.++++++++.-++.-.-..+|.+.+.-..|.+. ++.-+-+++
T Consensus 4 ~lkf~lv~imlaqllsctpsapyeikspcvs~did-d~s~ls~np 47 (60)
T PF10913_consen 4 SLKFLLVLIMLAQLLSCTPSAPYEIKSPCVSADID-DNSSLSVNP 47 (60)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCccccCCccccccC-CCccccccc
Confidence 34444445555444443345678888888888887 777766665
No 77
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=30.08 E-value=1.2e+02 Score=20.52 Aligned_cols=27 Identities=11% Similarity=0.206 Sum_probs=17.8
Q ss_pred CCCCCCCcEEEEeeCCCCCceEEEEEEe
Q 031410 63 VGRLGPGDIVFVRSPVDPNKIVTKRIVG 90 (160)
Q Consensus 63 ~~~~~~GDiVvf~~p~~~~~~~iKRVv~ 90 (160)
.+.++.||.++|+.-.+ +..+.-+|+.
T Consensus 29 r~~ikvGD~I~f~~~~~-~~~l~v~V~~ 55 (109)
T cd06555 29 RQQIKVGDKILFNDLDT-GQQLLVKVVD 55 (109)
T ss_pred hhcCCCCCEEEEEEcCC-CcEEEEEEEE
Confidence 35799999999986433 3344445554
No 78
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=29.92 E-value=78 Score=23.10 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=18.9
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEee
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVGV 91 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~~ 91 (160)
-++.||-|.++.+. +..++|.||..+
T Consensus 3 ~yrvGD~Vy~~~~~-~~Py~I~rI~e~ 28 (164)
T cd04709 3 MYRVGDYVYFESSP-NNPYLIRRIEEL 28 (164)
T ss_pred EEecCCEEEEECCC-CCCCEEEEEEEE
Confidence 35788999998763 345788888865
No 79
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=29.81 E-value=75 Score=18.77 Aligned_cols=15 Identities=33% Similarity=0.550 Sum_probs=6.1
Q ss_pred CCCCCCcEEEEeeCC
Q 031410 64 GRLGPGDIVFVRSPV 78 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~ 78 (160)
..++.||-|-+.+|.
T Consensus 4 Gpf~~GdrVQlTD~K 18 (54)
T PF14801_consen 4 GPFRAGDRVQLTDPK 18 (54)
T ss_dssp -S--TT-EEEEEETT
T ss_pred CCCCCCCEEEEccCC
Confidence 345556666665543
No 80
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.33 E-value=2.2e+02 Score=20.54 Aligned_cols=54 Identities=17% Similarity=0.164 Sum_probs=27.4
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEE----eeCCCEEEEecCCCCCCcceEEccCCcEEE
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIV----GVEGDRVTYFKPRNGDSCHTVVVPKGHVWI 119 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv----~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v 119 (160)
-+++||.|...... ++-.+--.-. |-.||.|.++|.............+|.+-+
T Consensus 100 ~V~rG~~V~i~~~~-~g~~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv~g~V~~~g~V~V 157 (160)
T PRK06005 100 LVTRGSPVKLVFSA-GGLTITAAGTPLQSGAAGDLIRVRNVDSGVIVSGTVLADGTIQV 157 (160)
T ss_pred EEeCCCEEEEEEec-CCEEEEEEEEEcccCCCCCEEEEEECCCCCEEEEEEecCCEEEE
Confidence 35677777666532 2222222223 335888888875544433444444454433
No 81
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=28.42 E-value=1.2e+02 Score=20.25 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=22.8
Q ss_pred CCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC
Q 031410 63 VGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD 94 (160)
Q Consensus 63 ~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd 94 (160)
-.+++.||++.+.. ++..+.-+|.+++..
T Consensus 46 S~~VK~GD~l~i~~---~~~~~~v~Vl~~~~~ 74 (100)
T COG1188 46 SKEVKVGDILTIRF---GNKEFTVKVLALGEQ 74 (100)
T ss_pred ccccCCCCEEEEEe---CCcEEEEEEEecccc
Confidence 36899999999997 445777888887763
No 82
>KOG3858 consensus Ephrin, ligand for Eph receptor tyrosine kinase [Signal transduction mechanisms]
Probab=28.26 E-value=1e+02 Score=23.87 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=24.9
Q ss_pred eEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeC
Q 031410 35 PTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSP 77 (160)
Q Consensus 35 ~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p 77 (160)
...|.-+|..|-+. .||+++ +++.||.+-+.=|
T Consensus 26 ~~~VyWNSSNp~F~-~~d~vI---------~v~igD~ldIiCP 58 (233)
T KOG3858|consen 26 LHPVYWNSSNPRFR-RGDYVI---------YVQIGDYLDIICP 58 (233)
T ss_pred ccceEecCCCccee-cCCceE---------EeccCCEEEEECC
Confidence 57788899999998 888554 5677888866544
No 83
>PF10222 DUF2152: Uncharacterized conserved protein (DUF2152); InterPro: IPR018795 This entry includes mainly uncharacterised proteins, though some are described as belonging to the glycoside hydrolase family 65.
