Query psy15887
Match_columns 104
No_of_seqs 106 out of 1106
Neff 8.4
Searched_HMMs 46136
Date Sat Aug 17 00:08:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15887.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15887hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842|consensus 99.8 2.4E-19 5.2E-24 127.9 7.5 56 46-101 150-205 (307)
2 TIGR01565 homeo_ZF_HD homeobox 99.8 2.8E-19 6.1E-24 99.5 5.3 52 49-100 1-56 (58)
3 KOG0484|consensus 99.8 1.1E-19 2.4E-24 110.8 0.2 55 46-100 14-68 (125)
4 KOG0850|consensus 99.7 2E-18 4.3E-23 118.1 5.3 60 43-102 116-175 (245)
5 KOG0489|consensus 99.7 5.1E-19 1.1E-23 124.9 1.9 55 46-100 156-210 (261)
6 KOG0487|consensus 99.7 6.1E-18 1.3E-22 120.8 6.3 58 44-101 230-287 (308)
7 KOG0488|consensus 99.7 4.8E-18 1E-22 122.3 5.6 56 44-99 167-222 (309)
8 KOG0843|consensus 99.7 2.5E-18 5.5E-23 113.8 3.6 55 46-100 99-153 (197)
9 KOG0485|consensus 99.7 4.3E-17 9.3E-22 110.9 4.7 56 45-100 100-155 (268)
10 KOG0494|consensus 99.7 1.1E-16 2.4E-21 111.4 5.3 56 45-100 137-192 (332)
11 KOG2251|consensus 99.6 2.4E-16 5.3E-21 107.3 4.9 61 42-102 30-90 (228)
12 KOG0493|consensus 99.6 3.7E-16 7.9E-21 109.0 4.3 52 50-101 247-298 (342)
13 KOG0492|consensus 99.6 4E-16 8.8E-21 105.5 3.9 55 46-100 141-195 (246)
14 PF00046 Homeobox: Homeobox do 99.6 2.2E-16 4.8E-21 87.5 1.9 51 50-100 1-51 (57)
15 KOG0848|consensus 99.6 1E-15 2.2E-20 106.9 1.7 50 51-100 201-250 (317)
16 COG5576 Homeodomain-containing 99.5 1.9E-14 4.1E-19 94.6 4.8 54 47-100 49-102 (156)
17 KOG0486|consensus 99.5 1.6E-14 3.4E-19 102.8 4.7 58 43-100 106-163 (351)
18 smart00389 HOX Homeodomain. DN 99.5 1.4E-14 3E-19 79.7 3.3 52 50-101 1-52 (56)
19 cd00086 homeodomain Homeodomai 99.5 5.3E-14 1.2E-18 78.0 3.1 51 51-101 2-52 (59)
20 KOG0491|consensus 99.4 4.7E-15 1E-19 97.2 -2.0 55 48-102 99-153 (194)
21 KOG0844|consensus 99.4 9E-14 2E-18 98.9 2.6 57 45-101 177-233 (408)
22 KOG0490|consensus 99.4 3.3E-13 7.1E-18 92.9 2.7 56 46-101 57-112 (235)
23 KOG4577|consensus 99.3 6.7E-13 1.5E-17 93.9 3.4 53 48-100 166-218 (383)
24 KOG0483|consensus 99.3 1.4E-12 3.1E-17 88.6 2.6 50 51-100 52-101 (198)
25 KOG0847|consensus 99.2 1.2E-11 2.6E-16 84.7 3.7 57 45-101 163-219 (288)
26 KOG0849|consensus 99.2 1.8E-11 3.9E-16 89.8 3.8 58 44-101 171-228 (354)
27 KOG3802|consensus 99.1 1.1E-10 2.5E-15 85.6 5.5 53 48-100 293-345 (398)
28 KOG1168|consensus 98.5 7.7E-08 1.7E-12 68.6 2.9 55 47-101 307-361 (385)
29 KOG2252|consensus 98.5 1.1E-07 2.3E-12 72.6 2.8 55 47-101 418-472 (558)
30 KOG0490|consensus 98.4 3.1E-07 6.8E-12 63.1 3.4 58 43-100 147-204 (235)
31 KOG1146|consensus 98.2 1.2E-06 2.5E-11 72.5 2.9 55 46-100 900-954 (1406)
32 PF05920 Homeobox_KN: Homeobox 98.0 7.5E-07 1.6E-11 46.0 -0.7 31 70-100 7-37 (40)
33 KOG0775|consensus 97.9 1.4E-05 3E-10 56.7 3.4 45 56-100 183-227 (304)
34 KOG0774|consensus 97.7 3.6E-05 7.8E-10 54.4 3.5 53 50-102 189-244 (334)
35 PF11569 Homez: Homeodomain le 96.8 0.00031 6.8E-09 38.6 0.0 38 61-98 10-47 (56)
36 KOG3623|consensus 95.8 0.0047 1E-07 49.5 1.6 40 61-100 568-607 (1007)
37 KOG0773|consensus 95.6 0.037 8E-07 40.5 5.5 53 49-101 239-294 (342)
38 PF04218 CENP-B_N: CENP-B N-te 94.0 0.064 1.4E-06 29.0 2.5 45 50-99 1-45 (53)
39 PF04967 HTH_10: HTH DNA bindi 91.8 0.19 4E-06 27.3 2.3 37 56-92 1-39 (53)
40 COG3413 Predicted DNA binding 84.5 1.1 2.4E-05 30.7 2.9 38 55-92 155-194 (215)
41 KOG1146|consensus 79.3 1.6 3.5E-05 37.6 2.4 52 48-99 443-494 (1406)
42 PF13518 HTH_28: Helix-turn-he 79.0 0.34 7.4E-06 25.2 -1.1 23 79-101 15-37 (52)
43 PRK15451 tRNA cmo(5)U34 methyl 77.0 2.5 5.5E-05 29.4 2.6 46 56-103 190-236 (247)
44 PF10668 Phage_terminase: Phag 71.7 1.1 2.5E-05 24.9 -0.2 20 79-98 25-44 (60)
45 PF13384 HTH_23: Homeodomain-l 70.0 0.76 1.6E-05 23.8 -1.1 24 78-101 19-42 (50)
46 PF08281 Sigma70_r4_2: Sigma-7 66.2 4.1 8.8E-05 21.3 1.3 38 56-98 11-48 (54)
47 PF01527 HTH_Tnp_1: Transposas 66.2 4 8.7E-05 22.8 1.4 45 51-100 2-47 (76)
48 PF13936 HTH_38: Helix-turn-he 65.3 4.5 9.7E-05 20.7 1.3 36 54-94 3-38 (44)
49 PRK09413 IS2 repressor TnpA; R 60.6 9.5 0.00021 23.7 2.4 44 53-100 10-53 (121)
50 PF04545 Sigma70_r4: Sigma-70, 60.3 8.9 0.00019 19.7 2.0 37 55-96 4-40 (50)
51 KOG2971|consensus 55.3 5.3 0.00011 28.7 0.6 9 94-102 204-212 (299)
52 PF09607 BrkDBD: Brinker DNA-b 53.7 11 0.00024 20.8 1.6 19 81-99 30-48 (58)
53 PHA02955 hypothetical protein; 52.9 21 0.00045 24.9 3.2 43 58-100 60-103 (213)
54 PF06056 Terminase_5: Putative 52.5 3.3 7.2E-05 22.7 -0.6 24 78-101 15-38 (58)
55 PF08880 QLQ: QLQ; InterPro: 51.4 17 0.00037 18.1 2.0 15 55-69 2-16 (37)
56 cd06171 Sigma70_r4 Sigma70, re 49.6 13 0.00029 18.3 1.5 39 56-99 11-49 (55)
57 PF08280 HTH_Mga: M protein tr 49.2 14 0.0003 19.9 1.6 33 59-95 6-38 (59)
58 PF00196 GerE: Bacterial regul 49.0 7.1 0.00015 20.8 0.4 38 55-98 3-40 (58)
59 PRK03975 tfx putative transcri 48.6 14 0.0003 24.0 1.8 40 53-98 4-43 (141)
60 cd00569 HTH_Hin_like Helix-tur 48.3 25 0.00055 15.3 2.6 36 56-96 6-41 (42)
61 cd02413 40S_S3_KH K homology R 46.5 27 0.0006 20.3 2.7 21 79-99 56-76 (81)
62 cd04761 HTH_MerR-SF Helix-Turn 46.5 4.6 0.0001 20.4 -0.6 21 80-100 4-24 (49)
63 PF06032 DUF917: Protein of un 46.2 8.1 0.00018 28.8 0.5 15 89-103 267-281 (353)
64 COG4367 Uncharacterized protei 44.8 21 0.00046 21.5 2.0 36 56-91 3-38 (97)
65 cd04764 HTH_MlrA-like_sg1 Heli 44.8 5.5 0.00012 21.8 -0.5 23 80-102 4-26 (67)
66 PF09292 Neil1-DNA_bind: Endon 42.6 12 0.00025 18.9 0.5 6 94-99 27-32 (39)
67 TIGR03879 near_KaiC_dom probab 41.4 2.4 5.1E-05 24.5 -2.4 23 77-99 33-55 (73)
68 cd04763 HTH_MlrA-like Helix-Tu 41.2 6.4 0.00014 21.7 -0.6 22 80-101 4-25 (68)
69 PF12824 MRP-L20: Mitochondria 40.9 63 0.0014 21.5 4.0 40 52-93 82-121 (164)
70 PF13411 MerR_1: MerR HTH fami 40.7 7.5 0.00016 21.2 -0.4 21 80-100 4-24 (69)
71 PRK13558 bacterio-opsin activa 40.4 34 0.00073 27.0 3.1 39 54-92 606-646 (665)
72 PF11516 DUF3220: Protein of u 39.3 4.2 9.1E-05 24.0 -1.6 10 92-101 32-41 (106)
73 cd01104 HTH_MlrA-CarA Helix-Tu 38.5 7.1 0.00015 21.2 -0.7 23 80-102 4-26 (68)
74 smart00421 HTH_LUXR helix_turn 36.9 39 0.00084 16.9 2.1 38 55-98 3-40 (58)
75 PF13551 HTH_29: Winged helix- 36.7 5.8 0.00013 23.6 -1.3 23 79-101 15-37 (112)
76 PF02796 HTH_7: Helix-turn-hel 34.6 32 0.0007 17.3 1.5 34 56-94 6-39 (45)
77 PRK06759 RNA polymerase factor 32.8 33 0.00072 21.5 1.7 37 56-97 107-143 (154)
78 COG1905 NuoE NADH:ubiquinone o 32.6 67 0.0015 21.4 3.1 36 58-93 25-60 (160)
79 PF13223 DUF4031: Protein of u 32.5 32 0.00069 20.4 1.4 19 77-99 24-42 (83)
80 cd06170 LuxR_C_like C-terminal 31.8 49 0.0011 16.6 2.0 20 78-97 17-36 (57)
81 COG5484 Uncharacterized conser 31.0 17 0.00036 26.2 0.0 25 78-102 21-45 (279)
82 PRK10072 putative transcriptio 30.0 49 0.0011 20.0 2.0 37 57-100 34-70 (96)
83 cd04762 HTH_MerR-trunc Helix-T 29.4 14 0.0003 18.1 -0.5 21 80-100 4-24 (49)
