Query psy15749
Match_columns 164
No_of_seqs 211 out of 1149
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 20:23:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15749.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15749hhsearch_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 3E-41 6.5E-46 256.1 15.5 135 4-144 1-163 (163)
2 KOG1568|consensus 100.0 5.2E-39 1.1E-43 239.0 9.0 154 4-159 10-167 (174)
3 KOG0171|consensus 100.0 2.5E-37 5.5E-42 230.3 11.5 133 13-150 23-165 (176)
4 PRK10861 signal peptidase I; P 100.0 1.4E-36 3E-41 251.3 15.9 138 3-144 62-305 (324)
5 PRK13838 conjugal transfer pil 99.9 6.1E-25 1.3E-29 168.6 12.6 93 45-140 37-172 (176)
6 TIGR02771 TraF_Ti conjugative 99.9 4.1E-24 9E-29 163.3 13.5 105 20-140 21-169 (171)
7 PRK13884 conjugal transfer pep 99.9 1.4E-23 3.1E-28 161.3 13.0 82 59-140 49-176 (178)
8 TIGR02754 sod_Ni_protease nick 99.9 1.2E-22 2.5E-27 139.6 9.4 89 27-138 2-90 (90)
9 PF10502 Peptidase_S26: Signal 99.9 8.3E-24 1.8E-28 156.6 2.9 82 59-140 20-137 (138)
10 cd06530 S26_SPase_I The S26 Ty 99.9 3.3E-21 7.2E-26 130.8 8.9 84 25-136 2-85 (85)
11 TIGR02228 sigpep_I_arch signal 99.8 5.2E-18 1.1E-22 128.1 11.5 110 3-138 5-120 (158)
12 COG0681 LepB Signal peptidase 99.7 2.1E-16 4.5E-21 118.8 10.4 135 2-146 8-152 (166)
13 COG4959 TraF Type IV secretory 99.6 7.4E-15 1.6E-19 108.9 7.1 82 58-139 51-168 (173)
14 PF00717 Peptidase_S24: Peptid 99.3 8.9E-12 1.9E-16 81.0 7.2 58 27-95 1-58 (70)
15 cd06462 Peptidase_S24_S26 The 99.3 4E-11 8.6E-16 80.0 9.0 82 25-135 2-83 (84)
16 COG2932 Predicted transcriptio 98.9 1E-08 2.2E-13 80.7 10.6 87 24-143 124-213 (214)
17 cd06529 S24_LexA-like Peptidas 98.8 3.3E-08 7.2E-13 65.6 8.9 52 25-89 2-53 (81)
18 KOG3342|consensus 98.8 4.8E-08 1E-12 72.7 8.3 89 25-138 50-145 (180)
19 PRK10276 DNA polymerase V subu 98.5 1.6E-06 3.4E-11 64.1 10.8 85 24-142 52-137 (139)
20 PRK00215 LexA repressor; Valid 98.5 2.5E-06 5.5E-11 66.5 11.0 86 22-141 117-203 (205)
21 TIGR00498 lexA SOS regulatory 98.4 3.8E-06 8.2E-11 65.2 11.1 88 22-143 110-198 (199)
22 PRK12423 LexA repressor; Provi 98.3 6.8E-06 1.5E-10 64.3 10.8 85 24-141 115-200 (202)
23 COG1974 LexA SOS-response tran 97.8 0.00043 9.4E-09 54.3 11.1 88 23-143 112-200 (201)
24 COG0681 LepB Signal peptidase 87.2 0.7 1.5E-05 34.0 3.2 12 60-71 84-95 (166)
25 COG0234 GroS Co-chaperonin Gro 87.2 4.1 8.9E-05 28.2 6.7 71 43-114 6-88 (96)
26 PTZ00414 10 kDa heat shock pro 81.6 10 0.00022 26.5 6.8 65 44-113 16-91 (100)
27 PRK00364 groES co-chaperonin G 81.5 13 0.00028 25.5 7.3 27 86-112 60-86 (95)
28 PRK14533 groES co-chaperonin G 78.4 17 0.00036 24.9 6.9 65 44-113 7-82 (91)
29 cd00320 cpn10 Chaperonin 10 Kd 74.0 25 0.00054 24.0 7.4 26 86-111 59-84 (93)
30 KOG1641|consensus 72.8 30 0.00065 24.3 7.1 28 86-113 68-96 (104)
31 PF05257 CHAP: CHAP domain; I 71.9 9.9 0.00021 26.8 4.7 38 58-95 60-98 (124)
32 TIGR02594 conserved hypothetic 67.9 28 0.0006 25.2 6.4 14 58-71 71-84 (129)
33 PF06890 Phage_Mu_Gp45: Bacter 58.5 61 0.0013 24.6 6.9 37 58-96 72-111 (162)
34 PF14118 YfzA: YfzA-like prote 57.9 8.9 0.00019 26.5 2.1 32 2-40 11-42 (94)
35 PF15057 DUF4537: Domain of un 57.7 15 0.00032 26.5 3.3 54 59-112 54-113 (124)
36 COG0093 RplN Ribosomal protein 56.7 73 0.0016 23.0 7.7 30 101-131 77-106 (122)
37 PF00166 Cpn10: Chaperonin 10 52.9 69 0.0015 21.6 6.3 24 87-110 60-83 (93)
38 PF02736 Myosin_N: Myosin N-te 48.4 28 0.00061 20.0 2.9 35 72-106 7-41 (42)
39 PF10000 ACT_3: ACT domain; I 47.0 11 0.00023 24.7 1.1 17 31-51 12-28 (72)
40 cd04717 BAH_polybromo BAH, or 46.0 56 0.0012 22.9 4.8 26 61-86 4-29 (121)
41 cd04714 BAH_BAHCC1 BAH, or Bro 45.9 32 0.00069 24.5 3.5 28 60-87 3-30 (121)
42 COG0361 InfA Translation initi 45.7 22 0.00048 23.5 2.4 18 45-67 51-68 (75)
43 TIGR00008 infA translation ini 44.9 26 0.00056 22.7 2.6 18 45-67 49-66 (68)
44 cd04712 BAH_DCM_I BAH, or Brom 44.7 1.2E+02 0.0025 21.9 8.1 78 59-144 4-103 (130)
45 PF01176 eIF-1a: Translation i 44.6 33 0.00073 21.6 3.1 13 59-71 40-52 (65)
46 PF05382 Amidase_5: Bacterioph 42.6 49 0.0011 24.6 4.1 38 27-72 50-87 (145)
47 cd03695 CysN_NodQ_II CysN_NodQ 38.9 70 0.0015 20.8 4.1 34 58-93 24-65 (81)
48 PF07039 DUF1325: SGF29 tudor- 37.8 92 0.002 22.6 4.9 52 62-113 1-60 (130)
49 PF10913 DUF2706: Protein of u 37.6 51 0.0011 20.3 2.9 47 1-51 1-47 (60)
50 PF14085 DUF4265: Domain of un 36.8 1.2E+02 0.0026 21.4 5.3 45 45-93 12-57 (117)
51 cd05793 S1_IF1A S1_IF1A: Trans 36.5 44 0.00095 22.0 2.8 10 61-70 39-48 (77)
52 PF01426 BAH: BAH domain; Int 35.9 49 0.0011 22.6 3.2 26 61-86 3-28 (119)
53 cd04456 S1_IF1A_like S1_IF1A_l 35.8 45 0.00097 22.0 2.8 10 61-70 39-48 (78)
54 cd04760 BAH_Dnmt1_I BAH, or Br 35.5 71 0.0015 23.1 4.0 21 124-144 67-87 (124)
55 smart00652 eIF1a eukaryotic tr 35.4 47 0.001 22.2 2.8 10 61-70 44-53 (83)
56 PF10377 ATG11: Autophagy-rela 34.9 1.7E+02 0.0038 21.1 6.8 60 58-139 40-99 (129)
57 cd03698 eRF3_II_like eRF3_II_l 33.0 92 0.002 20.2 4.0 34 58-93 24-65 (83)
58 KOG2915|consensus 32.2 48 0.001 27.7 2.9 15 123-137 42-56 (314)
59 PF10030 DUF2272: Uncharacteri 31.0 2E+02 0.0044 22.2 6.1 15 58-72 91-105 (183)
60 smart00439 BAH Bromo adjacent 30.5 89 0.0019 21.2 3.8 17 126-142 70-86 (120)
61 COG3602 Uncharacterized protei 30.2 32 0.00069 24.8 1.4 17 31-51 12-28 (134)
62 PRK04012 translation initiatio 29.8 63 0.0014 22.5 2.8 10 61-70 60-69 (100)
63 cd04089 eRF3_II eRF3_II: domai 28.7 1.1E+02 0.0024 19.8 3.8 34 58-93 23-64 (82)
64 TIGR01067 rplN_bact ribosomal 28.5 2.3E+02 0.0049 20.4 7.4 30 101-131 77-106 (122)
65 PF00238 Ribosomal_L14: Riboso 28.3 43 0.00093 24.1 1.8 30 100-130 76-105 (122)
66 smart00002 PLP Myelin proteoli 28.2 15 0.00032 23.3 -0.5 20 117-136 22-41 (60)
67 CHL00057 rpl14 ribosomal prote 26.7 2.5E+02 0.0054 20.2 7.7 30 101-131 77-106 (122)
68 cd03694 GTPBP_II Domain II of 26.4 1.4E+02 0.0031 19.5 4.1 37 58-94 24-70 (87)
69 PF00278 Orn_DAP_Arg_deC: Pyri 26.1 96 0.0021 21.1 3.3 12 60-71 82-93 (116)
70 PRK12442 translation initiatio 26.0 76 0.0017 21.6 2.6 9 62-70 48-56 (87)
71 cd06555 ASCH_PF0470_like ASC-1 25.5 1.1E+02 0.0023 21.7 3.4 27 58-85 29-55 (109)
72 PF08169 RBB1NT: RBB1NT (NUC16 25.4 1.6E+02 0.0035 20.4 4.1 56 63-133 8-63 (96)
73 COG1097 RRP4 RNA-binding prote 24.6 2.2E+02 0.0047 23.1 5.4 76 30-115 106-194 (239)
74 PF14900 DUF4493: Domain of un 22.3 1.8E+02 0.0039 22.8 4.5 46 79-124 35-86 (235)
75 cd03696 selB_II selB_II: this 22.0 1.9E+02 0.0042 18.5 4.0 35 58-94 24-66 (83)
76 PF13759 2OG-FeII_Oxy_5: Putat 21.6 1.1E+02 0.0025 20.4 2.9 24 60-89 69-92 (101)
77 PF10222 DUF2152: Uncharacteri 21.2 98 0.0021 28.5 3.1 104 3-124 13-118 (604)
78 PRK00276 infA translation init 20.3 1E+02 0.0023 19.7 2.3 11 60-70 46-56 (72)
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=3e-41 Score=256.12 Aligned_cols=135 Identities=30% Similarity=0.520 Sum_probs=123.4
Q ss_pred HHHHHHHHHHHHHHHhhceeEEEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEE
Q psy15749 4 IFKSMLVGIPISITFCDSIGYVARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRI 83 (164)
Q Consensus 4 ~l~~~~~~i~i~~~i~~~~~~~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRV 83 (164)
|+..++++++++++++.|++..+.|+|+||+|||++| |+++++|..+. ..++++||+|+|+.|.++++.++|||
T Consensus 1 ~~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~G----d~vlv~k~~~~--~~~~~rGDiVvf~~~~~~~~~~iKRV 74 (163)
T TIGR02227 1 LILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKEG----DRILVNKFAYG--TSDPKRGDIVVFKDPDDNKNIYVKRV 74 (163)
T ss_pred CHHHHHHHHHHHHHHHhhEEEEEEECCcccccchhCC----CEEEEEEeEcC--CCCCCCCcEEEEecCCCCCceeEEEE
Confidence 5677888899999999999999999999999999999 99999999876 68999999999999877788999999
Q ss_pred EeeCCCEEEeccCc----------------------------cceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEE
Q psy15749 84 VGVEGDVVSTLDYK----------------------------SNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAK 135 (164)
Q Consensus 84 ialpGD~v~~~~~~----------------------------~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gk 135 (164)
+|+|||+|++++.. ....+||+|+|||+|||+++|.|||+||+|++++|+||
T Consensus 75 ig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk 154 (163)
T TIGR02227 75 IGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGK 154 (163)
T ss_pred EecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEE
Confidence 99999999997621 12358999999999999999999999999999999999
Q ss_pred EEEEEeCCC
Q psy15749 136 ASSIIWPPS 144 (164)
Q Consensus 136 v~~~~~p~~ 144 (164)
|.+++||++
T Consensus 155 ~~~~~~p~~ 163 (163)
T TIGR02227 155 VSFVFYPFD 163 (163)
T ss_pred EEEEECCCC
Confidence 999999985
No 2
>KOG1568|consensus
Probab=100.00 E-value=5.2e-39 Score=238.98 Aligned_cols=154 Identities=49% Similarity=0.829 Sum_probs=137.6
Q ss_pred HHHHHHHHHH--HHHHHhhceeEEEEEeCCCCCcccCCCCCC--ceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcce
Q psy15749 4 IFKSMLVGIP--ISITFCDSIGYVARVDGTSMQPVFNPDRNH--QDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKI 79 (164)
Q Consensus 4 ~l~~~~~~i~--i~~~i~~~~~~~~~V~g~SM~Ptl~~g~~~--~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~ 79 (164)
+.+.+..++. +.+.+...+.....|.|.||+|+++++.++ .|+||++|+... ...+.|||+|+|.+|.++++.+
T Consensus 10 ~~ksl~~s~~~~v~~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~--n~~~~rGDiVvl~sP~~p~~~~ 87 (174)
