Query 028679
Match_columns 205
No_of_seqs 183 out of 1288
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 15:17:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028679.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028679hhsearch_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 4.5E-35 9.7E-40 237.4 15.1 130 36-171 6-163 (163)
2 KOG0171 Mitochondrial inner me 100.0 3.8E-35 8.1E-40 235.5 10.9 141 35-180 18-168 (176)
3 KOG1568 Mitochondrial inner me 100.0 6.7E-35 1.4E-39 233.7 12.2 155 6-179 1-160 (174)
4 PRK10861 signal peptidase I; P 100.0 7.1E-31 1.5E-35 233.1 14.9 129 38-171 70-305 (324)
5 TIGR02754 sod_Ni_protease nick 99.9 2.6E-21 5.5E-26 141.7 10.1 89 54-165 2-90 (90)
6 PRK13838 conjugal transfer pil 99.9 2.3E-21 5E-26 159.4 10.4 92 71-168 39-173 (176)
7 TIGR02771 TraF_Ti conjugative 99.9 7.7E-21 1.7E-25 155.6 13.2 102 50-167 24-169 (171)
8 PF10502 Peptidase_S26: Signal 99.8 4.4E-22 9.5E-27 157.7 3.1 82 82-167 20-137 (138)
9 PRK13884 conjugal transfer pep 99.8 6.5E-20 1.4E-24 151.0 12.1 103 49-167 28-176 (178)
10 cd06530 S26_SPase_I The S26 Ty 99.8 2.2E-19 4.7E-24 129.7 9.3 84 52-163 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.6 6.1E-15 1.3E-19 119.4 11.6 86 54-165 35-120 (158)
12 COG4959 TraF Type IV secretory 99.5 7.5E-15 1.6E-19 117.3 4.5 82 82-167 52-169 (173)
13 COG0681 LepB Signal peptidase 99.4 4E-12 8.7E-17 101.4 10.5 122 38-163 17-144 (166)
14 PF00717 Peptidase_S24: Peptid 99.3 2.5E-11 5.4E-16 84.0 7.7 57 54-117 1-57 (70)
15 cd06462 Peptidase_S24_S26 The 99.2 1.5E-10 3.3E-15 82.0 9.2 83 52-163 2-84 (84)
16 COG2932 Predicted transcriptio 98.9 1.3E-08 2.7E-13 85.6 10.9 90 51-170 124-213 (214)
17 cd06529 S24_LexA-like Peptidas 98.9 1.7E-08 3.6E-13 71.3 9.1 62 52-139 2-63 (81)
18 KOG3342 Signal peptidase I [In 98.8 8.8E-09 1.9E-13 82.6 5.6 91 50-165 48-145 (180)
19 PRK10276 DNA polymerase V subu 98.7 1.7E-07 3.7E-12 74.0 11.2 87 49-169 50-137 (139)
20 PRK00215 LexA repressor; Valid 98.6 3.8E-07 8.1E-12 75.9 11.4 89 47-169 115-204 (205)
21 TIGR00498 lexA SOS regulatory 98.6 4.5E-07 9.9E-12 75.1 11.7 89 48-170 109-198 (199)
22 PRK12423 LexA repressor; Provi 98.5 9.2E-07 2E-11 73.9 11.1 87 50-169 114-201 (202)
23 COG1974 LexA SOS-response tran 97.8 0.00036 7.8E-09 58.8 12.0 89 49-170 111-200 (201)
24 PRK00364 groES co-chaperonin G 81.8 12 0.00027 27.6 7.8 92 64-163 3-94 (95)
25 PRK14533 groES co-chaperonin G 76.6 21 0.00045 26.3 7.5 86 64-163 3-89 (91)
26 COG0234 GroS Co-chaperonin Gro 74.1 18 0.00039 27.1 6.6 73 64-137 3-88 (96)
27 PTZ00414 10 kDa heat shock pro 72.2 34 0.00073 25.7 7.8 43 62-109 10-52 (100)
28 TIGR02594 conserved hypothetic 72.0 18 0.00039 28.2 6.6 55 82-161 72-126 (129)
29 COG0681 LepB Signal peptidase 70.4 5.6 0.00012 31.0 3.5 13 83-95 84-96 (166)
30 COG0093 RplN Ribosomal protein 68.7 51 0.0011 25.6 8.2 87 50-158 19-106 (122)
31 cd04714 BAH_BAHCC1 BAH, or Bro 65.7 14 0.0003 28.3 4.7 28 83-110 3-30 (121)
32 cd00320 cpn10 Chaperonin 10 Kd 64.2 54 0.0012 24.0 8.1 91 64-162 2-92 (93)
33 PF00166 Cpn10: Chaperonin 10 63.3 21 0.00045 26.0 5.1 91 65-163 3-93 (93)
34 cd04717 BAH_polybromo BAH, or 59.4 20 0.00044 27.1 4.6 28 83-110 3-30 (121)
35 PF00238 Ribosomal_L14: Riboso 58.7 47 0.001 25.7 6.5 88 49-157 18-105 (122)
36 CHL00057 rpl14 ribosomal prote 57.3 89 0.0019 24.3 7.9 86 49-158 18-106 (122)
37 TIGR01067 rplN_bact ribosomal 55.4 94 0.002 24.1 7.7 89 49-158 18-106 (122)
38 PF05257 CHAP: CHAP domain; I 51.8 40 0.00086 25.2 5.1 38 81-118 60-98 (124)
39 PF05382 Amidase_5: Bacterioph 43.9 86 0.0019 25.1 6.0 80 6-95 7-87 (145)
40 KOG3265 Histone chaperone invo 43.7 32 0.00069 29.8 3.7 66 126-202 65-138 (250)
41 PF10000 ACT_3: ACT domain; I 42.7 15 0.00033 25.8 1.4 18 58-76 12-29 (72)
42 COG1097 RRP4 RNA-binding prote 42.0 51 0.0011 28.6 4.8 77 56-139 105-195 (239)
43 cd04721 BAH_plant_1 BAH, or Br 40.6 73 0.0016 24.7 5.1 28 82-111 6-33 (130)
44 COG3602 Uncharacterized protei 39.7 18 0.0004 28.1 1.5 17 58-75 12-28 (134)
45 PRK05483 rplN 50S ribosomal pr 39.6 1.8E+02 0.0039 22.6 7.9 88 50-158 19-106 (122)
46 PF07039 DUF1325: SGF29 tudor- 39.6 92 0.002 24.2 5.5 52 85-136 1-60 (130)
47 cd04709 BAH_MTA BAH, or Bromo 39.4 1.1E+02 0.0023 25.0 6.1 24 146-169 85-108 (164)
48 PTZ00054 60S ribosomal protein 39.4 1.8E+02 0.0038 23.2 7.1 86 49-158 35-124 (139)
49 PF01426 BAH: BAH domain; Int 38.6 44 0.00096 24.4 3.5 27 84-110 3-29 (119)
50 cd04760 BAH_Dnmt1_I BAH, or Br 36.6 98 0.0021 24.1 5.2 79 83-171 3-87 (124)
51 COG1188 Ribosome-associated he 32.8 1E+02 0.0022 23.3 4.5 49 59-111 25-73 (100)
52 cd05792 S1_eIF1AD_like S1_eIF1 32.0 1E+02 0.0022 22.1 4.2 44 49-94 3-49 (78)
53 smart00002 PLP Myelin proteoli 31.7 12 0.00026 25.7 -0.6 19 145-163 23-41 (60)
54 TIGR03673 rpl14p_arch 50S ribo 31.7 2.6E+02 0.0056 22.0 7.8 29 125-158 88-116 (131)
55 smart00439 BAH Bromo adjacent 31.6 83 0.0018 22.8 4.0 17 153-169 70-86 (120)
56 PF01176 eIF-1a: Translation i 31.0 52 0.0011 22.3 2.5 46 49-94 6-52 (65)
57 cd04456 S1_IF1A_like S1_IF1A_l 30.1 54 0.0012 23.3 2.6 45 50-94 4-49 (78)
58 PRK08571 rpl14p 50S ribosomal 27.4 3.1E+02 0.0067 21.6 7.5 28 126-158 90-117 (132)
59 TIGR00008 infA translation ini 27.1 69 0.0015 22.4 2.6 19 68-90 48-66 (68)
60 PF10377 ATG11: Autophagy-rela 26.9 3E+02 0.0065 21.3 6.6 34 99-133 89-122 (129)
61 COG0361 InfA Translation initi 26.8 69 0.0015 22.9 2.6 19 68-90 50-68 (75)
62 smart00652 eIF1a eukaryotic tr 25.6 68 0.0015 23.1 2.5 47 48-94 7-54 (83)
63 cd05793 S1_IF1A S1_IF1A: Trans 25.3 69 0.0015 22.7 2.4 10 84-93 39-48 (77)
64 PF15057 DUF4537: Domain of un 24.8 1E+02 0.0022 23.7 3.5 27 82-108 54-80 (124)
65 PF14085 DUF4265: Domain of un 24.8 2.7E+02 0.0059 21.0 5.8 34 81-116 23-57 (117)
66 cd06555 ASCH_PF0470_like ASC-1 24.4 2E+02 0.0043 21.8 4.9 28 81-109 29-56 (109)
67 PTZ00320 ribosomal protein L14 24.2 3.1E+02 0.0067 22.9 6.3 29 125-158 144-172 (188)
68 PF06890 Phage_Mu_Gp45: Bacter 22.0 4.4E+02 0.0094 21.4 7.8 37 80-118 71-110 (162)
69 cd04370 BAH BAH, or Bromo Adja 21.6 2E+02 0.0043 20.7 4.5 28 83-110 3-32 (123)
70 cd04712 BAH_DCM_I BAH, or Brom 21.1 1.3E+02 0.0028 23.3 3.4 29 82-110 4-42 (130)
71 KOG4146 Ubiquitin-like protein 21.1 1.5E+02 0.0032 22.2 3.5 37 53-94 56-96 (101)
72 cd04720 BAH_Orc1p_Yeast BAH, o 20.2 2E+02 0.0043 23.5 4.6 37 71-110 42-78 (179)
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=4.5e-35 Score=237.36 Aligned_cols=130 Identities=28% Similarity=0.481 Sum_probs=115.2
Q ss_pred HHHHHHHHHhhceeEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEE
Q 028679 36 LRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV 115 (205)
Q Consensus 36 i~~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~ 115 (205)
+.++++..++..++++.+.|+|+||+|||+ .||+++++|+.+ ...++++||+|+|+.|.+.++.++|||+|+|||+|+
T Consensus 6 ~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~-~Gd~vlv~k~~~-~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~ 83 (163)
T TIGR02227 6 LIAILLALLIRTFVFFPYKIPGGSMEPTLK-EGDRILVNKFAY-GTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVE 83 (163)
T ss_pred HHHHHHHHHHHhhEEEEEEECCcccccchh-CCCEEEEEEeEc-CCCCCCCCcEEEEecCCCCCceeEEEEEecCCCEEE
Confidence 345666778889999999999999999999 799999999866 247899999999999887788999999999999999
Q ss_pred ecCCC----------------------------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEE
Q 028679 116 STDEK----------------------------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL 167 (205)
Q Consensus 116 ~~~~~----------------------------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~ 167 (205)
++++. ..+.+||+|+|||+|||+. +|+|||+||+||+++|+|||.+++
T Consensus 84 i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~----~S~DSR~~G~V~~~~I~Gk~~~~~ 159 (163)
T TIGR02227 84 FRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRD----NSLDSRYFGFVPIDDIIGKVSFVF 159 (163)
T ss_pred EECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCC----CCcccCCcCcCCHHHeEEEEEEEE
Confidence 86530 1236899999999999998 999999999999999999999999
Q ss_pred ecCC
Q 028679 168 RTAV 171 (205)
Q Consensus 168 ~p~~ 171 (205)
||++
T Consensus 160 ~p~~ 163 (163)
T TIGR02227 160 YPFD 163 (163)
T ss_pred CCCC
Confidence 9974
No 2
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.8e-35 Score=235.48 Aligned_cols=141 Identities=26% Similarity=0.409 Sum_probs=126.1
Q ss_pred HHHHHHHHHHhhceeEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceE
Q 028679 35 ELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEM 114 (205)
Q Consensus 35 ~i~~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V 114 (205)
+++..+|.+++..|+.++..++|.||+||+++.||+++.+|+++ .++++++||||+++.|.++++.+||||+|+|||.|
T Consensus 18 ~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~-~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v 96 (176)
T KOG0171|consen 18 EIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSY-RFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDLV 96 (176)
T ss_pred HHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhH-hhcCCCCCCEEEEeCCCCchhhhhheeeccCCceE
Confidence 35667788999999999999999999999997788888899988 47889999999999999999999999999999988
Q ss_pred EecCCC----------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCCCCCCccCCC
Q 028679 115 VSTDEK----------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180 (205)
Q Consensus 115 ~~~~~~----------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~~~g~~~~~~ 180 (205)
.+.++. ..+..||.||+||+|||+. +|+|||+|||+|.+.|+||+++++||+++++...-+.
