Query psy7434
Match_columns 91
No_of_seqs 130 out of 1058
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 18:13:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7434.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7434hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842|consensus 99.4 1.2E-13 2.6E-18 95.6 4.6 50 42-91 150-199 (307)
2 KOG0484|consensus 99.4 6.6E-14 1.4E-18 83.1 0.5 49 42-90 14-62 (125)
3 KOG0850|consensus 99.4 4.4E-13 9.6E-18 89.1 3.8 50 42-91 119-168 (245)
4 KOG0488|consensus 99.4 5.6E-13 1.2E-17 92.8 4.3 50 42-91 169-218 (309)
5 KOG0489|consensus 99.4 1.7E-13 3.7E-18 93.5 1.5 49 43-91 157-205 (261)
6 TIGR01565 homeo_ZF_HD homeobox 99.3 2E-12 4.4E-17 69.8 4.7 46 46-91 2-51 (58)
7 KOG0487|consensus 99.3 8.3E-13 1.8E-17 91.5 3.9 50 42-91 232-281 (308)
8 KOG2251|consensus 99.3 1.4E-12 3E-17 86.3 4.5 52 40-91 32-83 (228)
9 KOG0485|consensus 99.3 1.5E-12 3.2E-17 86.2 4.3 52 40-91 99-150 (268)
10 KOG0843|consensus 99.3 3E-12 6.5E-17 82.5 3.7 48 44-91 101-148 (197)
11 KOG0492|consensus 99.2 1.3E-11 2.7E-16 81.3 4.3 50 42-91 141-190 (246)
12 KOG0493|consensus 99.1 7.2E-11 1.6E-15 80.2 3.7 46 46-91 247-292 (342)
13 KOG0494|consensus 99.0 1.3E-10 2.9E-15 78.8 3.2 46 45-90 141-186 (332)
14 PF00046 Homeobox: Homeobox do 99.0 1.5E-10 3.2E-15 61.9 2.3 45 46-90 1-45 (57)
15 KOG0848|consensus 99.0 7.8E-11 1.7E-15 80.1 1.0 46 46-91 200-245 (317)
16 KOG0486|consensus 99.0 2.3E-10 4.9E-15 79.3 2.7 47 44-90 111-157 (351)
17 smart00389 HOX Homeodomain. DN 98.9 3.7E-09 8E-14 56.0 3.7 44 47-90 2-45 (56)
18 cd00086 homeodomain Homeodomai 98.8 1.1E-08 2.5E-13 54.5 3.5 44 47-90 2-45 (59)
19 KOG0491|consensus 98.8 8.1E-10 1.8E-14 70.5 -1.2 47 44-90 99-145 (194)
20 KOG0844|consensus 98.7 7.5E-09 1.6E-13 71.8 1.8 50 42-91 178-227 (408)
21 KOG0490|consensus 98.6 2.2E-08 4.8E-13 66.4 2.8 50 42-91 57-106 (235)
22 COG5576 Homeodomain-containing 98.6 1.8E-07 3.9E-12 59.7 5.5 52 40-91 46-97 (156)
23 KOG0849|consensus 98.5 8E-08 1.7E-12 68.3 3.4 50 41-90 172-221 (354)
24 KOG3802|consensus 97.9 1.4E-05 3E-10 57.3 4.5 47 44-90 293-339 (398)
25 KOG0483|consensus 97.8 1.2E-05 2.6E-10 53.2 2.6 44 48-91 53-96 (198)
26 KOG0847|consensus 97.6 6.4E-05 1.4E-09 50.5 3.3 47 44-90 166-212 (288)
27 KOG2252|consensus 97.3 0.00035 7.5E-09 52.1 4.3 48 42-89 417-464 (558)
28 KOG4577|consensus 97.0 0.00093 2E-08 46.6 3.5 49 42-90 164-212 (383)
29 KOG0774|consensus 96.4 0.0041 8.9E-08 42.9 3.2 44 46-89 189-235 (334)
30 KOG0490|consensus 95.8 0.012 2.7E-07 38.8 3.4 51 40-90 148-198 (235)
31 KOG0775|consensus 95.8 0.015 3.3E-07 40.3 3.8 42 48-89 170-220 (304)
32 PF05920 Homeobox_KN: Homeobox 95.7 0.0028 6E-08 31.6 -0.0 25 66-90 7-31 (40)
33 KOG1168|consensus 94.6 0.02 4.4E-07 40.1 1.6 47 44-90 308-354 (385)
34 PF04967 HTH_10: HTH DNA bindi 90.0 0.24 5.3E-06 26.0 1.6 36 52-87 1-38 (53)
35 PF04218 CENP-B_N: CENP-B N-te 88.8 0.87 1.9E-05 23.7 3.2 39 46-89 1-39 (53)
36 KOG1146|consensus 83.5 1.1 2.4E-05 37.3 2.7 46 45-90 903-948 (1406)
37 COG3413 Predicted DNA binding 81.5 1.9 4.2E-05 28.5 3.0 37 51-87 155-193 (215)
38 PF11569 Homez: Homeodomain le 81.1 0.48 1E-05 25.3 -0.0 34 57-90 10-43 (56)
39 PF12824 MRP-L20: Mitochondria 68.6 29 0.00062 22.4 7.1 38 48-87 82-119 (164)
40 PF04545 Sigma70_r4: Sigma-70, 63.8 3.6 7.8E-05 20.6 0.8 34 52-90 5-38 (50)
41 PF08280 HTH_Mga: M protein tr 61.0 3.8 8.3E-05 21.5 0.6 32 55-90 6-37 (59)
42 PF13936 HTH_38: Helix-turn-he 59.3 3.8 8.3E-05 20.3 0.4 35 50-89 3-37 (44)
43 PF08880 QLQ: QLQ; InterPro: 57.7 12 0.00026 18.1 2.0 15 51-65 2-16 (37)
44 COG4367 Uncharacterized protei 55.4 16 0.00036 21.3 2.6 36 52-87 3-38 (97)
45 PF01527 HTH_Tnp_1: Transposas 46.9 15 0.00033 19.7 1.5 37 47-88 2-39 (76)
46 KOG0773|consensus 42.1 54 0.0012 23.1 4.1 45 46-90 240-287 (342)
47 PRK13558 bacterio-opsin activa 38.9 37 0.00081 25.9 3.0 38 50-87 606-645 (665)
48 PF02796 HTH_7: Helix-turn-hel 38.6 16 0.00035 18.0 0.7 33 52-89 6-38 (45)
49 PRK03975 tfx putative transcri 37.7 26 0.00056 22.1 1.7 34 50-89 5-38 (141)
50 PF08281 Sigma70_r4_2: Sigma-7 34.9 26 0.00057 17.5 1.2 21 69-89 23-43 (54)
51 PRK15183 Vi polysaccharide bio 34.6 46 0.001 20.2 2.3 39 49-87 93-131 (143)
52 COG1905 NuoE NADH:ubiquinone o 32.7 65 0.0014 20.8 3.0 36 54-89 25-60 (160)
53 PF08279 HTH_11: HTH domain; 32.0 24 0.00052 17.7 0.8 16 74-89 17-32 (55)
54 cd06171 Sigma70_r4 Sigma70, re 31.6 36 0.00079 16.0 1.4 33 52-89 11-43 (55)
