Query 032329
Match_columns 143
No_of_seqs 175 out of 1062
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 12:40:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032329.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032329hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0171 Mitochondrial inner me 100.0 4.4E-31 9.5E-36 201.3 8.8 108 34-142 17-134 (176)
2 TIGR02227 sigpep_I_bact signal 100.0 1.8E-28 3.8E-33 186.7 13.7 106 35-142 5-138 (163)
3 KOG1568 Mitochondrial inner me 100.0 7.8E-29 1.7E-33 188.7 10.6 121 6-141 1-126 (174)
4 PRK10861 signal peptidase I; P 99.9 6.3E-26 1.4E-30 189.7 14.7 79 37-116 69-158 (324)
5 TIGR02754 sod_Ni_protease nick 99.7 9.4E-17 2E-21 110.5 9.2 70 54-142 2-71 (90)
6 cd06530 S26_SPase_I The S26 Ty 99.7 6.5E-16 1.4E-20 104.8 9.0 67 52-142 2-68 (85)
7 COG0681 LepB Signal peptidase 99.6 3.8E-15 8.3E-20 111.2 7.8 100 35-138 14-116 (166)
8 TIGR02228 sigpep_I_arch signal 99.5 7.4E-14 1.6E-18 106.5 10.1 53 55-112 36-88 (158)
9 PRK13838 conjugal transfer pil 99.5 4.1E-13 8.9E-18 104.0 11.4 71 69-141 37-150 (176)
10 PF00717 Peptidase_S24: Peptid 99.5 3.1E-13 6.7E-18 88.1 8.0 68 54-128 1-69 (70)
11 TIGR02771 TraF_Ti conjugative 99.4 3.1E-12 6.8E-17 98.6 11.7 60 82-142 45-148 (171)
12 PF10502 Peptidase_S26: Signal 99.2 2.8E-12 6.2E-17 95.5 1.7 60 82-141 20-115 (138)
13 cd06462 Peptidase_S24_S26 The 99.2 1.1E-10 2.3E-15 77.7 8.9 53 52-111 2-54 (84)
14 PRK13884 conjugal transfer pep 99.2 4.5E-11 9.9E-16 92.7 7.9 61 82-142 49-155 (178)
15 cd06529 S24_LexA-like Peptidas 99.0 5.7E-09 1.2E-13 69.3 9.6 68 52-128 2-71 (81)
16 COG2932 Predicted transcriptio 98.8 3.7E-08 8.1E-13 77.5 9.4 56 51-114 124-179 (214)
17 PRK00215 LexA repressor; Valid 98.6 5.5E-07 1.2E-11 70.2 10.7 78 49-135 117-196 (205)
18 PRK10276 DNA polymerase V subu 98.6 6.8E-07 1.5E-11 66.3 10.5 75 51-135 52-129 (139)
19 TIGR00498 lexA SOS regulatory 98.5 8.4E-07 1.8E-11 68.8 10.1 78 49-135 110-189 (199)
20 PRK12423 LexA repressor; Provi 98.5 2.3E-06 5.1E-11 67.1 10.5 75 51-135 115-193 (202)
21 KOG3342 Signal peptidase I [In 98.1 5.8E-06 1.2E-10 63.3 4.4 55 52-111 50-104 (180)
22 COG1974 LexA SOS-response tran 97.5 0.0013 2.9E-08 52.1 10.2 78 49-135 111-191 (201)
23 COG4959 TraF Type IV secretory 94.7 0.026 5.6E-07 43.5 2.6 60 82-141 52-147 (173)
24 COG0681 LepB Signal peptidase 86.8 0.78 1.7E-05 33.6 3.2 12 83-94 84-95 (166)
25 PF05382 Amidase_5: Bacterioph 80.3 8 0.00017 29.2 6.4 81 5-95 6-87 (145)
26 PRK00364 groES co-chaperonin G 73.8 26 0.00057 24.3 7.1 25 111-135 62-86 (95)
27 TIGR00008 infA translation ini 66.5 6.5 0.00014 26.1 2.6 9 85-93 46-54 (68)
28 COG0361 InfA Translation initi 66.2 6.6 0.00014 26.6 2.6 8 69-76 51-58 (75)
29 PTZ00414 10 kDa heat shock pro 64.9 47 0.001 23.5 7.1 70 62-136 10-91 (100)
30 cd04714 BAH_BAHCC1 BAH, or Bro 62.0 11 0.00025 27.0 3.4 28 83-110 3-30 (121)
31 PF01426 BAH: BAH domain; Int 60.3 12 0.00026 25.7 3.2 27 84-110 3-29 (119)
32 COG0234 GroS Co-chaperonin Gro 56.0 67 0.0014 22.8 6.3 73 64-137 3-88 (96)
33 smart00439 BAH Bromo adjacent 55.4 22 0.00048 24.3 3.9 26 84-109 2-27 (120)
34 cd04717 BAH_polybromo BAH, or 55.3 16 0.00034 26.0 3.2 27 83-109 3-29 (121)
35 PF06890 Phage_Mu_Gp45: Bacter 54.9 95 0.0021 23.8 8.1 41 74-117 66-109 (162)
36 PF05257 CHAP: CHAP domain; I 54.8 45 0.00098 23.4 5.5 36 82-117 61-97 (124)
37 PRK14533 groES co-chaperonin G 54.7 69 0.0015 22.2 7.0 67 64-135 3-81 (91)
38 PF09285 Elong-fact-P_C: Elong 54.4 31 0.00068 21.9 4.1 39 57-105 18-56 (56)
39 PRK12442 translation initiatio 51.7 17 0.00037 25.3 2.7 9 85-93 48-56 (87)
40 TIGR02594 conserved hypothetic 48.4 62 0.0013 23.6 5.5 13 82-94 72-84 (129)
41 PF10000 ACT_3: ACT domain; I 47.5 13 0.00029 24.6 1.6 17 58-75 12-28 (72)
42 PF01176 eIF-1a: Translation i 45.7 23 0.00049 22.7 2.5 11 83-93 41-51 (65)
43 cd05793 S1_IF1A S1_IF1A: Trans 45.4 22 0.00047 23.9 2.4 10 84-93 39-48 (77)
44 PF15057 DUF4537: Domain of un 44.7 58 0.0012 23.6 4.8 52 83-134 55-112 (124)
45 cd04370 BAH BAH, or Bromo Adja 42.8 33 0.00071 23.3 3.1 28 83-110 3-32 (123)
46 TIGR00498 lexA SOS regulatory 41.6 1.3E+02 0.0028 22.8 6.6 50 83-141 125-176 (199)
47 cd00320 cpn10 Chaperonin 10 Kd 41.0 1.2E+02 0.0025 20.9 7.3 13 65-77 3-15 (93)
48 smart00652 eIF1a eukaryotic tr 40.7 28 0.00061 23.6 2.4 43 49-93 8-53 (83)
49 smart00841 Elong-fact-P_C Elon 40.0 54 0.0012 20.8 3.5 39 57-105 18-56 (56)
50 KOG4146 Ubiquitin-like protein 39.8 42 0.00091 23.8 3.2 56 34-96 39-98 (101)
51 COG5131 URM1 Ubiquitin-like pr 38.7 45 0.00097 23.5 3.2 31 64-95 58-92 (96)
52 PRK02135 hypothetical protein; 38.3 31 0.00068 27.5 2.7 19 124-142 142-160 (201)
53 PRK04012 translation initiatio 37.4 33 0.00072 24.2 2.5 44 49-94 24-70 (100)
54 PF02736 Myosin_N: Myosin N-te 36.9 36 0.00078 19.9 2.2 35 95-129 7-41 (42)
55 cd04720 BAH_Orc1p_Yeast BAH, o 36.3 70 0.0015 24.7 4.3 28 82-110 51-78 (179)
56 cd04456 S1_IF1A_like S1_IF1A_l 35.0 40 0.00087 22.6 2.5 41 51-93 5-48 (78)
57 COG1188 Ribosome-associated he 34.9 1.1E+02 0.0023 21.8 4.7 42 69-113 34-75 (100)
58 KOG4680 Uncharacterized conser 34.9 54 0.0012 25.0 3.3 28 94-134 97-124 (153)
59 cd06555 ASCH_PF0470_like ASC-1 34.6 74 0.0016 22.8 3.9 27 82-109 30-56 (109)
60 cd04712 BAH_DCM_I BAH, or Brom 33.8 52 0.0011 24.1 3.1 29 82-110 4-42 (130)
61 cd04710 BAH_fungalPHD BAH, or 31.9 63 0.0014 23.8 3.3 29 82-110 10-38 (135)
62 cd02393 PNPase_KH Polynucleoti 29.7 6.8 0.00015 24.8 -2.0 39 101-139 11-51 (61)
63 COG1097 RRP4 RNA-binding prote 29.4 94 0.002 25.5 4.1 77 56-139 105-195 (239)
64 cd05794 S1_EF-P_repeat_2 S1_EF 29.3 96 0.0021 19.7 3.4 39 57-105 18-56 (56)
65 cd04709 BAH_MTA BAH, or Bromo 28.5 80 0.0017 24.2 3.4 25 84-109 4-28 (164)
66 COG3602 Uncharacterized protei 28.1 31 0.00067 25.5 1.0 16 58-74 12-27 (134)
67 COG4043 Preprotein translocase 27.2 98 0.0021 22.3 3.4 23 82-109 32-54 (111)
68 PF07497 Rho_RNA_bind: Rho ter 25.8 2E+02 0.0044 19.4 4.7 32 82-113 41-75 (78)
69 PF14085 DUF4265: Domain of un 24.3 2.7E+02 0.0058 19.8 6.8 44 69-115 12-55 (117)
70 PF13856 Gifsy-2: ATP-binding 24.3 2.1E+02 0.0045 19.3 4.7 61 47-113 18-91 (95)
71 PF15428 Imm14: Immunity prote 23.7 1.3E+02 0.0027 21.3 3.6 22 85-108 1-22 (129)
72 PF13550 Phage-tail_3: Putativ 23.5 1.1E+02 0.0025 21.8 3.4 25 82-109 138-162 (164)
73 PF00278 Orn_DAP_Arg_deC: Pyri 22.7 1.1E+02 0.0024 20.8 3.0 12 83-94 82-93 (116)
74 PF02452 PemK: PemK-like prote 20.6 88 0.0019 20.9 2.2 13 85-97 1-13 (110)
75 PLN03148 Blue copper-like prot 20.2 4E+02 0.0087 20.5 5.9 21 73-95 37-57 (167)
76 PF11330 DUF3132: Protein of u 20.1 1.8E+02 0.0038 20.7 3.6 19 86-104 86-104 (124)
77 PTZ00329 eukaryotic translatio 20.1 94 0.002 23.8 2.4 45 49-94 35-81 (155)
No 1
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4.4e-31 Score=201.34 Aligned_cols=108 Identities=25% Similarity=0.356 Sum_probs=95.3
Q ss_pred HHHHHHHHHHHhhhccEEEEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcE
Q 032329 34 IELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYE 113 (143)
Q Consensus 34 ~~~~~~~~~~~~~~~v~~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~ 113 (143)
.+....++.|++..|++++..++|+||+|||+++||+++.+|+++++ +++++||||++++|.++++.+||||+|+|||.