T KOG1568|consen 10 FEKSLTGSLKWHVLLTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVK--NRKVSRGDIVVLKSPNDPDKVI 87 (174)
T ss_pred HHhceeeeeeeheeeeeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccc--cceeccCCEEEEeCCCChhhee
Confidence 3444444444 445666778888999999999999999863 399999999766 5678999999999999999999
Q ss_pred EEEEEeeCCCEEEeccCccceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEEeCCCccccCCcCCCCCcee
Q psy15749 80 IKRIVGVEGDVVSTLDYKSNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSIIWPPSRWQYLKSEVPVHRLN 159 (164)
Q Consensus 80 iKRVialpGD~v~~~~~~~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~~~~~~~~~~~ 159 (164)
||||+|+|||.+...++..+.+.+|+|||||+|||..+|+|||.||||+...|.|||++++||+.|++.+.+..+..|++
T Consensus 88 iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~~~~~~~~~~~~~ 167 (174)
T KOG1568|consen 88 IKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQRLDKESPGRRVP 167 (174)
T ss_pred eeeeecccccEeccCCCCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhhhhcccCCccccc
Confidence 99999999999999888999999999999999999999999999999999999999999999999999999999888765
No 3
>KOG0171|consensus
Probab=100.00 E-value=2.5e-37 Score=230.31 Aligned_cols=133 Identities=36% Similarity=0.599 Sum_probs=118.4
Q ss_pred HHHHHHhhceeEEEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEE
Q psy15749 13 PISITFCDSIGYVARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVS 92 (164)
Q Consensus 13 ~i~~~i~~~~~~~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~ 92 (164)
.++.....+++++...+|.||+||++++ +|+++.+|+++. ++++++||||+++.|.++.+.++|||+|+|||.++
T Consensus 23 ~f~h~t~~yl~e~~~~~gpSM~PTl~~~---gd~l~aEkls~~--f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v~ 97 (176)
T KOG0171|consen 23 AFTHVTHEYLGEFVMCSGPSMEPTLHDG---GDVLLAEKLSYR--FRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDLVE 97 (176)
T ss_pred HHHHHHHHHhcceeeccCCCcCceecCC---CcEEehhhhhHh--hcCCCCCCEEEEeCCCCchhhhhheeeccCCceEE
Confidence 3344456689999999999999999988 478888999999 89999999999999999999999999999999888
Q ss_pred eccCcc----------ceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEEeCCCccccCC
Q psy15749 93 TLDYKS----------NVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSIIWPPSRWQYLK 150 (164)
Q Consensus 93 ~~~~~~----------~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~~~~~~~~ 150 (164)
+..... .+..||+||+||+|||+++|.|||+|||+|.++|+||+++++||.++++.+.
T Consensus 98 v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~ 165 (176)
T KOG0171|consen 98 VHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLI 165 (176)
T ss_pred EecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhcceee
Confidence 765321 3469999999999999999999999999999999999999999999988764
No 4
>PRK10861 signal peptidase I; Provisional
Probab=100.00 E-value=1.4e-36 Score=251.34 Aligned_cols=138 Identities=26% Similarity=0.332 Sum_probs=122.3
Q ss_pred HHHHHHHHHHHHHHHHhhceeEEEEEeCCCCCcccCCCCCCceEEEEEeeeccC----------CCCCcceeeEEEEecC
Q psy15749 3 RIFKSMLVGIPISITFCDSIGYVARVDGTSMQPVFNPDRNHQDYVFLNRWIIKG----------DDIGLQRGDIVSLVSP 72 (164)
Q Consensus 3 ~~l~~~~~~i~i~~~i~~~~~~~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~----------~~~~~~rGDiVvf~~p 72 (164)
++++.++++++++++++.|+++++.|+|+||+|||..| |+++++|++|.. ...+++|||||+|+.|
T Consensus 62 ~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~G----D~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P 137 (324)
T PRK10861 62 ETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIG----DFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYP 137 (324)
T ss_pred HHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccCC----CEEEEEEeecCccCccccccccccCCCCCCCEEEEecC
Confidence 56667778888999999999999999999999999999 999999998752 1257999999999999
Q ss_pred CCCCcceEEEEEeeCCCEEEec--c------Cc-----------------------------------------------
Q psy15749 73 KDPGQKIIKRIVGVEGDVVSTL--D------YK----------------------------------------------- 97 (164)
Q Consensus 73 ~~~~~~~iKRVialpGD~v~~~--~------~~----------------------------------------------- 97 (164)
.+++..+||||+|+|||+|+++ + .+
T Consensus 138 ~~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (324)
T PRK10861 138 EDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNET 217 (324)
T ss_pred CCCCCcEEEEeeecCCcEEEEEeCCCEEEEcCcccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 8888899999999999999985 1 00
Q ss_pred -----------------------------------------cceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEEE
Q psy15749 98 -----------------------------------------SNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKA 136 (164)
Q Consensus 98 -----------------------------------------~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv 136 (164)
...++||+|+||++|||+++|.||||||+||.++|+|||
T Consensus 218 ~~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a 297 (324)
T PRK10861 218 KENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKA 297 (324)
T ss_pred ccccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEE
Confidence 012389999999999999999999999999999999999
Q ss_pred EEEEeCCC
Q psy15749 137 SSIIWPPS 144 (164)
Q Consensus 137 ~~~~~p~~ 144 (164)
..++|+++
T Consensus 298 ~~i~~s~d 305 (324)
T PRK10861 298 TAIWMSFE 305 (324)
T ss_pred EEEEEEcC
Confidence 99999987
No 5
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.93 E-value=6.1e-25 Score=168.59 Aligned_cols=93 Identities=25% Similarity=0.324 Sum_probs=75.9
Q ss_pred eEEEEEeeeccCCCCCcceeeEEEEecCCCC-------------------CcceEEEEEeeCCCEEEeccC---------
Q psy15749 45 DYVFLNRWIIKGDDIGLQRGDIVSLVSPKDP-------------------GQKIIKRIVGVEGDVVSTLDY--------- 96 (164)
Q Consensus 45 d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~-------------------~~~~iKRVialpGD~v~~~~~--------- 96 (164)
+.+.+.++.+. ..++++||+|+|+.|+++ ...++|||+|+|||+|++++.
T Consensus 37 ~pig~y~~~~~--~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~ 114 (176)
T PRK13838 37 EPLGLWRIEAL--DRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLP 114 (176)
T ss_pred CEEEEEEEecc--CCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEcc
Confidence 66677776655 678999999999988543 135999999999999998740
Q ss_pred -------c--------cceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEE
Q psy15749 97 -------K--------SNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSII 140 (164)
Q Consensus 97 -------~--------~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~ 140 (164)
. ....++|+|+|||+||| ++|+||||||+|++++|+|+|.-.+
T Consensus 115 ~~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~-~~S~DSRy~G~V~~~~I~G~a~pi~ 172 (176)
T PRK13838 115 SSSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSF-AGSYDSRYFGPVPASGLLGLARPVL 172 (176)
T ss_pred ccccccccccCCcCCCCCccCcCCCeEEEECCC-CCCCcccccCcccHHHeEEEEEEEE
Confidence 0 01347999999999998 5899999999999999999997554
No 6
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=99.92 E-value=4.1e-24 Score=163.34 Aligned_cols=105 Identities=24% Similarity=0.323 Sum_probs=80.8
Q ss_pred hceeEEEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCC-------------------cceE
Q psy15749 20 DSIGYVARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPG-------------------QKII 80 (164)
Q Consensus 20 ~~~~~~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~-------------------~~~i 80 (164)
.|...+....++||...+. . ..+ ..+++|||+|+|+.|.++. ..++
T Consensus 21 ~~~~~~~~N~T~S~P~g~Y--------~-~~~------~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~v 85 (171)
T TIGR02771 21 LYCVGARINTTKSLPLGLY--------W-TTS------SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLL 85 (171)
T ss_pred cceeeEEEECCCCCcceEE--------E-eCC------CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceE
Confidence 3444455666677665542 2 222 5689999999999885432 2799
Q ss_pred EEEEeeCCCEEEeccCc-------------------------cceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEE
Q psy15749 81 KRIVGVEGDVVSTLDYK-------------------------SNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAK 135 (164)
Q Consensus 81 KRVialpGD~v~~~~~~-------------------------~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gk 135 (164)
|||+|+|||+|++++.. ....++|+| ||++|||+++|.||||||+|++++|+||
T Consensus 86 KRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk 164 (171)
T TIGR02771 86 KRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGR 164 (171)
T ss_pred EEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEE
Confidence 99999999999997620 124789999 9999999999999999999999999999
Q ss_pred EEEEE
Q psy15749 136 ASSII 140 (164)
Q Consensus 136 v~~~~ 140 (164)
|.-.+
T Consensus 165 ~~pl~ 169 (171)
T TIGR02771 165 VKPLF 169 (171)
T ss_pred EEEeE
Confidence 97543
No 7
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.91 E-value=1.4e-23 Score=161.35 Aligned_cols=82 Identities=22% Similarity=0.404 Sum_probs=69.0
Q ss_pred CCcceeeEEEEecCCCC-------------------CcceEEEEEeeCCCEEEeccCc----------------------
Q psy15749 59 IGLQRGDIVSLVSPKDP-------------------GQKIIKRIVGVEGDVVSTLDYK---------------------- 97 (164)
Q Consensus 59 ~~~~rGDiVvf~~p~~~-------------------~~~~iKRVialpGD~v~~~~~~---------------------- 97 (164)
.++++||+|+|+.|++. ...++|||+|+|||+|++++..