T Consensus 97 ~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~----nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~~~~ 168 (176)
T KOG0171|consen 97 EVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRN----NSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLILHW 168 (176)
T ss_pred EEecCCcccchhhhhccceeeccCceEEEecCCCC----CcccccccCCCchhheeeeEEEEecCchhcceeeecc
Confidence 776542 2347999999999999999 9999999999999999999999999999998876443
No 3
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.7e-35 Score=233.66 Aligned_cols=155 Identities=39% Similarity=0.621 Sum_probs=138.5
Q ss_pred hHHHHhhccceeEEEEeeecccCCccchHHHHHHHHHHHhhceeEEEEEecCCCcccccccC-----CcEEEEEecCCCC
Q 028679 6 TWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGL-----GGTLLVRKLPAAD 80 (205)
Q Consensus 6 ~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~-----GD~Vlv~k~~~~~ 80 (205)
.|+++++.+|++++..+.+....- -|...++.+..|.|.||.||++|. .|+||+.|+....
T Consensus 1 ~~~~~~~~~~~ksl~~s~~~~v~~--------------t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n 66 (174)
T KOG1568|consen 1 MWRRYIFKVFEKSLTGSLKWHVLL--------------TFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKN 66 (174)
T ss_pred CHHHHHHHHHHhceeeeeeeheee--------------eeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeecccc
Confidence 489999999999988887764322 255668999999999999999983 3999999997533
Q ss_pred CCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEE
Q 028679 81 PKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIV 160 (205)
Q Consensus 81 ~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~Ii 160 (205)
..+.+||+|+|..|.++++++||||+|++||+|...+...+.+.||+|||||+|||.. +|+|||.||||+...|.
T Consensus 67 -~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~----hs~DSntFGPVS~gli~ 141 (174)
T KOG1568|consen 67 -RKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQK----HSYDSNTFGPVSTGLIV 141 (174)
T ss_pred -ceeccCCEEEEeCCCChhheeeeeeecccccEeccCCCCCCceecCCCcEEEecCCcc----cccccCccCCcchhhee
Confidence 5689999999999999999999999999999999988888999999999999999998 99999999999999999
Q ss_pred EEEEEEEecCCCCCCccCC
Q 028679 161 GRAIYCLRTAVDHGPVQNS 179 (205)
Q Consensus 161 Gkv~~~~~p~~~~g~~~~~ 179 (205)
|||++++||+.|++++.++
T Consensus 142 grai~ilwpP~R~~~~~~~ 160 (174)
T KOG1568|consen 142 GRAIYILWPPVRWQRLDKE 160 (174)
T ss_pred eeEEEEEcChHHhhhhccc
Confidence 9999999999999988754
No 4
>PRK10861 signal peptidase I; Provisional
Probab=99.97 E-value=7.1e-31 Score=233.15 Aligned_cols=129 Identities=22% Similarity=0.326 Sum_probs=112.4
Q ss_pred HHHHHHHhhceeEEEEEecCCCcccccccCCcEEEEEecCCCC-----------CCCCccCeEEEEecCCCCCceEEEEE
Q 028679 38 DSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAAD-----------PKRVSVGDVVVMKDPEKSDNYIVRRL 106 (205)
Q Consensus 38 ~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~-----------~~~~~rGDIVvf~~P~~~~~~~VKRV 106 (205)
.++++.++..++++.+.|+|.||+|||. .||+|+++|++|.. ...++|||||+|+.|.+++..+||||
T Consensus 70 ~l~i~~~ir~fv~~~~~Ips~SM~PTL~-~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~~~~~yIKRV 148 (324)
T PRK10861 70 VLAIVLIVRSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDPKLDYIKRV 148 (324)
T ss_pred HHhHHHHHHhhEEEEEEECCCcCcCccc-CCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCCCCCcEEEEe
Confidence 3455567789999999999999999999 79999999998731 25799999999999998888999999
Q ss_pred EEecCceEEec--------CCC----------------------------------------------------------
Q 028679 107 AAIEGYEMVST--------DEK---------------------------------------------------------- 120 (205)
Q Consensus 107 ialpGd~V~~~--------~~~---------------------------------------------------------- 120 (205)
+|+|||+|+++ |+.
T Consensus 149 IGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (324)
T PRK10861 149 VGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENGIRLSERK 228 (324)
T ss_pred eecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccccccccccccccccccccceeEE
Confidence 99999999974 110
Q ss_pred ------------------------------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679 121 ------------------------------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA 170 (205)
Q Consensus 121 ------------------------------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~ 170 (205)
..+++||+|+||++|||+. +|+||||||+||.++|+|||.++++++
T Consensus 229 E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~----~S~DSRy~G~Vp~~~i~G~a~~i~~s~ 304 (324)
T PRK10861 229 ETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRD----NSADSRYWGFVPEANLVGKATAIWMSF 304 (324)
T ss_pred EecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCC----CCcccCcccccCHHHcEEEEEEEEEEc
Confidence 0123899999999999999 999999999999999999999999997
Q ss_pred C
Q 028679 171 V 171 (205)
Q Consensus 171 ~ 171 (205)
.
T Consensus 305 d 305 (324)
T PRK10861 305 E 305 (324)
T ss_pred C
Confidence 6
No 5
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.86 E-value=2.6e-21 Score=141.70 Aligned_cols=89 Identities=29% Similarity=0.561 Sum_probs=77.4
Q ss_pred EecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEE
Q 028679 54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV 133 (205)
Q Consensus 54 ~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~v 133 (205)
.|+|+||+|||+ +||+|++++... ....+++||+|+|+.|.+++..++||+++++ ++++|+
T Consensus 2 ~V~g~SM~P~l~-~GD~vlv~~~~~-~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~-----------------~~~~~l 62 (90)
T TIGR02754 2 KVTGVSMSPTLP-PGDRIIVVPWLK-IFRVPPIGNVVVVRHPLQPYGLIIKRLAAVD-----------------DNGLFL 62 (90)
T ss_pred EeeCCCccCccC-CCCEEEEEEccc-cCCCCCCCeEEEEecCCCCcceEEEEeeEEc-----------------CCeEEE
Confidence 689999999999 799999998532 1244567999999998866789999999984 468999
Q ss_pred EeCCCCCCCCCCCCCCccccccCCCEEEEEEE
Q 028679 134 LADNENMKPKEANDSRTFGPVPMRNIVGRAIY 165 (205)
Q Consensus 134 lGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~ 165 (205)
+|||+. .|.|||++|+|+..+|+|+|++
T Consensus 63 ~~dN~~----~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 63 LGDNPK----ASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred eCCCCC----CCCcccccCCCcHHHEEEEEEC
Confidence 999998 8999999999999999999863
No 6
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.86 E-value=2.3e-21 Score=159.37 Aligned_cols=92 Identities=26% Similarity=0.346 Sum_probs=73.4
Q ss_pred EEEEecCCCCCCCCccCeEEEEecCCCC-------------------CceEEEEEEEecCceEEecCC------------
Q 028679 71 LLVRKLPAADPKRVSVGDVVVMKDPEKS-------------------DNYIVRRLAAIEGYEMVSTDE------------ 119 (205)
Q Consensus 71 Vlv~k~~~~~~~~~~rGDIVvf~~P~~~-------------------~~~~VKRVialpGd~V~~~~~------------ 119 (205)
+.+.++.+ ...++++||+|+|+.|++. ...++|||+|+|||+|++.+.
T Consensus 39 ig~y~~~~-~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~~~ 117 (176)
T PRK13838 39 LGLWRIEA-LDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPSSS 117 (176)
T ss_pred EEEEEEec-cCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccccc
Confidence 55555433 2468999999999988643 135999999999999998631
Q ss_pred ------------CCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEe
Q 028679 120 ------------KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLR 168 (205)
Q Consensus 120 ------------~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~ 168 (205)
.....+||+|+|||+|||. +|+||||||+|+.++|+|+|.+++.