T Consensus 17 ~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f-~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~ 95 (176)
T KOG0171|consen 17 SEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRF-RKPQVGDIVIAKSPPDPKEHICKRIVAMEGDL 95 (176)
T ss_pred HHHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhh-cCCCCCCEEEEeCCCCchhhhhheeeccCCce
Confidence 34566788899999999999999999999999998999889999996 88999999999999999999999999999997
Q ss_pred EEEcCCC----------CCCEEecCCcEEEEecCCCCCC
Q 032329 114 MVSTDEK----------DEPFVLDKDECWVLADNENMKP 142 (143)
Q Consensus 114 vv~~~~~----------~~~~~VP~g~~wVlGDNr~~S~ 142 (143)
++..+.+ ..++.||+||+||+|||++||.
T Consensus 96 v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~ 134 (176)
T KOG0171|consen 96 VEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSL 134 (176)
T ss_pred EEEecCCcccchhhhhccceeeccCceEEEecCCCCCcc
Confidence 5543211 2458999999999999999985
No 2
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=99.96 E-value=1.8e-28 Score=186.68 Aligned_cols=106 Identities=25% Similarity=0.389 Sum_probs=91.2
Q ss_pred HHHHHHHHHHhhhccEEEEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEE
Q 032329 35 ELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEM 114 (143)
Q Consensus 35 ~~~~~~~~~~~~~~v~~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~v 114 (143)
.+++++++++++.++++++.|+|+||+|||++| |+++++|+.+.. ..+++||||+|+.|.++++.+||||+|+|||+|
T Consensus 5 ~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~G-d~vlv~k~~~~~-~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v 82 (163)
T TIGR02227 5 LLIAILLALLIRTFVFFPYKIPGGSMEPTLKEG-DRILVNKFAYGT-SDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKV 82 (163)
T ss_pred HHHHHHHHHHHHhhEEEEEEECCcccccchhCC-CEEEEEEeEcCC-CCCCCCcEEEEecCCCCCceeEEEEEecCCCEE
Confidence 455677888999999999999999999999998 999999987763 789999999999988788899999999999997
Q ss_pred EEcC-----------CC-----------------CCCEEecCCcEEEEecCCCCCC
Q 032329 115 VSTD-----------EK-----------------DEPFVLDKDECWVLADNENMKP 142 (143)
Q Consensus 115 v~~~-----------~~-----------------~~~~~VP~g~~wVlGDNr~~S~ 142 (143)
...+ +. ..+.+||+||||||||||.+|.
T Consensus 83 ~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~ 138 (163)
T TIGR02227 83 EFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSL 138 (163)
T ss_pred EEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCc
Confidence 6521 10 1246899999999999999884
No 3
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=7.8e-29 Score=188.73 Aligned_cols=121 Identities=37% Similarity=0.599 Sum_probs=103.8
Q ss_pred HHHHHHhhheeeeeeeeeeccCCCcchhHHHHHHHHHHHhhhccEEEEEeeCCCCcccccCCC-----cEEEEEeecCCC
Q 032329 6 TWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLG-----GTLLVRKLPAAD 80 (143)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~G~SM~PTl~~gg-----D~Vlv~k~~~~~ 80 (143)
.|++|++++|++++..+-+....-+ +...++.+..+.|.||+|||+++. |+||++|+....
T Consensus 1 ~~~~~~~~~~~ksl~~s~~~~v~~t--------------~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n 66 (174)
T KOG1568|consen 1 MWRRYIFKVFEKSLTGSLKWHVLLT--------------FSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKN 66 (174)
T ss_pred CHHHHHHHHHHhceeeeeeeheeee--------------eeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeecccc
Confidence 4999999999988777666553222 344588899999999999999863 899999998763
Q ss_pred CCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCCcEEEEecCCCCC
Q 032329 81 PKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMK 141 (143)
Q Consensus 81 ~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g~~wVlGDNr~~S 141 (143)
..+.|||||+|++|.++++++||||+|+|||++...+++.+++.||+|||||+|||..+|
T Consensus 67 -~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~hs 126 (174)
T KOG1568|consen 67 -RKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQKHS 126 (174)
T ss_pred -ceeccCCEEEEeCCCChhheeeeeeecccccEeccCCCCCCceecCCCcEEEecCCcccc
Confidence 668899999999999999999999999999997666777889999999999999999776
No 4
>PRK10861 signal peptidase I; Provisional
Probab=99.94 E-value=6.3e-26 Score=189.71 Aligned_cols=79 Identities=18% Similarity=0.187 Sum_probs=70.5
Q ss_pred HHHHHHHHhhhccEEEEEeeCCCCcccccCCCcEEEEEeecCCC-----------CCCCCcCeEEEEecCCCCCceEEEE
Q 032329 37 RDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAAD-----------PKRVSVGDVVVMKDPEKSDNYIVRR 105 (143)
Q Consensus 37 ~~~~~~~~~~~~v~~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~-----------~~~~~rGDVVvf~~P~~~~~~~VKR 105 (143)
.+++++.+++.|+++++.|+|.||+|||..| |++||+|+.+.. ...++|||||||+.|.+++..+|||
T Consensus 69 ~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~G-D~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~~~~~yIKR 147 (324)
T PRK10861 69 PVLAIVLIVRSFIYEPFQIPSGSMMPTLLIG-DFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDPKLDYIKR 147 (324)
T ss_pred HHHhHHHHHHhhEEEEEEECCCcCcCcccCC-CEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCCCCCcEEEE
Confidence 3556778899999999999999999999998 999999998752 1468999999999999989999999
Q ss_pred EEeeCCcEEEE
Q 032329 106 LAAIEGYEMVS 116 (143)
Q Consensus 106 ViglpGD~vv~ 116 (143)
|||+|||+|..
T Consensus 148 VIGlPGD~I~~ 158 (324)
T PRK10861 148 VVGLPGDKVTY 158 (324)
T ss_pred eeecCCcEEEE
Confidence 99999999875
No 5
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.70 E-value=9.4e-17 Score=110.46 Aligned_cols=70 Identities=24% Similarity=0.407 Sum_probs=58.5
Q ss_pred EeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCCcEEE
Q 032329 54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV 133 (143)
Q Consensus 54 ~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g~~wV 133 (143)
.|+|+||+|||++| |.|+++++... ...+++||+|+++.|.++++.++||+++++ +|++|+
T Consensus 2 ~V~g~SM~P~l~~G-D~vlv~~~~~~-~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~-----------------~~~~~l 62 (90)
T TIGR02754 2 KVTGVSMSPTLPPG-DRIIVVPWLKI-FRVPPIGNVVVVRHPLQPYGLIIKRLAAVD-----------------DNGLFL 62 (90)
T ss_pred EeeCCCccCccCCC-CEEEEEEcccc-CCCCCCCeEEEEecCCCCcceEEEEeeEEc-----------------CCeEEE
Confidence 58999999999998 99999986433 244568999999998777789999999985 356899
Q ss_pred EecCCCCCC
Q 032329 134 LADNENMKP 142 (143)
Q Consensus 134 lGDNr~~S~ 142 (143)
+|||+..|.
T Consensus 63 ~~dN~~~~~ 71 (90)
T TIGR02754 63 LGDNPKAST 71 (90)
T ss_pred eCCCCCCCC
Confidence 999998764
No 6
>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=99.66 E-value=6.5e-16 Score=104.84 Aligned_cols=67 Identities=31% Similarity=0.408 Sum_probs=57.6
Q ss_pred EEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCCcE
Q 032329 52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 131 (143)
Q Consensus 52 ~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g~~ 131 (143)
++.|.|+||+||+.+| |.+++++....+ ..+++||+|+|+.|.++++.++|||++ |
T Consensus 2 ~~~v~g~SM~P~i~~g-d~v~v~~~~~~~-~~~~~GDiv~~~~~~~~~~~~vkRv~~----------------------~ 57 (85)
T cd06530 2 PVVVPGGSMEPTLQPG-DLVLVNKLSYGF-REPKRGDVVVFKSPGDPGKPIIKRVIG----------------------Y 57 (85)
T ss_pred eeEEcCCCCcCcccCC-CEEEEEEeeccc-CCCCCCCEEEEeCCCCCCCEEEEEEEE----------------------E
Confidence 5789999999999997 999999875331 369999999999987657899999999 9
Q ss_pred EEEecCCCCCC
Q 032329 132 WVLADNENMKP 142 (143)
Q Consensus 132 wVlGDNr~~S~ 142 (143)
|+.|||+.+|.
T Consensus 58 ~~~gDn~~ns~ 68 (85)
T cd06530 58 FVLGDNRNNSL 68 (85)
T ss_pred EEeeCCCCCCC
Confidence 99999987764
No 7
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.59 E-value=3.8e-15 Score=111.19 Aligned_cols=100 Identities=16% Similarity=0.164 Sum_probs=76.1
Q ss_pred HHHHHHHHHHh--hhccEEEEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCc
Q 032329 35 ELRDSVWKYLF--QGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGY 112 (143)
Q Consensus 35 ~~~~~~~~~~~--~~~v~~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD 112 (143)
.+.+++++.++ +.++++++.|+|+||+|||+.| |+++++|+.+.. ..++.+|++ ..|...+..++||+++++||
T Consensus 14 ~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~G-D~v~v~k~~~~~-~~~~~~~~~--~~~~~~~~~~~kr~~~~~GD 89 (166)
T COG0681 14 LLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVG-DRVLVKKFSYGF-GKLKVPDII--VLPAVVEGDLIKRVIGLRGD 89 (166)
T ss_pred HHHHHHHhheeeeEEEEEEEEEECCCccccccccC-CEEEEEeccccc-cCCccceee--ecCCCCCcceEEEeccCCCC
Confidence 34445555566 7999999999999999999997 999999998874 678888888 56667888999999999999
Q ss_pred EEEEcCCCCC-CEEecCCcEEEEecCC
Q 032329 113 EMVSTDEKDE-PFVLDKDECWVLADNE 138 (143)
Q Consensus 113 ~vv~~~~~~~-~~~VP~g~~wVlGDNr 138 (143)
.++..++... ...+|+++.|+.++|.
