Query 047575
Match_columns 176
No_of_seqs 123 out of 659
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 12:24:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047575.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047575hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 2.1E-39 4.5E-44 285.9 14.2 172 4-176 171-359 (846)
2 PF10551 MULE: MULE transposas 99.7 4E-17 8.7E-22 109.5 5.7 65 109-176 1-68 (93)
3 PF00872 Transposase_mut: Tran 97.9 3.6E-06 7.9E-11 70.1 1.8 140 29-176 94-239 (381)
4 PF08069 Ribosomal_S13_N: Ribo 95.3 0.03 6.6E-07 34.1 3.6 33 32-64 26-59 (60)
5 PF00665 rve: Integrase core d 94.3 0.27 5.8E-06 33.4 6.8 72 102-175 6-78 (120)
6 PRK08561 rps15p 30S ribosomal 93.7 0.1 2.3E-06 37.7 3.9 81 32-112 26-142 (151)
7 COG3328 Transposase and inacti 93.4 0.26 5.7E-06 41.2 6.3 125 40-175 91-217 (379)
8 PTZ00072 40S ribosomal protein 90.7 0.66 1.4E-05 33.3 4.8 32 32-63 23-55 (148)
9 PF13936 HTH_38: Helix-turn-he 90.0 0.2 4.3E-06 28.5 1.4 31 31-61 2-32 (44)
10 PF13610 DDE_Tnp_IS240: DDE do 88.3 0.21 4.5E-06 35.7 0.9 69 102-175 1-69 (140)
11 PF02796 HTH_7: Helix-turn-hel 85.5 1.1 2.3E-05 25.5 2.6 40 32-78 4-43 (45)
12 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 81.0 1.7 3.7E-05 25.5 2.3 31 32-62 3-33 (50)
13 TIGR03147 cyt_nit_nrfF cytochr 74.0 3.9 8.4E-05 28.8 2.9 34 33-66 57-90 (126)
14 PF04218 CENP-B_N: CENP-B N-te 73.5 9 0.00019 22.5 4.0 47 31-81 4-50 (53)
15 KOG0400 40S ribosomal protein 73.0 1.4 3.1E-05 31.1 0.5 80 33-112 27-140 (151)
16 PF02171 Piwi: Piwi domain; I 71.2 29 0.00063 27.7 7.8 99 71-173 45-156 (302)
17 PRK10144 formate-dependent nit 67.3 6.8 0.00015 27.6 2.9 34 33-66 57-90 (126)
18 PF00076 RRM_1: RNA recognitio 62.9 17 0.00037 21.4 3.9 49 92-157 13-61 (70)
19 PHA02517 putative transposase 61.2 45 0.00097 26.2 7.0 132 37-175 30-180 (277)
20 KOG0125 Ataxin 2-binding prote 60.9 16 0.00035 30.0 4.3 64 83-164 100-165 (376)
21 PF00292 PAX: 'Paired box' dom 58.1 11 0.00025 26.5 2.7 33 31-63 15-47 (125)
22 PF12554 MOZART1: Mitotic-spin 56.5 17 0.00037 21.1 2.8 30 32-61 17-46 (48)
23 PF08671 SinI: Anti-repressor 55.9 15 0.00034 19.0 2.3 26 35-60 2-27 (30)
24 PF04189 Gcd10p: Gcd10p family 54.6 31 0.00068 28.0 5.1 31 31-64 105-135 (299)
25 PRK14702 insertion element IS2 53.3 1E+02 0.0022 24.3 7.8 134 39-174 14-162 (262)
26 PF14420 Clr5: Clr5 domain 50.6 47 0.001 19.5 4.2 40 36-76 6-46 (54)
27 PF13565 HTH_32: Homeodomain-l 50.2 41 0.00089 20.7 4.2 44 32-76 30-76 (77)
28 KOG4027 Uncharacterized conser 49.6 25 0.00054 25.9 3.4 37 105-141 68-107 (187)
29 PF03918 CcmH: Cytochrome C bi 48.4 11 0.00025 27.2 1.5 34 33-66 57-90 (148)
30 PF15299 ALS2CR8: Amyotrophic 48.0 45 0.00097 25.8 4.9 72 8-81 132-221 (225)
31 PRK09409 IS2 transposase TnpB; 47.2 1.5E+02 0.0033 23.9 8.1 134 39-174 53-201 (301)
32 cd02826 Piwi-like Piwi-like: P 46.2 1.2E+02 0.0027 25.3 7.6 66 104-173 174-251 (393)
33 TIGR01645 half-pint poly-U bin 45.5 51 0.0011 29.6 5.3 106 32-156 53-170 (612)
34 KOG0124 Polypyrimidine tract-b 45.0 65 0.0014 27.1 5.5 116 32-166 59-186 (544)
35 KOG0149 Predicted RNA-binding 44.5 42 0.00091 26.3 4.1 51 86-152 19-71 (247)
36 PF13551 HTH_29: Winged helix- 44.3 67 0.0015 21.0 4.8 45 34-79 58-110 (112)
37 PF00196 GerE: Bacterial regul 43.4 54 0.0012 19.1 3.8 41 33-81 3-43 (58)
38 cd01104 HTH_MlrA-CarA Helix-Tu 43.0 50 0.0011 19.7 3.7 30 30-59 35-67 (68)
39 cd04769 HTH_MerR2 Helix-Turn-H 42.6 89 0.0019 21.2 5.2 35 29-63 33-70 (116)
40 PF13384 HTH_23: Homeodomain-l 42.2 26 0.00056 19.7 2.1 40 36-82 4-43 (50)
41 smart00351 PAX Paired Box doma 42.1 51 0.0011 22.9 4.0 45 31-82 15-59 (125)
42 PF10264 Stork_head: Winged he 41.5 58 0.0012 21.1 3.8 48 33-80 11-61 (80)
43 smart00422 HTH_MERR helix_turn 41.3 59 0.0013 19.4 3.8 31 30-60 35-68 (70)
44 PF03106 WRKY: WRKY DNA -bindi 40.3 27 0.00057 21.2 2.0 17 4-20 43-59 (60)
45 PF04684 BAF1_ABF1: BAF1 / ABF 39.4 44 0.00095 28.9 3.8 22 5-26 164-185 (496)
46 cd00131 PAX Paired Box domain 39.0 60 0.0013 22.7 4.0 48 28-82 12-59 (128)
47 PF15652 Tox-SHH: HNH/Endo VII 38.4 21 0.00047 24.0 1.5 26 37-62 70-95 (100)
48 PF06056 Terminase_5: Putative 38.3 55 0.0012 19.6 3.2 37 38-81 2-38 (58)
49 cd04657 Piwi_ago-like Piwi_ago 38.2 2.1E+02 0.0045 24.3 7.8 68 104-173 201-278 (426)
50 PF13082 DUF3931: Protein of u 37.0 90 0.002 18.4 4.1 20 102-121 8-28 (66)
51 KOG3517 Transcription factor P 36.9 23 0.00049 28.1 1.6 33 32-64 19-51 (334)
52 PF04814 HNF-1_N: Hepatocyte n 36.8 16 0.00034 27.4 0.7 31 33-63 4-34 (180)
53 PF12762 DDE_Tnp_IS1595: ISXO2 36.6 1.5E+02 0.0032 20.8 6.3 46 123-175 38-85 (151)
54 PF11293 DUF3094: Protein of u 36.5 30 0.00064 20.6 1.7 21 32-52 2-22 (55)
55 PF10045 DUF2280: Uncharacteri 35.1 62 0.0013 22.0 3.3 32 33-64 3-34 (104)
56 cd00569 HTH_Hin_like Helix-tur 34.5 60 0.0013 15.6 2.8 28 32-59 4-31 (42)
57 cd04764 HTH_MlrA-like_sg1 Heli 33.0 46 0.00099 20.0 2.3 30 30-59 34-66 (67)
58 cd01105 HTH_GlnR-like Helix-Tu 32.2 92 0.002 20.1 3.8 34 30-63 36-72 (88)
59 cd04766 HTH_HspR Helix-Turn-He 31.8 85 0.0018 20.2 3.6 51 30-81 35-89 (91)
60 KOG0121 Nuclear cap-binding pr 31.3 1.1E+02 0.0023 21.9 4.1 73 84-175 41-115 (153)
61 PF13411 MerR_1: MerR HTH fami 31.2 38 0.00082 20.3 1.7 31 31-61 35-68 (69)
62 smart00421 HTH_LUXR helix_turn 30.9 99 0.0022 17.0 3.8 40 33-80 3-42 (58)
63 PF14386 DUF4417: Domain of un 30.8 2.4E+02 0.0052 21.4 6.5 76 69-171 89-175 (200)
64 cd04774 HTH_YfmP Helix-Turn-He 30.4 1.6E+02 0.0035 19.3 5.0 49 30-78 34-86 (96)
65 PF14638 FNIP_C: Folliculin-in 30.2 83 0.0018 23.9 3.7 74 4-77 80-153 (192)
66 KOG3862 Transcription factor P 29.9 53 0.0011 26.4 2.6 34 31-64 23-56 (327)
67 cd04658 Piwi_piwi-like_Euk Piw 29.4 3.6E+02 0.0077 23.0 8.3 67 104-173 231-306 (448)
68 PF07750 GcrA: GcrA cell cycle 29.2 54 0.0012 24.1 2.5 27 34-60 3-29 (162)
69 COG0735 Fur Fe2+/Zn2+ uptake r 29.1 1.2E+02 0.0026 21.7 4.2 49 32-82 17-67 (145)
70 cd04763 HTH_MlrA-like Helix-Tu 28.7 74 0.0016 19.1 2.7 30 30-59 35-67 (68)
71 COG1710 Uncharacterized protei 28.4 59 0.0013 22.7 2.4 43 30-79 90-132 (139)
72 PF12759 HTH_Tnp_IS1: InsA C-t 27.5 42 0.00092 19.2 1.3 27 35-61 7-33 (46)
73 PF09862 DUF2089: Protein of u 27.0 1.2E+02 0.0025 21.0 3.7 59 6-64 6-64 (113)
74 PF11829 DUF3349: Protein of u 26.2 1.3E+02 0.0029 20.1 3.7 50 31-81 33-86 (96)
75 cd01110 HTH_SoxR Helix-Turn-He 25.8 2E+02 0.0044 20.3 4.9 32 30-61 35-69 (139)
76 PF02838 Glyco_hydro_20b: Glyc 25.6 62 0.0014 21.9 2.2 34 139-172 88-124 (124)
77 PRK09413 IS2 repressor TnpA; R 25.6 1.7E+02 0.0037 20.0 4.4 45 31-82 10-55 (121)
78 COG3915 Uncharacterized protei 25.3 1.1E+02 0.0024 22.0 3.3 38 94-131 96-135 (155)
79 TIGR02937 sigma70-ECF RNA poly 25.3 87 0.0019 21.2 3.0 44 32-82 109-152 (158)
80 PRK13877 conjugal transfer rel 24.9 70 0.0015 22.1 2.3 45 33-77 16-62 (114)
81 PLN03134 glycine-rich RNA-bind 24.0 2E+02 0.0044 20.4 4.7 48 93-156 50-97 (144)
82 cd06171 Sigma70_r4 Sigma70, re 23.8 1.3E+02 0.0028 16.0 3.8 41 33-80 10-50 (55)
83 PF01644 Chitin_synth_1: Chiti 23.2 2.1E+02 0.0045 21.1 4.6 39 130-172 106-147 (163)
84 PF01527 HTH_Tnp_1: Transposas 23.1 77 0.0017 19.3 2.1 44 31-81 4-48 (76)
85 KOG1378 Purple acid phosphatas 22.8 2.1E+02 0.0046 24.8 5.2 30 140-170 269-298 (452)
86 cd01282 HTH_MerR-like_sg3 Heli 22.3 1.9E+02 0.0042 19.4 4.1 34 29-62 33-69 (112)
87 COG0552 FtsY Signal recognitio 22.2 2.1E+02 0.0046 23.8 4.9 16 119-134 140-155 (340)
88 PRK04217 hypothetical protein; 22.1 2.2E+02 0.0048 19.5 4.3 30 31-60 40-69 (110)
89 smart00165 UBA Ubiquitin assoc 22.1 1.1E+02 0.0025 15.8 2.4 26 40-65 3-28 (37)
90 COG2826 Tra8 Transposase and i 22.0 91 0.002 25.5 2.7 31 33-63 7-37 (318)
91 PF07299 FBP: Fibronectin-bind 21.9 39 0.00085 26.0 0.6 63 33-96 47-125 (208)
92 KOG1370 S-adenosylhomocysteine 21.8 82 0.0018 26.1 2.4 32 141-174 104-135 (434)
93 KOG1041 Translation initiation 21.5 3.7E+02 0.008 25.5 6.9 69 104-174 608-687 (876)
94 KOG3368 Transport protein part 21.0 1E+02 0.0022 22.0 2.4 40 110-157 63-102 (140)
95 PF12926 MOZART2: Mitotic-spin 20.2 1.2E+02 0.0027 19.9 2.6 20 32-51 21-40 (88)
96 PRK02126 ribonuclease Z; Provi 20.1 5E+02 0.011 21.3 7.3 52 4-61 149-200 (334)
97 COG3316 Transposase and inacti 20.0 2.6E+02 0.0056 21.7 4.7 68 102-175 70-137 (215)
98 cd04659 Piwi_piwi-like_ProArk 20.0 5.2E+02 0.011 21.6 7.6 70 104-174 192-269 (404)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=2.1e-39 Score=285.88 Aligned_cols=172 Identities=16% Similarity=0.271 Sum_probs=130.0
Q ss_pred cCCceEEEEecCCCCCCCCCCCCccccCCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCC--CccchHHHHHHHHhhcc
Q 047575 4 NNQDWMLKVICGLHNHHVAQHLEGHSFAGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDT--FSVTMMKAICNARYKYK 81 (176)
Q Consensus 4 ~~~~W~i~~~~~~HNH~~~~~~~~h~~~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~--~~~~t~kdi~N~~~k~r 81 (176)
.+|+|+|..+..+|||++.++.......|++-......+......+..+.+....+.+... -.....+.+.++.++++
T Consensus 171 ~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~r~~~~~~gD~~~ll~yf~~~q 250 (846)
T PLN03097 171 PDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMARQFAEYKNVVGLKNDSKSSFDKGRNLGLEAGDTKILLDFFTQMQ 250 (846)
T ss_pred CCCeEEEEEEecCCCCCCCCccccchhhhhhHHHHHhhhhccccccccchhhcchhhHHHhhhcccchHHHHHHHHHHHH
Confidence 5789999999999999999865433333443332222222111111111111111111000 01124566777777665
Q ss_pred c---------------cccceEEeChHhHHHHHhCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccc
Q 047575 82 V---------------CELDIFWAYPLTFELLKAFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKRED 146 (176)
Q Consensus 82 ~---------------~i~~if~~~~~~~~~~~~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~ 146 (176)
. +|++|||+|++|+..|..|||||.||+||+||+|+|||+.|+|+|+|+++++||||||.+|+.|
T Consensus 251 ~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~e 330 (846)
T PLN03097 251 NMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAA 330 (846)
T ss_pred hhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchh
Confidence 5 7999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhcCCCCCeEEEecCCCCC
Q 047575 147 NYIWALKRLKTIMQDDMLPSVIVIKRELTL 176 (176)
Q Consensus 147 s~~w~l~~~~~~~~~~~~p~~iitD~d~al 176 (176)
||.|+|++|+++|+ ++.|++||||+|.||
T Consensus 331 Sf~WLf~tfl~aM~-gk~P~tIiTDqd~am 359 (846)
T PLN03097 331 TYSWLMQTWLRAMG-GQAPKVIITDQDKAM 359 (846)
T ss_pred hHHHHHHHHHHHhC-CCCCceEEecCCHHH
Confidence 99999999999998 799999999999986
No 2
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.69 E-value=4e-17 Score=109.46 Aligned_cols=65 Identities=42% Similarity=0.632 Sum_probs=61.1
Q ss_pred ccccccccCcceeE---EEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCeEEEecCCCCC
