Query 047187
Match_columns 339
No_of_seqs 159 out of 378
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 08:35:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047187.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047187hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03162 golden-2 like transcr 100.0 3E-28 6.5E-33 238.6 11.3 100 151-252 230-329 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.9 8.7E-22 1.9E-26 147.6 6.4 55 156-210 1-56 (57)
3 PF00249 Myb_DNA-binding: Myb- 98.1 8.5E-06 1.9E-10 57.6 5.3 48 158-208 1-48 (48)
4 smart00426 TEA TEA domain. 95.5 0.015 3.3E-07 46.2 3.5 46 160-206 5-67 (68)
5 smart00717 SANT SANT SWI3, AD 94.9 0.11 2.4E-06 34.3 5.7 43 159-206 2-45 (49)
6 cd00167 SANT 'SWI3, ADA2, N-Co 94.4 0.16 3.6E-06 33.1 5.6 44 160-207 1-44 (45)
7 PF01285 TEA: TEA/ATTS domain 87.8 0.53 1.1E-05 48.1 3.6 53 155-207 46-112 (431)
8 PF12776 Myb_DNA-bind_3: Myb/S 82.4 2.2 4.8E-05 33.0 4.1 52 160-211 1-65 (96)
9 PF13921 Myb_DNA-bind_6: Myb-l 79.2 6.2 0.00014 28.5 5.3 41 161-206 1-41 (60)
10 KOG3841 TEF-1 and related tran 70.9 11 0.00024 39.1 6.3 54 157-210 75-144 (455)
11 KOG0457 Histone acetyltransfer 63.0 15 0.00032 38.4 5.5 52 155-210 69-120 (438)
12 PF04624 Dec-1: Dec-1 repeat; 60.6 1.6 3.5E-05 29.6 -1.1 11 301-311 2-12 (27)
13 PLN03212 Transcription repress 58.8 23 0.0005 34.5 5.7 45 154-201 21-65 (249)
14 PLN03091 hypothetical protein; 53.9 26 0.00057 36.8 5.6 37 153-191 9-45 (459)
15 cd00086 homeodomain Homeodomai 51.5 65 0.0014 22.3 5.8 56 156-213 2-57 (59)
16 PF00046 Homeobox: Homeobox do 47.7 55 0.0012 23.1 4.9 57 155-213 1-57 (57)
17 KOG0724 Zuotin and related mol 45.9 7.3 0.00016 37.2 0.2 53 157-214 52-104 (335)
18 PLN03212 Transcription repress 45.2 90 0.0019 30.6 7.4 40 159-203 79-118 (249)
19 PRK11923 algU RNA polymerase s 44.0 67 0.0015 27.5 5.8 48 163-213 126-184 (193)
20 cd06171 Sigma70_r4 Sigma70, re 43.4 83 0.0018 20.3 5.0 30 180-212 26-55 (55)
21 KOG0848 Transcription factor C 43.2 2.3E+02 0.0049 28.7 9.8 61 147-213 192-256 (317)
22 TIGR02894 DNA_bind_RsfA transc 42.0 15 0.00033 33.7 1.6 56 149-209 39-94 (161)
23 PLN03091 hypothetical protein; 38.0 1E+02 0.0022 32.6 7.0 40 159-203 68-107 (459)
24 PRK09642 RNA polymerase sigma 37.4 1E+02 0.0022 25.5 5.7 48 164-214 95-153 (160)
25 KOG0842 Transcription factor t 36.6 13 0.00028 37.0 0.3 63 148-216 147-213 (307)
26 cd08783 Death_MALT1 Death doma 36.0 64 0.0014 27.7 4.3 47 158-207 37-84 (97)
27 smart00501 BRIGHT BRIGHT, ARID 35.9 89 0.0019 24.7 4.9 48 163-211 32-87 (93)
28 COG5114 Histone acetyltransfer 35.2 54 0.0012 33.8 4.4 48 159-210 64-111 (432)
29 PRK12541 RNA polymerase sigma 34.1 1.3E+02 0.0029 24.9 5.9 46 166-214 103-159 (161)
30 PRK13919 putative RNA polymera 33.0 1.3E+02 0.0028 25.6 5.8 44 167-213 127-181 (186)
31 KOG0850 Transcription factor D 32.6 1.1E+02 0.0023 30.1 5.7 63 148-216 116-182 (245)
32 PF00690 Cation_ATPase_N: Cati 31.8 59 0.0013 24.2 3.1 28 182-209 5-35 (69)
33 TIGR02983 SigE-fam_strep RNA p 31.4 1.4E+02 0.003 24.7 5.6 49 163-214 98-157 (162)
34 TIGR02989 Sig-70_gvs1 RNA poly 30.7 1.4E+02 0.0031 24.4 5.5 49 162-213 98-157 (159)
35 PRK11924 RNA polymerase sigma 30.0 1.5E+02 0.0033 24.3 5.6 46 165-213 115-171 (179)
36 PF14075 UBN_AB: Ubinuclein co 29.9 73 0.0016 30.0 4.1 24 151-174 145-168 (214)
37 TIGR02950 SigM_subfam RNA poly 29.4 1.8E+02 0.0039 23.7 5.9 46 165-213 95-151 (154)
38 TIGR02985 Sig70_bacteroi1 RNA 29.3 1.8E+02 0.004 23.4 5.8 48 163-213 101-159 (161)
39 PRK09646 RNA polymerase sigma 29.3 1.6E+02 0.0035 25.5 5.9 49 163-214 130-189 (194)
40 PRK06759 RNA polymerase factor 29.2 1.7E+02 0.0037 23.9 5.7 47 164-213 95-152 (154)
41 PRK09640 RNA polymerase sigma 28.8 2E+02 0.0042 24.8 6.3 51 160-213 119-180 (188)
42 PRK12519 RNA polymerase sigma 28.1 1.7E+02 0.0038 25.0 5.8 29 182-213 159-187 (194)
43 PRK12530 RNA polymerase sigma 27.6 98 0.0021 26.9 4.2 47 164-213 123-180 (189)
44 PRK09415 RNA polymerase factor 27.3 1.9E+02 0.004 24.8 5.8 48 163-213 115-173 (179)
45 TIGR02960 SigX5 RNA polymerase 27.2 1E+02 0.0022 28.8 4.5 47 165-214 132-189 (324)
46 PRK12514 RNA polymerase sigma 27.1 1.8E+02 0.0039 24.6 5.7 30 182-214 147-176 (179)
47 KOG0843 Transcription factor E 26.9 1.1E+02 0.0025 29.0 4.7 62 153-217 101-163 (197)
48 PRK09652 RNA polymerase sigma 26.8 2E+02 0.0044 23.7 5.8 46 165-213 118-174 (182)
49 PF13837 Myb_DNA-bind_4: Myb/S 26.5 84 0.0018 23.9 3.2 49 158-206 1-62 (90)
50 PRK09644 RNA polymerase sigma 26.5 1.1E+02 0.0025 25.6 4.3 50 162-214 95-155 (165)
