Query 017042
Match_columns 378
No_of_seqs 135 out of 168
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 05:06:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017042.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017042hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04504 DUF573: Protein of un 100.0 1.7E-36 3.7E-41 252.9 11.7 97 159-256 2-98 (98)
2 PF12776 Myb_DNA-bind_3: Myb/S 96.7 0.0028 6.2E-08 51.3 4.9 64 163-227 1-70 (96)
3 PF13837 Myb_DNA-bind_4: Myb/S 92.5 0.23 4.9E-06 39.5 4.6 63 162-227 2-72 (90)
4 PF07904 Eaf7: Chromatin modif 88.0 0.79 1.7E-05 38.1 4.2 56 167-226 1-61 (91)
5 PF11081 DUF2890: Protein of u 87.8 0.99 2.1E-05 42.4 5.2 23 159-182 116-138 (187)
6 PF00249 Myb_DNA-binding: Myb- 79.6 3.6 7.8E-05 29.5 4.2 47 162-219 2-48 (48)
7 smart00717 SANT SANT SWI3, AD 75.8 6 0.00013 26.8 4.3 45 162-218 2-46 (49)
8 cd00167 SANT 'SWI3, ADA2, N-Co 63.8 15 0.00032 24.5 4.1 41 163-215 1-41 (45)
9 PF10545 MADF_DNA_bdg: Alcohol 60.2 24 0.00053 27.0 5.3 37 191-227 25-61 (85)
10 PF01726 LexA_DNA_bind: LexA D 59.1 19 0.00042 28.0 4.4 46 169-221 8-53 (65)
11 PF00486 Trans_reg_C: Transcri 56.6 19 0.0004 27.3 4.0 53 167-225 8-60 (77)
12 KOG4282 Transcription factor G 55.7 91 0.002 31.2 9.8 64 160-227 53-121 (345)
13 KOG2266 Chromatin-associated p 47.6 94 0.002 33.6 8.6 41 182-224 514-556 (594)
14 PF05110 AF-4: AF-4 proto-onco 45.2 33 0.00072 40.6 5.3 15 85-99 444-458 (1191)
15 PF13921 Myb_DNA-bind_6: Myb-l 42.1 33 0.00071 25.3 3.2 41 164-217 1-41 (60)
16 KOG3064 RNA-binding nuclear pr 38.5 20 0.00044 35.6 2.0 9 28-36 207-215 (303)
17 smart00595 MADF subfamily of S 36.5 70 0.0015 25.2 4.5 34 192-227 27-60 (89)
18 PF04147 Nop14: Nop14-like fam 36.3 1.3E+02 0.0028 34.5 8.1 50 207-260 510-559 (840)
19 cd00383 trans_reg_C Effector d 34.5 62 0.0013 25.3 3.9 52 167-224 26-77 (95)
20 PF12186 AcylCoA_dehyd_C: Acyl 34.3 67 0.0014 28.2 4.3 61 193-254 4-66 (114)
21 PF07914 DUF1679: Protein of u 32.0 1.2E+02 0.0027 31.6 6.6 82 160-249 278-361 (414)
22 PF11728 DUF939_C: DUF939 C-te 31.4 86 0.0019 28.6 4.8 59 168-226 77-137 (167)
23 smart00862 Trans_reg_C Transcr 31.3 1.1E+02 0.0023 23.0 4.6 53 167-224 8-60 (78)
24 PF03109 ABC1: ABC1 family; I 30.9 1.2E+02 0.0026 25.8 5.4 58 167-224 52-109 (119)
25 COG4047 Uncharacterized protei 26.9 1.3E+02 0.0029 29.2 5.3 52 170-221 44-106 (243)
26 PF14584 DUF4446: Protein of u 26.5 58 0.0013 29.6 2.7 35 211-253 21-55 (151)
27 PF09756 DDRGK: DDRGK domain; 25.5 46 0.001 31.4 2.0 40 170-218 98-137 (188)
28 KOG1060 Vesicle coat complex A 23.1 1.4E+02 0.0029 34.4 5.2 16 86-101 697-712 (968)
29 KOG0772 Uncharacterized conser 23.0 58 0.0013 35.5 2.3 17 160-176 292-308 (641)
30 TIGR01557 myb_SHAQKYF myb-like 22.8 1.5E+02 0.0033 22.5 4.0 20 161-180 3-22 (57)
31 PRK13923 putative spore coat p 22.8 1.1E+02 0.0024 28.5 3.9 26 160-185 4-29 (170)
32 PRK13280 N-glycosylase/DNA lya 22.1 1.6E+02 0.0034 29.4 5.0 80 170-253 51-143 (269)
33 PF13404 HTH_AsnC-type: AsnC-t 22.0 1.1E+02 0.0023 21.8 2.9 37 170-219 6-42 (42)
34 KOG0457 Histone acetyltransfer 22.0 85 0.0018 33.3 3.3 34 159-199 70-103 (438)
35 PF14797 SEEEED: Serine-rich r 21.6 56 0.0012 29.0 1.6 14 85-98 48-61 (130)
36 PF04931 DNA_pol_phi: DNA poly 21.5 53 0.0012 36.9 1.8 7 167-173 731-737 (784)
37 PF14178 YppF: YppF-like prote 21.4 2.3E+02 0.0049 22.3 4.7 42 177-219 8-50 (60)
38 PRK11173 two-component respons 21.1 1.2E+02 0.0027 27.3 3.8 51 167-223 163-213 (237)
39 PRK08055 chorismate mutase; Pr 21.0 1.5E+02 0.0032 27.8 4.4 49 171-219 130-178 (181)
40 PF13730 HTH_36: Helix-turn-he 20.3 3.3E+02 0.0071 19.4 5.4 47 167-220 5-51 (55)
No 1
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=100.00 E-value=1.7e-36 Score=252.92 Aligned_cols=97 Identities=52% Similarity=0.921 Sum_probs=94.7
Q ss_pred cccCCCCchhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCC
Q 017042 159 LFQRLWSEDDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVNNLRKSAKKGGVRTF 238 (378)
Q Consensus 159 ~fqR~WS~eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~~~~~k~k~G~~p~f 238 (378)
+|||+||++|||+||+|||+|+++||..|+.||++||++|+++|+++||++||++||||||+||.+++. ++++|.+|.|
T Consensus 2 ~~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~-k~~~g~~~~~ 80 (98)
T PF04504_consen 2 LFQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVK-KSKNGKDPSF 80 (98)
T ss_pred CCcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhh-hcccCcCCCC
Confidence 699999999999999999999999999999999999999999999999999999999999999999998 7889999999
Q ss_pred CChhHHHHHHHHHHhcCC
Q 017042 239 SNPHEQRAYDLSKKLWEG 256 (378)
Q Consensus 239 ~~~HD~~~feLSk~IWG~ 256 (378)
++|||++||+||++|||.