Q 047575 109 CTYKVNKYKFPLLE---IVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPSVIVIKRELTL 176 (176)
Q Consensus 109 ~ty~tn~~~~pl~~---~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~~iitD~d~al 176 (176)
+||+||+| +|++. ++|+|++++++++||+++.+|++++|.|+|+.+++.++. . |++||+|+|.|+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~-~-p~~ii~D~~~~~ 68 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ-K-PKVIISDFDKAL 68 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc-C-ceeeeccccHHH
Confidence 69999999 88886 999999999999999999999999999999999999984 5 999999999875
No 3
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=97.94 E-value=3.6e-06 Score=70.15 Aligned_cols=140 Identities=14% Similarity=0.038 Sum_probs=101.0
Q ss_pred ccCCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccccccceEEeChHhHHHHHhC-CcEEEE
Q 047575 29 SFAGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKVCELDIFWAYPLTFELLKAF-TNVLIM 107 (176)
Q Consensus 29 ~~~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~~i~~if~~~~~~~~~~~~f-~dvv~~ 107 (176)
+.+++-+++.-+.|..|.-.|+++++|-..|+...++..+....|.+...++...+.. | +.+ ..... -.+|.+
T Consensus 94 ~~y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~--w---~~R-~L~~~~y~~l~i 167 (381)
T PF00872_consen 94 PKYQRREDSLEELIISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEA--W---RNR-PLESEPYPYLWI 167 (381)
T ss_pred chhhhhhhhhhhhhhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHH--H---hhh-ccccccccceee
Confidence 3344446666678888999999999999999888774445556666665554431111 0 111 12223 257899
Q ss_pred eccccccc-----cCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCeEEEecCCCCC
Q 047575 108 DCTYKVNK-----YKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPSVIVIKRELTL 176 (176)
Q Consensus 108 D~ty~tn~-----~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~~iitD~d~al 176 (176)
|++|-.-+ -+.+++.++|++..|+-.++|+.....|+.++|.=+|..+++- +-..|..||+|...+|
T Consensus 168 D~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R--Gl~~~~lvv~Dg~~gl 239 (381)
T PF00872_consen 168 DGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER--GLKDILLVVSDGHKGL 239 (381)
T ss_pred eeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc--cccccceeeccccccc
Confidence 99997544 2467899999999999999999999999999999888887543 2456999999998765
No 4
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=95.31 E-value=0.03 Score=34.12 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=26.5
Q ss_pred CCCCHHH-HHhhhhhccCCCChhHHHHHhhhcCC
Q 047575 32 GRLTNEE-VSTLVDLSKNNVRPKEIFHTLKTRDT 64 (176)
Q Consensus 32 r~ls~~~-~~~i~~l~~~g~~~~~I~~~l~~~~~ 64 (176)
=++++++ .+.|.+|.+.|+.|++|-.+|+++++
T Consensus 26 ~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~~G 59 (60)
T PF08069_consen 26 LKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYG 59 (60)
T ss_dssp --S-HHHHHHHHHHHCCTTHCHHHHHHHHHHSCT
T ss_pred cCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhccC
Confidence 3567666 48899999999999999999999875
No 5
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=94.29 E-value=0.27 Score=33.36 Aligned_cols=72 Identities=15% Similarity=-0.008 Sum_probs=43.3
Q ss_pred CcEEEEeccccc-cccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCeEEEecCCCC
Q 047575 102 TNVLIMDCTYKV-NKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPSVIVIKRELT 175 (176)
Q Consensus 102 ~dvv~~D~ty~t-n~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~~iitD~d~a 175 (176)
++.+.+|.+... ...+...+.++.+|...+- ..++.+-..++.+.+.-+|.......+ +..|++|++|++.+
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~p~~i~tD~g~~ 78 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRG-GRPPRVIRTDNGSE 78 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS--SE-SEEEEESCHH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeecccccccccccccccccccc-cccceecccccccc
Confidence 467888888543 2334467777888877664 445555555455555555554444443 23399999999754
No 6
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=93.74 E-value=0.1 Score=37.68 Aligned_cols=81 Identities=21% Similarity=0.180 Sum_probs=52.4
Q ss_pred CCCCHHHH-HhhhhhccCCCChhHHHHHhhhcCCC---------c-----------cchHHHHHHHHhhccc---c----
Q 047575 32 GRLTNEEV-STLVDLSKNNVRPKEIFHTLKTRDTF---------S-----------VTMMKAICNARYKYKV---C---- 83 (176)
Q Consensus 32 r~ls~~~~-~~i~~l~~~g~~~~~I~~~l~~~~~~---------~-----------~~t~kdi~N~~~k~r~---~---- 83 (176)
-++++++. +.|.+|.+.|.+|++|-..|++++|- . +--..|+||+-.++.+ +
T Consensus 26 ~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~~L~~HL~~n 105 (151)
T PRK08561 26 VDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEEN 105 (151)
T ss_pred ccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHhC
Confidence 46777664 88899999999999999999999851 0 1126688888665433 1
Q ss_pred ------ccceEEeChHhHHHHHhC--CcEEEEecccc
Q 047575 84 ------ELDIFWAYPLTFELLKAF--TNVLIMDCTYK 112 (176)
Q Consensus 84 ------i~~if~~~~~~~~~~~~f--~dvv~~D~ty~ 112 (176)
-.++.-.-++.+.+..+| -+++--|..|.
T Consensus 106 kKD~~skRgL~~~~skrrRLl~Yyk~~~~LP~~WkY~ 142 (151)
T PRK08561 106 PKDLHNKRGLQLIESKIRRLVKYYKRTGVLPADWRYS 142 (151)
T ss_pred CCcchhHHHHHHHHHHHHHHHHHHHhcCCCCCCCcCC
Confidence 112222334455566666 45666666554
No 7
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.43 E-value=0.26 Score=41.21 Aligned_cols=125 Identities=12% Similarity=-0.011 Sum_probs=76.5
Q ss_pred HhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccccccceEEeChHhHHHHHhCCcEEEEeccccccc--cC
Q 047575 40 STLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKVCELDIFWAYPLTFELLKAFTNVLIMDCTYKVNK--YK 117 (176)
Q Consensus 40 ~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~~i~~if~~~~~~~~~~~~f~dvv~~D~ty~tn~--~~ 117 (176)
..|..|-..|+.+++|-..++..... ....-.+.....++...+.. .+++.+ ..| .+|.+|++|..-+ -+
T Consensus 91 ~~v~~~y~~gv~Tr~i~~~~~~~~~~-~~s~~~iS~~~~~~~e~v~~-----~~~r~l-~~~-~~v~~D~~~~k~r~v~~ 162 (379)
T COG3328 91 LPVLSMYAKGVTTREIEALLEELYGH-KVSPSVISVVTDRLDEKVKA-----WQNRPL-GDY-PYVYLDAKYVKVRSVRN 162 (379)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHhhCc-ccCHHHhhhHHHHHHHHHHH-----HHhccc-cCc-eEEEEecceeehhhhhh
Confidence 56777889999999999999887543 22222223332222221111 012222 222 4788999998877 56
Q ss_pred cceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCeEEEecCCCC
Q 047575 118 FPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPSVIVIKRELT 175 (176)
Q Consensus 118 ~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~~iitD~d~a 175 (176)
..++..+|++..|+-..+|+-.-..|. ..|.-++.-|+. -+ -..-..+++|.-++
T Consensus 163 ~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~-rg-l~~v~l~v~Dg~~g 217 (379)
T COG3328 163 KAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKN-RG-LSDVLLVVVDGLKG 217 (379)
T ss_pred heeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHh-cc-ccceeEEecchhhh
Confidence 788999999999999999998888888 555522322222 11 22334555576543
No 8
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=90.70 E-value=0.66 Score=33.35 Aligned_cols=32 Identities=22% Similarity=0.320 Sum_probs=27.6
Q ss_pred CCCCHHH-HHhhhhhccCCCChhHHHHHhhhcC
Q 047575 32 GRLTNEE-VSTLVDLSKNNVRPKEIFHTLKTRD 63 (176)
Q Consensus 32 r~ls~~~-~~~i~~l~~~g~~~~~I~~~l~~~~ 63 (176)
-+.++++ .+.|.+|.+.|+.|+||-..|++++
T Consensus 23 ~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~ 55 (148)
T PTZ00072 23 LKLSSSEVEDQICKLAKKGLTPSQIGVILRDSM 55 (148)
T ss_pred hcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhcc
Confidence 3567666 4889999999999999999999998
No 9
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=90.02 E-value=0.2 Score=28.45 Aligned_cols=31 Identities=26% Similarity=0.257 Sum_probs=15.9
Q ss_pred CCCCCHHHHHhhhhhccCCCChhHHHHHhhh
Q 047575 31 AGRLTNEEVSTLVDLSKNNVRPKEIFHTLKT 61 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~ 61 (176)
.++||++++..|..|.+.|.+.++|...|..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~ 32 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLGR 32 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT-
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHCc
Confidence 3589999999999999999999999998854
No 10
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=88.33 E-value=0.21 Score=35.68 Aligned_cols=69 Identities=19% Similarity=0.031 Sum_probs=51.1
Q ss_pred CcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCeEEEecCCCC
Q 047575 102 TNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPSVIVIKRELT 175 (176)
Q Consensus 102 ~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~~iitD~d~a 175 (176)
|+.+.+|=||-.=+ |---+.+-.+|..|+ .+.+-+-..-+...=..+|+..++... ..|.+|+||+-.|
T Consensus 1 ~~~w~~DEt~iki~-G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~--~~p~~ivtDk~~a 69 (140)
T PF13610_consen 1 GDSWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR--GEPRVIVTDKLPA 69 (140)
T ss_pred CCEEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec--cccceeecccCCc
Confidence 57889999996544 334566888999988 566666666677777777766666653 5899999999765
No 11
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=85.50 E-value=1.1 Score=25.46 Aligned_cols=40 Identities=13% Similarity=0.190 Sum_probs=28.6
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHh
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARY 78 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~ 78 (176)
+++++++.+.+..|.+.|.+..+|...+. +....||.+..
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~g-------vsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQFG-------VSRSTVYRYLN 43 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHHTT-------S-HHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHC-------cCHHHHHHHHh
Confidence 56888888999999999999999887753 34566666653
No 12
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=81.02 E-value=1.7 Score=25.48 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=21.8
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHhhhc
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTLKTR 62 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~ 62 (176)
..||++|+.+|..|.+.|++..+|-..+.+.
T Consensus 3 ~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RS 33 (50)
T PF11427_consen 3 KTLTDAEQAQIDVMHQLGMSLREISRRIGRS 33 (50)
T ss_dssp ----HHHHHHHHHHHHTT--HHHHHHHHT--
T ss_pred CcCCHHHHHHHHHHHHhchhHHHHHHHhCcc
Confidence 3589999999999999999999999988653
No 13
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=73.97 E-value=3.9 Score=28.83 Aligned_cols=34 Identities=6% Similarity=0.029 Sum_probs=28.5
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCc
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFS 66 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~ 66 (176)
.+..+++..|+++.+.|-+..+|+++|.+++|+.