T Consensus 118 ~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-----~S~DSRy~G~V~~~~I~G~a~pi~t 173 (176)
T PRK13838 118 VRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-----GSYDSRYFGPVPASGLLGLARPVLT 173 (176)
T ss_pred cccccccCCcCCCCCccCcCCCeEEEECCCC-----CCCcccccCcccHHHeEEEEEEEEe
Confidence 0113479999999999985 7999999999999999999998753
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=99.85 E-value=7.7e-21 Score=155.63 Aligned_cols=102 Identities=22% Similarity=0.308 Sum_probs=79.9
Q ss_pred EEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCC-------------------ceEEEEEEEec
Q 028679 50 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSD-------------------NYIVRRLAAIE 110 (205)
Q Consensus 50 ~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~-------------------~~~VKRVialp 110 (205)
..+..-.++||-. |-+. +.+ ..+++|||+|+|+.|+++. ..++|||+|+|
T Consensus 24 ~~~~~N~T~S~P~-----g~Y~-~~~-----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglp 92 (171)
T TIGR02771 24 VGARINTTKSLPL-----GLYW-TTS-----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLP 92 (171)
T ss_pred eeEEEECCCCCcc-----eEEE-eCC-----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeC
Confidence 3444556677664 4444 322 2689999999999886432 27999999999
Q ss_pred CceEEecCC-------------------------CCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEE
Q 028679 111 GYEMVSTDE-------------------------KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIY 165 (205)
Q Consensus 111 Gd~V~~~~~-------------------------~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~ 165 (205)
||+|+++++ ...+.+||+| ||++|||+. +|+||||||+||.++|+|||.+
T Consensus 93 GD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~----~S~DSRy~G~V~~~~IiGk~~p 167 (171)
T TIGR02771 93 GDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSP----TSFDSRYFGPISREQVIGRVKP 167 (171)
T ss_pred CCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCC----CCCcccccceecHHHeEEEEEE
Confidence 999998653 0125789999 999999998 9999999999999999999998
Q ss_pred EE
Q 028679 166 CL 167 (205)
Q Consensus 166 ~~ 167 (205)
++
T Consensus 168 l~ 169 (171)
T TIGR02771 168 LF 169 (171)
T ss_pred eE
Confidence 65
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=99.84 E-value=4.4e-22 Score=157.65 Aligned_cols=82 Identities=33% Similarity=0.520 Sum_probs=32.5
Q ss_pred CCCccCeEEEEecCCC------------CCceEEEEEEEecCceEEecCC------------------------CCCcee
Q 028679 82 KRVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTDE------------------------KDEPFV 125 (205)
Q Consensus 82 ~~~~rGDIVvf~~P~~------------~~~~~VKRVialpGd~V~~~~~------------------------~~~~~~ 125 (205)
..+++||+|+|+.|.. .+..++|||+|+|||+|+++++ .....+
T Consensus 20 ~~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~ 99 (138)
T PF10502_consen 20 DKIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGT 99 (138)
T ss_dssp ---------------------------------------------------------------------S-T----TEEE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceE
Confidence 3489999999999873 2358999999999999998753 013579
Q ss_pred eeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEE
Q 028679 126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL 167 (205)
Q Consensus 126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~ 167 (205)
||+|+|||+|||+. +|+||||||+|+.++|+|+|.+++
T Consensus 100 vp~g~~~v~gd~~~----~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 100 VPEGEYFVLGDNRP----NSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp --TTEEEEE-SBTT----S--SHHHH--EEGGGEEEEEEEEE
T ss_pred eCCCEEEEecCCCC----CccccCEecccCHHHEEEEEEEEE
Confidence 99999999999998 999999999999999999999886
No 9
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.83 E-value=6.5e-20 Score=151.01 Aligned_cols=103 Identities=19% Similarity=0.293 Sum_probs=79.2
Q ss_pred eEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCC-------------------CceEEEEEEEe
Q 028679 49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKS-------------------DNYIVRRLAAI 109 (205)
Q Consensus 49 ~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~-------------------~~~~VKRVial 109 (205)
...+....++||-..+. .+ .. .++++||+|+|++|+.. ..+++|||+|+
T Consensus 28 ~~~~~~N~T~S~P~glY-----~~-~~------~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~ 95 (178)
T PRK13884 28 AAGARVNTTKSIPVGLY-----WT-SS------APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAA 95 (178)
T ss_pred hCcEEEECCCCCcceEE-----EE-eC------CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEee
Confidence 34455555666653333 32 21 47999999999987631 13799999999
Q ss_pred cCceEEecCC---------------------C------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEE
Q 028679 110 EGYEMVSTDE---------------------K------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGR 162 (205)
Q Consensus 110 pGd~V~~~~~---------------------~------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGk 162 (205)
|||+|++.++ . ...++||+|+||++|||+. +|+||||||+|+.++|+|+
T Consensus 96 pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~----~S~DSRYfG~V~~~~I~G~ 171 (178)
T PRK13884 96 KGDAVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSA----TSFDGRYFGPINRSQIKTV 171 (178)
T ss_pred CCcEEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCC----CCCcccccCcccHHHEEEE
Confidence 9999998653 0 0124899999999999998 9999999999999999999
Q ss_pred EEEEE
Q 028679 163 AIYCL 167 (205)
Q Consensus 163 v~~~~ 167 (205)
+.+++
T Consensus 172 ~~Pl~ 176 (178)
T PRK13884 172 IRPVI 176 (178)
T ss_pred EEEeE
Confidence 99875
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=99.80 E-value=2.2e-19 Score=129.74 Aligned_cols=84 Identities=38% Similarity=0.600 Sum_probs=74.7
Q ss_pred EEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeE
Q 028679 52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 131 (205)
Q Consensus 52 i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~ 131 (205)
++.|.|+||+|++. .||++++++... ....+++||+|+|+.|...+..++|||++ |
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~v~~~~~-~~~~~~~GDiv~~~~~~~~~~~~vkRv~~----------------------~ 57 (85)
T cd06530 2 PVVVPGGSMEPTLQ-PGDLVLVNKLSY-GFREPKRGDVVVFKSPGDPGKPIIKRVIG----------------------Y 57 (85)
T ss_pred eeEEcCCCCcCccc-CCCEEEEEEeec-ccCCCCCCCEEEEeCCCCCCCEEEEEEEE----------------------E
Confidence 68899999999999 799999998642 12379999999999987656799999998 8
Q ss_pred EEEeCCCCCCCCCCCCCCccccccCCCEEEEE
Q 028679 132 WVLADNENMKPKEANDSRTFGPVPMRNIVGRA 163 (205)
Q Consensus 132 ~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv 163 (205)
|+.|||+. +|.|||+||+++.++|+|++
T Consensus 58 ~~~gDn~~----ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 58 FVLGDNRN----NSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred EEeeCCCC----CCCccCCcCCCcHHHeEEeC
Confidence 99999987 89999999999999999985
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=99.61 E-value=6.1e-15 Score=119.42 Aligned_cols=86 Identities=27% Similarity=0.402 Sum_probs=69.9
Q ss_pred EecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEE
Q 028679 54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV 133 (205)
Q Consensus 54 ~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~v 133 (205)
.|.|+||+||++ .||++++++.. ..++++||+|+|+.|+.+ +.++|||+++.++ + .+..++.
T Consensus 35 ~V~g~SM~Ptl~-~GD~vlv~~~~---~~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~-----~--------g~~~~~t 96 (158)
T TIGR02228 35 VVLSGSMEPTFN-TGDLILVTGAD---PNDIQVGDVITYKSPGFN-TPVTHRVIEINNS-----G--------GELGFIT 96 (158)
T ss_pred EEcCCCCcCCcc-CCCEEEEEecc---cCCCCCCCEEEEEECCCC-ccEEEEEEEEECC-----C--------CcEEEEE
Confidence 399999999999 79999999853 368999999999998743 7899999999643 0 1123667
Q ss_pred EeCCCCCCCCCCCCCCccccccCCCEEEEEEE
Q 028679 134 LADNENMKPKEANDSRTFGPVPMRNIVGRAIY 165 (205)
Q Consensus 134 lGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~ 165 (205)
.|||+. ..| .++|+.++|+|++..
T Consensus 97 kGDnN~-----~~D---~~~v~~~~IiG~v~~ 120 (158)
T TIGR02228 97 KGDNNP-----APD---GEPVPSENVIGKYLG 120 (158)
T ss_pred EecCCC-----CCC---cccCCHHHEEEEEEE
Confidence 799985 556 689999999999984
No 12
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.52 E-value=7.5e-15 Score=117.32 Aligned_cols=82 Identities=27% Similarity=0.445 Sum_probs=68.4
Q ss_pred CCCccCeEEEEecCCC------------CCceEEEEEEEecCceEEecCC-------------------C-----CCcee
Q 028679 82 KRVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTDE-------------------K-----DEPFV 125 (205)
Q Consensus 82 ~~~~rGDIVvf~~P~~------------~~~~~VKRVialpGd~V~~~~~-------------------~-----~~~~~ 125 (205)
.++.+||+|++++|+. ...+++|||.|+|||+|++.++ . ...-.
T Consensus 52 ~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~ 131 (173)
T COG4959 52 APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRY 131 (173)
T ss_pred CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCce
Confidence 4579999999999884 2357899999999999997542 0 12235
Q ss_pred eeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEE
Q 028679 126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL 167 (205)
Q Consensus 126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~ 167 (205)
+-++++|+++|... .|+|||||||||.++|+|.+.+++
T Consensus 132 l~~~el~lL~~~~~----~SfDsRYfGpipas~vig~aRPvw 169 (173)
T COG4959 132 LAPSELLLLTDRSS----TSFDSRYFGPIPASQVIGVARPVW 169 (173)
T ss_pred ecCCeEEEEeccCC----cccccceecccCHHHcceeeeeee
Confidence 88899999999998 899999999999999999998765
No 13
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.38 E-value=4e-12 Score=101.39 Aligned_cols=122 Identities=19% Similarity=0.271 Sum_probs=89.1
Q ss_pred HHHHHHHh--hceeEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEE
Q 028679 38 DSVWKYLF--QGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV 115 (205)
Q Consensus 38 ~~~~~~~~--~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~ 115 (205)
+++++.++ +.++++++.|+|+||+|||+ .||+++++|.++. ...++.++++ ..|......++||+++.+||.|.
T Consensus 17 ~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~-~GD~v~v~k~~~~-~~~~~~~~~~--~~~~~~~~~~~kr~~~~~GD~i~ 92 (166)
T COG0681 17 AIILALIIGVRTFVFEPVVVPSGSMEPTLN-VGDRVLVKKFSYG-FGKLKVPDII--VLPAVVEGDLIKRVIGLRGDIVV 92 (166)
T ss_pred HHHHhheeeeEEEEEEEEEECCCccccccc-cCCEEEEEecccc-ccCCccceee--ecCCCCCcceEEEeccCCCCEEE
Confidence 44444555 68899999999999999999 7999999999873 5567888887 55555677899999999999999
Q ss_pred ecCCCCC-ceeeeCCeEEEEeCCCCC---CCCCCCCCCccccccCCCEEEEE
Q 028679 116 STDEKDE-PFVLDKDECWVLADNENM---KPKEANDSRTFGPVPMRNIVGRA 163 (205)
Q Consensus 116 ~~~~~~~-~~~vp~g~~~vlGDN~~~---~~~~S~DSR~~GpV~~~~IiGkv 163 (205)
..++... ...+|++..++.++|... ....+.+++.++.......+.++
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (166)
T COG0681 93 FKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV 144 (166)
T ss_pred EECCEEEeecccCcchhhhhcccccccccccccccCccccccccccccccce
Confidence 9875322 234455555555443310 00157777878777777777777
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=99.26 E-value=2.5e-11 Score=84.02 Aligned_cols=57 Identities=25% Similarity=0.365 Sum_probs=46.1
Q ss_pred EecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEec
Q 028679 54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVST 117 (205)
Q Consensus 54 ~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~ 117 (205)
+|.|+||+|+|+ +||+|++++. ..++.||+|+|..+... ..++||+.+.+|+.+.+.
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 7999999985 48999999999986532 489999999999877654
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=99.19 E-value=1.5e-10 Score=81.99 Aligned_cols=83 Identities=34% Similarity=0.547 Sum_probs=63.6
Q ss_pred EEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeE
Q 028679 52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 131 (205)
Q Consensus 52 i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~ 131 (205)
.+.|.|+||+|++. +||++++++.. ..++.||+|++..+. +..++||+...++ ++++
T Consensus 2 ~~~v~g~SM~P~i~-~gd~v~i~~~~----~~~~~G~iv~~~~~~--~~~~ikrl~~~~~----------------~~~~ 58 (84)
T cd06462 2 ALRVEGDSMEPTIP-DGDLVLVDKSS----YEPKRGDIVVFRLPG--GELTVKRVIGLPG----------------EGHY 58 (84)
T ss_pred eeEEcCCCccCccc-CCCEEEEEecC----CCCcCCEEEEEEcCC--CcEEEEEEEEECC----------------CCEE
Confidence 57899999999999 79999999852 248999999999864 4789999999863 3689
Q ss_pred EEEeCCCCCCCCCCCCCCccccccCCCEEEEE
Q 028679 132 WVLADNENMKPKEANDSRTFGPVPMRNIVGRA 163 (205)
Q Consensus 132 ~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv 163 (205)
++.+||+ ++.+.+..+. ....++|++
T Consensus 59 ~l~~~N~-----~~~~~~~~~~-~~~~i~g~v 84 (84)
T cd06462 59 FLLGDNP-----NSPDSRIDGP-PELDIVGVV 84 (84)
T ss_pred EEECCCC-----CCCcccccCC-CHHHEEEeC
Confidence 9999995 3555443332 455666653
No 16
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.91 E-value=1.3e-08 Score=85.58 Aligned_cols=90 Identities=23% Similarity=0.306 Sum_probs=64.6
Q ss_pred EEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCe
Q 028679 51 YLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDE 130 (205)
Q Consensus 51 ~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~ 130 (205)
....|.|+||+|++. +||.++|+.- .+..+||.|++..- .+..+|||+...+| |.
T Consensus 124 ~~i~V~GDSMeP~~~-~Gd~ilVd~~-----~~~~~gd~v~v~~~--g~~~~VK~l~~~~~-----------------~~ 178 (214)
T COG2932 124 FALRVTGDSMEPTYE-DGDTLLVDPG-----VNTRRGDRVYVETD--GGELYVKKLQREPG-----------------GL 178 (214)
T ss_pred EEEEEeCCccccccc-CCCEEEECCC-----CceeeCCEEEEEEe--CCeEEEEEEEEecC-----------------Ce
Confidence 678999999999999 7999999974 56778886655542 35789999999854 57
Q ss_pred EEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679 131 CWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA 170 (205)
Q Consensus 131 ~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~ 170 (205)
+.+..+|+. ..+...+-.=..=+|+|||++.....