Probab=27.85 E-value=57 Score=28.97 Aligned_cols=67 Identities=16% Similarity=0.180 Sum_probs=36.0
Q ss_pred cEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEEcCCCCCCCCCC
Q 031410 52 DVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSR 131 (160)
Q Consensus 52 d~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR 131 (160)
+..+-+++........+||.++...|...+..++--| | +. .....|..++.|+.|.+|..+.+.+
T Consensus 52 ~~Cl~~~l~~w~~~~~e~da~i~~~~~p~e~~~~P~V-G--NG------------~iGl~V~~d~L~I~~~~R~l~~~~~ 116 (604)
T PF10222_consen 52 GKCLQDRLAPWYSQAEEGDAVILHPPKPQEKNYLPFV-G--NG------------YIGLDVDSDNLYIKGSGRALSLPVP 116 (604)
T ss_pred chhHHHHHHHHHHHHhcCCEEEccCCCCCcccCCcee-c--CC------------EEEEEEcCCeEEEEecCcccccccC
Confidence 4555555554445788999999985431221222111 1 11 1233455567777766655566666
Q ss_pred cc
Q 031410 132 QF 133 (160)
Q Consensus 132 ~~ 133 (160)
+.
T Consensus 117 f~ 118 (604)
T PF10222_consen 117 FH 118 (604)
T ss_pred CC
Confidence 54
No 84
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=27.73 E-value=1.6e+02 Score=18.61 Aligned_cols=36 Identities=19% Similarity=0.278 Sum_probs=23.2
Q ss_pred CCCCCCcEEEEeeCCCC--CceEEEEEE--------eeCCCEEEEe
Q 031410 64 GRLGPGDIVFVRSPVDP--NKIVTKRIV--------GVEGDRVTYF 99 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~--~~~~iKRVv--------~~~Gd~v~~~ 99 (160)
..++.||-+.+.+..+. ...-+|.+- |.+||++.+.
T Consensus 25 G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 25 GVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred CEEeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEE
Confidence 67888888888753211 244556655 7778877764
No 85
>PRK10507 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional
Probab=27.59 E-value=3.1e+02 Score=24.55 Aligned_cols=58 Identities=12% Similarity=0.064 Sum_probs=36.9
Q ss_pred CCCCCCCcEEEEeeC-CCCCceEEEEEEeeCCCEEEEecCC----------CCCCcceEEccCCcEEEE
Q 031410 63 VGRLGPGDIVFVRSP-VDPNKIVTKRIVGVEGDRVTYFKPR----------NGDSCHTVVVPKGHVWIQ 120 (160)
Q Consensus 63 ~~~~~~GDiVvf~~p-~~~~~~~iKRVv~~~Gd~v~~~~~~----------~~~~~~~~~vp~~~~~v~ 120 (160)
...|+.||++++... +...-=.|-=|+.+..+.|.+-+.. +.....+.+..+|.|++.