84 PF12793 SgrR_N: Sugar transpo 29.1 45 0.00098 20.7 1.8 34 59-94 4-37 (115)
85 TIGR00721 tfx DNA-binding prot 27.7 66 0.0014 20.8 2.4 38 53-96 4-41 (137)
86 PRK09652 RNA polymerase sigma 27.4 43 0.00093 21.3 1.5 38 55-97 128-165 (182)
87 PRK12537 RNA polymerase sigma 27.1 61 0.0013 21.1 2.3 37 56-97 134-170 (182)
88 PF08279 HTH_11: HTH domain; 26.9 61 0.0013 16.6 1.8 16 79-94 18-33 (55)
89 PRK12526 RNA polymerase sigma 26.4 39 0.00084 22.7 1.2 21 78-98 171-191 (206)
90 PRK09646 RNA polymerase sigma 26.3 59 0.0013 21.4 2.1 37 56-97 143-179 (194)
91 TIGR02989 Sig-70_gvs1 RNA poly 26.2 54 0.0012 20.6 1.8 37 55-96 111-147 (159)
92 PF00376 MerR: MerR family reg 26.1 12 0.00027 18.5 -1.0 17 80-96 3-19 (38)
93 COG1136 SalX ABC-type antimicr 25.6 27 0.00059 24.5 0.3 14 90-103 82-95 (226)
94 PRK00118 putative DNA-binding 25.6 56 0.0012 20.1 1.7 37 56-97 18-54 (104)
95 PF09792 But2: Ubiquitin 3 bin 25.2 34 0.00075 22.1 0.8 10 92-101 132-141 (143)
96 TIGR02959 SigZ RNA polymerase 24.4 57 0.0012 21.0 1.7 37 55-96 100-136 (170)
97 smart00351 PAX Paired Box doma 23.9 45 0.00097 20.9 1.1 41 55-100 17-57 (125)
98 PRK12514 RNA polymerase sigma 23.2 61 0.0013 20.9 1.7 20 79-98 148-167 (179)
99 PRK12519 RNA polymerase sigma 22.6 41 0.00089 22.0 0.8 21 78-98 159-179 (194)
100 PF12578 3-PAP: Myotubularin-a 22.6 15 0.00032 23.7 -1.3 13 88-100 81-93 (142)
101 PRK12530 RNA polymerase sigma 22.5 62 0.0013 21.3 1.6 37 56-97 135-171 (189)
102 PRK11511 DNA-binding transcrip 22.4 21 0.00045 22.3 -0.7 24 77-100 26-49 (127)
103 PF11388 DotA: Phagosome traff 22.2 27 0.00059 21.2 -0.1 9 92-100 31-39 (105)
104 COG5154 BRX1 RNA-binding prote 22.2 40 0.00086 23.7 0.6 11 92-102 183-193 (283)
105 TIGR01958 nuoE_fam NADH-quinon 22.0 1.2E+02 0.0027 19.4 2.9 33 61-93 19-51 (148)
106 PRK05988 formate dehydrogenase 21.9 1.3E+02 0.0028 19.7 3.0 33 61-93 26-58 (156)
107 TIGR02983 SigE-fam_strep RNA p 21.7 65 0.0014 20.3 1.5 18 79-96 129-146 (162)
108 PF14229 DUF4332: Domain of un 21.3 41 0.00088 21.0 0.5 23 74-96 27-49 (122)
109 PRK10100 DNA-binding transcrip 21.2 69 0.0015 21.9 1.7 39 55-99 155-193 (216)
110 PF13412 HTH_24: Winged helix- 21.2 1.3E+02 0.0028 14.9 2.5 32 58-93 3-34 (48)
111 PRK09648 RNA polymerase sigma 21.2 70 0.0015 20.9 1.7 38 55-97 139-176 (189)
112 PF13730 HTH_36: Helix-turn-he 21.1 56 0.0012 16.8 1.0 22 75-96 24-45 (55)
113 PRK10403 transcriptional regul 20.9 65 0.0014 20.5 1.5 39 55-99 153-191 (215)
114 KOG3623|consensus 20.7 78 0.0017 26.5 2.0 50 51-100 628-677 (1007)
115 PF06971 Put_DNA-bind_N: Putat 20.7 33 0.00071 18.2 -0.0 15 80-94 32-46 (50)
116 PRK10360 DNA-binding transcrip 20.6 71 0.0015 20.3 1.6 39 55-99 137-175 (196)
117 PRK15369 two component system 20.5 55 0.0012 20.6 1.0 39 55-99 149-187 (211)
118 PF10078 DUF2316: Uncharacteri 20.3 36 0.00079 20.4 0.1 27 63-93 14-40 (89)
119 PRK07539 NADH dehydrogenase su 20.3 1.4E+02 0.003 19.3 2.9 33 61-93 25-57 (154)
120 PF05848 CtsR: Firmicute trans 20.2 54 0.0012 21.7 0.9 16 78-93 27-42 (152)
121 smart00422 HTH_MERR helix_turn 20.2 26 0.00057 18.9 -0.5 18 80-97 4-21 (70)
122 PRK12512 RNA polymerase sigma 20.1 74 0.0016 20.6 1.6 37 56-97 132-168 (184)
No 1
>KOG0842|consensus
Probab=99.79 E-value=2.4e-19 Score=127.90 Aligned_cols=56 Identities=27% Similarity=0.392 Sum_probs=52.3
Q ss_pred ccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 46 SKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 46 ~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
..++||.|..|+..|+.+||+.|...+|++..+|++||..|.|++.||||||||-.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrR 205 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRR 205 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecch
Confidence 45667788999999999999999999999999999999999999999999999964
No 2
>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=99.78 E-value=2.8e-19 Score=99.49 Aligned_cols=52 Identities=15% Similarity=0.192 Sum_probs=50.2
Q ss_pred cCCCCCCCCHHHHHHHHHHhhcCCC----CCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 49 QRRQRTHFTSQQLQELEATFARNRY----PDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 49 ~rr~Rt~~t~~Q~~~L~~~F~~~~~----p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
+||.||.||.+|+..|+..|+.++| |+..++.+||..|||++++|||||||-
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~ 56 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN 56 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence 3789999999999999999999999 999999999999999999999999995
No 3
>KOG0484|consensus
Probab=99.75 E-value=1.1e-19 Score=110.81 Aligned_cols=55 Identities=51% Similarity=0.670 Sum_probs=52.5
Q ss_pred ccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 46 SKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 46 ~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
.++.||-||.||..|+.+|++.|...+||+...|++||.++.|++.+|||||||-
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNR 68 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNR 68 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhh
Confidence 5667889999999999999999999999999999999999999999999999995
No 4
>KOG0850|consensus
Probab=99.74 E-value=2e-18 Score=118.08 Aligned_cols=60 Identities=27% Similarity=0.350 Sum_probs=55.8
Q ss_pred CcCccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecccc
Q psy15887 43 TKNSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYNF 102 (104)
Q Consensus 43 ~~~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~~ 102 (104)
.++++|.|+.||.|+.-||..|.+.|+.+.|+...+|.+||..|||+..||||||||-.+
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRS 175 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRS 175 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHH
Confidence 356778889999999999999999999999999999999999999999999999999643
No 5
>KOG0489|consensus
Probab=99.74 E-value=5.1e-19 Score=124.89 Aligned_cols=55 Identities=40% Similarity=0.402 Sum_probs=52.3
Q ss_pred ccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 46 SKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 46 ~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
..+.||.||.||..|+.+||+.|+.++|++...|-+||..|+|+++||||||||-
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNR 210 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNR 210 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHH
Confidence 3557899999999999999999999999999999999999999999999999994
No 6
>KOG0487|consensus
Probab=99.73 E-value=6.1e-18 Score=120.80 Aligned_cols=58 Identities=29% Similarity=0.326 Sum_probs=53.4
Q ss_pred cCccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 44 KNSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 44 ~~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
...+.-|++|..||..|+.+||+.|..|.|.+...|.+|++.|+|++|||||||||=.