T Consensus 179 ~~l~S~N~~-----~~~~~~~~~~~~v~iIgrVv~~~~~~ 213 (214)
T COG2932 179 LRLVSLNPD-----YYPDEIFSEDDDVEIIGRVVWVSRLL 213 (214)
T ss_pred EEEEeCCCC-----CCcccccCccceEEEEEEEEEEeeec
Confidence 778899986 22222221110135899999887653
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=98.88 E-value=1.7e-08 Score=71.33 Aligned_cols=62 Identities=29% Similarity=0.390 Sum_probs=52.1
Q ss_pred EEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeE
Q 028679 52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 131 (205)
Q Consensus 52 i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~ 131 (205)
.+.|.|+||+|+++ +||.+++++. ..++.||++++..+. ..++||+...++ +.+
T Consensus 2 ~~~v~g~sM~p~i~-~gd~lii~~~-----~~~~~g~i~~~~~~~---~~~ikr~~~~~~-----------------~~~ 55 (81)
T cd06529 2 ALRVKGDSMEPTIP-DGDLVLVDPS-----DTPRDGDIVVARLDG---ELTVKRLQRRGG-----------------GRL 55 (81)
T ss_pred EEEEECCCcCCccC-CCCEEEEcCC-----CCCCCCCEEEEEECC---EEEEEEEEECCC-----------------CcE
Confidence 57899999999999 7999999974 358999999999853 689999998853 467
Q ss_pred EEEeCCCC
Q 028679 132 WVLADNEN 139 (205)
Q Consensus 132 ~vlGDN~~ 139 (205)
++.++|+.
T Consensus 56 ~L~s~N~~ 63 (81)
T cd06529 56 RLISDNPA 63 (81)
T ss_pred EEEeCCCC
Confidence 78888864
No 18
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.79 E-value=8.8e-09 Score=82.58 Aligned_cols=91 Identities=23% Similarity=0.299 Sum_probs=68.5
Q ss_pred EEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCC
Q 028679 50 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKD 129 (205)
Q Consensus 50 ~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g 129 (205)
-.+..|-+.||+|.++ .||+++.... .....+.||||+|+.+. ...+++|||+.+-+. .+|
T Consensus 48 SPiVVVLSgSMePaF~-RGDlLfL~N~---~~~p~~vGdivVf~veg-R~IPiVHRviK~he~--------------~~~ 108 (180)
T KOG3342|consen 48 SPIVVVLSGSMEPAFH-RGDLLFLTNR---NEDPIRVGDIVVFKVEG-REIPIVHRVIKQHEK--------------SNG 108 (180)
T ss_pred CCEEEEEcCCcCcccc-cccEEEEecC---CCCcceeccEEEEEECC-ccCchhHHHHHHhcc--------------cCC
Confidence 3588999999999999 8999998854 24678999999999865 357899999998642 334
Q ss_pred eE--EEEeCCCCCCCCCCCCCCc-c----ccccCCCEEEEEEE
Q 028679 130 EC--WVLADNENMKPKEANDSRT-F----GPVPMRNIVGRAIY 165 (205)
Q Consensus 130 ~~--~vlGDN~~~~~~~S~DSR~-~----GpV~~~~IiGkv~~ 165 (205)
+. ..-|||+. .|-|. | -...++.|+|+|.-
T Consensus 109 ~~~~LTKGDNN~------~dD~~Ly~~gq~~L~r~~Ivg~~~G 145 (180)
T KOG3342|consen 109 HIKFLTKGDNNA------VDDRGLYAQGQNWLERKDIVGRVRG 145 (180)
T ss_pred cEEEEecCCCCc------ccchhcccccccceeccceeeEEee
Confidence 44 44499975 45442 1 23778999999864
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.73 E-value=1.7e-07 Score=73.98 Aligned_cols=87 Identities=20% Similarity=0.282 Sum_probs=61.6
Q ss_pred eEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeee
Q 028679 49 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD 127 (205)
Q Consensus 49 ~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp 127 (205)
-....+|.|+||. |++. +||++++++- .+++.||+|++.. .+...+||+...
T Consensus 50 ~~f~l~V~GdSM~~~~I~-~GD~liVd~~-----~~~~~Gdivv~~~---~g~~~vKrl~~~------------------ 102 (139)
T PRK10276 50 ATYFVKASGDSMIDAGIS-DGDLLIVDSA-----ITASHGDIVIAAV---DGEFTVKKLQLR------------------ 102 (139)
T ss_pred CEEEEEEecCCCCCCCCC-CCCEEEEECC-----CCCCCCCEEEEEE---CCEEEEEEEEEC------------------
Confidence 3567999999998 6899 8999999963 3578899999986 346789998742
Q ss_pred CCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEec
Q 028679 128 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT 169 (205)
Q Consensus 128 ~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p 169 (205)
+++++..+|+. +....+-.-..=.|+|+|++++..
T Consensus 103 -~~~~L~s~N~~------y~~i~i~~~~~~~IiG~V~~~~~~ 137 (139)
T PRK10276 103 -PTVQLIPMNSA------YSPITISSEDTLDVFGVVTHIVKA 137 (139)
T ss_pred -CcEEEEcCCCC------CCCEEcCCCCcEEEEEEEEEEEEe
Confidence 24677888875 111111111122799999988764
No 20
>PRK00215 LexA repressor; Validated
Probab=98.65 E-value=3.8e-07 Score=75.94 Aligned_cols=89 Identities=21% Similarity=0.260 Sum_probs=65.1
Q ss_pred ceeEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCcee
Q 028679 47 GKLTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFV 125 (205)
Q Consensus 47 ~~~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~ 125 (205)
..-+.+..|.|+||. |++. +||++++++- ..++.||+|++... +...+||+.-.
T Consensus 115 ~~~~~~~~V~GdSM~~~~i~-~Gd~v~v~~~-----~~~~~G~ivv~~~~---~~~~vKrl~~~---------------- 169 (205)
T PRK00215 115 PGEDFLLRVRGDSMIDAGIL-DGDLVIVRKQ-----QTARNGQIVVALID---DEATVKRFRRE---------------- 169 (205)
T ss_pred CCCeEEEEEccCCCCCCCcC-CCCEEEEeCC-----CCCCCCCEEEEEEC---CEEEEEEEEEe----------------
Confidence 345678999999995 7999 7999999963 45788999999874 36899999764
Q ss_pred eeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEec
Q 028679 126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT 169 (205)
Q Consensus 126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p 169 (205)
.|.+++..+|+. ++.....+= .-.|+|+|+..+..
T Consensus 170 --~~~~~L~s~Np~------y~~~~~~~~-~~~IiG~Vv~~~r~ 204 (205)
T PRK00215 170 --GGHIRLEPENPA------YEPIIVDPD-RVTIEGKVVGLIRN 204 (205)
T ss_pred --CCEEEEEcCCCC------CCCEEeCCC-cEEEEEEEEEEEEc
Confidence 246788888885 222211110 35799999987753
No 21
>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=98.64 E-value=4.5e-07 Score=75.10 Aligned_cols=89 Identities=19% Similarity=0.259 Sum_probs=66.0
Q ss_pred eeEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceee
Q 028679 48 KLTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVL 126 (205)
Q Consensus 48 ~~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~v 126 (205)
.-+.++.|.|+||. |++. +||++++++. ..++.||+|++.. .+...+||+.--
T Consensus 109 ~~~f~~~V~GdSM~~~~i~-~Gd~v~v~~~-----~~~~~G~ivvv~~---~~~~~vKrl~~~----------------- 162 (199)
T TIGR00498 109 SAVFLLKVMGDSMVDAGIC-DGDLLIVRSQ-----KDARNGEIVAAMI---DGEVTVKRFYKD----------------- 162 (199)
T ss_pred CCEEEEEecCCCCCCCCCC-CCCEEEEecC-----CCCCCCCEEEEEE---CCEEEEEEEEEE-----------------
Confidence 34678999999996 5899 7999999863 4788999999998 456899998753
Q ss_pred eCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679 127 DKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA 170 (205)
Q Consensus 127 p~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~ 170 (205)
.+.+++..+|+.++ ...... ..=.|+|+|+..++.+
T Consensus 163 -~~~i~L~s~N~~y~------~i~~~~-~~~~IiG~Vv~~~r~~ 198 (199)
T TIGR00498 163 -GTKVELKPENPEFD------PIVLNA-EDVTILGKVVGVIRNF 198 (199)
T ss_pred -CCEEEEEcCCCCCc------CCcCCC-CcEEEEEEEEEEEEec
Confidence 24788889998521 111100 1348999999988754
No 22
>PRK12423 LexA repressor; Provisional
Probab=98.55 E-value=9.2e-07 Score=73.95 Aligned_cols=87 Identities=22% Similarity=0.221 Sum_probs=64.1
Q ss_pred EEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679 50 TYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK 128 (205)
Q Consensus 50 ~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~ 128 (205)
.....|.|+||. |+|. +||+|++++- ..++.||+|++.. .+...+||+.-..
T Consensus 114 ~f~l~V~GdSM~~~~i~-~Gd~viv~~~-----~~~~~Gdivv~~~---~~~~~vKrl~~~~------------------ 166 (202)
T PRK12423 114 DYLLQVQGDSMIDDGIL-DGDLVGVHRS-----PEARDGQIVVARL---DGEVTIKRLERSG------------------ 166 (202)
T ss_pred cEEEEEecCcCCCCCcC-CCCEEEEeCC-----CcCCCCCEEEEEE---CCEEEEEEEEEeC------------------
Confidence 357899999997 7999 8999999963 4678899999987 3468899997542
Q ss_pred CeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEec
Q 028679 129 DECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT 169 (205)
Q Consensus 129 g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p 169 (205)
+.+++..+|+. ++...+-+-..-.|+|+|+.+++.
T Consensus 167 ~~~~L~s~N~~------y~~i~~~~~~~~~I~Gvv~g~~r~ 201 (202)
T PRK12423 167 DRIRLLPRNPA------YAPIVVAPDQDFAIEGVFCGLIRQ 201 (202)
T ss_pred CEEEEEcCCCC------CCCEEcCCCCcEEEEEEEEEEEEC
Confidence 46888889875 222222111134799999988764
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.84 E-value=0.00036 Score=58.75 Aligned_cols=89 Identities=19% Similarity=0.231 Sum_probs=67.5
Q ss_pred eEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeee
Q 028679 49 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD 127 (205)
Q Consensus 49 ~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp 127 (205)
-.++.+|.|+||. +.+. +||.|+|++- ..++.||+|+....+ ++..+||..--
T Consensus 111 ~~f~L~V~GdSM~~~gi~-dGDlvvV~~~-----~~a~~GdiVvA~i~g--~e~TvKrl~~~------------------ 164 (201)
T COG1974 111 ATFFLRVSGDSMIDAGIL-DGDLVVVDPT-----EDAENGDIVVALIDG--EEATVKRLYRD------------------ 164 (201)
T ss_pred ceEEEEecCCccccCcCC-CCCEEEEcCC-----CCCCCCCEEEEEcCC--CcEEEEEEEEe------------------
Confidence 5778999999996 4566 8999999974 688999999999865 55789998874
Q ss_pred CCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679 128 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA 170 (205)
Q Consensus 128 ~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~ 170 (205)
.+++++..-|+. +.+..+..- .-.|+|+++.++|+.
T Consensus 165 g~~i~L~p~Np~------~~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 165 GNQILLKPENPA------YPPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred CCEEEEEeCCCC------CCCcccCcc-ceEEEEEEEEEEecC
Confidence 247888888886 222222211 347999999999874
No 24
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=81.83 E-value=12 Score=27.57 Aligned_cols=92 Identities=12% Similarity=0.172 Sum_probs=49.9
Q ss_pred cccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCC
Q 028679 64 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPK 143 (205)
Q Consensus 64 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~ 143 (205)
|.|-||+||+.+.. ..+-..|-|++=.. ...+...-+|+|+.-. ....+|...+..+..|..-+..+.... .
