Query psy14571
Match_columns 123
No_of_seqs 142 out of 1423
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 23:15:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14571.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14571hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0850|consensus 99.5 8.3E-14 1.8E-18 105.0 6.3 56 67-122 113-168 (245)
2 KOG0842|consensus 99.4 6.3E-13 1.4E-17 104.4 7.1 50 73-122 150-199 (307)
3 KOG0488|consensus 99.4 5.1E-13 1.1E-17 105.5 6.0 51 72-122 168-218 (309)
4 KOG0489|consensus 99.4 4.1E-13 8.8E-18 103.8 3.5 50 73-122 156-205 (261)
5 KOG0484|consensus 99.3 3.1E-13 6.7E-18 91.0 0.8 51 72-122 13-63 (125)
6 KOG2251|consensus 99.3 1E-11 2.2E-16 93.2 6.4 53 71-123 32-84 (228)
7 KOG0843|consensus 99.3 3.7E-12 7.9E-17 93.1 3.6 48 75-122 101-148 (197)
8 TIGR01565 homeo_ZF_HD homeobox 99.3 8.9E-12 1.9E-16 76.0 4.7 46 77-122 2-51 (58)
9 KOG0487|consensus 99.2 2.4E-11 5.3E-16 95.5 5.7 49 74-122 233-281 (308)
10 KOG0492|consensus 99.2 4.5E-11 9.7E-16 89.3 6.6 49 74-122 142-190 (246)
11 KOG0485|consensus 99.2 2.3E-11 5E-16 91.4 5.0 51 72-122 100-150 (268)
12 KOG0848|consensus 99.0 2.2E-10 4.7E-15 88.4 3.7 45 78-122 201-245 (317)
13 PF00046 Homeobox: Homeobox do 98.9 9.3E-10 2E-14 66.0 2.7 46 77-122 1-46 (57)
14 KOG0493|consensus 98.9 2.9E-09 6.2E-14 82.2 5.6 46 77-122 247-292 (342)
15 KOG0494|consensus 98.9 3.4E-09 7.4E-14 81.7 5.7 48 75-122 140-187 (332)
16 KOG0486|consensus 98.8 1.6E-09 3.4E-14 85.2 2.5 48 75-122 111-158 (351)
17 KOG0491|consensus 98.8 1.5E-09 3.4E-14 78.5 0.8 48 75-122 99-146 (194)
18 KOG0844|consensus 98.7 9E-09 2E-13 80.9 3.4 50 73-122 178-227 (408)
19 smart00389 HOX Homeodomain. DN 98.7 2.1E-08 4.5E-13 59.5 3.6 45 78-122 2-46 (56)
20 cd00086 homeodomain Homeodomai 98.6 6.2E-08 1.3E-12 57.8 3.5 45 78-122 2-46 (59)
21 KOG0490|consensus 98.4 1.6E-07 3.5E-12 70.0 2.6 50 73-122 57-106 (235)
22 KOG0849|consensus 98.3 6.3E-07 1.4E-11 72.2 4.8 51 72-122 172-222 (354)
23 COG5576 Homeodomain-containing 98.2 2.6E-06 5.7E-11 61.5 4.7 51 72-122 47-97 (156)
24 KOG0847|consensus 98.1 4.6E-06 1E-10 63.2 4.2 50 73-122 164-213 (288)
25 KOG0483|consensus 97.8 3.2E-05 7E-10 57.8 5.0 46 77-122 51-96 (198)
26 KOG3802|consensus 97.2 0.0005 1.1E-08 56.0 4.6 49 74-122 292-340 (398)
27 KOG4577|consensus 96.8 0.0015 3.2E-08 51.6 3.7 49 74-122 165-213 (383)
28 KOG2252|consensus 96.6 0.0027 5.8E-08 53.6 3.9 46 75-120 419-464 (558)
29 KOG0490|consensus 95.4 0.016 3.4E-07 43.0 3.2 51 72-122 149-199 (235)
30 PF05920 Homeobox_KN: Homeobox 93.4 0.031 6.6E-07 31.4 0.5 25 97-121 7-31 (40)
31 KOG0774|consensus 92.2 0.15 3.3E-06 39.9 3.1 45 76-120 188-235 (334)
32 KOG0775|consensus 91.9 0.23 4.9E-06 39.1 3.8 42 79-120 170-220 (304)
33 KOG1168|consensus 89.3 0.26 5.6E-06 39.2 2.0 49 74-122 307-355 (385)
34 PF13945 NST1: Salt tolerance 79.5 5.5 0.00012 29.7 5.1 11 100-110 113-123 (190)
35 PF04967 HTH_10: HTH DNA bindi 76.6 2.1 4.5E-05 25.4 1.8 37 83-119 1-39 (53)
36 PF04218 CENP-B_N: CENP-B N-te 72.5 8 0.00017 22.6 3.6 40 77-121 1-40 (53)
37 KOG1146|consensus 66.4 9.6 0.00021 36.1 4.4 48 75-122 902-949 (1406)
38 PF11569 Homez: Homeodomain le 66.1 2.4 5.2E-05 25.5 0.4 34 88-121 10-43 (56)
39 COG3413 Predicted DNA binding 49.9 19 0.00042 26.6 3.0 37 82-118 155-193 (215)
40 PF08880 QLQ: QLQ; InterPro: 43.0 21 0.00045 19.5 1.7 16 82-97 2-17 (37)
41 PF08280 HTH_Mga: M protein tr 41.5 13 0.00028 21.9 0.8 32 86-121 6-37 (59)
42 KOG3794|consensus 40.6 29 0.00062 29.0 2.8 7 4-10 232-238 (453)
43 PF12824 MRP-L20: Mitochondria 34.3 1.8E+02 0.0039 21.0 6.2 39 80-120 83-121 (164)
44 PF04545 Sigma70_r4: Sigma-70, 32.8 28 0.00062 19.4 1.3 34 83-121 5-38 (50)
45 PF13936 HTH_38: Helix-turn-he 32.7 20 0.00043 19.9 0.5 35 81-120 3-37 (44)
46 PF01527 HTH_Tnp_1: Transposas 24.1 68 0.0015 19.1 2.0 37 78-119 2-39 (76)
47 PF15012 DUF4519: Domain of un 22.6 47 0.001 20.0 0.9 23 13-35 15-37 (56)
48 PF15086 UPF0542: Uncharacteri 22.4 95 0.0021 19.7 2.3 10 5-14 49-58 (74)
49 PF06971 Put_DNA-bind_N: Putat 21.4 26 0.00056 20.4 -0.4 15 107-121 32-46 (50)
50 PF08279 HTH_11: HTH domain; 21.3 54 0.0012 18.4 1.0 28 90-120 5-32 (55)
51 TIGR03879 near_KaiC_dom probab 21.2 13 0.00029 23.5 -1.7 28 94-121 23-50 (73)
52 PF08281 Sigma70_r4_2: Sigma-7 20.0 17 0.00037 20.5 -1.4 24 98-121 21-44 (54)