55 TIGR01958 nuoE_fam NADH-quinon 31.2 53 0.0011 20.5 2.4 31 59-89 21-51 (148)
56 PF00196 GerE: Bacterial regul 30.8 24 0.00053 18.0 0.7 33 51-89 3-35 (58)
57 PF10668 Phage_terminase: Phag 30.0 13 0.00029 20.0 -0.5 17 74-90 24-40 (60)
58 PRK05988 formate dehydrogenase 29.9 59 0.0013 20.6 2.4 33 57-89 26-58 (156)
59 PRK07539 NADH dehydrogenase su 29.8 57 0.0012 20.5 2.4 31 59-89 27-57 (154)
60 TIGR00721 tfx DNA-binding prot 29.2 47 0.001 20.8 1.9 35 49-89 4-38 (137)
61 TIGR03879 near_KaiC_dom probab 28.7 5.5 0.00012 22.3 -2.1 27 64-90 24-50 (73)
62 TIGR03209 P21_Cbot clostridium 27.5 81 0.0018 18.8 2.7 17 74-90 125-141 (142)
63 PRK06759 RNA polymerase factor 27.1 46 0.001 20.1 1.6 18 73-90 123-140 (154)
64 PRK07571 bidirectional hydroge 26.9 70 0.0015 20.7 2.4 25 65-89 47-71 (169)
65 PRK04217 hypothetical protein; 26.7 49 0.0011 19.9 1.6 35 50-89 41-75 (110)
66 KOG0041|consensus 25.1 1.2E+02 0.0025 20.8 3.2 37 51-87 92-133 (244)
67 TIGR02959 SigZ RNA polymerase 24.7 54 0.0012 20.4 1.6 17 74-90 118-134 (170)
68 PF06971 Put_DNA-bind_N: Putat 24.7 13 0.00027 19.2 -1.1 15 76-90 32-46 (50)
69 PRK12529 RNA polymerase sigma 24.6 56 0.0012 20.5 1.6 17 74-90 145-161 (178)
70 cd00569 HTH_Hin_like Helix-tur 24.1 71 0.0015 13.1 2.4 32 52-88 6-37 (42)
71 cd08313 Death_TNFR1 Death doma 24.1 30 0.00066 19.6 0.3 15 75-89 14-28 (80)
72 PF13404 HTH_AsnC-type: AsnC-t 23.9 16 0.00035 17.9 -0.8 15 75-89 20-34 (42)
73 PF13730 HTH_36: Helix-turn-he 23.5 28 0.00061 17.4 0.1 19 71-89 24-42 (55)
74 PF01257 2Fe-2S_thioredx: Thio 23.1 51 0.0011 20.5 1.2 31 59-89 18-48 (145)
75 smart00421 HTH_LUXR helix_turn 22.7 86 0.0019 15.0 1.9 32 52-89 4-35 (58)
76 PRK12537 RNA polymerase sigma 22.3 96 0.0021 19.4 2.4 17 74-90 151-167 (182)
77 PRK09646 RNA polymerase sigma 22.2 87 0.0019 19.9 2.2 17 74-90 160-176 (194)
78 PF10078 DUF2316: Uncharacteri 22.0 22 0.00047 20.7 -0.6 27 59-89 14-40 (89)
79 PRK09645 RNA polymerase sigma 21.3 86 0.0019 19.3 2.0 17 74-90 136-152 (173)
80 PRK09642 RNA polymerase sigma 21.3 73 0.0016 19.4 1.7 17 74-90 124-140 (160)
81 TIGR02989 Sig-70_gvs1 RNA poly 21.3 75 0.0016 19.2 1.7 17 74-90 129-145 (159)
82 COG2197 CitB Response regulato 21.2 1.1E+02 0.0024 20.0 2.6 35 50-90 147-181 (211)
83 PF04539 Sigma70_r3: Sigma-70 20.8 26 0.00055 18.9 -0.4 16 74-89 22-37 (78)
84 TIGR02999 Sig-70_X6 RNA polyme 20.8 72 0.0016 19.9 1.6 17 74-90 152-168 (183)
85 PRK07037 extracytoplasmic-func 20.7 75 0.0016 19.4 1.6 17 74-90 127-143 (163)
86 PRK09047 RNA polymerase factor 20.7 73 0.0016 19.3 1.6 17 74-90 124-140 (161)
87 PRK09648 RNA polymerase sigma 20.4 73 0.0016 20.1 1.6 17 74-90 157-173 (189)
88 PF12793 SgrR_N: Sugar transpo 20.1 58 0.0013 19.6 1.0 33 56-90 5-37 (115)
No 1
>KOG0842|consensus
Probab=99.44 E-value=1.2e-13 Score=95.58 Aligned_cols=50 Identities=30% Similarity=0.517 Sum_probs=47.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
..++||.|..||..|..+||+.|..++|++.++|++||..|.|++.||||
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKI 199 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKI 199 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheee
Confidence 45677789999999999999999999999999999999999999999998
No 2
>KOG0484|consensus
Probab=99.38 E-value=6.6e-14 Score=83.09 Aligned_cols=49 Identities=53% Similarity=0.895 Sum_probs=46.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
.++.||-||.||..||.+||+.|...|||++.+|++||.++.|+|.+||
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQ 62 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQ 62 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHH
Confidence 5667899999999999999999999999999999999999999999886
No 3
>KOG0850|consensus
Probab=99.37 E-value=4.4e-13 Score=89.08 Aligned_cols=50 Identities=32% Similarity=0.504 Sum_probs=47.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
.+|.|+.||+|+..||..|.+.|+++.|+..++|.+||..|||+..||||
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKI 168 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKI 168 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhh
Confidence 56668899999999999999999999999999999999999999999997
No 4
>KOG0488|consensus
Probab=99.37 E-value=5.6e-13 Score=92.82 Aligned_cols=50 Identities=40% Similarity=0.645 Sum_probs=47.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
.+|+|+.||.||..|+.+||+.|++.+|++..+|.+||..|||+++|||.