T Consensus 57 ~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~ 90 (126)
T TIGR03147 57 PIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDF 90 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCe
Confidence 5666778888889999999999999999888863
No 14
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=73.53 E-value=9 Score=22.48 Aligned_cols=47 Identities=17% Similarity=0.159 Sum_probs=32.5
Q ss_pred CCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhcc
Q 047575 31 AGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYK 81 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r 81 (176)
.+.||.+++..|..+.+.|.+.++|...+ +-...|..+|...+.+++
T Consensus 4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~f----gv~~sTv~~I~K~k~~i~ 50 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGESKRDIAREF----GVSRSTVSTILKNKDKIL 50 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT-HHHHHHHH----T--CCHHHHHHHCHHHHC
T ss_pred CccCCHHHHHHHHHHHHcCCCHHHHHHHh----CCCHHHHHHHHHhHHHHH
Confidence 35789999999999999999777766554 333467888888777665
No 15
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=73.05 E-value=1.4 Score=31.10 Aligned_cols=80 Identities=13% Similarity=0.207 Sum_probs=52.8
Q ss_pred CCCH-HHHHhhhhhccCCCChhHHHHHhhhcCCCc--------------------cchHHHHHHHHhhc---cccc----
Q 047575 33 RLTN-EEVSTLVDLSKNNVRPKEIFHTLKTRDTFS--------------------VTMMKAICNARYKY---KVCE---- 84 (176)
Q Consensus 33 ~ls~-~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~--------------------~~t~kdi~N~~~k~---r~~i---- 84 (176)
+++. +.+++|..|.+-|++|+||-.+|++.++-. +-...|+|++..+. |+++
T Consensus 27 K~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~PeiPeDLy~likkAv~iRkHLer~R 106 (151)
T KOG0400|consen 27 KLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPEIPEDLYHLIKKAVAIRKHLERNR 106 (151)
T ss_pred hcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHhc
Confidence 5554 567999999999999999999999877520 11256888876542 2211
Q ss_pred ------cceEEeChHhHHHHHhCCcEEEEecccc
Q 047575 85 ------LDIFWAYPLTFELLKAFTNVLIMDCTYK 112 (176)
Q Consensus 85 ------~~if~~~~~~~~~~~~f~dvv~~D~ty~ 112 (176)
=.+.....+.-.+.++|..+..+-.++|
T Consensus 107 KD~d~K~RLILveSRihRlARYYk~~~~lPp~WK 140 (151)
T KOG0400|consen 107 KDKDAKFRLILVESRIHRLARYYKTKMVLPPNWK 140 (151)
T ss_pred cccccceEEEeehHHHHHHHHHHHhcccCCCCCC
Confidence 1244555666667777776666555543
No 16
>PF02171 Piwi: Piwi domain; InterPro: IPR003165 This domain is found in the stem cell self-renewal protein Piwi and its relatives in Drosophila melanogaster []. It has been found in the C-terminal of a number of proteins which also contain the PAZ domain (IPR003100 from INTERPRO) in their central region, for example the Argonaute proteins. Several of these proteins have been implicated in the development and maintenance of stem cells through the RNA-mediated gene-quelling mechanisms associated with the protein DICER. ; GO: 0005515 protein binding; PDB: 4F1N_B 3LUH_B 4EI1_A 3QX8_A 3LUC_C 3LUJ_B 3LUD_B 3QX9_A 3LUG_B 3LUK_B ....
Probab=71.17 E-value=29 Score=27.66 Aligned_cols=99 Identities=19% Similarity=0.153 Sum_probs=53.7
Q ss_pred HHHHHHHhhccccccce-EEeChHhHHH-HHhCCc--EEEEecccccccc-Ccc-eeEEEeeccCCCeEEEEEEeecC--
Q 047575 71 KAICNARYKYKVCELDI-FWAYPLTFEL-LKAFTN--VLIMDCTYKVNKY-KFP-LLEIVGVTLTTMTFNVDFAYLES-- 142 (176)
Q Consensus 71 kdi~N~~~k~r~~i~~i-f~~~~~~~~~-~~~f~d--vv~~D~ty~tn~~-~~p-l~~~~g~~~~~~~~~~~~~~~~~-- 142 (176)
.-+.|...++..++-++ .|........ + .+ |+.+|.++..... +.| +.-+++.-+.+.+...+......
T Consensus 45 ~~~~ni~lkinaKlGG~n~~~~~~~~~~~~---~~~miIGidv~h~~~~~~~~~sv~g~~~s~~~~~~~~~~~~~~~~~~ 121 (302)
T PF02171_consen 45 QILNNIALKINAKLGGINPWLLDSPPSIDL---KNTMIIGIDVSHPSPGSDKNPSVVGFVASFDSDGSKYFSSVRFQDSG 121 (302)
T ss_dssp HHHHHHHHHHHHHTTTBSEEECSCSSGSSE---SEEEEEEEEEEEESSTCTCSCEEEEEEEEESTTTCEEEEEEEEECTT
T ss_pred HHHHHHHHHHHHhCCCeeeeeccccccccc---CceEEEEEEEEecCcccCCcceeeEEEEeccCccccccceeEEeccc
Confidence 33556555555556666 6765443211 1 22 7889999988876 344 33444444334444444443432
Q ss_pred -Ccc----chHHHHHHHHHHHhcCCCCCeEEEecCC
Q 047575 143 -KRE----DNYIWALKRLKTIMQDDMLPSVIVIKRE 173 (176)
Q Consensus 143 -E~~----~s~~w~l~~~~~~~~~~~~p~~iitD~d 173 (176)
|.. +.+.++++.|.+... ...|+-||.-||
T Consensus 122 ~e~~~~l~~~~~~~L~~~~~~~~-~~~P~~IiiyRd 156 (302)
T PF02171_consen 122 QEIIDNLEEIIKEALKEFKKNNG-KWLPERIIIYRD 156 (302)
T ss_dssp CCCHHHHHHHHHHHHHHHHHTTT-T-TTSEEEEEEE
T ss_pred hhhhcchhhHHHHHHHHHHHHcC-CCCCceEEEEEc
Confidence 222 236666666666654 348988777665
No 17
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=67.30 E-value=6.8 Score=27.61 Aligned_cols=34 Identities=9% Similarity=-0.045 Sum_probs=28.0
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCc
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFS 66 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~ 66 (176)
.+..+.+..|+++.+.|-+..+|+++|.+++|+.
T Consensus 57 ~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~ 90 (126)
T PRK10144 57 PVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDF 90 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCe
Confidence 4566778888888889999999999998888763
No 18
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=62.88 E-value=17 Score=21.39 Aligned_cols=49 Identities=14% Similarity=0.195 Sum_probs=33.7
Q ss_pred hHhHHHHHhCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHH
Q 047575 92 PLTFELLKAFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKT 157 (176)
Q Consensus 92 ~~~~~~~~~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~ 157 (176)
.....+|..||++..+.-..+ .....-++||+.=++.++-..+++.+..
T Consensus 13 ~~l~~~f~~~g~i~~~~~~~~-----------------~~~~~~~~a~V~F~~~~~a~~a~~~l~g 61 (70)
T PF00076_consen 13 EELRDFFSQFGKIESIKVMRN-----------------SSGKSKGYAFVEFESEEDAEKALEELNG 61 (70)
T ss_dssp HHHHHHHHTTSTEEEEEEEEE-----------------TTSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhhhccccccccc-----------------ccccccceEEEEEcCHHHHHHHHHHcCC
Confidence 455678899999865543221 2223457889999999999988887654
No 19
>PHA02517 putative transposase OrfB; Reviewed
Probab=61.18 E-value=45 Score=26.18 Aligned_cols=132 Identities=10% Similarity=-0.004 Sum_probs=72.1
Q ss_pred HHHHhhhhhc-c--CCCChhHHHHHhhhcCCCccchHHHHHHHHhhccc---------ccc--ceEEeChH-hHHHHH--
Q 047575 37 EEVSTLVDLS-K--NNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV---------CEL--DIFWAYPL-TFELLK-- 99 (176)
Q Consensus 37 ~~~~~i~~l~-~--~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~---------~i~--~if~~~~~-~~~~~~-- 99 (176)
+.++.|.++. + .....++|...|++. |..+..+.|+.+.++..- .-. .-.-..+. ....|.
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~--g~~vs~~tV~Rim~~~gl~~~~~~k~~~~~~~~~~~~~~n~~~r~f~~~ 107 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE--GIRVARCTVGRLMKELGLAGVLRGKKVRTTISRKAVAAPDRVNRQFVAT 107 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc--CcccCHHHHHHHHHHcCCceEecCCCcCCCCCCCCCCCCCcccCCCCCC
Confidence 4456777773 3 246889999999865 344566667766443221 000 00000000 000111
Q ss_pred hCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCe--EEEecCCCC
Q 047575 100 AFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPS--VIVIKRELT 175 (176)
Q Consensus 100 ~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~--~iitD~d~a 175 (176)
.=.+++..|.||-....+ ..+.++.+|.+.+- ++|+.+-..++.+ +++..|..++.....|. .|.||+...
T Consensus 108 ~pn~~w~~D~t~~~~~~g-~~yl~~iiD~~sr~-i~~~~~~~~~~~~---~~~~~l~~a~~~~~~~~~~i~~sD~G~~ 180 (277)
T PHA02517 108 RPNQLWVADFTYVSTWQG-WVYVAFIIDVFARR-IVGWRVSSSMDTD---FVLDALEQALWARGRPGGLIHHSDKGSQ 180 (277)
T ss_pred CCCCeEEeceeEEEeCCC-CEEEEEecccCCCe-eeecccCCCCChH---HHHHHHHHHHHhcCCCcCcEeecccccc
Confidence 223689999999654434 35666667766654 5577776655555 45666666664223453 666998653
No 20
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=60.87 E-value=16 Score=30.02 Aligned_cols=64 Identities=13% Similarity=0.105 Sum_probs=48.0
Q ss_pred cccce--EEeChHhHHHHHhCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhc
Q 047575 83 CELDI--FWAYPLTFELLKAFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQ 160 (176)
Q Consensus 83 ~i~~i--f~~~~~~~~~~~~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~ 160 (176)
++.|| -|-++..+.+|.+||.|+-+. +.+|..|. =|||||.=|..++-+.+-+.|...+-
T Consensus 100 hVSNIPFrFRdpDL~aMF~kfG~VldVE---------------IIfNERGS---KGFGFVTmen~~dadRARa~LHgt~V 161 (376)
T KOG0125|consen 100 HVSNIPFRFRDPDLRAMFEKFGKVLDVE---------------IIFNERGS---KGFGFVTMENPADADRARAELHGTVV 161 (376)
T ss_pred EeecCCccccCccHHHHHHhhCceeeEE---------------EEeccCCC---CccceEEecChhhHHHHHHHhhccee
Confidence 45554 456789999999999997653 33444443 38999999999999999999988875
Q ss_pred CCCC
Q 047575 161 DDML 164 (176)
Q Consensus 161 ~~~~ 164 (176)
+|+.
T Consensus 162 EGRk 165 (376)
T KOG0125|consen 162 EGRK 165 (376)
T ss_pred eceE
Confidence 4544
No 21
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=58.06 E-value=11 Score=26.48 Aligned_cols=33 Identities=33% Similarity=0.487 Sum_probs=24.6
Q ss_pred CCCCCHHHHHhhhhhccCCCChhHHHHHhhhcC
Q 047575 31 AGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRD 63 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~ 63 (176)
-|.|..+.+..|.+|...|++|++|-..|.-.+
T Consensus 15 GrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~ 47 (125)
T PF00292_consen 15 GRPLPNELRQRIVELAKEGVRPCDISRQLRVSH 47 (125)
T ss_dssp TSSS-HHHHHHHHHHHHTT--HHHHHHHHT--H
T ss_pred CccCcHHHHHHHHHHhhhcCCHHHHHHHHccch
Confidence 378889999999999999999999998776544
No 22
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=56.49 E-value=17 Score=21.06 Aligned_cols=30 Identities=27% Similarity=0.457 Sum_probs=24.8
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHhhh
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTLKT 61 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~ 61 (176)
-.|+.+..+....|.++|+.|...-..+++
T Consensus 17 tgLd~etL~ici~L~e~GVnPeaLA~vI~e 46 (48)
T PF12554_consen 17 TGLDRETLSICIELCENGVNPEALAAVIKE 46 (48)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 368889999999999999999887776654
No 23
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=55.94 E-value=15 Score=19.01 Aligned_cols=26 Identities=19% Similarity=0.229 Sum_probs=18.9
Q ss_pred CHHHHHhhhhhccCCCChhHHHHHhh
Q 047575 35 TNEEVSTLVDLSKNNVRPKEIFHTLK 60 (176)
Q Consensus 35 s~~~~~~i~~l~~~g~~~~~I~~~l~ 60 (176)
++|=.+.|.+..+.|+++.+|..+|.
T Consensus 2 D~EW~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 2 DEEWVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 44556778888999999999999885
No 24
>PF04189 Gcd10p: Gcd10p family; InterPro: IPR007316 eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit of eIF3 [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation
Probab=54.57 E-value=31 Score=28.01 Aligned_cols=31 Identities=32% Similarity=0.489 Sum_probs=25.1
Q ss_pred CCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCC
Q 047575 31 AGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDT 64 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~ 64 (176)
..+||.++ |.+|.+.|....+|++.|-+.+.
T Consensus 105 ~QkLt~ee---Ie~LK~~g~sg~eII~kLiens~ 135 (299)
T PF04189_consen 105 SQKLTQEE---IEELKKEGVSGEEIIEKLIENSS 135 (299)
T ss_pred cccCCHHH---HHHHHHcCCCHHHHHHHHHHhcc
Confidence 45677766 88888889999999999987654
No 25
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=53.30 E-value=1e+02 Score=24.28 Aligned_cols=134 Identities=6% Similarity=-0.131 Sum_probs=71.5
Q ss_pred HHhhhhh-cc-CCCChhHHHHHhhhcCC--Cc-cchHHHHHHHHhhccc------cccceEEeChHhHHHHHhCCcEEEE
Q 047575 39 VSTLVDL-SK-NNVRPKEIFHTLKTRDT--FS-VTMMKAICNARYKYKV------CELDIFWAYPLTFELLKAFTNVLIM 107 (176)
Q Consensus 39 ~~~i~~l-~~-~g~~~~~I~~~l~~~~~--~~-~~t~kdi~N~~~k~r~------~i~~if~~~~~~~~~~~~f~dvv~~ 107 (176)
...|.++ .+ .....+.|...|++... |. ....+-|+.+.+..-- .-..-.-.... ...-..=..+.+.
T Consensus 14 ~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~r~~~~~~~~~~~~-~~~~~~pn~~W~~ 92 (262)
T PRK14702 14 LLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLERKPAVPPSKRAHTG-RVAVKESNQRWCS 92 (262)
T ss_pred HHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCccccCCCCCCCCcCCCC-ccccCCCCCEEEe
Confidence 3455554 22 34677888888876421 33 2567777776544211 00000000000 0011122368899
Q ss_pred eccccccccCcceeEEEeeccCCCeEEEEEEeecC-CccchHHHHHHHHHHHh-c--CCCCCeEEEecCCC
Q 047575 108 DCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLES-KREDNYIWALKRLKTIM-Q--DDMLPSVIVIKREL 174 (176)
Q Consensus 108 D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~-E~~~s~~w~l~~~~~~~-~--~~~~p~~iitD~d~ 174 (176)
|-||..-.-+..++..+.+|.+.+ .++|+++-.+ .+.+...=+|+...+.. + ....|..|.||+..