51 TIGR02943 Sig70_famx1 RNA poly 25.8 2E+02 0.0042 25.1 5.8 48 164-214 120-178 (188)
52 PRK12544 RNA polymerase sigma 25.8 1.8E+02 0.004 26.0 5.7 48 164-214 137-195 (206)
53 PRK09643 RNA polymerase sigma 25.7 2.1E+02 0.0046 24.9 6.0 49 163-214 122-181 (192)
54 COG1595 RpoE DNA-directed RNA 25.0 1.5E+02 0.0032 25.5 4.8 50 163-215 115-175 (182)
55 TIGR02947 SigH_actino RNA poly 24.8 1.9E+02 0.0041 25.0 5.5 46 166-214 122-178 (193)
56 PF11888 DUF3408: Protein of u 24.5 2.2E+02 0.0047 24.6 5.7 46 159-213 83-128 (136)
57 smart00389 HOX Homeodomain. DN 23.8 2.4E+02 0.0051 19.5 4.9 52 156-209 2-53 (56)
58 PRK12545 RNA polymerase sigma 23.2 2.3E+02 0.005 24.9 5.8 44 167-213 131-185 (201)
59 PRK12515 RNA polymerase sigma 22.7 2.5E+02 0.0054 24.1 5.8 48 164-214 120-178 (189)
60 TIGR02948 SigW_bacill RNA poly 22.5 2.2E+02 0.0048 24.0 5.3 47 164-213 125-182 (187)
61 PRK12533 RNA polymerase sigma 22.4 2.4E+02 0.0052 25.7 5.9 49 163-214 122-181 (216)
62 TIGR02952 Sig70_famx2 RNA poly 22.0 1.8E+02 0.004 23.9 4.7 46 165-213 112-168 (170)
63 PRK09047 RNA polymerase factor 21.7 2.6E+02 0.0057 22.9 5.5 49 162-213 93-152 (161)
64 PRK09636 RNA polymerase sigma 21.6 2.3E+02 0.0049 26.6 5.7 51 162-215 102-163 (293)
65 TIGR02937 sigma70-ECF RNA poly 21.6 2.9E+02 0.0062 21.3 5.4 28 183-213 129-156 (158)
66 PRK12520 RNA polymerase sigma 21.5 2.6E+02 0.0057 24.0 5.7 46 165-213 121-177 (191)
67 PRK12536 RNA polymerase sigma 21.4 2.7E+02 0.0058 23.8 5.7 47 164-213 118-175 (181)
68 TIGR03001 Sig-70_gmx1 RNA poly 20.9 2.3E+02 0.0051 26.4 5.6 50 161-213 147-207 (244)
69 PRK11922 RNA polymerase sigma 20.9 2.7E+02 0.0059 25.1 5.9 52 160-214 134-196 (231)
70 PRK12522 RNA polymerase sigma 20.9 1.7E+02 0.0037 24.7 4.3 51 160-213 104-165 (173)
71 KOG0493 Transcription factor E 20.6 3E+02 0.0066 27.9 6.5 65 153-219 245-309 (342)
72 PRK08241 RNA polymerase factor 20.0 2.4E+02 0.0052 26.7 5.5 46 165-213 143-199 (339)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.95 E-value=3e-28 Score=238.62 Aligned_cols=100 Identities=35% Similarity=0.600 Sum_probs=84.3
Q ss_pred ccCCCCCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhhcCCCCCCCCCCccccc
Q 047187 151 ARTLKRPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQGLSNDDPSSSDHQLF 230 (339)
Q Consensus 151 ~~~~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~~~l~~~gps~sd~~l~ 230 (339)
+...||+||+||+|||+|||+||++||+++||||+||++|+|+||||+||||||||||+++||+.....+..+.++++++
T Consensus 230 ~~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~swt~kr~~ 309 (526)
T PLN03162 230 APGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWTHRRAY 309 (526)
T ss_pred CCCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhccchhhhhh
Confidence 34589999999999999999999999999999999999999999999999999999999999887777777777776778
Q ss_pred ccCCCCCCCCCCCCCCcccccc
Q 047187 231 ASTPVPPHNNGSGNSGHVGMAA 252 (339)
Q Consensus 231 ~stpvp~s~~~~~~~g~~~~P~ 252 (339)
..+|.+.+...++ .+..+||
T Consensus 310 ~~~P~~rs~~~~g--~p~~~pi 329 (526)
T PLN03162 310 TQAPWPRSSRRDG--LPYLVPI 329 (526)
T ss_pred ccCCcccCCCCCC--Ccccccc
Confidence 7777666544333 3444554
No 2
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.85 E-value=8.7e-22 Score=147.55 Aligned_cols=55 Identities=60% Similarity=0.983 Sum_probs=53.0
Q ss_pred CCCeecChHHHHHHHHHHHHhCC-CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHH
Q 047187 156 RPRLVWTPQLHKRFVDVVAHLGI-KNAVPKTIMQLMNVEGLTRENVASHLQKYRLY 210 (339)
Q Consensus 156 KpRl~WT~ELH~rFVeAV~qLG~-dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~ 210 (339)
|+|++||+|||++||+||++||. +.|+||+|+++|++++||+.||+|||||||++
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 68999999999999999999995 89999999999999999999999999999985
No 3
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=98.06 E-value=8.5e-06 Score=57.60 Aligned_cols=48 Identities=25% Similarity=0.322 Sum_probs=42.3
Q ss_pred CeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhH
Q 047187 158 RLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYR 208 (339)
Q Consensus 158 Rl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYR 208 (339)
|..||+|.+.+|++||.++|.+ .++.|.+.|+ .+.|..++++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~--~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD--NWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT--HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCc--HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 5689999999999999999965 5999999999 7899999999999985
No 4
>smart00426 TEA TEA domain.
