Query 036050
Match_columns 393
No_of_seqs 146 out of 173
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:54:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036050.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036050hhsearch_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 8.5E-37 1.8E-41 255.9 11.1 97 163-260 2-98 (98)
2 PF12776 Myb_DNA-bind_3: Myb/S 96.3 0.0047 1E-07 50.3 4.2 63 167-230 1-69 (96)
3 PF13837 Myb_DNA-bind_4: Myb/S 92.5 0.29 6.2E-06 39.2 5.2 66 166-232 2-73 (90)
4 PF07904 Eaf7: Chromatin modif 88.2 0.69 1.5E-05 38.7 4.1 51 171-222 1-56 (91)
5 PF00249 Myb_DNA-binding: Myb- 77.8 4.8 0.0001 29.0 4.4 47 166-223 2-48 (48)
6 PF11081 DUF2890: Protein of u 71.8 59 0.0013 30.9 11.1 13 174-186 126-138 (187)
7 smart00717 SANT SANT SWI3, AD 68.4 9.7 0.00021 25.9 4.0 46 166-223 2-47 (49)
8 PF01726 LexA_DNA_bind: LexA D 60.4 25 0.00054 27.5 5.3 44 173-225 8-53 (65)
9 PF05110 AF-4: AF-4 proto-onco 57.0 13 0.00028 44.0 4.5 13 78-90 446-458 (1191)
10 cd00167 SANT 'SWI3, ADA2, N-Co 54.0 25 0.00054 23.5 3.9 17 167-183 1-17 (45)
11 PF10545 MADF_DNA_bdg: Alcohol 52.8 21 0.00046 27.5 3.9 38 196-233 26-63 (85)
12 PF03546 Treacle: Treacher Col 51.8 30 0.00064 37.4 5.7 33 76-109 88-122 (519)
13 PF00486 Trans_reg_C: Transcri 44.2 68 0.0015 24.3 5.4 53 171-229 8-60 (77)
14 PLN03237 DNA topoisomerase 2; 38.6 1.2E+02 0.0026 37.0 8.6 33 157-192 1350-1382(1465)
15 PF07914 DUF1679: Protein of u 38.0 53 0.0012 34.4 5.1 82 164-253 278-361 (414)
16 PF13921 Myb_DNA-bind_6: Myb-l 37.6 25 0.00055 26.0 2.0 41 168-221 1-41 (60)
17 PF03109 ABC1: ABC1 family; I 32.3 1.1E+02 0.0025 26.1 5.5 59 171-229 52-110 (119)
18 PRK13280 N-glycosylase/DNA lya 31.5 1.5E+02 0.0032 29.8 6.7 77 174-257 51-143 (269)
19 PF11728 DUF939_C: DUF939 C-te 31.0 86 0.0019 28.7 4.8 59 172-230 77-137 (167)
20 PF05432 BSP_II: Bone sialopro 29.2 66 0.0014 32.3 3.8 28 7-34 37-65 (292)
21 PF12186 AcylCoA_dehyd_C: Acyl 26.7 49 0.0011 29.1 2.2 62 196-258 3-66 (114)
22 PF14584 DUF4446: Protein of u 25.2 67 0.0015 29.3 2.9 22 214-237 20-41 (151)
23 PF13404 HTH_AsnC-type: AsnC-t 24.8 1.1E+02 0.0025 21.7 3.5 37 174-223 6-42 (42)
24 KOG4282 Transcription factor G 24.7 5.1E+02 0.011 26.0 9.5 64 165-232 54-122 (345)
25 TIGR01557 myb_SHAQKYF myb-like 22.8 1.3E+02 0.0027 23.1 3.6 19 165-183 3-21 (57)
26 PF09171 DUF1886: Domain of un 20.4 70 0.0015 31.6 2.2 52 174-229 41-107 (246)
27 smart00595 MADF subfamily of S 20.3 1.5E+02 0.0033 23.4 3.8 36 196-233 27-62 (89)
28 PF08031 BBE: Berberine and be 20.1 77 0.0017 23.0 1.8 13 216-228 24-36 (47)
No 1
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=100.00 E-value=8.5e-37 Score=255.94 Aligned_cols=97 Identities=59% Similarity=1.067 Sum_probs=94.8
Q ss_pred ccccCCCchhHHHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhhhcccccCCCCCCC
Q 036050 163 LFQRLWSEDDEIVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENNLGKGKKKGEDRTF 242 (393)
Q Consensus 163 ~fqR~WS~eDEI~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~~~K~~k~G~~p~f 242 (393)
+|||+||++|||+||+|||+|+++||..|..||++||++|+++|+++||++||++||||||+||.+++.|+ ++|.+|.|
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 LFQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKKS-KNGKDPSF 80 (98)
T ss_pred CCcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhhc-ccCcCCCC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999887 89999999
Q ss_pred CChhHHHHHHHHhhhcCC
Q 036050 243 SKPHEQKAYDLSKKFWGG 260 (393)
Q Consensus 243 ~~~HD~~~feLSk~IWG~ 260 (393)
++|||++||+||++|||+
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=96.35 E-value=0.0047 Score=50.31 Aligned_cols=63 Identities=19% Similarity=0.282 Sum_probs=51.5
