Query 016585
Match_columns 387
No_of_seqs 168 out of 453
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 08:10:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016585.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016585hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03162 golden-2 like transcr 99.9 1.1E-23 2.4E-28 209.8 8.4 66 212-278 230-295 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.8 1.5E-21 3.2E-26 149.2 6.4 56 217-272 1-56 (57)
3 PF00249 Myb_DNA-binding: Myb- 97.5 0.00024 5.3E-09 51.4 5.2 48 219-270 1-48 (48)
4 smart00426 TEA TEA domain. 90.2 0.29 6.3E-06 39.7 3.0 47 221-268 5-67 (68)
5 smart00717 SANT SANT SWI3, AD 86.0 2.4 5.3E-05 28.6 5.2 43 220-268 2-45 (49)
6 cd00167 SANT 'SWI3, ADA2, N-Co 84.8 2.8 6.1E-05 28.0 4.9 43 221-269 1-44 (45)
7 KOG1588 RNA-binding protein Sa 66.0 8.9 0.00019 38.2 4.5 46 5-51 25-70 (259)
8 PF01285 TEA: TEA/ATTS domain 64.9 7.5 0.00016 40.9 4.0 53 216-269 46-112 (431)
9 PF12776 Myb_DNA-bind_3: Myb/S 63.1 17 0.00036 29.0 4.8 52 221-272 1-64 (96)
10 PF11014 DUF2852: Protein of u 60.0 5.8 0.00013 35.2 1.8 20 12-31 78-97 (115)
11 PF13921 Myb_DNA-bind_6: Myb-l 39.0 91 0.002 22.9 5.2 41 222-268 1-41 (60)
12 cd06171 Sigma70_r4 Sigma70, re 38.7 88 0.0019 20.8 4.7 28 243-273 27-54 (55)
13 PRK14069 exodeoxyribonuclease 37.9 62 0.0013 27.9 4.5 37 1-46 8-46 (95)
14 PF00046 Homeobox: Homeobox do 37.8 56 0.0012 23.7 3.8 56 216-274 1-56 (57)
15 KOG3841 TEF-1 and related tran 35.4 20 0.00044 37.8 1.5 50 221-272 78-144 (455)
16 PRK14063 exodeoxyribonuclease 35.4 1E+02 0.0022 25.2 5.3 38 1-47 5-44 (76)
17 PRK11923 algU RNA polymerase s 35.3 37 0.0008 30.0 3.0 48 225-275 127-184 (193)
18 cd00086 homeodomain Homeodomai 32.7 1.6E+02 0.0034 21.0 5.5 56 217-275 2-57 (59)
19 smart00501 BRIGHT BRIGHT, ARID 31.6 46 0.001 27.0 2.8 46 224-270 32-84 (93)
20 PRK14066 exodeoxyribonuclease 31.1 1.3E+02 0.0029 24.6 5.3 37 2-47 5-43 (75)
21 PF15035 Rootletin: Ciliary ro 30.1 71 0.0015 30.0 4.0 19 8-26 60-78 (182)
22 TIGR02894 DNA_bind_RsfA transc 30.1 66 0.0014 30.2 3.8 52 213-272 42-95 (161)
23 PF07384 DUF1497: Protein of u 29.2 43 0.00094 26.3 2.0 21 221-241 37-57 (59)
24 KOG0457 Histone acetyltransfer 28.9 79 0.0017 33.8 4.5 47 220-272 73-120 (438)
25 PF00690 Cation_ATPase_N: Cati 28.4 62 0.0013 24.7 2.8 30 244-273 5-37 (69)
26 TIGR01280 xseB exodeoxyribonuc 24.7 1.1E+02 0.0025 24.3 3.7 38 1-47 1-40 (67)
27 PF10267 Tmemb_cc2: Predicted 24.5 1.4E+02 0.0031 31.5 5.4 40 11-50 247-286 (395)
28 PRK12541 RNA polymerase sigma 24.2 1.3E+02 0.0029 25.7 4.4 45 228-275 104-158 (161)
29 TIGR02960 SigX5 RNA polymerase 24.1 72 0.0016 30.7 3.1 49 226-278 132-191 (324)
30 PRK12530 RNA polymerase sigma 24.0 72 0.0016 28.6 2.8 48 225-275 123-180 (189)
31 PRK06759 RNA polymerase factor 24.0 92 0.002 26.3 3.3 47 225-275 95-152 (154)
32 TIGR02989 Sig-70_gvs1 RNA poly 23.8 1.4E+02 0.0031 25.2 4.5 49 223-274 98-156 (159)
33 PF02970 TBCA: Tubulin binding 23.6 1.4E+02 0.003 25.0 4.2 43 9-51 15-77 (90)
34 PF12638 Staygreen: Staygreen 23.2 47 0.001 30.8 1.5 15 23-37 93-107 (151)
35 PF11888 DUF3408: Protein of u 23.1 63 0.0014 28.5 2.3 48 215-273 79-126 (136)
36 KOG0850 Transcription factor D 22.4 78 0.0017 31.5 2.9 60 212-278 119-182 (245)
37 KOG0842 Transcription factor t 22.2 50 0.0011 33.7 1.6 59 212-277 150-212 (307)
38 PF07638 Sigma70_ECF: ECF sigm 21.5 1.4E+02 0.003 26.9 4.2 43 225-268 121-163 (185)
39 PRK09642 RNA polymerase sigma 21.4 1E+02 0.0022 26.3 3.2 48 225-275 95-152 (160)
40 TIGR01232 lacD tagatose 1,6-di 21.2 48 0.001 34.2 1.2 50 7-56 183-244 (325)
41 PF01527 HTH_Tnp_1: Transposas 20.6 1.2E+02 0.0025 23.0 3.0 47 217-270 2-48 (76)
42 PRK09643 RNA polymerase sigma 20.4 1.3E+02 0.0029 26.9 3.8 40 243-285 151-190 (192)
43 PRK13919 putative RNA polymera 20.3 1.8E+02 0.0038 25.5 4.5 31 242-275 151-181 (186)
44 PF14336 DUF4392: Domain of un 20.2 1.2E+02 0.0027 30.1 3.9 42 217-261 239-280 (291)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.89 E-value=1.1e-23 Score=209.84 Aligned_cols=66 Identities=48% Similarity=0.816 Sum_probs=61.5
Q ss_pred CCCCCCCcccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccCCCC
Q 016585 212 GQPQRKQRRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRRPSP 278 (387)
Q Consensus 212 ~~~~rK~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr~~~ 278 (387)
....||+||+||+|||++||+||++|| .++||||+||++|+|+|||++||||||||||+++++...