T Consensus 81 ~~~hd~~~f~Lsk~IWG~ 98 (98)
T PF04504_consen 81 SKPHDRRLFELSKKIWGS 98 (98)
T ss_pred CCHhHHHHHHHHHHHcCC
Confidence 999999999999999995
No 2
>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=96.69 E-value=0.0028 Score=51.28 Aligned_cols=64 Identities=22% Similarity=0.251 Sum_probs=53.4
Q ss_pred CCCchhHHHHHHHHHHHHHhhCCCC------CccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 017042 163 LWSEDDEIIVLKRMIEYSTEKGIDP------SQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVNNLR 227 (378)
Q Consensus 163 ~WS~eDEI~ILqgli~~~~~~G~~P------~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~~~~ 227 (378)
.||++.+-.||..|++.....+. | ...+......+.......++..||..|++.||++|.....
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~-~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~ 70 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNR-PTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKE 70 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCC-CCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHH
Confidence 49999999999999999866544 4 2356777777777778899999999999999999998753
No 3
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=92.50 E-value=0.23 Score=39.54 Aligned_cols=63 Identities=19% Similarity=0.298 Sum_probs=38.8
Q ss_pred CCCCchhHHHHHHHHHH--HHHh--h-CCCCCccHHHHHHHHHhcc---CCCCCHHHHHHHHHHHHHHHHHHhh
Q 017042 162 RLWSEDDEIIVLKRMIE--YSTE--K-GIDPSQDTQAFYDYVKNSL---HGDYTKAQLMDKIRRLKKKCVNNLR 227 (378)
Q Consensus 162 R~WS~eDEI~ILqgli~--~~~~--~-G~~P~~D~~af~~~ik~sL---~~~~s~~QL~~KvRrLKkKY~~~~~ 227 (378)
+.|+.+.-..||..+.. +... . +..... .+|..|...| .+..|..|+.+|+..|+++|.....
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~---~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~ 72 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNK---KVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKD 72 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--H---HHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccch---HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 47999988888888877 3321 2 233322 2455444443 4677999999999999999998754
No 4
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=87.98 E-value=0.79 Score=38.13 Aligned_cols=56 Identities=23% Similarity=0.373 Sum_probs=45.8
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhc-----cCCCCCHHHHHHHHHHHHHHHHHHh
Q 017042 167 DDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNS-----LHGDYTKAQLMDKIRRLKKKCVNNL 226 (378)
Q Consensus 167 eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~s-----L~~~~s~~QL~~KvRrLKkKY~~~~ 226 (378)
++||+||++|+.|+=. |..=+-.|-++.+.|... +...++..+|-+||++| |.-..
T Consensus 1 e~Ei~Lf~a~~~~KPv-Gi~KHF~M~~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~---YdL~~ 61 (91)
T PF07904_consen 1 EDEIRLFRAMCRYKPV-GIHKHFHMICIVERLNNPGFDPKLNKHFTIDDIWKKLRTL---YDLEA 61 (91)
T ss_pred ChHHHHHHHHHhcCCC-ccchHHHHHHHHHHHhccccCCccCCcCCHHHHHHHHHHh---cCHHH
Confidence 5899999999999733 644455788999999999 88999999999999887 66543
No 5
>PF11081 DUF2890: Protein of unknown function (DUF2890); InterPro: IPR021304 This entry contains the 33kDa and 22kDa phosphoproteins from vertebrate adenoviruses.
Probab=87.80 E-value=0.99 Score=42.45 Aligned_cols=23 Identities=13% Similarity=0.130 Sum_probs=12.1
Q ss_pred cccCCCCchhHHHHHHHHHHHHHh
Q 017042 159 LFQRLWSEDDEIIVLKRMIEYSTE 182 (378)
Q Consensus 159 ~fqR~WS~eDEI~ILqgli~~~~~ 182 (378)
.-.+.|..= =..||..|.+-...