Probab=95.51 E-value=0.015 Score=46.24 Aligned_cols=46 Identities=28% Similarity=0.486 Sum_probs=30.7
Q ss_pred ecChHHHHHHHHHHHHhCCCCCChH-HHHHh-------------hC-CCC--CCHHHHHHHhhh
Q 047187 160 VWTPQLHKRFVDVVAHLGIKNAVPK-TIMQL-------------MN-VEG--LTRENVASHLQK 206 (339)
Q Consensus 160 ~WT~ELH~rFVeAV~qLG~dkAtPK-~ILel-------------M~-V~G--LTr~nVkSHLQK 206 (339)
+|.++|-..|++|+..+=. ..+-| +|+.. +- ..| .|++||.||||-
T Consensus 5 vWp~~lE~Af~~aL~~~~~-~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYPP-CGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcCc-cCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhee
Confidence 7999999999999997652 22222 22211 11 133 699999999994
No 5
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=94.85 E-value=0.11 Score=34.25 Aligned_cols=43 Identities=19% Similarity=0.295 Sum_probs=36.8
Q ss_pred eecChHHHHHHHHHHHHhC-CCCCChHHHHHhhCCCCCCHHHHHHHhhh
Q 047187 159 LVWTPQLHKRFVDVVAHLG-IKNAVPKTIMQLMNVEGLTRENVASHLQK 206 (339)
Q Consensus 159 l~WT~ELH~rFVeAV~qLG-~dkAtPK~ILelM~V~GLTr~nVkSHLQK 206 (339)
-.||++-...|+.++.++| .+ ++.|.+.|. +-|..+|+.+..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~---w~~Ia~~~~--~rt~~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNN---WEKIAKELP--GRTAEQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCC---HHHHHHHcC--CCCHHHHHHHHHH
Confidence 4699999999999999999 54 899998886 7899999876443
No 6
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=94.36 E-value=0.16 Score=33.11 Aligned_cols=44 Identities=14% Similarity=0.191 Sum_probs=36.9
Q ss_pred ecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhh
Q 047187 160 VWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKY 207 (339)
Q Consensus 160 ~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKY 207 (339)
.||.+-.+.|+.++.++|. ..++.|.+.|+- -|..+|+.+.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~--~~w~~Ia~~~~~--rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK--NNWEKIAKELPG--RTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc--CCHHHHHhHcCC--CCHHHHHHHHHHh
Confidence 4999999999999999993 238999998854 8999999886654
No 7
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=87.76 E-value=0.53 Score=48.07 Aligned_cols=53 Identities=25% Similarity=0.436 Sum_probs=29.4
Q ss_pred CCCCeecChHHHHHHHHHHHHh---CCCCC--------ChHHHHHhhCC---CCCCHHHHHHHhhhh
Q 047187 155 KRPRLVWTPQLHKRFVDVVAHL---GIKNA--------VPKTIMQLMNV---EGLTRENVASHLQKY 207 (339)
Q Consensus 155 kKpRl~WT~ELH~rFVeAV~qL---G~dkA--------tPK~ILelM~V---~GLTr~nVkSHLQKY 207 (339)
++..-+|++++...|++|+..+ |..|- .=+-|.+.+.. .-.|++||+||||--
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 4567899999999999999976 32220 00111111111 347999999999998
No 8
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=82.43 E-value=2.2 Score=33.03 Aligned_cols=52 Identities=15% Similarity=0.318 Sum_probs=38.1
Q ss_pred ecChHHHHHHHHHHHHh---CCC-------CCChHHHHHhhCC---CCCCHHHHHHHhhhhHHHH
Q 047187 160 VWTPQLHKRFVDVVAHL---GIK-------NAVPKTIMQLMNV---EGLTRENVASHLQKYRLYL 211 (339)
Q Consensus 160 ~WT~ELH~rFVeAV~qL---G~d-------kAtPK~ILelM~V---~GLTr~nVkSHLQKYRl~l 211 (339)
.||++..+.||+++... |.. +...+.|.+.++- ..+|..||++|++..|...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHH
Confidence 59999999999998643 422 2346677777763 4579999999998766544
No 9
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=79.21 E-value=6.2 Score=28.47 Aligned_cols=41 Identities=17% Similarity=0.322 Sum_probs=33.7
Q ss_pred cChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhh
Q 047187 161 WTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQK 206 (339)
Q Consensus 161 WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQK 206 (339)
||+|--++.+++|...|.+ ++.|-+.|+ .-|..+|+.+..+
T Consensus 1 WT~eEd~~L~~~~~~~g~~---W~~Ia~~l~--~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGND---WKKIAEHLG--NRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS----HHHHHHHST--TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcC---HHHHHHHHC--cCCHHHHHHHHHH
Confidence 9999999999999999954 999999986 5899999876665
No 10
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=70.94 E-value=11 Score=39.12 Aligned_cols=54 Identities=24% Similarity=0.418 Sum_probs=35.1
Q ss_pred CCeecChHHHHHHHHHHHHh---CCCC----------CChHHHHHhhC---CCCCCHHHHHHHhhhhHHH
Q 047187 157 PRLVWTPQLHKRFVDVVAHL---GIKN----------AVPKTIMQLMN---VEGLTRENVASHLQKYRLY 210 (339)
Q Consensus 157 pRl~WT~ELH~rFVeAV~qL---G~dk----------AtPK~ILelM~---V~GLTr~nVkSHLQKYRl~ 210 (339)
.--+|+++.-+.|.||+..+ |..| ..=.-|-..++ =+-.||+||.||+|-...+
T Consensus 75 aegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarr 144 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARR 144 (455)
T ss_pred cccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHH
Confidence 35689999999999999976 3211 01111222222 2457999999999976443
No 11
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=63.00 E-value=15 Score=38.37 Aligned_cols=52 Identities=17% Similarity=0.199 Sum_probs=45.5
Q ss_pred CCCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHH
Q 047187 155 KRPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLY 210 (339)
Q Consensus 155 kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~ 210 (339)
..-...||.+--..||+|++.+|+.+ |.-|-+.|+. -|.++++.|--|+.+.
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GN--W~dIA~hIGt--Ktkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGN--WQDIADHIGT--KTKEECKEHYLKHFVN 120 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCc--HHHHHHHHcc--cchHHHHHHHHHHHhc
Confidence 33456899999999999999999776 9999999994 8999999998888764
No 12
>PF04624 Dec-1: Dec-1 repeat; InterPro: IPR006718 The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing []. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). This repeat is usually found in 12 copies in the central region of the protein. Its function is unknown. Length polymorphisms of Dec-1 have been observed in wild-type strains, and are caused by changes in the numbers of the first five repeats [].; GO: 0005213 structural constituent of chorion, 0007304 chorion-containing eggshell formation, 0005576 extracellular region, 0042600 chorion
Probab=60.62 E-value=1.6 Score=29.56 Aligned_cols=11 Identities=73% Similarity=1.138 Sum_probs=9.8
Q ss_pred ccccccccCCC
Q 047187 301 NNMMHQQRDWS 311 (339)
Q Consensus 301 ~~~~~~q~~w~ 311 (339)
+.||||||-|+
T Consensus 2 npmMMqqRQws 12 (27)
T PF04624_consen 2 NPMMMQQRQWS 12 (27)
T ss_pred CcHHHHHHHhh
Confidence 57899999998
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=58.77 E-value=23 Score=34.52 Aligned_cols=45 Identities=11% Similarity=0.057 Sum_probs=32.1
Q ss_pred CCCCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHH
Q 047187 154 LKRPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVA 201 (339)
Q Consensus 154 ~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVk 201 (339)
..-.|-.||+|.-++.+++|+++|.. .++.|.+.|+ ++.|..|.+
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~~--nW~~IAk~~g-~gRT~KQCR 65 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGEG--RWRSLPKRAG-LLRCGKSCR 65 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcc--cHHHHHHhhh-cCCCcchHH
Confidence 33457789999999999999999953 3788877664 234444443
No 14
>PLN03091 hypothetical protein; Provisional
Probab=53.91 E-value=26 Score=36.79 Aligned_cols=37 Identities=11% Similarity=0.283 Sum_probs=29.1
Q ss_pred CCCCCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhC
Q 047187 153 TLKRPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMN 191 (339)
Q Consensus 153 ~~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~ 191 (339)
..+..|-+||+|.-++.+++|.++|.. .++.|-++|+
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~--nWs~IAk~~g 45 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHG--CWSSVPKQAG 45 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcC--CHHHHhhhhc
Confidence 345567789999999999999999953 3777776664
No 15
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=51.54 E-value=65 Score=22.35 Aligned_cols=56 Identities=25% Similarity=0.223 Sum_probs=40.4
Q ss_pred CCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 156 RPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 156 KpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
+.|..++.+- ...++++.... ...+...|.++...-|||..+|..-.+.-|...++
T Consensus 2 ~~r~~~~~~~-~~~Le~~f~~~-~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQ-LEELEKEFEKN-PYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHH-HHHHHHHHHhC-CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4555666665 45555555554 34567888888888999999999988888877654
No 16
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=47.69 E-value=55 Score=23.12 Aligned_cols=57 Identities=23% Similarity=0.195 Sum_probs=39.3
Q ss_pred CCCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 155 KRPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 155 kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
||+|..+|.+-.. .++++.... ...+...+.+|...-|||..+|..=.|.-|...||
T Consensus 1 kr~r~~~t~~q~~-~L~~~f~~~-~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLK-VLEEYFQEN-PYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHH-HHHHHHHHS-SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHH-HHHHHHHHh-ccccccccccccccccccccccccCHHHhHHHhCc
Confidence 5678888866544 455555544 23445666666666699999999988888877664
No 17
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=45.86 E-value=7.3 Score=37.22 Aligned_cols=53 Identities=13% Similarity=0.113 Sum_probs=42.1
Q ss_pred CCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 157 PRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 157 pRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
..-+||++.|.+|.+||-.. +..+.+|.+..+. .+..++.+|-|+|...+.+.