T Consensus 109 ~~~P~~gdLlI~~~~~~~~p~GHVAVVt~V~~~~V~iaeQN~~~~~w~~~~~~sR~l~l~~~~g~~~i~ 177 (619)
T PRK10507 109 PRAPEAGALLIWDKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLK 177 (619)
T ss_pred CCCCCCCcEEEeCCCCCCCCCceEEEEEEEcCCeEEEEeccccccCCCCCCCeeeEEEEEEeCCEEEEE
Confidence 358999999999953 2112235666778888999996321 112233445567888886
No 86
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=27.23 E-value=1.8e+02 Score=18.88 Aligned_cols=87 Identities=16% Similarity=0.087 Sum_probs=42.2
Q ss_pred CCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEEcCCCC--C
Q 031410 49 LTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLY--A 126 (160)
Q Consensus 49 ~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~--~ 126 (160)
|-||+|++.+... .+-..|-+++=.. ..+......|+|+.-+...-+ + ...+..+..|..-+..+... -
T Consensus 4 Pl~DrVLV~~~~~--e~~T~~GI~Lp~~--~~~k~~~g~VvAVG~g~~~~~-g----~~~~~~vk~GD~Vl~~~~~g~~v 74 (93)
T cd00320 4 PLGDRVLVKRIEA--EEKTKGGIILPDS--AKEKPQEGKVVAVGPGRRNEN-G----ERVPLSVKVGDKVLFPKYAGTEV 74 (93)
T ss_pred ecCCEEEEEEccc--cceecceEEeCCC--cCCCceEEEEEEECCCeECCC-C----CCccccccCCCEEEECCCCceEE
Confidence 5789999987531 3445666665332 224556677777654322111 0 11122333443333333221 1
Q ss_pred CCCCCcccceeCCCeEEE
Q 031410 127 SRDSRQFGPVPYGLIEGK 144 (160)
Q Consensus 127 s~DSR~~G~V~~~~I~G~ 144 (160)
..|.-.|=.++.++|+|+
T Consensus 75 ~~~~~~y~i~~~~DIla~ 92 (93)
T cd00320 75 KLDGEEYLILRESDILAV 92 (93)
T ss_pred EECCEEEEEEEHHHEEEE
Confidence 223334446777777765
No 87
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=26.90 E-value=1.8e+02 Score=18.73 Aligned_cols=27 Identities=22% Similarity=0.107 Sum_probs=18.9
Q ss_pred cEEEEEecccCCCCCCCCcEEEEeeCC
Q 031410 52 DVILAEYVSHRVGRLGPGDIVFVRSPV 78 (160)
Q Consensus 52 d~vlv~~~~~~~~~~~~GDiVvf~~p~ 78 (160)
.++.+++-......++.||.|.+..+.
T Consensus 30 ~~v~inp~dA~~~Gi~~Gd~V~v~s~~ 56 (110)
T PF01568_consen 30 PFVEINPEDAAKLGIKDGDWVRVSSPR 56 (110)
T ss_dssp EEEEEEHHHHHHCT--TTCEEEEEETT
T ss_pred CEEEEcHHHHHHhcCcCCCEEEEEecc
Confidence 478887755445689999999999865
No 88
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.83 E-value=2.8e+02 Score=21.14 Aligned_cols=51 Identities=12% Similarity=0.053 Sum_probs=27.2
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEe----eCCCEEEEecCCCCCCcceEEccCCcE
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVG----VEGDRVTYFKPRNGDSCHTVVVPKGHV 117 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~----~~Gd~v~~~~~~~~~~~~~~~vp~~~~ 117 (160)
-+++||.|...... ++-.+.-.-.| ..||.|.+++ ..........+.+|++
T Consensus 165 lV~rGd~V~i~~~~-gg~~I~~~G~Al~~G~~Gd~IrVrN-~Sgkii~g~V~~~g~V 219 (222)
T PRK08515 165 LVRKNDIINGVLKE-GGVSIEISLKALQDGNLGDIIQAKN-KSNKILKAKVLSKNKA 219 (222)
T ss_pred eEecCCEEEEEEEC-CCEEEEEEEEEcccCCCCCEEEEEe-CCCCEEEEEEecCCEE
Confidence 56788888777643 22223333333 3588888887 4333333333444443
No 89
>PTZ00320 ribosomal protein L14; Provisional
Probab=26.81 E-value=1.1e+02 Score=22.80 Aligned_cols=32 Identities=6% Similarity=-0.035 Sum_probs=24.1
Q ss_pred ceEEccCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 108 HTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 108 ~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
..+..-+|.+-++.++. +..-+|-||||++|.