T Consensus 3 i~Pl~drVLV~~~~---~e~~T~gGI~Lp~~--a~~k~~~G~VvaVG~G-~~~~~G~~~~~~vk~GD~Vlf~~~~g~--e 74 (95)
T PRK00364 3 LKPLGDRVLVKRLE---EEEKTAGGIVLPDS--AKEKPQEGEVVAVGPG-RRLDNGERVPLDVKVGDKVLFGKYAGT--E 74 (95)
T ss_pred ceEcCCEEEEEEcc---cCccccceEEcCcc--ccCCcceEEEEEECCC-eECCCCCEeecccCCCCEEEEcCCCCe--E
Confidence 56779999999863 24455666666221 1345667778887421 112233333444555554444443320 0
Q ss_pred CCCCCCccccccCCCEEEEE
Q 028679 144 EANDSRTFGPVPMRNIVGRA 163 (205)
Q Consensus 144 ~S~DSR~~GpV~~~~IiGkv 163 (205)
--+|...|=.++.++|+|++
T Consensus 75 v~~~~~~y~iv~~~DIlavi 94 (95)
T PRK00364 75 VKIDGEEYLILRESDILAIV 94 (95)
T ss_pred EEECCEEEEEEEHHHEEEEe
Confidence 12344556677777887764
No 25
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=76.64 E-value=21 Score=26.29 Aligned_cols=86 Identities=13% Similarity=0.259 Sum_probs=45.3
Q ss_pred cccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEec-CceEEecCCCCCceeeeCCeEEEEeCCCCCCC
Q 028679 64 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIE-GYEMVSTDEKDEPFVLDKDECWVLADNENMKP 142 (205)
Q Consensus 64 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialp-Gd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~ 142 (205)
|.|-||+||+.+.. ...-..|-|++=... ..+.....|+|+. |.. ..+..+..|.--+.++....
T Consensus 3 i~Pl~DRVLVk~~~---~e~~T~gGI~Lp~~a--~ek~~~G~VvavG~g~~-------~~~~~Vk~GD~Vl~~~y~g~-- 68 (91)
T PRK14533 3 VIPLGERLLIKPIK---EEKKTEGGIVLPDSA--KEKPMKAEVVAVGKLDD-------EEDFDIKVGDKVIFSKYAGT-- 68 (91)
T ss_pred ceEcCCEEEEEEcc---ccceecccEEecccc--cCCcceEEEEEECCCCc-------cccccccCCCEEEEccCCCe--
Confidence 55679999999863 234455666663322 2345566677663 321 12334445544444444320
Q ss_pred CCCCCCCccccccCCCEEEEE
Q 028679 143 KEANDSRTFGPVPMRNIVGRA 163 (205)
Q Consensus 143 ~~S~DSR~~GpV~~~~IiGkv 163 (205)
.--+|...|=.++.++|+|++
T Consensus 69 ev~~~~~~y~iv~e~DILa~i 89 (91)
T PRK14533 69 EIKIDDEDYIIIDVNDILAKI 89 (91)
T ss_pred EEEECCEEEEEEEhHhEEEEe
Confidence 012344445567777777764
No 26
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=74.07 E-value=18 Score=27.10 Aligned_cols=73 Identities=18% Similarity=0.314 Sum_probs=39.2
Q ss_pred cccCCcEEEEEecCCC------------CCCCCccCeEEEEecCC-CCCceEEEEEEEecCceEEecCCCCCceeeeCCe
Q 028679 64 MGGLGGTLLVRKLPAA------------DPKRVSVGDVVVMKDPE-KSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDE 130 (205)
Q Consensus 64 L~~~GD~Vlv~k~~~~------------~~~~~~rGDIVvf~~P~-~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~ 130 (205)
|.|-||+|++.+..-. .-.++++|.+|++-.-. ..+.-.+. .----||+|.+.......+++...+
T Consensus 3 ikPL~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~~~~g~~~~-~~VkvGD~Vlf~ky~G~evk~dgee 81 (96)
T COG0234 3 IKPLGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENGELVP-LDVKVGDRVLFGKYAGTEVKIDGEE 81 (96)
T ss_pred ceecCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEccceecCCCCEec-cccccCCEEEECccCCcEEEECCEE
Confidence 4567899999887320 12356666666665411 11111111 1112377777766555556666666
Q ss_pred EEEEeCC
Q 028679 131 CWVLADN 137 (205)
Q Consensus 131 ~~vlGDN 137 (205)
|.++.+.
T Consensus 82 ylil~e~ 88 (96)
T COG0234 82 YLILSES 88 (96)
T ss_pred EEEechH
Confidence 7666544
No 27
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=72.24 E-value=34 Score=25.73 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=25.3
Q ss_pred cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEe
Q 028679 62 PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAI 109 (205)
Q Consensus 62 PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVial 109 (205)
+.|+|-||+|++.+.. ...-..|-|++=..- ..+...-.|+|+
T Consensus 10 ~~ikPL~dRVLVk~~~---~e~kT~gGIiLP~sa--kekp~~g~VvAV 52 (100)
T PTZ00414 10 KKLQPLGQRVLVKRTL---AAKQTKAGVLIPEQV--AGKVNEGTVVAV 52 (100)
T ss_pred ccceecCCEEEEEEcc---cccccccCEEccccc--ccCCceeEEEEE
Confidence 6688889999999863 234445666553321 223444555555
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=71.96 E-value=18 Score=28.16 Aligned_cols=55 Identities=15% Similarity=0.120 Sum_probs=33.2
Q ss_pred CCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEE
Q 028679 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVG 161 (205)
Q Consensus 82 ~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiG 161 (205)
..+++||+|+|+... .-.|--+++... ..|++.++|=|.. +..-.+ ..+.++|+|
T Consensus 72 ~~p~~GDiv~f~~~~---~~HVGi~~g~~~---------------~~g~i~~lgGNq~----~~V~~~---~~~~~~~~~ 126 (129)
T TIGR02594 72 SKPAYGCIAVKRRGG---GGHVGFVVGKDK---------------QTGTIIVLGGNQG----DRVREA---LYSRSRIVA 126 (129)
T ss_pred CCCCccEEEEEECCC---CCEEEEEEeEcC---------------CCCEEEEeeCCCC----CeEEEE---EEecccEEE
Confidence 468999999998532 224444444321 2368889988876 544222 335556655
No 29
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=70.40 E-value=5.6 Score=31.03 Aligned_cols=13 Identities=46% Similarity=0.519 Sum_probs=10.6
Q ss_pred CCccCeEEEEecC
Q 028679 83 RVSVGDVVVMKDP 95 (205)
Q Consensus 83 ~~~rGDIVvf~~P 95 (205)
...+||+|+|+.+
T Consensus 84 ~~~~GD~i~~~~~ 96 (166)
T COG0681 84 IGLRGDIVVFKDD 96 (166)
T ss_pred ccCCCCEEEEECC
Confidence 4667999999984
No 30
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=68.74 E-value=51 Score=25.64 Aligned_cols=87 Identities=22% Similarity=0.281 Sum_probs=45.3
Q ss_pred EEEEEecCCCcccccccCCcEEEEEecCCCCC-CCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679 50 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADP-KRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK 128 (205)
Q Consensus 50 ~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~-~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~ 128 (205)
+..+.|.|.|-.-.-. -||.+.+.--.- .+ ...++||++-.-.-... |.+---.|.+|.+ .+
T Consensus 19 v~~I~V~gg~~r~~A~-vGD~ivvsVKka-~P~~~vKkg~V~~AViVRtk-----k~~rR~DGs~i~F----------dd 81 (122)
T COG0093 19 VMCIKVLGGSRRRYAG-VGDIIVVSVKKA-IPRGMVKKGDVVKAVVVRTK-----KEVRRPDGSYIKF----------DD 81 (122)
T ss_pred EEEEEEeccccccccC-CCCEEEEEEeec-cCCcceeccceEEEEEEEeC-----CceEcCCCCEEEe----------CC
Confidence 4556666666544333 477776552211 12 45677776533210000 1111122444444 44
Q ss_pred CeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 129 DECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 129 g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
+.+-+..++. +..-+|-||||.++.
T Consensus 82 NA~Viin~~g-----~P~GtrI~GPVaREl 106 (122)
T COG0093 82 NAAVIINPDG-----EPRGTRIFGPVAREL 106 (122)
T ss_pred ceEEEECCCC-----CcccceEecchhHHH
Confidence 6666665553 578899999998763
No 31
>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=65.69 E-value=14 Score=28.29 Aligned_cols=28 Identities=29% Similarity=0.468 Sum_probs=22.2
Q ss_pred CCccCeEEEEecCCCCCceEEEEEEEec
Q 028679 83 RVSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (205)
Q Consensus 83 ~~~rGDIVvf~~P~~~~~~~VKRVialp 110 (205)
.++.||.|.++.++.++..+|-||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~ 30 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLW 30 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 4677999999987765678899998874
No 32
>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=64.23 E-value=54 Score=23.97 Aligned_cols=91 Identities=10% Similarity=0.193 Sum_probs=47.4
Q ss_pred cccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCC
Q 028679 64 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPK 143 (205)
Q Consensus 64 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~ 143 (205)
|.|-||+|++.+.. ...-..|-|++=... ..+...-.|+|+.-.. .-.++...+..+..|..-+..+.... .