T Consensus 90 ~i~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (166)
T COG0681 90 IVVFKDDRLYVVPIIPRVYGLVEKDNG 116 (166)
T ss_pred EEEEECCEEEeecccCcchhhhhcccc
Confidence 9776542211 2345666666555543
No 8
>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=99.53 E-value=7.4e-14 Score=106.53 Aligned_cols=53 Identities=25% Similarity=0.387 Sum_probs=45.9
Q ss_pred eeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCc
Q 032329 55 NKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGY 112 (143)
Q Consensus 55 v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD 112 (143)
|.|+||+|||++| |.+++++.. ..++++||||+|+.|.++ +.++|||+++.++
T Consensus 36 V~g~SM~Ptl~~G-D~vlv~~~~---~~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~ 88 (158)
T TIGR02228 36 VLSGSMEPTFNTG-DLILVTGAD---PNDIQVGDVITYKSPGFN-TPVTHRVIEINNS 88 (158)
T ss_pred EcCCCCcCCccCC-CEEEEEecc---cCCCCCCCEEEEEECCCC-ccEEEEEEEEECC
Confidence 8999999999998 999999843 257999999999988644 7899999999754
No 9
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=99.49 E-value=4.1e-13 Score=104.03 Aligned_cols=71 Identities=20% Similarity=0.232 Sum_probs=52.9
Q ss_pred cEEEEEeecCCCCCCCCcCeEEEEecCCCC-------------------CceEEEEEEeeCCcEEEEc-----C-----C
Q 032329 69 GTLLVRKLPAADPKRVSVGDVVVMKDPEKS-------------------DNYIVRRLAAIEGYEMVST-----D-----E 119 (143)
Q Consensus 69 D~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~-------------------~~~~VKRViglpGD~vv~~-----~-----~ 119 (143)
+.+.+.++... ...+++||+|+|+.|.++ ...++|||+|+|||+|... + +
T Consensus 37 ~pig~y~~~~~-~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~ 115 (176)
T PRK13838 37 EPLGLWRIEAL-DRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPS 115 (176)
T ss_pred CEEEEEEEecc-CCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccc
Confidence 77778887654 368999999999987643 1259999999999997642 1 1
Q ss_pred C--------------CCCEEecCCcEEEEecCCCCC
Q 032329 120 K--------------DEPFVLDKDECWVLADNENMK 141 (143)
Q Consensus 120 ~--------------~~~~~VP~g~~wVlGDNr~~S 141 (143)
. ....+||+|||||+|||. +|
T Consensus 116 ~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S 150 (176)
T PRK13838 116 SSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GS 150 (176)
T ss_pred cccccccccCCcCCCCCccCcCCCeEEEECCCC-CC
Confidence 0 113479999999999984 55
No 10
>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=99.47 E-value=3.1e-13 Score=88.11 Aligned_cols=68 Identities=21% Similarity=0.331 Sum_probs=52.2
Q ss_pred EeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEEc-CCCCCCEEecC
Q 032329 54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVST-DEKDEPFVLDK 128 (143)
Q Consensus 54 ~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~~-~~~~~~~~VP~ 128 (143)
+|.|+||+|+|.+| |.|++++. ..++.||+|++..+.+. ..++||+++.+|+.+... +..++++.|++
T Consensus 1 ~V~GdSM~P~i~~G-d~v~v~~~-----~~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~~~n~~~~~~i~~ 69 (70)
T PF00717_consen 1 RVEGDSMEPTIKDG-DIVLVDPS-----SEPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILISSNNNYPPIYING 69 (70)
T ss_dssp EEESSTTGGTSSTT-EEEEEEET-----S---TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-SSTTSETEEEST
T ss_pred CeECcCcccCeeCC-CEEEEEEc-----CCCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEeccCCCCCEEeCC
Confidence 48999999999998 99999985 47899999999976432 389999999999996653 22466777765
No 11
>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=99.42 E-value=3.1e-12 Score=98.63 Aligned_cols=60 Identities=20% Similarity=0.272 Sum_probs=47.5
Q ss_pred CCCCcCeEEEEecCCCCC-------------------ceEEEEEEeeCCcEEEEcC------C-----------------
Q 032329 82 KRVSVGDVVVMKDPEKSD-------------------NYIVRRLAAIEGYEMVSTD------E----------------- 119 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~~-------------------~~~VKRViglpGD~vv~~~------~----------------- 119 (143)
..++|||+|+|+.|.++. ..++|||+|+|||+|...+ +
T Consensus 45 ~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~ 124 (171)
T TIGR02771 45 KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRP 124 (171)
T ss_pred CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCc
Confidence 579999999999886432 2799999999999976521 0
Q ss_pred --CCCCEEecCCcEEEEecCCCCCC
Q 032329 120 --KDEPFVLDKDECWVLADNENMKP 142 (143)
Q Consensus 120 --~~~~~~VP~g~~wVlGDNr~~S~ 142 (143)
...+.+||+| ||+||||+.+|-
T Consensus 125 l~~~~~~~vp~g-yf~lgdn~~~S~ 148 (171)
T TIGR02771 125 LPPFPEGVIPPG-FFVVHDTSPTSF 148 (171)
T ss_pred cccCCCcEECCC-EEEECCCCCCCC
Confidence 0135789999 999999999884
No 12
>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=99.23 E-value=2.8e-12 Score=95.54 Aligned_cols=60 Identities=27% Similarity=0.444 Sum_probs=14.1
Q ss_pred CCCCcCeEEEEecCCC------------CCceEEEEEEeeCCcEEEEcCC-----------------------C-CCCEE
Q 032329 82 KRVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTDE-----------------------K-DEPFV 125 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~------------~~~~~VKRViglpGD~vv~~~~-----------------------~-~~~~~ 125 (143)
..+++||+|+|..|.. .+..++|||+|+|||+|...++ . ....+
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 3489999999998752 2458899999999999765311 0 13578
Q ss_pred ecCCcEEEEecCCCCC
Q 032329 126 LDKDECWVLADNENMK 141 (143)
Q Consensus 126 VP~g~~wVlGDNr~~S 141 (143)
||+|+|||+|||+.+|
T Consensus 100 vp~g~~~v~gd~~~~S 115 (138)
T PF10502_consen 100 VPEGEYFVLGDNRPNS 115 (138)
T ss_dssp --TTEEEEE-SBTTS-
T ss_pred eCCCEEEEecCCCCCc
Confidence 9999999999999887
No 13
>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=99.22 E-value=1.1e-10 Score=77.65 Aligned_cols=53 Identities=28% Similarity=0.444 Sum_probs=45.0
Q ss_pred EEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCC
Q 032329 52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEG 111 (143)
Q Consensus 52 ~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpG 111 (143)
.+.++|+||+|++.+| |.+++++.. ..++.||+++++.+. +..++||+...++
T Consensus 2 ~~~v~g~SM~P~i~~g-d~v~i~~~~----~~~~~G~iv~~~~~~--~~~~ikrl~~~~~ 54 (84)
T cd06462 2 ALRVEGDSMEPTIPDG-DLVLVDKSS----YEPKRGDIVVFRLPG--GELTVKRVIGLPG 54 (84)
T ss_pred eeEEcCCCccCcccCC-CEEEEEecC----CCCcCCEEEEEEcCC--CcEEEEEEEEECC
Confidence 4679999999999998 999999752 248999999999753 4799999999986
No 14
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=99.21 E-value=4.5e-11 Score=92.69 Aligned_cols=61 Identities=21% Similarity=0.404 Sum_probs=46.2
Q ss_pred CCCCcCeEEEEecCCCC-------------------CceEEEEEEeeCCcEEEEcCC-----------------------
Q 032329 82 KRVSVGDVVVMKDPEKS-------------------DNYIVRRLAAIEGYEMVSTDE----------------------- 119 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~-------------------~~~~VKRViglpGD~vv~~~~----------------------- 119 (143)
..+++||+|+|..|... ...++|||+|+|||+|...++
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 46899999999866421 136899999999999765210
Q ss_pred ----CCCCEEecCCcEEEEecCCCCCC
Q 032329 120 ----KDEPFVLDKDECWVLADNENMKP 142 (143)
Q Consensus 120 ----~~~~~~VP~g~~wVlGDNr~~S~ 142 (143)
.....+||+|+|||+|||+.+|-
T Consensus 129 l~~~~~~~~~lp~g~~fvlgd~~~~S~ 155 (178)
T PRK13884 129 LPRYQANSYTLGESELLLMSDVSATSF 155 (178)
T ss_pred ccccCCCceEECCCEEEEECCCCCCCC
Confidence 01135899999999999999884
No 15
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=99.00 E-value=5.7e-09 Score=69.28 Aligned_cols=68 Identities=25% Similarity=0.315 Sum_probs=53.6
Q ss_pred EEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEE--cCCCCCCEEecC
Q 032329 52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVS--TDEKDEPFVLDK 128 (143)
Q Consensus 52 ~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~--~~~~~~~~~VP~ 128 (143)
.+.++|+||+|++++| |.+++++. ..++.||++++..+ ++.++||+...+++.+.. .++.+++..++.