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKt 218 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKT 218 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHH
Confidence 46778899999999999999999999999999999999999999999984
No 5
>KOG0489|consensus
Probab=99.36 E-value=1.7e-13 Score=93.54 Aligned_cols=49 Identities=31% Similarity=0.432 Sum_probs=46.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 43 KRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 43 ~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
.+.||.||.||..|+.+||++|+.|+|++...|.|||..|+|+|+||||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKI 205 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKI 205 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHH
Confidence 3468899999999999999999999999999999999999999999997
No 6
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.34 E-value=2e-12 Score=69.78 Aligned_cols=46 Identities=22% Similarity=0.263 Sum_probs=44.2
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHhcCCCCCCCCC
Q psy7434 46 RRHRTIFTEEQLEQLEATFEKTHY----PDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 46 rr~Rt~~t~~Q~~~Le~~F~~~~y----p~~~~r~~La~~l~l~~~qVk~ 91 (91)
||.||.||..|+..|+..|..+.| |+..++++||..|||++.+||+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKV 51 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKV 51 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeee
Confidence 688999999999999999999999 9999999999999999999984
No 7
>KOG0487|consensus
Probab=99.34 E-value=8.3e-13 Score=91.47 Aligned_cols=50 Identities=28% Similarity=0.365 Sum_probs=47.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
.++.|++|.+||+.|+.+||++|..|.|+....|.+|++.|+|+|+||||
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKI 281 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKI 281 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheee
Confidence 35678899999999999999999999999999999999999999999998
No 8
>KOG2251|consensus
Probab=99.34 E-value=1.4e-12 Score=86.27 Aligned_cols=52 Identities=58% Similarity=0.906 Sum_probs=49.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 40 PPPKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 40 ~~~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
...++.||.||.|+..|+.+||..|.+..||++..|++||.+|+|+|.+||+
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 4567789999999999999999999999999999999999999999999984
No 9
>KOG0485|consensus
Probab=99.33 E-value=1.5e-12 Score=86.19 Aligned_cols=52 Identities=37% Similarity=0.494 Sum_probs=49.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 40 PPPKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 40 ~~~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
.+..++|+.||.|+..|+..||..|+..+|++..+|..||.+|.|+|.||||
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKI 150 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKI 150 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhh
Confidence 4566788899999999999999999999999999999999999999999997
No 10
>KOG0843|consensus
Probab=99.29 E-value=3e-12 Score=82.51 Aligned_cols=48 Identities=44% Similarity=0.536 Sum_probs=46.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 44 RKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 44 ~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
+.+|.||.||..|+..||..|..++|....+|++||+.|+|+|.|||+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkv 148 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKV 148 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhh
Confidence 678899999999999999999999999999999999999999999995
No 11
>KOG0492|consensus
Probab=99.22 E-value=1.3e-11 Score=81.29 Aligned_cols=50 Identities=32% Similarity=0.496 Sum_probs=47.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
.+..|+.||.||..||..||+.|...+|+++.+|.+++..|.|+|.||||
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKI 190 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKI 190 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheeh
Confidence 44457889999999999999999999999999999999999999999997
No 12
>KOG0493|consensus
Probab=99.10 E-value=7.2e-11 Score=80.17 Aligned_cols=46 Identities=37% Similarity=0.594 Sum_probs=44.3
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 46 RRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 46 rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
+|.||.||.+||..|+.+|+.|+|+....|.+||+.|+|.|.||||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKI 292 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKI 292 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhH
Confidence 5689999999999999999999999999999999999999999997
No 13
>KOG0494|consensus
Probab=99.05 E-value=1.3e-10 Score=78.79 Aligned_cols=46 Identities=54% Similarity=0.854 Sum_probs=42.9
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 45 KRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 45 ~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
+|+-||.||..|+.+||..|++.+||+...|+-||.++.|+|.+|+
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIq 186 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQ 186 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhh
Confidence 3445999999999999999999999999999999999999999886
No 14
>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=99.03 E-value=1.5e-10 Score=61.90 Aligned_cols=45 Identities=44% Similarity=0.664 Sum_probs=42.5
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 46 RRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 46 rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
|+.|+.||..|+..|+..|..++||+..++++||..+||+..+|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccc
Confidence 567899999999999999999999999999999999999998875
No 15
>KOG0848|consensus
Probab=99.02 E-value=7.8e-11 Score=80.10 Aligned_cols=46 Identities=26% Similarity=0.452 Sum_probs=43.8
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 46 RRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 46 rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
-+.|.+||..|..+||++|..++|+.+..+.|||..|+|+|+||||
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI 245 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI 245 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence 3568999999999999999999999999999999999999999997
No 16
>KOG0486|consensus
Probab=98.99 E-value=2.3e-10 Score=79.25 Aligned_cols=47 Identities=49% Similarity=0.834 Sum_probs=45.3
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 44 RKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 44 ~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
|+||.||.||..|+++||..|++|.||+..+|+|||..++|+|.+|+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr 157 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 157 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence 67899999999999999999999999999999999999999999885
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.85 E-value=3.7e-09 Score=56.01 Aligned_cols=44 Identities=52% Similarity=0.738 Sum_probs=41.3
Q ss_pred CCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 47 RHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 47 r~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVK 45 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 46778999999999999999999999999999999999998875
No 18
>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=98.75 E-value=1.1e-08 Score=54.49 Aligned_cols=44 Identities=52% Similarity=0.726 Sum_probs=41.3
Q ss_pred CCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 47 RHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 47 r~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
+.++.|+..|+..|+..|..++||+..++..||..+||++.+|+
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 46778999999999999999999999999999999999998885
No 19
>KOG0491|consensus
Probab=98.75 E-value=8.1e-10 Score=70.55 Aligned_cols=47 Identities=38% Similarity=0.641 Sum_probs=44.4
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 44 RKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 44 ~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
++++.||.|+..|+..||..|+..+|++..+|.|||..|+|++.|||
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVK 145 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVK 145 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHH
Confidence 34668999999999999999999999999999999999999999997
No 20
>KOG0844|consensus
Probab=98.68 E-value=7.5e-09 Score=71.81 Aligned_cols=50 Identities=34% Similarity=0.475 Sum_probs=46.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
...-||.||.||.+|+-.||++|-+..|.+.+.|-|||..|+|+|..||.