T Consensus 93 DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gs 162 (262)
T PRK14702 93 DGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 162 (262)
T ss_pred eeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCc
Confidence 999865444445777777887777 5678888764 45555444554433332 2 12356788999864
No 26
>PF14420 Clr5: Clr5 domain
Probab=50.63 E-value=47 Score=19.46 Aligned_cols=40 Identities=10% Similarity=0.091 Sum_probs=29.6
Q ss_pred HHHHHhhhhhc-cCCCChhHHHHHhhhcCCCccchHHHHHHH
Q 047575 36 NEEVSTLVDLS-KNNVRPKEIFHTLKTRDTFSVTMMKAICNA 76 (176)
Q Consensus 36 ~~~~~~i~~l~-~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~ 76 (176)
+..+..|..|- ..+.+-.+|.++|+..++ ...+.+...+.
T Consensus 6 e~~K~~I~~LY~~e~~tl~~v~~~M~~~~~-F~at~rqy~~r 46 (54)
T PF14420_consen 6 EPHKEEIERLYIDENKTLEEVMEIMKEEHG-FKATKRQYKRR 46 (54)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHHHHhC-CCcCHHHHHHH
Confidence 35578888885 789999999999998887 44555554443
No 27
>PF13565 HTH_32: Homeodomain-like domain
Probab=50.22 E-value=41 Score=20.69 Aligned_cols=44 Identities=16% Similarity=0.202 Sum_probs=31.5
Q ss_pred CCCCHHHHHhhhhhccC--CCChhHHHHHhhhcCCCc-cchHHHHHHH
Q 047575 32 GRLTNEEVSTLVDLSKN--NVRPKEIFHTLKTRDTFS-VTMMKAICNA 76 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~--g~~~~~I~~~l~~~~~~~-~~t~kdi~N~ 76 (176)
++ ++++.+.|.++... ...+.+|...|.++++.. .+....||.+
T Consensus 30 ~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 30 RK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred CC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 55 67877888887554 589999999999987632 2355666553
No 28
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.61 E-value=25 Score=25.89 Aligned_cols=37 Identities=22% Similarity=0.445 Sum_probs=29.7
Q ss_pred EEEecccc-ccccCcc--eeEEEeeccCCCeEEEEEEeec
Q 047575 105 LIMDCTYK-VNKYKFP--LLEIVGVTLTTMTFNVDFAYLE 141 (176)
Q Consensus 105 v~~D~ty~-tn~~~~p--l~~~~g~~~~~~~~~~~~~~~~ 141 (176)
+-||.||| ||-|+-| ++.+.|-|+.|+-...|+|-+.
T Consensus 68 ~Pievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~h 107 (187)
T KOG4027|consen 68 LPIEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLH 107 (187)
T ss_pred cceEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEe
Confidence 45889996 6788887 5667888999999998988764
No 29
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=48.40 E-value=11 Score=27.24 Aligned_cols=34 Identities=9% Similarity=0.064 Sum_probs=24.6
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCc
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFS 66 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~ 66 (176)
.+..+++..|.++.+.|.+..+|+++|..++|+.
T Consensus 57 ~~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG~~ 90 (148)
T PF03918_consen 57 PIARDMRREIREMLAEGKSDEEIIDYFVERYGEF 90 (148)
T ss_dssp HHHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCcc
Confidence 3455677888888888888888888888888763
No 30
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=48.05 E-value=45 Score=25.78 Aligned_cols=72 Identities=22% Similarity=0.221 Sum_probs=45.3
Q ss_pred eEEEEe-cCCC-CCCCCCCCCccccCCCCCHHHHHhhhhhccCCCCh-hHHHHHhhh-----cC-----CC-----ccch
Q 047575 8 WMLKVI-CGLH-NHHVAQHLEGHSFAGRLTNEEVSTLVDLSKNNVRP-KEIFHTLKT-----RD-----TF-----SVTM 69 (176)
Q Consensus 8 W~i~~~-~~~H-NH~~~~~~~~h~~~r~ls~~~~~~i~~l~~~g~~~-~~I~~~l~~-----~~-----~~-----~~~t 69 (176)
|+|..- ..+| +|+....... .-..+.++..+.|.+|...|+.. .+|...|+. -+ |. ..+|
T Consensus 132 ~yv~lP~~~~H~~H~~~~~~~~--~~q~~~~~v~~ki~eLv~~gv~~v~e~k~~l~~fV~~~lf~~~~~p~~~n~~y~Pt 209 (225)
T PF15299_consen 132 FYVQLPSPEEHSGHPIGQEAAG--LKQPLDPRVVEKIHELVAQGVTSVPEMKRHLKKFVEEELFKDQEPPPPTNRRYFPT 209 (225)
T ss_pred EEEECCChHhcCCCcccccccc--ccccCCHHHHHHHHHHHHcccccHHHHHHHHHHHhhhhccCCCCCCCCCccccCCc
Confidence 444443 2477 7887663211 22467788889999999999766 566665532 12 10 2368
Q ss_pred HHHHHHHHhhcc
Q 047575 70 MKAICNARYKYK 81 (176)
Q Consensus 70 ~kdi~N~~~k~r 81 (176)
.+||.|......
T Consensus 210 ~~di~n~~~~~~ 221 (225)
T PF15299_consen 210 DKDIRNHMYSAK 221 (225)
T ss_pred hHHHHHHHHHHH
Confidence 999999876544
No 31
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=47.17 E-value=1.5e+02 Score=23.88 Aligned_cols=134 Identities=6% Similarity=-0.095 Sum_probs=72.2
Q ss_pred HHhhhhhcc--CCCChhHHHHHhhhcCC--Cc-cchHHHHHHHHhhccc------cccceEEeChHhHHHHHhCCcEEEE
Q 047575 39 VSTLVDLSK--NNVRPKEIFHTLKTRDT--FS-VTMMKAICNARYKYKV------CELDIFWAYPLTFELLKAFTNVLIM 107 (176)
Q Consensus 39 ~~~i~~l~~--~g~~~~~I~~~l~~~~~--~~-~~t~kdi~N~~~k~r~------~i~~if~~~~~~~~~~~~f~dvv~~ 107 (176)
.+.|.++.+ .....+.|...|+++.. +. .+..+.|+.+.+..-- .-..-.-.+... ..-..=..+.+.
T Consensus 53 ~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~Gl~~~~~~~~~~~~~~~~~~-~~~~~pN~~W~t 131 (301)
T PRK09409 53 LLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLERKPAVPPSKRAHTGR-VAVKESNQRWCS 131 (301)
T ss_pred HHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcCCcccccCCCCCCCCCCCCC-cCCCCCCCEEEe
Confidence 345555422 34677889888876532 34 3567777776554211 000000000000 001122368999
Q ss_pred eccccccccCcceeEEEeeccCCCeEEEEEEeecC-CccchHHHHHHH-HHHHhcC--CCCCeEEEecCCC
Q 047575 108 DCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLES-KREDNYIWALKR-LKTIMQD--DMLPSVIVIKREL 174 (176)
Q Consensus 108 D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~-E~~~s~~w~l~~-~~~~~~~--~~~p~~iitD~d~ 174 (176)
|-||..-.-+.-++..+.+|.+.+ .++|+++-.. .+.+...=+|+. +....+. ...|..|-||+-.
T Consensus 132 DiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGs 201 (301)
T PRK09409 132 DGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 201 (301)
T ss_pred eeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCc
Confidence 999954433434666666777776 5778888765 465555555554 3333321 1346688999864
No 32
>cd02826 Piwi-like Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism.
Probab=46.16 E-value=1.2e+02 Score=25.33 Aligned_cols=66 Identities=27% Similarity=0.329 Sum_probs=35.6
Q ss_pred EEEEeccccccc--cCcceeEEEeeccC--CCeEEEEEEeecCCcc-------chHHHHHHHHHHHhcCCC-CCeEEEec
Q 047575 104 VLIMDCTYKVNK--YKFPLLEIVGVTLT--TMTFNVDFAYLESKRE-------DNYIWALKRLKTIMQDDM-LPSVIVIK 171 (176)
Q Consensus 104 vv~~D~ty~tn~--~~~pl~~~~g~~~~--~~~~~~~~~~~~~E~~-------~s~~w~l~~~~~~~~~~~-~p~~iitD 171 (176)
++.+|.++.... .+.|. ++|+.+. +.++..++.+.....+ +.+.-+|+.|++.. +. .|.-||.-
T Consensus 174 iiGiDv~h~~~~~~~~~~s--i~~~vas~~~~~~~g~~~~~~~~~~~~~~~l~~~~~~~L~~y~~~~--~~~~P~~Iiiy 249 (393)
T cd02826 174 FIGFDVSHPDRRTVNGGPS--AVGFAANLSNHTFLGGFLYVQPSREVKLQDLGEVIKKCLDGFKKST--GEGLPEKIVIY 249 (393)
T ss_pred EEEEEeeCCCCCCCCCCCc--EEEEEeecCCccccceEEEEecCccchHHHHHHHHHHHHHHHHHHc--CCCCcceeEEE
Confidence 578898888763 33443 2333332 2234444444443322 34455555555543 35 89888877
Q ss_pred CC
Q 047575 172 RE 173 (176)
Q Consensus 172 ~d 173 (176)
||
T Consensus 250 RD 251 (393)
T cd02826 250 RD 251 (393)
T ss_pred ec
Confidence 66
No 33
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=45.51 E-value=51 Score=29.61 Aligned_cols=106 Identities=12% Similarity=0.120 Sum_probs=56.0
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhh-----ccc-----cccceEE--eChHhHHHHH
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYK-----YKV-----CELDIFW--AYPLTFELLK 99 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k-----~r~-----~i~~if~--~~~~~~~~~~ 99 (176)
-+|+++|++.+..+.+.-+..+--...+++.-. --.++..|.++. ... -+.+|-+ .....+++|.
T Consensus 53 ~~~~~~q~~~~~~~~~~~~~~s~~~~~lkQ~~~---~qqqq~~~q~~~~~r~~a~~~~~rLfVGnLp~~~tEe~Lr~lF~ 129 (612)
T TIGR01645 53 PKLSSEQKDDIQKAKKYAMEQSIKQVLLKQTKA---HQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFD 129 (612)
T ss_pred CCCCHHHHHHHHHHHHHHhhhhhHHHHhhhHHH---HHHHHHHHHHHHHHHhhhhcCCCEEEEcCCCCCCCHHHHHHHHH
Confidence 378999998888876654433222222222110 011222222211 111 1223322 3445677999
Q ss_pred hCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHH
Q 047575 100 AFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLK 156 (176)
Q Consensus 100 ~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~ 156 (176)
.||+|.-+.--+ +. .....-|||||.-++.+.-.-+++.+.
T Consensus 130 ~fG~I~sV~I~~---------------D~-~TgkskGfAFVeF~s~e~A~~Ai~~ln 170 (612)
T TIGR01645 130 PFGPIKSINMSW---------------DP-ATGKHKGFAFVEYEVPEAAQLALEQMN 170 (612)
T ss_pred ccCCEEEEEEee---------------cC-CCCCcCCeEEEEeCcHHHHHHHHHhcC
Confidence 999986543211 10 011235899999999998888887653
No 34
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=45.04 E-value=65 Score=27.08 Aligned_cols=116 Identities=13% Similarity=0.155 Sum_probs=69.0
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccc----------cccceEEe--ChHhHHHHH
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV----------CELDIFWA--YPLTFELLK 99 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~----------~i~~if~~--~~~~~~~~~ 99 (176)
-+||+++++.|....+..+.. .|...|.++. .--..+++-+.|+.+.+ -+-.|-|- ...-+..|.
T Consensus 59 pkLsseq~d~iqkAKKYAMeq-SIK~vL~kQt--iahqQQQl~~qr~q~qrqqALaiMcRvYVGSIsfEl~EDtiR~AF~ 135 (544)
T KOG0124|consen 59 PKLSSEQKDDIQKAKKYAMEQ-SIKQVLLKQT--IAHQQQQLNQQRQQMQRQQALAIMCRVYVGSISFELREDTIRRAFD 135 (544)
T ss_pred CCCChhHHHHHHHHHHHHHHH-HHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhHheeeeeeEEEechHHHHhhcc
Confidence 488999988887766554322 2333333321 00123445555555443 22344432 234566899
Q ss_pred hCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCe
Q 047575 100 AFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPS 166 (176)
Q Consensus 100 ~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~ 166 (176)
-||.+-.+|-.+.- ++| + .=||||++.|-.|.-.-++++.--.|-+|+..+
T Consensus 136 PFGPIKSInMSWDp---------~T~---k----HKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiK 186 (544)
T KOG0124|consen 136 PFGPIKSINMSWDP---------ATG---K----HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK 186 (544)
T ss_pred CCCCcceeeccccc---------ccc---c----ccceEEEEEeCcHHHHHHHHHhccccccCcccc
Confidence 99999888755432 222 1 238999999999999999999888874344433
No 35
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=44.49 E-value=42 Score=26.34 Aligned_cols=51 Identities=10% Similarity=0.169 Sum_probs=36.0
Q ss_pred ceEEe--ChHhHHHHHhCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHH
Q 047575 86 DIFWA--YPLTFELLKAFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWAL 152 (176)
Q Consensus 86 ~if~~--~~~~~~~~~~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l 152 (176)
++-|- ...+++.|.+|||||- .+.|+.-.....-|+|||.=-+.|+-+.+.