T Consensus 2 ~~~v~g~sM~p~i~~g-d~lii~~~-----~~~~~g~i~~~~~~---~~~~ikr~~~~~~~~~~L~s~N~~~~~~~~~~ 71 (81)
T cd06529 2 ALRVKGDSMEPTIPDG-DLVLVDPS-----DTPRDGDIVVARLD---GELTVKRLQRRGGGRLRLISDNPAYPPIEIDE 71 (81)
T ss_pred EEEEECCCcCCccCCC-CEEEEcCC-----CCCCCCCEEEEEEC---CEEEEEEEEECCCCcEEEEeCCCCCCCEeeCh
Confidence 4679999999999998 99999874 45899999999964 378999999999655443 344566666664
No 16
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.80 E-value=3.7e-08 Score=77.50 Aligned_cols=56 Identities=25% Similarity=0.305 Sum_probs=46.0
Q ss_pred EEEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEE
Q 032329 51 YLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEM 114 (143)
Q Consensus 51 ~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~v 114 (143)
..+.|.|+||+|++++| |.++|+.- .+..+||.|++.. .+++.+|||+...+|-.+
T Consensus 124 ~~i~V~GDSMeP~~~~G-d~ilVd~~-----~~~~~gd~v~v~~--~g~~~~VK~l~~~~~~~~ 179 (214)
T COG2932 124 FALRVTGDSMEPTYEDG-DTLLVDPG-----VNTRRGDRVYVET--DGGELYVKKLQREPGGLL 179 (214)
T ss_pred EEEEEeCCcccccccCC-CEEEECCC-----CceeeCCEEEEEE--eCCeEEEEEEEEecCCeE
Confidence 46889999999999998 99999874 4567888666553 357899999999997765
No 17
>PRK00215 LexA repressor; Validated
Probab=98.61 E-value=5.5e-07 Score=70.17 Aligned_cols=78 Identities=23% Similarity=0.296 Sum_probs=58.8
Q ss_pred cEEEEEeeCCCCc-ccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEE-EcCCCCCCEEe
Q 032329 49 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV-STDEKDEPFVL 126 (143)
Q Consensus 49 v~~~~~v~G~SM~-PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv-~~~~~~~~~~V 126 (143)
-.+.+.|.|+||. |++.+| |.+++++- ..++.||+|++... ++..|||+.-..|.... +.++.++++.+
T Consensus 117 ~~~~~~V~GdSM~~~~i~~G-d~v~v~~~-----~~~~~G~ivv~~~~---~~~~vKrl~~~~~~~~L~s~Np~y~~~~~ 187 (205)
T PRK00215 117 EDFLLRVRGDSMIDAGILDG-DLVIVRKQ-----QTARNGQIVVALID---DEATVKRFRREGGHIRLEPENPAYEPIIV 187 (205)
T ss_pred CeEEEEEccCCCCCCCcCCC-CEEEEeCC-----CCCCCCCEEEEEEC---CEEEEEEEEEeCCEEEEEcCCCCCCCEEe
Confidence 3457889999995 799998 99999863 45789999999863 37899999977554322 23556778888
Q ss_pred cCCcEEEEe
Q 032329 127 DKDECWVLA 135 (143)
Q Consensus 127 P~g~~wVlG 135 (143)
+++.+-+.|
T Consensus 188 ~~~~~~IiG 196 (205)
T PRK00215 188 DPDRVTIEG 196 (205)
T ss_pred CCCcEEEEE
Confidence 776666665
No 18
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.60 E-value=6.8e-07 Score=66.28 Aligned_cols=75 Identities=20% Similarity=0.322 Sum_probs=53.6
Q ss_pred EEEEeeCCCCc-ccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcE-EEEcCCCCCCEEecC
Q 032329 51 YLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYE-MVSTDEKDEPFVLDK 128 (143)
Q Consensus 51 ~~~~v~G~SM~-PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~-vv~~~~~~~~~~VP~ 128 (143)
+...|+|+||. |++.+| |.+++++- ..++.||+|++.. .++..+||+.--+ +. +.+.+..+.++.+.+
T Consensus 52 f~l~V~GdSM~~~~I~~G-D~liVd~~-----~~~~~Gdivv~~~---~g~~~vKrl~~~~-~~~L~s~N~~y~~i~i~~ 121 (139)
T PRK10276 52 YFVKASGDSMIDAGISDG-DLLIVDSA-----ITASHGDIVIAAV---DGEFTVKKLQLRP-TVQLIPMNSAYSPITISS 121 (139)
T ss_pred EEEEEecCCCCCCCCCCC-CEEEEECC-----CCCCCCCEEEEEE---CCEEEEEEEEECC-cEEEEcCCCCCCCEEcCC
Confidence 46889999998 689997 99999863 4578999999975 3568999998653 43 223345566777654
Q ss_pred -CcEEEEe
Q 032329 129 -DECWVLA 135 (143)
Q Consensus 129 -g~~wVlG 135 (143)
+++=+.|
T Consensus 122 ~~~~~IiG 129 (139)
T PRK10276 122 EDTLDVFG 129 (139)
T ss_pred CCcEEEEE
Confidence 3444443
No 19
>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=98.55 E-value=8.4e-07 Score=68.82 Aligned_cols=78 Identities=21% Similarity=0.275 Sum_probs=59.2
Q ss_pred cEEEEEeeCCCCc-ccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEE-EcCCCCCCEEe
Q 032329 49 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV-STDEKDEPFVL 126 (143)
Q Consensus 49 v~~~~~v~G~SM~-PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv-~~~~~~~~~~V 126 (143)
-...+.+.|+||. |++.+| |.+++++. ..++.||+|++.. +++..|||+.--+|.... ..++.++++.+
T Consensus 110 ~~f~~~V~GdSM~~~~i~~G-d~v~v~~~-----~~~~~G~ivvv~~---~~~~~vKrl~~~~~~i~L~s~N~~y~~i~~ 180 (199)
T TIGR00498 110 AVFLLKVMGDSMVDAGICDG-DLLIVRSQ-----KDARNGEIVAAMI---DGEVTVKRFYKDGTKVELKPENPEFDPIVL 180 (199)
T ss_pred CEEEEEecCCCCCCCCCCCC-CEEEEecC-----CCCCCCCEEEEEE---CCEEEEEEEEEECCEEEEEcCCCCCcCCcC
Confidence 3458899999996 589997 99999863 4688999999986 467899999876544322 23556777888
Q ss_pred cCCcEEEEe
Q 032329 127 DKDECWVLA 135 (143)
Q Consensus 127 P~g~~wVlG 135 (143)
+++.+-+.|
T Consensus 181 ~~~~~~IiG 189 (199)
T TIGR00498 181 NAEDVTILG 189 (199)
T ss_pred CCCcEEEEE
Confidence 776777666
No 20
>PRK12423 LexA repressor; Provisional
Probab=98.45 E-value=2.3e-06 Score=67.08 Aligned_cols=75 Identities=17% Similarity=0.210 Sum_probs=55.0
Q ss_pred EEEEeeCCCCc-ccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEE--cCCCCCCEEec
Q 032329 51 YLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVS--TDEKDEPFVLD 127 (143)
Q Consensus 51 ~~~~v~G~SM~-PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~--~~~~~~~~~VP 127 (143)
+...|.|+||. |+|.+| |.++|++- ..++.||||++.. .++..+||+.-..+. +.. .+..++++.+.
T Consensus 115 f~l~V~GdSM~~~~i~~G-d~viv~~~-----~~~~~Gdivv~~~---~~~~~vKrl~~~~~~-~~L~s~N~~y~~i~~~ 184 (202)
T PRK12423 115 YLLQVQGDSMIDDGILDG-DLVGVHRS-----PEARDGQIVVARL---DGEVTIKRLERSGDR-IRLLPRNPAYAPIVVA 184 (202)
T ss_pred EEEEEecCcCCCCCcCCC-CEEEEeCC-----CcCCCCCEEEEEE---CCEEEEEEEEEeCCE-EEEEcCCCCCCCEEcC
Confidence 46899999997 799998 99999863 4678999999985 357899999877544 333 34556677765
Q ss_pred C-CcEEEEe
Q 032329 128 K-DECWVLA 135 (143)
Q Consensus 128 ~-g~~wVlG 135 (143)
+ ..+=+.|
T Consensus 185 ~~~~~~I~G 193 (202)
T PRK12423 185 PDQDFAIEG 193 (202)
T ss_pred CCCcEEEEE
Confidence 4 3444443
No 21
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.05 E-value=5.8e-06 Score=63.27 Aligned_cols=55 Identities=22% Similarity=0.247 Sum_probs=42.3
Q ss_pred EEEeeCCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCC
Q 032329 52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEG 111 (143)
Q Consensus 52 ~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpG 111 (143)
++.|=+.||+|.++-| |.+++.... ....+.||||||+-+. .+-..|+||+.+-+
T Consensus 50 iVVVLSgSMePaF~RG-DlLfL~N~~---~~p~~vGdivVf~veg-R~IPiVHRviK~he 104 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHRG-DLLFLTNRN---EDPIRVGDIVVFKVEG-REIPIVHRVIKQHE 104 (180)
T ss_pred EEEEEcCCcCcccccc-cEEEEecCC---CCcceeccEEEEEECC-ccCchhHHHHHHhc
Confidence 3456789999999997 999886543 2457899999999753 34468999997753
No 22
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.52 E-value=0.0013 Score=52.14 Aligned_cols=78 Identities=21% Similarity=0.219 Sum_probs=57.4
Q ss_pred cEEEEEeeCCCCcc-cccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEE--cCCCCCCEE
Q 032329 49 LTYLYGNKGDQMAP-VMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVS--TDEKDEPFV 125 (143)
Q Consensus 49 v~~~~~v~G~SM~P-Tl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~--~~~~~~~~~ 125 (143)
-.+...|.|+||.. .+.+| |.|+|++ ....+.||||++.-+. ++.-+||..--.+.. .. .++.++++.
T Consensus 111 ~~f~L~V~GdSM~~~gi~dG-DlvvV~~-----~~~a~~GdiVvA~i~g--~e~TvKrl~~~g~~i-~L~p~Np~~~~i~ 181 (201)
T COG1974 111 ATFFLRVSGDSMIDAGILDG-DLVVVDP-----TEDAENGDIVVALIDG--EEATVKRLYRDGNQI-LLKPENPAYPPIP 181 (201)
T ss_pred ceEEEEecCCccccCcCCCC-CEEEEcC-----CCCCCCCCEEEEEcCC--CcEEEEEEEEeCCEE-EEEeCCCCCCCcc
Confidence 34578899999975 56665 9999986 3688999999998643 668999998765544 43 355677777
Q ss_pred ecCCcEEEEe
Q 032329 126 LDKDECWVLA 135 (143)
Q Consensus 126 VP~g~~wVlG 135 (143)
+..+.|=++|
T Consensus 182 ~~~~~~~I~G 191 (201)
T COG1974 182 VDADSVTILG 191 (201)
T ss_pred cCccceEEEE
Confidence 7665666655
No 23
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=94.73 E-value=0.026 Score=43.48 Aligned_cols=60 Identities=22% Similarity=0.310 Sum_probs=42.6
Q ss_pred CCCCcCeEEEEecCCC------------CCceEEEEEEeeCCcEEEEcC------C-----------C-------CCCEE
Q 032329 82 KRVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTD------E-----------K-------DEPFV 125 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~------------~~~~~VKRViglpGD~vv~~~------~-----------~-------~~~~~ 125 (143)
..+++||+|++..|+. ..-.++|||.|+|||+|...+ + . ..--.
T Consensus 52 ~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~ 131 (173)
T COG4959 52 APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRY 131 (173)
T ss_pred CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCce
Confidence 3469999999987763 234579999999999976421 1 0 01112
Q ss_pred ecCCcEEEEecCCCCC
Q 032329 126 LDKDECWVLADNENMK 141 (143)
Q Consensus 126 VP~g~~wVlGDNr~~S 141 (143)
+-++++|+|+|.-+.|
T Consensus 132 l~~~el~lL~~~~~~S 147 (173)
T COG4959 132 LAPSELLLLTDRSSTS 147 (173)
T ss_pred ecCCeEEEEeccCCcc
Confidence 7788999999987766
No 24
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=86.77 E-value=0.78 Score=33.64 Aligned_cols=12 Identities=50% Similarity=0.581 Sum_probs=10.2
Q ss_pred CCCcCeEEEEec
Q 032329 83 RVSVGDVVVMKD 94 (143)
Q Consensus 83 ~~~rGDVVvf~~ 94 (143)
...+||+|+|++
T Consensus 84 ~~~~GD~i~~~~ 95 (166)
T COG0681 84 IGLRGDIVVFKD 95 (166)
T ss_pred ccCCCCEEEEEC
Confidence 457899999997
No 25
>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=80.34 E-value=8 Score=29.20 Aligned_cols=81 Identities=12% Similarity=0.104 Sum_probs=50.4
Q ss_pred hHHHHHHhhheeeeeeeeeeccCCCcchhHHHHHHHHHHHh-hhccEEEEEeeCCCCcccccCCCcEEEEEeecCCCCCC
Q 032329 5 STWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLF-QGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKR 83 (143)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~v~~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~~~ 83 (143)
=.||+-.++++.|+|+.++..... -|...+...+. .++...-......+|...|... -...+..-. ...
T Consensus 6 I~w~~~r~~~v~YSm~~R~G~~s~------DCSs~V~~ALr~aG~~~~g~~~nT~tl~~~L~~~-G~~~I~~~~---~~~ 75 (145)
T PF05382_consen 6 INWMEARKGKVTYSMDSRNGPDSY------DCSSFVYQALRAAGFKIPGSAGNTETLHDWLKKN-GFKKISENV---DWN 75 (145)
T ss_pred HHHHHHhcCCceEhhhhcCCCCcC------chHHHHHHHHHHcCCCCCCCccCHHHHHHHHhhC-CcEEeccCC---ccc
Confidence 369999999999998866665432 34444444332 2222222235678898888876 354453311 147
Q ss_pred CCcCeEEEEecC
Q 032329 84 VSVGDVVVMKDP 95 (143)
Q Consensus 84 ~~rGDVVvf~~P 95 (143)
+|+|||++....