T Consensus 116 ~~~~swr~l-R~~I~~tLyaifqq 138 (187)
T PF11081_consen 116 QEYRSWREL-RNRIFPTLYAIFQQ 138 (187)
T ss_pred cCchHHHHH-HHHHHHHHHHHHHH
Confidence 345566532 24677877444333
No 6
>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=79.64 E-value=3.6 Score=29.48 Aligned_cols=47 Identities=21% Similarity=0.430 Sum_probs=31.1
Q ss_pred CCCCchhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHH
Q 017042 162 RLWSEDDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLK 219 (378)
Q Consensus 162 R~WS~eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLK 219 (378)
..||.+++..|++++..| |.. +|.. |...+...-|..|+..+.++|+
T Consensus 2 ~~Wt~eE~~~l~~~v~~~----g~~---~W~~----Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKY----GKD---NWKK----IAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp -SS-HHHHHHHHHHHHHS----TTT---HHHH----HHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHh----CCc---HHHH----HHHHcCCCCCHHHHHHHHHhhC
Confidence 469999999999998877 421 3444 4444445668888887776653
No 7
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=75.77 E-value=6 Score=26.81 Aligned_cols=45 Identities=13% Similarity=0.316 Sum_probs=28.6
Q ss_pred CCCCchhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHH
Q 017042 162 RLWSEDDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRL 218 (378)
Q Consensus 162 R~WS~eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrL 218 (378)
..||.+++..|+.++..|.. .+|..+...| . .-+..|+..+.+.|
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~-------~~w~~Ia~~~----~-~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK-------NNWEKIAKEL----P-GRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc-------CCHHHHHHHc----C-CCCHHHHHHHHHHH
Confidence 47999999999999887732 4454443333 2 33566666555444
No 8
>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=63.83 E-value=15 Score=24.47 Aligned_cols=41 Identities=17% Similarity=0.378 Sum_probs=26.1
Q ss_pred CCCchhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHH
Q 017042 163 LWSEDDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKI 215 (378)
Q Consensus 163 ~WS~eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~Kv 215 (378)
.||.+++..|++++..| |. .++..+...+.+ -+..|+..+.
T Consensus 1 ~Wt~eE~~~l~~~~~~~----g~---~~w~~Ia~~~~~-----rs~~~~~~~~ 41 (45)
T cd00167 1 PWTEEEDELLLEAVKKY----GK---NNWEKIAKELPG-----RTPKQCRERW 41 (45)
T ss_pred CCCHHHHHHHHHHHHHH----Cc---CCHHHHHhHcCC-----CCHHHHHHHH
Confidence 49999999999999877 32 455555544433 2455554443
No 9
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=60.25 E-value=24 Score=26.99 Aligned_cols=37 Identities=8% Similarity=0.283 Sum_probs=32.3
Q ss_pred HHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 017042 191 TQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVNNLR 227 (378)
Q Consensus 191 ~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~~~~ 227 (378)
...++..|...|...++..++..+++.||.+|.....
T Consensus 25 r~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~ 61 (85)
T PF10545_consen 25 REEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELK 61 (85)
T ss_pred HHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHH
Confidence 3467778888888889999999999999999999986
No 10
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=59.06 E-value=19 Score=27.99 Aligned_cols=46 Identities=22% Similarity=0.378 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHH
Q 017042 169 EIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKK 221 (378)
Q Consensus 169 EI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkK 221 (378)
.-.||.-|.+|..++|..|... . |..-|.+. |.+-+..-|+.|.+|
T Consensus 8 Q~~vL~~I~~~~~~~G~~Pt~r--E----Ia~~~g~~-S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGYPPTVR--E----IAEALGLK-STSTVQRHLKALERK 53 (65)
T ss_dssp HHHHHHHHHHHHHHHSS---HH--H----HHHHHTSS-SHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcCCCCCHH--H----HHHHhCCC-ChHHHHHHHHHHHHC
Confidence 4579999999999999999632 2 22222333 588888888888765
No 11
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=56.58 E-value=19 Score=27.33 Aligned_cols=53 Identities=19% Similarity=0.231 Sum_probs=39.9
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHH
Q 017042 167 DDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVNN 225 (378)
Q Consensus 167 eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~~ 225 (378)
.-|..||..|+.+. |.. .....|++.|-+.-. ..+.+.|..-|.|||+|+...
T Consensus 8 ~~e~~lL~~L~~~~---~~~--vs~~~l~~~~w~~~~-~~~~~~l~~~I~rLR~kL~~~ 60 (77)
T PF00486_consen 8 PKEFRLLELLLRNP---GRV--VSREELIEALWGDEE-DVSDNSLDVHISRLRKKLEDA 60 (77)
T ss_dssp HHHHHHHHHHHHTT---TSE--EEHHHHHHHHTSSSS-TTCTHHHHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHhCC---CCC--CCHHHhCChhhhccc-ccchhhHHHHHHHHHHHHhhc
Confidence 35788999888774 321 234578888877644 788999999999999999864
No 12
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=55.68 E-value=91 Score=31.23 Aligned_cols=64 Identities=20% Similarity=0.296 Sum_probs=44.2
Q ss_pred ccCCCCchhHHHHHHHH--HHHHHhhCCCCCccHHHHHHHHHhc---cCCCCCHHHHHHHHHHHHHHHHHHhh
Q 017042 160 FQRLWSEDDEIIVLKRM--IEYSTEKGIDPSQDTQAFYDYVKNS---LHGDYTKAQLMDKIRRLKKKCVNNLR 227 (378)
Q Consensus 160 fqR~WS~eDEI~ILqgl--i~~~~~~G~~P~~D~~af~~~ik~s---L~~~~s~~QL~~KvRrLKkKY~~~~~ 227 (378)
+.+.|+.+.=+.||+.. .++.-..|.+=. .+|+.|... +.+.-|..|+..||..|++||.....