T Consensus 141 s~IrFDdNAaVLIN~qg-ePlGTRIfGPVaREL 172 (188)
T PTZ00320 141 LQTNFDRNTCILMNDQR-VPLGTRVMYCAGRHV 172 (188)
T ss_pred CEEEeCCcEEEEECCCC-CEeeeEEecchhHHH
Confidence 34555667787887774 778899999998764
No 90
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=26.79 E-value=1.1e+02 Score=20.23 Aligned_cols=36 Identities=22% Similarity=0.268 Sum_probs=24.7
Q ss_pred EEEeCCCCccccCCCCcEEEEEecccC-----CCCCCCCcEEEEee
Q 031410 36 TLVFGPSMLPTLNLTGDVILAEYVSHR-----VGRLGPGDIVFVRS 76 (160)
Q Consensus 36 ~~v~g~SM~Ptl~~~Gd~vlv~~~~~~-----~~~~~~GDiVvf~~ 76 (160)
..+.++|..| |-.+++|...+- ...++.||.|+|-+
T Consensus 56 lFi~~gsvrp-----Gii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 56 LFIHHGSVRP-----GIIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred eEeeCCcCcC-----cEEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 5566777655 667788764421 23688999999975
No 91
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=26.77 E-value=2e+02 Score=19.14 Aligned_cols=28 Identities=25% Similarity=0.339 Sum_probs=16.7
Q ss_pred CCCcEEEEEeccc-------------CCCCCCCCcEEEEee
Q 031410 49 LTGDVILAEYVSH-------------RVGRLGPGDIVFVRS 76 (160)
Q Consensus 49 ~~Gd~vlv~~~~~-------------~~~~~~~GDiVvf~~ 76 (160)
|-||+|++.+... ....+++|.+|+...
T Consensus 5 PL~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~ 45 (96)
T COG0234 5 PLGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGP 45 (96)
T ss_pred ecCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEcc
Confidence 4678888876531 123456666666663
No 92
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=26.69 E-value=1.7e+02 Score=23.79 Aligned_cols=14 Identities=29% Similarity=0.325 Sum_probs=8.7
Q ss_pred EEEEEEeeCCCEEE
Q 031410 84 VTKRIVGVEGDRVT 97 (160)
Q Consensus 84 ~iKRVv~~~Gd~v~ 97 (160)
.++++...+||+|.
T Consensus 71 ~V~~v~v~~G~~V~ 84 (370)
T PRK11578 71 QLKTLSVAIGDKVK 84 (370)
T ss_pred EEEEEEcCCCCEEc
Confidence 55666666777553
No 93
>PF14118 YfzA: YfzA-like protein
Probab=26.16 E-value=60 Score=21.45 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=12.6
Q ss_pred EEeCCCCccccCCCCcE
Q 031410 37 LVFGPSMLPTLNLTGDV 53 (160)
Q Consensus 37 ~v~g~SM~Ptl~~~Gd~ 53 (160)
.+.+.|+.|.+. +|++
T Consensus 29 ~~d~t~w~pnf~-~g~~ 44 (94)
T PF14118_consen 29 IFDGTGWGPNFN-EGDF 44 (94)
T ss_pred HhhccccccccC-CCch
Confidence 356899999998 6774
No 94
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=25.92 E-value=1.2e+02 Score=21.02 Aligned_cols=13 Identities=31% Similarity=0.582 Sum_probs=11.2
Q ss_pred CCCCCCcEEEEee
Q 031410 64 GRLGPGDIVFVRS 76 (160)
Q Consensus 64 ~~~~~GDiVvf~~ 76 (160)
.++++||+|.|..
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 4789999999985
No 95
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=25.81 E-value=94 Score=16.95 Aligned_cols=22 Identities=32% Similarity=0.348 Sum_probs=18.1
Q ss_pred CCCCceEEEEEEeeCCCEEEEe
Q 031410 78 VDPNKIVTKRIVGVEGDRVTYF 99 (160)
Q Consensus 78 ~~~~~~~iKRVv~~~Gd~v~~~ 99 (160)
+....+...+|+...||.+.++
T Consensus 8 D~~egfv~g~I~~~~g~~vtV~ 29 (42)
T PF02736_consen 8 DPKEGFVKGEIIEEEGDKVTVK 29 (42)
T ss_dssp ESSSSEEEEEEEEEESSEEEEE
T ss_pred CCcccEEEEEEEEEcCCEEEEE
Confidence 3456788899999999999886
No 96
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=25.76 E-value=1e+02 Score=18.95 Aligned_cols=12 Identities=50% Similarity=0.634 Sum_probs=9.8
Q ss_pred CCCCCcEEEEee
Q 031410 65 RLGPGDIVFVRS 76 (160)
Q Consensus 65 ~~~~GDiVvf~~ 76 (160)
.+..||.|.++.