T Consensus 76 ~q~GDI~I~g~~ 87 (145)
T PF05382_consen 76 LQRGDIFIWGRR 87 (145)
T ss_pred ccCCCEEEEcCC
Confidence 899999998644
No 26
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=73.84 E-value=26 Score=24.28 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=14.4
Q ss_pred CcEEEEcCCCCCCEEecCCcEEEEe
Q 032329 111 GYEMVSTDEKDEPFVLDKDECWVLA 135 (143)
Q Consensus 111 GD~vv~~~~~~~~~~VP~g~~wVlG 135 (143)
||+|+........+++-...|.++-
T Consensus 62 GD~Vlf~~~~g~ev~~~~~~y~iv~ 86 (95)
T PRK00364 62 GDKVLFGKYAGTEVKIDGEEYLILR 86 (95)
T ss_pred CCEEEEcCCCCeEEEECCEEEEEEE
Confidence 7776655444455666555555553
No 27
>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=66.47 E-value=6.5 Score=26.09 Aligned_cols=9 Identities=33% Similarity=0.379 Sum_probs=4.3
Q ss_pred CcCeEEEEe
Q 032329 85 SVGDVVVMK 93 (143)
Q Consensus 85 ~rGDVVvf~ 93 (143)
..||.|.+.
T Consensus 46 ~~GD~V~Ve 54 (68)
T TIGR00008 46 LPGDKVKVE 54 (68)
T ss_pred CCCCEEEEE
Confidence 345555443
No 28
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=66.23 E-value=6.6 Score=26.60 Aligned_cols=8 Identities=25% Similarity=0.231 Sum_probs=3.8
Q ss_pred cEEEEEee
Q 032329 69 GTLLVRKL 76 (143)
Q Consensus 69 D~Vlv~k~ 76 (143)
|.|+|+.+
T Consensus 51 D~V~Ve~~ 58 (75)
T COG0361 51 DVVLVELS 58 (75)
T ss_pred CEEEEEec
Confidence 55555443
No 29
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=64.92 E-value=47 Score=23.55 Aligned_cols=70 Identities=17% Similarity=0.224 Sum_probs=39.6
Q ss_pred ccccCCCcEEEEEeecCCC------------CCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCC
Q 032329 62 PVMGGLGGTLLVRKLPAAD------------PKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKD 129 (143)
Q Consensus 62 PTl~~ggD~Vlv~k~~~~~------------~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g 129 (143)
+.|.+=+|+||+.+..... ..+++.|.||.+-. .. ... -.-=-+||+|+........+++-..
T Consensus 10 ~~ikPL~dRVLVk~~~~e~kT~gGIiLP~sakekp~~g~VvAVG~-G~---~~~-~~~Vk~GD~Vl~~~y~Gtevk~dg~ 84 (100)
T PTZ00414 10 KKLQPLGQRVLVKRTLAAKQTKAGVLIPEQVAGKVNEGTVVAVAA-AT---KDW-TPTVKVGDTVLLPEFGGSSVKVEGE 84 (100)
T ss_pred ccceecCCEEEEEEcccccccccCEEcccccccCCceeEEEEECC-CC---ccc-cceecCCCEEEEcCCCCcEEEECCE
Confidence 5677767999998754220 13456666666642 11 000 0112258887766555666777666
Q ss_pred cEEEEec
Q 032329 130 ECWVLAD 136 (143)
Q Consensus 130 ~~wVlGD 136 (143)
+|.++-+
T Consensus 85 ey~i~~e 91 (100)
T PTZ00414 85 EFFLYNE 91 (100)
T ss_pred EEEEEEh
Confidence 6766643
No 30
>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=62.05 E-value=11 Score=27.03 Aligned_cols=28 Identities=29% Similarity=0.468 Sum_probs=21.8
Q ss_pred CCCcCeEEEEecCCCCCceEEEEEEeeC
Q 032329 83 RVSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (143)
Q Consensus 83 ~~~rGDVVvf~~P~~~~~~~VKRViglp 110 (143)
.++.||-|.++++..++..+|.||..+-
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~ 30 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLW 30 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 4678999999887665667899998764
No 31
>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=60.27 E-value=12 Score=25.70 Aligned_cols=27 Identities=30% Similarity=0.372 Sum_probs=21.3
Q ss_pred CCcCeEEEEecCCCCCceEEEEEEeeC
Q 032329 84 VSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (143)
Q Consensus 84 ~~rGDVVvf~~P~~~~~~~VKRViglp 110 (143)
++.||.|.+..+..++..+|.||..+-
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~ 29 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIW 29 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 567888888876656778999998774
No 32
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=56.05 E-value=67 Score=22.76 Aligned_cols=73 Identities=16% Similarity=0.307 Sum_probs=40.4
Q ss_pred ccCCCcEEEEEeecCCC------------CCCCCcCeEEEEec-CCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCCc
Q 032329 64 MGGLGGTLLVRKLPAAD------------PKRVSVGDVVVMKD-PEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDE 130 (143)
Q Consensus 64 l~~ggD~Vlv~k~~~~~------------~~~~~rGDVVvf~~-P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g~ 130 (143)
|.+=||+|+|.+.-... ..++++|.||.+-. ..+.+... ...-=--||+|+........+++-..+
T Consensus 3 ikPL~DRVlVk~~e~EekT~gGIvlpdsakeK~~~g~VvAVG~G~~~~~g~~-~~~~VkvGD~Vlf~ky~G~evk~dgee 81 (96)
T COG0234 3 IKPLGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENGEL-VPLDVKVGDRVLFGKYAGTEVKIDGEE 81 (96)
T ss_pred ceecCCEEEEEEchhhccccCcEEecCccccCCcceEEEEEccceecCCCCE-eccccccCCEEEECccCCcEEEECCEE
Confidence 34445999998753210 14578888888753 11122111 111112388877665555667777777
Q ss_pred EEEEecC
Q 032329 131 CWVLADN 137 (143)
Q Consensus 131 ~wVlGDN 137 (143)
|-++.+.
T Consensus 82 ylil~e~ 88 (96)
T COG0234 82 YLILSES 88 (96)
T ss_pred EEEechH
Confidence 7777653
No 33
>smart00439 BAH Bromo adjacent homology domain.
Probab=55.40 E-value=22 Score=24.34 Aligned_cols=26 Identities=27% Similarity=0.636 Sum_probs=16.0
Q ss_pred CCcCeEEEEecCCCCCceEEEEEEee
Q 032329 84 VSVGDVVVMKDPEKSDNYIVRRLAAI 109 (143)
Q Consensus 84 ~~rGDVVvf~~P~~~~~~~VKRVigl 109 (143)
++.||.|.+.++......+|-||..+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i 27 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEI 27 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEE
Confidence 45677777766543345666666665
No 34
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=55.32 E-value=16 Score=26.00 Aligned_cols=27 Identities=30% Similarity=0.550 Sum_probs=20.7
Q ss_pred CCCcCeEEEEecCCCCCceEEEEEEee
Q 032329 83 RVSVGDVVVMKDPEKSDNYIVRRLAAI 109 (143)
Q Consensus 83 ~~~rGDVVvf~~P~~~~~~~VKRVigl 109 (143)
.++.||-|.+.++.+++..+|-||..+
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i 29 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERL 29 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEE
Confidence 357899999988766577788888776
No 35
>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=54.89 E-value=95 Score=23.81 Aligned_cols=41 Identities=15% Similarity=0.294 Sum_probs=28.3
Q ss_pred EeecCCCCCCCCcCeEEEEecCCCCCceEEEE---EEeeCCcEEEEc
Q 032329 74 RKLPAADPKRVSVGDVVVMKDPEKSDNYIVRR---LAAIEGYEMVST 117 (143)
Q Consensus 74 ~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKR---ViglpGD~vv~~ 117 (143)
+.-.++ +..++.|++.++.. .....++|| +|.+.++.+...
T Consensus 66 ~d~~yR-~~~L~~GEvalY~~--~G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 66 EDRRYR-PKGLKPGEVALYDD--EGQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred CCcccc-ccCCCCCcEEEEcC--CCCEEEEEecceEEeccCceEEEe
Confidence 444455 36799999999985 455566765 777888876543
No 36
>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=54.84 E-value=45 Score=23.35 Aligned_cols=36 Identities=17% Similarity=0.193 Sum_probs=21.3
Q ss_pred CCCCcCeEEEEecCCCCCceEEEEEEee-CCcEEEEc
Q 032329 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAI-EGYEMVST 117 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~~~~~VKRVigl-pGD~vv~~ 117 (143)
..|+.|||++|.......-=.|-=|.++ .+++|...
T Consensus 61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~ 97 (124)
T PF05257_consen 61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVI 97 (124)
T ss_dssp S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEE
T ss_pred cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEE
Confidence 6799999999953222233366667788 78886543
No 37
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=54.70 E-value=69 Score=22.17 Aligned_cols=67 Identities=12% Similarity=0.189 Sum_probs=32.6
Q ss_pred ccCCCcEEEEEeecCCC------------CCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCCcE
Q 032329 64 MGGLGGTLLVRKLPAAD------------PKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC 131 (143)
Q Consensus 64 l~~ggD~Vlv~k~~~~~------------~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g~~ 131 (143)
|.+=+|+||+.+..... ..+++.|.||..- |.. ... -.---+||+|+........+++-...|
T Consensus 3 i~Pl~DRVLVk~~~~e~~T~gGI~Lp~~a~ek~~~G~VvavG-~g~---~~~-~~~Vk~GD~Vl~~~y~g~ev~~~~~~y 77 (91)
T PRK14533 3 VIPLGERLLIKPIKEEKKTEGGIVLPDSAKEKPMKAEVVAVG-KLD---DEE-DFDIKVGDKVIFSKYAGTEIKIDDEDY 77 (91)
T ss_pred ceEcCCEEEEEEccccceecccEEecccccCCcceEEEEEEC-CCC---ccc-cccccCCCEEEEccCCCeEEEECCEEE
Confidence 33435999998754220 1234556555553 211 000 011224788766554445566655555
Q ss_pred EEEe
Q 032329 132 WVLA 135 (143)
Q Consensus 132 wVlG 135 (143)
.++-
T Consensus 78 ~iv~ 81 (91)
T PRK14533 78 IIID 81 (91)
T ss_pred EEEE
Confidence 5553
No 38
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=54.40 E-value=31 Score=21.93 Aligned_cols=39 Identities=21% Similarity=0.273 Sum_probs=22.7
Q ss_pred CCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEE
Q 032329 57 GDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRR 105 (143)
Q Consensus 57 G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKR 105 (143)
+.++.|..-..|-.+.|- .-++.||.|.++. .+..|++|
T Consensus 18 ~~~~K~A~letG~~i~VP-------~FI~~Gd~I~VdT---~~g~Yv~R 56 (56)
T PF09285_consen 18 SSSYKPATLETGAEIQVP-------LFIEEGDKIKVDT---RDGSYVER 56 (56)
T ss_dssp STTEEEEEETTS-EEEEE-------TT--TT-EEEEET---TTTEEEEE
T ss_pred CCCccEEEEcCCCEEEcc-------ceecCCCEEEEEC---CCCeEeCC
Confidence 455677555444666663 3478999999984 34567777
No 39
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=51.71 E-value=17 Score=25.30 Aligned_cols=9 Identities=33% Similarity=0.545 Sum_probs=4.5
Q ss_pred CcCeEEEEe
Q 032329 85 SVGDVVVMK 93 (143)
Q Consensus 85 ~rGDVVvf~ 93 (143)
..||.|.+.