No 1
>KOG0850|consensus
Probab=99.47 E-value=8.3e-14 Score=104.97 Aligned_cols=56 Identities=27% Similarity=0.373 Sum_probs=52.3
Q ss_pred cccccccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 67 ALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 67 ~~~~~~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
...++.+.|.|+.||+|+..||..|.++|+.++|+...+|++||+.||||.+||||
T Consensus 113 ~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKI 168 (245)
T KOG0850|consen 113 RRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKI 168 (245)
T ss_pred eccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhh
Confidence 35566778889999999999999999999999999999999999999999999998
No 2
>KOG0842|consensus
Probab=99.40 E-value=6.3e-13 Score=104.41 Aligned_cols=50 Identities=32% Similarity=0.466 Sum_probs=47.4
Q ss_pred cCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 73 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 73 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
..++|+.|..||..|+.+||++|..++|++++||++||..|+||++||||
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKI 199 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKI 199 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheee
Confidence 34677889999999999999999999999999999999999999999998
No 3
>KOG0488|consensus
Probab=99.39 E-value=5.1e-13 Score=105.47 Aligned_cols=51 Identities=41% Similarity=0.557 Sum_probs=48.1
Q ss_pred ccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 72 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 72 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
..++.|+.||.||..||.+||..|+++.|++..+|++||..|||+++||||
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKt 218 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKT 218 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHH
Confidence 346778899999999999999999999999999999999999999999986
No 4
>KOG0489|consensus
Probab=99.36 E-value=4.1e-13 Score=103.78 Aligned_cols=50 Identities=60% Similarity=0.791 Sum_probs=47.7
Q ss_pred cCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 73 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 73 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
....+|.||.||..|+.+||.+|+.++|++...|.+||..|.|+|+||||
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKI 205 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKI 205 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHH
Confidence 34678999999999999999999999999999999999999999999998
No 5
>KOG0484|consensus
Probab=99.32 E-value=3.1e-13 Score=91.03 Aligned_cols=51 Identities=33% Similarity=0.372 Sum_probs=48.4
Q ss_pred ccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 72 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 72 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
..++.||-||.||..||.+||+.|...+||++.+|++||..|.|+|.+|||
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQV 63 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQV 63 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHH
Confidence 456789999999999999999999999999999999999999999999987
No 6
>KOG2251|consensus
Probab=99.27 E-value=1e-11 Score=93.19 Aligned_cols=53 Identities=32% Similarity=0.294 Sum_probs=49.8
Q ss_pred cccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCcccC
Q psy14571 71 HQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSFE 123 (123)
Q Consensus 71 ~~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI~ 123 (123)
...++.||.||.|+..|+.+||..|...+||++.+|++||..|+|.|.+|||.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVW 84 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVW 84 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhh
Confidence 44567899999999999999999999999999999999999999999999984
No 7
>KOG0843|consensus
Probab=99.26 E-value=3.7e-12 Score=93.11 Aligned_cols=48 Identities=40% Similarity=0.488 Sum_probs=46.9
Q ss_pred CCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 75 k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
+.+|.||.||.+||..||..|..++|+...+|..||+.|+|++.||||
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 788999999999999999999999999999999999999999999998
No 8