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~ 128 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP 128 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence 47899999999987531 1379999999999999997620
Q ss_pred -----cceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEE
Q psy15749 98 -----SNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSII 140 (164)
Q Consensus 98 -----~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~ 140 (164)
...+++|+|+||++|||+++|+||||||+|++++|+|++.-.+
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~ 176 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVI 176 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeE
Confidence 1124899999999999999999999999999999999997543
No 8
>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=99.89 E-value=1.2e-22 Score=139.62 Aligned_cols=89 Identities=30% Similarity=0.484 Sum_probs=77.8
Q ss_pred EEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeecCC
Q psy15749 27 RVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVPQG 106 (164)
Q Consensus 27 ~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp~~ 106 (164)
.|.|+||+|+|++| |++++++.... ...+++||+|+|+.|.+++..++||+++++ ++
T Consensus 2 ~V~g~SM~P~l~~G----D~vlv~~~~~~--~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~-----------------~~ 58 (90)
T TIGR02754 2 KVTGVSMSPTLPPG----DRIIVVPWLKI--FRVPPIGNVVVVRHPLQPYGLIIKRLAAVD-----------------DN 58 (90)
T ss_pred EeeCCCccCccCCC----CEEEEEEcccc--CCCCCCCeEEEEecCCCCcceEEEEeeEEc-----------------CC
Confidence 68999999999999 99999985443 445678999999998766789999998864 45
Q ss_pred eEEEecCCCCCCCCCCccccccCCCeEEEEEE
Q psy15749 107 HIWVEGDHVGHSMDSNMFGPVSMGLVTAKASS 138 (164)
Q Consensus 107 ~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~ 138 (164)
++|++|||+..|.|||++|+|+..+|+|||++
T Consensus 59 ~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~ 90 (90)
T TIGR02754 59 GLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW 90 (90)
T ss_pred eEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence 78999999999999999999999999999853
No 9
>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=99.88 E-value=8.3e-24 Score=156.55 Aligned_cols=82 Identities=38% Similarity=0.611 Sum_probs=32.3
Q ss_pred CCcceeeEEEEecCCC------------CCcceEEEEEeeCCCEEEeccCc------------------------cceee
Q psy15749 59 IGLQRGDIVSLVSPKD------------PGQKIIKRIVGVEGDVVSTLDYK------------------------SNVVK 102 (164)
Q Consensus 59 ~~~~rGDiVvf~~p~~------------~~~~~iKRVialpGD~v~~~~~~------------------------~~~~~ 102 (164)
..+++||+|+|+.|.. .+..++|||+|+|||+|++++.+ ....+
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 4589999999999852 24589999999999999998721 13689
Q ss_pred ecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEE
Q psy15749 103 VPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSII 140 (164)
Q Consensus 103 vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~ 140 (164)
+|+|+||++|||+.+|+||||||+|++++|+|||..++
T Consensus 100 vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~ 137 (138)
T PF10502_consen 100 VPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW 137 (138)
T ss_dssp --TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred eCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence 99999999999999999999999999999999998765
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=99.85 E-value=3.3e-21 Score=130.77 Aligned_cols=84 Identities=39% Similarity=0.657 Sum_probs=75.3
Q ss_pred EEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeec
Q psy15749 25 VARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVP 104 (164)
Q Consensus 25 ~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp 104 (164)
++.|.|+||+|++..| |++++++.... ...+++||+|+|+.|.+++..++|||++
T Consensus 2 ~~~v~g~SM~P~i~~g----d~v~v~~~~~~--~~~~~~GDiv~~~~~~~~~~~~vkRv~~------------------- 56 (85)
T cd06530 2 PVVVPGGSMEPTLQPG----DLVLVNKLSYG--FREPKRGDVVVFKSPGDPGKPIIKRVIG------------------- 56 (85)
T ss_pred eeEEcCCCCcCcccCC----CEEEEEEeecc--cCCCCCCCEEEEeCCCCCCCEEEEEEEE-------------------
Confidence 5789999999999999 99999987432 3479999999999986556899999987
Q ss_pred CCeEEEecCCCCCCCCCCccccccCCCeEEEE
Q psy15749 105 QGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKA 136 (164)
Q Consensus 105 ~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv 136 (164)
||+.|||+++|.|||+||+++.++|+|++
T Consensus 57 ---~~~~gDn~~ns~d~~~~g~~~~~~i~G~~ 85 (85)
T cd06530 57 ---YFVLGDNRNNSLDSRYWGPVPEDDIVGKV 85 (85)
T ss_pred ---EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence 99999999999999999999999999985
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=99.77 E-value=5.2e-18 Score=128.15 Aligned_cols=110 Identities=19% Similarity=0.261 Sum_probs=80.8
Q ss_pred HHHHHHHHHHHHHHHHhhceeEEE------EEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCC
Q psy15749 3 RIFKSMLVGIPISITFCDSIGYVA------RVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPG 76 (164)
Q Consensus 3 ~~l~~~~~~i~i~~~i~~~~~~~~------~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~ 76 (164)
+.+..+++++++++++....+... .|.|+||+||+++| |++++++.. ..++++||+|+|+.|.++
T Consensus 5 ~ii~~~~~~~l~~~~~~~l~~~~~~~~p~v~V~g~SM~Ptl~~G----D~vlv~~~~----~~~~~~GDIVvf~~~~~~- 75 (158)
T TIGR02228 5 NVIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFNTG----DLILVTGAD----PNDIQVGDVITYKSPGFN- 75 (158)
T ss_pred HHHHHHHHHHHHHHHHHHheeeccCCCcEEEEcCCCCcCCccCC----CEEEEEecc----cCCCCCCCEEEEEECCCC-
Confidence 444555555555555444444422 39999999999999 999999853 358999999999988543
Q ss_pred cceEEEEEeeCCCEEEeccCccceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEE
Q psy15749 77 QKIIKRIVGVEGDVVSTLDYKSNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASS 138 (164)
Q Consensus 77 ~~~iKRVialpGD~v~~~~~~~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~ 138 (164)
+.++|||+++.++ + .+..|++.|||+ ...| .++|+.++|+||+..
T Consensus 76 ~~iihRVi~v~~~-----~--------g~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~~ 120 (158)
T TIGR02228 76 TPVTHRVIEINNS-----G--------GELGFITKGDNN-PAPD---GEPVPSENVIGKYLG 120 (158)
T ss_pred ccEEEEEEEEECC-----C--------CcEEEEEEecCC-CCCC---cccCCHHHEEEEEEE
Confidence 7899999997643 0 012477779996 4556 689999999999984
No 12
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.69 E-value=2.1e-16 Score=118.78 Aligned_cols=135 Identities=24% Similarity=0.322 Sum_probs=106.9
Q ss_pred hHHHHHHHHHHHHHHHH--hhceeEEEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcce
Q psy15749 2 FRIFKSMLVGIPISITF--CDSIGYVARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKI 79 (164)
Q Consensus 2 ~~~l~~~~~~i~i~~~i--~~~~~~~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~ 79 (164)
.+|+..+++++++++++ +.+++.++.|+|+||+|||+.| |+++++|.++. ...+..+|++ ..|......+
T Consensus 8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~G----D~v~v~k~~~~--~~~~~~~~~~--~~~~~~~~~~ 79 (166)
T COG0681 8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVG----DRVLVKKFSYG--FGKLKVPDII--VLPAVVEGDL 79 (166)
T ss_pred HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccccC----CEEEEEecccc--ccCCccceee--ecCCCCCcce
Confidence 46888888999999888 8999999999999999999999 99999999988 7888999888 4455667889
Q ss_pred EEEEEeeCCCEEEeccCccc-eeeecCCeEEEecCC-------CCCCCCCCccccccCCCeEEEEEEEEeCCCcc
Q psy15749 80 IKRIVGVEGDVVSTLDYKSN-VVKVPQGHIWVEGDH-------VGHSMDSNMFGPVSMGLVTAKASSIIWPPSRW 146 (164)
Q Consensus 80 iKRVialpGD~v~~~~~~~~-~~~vp~~~~~vlgDn-------~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~~~~ 146 (164)
+||+++++||.+.+++.... ...+|++..++.++| ...+.+++.++.......+.++ ...|-+..
T Consensus 80 ~kr~~~~~GD~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~gd~~ 152 (166)
T COG0681 80 IKRVIGLRGDIVVFKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV--IGLPGDNI 152 (166)
T ss_pred EEEeccCCCCEEEEECCEEEeecccCcchhhhhcccccccccccccccCccccccccccccccce--EEeeccce
Confidence 99999999999999874322 345566666665543 4467777878777777777777 34454443
No 13
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.57 E-value=7.4e-15 Score=108.94 Aligned_cols=82 Identities=23% Similarity=0.410 Sum_probs=68.5
Q ss_pred CCCcceeeEEEEecCCC------------CCcceEEEEEeeCCCEEEeccCc------------------------ccee
Q psy15749 58 DIGLQRGDIVSLVSPKD------------PGQKIIKRIVGVEGDVVSTLDYK------------------------SNVV 101 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~------------~~~~~iKRVialpGD~v~~~~~~------------------------~~~~ 101 (164)
..++.+||+|+++.|+. ....++|||.|+|||+|.+.+.. ....
T Consensus 51 ~~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR 130 (173)
T COG4959 51 SAPVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCR 130 (173)
T ss_pred CCCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCc
Confidence 44679999999999963 34679999999999999987511 1234
Q ss_pred eecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEE
Q psy15749 102 KVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSI 139 (164)
Q Consensus 102 ~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~ 139 (164)
.+-++++|+++|..+.|+|||||||||.++|+|.+.-+
T Consensus 131 ~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPv 168 (173)
T COG4959 131 YLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPV 168 (173)
T ss_pred eecCCeEEEEeccCCcccccceecccCHHHcceeeeee
Confidence 58889999999999999999999999999999988654
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=99.31 E-value=8.9e-12 Score=81.01 Aligned_cols=58 Identities=33% Similarity=0.531 Sum_probs=47.1
Q ss_pred EEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEecc
Q psy15749 27 RVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLD 95 (164)
Q Consensus 27 ~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~ 95 (164)
+|.|+||+|++.+| |++++++ ...++.||+|+|..+.+. ..++||+++.+|+.+.+..
T Consensus 1 ~V~GdSM~P~i~~G----d~v~v~~------~~~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~~ 58 (70)
T PF00717_consen 1 RVEGDSMEPTIKDG----DIVLVDP------SSEPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILISS 58 (70)
T ss_dssp EEESSTTGGTSSTT----EEEEEEE------TS---TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-S
T ss_pred CeECcCcccCeeCC----CEEEEEE------cCCCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEec
Confidence 58999999999999 9999998 568999999999986432 3899999999999888764
No 15
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=99.27 E-value=4e-11 Score=79.98 Aligned_cols=82 Identities=34% Similarity=0.597 Sum_probs=62.8
Q ss_pred EEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeec
Q psy15749 25 VARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVP 104 (164)
Q Consensus 25 ~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp 104 (164)
.+.+.|+||+|++..| |.+++++. ...++.||+++++.+. +..++||+...++
T Consensus 2 ~~~v~g~SM~P~i~~g----d~v~i~~~-----~~~~~~G~iv~~~~~~--~~~~ikrl~~~~~---------------- 54 (84)
T cd06462 2 ALRVEGDSMEPTIPDG----DLVLVDKS-----SYEPKRGDIVVFRLPG--GELTVKRVIGLPG---------------- 54 (84)
T ss_pred eeEEcCCCccCcccCC----CEEEEEec-----CCCCcCCEEEEEEcCC--CcEEEEEEEEECC----------------
Confidence 4689999999999999 99999983 2238999999999863 4899999987654
Q ss_pred CCeEEEecCCCCCCCCCCccccccCCCeEEE
Q psy15749 105 QGHIWVEGDHVGHSMDSNMFGPVSMGLVTAK 135 (164)
Q Consensus 105 ~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gk 135 (164)
++++++.+|| +++.+.+..+. ....++|+
T Consensus 55 ~~~~~l~~~N-~~~~~~~~~~~-~~~~i~g~ 83 (84)
T cd06462 55 EGHYFLLGDN-PNSPDSRIDGP-PELDIVGV 83 (84)
T ss_pred CCEEEEECCC-CCCCcccccCC-CHHHEEEe
Confidence 3688899999 35555554333 45566665
No 16
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.94 E-value=1e-08 Score=80.73 Aligned_cols=87 Identities=21% Similarity=0.329 Sum_probs=63.6
Q ss_pred EEEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeee
Q psy15749 24 YVARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKV 103 (164)
Q Consensus 24 ~~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~v 103 (164)
....|.|+||+|++.+| |.++|+. ..+..+||.|.+.. .+++.++||+.-.