T Consensus 48 l~GD~V~VE 56 (87)
T PRK12442 48 LAGDRVTLE 56 (87)
T ss_pred cCCCEEEEE
Confidence 345555553
No 40
>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=48.43 E-value=62 Score=23.62 Aligned_cols=13 Identities=15% Similarity=0.309 Sum_probs=11.0
Q ss_pred CCCCcCeEEEEec
Q 032329 82 KRVSVGDVVVMKD 94 (143)
Q Consensus 82 ~~~~rGDVVvf~~ 94 (143)
..+++||||+|+.
T Consensus 72 ~~p~~GDiv~f~~ 84 (129)
T TIGR02594 72 SKPAYGCIAVKRR 84 (129)
T ss_pred CCCCccEEEEEEC
Confidence 4689999999975
No 41
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=47.52 E-value=13 Score=24.64 Aligned_cols=17 Identities=12% Similarity=0.147 Sum_probs=11.6
Q ss_pred CCCcccccCCCcEEEEEe
Q 032329 58 DQMAPVMGGLGGTLLVRK 75 (143)
Q Consensus 58 ~SM~PTl~~ggD~Vlv~k 75 (143)
.||+|.|++| ++|+..-
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 4899999998 9998854
No 42
>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=45.66 E-value=23 Score=22.72 Aligned_cols=11 Identities=27% Similarity=0.577 Sum_probs=6.8
Q ss_pred CCCcCeEEEEe
Q 032329 83 RVSVGDVVVMK 93 (143)
Q Consensus 83 ~~~rGDVVvf~ 93 (143)
-+++||.|++.
T Consensus 41 wI~~GD~V~V~ 51 (65)
T PF01176_consen 41 WIKRGDFVLVE 51 (65)
T ss_dssp ---TTEEEEEE
T ss_pred ecCCCCEEEEE
Confidence 46788888887
No 43
>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=45.41 E-value=22 Score=23.88 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=7.5
Q ss_pred CCcCeEEEEe
Q 032329 84 VSVGDVVVMK 93 (143)
Q Consensus 84 ~~rGDVVvf~ 93 (143)
+++||.|++.
T Consensus 39 I~~GD~V~Ve 48 (77)
T cd05793 39 INEGDIVLVA 48 (77)
T ss_pred EcCCCEEEEE
Confidence 5678888885
No 44
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=44.69 E-value=58 Score=23.62 Aligned_cols=52 Identities=15% Similarity=0.043 Sum_probs=24.4
Q ss_pred CCCcCeEEEEecCCCCCceEEEEEEeeC------CcEEEEcCCCCCCEEecCCcEEEE
Q 032329 83 RVSVGDVVVMKDPEKSDNYIVRRLAAIE------GYEMVSTDEKDEPFVLDKDECWVL 134 (143)
Q Consensus 83 ~~~rGDVVvf~~P~~~~~~~VKRViglp------GD~vv~~~~~~~~~~VP~g~~wVl 134 (143)
.++.||-|+...+.....+.=..|++.| +..+...-.+.....+|.++++-.
T Consensus 55 ~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~~~~~I 112 (124)
T PF15057_consen 55 SLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAKVPRGEVIWI 112 (124)
T ss_pred cCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECCCCCccchhhEEEC
Confidence 4555555555544333334445666432 222222111223456777776654
No 45
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=42.78 E-value=33 Score=23.34 Aligned_cols=28 Identities=25% Similarity=0.356 Sum_probs=19.7
Q ss_pred CCCcCeEEEEecCCC--CCceEEEEEEeeC
Q 032329 83 RVSVGDVVVMKDPEK--SDNYIVRRLAAIE 110 (143)
Q Consensus 83 ~~~rGDVVvf~~P~~--~~~~~VKRViglp 110 (143)
.++.||.|.+..+.. ++..+|-||..+-
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~ 32 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELW 32 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeee
Confidence 456788888876543 3567888888774
No 46
>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=41.65 E-value=1.3e+02 Score=22.82 Aligned_cols=50 Identities=12% Similarity=0.314 Sum_probs=29.4
Q ss_pred CCCcCeEEEEecCC--CCCceEEEEEEeeCCcEEEEcCCCCCCEEecCCcEEEEecCCCCC
Q 032329 83 RVSVGDVVVMKDPE--KSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMK 141 (143)
Q Consensus 83 ~~~rGDVVvf~~P~--~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g~~wVlGDNr~~S 141 (143)
.+..||+|+++... .+++.++=++ .|+. ... .+..-.|++++..||++-+
T Consensus 125 ~i~~Gd~v~v~~~~~~~~G~ivvv~~---~~~~-~vK-----rl~~~~~~i~L~s~N~~y~ 176 (199)
T TIGR00498 125 GICDGDLLIVRSQKDARNGEIVAAMI---DGEV-TVK-----RFYKDGTKVELKPENPEFD 176 (199)
T ss_pred CCCCCCEEEEecCCCCCCCCEEEEEE---CCEE-EEE-----EEEEECCEEEEEcCCCCCc
Confidence 47889999997321 2344443333 4443 221 2333468899999998653
No 47
>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=41.05 E-value=1.2e+02 Score=20.86 Aligned_cols=13 Identities=31% Similarity=0.634 Sum_probs=8.9
Q ss_pred cCCCcEEEEEeec
Q 032329 65 GGLGGTLLVRKLP 77 (143)
Q Consensus 65 ~~ggD~Vlv~k~~ 77 (143)
.+-+|+||+.+..
T Consensus 3 ~Pl~DrVLV~~~~ 15 (93)
T cd00320 3 KPLGDRVLVKRIE 15 (93)
T ss_pred eecCCEEEEEEcc
Confidence 3435899998764
No 48
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=40.68 E-value=28 Score=23.64 Aligned_cols=43 Identities=19% Similarity=0.269 Sum_probs=22.9
Q ss_pred cEEEEEeeCCCCcc-cccCCCcEEEEEeecCCCCC--CCCcCeEEEEe
Q 032329 49 LTYLYGNKGDQMAP-VMGGLGGTLLVRKLPAADPK--RVSVGDVVVMK 93 (143)
Q Consensus 49 v~~~~~v~G~SM~P-Tl~~ggD~Vlv~k~~~~~~~--~~~rGDVVvf~ 93 (143)
++.+....|+.+.= .+.+| ..+++. +...+.+ -+++||+|++.
T Consensus 8 ~g~V~~~lG~~~~~V~~~dG-~~~la~-ipgK~Rk~iwI~~GD~VlVe 53 (83)
T smart00652 8 IAQVVKMLGNGRLEVMCADG-KERLAR-IPGKMRKKVWIRRGDIVLVD 53 (83)
T ss_pred EEEEEEEcCCCEEEEEECCC-CEEEEE-EchhhcccEEEcCCCEEEEE
Confidence 34455566666665 33444 555553 2222111 25788888886
No 49
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=40.05 E-value=54 Score=20.84 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=23.6
Q ss_pred CCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEE
Q 032329 57 GDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRR 105 (143)
Q Consensus 57 G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKR 105 (143)
+.|+.|..-..|-.+.| +.-++.||.|.++.. +..|+.|
T Consensus 18 ~~~~K~A~letG~~i~V-------P~FI~~Gd~I~V~T~---~g~Y~~R 56 (56)
T smart00841 18 SGGTKPATLETGAVVQV-------PLFINEGDKIKVDTR---TGEYVSR 56 (56)
T ss_pred CCCcceEEECCCCEEEc-------CCcccCCCEEEEECC---CCcEEcC
Confidence 44556654443466666 344789999999853 2345554
No 50
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=39.78 E-value=42 Score=23.83 Aligned_cols=56 Identities=13% Similarity=0.055 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhhhccEEEEEeeCCCCcccccCCCcEEEEEeecCCC----CCCCCcCeEEEEecCC
Q 032329 34 IELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAAD----PKRVSVGDVVVMKDPE 96 (143)
Q Consensus 34 ~~~~~~~~~~~~~~~v~~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~----~~~~~rGDVVvf~~P~ 96 (143)
..++-.++..++.+.- -..+.+.|..|- -.+|+|..-+.. .+.++.||.|+|-+..
T Consensus 39 gdll~yi~~~~ie~r~--~lFi~~gsvrpG-----ii~lINd~DWEllekedy~ledgD~ivfiSTl 98 (101)
T KOG4146|consen 39 GDLLDYIFGKYIETRD--SLFIHHGSVRPG-----IIVLINDMDWELLEKEDYPLEDGDHIVFISTL 98 (101)
T ss_pred HHHHHHHHHHHhcCCc--ceEeeCCcCcCc-----EEEEEeccchhhhcccccCcccCCEEEEEEec
Confidence 3444445554443331 244788886663 445555432110 3568999999998643
No 51
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=38.67 E-value=45 Score=23.50 Aligned_cols=31 Identities=13% Similarity=0.086 Sum_probs=19.4
Q ss_pred ccCCCcEEEEEeecCCC----CCCCCcCeEEEEecC
Q 032329 64 MGGLGGTLLVRKLPAAD----PKRVSVGDVVVMKDP 95 (143)
Q Consensus 64 l~~ggD~Vlv~k~~~~~----~~~~~rGDVVvf~~P 95 (143)
+.+| -.+|+|..-+.. .+.++.||+|+|-+.
T Consensus 58 lrpG-iI~LINd~DWeLleke~y~ledgDiIvfist 92 (96)
T COG5131 58 LRPG-IICLINDMDWELLEKERYPLEDGDIIVFIST 92 (96)
T ss_pred Cccc-EEEEEcCccHhhhhcccccCCCCCEEEEEec
Confidence 5554 566666533221 246889999999764
No 52
>PRK02135 hypothetical protein; Provisional
Probab=38.30 E-value=31 Score=27.51 Aligned_cols=19 Identities=16% Similarity=0.330 Sum_probs=15.5
Q ss_pred EEecCCcEEEEecCCCCCC
Q 032329 124 FVLDKDECWVLADNENMKP 142 (143)
Q Consensus 124 ~~VP~g~~wVlGDNr~~S~ 142 (143)
...|++-+||+||+...+.