Q ss_pred CCCchhHHHHHHHHHHHHHhhCCCC-c-----cchHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhhh
Q 036050 167 LWSEDDEIVVLKGMTDYSTKKGLDP-N-----QDMQGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENNL 230 (393)
Q Consensus 167 ~WS~eDEI~IL~gli~~~~~~G~~P-~-----~D~~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~~ 230 (393)
-||++.+-.||..|++.....+. | . ..+......+.......++..||..|++.||++|....
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~-~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~ 69 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNR-PTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWK 69 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCC-CCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHH
Confidence 39999999999999999776554 4 2 24566666666777788999999999999999999875
No 3
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=92.48 E-value=0.29 Score=39.20 Aligned_cols=66 Identities=15% Similarity=0.301 Sum_probs=39.2
Q ss_pred cCCCchhHHHHHHHHHH--HHHh--h-CCCCcc-chHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhhhcc
Q 036050 166 RLWSEDDEIVVLKGMTD--YSTK--K-GLDPNQ-DMQGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENNLGK 232 (393)
Q Consensus 166 R~WS~eDEI~IL~gli~--~~~~--~-G~~P~~-D~~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~~~K 232 (393)
+.|+.+.-..||+.+.. +... . +..... -+....+.+. ...+..|..|+..|+..|+++|......
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~-~~G~~rt~~qc~~Kw~~L~~~Yk~~k~~ 73 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELA-EHGYNRTPEQCRNKWKNLKKKYKKIKDR 73 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHH-HHC----HHHHHHHHHHHHHHHHCSSSS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHH-HcCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 47999988889888888 3331 2 222222 2333333333 2356779999999999999999988644
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=88.24 E-value=0.69 Score=38.65 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=42.5
Q ss_pred hhHHHHHHHHHHHHHhhCCCCccchHHHHHHHHhh-----cccCCCHHHHHHHHHHH
Q 036050 171 DDEIVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNS-----LHVDVSKAQLVDKIRRL 222 (393)
Q Consensus 171 eDEI~IL~gli~~~~~~G~~P~~D~~af~d~ik~s-----l~~~~s~~QL~~KiRrL 222 (393)
++||+||++|+.|+= -|..=+-.|.+..+.|++. +...++..+|-.||++|
T Consensus 1 e~Ei~Lf~a~~~~KP-vGi~KHF~M~~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~ 56 (91)
T PF07904_consen 1 EDEIRLFRAMCRYKP-VGIHKHFHMICIVERLNNPGFDPKLNKHFTIDDIWKKLRTL 56 (91)
T ss_pred ChHHHHHHHHHhcCC-CccchHHHHHHHHHHHhccccCCccCCcCCHHHHHHHHHHh
Confidence 589999999999943 3543334789999999999 89999999999998876
No 5
>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=77.82 E-value=4.8 Score=28.96 Aligned_cols=47 Identities=15% Similarity=0.318 Sum_probs=31.7
Q ss_pred cCCCchhHHHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHHHH
Q 036050 166 RLWSEDDEIVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRRLK 223 (393)
Q Consensus 166 R~WS~eDEI~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRrLK 223 (393)
..||.+++..|++++.-|-.. ++ ..|...+...-|..|+..+.++|+
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~-------~W----~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKD-------NW----KKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTT-------HH----HHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHhCCc-------HH----HHHHHHcCCCCCHHHHHHHHHhhC
Confidence 469999999999999877321 23 444444445678888888777663
No 6
>PF11081 DUF2890: Protein of unknown function (DUF2890); InterPro: IPR021304 This entry contains the 33kDa and 22kDa phosphoproteins from vertebrate adenoviruses.