T Consensus 19 gL~w~T~~~~l~~yFeqfGeI~e----------------avvitd~~t~rskGyGfVTf~d~~aa~rAc 71 (247)
T KOG0149|consen 19 GLAWETHKETLRRYFEQFGEIVE----------------AVVITDKNTGRSKGYGFVTFRDAEAATRAC 71 (247)
T ss_pred CcccccchHHHHHHHHHhCceEE----------------EEEEeccCCccccceeeEEeecHHHHHHHh
Confidence 45563 3468999999999863 555566666667788888877777766544
No 36
>PF13551 HTH_29: Winged helix-turn helix
Probab=44.29 E-value=67 Score=21.00 Aligned_cols=45 Identities=18% Similarity=0.141 Sum_probs=31.1
Q ss_pred CCHHHHHhhhhhccCC-------CChhHHHHHh-hhcCCCccchHHHHHHHHhh
Q 047575 34 LTNEEVSTLVDLSKNN-------VRPKEIFHTL-KTRDTFSVTMMKAICNARYK 79 (176)
Q Consensus 34 ls~~~~~~i~~l~~~g-------~~~~~I~~~l-~~~~~~~~~t~kdi~N~~~k 79 (176)
|++++++.|.++.... ..+..|...| .+.++ ..+....|+++..+
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~-~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFG-IDVSPSTIRRILKR 110 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccC-ccCCHHHHHHHHHH
Confidence 9999999998875542 4577888766 54443 55567777776554
No 37
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=43.41 E-value=54 Score=19.07 Aligned_cols=41 Identities=24% Similarity=0.286 Sum_probs=27.0
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhcc
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYK 81 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r 81 (176)
.||+.|.+ +..+...|.++.+|-..+. .+.+.|++.+..++
T Consensus 3 ~LT~~E~~-vl~~l~~G~~~~eIA~~l~-------is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 3 SLTERELE-VLRLLAQGMSNKEIAEELG-------ISEKTVKSHRRRIM 43 (58)
T ss_dssp SS-HHHHH-HHHHHHTTS-HHHHHHHHT-------SHHHHHHHHHHHHH
T ss_pred ccCHHHHH-HHHHHHhcCCcchhHHhcC-------cchhhHHHHHHHHH
Confidence 57887754 6677788999999999874 34555665555444
No 38
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=43.03 E-value=50 Score=19.70 Aligned_cols=30 Identities=13% Similarity=0.070 Sum_probs=22.6
Q ss_pred cCCCCCHHHH---HhhhhhccCCCChhHHHHHh
Q 047575 30 FAGRLTNEEV---STLVDLSKNNVRPKEIFHTL 59 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l 59 (176)
.+|..++++. ..+..|.+.|++..+|.+.+
T Consensus 35 ~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 35 GHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred CCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 4577888775 44556788999999998764
No 39
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.56 E-value=89 Score=21.22 Aligned_cols=35 Identities=6% Similarity=0.012 Sum_probs=27.2
Q ss_pred ccCCCCCHHHHHh---hhhhccCCCChhHHHHHhhhcC
Q 047575 29 SFAGRLTNEEVST---LVDLSKNNVRPKEIFHTLKTRD 63 (176)
Q Consensus 29 ~~~r~ls~~~~~~---i~~l~~~g~~~~~I~~~l~~~~ 63 (176)
+..|.-++++... |..+.+.|++..+|..++....
T Consensus 33 ~~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~ 70 (116)
T cd04769 33 GNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHE 70 (116)
T ss_pred CCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 3457778877644 6679999999999999997644
No 40
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=42.21 E-value=26 Score=19.67 Aligned_cols=40 Identities=15% Similarity=0.211 Sum_probs=20.3
Q ss_pred HHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccc
Q 047575 36 NEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV 82 (176)
Q Consensus 36 ~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~ 82 (176)
.+.+..+..+...|.+.++|...+. .+...|++.++++++
T Consensus 4 ~~~R~~ii~l~~~G~s~~~ia~~lg-------vs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 4 EERRAQIIRLLREGWSIREIAKRLG-------VSRSTVYRWIKRYRE 43 (50)
T ss_dssp ------HHHHHHHT--HHHHHHHHT-------S-HHHHHHHHT----
T ss_pred hhHHHHHHHHHHCCCCHHHHHHHHC-------cCHHHHHHHHHHccc
Confidence 3445566666666999999988874 356778888777653
No 41
>smart00351 PAX Paired Box domain.
Probab=42.11 E-value=51 Score=22.87 Aligned_cols=45 Identities=27% Similarity=0.361 Sum_probs=33.8
Q ss_pred CCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccc
Q 047575 31 AGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV 82 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~ 82 (176)
.+.++.++++.|..+.+.|.+.++|...+. ++...+++..+++++
T Consensus 15 ~~~~s~~~R~riv~~~~~G~s~~~iA~~~g-------vs~~tV~kwi~r~~~ 59 (125)
T smart00351 15 GRPLPDEERQRIVELAQNGVRPCDISRQLC-------VSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHHC-------cCHHHHHHHHHHHHH
Confidence 467999999999999889999988876653 345666777665543
No 42
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=41.51 E-value=58 Score=21.06 Aligned_cols=48 Identities=10% Similarity=0.043 Sum_probs=36.2
Q ss_pred CCCHHHHHhhhhhccCCCC--hhHHHHHhhhcCCCc-cchHHHHHHHHhhc
Q 047575 33 RLTNEEVSTLVDLSKNNVR--PKEIFHTLKTRDTFS-VTMMKAICNARYKY 80 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~--~~~I~~~l~~~~~~~-~~t~kdi~N~~~k~ 80 (176)
.|.+.-...|.+|..+|.+ -..|++.|.+.+|+. .+..+.||+....+
T Consensus 11 PL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~L 61 (80)
T PF10264_consen 11 PLPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTL 61 (80)
T ss_pred eHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHH
Confidence 4555667889999887754 478999999999984 35677888876654
No 43
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=41.27 E-value=59 Score=19.44 Aligned_cols=31 Identities=16% Similarity=0.106 Sum_probs=23.4
Q ss_pred cCCCCCHHHH---HhhhhhccCCCChhHHHHHhh
Q 047575 30 FAGRLTNEEV---STLVDLSKNNVRPKEIFHTLK 60 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l~ 60 (176)
.+|..++++. ..+..|.+.|+++.+|...|.
T Consensus 35 g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 35 GYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred CCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4577888775 455567889999999988764
No 44
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=40.31 E-value=27 Score=21.17 Aligned_cols=17 Identities=24% Similarity=0.434 Sum_probs=10.3
Q ss_pred cCCceEEEEecCCCCCC
Q 047575 4 NNQDWMLKVICGLHNHH 20 (176)
Q Consensus 4 ~~~~W~i~~~~~~HNH~ 20 (176)
+++.=.+....++|||+
T Consensus 43 ~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 43 DDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp TCCCEEEEEEES--SS-
T ss_pred CCCCEEEEEEeeeeCCC
Confidence 45666677778999996
No 45
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=39.35 E-value=44 Score=28.85 Aligned_cols=22 Identities=23% Similarity=0.395 Sum_probs=19.3
Q ss_pred CCceEEEEecCCCCCCCCCCCC
Q 047575 5 NQDWMLKVICGLHNHHVAQHLE 26 (176)
Q Consensus 5 ~~~W~i~~~~~~HNH~~~~~~~ 26 (176)
.|.+.|+...+-||||+...++
T Consensus 164 ~g~f~v~k~~~~h~h~l~~nl~ 185 (496)
T PF04684_consen 164 KGPFVVTKIEPYHNHPLESNLS 185 (496)
T ss_pred cCceEEEeeccccCCccccccc
Confidence 5789999999999999988654
No 46
>cd00131 PAX Paired Box domain
Probab=38.96 E-value=60 Score=22.69 Aligned_cols=48 Identities=17% Similarity=0.277 Sum_probs=35.0
Q ss_pred cccCCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccc
Q 047575 28 HSFAGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV 82 (176)
Q Consensus 28 h~~~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~ 82 (176)
+..-+.+|.+.++.|..+.+.|.++++|...+. .+...|+..++++++
T Consensus 12 ~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~-------Vs~~tV~r~i~r~~e 59 (128)
T cd00131 12 FVNGRPLPDSIRQRIVELAQSGIRPCDISRQLR-------VSHGCVSKILNRYYE 59 (128)
T ss_pred ccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHC-------cCHHHHHHHHHHHHH
Confidence 334478999999999999999999999977654 334556666555543
No 47
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=38.42 E-value=21 Score=24.00 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=19.1
Q ss_pred HHHHhhhhhccCCCChhHHHHHhhhc
Q 047575 37 EEVSTLVDLSKNNVRPKEIFHTLKTR 62 (176)
Q Consensus 37 ~~~~~i~~l~~~g~~~~~I~~~l~~~ 62 (176)
|.....++|.++|+++....++|++.
T Consensus 70 Ef~~~~~eM~dAGV~~~~~~~~l~~~ 95 (100)
T PF15652_consen 70 EFNNSYREMFDAGVSKECRKKALKAQ 95 (100)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 44455677888888888888887763
No 48
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=38.26 E-value=55 Score=19.58 Aligned_cols=37 Identities=19% Similarity=0.105 Sum_probs=28.1
Q ss_pred HHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhcc
Q 047575 38 EVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYK 81 (176)
Q Consensus 38 ~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r 81 (176)
-+..++.|.-.|.++++|-+.|.- ..+.||+.+++.+
T Consensus 2 ~k~~A~~LY~~G~~~~eIA~~Lg~-------~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 2 VKEQARSLYLQGWSIKEIAEELGV-------PRSTVYSWKDRYK 38 (58)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCC-------ChHHHHHHHHhhC
Confidence 356678888889999999998843 2677888877654
No 49
>cd04657 Piwi_ago-like Piwi_ago-like: PIWI domain, Argonaute-like subfamily. Argonaute is the central component of the RNA-induced silencing complex (RISC) and related complexes. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
Probab=38.20 E-value=2.1e+02 Score=24.32 Aligned_cols=68 Identities=21% Similarity=0.196 Sum_probs=35.9
Q ss_pred EEEEeccccccc--cCcce-eEEEe-eccCCCeEEEEEEeecCCc------cchHHHHHHHHHHHhcCCCCCeEEEecCC
Q 047575 104 VLIMDCTYKVNK--YKFPL-LEIVG-VTLTTMTFNVDFAYLESKR------EDNYIWALKRLKTIMQDDMLPSVIVIKRE 173 (176)
Q Consensus 104 vv~~D~ty~tn~--~~~pl-~~~~g-~~~~~~~~~~~~~~~~~E~------~~s~~w~l~~~~~~~~~~~~p~~iitD~d 173 (176)
++.+|.++.+.. .+.|- .-+++ +|.+...+...+.+-.... .+.+..+|+.|.+.. +..|.-||..||
T Consensus 201 iiG~Dv~H~~~~~~~~~pSiaa~Vas~d~~~~~y~~~~~~q~~~~e~i~~l~~~~~~~l~~~~~~~--~~~P~~IiiyRD 278 (426)
T cd04657 201 VLGADVTHPSPGDPAGAPSIAAVVASVDWHLAQYPASVRLQSHRQEIIDDLESMVRELLRAFKKAT--GKLPERIIYYRD 278 (426)
T ss_pred EEEEeeecCCCCCCCCCCcEEEEEEecCCcccccceEEEEeCCCcchHHHHHHHHHHHHHHHHHHh--CCCCceEEEEEc
Confidence 578899998765 34452 22333 3333333333333333222 233445555555544 469988887776
No 50
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=36.98 E-value=90 Score=18.38 Aligned_cols=20 Identities=35% Similarity=0.632 Sum_probs=10.9
Q ss_pred CcEEEEecccc-ccccCccee
Q 047575 102 TNVLIMDCTYK-VNKYKFPLL 121 (176)
Q Consensus 102 ~dvv~~D~ty~-tn~~~~pl~ 121 (176)
++|+.+|+.-+ ..-|.+|-+
T Consensus 8 cnvisidgkkkksdtysypkl 28 (66)
T PF13082_consen 8 CNVISIDGKKKKSDTYSYPKL 28 (66)
T ss_pred ccEEEeccccccCCcccCceE
Confidence 45677776553 334555543
No 51
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=36.89 E-value=23 Score=28.06 Aligned_cols=33 Identities=24% Similarity=0.365 Sum_probs=28.5
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHhhhcCC
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDT 64 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~ 64 (176)
|.|-.+.+-.|.+|.+.|++|++|-+.|+-.++
T Consensus 19 RPLPna~RlrIVELarlGiRPCDISRQLrvSHG 51 (334)
T KOG3517|consen 19 RPLPNAIRLRIVELARLGIRPCDISRQLRVSHG 51 (334)
T ss_pred ccCcchhhhhHHHHHHcCCCccchhhhhhhccc
Confidence 677778888999999999999999998876654
No 52
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=36.81 E-value=16 Score=27.41 Aligned_cols=31 Identities=35% Similarity=0.550 Sum_probs=25.0
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcC
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRD 63 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~ 63 (176)
+||.+|++.+..|..+|+..-+|+..|.+-.
T Consensus 4 ~l~~~QieLLqrL~~SG~TK~~ii~ALe~l~ 34 (180)
T PF04814_consen 4 KLTIEQIELLQRLRRSGMTKEEIIHALETLD 34 (180)
T ss_dssp HHHHHHHHHHHHHHHCT--HHHHHHHHTT--
T ss_pred cccHHHHHHHHHHHHcCCCHHHHHHHHhccC
Confidence 5788999999999999999999999998655
No 53
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=36.56 E-value=1.5e+02 Score=20.79 Aligned_cols=46 Identities=13% Similarity=0.010 Sum_probs=25.7
Q ss_pred EEeeccC-CCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCC-eEEEecCCCC
Q 047575 123 IVGVTLT-TMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLP-SVIVIKRELT 175 (176)
Q Consensus 123 ~~g~~~~-~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p-~~iitD~d~a 175 (176)
+++++-. +.+--+....+.+.+.++..=++ .+.. .| .+|+||.-.|
T Consensus 38 ~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i---~~~i----~~gs~i~TD~~~a 85 (151)
T PF12762_consen 38 FGAVERNDGGTGRVFMFVVPDRSAETLKPII---QEHI----EPGSTIITDGWRA 85 (151)
T ss_pred EEEEeecccCCceEEEEeecccccchhHHHH---HHhh----hccceeeecchhh
Confidence 5555554 33334444556778888775443 2222 23 4788997654
No 54
>PF11293 DUF3094: Protein of unknown function (DUF3094); InterPro: IPR021444 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=36.50 E-value=30 Score=20.58 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=18.1
Q ss_pred CCCCHHHHHhhhhhccCCCCh
Q 047575 32 GRLTNEEVSTLVDLSKNNVRP 52 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~ 52 (176)
++|++|.++.+++..++|..+
T Consensus 2 ~rL~pEDQ~~Vd~yL~a~~~~ 22 (55)
T PF11293_consen 2 SRLNPEDQQRVDEYLQAGVNQ 22 (55)
T ss_pred CCCCHHHHHHHHHHHhCCCCc
Confidence 689999999999998888755
No 55
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=35.05 E-value=62 Score=21.98 Aligned_cols=32 Identities=19% Similarity=0.112 Sum_probs=28.9
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCC
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDT 64 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~ 64 (176)
.|+++.|..|......=-.|+++.+.+++.++
T Consensus 3 ~L~~~vK~FIVQ~LAcfdTPs~v~~aVk~eFg 34 (104)
T PF10045_consen 3 ALKKEVKAFIVQSLACFDTPSEVAEAVKEEFG 34 (104)
T ss_pred CccHHHHHHHHHHHHhhCCHHHHHHHHHHHhC
Confidence 68899999999988888899999999999886
No 56
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=34.48 E-value=60 Score=15.57 Aligned_cols=28 Identities=25% Similarity=0.224 Sum_probs=20.1
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHh
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTL 59 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l 59 (176)
++++++++..+..+.+.|.+..+|...+
T Consensus 4 ~~~~~~~~~~i~~~~~~~~s~~~ia~~~ 31 (42)
T cd00569 4 PKLTPEQIEEARRLLAAGESVAEIARRL 31 (42)
T ss_pred CcCCHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3567777777777777788777777655
No 57
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=33.00 E-value=46 Score=19.99 Aligned_cols=30 Identities=23% Similarity=0.239 Sum_probs=22.8
Q ss_pred cCCCCCHHHH---HhhhhhccCCCChhHHHHHh
Q 047575 30 FAGRLTNEEV---STLVDLSKNNVRPKEIFHTL 59 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l 59 (176)
.+|.-++++. ..|..+.+.|++..+|...|
T Consensus 34 g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 34 GRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 4577787775 55566788999999998876
No 58
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=32.16 E-value=92 Score=20.05 Aligned_cols=34 Identities=12% Similarity=0.141 Sum_probs=27.1
Q ss_pred cCCCCCHHHH---HhhhhhccCCCChhHHHHHhhhcC
Q 047575 30 FAGRLTNEEV---STLVDLSKNNVRPKEIFHTLKTRD 63 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l~~~~ 63 (176)
.+|.-++++. ..|..|.+.|++..+|.+.+....