T Consensus 52 ~~~~~t~~~~~~~~~~l~~~---~~~~~~~~~~~~~--~~~v~~~~~~~~~~p~~~~~ 104 (335)
T KOG0724|consen 52 DEPRRTPDSWDKFAEALPLE---KRLEDKIEEYIGL--VFDVNIRESGQKPFPKYGKS 104 (335)
T ss_pred cccccchhhhhHHHhcCccc---cccchhHHhhhhh--HHHHhhhhccCCCccccCcc
Confidence 34569999999998887543 4558888877776 78899999999999888765
No 18
>PLN03212 Transcription repressor MYB5; Provisional
Probab=45.24 E-value=90 Score=30.58 Aligned_cols=40 Identities=15% Similarity=0.054 Sum_probs=33.7
Q ss_pred eecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHH
Q 047187 159 LVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASH 203 (339)
Q Consensus 159 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSH 203 (339)
-.||.|.-+.-++++..+|-+ +..|-+.| +|.|-.+||.+
T Consensus 79 gpWT~EED~lLlel~~~~GnK---Ws~IAk~L--pGRTDnqIKNR 118 (249)
T PLN03212 79 GGITSDEEDLILRLHRLLGNR---WSLIAGRI--PGRTDNEIKNY 118 (249)
T ss_pred CCCChHHHHHHHHHHHhcccc---HHHHHhhc--CCCCHHHHHHH
Confidence 468889888899999999954 89998866 88999999865
No 19
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=44.04 E-value=67 Score=27.54 Aligned_cols=48 Identities=13% Similarity=0.140 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 163 PQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
.++++.+.+|+..|... .-+.+.|-+.|| +|...|+++|++=|.+|++
T Consensus 126 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lg---is~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 126 DEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQ---CPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred HHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Confidence 34566778888877632 123455555554 4688899999988888875
No 20
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=43.39 E-value=83 Score=20.33 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=21.8
Q ss_pred CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHh
Q 047187 180 NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLK 212 (339)
Q Consensus 180 kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lk 212 (339)
.-+.+.|-+.|+ ++...|++++++.+..+|
T Consensus 26 ~~~~~~ia~~~~---~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 26 GLSYEEIAEILG---ISRSTVRQRLHRALKKLR 55 (55)
T ss_pred CCCHHHHHHHHC---cCHHHHHHHHHHHHHHcC
Confidence 345788887777 577888888888776653
No 21
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=43.17 E-value=2.3e+02 Score=28.70 Aligned_cols=61 Identities=25% Similarity=0.343 Sum_probs=37.4
Q ss_pred CCCCccCCCCCCeecChH----HHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 147 EDPSARTLKRPRLVWTPQ----LHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 147 ~~~~~~~~kKpRl~WT~E----LH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
.+.+.|+.-|-|+|.|+. |-+.|-- -..+-++ +--||--.=|||..|||.-.|.-|.+-+|
T Consensus 192 ~~~KtRTkDKYRvVYTDhQRLELEKEfh~-SryITir-----RKSELA~~LgLsERQVKIWFQNRRAKERK 256 (317)
T KOG0848|consen 192 QNVKTRTKDKYRVVYTDHQRLELEKEFHT-SRYITIR-----RKSELAATLGLSERQVKIWFQNRRAKERK 256 (317)
T ss_pred CCceeecccceeEEecchhhhhhhhhhcc-ccceeee-----hhHHHHHhhCccHhhhhHhhhhhhHHHHH
Confidence 456778899999999972 3222210 0011111 11244444589999999999988876443
No 22
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=42.01 E-value=15 Score=33.66 Aligned_cols=56 Identities=20% Similarity=0.246 Sum_probs=41.4
Q ss_pred CCccCCCCCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHH
Q 047187 149 PSARTLKRPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRL 209 (339)
Q Consensus 149 ~~~~~~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl 209 (339)
.-.||..-..|||...+-+++.++|+.---.+-.+++. ...||.++|-+-||.|..
T Consensus 39 ~L~RTsAACGFRWNs~VRkqY~~~i~~AKkqRk~~~~~-----~~~ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 39 ALNRTAAACGFRWNAYVRKQYEEAIELAKKQRKELKRE-----AGSLTLQDVISFLQNLKT 94 (161)
T ss_pred HHcccHHHhcchHHHHHHHHHHHHHHHHHHHHhccccC-----cccCCHHHHHHHHHHHHh
Confidence 34577888999999999999999998654211111111 256999999999999984
No 23
>PLN03091 hypothetical protein; Provisional
Probab=37.96 E-value=1e+02 Score=32.56 Aligned_cols=40 Identities=18% Similarity=0.218 Sum_probs=35.1
Q ss_pred eecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHH
Q 047187 159 LVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASH 203 (339)
Q Consensus 159 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSH 203 (339)
-.||.|.-++.++++..+|-+ +.+|-+.| +|.|-.+||.+
T Consensus 68 gpWT~EED~lLLeL~k~~GnK---WskIAk~L--PGRTDnqIKNR 107 (459)
T PLN03091 68 GTFSQQEENLIIELHAVLGNR---WSQIAAQL--PGRTDNEIKNL 107 (459)
T ss_pred CCCCHHHHHHHHHHHHHhCcc---hHHHHHhc--CCCCHHHHHHH
Confidence 369999999999999999964 99999876 89999999855
No 24
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=37.36 E-value=1e+02 Score=25.53 Aligned_cols=48 Identities=13% Similarity=0.110 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 164 QLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 164 ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
++-..+..|+++|..+ .-+.+.|-+.| |++...|++||.+-|..|++.