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKV 227 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKV 227 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeeh
Confidence 44568899999999999999999999999999999999999999999884
No 21
>KOG0490|consensus
Probab=98.63 E-value=2.2e-08 Score=66.41 Aligned_cols=50 Identities=44% Similarity=0.476 Sum_probs=46.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
..++|+.||.|+.+|+.+||+.|+..+||+...|+.||..++++|..||+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqv 106 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQV 106 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeeh
Confidence 45678899999999999999999999999999999999999999999874
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.56 E-value=1.8e-07 Score=59.69 Aligned_cols=52 Identities=29% Similarity=0.404 Sum_probs=46.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 40 PPPKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 40 ~~~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
......++.|++-|.+|+..|++.|..++||+..+|.+|+..++|++.-|||
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqI 97 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQI 97 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhh
Confidence 3344556677778999999999999999999999999999999999999986
No 23
>KOG0849|consensus
Probab=98.52 E-value=8e-08 Score=68.30 Aligned_cols=50 Identities=48% Similarity=0.698 Sum_probs=46.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 41 PPKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 41 ~~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
..++.+|.||.|+..|+..|+..|+.++||++..|++||.+++++|.+|+
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riq 221 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQ 221 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHH
Confidence 35556788999999999999999999999999999999999999998876
No 24
>KOG3802|consensus
Probab=97.95 E-value=1.4e-05 Score=57.29 Aligned_cols=47 Identities=30% Similarity=0.328 Sum_probs=44.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 44 RKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 44 ~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
|+|++||.+.......||..|.+|..|+..+..+||.+|+|....|+
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR 339 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR 339 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence 67889999999999999999999999999999999999999988775
No 25
>KOG0483|consensus
Probab=97.85 E-value=1.2e-05 Score=53.16 Aligned_cols=44 Identities=25% Similarity=0.348 Sum_probs=40.1
Q ss_pred CCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCCC
Q psy7434 48 HRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVEP 91 (91)
Q Consensus 48 ~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk~ 91 (91)
++.+||..|...||..|+.+.++....+..||+.|||.++||++
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVav 96 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAV 96 (198)
T ss_pred ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHH
Confidence 33468999999999999999999999999999999999999863
No 26
>KOG0847|consensus
Probab=97.62 E-value=6.4e-05 Score=50.46 Aligned_cols=47 Identities=36% Similarity=0.550 Sum_probs=43.0
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 44 RKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 44 ~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
+++..|..|+..|+..||..|+..+|+-..+|.+||..+|+++.|||
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvk 212 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVK 212 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHH
Confidence 34446778999999999999999999999999999999999999987
No 27
>KOG2252|consensus
Probab=97.32 E-value=0.00035 Score=52.06 Aligned_cols=48 Identities=23% Similarity=0.420 Sum_probs=43.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
.-..++.|.+||..|...|...|+.+++|+....+.|+.+|+|....|
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV 464 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTV 464 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHH
Confidence 344577899999999999999999999999999999999999987655
No 28
>KOG4577|consensus
Probab=96.98 E-value=0.00093 Score=46.61 Aligned_cols=49 Identities=31% Similarity=0.435 Sum_probs=44.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 42 PKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 42 ~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
...-+|.||.+|..||+-|+..+....-|....|+.|+..+||.-+.||
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQ 212 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQ 212 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehh
Confidence 3445789999999999999999999999999999999999999988776
No 29
>KOG0774|consensus
Probab=96.38 E-value=0.0041 Score=42.90 Aligned_cols=44 Identities=30% Similarity=0.479 Sum_probs=39.5
Q ss_pred CCCCCCCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 46 RRHRTIFTEEQLEQLEATFE---KTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 46 rr~Rt~~t~~Q~~~Le~~F~---~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
||+|..|+..-...|...|. .|+||+..++++||++-+++-.||
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 56778899999999999986 578999999999999999998876
No 30
>KOG0490|consensus
Probab=95.80 E-value=0.012 Score=38.78 Aligned_cols=51 Identities=49% Similarity=0.634 Sum_probs=45.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 40 PPPKRKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 40 ~~~~~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
....+.++.|+.++..|+..++..|..+++|+...+..|+..+++++..|+
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q 198 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQ 198 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhh
Confidence 334566788999999999999999999999999999999999999998765
No 31
>KOG0775|consensus
Probab=95.78 E-value=0.015 Score=40.28 Aligned_cols=42 Identities=26% Similarity=0.337 Sum_probs=35.4
Q ss_pred CCCCCCHHH---------HHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 48 HRTIFTEEQ---------LEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 48 ~Rt~~t~~Q---------~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
.||.+..++ ...|...|..+.||+..++.+||+.+||+..||
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 466655444 557888899999999999999999999999987
No 32
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=95.68 E-value=0.0028 Score=31.58 Aligned_cols=25 Identities=24% Similarity=0.453 Sum_probs=19.4
Q ss_pred hcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 66 KTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 66 ~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
.++||+..++.+|+..+||+..||.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~ 31 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQIS 31 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 3789999999999999999988763
No 33
>KOG1168|consensus
Probab=94.57 E-value=0.02 Score=40.12 Aligned_cols=47 Identities=32% Similarity=0.357 Sum_probs=41.9
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 44 RKRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 44 ~~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
.++|+||.+-.-....||..|...+-|+......+|.+|+|....|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR 354 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 354 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence 35678899999899999999999999999999999999999887664