T Consensus 36 g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~~ 72 (88)
T cd01105 36 GQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRR 72 (88)
T ss_pred CceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcc
Confidence 5678888776 556678889999999999998654
No 59
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=31.84 E-value=85 Score=20.24 Aligned_cols=51 Identities=10% Similarity=0.168 Sum_probs=32.2
Q ss_pred cCCCCCHHHH---Hhhhhhcc-CCCChhHHHHHhhhcCCCccchHHHHHHHHhhcc
Q 047575 30 FAGRLTNEEV---STLVDLSK-NNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYK 81 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~-~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r 81 (176)
.+|..++++. ..|..|.+ .|++...|..+|.-... .....+++..++++++
T Consensus 35 g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~-~~~l~~~l~~l~~~~~ 89 (91)
T cd04766 35 GTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEE-LAELRAELDELRARLR 89 (91)
T ss_pred CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHhc
Confidence 4678888776 55556776 99999999888752211 1123445555555544
No 60
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=31.34 E-value=1.1e+02 Score=21.94 Aligned_cols=73 Identities=18% Similarity=0.188 Sum_probs=42.9
Q ss_pred ccce-EEeChHhH-HHHHhCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcC
Q 047575 84 ELDI-FWAYPLTF-ELLKAFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQD 161 (176)
Q Consensus 84 i~~i-f~~~~~~~-~~~~~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~ 161 (176)
+-|+ |......+ ++|..+|+|-- .++|+|-+..+ +.|||||.-=..++-.-+++.+...-
T Consensus 41 VgNlSfyttEEqiyELFs~cG~irr---------------iiMGLdr~kkt-pCGFCFVeyy~~~dA~~Alryisgtr-- 102 (153)
T KOG0121|consen 41 VGNLSFYTTEEQIYELFSKCGDIRR---------------IIMGLDRFKKT-PCGFCFVEYYSRDDAEDALRYISGTR-- 102 (153)
T ss_pred EeeeeeeecHHHHHHHHHhccchhe---------------eEeccccCCcC-ccceEEEEEecchhHHHHHHHhccCc--
Confidence 3444 33444333 48888888732 27788877666 45999998766666554444433221
Q ss_pred CCCCeEEEecCCCC
Q 047575 162 DMLPSVIVIKRELT 175 (176)
Q Consensus 162 ~~~p~~iitD~d~a 175 (176)
.--+.|-+|.|..
T Consensus 103 -Lddr~ir~D~D~G 115 (153)
T KOG0121|consen 103 -LDDRPIRIDWDAG 115 (153)
T ss_pred -ccccceeeecccc
Confidence 2235666777653
No 61
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=31.25 E-value=38 Score=20.33 Aligned_cols=31 Identities=26% Similarity=0.322 Sum_probs=22.2
Q ss_pred CCCCCHHHH---HhhhhhccCCCChhHHHHHhhh
Q 047575 31 AGRLTNEEV---STLVDLSKNNVRPKEIFHTLKT 61 (176)
Q Consensus 31 ~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l~~ 61 (176)
+|..++++. ..|..|.+.|++..+|.+.|+.
T Consensus 35 ~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 35 YRYYSEEDVERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp SEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred eeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 467777765 5566688899999999998865
No 62
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=30.88 E-value=99 Score=17.02 Aligned_cols=40 Identities=23% Similarity=0.184 Sum_probs=26.3
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhc
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKY 80 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~ 80 (176)
.|++.++. +..+...|.+..+|...+. .+...+++.+.+.
T Consensus 3 ~l~~~e~~-i~~~~~~g~s~~eia~~l~-------is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPRERE-VLRLLAEGLTNKEIAERLG-------ISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHH-HHHHHHcCCCHHHHHHHHC-------CCHHHHHHHHHHH
Confidence 57888876 4455678999999988764 2344555554443
No 63
>PF14386 DUF4417: Domain of unknown function (DUF4417)
Probab=30.82 E-value=2.4e+02 Score=21.42 Aligned_cols=76 Identities=12% Similarity=0.181 Sum_probs=46.2
Q ss_pred hHHHHHHHHhhccc----------cccceEEeChHhHHHHHhCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEE
Q 047575 69 MMKAICNARYKYKV----------CELDIFWAYPLTFELLKAFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFA 138 (176)
Q Consensus 69 t~kdi~N~~~k~r~----------~i~~if~~~~~~~~~~~~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~ 138 (176)
...+++|..+...- .|-+|-|++.++...+ +-|+ ..+....++.-
T Consensus 89 ~~~qi~n~yR~r~~g~~~q~~Gi~VIP~v~W~~~~s~~~~------------------------~~gi-~~~~ivaist~ 143 (200)
T PF14386_consen 89 RAMQIWNIYRSRWLGAYWQSNGIKVIPNVSWSDKRSFDFC------------------------FDGI-PKGSIVAISTN 143 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCeEcceEEecCcchHHHH------------------------Hhhc-ccCCEEEEEEe
Confidence 46788888765332 4667888888776542 3333 22222222222
Q ss_pred eecCCccchHHHHHHHHHHHhcCCCCCe-EEEec
Q 047575 139 YLESKREDNYIWALKRLKTIMQDDMLPS-VIVIK 171 (176)
Q Consensus 139 ~~~~E~~~s~~w~l~~~~~~~~~~~~p~-~iitD 171 (176)
. ...+.+...+++.-+.+.... ..|+ +++..
T Consensus 144 g-~~~~~~~~~~f~~Gl~em~~r-l~P~~ilvyG 175 (200)
T PF14386_consen 144 G-CINNKEDKKLFLDGLREMLKR-LRPKHILVYG 175 (200)
T ss_pred c-ccCCHHHHHHHHHHHHHHHhc-cCCCeEEEEC
Confidence 2 355678899999999998874 4675 44544
No 64
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.36 E-value=1.6e+02 Score=19.29 Aligned_cols=49 Identities=10% Similarity=-0.000 Sum_probs=32.3
Q ss_pred cCCCCCHHHH---Hhhhhhcc-CCCChhHHHHHhhhcCCCccchHHHHHHHHh
Q 047575 30 FAGRLTNEEV---STLVDLSK-NNVRPKEIFHTLKTRDTFSVTMMKAICNARY 78 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~-~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~ 78 (176)
.+|.-++++. ..|..|.+ .|++..+|..++.....+.-...++..+...
T Consensus 34 g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~~~~~~~~~~~~l~ 86 (96)
T cd04774 34 RYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEPVDGGHRYSAESLR 86 (96)
T ss_pred CCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccccchhHHHHHHHHH
Confidence 4567777665 55666888 8999999999997644332234455555433
No 65
>PF14638 FNIP_C: Folliculin-interacting protein C-terminus
Probab=30.22 E-value=83 Score=23.86 Aligned_cols=74 Identities=15% Similarity=0.135 Sum_probs=46.5
Q ss_pred cCCceEEEEecCCCCCCCCCCCCccccCCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHH
Q 047575 4 NNQDWMLKVICGLHNHHVAQHLEGHSFAGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNAR 77 (176)
Q Consensus 4 ~~~~W~i~~~~~~HNH~~~~~~~~h~~~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~ 77 (176)
+..+|.+++...+..+.....+..--..-.+-....+.+..|.+.|++|..-+.+|+.+=.+.+..-+.+..+.
T Consensus 80 Dtd~wtV~v~ss~~~~~~~~~~~~~v~~S~lVs~mLes~~~l~~~~~~~~fCl~~lEd~L~el~~KS~~Lae~l 153 (192)
T PF14638_consen 80 DTDTWTVKVISSQRSNLWSNKPGIPVGMSELVSSMLESFVQLWKLGMPPEFCLMHLEDKLRELYLKSKTLAEYL 153 (192)
T ss_pred eCCCCEEEEEEecCccCcCCcCCcccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999887665533221111112333455688888999999999888888765333344444555554
No 66
>KOG3862 consensus Transcription factor PAX2/5/8, contains PAX domain [Transcription]
Probab=29.90 E-value=53 Score=26.39 Aligned_cols=34 Identities=26% Similarity=0.413 Sum_probs=30.9
Q ss_pred CCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCC
Q 047575 31 AGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDT 64 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~ 64 (176)
-|.|.+.....|.+|...|+.|++|-..++-.++
T Consensus 23 GRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShG 56 (327)
T KOG3862|consen 23 GRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHG 56 (327)
T ss_pred CccCchHHHHHHHHHHHcCCcchhHHHHHhhccC
Confidence 3889999999999999999999999999887776
No 67
>cd04658 Piwi_piwi-like_Euk Piwi_piwi-like_Euk: PIWI domain, Piwi-like subfamily found in eukaryotes. This domain is found in Piwi and closely related proteins, where it is believed to perform a crucial role in germline cells, via RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The mechanism in Piwi is believed to be similar to that in Argonaute, the central component of the RNA-induced silencing complex (RISC). The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
Probab=29.45 E-value=3.6e+02 Score=22.98 Aligned_cols=67 Identities=19% Similarity=0.176 Sum_probs=32.7
Q ss_pred EEEEeccccccccCcceeEEEe-eccCCCeEEEEEEeecCCcc--------chHHHHHHHHHHHhcCCCCCeEEEecCC
Q 047575 104 VLIMDCTYKVNKYKFPLLEIVG-VTLTTMTFNVDFAYLESKRE--------DNYIWALKRLKTIMQDDMLPSVIVIKRE 173 (176)
Q Consensus 104 vv~~D~ty~tn~~~~pl~~~~g-~~~~~~~~~~~~~~~~~E~~--------~s~~w~l~~~~~~~~~~~~p~~iitD~d 173 (176)
++.+|.++....-.--...+++ +|.+...+. +......... +.+..+++.|++.. +..|.-||.-||
T Consensus 231 iiGidv~h~~~~~~~Si~a~vas~~~~~~~~~-~~~~~q~~~~e~~~~~l~~~~~~~l~~y~~~~--~~~P~~IiiyRd 306 (448)
T cd04658 231 IVGIDVYHDTITKKKSVVGFVASLNKSITKWF-SKYISQVRGQEEIIDSLGKSMKKALKAYKKEN--KKLPSRIIIYRD 306 (448)
T ss_pred EEEEeeecCCCCCCCcEEEEEEEcCCCCceEe-eEEEEeCCCceeeHHHHHHHHHHHHHHHHHHh--CCCCceEEEEec
Confidence 5788888877532222222222 233333333 3233332221 23444555555543 578987777666
No 68
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=29.20 E-value=54 Score=24.05 Aligned_cols=27 Identities=26% Similarity=0.303 Sum_probs=25.0
Q ss_pred CCHHHHHhhhhhccCCCChhHHHHHhh
Q 047575 34 LTNEEVSTLVDLSKNNVRPKEIFHTLK 60 (176)
Q Consensus 34 ls~~~~~~i~~l~~~g~~~~~I~~~l~ 60 (176)
.|+|..+.++.|...|++.++|-..|.
T Consensus 3 Wtde~~~~L~~lw~~G~SasqIA~~lg 29 (162)
T PF07750_consen 3 WTDERVERLRKLWAEGLSASQIARQLG 29 (162)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 478889999999999999999999997
No 69
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=29.10 E-value=1.2e+02 Score=21.67 Aligned_cols=49 Identities=14% Similarity=0.188 Sum_probs=32.7
Q ss_pred CCCCHHHHHhhhhhccC--CCChhHHHHHhhhcCCCccchHHHHHHHHhhccc
Q 047575 32 GRLTNEEVSTLVDLSKN--NVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV 82 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~--g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~ 82 (176)
-|+|+.-...+.-|.++ .+++.+|+..|++..|+ +.+-.|||....+..