>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=99.26 E-value=8.9e-12 Score=76.04 Aligned_cols=46 Identities=15% Similarity=0.127 Sum_probs=44.9
Q ss_pred CCCCcccCHHHHHHHHHhhhhCCC----CCHHHHHHHHHHhCCCCCCccc
Q psy14571 77 NSGRTNFTNKQLTELEKEFHFNKY----LTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 77 rr~Rt~ft~~Ql~~LE~~F~~~~Y----p~~~~R~~LA~~L~Lte~qVKI 122 (123)
+|.||.||..|+..||..|+.+.| |+..+|.+||..|||++.+|||
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 789999999999999999999999 9999999999999999999997
No 9
>KOG0487|consensus
Probab=99.20 E-value=2.4e-11 Score=95.54 Aligned_cols=49 Identities=39% Similarity=0.612 Sum_probs=47.3
Q ss_pred CCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 74 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 74 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
+..|++|..||..|+.+||++|..|.|++...|.+|++.|+|||+||||
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKI 281 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKI 281 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheee
Confidence 5678899999999999999999999999999999999999999999998
No 10
>KOG0492|consensus
Probab=99.19 E-value=4.5e-11 Score=89.27 Aligned_cols=49 Identities=43% Similarity=0.569 Sum_probs=46.5
Q ss_pred CCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 74 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 74 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
...|.+||.||..||..||+.|...+|+++.+|.+++..|.||++||||
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKI 190 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKI 190 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheeh
Confidence 3457789999999999999999999999999999999999999999998
No 11
>KOG0485|consensus
Probab=99.19 E-value=2.3e-11 Score=91.41 Aligned_cols=51 Identities=35% Similarity=0.505 Sum_probs=48.1
Q ss_pred ccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 72 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 72 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
.+.+.++.||+|+..|+..||.+|+..+|++..+|..||+.|.|+|.||||
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKI 150 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKI 150 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhh
Confidence 445678899999999999999999999999999999999999999999998
No 12
>KOG0848|consensus
Probab=99.02 E-value=2.2e-10 Score=88.40 Aligned_cols=45 Identities=42% Similarity=0.603 Sum_probs=43.0
Q ss_pred CCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 78 r~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
+-|.+||..|..+||++|+.++|+++....+||..|+|+|+||||
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI 245 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI 245 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence 457899999999999999999999999999999999999999998
No 13
>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=98.90 E-value=9.3e-10 Score=65.95 Aligned_cols=46 Identities=39% Similarity=0.484 Sum_probs=43.5
Q ss_pred CCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 77 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 77 rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
++.|+.||..|+..||..|..++||+..++..||..|||+..+|++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 46 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKN 46 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence 5789999999999999999999999999999999999999998863
No 14
>KOG0493|consensus
Probab=98.89 E-value=2.9e-09 Score=82.15 Aligned_cols=46 Identities=48% Similarity=0.658 Sum_probs=44.6
Q ss_pred CCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 77 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 77 rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
+|+||.||.+||..|..+|+.++|++...|.+||+.|+|.|.||||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKI 292 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKI 292 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhH
Confidence 5789999999999999999999999999999999999999999998
No 15
>KOG0494|consensus
Probab=98.88 E-value=3.4e-09 Score=81.65 Aligned_cols=48 Identities=33% Similarity=0.306 Sum_probs=44.7
Q ss_pred CCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 75 k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