No 34
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=89.98 E-value=0.24 Score=26.04 Aligned_cols=36 Identities=28% Similarity=0.442 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhhhhcCC--CCHHHHHHHHHhcCCCCC
Q psy7434 52 FTEEQLEQLEATFEKTHY--PDVVLREQLALKVDLKEE 87 (91)
Q Consensus 52 ~t~~Q~~~Le~~F~~~~y--p~~~~r~~La~~l~l~~~ 87 (91)
+|..|...|...+....| |-...-.+||..||++..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~s 38 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKS 38 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHH
Confidence 478899999999998776 555566799999999864
No 35
>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=88.79 E-value=0.87 Score=23.70 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=28.2
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 46 RRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 46 rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
++.|..+|-.+-..+-..++.+. ...++|..+|++..+|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv 39 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTV 39 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHH
Confidence 46788899999988888888776 5678999999998876
No 36
>KOG1146|consensus
Probab=83.52 E-value=1.1 Score=37.33 Aligned_cols=46 Identities=24% Similarity=0.311 Sum_probs=42.1
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 45 KRRHRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 45 ~rr~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
+|+.||.++..|+..+...|....|+...+.+.|...++++.+.|+
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~ 948 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQ 948 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhH
Confidence 4678999999999999999999999999999999999999988764
No 37
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=81.55 E-value=1.9 Score=28.47 Aligned_cols=37 Identities=24% Similarity=0.373 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHhcCCCCC
Q psy7434 51 IFTEEQLEQLEATFEKTHY--PDVVLREQLALKVDLKEE 87 (91)
Q Consensus 51 ~~t~~Q~~~Le~~F~~~~y--p~~~~r~~La~~l~l~~~ 87 (91)
.+|..|+..|...|....| |-...-.+||+.||++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISks 193 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKS 193 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 6999999999999998775 555666799999999864
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=81.09 E-value=0.48 Score=25.26 Aligned_cols=34 Identities=18% Similarity=0.163 Sum_probs=23.8
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 57 LEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 57 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
+..|+..|...+++....-.+|..+.+|+..||+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr 43 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVR 43 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHH
Confidence 3458999999999999999999999999988875
No 39
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 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 entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=68.63 E-value=29 Score=22.40 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=31.3
Q ss_pred CCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCC
Q psy7434 48 HRTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEE 87 (91)
Q Consensus 48 ~Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 87 (91)
....+|.+++.++.+.-..+ |..+++..||+++|++..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~ 119 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPL 119 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHH
Confidence 45789999999998765554 677899999999999864
No 40
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=63.84 E-value=3.6 Score=20.60 Aligned_cols=34 Identities=12% Similarity=0.241 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 52 FTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 52 ~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
++..+...+...|..+ .+-.++|..+|++...|+
T Consensus 5 L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~ 38 (50)
T PF04545_consen 5 LPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVR 38 (50)
T ss_dssp S-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHH
T ss_pred CCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHH
Confidence 5677778888777433 256789999999886653
No 41
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=61.03 E-value=3.8 Score=21.53 Aligned_cols=32 Identities=25% Similarity=0.438 Sum_probs=21.9
Q ss_pred HHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 55 EQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 55 ~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
-|+..|+-.+. +...... +||..+++++..|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 36667777777 6666544 89999999986553
No 42
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=59.30 E-value=3.8 Score=20.29 Aligned_cols=35 Identities=23% Similarity=0.294 Sum_probs=15.3
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 50 TIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 50 t~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
..+|..+...++.....+ ....++|..||.+...|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV 37 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTV 37 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHH
Confidence 357788888888766544 35668999999876543
No 43
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=57.70 E-value=12 Score=18.07 Aligned_cols=15 Identities=40% Similarity=0.479 Sum_probs=12.3
Q ss_pred CCCHHHHHHHHHhhh
Q psy7434 51 IFTEEQLEQLEATFE 65 (91)
Q Consensus 51 ~~t~~Q~~~Le~~F~ 65 (91)
.||..|+.+|+.-..
T Consensus 2 ~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 2 PFTPAQLQELRAQIL 16 (37)
T ss_pred CCCHHHHHHHHHHHH
Confidence 699999999987543
No 44
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.40 E-value=16 Score=21.32 Aligned_cols=36 Identities=14% Similarity=0.150 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCC
Q psy7434 52 FTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEE 87 (91)
Q Consensus 52 ~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 87 (91)
+++.|...-...|+.|--++.-..+++|..|+.++-
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~ 38 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEV 38 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHH
Confidence 567777777777777766666677889999998874
No 45
>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=46.86 E-value=15 Score=19.67 Aligned_cols=37 Identities=16% Similarity=0.153 Sum_probs=21.0
Q ss_pred CCCCCCCHHHHHHHHHhh-hhcCCCCHHHHHHHHHhcCCCCCC
Q psy7434 47 RHRTIFTEEQLEQLEATF-EKTHYPDVVLREQLALKVDLKEER 88 (91)
Q Consensus 47 r~Rt~~t~~Q~~~Le~~F-~~~~yp~~~~r~~La~~l~l~~~q 88 (91)
+.|..||..+...+-... ... ....++|..+|++..+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~ 39 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPST 39 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeeccccccccc
Confidence 346678998888776655 333 3567888888887543
No 46
>KOG0773|consensus
Probab=42.06 E-value=54 Score=23.15 Aligned_cols=45 Identities=27% Similarity=0.277 Sum_probs=34.3
Q ss_pred CCCCCCCCHHHHHHHHHh-hh--hcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 46 RRHRTIFTEEQLEQLEAT-FE--KTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 46 rr~Rt~~t~~Q~~~Le~~-F~--~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
+|.+..+.......|+.. |+ ..+||+..++..|+..+||+..||.