T Consensus 142 ~~~~~~~~FvLgDH~~~~~ 160 (201)
T PRK02135 142 VEFPENPVFVLGDHIGFTE 160 (201)
T ss_pred ccCCCCCEEEEeCCCCCCH
Confidence 3578899999999987764
No 53
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=37.37 E-value=33 Score=24.25 Aligned_cols=44 Identities=20% Similarity=0.167 Sum_probs=22.5
Q ss_pred cEEEEEeeCCCCcccc-cCCCcEEEEEeecCCCCC--CCCcCeEEEEec
Q 032329 49 LTYLYGNKGDQMAPVM-GGLGGTLLVRKLPAADPK--RVSVGDVVVMKD 94 (143)
Q Consensus 49 v~~~~~v~G~SM~PTl-~~ggD~Vlv~k~~~~~~~--~~~rGDVVvf~~ 94 (143)
++.+...-|+.|.=-. .+| ..+++. ++..+.. -+++||.|++..
T Consensus 24 ~g~V~~~lG~~~~~V~~~dG-~~~la~-i~GK~Rk~IwI~~GD~VlVe~ 70 (100)
T PRK04012 24 FGVVEQMLGANRVRVRCMDG-VERMGR-IPGKMKKRMWIREGDVVIVAP 70 (100)
T ss_pred EEEEEEEcCCCEEEEEeCCC-CEEEEE-EchhhcccEEecCCCEEEEEe
Confidence 3344555566665533 344 555542 2222111 257788888863
No 54
>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=36.89 E-value=36 Score=19.95 Aligned_cols=35 Identities=17% Similarity=0.407 Sum_probs=23.6
Q ss_pred CCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCC
Q 032329 95 PEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKD 129 (143)
Q Consensus 95 P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g 129 (143)
|.....+..-+|+...||.+..........+|+++
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 33456688899999999997654333555666653
No 55
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=36.29 E-value=70 Score=24.67 Aligned_cols=28 Identities=29% Similarity=0.387 Sum_probs=21.6
Q ss_pred CCCCcCeEEEEecCCCCCceEEEEEEeeC
Q 032329 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~~~~~VKRViglp 110 (143)
..++.||.|+++.+.. +..+|..|..+-
T Consensus 51 ~~~~vGD~Vlik~~~~-~~~~V~iI~ei~ 78 (179)
T cd04720 51 LELSVGDTILVKDDVA-NSPSVYLIHEIR 78 (179)
T ss_pred eEEeCCCEEEEeCCCC-CCCEEEEEEEEE
Confidence 4689999999998754 667777777664
No 56
>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=35.03 E-value=40 Score=22.64 Aligned_cols=41 Identities=20% Similarity=0.241 Sum_probs=21.1
Q ss_pred EEEEeeCCCCcccc-cCCCcEEEEEeecCCCCC--CCCcCeEEEEe
Q 032329 51 YLYGNKGDQMAPVM-GGLGGTLLVRKLPAADPK--RVSVGDVVVMK 93 (143)
Q Consensus 51 ~~~~v~G~SM~PTl-~~ggD~Vlv~k~~~~~~~--~~~rGDVVvf~ 93 (143)
.+...-|+.+.=-. .+| ..+++. ++..+.. -+++||.|++.
T Consensus 5 ~V~~~lG~~~~~V~~~dg-~~~l~~-i~gK~Rk~iwI~~GD~VlV~ 48 (78)
T cd04456 5 RVLRMLGNNRHEVECADG-QRRLVS-IPGKLRKNIWIKRGDFLIVD 48 (78)
T ss_pred EEEEECCCCEEEEEECCC-CEEEEE-EchhhccCEEEcCCCEEEEE
Confidence 34455566655533 343 555553 2222111 25778888886
No 57
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=34.93 E-value=1.1e+02 Score=21.83 Aligned_cols=42 Identities=21% Similarity=0.324 Sum_probs=29.2
Q ss_pred cEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcE
Q 032329 69 GTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYE 113 (143)
Q Consensus 69 D~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~ 113 (143)
.+|-+|.-...-...++.||++.++. ++..+.=+|.+++...
T Consensus 34 GrV~vNG~~aKpS~~VK~GD~l~i~~---~~~~~~v~Vl~~~~~r 75 (100)
T COG1188 34 GRVKVNGQRAKPSKEVKVGDILTIRF---GNKEFTVKVLALGEQR 75 (100)
T ss_pred CeEEECCEEcccccccCCCCEEEEEe---CCcEEEEEEEeccccc
Confidence 36666544333247899999999995 4556778888888643
No 58
>KOG4680 consensus Uncharacterized conserved protein, contains ML domain [General function prediction only]
Probab=34.92 E-value=54 Score=24.96 Aligned_cols=28 Identities=14% Similarity=0.331 Sum_probs=19.2
Q ss_pred cCCCCCceEEEEEEeeCCcEEEEcCCCCCCEEecCCcEEEE
Q 032329 94 DPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVL 134 (143)
Q Consensus 94 ~P~~~~~~~VKRViglpGD~vv~~~~~~~~~~VP~g~~wVl 134 (143)
+|..++.+.++..+-+||.+ |+|.|-|.
T Consensus 97 CPVepG~f~~~hsq~LPg~t-------------PPG~Y~lk 124 (153)
T KOG4680|consen 97 CPVEPGDFLVAHSQVLPGYT-------------PPGSYVLK 124 (153)
T ss_pred CCcCcCceeeeeeEeccCcC-------------CCceEEEE
Confidence 45567777777777777765 67776654
No 59
>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=34.57 E-value=74 Score=22.81 Aligned_cols=27 Identities=19% Similarity=0.516 Sum_probs=18.0
Q ss_pred CCCCcCeEEEEecCCCCCceEEEEEEee
Q 032329 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAI 109 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~~~~~VKRVigl 109 (143)
..++.||.++|..-.+ ++.+.-+|+.+
T Consensus 30 ~~ikvGD~I~f~~~~~-~~~l~v~V~~i 56 (109)
T cd06555 30 QQIKVGDKILFNDLDT-GQQLLVKVVDI 56 (109)
T ss_pred hcCCCCCEEEEEEcCC-CcEEEEEEEEE
Confidence 4699999999986433 34455555554
No 60
>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=33.82 E-value=52 Score=24.06 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=19.2
Q ss_pred CCCCcCeEEEEecCCCC----------CceEEEEEEeeC
Q 032329 82 KRVSVGDVVVMKDPEKS----------DNYIVRRLAAIE 110 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~----------~~~~VKRViglp 110 (143)
..++.||+|.++.+... ...+|-||..+.
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~ 42 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMK 42 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEee
Confidence 45778998888754332 145788887764
No 61
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=31.88 E-value=63 Score=23.85 Aligned_cols=29 Identities=17% Similarity=0.346 Sum_probs=22.1
Q ss_pred CCCCcCeEEEEecCCCCCceEEEEEEeeC
Q 032329 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAIE 110 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~~~~~VKRViglp 110 (143)
..++.||-|.+.+...++.++|.||..+-
T Consensus 10 ~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~ 38 (135)
T cd04710 10 ELLKVNDHIYMSSEPPGEPYYIGRIMEFV 38 (135)
T ss_pred eEEeCCCEEEEecCCCCCCCEEEEEEEEE
Confidence 56788999999865445668899999763
No 62
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=29.74 E-value=6.8 Score=24.79 Aligned_cols=39 Identities=10% Similarity=0.230 Sum_probs=25.6
Q ss_pred eEEEEEEeeCCcEEEEc-CCCCCCEEecC-CcEEEEecCCC
Q 032329 101 YIVRRLAAIEGYEMVST-DEKDEPFVLDK-DECWVLADNEN 139 (143)
Q Consensus 101 ~~VKRViglpGD~vv~~-~~~~~~~~VP~-g~~wVlGDNr~ 139 (143)
..++++||..|..+-.. .+..-.+.|++ |.+++.|+|..
T Consensus 11 ~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~ 51 (61)
T cd02393 11 DKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKE 51 (61)
T ss_pred hheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHH
Confidence 37799999999985322 11222344554 88999998753
No 63
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=29.37 E-value=94 Score=25.48 Aligned_cols=77 Identities=14% Similarity=0.288 Sum_probs=47.0
Q ss_pred eCCCCcccccCCCcEEEEEeecCC------------CCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEEEc-CCCCC
Q 032329 56 KGDQMAPVMGGLGGTLLVRKLPAA------------DPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVST-DEKDE 122 (143)
Q Consensus 56 ~G~SM~PTl~~ggD~Vlv~k~~~~------------~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv~~-~~~~~ 122 (143)
....|.|+|+.| |.+...=.... .-.+++.|-+|-+. | ..+-|+++--|--+-.. ....-
T Consensus 105 ~~~~~r~~l~vG-D~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~-p-----~kVpRvig~~~sm~~~l~~~~~~ 177 (239)
T COG1097 105 AEKDLRPFLNVG-DLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIP-P-----SKVPRVIGKKGSMLNMLKEKTGC 177 (239)
T ss_pred cccccccccccC-CEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEc-h-----hhcceEecCCCcHHHHhhhhcCe
Confidence 478899999998 98865322111 01457778777664 2 36778887766542111 11112
Q ss_pred CEEe-cCCcEEEEecCCC
Q 032329 123 PFVL-DKDECWVLADNEN 139 (143)
Q Consensus 123 ~~~V-P~g~~wVlGDNr~ 139 (143)
.+.| -.|.+||-|.|..
T Consensus 178 ~I~VG~NG~IWV~~~~~~ 195 (239)
T COG1097 178 EIIVGQNGRIWVDGENES 195 (239)
T ss_pred EEEEecCCEEEecCCCcc
Confidence 2333 4699999999985
No 64
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=29.27 E-value=96 Score=19.67 Aligned_cols=39 Identities=18% Similarity=0.253 Sum_probs=23.2
Q ss_pred CCCCcccccCCCcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEE
Q 032329 57 GDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRR 105 (143)
Q Consensus 57 G~SM~PTl~~ggD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKR 105 (143)
+.++.|..-..|-.+.| +.-++.||.|.++.. +..|+.|
T Consensus 18 ~~~~K~A~letG~~i~V-------P~FI~~Gd~I~V~T~---~g~Y~~R 56 (56)
T cd05794 18 SSGTKPATLETGAEVQV-------PLFIKEGEKIKVDTR---TGEYVER 56 (56)
T ss_pred CCCcceEEECCCCEEEc-------CCeecCCCEEEEECC---CCcEecC
Confidence 45666654444355555 234788999999853 2335554
No 65
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=28.50 E-value=80 Score=24.20 Aligned_cols=25 Identities=28% Similarity=0.650 Sum_probs=16.6
Q ss_pred CCcCeEEEEecCCCCCceEEEEEEee
Q 032329 84 VSVGDVVVMKDPEKSDNYIVRRLAAI 109 (143)
Q Consensus 84 ~~rGDVVvf~~P~~~~~~~VKRVigl 109 (143)
++.||-|.+.++. ...++|.||..+
T Consensus 4 yrvGD~Vy~~~~~-~~Py~I~rI~e~ 28 (164)
T cd04709 4 YRVGDYVYFESSP-NNPYLIRRIEEL 28 (164)
T ss_pred EecCCEEEEECCC-CCCCEEEEEEEE
Confidence 5677888887652 234677888765
No 66
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.08 E-value=31 Score=25.51 Aligned_cols=16 Identities=13% Similarity=0.135 Sum_probs=13.6
Q ss_pred CCCcccccCCCcEEEEE
Q 032329 58 DQMAPVMGGLGGTLLVR 74 (143)
Q Consensus 58 ~SM~PTl~~ggD~Vlv~ 74 (143)
.||.|-|.+| |+|+-.