T Consensus 124 ~~i~V~GDSMeP~~~~G----d~ilVd~------~~~~~~gd~v~v~~--~g~~~~VK~l~~~----------------- 174 (214)
T COG2932 124 FALRVTGDSMEPTYEDG----DTLLVDP------GVNTRRGDRVYVET--DGGELYVKKLQRE----------------- 174 (214)
T ss_pred EEEEEeCCcccccccCC----CEEEECC------CCceeeCCEEEEEE--eCCeEEEEEEEEe-----------------
Confidence 46789999999999999 9999998 56778999666654 3368999999654
Q ss_pred cCCeEEEecCCCCCCCCCCccccccCC---CeEEEEEEEEeCC
Q psy15749 104 PQGHIWVEGDHVGHSMDSNMFGPVSMG---LVTAKASSIIWPP 143 (164)
Q Consensus 104 p~~~~~vlgDn~~~s~DSR~~G~V~~~---~I~Gkv~~~~~p~ 143 (164)
|.+.+.+.++|+....|--. ..+ .|+|||++..-++
T Consensus 175 ~~~~~~l~S~N~~~~~~~~~----~~~~~v~iIgrVv~~~~~~ 213 (214)
T COG2932 175 PGGLLRLVSLNPDYYPDEIF----SEDDDVEIIGRVVWVSRLL 213 (214)
T ss_pred cCCeEEEEeCCCCCCccccc----CccceEEEEEEEEEEeeec
Confidence 55566677888754333321 222 4899998876543
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=98.84 E-value=3.3e-08 Score=65.56 Aligned_cols=52 Identities=31% Similarity=0.447 Sum_probs=44.3
Q ss_pred EEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCC
Q psy15749 25 VARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGD 89 (164)
Q Consensus 25 ~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD 89 (164)
.+.+.|+||+|.+++| |.+++++ ...++.||++++..+ +..++||+...+++
T Consensus 2 ~~~v~g~sM~p~i~~g----d~lii~~------~~~~~~g~i~~~~~~---~~~~ikr~~~~~~~ 53 (81)
T cd06529 2 ALRVKGDSMEPTIPDG----DLVLVDP------SDTPRDGDIVVARLD---GELTVKRLQRRGGG 53 (81)
T ss_pred EEEEECCCcCCccCCC----CEEEEcC------CCCCCCCCEEEEEEC---CEEEEEEEEECCCC
Confidence 4689999999999999 9999998 456999999999975 37899999875543
No 18
>KOG3342|consensus
Probab=98.76 E-value=4.8e-08 Score=72.74 Aligned_cols=89 Identities=21% Similarity=0.367 Sum_probs=64.0
Q ss_pred EEEEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeec
Q psy15749 25 VARVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVP 104 (164)
Q Consensus 25 ~~~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp 104 (164)
+..|-++||||.++.| |.++..... ....+.||+|+|+.+ ..+-+.+|||+-+-+- .
T Consensus 50 iVVVLSgSMePaF~RG----DlLfL~N~~----~~p~~vGdivVf~ve-gR~IPiVHRviK~he~--------------~ 106 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHRG----DLLFLTNRN----EDPIRVGDIVVFKVE-GREIPIVHRVIKQHEK--------------S 106 (180)
T ss_pred EEEEEcCCcCcccccc----cEEEEecCC----CCcceeccEEEEEEC-CccCchhHHHHHHhcc--------------c
Confidence 4578899999999999 999987432 457899999999986 3467899999754211 2
Q ss_pred CCe--EEEecCCCCCCCCCCc-c----ccccCCCeEEEEEE
Q psy15749 105 QGH--IWVEGDHVGHSMDSNM-F----GPVSMGLVTAKASS 138 (164)
Q Consensus 105 ~~~--~~vlgDn~~~s~DSR~-~----G~V~~~~I~Gkv~~ 138 (164)
+|+ +...|||. ..|-|. | -...+++|.|+|.-
T Consensus 107 ~~~~~~LTKGDNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~G 145 (180)
T KOG3342|consen 107 NGHIKFLTKGDNN--AVDDRGLYAQGQNWLERKDIVGRVRG 145 (180)
T ss_pred CCcEEEEecCCCC--cccchhcccccccceeccceeeEEee
Confidence 233 45559984 334442 2 35778999999865
No 19
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.54 E-value=1.6e-06 Score=64.06 Aligned_cols=85 Identities=16% Similarity=0.168 Sum_probs=58.5
Q ss_pred EEEEEeCCCCC-cccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceee
Q psy15749 24 YVARVDGTSMQ-PVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVK 102 (164)
Q Consensus 24 ~~~~V~g~SM~-Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~ 102 (164)
....|.|+||+ |++.+| |++++++ ..+++.||+|++.. .++..+||+.-.
T Consensus 52 f~l~V~GdSM~~~~I~~G----D~liVd~------~~~~~~Gdivv~~~---~g~~~vKrl~~~---------------- 102 (139)
T PRK10276 52 YFVKASGDSMIDAGISDG----DLLIVDS------AITASHGDIVIAAV---DGEFTVKKLQLR---------------- 102 (139)
T ss_pred EEEEEecCCCCCCCCCCC----CEEEEEC------CCCCCCCCEEEEEE---CCEEEEEEEEEC----------------
Confidence 45789999998 689999 9999997 45678999999875 246789998521
Q ss_pred ecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEEeC
Q psy15749 103 VPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSIIWP 142 (164)
Q Consensus 103 vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p 142 (164)
+++++.++|+.. ....+-.-..=.|+|+|.+.+..
T Consensus 103 ---~~~~L~s~N~~y--~~i~i~~~~~~~IiG~V~~~~~~ 137 (139)
T PRK10276 103 ---PTVQLIPMNSAY--SPITISSEDTLDVFGVVTHIVKA 137 (139)
T ss_pred ---CcEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEEEEe
Confidence 246677777521 11111111112699999887653
No 20
>PRK00215 LexA repressor; Validated
Probab=98.47 E-value=2.5e-06 Score=66.50 Aligned_cols=86 Identities=22% Similarity=0.324 Sum_probs=61.4
Q ss_pred eeEEEEEeCCCCC-cccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccce
Q psy15749 22 IGYVARVDGTSMQ-PVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNV 100 (164)
Q Consensus 22 ~~~~~~V~g~SM~-Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~ 100 (164)
-.....|.|+||. |++.+| |++++++ ...++.||+|++... ++..+||+.-.
T Consensus 117 ~~~~~~V~GdSM~~~~i~~G----d~v~v~~------~~~~~~G~ivv~~~~---~~~~vKrl~~~-------------- 169 (205)
T PRK00215 117 EDFLLRVRGDSMIDAGILDG----DLVIVRK------QQTARNGQIVVALID---DEATVKRFRRE-------------- 169 (205)
T ss_pred CeEEEEEccCCCCCCCcCCC----CEEEEeC------CCCCCCCCEEEEEEC---CEEEEEEEEEe--------------
Confidence 3456789999995 799999 9999987 446789999999874 37899999632
Q ss_pred eeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEEe
Q psy15749 101 VKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSIIW 141 (164)
Q Consensus 101 ~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~~ 141 (164)
.|.+++.+||++. +.....+ ..-.|+|+|+..+.
T Consensus 170 ----~~~~~L~s~Np~y--~~~~~~~-~~~~IiG~Vv~~~r 203 (205)
T PRK00215 170 ----GGHIRLEPENPAY--EPIIVDP-DRVTIEGKVVGLIR 203 (205)
T ss_pred ----CCEEEEEcCCCCC--CCEEeCC-CcEEEEEEEEEEEE
Confidence 3567777888632 2221111 02479999988764
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=98.43 E-value=3.8e-06 Score=65.22 Aligned_cols=88 Identities=15% Similarity=0.188 Sum_probs=63.1
Q ss_pred eeEEEEEeCCCCC-cccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccce
Q psy15749 22 IGYVARVDGTSMQ-PVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNV 100 (164)
Q Consensus 22 ~~~~~~V~g~SM~-Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~ 100 (164)
-...+.|.|+||. |.+.+| |++++++ ...++.||+|++.. .++..+||+.-.
T Consensus 110 ~~f~~~V~GdSM~~~~i~~G----d~v~v~~------~~~~~~G~ivvv~~---~~~~~vKrl~~~-------------- 162 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGICDG----DLLIVRS------QKDARNGEIVAAMI---DGEVTVKRFYKD-------------- 162 (199)
T ss_pred CEEEEEecCCCCCCCCCCCC----CEEEEec------CCCCCCCCEEEEEE---CCEEEEEEEEEE--------------
Confidence 3467899999996 689999 9999987 45789999999987 357899998532
Q ss_pred eeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEEeCC
Q psy15749 101 VKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSIIWPP 143 (164)
Q Consensus 101 ~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~ 143 (164)
.+.+++..+|+... | ..... ..=.|+|+|+..+..+
T Consensus 163 ----~~~i~L~s~N~~y~-~-i~~~~-~~~~IiG~Vv~~~r~~ 198 (199)
T TIGR00498 163 ----GTKVELKPENPEFD-P-IVLNA-EDVTILGKVVGVIRNF 198 (199)
T ss_pred ----CCEEEEEcCCCCCc-C-CcCCC-CcEEEEEEEEEEEEec
Confidence 34677778886321 1 11110 1247999999887654
No 22
>PRK12423 LexA repressor; Provisional
Probab=98.35 E-value=6.8e-06 Score=64.28 Aligned_cols=85 Identities=21% Similarity=0.199 Sum_probs=60.5
Q ss_pred EEEEEeCCCCC-cccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceee
Q psy15749 24 YVARVDGTSMQ-PVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVK 102 (164)
Q Consensus 24 ~~~~V~g~SM~-Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~ 102 (164)
....|.|+||. |++.+| |.+++++ ...++.||+|++... ++..+||+.-.
T Consensus 115 f~l~V~GdSM~~~~i~~G----d~viv~~------~~~~~~Gdivv~~~~---~~~~vKrl~~~---------------- 165 (202)
T PRK12423 115 YLLQVQGDSMIDDGILDG----DLVGVHR------SPEARDGQIVVARLD---GEVTIKRLERS---------------- 165 (202)
T ss_pred EEEEEecCcCCCCCcCCC----CEEEEeC------CCcCCCCCEEEEEEC---CEEEEEEEEEe----------------
Confidence 35799999997 799999 9999987 457889999999862 46889998532
Q ss_pred ecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEEe
Q psy15749 103 VPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSIIW 141 (164)
Q Consensus 103 vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~~ 141 (164)
.+.+++..+|+. ++...+-+-..=.|+|+++..+.
T Consensus 166 --~~~~~L~s~N~~--y~~i~~~~~~~~~I~Gvv~g~~r 200 (202)
T PRK12423 166 --GDRIRLLPRNPA--YAPIVVAPDQDFAIEGVFCGLIR 200 (202)
T ss_pred --CCEEEEEcCCCC--CCCEEcCCCCcEEEEEEEEEEEE
Confidence 245777788752 22222211123379999988764
No 23
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.79 E-value=0.00043 Score=54.32 Aligned_cols=88 Identities=18% Similarity=0.203 Sum_probs=63.8
Q ss_pred eEEEEEeCCCCC-cccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCcccee
Q psy15749 23 GYVARVDGTSMQ-PVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVV 101 (164)
Q Consensus 23 ~~~~~V~g~SM~-Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~ 101 (164)
.++..|.|+||. +.+.+| |.++|++ ....+.||+|+...++ ++..+||..-
T Consensus 112 ~f~L~V~GdSM~~~gi~dG----DlvvV~~------~~~a~~GdiVvA~i~g--~e~TvKrl~~---------------- 163 (201)
T COG1974 112 TFFLRVSGDSMIDAGILDG----DLVVVDP------TEDAENGDIVVALIDG--EEATVKRLYR---------------- 163 (201)
T ss_pred eEEEEecCCccccCcCCCC----CEEEEcC------CCCCCCCCEEEEEcCC--CcEEEEEEEE----------------
Confidence 456789999995 777888 9999997 7889999999999753 5688999852
Q ss_pred eecCCeEEEecCCCCCCCCCCccccccCCCeEEEEEEEEeCC
Q psy15749 102 KVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKASSIIWPP 143 (164)
Q Consensus 102 ~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~~~~~p~ 143 (164)
..+++++..-|+. +.+..+..= .=.|+|+++.++|+.