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRR 287 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRR 287 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhh
Confidence 3446678899999999999999999999999999999999999999999999999943
No 7
>KOG0488|consensus
Probab=99.73 E-value=4.8e-18 Score=122.26 Aligned_cols=56 Identities=34% Similarity=0.494 Sum_probs=53.4
Q ss_pred cCccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 44 KNSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 44 ~~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
...+|+|+.||.||..|+..||+.|++..|++...|.+||..|||+..|||+||||
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQN 222 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQN 222 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhh
Confidence 44578888999999999999999999999999999999999999999999999999
No 8
>KOG0843|consensus
Probab=99.73 E-value=2.5e-18 Score=113.84 Aligned_cols=55 Identities=33% Similarity=0.390 Sum_probs=52.5
Q ss_pred ccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 46 SKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 46 ~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
..+.||.||.||.+|+..||..|+.++|....+|+.||+.|+|++.||||||||-
T Consensus 99 ~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNR 153 (197)
T KOG0843|consen 99 SMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNR 153 (197)
T ss_pred ccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhh
Confidence 3478999999999999999999999999999999999999999999999999995
No 9
>KOG0485|consensus
Probab=99.68 E-value=4.3e-17 Score=110.95 Aligned_cols=56 Identities=29% Similarity=0.379 Sum_probs=52.7
Q ss_pred CccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 45 NSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 45 ~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
...++|+.||+|+..|+..||..|+..+|++..+|..||.+|.|++.||||||||-
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNR 155 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNR 155 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhh
Confidence 34577889999999999999999999999999999999999999999999999995
No 10
>KOG0494|consensus
Probab=99.66 E-value=1.1e-16 Score=111.45 Aligned_cols=56 Identities=39% Similarity=0.481 Sum_probs=51.4
Q ss_pred CccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 45 NSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 45 ~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
..+++|+.||.||..|+.+||..|...+||+...|+-||.++.|++.+|||||||-
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNR 192 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNR 192 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhh
Confidence 33455566999999999999999999999999999999999999999999999995
No 11
>KOG2251|consensus
Probab=99.64 E-value=2.4e-16 Score=107.33 Aligned_cols=61 Identities=39% Similarity=0.561 Sum_probs=56.7
Q ss_pred CCcCccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecccc
Q psy15887 42 NTKNSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYNF 102 (104)
Q Consensus 42 ~~~~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~~ 102 (104)
....+++.||.||.||..|+.+||..|.+..||+...|++||.+|+|++.+|||||-|-.+
T Consensus 30 ~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRA 90 (228)
T KOG2251|consen 30 YSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRA 90 (228)
T ss_pred cCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccc
Confidence 3466888999999999999999999999999999999999999999999999999999653
No 12
>KOG0493|consensus
Probab=99.62 E-value=3.7e-16 Score=108.97 Aligned_cols=52 Identities=37% Similarity=0.459 Sum_probs=50.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 50 rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
||+||.||.+||..|+..|+.++|+....|.+||..|+|.+.||||||||-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKR 298 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKR 298 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhh
Confidence 5789999999999999999999999999999999999999999999999964
No 13
>KOG0492|consensus
Probab=99.61 E-value=4e-16 Score=105.53 Aligned_cols=55 Identities=33% Similarity=0.413 Sum_probs=51.5
Q ss_pred ccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 46 SKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 46 ~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
.+..|++||.||..||..||+.|....|+++.+|.+++..|.|++.||||||||-
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNR 195 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNR 195 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhh
Confidence 3445778999999999999999999999999999999999999999999999995
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=99.61 E-value=2.2e-16 Score=87.52 Aligned_cols=51 Identities=39% Similarity=0.505 Sum_probs=49.3
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 50 rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
||+|+.||.+|+..|+..|..++||+..+++.||..+||+..+|++||||.
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr 51 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNR 51 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHh
Confidence 578999999999999999999999999999999999999999999999995
No 15
>KOG0848|consensus
Probab=99.56 E-value=1e-15 Score=106.91 Aligned_cols=50 Identities=26% Similarity=0.321 Sum_probs=47.8
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 51 r~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
+.|.+||..|+.+||+.|..++|.+...+.+||..|+|++|||||||||-
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNR 250 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNR 250 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhh
Confidence 45789999999999999999999999999999999999999999999995
No 16
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.51 E-value=1.9e-14 Score=94.65 Aligned_cols=54 Identities=24% Similarity=0.302 Sum_probs=49.8
Q ss_pred cCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 47 KRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 47 ~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
...+++|++.|..|+..|++.|+.++||+...|..|+..++|+++-|||||||-
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNk 102 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNK 102 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchH
Confidence 445667777899999999999999999999999999999999999999999994
No 17
>KOG0486|consensus
Probab=99.51 E-value=1.6e-14 Score=102.83 Aligned_cols=58 Identities=72% Similarity=0.948 Sum_probs=53.7
Q ss_pred CcCccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 43 TKNSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 43 ~~~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
..+.+|+||.||.||.+|+.+||..|++++||++..|++||..++|++.+|+|||-|-
T Consensus 106 ~kki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknr 163 (351)
T KOG0486|consen 106 KKKISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNR 163 (351)
T ss_pred cchhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccc
Confidence 3444588899999999999999999999999999999999999999999999999874
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.51 E-value=1.4e-14 Score=79.75 Aligned_cols=52 Identities=40% Similarity=0.565 Sum_probs=48.8
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 50 rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
++.|+.|+..|+..|++.|..++||+..++..||..+||+..+|+.||+|-.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR 52 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRR 52 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHh
Confidence 3567889999999999999999999999999999999999999999999964
No 19
>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=99.45 E-value=5.3e-14 Score=77.99 Aligned_cols=51 Identities=41% Similarity=0.545 Sum_probs=48.3
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 51 r~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|+.||+|-.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR 52 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRR 52 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 567889999999999999999999999999999999999999999999954
No 20
>KOG0491|consensus
Probab=99.44 E-value=4.7e-15 Score=97.19 Aligned_cols=55 Identities=35% Similarity=0.475 Sum_probs=51.3
Q ss_pred CcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecccc
Q psy15887 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYNF 102 (104)
Q Consensus 48 ~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~~ 102 (104)
++++.||+|+..|+..|++.|+..+|++..+|.+||..|+|++.|||.||||..+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRM 153 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRM 153 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 3466799999999999999999999999999999999999999999999999753
No 21
>KOG0844|consensus
Probab=99.41 E-value=9e-14 Score=98.94 Aligned_cols=57 Identities=32% Similarity=0.375 Sum_probs=52.9
Q ss_pred CccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 45 NSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 45 ~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
....-||.||.||.+|+-.||+.|-+..|.+.+.|=+||..|+|++..|||||||-.
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRR 233 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRR 233 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhch
Confidence 345568899999999999999999999999999999999999999999999999964
No 22
>KOG0490|consensus
Probab=99.36 E-value=3.3e-13 Score=92.92 Aligned_cols=56 Identities=27% Similarity=0.284 Sum_probs=53.1
Q ss_pred ccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 46 SKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 46 ~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
..+.|+.||.|+..|+.+|++.|+..+||+...|+.||..+++++..|||||||+-
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrr 112 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRR 112 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhc
Confidence 55678999999999999999999999999999999999999999999999999974
No 23
>KOG4577|consensus
Probab=99.34 E-value=6.7e-13 Score=93.93 Aligned_cols=53 Identities=23% Similarity=0.321 Sum_probs=50.8
Q ss_pred CcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 48 ~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
..||+||.+|..|++.|+.++...+.|..+.|+.|+..+||.-++|||||||-
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNR 218 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNR 218 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhh
Confidence 35889999999999999999999999999999999999999999999999995
No 24
>KOG0483|consensus
Probab=99.29 E-value=1.4e-12 Score=88.59 Aligned_cols=50 Identities=16% Similarity=0.178 Sum_probs=46.4
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 51 r~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
+++-+||.+|+..|+..|+...++....+..||..|||.++||.|||||=
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNR 101 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNR 101 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhc
Confidence 34456899999999999999999999999999999999999999999994
No 25
>KOG0847|consensus
Probab=99.21 E-value=1.2e-11 Score=84.69 Aligned_cols=57 Identities=23% Similarity=0.340 Sum_probs=52.9
Q ss_pred CccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 45 NSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 45 ~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
...+++..|..|+..|+..|+..|+...|+...+|.+||..+|+++.+|+|||||-.
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRR 219 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRR 219 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcch
Confidence 446677889999999999999999999999999999999999999999999999953
No 26
>KOG0849|consensus
Probab=99.18 E-value=1.8e-11 Score=89.85 Aligned_cols=58 Identities=34% Similarity=0.469 Sum_probs=53.3
Q ss_pred cCccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 44 KNSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 44 ~~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
...++.+|.||.|+..|+..|+..|+.++||+...|++||.++++++..|+|||||-.