T Consensus 17 lr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~--islaTVYr~L~~l~e 67 (145)
T COG0735 17 LRLTPQRLAVLELLLEADGHLSAEELYEELREEGPG--ISLATVYRTLKLLEE 67 (145)
T ss_pred CCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCC--CCHhHHHHHHHHHHH
Confidence 36777666666666544 37788888888887664 346677877665544
No 70
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=28.71 E-value=74 Score=19.12 Aligned_cols=30 Identities=10% Similarity=0.109 Sum_probs=22.4
Q ss_pred cCCCCCHHHH---HhhhhhccCCCChhHHHHHh
Q 047575 30 FAGRLTNEEV---STLVDLSKNNVRPKEIFHTL 59 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l 59 (176)
.+|..+.++. ..|..|.+.|++..+|...|
T Consensus 35 g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 35 GHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 4577887775 55556778899999988775
No 71
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.40 E-value=59 Score=22.75 Aligned_cols=43 Identities=14% Similarity=0.226 Sum_probs=30.7
Q ss_pred cCCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhh
Q 047575 30 FAGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYK 79 (176)
Q Consensus 30 ~~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k 79 (176)
.-|+-+......|++|.++|.+|++|-..+. +..+.+|=...+
T Consensus 90 rprkyd~~t~~~i~emlr~gk~preIsk~lG-------IpirTvyY~l~k 132 (139)
T COG1710 90 RPRKYDRNTLLRIREMLRNGKTPREISKDLG-------IPIRTVYYLLKK 132 (139)
T ss_pred CCcccchhHHHHHHHHHHcCCCHHHHHHhhC-------CchhhhHHHHHH
Confidence 3467777778889999999999999987752 345655544433
No 72
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=27.51 E-value=42 Score=19.24 Aligned_cols=27 Identities=15% Similarity=0.163 Sum_probs=21.5
Q ss_pred CHHHHHhhhhhccCCCChhHHHHHhhh
Q 047575 35 TNEEVSTLVDLSKNNVRPKEIFHTLKT 61 (176)
Q Consensus 35 s~~~~~~i~~l~~~g~~~~~I~~~l~~ 61 (176)
.|..+++|.+|...|...+.+-..|+-
T Consensus 7 kpgikeqIvema~nG~GiRdtaRvL~I 33 (46)
T PF12759_consen 7 KPGIKEQIVEMAFNGSGIRDTARVLKI 33 (46)
T ss_pred CccHHHHHHHHHhcCCcchhhHhHhcc
Confidence 346677899999999988888887753
No 73
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=27.02 E-value=1.2e+02 Score=20.99 Aligned_cols=59 Identities=14% Similarity=0.025 Sum_probs=38.0
Q ss_pred CceEEEEecCCCCCCCCCCCCccccCCCCCHHHHHhhhhhccCCCChhHHHHHhhhcCC
Q 047575 6 QDWMLKVICGLHNHHVAQHLEGHSFAGRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDT 64 (176)
Q Consensus 6 ~~W~i~~~~~~HNH~~~~~~~~h~~~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~ 64 (176)
+.-.|+.+...|-+---.-....+.--+|++|+.+.|..+.++.-+-+++-+.+.-.+|
T Consensus 6 ~~l~vt~l~C~~C~t~i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYP 64 (113)
T PF09862_consen 6 GELVVTRLKCPSCGTEIEGEFELPWFARLSPEQLEFIKLFIKNRGNLKEMEKELGISYP 64 (113)
T ss_pred CceEEEEEEcCCCCCEEEeeeccchhhcCCHHHHHHHHHHHHhcCCHHHHHHHHCCCcH
Confidence 44556666665533222212223445689999999999998887777777777655444
No 74
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=26.19 E-value=1.3e+02 Score=20.11 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=31.2
Q ss_pred CCCCCHHHHHhhh-hhccCC---CChhHHHHHhhhcCCCccchHHHHHHHHhhcc
Q 047575 31 AGRLTNEEVSTLV-DLSKNN---VRPKEIFHTLKTRDTFSVTMMKAICNARYKYK 81 (176)
Q Consensus 31 ~r~ls~~~~~~i~-~l~~~g---~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r 81 (176)
.|+||++|..+|. .|.+.| ....+|...+.+-.. ...+..||...+.++.
T Consensus 33 ~r~Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~I~~vt~-~~P~~~di~RV~~~La 86 (96)
T PF11829_consen 33 RRRLTDDEVAEVAAELAARGDPPVDRIDIGVAITRVTD-ELPTPEDIERVRARLA 86 (96)
T ss_dssp TTTS-HHHHHHHHHHHHHHTSS-BSCCHHHHHHHHHCS-S-S-HHHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHc-CCcCHHHHHHHHHHHH
Confidence 5889999875554 454443 366778777766543 4567888888777653
No 75
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=25.78 E-value=2e+02 Score=20.28 Aligned_cols=32 Identities=16% Similarity=0.116 Sum_probs=25.3
Q ss_pred cCCCCCHHHH---HhhhhhccCCCChhHHHHHhhh
Q 047575 30 FAGRLTNEEV---STLVDLSKNNVRPKEIFHTLKT 61 (176)
Q Consensus 30 ~~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l~~ 61 (176)
.+|.-++++. ..|..+.+.|++..+|..+|..
T Consensus 35 g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (139)
T cd01110 35 NQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAT 69 (139)
T ss_pred CCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4577787765 5666688899999999999864
No 76
>PF02838 Glyco_hydro_20b: Glycosyl hydrolase family 20, domain 2; InterPro: IPR015882 Glycoside hydrolase family 20 GH20 from CAZY comprises enzymes with several known activities; beta-hexosaminidase (3.2.1.52 from EC); lacto-N-biosidase (3.2.1.140 from EC). Carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base in this family of enzymes. In the brain and other tissues, beta-hexosaminidase A degrades GM2 gangliosides; specifically, the enzyme hydrolyses terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor. Mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside []. This entry represents the alpha and beta subunit of beta-N-acetylhexosaminidase. It contains a similar fold but lacks the catalytic centre.; GO: 0004563 beta-N-acetylhexosaminidase activity, 0005975 carbohydrate metabolic process; PDB: 3SUT_A 3SUS_A 3GH7_A 3SUR_A 3SUW_A 3SUV_A 3SUU_A 3GH5_A 3GH4_A 2J4G_B ....
Probab=25.60 E-value=62 Score=21.89 Aligned_cols=34 Identities=18% Similarity=0.409 Sum_probs=27.5
Q ss_pred eecCCccchHHHHHHHHHHHhcC---CCCCeEEEecC
Q 047575 139 YLESKREDNYIWALKRLKTIMQD---DMLPSVIVIKR 172 (176)
Q Consensus 139 ~~~~E~~~s~~w~l~~~~~~~~~---~~~p~~iitD~ 172 (176)
-+...+...+-|.+++|++.+.. +..|.+.|.|.
T Consensus 88 ~I~a~~~~G~~yg~qTL~Qll~~~~~~~lp~~~I~D~ 124 (124)
T PF02838_consen 88 TIEASDPAGLFYGLQTLRQLLRQSGNGTLPCVEIEDY 124 (124)
T ss_dssp EEEESSHHHHHHHHHHHHHHSBTCS-CEEEEEEEEE-
T ss_pred EEEEcCchHHHHHHHHHHHHhhccCCCccceEEEEeC
Confidence 45667889999999999999963 46788889884
No 77
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.55 E-value=1.7e+02 Score=20.01 Aligned_cols=45 Identities=13% Similarity=0.076 Sum_probs=31.0
Q ss_pred CCCCCHHHHHhhhh-hccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccc
Q 047575 31 AGRLTNEEVSTLVD-LSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV 82 (176)
Q Consensus 31 ~r~ls~~~~~~i~~-l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~ 82 (176)
.|+-|++.|..+.. +.+.|.+.++|..-+ + ++...|||++++++.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~----g---Is~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQH----G---VAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHH----C---cCHHHHHHHHHHHhh
Confidence 46788888865554 577788888776553 2 356778888887653
No 78
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.34 E-value=1.1e+02 Score=21.99 Aligned_cols=38 Identities=13% Similarity=0.218 Sum_probs=31.4
Q ss_pred hHHHHHhCCcEE--EEeccccccccCcceeEEEeeccCCC
Q 047575 94 TFELLKAFTNVL--IMDCTYKVNKYKFPLLEIVGVTLTTM 131 (176)
Q Consensus 94 ~~~~~~~f~dvv--~~D~ty~tn~~~~pl~~~~g~~~~~~ 131 (176)
....++.|..++ -.|+.|.+-|.+.||+.+.-.++...
T Consensus 96 p~sDi~kynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 96 PYSDIEKYNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred cHHHhhhcccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 456778888876 56999999999999999998887653
No 79
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=25.30 E-value=87 Score=21.16 Aligned_cols=44 Identities=18% Similarity=0.105 Sum_probs=27.9
Q ss_pred CCCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhccc
Q 047575 32 GRLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYKV 82 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r~ 82 (176)
..|++.++..+....-.|.+..+|-..+. .+.+.|++.+.+.++
T Consensus 109 ~~L~~~~~~ii~~~~~~g~s~~eIA~~l~-------~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 109 EKLPEREREVLVLRYLEGLSYKEIAEILG-------ISVGTVKRRLKRARK 152 (158)
T ss_pred HhCCHHHHHHHhhHHhcCCCHHHHHHHHC-------CCHHHHHHHHHHHHH
Confidence 36777776665544456777777777654 346677777666554
No 80
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=24.88 E-value=70 Score=22.09 Aligned_cols=45 Identities=4% Similarity=0.012 Sum_probs=30.8
Q ss_pred CCCHHHHHhhhhh-ccCCCChhHHHHHhhhcCCC-ccchHHHHHHHH
Q 047575 33 RLTNEEVSTLVDL-SKNNVRPKEIFHTLKTRDTF-SVTMMKAICNAR 77 (176)
Q Consensus 33 ~ls~~~~~~i~~l-~~~g~~~~~I~~~l~~~~~~-~~~t~kdi~N~~ 77 (176)
++|+++++.|..- .++|++.++.+..+.-.+.- ..++.+++..+.
T Consensus 16 rvt~eE~~~I~~kA~~AGlS~SeYLR~~aLg~~I~s~~D~e~v~eL~ 62 (114)
T PRK13877 16 PVLPDEKAEIEANAAAAGLSVARYLRDVGQGYQIKGVIDYEYVRELA 62 (114)
T ss_pred EeCHHHHHHHHHHHHHhCCCHHHHHHHHHcCCCccccCCHHHHHHHH
Confidence 6899999999874 67899988888876653321 134555555553
No 81
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=24.02 E-value=2e+02 Score=20.36 Aligned_cols=48 Identities=13% Similarity=0.131 Sum_probs=31.6
Q ss_pred HhHHHHHhCCcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHH
Q 047575 93 LTFELLKAFTNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLK 156 (176)
Q Consensus 93 ~~~~~~~~f~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~ 156 (176)
.-+++|..|++|.-+.-. .+. .....-+||||.=++.++-..+++.+.
T Consensus 50 ~L~~~F~~~G~I~~v~i~---------------~d~-~tg~~kGfaFV~F~~~e~A~~Al~~ln 97 (144)
T PLN03134 50 SLRDAFAHFGDVVDAKVI---------------VDR-ETGRSRGFGFVNFNDEGAATAAISEMD 97 (144)
T ss_pred HHHHHHhcCCCeEEEEEE---------------ecC-CCCCcceEEEEEECCHHHHHHHHHHcC
Confidence 456688889987544311 111 112234899999999999999888653
No 82
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=23.76 E-value=1.3e+02 Score=16.05 Aligned_cols=41 Identities=12% Similarity=0.063 Sum_probs=26.5
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCCCccchHHHHHHHHhhc
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKY 80 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~ 80 (176)
.|+++++..+....-.|.+..+|-..+. .+...|+....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~~~~~~ia~~~~-------~s~~~i~~~~~~~ 50 (55)
T cd06171 10 KLPEREREVILLRFGEGLSYEEIAEILG-------ISRSTVRQRLHRA 50 (55)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHC-------cCHHHHHHHHHHH
Confidence 5677777666666668888888877753 3345555554443
No 83
>PF01644 Chitin_synth_1: Chitin synthase; InterPro: IPR004834 This region is found commonly in chitin synthases classes I, II and III 2.4.1.16 from EC. Chitin a linear homopolymer of GlcNAc residues, it is an important component of the cell wall of fungi and is synthesised on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases []. ; GO: 0004100 chitin synthase activity, 0006031 chitin biosynthetic process
Probab=23.16 E-value=2.1e+02 Score=21.15 Aligned_cols=39 Identities=13% Similarity=0.352 Sum_probs=25.7
Q ss_pred CCeEEEEEEeecCC--ccchHHHHHHHHHHHhcCCCCCe-EEEecC
Q 047575 130 TMTFNVDFAYLESK--REDNYIWALKRLKTIMQDDMLPS-VIVIKR 172 (176)
Q Consensus 130 ~~~~~~~~~~~~~E--~~~s~~w~l~~~~~~~~~~~~p~-~iitD~ 172 (176)
..+.-+-||+=+.. +-.|-.|+|+.|-+.++ |. |++.|-
T Consensus 106 ~~PvQ~ifclKe~N~kKinSHrWfFnaf~~~l~----P~vcvllDv 147 (163)
T PF01644_consen 106 IVPVQIIFCLKEKNAKKINSHRWFFNAFCRQLQ----PNVCVLLDV 147 (163)
T ss_pred CCCEEEEEEeccccccccchhhHHHHHHHhhcC----CcEEEEEec
Confidence 33344445553332 57899999999999885 54 666664
No 84
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=23.07 E-value=77 Score=19.28 Aligned_cols=44 Identities=16% Similarity=0.098 Sum_probs=24.1
Q ss_pred CCCCCHHHHHhhhhhc-cCCCChhHHHHHhhhcCCCccchHHHHHHHHhhcc
Q 047575 31 AGRLTNEEVSTLVDLS-KNNVRPKEIFHTLKTRDTFSVTMMKAICNARYKYK 81 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~-~~g~~~~~I~~~l~~~~~~~~~t~kdi~N~~~k~r 81 (176)
.|+-|+++|..+.... ..|.+..++...+ + +....|+|.+.+++
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~----g---i~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREY----G---ISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHH----T---S-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeeccc----c---cccccccHHHHHHh
Confidence 3567888887766654 5666555555443 2 35667777776653
No 85
>KOG1378 consensus Purple acid phosphatase [Carbohydrate transport and metabolism]
Probab=22.78 E-value=2.1e+02 Score=24.75 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=22.6
Q ss_pred ecCCccchHHHHHHHHHHHhcCCCCCeEEEe
Q 047575 140 LESKREDNYIWALKRLKTIMQDDMLPSVIVI 170 (176)
Q Consensus 140 ~~~E~~~s~~w~l~~~~~~~~~~~~p~~iit 170 (176)
...+..+-|.|+-+.|.++.+. +.|=+|+.