T Consensus 164 --~g~~i~L~p~Np~--~~~i~~~~~-~~~I~G~vvgv~r~~ 200 (201)
T COG1974 164 --DGNQILLKPENPA--YPPIPVDAD-SVTILGKVVGVIRDI 200 (201)
T ss_pred --eCCEEEEEeCCCC--CCCcccCcc-ceEEEEEEEEEEecC
Confidence 2345666666642 222222211 346999999999875
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=87.22 E-value=0.7 Score=34.03 Aligned_cols=12 Identities=42% Similarity=0.354 Sum_probs=10.6
Q ss_pred CcceeeEEEEec
Q psy15749 60 GLQRGDIVSLVS 71 (164)
Q Consensus 60 ~~~rGDiVvf~~ 71 (164)
...+||+|+|++
T Consensus 84 ~~~~GD~i~~~~ 95 (166)
T COG0681 84 IGLRGDIVVFKD 95 (166)
T ss_pred ccCCCCEEEEEC
Confidence 568899999998
No 25
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=87.21 E-value=4.1 Score=28.24 Aligned_cols=71 Identities=18% Similarity=0.208 Sum_probs=46.4
Q ss_pred CceEEEEEeeecc-----------CCCCCcceeeEEEEecC-CCCCcceEEEEEeeCCCEEEeccCccceeeecCCeEEE
Q psy15749 43 HQDYVFLNRWIIK-----------GDDIGLQRGDIVSLVSP-KDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVPQGHIWV 110 (164)
Q Consensus 43 ~~d~vlv~r~~~~-----------~~~~~~~rGDiVvf~~p-~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp~~~~~v 110 (164)
++|+|++.+.--. ....++++|.+|+.-.- .+.+...+. .-=.-||+|.+..|.....++...+|.+
T Consensus 6 L~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~~~~g~~~~-~~VkvGD~Vlf~ky~G~evk~dgeeyli 84 (96)
T COG0234 6 LGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENGELVP-LDVKVGDRVLFGKYAGTEVKIDGEEYLI 84 (96)
T ss_pred cCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEccceecCCCCEec-cccccCCEEEECccCCcEEEECCEEEEE
Confidence 4599999886322 12457889998888641 111111111 1113599999999988889998888988
Q ss_pred ecCC
Q psy15749 111 EGDH 114 (164)
Q Consensus 111 lgDn 114 (164)
+.+.
T Consensus 85 l~e~ 88 (96)
T COG0234 85 LSES 88 (96)
T ss_pred echH
Confidence 8754
No 26
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=81.65 E-value=10 Score=26.54 Aligned_cols=65 Identities=17% Similarity=0.198 Sum_probs=40.5
Q ss_pred ceEEEEEeeecc-----------CCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeecCCeEEEec
Q psy15749 44 QDYVFLNRWIIK-----------GDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVPQGHIWVEG 112 (164)
Q Consensus 44 ~d~vlv~r~~~~-----------~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp~~~~~vlg 112 (164)
+|+|++.+.... ....+++.|.+|..-+- .... -.-=.+||+|.+..|....+++...+|.++.
T Consensus 16 ~dRVLVk~~~~e~kT~gGIiLP~sakekp~~g~VvAVG~G----~~~~-~~~Vk~GD~Vl~~~y~Gtevk~dg~ey~i~~ 90 (100)
T PTZ00414 16 GQRVLVKRTLAAKQTKAGVLIPEQVAGKVNEGTVVAVAAA----TKDW-TPTVKVGDTVLLPEFGGSSVKVEGEEFFLYN 90 (100)
T ss_pred CCEEEEEEcccccccccCEEcccccccCCceeEEEEECCC----Cccc-cceecCCCEEEEcCCCCcEEEECCEEEEEEE
Confidence 499999875322 01345666777766431 1111 1112469999998888888888777787765
Q ss_pred C
Q psy15749 113 D 113 (164)
Q Consensus 113 D 113 (164)
+
T Consensus 91 e 91 (100)
T PTZ00414 91 E 91 (100)
T ss_pred h
Confidence 4
No 27
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=81.46 E-value=13 Score=25.51 Aligned_cols=27 Identities=22% Similarity=0.164 Sum_probs=16.8
Q ss_pred eCCCEEEeccCccceeeecCCeEEEec
Q psy15749 86 VEGDVVSTLDYKSNVVKVPQGHIWVEG 112 (164)
Q Consensus 86 lpGD~v~~~~~~~~~~~vp~~~~~vlg 112 (164)
.+||+|.+..|....+++....|.++.
T Consensus 60 k~GD~Vlf~~~~g~ev~~~~~~y~iv~ 86 (95)
T PRK00364 60 KVGDKVLFGKYAGTEVKIDGEEYLILR 86 (95)
T ss_pred CCCCEEEEcCCCCeEEEECCEEEEEEE
Confidence 357777777766666666555555543
No 28
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=78.35 E-value=17 Score=24.89 Aligned_cols=65 Identities=9% Similarity=0.036 Sum_probs=36.7
Q ss_pred ceEEEEEeeeccC-----------CCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeecCCeEEEec
Q psy15749 44 QDYVFLNRWIIKG-----------DDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVPQGHIWVEG 112 (164)
Q Consensus 44 ~d~vlv~r~~~~~-----------~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp~~~~~vlg 112 (164)
+|+||+.+..... ...+++.|.+|..-.. .... -.--.+||+|.+..|....+++....|.++.
T Consensus 7 ~DRVLVk~~~~e~~T~gGI~Lp~~a~ek~~~G~VvavG~g----~~~~-~~~Vk~GD~Vl~~~y~g~ev~~~~~~y~iv~ 81 (91)
T PRK14533 7 GERLLIKPIKEEKKTEGGIVLPDSAKEKPMKAEVVAVGKL----DDEE-DFDIKVGDKVIFSKYAGTEIKIDDEDYIIID 81 (91)
T ss_pred CCEEEEEEccccceecccEEecccccCCcceEEEEEECCC----Cccc-cccccCCCEEEEccCCCeEEEECCEEEEEEE
Confidence 4999998753210 1234566666666421 1000 1112468888888777777777666666654
Q ss_pred C
Q psy15749 113 D 113 (164)
Q Consensus 113 D 113 (164)
+
T Consensus 82 e 82 (91)
T PRK14533 82 V 82 (91)
T ss_pred h
Confidence 3
No 29
>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=74.01 E-value=25 Score=23.95 Aligned_cols=26 Identities=23% Similarity=0.193 Sum_probs=16.9
Q ss_pred eCCCEEEeccCccceeeecCCeEEEe
Q psy15749 86 VEGDVVSTLDYKSNVVKVPQGHIWVE 111 (164)
Q Consensus 86 lpGD~v~~~~~~~~~~~vp~~~~~vl 111 (164)
.+||+|.+..|....+++-...|.++
T Consensus 59 k~GD~Vl~~~~~g~~v~~~~~~y~i~ 84 (93)
T cd00320 59 KVGDKVLFPKYAGTEVKLDGEEYLIL 84 (93)
T ss_pred cCCCEEEECCCCceEEEECCEEEEEE
Confidence 46788887777666666655555554
No 30
>KOG1641|consensus
Probab=72.81 E-value=30 Score=24.29 Aligned_cols=28 Identities=25% Similarity=0.253 Sum_probs=18.6
Q ss_pred eCCCEEEeccCccceeeec-CCeEEEecC
Q psy15749 86 VEGDVVSTLDYKSNVVKVP-QGHIWVEGD 113 (164)
Q Consensus 86 lpGD~v~~~~~~~~~~~vp-~~~~~vlgD 113 (164)
.+||+|-+-+|....+.+. +++|.+.-|
T Consensus 68 k~Gd~VLlpeygGt~V~l~~~~~~~~fr~ 96 (104)
T KOG1641|consen 68 KVGDRVLLPEYGGTKVKLGDEDEYHLFRD 96 (104)
T ss_pred cCCCEEEeeccCCcEEeccCCceeEEecc
Confidence 4688888777777777777 346655544
No 31
>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=71.90 E-value=9.9 Score=26.75 Aligned_cols=38 Identities=24% Similarity=0.321 Sum_probs=23.9
Q ss_pred CCCcceeeEEEEecCCCCCcceEEEEEee-CCCEEEecc
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKRIVGV-EGDVVSTLD 95 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKRVial-pGD~v~~~~ 95 (164)
...|+.|||++|........-.+--|.+. .+++|++.+
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 56899999999953223334467777777 778887755
No 32
>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=67.92 E-value=28 Score=25.22 Aligned_cols=14 Identities=14% Similarity=-0.211 Sum_probs=11.5
Q ss_pred CCCcceeeEEEEec
Q psy15749 58 DIGLQRGDIVSLVS 71 (164)
Q Consensus 58 ~~~~~rGDiVvf~~ 71 (164)
..+++.||+|+|+.
T Consensus 71 v~~p~~GDiv~f~~ 84 (129)
T TIGR02594 71 LSKPAYGCIAVKRR 84 (129)
T ss_pred CCCCCccEEEEEEC
Confidence 34689999999975
No 33
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=58.53 E-value=61 Score=24.57 Aligned_cols=37 Identities=22% Similarity=0.289 Sum_probs=28.4
Q ss_pred CCCcceeeEEEEecCCCCCcceEEE---EEeeCCCEEEeccC
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKR---IVGVEGDVVSTLDY 96 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKR---VialpGD~v~~~~~ 96 (164)
...++.|++.+|.. +.....+|| ++...++++++...
T Consensus 72 ~~~L~~GEvalY~~--~G~~I~L~~~G~ii~~~~~~~~v~a~ 111 (162)
T PF06890_consen 72 PKGLKPGEVALYDD--EGQKIHLKRDGRIIEVTCKTVTVNAA 111 (162)
T ss_pred ccCCCCCcEEEEcC--CCCEEEEEecceEEeccCceEEEecC
Confidence 56789999999985 345666765 77788899988753
No 34
>PF14118 YfzA: YfzA-like protein
Probab=57.89 E-value=8.9 Score=26.46 Aligned_cols=32 Identities=28% Similarity=0.406 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHHHHHHHhhceeEEEEEeCCCCCcccCCC
Q psy15749 2 FRIFKSMLVGIPISITFCDSIGYVARVDGTSMQPVFNPD 40 (164)
Q Consensus 2 ~~~l~~~~~~i~i~~~i~~~~~~~~~V~g~SM~Ptl~~g 40 (164)
+.|+..+++.+++-+++. .+++.|+.|.+++|
T Consensus 11 k~W~~~L~iF~i~QLlFi-------~~d~t~w~pnf~~g 42 (94)
T PF14118_consen 11 KRWFITLGIFLIVQLLFI-------IFDGTGWGPNFNEG 42 (94)
T ss_pred hhHHHHHHHHHHHHHHHH-------HhhccccccccCCC
Confidence 578888888888777653 35789999999997
No 35
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=57.74 E-value=15 Score=26.50 Aligned_cols=54 Identities=22% Similarity=0.185 Sum_probs=29.2
Q ss_pred CCcceeeEEEEecCCCCCcceEEEEEe------eCCCEEEeccCccceeeecCCeEEEec
Q psy15749 59 IGLQRGDIVSLVSPKDPGQKIIKRIVG------VEGDVVSTLDYKSNVVKVPQGHIWVEG 112 (164)
Q Consensus 59 ~~~~rGDiVvf~~p~~~~~~~iKRVia------lpGD~v~~~~~~~~~~~vp~~~~~vlg 112 (164)
..++.||-|+...+.....+.=..|++ ..+..+++.-+......+|.++++-+.
T Consensus 54 ~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~~~~~I~ 113 (124)
T PF15057_consen 54 HSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAKVPRGEVIWIS 113 (124)
T ss_pred CcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECCCCCccchhhEEECC
Confidence 456666666666554433444456663 344555554444555566666655443
No 36
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=56.71 E-value=73 Score=23.01 Aligned_cols=30 Identities=23% Similarity=0.452 Sum_probs=20.4
Q ss_pred eeecCCeEEEecCCCCCCCCCCccccccCCC
Q psy15749 101 VKVPQGHIWVEGDHVGHSMDSNMFGPVSMGL 131 (164)
Q Consensus 101 ~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~ 131 (164)
+...+|.+-++.++ .+..-+|-||||.+|.