++|+.||.||..|+.+||..|...+||+...|+-||..+.|+|.+|+|
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqV 187 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQV 187 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhH
Confidence 444559999999999999999999999999999999999999999987
No 16
>KOG0486|consensus
Probab=98.83 E-value=1.6e-09 Score=85.21 Aligned_cols=48 Identities=38% Similarity=0.484 Sum_probs=46.6
Q ss_pred CCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 75 k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
++||.||.||..|+++||..|+++.||+..+|++||..++|+|.+|+|
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrv 158 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV 158 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhh
Confidence 788999999999999999999999999999999999999999999987
No 17
>KOG0491|consensus
Probab=98.78 E-value=1.5e-09 Score=78.53 Aligned_cols=48 Identities=40% Similarity=0.573 Sum_probs=45.2
Q ss_pred CCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 75 k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
+.++.||+|+..|+..||.+|+.++|++..+|.+||..|+|++.|||+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKT 146 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKT 146 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHH
Confidence 456689999999999999999999999999999999999999999974
No 18
>KOG0844|consensus
Probab=98.72 E-value=9e-09 Score=80.92 Aligned_cols=50 Identities=40% Similarity=0.526 Sum_probs=47.1
Q ss_pred cCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 73 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 73 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
...-||-||.||.+||-.||++|-+..|.+...|.+||..|+|+|..|||
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKV 227 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKV 227 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeeh
Confidence 34568899999999999999999999999999999999999999999987
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.68 E-value=2.1e-08 Score=59.53 Aligned_cols=45 Identities=49% Similarity=0.636 Sum_probs=42.1
Q ss_pred CCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 78 r~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..||++
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 568889999999999999999999999999999999999998863
No 20
>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=98.58 E-value=6.2e-08 Score=57.80 Aligned_cols=45 Identities=49% Similarity=0.620 Sum_probs=42.2
Q ss_pred CCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 78 r~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
+.|+.|+..|+..||..|..+.||+..++..||..+||+..||++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 467899999999999999999999999999999999999999863
No 21
>KOG0490|consensus
Probab=98.40 E-value=1.6e-07 Score=69.96 Aligned_cols=50 Identities=28% Similarity=0.266 Sum_probs=47.6
Q ss_pred cCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 73 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 73 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
..+.++.||.|+..|+.+||+.|+..+||+...|+.||..++++|..|+|
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 45678999999999999999999999999999999999999999999987
No 22
>KOG0849|consensus
Probab=98.34 E-value=6.3e-07 Score=72.17 Aligned_cols=51 Identities=25% Similarity=0.262 Sum_probs=47.2
Q ss_pred ccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 72 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 72 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
...+.+|.||.|+..|+..||..|+.++||++..|++||..++|++..|+|
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqv 222 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQV 222 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHH
Confidence 445677889999999999999999999999999999999999999998876
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.18 E-value=2.6e-06 Score=61.47 Aligned_cols=51 Identities=29% Similarity=0.412 Sum_probs=46.8
Q ss_pred ccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 72 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 72 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