Probab=71.83 E-value=59 Score=30.89 Aligned_cols=13 Identities=0% Similarity=-0.069 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHh
Q 036050 174 IVVLKGMTDYSTK 186 (393)
Q Consensus 174 I~IL~gli~~~~~ 186 (393)
..||..|.+-...
T Consensus 126 ~~I~~tLyaifqq 138 (187)
T PF11081_consen 126 NRIFPTLYAIFQQ 138 (187)
T ss_pred HHHHHHHHHHHHH
Confidence 4677777544444
No 7
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=68.41 E-value=9.7 Score=25.89 Aligned_cols=46 Identities=15% Similarity=0.357 Sum_probs=28.8
Q ss_pred cCCCchhHHHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHHHH
Q 036050 166 RLWSEDDEIVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRRLK 223 (393)
Q Consensus 166 R~WS~eDEI~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRrLK 223 (393)
..||.+++..|++++..|.. .++.. |...|. .-+..|+..+.+.|.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~-------~~w~~----Ia~~~~-~rt~~~~~~~~~~~~ 47 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK-------NNWEK----IAKELP-GRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc-------CCHHH----HHHHcC-CCCHHHHHHHHHHHc
Confidence 46999999999999887732 33433 333332 346666666555543
No 8
>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=60.37 E-value=25 Score=27.46 Aligned_cols=44 Identities=18% Similarity=0.396 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHhhCCCCcc-chHHHHHHHHhhcccCC-CHHHHHHHHHHHHHH
Q 036050 173 EIVVLKGMTDYSTKKGLDPNQ-DMQGFYDYIKNSLHVDV-SKAQLVDKIRRLKKK 225 (393)
Q Consensus 173 EI~IL~gli~~~~~~G~~P~~-D~~af~d~ik~sl~~~~-s~~QL~~KiRrLKkK 225 (393)
.-.||.-|.+|..++|..|.. ++... +.+ |.+-+..-|+.|.+|
T Consensus 8 Q~~vL~~I~~~~~~~G~~Pt~rEIa~~---------~g~~S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGYPPTVREIAEA---------LGLKSTSTVQRHLKALERK 53 (65)
T ss_dssp HHHHHHHHHHHHHHHSS---HHHHHHH---------HTSSSHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHH---------hCCCChHHHHHHHHHHHHC
Confidence 457999999999999998873 44433 333 588888889999865
No 9
>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=57.04 E-value=13 Score=44.02 Aligned_cols=13 Identities=69% Similarity=0.593 Sum_probs=5.0
Q ss_pred CCCCCCCCCCCCC
Q 036050 78 SLSSGESESESES 90 (393)
Q Consensus 78 s~s~~e~~s~s~s 90 (393)
|+|+|++||||||
T Consensus 446 SESsS~SDSESES 458 (1191)
T PF05110_consen 446 SESSSSSDSESES 458 (1191)
T ss_pred CCccCcccccccc
Confidence 3333344444433
No 10
>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=53.95 E-value=25 Score=23.45 Aligned_cols=17 Identities=24% Similarity=0.817 Sum_probs=15.1
Q ss_pred CCCchhHHHHHHHHHHH
Q 036050 167 LWSEDDEIVVLKGMTDY 183 (393)
Q Consensus 167 ~WS~eDEI~IL~gli~~ 183 (393)
.||.+++..|++++..|
T Consensus 1 ~Wt~eE~~~l~~~~~~~ 17 (45)
T cd00167 1 PWTEEEDELLLEAVKKY 17 (45)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 39999999999999877
No 11
>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=52.82 E-value=21 Score=27.49 Aligned_cols=38 Identities=16% Similarity=0.258 Sum_probs=33.2
Q ss_pred HHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhhhccc
Q 036050 196 QGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENNLGKG 233 (393)
Q Consensus 196 ~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~~~K~ 233 (393)
..++..|...|...++..++..+++.||.+|.....+.