T Consensus 95 e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l---gis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 95 EQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQE---KIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHHH
Confidence 4445567777777632 22344444444 468888999999999888753
No 25
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=36.59 E-value=13 Score=37.01 Aligned_cols=63 Identities=21% Similarity=0.248 Sum_probs=44.7
Q ss_pred CCCccCCCCCCeecCh----HHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhhcC
Q 047187 148 DPSARTLKRPRLVWTP----QLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQG 216 (339)
Q Consensus 148 ~~~~~~~kKpRl~WT~----ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~~~ 216 (339)
....+..||+|+-.|. ||-+||-..=..=+.++ ..| =..=.||-.|||.=.|..|=++||.+.
T Consensus 147 ~t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPER----E~L--A~~LrLT~TQVKIWFQNrRYK~KR~~~ 213 (307)
T KOG0842|consen 147 QTGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPER----EHL--ASSLRLTPTQVKIWFQNRRYKTKRQQK 213 (307)
T ss_pred ccccccccccccccchhHHHHHHHHHHhhhccccHhH----HHH--HHhcCCCchheeeeeecchhhhhhhhh
Confidence 3346678999999985 89999976544444332 111 112249999999999999999999754
No 26
>cd08783 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins
Probab=35.95 E-value=64 Score=27.66 Aligned_cols=47 Identities=19% Similarity=0.320 Sum_probs=39.2
Q ss_pred CeecCh-HHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhh
Q 047187 158 RLVWTP-QLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKY 207 (339)
Q Consensus 158 Rl~WT~-ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKY 207 (339)
||+-++ ||+++-+..+..-|-. -|.+|++|++.|-|..+.-.-||+-
T Consensus 37 ~fr~S~~el~~cslkvl~p~gSP---sk~LL~~~~~rg~Tv~~Ll~~L~~M 84 (97)
T cd08783 37 RFRLSCLDLEQCSLKVLEPEGSP---SRSLLKLLGERGCTVTELSEFLQAM 84 (97)
T ss_pred ccccCHHHHHHHHHHHhcCCCCc---hHHHHHHHHHcCCcHHHHHHHHHHh
Confidence 778777 8889888888877743 5778899999999999998888863
No 27
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=35.95 E-value=89 Score=24.74 Aligned_cols=48 Identities=19% Similarity=0.229 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHHhCC-----CCCChHHHHHhhCCCCC---CHHHHHHHhhhhHHHH
Q 047187 163 PQLHKRFVDVVAHLGI-----KNAVPKTIMQLMNVEGL---TRENVASHLQKYRLYL 211 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~-----dkAtPK~ILelM~V~GL---Tr~nVkSHLQKYRl~l 211 (339)
-+|++.|.. |..+|. .+..++.|.+.|+++.- ....++++-+||=+-.
T Consensus 32 vdL~~Ly~~-V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 32 LDLYRLYRL-VQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred CcHHHHHHH-HHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 469999985 666674 23569999999999742 2455677767664433
No 28
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=35.24 E-value=54 Score=33.76 Aligned_cols=48 Identities=19% Similarity=0.277 Sum_probs=41.9
Q ss_pred eecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHH
Q 047187 159 LVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLY 210 (339)
Q Consensus 159 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~ 210 (339)
--|+.+.--.|+++++-||+.+ |.-|.+.+| ..+.+.||+|-=||-+-
T Consensus 64 e~WgadEEllli~~~~TlGlGN--W~dIadyiG--sr~kee~k~HylK~y~e 111 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGN--WEDIADYIG--SRAKEEIKSHYLKMYDE 111 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCc--HHHHHHHHh--hhhhHHHHHHHHHHHhh
Confidence 3599999999999999999766 999999999 48999999998887663
No 29
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=34.14 E-value=1.3e+02 Score=24.95 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 166 HKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 166 H~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
...+++|+..|..+ .-+.+.|-+.|| +|...|++||.+=|..|++.
T Consensus 103 ~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lg---is~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 103 IASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTG---LSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHhh
Confidence 35677888877742 223444444444 57788999999988888764
No 30
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=33.02 E-value=1.3e+02 Score=25.59 Aligned_cols=44 Identities=14% Similarity=0.157 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 167 KRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 167 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
....+|+.+|.. +.-+.+.|-+.||+ |..+|+++|++-|.+|++
T Consensus 127 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi---s~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 127 TRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGL---PLGTLKTRARRALSRLKE 181 (186)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHH
Confidence 345667777653 23456677666664 688999999999988875
No 31
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=32.56 E-value=1.1e+02 Score=30.09 Aligned_cols=63 Identities=25% Similarity=0.506 Sum_probs=46.2
Q ss_pred CCCccCCCCCCeecCh----HHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhhcC
Q 047187 148 DPSARTLKRPRLVWTP----QLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQG 216 (339)
Q Consensus 148 ~~~~~~~kKpRl~WT~----ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~~~ 216 (339)
+...++.||+|-..+. .|.+||-.. +.| |.|.+- ||--.=|||..|||.-.|.=|.++||+..
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkT-QYL----ALPERA-eLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQT-QYL----ALPERA-ELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhc-chh----cCcHHH-HHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3455678899988875 577888653 222 445554 55556799999999999999999988754
No 32
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=31.76 E-value=59 Score=24.24 Aligned_cols=28 Identities=25% Similarity=0.458 Sum_probs=22.7
Q ss_pred ChHHHHHhhC---CCCCCHHHHHHHhhhhHH
Q 047187 182 VPKTIMQLMN---VEGLTRENVASHLQKYRL 209 (339)
Q Consensus 182 tPK~ILelM~---V~GLTr~nVkSHLQKYRl 209 (339)
....|++.++ ..|||.++|+..+++|=.
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G~ 35 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERRKKYGP 35 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHHHHHSS
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHHHhccc
Confidence 3567777777 489999999999999954
No 33
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=31.44 E-value=1.4e+02 Score=24.70 Aligned_cols=49 Identities=12% Similarity=0.209 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 163 PQLHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
.++.....+++.+|-. +.-+.+.|-+.|| ++...|++||.+=|..|++.
T Consensus 98 ~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lg---is~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 98 VALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALG---ISVGTVKSRLSRALARLREL 157 (162)
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHHH
Confidence 4455556666666653 2234555555555 47889999999999888864
No 34
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=30.74 E-value=1.4e+02 Score=24.43 Aligned_cols=49 Identities=12% Similarity=0.164 Sum_probs=31.1
Q ss_pred ChHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 162 TPQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 162 T~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
..+++..+.+|+..|..+ .-+.+.|-+.|| +|...|+++|.+=|..|+.