.....++.|++-|..|+..|++.|..++||+..+|.+|+..|+|++.-|||
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqI 97 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQI 97 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhh
Confidence 345567788889999999999999999999999999999999999999987
No 24
>KOG0847|consensus
Probab=98.07 E-value=4.6e-06 Score=63.22 Aligned_cols=50 Identities=32% Similarity=0.509 Sum_probs=46.2
Q ss_pred cCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 73 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 73 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
.++++-.|.+|+..||..||..|+..+|+-..+|.+||..+|+++.||+|
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkV 213 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKV 213 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHH
Confidence 34556678899999999999999999999999999999999999999987
No 25
>KOG0483|consensus
Probab=97.83 E-value=3.2e-05 Score=57.81 Aligned_cols=46 Identities=28% Similarity=0.375 Sum_probs=42.3
Q ss_pred CCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 77 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 77 rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
.+..-+||..|+..||..|+.+.|+....+..||..|||.++||.|
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVav 96 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAV 96 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHH
Confidence 3445579999999999999999999999999999999999999987
No 26
>KOG3802|consensus
Probab=97.22 E-value=0.0005 Score=55.99 Aligned_cols=49 Identities=27% Similarity=0.186 Sum_probs=46.3
Q ss_pred CCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 74 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 74 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
.++|+.||.|.......||..|..|.-|+..+...||..|+|....|+|
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRV 340 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRV 340 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEE
Confidence 3678899999999999999999999999999999999999999998887
No 27
>KOG4577|consensus
Probab=96.78 E-value=0.0015 Score=51.58 Aligned_cols=49 Identities=24% Similarity=0.258 Sum_probs=46.1
Q ss_pred CCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 74 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 74 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
...+|+||++|..||+.|...|....-|....|++|+..+||.-+.|||
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQV 213 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQV 213 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhh
Confidence 3468899999999999999999999999999999999999999999987
No 28
>KOG2252|consensus
Probab=96.56 E-value=0.0027 Score=53.65 Aligned_cols=46 Identities=26% Similarity=0.247 Sum_probs=42.5
Q ss_pred CCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCc
Q psy14571 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120 (123)
Q Consensus 75 k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qV 120 (123)
..+++|.+||+.|...|...|..++||+..+...|+..|+|....|
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV 464 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTV 464 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHH
Confidence 4567899999999999999999999999999999999999987665
No 29
>KOG0490|consensus
Probab=95.41 E-value=0.016 Score=42.99 Aligned_cols=51 Identities=25% Similarity=0.230 Sum_probs=46.6
Q ss_pred ccCCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 72 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 72 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
...+.++.|+.|+..|+..|+..|....||+...+..|+..+++++..|+|
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~ 199 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQV 199 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhh
Confidence 345678899999999999999999999999999999999999999988776
No 30
>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=93.36 E-value=0.031 Score=31.37 Aligned_cols=25 Identities=28% Similarity=0.375 Sum_probs=19.6
Q ss_pred hCCCCCHHHHHHHHHHhCCCCCCcc
Q psy14571 97 FNKYLTRARRIEIASVLQLNETQTS 121 (123)
Q Consensus 97 ~~~Yp~~~~R~~LA~~L~Lte~qVK 121 (123)
.+.||+..++..||..+||+..||.