T Consensus 26 ~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~~ 63 (85)
T PF10545_consen 26 EEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKKI 63 (85)
T ss_pred HHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 56778888888888999999999999999999988664
No 12
>PF03546 Treacle: Treacher Collins syndrome protein Treacle; InterPro: IPR003993 Treacher Collins Syndrome (TCS) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate [, ]; it is the most common of the human mandibulo-facial dysostosis disorders []. The TCS locus has been mapped to human chromosome 5q31.3-32 and the mutated gene identified (TCOF1) []. To date, 35 mutations have been reported in TCOF1, all but one of which result in the introduction of a premature-termination codon into the predicted protein, Treacle. The observed mutational spectrum supports the hypothesis that TCS results from haploinsufficiency. Treacle is a low complexity protein of 1,411 amino acids whose predicted protein structure contains a set of highly polar repeated motifs []. These motifs are common to nucleolar trafficking proteins in other species and are predicted to be phosphorylated by casein kinase. In concert with this observation, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localisation signals []. Throughout the open reading frame are found mutations in TCS families and several polymorphisms. It has thus been suggested that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.
Probab=51.80 E-value=30 Score=37.39 Aligned_cols=33 Identities=33% Similarity=0.390 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC--CCcccCCCCCC
Q 036050 76 TKSLSSGESESESESESEPDATP--KPIATKPMEET 109 (393)
Q Consensus 76 s~s~s~~e~~s~s~s~~~p~~~~--kpi~~kp~~~~ 109 (393)
.++.|. +.+|||+.+.+-..++ .|.-.||+..+
T Consensus 88 ~~s~SS-seeSds~~etpaa~~~t~s~aqvKPsgk~ 122 (519)
T PF03546_consen 88 EDSESS-SEESDSEGETPAAQPLTRSPAQVKPSGKN 122 (519)
T ss_pred cccccc-cccccccccCccccccccccccccccccC
Confidence 444443 3366666666654333 45556666554
No 13
>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=44.15 E-value=68 Score=24.29 Aligned_cols=53 Identities=25% Similarity=0.277 Sum_probs=38.6
Q ss_pred hhHHHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhh
Q 036050 171 DDEIVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENN 229 (393)
Q Consensus 171 eDEI~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~ 229 (393)
.-|..||..|+.+. |. ......+++.|-+.-. ..+.+.|..-|.|||+|+...
