Query 040570
Match_columns 210
No_of_seqs 130 out of 765
Neff 9.2
Searched_HMMs 46136
Date Fri Mar 29 09:41:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040570.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040570hhsearch_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 8.1E-42 1.7E-46 306.3 16.9 186 2-210 170-362 (846)
2 PF10551 MULE: MULE transposas 99.7 6.1E-18 1.3E-22 115.3 4.7 68 140-210 1-71 (93)
3 PF00872 Transposase_mut: Tran 98.2 1.3E-06 2.8E-11 74.2 3.4 141 30-210 96-242 (381)
4 PF00665 rve: Integrase core d 94.4 0.24 5.1E-06 34.3 6.8 71 134-207 7-79 (120)
5 COG3328 Transposase and inacti 94.2 0.45 9.8E-06 40.5 9.2 129 37-208 89-219 (379)
6 PF08069 Ribosomal_S13_N: Ribo 93.9 0.1 2.3E-06 32.0 3.6 34 30-63 25-59 (60)
7 PRK08561 rps15p 30S ribosomal 90.6 1.9 4E-05 31.7 7.1 33 31-63 26-59 (151)
8 PF13936 HTH_38: Helix-turn-he 88.4 0.35 7.7E-06 27.6 1.7 29 30-58 2-30 (44)
9 PTZ00072 40S ribosomal protein 86.8 4.1 9E-05 29.6 6.7 32 32-63 24-56 (148)
10 PF13610 DDE_Tnp_IS240: DDE do 86.8 0.17 3.6E-06 36.8 -0.4 72 133-209 1-72 (140)
11 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 80.0 2.7 5.9E-05 24.8 2.9 29 31-59 3-31 (50)
12 PF02796 HTH_7: Helix-turn-hel 78.4 2.5 5.5E-05 24.1 2.5 39 31-76 4-42 (45)
13 TIGR03147 cyt_nit_nrfF cytochr 76.5 5.5 0.00012 28.4 4.2 34 32-65 57-90 (126)
14 PF04218 CENP-B_N: CENP-B N-te 76.1 6.3 0.00014 23.4 3.8 47 30-80 4-50 (53)
15 PF13082 DUF3931: Protein of u 70.9 10 0.00022 22.4 3.7 42 133-174 8-62 (66)
16 PRK10144 formate-dependent nit 70.8 9.2 0.0002 27.3 4.2 34 32-65 57-90 (126)
17 PF10045 DUF2280: Uncharacteri 70.7 21 0.00046 24.4 5.7 40 32-72 3-42 (104)
18 COG3915 Uncharacterized protei 69.9 22 0.00047 25.7 5.8 66 89-162 68-135 (155)
19 PRK14702 insertion element IS2 67.1 38 0.00083 27.3 7.7 71 134-205 88-162 (262)
20 KOG0400 40S ribosomal protein 66.1 2.9 6.2E-05 29.8 0.8 34 30-63 25-59 (151)
21 PHA02517 putative transposase 62.8 29 0.00064 27.9 6.3 69 134-207 111-181 (277)
22 PF13384 HTH_23: Homeodomain-l 61.5 11 0.00025 21.5 2.8 39 36-81 5-43 (50)
23 PF03918 CcmH: Cytochrome C bi 60.7 8.5 0.00018 28.3 2.5 33 33-65 58-90 (148)
24 PF00292 PAX: 'Paired box' dom 60.1 14 0.00029 26.4 3.4 33 30-62 15-47 (125)
25 PRK09409 IS2 transposase TnpB; 60.0 64 0.0014 26.6 7.9 71 134-205 127-201 (301)
26 KOG0149 Predicted RNA-binding 58.6 37 0.00079 27.0 5.8 44 123-182 27-70 (247)
27 PF06056 Terminase_5: Putative 58.6 39 0.00084 20.5 5.7 42 37-85 2-43 (58)
28 PF10264 Stork_head: Winged he 57.3 44 0.00095 21.8 5.1 48 32-79 11-61 (80)
29 PF04937 DUF659: Protein of un 57.0 48 0.001 24.4 6.0 77 130-210 30-108 (153)
30 PF13565 HTH_32: Homeodomain-l 55.8 46 0.001 20.8 5.2 44 31-75 30-76 (77)
31 smart00351 PAX Paired Box doma 55.7 51 0.0011 23.3 5.8 45 30-81 15-59 (125)
32 cd04769 HTH_MerR2 Helix-Turn-H 53.4 73 0.0016 22.0 8.0 35 28-62 33-70 (116)
33 KOG0121 Nuclear cap-binding pr 53.3 39 0.00085 24.3 4.7 73 116-207 42-116 (153)
34 cd01110 HTH_SoxR Helix-Turn-He 53.1 84 0.0018 22.6 8.0 32 29-60 35-69 (139)
35 cd00131 PAX Paired Box domain 52.7 60 0.0013 23.1 5.8 46 29-81 14-59 (128)
36 PF06135 DUF965: Bacterial pro 50.4 68 0.0015 20.8 5.1 49 42-95 26-75 (79)
37 PF12554 MOZART1: Mitotic-spin 50.2 50 0.0011 19.3 4.1 31 30-60 16-46 (48)
38 PF06163 DUF977: Bacterial pro 50.0 76 0.0016 22.7 5.7 56 30-104 2-57 (127)
39 PF13551 HTH_29: Winged helix- 47.1 84 0.0018 20.9 6.0 45 33-78 58-110 (112)
40 PF11293 DUF3094: Protein of u 43.7 32 0.00069 20.6 2.6 21 31-51 2-22 (55)
41 cd08309 Death_IRAK Death domai 43.5 98 0.0021 20.7 6.7 66 31-100 4-71 (95)
42 COG4472 Uncharacterized protei 42.3 96 0.0021 20.2 5.8 53 42-99 29-83 (88)
43 PF15299 ALS2CR8: Amyotrophic 41.9 1.1E+02 0.0025 24.0 6.4 67 13-81 139-222 (225)
44 PF15652 Tox-SHH: HNH/Endo VII 41.9 35 0.00075 23.3 2.9 24 39-62 73-96 (100)
45 KOG3517 Transcription factor P 41.8 22 0.00047 28.4 2.2 34 30-63 18-51 (334)
46 KOG4027 Uncharacterized conser 41.2 38 0.00082 25.2 3.2 37 137-173 69-108 (187)
47 PF02171 Piwi: Piwi domain; I 40.8 1.9E+02 0.004 23.5 7.8 70 135-205 79-157 (302)
48 PF08671 SinI: Anti-repressor 40.6 56 0.0012 17.0 3.5 25 35-59 3-27 (30)
49 PF03106 WRKY: WRKY DNA -bindi 40.4 25 0.00055 21.5 1.9 17 3-19 43-59 (60)
50 cd02826 Piwi-like Piwi-like: P 40.2 1.9E+02 0.0041 24.8 7.9 68 135-204 174-251 (393)
51 COG1710 Uncharacterized protei 38.6 1.1E+02 0.0024 21.6 5.0 44 31-81 92-135 (139)
52 cd01104 HTH_MlrA-CarA Helix-Tu 36.9 96 0.0021 18.7 4.6 30 29-58 35-67 (68)
53 PRK05473 hypothetical protein; 36.5 1.3E+02 0.0027 19.9 5.6 48 43-95 30-78 (86)
54 PF04814 HNF-1_N: Hepatocyte n 35.8 26 0.00057 26.6 1.8 31 32-62 4-34 (180)
55 PRK07708 hypothetical protein; 35.1 2.2E+02 0.0048 22.3 11.4 109 92-205 31-151 (219)
56 COG3316 Transposase and inacti 35.1 52 0.0011 25.8 3.3 116 46-207 23-138 (215)
57 KOG3368 Transport protein part 34.8 31 0.00067 24.8 1.9 41 141-189 63-103 (140)
58 COG0046 PurL Phosphoribosylfor 34.0 28 0.0006 32.5 2.0 21 4-24 92-112 (743)
59 COG0735 Fur Fe2+/Zn2+ uptake r 34.0 1.8E+02 0.004 21.0 6.1 57 43-103 11-71 (145)
60 cd06222 RnaseH RNase H (RNase 33.7 1.4E+02 0.003 19.6 6.7 71 135-206 1-73 (130)
61 KOG3862 Transcription factor P 32.7 63 0.0014 26.3 3.5 34 30-63 23-56 (327)
62 PF04684 BAF1_ABF1: BAF1 / ABF 31.6 82 0.0018 27.7 4.2 23 4-26 164-186 (496)
63 PF01527 HTH_Tnp_1: Transposas 30.8 94 0.002 19.2 3.6 44 30-80 4-48 (76)
64 cd04657 Piwi_ago-like Piwi_ago 30.5 3.1E+02 0.0068 23.8 7.8 69 135-205 201-279 (426)
65 PF01644 Chitin_synth_1: Chiti 30.3 1.1E+02 0.0025 22.8 4.4 40 160-203 105-147 (163)
66 PF12017 Tnp_P_element: Transp 30.1 2.7E+02 0.0058 22.2 6.7 151 30-206 69-222 (236)
67 PRK13907 rnhA ribonuclease H; 29.8 1.9E+02 0.0042 20.0 7.8 68 135-204 3-71 (128)
68 PF06755 DUF1219: Protein of u 29.6 1.6E+02 0.0034 20.5 4.5 27 37-63 45-71 (114)
69 PHA00675 hypothetical protein 28.9 1.5E+02 0.0033 19.2 4.1 39 32-77 22-61 (78)
70 smart00422 HTH_MERR helix_turn 27.4 1.5E+02 0.0032 17.9 4.7 31 29-59 35-68 (70)
71 TIGR03676 aRF1/eRF1 peptide ch 27.3 4.1E+02 0.0089 23.0 9.4 28 180-207 118-145 (403)
72 PRK03573 transcriptional regul 27.3 2.3E+02 0.005 20.1 6.7 76 44-130 24-101 (144)
73 PF14420 Clr5: Clr5 domain 27.1 1.4E+02 0.0031 17.6 5.5 38 36-74 7-45 (54)
74 PF05066 HARE-HTH: HB1, ASXL, 26.2 1.6E+02 0.0034 18.2 4.0 38 54-93 7-44 (72)
75 PF12926 MOZART2: Mitotic-spin 26.0 1.5E+02 0.0032 19.8 3.8 19 32-50 22-40 (88)
76 PF13411 MerR_1: MerR HTH fami 25.0 90 0.0019 18.9 2.7 31 30-60 35-68 (69)
77 cd01105 HTH_GlnR-like Helix-Tu 24.9 2E+02 0.0044 18.7 4.8 34 29-62 36-72 (88)
78 PF06720 Phi-29_GP16_7: Bacter 24.7 2.5E+02 0.0054 19.6 5.5 45 33-80 68-113 (130)
79 cd04764 HTH_MlrA-like_sg1 Heli 24.6 1.3E+02 0.0028 18.2 3.4 30 29-58 34-66 (67)
80 COG2826 Tra8 Transposase and i 24.3 89 0.0019 25.9 3.1 32 32-63 7-38 (318)
81 cd00569 HTH_Hin_like Helix-tur 23.6 1E+02 0.0023 14.8 3.8 28 31-58 4-31 (42)
82 KOG3095 Transcription initiati 23.5 2.8E+02 0.0062 22.7 5.7 39 86-125 165-203 (284)
83 PRK14994 SAM-dependent 16S rib 23.4 2.2E+02 0.0047 23.4 5.3 32 44-78 252-283 (287)
84 cd04763 HTH_MlrA-like Helix-Tu 23.3 1.7E+02 0.0038 17.7 3.8 30 29-58 35-67 (68)
85 PF12762 DDE_Tnp_IS1595: ISXO2 23.3 2.8E+02 0.0061 19.7 6.1 48 153-207 37-86 (151)
86 cd01109 HTH_YyaN Helix-Turn-He 23.1 2.5E+02 0.0055 19.1 7.4 34 29-62 35-71 (113)
87 TIGR02043 ZntR Zn(II)-responsi 22.8 2.8E+02 0.0061 19.6 6.9 33 29-61 36-71 (131)
88 PF00196 GerE: Bacterial regul 22.7 1.7E+02 0.0038 17.1 5.6 42 32-81 3-44 (58)
89 PF03564 DUF1759: Protein of u 22.0 2.1E+02 0.0046 20.2 4.6 35 31-65 36-70 (145)
90 cd01903 Ntn_AC_NAAA AC_NAAA Th 21.6 2.7E+02 0.0058 21.9 5.3 52 3-61 162-213 (231)
91 TIGR02047 CadR-PbrR Cd(II)/Pb( 21.6 3E+02 0.0064 19.3 7.5 33 29-61 35-70 (127)
92 PLN03134 glycine-rich RNA-bind 21.4 2.5E+02 0.0054 20.2 4.8 48 123-186 49-96 (144)
93 PF09713 A_thal_3526: Plant pr 21.0 2E+02 0.0044 17.2 4.7 42 39-80 3-44 (54)
94 PF01402 RHH_1: Ribbon-helix-h 20.7 95 0.0021 16.5 1.9 29 32-60 5-34 (39)
95 KOG2599 Pyridoxal/pyridoxine/p 20.7 4.9E+02 0.011 21.5 8.5 32 6-41 37-70 (308)
96 TIGR00625 tfb2 Transcription f 20.4 6E+02 0.013 22.5 8.9 24 39-62 336-359 (448)
97 PRK09413 IS2 repressor TnpA; R 20.4 3.1E+02 0.0066 19.0 5.8 46 30-82 10-56 (121)
98 TIGR01950 SoxR redox-sensitive 20.2 3.4E+02 0.0075 19.6 7.9 32 29-60 35-69 (142)
99 TIGR00824 EIIA-man PTS system, 20.0 2.7E+02 0.0059 19.2 4.6 38 165-203 30-67 (116)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=8.1e-42 Score=306.31 Aligned_cols=186 Identities=17% Similarity=0.210 Sum_probs=152.1
Q ss_pred CCCCCcEEEEecCCCCCCCCCCCccccccCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCC---CcchHhHHhHHHHH
Q 040570 2 ENNDDWALIVKYGFHNHLATQYLEGHSFAGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMH---NATTIRAIYNARQK 78 (210)
Q Consensus 2 ~~~~~W~v~~~~~~HNH~~~~~~~~h~~~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~---~~~t~~di~N~~~k 78 (210)
..+|+|.|+.++.+|||||.++...+ ..++.++..+.+..++ ...+..|..|...+
T Consensus 170 ~~~gkW~V~~fv~eHNH~L~p~~~~~---------------------~~~r~~~~~~~~~~~~~~~v~~~~~d~~~~~~~ 228 (846)
T PLN03097 170 RPDGKWVIHSFVKEHNHELLPAQAVS---------------------EQTRKMYAAMARQFAEYKNVVGLKNDSKSSFDK 228 (846)
T ss_pred cCCCeEEEEEEecCCCCCCCCccccc---------------------hhhhhhHHHHHhhhhccccccccchhhcchhhH
Confidence 46899999999999999998664311 1123333333332221 12344566666555
Q ss_pred HhhhhcccchHHHHHHHHhhc----cceeEEEeeecCCCceEEEEEeChhhHHHHHhCCcEEEEecccccCcCCCceeeE
Q 040570 79 YKVREQVGHSQMQLLMSKLIE----QKYIERHKSDVDTNCVKALFLAHPSAIELLQAFPRVLIMDCTYKTNRYDMPLLEI 154 (210)
Q Consensus 79 ~~~~~~~g~~~~~~L~~~l~~----~~~~~~~~~~d~~~~~~~lf~a~~~~~~~~~~f~~vl~~D~Ty~tn~~~~pl~~~ 154 (210)
.++..+. ..+++.|+++|++ +|.|||.+++|++|++++|||+++.|+..|..|||||.||+||+||+|+|||+.|
T Consensus 229 ~r~~~~~-~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~F 307 (846)
T PLN03097 229 GRNLGLE-AGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALF 307 (846)
T ss_pred HHhhhcc-cchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEEEEE
Confidence 5544443 3478889988864 4678899999999999999999999999999999999999999999999999999
Q ss_pred EeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcCCCCeEEEecCcccCCCC
Q 040570 155 AGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELAWHPV 210 (210)
Q Consensus 155 ~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~p~~iitD~d~al~~~ 210 (210)
+|+|+|+++++|||||+.+|+.|||.|+|++|+++|+ ++.|++||||+|.||.+|
T Consensus 308 vGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~-gk~P~tIiTDqd~am~~A 362 (846)
T PLN03097 308 VGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMG-GQAPKVIITDQDKAMKSV 362 (846)
T ss_pred EEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhC-CCCCceEEecCCHHHHHH
Confidence 9999999999999999999999999999999999997 799999999999999765
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=99.72 E-value=6.1e-18 Score=115.32 Aligned_cols=68 Identities=35% Similarity=0.520 Sum_probs=63.7
Q ss_pred cccccCcCCCceee---EEeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcCCCCeEEEecCcccCCCC
Q 040570 140 CTYKTNRYDMPLLE---IAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELAWHPV 210 (210)
Q Consensus 140 ~Ty~tn~~~~pl~~---~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~p~~iitD~d~al~~~ 210 (210)
+||+||+| +|++. ++|+|++++++++||+++++|++++|.|+|+.+++.+.. . |++||||+|.|+++|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~-~-p~~ii~D~~~~~~~A 71 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ-K-PKVIISDFDKALINA 71 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc-C-ceeeeccccHHHHHH
Confidence 69999999 88886 999999999999999999999999999999999999974 5 999999999999765
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=98.17 E-value=1.3e-06 Score=74.23 Aligned_cols=141 Identities=12% Similarity=0.043 Sum_probs=102.3
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhccceeEEEeee
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQKYIERHKSD 109 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~~~~~~~~~~ 109 (210)
.++.+++.-+.|..|...|+++++|-..|.+.+|+..+....|.+....... -++.++..+
T Consensus 96 y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~-----------~~~~w~~R~-------- 156 (381)
T PF00872_consen 96 YQRREDSLEELIISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDE-----------EVEAWRNRP-------- 156 (381)
T ss_pred hhhhhhhhhhhhhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhh-----------hHHHHhhhc--------
Confidence 4444566667788889999999999999999888444555556555444321 112222211
Q ss_pred cCCCceEEEEEeChhhHHHHHhC-CcEEEEecccccCc-----CCCceeeEEeeecCCceEEEEEEeecCccchhHHHHH
Q 040570 110 VDTNCVKALFLAHPSAIELLQAF-PRVLIMDCTYKTNR-----YDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWAL 183 (210)
Q Consensus 110 d~~~~~~~lf~a~~~~~~~~~~f-~~vl~~D~Ty~tn~-----~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l 183 (210)
+... -++|.+|++|-+-+ -+.++++++|++..|+-.++|+.....|+.++|.-+|
T Consensus 157 -------------------L~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l 217 (381)
T PF00872_consen 157 -------------------LESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFL 217 (381)
T ss_pred -------------------cccccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecc
Confidence 1111 13788899987644 2467899999999999999999999999999999999
Q ss_pred HHHHHHHhcCCCCeEEEecCcccCCCC
Q 040570 184 ERLKSIMEENMLASVIVTDRELAWHPV 210 (210)
Q Consensus 184 ~~~~~~~~~~~~p~~iitD~d~al~~~ 210 (210)
+.|++- .-..|..||+|...+|.+|
T Consensus 218 ~~L~~R--Gl~~~~lvv~Dg~~gl~~a 242 (381)
T PF00872_consen 218 QDLKER--GLKDILLVVSDGHKGLKEA 242 (381)
T ss_pred hhhhhc--cccccceeecccccccccc
Confidence 998764 2356899999999999765
No 4
>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=94.39 E-value=0.24 Score=34.33 Aligned_cols=71 Identities=13% Similarity=-0.044 Sum_probs=45.5
Q ss_pred cEEEEeccccc-CcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcCCC-CeEEEecCcccC
Q 040570 134 RVLIMDCTYKT-NRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENML-ASVIVTDRELAW 207 (210)
Q Consensus 134 ~vl~~D~Ty~t-n~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~-p~~iitD~d~al 207 (210)
+.+.+|.+... ...+...+..+.+|...+-.. ++.+-..++.+.+..+|.......+ .. |++|+||+..+.
T Consensus 7 ~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~--~~~p~~i~tD~g~~f 79 (120)
T PF00665_consen 7 ERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFIY-AFPVSSKETAEAALRALKRAIEKRG--GRPPRVIRTDNGSEF 79 (120)
T ss_dssp TEEEEEEEEETGGCTT-CEEEEEEEETTTTEEE-EEEESSSSHHHHHHHHHHHHHHHHS---SE-SEEEEESCHHH
T ss_pred CEEEEeeEEEecCCCCccEEEEEEEECCCCcEE-EEEeecccccccccccccccccccc--cccceeccccccccc
Confidence 58889988433 344556777777777766554 5666556566666666665555443 44 999999998764
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=94.22 E-value=0.45 Score=40.50 Aligned_cols=129 Identities=12% Similarity=0.021 Sum_probs=80.1
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhccceeEEEeeecCCCceE
Q 040570 37 KSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQKYIERHKSDVDTNCVK 116 (210)
Q Consensus 37 ~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~~~~~~~~~~d~~~~~~ 116 (210)
.-..|..|...|+++++|-..+++.++. .+. .+.+...... +.+-+..++..+- .
T Consensus 89 ~~~~v~~~y~~gv~Tr~i~~~~~~~~~~-~~s-~~~iS~~~~~----------~~e~v~~~~~r~l--~----------- 143 (379)
T COG3328 89 LDLPVLSMYAKGVTTREIEALLEELYGH-KVS-PSVISVVTDR----------LDEKVKAWQNRPL--G----------- 143 (379)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHhhCc-ccC-HHHhhhHHHH----------HHHHHHHHHhccc--c-----------
Confidence 3445667889999999999999988753 222 2222222211 1111222222211 0
Q ss_pred EEEEeChhhHHHHHhCCcEEEEecccccCc--CCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcCC
Q 040570 117 ALFLAHPSAIELLQAFPRVLIMDCTYKTNR--YDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENM 194 (210)
Q Consensus 117 ~lf~a~~~~~~~~~~f~~vl~~D~Ty~tn~--~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~ 194 (210)
--.++.+|++|.+=+ -+..++.++|++..|+-.++++.+-.+|. ..|.-++.-|+.- + -.
T Consensus 144 ---------------~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-g-l~ 205 (379)
T COG3328 144 ---------------DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-G-LS 205 (379)
T ss_pred ---------------CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-c-cc
Confidence 012678899988777 56778899999999999999999999998 6665444444332 1 12
Q ss_pred CCeEEEecCcccCC
Q 040570 195 LASVIVTDRELAWH 208 (210)
Q Consensus 195 ~p~~iitD~d~al~ 208 (210)
.-..+++|.-.++-
T Consensus 206 ~v~l~v~Dg~~gl~ 219 (379)
T COG3328 206 DVLLVVVDGLKGLP 219 (379)
T ss_pred ceeEEecchhhhhH
Confidence 23456668776654
No 6
>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=93.93 E-value=0.1 Score=31.98 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=26.1
Q ss_pred cCCCCH-HHHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 30 AGILNK-EKSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 30 ~R~lt~-~~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
.-++++ +..+.|..|.+.|++|.+|-.+|++++|
T Consensus 25 W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~~G 59 (60)
T PF08069_consen 25 WLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYG 59 (60)
T ss_dssp T--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHSCT
T ss_pred CcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhccC
Confidence 335665 4556688999999999999999999986
No 7
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=90.56 E-value=1.9 Score=31.66 Aligned_cols=33 Identities=18% Similarity=0.231 Sum_probs=27.4
Q ss_pred CCCCHH-HHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 31 GILNKE-KSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 31 R~lt~~-~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
-+.+++ ..+.|..|.+.|++|++|--.|++++|
T Consensus 26 ~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~g 59 (151)
T PRK08561 26 VDYSPEEIEELVVELAKQGYSPSMIGIILRDQYG 59 (151)
T ss_pred ccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccC
Confidence 456654 455688999999999999999999995
No 8
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=88.37 E-value=0.35 Score=27.64 Aligned_cols=29 Identities=14% Similarity=0.203 Sum_probs=14.3
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHH
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVL 58 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l 58 (210)
.++||++++..|..|.+.|.+.++|-..|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~l 30 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRL 30 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHT
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 36799999999999999999999997765
No 9
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=86.84 E-value=4.1 Score=29.63 Aligned_cols=32 Identities=13% Similarity=0.263 Sum_probs=26.5
Q ss_pred CCCHH-HHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 32 ILNKE-KSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 32 ~lt~~-~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
+.+++ ..+.|..|.+.|++|++|-..|++++|
T Consensus 24 ~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~g 56 (148)
T PTZ00072 24 KLSSSEVEDQICKLAKKGLTPSQIGVILRDSMG 56 (148)
T ss_pred cCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccC
Confidence 45554 556688999999999999999999994
No 10
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=86.81 E-value=0.17 Score=36.81 Aligned_cols=72 Identities=17% Similarity=-0.043 Sum_probs=51.9
Q ss_pred CcEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcCCCCeEEEecCcccCCC
Q 040570 133 PRVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDRELAWHP 209 (210)
Q Consensus 133 ~~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~p~~iitD~d~al~~ 209 (210)
++.+.+|=||-+=+-. -.+....+|..++ ++.+-+....+...=..+|+.+++... ..|..|+||+-.+...
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~--~~p~~ivtDk~~aY~~ 72 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR--GEPRVIVTDKLPAYPA 72 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec--cccceeecccCCccch
Confidence 4678889898553322 3455788888888 667777777777777777777666653 6899999999887644
No 11
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=80.00 E-value=2.7 Score=24.79 Aligned_cols=29 Identities=7% Similarity=0.101 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHH
Q 040570 31 GILNKEKSNLLVDMSKNNVRPKDVLHVLK 59 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~~g~~p~~I~~~l~ 59 (210)
..||+.++++|+.|.+.|++-++|-..+.