T Consensus 46 ~i~vGD~V~ve~ 57 (72)
T PRK00276 46 RILPGDKVTVEL 57 (72)
T ss_pred ccCCCCEEEEEE
Confidence 378899999994
No 97
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=25.66 E-value=1.5e+02 Score=17.52 Aligned_cols=36 Identities=28% Similarity=0.344 Sum_probs=19.5
Q ss_pred CCccc-cCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEE
Q 031410 42 SMLPT-LNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKR 87 (160)
Q Consensus 42 SM~Pt-l~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKR 87 (160)
++.|. |. .|-.+.+.. -++.||.|.++.. +..|+.|
T Consensus 20 ~~K~A~le-tG~~i~VP~------FI~~Gd~I~VdT~---~g~Yv~R 56 (56)
T PF09285_consen 20 SYKPATLE-TGAEIQVPL------FIEEGDKIKVDTR---DGSYVER 56 (56)
T ss_dssp TEEEEEET-TS-EEEEET------T--TT-EEEEETT---TTEEEEE
T ss_pred CccEEEEc-CCCEEEccc------eecCCCEEEEECC---CCeEeCC
Confidence 34443 44 666666654 6799999999863 3456665
No 98
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.28 E-value=3.4e+02 Score=21.36 Aligned_cols=51 Identities=12% Similarity=0.105 Sum_probs=24.8
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEe----eCCCEEEEecCCCCCCcceEEccCCc
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVG----VEGDRVTYFKPRNGDSCHTVVVPKGH 116 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~----~~Gd~v~~~~~~~~~~~~~~~vp~~~ 116 (160)
-+++||.|...... ++-.+--.-.| -.||.|.++|......-......+|.
T Consensus 202 lV~rG~~V~Iva~~-gg~~i~~~G~AL~~G~~Gd~IrVrN~~SgkvV~a~V~~~g~ 256 (261)
T PRK06804 202 LVERGQHVLMIAAQ-DGIEAQTLGIAQKNGRKGELIKVKNLSSGRVVTATVDGSGR 256 (261)
T ss_pred EEecCCEEEEEEec-CCEEEEEEEEEccCCCCCCEEEEEECCCCCEEEEEEecCCE
Confidence 35677777766532 22222223333 35788888764433333333333343
No 99
>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=25.09 E-value=93 Score=20.35 Aligned_cols=74 Identities=16% Similarity=0.157 Sum_probs=37.7
Q ss_pred CCCCCcEEEEeeCCC--CCceEEEEEEeeCCC---EEEEec-----CCCCCCcceEEccCCcEEEEcCCCCCCCCCCccc
Q 031410 65 RLGPGDIVFVRSPVD--PNKIVTKRIVGVEGD---RVTYFK-----PRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFG 134 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~--~~~~~iKRVv~~~Gd---~v~~~~-----~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G 134 (160)
.++.||.|.+..+.+ ...+++-||..+-.+ ...+.- +............+++.|...+. .
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~----------~ 72 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHL----------D 72 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCc----------c
Confidence 456778777776543 356777777765432 111110 00000000012344566664332 2
Q ss_pred ceeCCCeEEEEEEE
Q 031410 135 PVPYGLIEGKAFFR 148 (160)
Q Consensus 135 ~V~~~~I~G~v~~~ 148 (160)
-++.+.|.|++.-.
T Consensus 73 ~i~v~~I~gkc~V~ 86 (123)
T cd04370 73 EIPVESIIGKCKVL 86 (123)
T ss_pred ccCHHHhccccEEE
Confidence 67778888888665
No 100
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=23.86 E-value=2e+02 Score=18.55 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=16.4
Q ss_pred CCCCCCCcEEEEeeCCCCCceEEEEEEeeCC
Q 031410 63 VGRLGPGDIVFVRSPVDPNKIVTKRIVGVEG 93 (160)
Q Consensus 63 ~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~G 93 (160)
...|++||.|.+. +..+.++++.--.|
T Consensus 63 ~~~P~~gd~v~~d----G~~y~V~~~~~~~G 89 (95)
T PF13856_consen 63 YPKPRRGDRVVID----GESYTVTRFQEEDG 89 (95)
T ss_dssp -----TT-EEEET----TEEEEEEEEEEETT
T ss_pred CCCCCCCCEEEEC----CeEEEEeEEecCCC
Confidence 3459999999886 56788888776554
No 101
>CHL00010 infA translation initiation factor 1
Probab=23.79 E-value=1.2e+02 Score=19.12 Aligned_cols=12 Identities=50% Similarity=0.595 Sum_probs=9.4
Q ss_pred CCCCCcEEEEee
Q 031410 65 RLGPGDIVFVRS 76 (160)
Q Consensus 65 ~~~~GDiVvf~~ 76 (160)
.+..||.|.|+.