T Consensus 53 ~~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~----~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~ 121 (345)
T KOG4282|consen 53 SEPRWSEEETLTLIEIRGEMDVALRRGKLKG----PLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKA 121 (345)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHhhhhcc----cHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 36899998888888766 333333343222 345555443 34677899999999999999998754
No 13
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=47.63 E-value=94 Score=33.60 Aligned_cols=41 Identities=27% Similarity=0.464 Sum_probs=30.1
Q ss_pred hhCC-CCCccHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHHHHH
Q 017042 182 EKGI-DPSQDTQAFYDYVKNSLH-GDYTKAQLMDKIRRLKKKCVN 224 (378)
Q Consensus 182 ~~G~-~P~~D~~af~~~ik~sL~-~~~s~~QL~~KvRrLKkKY~~ 224 (378)
..|. -|..- .|..+|...|. ++|+..-|.+-+++|=.+|.-
T Consensus 514 kKGKaePTde--elk~~V~kILk~vdfntaTm~dIlKkl~~~f~~ 556 (594)
T KOG2266|consen 514 KKGKAEPTDE--ELKEVVKKILKEVDFNTATMKDILKKLYAKFPI 556 (594)
T ss_pred ccCCCCCcHH--HHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCc
Confidence 3444 34433 67888888887 899998899988888777763
No 14
>PF05110 AF-4: AF-4 proto-oncoprotein; InterPro: IPR007797 This family consist of family member 1 (proto-oncogene AF4), family member 2 or FMR2 (Fragile X E mental retardation syndrome), family member 3 or LAF4 (lymphoid nuclear protein related to AF4) and family member 4 (protein lilliputian). Lilliputian is a Drosophila AF4 protein homologue which contains an AT-hook domain. It represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila []. These proteins have been linked to Homo sapiens diseases such as acute lymphoblastic leukemia and mental retardation [].
Probab=45.18 E-value=33 Score=40.62 Aligned_cols=15 Identities=60% Similarity=0.561 Sum_probs=6.7
Q ss_pred CCCccccCCCCCCCC
Q 017042 85 SESESESESGSEPGA 99 (378)
Q Consensus 85 s~s~~~~~s~~~~~~ 99 (378)
|+||+.|+|+||+|+
T Consensus 444 S~SESsS~SDSESES 458 (1191)
T PF05110_consen 444 SESESSSSSDSESES 458 (1191)
T ss_pred CCCCccCcccccccc
Confidence 334444444444444
No 15
>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=42.12 E-value=33 Score=25.27 Aligned_cols=41 Identities=20% Similarity=0.438 Sum_probs=23.7
Q ss_pred CCchhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHH
Q 017042 164 WSEDDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRR 217 (378)
Q Consensus 164 WS~eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRr 217 (378)
||.++...|++.+..| |. +|.....+| . .-+..|+..+.++
T Consensus 1 WT~eEd~~L~~~~~~~----g~----~W~~Ia~~l----~-~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKY----GN----DWKKIAEHL----G-NRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHH----TS-----HHHHHHHS----T-TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHH----Cc----CHHHHHHHH----C-cCCHHHHHHHHHH
Confidence 8988888888877776 42 555444433 1 3456666655555
No 16
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=38.48 E-value=20 Score=35.62 Aligned_cols=9 Identities=33% Similarity=0.280 Sum_probs=3.8
Q ss_pred cCCcchhhc
Q 017042 28 DSSGSELEV 36 (378)
Q Consensus 28 ~~~~ee~e~ 36 (378)
+.+++-|++
T Consensus 207 ~~~~e~E~v 215 (303)
T KOG3064|consen 207 DEDAELEEV 215 (303)
T ss_pred chhhhhhhc
Confidence 344444444
No 17
>smart00595 MADF subfamily of SANT domain.
Probab=36.55 E-value=70 Score=25.20 Aligned_cols=34 Identities=9% Similarity=0.229 Sum_probs=27.8
Q ss_pred HHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhh
Q 017042 192 QAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVNNLR 227 (378)
Q Consensus 192 ~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~~~~ 227 (378)
..++..|...|.. +..++..|++.||.+|.....
T Consensus 27 ~~aW~~Ia~~l~~--~~~~~~~kw~~LR~~y~~e~~ 60 (89)
T smart00595 27 RKAWEEIAEELGL--SVEECKKRWKNLRDRYRRELK 60 (89)
T ss_pred HHHHHHHHHHHCc--CHHHHHHHHHHHHHHHHHHHH
Confidence 3566667666655 899999999999999999876
No 18
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=36.27 E-value=1.3e+02 Score=34.45 Aligned_cols=50 Identities=12% Similarity=0.188 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCCCChhHHHHHHHHHHhcCCCCCC
Q 017042 207 TKAQLMDKIRRLKKKCVNNLRKSAKKGGVRTFSNPHEQRAYDLSKKLWEGSEES 260 (378)
Q Consensus 207 s~~QL~~KvRrLKkKY~~~~~~k~k~G~~p~f~~~HD~~~feLSk~IWG~~~~~ 260 (378)
...-+...|..+..+|..... + ..+ -.|..-.+.-+|.|.-.||....-.