T Consensus 98 ~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~---is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 98 SEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLG---RTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHh
Confidence 456677788888888743 123444444443 5677788887777776653
No 35
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.01 E-value=1.5e+02 Score=24.31 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 165 LHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 165 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
+-..+..++++|.. +.-+.+.|-+.|| +|...|++++.+-|.+|++
T Consensus 115 ~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lg---is~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 115 DLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILG---VPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred HHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Confidence 34455566666552 2233555555555 5788888999888888875
No 36
>PF14075 UBN_AB: Ubinuclein conserved middle domain
Probab=29.87 E-value=73 Score=29.96 Aligned_cols=24 Identities=17% Similarity=0.412 Sum_probs=19.6
Q ss_pred ccCCCCCCeecChHHHHHHHHHHH
Q 047187 151 ARTLKRPRLVWTPQLHKRFVDVVA 174 (339)
Q Consensus 151 ~~~~kKpRl~WT~ELH~rFVeAV~ 174 (339)
.....|.|+.||+++-..+.+.|.
T Consensus 145 ~~~~PrKkF~Wtde~R~lL~~lv~ 168 (214)
T PF14075_consen 145 KVKGPRKKFQWTDEIRELLCELVK 168 (214)
T ss_pred CCCCCCcCCCCCHHHHHHHHHHHH
Confidence 345667899999999999988776
No 37
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=29.36 E-value=1.8e+02 Score=23.67 Aligned_cols=46 Identities=26% Similarity=0.283 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 165 LHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 165 LH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
....+.+++++|... .-+-+.|-+.|| +|...|+++|.+-|.+|++
T Consensus 95 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lg---is~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 95 EQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLN---LSLAKVKSNLFRARKELKK 151 (154)
T ss_pred HHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Confidence 345678888888732 123445555544 4677888888888888775
No 38
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=29.30 E-value=1.8e+02 Score=23.35 Aligned_cols=48 Identities=17% Similarity=0.205 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 163 PQLHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
.++...+.+++..|.. +.-+.+.|-+.|| ++...|+++|..=|.+|++
T Consensus 101 ~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lg---is~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 101 KELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELG---ISVKTVEYHISKALKELRK 159 (161)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHh
Confidence 4556667777776653 2234455554444 5888888888887777764
No 39
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=29.27 E-value=1.6e+02 Score=25.53 Aligned_cols=49 Identities=10% Similarity=0.115 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 163 PQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
.++...+.+|+.+|..+ .-+-+.|-+.|| ++..+|+++|.+=|.+|++.
T Consensus 130 ~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lg---is~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 130 RLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLA---VPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred HhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhC---CChHhHHHHHHHHHHHHHHH
Confidence 45667788888888742 123444444444 47788888888877777754
No 40
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=29.17 E-value=1.7e+02 Score=23.91 Aligned_cols=47 Identities=13% Similarity=0.039 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 164 QLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 164 ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
++.....+|+.+|..+ .-+-+.|-+.| |++...|+++|.+=+.+|++
T Consensus 95 ~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l---~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 95 DVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALET---EMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHhh
Confidence 4456677778777632 22333443333 45777788888877777764
No 41
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=28.79 E-value=2e+02 Score=24.82 Aligned_cols=51 Identities=10% Similarity=0.059 Sum_probs=36.4
Q ss_pred ecChHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 160 VWTPQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 160 ~WT~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
.+..++.....+++++|..+ .-+.+.|-+.|| +|...|+++|.+=|..|++
T Consensus 119 ~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 119 APKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMH---MGLSATKMRYKRALDKLRE 180 (188)
T ss_pred cccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Confidence 45667888899999999732 123555555555 5778899999888888775
No 42
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.15 E-value=1.7e+02 Score=25.03 Aligned_cols=29 Identities=14% Similarity=0.166 Sum_probs=21.5
Q ss_pred ChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 182 VPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 182 tPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
+-+.|-+.|| +|...|+++|++-|.+|++
T Consensus 159 s~~EIA~~lg---is~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 159 SQSEIAKRLG---IPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CHHHHHHHhC---CCHHHHHHHHHHHHHHHHH
Confidence 3555555554 4888899999999998875
No 43
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=27.55 E-value=98 Score=26.92 Aligned_cols=47 Identities=21% Similarity=0.251 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 164 QLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 164 ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
++...+..|+++|..+ .-+-+.|-+. -|++...|++||.+=|..||+
T Consensus 123 ~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~---lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 123 EFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQE---CDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred HHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHH
Confidence 4556677888888742 1123333333 346888899999988888875
No 44
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=27.26 E-value=1.9e+02 Score=24.82 Aligned_cols=48 Identities=25% Similarity=0.338 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 163 PQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
.++..+...++.+|..+ .-+.+.|-+.|| ++...|++||.+-|..|++
T Consensus 115 ~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~---is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 115 NAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTG---VNENTVKTRLKKAKELLKK 173 (179)
T ss_pred HHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Confidence 45556677777877732 223455555555 4788899999999988875
No 45
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=27.18 E-value=1e+02 Score=28.78 Aligned_cols=47 Identities=23% Similarity=0.303 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhCCCC-----------CChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 165 LHKRFVDVVAHLGIKN-----------AVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 165 LH~rFVeAV~qLG~dk-----------AtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
+...+.+|+.+|..+. -+-+.|-+.| |++...|++||++=|.+||+.
T Consensus 132 ~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~l---gis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 132 VRLAFVAAIQYLPPRQRAVLLLRDVLGWRAAETAELL---GTSTASVNSALQRARATLDEV 189 (324)
T ss_pred HHHHHHHHHHhCCHHHhhHhhhHHHhCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHHh
Confidence 5566888888887431 1233333333 457888999999999999864
No 46
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=27.07 E-value=1.8e+02 Score=24.59 Aligned_cols=30 Identities=13% Similarity=0.185 Sum_probs=21.6
Q ss_pred ChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 182 VPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 182 tPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
+.+.|-+.|| +|...|+++|+.-|..||+.
T Consensus 147 s~~eIA~~lg---is~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHD---VPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHC---CChHHHHHHHHHHHHHHHHH
Confidence 4555555555 57788899999988888753
No 47
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=26.93 E-value=1.1e+02 Score=29.02 Aligned_cols=62 Identities=26% Similarity=0.252 Sum_probs=50.3
Q ss_pred CCCCCCeecChHHHHHHHHHHHHhC-CCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhhcCC
Q 047187 153 TLKRPRLVWTPQLHKRFVDVVAHLG-IKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQGL 217 (339)
Q Consensus 153 ~~kKpRl~WT~ELH~rFVeAV~qLG-~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~~~l 217 (339)
++||.|-..|++--.+.-.+++.-. +-.+.=|++.+.+ +||-.|||--.|.-|.+-||++..