T Consensus 2 i~Pl~DrVLV~~~~---~e~~T~~GI~Lp~~~--~~k~~~g~VvAVG~g~-~~~~g~~~~~~vk~GD~Vl~~~~~g~-~- 73 (93)
T cd00320 2 IKPLGDRVLVKRIE---AEEKTKGGIILPDSA--KEKPQEGKVVAVGPGR-RNENGERVPLSVKVGDKVLFPKYAGT-E- 73 (93)
T ss_pred ceecCCEEEEEEcc---ccceecceEEeCCCc--CCCceEEEEEEECCCe-ECCCCCCccccccCCCEEEECCCCce-E-
Confidence 45679999999863 244556666663321 2456777888874221 11133333444455554444433210 0
Q ss_pred CCCCCCccccccCCCEEEE
Q 028679 144 EANDSRTFGPVPMRNIVGR 162 (205)
Q Consensus 144 ~S~DSR~~GpV~~~~IiGk 162 (205)
--+|...|=.++.++|+|+
T Consensus 74 v~~~~~~y~i~~~~DIla~ 92 (93)
T cd00320 74 VKLDGEEYLILRESDILAV 92 (93)
T ss_pred EEECCEEEEEEEHHHEEEE
Confidence 1234444556777777764
No 33
>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=63.29 E-value=21 Score=26.04 Aligned_cols=91 Identities=11% Similarity=0.175 Sum_probs=51.1
Q ss_pred ccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCCC
Q 028679 65 GGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKE 144 (205)
Q Consensus 65 ~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~~ 144 (205)
.|-||+|++.+.. ...-..|-+++=.. .......-+|+|+...... .++...+..+..|..-+..+.... .-
T Consensus 3 ~Pl~drVLV~~~~---~e~~T~~GiiLp~~--~~~~~~~G~VvaVG~G~~~-~~g~~~~~~vk~GD~Vl~~~~~g~--~v 74 (93)
T PF00166_consen 3 KPLGDRVLVKKIE---AEEKTASGIILPES--AKEKPNQGKVVAVGPGRYN-ENGEEVPMDVKVGDKVLFPKYAGT--EV 74 (93)
T ss_dssp EESTTEEEEEECS---CTCTCTTSCCE-CC--SSSSEEEEEEEEE-SEEET-TTSSEEETSS-TTSEEEEETTTSE--EE
T ss_pred eecCCEEEEEEcc---ccceecceEEeccc--cccccceeEEEEcCCcccc-CCCcEeeeeeeeccEEeccccCce--EE
Confidence 4568999999863 35556677776632 2336778888888543222 333322334555655555554420 01
Q ss_pred CCCCCccccccCCCEEEEE
Q 028679 145 ANDSRTFGPVPMRNIVGRA 163 (205)
Q Consensus 145 S~DSR~~GpV~~~~IiGkv 163 (205)
-+|...|=.++.++|+|++
T Consensus 75 ~~~~~~~~~~~~~dIlavi 93 (93)
T PF00166_consen 75 KFDGEKYLIVREDDILAVI 93 (93)
T ss_dssp EETTEEEEEEEGGGEEEEE
T ss_pred EECCEEEEEEEHHHeEEEC
Confidence 2456667678888888753
No 34
>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=59.36 E-value=20 Score=27.09 Aligned_cols=28 Identities=29% Similarity=0.480 Sum_probs=21.1
Q ss_pred CCccCeEEEEecCCCCCceEEEEEEEec
Q 028679 83 RVSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (205)
Q Consensus 83 ~~~rGDIVvf~~P~~~~~~~VKRVialp 110 (205)
.++.||.|.++.++.+....|-||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~ 30 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLW 30 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEE
Confidence 4577999999987765667787777763
No 35
>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=58.66 E-value=47 Score=25.68 Aligned_cols=88 Identities=17% Similarity=0.213 Sum_probs=51.0
Q ss_pred eEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679 49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK 128 (205)
Q Consensus 49 ~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~ 128 (205)
....+.+.+.+=.+.-. -||.+++.=-.......+++||++-.---... +..--..|..+.+ .+
T Consensus 18 ~v~cI~v~~~~~~~~a~-vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk-----~~~~r~dg~~i~F----------~~ 81 (122)
T PF00238_consen 18 KVKCIKVLGGKRRKYAS-VGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTK-----KPIRRKDGSFIKF----------DD 81 (122)
T ss_dssp EEEEEEETSSTTTSEE--TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECS-----SEEETTTSEEEEE----------SS
T ss_pred EEEEEEEeCCcCccccc-cceEEEEEEeecccCccccccceEEEEEEEEe-----EEEEEeCCcEEEe----------CC
Confidence 35566777666666666 68887765211111356777776543210000 0111233444444 55
Q ss_pred CeEEEEeCCCCCCCCCCCCCCccccccCC
Q 028679 129 DECWVLADNENMKPKEANDSRTFGPVPMR 157 (205)
Q Consensus 129 g~~~vlGDN~~~~~~~S~DSR~~GpV~~~ 157 (205)
+.+-++.++. +...+|-+||||.+
T Consensus 82 Na~VLln~~~-----~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 82 NAVVLLNKKG-----NPLGTRIFGPVPRE 105 (122)
T ss_dssp EEEEEEETTS-----SBSSSSBCSEEEHH
T ss_pred ccEEEEcCCC-----CEeeeEEEeeehHH
Confidence 7888888886 58999999999865
No 36
>CHL00057 rpl14 ribosomal protein L14
Probab=57.34 E-value=89 Score=24.25 Aligned_cols=86 Identities=17% Similarity=0.197 Sum_probs=47.6
Q ss_pred eEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEE---EEecCceEEecCCCCCcee
Q 028679 49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRL---AAIEGYEMVSTDEKDEPFV 125 (205)
Q Consensus 49 ~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRV---ialpGd~V~~~~~~~~~~~ 125 (205)
....+.|.|.+..+.-. -||.+++.=-.......+++||++-.- +|..= --..|-.+.+
T Consensus 18 ~v~cI~v~~~~~~~~a~-vGD~IvvsVk~~~~~~k~kkg~v~kAv--------IVrtk~~~~r~dG~~i~F--------- 79 (122)
T CHL00057 18 KLMCIRVLGASNRKYAH-IGDVIIAVVKEAVPNMPLKRSEVVRAV--------IVRTCKELKRDNGMIIRF--------- 79 (122)
T ss_pred EEEEEEEeCCCCCcccc-CCCEEEEEEEeccCCCceecCCEEEEE--------EEEeccccCcCCCcEEEc---------
Confidence 34556666766777777 688877642111011236667665221 11110 0112333333
Q ss_pred eeCCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
.++.+-++.++. +-.-+|-+|||+.+.
T Consensus 80 -~~Na~VLin~~~-----~p~GTrI~Gpv~~el 106 (122)
T CHL00057 80 -DDNAAVVIDQEG-----NPKGTRVFGPIAREL 106 (122)
T ss_pred -CCceEEEECCCC-----CEeEeEEEccchHHH
Confidence 456777777665 578899999999765
No 37
>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=55.43 E-value=94 Score=24.10 Aligned_cols=89 Identities=25% Similarity=0.282 Sum_probs=49.0
Q ss_pred eEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679 49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK 128 (205)
Q Consensus 49 ~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~ 128 (205)
....+.|.|.+..+.-. -||.+++.=-.......+++|+++-.---... .-++| ..|-.+.+ .+
T Consensus 18 ~v~cI~v~~~~~~~~a~-iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtk--k~~~r---~dG~~i~F----------~~ 81 (122)
T TIGR01067 18 KVQCIKVLGGSRRRYAT-VGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTK--KGVRR---KDGSYIRF----------DD 81 (122)
T ss_pred EEEEEEEeCCCCCCccc-cCCEEEEEEEEcCCCCccccccEEEEEEEEee--cceEe---CCCCEEEC----------CC
Confidence 34556666777777777 69988765321111124667776522110000 01122 22333333 55
Q ss_pred CeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 129 DECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 129 g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
+.+-++.++. +-.-+|-+|||+.+.
T Consensus 82 Na~VLin~~~-----~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 82 NACVLINKNK-----EPRGTRIFGPVAREL 106 (122)
T ss_pred ceEEEECCCC-----CEeeeEEEccchHHH
Confidence 6776776664 468899999999765
No 38
>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=51.81 E-value=40 Score=25.24 Aligned_cols=38 Identities=16% Similarity=0.192 Sum_probs=22.1
Q ss_pred CCCCccCeEEEEecCCCCCceEEEEEEEe-cCceEEecC
Q 028679 81 PKRVSVGDVVVMKDPEKSDNYIVRRLAAI-EGYEMVSTD 118 (205)
Q Consensus 81 ~~~~~rGDIVvf~~P~~~~~~~VKRVial-pGd~V~~~~ 118 (205)
...|++|||++|.......-=.|--|.++ .+++|.+.+
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e 98 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIE 98 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEE
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEE
Confidence 36899999999952222233367777888 677666543
No 39
>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=43.93 E-value=86 Score=25.06 Aligned_cols=80 Identities=13% Similarity=0.084 Sum_probs=46.7
Q ss_pred hHHHHhhccceeEEEEeeecccCCccchHHHHHHHHHHH-hhceeEEEEEecCCCcccccccCCcEEEEEecCCCCCCCC
Q 028679 6 TWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYL-FQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRV 84 (205)
Q Consensus 6 ~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~i~~~~~~~~-~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~ 84 (205)
.||+-+.++..|+++.-++.-. .+= ..+++..| -..+...-......+|...|. ..-+..+..- ....+
T Consensus 7 ~w~~~r~~~v~YSm~~R~G~~s-----~DC-Ss~V~~ALr~aG~~~~g~~~nT~tl~~~L~-~~G~~~I~~~---~~~~~ 76 (145)
T PF05382_consen 7 NWMEARKGKVTYSMDSRNGPDS-----YDC-SSFVYQALRAAGFKIPGSAGNTETLHDWLK-KNGFKKISEN---VDWNL 76 (145)
T ss_pred HHHHHhcCCceEhhhhcCCCCc-----Cch-HHHHHHHHHHcCCCCCCCccCHHHHHHHHh-hCCcEEeccC---Ccccc
Confidence 5999999999998885444321 111 11221111 112222223457789999888 4446656542 12478
Q ss_pred ccCeEEEEecC
Q 028679 85 SVGDVVVMKDP 95 (205)
Q Consensus 85 ~rGDIVvf~~P 95 (205)
++|||++....
T Consensus 77 q~GDI~I~g~~ 87 (145)
T PF05382_consen 77 QRGDIFIWGRR 87 (145)
T ss_pred cCCCEEEEcCC
Confidence 99999998664
No 40
>KOG3265 consensus Histone chaperone involved in gene silencing [Transcription; Chromatin structure and dynamics]
Probab=43.73 E-value=32 Score=29.80 Aligned_cols=66 Identities=18% Similarity=0.220 Sum_probs=47.0
Q ss_pred eeCC-eEEEE-eCCCCCCCCCCCCCCccccccCCCEEEEEEEEEe------cCCCCCCccCCCCCCCCCCCeeeeeecHH
Q 028679 126 LDKD-ECWVL-ADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLR------TAVDHGPVQNSNDSMRKDSPVLEVELDVD 197 (205)
Q Consensus 126 vp~g-~~~vl-GDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~------p~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 197 (205)
||.| +-||. +|.+. -..||.+.|+|.-+.++. -+-|.|...|+.+..++.--+=++.-+.+
T Consensus 65 VP~G~~~FVf~AD~Pd-----------~~kIP~~d~vGVTviLltC~Y~gQEFIRvGYyVnNeY~~~elrEnpP~k~~id 133 (250)
T KOG3265|consen 65 VPVGRHKFVFQADAPD-----------PSKIPEDDIVGVTVILLTCSYRGQEFIRVGYYVNNEYTEEELRENPPSKPLID 133 (250)
T ss_pred ccccceEEEEecCCCC-----------cccCcccceeeeEEEEEEEEEcCceeEEEEEEecCCCCchhhccCCCCchhHH
Confidence 4666 34444 78775 457999999998776552 36788999999999876666666666666
Q ss_pred HHhhc
Q 028679 198 EMMKN 202 (205)
Q Consensus 198 ~~~~~ 202 (205)
.+-||
T Consensus 134 Kv~Rn 138 (250)
T KOG3265|consen 134 KLQRN 138 (250)
T ss_pred HHHHH
Confidence 66655
No 41
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=42.73 E-value=15 Score=25.83 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=12.1
Q ss_pred CCcccccccCCcEEEEEec
Q 028679 58 DQMAPVMGGLGGTLLVRKL 76 (205)
Q Consensus 58 ~SM~PTL~~~GD~Vlv~k~ 76 (205)
.||.|.|+ +|++|++.--
T Consensus 12 ~~m~P~L~-~~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELN-PGEYVFCTVP 29 (72)
T ss_dssp ST-EEEE--SS-EEEEEE-
T ss_pred hhCCcEeC-CCCEEEEEec
Confidence 58999999 6999998754
No 42
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=42.00 E-value=51 Score=28.61 Aligned_cols=77 Identities=14% Similarity=0.323 Sum_probs=46.4
Q ss_pred cCCCcccccccCCcEEEEEecCC------------CCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEec-CCCCC
Q 028679 56 KGDQMAPVMGGLGGTLLVRKLPA------------ADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVST-DEKDE 122 (205)
Q Consensus 56 ~g~SM~PTL~~~GD~Vlv~k~~~------------~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~-~~~~~ 122 (205)
....|.|.|+ .||.|...=... .....++.|.+|.+.+ ..+-|+++-.|--+..- ....-
T Consensus 105 ~~~~~r~~l~-vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p------~kVpRvig~~~sm~~~l~~~~~~ 177 (239)
T COG1097 105 AEKDLRPFLN-VGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPP------SKVPRVIGKKGSMLNMLKEKTGC 177 (239)
T ss_pred cccccccccc-cCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEch------hhcceEecCCCcHHHHhhhhcCe
Confidence 3688999999 799987542221 1346778888888775 24566666554332110 00011
Q ss_pred ceee-eCCeEEEEeCCCC
Q 028679 123 PFVL-DKDECWVLADNEN 139 (205)
Q Consensus 123 ~~~v-p~g~~~vlGDN~~ 139 (205)
.+.| -+|.+||-|.|..
T Consensus 178 ~I~VG~NG~IWV~~~~~~ 195 (239)
T COG1097 178 EIIVGQNGRIWVDGENES 195 (239)
T ss_pred EEEEecCCEEEecCCCcc
Confidence 1222 4689999999974
No 43
>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=40.64 E-value=73 Score=24.72 Aligned_cols=28 Identities=21% Similarity=0.249 Sum_probs=19.9
Q ss_pred CCCccCeEEEEecCCCCCceEEEEEEEecC
Q 028679 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAIEG 111 (205)
Q Consensus 82 ~~~~rGDIVvf~~P~~~~~~~VKRVialpG 111 (205)
..++.||.|.+++++ +...|-+|-.+-.