T Consensus 3 ~~Lt~~Eqaqid~m~qlG~s~~~isr~i~ 31 (50)
T PF11427_consen 3 KTLTDAEQAQIDVMHQLGMSLREISRRIG 31 (50)
T ss_dssp ----HHHHHHHHHHHHTT--HHHHHHHHT
T ss_pred CcCCHHHHHHHHHHHHhchhHHHHHHHhC
Confidence 35899999999999999999999877664
No 12
>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=78.43 E-value=2.5 Score=24.08 Aligned_cols=39 Identities=10% Similarity=0.158 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHH
Q 040570 31 GILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNAR 76 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~ 76 (210)
+.+++++.++|..|.+.|.+..+|...+ + +....||.+.
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~----g---vsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQF----G---VSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHHT----T---S-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHH----C---cCHHHHHHHH
Confidence 4678888899999999999888885553 2 4455566553
No 13
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=76.46 E-value=5.5 Score=28.43 Aligned_cols=34 Identities=6% Similarity=0.072 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCC
Q 040570 32 ILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHN 65 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~ 65 (210)
.+..+++.+|..+...|-+..+|++++.+++|+.
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 5666788888888889999999999999999864
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=76.14 E-value=6.3 Score=23.39 Aligned_cols=47 Identities=13% Similarity=0.153 Sum_probs=31.2
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHh
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYK 80 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~ 80 (210)
.+.||.++|..|..+.+.|.+.+.| .+.+|-...|..+|..-+.+..
T Consensus 4 R~~LTl~eK~~iI~~~e~g~s~~~i----a~~fgv~~sTv~~I~K~k~~i~ 50 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGESKRDI----AREFGVSRSTVSTILKNKDKIL 50 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT-HHHH----HHHHT--CCHHHHHHHCHHHHC
T ss_pred CccCCHHHHHHHHHHHHcCCCHHHH----HHHhCCCHHHHHHHHHhHHHHH
Confidence 3569999999999999999865555 5556644578888877666543
No 15
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=70.87 E-value=10 Score=22.38 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=24.2
Q ss_pred CcEEEEeccc-ccCcCCCcee------------eEEeeecCCceEEEEEEeecCc
Q 040570 133 PRVLIMDCTY-KTNRYDMPLL------------EIAGVTSIDLTFSVCCVYLKLK 174 (210)
Q Consensus 133 ~~vl~~D~Ty-~tn~~~~pl~------------~~~g~~~~~~~~~~~~~~~~~E 174 (210)
++|++||+.- +...|.+|-+ +.+|.+..|+..++..-+-.+|
T Consensus 8 cnvisidgkkkksdtysypklvvenktyefssfvlcgetpdgrrlvlthmistde 62 (66)
T PF13082_consen 8 CNVISIDGKKKKSDTYSYPKLVVENKTYEFSSFVLCGETPDGRRLVLTHMISTDE 62 (66)
T ss_pred ccEEEeccccccCCcccCceEEEeCceEEEEEEEEEccCCCCcEEEEEEEecchh
Confidence 5678888753 4445666654 4556666666655544444333
No 16
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=70.80 E-value=9.2 Score=27.29 Aligned_cols=34 Identities=6% Similarity=0.027 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCC
Q 040570 32 ILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHN 65 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~ 65 (210)
.+..+++.+|..+...|-+..+|++++.+++|+.
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 4556778888888888888888888888888864
No 17
>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=70.74 E-value=21 Score=24.43 Aligned_cols=40 Identities=18% Similarity=0.165 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHH
Q 040570 32 ILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAI 72 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di 72 (210)
.|+++.|.+|+....+=-+|.++.+.+++.|| ..++...+
T Consensus 3 ~L~~~vK~FIVQ~LAcfdTPs~v~~aVk~eFg-i~vsrQqv 42 (104)
T PF10045_consen 3 ALKKEVKAFIVQSLACFDTPSEVAEAVKEEFG-IDVSRQQV 42 (104)
T ss_pred CccHHHHHHHHHHHHhhCCHHHHHHHHHHHhC-CccCHHHH
Confidence 58899999999988888899999999999997 33444443
No 18
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.87 E-value=22 Score=25.75 Aligned_cols=66 Identities=15% Similarity=0.051 Sum_probs=44.6
Q ss_pred HHHHHHHHhhccceeEEEeeecCCCceEEEEEeChhhHHHHHhCCcEE--EEecccccCcCCCceeeEEeeecCCc
Q 040570 89 QMQLLMSKLIEQKYIERHKSDVDTNCVKALFLAHPSAIELLQAFPRVL--IMDCTYKTNRYDMPLLEIAGVTSIDL 162 (210)
Q Consensus 89 ~~~~L~~~l~~~~~~~~~~~~d~~~~~~~lf~a~~~~~~~~~~f~~vl--~~D~Ty~tn~~~~pl~~~~g~~~~~~ 162 (210)
.+..|++.+..++.-.-.+..++ ++-.-..+.+++|.+++ -.|+.|++-|.++||+.+.-.++..+
T Consensus 68 sls~Ll~~l~ak~tslt~iALNd--------Y~a~Ip~sDi~kynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 68 SLSALLAWLGAKQTSLTVIALND--------YWAEIPYSDIEKYNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred eHHHHHHHhhccCcceEEEEecc--------eeccCcHHHhhhcccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 36778888875543211122111 22234567889999865 57999999999999999988877653
No 19
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=67.10 E-value=38 Score=27.26 Aligned_cols=71 Identities=7% Similarity=-0.242 Sum_probs=45.8
Q ss_pred cEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecC-ccchhHHHHHHHHHHHH-h--cCCCCeEEEecCcc
Q 040570 134 RVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKL-KWENNYIWALERLKSIM-E--ENMLASVIVTDREL 205 (210)
Q Consensus 134 ~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~-E~~e~~~w~l~~~~~~~-~--~~~~p~~iitD~d~ 205 (210)
.++..|-||-...-+.-++..+.+|.+.+ .++|+++-.. .+.+...-+|....+.. + ....|..|.||+-.
T Consensus 88 ~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gs 162 (262)
T PRK14702 88 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 162 (262)
T ss_pred CEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCc
Confidence 59999999865544545777777887777 6668888764 45555555555433332 2 12456788999754
No 20
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=66.12 E-value=2.9 Score=29.82 Aligned_cols=34 Identities=12% Similarity=0.203 Sum_probs=29.0
Q ss_pred cCCCC-HHHHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 30 AGILN-KEKSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 30 ~R~lt-~~~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
.-+++ ++.+++|..|.+-|++|.||--.|++.+|
T Consensus 25 WlK~~~ddvkeqI~K~akKGltpsqIGviLRDshG 59 (151)
T KOG0400|consen 25 WLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHG 59 (151)
T ss_pred HHhcCHHHHHHHHHHHHHcCCChhHceeeeecccC
Confidence 33455 46889999999999999999999999887
No 21
>PHA02517 putative transposase OrfB; Reviewed
Probab=62.84 E-value=29 Score=27.85 Aligned_cols=69 Identities=10% Similarity=-0.004 Sum_probs=41.9
Q ss_pred cEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcCCCC--eEEEecCcccC
Q 040570 134 RVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLA--SVIVTDRELAW 207 (210)
Q Consensus 134 ~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~p--~~iitD~d~al 207 (210)
+++..|-||-...-+ -.+..+.+|...+- ++|+.+...++.+. ++..|..++.....| ..|.||+-...
T Consensus 111 ~~w~~D~t~~~~~~g-~~yl~~iiD~~sr~-i~~~~~~~~~~~~~---~~~~l~~a~~~~~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 111 QLWVADFTYVSTWQG-WVYVAFIIDVFARR-IVGWRVSSSMDTDF---VLDALEQALWARGRPGGLIHHSDKGSQY 181 (277)
T ss_pred CeEEeceeEEEeCCC-CEEEEEecccCCCe-eeecccCCCCChHH---HHHHHHHHHHhcCCCcCcEeeccccccc
Confidence 589999998654434 34556666666654 45677766666664 445555555322234 36679986543
No 22
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=61.46 E-value=11 Score=21.50 Aligned_cols=39 Identities=10% Similarity=0.318 Sum_probs=20.7
Q ss_pred HHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhh
Q 040570 36 EKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKV 81 (210)
Q Consensus 36 ~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~ 81 (210)
+.+..|..+...|.+.++|...+ .++...|++.+.+++.
T Consensus 5 ~~R~~ii~l~~~G~s~~~ia~~l-------gvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 5 ERRAQIIRLLREGWSIREIAKRL-------GVSRSTVYRWIKRYRE 43 (50)
T ss_dssp -----HHHHHHHT--HHHHHHHH-------TS-HHHHHHHHT----
T ss_pred hHHHHHHHHHHCCCCHHHHHHHH-------CcCHHHHHHHHHHccc
Confidence 45666777766699999997775 2566788888888764
No 23
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=60.68 E-value=8.5 Score=28.30 Aligned_cols=33 Identities=6% Similarity=0.159 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCC
Q 040570 33 LNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHN 65 (210)
Q Consensus 33 lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~ 65 (210)
+..+++.+|..+...|.+..+|++++.++||+.
T Consensus 58 ~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG~~ 90 (148)
T PF03918_consen 58 IARDMRREIREMLAEGKSDEEIIDYFVERYGEF 90 (148)
T ss_dssp HHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCcc
Confidence 445677778888888888888888888888764
No 24
>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=60.14 E-value=14 Score=26.41 Aligned_cols=33 Identities=27% Similarity=0.421 Sum_probs=24.5
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhC
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRN 62 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~ 62 (210)
-|.|..+.+..|..|...|++|.+|-..|.-.+
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 478999999999999999999999977775444
No 25
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=60.05 E-value=64 Score=26.56 Aligned_cols=71 Identities=7% Similarity=-0.184 Sum_probs=45.8
Q ss_pred cEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecC-ccchhHHHHHHH-HHHHHhc--CCCCeEEEecCcc
Q 040570 134 RVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKL-KWENNYIWALER-LKSIMEE--NMLASVIVTDREL 205 (210)
Q Consensus 134 ~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~-E~~e~~~w~l~~-~~~~~~~--~~~p~~iitD~d~ 205 (210)
.++..|-||-...-+.-++..+.+|..++ .++|+++-.. .+.+...-+|+. +....+. ...|..|-||+-.
T Consensus 127 ~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGs 201 (301)
T PRK09409 127 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 201 (301)
T ss_pred CEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCc
Confidence 59999999865444445676777777776 6678888765 566665555554 3333321 2346688999754
No 26
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=58.57 E-value=37 Score=26.99 Aligned_cols=44 Identities=9% Similarity=0.046 Sum_probs=34.8
Q ss_pred hhhHHHHHhCCcEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHH
Q 040570 123 PSAIELLQAFPRVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWA 182 (210)
Q Consensus 123 ~~~~~~~~~f~~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~ 182 (210)
..+++.|.+|+||+- ++.|+..+....-||+||.=.+.|+=+.+
T Consensus 27 ~~l~~yFeqfGeI~e----------------avvitd~~t~rskGyGfVTf~d~~aa~rA 70 (247)
T KOG0149|consen 27 ETLRRYFEQFGEIVE----------------AVVITDKNTGRSKGYGFVTFRDAEAATRA 70 (247)
T ss_pred HHHHHHHHHhCceEE----------------EEEEeccCCccccceeeEEeecHHHHHHH
Confidence 678889999999984 77888888888889999986666655433
No 27
>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=58.55 E-value=39 Score=20.46 Aligned_cols=42 Identities=14% Similarity=0.186 Sum_probs=31.6
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcc
Q 040570 37 KSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKVREQV 85 (210)
Q Consensus 37 ~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~ 85 (210)
.|..+..|.-.|.++++|-..|. +..+.||+.+.+..-+...
T Consensus 2 ~k~~A~~LY~~G~~~~eIA~~Lg-------~~~~TV~~W~~r~~W~~~~ 43 (58)
T PF06056_consen 2 VKEQARSLYLQGWSIKEIAEELG-------VPRSTVYSWKDRYKWDELL 43 (58)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHC-------CChHHHHHHHHhhCccccC
Confidence 35677788889999999988762 3467899999987655443
No 28
>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=57.32 E-value=44 Score=21.82 Aligned_cols=48 Identities=15% Similarity=0.137 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHhCCCC--hHHHHHHHHHhCCCCc-chHhHHhHHHHHH
Q 040570 32 ILNKEKSNLLVDMSKNNVR--PKDVLHVLKKRNMHNA-TTIRAIYNARQKY 79 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~--p~~I~~~l~~~~~~~~-~t~~di~N~~~k~ 79 (210)
+|.+.....|.+|..+|.+ -..|++.|.+.+|+.. ...+.+||....+
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 3555666778888877654 6689999999999864 4556667765543
No 29
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=56.97 E-value=48 Score=24.42 Aligned_cols=77 Identities=14% Similarity=0.035 Sum_probs=39.7
Q ss_pred HhCCcEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecC--ccchhHHHHHHHHHHHHhcCCCCeEEEecCcccC
Q 040570 130 QAFPRVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKL--KWENNYIWALERLKSIMEENMLASVIVTDRELAW 207 (210)
Q Consensus 130 ~~f~~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~--E~~e~~~w~l~~~~~~~~~~~~p~~iitD~d~al 207 (210)
..+|--|..|+= ++.-+.+++.|+.....|..|.-. .=.++ .+.+.+--++....+-.+ .....-||||....+
T Consensus 30 ~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flks-vd~s~~~~~a~~l~~ll~~vIeeVG-~~nVvqVVTDn~~~~ 105 (153)
T PF04937_consen 30 KRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKS-VDASSIIKTAEYLFELLDEVIEEVG-EENVVQVVTDNASNM 105 (153)
T ss_pred HhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEE-EecccccccHHHHHHHHHHHHHHhh-hhhhhHHhccCchhH
Confidence 334444444543 334455666666655555444322 22222 345555555555555444 244456789988877
Q ss_pred CCC
Q 040570 208 HPV 210 (210)
Q Consensus 208 ~~~ 210 (210)
++|
T Consensus 106 ~~a 108 (153)
T PF04937_consen 106 KKA 108 (153)
T ss_pred HHH
Confidence 654
No 30
>PF13565 HTH_32: Homeodomain-like domain
Probab=55.83 E-value=46 Score=20.77 Aligned_cols=44 Identities=9% Similarity=0.221 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHHHHHh--CCCChHHHHHHHHHhCCCC-cchHhHHhHH
Q 040570 31 GILNKEKSNLLVDMSK--NNVRPKDVLHVLKKRNMHN-ATTIRAIYNA 75 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~--~g~~p~~I~~~l~~~~~~~-~~t~~di~N~ 75 (210)
|+ ++++.+.|..+.. ...++.+|...|.+++|.. .+....||++
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 45 6788788887754 4689999999999998742 2455666653
No 31
>smart00351 PAX Paired Box domain.