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~ 287 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVS 287 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCC
Confidence 344456777777777765 33 2569999999999999999999875
No 47
>PRK13558 bacterio-opsin activator; Provisional
Probab=38.89 E-value=37 Score=25.85 Aligned_cols=38 Identities=24% Similarity=0.359 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHhcCCCCC
Q psy7434 50 TIFTEEQLEQLEATFEKTHY--PDVVLREQLALKVDLKEE 87 (91)
Q Consensus 50 t~~t~~Q~~~Le~~F~~~~y--p~~~~r~~La~~l~l~~~ 87 (91)
..+|..|...|+..+....| |-..+-++||..||++..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~ 645 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRS 645 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 36999999999999998887 666677899999999864
No 48
>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=38.62 E-value=16 Score=17.96 Aligned_cols=33 Identities=15% Similarity=0.339 Sum_probs=20.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 52 FTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 52 ~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
++.+|...+...+.... ...++|..+|++...|
T Consensus 6 ~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~Tv 38 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRSTV 38 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHH
T ss_pred CCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHH
Confidence 56656666666666552 4668999999886543
No 49
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=37.67 E-value=26 Score=22.08 Aligned_cols=34 Identities=24% Similarity=0.355 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 50 TIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 50 t~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
..++..|...|... ..+ ....++|..||++...|
T Consensus 5 ~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tV 38 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANV 38 (141)
T ss_pred cCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHH
Confidence 46788888888773 323 25779999999988655
No 50
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=34.86 E-value=26 Score=17.45 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=12.9
Q ss_pred CCCHHHHHHHHHhcCCCCCCC
Q psy7434 69 YPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 69 yp~~~~r~~La~~l~l~~~qV 89 (91)
|.....-.++|..+|+++..|
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v 43 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTV 43 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHH
Confidence 344446789999999987655
No 51
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=34.56 E-value=46 Score=20.24 Aligned_cols=39 Identities=23% Similarity=0.400 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCC
Q psy7434 49 RTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEE 87 (91)
Q Consensus 49 Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 87 (91)
..-++..-.++|+..|-...---..=|.+||.+.|+.+.
T Consensus 93 kyflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~p 131 (143)
T PRK15183 93 KYFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREP 131 (143)
T ss_pred hhhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCC
Confidence 344567777888888876554333457899999998764
No 52
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=32.74 E-value=65 Score=20.79 Aligned_cols=36 Identities=17% Similarity=0.131 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 54 EEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 54 ~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
..-+..|...+...-|........+|..|+++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 445667788888888999999999999999998665
No 53
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=32.05 E-value=24 Score=17.71 Aligned_cols=16 Identities=13% Similarity=0.279 Sum_probs=11.0
Q ss_pred HHHHHHHhcCCCCCCC
Q psy7434 74 LREQLALKVDLKEERV 89 (91)
Q Consensus 74 ~r~~La~~l~l~~~qV 89 (91)
.-.+||..++++...|
T Consensus 17 t~~eLa~~l~vS~rTi 32 (55)
T PF08279_consen 17 TAKELAEELGVSRRTI 32 (55)
T ss_dssp EHHHHHHHCTS-HHHH
T ss_pred CHHHHHHHhCCCHHHH
Confidence 3458899999987654
No 54
>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=31.57 E-value=36 Score=16.01 Aligned_cols=33 Identities=18% Similarity=0.251 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 52 FTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 52 ~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
++..+...+...+..+ ..-.++|..+|++...|
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i 43 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTV 43 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHH
Confidence 4555555555544222 24567888899887655
No 55
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=31.15 E-value=53 Score=20.48 Aligned_cols=31 Identities=13% Similarity=0.014 Sum_probs=23.1
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 59 QLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 59 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
.|...=+...|.+......+|..++++..+|
T Consensus 21 ~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 21 ALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3333334456999999999999999998765
No 56
>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=30.83 E-value=24 Score=18.03 Aligned_cols=33 Identities=24% Similarity=0.321 Sum_probs=20.3
Q ss_pred CCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 51 IFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 51 ~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
.+|..++..|.....-. ...++|..+++++..|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV 35 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTV 35 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhH
Confidence 46777777776655433 4567788777766544
No 57
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=30.03 E-value=13 Score=19.99 Aligned_cols=17 Identities=18% Similarity=0.282 Sum_probs=13.5
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-.+||..||+++.+|+
T Consensus 24 ~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIR 40 (60)
T ss_pred cHHHHHHHHCCCHHHHH
Confidence 34589999999988774
No 58
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=29.93 E-value=59 Score=20.64 Aligned_cols=33 Identities=21% Similarity=0.155 Sum_probs=24.2
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 57 LEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 57 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
+..|...=+...|++...-..+|..|+++..+|
T Consensus 26 i~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V 58 (156)
T PRK05988 26 LPILHAIQDEFGYVPEDAVPVIAEALNLSRAEV 58 (156)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 334433334556999999999999999998765
No 59
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=29.82 E-value=57 Score=20.50 Aligned_cols=31 Identities=16% Similarity=0.049 Sum_probs=23.2
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 59 QLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 59 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
.|...=....|.+......+|..++++..+|
T Consensus 27 ~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 27 ALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3333334457899999999999999998765
No 60
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=29.16 E-value=47 Score=20.77 Aligned_cols=35 Identities=29% Similarity=0.398 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 49 RTIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 49 Rt~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
.+.++..|...|+.. ..+. ...++|..+|++...|
T Consensus 4 ~~~Lte~qr~VL~Lr-~~Gl-----Tq~EIAe~LgiS~stV 38 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKGL-----SQKEIAKELKTTRANV 38 (137)
T ss_pred cCCCCHHHHHHHHHH-HcCC-----CHHHHHHHHCcCHHHH
Confidence 456788888888763 2222 5778999999987655
No 61
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=28.73 E-value=5.5 Score=22.30 Aligned_cols=27 Identities=11% Similarity=0.010 Sum_probs=18.0
Q ss_pred hhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 64 FEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 64 F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
|....|.......++|..+|+++..|+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk 50 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVR 50 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHH
Confidence 444444444467789999999987654
No 62
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=27.47 E-value=81 Score=18.82 Aligned_cols=17 Identities=18% Similarity=0.208 Sum_probs=13.8
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-+++|..||+++..|+
T Consensus 125 s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 125 KEIDIAKKLHISRQSVY 141 (142)
T ss_pred CHHHHHHHHCcCHHhhc
Confidence 45688999999988776
No 63
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=27.06 E-value=46 Score=20.08 Aligned_cols=18 Identities=17% Similarity=0.226 Sum_probs=13.7
Q ss_pred HHHHHHHHhcCCCCCCCC
Q psy7434 73 VLREQLALKVDLKEERVE 90 (91)
Q Consensus 73 ~~r~~La~~l~l~~~qVk 90 (91)
..-.++|..+|+++..|+
T Consensus 123 ~s~~EIA~~l~is~~tV~ 140 (154)
T PRK06759 123 KTMGEIALETEMTYYQVR 140 (154)
T ss_pred CCHHHHHHHHCCCHHHHH
Confidence 356789999999887664
No 64
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=26.94 E-value=70 Score=20.68 Aligned_cols=25 Identities=28% Similarity=0.178 Sum_probs=20.9
Q ss_pred hhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 65 EKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 65 ~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
....|++....+.+|..||++..+|
T Consensus 47 ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 47 ELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 4456899999999999999998665
No 65
>PRK04217 hypothetical protein; Provisional
Probab=26.66 E-value=49 Score=19.91 Aligned_cols=35 Identities=17% Similarity=0.178 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 50 TIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 50 t~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
..++..|...+...+.... ...++|..+|++...|
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV 75 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTV 75 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHH
Confidence 3467888777765554333 5668999999987655
No 66
>KOG0041|consensus
Probab=25.08 E-value=1.2e+02 Score=20.77 Aligned_cols=37 Identities=16% Similarity=0.361 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHhhh-----hcCCCCHHHHHHHHHhcCCCCC
Q psy7434 51 IFTEEQLEQLEATFE-----KTHYPDVVLREQLALKVDLKEE 87 (91)
Q Consensus 51 ~~t~~Q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~ 87 (91)
-|+..|+..++..|. .+.|++.-+-..+-.+||.+..