T Consensus 8 ~~e~~lL~~L~~~~---~~--~vs~~~l~~~~w~~~~-~~~~~~l~~~I~rLR~kL~~~ 60 (77)
T PF00486_consen 8 PKEFRLLELLLRNP---GR--VVSREELIEALWGDEE-DVSDNSLDVHISRLRKKLEDA 60 (77)
T ss_dssp HHHHHHHHHHHHTT---TS--EEEHHHHHHHHTSSSS-TTCTHHHHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHhCC---CC--CCCHHHhCChhhhccc-ccchhhHHHHHHHHHHHHhhc
Confidence 35788999998772 22 1244556666666433 689999999999999999975
No 14
>PLN03237 DNA topoisomerase 2; Provisional
Probab=38.58 E-value=1.2e+02 Score=37.04 Aligned_cols=33 Identities=21% Similarity=0.243 Sum_probs=19.7
Q ss_pred ccccccccccCCCchhHHHHHHHHHHHHHhhCCCCc
Q 036050 157 EDTKKQLFQRLWSEDDEIVVLKGMTDYSTKKGLDPN 192 (393)
Q Consensus 157 ~~~kk~~fqR~WS~eDEI~IL~gli~~~~~~G~~P~ 192 (393)
--+||+..+..=+..+ +|-.|+.=....|..|-
T Consensus 1350 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~p~ 1382 (1465)
T PLN03237 1350 AAAKKRGPATVQSGQK---LLTEMLKPAEAIGISPE 1382 (1465)
T ss_pred ccccCCCcccCCCcch---hHHHHhchhhcCCCCCc
Confidence 3445555555545444 67777766666777665
No 15
>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=38.04 E-value=53 Score=34.41 Aligned_cols=82 Identities=17% Similarity=0.332 Sum_probs=53.6
Q ss_pred cccCCCchhH-HHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhhhcccccCC-CCCC
Q 036050 164 FQRLWSEDDE-IVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENNLGKGKKKG-EDRT 241 (393)
Q Consensus 164 fqR~WS~eDE-I~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~~~K~~k~G-~~p~ 241 (393)
..=+|+.+++ -.-|.+||||..-|-.+|..|+.-++ ...+|...=...-.+|=..|.....+....| ..|
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-------VSCLSGEDRREHTEELLEYYYDTFTEALEDGGKAP- 349 (414)
T ss_pred HheeeecCCchhHHHHHHHHHHHhhcCchHHHHHHHH-------HhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCC-
Confidence 3557888666 67899999999999889988876543 3455555555566666666665544432334 444
Q ss_pred CCChhHHHHHHH
Q 036050 242 FSKPHEQKAYDL 253 (393)
Q Consensus 242 f~~~HD~~~feL 253 (393)
|+-..=+.+|+|
T Consensus 350 fT~eqL~~sY~l 361 (414)
T PF07914_consen 350 FTLEQLKDSYRL 361 (414)
T ss_pred ccHHHHHHHHHH
Confidence 665555566665
No 16
>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=37.60 E-value=25 Score=26.01 Aligned_cols=41 Identities=20% Similarity=0.443 Sum_probs=23.7
Q ss_pred CCchhHHHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHH
Q 036050 168 WSEDDEIVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRR 221 (393)
Q Consensus 168 WS~eDEI~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRr 221 (393)
||.++...|++++..| |. ++.....+ |. .-|..|+..+.++
T Consensus 1 WT~eEd~~L~~~~~~~----g~----~W~~Ia~~----l~-~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKY----GN----DWKKIAEH----LG-NRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHH----TS-----HHHHHHH----ST-TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHH----Cc----CHHHHHHH----HC-cCCHHHHHHHHHH
Confidence 8998888888887777 42 44433333 31 3566676666655
No 17
>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=32.33 E-value=1.1e+02 Score=26.13 Aligned_cols=59 Identities=14% Similarity=0.291 Sum_probs=48.6
Q ss_pred hhHHHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhh
Q 036050 171 DDEIVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENN 229 (393)
Q Consensus 171 eDEI~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~ 229 (393)
..++.||+.++.+....+.....++..+++.++..|...++-..=..-++++++.|...