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrr 228 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRR 228 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhh
Confidence 3455667789999999999999999999999999999999999999999999999954
No 27
>KOG3802|consensus
Probab=99.11 E-value=1.1e-10 Score=85.60 Aligned_cols=53 Identities=23% Similarity=0.251 Sum_probs=50.6
Q ss_pred CcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 48 ~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
++||+||.+....+..||+.|..|..|+..+...||.+|+|.+.+|+|||=|-
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNR 345 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNR 345 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecc
Confidence 67888999999999999999999999999999999999999999999999773
No 28
>KOG1168|consensus
Probab=98.50 E-value=7.7e-08 Score=68.59 Aligned_cols=55 Identities=22% Similarity=0.241 Sum_probs=50.4
Q ss_pred cCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 47 KRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 47 ~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
..+||+||.+-.-..+.||+.|...+-|+......+|++|.|.+.+|+|||=|+.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQR 361 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQR 361 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccH
Confidence 3467889998888889999999999999999999999999999999999998874
No 29
>KOG2252|consensus
Probab=98.46 E-value=1.1e-07 Score=72.57 Aligned_cols=55 Identities=24% Similarity=0.264 Sum_probs=51.5
Q ss_pred cCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 47 KRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 47 ~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
...||+|.+||..|...|.+.|+.+.+|+..+...|+.+|+|....|..||=|+.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaR 472 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNAR 472 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhh
Confidence 3457789999999999999999999999999999999999999999999999974
No 30
>KOG0490|consensus
Probab=98.38 E-value=3.1e-07 Score=63.11 Aligned_cols=58 Identities=34% Similarity=0.450 Sum_probs=53.1
Q ss_pred CcCccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 43 TKNSKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 43 ~~~~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
.....+.++.|+.++..|+..+...|...++|+...+..|+..++++...|+|||||-
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~ 204 (235)
T KOG0490|consen 147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNR 204 (235)
T ss_pred CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccH
Confidence 3445667889999999999999999999999999999999999999999999999994
No 31
>KOG1146|consensus
Probab=98.18 E-value=1.2e-06 Score=72.46 Aligned_cols=55 Identities=20% Similarity=0.202 Sum_probs=51.1
Q ss_pred ccCcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 46 SKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 46 ~~~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
...+|+.||+++..|+..+...|....||...+.+.|...++++.++|+|||||-
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna 954 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNA 954 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhh
Confidence 3446778999999999999999999999999999999999999999999999994
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=98.02 E-value=7.5e-07 Score=45.97 Aligned_cols=31 Identities=26% Similarity=0.314 Sum_probs=25.9
Q ss_pred cCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 70 RNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 70 ~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
.++||+..++..||..+||+..||..||=|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~Na 37 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINA 37 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 4789999999999999999999999999774
No 33
>KOG0775|consensus
Probab=97.88 E-value=1.4e-05 Score=56.70 Aligned_cols=45 Identities=22% Similarity=0.233 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
|...-+..|...|..++||+..++.+||+.+||+..||-.||-|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNR 227 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNR 227 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhh
Confidence 444556689999999999999999999999999999999999984
No 34
>KOG0774|consensus
Probab=97.72 E-value=3.6e-05 Score=54.45 Aligned_cols=53 Identities=28% Similarity=0.376 Sum_probs=48.1
Q ss_pred CCCCCCCCHHHHHHHHHHhh---cCCCCCHHHHHHHHHHcCCCcCccceeeecccc
Q psy15887 50 RRQRTHFTSQQLQELEATFA---RNRYPDMSTREEIAMWTNLTEALRETHAYSYNF 102 (104)
Q Consensus 50 rr~Rt~~t~~Q~~~L~~~F~---~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~~ 102 (104)
+|+|..|+..-...|...|. .++||+..++++||++-+++..||--||-|-.+
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrI 244 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRI 244 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccccee
Confidence 67788899999999999996 588999999999999999999999999998654
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.80 E-value=0.00031 Score=38.61 Aligned_cols=38 Identities=11% Similarity=0.104 Sum_probs=28.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeee
Q psy15887 61 LQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 61 ~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQ 98 (104)
+..|++.|...+++.......|..+.+|+..+|+.||=
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa 47 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFA 47 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHH
Confidence 45699999999999888889999999999999999993
No 36
>KOG3623|consensus
Probab=95.82 E-value=0.0047 Score=49.48 Aligned_cols=40 Identities=23% Similarity=0.124 Sum_probs=37.6
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 61 LQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 61 ~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
+..|++.|..+..|+..+...+|.+.|++.+.|++||++-
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~ 607 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDE 607 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhh
Confidence 6778999999999999999999999999999999999974
No 37
>KOG0773|consensus
Probab=95.58 E-value=0.037 Score=40.51 Aligned_cols=53 Identities=17% Similarity=0.187 Sum_probs=42.6
Q ss_pred cCCCCCCCCHHHHHHHHHH-hh--cCCCCCHHHHHHHHHHcCCCcCccceeeeccc
Q psy15887 49 QRRQRTHFTSQQLQELEAT-FA--RNRYPDMSTREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 49 ~rr~Rt~~t~~Q~~~L~~~-F~--~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
..|.+..+.......|+.. |+ ..+||+...+..||.++||+..||-.||-|..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR 294 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINAR 294 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcc
Confidence 3445557888888888766 33 35799999999999999999999999999864
No 38
>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=93.99 E-value=0.064 Score=28.98 Aligned_cols=45 Identities=16% Similarity=0.205 Sum_probs=33.9
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 50 rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
||+|..+|-.+-..+-..++... ....+|..+|++..+|..|.-|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHC
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHh
Confidence 56788999999988888888776 4678999999999999888765
No 39
>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=91.79 E-value=0.19 Score=27.31 Aligned_cols=37 Identities=24% Similarity=0.320 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHhhcCCC--CCHHHHHHHHHHcCCCcCc
Q psy15887 56 FTSQQLQELEATFARNRY--PDMSTREEIAMWTNLTEAL 92 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~--p~~~~r~~La~~l~l~~~~ 92 (104)
+|+.|...|...++...| |-...-.+||..+|++...
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 588999999999998876 5556678999999998754
No 40
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=84.55 E-value=1.1 Score=30.66 Aligned_cols=38 Identities=16% Similarity=0.314 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHhhcCCC--CCHHHHHHHHHHcCCCcCc
Q psy15887 55 HFTSQQLQELEATFARNRY--PDMSTREEIAMWTNLTEAL 92 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~--p~~~~r~~La~~l~l~~~~ 92 (104)
.+|..|+..|..+|....| |-...-.+||..+|+++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 6999999999999998876 6666678999999998753
No 41
>KOG1146|consensus
Probab=79.28 E-value=1.6 Score=37.60 Aligned_cols=52 Identities=12% Similarity=0.038 Sum_probs=44.1
Q ss_pred CcCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 48 ~~rr~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
..+-.|++++.-|.+.|...|....||.-.....++..|++..+.+-.|||+
T Consensus 443 e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~ 494 (1406)
T KOG1146|consen 443 EPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS 494 (1406)
T ss_pred hhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch
Confidence 3445678889999999999999999999999999999999999995555554
No 42
>PF13518 HTH_28: Helix-turn-helix domain
Probab=78.97 E-value=0.34 Score=25.22 Aligned_cols=23 Identities=17% Similarity=0.066 Sum_probs=20.4
Q ss_pred HHHHHHHcCCCcCccceeeeccc
Q psy15887 79 REEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 79 r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
..++|..+|++..+|.-|-+.|+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHH
Confidence 45789999999999999998885
No 43
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=76.97 E-value=2.5 Score=29.40 Aligned_cols=46 Identities=9% Similarity=0.125 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHhhcCCCC-CHHHHHHHHHHcCCCcCccceeeeccccc
Q psy15887 56 FTSQQLQELEATFARNRYP-DMSTREEIAMWTNLTEALRETHAYSYNFL 103 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p-~~~~r~~La~~l~l~~~~VqvWFQN~~~~ 103 (104)
++..++......+.....| +..+..++.++.|.. .|..|||+++|-
T Consensus 190 ~s~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~--~v~~~~~~~~f~ 236 (247)
T PRK15451 190 YSELEISQKRSMLENVMLTDSVETHKARLHKAGFE--HSELWFQCFNFG 236 (247)
T ss_pred CCHHHHHHHHHHHHhhcccCCHHHHHHHHHHcCch--hHHHHHHHHhHH
Confidence 4555554444444444444 445556778888865 689999999983
No 44
>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=71.68 E-value=1.1 Score=24.89 Aligned_cols=20 Identities=15% Similarity=0.059 Sum_probs=17.1
Q ss_pred HHHHHHHcCCCcCccceeee
Q psy15887 79 REEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 79 r~~La~~l~l~~~~VqvWFQ 98 (104)
-..||..||+++.+|..|=-
T Consensus 25 lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHHCCCHHHHHHHhh
Confidence 45799999999999999843
No 45
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=69.98 E-value=0.76 Score=23.81 Aligned_cols=24 Identities=17% Similarity=0.119 Sum_probs=17.4
Q ss_pred HHHHHHHHcCCCcCccceeeeccc
Q psy15887 78 TREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 78 ~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
...++|..+|++...|.-|...|+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcc
Confidence 466899999999999999988875
No 46
>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=66.21 E-value=4.1 Score=21.29 Aligned_cols=38 Identities=13% Similarity=0.122 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQ 98 (104)
+++.+...+.-.|... ..-.++|..+|++...|+.|.+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHH
Confidence 4455555555444433 3577899999999999988764
No 47
>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=66.21 E-value=4 Score=22.78 Aligned_cols=45 Identities=11% Similarity=0.166 Sum_probs=28.2
Q ss_pred CCCCCCCHHHHHHHHHHh-hcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 51 RQRTHFTSQQLQELEATF-ARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 51 r~Rt~~t~~Q~~~L~~~F-~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
+.|..||.++...+-... ... .....+|..+|++...+.-|=.-|
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHHH
Confidence 346678888877766555 333 256789999999999998886544
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=65.34 E-value=4.5 Score=20.66 Aligned_cols=36 Identities=19% Similarity=0.257 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccc
Q psy15887 54 THFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRE 94 (104)
Q Consensus 54 t~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~Vq 94 (104)
..+|.++...++....... ...++|..+|.+...|-
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~-----s~~~IA~~lg~s~sTV~ 38 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM-----SIREIAKRLGRSRSTVS 38 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHH
T ss_pred cchhhhHHHHHHHHHHcCC-----CHHHHHHHHCcCcHHHH
Confidence 4578888888887766442 46679999999876653
No 49
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=60.58 E-value=9.5 Score=23.72 Aligned_cols=44 Identities=14% Similarity=-0.010 Sum_probs=29.1
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 53 RTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 53 Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
|..||.++....-.....+.+ ....+|..+|++...|--|-+-|
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 445777765544333332332 24578999999999999997765
No 50
>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=60.30 E-value=8.9 Score=19.71 Aligned_cols=37 Identities=14% Similarity=0.161 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcccee
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETH 96 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 96 (104)
.+++.+...+...|.... .-.++|..+|++...|+.+
T Consensus 4 ~L~~~er~vi~~~y~~~~-----t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL-----TLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC-----CHHHHHHHHCCcHHHHHHH
Confidence 467788888888884332 4668999999998877643
No 51
>KOG2971|consensus
Probab=55.26 E-value=5.3 Score=28.70 Aligned_cols=9 Identities=11% Similarity=0.228 Sum_probs=8.1
Q ss_pred ceeeecccc
Q psy15887 94 ETHAYSYNF 102 (104)
Q Consensus 94 qvWFQN~~~ 102 (104)
+|||.||.+
T Consensus 204 ~IWfRnyqI 212 (299)
T KOG2971|consen 204 KIWFRNYQI 212 (299)
T ss_pred eEEEEEeEe
Confidence 899999976
No 52
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=53.75 E-value=11 Score=20.81 Aligned_cols=19 Identities=11% Similarity=-0.090 Sum_probs=15.1
Q ss_pred HHHHHcCCCcCccceeeec
Q psy15887 81 EIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 81 ~La~~l~l~~~~VqvWFQN 99 (104)
..|.++++++++|+-|-+.