T Consensus 92 eFsrkqIk~~~~~Fk~yDe~rDgfIdl~ELK~mmEKLgapQT 133 (244)
T KOG0041|consen 92 EFSRKQIKDAESMFKQYDEDRDGFIDLMELKRMMEKLGAPQT 133 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHhCCchh
Confidence 477889999999996 4679999999999999987754
No 67
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=24.74 E-value=54 Score=20.43 Aligned_cols=17 Identities=18% Similarity=0.239 Sum_probs=12.7
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-+++|..+|+++..|+
T Consensus 118 s~~eIA~~lgis~~tV~ 134 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAK 134 (170)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688888888876654
No 68
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=24.71 E-value=13 Score=19.24 Aligned_cols=15 Identities=20% Similarity=0.361 Sum_probs=11.2
Q ss_pred HHHHHhcCCCCCCCC
Q psy7434 76 EQLALKVDLKEERVE 90 (91)
Q Consensus 76 ~~La~~l~l~~~qVk 90 (91)
.+||..+|++..||+
T Consensus 32 ~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 32 QELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHTS-HHHHH
T ss_pred HHHHHHHCCCHHHhc
Confidence 478999999888774
No 69
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.58 E-value=56 Score=20.55 Aligned_cols=17 Identities=18% Similarity=0.290 Sum_probs=13.1
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-+++|..||+++..||
T Consensus 145 s~~EIA~~lgis~~tVk 161 (178)
T PRK12529 145 KQKDIAQALDIALPTVK 161 (178)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999887664
No 70
>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=24.12 E-value=71 Score=13.12 Aligned_cols=32 Identities=16% Similarity=0.221 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCC
Q psy7434 52 FTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEER 88 (91)
Q Consensus 52 ~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~q 88 (91)
++..+...+...+... + ...+++..++++...
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~t 37 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRST 37 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHH
Confidence 5566666565555533 2 345778888877543
No 71
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=24.11 E-value=30 Score=19.55 Aligned_cols=15 Identities=7% Similarity=0.379 Sum_probs=12.1
Q ss_pred HHHHHHhcCCCCCCC
Q psy7434 75 REQLALKVDLKEERV 89 (91)
Q Consensus 75 r~~La~~l~l~~~qV 89 (91)
=.+++++|||++.+|
T Consensus 14 wk~~~R~LGlse~~I 28 (80)
T cd08313 14 WKEFVRRLGLSDNEI 28 (80)
T ss_pred HHHHHHHcCCCHHHH
Confidence 357999999998765
No 72
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=23.89 E-value=16 Score=17.90 Aligned_cols=15 Identities=33% Similarity=0.395 Sum_probs=10.9
Q ss_pred HHHHHHhcCCCCCCC
Q psy7434 75 REQLALKVDLKEERV 89 (91)
Q Consensus 75 r~~La~~l~l~~~qV 89 (91)
-.+||..+|+++..|
T Consensus 20 ~~~la~~lglS~~~v 34 (42)
T PF13404_consen 20 YAELAEELGLSESTV 34 (42)
T ss_dssp HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHCcCHHHH
Confidence 457999999998654
No 73
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.53 E-value=28 Score=17.41 Aligned_cols=19 Identities=21% Similarity=0.190 Sum_probs=13.9
Q ss_pred CHHHHHHHHHhcCCCCCCC
Q psy7434 71 DVVLREQLALKVDLKEERV 89 (91)
Q Consensus 71 ~~~~r~~La~~l~l~~~qV 89 (91)
+.+..+.||..+|++...|
T Consensus 24 ~~pS~~~la~~~g~s~~Tv 42 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTV 42 (55)
T ss_pred CCcCHHHHHHHHCcCHHHH
Confidence 4445678899999887655
No 74
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=23.08 E-value=51 Score=20.48 Aligned_cols=31 Identities=19% Similarity=0.146 Sum_probs=20.4
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 59 QLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 59 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
.|...=+...|.+...-..+|..++++..+|
T Consensus 18 ~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v 48 (145)
T PF01257_consen 18 ILHEVQEEYGYIPEEALEEIAEALGIPPAEV 48 (145)
T ss_dssp HHHHHHHHHSS--HHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHCCCHHHH
Confidence 3443334456999999999999999987665
No 75
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.71 E-value=86 Score=14.98 Aligned_cols=32 Identities=22% Similarity=0.272 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 52 FTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 52 ~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
++..+...+...+. .. ...++|..++++...|
T Consensus 4 l~~~e~~i~~~~~~-g~-----s~~eia~~l~is~~tv 35 (58)
T smart00421 4 LTPREREVLRLLAE-GL-----TNKEIAERLGISEKTV 35 (58)
T ss_pred CCHHHHHHHHHHHc-CC-----CHHHHHHHHCCCHHHH
Confidence 56666666654322 21 4567888898887654
No 76
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.29 E-value=96 Score=19.44 Aligned_cols=17 Identities=12% Similarity=0.147 Sum_probs=13.4
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-.++|..+|+++..|+
T Consensus 151 s~~eIA~~lgis~~tV~ 167 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVK 167 (182)
T ss_pred CHHHHHHHHCCChhhHH
Confidence 45688999999987765
No 77
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=22.19 E-value=87 Score=19.92 Aligned_cols=17 Identities=12% Similarity=0.132 Sum_probs=13.2
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-.++|..||+++..|+