T Consensus 46 ~~~vGD~V~ve~ 57 (78)
T CHL00010 46 RILPGDRVKVEL 57 (78)
T ss_pred ccCCCCEEEEEE
Confidence 367899999984
No 102
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.55 E-value=3.5e+02 Score=22.12 Aligned_cols=55 Identities=22% Similarity=0.301 Sum_probs=35.5
Q ss_pred CCCCCcEEEEeeCCCCCceEEEEEEee----CCCEEEEecCCCCCCcceEEccCCcEEEE
Q 031410 65 RLGPGDIVFVRSPVDPNKIVTKRIVGV----EGDRVTYFKPRNGDSCHTVVVPKGHVWIQ 120 (160)
Q Consensus 65 ~~~~GDiVvf~~p~~~~~~~iKRVv~~----~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~ 120 (160)
-+++||.|...... ++-.+.-+-.|+ .||.|.++|.............+|.+-+.
T Consensus 258 lV~rGd~V~i~~~~-ggl~v~~~G~ALe~G~~Gd~IrV~N~~S~kiv~g~V~g~g~V~V~ 316 (338)
T PRK12786 258 LVQRGQLVTLIYQT-PGIYLTARGKALEDGAEGDVVRVLNLQSKRTVTGTVTGRGQVSVD 316 (338)
T ss_pred EEcCCCEEEEEEEc-CCEEEEEEEEEccccCCCCEEEEEECCCCCEEEEEEecCCEEEEe
Confidence 46789988887643 333444444444 59999998765555555566677777665
No 103
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=23.20 E-value=77 Score=22.33 Aligned_cols=31 Identities=16% Similarity=0.115 Sum_probs=22.9
Q ss_pred eEEccCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410 109 TVVVPKGHVWIQGDNLYASRDSRQFGPVPYGL 140 (160)
Q Consensus 109 ~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~ 140 (160)
....-+|.+-++.++. +..-+|-+|||++|.
T Consensus 87 ~i~F~dNa~VLin~~~-~p~GTRI~GpV~~El 117 (132)
T PRK08571 87 RVKFEDNAAVIVTPEG-TPKGTEIKGPVAREA 117 (132)
T ss_pred EEEeCCcEEEEECCCC-CEeeeEEeccchHHH
Confidence 3344556777777664 677899999999987
No 104
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.85 E-value=2.9e+02 Score=20.73 Aligned_cols=32 Identities=38% Similarity=0.408 Sum_probs=25.1
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEEeeCCCE
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDR 95 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~ 95 (160)
.-+++||+|.-+...-....++-||.++.+..
T Consensus 60 ~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~ 91 (188)
T COG1096 60 PLPKGGDIVYGRVTDVREQRALVRIVGVEGKE 91 (188)
T ss_pred CCCCCCCEEEEEEeeccceEEEEEEEEEeccc
Confidence 46788899988877667778888888887743
No 105
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=22.62 E-value=2.1e+02 Score=17.95 Aligned_cols=36 Identities=25% Similarity=0.241 Sum_probs=20.4
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEE--------eeCCCEEEEe
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIV--------GVEGDRVTYF 99 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv--------~~~Gd~v~~~ 99 (160)
..++.||-+.+.++......-+|.+- |.+||++.+.
T Consensus 25 G~v~~gd~v~~~p~~~~~~~~V~si~~~~~~~~~a~~G~~v~l~ 68 (87)
T cd03697 25 GTIKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAEAGDNVGVL 68 (87)
T ss_pred CCCccCCEEEEeCCCCCceEEEEEEEECCcCCCEECCCCEEEEE
Confidence 56777777776543212233444443 5678877764
No 106
>KOG2915 consensus tRNA(1-methyladenosine) methyltransferase, subunit GCD14 [Translation, ribosomal structure and biogenesis]
Probab=22.42 E-value=1.4e+02 Score=24.02 Aligned_cols=15 Identities=33% Similarity=0.747 Sum_probs=11.6
Q ss_pred cccceeCCCeEEEEE
Q 031410 132 QFGPVPYGLIEGKAF 146 (160)
Q Consensus 132 ~~G~V~~~~I~G~v~ 146 (160)
.||.+|-++|+||-+
T Consensus 42 ~yGa~~h~~iIGK~~ 56 (314)
T KOG2915|consen 42 RYGALPHSDIIGKPY 56 (314)
T ss_pred cccccchhheecCCc
Confidence 478888888888754
No 107
>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=22.41 E-value=1.4e+02 Score=19.48 Aligned_cols=25 Identities=28% Similarity=0.417 Sum_probs=13.3
Q ss_pred CCcEEEEEecccCCCCCCCCcEEEEee
Q 031410 50 TGDVILAEYVSHRVGRLGPGDIVFVRS 76 (160)
Q Consensus 50 ~Gd~vlv~~~~~~~~~~~~GDiVvf~~ 76 (160)
.+|.+.-...- .++++.||+++|..