T Consensus 230 ~~g~KKpRLrWTpELH~rFVeAV~qLG-~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~ 295 (526)
T PLN03162 230 APGKKKAKVDWTPELHRRFVHAVEQLG-VEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAA 295 (526)
T ss_pred CCCCCCCcccCCHHHHHHHHHHHHHhC-cCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccc
Confidence 355889999999999999999999999 799999999999999999999999999999999986543
No 2
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.85 E-value=1.5e-21 Score=149.21 Aligned_cols=56 Identities=64% Similarity=0.992 Sum_probs=54.1
Q ss_pred CCcccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhh
Q 016585 217 KQRRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLH 272 (387)
Q Consensus 217 K~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~ 272 (387)
|+|+.||+|+|++||+||++||+.+.|+||.|+++|++++||+.||+|||||||++
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 68999999999999999999998789999999999999999999999999999986
No 3
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=97.48 E-value=0.00024 Score=51.41 Aligned_cols=48 Identities=27% Similarity=0.452 Sum_probs=41.0
Q ss_pred cccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhh
Q 016585 219 RRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYR 270 (387)
Q Consensus 219 Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYR 270 (387)
|..||+|-+..|++||.++|.- .-+.|.+.|+ .|-|..+|++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~---~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD---NWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT---HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCc---HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 5689999999999999999942 4589999998 7889999999999985
No 4
>smart00426 TEA TEA domain.
Probab=90.20 E-value=0.29 Score=39.70 Aligned_cols=47 Identities=26% Similarity=0.455 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHHHHhcCCCCCChHHHHh-------------Hhc-CCC--CCHHHHHHhhhh
Q 016585 221 SWSPELHRRFLHALQQLGGSHAATPKQIRE-------------LMN-VDG--LTNDEVKSHLQK 268 (387)
Q Consensus 221 ~WT~ELH~rFv~Av~~LGG~~~AtPK~Ile-------------lM~-V~g--LT~~~VkSHLQK 268 (387)
+|.++|-..|++|+..+- .....+-+|+. -+- ..| =|+.||.||||-
T Consensus 5 vWp~~lE~Af~~aL~~~~-~~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYP-PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcC-ccCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhee
Confidence 799999999999999775 11111112221 111 233 478899999994
No 5
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=86.04 E-value=2.4 Score=28.60 Aligned_cols=43 Identities=14% Similarity=0.400 Sum_probs=35.2
Q ss_pred ccCCHHHHHHHHHHHHHhc-CCCCCChHHHHhHhcCCCCCHHHHHHhhhh
Q 016585 220 RSWSPELHRRFLHALQQLG-GSHAATPKQIRELMNVDGLTNDEVKSHLQK 268 (387)
Q Consensus 220 l~WT~ELH~rFv~Av~~LG-G~~~AtPK~IlelM~V~gLT~~~VkSHLQK 268 (387)
-.||++=...|+.++.++| +-. ..|.+.|+ +=|..+|+.+-..
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w----~~Ia~~~~--~rt~~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNW----EKIAKELP--GRTAEQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCH----HHHHHHcC--CCCHHHHHHHHHH
Confidence 4699999999999999999 544 77888876 6688888877554
No 6
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=84.79 E-value=2.8 Score=27.96 Aligned_cols=43 Identities=19% Similarity=0.398 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHHHhc-CCCCCChHHHHhHhcCCCCCHHHHHHhhhhh
Q 016585 221 SWSPELHRRFLHALQQLG-GSHAATPKQIRELMNVDGLTNDEVKSHLQKY 269 (387)
Q Consensus 221 ~WT~ELH~rFv~Av~~LG-G~~~AtPK~IlelM~V~gLT~~~VkSHLQKY 269 (387)
.||.+=+..|+.++..+| +. =..|.+.|+ +=|..+|+.|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~----w~~Ia~~~~--~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNN----WEKIAKELP--GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCC----HHHHHhHcC--CCCHHHHHHHHHHh
Confidence 499999999999999999 44 377888875 35888898886654
No 7
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=65.96 E-value=8.9 Score=38.17 Aligned_cols=46 Identities=15% Similarity=0.309 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhcccchhhHHHHHHHHHHHHHHhcc
Q 016585 5 EKMQRCHEYVEALEEEKRKIQVFQRELPLCLELVTQAIQACRRELSG 51 (387)
Q Consensus 5 ~k~~k~~d~v~~LEEErrKIevFkRELPLCm~Ll~~aIe~~K~el~~ 51 (387)
...++...|+.-|..||.+++.|-- |+.|++||.+.|+.+..-+..