T Consensus 30 Aaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 30 AAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp HHHHHTTS-HHHHHHHHTT
T ss_pred HHHHHhCccHHHHHHHHHH
Confidence 3599999999999999653
No 53
>PHA02955 hypothetical protein; Provisional
Probab=52.87 E-value=21 Score=24.90 Aligned_cols=43 Identities=12% Similarity=-0.009 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhhcC-CCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 58 SQQLQELEATFARN-RYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 58 ~~Q~~~L~~~F~~~-~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
..++..|-..|.+. --+...++.+++..||.....+.-||++|
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 44666666666654 45677789999999999887789999887
No 54
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=52.49 E-value=3.3 Score=22.70 Aligned_cols=24 Identities=17% Similarity=0.091 Sum_probs=20.0
Q ss_pred HHHHHHHHcCCCcCccceeeeccc
Q psy15887 78 TREEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 78 ~r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
.-.++|..||++...|..|-+-|+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhC
Confidence 356899999999999999977654
No 55
>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=51.45 E-value=17 Score=18.07 Aligned_cols=15 Identities=53% Similarity=0.627 Sum_probs=12.3
Q ss_pred CCCHHHHHHHHHHhh
Q psy15887 55 HFTSQQLQELEATFA 69 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~ 69 (104)
.||..|+..|+.-..
T Consensus 2 ~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 2 PFTPAQLQELRAQIL 16 (37)
T ss_pred CCCHHHHHHHHHHHH
Confidence 699999999986544
No 56
>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=49.58 E-value=13 Score=18.30 Aligned_cols=39 Identities=13% Similarity=0.142 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
++..+...+...+... .....+|..+|++...|..|.+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 4566666666555322 23567899999999988877543
No 57
>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=49.17 E-value=14 Score=19.94 Aligned_cols=33 Identities=27% Similarity=0.367 Sum_probs=22.9
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccce
Q psy15887 59 QQLQELEATFARNRYPDMSTREEIAMWTNLTEALRET 95 (104)
Q Consensus 59 ~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 95 (104)
.|+..|+-.+. +...... +||..++++++.|+-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 46677777777 5555443 899999999988754
No 58
>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=49.00 E-value=7.1 Score=20.79 Aligned_cols=38 Identities=21% Similarity=0.212 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeee
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQ 98 (104)
.+|+.++..|.-...-. ...++|..+++++..|..+..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHH
Confidence 57888888887766644 366889999998887766543
No 59
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=48.60 E-value=14 Score=24.02 Aligned_cols=40 Identities=23% Similarity=0.174 Sum_probs=29.7
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeee
Q psy15887 53 RTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 53 Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQ 98 (104)
...+|+.|...|...+ ... ...++|..+|++...|+.|-+
T Consensus 4 ~~~Lt~rqreVL~lr~-~Gl-----Tq~EIAe~LGiS~~tVs~ie~ 43 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RGL-----TQQEIADILGTSRANVSSIEK 43 (141)
T ss_pred ccCCCHHHHHHHHHHH-cCC-----CHHHHHHHHCCCHHHHHHHHH
Confidence 3467899999987743 222 467899999999988877654
No 60
>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=48.29 E-value=25 Score=15.27 Aligned_cols=36 Identities=19% Similarity=0.195 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcccee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETH 96 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 96 (104)
++..+...+...+.... ....+|..++++...|.-|
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHh
Confidence 45666666666665332 3457788999888766555
No 61
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=46.47 E-value=27 Score=20.29 Aligned_cols=21 Identities=19% Similarity=0.014 Sum_probs=18.2
Q ss_pred HHHHHHHcCCCcCccceeeec
Q psy15887 79 REEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 79 r~~La~~l~l~~~~VqvWFQN 99 (104)
+..|...++|..-++.||+..
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~~ 76 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAEK 76 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEEE
Confidence 567888899999999999975
No 62
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.46 E-value=4.6 Score=20.41 Aligned_cols=21 Identities=14% Similarity=-0.031 Sum_probs=17.2
Q ss_pred HHHHHHcCCCcCccceeeecc
Q psy15887 80 EEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvWFQN~ 100 (104)
.++|..+|++...|+.|-++.
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 478899999999999887654
No 63
>PF06032 DUF917: Protein of unknown function (DUF917); InterPro: IPR010318 This family consists of hypothetical bacterial and archaeal proteins of unknown function.; PDB: 2O3I_B.
Probab=46.24 E-value=8.1 Score=28.78 Aligned_cols=15 Identities=13% Similarity=-0.011 Sum_probs=12.1
Q ss_pred CcCccceeeeccccc
Q psy15887 89 TEALRETHAYSYNFL 103 (104)
Q Consensus 89 ~~~~VqvWFQN~~~~ 103 (104)
..+.++|||||-|.+
T Consensus 267 ~~~~~~i~fqNEnL~ 281 (353)
T PF06032_consen 267 KGRTLRIEFQNENLL 281 (353)
T ss_dssp TTEEEEEEESSSEEE
T ss_pred CCCEEEEEEEcCcEE
Confidence 456789999998865
No 64
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.82 E-value=21 Score=21.47 Aligned_cols=36 Identities=28% Similarity=0.146 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcC
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~ 91 (104)
+.++|...-...|+.+.-.+....+++|..|+.++-
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 456677766666666666666667788999888764
No 65
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=44.82 E-value=5.5 Score=21.82 Aligned_cols=23 Identities=9% Similarity=0.109 Sum_probs=18.7
Q ss_pred HHHHHHcCCCcCccceeeecccc
Q psy15887 80 EEIAMWTNLTEALRETHAYSYNF 102 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvWFQN~~~ 102 (104)
.++|+.+|++...++-|-++..+
T Consensus 4 ~evA~~~gvs~~tlR~~~~~g~l 26 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKEFNL 26 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHhcCC
Confidence 47899999999999999876543
No 66
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=42.61 E-value=12 Score=18.85 Aligned_cols=6 Identities=0% Similarity=-0.280 Sum_probs=4.9
Q ss_pred ceeeec
Q psy15887 94 ETHAYS 99 (104)
Q Consensus 94 qvWFQN 99 (104)
.||||.
T Consensus 27 TiWFqG 32 (39)
T PF09292_consen 27 TIWFQG 32 (39)
T ss_dssp EEEESS
T ss_pred EEEeeC
Confidence 699985
No 67
>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=41.43 E-value=2.4 Score=24.53 Aligned_cols=23 Identities=30% Similarity=0.139 Sum_probs=19.4
Q ss_pred HHHHHHHHHcCCCcCccceeeec
Q psy15887 77 STREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 77 ~~r~~La~~l~l~~~~VqvWFQN 99 (104)
....++|..+|+++..|+.|+-+
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhc
Confidence 34678999999999999998764
No 68
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=41.21 E-value=6.4 Score=21.67 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=18.0
Q ss_pred HHHHHHcCCCcCccceeeeccc
Q psy15887 80 EEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvWFQN~~ 101 (104)
.++|+.+|++...++.|.+...