T Consensus 69 ~~D~i~~~~~l--P~~l~~GD~l~f~~ 93 (116)
T PF00278_consen 69 SGDVIARDVML--PKELEVGDWLVFEN 93 (116)
T ss_dssp TTSEEEEEEEE--ESTTTTT-EEEESS
T ss_pred CCceEeeeccC--CCCCCCCCEEEEec
Confidence 56666532211 12677777777775
No 108
>COG3764 SrtA Sortase (surface protein transpeptidase) [Cell envelope biogenesis, outer membrane]
Probab=22.32 E-value=2.6e+02 Score=21.31 Aligned_cols=36 Identities=25% Similarity=0.356 Sum_probs=21.4
Q ss_pred CCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEE
Q 031410 63 VGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTY 98 (160)
Q Consensus 63 ~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~ 98 (160)
..+++.||.|.+......-.+.+.-+.=+.-+.+++
T Consensus 132 L~~lk~GD~iyv~~~~~~~~Y~v~~~~~V~p~~v~~ 167 (210)
T COG3764 132 LGKLKVGDKIYVTTKNETYVYKVTDISIVDPDDVDV 167 (210)
T ss_pred hhhhcCCCEEEEEeCCcEEEEEEEEEEEeCcceeee
Confidence 457899999999986543344333333333444444
No 109
>PLN00208 translation initiation factor (eIF); Provisional
Probab=21.80 E-value=78 Score=22.70 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=8.4
Q ss_pred CCCCcEEEEeeC
Q 031410 66 LGPGDIVFVRSP 77 (160)
Q Consensus 66 ~~~GDiVvf~~p 77 (160)
+++||+|++...
T Consensus 71 I~~GD~VlVel~ 82 (145)
T PLN00208 71 IAAGDIILVGLR 82 (145)
T ss_pred ecCCCEEEEEcc
Confidence 677777777643
No 110
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=21.60 E-value=1.1e+02 Score=18.13 Aligned_cols=12 Identities=50% Similarity=0.595 Sum_probs=9.9
Q ss_pred CCCCCcEEEEee
Q 031410 65 RLGPGDIVFVRS 76 (160)
Q Consensus 65 ~~~~GDiVvf~~ 76 (160)
.+..||.|.++.
T Consensus 40 ~~~vGD~V~~~~ 51 (64)
T cd04451 40 RILPGDRVKVEL 51 (64)
T ss_pred ccCCCCEEEEEE
Confidence 478899999985
No 111
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=21.36 E-value=89 Score=23.07 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=20.6
Q ss_pred CcceEEccCCcEEEEcCCCCCCCCCCcc
Q 031410 106 SCHTVVVPKGHVWIQGDNLYASRDSRQF 133 (160)
Q Consensus 106 ~~~~~~vp~~~~~v~gdn~~~s~DSR~~ 133 (160)
.+-+++.++|..+-...+....+|.|||
T Consensus 95 pclEf~~~~~~~~r~~~~s~~yyD~rYW 122 (176)
T PLN02289 95 PCLEFELEHGFVYREHHRSPGYYDGRYW 122 (176)
T ss_pred eeeeeccCCceeEecCCCCCCcccCcee
Confidence 3456666777787777776778999987
No 112
>PF14900 DUF4493: Domain of unknown function (DUF4493)
Probab=21.34 E-value=2.4e+02 Score=21.33 Aligned_cols=27 Identities=26% Similarity=0.455 Sum_probs=21.7
Q ss_pred cceEEccCCcEEEE---cCCCCCCCCCCcc
Q 031410 107 CHTVVVPKGHVWIQ---GDNLYASRDSRQF 133 (160)
Q Consensus 107 ~~~~~vp~~~~~v~---gdn~~~s~DSR~~ 133 (160)
...+.+|.|.|-+. ||+...++|..||
T Consensus 57 ~~~i~L~~G~Ytv~A~~g~~~~~~~d~pyy 86 (235)
T PF14900_consen 57 GESIELPVGSYTVKASYGDNVAAGFDKPYY 86 (235)
T ss_pred cceEeecCCcEEEEEEcCCCccccccCcee
Confidence 36688899998777 7887778998887
No 113
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=21.29 E-value=2.3e+02 Score=17.94 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=18.1
Q ss_pred CCCCCcEEEEeeCC-----CCCceEEEEEEeeCCC
Q 031410 65 RLGPGDIVFVRSPV-----DPNKIVTKRIVGVEGD 94 (160)
Q Consensus 65 ~~~~GDiVvf~~p~-----~~~~~~iKRVv~~~Gd 94 (160)
.++.||.|+++... ..+...+..|+-..|.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg 39 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG 39 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEecc
Confidence 56677777777543 1345677777765553
No 114
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=21.20 E-value=82 Score=22.86 Aligned_cols=11 Identities=36% Similarity=0.670 Sum_probs=7.1
Q ss_pred CCCCcEEEEee
Q 031410 66 LGPGDIVFVRS 76 (160)
Q Consensus 66 ~~~GDiVvf~~ 76 (160)
+..||+|++..