T Consensus 25 ~~~~~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~ 70 (259)
T KOG1588|consen 25 QLNEKASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQ 70 (259)
T ss_pred chhhHHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhh
Confidence 3456788999999999999999887 999999999999998876654
No 8
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=64.88 E-value=7.5 Score=40.89 Aligned_cols=53 Identities=21% Similarity=0.365 Sum_probs=29.1
Q ss_pred CCCcccCCHHHHHHHHHHHHHhcCCCCCChHH-----------HHhHhcC---CCCCHHHHHHhhhhh
Q 016585 216 RKQRRSWSPELHRRFLHALQQLGGSHAATPKQ-----------IRELMNV---DGLTNDEVKSHLQKY 269 (387)
Q Consensus 216 rK~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~-----------IlelM~V---~gLT~~~VkSHLQKY 269 (387)
.+..-+|+++|...|++|+...-=...+. -. |-+-+.. .-=|+.||.||||-.
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k-~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRK-LSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS----HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcc-cccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 45667999999999999998764111121 11 2221111 235889999999998
No 9
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=63.12 E-value=17 Score=28.98 Aligned_cols=52 Identities=25% Similarity=0.397 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHHHHHh---cCC-CCCCh-----HHHHhHhcC---CCCCHHHHHHhhhhhhhh
Q 016585 221 SWSPELHRRFLHALQQL---GGS-HAATP-----KQIRELMNV---DGLTNDEVKSHLQKYRLH 272 (387)
Q Consensus 221 ~WT~ELH~rFv~Av~~L---GG~-~~AtP-----K~IlelM~V---~gLT~~~VkSHLQKYRl~ 272 (387)
.||++..+-||+.+-.. |.- ..... ..|.+.|+- -.+|..||++|+...|..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 59999999999988433 433 23333 336666663 348999999999876655
No 10
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=60.00 E-value=5.8 Score=35.20 Aligned_cols=20 Identities=35% Similarity=0.577 Sum_probs=15.9
Q ss_pred HHHHHHHHHHhhhhhhcccc
Q 016585 12 EYVEALEEEKRKIQVFQREL 31 (387)
Q Consensus 12 d~v~~LEEErrKIevFkREL 31 (387)
+=|+||||||+--+.|-+||
T Consensus 78 ~tL~RLEeEq~eF~~Fl~rL 97 (115)
T PF11014_consen 78 DTLRRLEEEQREFEDFLERL 97 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34899999999888887654
No 11
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=39.01 E-value=91 Score=22.94 Aligned_cols=41 Identities=20% Similarity=0.386 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhh
Q 016585 222 WSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQK 268 (387)
Q Consensus 222 WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQK 268 (387)
||+|=-...+.+|...|. .-+.|-+.|+ .=|..+|+.|...
T Consensus 1 WT~eEd~~L~~~~~~~g~----~W~~Ia~~l~--~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN----DWKKIAEHLG--NRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-----HHHHHHHST--TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc----CHHHHHHHHC--cCCHHHHHHHHHH
Confidence 999999999999999984 3689999986 4688999987776
No 12
>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=38.67 E-value=88 Score=20.84 Aligned_cols=28 Identities=14% Similarity=0.311 Sum_probs=22.6
Q ss_pred CChHHHHhHhcCCCCCHHHHHHhhhhhhhhc
Q 016585 243 ATPKQIRELMNVDGLTNDEVKSHLQKYRLHT 273 (387)
Q Consensus 243 AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~ 273 (387)
-+.+.|-+.|++ +...|..++++.+..+
T Consensus 27 ~~~~~ia~~~~~---s~~~i~~~~~~~~~~l 54 (55)
T cd06171 27 LSYEEIAEILGI---SRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHHHHHHHc
Confidence 577888888886 8889999988877654
No 13
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=37.89 E-value=62 Score=27.90 Aligned_cols=37 Identities=14% Similarity=0.406 Sum_probs=26.2
Q ss_pred CchHHHHHHHHHHHHHHHHHHhhhhhhcccchh--hHHHHHHHHHHHH
Q 016585 1 MDYAEKMQRCHEYVEALEEEKRKIQVFQRELPL--CLELVTQAIQACR 46 (387)
Q Consensus 1 ~~~~~k~~k~~d~v~~LEEErrKIevFkRELPL--Cm~Ll~~aIe~~K 46 (387)
|.|-+.+.+|++.|++||.. +||| .|.|...+|+.+|
T Consensus 8 ~sFEeal~~LEeIV~~LEsg---------dl~LEesl~lyeeGv~L~k 46 (95)
T PRK14069 8 ISFEDALRELEQIAEKLERQ---------DFSLEESLKAYERGMELKK 46 (95)
T ss_pred CCHHHHHHHHHHHHHHHHCC---------CCCHHHHHHHHHHHHHHHH
Confidence 46888999999999999965 5555 4556666555433
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=37.85 E-value=56 Score=23.71 Aligned_cols=56 Identities=23% Similarity=0.316 Sum_probs=40.0
Q ss_pred CCCcccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhcc
Q 016585 216 RKQRRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTR 274 (387)
Q Consensus 216 rK~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~r 274 (387)
|+.|..+|.+-. ..++++...+ ...+...|.+|...=||+..+|..-.|.-|...+
T Consensus 1 kr~r~~~t~~q~-~~L~~~f~~~--~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 1 KRKRTRFTKEQL-KVLEEYFQEN--PYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSSSSHHHH-HHHHHHHHHS--SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHH-HHHHHHHHHh--ccccccccccccccccccccccccCHHHhHHHhC
Confidence 577888887654 4555555554 3566677777777678999999998888776654
No 15
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=35.42 E-value=20 Score=37.83 Aligned_cols=50 Identities=26% Similarity=0.412 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHHHHhcCCCCCChHHHH--------------hHhcC---CCCCHHHHHHhhhhhhhh
Q 016585 221 SWSPELHRRFLHALQQLGGSHAATPKQIR--------------ELMNV---DGLTNDEVKSHLQKYRLH 272 (387)
Q Consensus 221 ~WT~ELH~rFv~Av~~LGG~~~AtPK~Il--------------elM~V---~gLT~~~VkSHLQKYRl~ 272 (387)
+|+++.-+.|.+|+..+- ..-+=|-|| .-++. +-=|+.||.||+|..-..