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~~g 25 (68)
T cd04763 4 GEVALLTGIKPHVLRAWEREFG 25 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHhcC
Confidence 4789999999999999977543
No 69
>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=40.86 E-value=63 Score=21.51 Aligned_cols=40 Identities=25% Similarity=0.363 Sum_probs=32.0
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcc
Q psy15887 52 QRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALR 93 (104)
Q Consensus 52 ~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 93 (104)
+...+|.+++.++.+.-..+ |....+..||.++|++..-|
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV 121 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFV 121 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHH
Confidence 45689999999988776655 56778999999999987543
No 70
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=40.73 E-value=7.5 Score=21.21 Aligned_cols=21 Identities=10% Similarity=-0.023 Sum_probs=17.4
Q ss_pred HHHHHHcCCCcCccceeeecc
Q psy15887 80 EEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvWFQN~ 100 (104)
.++|..+|++...|+.|=+..
T Consensus 4 ~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHCcCHHHHHHHHHhc
Confidence 478999999999999986544
No 71
>PRK13558 bacterio-opsin activator; Provisional
Probab=40.38 E-value=34 Score=27.03 Aligned_cols=39 Identities=21% Similarity=0.374 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHHHhhcCCC--CCHHHHHHHHHHcCCCcCc
Q psy15887 54 THFTSQQLQELEATFARNRY--PDMSTREEIAMWTNLTEAL 92 (104)
Q Consensus 54 t~~t~~Q~~~L~~~F~~~~~--p~~~~r~~La~~l~l~~~~ 92 (104)
..+|..|...|+..+....| |-...-.+||..||++...
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t 646 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRST 646 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 46999999999999998887 6666678999999998753
No 72
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=39.30 E-value=4.2 Score=24.00 Aligned_cols=10 Identities=0% Similarity=-0.203 Sum_probs=7.9
Q ss_pred ccceeeeccc
Q psy15887 92 LRETHAYSYN 101 (104)
Q Consensus 92 ~VqvWFQN~~ 101 (104)
-|+||.||..
T Consensus 32 dvkvwmqnle 41 (106)
T PF11516_consen 32 DVKVWMQNLE 41 (106)
T ss_dssp HHHHHHHHHH
T ss_pred cHHHHHHHHH
Confidence 4899999864
No 73
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=38.47 E-value=7.1 Score=21.24 Aligned_cols=23 Identities=13% Similarity=0.185 Sum_probs=18.1
Q ss_pred HHHHHHcCCCcCccceeeecccc
Q psy15887 80 EEIAMWTNLTEALRETHAYSYNF 102 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvWFQN~~~ 102 (104)
.++|+.+|++...++-|-+.+.+
T Consensus 4 ~eva~~~gvs~~tlr~w~~~~g~ 26 (68)
T cd01104 4 GAVARLTGVSPDTLRAWERRYGL 26 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHhCCC
Confidence 46889999999999888875443
No 74
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=36.85 E-value=39 Score=16.88 Aligned_cols=38 Identities=24% Similarity=0.209 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeee
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQ 98 (104)
.++..+...+...+. .. ...++|..++++...|..|.+
T Consensus 3 ~l~~~e~~i~~~~~~-g~-----s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLAE-GL-----TNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHHc-CC-----CHHHHHHHHCCCHHHHHHHHH
Confidence 356777776655332 21 356889999999988776643
No 75
>PF13551 HTH_29: Winged helix-turn helix
Probab=36.73 E-value=5.8 Score=23.56 Aligned_cols=23 Identities=17% Similarity=0.076 Sum_probs=20.2
Q ss_pred HHHHHHHcCCCcCccceeeeccc
Q psy15887 79 REEIAMWTNLTEALRETHAYSYN 101 (104)
Q Consensus 79 r~~La~~l~l~~~~VqvWFQN~~ 101 (104)
..++|..+|++.+.|.-|.+.|+
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHH
Confidence 56889999999999999988875
No 76
>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=34.64 E-value=32 Score=17.34 Aligned_cols=34 Identities=18% Similarity=0.285 Sum_probs=22.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccc
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRE 94 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~Vq 94 (104)
++.++...+...+... + ...++|..+|++...|.
T Consensus 6 ~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~Tvy 39 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVY 39 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHH
T ss_pred CCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHH
Confidence 5565666666666665 2 36689999999887653
No 77
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.79 E-value=33 Score=21.46 Aligned_cols=37 Identities=19% Similarity=0.044 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
+++.+...+...|-... ...++|..+|++...|+.|.
T Consensus 107 L~~~~r~ii~l~~~~~~-----s~~EIA~~l~is~~tV~~~~ 143 (154)
T PRK06759 107 LDEKEKYIIFERFFVGK-----TMGEIALETEMTYYQVRWIY 143 (154)
T ss_pred CCHHHHHHHHHHHhcCC-----CHHHHHHHHCCCHHHHHHHH
Confidence 45555555554443322 36689999999999888764
No 78
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=32.60 E-value=67 Score=21.37 Aligned_cols=36 Identities=19% Similarity=0.063 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcc
Q psy15887 58 SQQLQELEATFARNRYPDMSTREEIAMWTNLTEALR 93 (104)
Q Consensus 58 ~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 93 (104)
..-+..|+......-|........+|..|+++...|
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 345667888888888999999999999999998764
No 79
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=32.53 E-value=32 Score=20.38 Aligned_cols=19 Identities=5% Similarity=-0.057 Sum_probs=15.1
Q ss_pred HHHHHHHHHcCCCcCccceeeec
Q psy15887 77 STREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 77 ~~r~~La~~l~l~~~~VqvWFQN 99 (104)
.+...+|..+|++. -|||.
T Consensus 24 ~ELHafA~riGv~r----r~fq~ 42 (83)
T PF13223_consen 24 DELHAFAARIGVPR----RWFQR 42 (83)
T ss_pred HHHHHHHHHcCCCH----HHHcC
Confidence 35557899999987 58887
No 80
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=31.79 E-value=49 Score=16.60 Aligned_cols=20 Identities=35% Similarity=0.351 Sum_probs=15.3
Q ss_pred HHHHHHHHcCCCcCccceee
Q psy15887 78 TREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 78 ~r~~La~~l~l~~~~VqvWF 97 (104)
...++|..++++...|+.|.
T Consensus 17 s~~eia~~l~~s~~tv~~~~ 36 (57)
T cd06170 17 TNKEIADILGISEKTVKTHL 36 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 35678999999988877664
No 81
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=31.00 E-value=17 Score=26.20 Aligned_cols=25 Identities=8% Similarity=0.020 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCCcCccceeeecccc
Q psy15887 78 TREEIAMWTNLTEALRETHAYSYNF 102 (104)
Q Consensus 78 ~r~~La~~l~l~~~~VqvWFQN~~~ 102 (104)
--.+||..+|+++-+|+.|=+-+..
T Consensus 21 k~~dIAeklGvspntiksWKrr~gW 45 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWKRRDGW 45 (279)
T ss_pred cHHHHHHHhCCChHHHHHHHHhcCC
Confidence 3568999999999999999887764
No 82
>PRK10072 putative transcriptional regulator; Provisional
Probab=30.02 E-value=49 Score=19.96 Aligned_cols=37 Identities=8% Similarity=0.066 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 57 TSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 57 t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
+...+..|...-.. ...+||..+|++...|.-|.+..
T Consensus 34 ~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 34 SFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred ChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCC
Confidence 55555555332222 36789999999999999998754
No 83
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=29.38 E-value=14 Score=18.14 Aligned_cols=21 Identities=10% Similarity=-0.048 Sum_probs=15.5
Q ss_pred HHHHHHcCCCcCccceeeecc
Q psy15887 80 EEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvWFQN~ 100 (104)
.++|..+|++...|.-|-++-
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHcC
Confidence 467888888888887776554
No 84
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=29.12 E-value=45 Score=20.73 Aligned_cols=34 Identities=21% Similarity=0.126 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccc
Q psy15887 59 QQLQELEATFARNRYPDMSTREEIAMWTNLTEALRE 94 (104)
Q Consensus 59 ~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~Vq 94 (104)
++...|...|. .-+......+||..+.++.+.++
T Consensus 4 ~~y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 4 EQYQRLWQHYG--GQPVEVTLDELAELLFCSRRNAR 37 (115)
T ss_pred HHHHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHH
Confidence 34555666666 33444556799999999998775
No 85
>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=27.69 E-value=66 Score=20.77 Aligned_cols=38 Identities=26% Similarity=0.223 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcccee
Q psy15887 53 RTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETH 96 (104)
Q Consensus 53 Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 96 (104)
.+.+|..|...+.-.. ... ...++|..+|++...|+.+
T Consensus 4 ~~~Lte~qr~VL~Lr~-~Gl-----Tq~EIAe~LgiS~stV~~~ 41 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KGL-----SQKEIAKELKTTRANVSAI 41 (137)
T ss_pred cCCCCHHHHHHHHHHH-cCC-----CHHHHHHHHCcCHHHHHHH
Confidence 4567888988887743 222 4678999999998877654
No 86
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=27.42 E-value=43 Score=21.33 Aligned_cols=38 Identities=11% Similarity=-0.004 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
.+++.+...+...|.... .-.++|..+|++...|+.|.