T Consensus 6 ~~i~vGD~V~v~~~~--~~~~va~Ie~i~e 33 (130)
T cd04721 6 VTISVHDFVYVLSEE--EDRYVAYIEDLYE 33 (130)
T ss_pred EEEECCCEEEEeCCC--CCcEEEEEEEEEE
Confidence 457889999999765 4456777766643
No 44
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.73 E-value=18 Score=28.08 Aligned_cols=17 Identities=18% Similarity=0.229 Sum_probs=14.8
Q ss_pred CCcccccccCCcEEEEEe
Q 028679 58 DQMAPVMGGLGGTLLVRK 75 (205)
Q Consensus 58 ~SM~PTL~~~GD~Vlv~k 75 (205)
.||.|.|. +||+|++.-
T Consensus 12 ~smtPeL~-~G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELL-DGDYVFCTV 28 (134)
T ss_pred HhcCcccc-CCceEEEEe
Confidence 38999999 799999864
No 45
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=39.60 E-value=1.8e+02 Score=22.55 Aligned_cols=88 Identities=24% Similarity=0.277 Sum_probs=46.0
Q ss_pred EEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCC
Q 028679 50 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKD 129 (205)
Q Consensus 50 ~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g 129 (205)
...+.|.|.+-.+.-. -||.+++.=-.......+++|+++-.---. .+.-++| ..|-++.+ .++
T Consensus 19 v~cI~v~g~~~~~~a~-iGD~I~vsVkk~~~~~~~kkg~v~~AvIVr--tkk~~~r---~dG~~i~F----------~dN 82 (122)
T PRK05483 19 VMCIKVLGGSKRRYAS-IGDVIVVSVKEAIPRGKVKKGDVVKAVVVR--TKKGVRR---PDGSYIRF----------DDN 82 (122)
T ss_pred EEEEEEeCCCCCCccc-cCCEEEEEEEEcCCCCcccCCCEeeEEEEE--eccceec---CCCCEEEc----------CCC
Confidence 4455556655556666 588876652211111236667654221000 0001122 22333433 456
Q ss_pred eEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 130 ECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 130 ~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
.+-++.++. +..-+|-+|||+.+.
T Consensus 83 avVLin~~~-----~p~GTrI~Gpv~~el 106 (122)
T PRK05483 83 AAVLLNNDG-----EPRGTRIFGPVAREL 106 (122)
T ss_pred EEEEECCCC-----CEeEeEEeccchHHH
Confidence 776776654 578899999998764
No 46
>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=39.57 E-value=92 Score=24.25 Aligned_cols=52 Identities=15% Similarity=0.258 Sum_probs=36.8
Q ss_pred ccCeEEEEecC--CCCCceEEEEEEEecCce--EEecCCC----CCceeeeCCeEEEEeC
Q 028679 85 SVGDVVVMKDP--EKSDNYIVRRLAAIEGYE--MVSTDEK----DEPFVLDKDECWVLAD 136 (205)
Q Consensus 85 ~rGDIVvf~~P--~~~~~~~VKRVialpGd~--V~~~~~~----~~~~~vp~g~~~vlGD 136 (205)
+.||-|+++.+ +..+.+++-+|+..-+++ ..+.|.. ...++++..++..+=.
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 47999999876 345689999999998765 6665532 2467888888888855
No 47
>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=39.40 E-value=1.1e+02 Score=24.97 Aligned_cols=24 Identities=25% Similarity=0.274 Sum_probs=18.7
Q ss_pred CCCCccccccCCCEEEEEEEEEec
Q 028679 146 NDSRTFGPVPMRNIVGRAIYCLRT 169 (205)
Q Consensus 146 ~DSR~~GpV~~~~IiGkv~~~~~p 169 (205)
|=|+..-.+|.+.|.||..-....
T Consensus 85 F~S~~~d~~p~~~IrGKC~V~~~~ 108 (164)
T cd04709 85 FLSRQVETLPATHIRGKCSVTLLN 108 (164)
T ss_pred EEecccccccHHHeeeeEEEEEeh
Confidence 455677889999999999766443
No 48
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=39.39 E-value=1.8e+02 Score=23.22 Aligned_cols=86 Identities=17% Similarity=0.157 Sum_probs=45.6
Q ss_pred eEEEEEecC---CCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCce
Q 028679 49 LTYLYGNKG---DQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPF 124 (205)
Q Consensus 49 ~~~i~~V~g---~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~ 124 (205)
....+.|.| .+-. |.-. -||.+++.=-. ..+.++||++-.---... |-+--..|-+|.+
T Consensus 35 ~v~cI~vlg~~g~~~r~~~a~-iGD~IvvsVKk---~~p~~kg~V~kAVIVRtK-----k~~rR~dGs~i~F-------- 97 (139)
T PTZ00054 35 NLYIIAVKGIHGRLNRLPSAS-LGDMVLATVKK---GKPELRKKVLNAVIIRQR-----KAWRRKDGVFIYF-------- 97 (139)
T ss_pred EEEEEEEeccCcCCccCcccc-cCCEEEEEEEE---CCCcccCCEeeEEEEEEC-----cceEcCCCcEEEe--------
Confidence 345556655 4444 6666 58887665321 234566665421110000 0011122333333
Q ss_pred eeeCCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 125 VLDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 125 ~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
.+|.+-++.++. +-.-+|-||||+.+.
T Consensus 98 --~dNA~VLin~~~-----~p~GTRI~GpV~rEl 124 (139)
T PTZ00054 98 --EDNAGVIVNPKG-----EMKGSAITGPVAKEC 124 (139)
T ss_pred --CCcEEEEECCCC-----CEeeeEEeCchhHHH
Confidence 556777776654 468889999999886
No 49
>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=38.55 E-value=44 Score=24.37 Aligned_cols=27 Identities=30% Similarity=0.372 Sum_probs=20.7
Q ss_pred CccCeEEEEecCCCCCceEEEEEEEec
Q 028679 84 VSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (205)
Q Consensus 84 ~~rGDIVvf~~P~~~~~~~VKRVialp 110 (205)
++.||.|.+..+.....+.|.||..+-
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~ 29 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIW 29 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 467888888877656678888888774
No 50
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. 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=36.65 E-value=98 Score=24.13 Aligned_cols=79 Identities=15% Similarity=0.165 Sum_probs=42.6
Q ss_pred CCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCC-Cc---eeeeCCeEEEEeC--CCCCCCCCCCCCCccccccC
Q 028679 83 RVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKD-EP---FVLDKDECWVLAD--NENMKPKEANDSRTFGPVPM 156 (205)
Q Consensus 83 ~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~-~~---~~vp~g~~~vlGD--N~~~~~~~S~DSR~~GpV~~ 156 (205)
.++.||.|.++.++....++|-||..+-.+. ++.. -. +.=|++. |+|. |+. .-+-|+..--.+.
T Consensus 3 ~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~----~g~k~~h~rWf~Rg~dT--VlG~~~~~k----EvFlsd~c~d~~l 72 (124)
T cd04760 3 ELEAGDCVSVKPDDPTKPLYIARVTYMWKDS----IGGKMFHAHWFCRGSDT--VLGETSDPL----ELFLVDECEDMAL 72 (124)
T ss_pred EEecCCEEEEecCCCCCCcEEEEEhhheecC----CCCcEEEEEEEEECCcc--cccccCCCc----EEEeecccCCcch
Confidence 3566888888865544556888887764331 0100 00 0001111 1111 111 2344444555788
Q ss_pred CCEEEEEEEEEecCC
Q 028679 157 RNIVGRAIYCLRTAV 171 (205)
Q Consensus 157 ~~IiGkv~~~~~p~~ 171 (205)
+.|.||+...+.+++
T Consensus 73 ~~I~~Kv~V~~~~p~ 87 (124)
T cd04760 73 SSIHGKVNVIYKAPS 87 (124)
T ss_pred HHheeeeEEEEeCCC
Confidence 899999999998877
No 51
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=32.78 E-value=1e+02 Score=23.28 Aligned_cols=49 Identities=24% Similarity=0.317 Sum_probs=32.6
Q ss_pred CcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecC
Q 028679 59 QMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEG 111 (205)
Q Consensus 59 SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpG 111 (205)
|..-.+. ++.+|.+|...-.....++.||++.+... +..+.=+|.+++.
T Consensus 25 slAk~~~-~~GrV~vNG~~aKpS~~VK~GD~l~i~~~---~~~~~v~Vl~~~~ 73 (100)
T COG1188 25 SLAKEMI-EGGRVKVNGQRAKPSKEVKVGDILTIRFG---NKEFTVKVLALGE 73 (100)
T ss_pred HHHHHHH-HCCeEEECCEEcccccccCCCCEEEEEeC---CcEEEEEEEeccc
Confidence 3333344 46666666543333468999999999983 4567778888875
No 52
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=32.03 E-value=1e+02 Score=22.10 Aligned_cols=44 Identities=23% Similarity=0.393 Sum_probs=26.5
Q ss_pred eEEEEEecCCCcccccccCCcEEEEEecCCCCCCC---CccCeEEEEec
Q 028679 49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKR---VSVGDVVVMKD 94 (205)
Q Consensus 49 ~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~---~~rGDIVvf~~ 94 (205)
++.+....|.+..-...++|...++.-..+ ++. +++||+|++.+
T Consensus 3 i~rV~~~~G~n~~~V~~~dG~~~l~~iP~K--fRk~iWIkrGd~VlV~p 49 (78)
T cd05792 3 IVRVLGSKGNNLHEVETPNGSRYLVSMPTK--FRKNIWIKRGDFVLVEP 49 (78)
T ss_pred EEEEEEcCCCcEEEEEcCCCCEEEEEechh--hcccEEEEeCCEEEEEe
Confidence 445555666666655555677776663321 222 77888888864
No 53
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=31.73 E-value=12 Score=25.66 Aligned_cols=19 Identities=26% Similarity=0.613 Sum_probs=16.5
Q ss_pred CCCCCccccccCCCEEEEE
Q 028679 145 ANDSRTFGPVPMRNIVGRA 163 (205)
Q Consensus 145 S~DSR~~GpV~~~~IiGkv 163 (205)
+.|-|.||.+|-++.-|||
T Consensus 23 C~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 23 CVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EeechhcceeecCCCCCch
Confidence 7899999999988877775
No 54
>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=31.71 E-value=2.6e+02 Score=22.04 Aligned_cols=29 Identities=14% Similarity=0.328 Sum_probs=21.9
Q ss_pred eeeCCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 125 VLDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 125 ~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
...++.+-++.++. +-.-+|-||||+.+.
T Consensus 88 ~FddNa~VLin~~~-----~P~GTRI~GpV~rEl 116 (131)
T TIGR03673 88 KFEDNAVVIVTPDG-----EPKGTEIKGPVAREA 116 (131)
T ss_pred EeCCcEEEEECCCC-----CEeeeEEEccchHHH
Confidence 33567777777665 468889999999876
No 55
>smart00439 BAH Bromo adjacent homology domain.
Probab=31.57 E-value=83 Score=22.85 Aligned_cols=17 Identities=24% Similarity=0.579 Sum_probs=13.6
Q ss_pred cccCCCEEEEEEEEEec
Q 028679 153 PVPMRNIVGRAIYCLRT 169 (205)
Q Consensus 153 pV~~~~IiGkv~~~~~p 169 (205)
-++.+.|+|++.-...+
T Consensus 70 ~i~~~~I~~kc~V~~~~ 86 (120)
T smart00439 70 TVPLSDIIGKCNVLSKS 86 (120)
T ss_pred cCChHHeeeEEEEEEcc
Confidence 58999999999876444
No 56
>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=31.04 E-value=52 Score=22.30 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=21.3
Q ss_pred eEEEEEecCCCcccccccCCcEEEEEecCC-CCCCCCccCeEEEEec
Q 028679 49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPA-ADPKRVSVGDVVVMKD 94 (205)
Q Consensus 49 ~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~-~~~~~~~rGDIVvf~~ 94 (205)
++.+....|..+.=-..++|..+++.-... +..--+++||.|++..