T Consensus 510 ~a~~~r~~L~~~~~~~~~~~l-~-~~~--~~~P~l~~Lvllklv~~lFPTSD~~ 559 (840)
T PF04147_consen 510 AAECFREVLKEMQKRFRKGAL-K-PKE--RSWPSLSDLVLLKLVGTLFPTSDFR 559 (840)
T ss_pred HHHHHHHHHHHHHHHHhhhcc-c-ccC--CCCCChhHHHHHHHHHHhcCccccc
Confidence 345556667777666665221 0 111 1267788999999999999876433
No 19
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=34.46 E-value=62 Score=25.33 Aligned_cols=52 Identities=21% Similarity=0.181 Sum_probs=36.6
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHH
Q 017042 167 DDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVN 224 (378)
Q Consensus 167 eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~ 224 (378)
.-|..||..|+.+. |..-. ...+++.|-+.-. .++..-|..=|.|||+++..
T Consensus 26 ~~e~~lL~~L~~~~---~~~vs--~~~l~~~lw~~~~-~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 26 PKEFELLELLARNP---GRVLS--REQLLEAVWGDDY-DVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred HHHHHHHHHHHhCC---CCcCC--HHHHHHHhcCCCC-CCCcccHHHHHHHHHHHhcc
Confidence 67899999998874 43322 2367777765322 35667788999999999874
No 20
>PF12186 AcylCoA_dehyd_C: Acyl-CoA dehydrogenase C terminal; InterPro: IPR020964 This entry represents the C-terminal alpha helical domain of some bacterial Acyl-CoA dehydrogenases. It is found in association with PF02770 from PFAM, PF00441 from PFAM, PF02771 from PFAM. There is a conserved ARRL sequence motif. ; PDB: 2OKU_A.
Probab=34.26 E-value=67 Score=28.16 Aligned_cols=61 Identities=8% Similarity=0.293 Sum_probs=45.5
Q ss_pred HHHHHHHhccCCCCC--HHHHHHHHHHHHHHHHHHhhhhhhcCCCCCCCChhHHHHHHHHHHhc
Q 017042 193 AFYDYVKNSLHGDYT--KAQLMDKIRRLKKKCVNNLRKSAKKGGVRTFSNPHEQRAYDLSKKLW 254 (378)
Q Consensus 193 af~~~ik~sL~~~~s--~~QL~~KvRrLKkKY~~~~~~k~k~G~~p~f~~~HD~~~feLSk~IW 254 (378)
.++..|+..+...++ ..-|.++|..|..+|...+. +.+.-.+..+..=|=||||++.-.|-
T Consensus 4 tYl~~i~E~~~~~~~~el~~l~~rl~~m~~~yeeav~-~Vke~~nqe~~Df~ARRLvEMa~~ii 66 (114)
T PF12186_consen 4 TYLAIIREYEQAEVSPELQPLKERLKKMTEKYEEAVA-KVKEAKNQELQDFHARRLVEMAAHII 66 (114)
T ss_dssp HHHHHHHTGGGS---GGGHHHHHHHHHHHHHHHHHHH-HHHTT--HHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHH-HHHhhcChHHHHHHHHHHHHHHHHHH
Confidence 577788887776664 57899999999999999998 66655566666777899999887775
No 21
>PF07914 DUF1679: Protein of unknown function (DUF1679); InterPro: IPR012877 This region is found in a number of Caenorhabditis elegans and Caenorhabditis briggsae proteins, in one case (Q19034 from SWISSPROT) as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in zinc finger-C4 and HLH domain-containing kinases. In fact, one member of this family (Q9GUC1 from SWISSPROT) is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (IPR000536 from INTERPRO, IPR008946 from INTERPRO, and IPR001628 from INTERPRO).
Probab=31.99 E-value=1.2e+02 Score=31.58 Aligned_cols=82 Identities=16% Similarity=0.309 Sum_probs=50.3
Q ss_pred ccCCCCchhH-HHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhhhhhhc-CCCCC
Q 017042 160 FQRLWSEDDE-IIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVNNLRKSAKK-GGVRT 237 (378)
Q Consensus 160 fqR~WS~eDE-I~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~~~~~k~k~-G~~p~ 237 (378)
.+-+|+.+++ -.-|.+||||...|-..|..|+.-++ . +.+|...=...-.+|=..|-....+.... |..|
T Consensus 278 ~NiLw~k~~~g~~~l~AIIDwQ~vh~G~~~eDl~Rll---~----~~lS~edRR~~~~~lL~~Yy~~f~~~l~~~~~~P- 349 (414)
T PF07914_consen 278 SNILWDKDSDGKLKLKAIIDWQCVHRGSPAEDLARLL---V----SCLSGEDRREHTEELLEYYYDTFTEALEDGGKAP- 349 (414)
T ss_pred HheeeecCCchhHHHHHHHHHHHhhcCchHHHHHHHH---H----hcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCC-
Confidence 3457888665 67899999999999889988744433 2 33344333445555555565555433333 4566
Q ss_pred CCChhHHHHHHH
Q 017042 238 FSNPHEQRAYDL 249 (378)
Q Consensus 238 f~~~HD~~~feL 249 (378)
|+-..=+.+|+|
T Consensus 350 fT~eqL~~sY~l 361 (414)
T PF07914_consen 350 FTLEQLKDSYRL 361 (414)
T ss_pred ccHHHHHHHHHH
Confidence 665555556665
No 22
>PF11728 DUF939_C: DUF939 C-terminal domain; InterPro: IPR021062 This entry represents a C-terminal domain found in a set of bacterial proteins. The proteins are about 160 amino acids in length and are predicted to be multi-pass membrane proteins. ; PDB: 3KMI_B.