T Consensus 128 ~L~~~~r~vl~l~~~~~~-----s~~eIA~~lgis~~tV~~~l 165 (182)
T PRK09652 128 SLPEELRTAITLREIEGL-----SYEEIAEIMGCPIGTVRSRI 165 (182)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHH
Confidence 356666666655543221 35588999999999887764
No 87
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.12 E-value=61 Score=21.08 Aligned_cols=37 Identities=8% Similarity=0.039 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
+++.+...+...|..+. .-+++|..+|++...|++|-
T Consensus 134 L~~~~r~i~~l~~~~~~-----s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 134 LEPARRNCILHAYVDGC-----SHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCChhhHHHHH
Confidence 34444444444432221 35689999999999888763
No 88
>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=26.85 E-value=61 Score=16.65 Aligned_cols=16 Identities=13% Similarity=0.044 Sum_probs=11.7
Q ss_pred HHHHHHHcCCCcCccc
Q psy15887 79 REEIAMWTNLTEALRE 94 (104)
Q Consensus 79 r~~La~~l~l~~~~Vq 94 (104)
-.+||..++++.+.|+
T Consensus 18 ~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 18 AKELAEELGVSRRTIR 33 (55)
T ss_dssp HHHHHHHCTS-HHHHH
T ss_pred HHHHHHHhCCCHHHHH
Confidence 4578999999987653
No 89
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=26.36 E-value=39 Score=22.67 Aligned_cols=21 Identities=14% Similarity=0.143 Sum_probs=16.9
Q ss_pred HHHHHHHHcCCCcCccceeee
Q psy15887 78 TREEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 78 ~r~~La~~l~l~~~~VqvWFQ 98 (104)
...++|..+|++...|+++..
T Consensus 171 s~~EIA~~lgis~~tV~~~l~ 191 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLR 191 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456899999999998887643
No 90
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=26.26 E-value=59 Score=21.43 Aligned_cols=37 Identities=16% Similarity=0.125 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
++..+...|.-.|... ..-.++|..+|++...|+++.
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l 179 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRM 179 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHH
Confidence 5555555555443322 135689999999999888764
No 91
>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=26.24 E-value=54 Score=20.55 Aligned_cols=37 Identities=14% Similarity=0.069 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcccee
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETH 96 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 96 (104)
.+++.+...+...|... ..-+++|..+|++...|+++
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~ 147 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKA 147 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHH
Confidence 35555555555533322 23568999999999888765
No 92
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=26.07 E-value=12 Score=18.48 Aligned_cols=17 Identities=12% Similarity=0.008 Sum_probs=12.4
Q ss_pred HHHHHHcCCCcCcccee
Q psy15887 80 EEIAMWTNLTEALRETH 96 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvW 96 (104)
.++|+.+|++.+.|+-|
T Consensus 3 ~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHH
Confidence 36788888888887776
No 93
>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=25.64 E-value=27 Score=24.49 Aligned_cols=14 Identities=14% Similarity=0.057 Sum_probs=10.7
Q ss_pred cCccceeeeccccc
Q psy15887 90 EALRETHAYSYNFL 103 (104)
Q Consensus 90 ~~~VqvWFQN~~~~ 103 (104)
...|-.=||+||++
T Consensus 82 ~~~iGfvFQ~~nLl 95 (226)
T COG1136 82 RKKIGFVFQNFNLL 95 (226)
T ss_pred HHhEEEECccCCCC
Confidence 34567889999986
No 94
>PRK00118 putative DNA-binding protein; Validated
Probab=25.63 E-value=56 Score=20.07 Aligned_cols=37 Identities=19% Similarity=0.127 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
++..|...+...|.... ...++|..+|++...|..|.
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L 54 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNI 54 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHH
Confidence 45666666655554432 45689999999998887664
No 95
>PF09792 But2: Ubiquitin 3 binding protein But2 C-terminal domain; InterPro: IPR018620 This entry represents a presumed C-terminal domain of ubiquitin 3 binding proteins (But2). But2 is conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway [].
Probab=25.17 E-value=34 Score=22.13 Aligned_cols=10 Identities=20% Similarity=0.175 Sum_probs=7.4
Q ss_pred ccceeeeccc
Q psy15887 92 LRETHAYSYN 101 (104)
Q Consensus 92 ~VqvWFQN~~ 101 (104)
..=.|||.||
T Consensus 132 t~l~~fq~~~ 141 (143)
T PF09792_consen 132 TSLSFFQDYN 141 (143)
T ss_pred CeEEEEeecC
Confidence 4457999887
No 96
>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=24.40 E-value=57 Score=21.03 Aligned_cols=37 Identities=14% Similarity=0.100 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcccee
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETH 96 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 96 (104)
.+++.+...+.-.|-... ..+++|..+|++...|+.+
T Consensus 100 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~lgis~~tV~~~ 136 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL-----SQQEIAEKLGLSLSGAKSR 136 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHH
Confidence 355555555555443332 3568899999999887654
No 97
>smart00351 PAX Paired Box domain.
Probab=23.90 E-value=45 Score=20.85 Aligned_cols=41 Identities=7% Similarity=-0.006 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
.++.++...+-..+.... ...++|..+|++...|.-|.+.|
T Consensus 17 ~~s~~~R~riv~~~~~G~-----s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 17 PLPDEERQRIVELAQNGV-----RPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 367777666666665432 34588999999999999997765
No 98
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.23 E-value=61 Score=20.90 Aligned_cols=20 Identities=15% Similarity=0.026 Sum_probs=16.8
Q ss_pred HHHHHHHcCCCcCccceeee
Q psy15887 79 REEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 79 r~~La~~l~l~~~~VqvWFQ 98 (104)
.+++|..+|++...|+++.+
T Consensus 148 ~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 148 YKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 56899999999999887654
No 99
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=22.64 E-value=41 Score=22.04 Aligned_cols=21 Identities=19% Similarity=0.155 Sum_probs=17.3
Q ss_pred HHHHHHHHcCCCcCccceeee
Q psy15887 78 TREEIAMWTNLTEALRETHAY 98 (104)
Q Consensus 78 ~r~~La~~l~l~~~~VqvWFQ 98 (104)
...++|..+|++...|+.|.+
T Consensus 159 s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 456899999999999988754
No 100
>PF12578 3-PAP: Myotubularin-associated protein; InterPro: IPR022587 The proteins in this entry are found in eukaryotes, and are typically between 115 and 138 amino acids in length. This entry contains myotubularin-associated protein 12 (also known as the phosphatidylinositol-3 phosphate 3-phosphatase adapter subunit, 3-PAP). 3-PAP is a catalytically inactive member of the myotubularin gene family, which coprecipitates lipid phosphatidylinositol 3-phosphate-3-phosphatase activity from lysates of human platelets [].
Probab=22.58 E-value=15 Score=23.74 Aligned_cols=13 Identities=15% Similarity=0.192 Sum_probs=10.5
Q ss_pred CCcCccceeeecc
Q psy15887 88 LTEALRETHAYSY 100 (104)
Q Consensus 88 l~~~~VqvWFQN~ 100 (104)
+...+|++|.|+|
T Consensus 81 ~~~~~i~lW~qcY 93 (142)
T PF12578_consen 81 LSGPQIKLWSQCY 93 (142)
T ss_pred cccccHHHHHHHH
Confidence 3456889999998
No 101
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.46 E-value=62 Score=21.31 Aligned_cols=37 Identities=11% Similarity=0.015 Sum_probs=23.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
+++.+...+.-.+-... .-+++|..+|+++..|+++.
T Consensus 135 Lp~~~R~v~~L~~~~g~-----s~~EIA~~lgis~~tVk~~l 171 (189)
T PRK12530 135 LPAQQARVFMMREYLEL-----SSEQICQECDISTSNLHVLL 171 (189)
T ss_pred CCHHHHHHHhHHHHcCC-----CHHHHHHHHCCCHHHHHHHH
Confidence 34455555544432221 35689999999999887653
No 102
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=22.38 E-value=21 Score=22.27 Aligned_cols=24 Identities=4% Similarity=-0.098 Sum_probs=19.6
Q ss_pred HHHHHHHHHcCCCcCccceeeecc
Q psy15887 77 STREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 77 ~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
....+||..+|++++.+.-+|+.+
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 456789999999999988888754
No 103
>PF11388 DotA: Phagosome trafficking protein DotA; InterPro: IPR021528 DotA is essential for intracellular growth in Legionella []. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake [].