T Consensus 6 ~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 6 IGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEE
T ss_pred EEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEe
Confidence 344555555555444444566555542110 1123467777777774
No 57
>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=30.06 E-value=54 Score=23.31 Aligned_cols=45 Identities=16% Similarity=0.116 Sum_probs=22.7
Q ss_pred EEEEEecCCCcccccccCCcEEEEEecCC-CCCCCCccCeEEEEec
Q 028679 50 TYLYGNKGDQMAPVMGGLGGTLLVRKLPA-ADPKRVSVGDVVVMKD 94 (205)
Q Consensus 50 ~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~-~~~~~~~rGDIVvf~~ 94 (205)
+.+....|+.+.=...++|..+++.-... +..--+++||+|++..
T Consensus 4 ~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~ 49 (78)
T cd04456 4 VRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDP 49 (78)
T ss_pred EEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEe
Confidence 44555556665554433566666552211 0012366777777764
No 58
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=27.43 E-value=3.1e+02 Score=21.61 Aligned_cols=28 Identities=11% Similarity=0.306 Sum_probs=21.3
Q ss_pred eeCCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
..++.+-++.++. +-.-+|-+|||+.+.
T Consensus 90 F~dNa~VLin~~~-----~p~GTRI~GpV~~El 117 (132)
T PRK08571 90 FEDNAAVIVTPEG-----TPKGTEIKGPVAREA 117 (132)
T ss_pred eCCcEEEEECCCC-----CEeeeEEeccchHHH
Confidence 3557777777665 468889999999876
No 59
>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=27.06 E-value=69 Score=22.39 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=9.8
Q ss_pred CcEEEEEecCCCCCCCCccCeEE
Q 028679 68 GGTLLVRKLPAADPKRVSVGDVV 90 (205)
Q Consensus 68 GD~Vlv~k~~~~~~~~~~rGDIV 90 (205)
||+|.|.... .++.+|+|+
T Consensus 48 GD~V~Ve~sp----yd~tkgrIi 66 (68)
T TIGR00008 48 GDKVKVELSP----YDLTRGRIT 66 (68)
T ss_pred CCEEEEEECc----ccCCcEeEE
Confidence 5666655432 345555554
No 60
>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=26.85 E-value=3e+02 Score=21.29 Aligned_cols=34 Identities=24% Similarity=0.470 Sum_probs=21.1
Q ss_pred CceEEEEEEEecCceEEecCCCCCceeeeCCeEEE
Q 028679 99 DNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV 133 (205)
Q Consensus 99 ~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~v 133 (205)
..+++.||+.++--++.- +....++.+|.|..|.
T Consensus 89 ~~w~vgrI~~~e~~~v~~-~~~~Npy~Lp~Gt~~y 122 (129)
T PF10377_consen 89 REWIVGRIVSIEECQVKD-DKDSNPYNLPVGTKFY 122 (129)
T ss_pred CCEEEEEEEEEEEEEecc-CCCCCCCcCCCCCEEE
Confidence 357888888886433321 2445677778776653
No 61
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=26.79 E-value=69 Score=22.86 Aligned_cols=19 Identities=32% Similarity=0.557 Sum_probs=9.6
Q ss_pred CcEEEEEecCCCCCCCCccCeEE
Q 028679 68 GGTLLVRKLPAADPKRVSVGDVV 90 (205)
Q Consensus 68 GD~Vlv~k~~~~~~~~~~rGDIV 90 (205)
||+|++... +.+..+|||+
T Consensus 50 GD~V~Ve~~----~~d~~kg~I~ 68 (75)
T COG0361 50 GDVVLVELS----PYDLTKGRIV 68 (75)
T ss_pred CCEEEEEec----ccccccccEE
Confidence 555555543 2345555554
No 62
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=25.64 E-value=68 Score=23.08 Aligned_cols=47 Identities=19% Similarity=0.203 Sum_probs=24.5
Q ss_pred eeEEEEEecCCCcccccccCCcEEEEEecCC-CCCCCCccCeEEEEec
Q 028679 48 KLTYLYGNKGDQMAPVMGGLGGTLLVRKLPA-ADPKRVSVGDVVVMKD 94 (205)
Q Consensus 48 ~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~-~~~~~~~rGDIVvf~~ 94 (205)
.++.+....|+.+.=...++|..+++.-... +..--+++||+|++..
T Consensus 7 ~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~ 54 (83)
T smart00652 7 EIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDP 54 (83)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence 3455566666666654433566665542211 0111266777777764
No 63
>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=25.25 E-value=69 Score=22.68 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=6.1
Q ss_pred CccCeEEEEe
Q 028679 84 VSVGDVVVMK 93 (205)
Q Consensus 84 ~~rGDIVvf~ 93 (205)
+++||.|++.
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 5566666665
No 64
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=24.83 E-value=1e+02 Score=23.71 Aligned_cols=27 Identities=22% Similarity=0.186 Sum_probs=13.0
Q ss_pred CCCccCeEEEEecCCCCCceEEEEEEE
Q 028679 82 KRVSVGDVVVMKDPEKSDNYIVRRLAA 108 (205)
Q Consensus 82 ~~~~rGDIVvf~~P~~~~~~~VKRVia 108 (205)
..++.||-|+...+.....+.=..|++
T Consensus 54 ~~L~~GD~VLA~~~~~~~~Y~Pg~V~~ 80 (124)
T PF15057_consen 54 HSLQVGDKVLAPWEPDDCRYGPGTVIA 80 (124)
T ss_pred CcCCCCCEEEEecCcCCCEEeCEEEEE
Confidence 345555555555444333333355554
No 65
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=24.78 E-value=2.7e+02 Score=20.99 Aligned_cols=34 Identities=12% Similarity=0.213 Sum_probs=21.8
Q ss_pred CCCCccCeEEEEecCCCCCceEEEEE-EEecCceEEe
Q 028679 81 PKRVSVGDVVVMKDPEKSDNYIVRRL-AAIEGYEMVS 116 (205)
Q Consensus 81 ~~~~~rGDIVvf~~P~~~~~~~VKRV-ialpGd~V~~ 116 (205)
...+..||+|.+...+ +.+.+.++ .+-.+-|+++
T Consensus 23 a~glA~gDvV~~~~~~--g~~~~~~~v~~sGnsTiRv 57 (117)
T PF14085_consen 23 AYGLALGDVVRAEPDD--GELWFQKVVESSGNSTIRV 57 (117)
T ss_pred cCCCCCCCEEEEEeCC--CeEEEEEEEecCCCEEEEE
Confidence 4789999999999765 44444444 4433455543
No 66
>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=24.38 E-value=2e+02 Score=21.84 Aligned_cols=28 Identities=18% Similarity=0.487 Sum_probs=19.8
Q ss_pred CCCCccCeEEEEecCCCCCceEEEEEEEe
Q 028679 81 PKRVSVGDVVVMKDPEKSDNYIVRRLAAI 109 (205)
Q Consensus 81 ~~~~~rGDIVvf~~P~~~~~~~VKRVial 109 (205)
.+.++.||.++|..-.+ ++.+.-+|+.+
T Consensus 29 r~~ikvGD~I~f~~~~~-~~~l~v~V~~i 56 (109)
T cd06555 29 RQQIKVGDKILFNDLDT-GQQLLVKVVDI 56 (109)
T ss_pred hhcCCCCCEEEEEEcCC-CcEEEEEEEEE
Confidence 35799999999986433 44566667665
No 67
>PTZ00320 ribosomal protein L14; Provisional
Probab=24.23 E-value=3.1e+02 Score=22.93 Aligned_cols=29 Identities=14% Similarity=0.237 Sum_probs=22.0
Q ss_pred eeeCCeEEEEeCCCCCCCCCCCCCCccccccCCC
Q 028679 125 VLDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158 (205)
Q Consensus 125 ~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~ 158 (205)
...++.+-++.++. +..-+|-||||+++.
T Consensus 144 rFDdNAaVLIN~qg-----ePlGTRIfGPVaREL 172 (188)
T PTZ00320 144 NFDRNTCILMNDQR-----VPLGTRVMYCAGRHV 172 (188)
T ss_pred EeCCcEEEEECCCC-----CEeeeEEecchhHHH
Confidence 34567887887775 578899999998754
No 68
>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=21.98 E-value=4.4e+02 Score=21.41 Aligned_cols=37 Identities=16% Similarity=0.350 Sum_probs=27.4
Q ss_pred CCCCCccCeEEEEecCCCCCceEEEE---EEEecCceEEecC
Q 028679 80 DPKRVSVGDVVVMKDPEKSDNYIVRR---LAAIEGYEMVSTD 118 (205)
Q Consensus 80 ~~~~~~rGDIVvf~~P~~~~~~~VKR---VialpGd~V~~~~ 118 (205)
.+..++.|++.++..- .....+|| ++.+.++++.+..
T Consensus 71 R~~~L~~GEvalY~~~--G~~I~L~~~G~ii~~~~~~~~v~a 110 (162)
T PF06890_consen 71 RPKGLKPGEVALYDDE--GQKIHLKRDGRIIEVTCKTVTVNA 110 (162)
T ss_pred cccCCCCCcEEEEcCC--CCEEEEEecceEEeccCceEEEec
Confidence 3567899999999952 34566665 7778888888864
No 69
>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=21.56 E-value=2e+02 Score=20.65 Aligned_cols=28 Identities=25% Similarity=0.356 Sum_probs=18.3
Q ss_pred CCccCeEEEEecCCC--CCceEEEEEEEec
Q 028679 83 RVSVGDVVVMKDPEK--SDNYIVRRLAAIE 110 (205)
Q Consensus 83 ~~~rGDIVvf~~P~~--~~~~~VKRVialp 110 (205)
.++.||.|.+..+.. ...+.+-||..+-
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~ 32 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELW 32 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeee
Confidence 356688888876553 3456777777764
No 70
>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=21.15 E-value=1.3e+02 Score=23.35 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=20.0
Q ss_pred CCCccCeEEEEecCCCCC----------ceEEEEEEEec
Q 028679 82 KRVSVGDVVVMKDPEKSD----------NYIVRRLAAIE 110 (205)
Q Consensus 82 ~~~~rGDIVvf~~P~~~~----------~~~VKRVialp 110 (205)
..++.||+|+++.++... ..+|-||..+.
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~ 42 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMK 42 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEee
Confidence 457789999998765431 45677777764
No 71
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.09 E-value=1.5e+02 Score=22.25 Aligned_cols=37 Identities=14% Similarity=0.126 Sum_probs=26.1
Q ss_pred EEecCCCcccccccCCcEEEEEecCCC----CCCCCccCeEEEEec
Q 028679 53 YGNKGDQMAPVMGGLGGTLLVRKLPAA----DPKRVSVGDVVVMKD 94 (205)
Q Consensus 53 ~~V~g~SM~PTL~~~GD~Vlv~k~~~~----~~~~~~rGDIVvf~~ 94 (205)
+.+.++|..|- =++++++.... ...+++.||.|+|-.
T Consensus 56 lFi~~gsvrpG-----ii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 56 LFIHHGSVRPG-----IIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred eEeeCCcCcCc-----EEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 67788888864 44777765421 235899999999975
No 72
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.24 E-value=2e+02 Score=23.55 Aligned_cols=37 Identities=24% Similarity=0.367 Sum_probs=24.7
Q ss_pred EEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEec
Q 028679 71 LLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (205)
Q Consensus 71 Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialp 110 (205)
+...|.. ....++.||.|+++.+.. +...|..|..+-
T Consensus 42 i~l~R~~--d~~~~~vGD~Vlik~~~~-~~~~V~iI~ei~ 78 (179)
T cd04720 42 IFLARDS--DGLELSVGDTILVKDDVA-NSPSVYLIHEIR 78 (179)
T ss_pred EEEEEcc--CCeEEeCCCEEEEeCCCC-CCCEEEEEEEEE
Confidence 4444442 246799999999998764 556666666653
Done!