Probab=31.42 E-value=86 Score=28.59 Aligned_cols=59 Identities=22% Similarity=0.362 Sum_probs=43.0
Q ss_pred hHHHHHHHHHHHHHhhCCCC-C-ccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHh
Q 017042 168 DEIIVLKRMIEYSTEKGIDP-S-QDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVNNL 226 (378)
Q Consensus 168 DEI~ILqgli~~~~~~G~~P-~-~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~~~ 226 (378)
..+.||+.|..+...--..| + ..++.|++.+..+++..-+...|.++|..|+..|+..-
T Consensus 77 ~Q~~iL~~M~~~l~~i~~~~~q~~~ia~~~~~~a~~~~e~n~~~~ll~~L~~l~~~fr~~~ 137 (167)
T PF11728_consen 77 KQLEILKRMYPNLSKIYMSPKQAEIIADFLEELAESLHENNTAEELLEELEELKEEFREMP 137 (167)
T ss_dssp HHHHHHHHHHHHHTT-SS--HHHHHHHHHHHHHHH----TTHHHHHHHHHHHHHHHHHTS-
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhcCC
Confidence 45789999998876644433 2 45889999999999999999999999999999998764
No 23
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=31.34 E-value=1.1e+02 Score=23.01 Aligned_cols=53 Identities=21% Similarity=0.230 Sum_probs=34.9
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHH
Q 017042 167 DDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVN 224 (378)
Q Consensus 167 eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~ 224 (378)
.-|+.||.-|+.+. |.. .....+++.|-+.-....+..-|..-|.+||+++..
T Consensus 8 ~~e~~lL~~L~~~~---~~~--vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 8 PKEFRLLELLLRNP---GRV--VSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred HHHHHHHHHHHhCC---CCc--cCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 44777888888774 431 223367776665321255678899999999999864
No 24
>PF03109 ABC1: ABC1 family; InterPro: IPR004147 This entry includes ABC1 from yeast [] and AarF from Escherichia coli []. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex [] and E. coli AarF is required for ubiquinone production []. It has been suggested that members of the ABC1 family are novel chaperonins []. These proteins are unrelated to the ABC transporter proteins.
Probab=30.85 E-value=1.2e+02 Score=25.81 Aligned_cols=58 Identities=14% Similarity=0.220 Sum_probs=45.7
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHH
Q 017042 167 DDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCVN 224 (378)
Q Consensus 167 eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~~ 224 (378)
..++.||+.++.+....+.....++..+++.++..|...++-..=..-++++++.|..
T Consensus 52 ~~Dl~~l~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~ElDf~~Ea~n~~~~~~~~~~ 109 (119)
T PF03109_consen 52 EADLRILRRLARLLERLPPFRRLDLEEIVDEFRDSLLEELDFRREAANLERFRKNFAD 109 (119)
T ss_pred HHHHHHHHHHHHHHHHcccccccCHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHhCC
Confidence 5678999999888877665446788899999999888777777777778888777764
No 25
>COG4047 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.90 E-value=1.3e+02 Score=29.23 Aligned_cols=52 Identities=15% Similarity=0.409 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhh-CCCC---------CccHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHH
Q 017042 170 IIVLKRMIEYSTEK-GIDP---------SQDTQAFYDYVKNSLH-GDYTKAQLMDKIRRLKKK 221 (378)
Q Consensus 170 I~ILqgli~~~~~~-G~~P---------~~D~~af~~~ik~sL~-~~~s~~QL~~KvRrLKkK 221 (378)
++||+||+.|+-.. |-.- ..+.-.+|...++.|. ..|+..-+-.|+||+++=
T Consensus 44 laianaLvSYqLtgkGEewW~eF~kyf~~~~vr~i~ray~~fLp~s~fnrrlieqKlrRi~ra 106 (243)
T COG4047 44 LAIANALVSYQLTGKGEEWWWEFAKYFRGREVRDIYRAYKEFLPNSRFNRRLIEQKLRRIRRA 106 (243)
T ss_pred HHHHHHHHHHhhccCcHHHHHHHHHHHhhccHHHHHHHHHHhccCCchhHHHHHHHHHHHHHH
Confidence 68999999998543 2110 1233344555555665 688888888999999763
No 26
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=26.49 E-value=58 Score=29.60 Aligned_cols=35 Identities=26% Similarity=0.337 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHhhhhhhcCCCCCCCChhHHHHHHHHHHh
Q 017042 211 LMDKIRRLKKKCVNNLRKSAKKGGVRTFSNPHEQRAYDLSKKL 253 (378)
Q Consensus 211 L~~KvRrLKkKY~~~~~~k~k~G~~p~f~~~HD~~~feLSk~I 253 (378)
+.-|++||++||.... ++..|. ..+..+-++...|
T Consensus 21 ~~~kl~kl~r~Y~~lm--~g~~~~------~lE~~l~~~~~~~ 55 (151)
T PF14584_consen 21 LNIKLRKLKRRYDALM--RGKDGK------NLEDLLNELFDQI 55 (151)
T ss_pred HHHHHHHHHHHHHHHh--CCCCcc------cHHHHHHHHHHHH
Confidence 5689999999999987 455553 2344444444444
No 27
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=25.48 E-value=46 Score=31.39 Aligned_cols=40 Identities=20% Similarity=0.328 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHH
Q 017042 170 IIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRL 218 (378)
Q Consensus 170 I~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrL 218 (378)
-.+|+.+|+|...+-.++..|+.+ +|++++..+++.|..|
T Consensus 98 ~~lL~~Fi~yIK~~Kvv~ledla~---------~f~l~t~~~i~ri~~L 137 (188)