T Consensus 77 i~FddNA~Viin~~-g~P~GtrI~GPVaREl 106 (122)
T COG0093 77 IKFDDNAAVIINPD-GEPRGTRIFGPVAREL 106 (122)
T ss_pred EEeCCceEEEECCC-CCcccceEecchhHHH
Confidence 34445555555544 4778899999999863
No 37
>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=52.93 E-value=69 Score=21.62 Aligned_cols=24 Identities=25% Similarity=0.250 Sum_probs=12.9
Q ss_pred CCCEEEeccCccceeeecCCeEEE
Q psy15749 87 EGDVVSTLDYKSNVVKVPQGHIWV 110 (164)
Q Consensus 87 pGD~v~~~~~~~~~~~vp~~~~~v 110 (164)
+||+|.+.++....++.....|.+
T Consensus 60 ~GD~Vl~~~~~g~~v~~~~~~~~~ 83 (93)
T PF00166_consen 60 VGDKVLFPKYAGTEVKFDGEKYLI 83 (93)
T ss_dssp TTSEEEEETTTSEEEEETTEEEEE
T ss_pred eccEEeccccCceEEEECCEEEEE
Confidence 477777766555455553333433
No 38
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=48.39 E-value=28 Score=19.98 Aligned_cols=35 Identities=23% Similarity=0.263 Sum_probs=24.9
Q ss_pred CCCCCcceEEEEEeeCCCEEEeccCccceeeecCC
Q psy15749 72 PKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVPQG 106 (164)
Q Consensus 72 p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp~~ 106 (164)
|+....+...+|+...||.++++-......+++++
T Consensus 7 pD~~egfv~g~I~~~~g~~vtV~~~~G~~~tv~~d 41 (42)
T PF02736_consen 7 PDPKEGFVKGEIIEEEGDKVTVKTEDGKEVTVKKD 41 (42)
T ss_dssp EESSSSEEEEEEEEEESSEEEEEETTTEEEEEEGG
T ss_pred eCCcccEEEEEEEEEcCCEEEEEECCCCEEEeCCC
Confidence 33446788899999999999987544555666543
No 39
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=47.03 E-value=11 Score=24.65 Aligned_cols=17 Identities=47% Similarity=0.870 Sum_probs=12.1
Q ss_pred CCCCcccCCCCCCceEEEEEe
Q psy15749 31 TSMQPVFNPDRNHQDYVFLNR 51 (164)
Q Consensus 31 ~SM~Ptl~~g~~~~d~vlv~r 51 (164)
.||+|.+++| ++|++.-
T Consensus 12 ~~m~P~L~~~----~yVF~t~ 28 (72)
T PF10000_consen 12 ASMSPELNPG----EYVFCTV 28 (72)
T ss_dssp ST-EEEE-SS-----EEEEEE
T ss_pred hhCCcEeCCC----CEEEEEe
Confidence 4899999999 9999965
No 40
>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=46.04 E-value=56 Score=22.95 Aligned_cols=26 Identities=38% Similarity=0.625 Sum_probs=19.6
Q ss_pred cceeeEEEEecCCCCCcceEEEEEee
Q psy15749 61 LQRGDIVSLVSPKDPGQKIIKRIVGV 86 (164)
Q Consensus 61 ~~rGDiVvf~~p~~~~~~~iKRVial 86 (164)
++.||-|.+++++++....+.||..+
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i 29 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERL 29 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEE
Confidence 57789999988766566778887664
No 41
>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=45.91 E-value=32 Score=24.46 Aligned_cols=28 Identities=29% Similarity=0.364 Sum_probs=21.3
Q ss_pred CcceeeEEEEecCCCCCcceEEEEEeeC
Q psy15749 60 GLQRGDIVSLVSPKDPGQKIIKRIVGVE 87 (164)
Q Consensus 60 ~~~rGDiVvf~~p~~~~~~~iKRVialp 87 (164)
.++.||-|.++.++++...+|.||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~ 30 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLW 30 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 3578999999987655678899987653
No 42
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=45.69 E-value=22 Score=23.53 Aligned_cols=18 Identities=33% Similarity=0.434 Sum_probs=9.5
Q ss_pred eEEEEEeeeccCCCCCcceeeEE
Q psy15749 45 DYVFLNRWIIKGDDIGLQRGDIV 67 (164)
Q Consensus 45 d~vlv~r~~~~~~~~~~~rGDiV 67 (164)
|.|++.... .+.++|||+
T Consensus 51 D~V~Ve~~~-----~d~~kg~I~ 68 (75)
T COG0361 51 DVVLVELSP-----YDLTKGRIV 68 (75)
T ss_pred CEEEEEecc-----cccccccEE
Confidence 666665542 235556654
No 43
>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=44.95 E-value=26 Score=22.73 Aligned_cols=18 Identities=33% Similarity=0.292 Sum_probs=8.7
Q ss_pred eEEEEEeeeccCCCCCcceeeEE
Q psy15749 45 DYVFLNRWIIKGDDIGLQRGDIV 67 (164)
Q Consensus 45 d~vlv~r~~~~~~~~~~~rGDiV 67 (164)
|.|.+....| ++.+|||+
T Consensus 49 D~V~Ve~spy-----d~tkgrIi 66 (68)
T TIGR00008 49 DKVKVELSPY-----DLTRGRIT 66 (68)
T ss_pred CEEEEEECcc-----cCCcEeEE
Confidence 5555554422 34555554
No 44
>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=44.74 E-value=1.2e+02 Score=21.93 Aligned_cols=78 Identities=6% Similarity=-0.001 Sum_probs=41.1
Q ss_pred CCcceeeEEEEecCCCC----------CcceEEEEEeeCCC---EEEecc------Cc--cceeeecCCeEEEecCCC-C
Q psy15749 59 IGLQRGDIVSLVSPKDP----------GQKIIKRIVGVEGD---VVSTLD------YK--SNVVKVPQGHIWVEGDHV-G 116 (164)
Q Consensus 59 ~~~~rGDiVvf~~p~~~----------~~~~iKRVialpGD---~v~~~~------~~--~~~~~vp~~~~~vlgDn~-~ 116 (164)
..++.||+|+++.++.+ ...+|-||..+.-+ .-.+.. .+ ... .-.+.++|+ +|+. +
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~-~~~~~ElFL-Sd~c~~ 81 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN-YANERELFL-TNECTC 81 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc-cCCCceEEE-eccccc
Confidence 45788998888876433 24577777665322 111110 00 011 334455555 4443 1
Q ss_pred CCCCCCccccccCCCeEEEEEEEEeCCC
Q psy15749 117 HSMDSNMFGPVSMGLVTAKASSIIWPPS 144 (164)
Q Consensus 117 ~s~DSR~~G~V~~~~I~Gkv~~~~~p~~ 144 (164)
.+.++. .+.|.||+..-+.+..
T Consensus 82 ~~~~~~------~~~I~~k~~V~~~~~~ 103 (130)
T cd04712 82 LELDLL------STEIKGVHKVDWSGTP 103 (130)
T ss_pred cccccc------cceeEEEEEEEEecCc
Confidence 222211 4599999988876644
No 45
>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=44.57 E-value=33 Score=21.59 Aligned_cols=13 Identities=38% Similarity=0.588 Sum_probs=6.9
Q ss_pred CCcceeeEEEEec
Q psy15749 59 IGLQRGDIVSLVS 71 (164)
Q Consensus 59 ~~~~rGDiVvf~~ 71 (164)
--+++||.|+...
T Consensus 40 iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 40 IWIKRGDFVLVEP 52 (65)
T ss_dssp C---TTEEEEEEE
T ss_pred EecCCCCEEEEEe
Confidence 3567777777764
No 46
>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=42.64 E-value=49 Score=24.63 Aligned_cols=38 Identities=18% Similarity=0.271 Sum_probs=25.6
Q ss_pred EEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecC
Q psy15749 27 RVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSP 72 (164)
Q Consensus 27 ~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p 72 (164)
...+.+|...|... -+..+.+-. ..++++|||+++...
T Consensus 50 ~~nT~tl~~~L~~~----G~~~I~~~~----~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 50 AGNTETLHDWLKKN----GFKKISENV----DWNLQRGDIFIWGRR 87 (145)
T ss_pred ccCHHHHHHHHhhC----CcEEeccCC----cccccCCCEEEEcCC
Confidence 34667787877766 555554421 247899999998654
No 47
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=38.88 E-value=70 Score=20.82 Aligned_cols=34 Identities=21% Similarity=0.261 Sum_probs=24.2
Q ss_pred CCCcceeeEEEEecCCCCCcceEEEEE--------eeCCCEEEe
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKRIV--------GVEGDVVST 93 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKRVi--------alpGD~v~~ 93 (164)
.+.++.||-|.+.+. .....+|.+. |.+||.+.+
T Consensus 24 ~G~v~~Gd~v~~~P~--~~~~~V~si~~~~~~~~~a~aGd~v~l 65 (81)
T cd03695 24 SGSIRVGDEVVVLPS--GKTSRVKSIETFDGELDEAGAGESVTL 65 (81)
T ss_pred cceEECCCEEEEcCC--CCeEEEEEEEECCcEeCEEcCCCEEEE
Confidence 457889999988753 2355677776 677887776
No 48
>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=37.83 E-value=92 Score=22.57 Aligned_cols=52 Identities=19% Similarity=0.167 Sum_probs=36.6
Q ss_pred ceeeEEEEecC--CCCCcceEEEEEeeCCCE--EEeccC----ccceeeecCCeEEEecC
Q psy15749 62 QRGDIVSLVSP--KDPGQKIIKRIVGVEGDV--VSTLDY----KSNVVKVPQGHIWVEGD 113 (164)
Q Consensus 62 ~rGDiVvf~~p--~~~~~~~iKRVialpGD~--v~~~~~----~~~~~~vp~~~~~vlgD 113 (164)
+.||-|+|+.+ ++++.+++-+|+..-++. .++.+. +...++++..++.-+-.
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 57999999876 455789999999988764 777652 23467888888877755
No 49
>PF10913 DUF2706: Protein of unknown function (DUF2706); InterPro: IPR024444 This family of proteins with unknown function appears to be restricted to Rickettsia spp.
Probab=37.62 E-value=51 Score=20.30 Aligned_cols=47 Identities=13% Similarity=0.147 Sum_probs=35.1
Q ss_pred ChHHHHHHHHHHHHHHHHhhceeEEEEEeCCCCCcccCCCCCCceEEEEEe
Q psy15749 1 MFRIFKSMLVGIPISITFCDSIGYVARVDGTSMQPVFNPDRNHQDYVFLNR 51 (164)
Q Consensus 1 ~~~~l~~~~~~i~i~~~i~~~~~~~~~V~g~SM~Ptl~~g~~~~d~vlv~r 51 (164)
|.+.++.+++.++++-++...=-.+|.+.+.-..|.+.++ .-+-++.
T Consensus 1 mlk~lkf~lv~imlaqllsctpsapyeikspcvs~didd~----s~ls~np 47 (60)
T PF10913_consen 1 MLKSLKFLLVLIMLAQLLSCTPSAPYEIKSPCVSADIDDN----SSLSVNP 47 (60)
T ss_pred ChhHHHHHHHHHHHHHHHcCCCCCCccccCCccccccCCC----ccccccc
Confidence 4567777788888887777666678899988888888887 5555544
No 50
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=36.76 E-value=1.2e+02 Score=21.42 Aligned_cols=45 Identities=22% Similarity=0.333 Sum_probs=27.8
Q ss_pred eEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceEEEEEeeCC-CEEEe
Q psy15749 45 DYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEG-DVVST 93 (164)
Q Consensus 45 d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpG-D~v~~ 93 (164)
|..-+...... ...+..||+|.++..+ +...+.+++.--| -++++
T Consensus 12 ~~y~l~n~Pf~--a~glA~gDvV~~~~~~--g~~~~~~~v~~sGnsTiRv 57 (117)
T PF14085_consen 12 DTYRLDNIPFF--AYGLALGDVVRAEPDD--GELWFQKVVESSGNSTIRV 57 (117)
T ss_pred CEEEEEecccc--cCCCCCCCEEEEEeCC--CeEEEEEEEecCCCEEEEE
Confidence 55555555444 6789999999999754 4455555544333 44444
No 51
>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=36.46 E-value=44 Score=22.01 Aligned_cols=10 Identities=40% Similarity=0.747 Sum_probs=6.0
Q ss_pred cceeeEEEEe
Q psy15749 61 LQRGDIVSLV 70 (164)
Q Consensus 61 ~~rGDiVvf~ 70 (164)
+++||+|+..