Probab=55.68 E-value=51 Score=23.27 Aligned_cols=45 Identities=22% Similarity=0.344 Sum_probs=34.7
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhh
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKV 81 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~ 81 (210)
.|.++.++++.|..+...|.+.++|...+ + ++...+++..++++.
T Consensus 15 ~~~~s~~~R~riv~~~~~G~s~~~iA~~~----g---vs~~tV~kwi~r~~~ 59 (125)
T smart00351 15 GRPLPDEERQRIVELAQNGVRPCDISRQL----C---VSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHH----C---cCHHHHHHHHHHHHH
Confidence 57799999999999988999998885443 2 556678887777653
No 32
>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=53.37 E-value=73 Score=22.03 Aligned_cols=35 Identities=0% Similarity=0.054 Sum_probs=27.2
Q ss_pred cccCCCCHHHHHH---HHHHHhCCCChHHHHHHHHHhC
Q 040570 28 SFAGILNKEKSNL---LVDMSKNNVRPKDVLHVLKKRN 62 (210)
Q Consensus 28 ~~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l~~~~ 62 (210)
+..|..++.+... |..|.+.|++..+|..++....
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 3457777776665 6678999999999999997544
No 33
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=53.33 E-value=39 Score=24.33 Aligned_cols=73 Identities=18% Similarity=0.156 Sum_probs=43.5
Q ss_pred EEE-EEeChhhH-HHHHhCCcEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcC
Q 040570 116 KAL-FLAHPSAI-ELLQAFPRVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEEN 193 (210)
Q Consensus 116 ~~l-f~a~~~~~-~~~~~f~~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~ 193 (210)
.+| |....+++ ++|.++++|=- +++|+|.+..+.. |||||.-=..++=.-+++ -+.+--
T Consensus 42 gNlSfyttEEqiyELFs~cG~irr---------------iiMGLdr~kktpC-GFCFVeyy~~~dA~~Alr---yisgtr 102 (153)
T KOG0121|consen 42 GNLSFYTTEEQIYELFSKCGDIRR---------------IIMGLDRFKKTPC-GFCFVEYYSRDDAEDALR---YISGTR 102 (153)
T ss_pred eeeeeeecHHHHHHHHHhccchhe---------------eEeccccCCcCcc-ceEEEEEecchhHHHHHH---HhccCc
Confidence 344 44555655 79999998642 3788888877765 777776433343333333 333211
Q ss_pred CCCeEEEecCcccC
Q 040570 194 MLASVIVTDRELAW 207 (210)
Q Consensus 194 ~~p~~iitD~d~al 207 (210)
.--+.|-+|.|.+.
T Consensus 103 Lddr~ir~D~D~GF 116 (153)
T KOG0121|consen 103 LDDRPIRIDWDAGF 116 (153)
T ss_pred ccccceeeeccccc
Confidence 22367888888764
No 34
>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=53.10 E-value=84 Score=22.65 Aligned_cols=32 Identities=3% Similarity=-0.022 Sum_probs=25.3
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHHHH
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVLKK 60 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l~~ 60 (210)
.+|.-++++... |..|.+.|++..+|..++..
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 467788876665 55678899999999999874
No 35
>cd00131 PAX Paired Box domain
Probab=52.66 E-value=60 Score=23.07 Aligned_cols=46 Identities=15% Similarity=0.249 Sum_probs=35.5
Q ss_pred ccCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhh
Q 040570 29 FAGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKV 81 (210)
Q Consensus 29 ~~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~ 81 (210)
..|.++.+.++.|..+.+.|.++++|-..+ + ++...|++.+++.+.
T Consensus 14 m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~----~---Vs~~tV~r~i~r~~e 59 (128)
T cd00131 14 NGRPLPDSIRQRIVELAQSGIRPCDISRQL----R---VSHGCVSKILNRYYE 59 (128)
T ss_pred CCCcCCHHHHHHHHHHHHcCCCHHHHHHHH----C---cCHHHHHHHHHHHHH
Confidence 358899999999999999999999995554 2 455667777777653
No 36
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=50.42 E-value=68 Score=20.83 Aligned_cols=49 Identities=14% Similarity=0.174 Sum_probs=33.4
Q ss_pred HHHHhCCCCh-HHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHH
Q 040570 42 VDMSKNNVRP-KDVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMS 95 (210)
Q Consensus 42 ~~l~~~g~~p-~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~ 95 (210)
..|.+.|..| .||..+|..-.|.....-++.+|..++.-+.. -++.|++
T Consensus 26 ~AL~EKGYnPinQivGYllSGDPaYItsh~nAR~lIr~~eRDe-----llEeLv~ 75 (79)
T PF06135_consen 26 AALEEKGYNPINQIVGYLLSGDPAYITSHNNARNLIRKIERDE-----LLEELVR 75 (79)
T ss_pred HHHHHcCCChHHHHHhheecCCCccccCcccHHHHHHHHhHHH-----HHHHHHH
Confidence 3577889876 48888887777765566678888877765543 2455554
No 37
>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=50.24 E-value=50 Score=19.26 Aligned_cols=31 Identities=23% Similarity=0.469 Sum_probs=24.0
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHH
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKK 60 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~ 60 (210)
+=.|+.+.-..+..|.+.|+.|...-..+++
T Consensus 16 ntgLd~etL~ici~L~e~GVnPeaLA~vI~e 46 (48)
T PF12554_consen 16 NTGLDRETLSICIELCENGVNPEALAAVIKE 46 (48)
T ss_pred cCCCCHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 3467778888888899999999887776654
No 38
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=50.01 E-value=76 Score=22.66 Aligned_cols=56 Identities=11% Similarity=0.258 Sum_probs=38.5
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhccceeE
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQKYIE 104 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~~~~~ 104 (210)
.|..|+++++.+ ..+|++.++++.- +|.+|+-..-.. ++..+..+++.|.+.|.++
T Consensus 2 a~~~T~eer~eL---------k~rIvElVRe~GR---iTi~ql~~~TGa-------sR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 2 ARVFTPEEREEL---------KARIVELVREHGR---ITIKQLVAKTGA-------SRNTVKRYLRELVARGDLY 57 (127)
T ss_pred CCcCCHHHHHHH---------HHHHHHHHHHcCC---ccHHHHHHHHCC-------CHHHHHHHHHHHHHcCCeE
Confidence 477899999988 4688888887653 566666543322 3445677788888887764
No 39
>PF13551 HTH_29: Winged helix-turn helix
Probab=47.06 E-value=84 Score=20.93 Aligned_cols=45 Identities=11% Similarity=0.156 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhC-------CCChHHHHHHH-HHhCCCCcchHhHHhHHHHH
Q 040570 33 LNKEKSNLLVDMSKN-------NVRPKDVLHVL-KKRNMHNATTIRAIYNARQK 78 (210)
Q Consensus 33 lt~~~k~~i~~l~~~-------g~~p~~I~~~l-~~~~~~~~~t~~di~N~~~k 78 (210)
+++++++.|..+... ...+..|...| .+.++ ..+....|+++..+
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 999999998876653 25678888866 55554 45667777776654
No 40
>PF11293 DUF3094: Protein of unknown function (DUF3094); InterPro: IPR021444 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=43.72 E-value=32 Score=20.56 Aligned_cols=21 Identities=19% Similarity=0.199 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHHHHhCCCCh
Q 040570 31 GILNKEKSNLLVDMSKNNVRP 51 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~~g~~p 51 (210)
++|++|+++.++...++|..+
T Consensus 2 ~rL~pEDQ~~Vd~yL~a~~~~ 22 (55)
T PF11293_consen 2 SRLNPEDQQRVDEYLQAGVNQ 22 (55)
T ss_pred CCCCHHHHHHHHHHHhCCCCc
Confidence 689999999999998888764
No 41
>cd08309 Death_IRAK Death domain of Interleukin-1 Receptor-Associated Kinases. Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinase pathways. IRAK1 and IRAK4 are active kinases while IRAK2 and IRAK-M (also called IRAK3) are inactive. In general, IRAKs are expressed ubiquitously, except for IRAK-M which is detected only in macrophages. The insect homologs, Pelle and Tube, are important components of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in the innate immune response. Most members have an N-terminal DD followed by a kinase domain. In general, DDs are protein-protein interaction domains found in a variety of domain a
Probab=43.55 E-value=98 Score=20.69 Aligned_cols=66 Identities=11% Similarity=-0.035 Sum_probs=44.4
Q ss_pred CCCCHHHHHHHHHHHhC--CCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhcc
Q 040570 31 GILNKEKSNLLVDMSKN--NVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQ 100 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~~--g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~ 100 (210)
|.|....+..+..+.++ +-.=+++...+.+..++..+...+|.++..+.++ |.+|...|+......
T Consensus 4 ~~Lp~~~~~~L~~~LD~~~~~~W~~LA~~i~~~~~~~~~~~~~i~~~e~~~~~----g~SPt~~LL~~W~~~ 71 (95)
T cd08309 4 RQLPYSVLARLCKVLDPLELKGWRQLASLIPKGLGGPRYDLTDVRQIESMKQR----GRSPTRELLWDWGTQ 71 (95)
T ss_pred eeCCHHHHHHHHHHhCCcccCChHHHHHHhccccccCCcCHHHHHHHHHHhhc----CCChHHHHHHHHHhc
Confidence 56777777777777776 6666777777765555545666778887666543 556777777766443
No 42
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.32 E-value=96 Score=20.21 Aligned_cols=53 Identities=13% Similarity=0.114 Sum_probs=36.0
Q ss_pred HHHHhCCCChH-HHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHH-Hhhc
Q 040570 42 VDMSKNNVRPK-DVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMS-KLIE 99 (210)
Q Consensus 42 ~~l~~~g~~p~-~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~-~l~~ 99 (210)
..|-+-|..|. ||..+|-.-.|.......|.+|..+++-+.. -++.|++ +|+.
T Consensus 29 ~sL~ekGYNpiNQiVGYllSGDPaYIpr~ndARn~IRk~eRDe-----IvEElvk~YLk~ 83 (88)
T COG4472 29 NSLEEKGYNPINQIVGYLLSGDPAYIPRYNDARNQIRKLERDE-----IVEELVKYYLKG 83 (88)
T ss_pred HHHHHcCCChHHHHHhhhccCCccccCccccHHHHHHHHhHHH-----HHHHHHHHHHhh
Confidence 35667788764 8888887666655566789999888876543 3566665 4544
No 43
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=41.93 E-value=1.1e+02 Score=23.97 Aligned_cols=67 Identities=18% Similarity=0.084 Sum_probs=41.6
Q ss_pred cCCC-CCCCCCCCccccccCCCCHHHHHHHHHHHhCCCCh-HHHHHHHH-----HhCCC----------CcchHhHHhHH
Q 040570 13 YGFH-NHLATQYLEGHSFAGILNKEKSNLLVDMSKNNVRP-KDVLHVLK-----KRNMH----------NATTIRAIYNA 75 (210)
Q Consensus 13 ~~~H-NH~~~~~~~~h~~~R~lt~~~k~~i~~l~~~g~~p-~~I~~~l~-----~~~~~----------~~~t~~di~N~ 75 (210)
..+| +|+....... ...++.+...+.|..|...|+.. .+|...|+ +.+.+ ...|.+||+|.
T Consensus 139 ~~~H~~H~~~~~~~~--~~q~~~~~v~~ki~eLv~~gv~~v~e~k~~l~~fV~~~lf~~~~~p~~~n~~y~Pt~~di~n~ 216 (225)
T PF15299_consen 139 PEEHSGHPIGQEAAG--LKQPLDPRVVEKIHELVAQGVTSVPEMKRHLKKFVEEELFKDQEPPPPTNRRYFPTDKDIRNH 216 (225)
T ss_pred hHhcCCCcccccccc--ccccCCHHHHHHHHHHHHcccccHHHHHHHHHHHhhhhccCCCCCCCCCccccCCchHHHHHH
Confidence 3577 6888753211 12456778888899999999764 45544442 11210 12677899998
Q ss_pred HHHHhh
Q 040570 76 RQKYKV 81 (210)
Q Consensus 76 ~~k~~~ 81 (210)
......