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 3689999999999999999998874
No 31
>KOG0774|consensus
Probab=92.22 E-value=0.15 Score=39.94 Aligned_cols=45 Identities=22% Similarity=0.306 Sum_probs=40.2
Q ss_pred CCCCCcccCHHHHHHHHHhhhh---CCCCCHHHHHHHHHHhCCCCCCc
Q psy14571 76 NNSGRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQT 120 (123)
Q Consensus 76 ~rr~Rt~ft~~Ql~~LE~~F~~---~~Yp~~~~R~~LA~~L~Lte~qV 120 (123)
.||.|..|+..-...|..-|.. +.||+....++||...+++-.||
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 3678889999999999999874 77999999999999999998887
No 32
>KOG0775|consensus
Probab=91.94 E-value=0.23 Score=39.11 Aligned_cols=42 Identities=24% Similarity=0.250 Sum_probs=35.1
Q ss_pred CCcccCHHH---------HHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCc
Q psy14571 79 GRTNFTNKQ---------LTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120 (123)
Q Consensus 79 ~Rt~ft~~Q---------l~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qV 120 (123)
+||++..+| ...|..-|..+.||+..+..+||..+||+..||
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 577654443 467888899999999999999999999999987
No 33
>KOG1168|consensus
Probab=89.26 E-value=0.26 Score=39.22 Aligned_cols=49 Identities=18% Similarity=0.158 Sum_probs=43.8
Q ss_pred CCCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 74 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 74 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
...+|.||.+-.-.-..||..|..+.-|+....+.||..|.|....|+|
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRV 355 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRV 355 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEE
Confidence 4467889998888888999999999999999999999999999888876
No 34
>PF13945 NST1: Salt tolerance down-regulator
Probab=79.54 E-value=5.5 Score=29.72 Aligned_cols=11 Identities=18% Similarity=0.298 Sum_probs=6.8
Q ss_pred CCCHHHHHHHH
Q psy14571 100 YLTRARRIEIA 110 (123)
Q Consensus 100 Yp~~~~R~~LA 110 (123)
-|+..+|..|-
T Consensus 113 SL~eeERr~LV 123 (190)
T PF13945_consen 113 SLSEEERRSLV 123 (190)
T ss_pred ccCHHHHHHHH
Confidence 36667776654
No 35
>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=76.63 E-value=2.1 Score=25.41 Aligned_cols=37 Identities=19% Similarity=0.322 Sum_probs=29.5
Q ss_pred cCHHHHHHHHHhhhhCCC--CCHHHHHHHHHHhCCCCCC
Q psy14571 83 FTNKQLTELEKEFHFNKY--LTRARRIEIASVLQLNETQ 119 (123)
Q Consensus 83 ft~~Ql~~LE~~F~~~~Y--p~~~~R~~LA~~L~Lte~q 119 (123)
+|..|...|...+....| |-...-.+||..||++...
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st 39 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKST 39 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHH
Confidence 478899999999998876 4445567999999998753
No 36
>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=72.50 E-value=8 Score=22.56 Aligned_cols=40 Identities=18% Similarity=0.239 Sum_probs=28.4
Q ss_pred CCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCcc
Q psy14571 77 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121 (123)
Q Consensus 77 rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVK 121 (123)
++.|..+|-.+-..+=..++.+. ...+||..+|++..+|.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~ 40 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVS 40 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHH
Confidence 46788899988888877788776 46789999999998873
No 37
>KOG1146|consensus
Probab=66.38 E-value=9.6 Score=36.07 Aligned_cols=48 Identities=13% Similarity=0.041 Sum_probs=42.8
Q ss_pred CCCCCCcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCccc
Q psy14571 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122 (123)
Q Consensus 75 k~rr~Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVKI 122 (123)
..|+.||.|+..||..|...|....|+...+-+.|...++|..+.|+|
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~v 949 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQV 949 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHH
Confidence 456789999999999999999999999888888899999999887765
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=66.08 E-value=2.4 Score=25.55 Aligned_cols=34 Identities=18% Similarity=0.169 Sum_probs=24.3
Q ss_pred HHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCcc
Q psy14571 88 LTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121 (123)
Q Consensus 88 l~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVK 121 (123)
+..|+..|...+++....-..|+...+|+..||+
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 4569999999999999888999999999998885
No 39
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=49.86 E-value=19 Score=26.62 Aligned_cols=37 Identities=19% Similarity=0.385 Sum_probs=30.8
Q ss_pred ccCHHHHHHHHHhhhhCCC--CCHHHHHHHHHHhCCCCC
Q psy14571 82 NFTNKQLTELEKEFHFNKY--LTRARRIEIASVLQLNET 118 (123)
Q Consensus 82 ~ft~~Ql~~LE~~F~~~~Y--p~~~~R~~LA~~L~Lte~ 118 (123)
.+|..|+..|...|....| |-...-.+||..||++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISks 193 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKS 193 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 6899999999999998875 545555789999999874
No 40
>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=42.96 E-value=21 Score=19.52 Aligned_cols=16 Identities=38% Similarity=0.420 Sum_probs=12.7
Q ss_pred ccCHHHHHHHHHhhhh
Q psy14571 82 NFTNKQLTELEKEFHF 97 (123)
Q Consensus 82 ~ft~~Ql~~LE~~F~~ 97 (123)
.||..|+.+|+.-...