T Consensus 12 ~smtPeL~~G-~yVfcT 27 (134)
T COG3602 12 ASMTPELLDG-DYVFCT 27 (134)
T ss_pred HhcCccccCC-ceEEEE
Confidence 3899999998 999764
No 67
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.21 E-value=98 Score=22.34 Aligned_cols=23 Identities=13% Similarity=0.433 Sum_probs=15.9
Q ss_pred CCCCcCeEEEEecCCCCCceEEEEEEee
Q 032329 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAI 109 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~~~~~VKRVigl 109 (143)
..+++||.|+|+. + .+--+|+++
T Consensus 32 r~ik~GD~IiF~~----~-~l~v~V~~v 54 (111)
T COG4043 32 RQIKPGDKIIFNG----D-KLKVEVIDV 54 (111)
T ss_pred cCCCCCCEEEEcC----C-eeEEEEEEE
Confidence 6799999999973 2 343455554
No 68
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=25.83 E-value=2e+02 Score=19.37 Aligned_cols=32 Identities=22% Similarity=0.533 Sum_probs=19.9
Q ss_pred CCCCcCeEEE--EecCCCCCce-EEEEEEeeCCcE
Q 032329 82 KRVSVGDVVV--MKDPEKSDNY-IVRRLAAIEGYE 113 (143)
Q Consensus 82 ~~~~rGDVVv--f~~P~~~~~~-~VKRViglpGD~ 113 (143)
..++.||.|. ++.|.+.+++ -+-||..+.|..
T Consensus 41 f~LR~GD~V~G~vr~p~~~ek~~aL~~V~~VNg~~ 75 (78)
T PF07497_consen 41 FGLRTGDLVEGQVRPPREGEKYFALLRVESVNGRP 75 (78)
T ss_dssp TT--TTEEEEEEEE--STTSSSEEECEECEETTEC
T ss_pred cCCCCCCEEEEEEeCCCCCCcceeeEEEEeECCcC
Confidence 5899999998 6777655543 477887777753
No 69
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=24.32 E-value=2.7e+02 Score=19.78 Aligned_cols=44 Identities=16% Similarity=0.305 Sum_probs=29.9
Q ss_pred cEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcEEE
Q 032329 69 GTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV 115 (143)
Q Consensus 69 D~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~vv 115 (143)
|..-+...... .+++..||+|.++... +.+.+.+++.-.|-.-+
T Consensus 12 ~~y~l~n~Pf~-a~glA~gDvV~~~~~~--g~~~~~~~v~~sGnsTi 55 (117)
T PF14085_consen 12 DTYRLDNIPFF-AYGLALGDVVRAEPDD--GELWFQKVVESSGNSTI 55 (117)
T ss_pred CEEEEEecccc-cCCCCCCCEEEEEeCC--CeEEEEEEEecCCCEEE
Confidence 56666655443 4789999999998643 66667777666665533
No 70
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=24.26 E-value=2.1e+02 Score=19.35 Aligned_cols=61 Identities=18% Similarity=0.172 Sum_probs=32.1
Q ss_pred hccEEEEEeeCCCCcccccC-----C--------CcEEEEEeecCCCCCCCCcCeEEEEecCCCCCceEEEEEEeeCCcE
Q 032329 47 GKLTYLYGNKGDQMAPVMGG-----L--------GGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYE 113 (143)
Q Consensus 47 ~~v~~~~~v~G~SM~PTl~~-----g--------gD~Vlv~k~~~~~~~~~~rGDVVvf~~P~~~~~~~VKRViglpGD~ 113 (143)
.-+...+.+.|.+|.=.+.+ + ....|+=+.. .. ..|++||.|+++ ...++|+|+.--.|-.
T Consensus 18 ~~fg~~~~InG~~~~~v~d~~~~~~~~~~~~v~g~~~~L~v~~~-d~-~~P~~gd~v~~d----G~~y~V~~~~~~~G~~ 91 (95)
T PF13856_consen 18 DEFGEEHTINGKPYRAVFDEPELEERGKRVGVEGTQPTLYVFSS-DY-PKPRRGDRVVID----GESYTVTRFQEEDGMY 91 (95)
T ss_dssp HHH-EEEEETTEEEEEEEGGGT--------------EEEEE--S-S------TT-EEEET----TEEEEEEEEEEETTEE
T ss_pred HHhCCeEEECCEEEEEEECCchhhhccccccccCCceEEEEEcC-CC-CCCCCCCEEEEC----CeEEEEeEEecCCCEE
Confidence 55667777877766533322 1 1233332222 11 349999999986 5778999998777654
No 71
>PF15428 Imm14: Immunity protein 14
Probab=23.72 E-value=1.3e+02 Score=21.30 Aligned_cols=22 Identities=18% Similarity=0.305 Sum_probs=15.9
Q ss_pred CcCeEEEEecCCCCCceEEEEEEe
Q 032329 85 SVGDVVVMKDPEKSDNYIVRRLAA 108 (143)
Q Consensus 85 ~rGDVVvf~~P~~~~~~~VKRVig 108 (143)
|.|||..+.-+ .+.+...||++
T Consensus 1 K~GDIF~ipL~--~~~y~~G~Vi~ 22 (129)
T PF15428_consen 1 KPGDIFCIPLD--DGKYGFGRVIG 22 (129)
T ss_pred CCceEEEEEcC--CCCEEEEEEEe
Confidence 46888888643 56778888883
No 72
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=23.47 E-value=1.1e+02 Score=21.82 Aligned_cols=25 Identities=24% Similarity=0.392 Sum_probs=18.2
Q ss_pred CCCCcCeEEEEecCCCCCceEEEEEEee
Q 032329 82 KRVSVGDVVVMKDPEKSDNYIVRRLAAI 109 (143)
Q Consensus 82 ~~~~rGDVVvf~~P~~~~~~~VKRVigl 109 (143)
..+++||+|.+.++ .....=||.++
T Consensus 138 ~~l~pGDvi~l~~~---~~~~~~RI~~i 162 (164)
T PF13550_consen 138 LALEPGDVIALSDD---GRDMRFRITEI 162 (164)
T ss_pred ccCCCCCEEEEEeC---CCceEEEEEEE
Confidence 35789999999876 33566677665
No 73
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=22.69 E-value=1.1e+02 Score=20.81 Aligned_cols=12 Identities=33% Similarity=0.686 Sum_probs=7.7
Q ss_pred CCCcCeEEEEec
Q 032329 83 RVSVGDVVVMKD 94 (143)
Q Consensus 83 ~~~rGDVVvf~~ 94 (143)
.++.||.++|.+
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 677777777763
No 74
>PF02452 PemK: PemK-like protein; InterPro: IPR003477 PemK is a growth inhibitor in Escherichia coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. It is responsible for mediating cell death through inhibiting protein synthesis through the cleavage of single-stranded RNA. PemK is part of the PemK-PemI system, where PemI is an antitoxin that inhibits the action of the PemK toxin []. PemK homologues have been found in a wide range of bacteria, which together form an endonuclease family that interfere with mRNA function. This family consists of the PemK protein in addition to ChpA, ChpB, Kid and MazF.; GO: 0003677 DNA binding; PDB: 1M1F_A 2C06_A 3NFC_F 1UB4_B 1NE8_A.
Probab=20.57 E-value=88 Score=20.87 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=7.6
Q ss_pred CcCeEEEEecCCC
Q 032329 85 SVGDVVVMKDPEK 97 (143)
Q Consensus 85 ~rGDVVvf~~P~~ 97 (143)
++|||+.++.|..
T Consensus 1 k~GdI~~v~~p~~ 13 (110)
T PF02452_consen 1 KRGDIVWVDFPDF 13 (110)
T ss_dssp STTEEEEEE-S--
T ss_pred CCceEEEEECCCC
Confidence 5788888877644
No 75
>PLN03148 Blue copper-like protein; Provisional
Probab=20.19 E-value=4e+02 Score=20.54 Aligned_cols=21 Identities=14% Similarity=0.240 Sum_probs=15.6
Q ss_pred EEeecCCCCCCCCcCeEEEEecC
Q 032329 73 VRKLPAADPKRVSVGDVVVMKDP 95 (143)
Q Consensus 73 v~k~~~~~~~~~~rGDVVvf~~P 95 (143)
++.+... +.++.||.++|+..
T Consensus 37 Y~~WA~~--k~F~VGD~LvF~Y~ 57 (167)
T PLN03148 37 YTLWANN--QTFYVGDLISFRYQ 57 (167)
T ss_pred hhHhhcC--CCCccCCEEEEEec
Confidence 4445443 68999999999975
No 76
>PF11330 DUF3132: Protein of unknown function (DUF3132); InterPro: IPR021479 This entry is represented by the Citrus psorosis virus, 54kDa protein; it is a family of uncharacterised viral proteins.
Probab=20.13 E-value=1.8e+02 Score=20.70 Aligned_cols=19 Identities=21% Similarity=0.450 Sum_probs=12.8
Q ss_pred cCeEEEEecCCCCCceEEE
Q 032329 86 VGDVVVMKDPEKSDNYIVR 104 (143)
Q Consensus 86 rGDVVvf~~P~~~~~~~VK 104 (143)
.|.||.+-+..+.+.++||
T Consensus 86 dgevvmildsrdegrmwik 104 (124)
T PF11330_consen 86 DGEVVMILDSRDEGRMWIK 104 (124)
T ss_pred CCcEEEEEeccccCceeee
Confidence 4667777666666666666
No 77
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=20.08 E-value=94 Score=23.83 Aligned_cols=45 Identities=11% Similarity=0.100 Sum_probs=22.2
Q ss_pred cEEEEEeeCCCCcccccCCCcEEEEEeecCCCC--CCCCcCeEEEEec
Q 032329 49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADP--KRVSVGDVVVMKD 94 (143)
Q Consensus 49 v~~~~~v~G~SM~PTl~~ggD~Vlv~k~~~~~~--~~~~rGDVVvf~~ 94 (143)
++.+...-|+.|.=.....|..++.. ++..+. --+.+||+|++..
T Consensus 35 ~g~V~~~LGn~~f~V~c~dG~~rLa~-I~GKmRK~IWI~~GD~VlVel 81 (155)
T PTZ00329 35 YAQVLRMLGNGRLEAYCFDGVKRLCH-IRGKMRKRVWINIGDIILVSL 81 (155)
T ss_pred EEEEEEEcCCCEEEEEECCCCEEEEE-eeccceeeEEecCCCEEEEec
Confidence 44455566666665443323555442 222111 1256788888753
Done!