T Consensus 217 ~~~~~~ 222 (225)
T PF15299_consen 217 MYSAKK 222 (225)
T ss_pred HHHHHh
Confidence 877643
No 44
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=41.89 E-value=35 Score=23.25 Aligned_cols=24 Identities=21% Similarity=0.122 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCChHHHHHHHHHhC
Q 040570 39 NLLVDMSKNNVRPKDVLHVLKKRN 62 (210)
Q Consensus 39 ~~i~~l~~~g~~p~~I~~~l~~~~ 62 (210)
....+|.++|+++....+.+++.+
T Consensus 73 ~~~~eM~dAGV~~~~~~~~l~~~Y 96 (100)
T PF15652_consen 73 NSYREMFDAGVSKECRKKALKAQY 96 (100)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHH
Confidence 334567788888888888877654
No 45
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=41.83 E-value=22 Score=28.44 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=30.9
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
-|.|..+.+-.|++|.+.|++|..|-..|+-.+|
T Consensus 18 GRPLPna~RlrIVELarlGiRPCDISRQLrvSHG 51 (334)
T KOG3517|consen 18 GRPLPNAIRLRIVELARLGIRPCDISRQLRVSHG 51 (334)
T ss_pred CccCcchhhhhHHHHHHcCCCccchhhhhhhccc
Confidence 4788889999999999999999999999988776
No 46
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.19 E-value=38 Score=25.24 Aligned_cols=37 Identities=19% Similarity=0.260 Sum_probs=29.6
Q ss_pred EEecccc-cCcCCCcee--eEEeeecCCceEEEEEEeecC
Q 040570 137 IMDCTYK-TNRYDMPLL--EIAGVTSIDLTFSVCCVYLKL 173 (210)
Q Consensus 137 ~~D~Ty~-tn~~~~pl~--~~~g~~~~~~~~~~~~~~~~~ 173 (210)
-||+||| ||.|+-|-+ .+.|-|+.|+-...|||-+.-
T Consensus 69 Pievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~hi 108 (187)
T KOG4027|consen 69 PIEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLHI 108 (187)
T ss_pred ceEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEec
Confidence 3788986 789999966 567888999998888887653
No 47
>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=40.79 E-value=1.9e+02 Score=23.50 Aligned_cols=70 Identities=16% Similarity=0.110 Sum_probs=39.0
Q ss_pred EEEEecccccCcC-CCcee--eEEeeecCCceEEEEEEeecC--ccchh----HHHHHHHHHHHHhcCCCCeEEEecCcc
Q 040570 135 VLIMDCTYKTNRY-DMPLL--EIAGVTSIDLTFSVCCVYLKL--KWENN----YIWALERLKSIMEENMLASVIVTDREL 205 (210)
Q Consensus 135 vl~~D~Ty~tn~~-~~pl~--~~~g~~~~~~~~~~~~~~~~~--E~~e~----~~w~l~~~~~~~~~~~~p~~iitD~d~ 205 (210)
|+-+|.++..... +.|-+ .+..+|..+..+.-.+.+... |..+. +.++|+.|.+..+ ...|+-||.-||-
T Consensus 79 iIGidv~h~~~~~~~~~sv~g~~~s~~~~~~~~~~~~~~~~~~~e~~~~l~~~~~~~L~~~~~~~~-~~~P~~IiiyRdG 157 (302)
T PF02171_consen 79 IIGIDVSHPSPGSDKNPSVVGFVASFDSDGSKYFSSVRFQDSGQEIIDNLEEIIKEALKEFKKNNG-KWLPERIIIYRDG 157 (302)
T ss_dssp EEEEEEEEESSTCTCSCEEEEEEEEESTTTCEEEEEEEEECTTCCCHHHHHHHHHHHHHHHHHTTT-T-TTSEEEEEEES
T ss_pred EEEEEEEecCcccCCcceeeEEEEeccCccccccceeEEeccchhhhcchhhHHHHHHHHHHHHcC-CCCCceEEEEEcc
Confidence 6778888877776 55533 233344455555544444332 32233 4555555555443 2389988887775
No 48
>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=40.61 E-value=56 Score=17.01 Aligned_cols=25 Identities=12% Similarity=0.300 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhCCCChHHHHHHHH
Q 040570 35 KEKSNLLVDMSKNNVRPKDVLHVLK 59 (210)
Q Consensus 35 ~~~k~~i~~l~~~g~~p~~I~~~l~ 59 (210)
++=.+.|....+.|+++.+|.++|.
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3445667777889999999999885
No 49
>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=40.36 E-value=25 Score=21.50 Aligned_cols=17 Identities=24% Similarity=0.423 Sum_probs=10.5
Q ss_pred CCCCcEEEEecCCCCCC
Q 040570 3 NNDDWALIVKYGFHNHL 19 (210)
Q Consensus 3 ~~~~W~v~~~~~~HNH~ 19 (210)
.|+.-.++.-.++|||+
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 35666677788999997
No 50
>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=40.17 E-value=1.9e+02 Score=24.76 Aligned_cols=68 Identities=19% Similarity=0.124 Sum_probs=36.8
Q ss_pred EEEEecccccCc--CCCceeeEEeeecCCceEEEEEEeecCccc-------hhHHHHHHHHHHHHhcCC-CCeEEEecCc
Q 040570 135 VLIMDCTYKTNR--YDMPLLEIAGVTSIDLTFSVCCVYLKLKWE-------NNYIWALERLKSIMEENM-LASVIVTDRE 204 (210)
Q Consensus 135 vl~~D~Ty~tn~--~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~-------e~~~w~l~~~~~~~~~~~-~p~~iitD~d 204 (210)
++-+|.++.... .+.|......-+..+.++.-++.+.+...+ +.+..+|+.|++.. +. .|.-||.-||
T Consensus 174 iiGiDv~h~~~~~~~~~~si~~~vas~~~~~~~g~~~~~~~~~~~~~~~l~~~~~~~L~~y~~~~--~~~~P~~IiiyRD 251 (393)
T cd02826 174 FIGFDVSHPDRRTVNGGPSAVGFAANLSNHTFLGGFLYVQPSREVKLQDLGEVIKKCLDGFKKST--GEGLPEKIVIYRD 251 (393)
T ss_pred EEEEEeeCCCCCCCCCCCcEEEEEeecCCccccceEEEEecCccchHHHHHHHHHHHHHHHHHHc--CCCCcceeEEEec
Confidence 677888888764 445544333333222244445555443322 23344445554433 46 8998888776
No 51
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.61 E-value=1.1e+02 Score=21.60 Aligned_cols=44 Identities=20% Similarity=0.331 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhh
Q 040570 31 GILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKV 81 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~ 81 (210)
|+-+......|..|.+.|.+|+.|-..+ .+.++.+|=...++.+
T Consensus 92 rkyd~~t~~~i~emlr~gk~preIsk~l-------GIpirTvyY~l~k~k~ 135 (139)
T COG1710 92 RKYDRNTLLRIREMLRNGKTPREISKDL-------GIPIRTVYYLLKKLKK 135 (139)
T ss_pred cccchhHHHHHHHHHHcCCCHHHHHHhh-------CCchhhhHHHHHHHhh
Confidence 4455556667888888898888885543 2556666665555543
No 52
>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=36.92 E-value=96 Score=18.68 Aligned_cols=30 Identities=7% Similarity=0.072 Sum_probs=22.1
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHH
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVL 58 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l 58 (210)
.+|..++++... |..|.+.|++..+|.+.+
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 467788776655 456778999999987764
No 53
>PRK05473 hypothetical protein; Provisional
Probab=36.52 E-value=1.3e+02 Score=19.94 Aligned_cols=48 Identities=13% Similarity=0.133 Sum_probs=33.7
Q ss_pred HHHhCCCChH-HHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHH
Q 040570 43 DMSKNNVRPK-DVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMS 95 (210)
Q Consensus 43 ~l~~~g~~p~-~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~ 95 (210)
.|.+-|..|. ||..+|..-.|.....-++.+|..++.-+.+ -++.|++
T Consensus 30 AL~EKGYNPinQiVGYllSGDPaYItsh~nAR~lIrkiERDE-----ilEeLv~ 78 (86)
T PRK05473 30 ALEEKGYNPINQIVGYLLSGDPAYIPRHNDARNLIRKLERDE-----ILEELVK 78 (86)
T ss_pred HHHHcCCChHHHHHhhhccCCCCccCCcccHHHHHHHHhHHH-----HHHHHHH
Confidence 4677888764 8999998777765666678888877765543 3566654
No 54
>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=35.84 E-value=26 Score=26.59 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHHhC
Q 040570 32 ILNKEKSNLLVDMSKNNVRPKDVLHVLKKRN 62 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~ 62 (210)
+|+.+|++.+..|+.+|++...|+..|....
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 5778899999999999999999999997555
No 55
>PRK07708 hypothetical protein; Validated
Probab=35.13 E-value=2.2e+02 Score=22.32 Aligned_cols=109 Identities=8% Similarity=-0.007 Sum_probs=59.8
Q ss_pred HHHHHhhccceeEEEeeecCCCceEEEEEeChhhHHHHHhCC---c--EEEEecccccCcCCCceeeEEeeecCC-ceEE
Q 040570 92 LLMSKLIEQKYIERHKSDVDTNCVKALFLAHPSAIELLQAFP---R--VLIMDCTYKTNRYDMPLLEIAGVTSID-LTFS 165 (210)
Q Consensus 92 ~L~~~l~~~~~~~~~~~~d~~~~~~~lf~a~~~~~~~~~~f~---~--vl~~D~Ty~tn~~~~pl~~~~g~~~~~-~~~~ 165 (210)
.|.+.|+..|..--..-.|++| ..|+-++..++...-. + ++.+|+.|..|.-+.=.. ++-.+..+ ..+.
T Consensus 31 ~~~~~~~~~~~~~~~~~~d~~~----~~~~~k~~~~~~~~~~~ep~~~~vY~DGs~~~n~g~aG~G-vVI~~~~g~~~~~ 105 (219)
T PRK07708 31 QLAEDFEKTGRVKELEFYDEMD----TEWSLKELKKLSKEVEEEPHEILVYFDGGFDKETKLAGLG-IVIYYKQGNKRYR 105 (219)
T ss_pred HHHHHHhhcCCceeEEEecCCC----CEeeHHHHhhhhhhhccCCCcEEEEEeeccCCCCCCcEEE-EEEEECCCCEEEE
Confidence 4556777766421111135555 4699999888887553 3 789999997665433222 22223333 2222
Q ss_pred EE----EEeecCccchhHHHHHHHHHHHHhcCC--CCeEEEecCcc
Q 040570 166 VC----CVYLKLKWENNYIWALERLKSIMEENM--LASVIVTDREL 205 (210)
Q Consensus 166 ~~----~~~~~~E~~e~~~w~l~~~~~~~~~~~--~p~~iitD~d~ 205 (210)
+. +......++.-|.-++..+..+...+. .|.+|-+|...
T Consensus 106 ~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSql 151 (219)
T PRK07708 106 IRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQV 151 (219)
T ss_pred EEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHH
Confidence 21 121234455567777777777765332 24567777543
No 56
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.10 E-value=52 Score=25.82 Aligned_cols=116 Identities=21% Similarity=0.117 Sum_probs=59.6
Q ss_pred hCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhccceeEEEeeecCCCceEEEEEeChhh
Q 040570 46 KNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQKYIERHKSDVDTNCVKALFLAHPSA 125 (210)
Q Consensus 46 ~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~~~~~~~~~~d~~~~~~~lf~a~~~~ 125 (210)
..++.-+.+-+++.+.+ ....-..|++..+++.. .+...+.+..- .
T Consensus 23 ~~~Ls~r~v~e~l~~rg--i~v~h~Ti~rwv~k~~~----------~~~~~~~~r~~-----~----------------- 68 (215)
T COG3316 23 RYGLSLRDVEEMLAERG--IEVDHETIHRWVQKYGP----------LLARRLKRRKR-----K----------------- 68 (215)
T ss_pred hcchhhccHHHHHHHcC--cchhHHHHHHHHHHHhH----------HHHHHhhhhcc-----c-----------------
Confidence 34777777777776665 33455667777776532 22333332210 0
Q ss_pred HHHHHhCCcEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHHHHHHhcCCCCeEEEecCcc
Q 040570 126 IELLQAFPRVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDREL 205 (210)
Q Consensus 126 ~~~~~~f~~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~p~~iitD~d~ 205 (210)
-.+.+.+|=||-+-+-+--- ..-.+|..|.+ +-+-|...-+...=.-+|..+++.. ..|.+|+||+..