T Consensus 269 ~~~~~~~QY~WL~~dL~~v~r~-~tPWlIv~ 298 (452)
T KOG1378|consen 269 NFLKGTAQYQWLERDLASVDRK-KTPWLIVQ 298 (452)
T ss_pred cccccchHHHHHHHHHHHhccc-CCCeEEEE
Confidence 3456689999999999999862 37766653
No 86
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.26 E-value=1.9e+02 Score=19.44 Aligned_cols=34 Identities=15% Similarity=0.024 Sum_probs=26.4
Q ss_pred ccCCCCCHHHH---HhhhhhccCCCChhHHHHHhhhc
Q 047575 29 SFAGRLTNEEV---STLVDLSKNNVRPKEIFHTLKTR 62 (176)
Q Consensus 29 ~~~r~ls~~~~---~~i~~l~~~g~~~~~I~~~l~~~ 62 (176)
..+|.-++++. ..|..|.+.|++..+|..++...
T Consensus 33 ~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~ 69 (112)
T cd01282 33 NGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCL 69 (112)
T ss_pred CCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 34677787765 56667888999999999998753
No 87
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=22.16 E-value=2.1e+02 Score=23.78 Aligned_cols=16 Identities=25% Similarity=0.144 Sum_probs=12.6
Q ss_pred ceeEEEeeccCCCeEE
Q 047575 119 PLLEIVGVTLTTMTFN 134 (176)
Q Consensus 119 pl~~~~g~~~~~~~~~ 134 (176)
-++.|+|+|+.|+|..
T Consensus 140 ~Vil~vGVNG~GKTTT 155 (340)
T COG0552 140 FVILFVGVNGVGKTTT 155 (340)
T ss_pred EEEEEEecCCCchHhH
Confidence 3566999999998854
No 88
>PRK04217 hypothetical protein; Provisional
Probab=22.09 E-value=2.2e+02 Score=19.47 Aligned_cols=30 Identities=17% Similarity=0.073 Sum_probs=24.1
Q ss_pred CCCCCHHHHHhhhhhccCCCChhHHHHHhh
Q 047575 31 AGRLTNEEVSTLVDLSKNNVRPKEIFHTLK 60 (176)
Q Consensus 31 ~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~ 60 (176)
-.+|++++++.+..+...|++..+|.+.+.
T Consensus 40 ~~~Lt~eereai~l~~~eGlS~~EIAk~LG 69 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGLTQEEAGKRMG 69 (110)
T ss_pred cccCCHHHHHHHHHHHHcCCCHHHHHHHHC
Confidence 468999998666666668999999998874
No 89
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=22.07 E-value=1.1e+02 Score=15.77 Aligned_cols=26 Identities=12% Similarity=0.173 Sum_probs=20.3
Q ss_pred HhhhhhccCCCChhHHHHHhhhcCCC
Q 047575 40 STLVDLSKNNVRPKEIFHTLKTRDTF 65 (176)
Q Consensus 40 ~~i~~l~~~g~~~~~I~~~l~~~~~~ 65 (176)
+.+..|.+.|++..++...|+...++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~~~d 28 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAANGN 28 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 34667777899999999999876653
No 90
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=22.03 E-value=91 Score=25.51 Aligned_cols=31 Identities=26% Similarity=0.206 Sum_probs=27.8
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcC
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRD 63 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~ 63 (176)
.||.+++..|..+.++|++.++|...|....
T Consensus 7 hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~ 37 (318)
T COG2826 7 HLTLFERYEIERLLKAKMSIREIAKQLNRHH 37 (318)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCc
Confidence 7899999999999999999999999886543
No 91
>PF07299 FBP: Fibronectin-binding protein (FBP); InterPro: IPR010841 This entry consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species [,].; PDB: 4ADO_B 4ADN_B 2YB5_F.
Probab=21.95 E-value=39 Score=25.96 Aligned_cols=63 Identities=19% Similarity=0.035 Sum_probs=41.8
Q ss_pred CCCHHHHHhhhhhccCCCChhHHHHHhhhcCC----CccchHHHHHHHHhhccc------------cccceEEeChHhHH
Q 047575 33 RLTNEEVSTLVDLSKNNVRPKEIFHTLKTRDT----FSVTMMKAICNARYKYKV------------CELDIFWAYPLTFE 96 (176)
Q Consensus 33 ~ls~~~~~~i~~l~~~g~~~~~I~~~l~~~~~----~~~~t~kdi~N~~~k~r~------------~i~~if~~~~~~~~ 96 (176)
.+++++++.+..+.+.. .+.++-.+|.+--| -..+|.++|..+..|.++ .+.-+-|.|..+.+
T Consensus 47 ~~~~eq~~ll~~i~~i~-~~~~~~~~L~~L~~yV~pF~~~t~~qi~kLF~K~KKLklP~l~~~d~~~l~YLgW~D~~~~R 125 (208)
T PF07299_consen 47 ELTEEQKELLEQIMDIK-TREEAEKYLEELKPYVIPFPPITEKQIKKLFPKAKKLKLPDLDEIDWDDLDYLGWRDKGSNR 125 (208)
T ss_dssp TTTHHHCCHHHHHTSTT--HHHHHHHHHHHHCCB-------HHHHHHHTTTSSS-----GCCHHCCC-SSEEEEECCCTE
T ss_pred cCCHHHHHHHHHHhccC-CHHHHHHHHHHHHHHhcCCCCCCHHHHHHHhhhhhccCCCCCCCCCcccCceeeeecCCCCc
Confidence 57888888777777777 77888888776433 345789999999888877 45566788765544
No 92
>KOG1370 consensus S-adenosylhomocysteine hydrolase [Coenzyme transport and metabolism]
Probab=21.80 E-value=82 Score=26.10 Aligned_cols=32 Identities=22% Similarity=0.486 Sum_probs=26.2
Q ss_pred cCCccchHHHHHHHHHHHhcCCCCCeEEEecCCC
Q 047575 141 ESKREDNYIWALKRLKTIMQDDMLPSVIVIKREL 174 (176)
Q Consensus 141 ~~E~~~s~~w~l~~~~~~~~~~~~p~~iitD~d~ 174 (176)
..|++|.|.|.+++-.. .++.+|..|+-|.-.
T Consensus 104 kget~ee~~wcie~~~~--~~g~~~nmIlDdggd 135 (434)
T KOG1370|consen 104 KGETEEEYWWCIERCLN--KDGWQPNMILDDGGD 135 (434)
T ss_pred ccccchhhhhhhhhhhc--cCCCCcceeecCCCc
Confidence 46899999999998776 457899999988754
No 93
>KOG1041 consensus Translation initiation factor 2C (eIF-2C) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=21.45 E-value=3.7e+02 Score=25.49 Aligned_cols=69 Identities=20% Similarity=0.196 Sum_probs=45.1
Q ss_pred EEEEeccccccccCc---ceeEEEeeccC-CCeEEEEEEeecCCc-------cchHHHHHHHHHHHhcCCCCCeEEEecC
Q 047575 104 VLIMDCTYKVNKYKF---PLLEIVGVTLT-TMTFNVDFAYLESKR-------EDNYIWALKRLKTIMQDDMLPSVIVIKR 172 (176)
Q Consensus 104 vv~~D~ty~tn~~~~---pl~~~~g~~~~-~~~~~~~~~~~~~E~-------~~s~~w~l~~~~~~~~~~~~p~~iitD~ 172 (176)
++.+|.|+-...... |-...++-+.. .-+.+.|+..+.... .+-+.+++..|.++-+ ..|.-||..|
T Consensus 608 ~IG~dVsHp~~~~~~~~~PSiagvv~s~~~~~~~y~g~~~~Q~~r~e~i~~~~~~~~~~l~~f~~~t~--~~P~~IIiyR 685 (876)
T KOG1041|consen 608 FIGFDVSHPAAGTSFDGNPSIVGVVYNLDWHPQKFAGFVRFQKSRQEVIQDLGEMIRELLRSFRKSTR--KLPDRIVIYR 685 (876)
T ss_pred EEEEeeeCCCcCCCcCCCccEEEEEecccccchhhcceEEEecCChhhhcchHHHHHHHHHHHHHhcc--CCCceEEEEe
Confidence 578899998877766 55544444444 334455665555444 4556677777777754 5999998888
Q ss_pred CC
Q 047575 173 EL 174 (176)
Q Consensus 173 d~ 174 (176)
|-
T Consensus 686 dG 687 (876)
T KOG1041|consen 686 DG 687 (876)
T ss_pred cC
Confidence 74
No 94
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.97 E-value=1e+02 Score=22.01 Aligned_cols=40 Identities=23% Similarity=0.335 Sum_probs=30.8
Q ss_pred cccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHH
Q 047575 110 TYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKT 157 (176)
Q Consensus 110 ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~ 157 (176)
.|+||+|++.++. +. ..+-+.++.+-+..+++=+|+.+=.
T Consensus 63 sy~Ts~Yklhfye----Tp----tglk~vl~Tdpk~~~ir~vLq~IYs 102 (140)
T KOG3368|consen 63 SYKTSKYKLHFYE----TP----TGLKFVLNTDPKAGSIRDVLQYIYS 102 (140)
T ss_pred EEeeceeEEEEEE----cC----CCcEEEEecCCCcccHHHHHHHHHH
Confidence 5899999998873 22 2356778899999999988887655
No 95
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=20.24 E-value=1.2e+02 Score=19.88 Aligned_cols=20 Identities=25% Similarity=0.089 Sum_probs=10.6
Q ss_pred CCCCHHHHHhhhhhccCCCC
Q 047575 32 GRLTNEEVSTLVDLSKNNVR 51 (176)
Q Consensus 32 r~ls~~~~~~i~~l~~~g~~ 51 (176)
..|++++++..+-...+|+.
T Consensus 21 ~~Ls~eE~EL~ELa~~AGv~ 40 (88)
T PF12926_consen 21 KVLSAEEVELYELAQLAGVP 40 (88)
T ss_pred hccCHHHHHHHHHHHHhCCC
Confidence 35777776444433445543
No 96
>PRK02126 ribonuclease Z; Provisional
Probab=20.09 E-value=5e+02 Score=21.33 Aligned_cols=52 Identities=10% Similarity=0.045 Sum_probs=31.0
Q ss_pred cCCceEEEEecCCCCCCCCCCCCccccCCCCCHHHHHhhhhhccCCCChhHHHHHhhh
Q 047575 4 NNQDWMLKVICGLHNHHVAQHLEGHSFAGRLTNEEVSTLVDLSKNNVRPKEIFHTLKT 61 (176)
Q Consensus 4 ~~~~W~i~~~~~~HNH~~~~~~~~h~~~r~ls~~~~~~i~~l~~~g~~~~~I~~~l~~ 61 (176)
+++.+.|+.+-..|.=+...-...-+...++..+ .+.+.|++|--.+..|++
T Consensus 149 ~~~~~~V~a~~~~H~vp~~gy~~~e~~~~~~~~e------k~~~~gi~~g~~~~~Lk~ 200 (334)
T PRK02126 149 DEPWFRVRAAFLDHGIPCLAFALEEKAHINIDKN------RLAELGLPPGPWLRELKH 200 (334)
T ss_pred eCCCEEEEEEEccCCCceeEEEEEecCCcCcCHH------HHHHcCCCCChHHHHHHh
Confidence 4567888888888874322211111222234433 366789999888877775
No 97
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.03 E-value=2.6e+02 Score=21.66 Aligned_cols=68 Identities=16% Similarity=0.074 Sum_probs=38.6
Q ss_pred CcEEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCccchHHHHHHHHHHHhcCCCCCeEEEecCCCC
Q 047575 102 TNVLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKREDNYIWALKRLKTIMQDDMLPSVIVIKRELT 175 (176)
Q Consensus 102 ~dvv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~~s~~w~l~~~~~~~~~~~~p~~iitD~d~a 175 (176)
+++..+|=||-+-+-+. -+..-.+|..|.+.- +=+-..-+...=.-++..+++.. ..|.+|+||+-.+
T Consensus 70 ~~~w~vDEt~ikv~gkw-~ylyrAid~~g~~Ld--~~L~~rRn~~aAk~Fl~kllk~~---g~p~v~vtDka~s 137 (215)
T COG3316 70 GDSWRVDETYIKVNGKW-HYLYRAIDADGLTLD--VWLSKRRNALAAKAFLKKLLKKH---GEPRVFVTDKAPS 137 (215)
T ss_pred ccceeeeeeEEeeccEe-eehhhhhccCCCeEE--EEEEcccCcHHHHHHHHHHHHhc---CCCceEEecCccc
Confidence 57888999995544333 333566676666533 32333323333333444444433 5799999998643
No 98
>cd04659 Piwi_piwi-like_ProArk Piwi_piwi-like_ProArk: PIWI domain, Piwi-like subfamily found in Archaea and Bacteria. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism.
Probab=20.01 E-value=5.2e+02 Score=21.58 Aligned_cols=70 Identities=9% Similarity=-0.056 Sum_probs=34.1
Q ss_pred EEEEeccccccccCcceeEEEeeccCCCeEEEEEEeecCCc--------cchHHHHHHHHHHHhcCCCCCeEEEecCCC
Q 047575 104 VLIMDCTYKVNKYKFPLLEIVGVTLTTMTFNVDFAYLESKR--------EDNYIWALKRLKTIMQDDMLPSVIVIKREL 174 (176)
Q Consensus 104 vv~~D~ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~--------~~s~~w~l~~~~~~~~~~~~p~~iitD~d~ 174 (176)
++.+|.++..+...........++..|.+..+.-.-...+. .+.+.-+++.+++... ...|+-||.-+|.
T Consensus 192 iIGidv~~~~~~~~~~~~~a~vf~~~g~g~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~y~~~~~-~~~P~rIiihrdg 269 (404)
T cd04659 192 YIGIGFARSRDGEVRVTGCAQVFDSDGLGLILRGAPIEEPTEDRSPADLKDLLKRVLEGYRESHR-GRDPKRLVLHKDG 269 (404)
T ss_pred EEEEEEEEcCCCCEEEEEEEEEEcCCCCEEEEecCccCCcccccCHHHHHHHHHHHHHHHHHHcC-CCCCeEEEEECCC
Confidence 57888888776422222333335666644444322222222 2333334444444443 2488877766553
Done!