T Consensus 78 vWSpdIEqsFqEALaiyp--pcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarr 144 (455)
T KOG3841|consen 78 VWSPDIEQSFQEALAIYP--PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARR 144 (455)
T ss_pred ccChhHHHHHHHHHhhcC--CCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHH
Confidence 899999999999998763 111112222 22222 346899999999975433
No 16
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=35.36 E-value=1e+02 Score=25.20 Aligned_cols=38 Identities=16% Similarity=0.461 Sum_probs=26.6
Q ss_pred CchHHHHHHHHHHHHHHHHHHhhhhhhcccchh--hHHHHHHHHHHHHH
Q 016585 1 MDYAEKMQRCHEYVEALEEEKRKIQVFQRELPL--CLELVTQAIQACRR 47 (387)
Q Consensus 1 ~~~~~k~~k~~d~v~~LEEErrKIevFkRELPL--Cm~Ll~~aIe~~K~ 47 (387)
|.|-+.+.+|++.|.+||.. +||| .+.|...+|+.+|.
T Consensus 5 ~sfEeal~~LE~Iv~~LE~~---------~l~Leesl~lyeeG~~L~k~ 44 (76)
T PRK14063 5 LSFEEAISQLEHLVSKLEQG---------DVPLEEAISYFKEGMELSKL 44 (76)
T ss_pred cCHHHHHHHHHHHHHHHHCC---------CCCHHHHHHHHHHHHHHHHH
Confidence 46888999999999999854 5555 45666666554443
No 17
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=35.32 E-value=37 Score=30.05 Aligned_cols=48 Identities=19% Similarity=0.238 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHhcCCC----------CCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccC
Q 016585 225 ELHRRFLHALQQLGGSH----------AATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRR 275 (387)
Q Consensus 225 ELH~rFv~Av~~LGG~~----------~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr 275 (387)
+++..|.+|+..|.... .-+.+.|-+.||+ |...|++||++-|..+++
T Consensus 127 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 127 EIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQC---PVGTVRSRIFRAREAIDK 184 (193)
T ss_pred HHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHH
Confidence 45667778887776321 2233444444444 566677888777776654
No 18
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=32.71 E-value=1.6e+02 Score=20.96 Aligned_cols=56 Identities=25% Similarity=0.297 Sum_probs=42.1
Q ss_pred CCcccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccC
Q 016585 217 KQRRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRR 275 (387)
Q Consensus 217 K~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr 275 (387)
+.|..++.+- ..+++++.... ...+...|.+|...-||+..+|..-.+.-|...++
T Consensus 2 ~~r~~~~~~~-~~~Le~~f~~~--~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQ-LEELEKEFEKN--PYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHH-HHHHHHHHHhC--CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4455666655 55666666654 36778889999999999999999999988877654
No 19
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=31.55 E-value=46 Score=27.03 Aligned_cols=46 Identities=22% Similarity=0.405 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHhcCCCCCCh----HHHHhHhcCCCC---CHHHHHHhhhhhh
Q 016585 224 PELHRRFLHALQQLGGSHAATP----KQIRELMNVDGL---TNDEVKSHLQKYR 270 (387)
Q Consensus 224 ~ELH~rFv~Av~~LGG~~~AtP----K~IlelM~V~gL---T~~~VkSHLQKYR 270 (387)
-+|++.|. +|..+||.+..+= +.|.+.|+++.- ...++++|-+||=
T Consensus 32 vdL~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L 84 (93)
T smart00501 32 LDLYRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYL 84 (93)
T ss_pred CcHHHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHh
Confidence 36899998 5889999765432 568899998742 2345777777663
No 20
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=31.12 E-value=1.3e+02 Score=24.60 Aligned_cols=37 Identities=22% Similarity=0.382 Sum_probs=27.1
Q ss_pred chHHHHHHHHHHHHHHHHHHhhhhhhcccchh--hHHHHHHHHHHHHH
Q 016585 2 DYAEKMQRCHEYVEALEEEKRKIQVFQRELPL--CLELVTQAIQACRR 47 (387)
Q Consensus 2 ~~~~k~~k~~d~v~~LEEErrKIevFkRELPL--Cm~Ll~~aIe~~K~ 47 (387)
.|-+.+.+|++.|++||. -+||| .|.|...+|+.+|.