T Consensus 71 I~~GD~VlVel 81 (155)
T PTZ00329 71 INIGDIILVSL 81 (155)
T ss_pred ecCCCEEEEec
Confidence 56666666664
No 115
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=21.09 E-value=95 Score=24.92 Aligned_cols=26 Identities=15% Similarity=0.314 Sum_probs=21.4
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEEe
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIVG 90 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv~ 90 (160)
.++++||.|+...+. .++++|.+|.+
T Consensus 71 neI~KGDlvi~y~k~-~r~y~IGkVts 96 (318)
T COG4127 71 NEIQKGDLVITYSKS-NRTYLIGKVTS 96 (318)
T ss_pred HHhccCcEEEeeccc-CceEEEEEecC
Confidence 489999999988765 57789998876
No 116
>COG5547 Small integral membrane protein [Function unknown]
Probab=20.37 E-value=1.6e+02 Score=17.75 Aligned_cols=14 Identities=7% Similarity=-0.081 Sum_probs=6.0
Q ss_pred ChhhhHHHHHHHHH
Q 031410 1 MRRWGLLAKEALTQ 14 (160)
Q Consensus 1 m~~~~~~~~~~~~~ 14 (160)
|.+.++....++.-
T Consensus 1 meflk~fkypIIgg 14 (62)
T COG5547 1 MEFLKKFKYPIIGG 14 (62)
T ss_pred CcHHHHhccchHHH
Confidence 44444444444433
No 117
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=20.26 E-value=2.4e+02 Score=17.83 Aligned_cols=34 Identities=26% Similarity=0.344 Sum_probs=23.3
Q ss_pred CCCCCCcEEEEeeCCCCCceEEEEEE--------eeCCCEEEEe
Q 031410 64 GRLGPGDIVFVRSPVDPNKIVTKRIV--------GVEGDRVTYF 99 (160)
Q Consensus 64 ~~~~~GDiVvf~~p~~~~~~~iKRVv--------~~~Gd~v~~~ 99 (160)
+.++.||-+.+-+. ....-+|.+- |.+||.+.+.
T Consensus 29 G~i~~gd~v~i~P~--~~~~~V~sI~~~~~~~~~a~aG~~v~i~ 70 (91)
T cd03693 29 GVLKPGMVVTFAPA--GVTGEVKSVEMHHEPLEEALPGDNVGFN 70 (91)
T ss_pred ceeecCCEEEECCC--CcEEEEEEEEECCcCcCEECCCCEEEEE
Confidence 57788888877742 2345666665 7788888775
No 118
>PF15428 Imm14: Immunity protein 14
Probab=20.03 E-value=1.7e+02 Score=19.78 Aligned_cols=22 Identities=32% Similarity=0.510 Sum_probs=16.2
Q ss_pred CCCcEEEEeeCCCCCceEEEEEEe
Q 031410 67 GPGDIVFVRSPVDPNKIVTKRIVG 90 (160)
Q Consensus 67 ~~GDiVvf~~p~~~~~~~iKRVv~ 90 (160)
|.|||..+..+ .+.+...||++
T Consensus 1 K~GDIF~ipL~--~~~y~~G~Vi~ 22 (129)
T PF15428_consen 1 KPGDIFCIPLD--DGKYGFGRVIG 22 (129)
T ss_pred CCceEEEEEcC--CCCEEEEEEEe
Confidence 57888888864 45778888883
Done!