T Consensus 69 ------~~~~w~vDEt~ikv~gkw~y-lyrAid~~g~~--Ld~~L~~rRn~~aAk~Fl~kllk~~---g~p~v~vtDka~ 136 (215)
T COG3316 69 ------AGDSWRVDETYIKVNGKWHY-LYRAIDADGLT--LDVWLSKRRNALAAKAFLKKLLKKH---GEPRVFVTDKAP 136 (215)
T ss_pred ------cccceeeeeeEEeeccEeee-hhhhhccCCCe--EEEEEEcccCcHHHHHHHHHHHHhc---CCCceEEecCcc
Confidence 01244445554332222211 23445555443 3344444444554455555555554 579999999876
Q ss_pred cC
Q 040570 206 AW 207 (210)
Q Consensus 206 al 207 (210)
..
T Consensus 137 s~ 138 (215)
T COG3316 137 SY 138 (215)
T ss_pred ch
Confidence 54
No 57
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.78 E-value=31 Score=24.78 Aligned_cols=41 Identities=22% Similarity=0.204 Sum_probs=32.4
Q ss_pred ccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHHHHH
Q 040570 141 TYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERLKSI 189 (210)
Q Consensus 141 Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~~~~ 189 (210)
.|+||+|++..+. +..| +-+.|..+-+..+++-+|+++=.+
T Consensus 63 sy~Ts~Yklhfye----Tptg----lk~vl~Tdpk~~~ir~vLq~IYs~ 103 (140)
T KOG3368|consen 63 SYKTSKYKLHFYE----TPTG----LKFVLNTDPKAGSIRDVLQYIYSH 103 (140)
T ss_pred EEeeceeEEEEEE----cCCC----cEEEEecCCCcccHHHHHHHHHHH
Confidence 4889999997772 2333 667799999999999999988773
No 58
>COG0046 PurL Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism]
Probab=33.96 E-value=28 Score=32.47 Aligned_cols=21 Identities=33% Similarity=0.534 Sum_probs=16.4
Q ss_pred CCCcEEEEecCCCCCCCCCCC
Q 040570 4 NDDWALIVKYGFHNHLATQYL 24 (210)
Q Consensus 4 ~~~W~v~~~~~~HNH~~~~~~ 24 (210)
++.|.+...+..||||-.-.+
T Consensus 92 ~d~~~v~fKvESHNHPSaIeP 112 (743)
T COG0046 92 GDGWAVVFKVESHNHPSAIEP 112 (743)
T ss_pred CCcEEEEEEeccCCCCCccCC
Confidence 345999999999999965444
No 59
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=33.95 E-value=1.8e+02 Score=21.03 Aligned_cols=57 Identities=14% Similarity=0.202 Sum_probs=26.0
Q ss_pred HHHhCCCCh----HHHHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhcccee
Q 040570 43 DMSKNNVRP----KDVLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQKYI 103 (210)
Q Consensus 43 ~l~~~g~~p----~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~~~~ 103 (210)
.|.+.|++. ..|+++|.+..+. ++..+||....+.-. --|.+.+-.-++.|.+.|.+
T Consensus 11 ~lk~~glr~T~qR~~vl~~L~~~~~~--~sAeei~~~l~~~~p--~islaTVYr~L~~l~e~Glv 71 (145)
T COG0735 11 RLKEAGLRLTPQRLAVLELLLEADGH--LSAEELYEELREEGP--GISLATVYRTLKLLEEAGLV 71 (145)
T ss_pred HHHHcCCCcCHHHHHHHHHHHhcCCC--CCHHHHHHHHHHhCC--CCCHhHHHHHHHHHHHCCCE
Confidence 445555531 1344444443322 566666665444211 11222334445566677764
No 60
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=33.67 E-value=1.4e+02 Score=19.58 Aligned_cols=71 Identities=13% Similarity=-0.016 Sum_probs=34.1
Q ss_pred EEEEecccccCcCCCceeeEEeeecCCceEEEEEEee--cCccchhHHHHHHHHHHHHhcCCCCeEEEecCccc
Q 040570 135 VLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYL--KLKWENNYIWALERLKSIMEENMLASVIVTDRELA 206 (210)
Q Consensus 135 vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~--~~E~~e~~~w~l~~~~~~~~~~~~p~~iitD~d~a 206 (210)
++++|+.+..+.-+.-. -++..+..+....-..... .+....-+.-++..+..+...+..+-.|.||...+
T Consensus 1 ~~~~Dgs~~~~~~~~g~-g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~ 73 (130)
T cd06222 1 VIYTDGSCRGNPGPAGA-GVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYV 73 (130)
T ss_pred CEEecccCCCCCCceEE-EEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHH
Confidence 36788888766422211 2233334433333333321 12222233344445555444356777899997643
No 61
>KOG3862 consensus Transcription factor PAX2/5/8, contains PAX domain [Transcription]
Probab=32.68 E-value=63 Score=26.29 Aligned_cols=34 Identities=24% Similarity=0.334 Sum_probs=31.1
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
-|.|.+..+..|+.|.+.|+.|..|-..++-.+|
T Consensus 23 GRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShG 56 (327)
T KOG3862|consen 23 GRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHG 56 (327)
T ss_pred CccCchHHHHHHHHHHHcCCcchhHHHHHhhccC
Confidence 4889999999999999999999999999887776
No 62
>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=31.59 E-value=82 Score=27.68 Aligned_cols=23 Identities=17% Similarity=0.189 Sum_probs=19.0
Q ss_pred CCCcEEEEecCCCCCCCCCCCcc
Q 040570 4 NDDWALIVKYGFHNHLATQYLEG 26 (210)
Q Consensus 4 ~~~W~v~~~~~~HNH~~~~~~~~ 26 (210)
.|-+.|+...+-||||+....+.
T Consensus 164 ~g~f~v~k~~~~h~h~l~~nl~l 186 (496)
T PF04684_consen 164 KGPFVVTKIEPYHNHPLESNLSL 186 (496)
T ss_pred cCceEEEeeccccCCcccccccH
Confidence 36689999999999999877643
No 63
>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=30.82 E-value=94 Score=19.21 Aligned_cols=44 Identities=16% Similarity=0.117 Sum_probs=28.6
Q ss_pred cCCCCHHHHHHHHHHH-hCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHh
Q 040570 30 AGILNKEKSNLLVDMS-KNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYK 80 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~-~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~ 80 (210)
.|+.|++.|..+.... ..|.+..++... +| +....++|.+.+++
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~----~g---i~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVARE----YG---ISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHH----HT---S-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecc----cc---cccccccHHHHHHh
Confidence 3678899999888765 677776665443 32 57788999999886
No 64
>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=30.50 E-value=3.1e+02 Score=23.75 Aligned_cols=69 Identities=19% Similarity=0.110 Sum_probs=40.6
Q ss_pred EEEEecccccCc--CCCcee--eEEeeecCCceEEEEEEeecCccc--hh----HHHHHHHHHHHHhcCCCCeEEEecCc
Q 040570 135 VLIMDCTYKTNR--YDMPLL--EIAGVTSIDLTFSVCCVYLKLKWE--NN----YIWALERLKSIMEENMLASVIVTDRE 204 (210)
Q Consensus 135 vl~~D~Ty~tn~--~~~pl~--~~~g~~~~~~~~~~~~~~~~~E~~--e~----~~w~l~~~~~~~~~~~~p~~iitD~d 204 (210)
++-+|.++.+.. -+.|-. .+..+|.+...+.-.+.+-....+ ++ +..+|+.|.+.. +..|.-||.-||
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 778999998766 355543 344455555555544555443322 23 344455555443 479998888777
Q ss_pred c
Q 040570 205 L 205 (210)
Q Consensus 205 ~ 205 (210)
-
T Consensus 279 G 279 (426)
T cd04657 279 G 279 (426)
T ss_pred C
Confidence 4
No 65
>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=30.28 E-value=1.1e+02 Score=22.82 Aligned_cols=40 Identities=10% Similarity=0.128 Sum_probs=26.0
Q ss_pred CCceEEEEEEeec--CccchhHHHHHHHHHHHHhcCCCCe-EEEecC
Q 040570 160 IDLTFSVCCVYLK--LKWENNYIWALERLKSIMEENMLAS-VIVTDR 203 (210)
Q Consensus 160 ~~~~~~~~~~~~~--~E~~e~~~w~l~~~~~~~~~~~~p~-~iitD~ 203 (210)
......+-||+=+ ..+-.|-+|+|+.|-..+. |. |+..|-
T Consensus 105 ~~~PvQ~ifclKe~N~kKinSHrWfFnaf~~~l~----P~vcvllDv 147 (163)
T PF01644_consen 105 NIVPVQIIFCLKEKNAKKINSHRWFFNAFCRQLQ----PNVCVLLDV 147 (163)
T ss_pred CCCCEEEEEEeccccccccchhhHHHHHHHhhcC----CcEEEEEec
Confidence 3334445555533 2257899999999999875 54 566664
No 66
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=30.08 E-value=2.7e+02 Score=22.23 Aligned_cols=151 Identities=11% Similarity=0.080 Sum_probs=78.4
Q ss_pred cCCCCHHHHHHHHHHHhCCCChHHHHHHHHHh-CCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhccceeEEEee
Q 040570 30 AGILNKEKSNLLVDMSKNNVRPKDVLHVLKKR-NMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQKYIERHKS 108 (210)
Q Consensus 30 ~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~-~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~~~~~~~~~ 108 (210)
.++.|.+++.....|...| .+.+++|.++ +| ++..+.+++..++..- ..| ....+++.|+....
T Consensus 69 ~~~wt~e~~~~Al~L~~~s---pr~Y~yL~kk~~p--LPs~rTL~r~l~~v~~--~pG--i~~~il~~l~~~~~------ 133 (236)
T PF12017_consen 69 RRRWTKEDKSFALSLYKCS---PRAYNYLRKKGYP--LPSVRTLQRWLSKVNI--DPG--ILDFILDLLKNKSM------ 133 (236)
T ss_pred ccccCHHHHHhhheeeecC---hHHHHHHHHcCCC--CCCHHHHHHHHHhCCC--CCC--chHHHHHHHHHccC------
Confidence 3568888888877776443 4678888744 43 5677888888776542 234 34566776664321
Q ss_pred ecCCCceEEEEEeChhhH--HHHHhCCcEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHH
Q 040570 109 DVDTNCVKALFLAHPSAI--ELLQAFPRVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERL 186 (210)
Q Consensus 109 ~d~~~~~~~lf~a~~~~~--~~~~~f~~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~ 186 (210)
++.+++.-|.|=--.-. -.|..=.|++ +....|- -++++-|+...++. |++|.|-..=+ -.++.+-.
T Consensus 134 -~~~dr~CvL~fDEm~l~~~~eYD~~~d~v-----~~~~~~~-~v~mvrGl~~~WKQ-pi~~~f~t~m~---~~~l~~iI 202 (236)
T PF12017_consen 134 -SEEDRICVLSFDEMKLSPHLEYDPSRDEV-----NEPANYV-QVFMVRGLFKSWKQ-PIYFDFDTSMD---ADILKNII 202 (236)
T ss_pred -chhccEEEEEEeEEEccceeeeccccCcc-----cChhhhh-hHHHHHHHHhcCCc-cEEEEecCcCC---HHHHHHHH
Confidence 22233333222110000 0011111222 3333332 25567788777765 44888833223 34444444
Q ss_pred HHHHhcCCCCeEEEecCccc
Q 040570 187 KSIMEENMLASVIVTDRELA 206 (210)
Q Consensus 187 ~~~~~~~~~p~~iitD~d~a 206 (210)
.++..-|-....+++|...+
T Consensus 203 ~~l~~~g~~VvAivsD~g~~ 222 (236)
T PF12017_consen 203 EKLHEIGYNVVAIVSDMGSN 222 (236)
T ss_pred HHHHHCCCEEEEEECCCCcc
Confidence 44443355567899997643
No 67
>PRK13907 rnhA ribonuclease H; Provisional
Probab=29.81 E-value=1.9e+02 Score=19.97 Aligned_cols=68 Identities=18% Similarity=-0.003 Sum_probs=34.5
Q ss_pred EEEEecccccCcCCCceeeEEeeecCCceEEEEEE-eecCccchhHHHHHHHHHHHHhcCCCCeEEEecCc
Q 040570 135 VLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCV-YLKLKWENNYIWALERLKSIMEENMLASVIVTDRE 204 (210)
Q Consensus 135 vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~-~~~~E~~e~~~w~l~~~~~~~~~~~~p~~iitD~d 204 (210)
.+.+|+.++.|.-..=.-.++ .+..+ .....+. -.......-|.-++..+..+...+..+..|-||..
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~-~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~ 71 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQP-AVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQ 71 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCe-eEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechH
Confidence 367899998875332222222 33333 2222221 11223344466667777776654445566777753
No 68
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=29.63 E-value=1.6e+02 Score=20.53 Aligned_cols=27 Identities=11% Similarity=0.314 Sum_probs=22.8
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 37 KSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 37 ~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
+...|....++|++|.+..+.|.+++.
T Consensus 45 de~vI~~hidaGIs~~~AVN~LVeKY~ 71 (114)
T PF06755_consen 45 DETVIQEHIDAGISPADAVNFLVEKYE 71 (114)
T ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 445677889999999999999998873
No 69
>PHA00675 hypothetical protein
Probab=28.86 E-value=1.5e+02 Score=19.18 Aligned_cols=39 Identities=8% Similarity=0.042 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHHH-hCCCChHHHHHHHHHhCCCCcchHhHHhHHHH
Q 040570 32 ILNKEKSNLLVDMS-KNNVRPKDVLHVLKKRNMHNATTIRAIYNARQ 77 (210)
Q Consensus 32 ~lt~~~k~~i~~l~-~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~ 77 (210)
+|++.+-..|..+. ..|.+-..| .+++| +....|++.+.