T PF09756_consen 98 SQLLQEFINYIKEHKVVNLEDLAA---------EFGLRTQDVINRIQEL 137 (188)
T ss_dssp --HHHHHHHHHHH-SEE-HHHHHH---------HH-S-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcceeeHHHHHH---------HcCCCHHHHHHHHHHH
Confidence 339999999999998888777544 5788888999988888
No 28
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.08 E-value=1.4e+02 Score=34.42 Aligned_cols=16 Identities=44% Similarity=0.582 Sum_probs=8.2
Q ss_pred CCccccCCCCCCCCCC
Q 017042 86 ESESESESGSEPGASP 101 (378)
Q Consensus 86 ~s~~~~~s~~~~~~~p 101 (378)
.|.++++|+|+.+++|
T Consensus 697 ss~~d~~s~se~e~e~ 712 (968)
T KOG1060|consen 697 SSAEDSESSSEAESEP 712 (968)
T ss_pred cccccccccccccccc
Confidence 3344555555555544
No 29
>KOG0772 consensus Uncharacterized conserved protein, contains WD40 repeat [Function unknown]
Probab=23.05 E-value=58 Score=35.48 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=9.2
Q ss_pred ccCCCCchhHHHHHHHH
Q 017042 160 FQRLWSEDDEIIVLKRM 176 (378)
Q Consensus 160 fqR~WS~eDEI~ILqgl 176 (378)
.-|+|.-++=..-|+-|
T Consensus 292 tlRiWdv~~~k~q~qVi 308 (641)
T KOG0772|consen 292 TLRIWDVNNTKSQLQVI 308 (641)
T ss_pred cEEEEecCCchhheeEE
Confidence 45666655555544443
No 30
>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=22.78 E-value=1.5e+02 Score=22.53 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=17.7
Q ss_pred cCCCCchhHHHHHHHHHHHH
Q 017042 161 QRLWSEDDEIIVLKRMIEYS 180 (378)
Q Consensus 161 qR~WS~eDEI~ILqgli~~~ 180 (378)
.+.||++....+|+||-.|-
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G 22 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLG 22 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhC
Confidence 45799999999999999883
No 31
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=22.76 E-value=1.1e+02 Score=28.53 Aligned_cols=26 Identities=15% Similarity=0.357 Sum_probs=22.9
Q ss_pred ccCCCCchhHHHHHHHHHHHHHhhCC
Q 017042 160 FQRLWSEDDEIIVLKRMIEYSTEKGI 185 (378)
Q Consensus 160 fqR~WS~eDEI~ILqgli~~~~~~G~ 185 (378)
.|..|+.+|++.+-+.+|.|..+.|+
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~t 29 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGT 29 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccch
Confidence 57899999999999999999977663
No 32
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=22.14 E-value=1.6e+02 Score=29.42 Aligned_cols=80 Identities=16% Similarity=0.217 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHhh-CCCCC---------ccHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHH--HHHHhhhhhhcCCCC
Q 017042 170 IIVLKRMIEYSTEK-GIDPS---------QDTQAFYDYVKNSLH-GDYTKAQLMDKIRRLKKK--CVNNLRKSAKKGGVR 236 (378)
Q Consensus 170 I~ILqgli~~~~~~-G~~P~---------~D~~af~~~ik~sL~-~~~s~~QL~~KvRrLKkK--Y~~~~~~k~k~G~~p 236 (378)
++|++||++|+-.. |-... .+...+++.+...|. ..+++.=+-.|||||++= |...+. ....+ .
T Consensus 51 Lvi~NaLvSYqLsgkGEe~W~eFs~yf~~~~~~~~~~~~~~Fl~~s~~nrrl~e~KikRi~r~~~fl~~L~-l~~~~--~ 127 (269)
T PRK13280 51 LVIANALVSYQLSGKGEEWWWEFSKYFSEKGVEDIVEAYIEFLKNSKGNRRLLEQKIKRIEKVEPFLESLT-LLDLP--L 127 (269)
T ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHhcccCchhHHHHHHHHHhcCchhHHHHHHHHHHHHHHHHHhhhhc-cchhh--h
Confidence 78899999998653 32210 111222233333334 466777788999999776 665552 11111 1
Q ss_pred CCCChhHHHHHHHHHHh
Q 017042 237 TFSNPHEQRAYDLSKKL 253 (378)
Q Consensus 237 ~f~~~HD~~~feLSk~I 253 (378)
-+ ..-+.-...|++.+
T Consensus 128 ~y-~~l~~l~~~La~~L 143 (269)
T PRK13280 128 YY-EDLEELLEQLAKIL 143 (269)
T ss_pred hH-hhHHHHHHHHHHHh
Confidence 12 33455556666644
No 33
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=22.03 E-value=1.1e+02 Score=21.75 Aligned_cols=37 Identities=19% Similarity=0.294 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHH
Q 017042 170 IIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLK 219 (378)
Q Consensus 170 I~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLK 219 (378)
..||..|- ..|..|+..++. ..++|...+...|++|+
T Consensus 6 ~~Il~~Lq----~d~r~s~~~la~---------~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 6 RKILRLLQ----EDGRRSYAELAE---------ELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHH----H-TTS-HHHHHH---------HHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHH----HcCCccHHHHHH---------HHCcCHHHHHHHHHHhC
Confidence 45555554 448888765433 35789999999999985
No 34
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=21.96 E-value=85 Score=33.30 Aligned_cols=34 Identities=26% Similarity=0.531 Sum_probs=27.5
Q ss_pred cccCCCCchhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHH
Q 017042 159 LFQRLWSEDDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVK 199 (378)
Q Consensus 159 ~fqR~WS~eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik 199 (378)
.+---|+-+|||.||+|+-.| | ..+|....++|.