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L---~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSL---SLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHc---CCChhHhhhhhhhhhHHHHHHHHH
Confidence 7899999999999999999998766 4445556665554 589999999999999999987643
No 48
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=26.80 E-value=2e+02 Score=23.68 Aligned_cols=46 Identities=20% Similarity=0.212 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 165 LHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 165 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
....+..++..|.. +.-+.+.|-+.|| ++...|+++|++=+.+|++
T Consensus 118 ~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lg---is~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 118 LEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMG---CPIGTVRSRIFRAREALRA 174 (182)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Confidence 45556666666652 2334666666655 4777788887777666664
No 49
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=26.49 E-value=84 Score=23.87 Aligned_cols=49 Identities=24% Similarity=0.377 Sum_probs=31.0
Q ss_pred CeecChHHHHHHHHHHHH------h---C-CCC-CChHHHHHhhCCCCC--CHHHHHHHhhh
Q 047187 158 RLVWTPQLHKRFVDVVAH------L---G-IKN-AVPKTIMQLMNVEGL--TRENVASHLQK 206 (339)
Q Consensus 158 Rl~WT~ELH~rFVeAV~q------L---G-~dk-AtPK~ILelM~V~GL--Tr~nVkSHLQK 206 (339)
|-.||.+.-..|++++.. + + ..+ .+.+.|.+.|..-|. |..|++...-.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~ 62 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKN 62 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 557999999999999887 2 1 122 368888888775555 88888765543
No 50
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=26.49 E-value=1.1e+02 Score=25.56 Aligned_cols=50 Identities=20% Similarity=0.291 Sum_probs=30.7
Q ss_pred ChHHHHHHHHHHHHhCCCCCChHHHHHhhCCC-----------CCCHHHHHHHhhhhHHHHhhh
Q 047187 162 TPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVE-----------GLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 162 T~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~-----------GLTr~nVkSHLQKYRl~lkR~ 214 (339)
..++...+..++..|..+ -+.|+.+.-+. |++...|+++|++-|..|++.
T Consensus 95 ~~~~~~~l~~~l~~L~~~---~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 95 AKNSYEKLIQIIHTLPVI---EAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HHHHHHHHHHHHHhCCHH---HHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345666777888887642 33344333333 346667888888888887753
No 51
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=25.82 E-value=2e+02 Score=25.11 Aligned_cols=48 Identities=21% Similarity=0.205 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 164 QLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 164 ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
++...+.+++.+|..+ .-+-+.|-+. -|+|...|+++|.+=|..|++.
T Consensus 120 e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~---lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 120 EFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQE---LEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHH---hCCCHHHHHHHHHHHHHHHHHH
Confidence 3345566677766521 1223333333 3568888999999998888753
No 52
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=25.77 E-value=1.8e+02 Score=25.98 Aligned_cols=48 Identities=23% Similarity=0.274 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 164 QLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 164 ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
++...+.+++.+|..+ .-+-+.|-+.| |+|...|++||++=|..|++.
T Consensus 137 e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~l---gis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 137 QFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAV---DLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH---CcCHHHHHHHHHHHHHHHHHH
Confidence 3445677788887632 12234444444 568899999999999888763
No 53
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=25.75 E-value=2.1e+02 Score=24.91 Aligned_cols=49 Identities=10% Similarity=0.118 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 163 PQLHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
.++.....+|+..|-. +.-+.+.|-+.|+ ++...|+++|.+=|..|++.
T Consensus 122 ~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg---~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 122 VETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLG---VAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHH
Confidence 3445556666666642 2234566666665 58888999998888777764
No 54
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=24.96 E-value=1.5e+02 Score=25.53 Aligned_cols=50 Identities=18% Similarity=0.238 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhhc
Q 047187 163 PQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQ 215 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~~ 215 (339)
.+...++.+|+..|-.+ .-+.+.|-+.|++ +...|+|+|..=|.+|++.-
T Consensus 115 ~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i---~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 115 EEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGI---SVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred HHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 45667777888777632 2345555555553 66779999999998887643
No 55
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=24.84 E-value=1.9e+02 Score=24.95 Aligned_cols=46 Identities=24% Similarity=0.281 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 166 HKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 166 H~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
...+.+|+.+|..+ .-+.+.|-+.| |++...|+++|.+=|..|++.
T Consensus 122 ~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~l---gis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 122 DQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIM---GTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred HHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHHH
Confidence 45567788888632 22344444444 468888999999999888763
No 56
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=24.52 E-value=2.2e+02 Score=24.58 Aligned_cols=46 Identities=17% Similarity=0.352 Sum_probs=35.9
Q ss_pred eecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 159 LVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 159 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
+-=+.++|++....|..||..+.+-..+++-+ ++-||..|+.-+.+
T Consensus 83 vyI~~e~h~~l~~Iv~~ig~~~~si~~yidNI---------L~~Hle~~~eeI~~ 128 (136)
T PF11888_consen 83 VYISRETHERLSRIVRVIGERKMSISGYIDNI---------LRHHLEEYREEINE 128 (136)
T ss_pred eEECHHHHHHHHHHHHHHCCCCCcHHHHHHHH---------HHHHHHHHHHHHHH
Confidence 88899999999999999997766666554321 56799999976654
No 57
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=23.75 E-value=2.4e+02 Score=19.50 Aligned_cols=52 Identities=19% Similarity=0.169 Sum_probs=34.1
Q ss_pred CCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHH
Q 047187 156 RPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRL 209 (339)
Q Consensus 156 KpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl 209 (339)
|.|..+|++- ...++++..... ..+...|.++...-|||..+|..=.+.-|.
T Consensus 2 k~r~~~~~~~-~~~L~~~f~~~~-~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 2 RKRTSFTPEQ-LEELEKEFQKNP-YPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCcCCHHH-HHHHHHHHHhCC-CCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 4566677664 344455554442 456778888888889999999765555443
No 58
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=23.15 E-value=2.3e+02 Score=24.95 Aligned_cols=44 Identities=20% Similarity=0.204 Sum_probs=29.0
Q ss_pred HHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 167 KRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 167 ~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
..+.+++.+|... .-+-+.|-+.| |++...|+++|.+=|..|++
T Consensus 131 ~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~l---gis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 131 TLFETCLDHLPEQIGRVFMMREFLDFEIDDICTEL---TLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH---CcCHHHHHHHHHHHHHHHHH
Confidence 4566777777632 22344444444 45788899999988888875
No 59
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=22.67 E-value=2.5e+02 Score=24.10 Aligned_cols=48 Identities=10% Similarity=0.158 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 164 QLHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 164 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
++...+.+++.+|.. +.-+.+.|-+.|| +|...|+++|.+=|..|++.
T Consensus 120 ~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lg---is~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 120 DTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVG---IPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHH
Confidence 445566777777763 2233455555554 47888999998888887754
No 60
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.48 E-value=2.2e+02 Score=23.97 Aligned_cols=47 Identities=15% Similarity=0.268 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 164 QLHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 164 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
++.....+++.+|.. +.-+.+.|-+.||+ |...|+++|++=|..|++
T Consensus 125 e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 125 ELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEILDL---PVGTVKTRIHRGREALRK 182 (187)
T ss_pred HHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHH
Confidence 334445566666652 33456666666654 788899999888877764
No 61
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.44 E-value=2.4e+02 Score=25.68 Aligned_cols=49 Identities=16% Similarity=0.185 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 163 PQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 163 ~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
.+..+.+.+|+..|... .-+-+.|-+.| |++...|++||.+=|.+|++.