T Consensus 5 ~fEeal~~LE~IV~~LE~---------g~l~Leesl~lyeeG~~L~k~ 43 (75)
T PRK14066 5 KFETALKKLEEVVKKLEG---------GELSLDDSLKAFEEGVKHAAF 43 (75)
T ss_pred cHHHHHHHHHHHHHHHHC---------CCCCHHHHHHHHHHHHHHHHH
Confidence 577888999999999985 45665 56677777665554
No 21
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=30.12 E-value=71 Score=29.99 Aligned_cols=19 Identities=26% Similarity=0.296 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHhhhhh
Q 016585 8 QRCHEYVEALEEEKRKIQV 26 (387)
Q Consensus 8 ~k~~d~v~~LEEErrKIev 26 (387)
..|++++.+||||+++-+-
T Consensus 60 ~dLe~~l~rLeEEqqR~~~ 78 (182)
T PF15035_consen 60 PDLEEALIRLEEEQQRSEE 78 (182)
T ss_pred ccHHHHHHHHHHHHHhHHH
Confidence 4688999999999998665
No 22
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=30.11 E-value=66 Score=30.22 Aligned_cols=52 Identities=21% Similarity=0.316 Sum_probs=38.4
Q ss_pred CCCCCCcccCCHHHHHHHHHHHHHhcCCCCCChHHHH-hHhc-CCCCCHHHHHHhhhhhhhh
Q 016585 213 QPQRKQRRSWSPELHRRFLHALQQLGGSHAATPKQIR-ELMN-VDGLTNDEVKSHLQKYRLH 272 (387)
Q Consensus 213 ~~~rK~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~Il-elM~-V~gLT~~~VkSHLQKYRl~ 272 (387)
++.-.-.|||+..+-+.+.+||+.-- +.+ +.+. ...||.++|=+.||.|...
T Consensus 42 RTsAACGFRWNs~VRkqY~~~i~~AK--------kqRk~~~~~~~~ltl~~vI~fLq~l~~~ 95 (161)
T TIGR02894 42 RTAAACGFRWNAYVRKQYEEAIELAK--------KQRKELKREAGSLTLQDVISFLQNLKTT 95 (161)
T ss_pred ccHHHhcchHHHHHHHHHHHHHHHHH--------HHHhccccCcccCCHHHHHHHHHHHHhc
Confidence 33445578999999999999998743 222 2233 2669999999999999853
No 23
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=29.23 E-value=43 Score=26.31 Aligned_cols=21 Identities=24% Similarity=0.651 Sum_probs=18.9
Q ss_pred cCCHHHHHHHHHHHHHhcCCC
Q 016585 221 SWSPELHRRFLHALQQLGGSH 241 (387)
Q Consensus 221 ~WT~ELH~rFv~Av~~LGG~~ 241 (387)
.+..|+|..|-+-|+.|||-.
T Consensus 37 kfnqem~aefheri~klggk~ 57 (59)
T PF07384_consen 37 KFNQEMQAEFHERIKKLGGKN 57 (59)
T ss_pred HhhHHHHHHHHHHHHHhcccc
Confidence 578999999999999999853
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=28.86 E-value=79 Score=33.84 Aligned_cols=47 Identities=26% Similarity=0.454 Sum_probs=40.9
Q ss_pred ccCCHHHHHHHHHHHHHhc-CCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhh
Q 016585 220 RSWSPELHRRFLHALQQLG-GSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLH 272 (387)
Q Consensus 220 l~WT~ELH~rFv~Av~~LG-G~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~ 272 (387)
..||.+=--.|++|++.+| |-+ .-|-+.||-. |.++++.|--||-+.
T Consensus 73 ~~WtadEEilLLea~~t~G~GNW----~dIA~hIGtK--tkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 73 PSWTADEEILLLEAAETYGFGNW----QDIADHIGTK--TKEECKEHYLKHFVN 120 (438)
T ss_pred CCCChHHHHHHHHHHHHhCCCcH----HHHHHHHccc--chHHHHHHHHHHHhc
Confidence 3799999999999999999 777 8899999954 899999998887654
No 25
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=28.39 E-value=62 Score=24.73 Aligned_cols=30 Identities=23% Similarity=0.465 Sum_probs=24.6
Q ss_pred ChHHHHhHhc---CCCCCHHHHHHhhhhhhhhc
Q 016585 244 TPKQIRELMN---VDGLTNDEVKSHLQKYRLHT 273 (387)
Q Consensus 244 tPK~IlelM~---V~gLT~~~VkSHLQKYRl~~ 273 (387)
+...|++.++ ..|||.++|+.++++|=...
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G~N~ 37 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERRKKYGPNE 37 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHHHHHSSSS
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHHHhccccc
Confidence 4567888887 48999999999999996553
No 26
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides.
Probab=24.66 E-value=1.1e+02 Score=24.31 Aligned_cols=38 Identities=26% Similarity=0.527 Sum_probs=27.8
Q ss_pred CchHHHHHHHHHHHHHHHHHHhhhhhhcccchh--hHHHHHHHHHHHHH
Q 016585 1 MDYAEKMQRCHEYVEALEEEKRKIQVFQRELPL--CLELVTQAIQACRR 47 (387)
Q Consensus 1 ~~~~~k~~k~~d~v~~LEEErrKIevFkRELPL--Cm~Ll~~aIe~~K~ 47 (387)
|.|-+.+.+|++.|+.||.. +||| .|.|...+++.+|.