T Consensus 70 i~~~~WtadEEilLLea~~t~----G---~GNW~dIA~hIG 103 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETY----G---FGNWQDIADHIG 103 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHh----C---CCcHHHHHHHHc
Confidence 455679999999999999988 3 457888777776
No 35
>PF14797 SEEEED: Serine-rich region of AP3B1, clathrin-adaptor complex
Probab=21.58 E-value=56 Score=29.02 Aligned_cols=14 Identities=64% Similarity=0.741 Sum_probs=8.6
Q ss_pred CCCccccCCCCCCC
Q 017042 85 SESESESESGSEPG 98 (378)
Q Consensus 85 s~s~~~~~s~~~~~ 98 (378)
|.++.++++|++++
T Consensus 48 SSse~~SEs~sese 61 (130)
T PF14797_consen 48 SSSEQDSESGSESE 61 (130)
T ss_pred ccccccccccchhh
Confidence 44555666666665
No 36
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=21.49 E-value=53 Score=36.88 Aligned_cols=7 Identities=29% Similarity=0.866 Sum_probs=2.7
Q ss_pred hhHHHHH
Q 017042 167 DDEIIVL 173 (378)
Q Consensus 167 eDEI~IL 173 (378)
+|+..-|
T Consensus 731 De~m~~l 737 (784)
T PF04931_consen 731 DEQMMAL 737 (784)
T ss_pred HHHHHHH
Confidence 3343333
No 37
>PF14178 YppF: YppF-like protein
Probab=21.42 E-value=2.3e+02 Score=22.30 Aligned_cols=42 Identities=17% Similarity=0.484 Sum_probs=31.9
Q ss_pred HHHHHhhCCCCCccHHHHHHHHHhc-cCCCCCHHHHHHHHHHHH
Q 017042 177 IEYSTEKGIDPSQDTQAFYDYVKNS-LHGDYTKAQLMDKIRRLK 219 (378)
Q Consensus 177 i~~~~~~G~~P~~D~~af~~~ik~s-L~~~~s~~QL~~KvRrLK 219 (378)
-.|.+.++..| .+++.|+||.|.. |.-.++.++..+-||-|-
T Consensus 8 ~~F~~~k~y~p-~~~NeLLDFar~~Yi~gei~i~eYR~lvreLE 50 (60)
T PF14178_consen 8 QKFMQKKKYEP-EDMNELLDFARKLYIQGEISINEYRNLVRELE 50 (60)
T ss_pred HHHHHHhccCc-ccHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence 35777777555 6789999999987 557888888777777763
No 38
>PRK11173 two-component response regulator; Provisional
Probab=21.14 E-value=1.2e+02 Score=27.28 Aligned_cols=51 Identities=16% Similarity=0.146 Sum_probs=35.8
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHH
Q 017042 167 DDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKKKCV 223 (378)
Q Consensus 167 eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKkKY~ 223 (378)
.=|..||.-|+.+. |..-..+ .+++.|-+. ....+...|.--|+|||+|+.
T Consensus 163 ~~E~~ll~~l~~~~---g~v~sr~--~l~~~vw~~-~~~~~~~~~~~~i~rlR~kl~ 213 (237)
T PRK11173 163 RSEFRAMLHFCENP---GKIQSRA--ELLKKMTGR-ELKPHDRTVDVTIRRIRKHFE 213 (237)
T ss_pred HHHHHHHHHHHhCC---CccCcHH--HHHHHhcCc-CCCCCCccHHHHHHHHHHHhc
Confidence 44777888776653 6555444 788888764 344456788889999999986
No 39
>PRK08055 chorismate mutase; Provisional
Probab=21.03 E-value=1.5e+02 Score=27.83 Aligned_cols=49 Identities=10% Similarity=0.136 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHH
Q 017042 171 IVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLK 219 (378)
Q Consensus 171 ~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLK 219 (378)
.||.+|.+|...+|..-..|+..|...|....-.+.++..|+.-+...|
T Consensus 130 ~il~~ia~~l~~~g~~~~~~~~~f~~~i~~~~ls~~dk~~l~~al~~i~ 178 (181)
T PRK08055 130 QILIQIAQRLKVCGPFSHGDMAWFRSTINQPNLSEADKSAIFAALSQVR 178 (181)
T ss_pred HHHHHHHHHHHhcCCCCcchHHHHHHHHhcccCCHHHHHHHHHHHHHhh
Confidence 4889999998777855567888888877665445666777766655544
No 40
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.29 E-value=3.3e+02 Score=19.35 Aligned_cols=47 Identities=11% Similarity=0.152 Sum_probs=31.6
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCccHHHHHHHHHhccCCCCCHHHHHHHHHHHHH
Q 017042 167 DDEIIVLKRMIEYSTEKGIDPSQDTQAFYDYVKNSLHGDYTKAQLMDKIRRLKK 220 (378)
Q Consensus 167 eDEI~ILqgli~~~~~~G~~P~~D~~af~~~ik~sL~~~~s~~QL~~KvRrLKk 220 (378)
..++.|+-.|+.|....|. .+.....+.+. ..++.+.++.-|..|..
T Consensus 5 ~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~------~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 5 PTAKLVYLYLASYANKNGG-CFPSQETLAKD------LGVSRRTVQRAIKELEE 51 (55)
T ss_pred HHHHHHHHHHHHhcCCCCC-CCcCHHHHHHH------HCcCHHHHHHHHHHHHH
Confidence 3578899999999866665 33333333332 36778888888888865
Done!