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 5566666664
No 52
>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=35.94 E-value=49 Score=22.57 Aligned_cols=26 Identities=23% Similarity=0.386 Sum_probs=19.8
Q ss_pred cceeeEEEEecCCCCCcceEEEEEee
Q psy15749 61 LQRGDIVSLVSPKDPGQKIIKRIVGV 86 (164)
Q Consensus 61 ~~rGDiVvf~~p~~~~~~~iKRVial 86 (164)
++.||.|.+..++.+....+.||..+
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i 28 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEI 28 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEE
Confidence 46788888887765677888888765
No 53
>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=35.80 E-value=45 Score=22.03 Aligned_cols=10 Identities=30% Similarity=0.674 Sum_probs=5.7
Q ss_pred cceeeEEEEe
Q psy15749 61 LQRGDIVSLV 70 (164)
Q Consensus 61 ~~rGDiVvf~ 70 (164)
+++||+|+..
T Consensus 39 I~~GD~VlV~ 48 (78)
T cd04456 39 IKRGDFLIVD 48 (78)
T ss_pred EcCCCEEEEE
Confidence 4556666554
No 54
>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=35.54 E-value=71 Score=23.12 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=16.5
Q ss_pred cccccCCCeEEEEEEEEeCCC
Q psy15749 124 FGPVSMGLVTAKASSIIWPPS 144 (164)
Q Consensus 124 ~G~V~~~~I~Gkv~~~~~p~~ 144 (164)
.--.+.+.|.||+...+-+++
T Consensus 67 c~d~~l~~I~~Kv~V~~~~p~ 87 (124)
T cd04760 67 CEDMALSSIHGKVNVIYKAPS 87 (124)
T ss_pred cCCcchHHheeeeEEEEeCCC
Confidence 345567789999999998876
No 55
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=35.35 E-value=47 Score=22.21 Aligned_cols=10 Identities=50% Similarity=0.816 Sum_probs=6.3
Q ss_pred cceeeEEEEe
Q psy15749 61 LQRGDIVSLV 70 (164)
Q Consensus 61 ~~rGDiVvf~ 70 (164)
+++||+|+..
T Consensus 44 I~~GD~VlVe 53 (83)
T smart00652 44 IRRGDIVLVD 53 (83)
T ss_pred EcCCCEEEEE
Confidence 5666666665
No 56
>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=34.92 E-value=1.7e+02 Score=21.07 Aligned_cols=60 Identities=17% Similarity=0.200 Sum_probs=31.9
Q ss_pred CCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeecCCeEEEecCCCCCCCCCCccccccCCCeEEEEE
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVTAKAS 137 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~Gkv~ 137 (164)
..+++.||+|+|-+..... -.+|..+ -+....=+||+-.|.-.. .+. -.++.++|++.
T Consensus 40 ~~~f~~GDlvLflpt~~~~--~~~~~~~--------------af~~~~~~YFL~~~s~~~-~~~-----~~~~w~vgrI~ 97 (129)
T PF10377_consen 40 FRNFQVGDLVLFLPTRNHN--NKKQPWA--------------AFNVGCPHYFLHEDSIAA-NEL-----KRREWIVGRIV 97 (129)
T ss_pred EecCCCCCEEEEEecCCCC--ccccceE--------------EeeCCCceEEEecccchh-ccC-----CCCCEEEEEEE
Confidence 3478999999997543222 1111111 133445578887665421 111 12667888886
Q ss_pred EE
Q psy15749 138 SI 139 (164)
Q Consensus 138 ~~ 139 (164)
-+
T Consensus 98 ~~ 99 (129)
T PF10377_consen 98 SI 99 (129)
T ss_pred EE
Confidence 54
No 57
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=32.98 E-value=92 Score=20.17 Aligned_cols=34 Identities=24% Similarity=0.360 Sum_probs=23.6
Q ss_pred CCCcceeeEEEEecCCCCCcceEEEEE--------eeCCCEEEe
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKRIV--------GVEGDVVST 93 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKRVi--------alpGD~v~~ 93 (164)
.+.++.||-|.+.+. + ...-+|.+. |.+||.+.+
T Consensus 24 ~G~i~~Gd~v~i~P~-~-~~~~V~si~~~~~~~~~a~aGd~v~~ 65 (83)
T cd03698 24 SGSIQKGDTLLVMPS-K-ESVEVKSIYVDDEEVDYAVAGENVRL 65 (83)
T ss_pred eeEEeCCCEEEEeCC-C-cEEEEEEEEECCeECCEECCCCEEEE
Confidence 457888999888643 2 345666666 678888775
No 58
>KOG2915|consensus
Probab=32.17 E-value=48 Score=27.67 Aligned_cols=15 Identities=13% Similarity=0.273 Sum_probs=12.4
Q ss_pred ccccccCCCeEEEEE
Q psy15749 123 MFGPVSMGLVTAKAS 137 (164)
Q Consensus 123 ~~G~V~~~~I~Gkv~ 137 (164)
.||.++.++|+||-.
T Consensus 42 ~yGa~~h~~iIGK~~ 56 (314)
T KOG2915|consen 42 RYGALPHSDIIGKPY 56 (314)
T ss_pred cccccchhheecCCc
Confidence 489999999999863
No 59
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=30.97 E-value=2e+02 Score=22.19 Aligned_cols=15 Identities=13% Similarity=0.264 Sum_probs=10.6
Q ss_pred CCCcceeeEEEEecC
Q psy15749 58 DIGLQRGDIVSLVSP 72 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p 72 (164)
...|+.||+|.+...
T Consensus 91 ~y~P~~GDlIc~~R~ 105 (183)
T PF10030_consen 91 EYKPRPGDLICYDRG 105 (183)
T ss_pred CCCCCCCCEEEecCC
Confidence 456788888887654
No 60
>smart00439 BAH Bromo adjacent homology domain.
Probab=30.51 E-value=89 Score=21.20 Aligned_cols=17 Identities=12% Similarity=0.151 Sum_probs=13.5
Q ss_pred cccCCCeEEEEEEEEeC
Q psy15749 126 PVSMGLVTAKASSIIWP 142 (164)
Q Consensus 126 ~V~~~~I~Gkv~~~~~p 142 (164)
-++.+.|+||+.....+
T Consensus 70 ~i~~~~I~~kc~V~~~~ 86 (120)
T smart00439 70 TVPLSDIIGKCNVLSKS 86 (120)
T ss_pred cCChHHeeeEEEEEEcc
Confidence 67889999999776544
No 61
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.18 E-value=32 Score=24.82 Aligned_cols=17 Identities=41% Similarity=0.610 Sum_probs=14.8
Q ss_pred CCCCcccCCCCCCceEEEEEe
Q psy15749 31 TSMQPVFNPDRNHQDYVFLNR 51 (164)
Q Consensus 31 ~SM~Ptl~~g~~~~d~vlv~r 51 (164)
.||+|-|.+| |+|+..-
T Consensus 12 ~smtPeL~~G----~yVfcT~ 28 (134)
T COG3602 12 ASMTPELLDG----DYVFCTV 28 (134)
T ss_pred HhcCccccCC----ceEEEEe
Confidence 3899999999 9999854
No 62
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=29.76 E-value=63 Score=22.46 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=5.9
Q ss_pred cceeeEEEEe
Q psy15749 61 LQRGDIVSLV 70 (164)
Q Consensus 61 ~~rGDiVvf~ 70 (164)
+.+||+|+..
T Consensus 60 I~~GD~VlVe 69 (100)
T PRK04012 60 IREGDVVIVA 69 (100)
T ss_pred ecCCCEEEEE
Confidence 4566666665
No 63
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=28.68 E-value=1.1e+02 Score=19.79 Aligned_cols=34 Identities=18% Similarity=0.208 Sum_probs=23.3
Q ss_pred CCCcceeeEEEEecCCCCCcceEEEEE--------eeCCCEEEe
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKRIV--------GVEGDVVST 93 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKRVi--------alpGD~v~~ 93 (164)
.+.++.||-|.+.+. .....+|.+. |.+||.+.+
T Consensus 23 ~G~i~~G~~v~i~P~--~~~~~V~si~~~~~~~~~a~aGd~v~l 64 (82)
T cd04089 23 SGTIKKGDKLLVMPN--KTQVEVLSIYNEDVEVRYARPGENVRL 64 (82)
T ss_pred eeEEecCCEEEEeCC--CcEEEEEEEEECCEECCEECCCCEEEE
Confidence 457889999888643 2355677766 667777765
No 64
>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=28.46 E-value=2.3e+02 Score=20.39 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=21.7
Q ss_pred eeecCCeEEEecCCCCCCCCCCccccccCCC
Q psy15749 101 VKVPQGHIWVEGDHVGHSMDSNMFGPVSMGL 131 (164)
Q Consensus 101 ~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~ 131 (164)
+...+|.+-++.++. +-.-+|-+|||++|.
T Consensus 77 i~F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T TIGR01067 77 IRFDDNACVLINKNK-EPRGTRIFGPVAREL 106 (122)
T ss_pred EECCCceEEEECCCC-CEeeeEEEccchHHH
Confidence 444566676666654 678899999999874
No 65
>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=28.27 E-value=43 Score=24.07 Aligned_cols=30 Identities=17% Similarity=0.393 Sum_probs=23.8
Q ss_pred eeeecCCeEEEecCCCCCCCCCCccccccCC
Q psy15749 100 VVKVPQGHIWVEGDHVGHSMDSNMFGPVSMG 130 (164)
Q Consensus 100 ~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~ 130 (164)
.....++.+-++.++. +...+|-+|||+.+
T Consensus 76 ~i~F~~Na~VLln~~~-~p~GtrI~Gpv~~e 105 (122)
T PF00238_consen 76 FIKFDDNAVVLLNKKG-NPLGTRIFGPVPRE 105 (122)
T ss_dssp EEEESSEEEEEEETTS-SBSSSSBCSEEEHH
T ss_pred EEEeCCccEEEEcCCC-CEeeeEEEeeehHH
Confidence 3455677888888774 88999999999975
No 66
>smart00002 PLP Myelin proteolipid protein (PLP or lipophilin).
Probab=28.17 E-value=15 Score=23.28 Aligned_cols=20 Identities=15% Similarity=0.308 Sum_probs=16.2
Q ss_pred CCCCCCccccccCCCeEEEE
Q psy15749 117 HSMDSNMFGPVSMGLVTAKA 136 (164)
Q Consensus 117 ~s~DSR~~G~V~~~~I~Gkv 136 (164)
-+.|-|.||.+|-...-|||
T Consensus 22 lC~D~RQyGilpwna~pgK~ 41 (60)
T smart00002 22 LCVDARQYGILPWNAFPGKV 41 (60)
T ss_pred EEeechhcceeecCCCCCch
Confidence 37899999999877777775
No 67
>CHL00057 rpl14 ribosomal protein L14
Probab=26.66 E-value=2.5e+02 Score=20.23 Aligned_cols=30 Identities=17% Similarity=0.354 Sum_probs=22.2
Q ss_pred eeecCCeEEEecCCCCCCCCCCccccccCCC
Q psy15749 101 VKVPQGHIWVEGDHVGHSMDSNMFGPVSMGL 131 (164)
Q Consensus 101 ~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~ 131 (164)
....+|.+-++.++. +-.-+|-+|||+.|.
T Consensus 77 i~F~~Na~VLin~~~-~p~GTrI~Gpv~~el 106 (122)
T CHL00057 77 IRFDDNAAVVIDQEG-NPKGTRVFGPIAREL 106 (122)
T ss_pred EEcCCceEEEECCCC-CEeEeEEEccchHHH
Confidence 445566777777664 678889999999864
No 68
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=26.37 E-value=1.4e+02 Score=19.51 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=23.4
Q ss_pred CCCcceeeEEEEecCCCC--CcceEEEEE--------eeCCCEEEec
Q psy15749 58 DIGLQRGDIVSLVSPKDP--GQKIIKRIV--------GVEGDVVSTL 94 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~--~~~~iKRVi--------alpGD~v~~~ 94 (164)
.+.++.||-+.+.+..+. ....+|.+- |.+||.+.+.