T Consensus 2 ~FT~~Ql~~L~~Qi~a 17 (37)
T PF08880_consen 2 PFTPAQLQELRAQILA 17 (37)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 6999999999865443
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=41.50 E-value=13 Score=21.92 Aligned_cols=32 Identities=34% Similarity=0.462 Sum_probs=23.0
Q ss_pred HHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCcc
Q psy14571 86 KQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121 (123)
Q Consensus 86 ~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVK 121 (123)
.|+.-|+-.+. +.+++.. +||..||+++..|+
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 46677777777 6666555 89999999987654
No 42
>KOG3794|consensus
Probab=40.60 E-value=29 Score=28.95 Aligned_cols=7 Identities=43% Similarity=0.302 Sum_probs=2.5
Q ss_pred hHHHHhh
Q psy14571 4 RKKEKKK 10 (123)
Q Consensus 4 ~~~~~~~ 10 (123)
+.+.+++
T Consensus 232 ldK~e~K 238 (453)
T KOG3794|consen 232 LDKLEKK 238 (453)
T ss_pred HHHHHHH
Confidence 3333333
No 43
>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=34.29 E-value=1.8e+02 Score=21.04 Aligned_cols=39 Identities=10% Similarity=0.114 Sum_probs=30.1
Q ss_pred CcccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCc
Q psy14571 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120 (123)
Q Consensus 80 Rt~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qV 120 (123)
....|.+++.++-+.-..+ |..-.|..||..+|++..-|
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV 121 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFV 121 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHH
Confidence 4578999999887766554 55667899999999987543
No 44
>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=32.81 E-value=28 Score=19.37 Aligned_cols=34 Identities=12% Similarity=0.146 Sum_probs=22.5
Q ss_pred cCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCcc
Q psy14571 83 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121 (123)
Q Consensus 83 ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qVK 121 (123)
.+..+...|...|..+ ..-.++|..+|++...|+
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 4566667777676332 346689999999987664
No 45
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=32.69 E-value=20 Score=19.92 Aligned_cols=35 Identities=17% Similarity=0.166 Sum_probs=15.4
Q ss_pred cccCHHHHHHHHHhhhhCCCCCHHHHHHHHHHhCCCCCCc
Q psy14571 81 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120 (123)
Q Consensus 81 t~ft~~Ql~~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qV 120 (123)
..+|..|...++...... ..-.+||..||.+...|
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 356777788887776544 34567999999887654
No 46
>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=24.14 E-value=68 Score=19.11 Aligned_cols=37 Identities=11% Similarity=0.174 Sum_probs=20.7
Q ss_pred CCCcccCHHHHHHHHHhh-hhCCCCCHHHHHHHHHHhCCCCCC
Q psy14571 78 SGRTNFTNKQLTELEKEF-HFNKYLTRARRIEIASVLQLNETQ 119 (123)
Q Consensus 78 r~Rt~ft~~Ql~~LE~~F-~~~~Yp~~~~R~~LA~~L~Lte~q 119 (123)