T Consensus 1 ~sfEe~l~~Le~Iv~~LE~~---------~l~Leesl~lyeeG~~L~k~ 40 (67)
T TIGR01280 1 LSFEEALSELEQIVQKLESG---------DLALEEALNLFERGMALARR 40 (67)
T ss_pred CCHHHHHHHHHHHHHHHHCC---------CCCHHHHHHHHHHHHHHHHH
Confidence 67999999999999999975 4554 45666666554443
No 27
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=24.51 E-value=1.4e+02 Score=31.46 Aligned_cols=40 Identities=28% Similarity=0.349 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhhhhhhcccchhhHHHHHHHHHHHHHHhc
Q 016585 11 HEYVEALEEEKRKIQVFQRELPLCLELVTQAIQACRRELS 50 (387)
Q Consensus 11 ~d~v~~LEEErrKIevFkRELPLCm~Ll~~aIe~~K~el~ 50 (387)
.-+.++|+|||-|++..--.|==-++|--+-|..||++|.
T Consensus 247 ~~~~~~LqEEr~R~erLEeqlNd~~elHq~Ei~~LKqeLa 286 (395)
T PF10267_consen 247 QFILEALQEERYRYERLEEQLNDLTELHQNEIYNLKQELA 286 (395)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466778888877777665555556666667778888875
No 28
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=24.24 E-value=1.3e+02 Score=25.73 Aligned_cols=45 Identities=24% Similarity=0.284 Sum_probs=28.7
Q ss_pred HHHHHHHHHhcCC----------CCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccC
Q 016585 228 RRFLHALQQLGGS----------HAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRR 275 (387)
Q Consensus 228 ~rFv~Av~~LGG~----------~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr 275 (387)
..+++|+..|... +.-+.+.|-+.||+ +...|++||.+-|..++.
T Consensus 104 ~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgi---s~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 104 ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGL---SLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHh
Confidence 4566777777632 23444555555555 677788888887777654
No 29
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=24.14 E-value=72 Score=30.70 Aligned_cols=49 Identities=27% Similarity=0.334 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcCCCCCChHHHHhHhcCCCC-----------CHHHHHHhhhhhhhhccCCCC
Q 016585 226 LHRRFLHALQQLGGSHAATPKQIRELMNVDGL-----------TNDEVKSHLQKYRLHTRRPSP 278 (387)
Q Consensus 226 LH~rFv~Av~~LGG~~~AtPK~IlelM~V~gL-----------T~~~VkSHLQKYRl~~rr~~~ 278 (387)
+...+..|+++|.-.+ +.|+.|..+.|+ +...|++||++-|..+++...
T Consensus 132 ~~~~l~~~l~~Lp~~~----R~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 132 VRLAFVAAIQYLPPRQ----RAVLLLRDVLGWRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HHHHHHHHHHhCCHHH----hhHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 5566778888887322 334443333333 666799999999988876554
No 30
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.97 E-value=72 Score=28.58 Aligned_cols=48 Identities=19% Similarity=0.274 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhcCCC----------CCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccC
Q 016585 225 ELHRRFLHALQQLGGSH----------AATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRR 275 (387)
Q Consensus 225 ELH~rFv~Av~~LGG~~----------~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr 275 (387)
++...+..|+.+|.... .-+-+.|-+.||+ +...|++||.+-|..++.
T Consensus 123 ~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 123 EFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDI---STSNLHVLLYRARLQLQA 180 (189)
T ss_pred HHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHH
Confidence 55566778888887321 2223333344433 666788888887777664
No 31
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.97 E-value=92 Score=26.29 Aligned_cols=47 Identities=15% Similarity=0.017 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCC-----------CHHHHHHhhhhhhhhccC
Q 016585 225 ELHRRFLHALQQLGGSHAATPKQIRELMNVDGL-----------TNDEVKSHLQKYRLHTRR 275 (387)
Q Consensus 225 ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gL-----------T~~~VkSHLQKYRl~~rr 275 (387)
++...+..|+.+|...+ +.|+.+.-+.|+ +...|+++|..-|..+|+
T Consensus 95 ~~~~~l~~~l~~L~~~~----r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 95 DVEMKVKDFMSVLDEKE----KYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HHHHHHHHHHHhCCHHH----HHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 34556677777776322 444444444444 555566666666655543
No 32
>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=23.77 E-value=1.4e+02 Score=25.21 Aligned_cols=49 Identities=18% Similarity=0.231 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHHHHhcCC----------CCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhcc
Q 016585 223 SPELHRRFLHALQQLGGS----------HAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTR 274 (387)
Q Consensus 223 T~ELH~rFv~Av~~LGG~----------~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~r 274 (387)
..+++..+..|+..|.-. +.-+.+.|-+.||+ +...|++||..-|..++
T Consensus 98 ~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~i---s~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 98 SEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGR---TVNAVYKALSRLRVRLR 156 (159)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCC---CHHHHHHHHHHHHHHHH
Confidence 345566677777777621 12334444444444 56667777766665544
No 33
>PF02970 TBCA: Tubulin binding cofactor A; InterPro: IPR004226 The folding pathway of tubulins includes highly specific interactions with a series of cofactors (A, B, C, D and E) after they are released from the eukaryotic chaperonin CCT. Cofactors A and D capture and stabilise tubulin in a quasi-native conformation. Cofactor E binds to the cofactor D-tubulin complex, and interaction with cofactor C then causes the release of tubulin poypeptides in the native state. This family is the tubulin-specific chaperone A.; GO: 0051082 unfolded protein binding, 0007021 tubulin complex assembly, 0005874 microtubule; PDB: 3MXZ_A 1QSD_A 1H7C_A.