T Consensus 24 ~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~ 70 (87)
T cd03694 24 KGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLA 70 (87)
T ss_pred cCEEeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEE
Confidence 457888998888653211 244566655 6678877763
No 69
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=26.13 E-value=96 Score=21.07 Aligned_cols=12 Identities=25% Similarity=0.396 Sum_probs=6.3
Q ss_pred CcceeeEEEEec
Q psy15749 60 GLQRGDIVSLVS 71 (164)
Q Consensus 60 ~~~rGDiVvf~~ 71 (164)
+++.||+++|.+
T Consensus 82 ~l~~GD~l~f~~ 93 (116)
T PF00278_consen 82 ELEVGDWLVFEN 93 (116)
T ss_dssp TTTTT-EEEESS
T ss_pred CCCCCCEEEEec
Confidence 556666666643
No 70
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=26.04 E-value=76 Score=21.60 Aligned_cols=9 Identities=44% Similarity=0.508 Sum_probs=4.0
Q ss_pred ceeeEEEEe
Q psy15749 62 QRGDIVSLV 70 (164)
Q Consensus 62 ~rGDiVvf~ 70 (164)
..||.|...
T Consensus 48 l~GD~V~VE 56 (87)
T PRK12442 48 LAGDRVTLE 56 (87)
T ss_pred cCCCEEEEE
Confidence 334444444
No 71
>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=25.53 E-value=1.1e+02 Score=21.65 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=17.7
Q ss_pred CCCcceeeEEEEecCCCCCcceEEEEEe
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKRIVG 85 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKRVia 85 (164)
.+.++.||.++|..-.+ +..+.-+|+.
T Consensus 29 r~~ikvGD~I~f~~~~~-~~~l~v~V~~ 55 (109)
T cd06555 29 RQQIKVGDKILFNDLDT-GQQLLVKVVD 55 (109)
T ss_pred hhcCCCCCEEEEEEcCC-CcEEEEEEEE
Confidence 34799999999976433 3445555543
No 72
>PF08169 RBB1NT: RBB1NT (NUC162) domain; InterPro: IPR012603 This domain is found N-terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family [].; PDB: 2YRV_A.
Probab=25.38 E-value=1.6e+02 Score=20.41 Aligned_cols=56 Identities=20% Similarity=0.188 Sum_probs=23.8
Q ss_pred eeeEEEEecCCCCCcceEEEEEeeCCCEEEeccCccceeeecCCeEEEecCCCCCCCCCCccccccCCCeE
Q psy15749 63 RGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTLDYKSNVVKVPQGHIWVEGDHVGHSMDSNMFGPVSMGLVT 133 (164)
Q Consensus 63 rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~~~~~~~~~vp~~~~~vlgDn~~~s~DSR~~G~V~~~~I~ 133 (164)
.|-+|..........++--=|+. | .....++|.+++|.|-+ =.||++| .|++.++.
T Consensus 8 lGkVV~V~~~~~k~~W~PALVVs-P--------sc~ddv~VkKD~~lVRS-----FkD~Kfy-sV~rkd~~ 63 (96)
T PF08169_consen 8 LGKVVCVESTKKKTSWFPALVVS-P--------SCNDDVTVKKDQCLVRS-----FKDGKFY-SVARKDVR 63 (96)
T ss_dssp TTSEEEEE-SS-SS-EEEEEEE-----------SS-SS----TT-EEEEE-----SSS--EE-EE-TTTEE
T ss_pred cCcEEEEEcCCCCCceeeEEEEc-C--------CccceeeeccceEEEEE-----eccCceE-EEEhhhhh
Confidence 46677775544444555555544 2 11223567788888832 2578877 57776653
No 73
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=24.62 E-value=2.2e+02 Score=23.08 Aligned_cols=76 Identities=24% Similarity=0.486 Sum_probs=46.0
Q ss_pred CCCCCcccCCCCCCceEEEEEeeecc-----------CCCCCcceeeEEEEecCCCCCcceEEEEEeeCCCEEEec-cCc
Q psy15749 30 GTSMQPVFNPDRNHQDYVFLNRWIIK-----------GDDIGLQRGDIVSLVSPKDPGQKIIKRIVGVEGDVVSTL-DYK 97 (164)
Q Consensus 30 g~SM~Ptl~~g~~~~d~vlv~r~~~~-----------~~~~~~~rGDiVvf~~p~~~~~~~iKRVialpGD~v~~~-~~~ 97 (164)
+..|.|.|+.| |.+...-.... .+.++++.|-+|-..+ ..+-|+++--|--+..- ...
T Consensus 106 ~~~~r~~l~vG----D~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p------~kVpRvig~~~sm~~~l~~~~ 175 (239)
T COG1097 106 EKDLRPFLNVG----DLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPP------SKVPRVIGKKGSMLNMLKEKT 175 (239)
T ss_pred ccccccccccC----CEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEch------hhcceEecCCCcHHHHhhhhc
Confidence 67899999999 99887433222 1245677777776643 35667777555444221 111
Q ss_pred cceeee-cCCeEEEecCCC
Q psy15749 98 SNVVKV-PQGHIWVEGDHV 115 (164)
Q Consensus 98 ~~~~~v-p~~~~~vlgDn~ 115 (164)
.-.+.| -.|.+|+-+.|.
T Consensus 176 ~~~I~VG~NG~IWV~~~~~ 194 (239)
T COG1097 176 GCEIIVGQNGRIWVDGENE 194 (239)
T ss_pred CeEEEEecCCEEEecCCCc
Confidence 112333 467889999886
No 74
>PF14900 DUF4493: Domain of unknown function (DUF4493)
Probab=22.34 E-value=1.8e+02 Score=22.80 Aligned_cols=46 Identities=26% Similarity=0.508 Sum_probs=31.2
Q ss_pred eEEEEEeeCCCEEEeccCcc---ceeeecCCeEEEe---cCCCCCCCCCCcc
Q psy15749 79 IIKRIVGVEGDVVSTLDYKS---NVVKVPQGHIWVE---GDHVGHSMDSNMF 124 (164)
Q Consensus 79 ~iKRVialpGD~v~~~~~~~---~~~~vp~~~~~vl---gDn~~~s~DSR~~ 124 (164)
+.=||....|..+....+.. ..+.+|.|.|=+. ||+...++|..||
T Consensus 35 ~~v~I~~~~~~~~~~~~~~~~~~~~i~L~~G~Ytv~A~~g~~~~~~~d~pyy 86 (235)
T PF14900_consen 35 FTVEIYNADGTVVKYWKYSEMPGESIELPVGSYTVKASYGDNVAAGFDKPYY 86 (235)
T ss_pred eEEEEEeCCCcEEEecchhccccceEeecCCcEEEEEEcCCCccccccCcee
Confidence 44455555555555544332 4588999998776 7888788998887
No 75
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=21.96 E-value=1.9e+02 Score=18.50 Aligned_cols=35 Identities=20% Similarity=0.255 Sum_probs=21.7
Q ss_pred CCCcceeeEEEEecCCCCCcceEEEEE--------eeCCCEEEec
Q psy15749 58 DIGLQRGDIVSLVSPKDPGQKIIKRIV--------GVEGDVVSTL 94 (164)
Q Consensus 58 ~~~~~rGDiVvf~~p~~~~~~~iKRVi--------alpGD~v~~~ 94 (164)
.+.++.||-+.+.+. .....+|.+. |.+||.+.+.
T Consensus 24 sG~i~~g~~v~~~p~--~~~~~V~sI~~~~~~~~~a~aGd~v~i~ 66 (83)
T cd03696 24 SGSVKVGDKVEILPL--GEETRVRSIQVHGKDVEEAKAGDRVALN 66 (83)
T ss_pred ecEEeCCCEEEECCC--CceEEEEEEEECCcCcCEEcCCCEEEEE
Confidence 456788888777642 2344555554 5677777653
No 76
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=21.60 E-value=1.1e+02 Score=20.44 Aligned_cols=24 Identities=21% Similarity=0.244 Sum_probs=13.0
Q ss_pred CcceeeEEEEecCCCCCcceEEEEEeeCCC
Q psy15749 60 GLQRGDIVSLVSPKDPGQKIIKRIVGVEGD 89 (164)
Q Consensus 60 ~~~rGDiVvf~~p~~~~~~~iKRVialpGD 89 (164)
+++.||+|+|-. .+.++|..-.+|
T Consensus 69 ~p~~G~lvlFPs------~l~H~v~p~~~~ 92 (101)
T PF13759_consen 69 EPEEGDLVLFPS------WLWHGVPPNNSD 92 (101)
T ss_dssp ---TTEEEEEET------TSEEEE----SS
T ss_pred CCCCCEEEEeCC------CCEEeccCcCCC
Confidence 678999999953 577777666554
No 77
>PF10222 DUF2152: Uncharacterized conserved protein (DUF2152); InterPro: IPR018795 This entry includes mainly uncharacterised proteins, though some are described as belonging to the glycoside hydrolase family 65.
Probab=21.18 E-value=98 Score=28.48 Aligned_cols=104 Identities=15% Similarity=0.136 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHHHhhceeEEE--EEeCCCCCcccCCCCCCceEEEEEeeeccCCCCCcceeeEEEEecCCCCCcceE
Q psy15749 3 RIFKSMLVGIPISITFCDSIGYVA--RVDGTSMQPVFNPDRNHQDYVFLNRWIIKGDDIGLQRGDIVSLVSPKDPGQKII 80 (164)
Q Consensus 3 ~~l~~~~~~i~i~~~i~~~~~~~~--~V~g~SM~Ptl~~g~~~~d~vlv~r~~~~~~~~~~~rGDiVvf~~p~~~~~~~i 80 (164)
+|.+-+++.+++.+++..|++... +..+.+-.+.-.. +..+-+++... .....+||.++...|...+...+
T Consensus 13 sw~RR~l~~ll~~~~~~~Yigp~~~r~~f~~~~~~~~~~-----~~Cl~~~l~~w--~~~~~e~da~i~~~~~p~e~~~~ 85 (604)
T PF10222_consen 13 SWARRLLALLLLCLIFYWYIGPPFFRWLFSSSGPPKDES-----GKCLQDRLAPW--YSQAEEGDAVILHPPKPQEKNYL 85 (604)
T ss_pred hHHHHHHHHHHHHHhhhhecccHhhhhhhcCCCCCCCcc-----chhHHHHHHHH--HHHHhcCCEEEccCCCCCcccCC
Confidence 466667766666666655655522 2222222222222 23333444333 45678999999885431111122
Q ss_pred EEEEeeCCCEEEeccCccceeeecCCeEEEecCCCCCCCCCCcc
Q psy15749 81 KRIVGVEGDVVSTLDYKSNVVKVPQGHIWVEGDHVGHSMDSNMF 124 (164)
Q Consensus 81 KRVialpGD~v~~~~~~~~~~~vp~~~~~vlgDn~~~s~DSR~~ 124 (164)
--| +.+.-...|..++.|+-|.+|.-+.+.+++
T Consensus 86 P~V-----------GNG~iGl~V~~d~L~I~~~~R~l~~~~~f~ 118 (604)
T PF10222_consen 86 PFV-----------GNGYIGLDVDSDNLYIKGSGRALSLPVPFH 118 (604)
T ss_pred cee-----------cCCEEEEEEcCCeEEEEecCcccccccCCC
Confidence 111 112233456667788887666666666654
No 78
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=20.31 E-value=1e+02 Score=19.69 Aligned_cols=11 Identities=27% Similarity=0.404 Sum_probs=9.2
Q ss_pred CcceeeEEEEe
Q psy15749 60 GLQRGDIVSLV 70 (164)
Q Consensus 60 ~~~rGDiVvf~ 70 (164)
.+..||+|.|.
T Consensus 46 ~i~vGD~V~ve 56 (72)
T PRK00276 46 RILPGDKVTVE 56 (72)
T ss_pred ccCCCCEEEEE
Confidence 47789999998
Done!