+.|..||..+-..+-... ... ....++|..+|++..+
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 356788888877665554 332 3566899999987654
No 47
>PF15012 DUF4519: Domain of unknown function (DUF4519)
Probab=22.62 E-value=47 Score=19.95 Aligned_cols=23 Identities=26% Similarity=0.592 Sum_probs=14.4
Q ss_pred HHHHHhhhHHhhhcccccccCCC
Q psy14571 13 KKKKKKKKKKKKKKRITKVQIPS 35 (123)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~p~ 35 (123)
-|+-+|++-.+....+.++.+|-
T Consensus 15 ~K~ERk~~~~e~~~kv~tVVlP~ 37 (56)
T PF15012_consen 15 QKKERKKEMQEAQQKVFTVVLPT 37 (56)
T ss_pred HHHHHHHHHHHHHHhheeEehhH
Confidence 34445556666667777777763
No 48
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=22.37 E-value=95 Score=19.67 Aligned_cols=10 Identities=60% Similarity=0.863 Sum_probs=3.9
Q ss_pred HHHHhhhHHH
Q psy14571 5 KKEKKKKKKK 14 (123)
Q Consensus 5 ~~~~~~~~~~ 14 (123)
+++++.+|++
T Consensus 49 e~~ere~K~k 58 (74)
T PF15086_consen 49 EKEEREKKKK 58 (74)
T ss_pred HHHHHHHHHH
Confidence 3344433333
No 49
>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=21.38 E-value=26 Score=20.40 Aligned_cols=15 Identities=27% Similarity=0.359 Sum_probs=11.8
Q ss_pred HHHHHHhCCCCCCcc
Q psy14571 107 IEIASVLQLNETQTS 121 (123)
Q Consensus 107 ~~LA~~L~Lte~qVK 121 (123)
.+||..+|++..||+
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 379999999998874
No 50
>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=21.28 E-value=54 Score=18.39 Aligned_cols=28 Identities=18% Similarity=0.134 Sum_probs=16.2
Q ss_pred HHHHhhhhCCCCCHHHHHHHHHHhCCCCCCc
Q psy14571 90 ELEKEFHFNKYLTRARRIEIASVLQLNETQT 120 (123)
Q Consensus 90 ~LE~~F~~~~Yp~~~~R~~LA~~L~Lte~qV 120 (123)
.|.-.+....+++ -.+||..|+++.+.|
T Consensus 5 il~~L~~~~~~it---~~eLa~~l~vS~rTi 32 (55)
T PF08279_consen 5 ILKLLLESKEPIT---AKELAEELGVSRRTI 32 (55)
T ss_dssp HHHHHHHTTTSBE---HHHHHHHCTS-HHHH
T ss_pred HHHHHHHcCCCcC---HHHHHHHhCCCHHHH
Confidence 3333334454443 347899999987654
No 51
>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=21.20 E-value=13 Score=23.45 Aligned_cols=28 Identities=18% Similarity=0.067 Sum_probs=19.8
Q ss_pred hhhhCCCCCHHHHHHHHHHhCCCCCCcc
Q psy14571 94 EFHFNKYLTRARRIEIASVLQLNETQTS 121 (123)
Q Consensus 94 ~F~~~~Yp~~~~R~~LA~~L~Lte~qVK 121 (123)
.|.-..|.......++|..||+++..|+
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk 50 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVR 50 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHH
Confidence 3444455555567799999999987765
No 52
>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=20.03 E-value=17 Score=20.53 Aligned_cols=24 Identities=25% Similarity=0.420 Sum_probs=15.3
Q ss_pred CCCCCHHHHHHHHHHhCCCCCCcc
Q psy14571 98 NKYLTRARRIEIASVLQLNETQTS 121 (123)
Q Consensus 98 ~~Yp~~~~R~~LA~~L~Lte~qVK 121 (123)
-.|.....-.++|..+|+++..|+
T Consensus 21 l~~~~g~s~~eIa~~l~~s~~~v~ 44 (54)
T PF08281_consen 21 LRYFQGMSYAEIAEILGISESTVK 44 (54)
T ss_dssp HHHTS---HHHHHHHCTS-HHHHH
T ss_pred HHHHHCcCHHHHHHHHCcCHHHHH
Confidence 445556678899999999987664
Done!