T Consensus 22 KLt~~qV~~IR~l~~r~G~s~~~I----A~~fG---VsrstV~~I~~ 61 (78)
T PHA00675 22 KLTDAEVERIRELHEVEGMSYAVL----AEKFE---QSKGAIAKICR 61 (78)
T ss_pred ccCHHHHHHHHHHHHhcCccHHHH----HHHhC---CCHHHHHHHHc
Confidence 79999999999888 788765444 45554 33344555443
No 70
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=27.44 E-value=1.5e+02 Score=17.88 Aligned_cols=31 Identities=6% Similarity=0.096 Sum_probs=21.4
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHHH
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVLK 59 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l~ 59 (210)
.+|..+.++... |..|.+.|+++..|...+.
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 467777765554 4457778888888877653
No 71
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=27.34 E-value=4.1e+02 Score=23.01 Aligned_cols=28 Identities=36% Similarity=0.424 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHhcCCCCeEEEecCcccC
Q 040570 180 IWALERLKSIMEENMLASVIVTDRELAW 207 (210)
Q Consensus 180 ~w~l~~~~~~~~~~~~p~~iitD~d~al 207 (210)
.+.++-+.++......--+|+.|+..|.
T Consensus 118 ~f~lepL~e~l~~~~~~g~VvvD~~~A~ 145 (403)
T TIGR03676 118 KFYLEPLEEMLEEKDVYGLIVLDRREAT 145 (403)
T ss_pred hHHHHHHHHHhcCCCCEEEEEEecCceE
Confidence 4456777777753222247888888664
No 72
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=27.28 E-value=2.3e+02 Score=20.05 Aligned_cols=76 Identities=14% Similarity=0.149 Sum_probs=45.1
Q ss_pred HHhCCCChHH--HHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHHHHHhhccceeEEEeeecCCCceEEEEEe
Q 040570 44 MSKNNVRPKD--VLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLLMSKLIEQKYIERHKSDVDTNCVKALFLA 121 (210)
Q Consensus 44 l~~~g~~p~~--I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L~~~l~~~~~~~~~~~~d~~~~~~~lf~a 121 (210)
+...|+++.+ ++..|.+..|+ .+..+|-....- ..+.+..+++.|++.|++... ...+|++...|..+
T Consensus 24 l~~~glt~~q~~vL~~l~~~~~~--~t~~eLa~~l~~-------~~~tvt~~v~~Le~~GlV~r~-~~~~DrR~~~l~LT 93 (144)
T PRK03573 24 LKPLELTQTHWVTLHNIHQLPPE--QSQIQLAKAIGI-------EQPSLVRTLDQLEEKGLISRQ-TCASDRRAKRIKLT 93 (144)
T ss_pred HHhcCCCHHHHHHHHHHHHcCCC--CCHHHHHHHhCC-------ChhhHHHHHHHHHHCCCEeee-cCCCCcCeeeeEEC
Confidence 5578999887 45555544333 455555333221 233577899999999987432 23456777776655
Q ss_pred ChhhHHHHH
Q 040570 122 HPSAIELLQ 130 (210)
Q Consensus 122 ~~~~~~~~~ 130 (210)
+...+.+.
T Consensus 94 -~~G~~~~~ 101 (144)
T PRK03573 94 -EKAEPLIS 101 (144)
T ss_pred -hHHHHHHH
Confidence 44444444
No 73
>PF14420 Clr5: Clr5 domain
Probab=27.06 E-value=1.4e+02 Score=17.56 Aligned_cols=38 Identities=13% Similarity=0.170 Sum_probs=28.5
Q ss_pred HHHHHHHHHH-hCCCChHHHHHHHHHhCCCCcchHhHHhH
Q 040570 36 EKSNLLVDMS-KNNVRPKDVLHVLKKRNMHNATTIRAIYN 74 (210)
Q Consensus 36 ~~k~~i~~l~-~~g~~p~~I~~~l~~~~~~~~~t~~di~N 74 (210)
..|..|..|. ..|.+-.+|++.|.+.++ ...+.+...+
T Consensus 7 ~~K~~I~~LY~~e~~tl~~v~~~M~~~~~-F~at~rqy~~ 45 (54)
T PF14420_consen 7 PHKEEIERLYIDENKTLEEVMEIMKEEHG-FKATKRQYKR 45 (54)
T ss_pred HHHHHHHHHHHhCCCcHHHHHHHHHHHhC-CCcCHHHHHH
Confidence 4577888876 789999999999998885 4455554433
No 74
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=26.18 E-value=1.6e+02 Score=18.23 Aligned_cols=38 Identities=16% Similarity=0.295 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCCcchHhHHhHHHHHHhhhhcccchHHHHH
Q 040570 54 VLHVLKKRNMHNATTIRAIYNARQKYKVREQVGHSQMQLL 93 (210)
Q Consensus 54 I~~~l~~~~~~~~~t~~di~N~~~k~~~~~~~g~~~~~~L 93 (210)
+..+|++.. .+.+.+||++.......-...|.+|...+
T Consensus 7 a~~vL~~~~--~pm~~~eI~~~i~~~~~~~~~~k~p~~~i 44 (72)
T PF05066_consen 7 AYEVLEEAG--RPMTFKEIWEEIQERGLYKKSGKTPEATI 44 (72)
T ss_dssp HHHHHHHH---S-EEHHHHHHHHHHHHTS---GGGGGHHH
T ss_pred HHHHHHhcC--CCcCHHHHHHHHHHhCCCCcccCCHHHHH
Confidence 445555544 35888999988777654443355554433
No 75
>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=25.99 E-value=1.5e+02 Score=19.76 Aligned_cols=19 Identities=21% Similarity=0.184 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHHHHhCCCC
Q 040570 32 ILNKEKSNLLVDMSKNNVR 50 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~ 50 (210)
-|++++++.......+|+.
T Consensus 22 ~Ls~eE~EL~ELa~~AGv~ 40 (88)
T PF12926_consen 22 VLSAEEVELYELAQLAGVP 40 (88)
T ss_pred ccCHHHHHHHHHHHHhCCC
Confidence 3777777655444445544
No 76
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.03 E-value=90 Score=18.89 Aligned_cols=31 Identities=13% Similarity=0.279 Sum_probs=21.9
Q ss_pred cCCCCHHHHHH---HHHHHhCCCChHHHHHHHHH
Q 040570 30 AGILNKEKSNL---LVDMSKNNVRPKDVLHVLKK 60 (210)
Q Consensus 30 ~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l~~ 60 (210)
+|..++++... |..|.+.|++..+|...|.+
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 46777766554 55688899999999998864
No 77
>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=24.93 E-value=2e+02 Score=18.67 Aligned_cols=34 Identities=6% Similarity=0.081 Sum_probs=26.1
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHHHHhC
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVLKKRN 62 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l~~~~ 62 (210)
.+|.-++++... |..|.+.|++..+|...+....
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 467788776654 5568889999999999997544
No 78
>PF06720 Phi-29_GP16_7: Bacteriophage phi-29 early protein GP16.7; InterPro: IPR009595 The early-expressed gene 16.7 is conserved in bacteriophage phi-29 and related phages. It encodes a membrane protein, GP16.7, consisting of an N-terminal transmembrane domain and a C-terminal DNA-binding and dimerisation domain. GP16.7 plays an important role in organising membrane-associated bacteriophage DNA replication [, ]. The C-terminal domain has a similar secondary structure similar to homeodomains, but forms a fundamentally different tertiary structure consisting of a six-helical dimeric fold []. Multimerisation of this dimer leads to efficient DNA binding.; PDB: 2C5R_B 2BNK_A 1ZAE_B.
Probab=24.71 E-value=2.5e+02 Score=19.59 Aligned_cols=45 Identities=22% Similarity=0.327 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhCCCC-hHHHHHHHHHhCCCCcchHhHHhHHHHHHh
Q 040570 33 LNKEKSNLLVDMSKNNVR-PKDVLHVLKKRNMHNATTIRAIYNARQKYK 80 (210)
Q Consensus 33 lt~~~k~~i~~l~~~g~~-p~~I~~~l~~~~~~~~~t~~di~N~~~k~~ 80 (210)
++..+.+..+.+-++|++ |..|++.+..+ .+-|.+++-|+....|
T Consensus 68 ~s~~e~~vLDlYe~SnIrIP~DIIEdl~~~---~L~Te~eVmnYiEnqR 113 (130)
T PF06720_consen 68 LSACESAVLDLYEQSNIRIPSDIIEDLVNQ---RLQTEQEVMNYIENQR 113 (130)
T ss_dssp S-HHHHHHHHHHHHTT----HHHHHHHHTT-----SSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHHHH---hhhhHHHHHHHHHhhH
Confidence 444445555666789998 88999888732 3567788877766544
No 79
>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=24.64 E-value=1.3e+02 Score=18.18 Aligned_cols=30 Identities=13% Similarity=0.205 Sum_probs=22.3
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHH
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVL 58 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l 58 (210)
.+|..++++... |..|.+.|++..+|...|
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 467787766655 456778999999988765
No 80
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=24.31 E-value=89 Score=25.93 Aligned_cols=32 Identities=9% Similarity=0.119 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHHhCC
Q 040570 32 ILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNM 63 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~ 63 (210)
.||..++..|..+.+.|++.++|-..|....+
T Consensus 7 hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~s 38 (318)
T COG2826 7 HLTLFERYEIERLLKAKMSIREIAKQLNRHHS 38 (318)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcc
Confidence 78999999999999999999999999987665
No 81
>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=23.56 E-value=1e+02 Score=14.84 Aligned_cols=28 Identities=11% Similarity=0.019 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHH
Q 040570 31 GILNKEKSNLLVDMSKNNVRPKDVLHVL 58 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~~g~~p~~I~~~l 58 (210)
+.++++.+..+..+...|.+..+|...+
T Consensus 4 ~~~~~~~~~~i~~~~~~~~s~~~ia~~~ 31 (42)
T cd00569 4 PKLTPEQIEEARRLLAAGESVAEIARRL 31 (42)
T ss_pred CcCCHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3466666777776777777777665443
No 82
>KOG3095 consensus Transcription initiation factor IIE, beta subunit [Transcription]
Probab=23.45 E-value=2.8e+02 Score=22.70 Aligned_cols=39 Identities=13% Similarity=0.084 Sum_probs=24.3
Q ss_pred cchHHHHHHHHhhccceeEEEeeecCCCceEEEEEeChhh
Q 040570 86 GHSQMQLLMSKLIEQKYIERHKSDVDTNCVKALFLAHPSA 125 (210)
Q Consensus 86 g~~~~~~L~~~l~~~~~~~~~~~~d~~~~~~~lf~a~~~~ 125 (210)
|.......++.|++++.++|....- |+.-.-+||-+.++
T Consensus 165 ~~pNv~~~lk~L~~s~eIl~l~t~~-d~k~kivf~ND~~~ 203 (284)
T KOG3095|consen 165 AWPNVDEDLKELEKSGEILVLRTPK-DDKPKIVFYNDKSC 203 (284)
T ss_pred cccchHHHHHHHhcCCcEEEEeccC-CCCCceEEecCCCC
Confidence 3445677788888888876655421 24455567766554
No 83
>PRK14994 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional
Probab=23.36 E-value=2.2e+02 Score=23.41 Aligned_cols=32 Identities=9% Similarity=0.094 Sum_probs=26.8
Q ss_pred HHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHH
Q 040570 44 MSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQK 78 (210)
Q Consensus 44 l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k 78 (210)
+...|++++++.+.+.+.++ +..+++|+....
T Consensus 252 ~~~~~~~~k~a~~~~a~~~~---~~k~~~Y~~~~~ 283 (287)
T PRK14994 252 LLQAELPLKKAAALAAEIHG---VKKNALYKYALE 283 (287)
T ss_pred HHHcCCCHHHHHHHHHHHHC---cCHHHHHHHHHH
Confidence 55679999999999999886 678999987665
No 84
>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=23.33 E-value=1.7e+02 Score=17.68 Aligned_cols=30 Identities=17% Similarity=0.168 Sum_probs=22.1
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHH
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVL 58 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l 58 (210)
.+|..+.++... |..|.+.|++..+|...|
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 467788776655 456778999988887765
No 85
>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=23.26 E-value=2.8e+02 Score=19.72 Aligned_cols=48 Identities=19% Similarity=0.059 Sum_probs=27.0
Q ss_pred eEEeeecC-CceEEEEEEeecCccchhHHHHHHHHHHHHhcCCCC-eEEEecCcccC
Q 040570 153 EIAGVTSI-DLTFSVCCVYLKLKWENNYIWALERLKSIMEENMLA-SVIVTDRELAW 207 (210)
Q Consensus 153 ~~~g~~~~-~~~~~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~p-~~iitD~d~al 207 (210)
++++++.. +.+--+....+.+.+.++..-++ ..... | .+|+||.-.|-
T Consensus 37 V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i---~~~i~----~gs~i~TD~~~aY 86 (151)
T PF12762_consen 37 VFGAVERNDGGTGRVFMFVVPDRSAETLKPII---QEHIE----PGSTIITDGWRAY 86 (151)
T ss_pred EEEEEeecccCCceEEEEeecccccchhHHHH---HHhhh----ccceeeecchhhc
Confidence 34445554 33334444555788888875443 33332 4 57889976653
No 86
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. 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 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=23.12 E-value=2.5e+02 Score=19.10 Aligned_cols=34 Identities=12% Similarity=0.073 Sum_probs=26.6
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHHHHhC
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVLKKRN 62 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l~~~~ 62 (210)
.+|.-++++... |..+.+.|++..+|..++....