T Consensus 122 ~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~L---giS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 122 AEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIA---DVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred HHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHHH
Confidence 34556788888888742 12233343444 468888999999999888764
No 62
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=22.04 E-value=1.8e+02 Score=23.95 Aligned_cols=46 Identities=17% Similarity=0.136 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhCCCCCChHHHHHhhCCCCC-----------CHHHHHHHhhhhHHHHhh
Q 047187 165 LHKRFVDVVAHLGIKNAVPKTIMQLMNVEGL-----------TRENVASHLQKYRLYLKR 213 (339)
Q Consensus 165 LH~rFVeAV~qLG~dkAtPK~ILelM~V~GL-----------Tr~nVkSHLQKYRl~lkR 213 (339)
....+.+|+.+|... =+.|+.+.-+.|+ +...|+++|.+=|..||+
T Consensus 112 ~~~~l~~~l~~L~~~---~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 112 ANEKLLKALKILTPK---QQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HHHHHHHHHHhCCHH---HHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345677888777742 2444444434444 455566666666666654
No 63
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=21.74 E-value=2.6e+02 Score=22.90 Aligned_cols=49 Identities=14% Similarity=0.195 Sum_probs=31.0
Q ss_pred ChHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 162 TPQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 162 T~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
..++...+..|+++|-.. .-+-+.|-+.| |++...|+++|.+=|..|++
T Consensus 93 ~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l---gis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 93 RAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAM---GCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHH
Confidence 345666777788877632 12233444444 45777888888888877765
No 64
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=21.56 E-value=2.3e+02 Score=26.59 Aligned_cols=51 Identities=10% Similarity=0.075 Sum_probs=34.6
Q ss_pred ChHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhhc
Q 047187 162 TPQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQ 215 (339)
Q Consensus 162 T~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~~ 215 (339)
..++...|..++++|-.+ .-.-+.|-+.| |+|...|+++|++=|..|++..
T Consensus 102 ~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~l---g~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 102 AEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTL---GRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHhhC
Confidence 345556688888888742 12234444444 4688889999999999998643
No 65
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=21.56 E-value=2.9e+02 Score=21.32 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=17.4
Q ss_pred hHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 183 PKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 183 PK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
.+.|-+.|| +|+..|..++++-+.++++
T Consensus 129 ~~eIA~~l~---~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 129 YKEIAEILG---ISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred HHHHHHHHC---CCHHHHHHHHHHHHHHHHh
Confidence 555555555 3677777777776666653
No 66
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=21.47 E-value=2.6e+02 Score=24.01 Aligned_cols=46 Identities=20% Similarity=0.211 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 165 LHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 165 LH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
+...+.+|+.+|-.+ .-+-+.|-+.| |++...|+++|.+=|..|++
T Consensus 121 ~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~l---gis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 121 FFEVLQACVDRLPPRTGRVFMMREWLELETEEICQEL---QITATNAWVLLYRARMRLRE 177 (191)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHH
Confidence 344566777777632 12233333333 45778889998888877765
No 67
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.40 E-value=2.7e+02 Score=23.82 Aligned_cols=47 Identities=13% Similarity=0.102 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 164 QLHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 164 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
++...+.++++.|.. +.-+.+.|-+.|+ ++...|+++|..=|.+|++
T Consensus 118 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~---is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 118 EARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTG---LSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Confidence 556667788887763 2233555555554 4777788888777777764
No 68
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=20.92 E-value=2.3e+02 Score=26.36 Aligned_cols=50 Identities=14% Similarity=0.204 Sum_probs=32.0
Q ss_pred cChHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 161 WTPQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 161 WT~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
|..++.....+|+.+|-.+ .-+-+.|-+.| |++...|++||.+=|..|++
T Consensus 147 ~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~L---gis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 147 YRQDFRQALREALAALSERERHLLRLHFVDGLSMDRIGAMY---QVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred hHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH---CcCHHHHHHHHHHHHHHHHH
Confidence 3445666777888888632 12233333333 35777799999988887765
No 69
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.87 E-value=2.7e+02 Score=25.12 Aligned_cols=52 Identities=15% Similarity=0.175 Sum_probs=34.6
Q ss_pred ecChHHHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhh
Q 047187 160 VWTPQLHKRFVDVVAHLGIK-----------NAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRM 214 (339)
Q Consensus 160 ~WT~ELH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~ 214 (339)
.+..++.+..-+++..|..+ .-+.+.|-+.|| ++...|+++|.+-|.+||+.
T Consensus 134 ~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lg---is~~tVk~~l~Rar~kLr~~ 196 (231)
T PRK11922 134 AARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALG---LPEETVKTRLHRARRLLRES 196 (231)
T ss_pred HHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHH
Confidence 34555666677788888732 223555555555 46888999998888888764
No 70
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=20.87 E-value=1.7e+02 Score=24.71 Aligned_cols=51 Identities=12% Similarity=0.119 Sum_probs=34.4
Q ss_pred ecChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 160 VWTPQLHKRFVDVVAHLGI-----------KNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 160 ~WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
.|..++-+....|+.+|.. +.-..+.|-+.|| ++...|++||.+=|..|++
T Consensus 104 ~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lg---is~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 104 FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILN---IPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHH
Confidence 4555666666777777763 2223555555555 5788999999998888875
No 71
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=20.61 E-value=3e+02 Score=27.86 Aligned_cols=65 Identities=22% Similarity=0.259 Sum_probs=45.5
Q ss_pred CCCCCCeecChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhhhcCCCC
Q 047187 153 TLKRPRLVWTPQLHKRFVDVVAHLGIKNAVPKTIMQLMNVEGLTRENVASHLQKYRLYLKRMQGLSN 219 (339)
Q Consensus 153 ~~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR~~~l~~ 219 (339)
-.||||--+|.|--+|.-.-++.-- --|=++-.+|-..-||...|||.-.|.-|.++||.++..+
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enR--YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn 309 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENR--YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKN 309 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhh--hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCC
Confidence 4789999999887666543333111 0123444566666789999999999999999998776543
No 72
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=20.01 E-value=2.4e+02 Score=26.74 Aligned_cols=46 Identities=24% Similarity=0.307 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhCCCC-----------CChHHHHHhhCCCCCCHHHHHHHhhhhHHHHhh
Q 047187 165 LHKRFVDVVAHLGIKN-----------AVPKTIMQLMNVEGLTRENVASHLQKYRLYLKR 213 (339)
Q Consensus 165 LH~rFVeAV~qLG~dk-----------AtPK~ILelM~V~GLTr~nVkSHLQKYRl~lkR 213 (339)
+...+..++.+|..+. -+-+.|-+.| |++...|+++|.+=|.+||+
T Consensus 143 ~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~l---gis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 143 VRLAFVAALQHLPPRQRAVLILRDVLGWSAAEVAELL---DTSVAAVNSALQRARATLAE 199 (339)
T ss_pred HHHHHHHHHHhCCHHHhhhhhhHHhhCCCHHHHHHHh---CCCHHHHHHHHHHHHHHHhh
Confidence 3456778888887421 2234444444 45778899999999998886
Done!