Probab=22.22 E-value=27 Score=21.24 Aligned_cols=9 Identities=22% Similarity=-0.171 Sum_probs=5.7
Q ss_pred ccceeeecc
Q psy15887 92 LRETHAYSY 100 (104)
Q Consensus 92 ~VqvWFQN~ 100 (104)
-+.+||||-
T Consensus 31 ~LC~WF~~~ 39 (105)
T PF11388_consen 31 LLCTWFQNK 39 (105)
T ss_pred HHHHHHccC
Confidence 345788774
No 104
>COG5154 BRX1 RNA-binding protein required for 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis]
Probab=22.20 E-value=40 Score=23.75 Aligned_cols=11 Identities=9% Similarity=0.090 Sum_probs=8.8
Q ss_pred ccceeeecccc
Q psy15887 92 LRETHAYSYNF 102 (104)
Q Consensus 92 ~VqvWFQN~~~ 102 (104)
--+|||.||.+
T Consensus 183 DgkIWvR~YeI 193 (283)
T COG5154 183 DGKIWVRCYEI 193 (283)
T ss_pred cCeEEEEEEee
Confidence 34899999975
No 105
>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=22.03 E-value=1.2e+02 Score=19.43 Aligned_cols=33 Identities=6% Similarity=0.031 Sum_probs=24.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcc
Q psy15887 61 LQELEATFARNRYPDMSTREEIAMWTNLTEALR 93 (104)
Q Consensus 61 ~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 93 (104)
+..|...=+...|.+......+|..++++...|
T Consensus 19 i~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 19 MPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 344444444556888888999999999998765
No 106
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=21.94 E-value=1.3e+02 Score=19.72 Aligned_cols=33 Identities=27% Similarity=0.078 Sum_probs=24.7
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcc
Q psy15887 61 LQELEATFARNRYPDMSTREEIAMWTNLTEALR 93 (104)
Q Consensus 61 ~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 93 (104)
+..|...=+...|.+......+|..++++...|
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 444444444566888999999999999998765
No 107
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=21.71 E-value=65 Score=20.32 Aligned_cols=18 Identities=6% Similarity=0.076 Sum_probs=14.9
Q ss_pred HHHHHHHcCCCcCcccee
Q psy15887 79 REEIAMWTNLTEALRETH 96 (104)
Q Consensus 79 r~~La~~l~l~~~~VqvW 96 (104)
-+++|..+|++...|+.+
T Consensus 129 ~~eIA~~lgis~~tV~~~ 146 (162)
T TIGR02983 129 EAQVAEALGISVGTVKSR 146 (162)
T ss_pred HHHHHHHhCCCHHHHHHH
Confidence 568899999999888765
No 108
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=21.34 E-value=41 Score=21.04 Aligned_cols=23 Identities=13% Similarity=-0.032 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHcCCCcCcccee
Q psy15887 74 PDMSTREEIAMWTNLTEALRETH 96 (104)
Q Consensus 74 p~~~~r~~La~~l~l~~~~VqvW 96 (104)
++...|..||..++++.+.|.-|
T Consensus 27 ~~~~~r~~La~~~~i~~~~l~~w 49 (122)
T PF14229_consen 27 DTPLGRKALAKKLGISERNLLKW 49 (122)
T ss_pred CCHHHHHHHHHhcCCCHHHHHHH
Confidence 45567888999999999999888
No 109
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.23 E-value=69 Score=21.91 Aligned_cols=39 Identities=23% Similarity=0.217 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
.+|+.+.+.|.-..+-. ...++|..+++++..|+.+.+|
T Consensus 155 ~Lt~rE~~Vl~l~~~G~------s~~eIA~~L~iS~~TVk~~~~~ 193 (216)
T PRK10100 155 LLTHREKEILNKLRIGA------SNNEIARSLFISENTVKTHLYN 193 (216)
T ss_pred CCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHH
Confidence 47888888887766632 3568899999999988876543
No 110
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.20 E-value=1.3e+02 Score=14.95 Aligned_cols=32 Identities=19% Similarity=0.099 Sum_probs=19.2
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcc
Q psy15887 58 SQQLQELEATFARNRYPDMSTREEIAMWTNLTEALR 93 (104)
Q Consensus 58 ~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 93 (104)
..+...|....+... . ...+||..+|++...|
T Consensus 3 ~~~~~Il~~l~~~~~-~---t~~ela~~~~is~~tv 34 (48)
T PF13412_consen 3 ETQRKILNYLRENPR-I---TQKELAEKLGISRSTV 34 (48)
T ss_dssp HHHHHHHHHHHHCTT-S----HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHHHcCC-C---CHHHHHHHhCCCHHHH
Confidence 455666655555332 2 4668899999987654
No 111
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.19 E-value=70 Score=20.85 Aligned_cols=38 Identities=16% Similarity=0.008 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
.+++.|...+...|.... ..+++|..+|++...|+.+.
T Consensus 139 ~L~~~~r~i~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 139 TLPEKQREILILRVVVGL-----SAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHH
Confidence 455556666655433321 35689999999998887653
No 112
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.09 E-value=56 Score=16.80 Aligned_cols=22 Identities=9% Similarity=0.056 Sum_probs=16.2
Q ss_pred CHHHHHHHHHHcCCCcCcccee
Q psy15887 75 DMSTREEIAMWTNLTEALRETH 96 (104)
Q Consensus 75 ~~~~r~~La~~l~l~~~~VqvW 96 (104)
+.+..+.||..+|++.+.|+-+
T Consensus 24 ~~pS~~~la~~~g~s~~Tv~~~ 45 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTVQRA 45 (55)
T ss_pred CCcCHHHHHHHHCcCHHHHHHH
Confidence 3335678999999998877644
No 113
>PRK10403 transcriptional regulator NarP; Provisional
Probab=20.94 E-value=65 Score=20.52 Aligned_cols=39 Identities=21% Similarity=0.223 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
.+|..+...|.-.... ..+.++|..++++++.|++...|
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~ 191 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRN 191 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHH
Confidence 4788888877655443 23678899999998888766543
No 114
>KOG3623|consensus
Probab=20.68 E-value=78 Score=26.50 Aligned_cols=50 Identities=16% Similarity=0.138 Sum_probs=26.2
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeecc
Q psy15887 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYSY 100 (104)
Q Consensus 51 r~Rt~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN~ 100 (104)
+.++.....+-..|....+.+.-+.--+--..+..+...+.+|.|||++-
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsr 677 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSR 677 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCC
Confidence 33444444444445555443333332222223444666778889999973
No 115
>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=20.67 E-value=33 Score=18.20 Aligned_cols=15 Identities=27% Similarity=0.180 Sum_probs=11.6
Q ss_pred HHHHHHcCCCcCccc
Q psy15887 80 EEIAMWTNLTEALRE 94 (104)
Q Consensus 80 ~~La~~l~l~~~~Vq 94 (104)
.+||..+|++..||+
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 478999999988874
No 116
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.63 E-value=71 Score=20.28 Aligned_cols=39 Identities=21% Similarity=0.105 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
.+|+.+...|.-..+. + .++++|..++++.+.|++..++
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~ 175 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRAN 175 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHH
Confidence 4777777777655543 2 4778899999988888766544
No 117
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=20.48 E-value=55 Score=20.64 Aligned_cols=39 Identities=23% Similarity=0.225 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceeeec
Q psy15887 55 HFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHAYS 99 (104)
Q Consensus 55 ~~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFQN 99 (104)
.+|..+...|.- +..+. ...++|..+++++..|+.+.+|
T Consensus 149 ~lt~~e~~vl~l-~~~g~-----~~~~Ia~~l~~s~~tv~~~~~~ 187 (211)
T PRK15369 149 LLTPRERQILKL-ITEGY-----TNRDIAEQLSISIKTVETHRLN 187 (211)
T ss_pred CCCHHHHHHHHH-HHCCC-----CHHHHHHHhCCCHHHHHHHHHH
Confidence 478877777765 33332 3568899999999888877655
No 118
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=20.32 E-value=36 Score=20.40 Aligned_cols=27 Identities=26% Similarity=0.195 Sum_probs=17.6
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHHcCCCcCcc
Q psy15887 63 ELEATFARNRYPDMSTREEIAMWTNLTEALR 93 (104)
Q Consensus 63 ~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 93 (104)
+|...|...-+. .+.+|..|+++...|
T Consensus 14 ELq~nf~~~~ls----~~~ia~dL~~s~~~l 40 (89)
T PF10078_consen 14 ELQANFELSGLS----LEQIAADLGTSPEHL 40 (89)
T ss_pred HHHHHHHHcCCC----HHHHHHHhCCCHHHH
Confidence 566777766654 456777777776544
No 119
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=20.28 E-value=1.4e+02 Score=19.33 Aligned_cols=33 Identities=9% Similarity=0.079 Sum_probs=24.3
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCcc
Q psy15887 61 LQELEATFARNRYPDMSTREEIAMWTNLTEALR 93 (104)
Q Consensus 61 ~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 93 (104)
+..|...=+...|.+......+|..++++...|
T Consensus 25 l~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 25 IPALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 334444444567888888899999999998765
No 120
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=20.25 E-value=54 Score=21.66 Aligned_cols=16 Identities=25% Similarity=0.158 Sum_probs=12.8
Q ss_pred HHHHHHHHcCCCcCcc
Q psy15887 78 TREEIAMWTNLTEALR 93 (104)
Q Consensus 78 ~r~~La~~l~l~~~~V 93 (104)
.|.+||.+++|.+.||
T Consensus 27 qR~eLA~~F~CvPSQI 42 (152)
T PF05848_consen 27 QRNELAERFNCVPSQI 42 (152)
T ss_dssp -HHHHHHHTTS-THHH
T ss_pred eHHHHHHHhCCchhhh
Confidence 5889999999999886
No 121
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.22 E-value=26 Score=18.91 Aligned_cols=18 Identities=11% Similarity=0.017 Sum_probs=14.0
Q ss_pred HHHHHHcCCCcCccceee
Q psy15887 80 EEIAMWTNLTEALRETHA 97 (104)
Q Consensus 80 ~~La~~l~l~~~~VqvWF 97 (104)
.++|+.+|++...|+-|-
T Consensus 4 ~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 467888888888887774
No 122
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=20.07 E-value=74 Score=20.60 Aligned_cols=37 Identities=11% Similarity=0.090 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHcCCCcCccceee
Q psy15887 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEALRETHA 97 (104)
Q Consensus 56 ~t~~Q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 97 (104)
+++.+...+...|.... .-.++|..+|++...|+.+.
T Consensus 132 L~~~~r~v~~l~~~~g~-----s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 132 LPPRQRDVVQSISVEGA-----SIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHH
Confidence 45555555555433222 35689999999998887654
Done!