T Consensus 160 s~~EIA~~Lgis~~tVk 176 (194)
T PRK09646 160 TYREVAERLAVPLGTVK 176 (194)
T ss_pred CHHHHHHHhCCChHhHH
Confidence 45688999999887764
No 78
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=21.98 E-value=22 Score=20.70 Aligned_cols=27 Identities=30% Similarity=0.391 Sum_probs=16.6
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHhcCCCCCCC
Q psy7434 59 QLEATFEKTHYPDVVLREQLALKVDLKEERV 89 (91)
Q Consensus 59 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 89 (91)
+|..-|....+ ..+.+|..|++++..|
T Consensus 14 ELq~nf~~~~l----s~~~ia~dL~~s~~~l 40 (89)
T PF10078_consen 14 ELQANFELSGL----SLEQIAADLGTSPEHL 40 (89)
T ss_pred HHHHHHHHcCC----CHHHHHHHhCCCHHHH
Confidence 45555555544 3567788888776543
No 79
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.34 E-value=86 Score=19.33 Aligned_cols=17 Identities=24% Similarity=0.319 Sum_probs=13.2
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-+++|..||+++..|+
T Consensus 136 s~~EIA~~lgis~~tV~ 152 (173)
T PRK09645 136 STAQIAADLGIPEGTVK 152 (173)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 45688999999887664
No 80
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=21.30 E-value=73 Score=19.37 Aligned_cols=17 Identities=24% Similarity=0.372 Sum_probs=12.8
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-.++|..+|+++..|+
T Consensus 124 s~~EIA~~lgis~~tV~ 140 (160)
T PRK09642 124 SYQEIALQEKIEVKTVE 140 (160)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 35588899998887664
No 81
>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=21.29 E-value=75 Score=19.17 Aligned_cols=17 Identities=18% Similarity=-0.009 Sum_probs=13.0
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-+++|..+|++...|+
T Consensus 129 ~~~eIA~~l~is~~tv~ 145 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVY 145 (159)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 56688999998887654
No 82
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=21.25 E-value=1.1e+02 Score=20.03 Aligned_cols=35 Identities=26% Similarity=0.360 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 50 TIFTEEQLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 50 t~~t~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
..+|..+...|.-.-+-. .-.++|.+|++++..||
T Consensus 147 ~~LT~RE~eVL~lla~G~------snkeIA~~L~iS~~TVk 181 (211)
T COG2197 147 ELLTPRELEVLRLLAEGL------SNKEIAEELNLSEKTVK 181 (211)
T ss_pred CCCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHhHHH
Confidence 368888888876443322 35689999999998886
No 83
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=20.83 E-value=26 Score=18.95 Aligned_cols=16 Identities=25% Similarity=0.368 Sum_probs=11.6
Q ss_pred HHHHHHHhcCCCCCCC
Q psy7434 74 LREQLALKVDLKEERV 89 (91)
Q Consensus 74 ~r~~La~~l~l~~~qV 89 (91)
+.++||..+|++...|
T Consensus 22 t~eEiA~~lgis~~~v 37 (78)
T PF04539_consen 22 TDEEIAEELGISVEEV 37 (78)
T ss_dssp BHHHHHHHHTS-HHHH
T ss_pred CHHHHHHHHcccHHHH
Confidence 5668999999987654
No 84
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=20.79 E-value=72 Score=19.85 Aligned_cols=17 Identities=24% Similarity=0.225 Sum_probs=12.7
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-.++|..+|+++..||
T Consensus 152 s~~EIA~~lgis~~tVk 168 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVE 168 (183)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45678888888887664
No 85
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.70 E-value=75 Score=19.36 Aligned_cols=17 Identities=12% Similarity=0.233 Sum_probs=12.8
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
...++|..+|++...|+
T Consensus 127 s~~EIA~~lgis~~tV~ 143 (163)
T PRK07037 127 TQKDIARELGVSPTLVN 143 (163)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 46688999998876654
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.69 E-value=73 Score=19.28 Aligned_cols=17 Identities=18% Similarity=0.055 Sum_probs=13.1
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-.++|..||+++..|+
T Consensus 124 s~~EIA~~lgis~~tV~ 140 (161)
T PRK09047 124 DVAETAAAMGCSEGSVK 140 (161)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999887664
No 87
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=20.38 E-value=73 Score=20.08 Aligned_cols=17 Identities=24% Similarity=0.079 Sum_probs=12.8
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy7434 74 LREQLALKVDLKEERVE 90 (91)
Q Consensus 74 ~r~~La~~l~l~~~qVk 90 (91)
.-.++|..+|++...|+
T Consensus 157 s~~EIA~~lgis~~tV~ 173 (189)
T PRK09648 157 SAEETAEAVGSTPGAVR 173 (189)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 46688999998876654
No 88
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=20.07 E-value=58 Score=19.58 Aligned_cols=33 Identities=18% Similarity=0.148 Sum_probs=21.4
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHhcCCCCCCCC
Q psy7434 56 QLEQLEATFEKTHYPDVVLREQLALKVDLKEERVE 90 (91)
Q Consensus 56 Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 90 (91)
|...|...|... +...+-.+||..+.++++.||
T Consensus 5 ~y~~L~~~~~~~--~~~vtl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 5 QYQRLWQHYGGQ--PVEVTLDELAELLFCSRRNAR 37 (115)
T ss_pred HHHHHHHHcCCC--CcceeHHHHHHHhCCCHHHHH
Confidence 445566656522 333456689999999987764
Done!