Probab=23.62 E-value=1.4e+02 Score=24.96 Aligned_cols=43 Identities=19% Similarity=0.400 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHhhhhhhccc--------------------chhhHHHHHHHHHHHHHHhcc
Q 016585 9 RCHEYVEALEEEKRKIQVFQRE--------------------LPLCLELVTQAIQACRRELSG 51 (387)
Q Consensus 9 k~~d~v~~LEEErrKIevFkRE--------------------LPLCm~Ll~~aIe~~K~el~~ 51 (387)
-..-|-.-++++..||+.|+.+ ||=|-.-|.+|+..|++-|..
T Consensus 15 E~~~Y~kE~~~q~~rle~~k~~~~de~~iKkq~~vl~Et~~mipd~~~RL~~a~~~L~~~l~~ 77 (90)
T PF02970_consen 15 EEASYEKEVEEQEARLEKMKAEGEDEYDIKKQEEVLEETKMMIPDCQQRLEKAVEDLEEFLEE 77 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3456888899999999999988 899999999999999887764
No 34
>PF12638 Staygreen: Staygreen protein; InterPro: IPR024438 This domain is found in a family of proteins have been implicated in chlorophyll degradation [, ]. Intriguingly members of this family are also found in non-photosynthetic bacteria.
Probab=23.17 E-value=47 Score=30.79 Aligned_cols=15 Identities=40% Similarity=0.851 Sum_probs=12.2
Q ss_pred hhhhhcccchhhHHH
Q 016585 23 KIQVFQRELPLCLEL 37 (387)
Q Consensus 23 KIevFkRELPLCm~L 37 (387)
..++|+|||||-|.-
T Consensus 93 Ry~IF~kELPl~L~A 107 (151)
T PF12638_consen 93 RYYIFRKELPLALKA 107 (151)
T ss_pred HHHHHHHHHHHHHHH
Confidence 578999999996653
No 35
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=23.08 E-value=63 Score=28.52 Aligned_cols=48 Identities=27% Similarity=0.483 Sum_probs=33.9
Q ss_pred CCCCcccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhc
Q 016585 215 QRKQRRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLHT 273 (387)
Q Consensus 215 ~rK~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~ 273 (387)
.|++ +-=..++|++....|..+|+.+ |.|.|+--.=+.-||..|+.-+
T Consensus 79 ~R~~-vyI~~e~h~~l~~Iv~~ig~~~----------~si~~yidNIL~~Hle~~~eeI 126 (136)
T PF11888_consen 79 ARKG-VYISRETHERLSRIVRVIGERK----------MSISGYIDNILRHHLEEYREEI 126 (136)
T ss_pred CCee-eEECHHHHHHHHHHHHHHCCCC----------CcHHHHHHHHHHHHHHHHHHHH
Confidence 4444 7778999999999999999632 3333333344677888888654
No 36
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=22.42 E-value=78 Score=31.50 Aligned_cols=60 Identities=33% Similarity=0.443 Sum_probs=44.0
Q ss_pred CCCCCCCcccCCH----HHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccCCCC
Q 016585 212 GQPQRKQRRSWSP----ELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRRPSP 278 (387)
Q Consensus 212 ~~~~rK~Rl~WT~----ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr~~~ 278 (387)
.+..||+|-..+. .|.+||-..=. -|.|.+ .||--.=|||..|||+-.|.-|.+.|+...
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQY------LALPER-AeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQY------LALPER-AELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcch------hcCcHH-HHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4678999988885 68888876522 244433 245556789999999999999998876543
No 37
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=22.17 E-value=50 Score=33.73 Aligned_cols=59 Identities=31% Similarity=0.380 Sum_probs=42.9
Q ss_pred CCCCCCCcccCCH----HHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccCCC
Q 016585 212 GQPQRKQRRSWSP----ELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRRPS 277 (387)
Q Consensus 212 ~~~~rK~Rl~WT~----ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr~~ 277 (387)
.+.+||+|+-.|. ||-|||-..=. |-+++ +.+|- ..=.||--|||+-.|.+|=++||..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRY-LSAPE----RE~LA--~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRY-LSAPE----REHLA--SSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhc-cccHh----HHHHH--HhcCCCchheeeeeecchhhhhhhh
Confidence 5678999999885 89999976543 44455 33321 2234699999999999999988764
No 38
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=21.51 E-value=1.4e+02 Score=26.95 Aligned_cols=43 Identities=23% Similarity=0.278 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhh
Q 016585 225 ELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQK 268 (387)
Q Consensus 225 ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQK 268 (387)
+.-..+.+|+++|-. -...-.+|++++.+.|+|.++|+-+|.-
T Consensus 121 ~~~~~l~e~l~~L~~-l~~~~~~~v~l~~~~Gls~~EIA~~lgi 163 (185)
T PF07638_consen 121 EELLELEEALERLLA-LDPRQRRVVELRFFEGLSVEEIAERLGI 163 (185)
T ss_pred HHHHHHHHHHHHHHc-cCHHHHHHHHHHHHCCCCHHHHHHHHCc
Confidence 333456677777763 3344467888888899999998877753
No 39
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=21.41 E-value=1e+02 Score=26.30 Aligned_cols=48 Identities=15% Similarity=0.157 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhcCC----------CCCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccC
Q 016585 225 ELHRRFLHALQQLGGS----------HAATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRR 275 (387)
Q Consensus 225 ELH~rFv~Av~~LGG~----------~~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr 275 (387)
++...+..|++.|... +.-+.+.|-+.||+ +...|++||..-|..++.