T Consensus 35 gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (113)
T cd01109 35 GIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRR 71 (113)
T ss_pred CCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHc
Confidence 468888876665 4568889999999999997544
No 87
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=22.81 E-value=2.8e+02 Score=19.56 Aligned_cols=33 Identities=6% Similarity=0.104 Sum_probs=25.6
Q ss_pred ccCCCCHHHHHH---HHHHHhCCCChHHHHHHHHHh
Q 040570 29 FAGILNKEKSNL---LVDMSKNNVRPKDVLHVLKKR 61 (210)
Q Consensus 29 ~~R~lt~~~k~~---i~~l~~~g~~p~~I~~~l~~~ 61 (210)
.+|.-++++... |..|.+.|++..+|..++...
T Consensus 36 gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~ 71 (131)
T TIGR02043 36 GYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIK 71 (131)
T ss_pred CceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 367777766554 567889999999999999754
No 88
>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=22.68 E-value=1.7e+02 Score=17.06 Aligned_cols=42 Identities=10% Similarity=0.224 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhh
Q 040570 32 ILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKV 81 (210)
Q Consensus 32 ~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~ 81 (210)
.||+.+.. |..+...|.++++|-..+ .++.+.|++.+....+
T Consensus 3 ~LT~~E~~-vl~~l~~G~~~~eIA~~l-------~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 3 SLTERELE-VLRLLAQGMSNKEIAEEL-------GISEKTVKSHRRRIMK 44 (58)
T ss_dssp SS-HHHHH-HHHHHHTTS-HHHHHHHH-------TSHHHHHHHHHHHHHH
T ss_pred ccCHHHHH-HHHHHHhcCCcchhHHhc-------CcchhhHHHHHHHHHH
Confidence 46776655 556778999999998876 2556677777666654
No 89
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=22.01 E-value=2.1e+02 Score=20.23 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHHHHHhCCCChHHHHHHHHHhCCCC
Q 040570 31 GILNKEKSNLLVDMSKNNVRPKDVLHVLKKRNMHN 65 (210)
Q Consensus 31 R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~~~~~ 65 (210)
..|+.+-++.|..+.-++..-..++..|.++||..
T Consensus 36 ~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~ 70 (145)
T PF03564_consen 36 SCLKGEAKELIRGLPLSEENYEEAWELLEERYGNP 70 (145)
T ss_pred HHhcchHHHHHHcccccchhhHHHHHHHHHHhCCc
Confidence 44555566666655555566678888899999864
No 90
>cd01903 Ntn_AC_NAAA AC_NAAA This conserved domain includes two closely related proteins, acid ceramidase (AC, also known as N-acylsphingosine amidohydrolase), and N-acylethanolamine-hydrolyzing acid amidase (NAAA). AC catalyzes the hydrolysis of ceramide to sphingosine and fatty acid. Ceramide is required for the biosynthesis of most sphingolipids and plays an important role in many signal transduction pathways by inducing apoptosis and/or arresting cell growth. An inherited deficiency of AC activity leads to the lysosomal storage disorder known as Farber disease. AC is considered a "rheostat" important for maintaining the proper intracellular levels of these lipids since hydrolysis of ceramide is the only source of sphingosine in cells. NAAA is a eukaryotic glycoprotein that hydrolyzes bioactive N-acylethanolamines, including anandamide (an endocannabinoid) and N-palmitoylethanolamine (an anti-inflammatory and neuroprotective substance), to fatty acids and ethanolamine at acidic pH
Probab=21.62 E-value=2.7e+02 Score=21.92 Aligned_cols=52 Identities=13% Similarity=0.119 Sum_probs=33.8
Q ss_pred CCCCcEEEEecCCCCCCCCCCCccccccCCCCHHHHHHHHHHHhCCCChHHHHHHHHHh
Q 040570 3 NNDDWALIVKYGFHNHLATQYLEGHSFAGILNKEKSNLLVDMSKNNVRPKDVLHVLKKR 61 (210)
Q Consensus 3 ~~~~W~v~~~~~~HNH~~~~~~~~h~~~R~lt~~~k~~i~~l~~~g~~p~~I~~~l~~~ 61 (210)
.++.|.+...|.+|--++-... .|| ++.+ +.+..+.+.++.+..+++.|...
T Consensus 162 ~~~~~~lv~TNyD~~~~~~~~d-----~rr-~~a~-~~l~~~~~~~~~~~~~~~vl~~~ 213 (231)
T cd01903 162 KNGTWFLVQTNYDRWKPPPFLD-----DRR-TPAI-KCMNALGQANISFKTLYDVLSTK 213 (231)
T ss_pred CCCCeEEEEecCCCCCCCcccc-----cCc-CHHH-HHHHHhccccCCHHHHHHHhccC
Confidence 3567888888888876653221 233 3333 34566778889999999887653
No 91
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.55 E-value=3e+02 Score=19.33 Aligned_cols=33 Identities=3% Similarity=0.102 Sum_probs=25.7
Q ss_pred ccCCCCHHHHH---HHHHHHhCCCChHHHHHHHHHh
Q 040570 29 FAGILNKEKSN---LLVDMSKNNVRPKDVLHVLKKR 61 (210)
Q Consensus 29 ~~R~lt~~~k~---~i~~l~~~g~~p~~I~~~l~~~ 61 (210)
..|.-++++.. .|..+.+.|++-.+|..++...
T Consensus 35 gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~ 70 (127)
T TIGR02047 35 NYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQ 70 (127)
T ss_pred CCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 46778877644 4667889999999999999743
No 92
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=21.38 E-value=2.5e+02 Score=20.23 Aligned_cols=48 Identities=13% Similarity=0.048 Sum_probs=31.0
Q ss_pred hhhHHHHHhCCcEEEEecccccCcCCCceeeEEeeecCCceEEEEEEeecCccchhHHHHHHHH
Q 040570 123 PSAIELLQAFPRVLIMDCTYKTNRYDMPLLEIAGVTSIDLTFSVCCVYLKLKWENNYIWALERL 186 (210)
Q Consensus 123 ~~~~~~~~~f~~vl~~D~Ty~tn~~~~pl~~~~g~~~~~~~~~~~~~~~~~E~~e~~~w~l~~~ 186 (210)
.+-+++|..|++|..+.-.. ......+-+||||.=++.++-..+++.+
T Consensus 49 ~~L~~~F~~~G~I~~v~i~~----------------d~~tg~~kGfaFV~F~~~e~A~~Al~~l 96 (144)
T PLN03134 49 ASLRDAFAHFGDVVDAKVIV----------------DRETGRSRGFGFVNFNDEGAATAAISEM 96 (144)
T ss_pred HHHHHHHhcCCCeEEEEEEe----------------cCCCCCcceEEEEEECCHHHHHHHHHHc
Confidence 44556888898876543211 1111223478899988899988888765
No 93
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=21.02 E-value=2e+02 Score=17.20 Aligned_cols=42 Identities=12% Similarity=0.179 Sum_probs=26.0
Q ss_pred HHHHHHHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHh
Q 040570 39 NLLVDMSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYK 80 (210)
Q Consensus 39 ~~i~~l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~ 80 (210)
..|.......++..+++..|.++.+-.+....-+|+...+..
T Consensus 3 ~lIErCl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN 44 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVRALQKQANIEPVFTSTVWQKLEKEN 44 (54)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHC
Confidence 445666677788888888888776533333344665554443
No 94
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=20.73 E-value=95 Score=16.48 Aligned_cols=29 Identities=10% Similarity=0.096 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHH-hCCCChHHHHHHHHH
Q 040570 32 ILNKEKSNLLVDMS-KNNVRPKDVLHVLKK 60 (210)
Q Consensus 32 ~lt~~~k~~i~~l~-~~g~~p~~I~~~l~~ 60 (210)
+++++..+.+..+. +.|.+...++..+-+
T Consensus 5 ~l~~~~~~~l~~~a~~~g~s~s~~ir~ai~ 34 (39)
T PF01402_consen 5 RLPDELYERLDELAKELGRSRSELIREAIR 34 (39)
T ss_dssp EEEHHHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred EeCHHHHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 35667777787775 478887777665543
No 95
>KOG2599 consensus Pyridoxal/pyridoxine/pyridoxamine kinase [Coenzyme transport and metabolism]
Probab=20.72 E-value=4.9e+02 Score=21.49 Aligned_cols=32 Identities=28% Similarity=0.390 Sum_probs=19.7
Q ss_pred CcEEEEecCCC--CCCCCCCCccccccCCCCHHHHHHH
Q 040570 6 DWALIVKYGFH--NHLATQYLEGHSFAGILNKEKSNLL 41 (210)
Q Consensus 6 ~W~v~~~~~~H--NH~~~~~~~~h~~~R~lt~~~k~~i 41 (210)
+|.|..++..| ||.- +.|-.-+.+++++...+
T Consensus 37 GwdVD~insVqFSNHtG----Y~~~kG~~~~~~eL~dL 70 (308)
T KOG2599|consen 37 GWDVDVINSVQFSNHTG----YAHVKGQVLNEEELEDL 70 (308)
T ss_pred ccccccccceeeccccC----CccccccccCHHHHHHH
Confidence 58888887755 7764 33444466777655443
No 96
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.39 E-value=6e+02 Score=22.45 Aligned_cols=24 Identities=13% Similarity=0.332 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCChHHHHHHHHHhC
Q 040570 39 NLLVDMSKNNVRPKDVLHVLKKRN 62 (210)
Q Consensus 39 ~~i~~l~~~g~~p~~I~~~l~~~~ 62 (210)
+.|....+.||+..||+++|+.+.
T Consensus 336 ~Sv~~A~~~GITa~qIi~fl~~~a 359 (448)
T TIGR00625 336 ESIRRALANGITAQQIIHYLRTHA 359 (448)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhcC
Confidence 456667789999999999998443
No 97
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.37 E-value=3.1e+02 Score=19.02 Aligned_cols=46 Identities=9% Similarity=0.049 Sum_probs=32.8
Q ss_pred cCCCCHHHHHHHHH-HHhCCCChHHHHHHHHHhCCCCcchHhHHhHHHHHHhhh
Q 040570 30 AGILNKEKSNLLVD-MSKNNVRPKDVLHVLKKRNMHNATTIRAIYNARQKYKVR 82 (210)
Q Consensus 30 ~R~lt~~~k~~i~~-l~~~g~~p~~I~~~l~~~~~~~~~t~~di~N~~~k~~~~ 82 (210)
.|+-|++.|..+.. +...|.+.++|..- +| ++...+||.+.+++..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e----~g---Is~~tl~~W~r~y~~~ 56 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQ----HG---VAASQLFLWRKQYQEG 56 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHH----HC---cCHHHHHHHHHHHhhc
Confidence 47788998888765 46788888777443 32 4667788888887653
No 98
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=20.20 E-value=3.4e+02 Score=19.55 Aligned_cols=32 Identities=3% Similarity=-0.002 Sum_probs=24.8
Q ss_pred ccCCCCHHHHH---HHHHHHhCCCChHHHHHHHHH
Q 040570 29 FAGILNKEKSN---LLVDMSKNNVRPKDVLHVLKK 60 (210)
Q Consensus 29 ~~R~lt~~~k~---~i~~l~~~g~~p~~I~~~l~~ 60 (210)
.+|.-++++.. .|..+.+.|++...|..++..
T Consensus 35 g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (142)
T TIGR01950 35 NQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAV 69 (142)
T ss_pred CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 35777776554 456788999999999999974
No 99
>TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components.
Probab=20.02 E-value=2.7e+02 Score=19.16 Aligned_cols=38 Identities=3% Similarity=-0.084 Sum_probs=26.9
Q ss_pred EEEEEeecCccchhHHHHHHHHHHHHhcCCCCeEEEecC
Q 040570 165 SVCCVYLKLKWENNYIWALERLKSIMEENMLASVIVTDR 203 (210)
Q Consensus 165 ~~~~~~~~~E~~e~~~w~l~~~~~~~~~~~~p~~iitD~ 203 (210)
+.+++|..+++.+.|.--++...+-.. ......|+||=
T Consensus 30 i~~i~~~~~~~~~~~~~~l~~~i~~~~-~~~~vivltDl 67 (116)
T TIGR00824 30 VGAVPFVPGENAETLQEKYNAALADLD-TEEEVLFLVDI 67 (116)
T ss_pred eEEEEcCCCcCHHHHHHHHHHHHHhcC-CCCCEEEEEeC
Confidence 456778888988888877766666553 24456888984
Done!