T Consensus 95 e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgi---s~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 95 EQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKI---EVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHH
Confidence 3344566666666522 23344555555544 677789999888877764
No 40
>TIGR01232 lacD tagatose 1,6-diphosphate aldolase. This family consists of Gram-positive proteins. Tagatose 1,6-diphosphate aldolase is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation.
Probab=21.16 E-value=48 Score=34.15 Aligned_cols=50 Identities=20% Similarity=0.362 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHhhhhhhcccchhhHHHH------------HHHHHHHHHHhccccccc
Q 016585 7 MQRCHEYVEALEEEKRKIQVFQRELPLCLELV------------TQAIQACRRELSGTTTEY 56 (387)
Q Consensus 7 ~~k~~d~v~~LEEErrKIevFkRELPLCm~Ll------------~~aIe~~K~el~~~~~~~ 56 (387)
-+++-+.++-+-+.|-.|||+|=|.|+-|..| .+|.+.+|++-..+..+|
T Consensus 183 P~~V~~a~kefs~~~~gvDVlKvEvPvn~~~veG~~~~e~~yt~~eA~~~f~eq~~~~~~P~ 244 (325)
T TIGR01232 183 PRKVNEAMKLFSEPRFNVDVLKVEVPVNVKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPY 244 (325)
T ss_pred hHHHHHHHHHhccCCCCCcEEEEecccccccccccCcccccccHHHHHHHHHHHhhccCCCE
Confidence 56778888888889999999999999999977 567777777777666666
No 41
>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=20.61 E-value=1.2e+02 Score=23.04 Aligned_cols=47 Identities=21% Similarity=0.466 Sum_probs=32.4
Q ss_pred CCcccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHHHHHhhhhhh
Q 016585 217 KQRRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDEVKSHLQKYR 270 (387)
Q Consensus 217 K~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~VkSHLQKYR 270 (387)
+.|-.||+|+-...|..+..-| ..|.++..--||+...|.-=+.+|+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-------~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-------ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-------CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-------CceEeeecccccccccccHHHHHHh
Confidence 4567999999999988884445 5666677777779999988888888
No 42
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.36 E-value=1.3e+02 Score=26.92 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=26.4
Q ss_pred CChHHHHhHhcCCCCCHHHHHHhhhhhhhhccCCCCCCCCCCC
Q 016585 243 ATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRRPSPAMHNGGN 285 (387)
Q Consensus 243 AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr~~~~~~~~~~ 285 (387)
-+++.|-+.||+ +...|++||..-|..+++.....+.++|
T Consensus 151 ~s~~EIA~~lg~---s~~tV~~rl~rar~~Lr~~l~~~~~~~~ 190 (192)
T PRK09643 151 YSVADAARMLGV---AEGTVKSRCARGRARLAELLGYLRAGGN 190 (192)
T ss_pred CCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 456666666665 7888999998777777665444433333
No 43
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.30 E-value=1.8e+02 Score=25.53 Aligned_cols=31 Identities=10% Similarity=0.179 Sum_probs=23.0
Q ss_pred CCChHHHHhHhcCCCCCHHHHHHhhhhhhhhccC
Q 016585 242 AATPKQIRELMNVDGLTNDEVKSHLQKYRLHTRR 275 (387)
Q Consensus 242 ~AtPK~IlelM~V~gLT~~~VkSHLQKYRl~~rr 275 (387)
.-+.+.|-+.||+ |...|+++|++-|..++.
T Consensus 151 ~~s~~eIA~~lgi---s~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 151 GYTHREAAQLLGL---PLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHH
Confidence 4566777777766 678888888888877764
No 44
>PF14336 DUF4392: Domain of unknown function (DUF4392)
Probab=20.16 E-value=1.2e+02 Score=30.09 Aligned_cols=42 Identities=31% Similarity=0.304 Sum_probs=36.7
Q ss_pred CCcccCCHHHHHHHHHHHHHhcCCCCCChHHHHhHhcCCCCCHHH
Q 016585 217 KQRRSWSPELHRRFLHALQQLGGSHAATPKQIRELMNVDGLTNDE 261 (387)
Q Consensus 217 K~Rl~WT~ELH~rFv~Av~~LGG~~~AtPK~IlelM~V~gLT~~~ 261 (387)
...+-++.+.+++.++++-.+|+.|..|-+. .|-||||..+.
T Consensus 239 ~~~~l~~~~~e~~~L~~lv~~G~vDGvt~~~---~~sVDGl~~~~ 280 (291)
T PF14336_consen 239 WKNLLPSPEEEEKLLEALVEAGAVDGVTGKP---EPSVDGLPFEV 280 (291)
T ss_pred chhhcCChHHHHHHHHHHHHcCCccCCcCCC---CCCccCCCHHH
Confidence 4678899999999999999999999888877 67899998844
Done!