T Consensus 52 ~~Dl~~l~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~ElDf~~Ea~n~~~~~~~~~~~ 110 (119)
T PF03109_consen 52 EADLRILRRLARLLERLPPFRRLDLEEIVDEFRDSLLEELDFRREAANLERFRKNFADS 110 (119)
T ss_pred HHHHHHHHHHHHHHHHcccccccCHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHhCCC
Confidence 46789999999887766655456899999999999988888888888899998888754
No 18
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=31.48 E-value=1.5e+02 Score=29.80 Aligned_cols=77 Identities=22% Similarity=0.357 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHh-hCCCC------------ccc-hHHHHHHHHhhcccCCCHHHHHHHHHHHHHH--HHhhhcccccCC
Q 036050 174 IVVLKGMTDYSTK-KGLDP------------NQD-MQGFYDYIKNSLHVDVSKAQLVDKIRRLKKK--FENNLGKGKKKG 237 (393)
Q Consensus 174 I~IL~gli~~~~~-~G~~P------------~~D-~~af~d~ik~sl~~~~s~~QL~~KiRrLKkK--Y~~~~~K~~k~G 237 (393)
++|++||++|+-. +|-.. ..| ..+|+.||.. ...++.=+--|||||++= |...+.-. ..+
T Consensus 51 Lvi~NaLvSYqLsgkGEe~W~eFs~yf~~~~~~~~~~~~~~Fl~~---s~~nrrl~e~KikRi~r~~~fl~~L~l~-~~~ 126 (269)
T PRK13280 51 LVIANALVSYQLSGKGEEWWWEFSKYFSEKGVEDIVEAYIEFLKN---SKGNRRLLEQKIKRIEKVEPFLESLTLL-DLP 126 (269)
T ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHhcccCchhHHHHHHHHHhc---CchhHHHHHHHHHHHHHHHHHhhhhccc-hhh
Confidence 7889999999763 22211 012 2455555555 467788888999999988 77666321 111
Q ss_pred CCCCCCChhHHHHHHHHhhh
Q 036050 238 EDRTFSKPHEQKAYDLSKKF 257 (393)
Q Consensus 238 ~~p~f~~~HD~~~feLSk~I 257 (393)
.-+ ..-+.-...||+.+
T Consensus 127 --~~y-~~l~~l~~~La~~L 143 (269)
T PRK13280 127 --LYY-EDLEELLEQLAKIL 143 (269)
T ss_pred --hhH-hhHHHHHHHHHHHh
Confidence 112 33445555666644
No 19
>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=31.02 E-value=86 Score=28.75 Aligned_cols=59 Identities=22% Similarity=0.393 Sum_probs=43.2
Q ss_pred hHHHHHHHHHHHHHhhCCCCc-c-chHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhhh
Q 036050 172 DEIVVLKGMTDYSTKKGLDPN-Q-DMQGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENNL 230 (393)
Q Consensus 172 DEI~IL~gli~~~~~~G~~P~-~-D~~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~~ 230 (393)
..+.||+.|..+..+=-..|. . .++.|+..+...++..-+...+.++|..|+..|+..-
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 457899999999765443443 2 5688999999999999999999999999999999764
No 20
>PF05432 BSP_II: Bone sialoprotein II (BSP-II); InterPro: IPR008412 The major non-collagenous matrix proteins (chondroitin-sulphate glycoproteins decorin and biglycan, sialoproteins osteopontin and bone sialoprotein, osteocalcin and osteonectin) have important roles in formation and organisation of the collagen matrix and nucleation and growth of hydroxyapatite crystals. Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully differentiated osteoblasts [], [] and is highly specific for mineralising tissues. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth; it is thought to be responsible for nucleation of hydroxyapatite crystals. BSP also displays a high affinity for calcium ions. The mature protein has a molecular weight of around 33 kDa and consists predominantly of Glu and Gly residues. It is subject to extensive posttranslational modification, and is predominantly phosphorylated at Ser residues. Posttranslational modifications can also cause BSP to act as an inhibitor of hydroxyapatite crystal formation. Ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone []. This entry represents the bone sialoprotein II group of proteins.; GO: 0001503 ossification, 0007155 cell adhesion, 0005576 extracellular region
Probab=29.23 E-value=66 Score=32.29 Aligned_cols=28 Identities=32% Similarity=0.469 Sum_probs=13.7
Q ss_pred CCCCCCCCCCCccc-ccccCCCCCccccc
Q 036050 7 NPMEEPPAASSSEE-VEEDDDSSGSEEVS 34 (393)
Q Consensus 7 ~~~~~pp~~sss~e-~~e~~~ss~eee~~ 34 (393)
+||.--|+.++||- +|..|.+|+||+++
T Consensus 37 PPlKR~~vq~~sDSSEEngdgdssEeEee 65 (292)
T PF05432_consen 37 PPLKRFPVQSNSDSSEENGDGDSSEEEEE 65 (292)
T ss_pred ChhhhccccCCCCcccccCCCcccccccc
Confidence 45555555555542 22234555555544
No 21
>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=26.73 E-value=49 Score=29.09 Aligned_cols=62 Identities=15% Similarity=0.373 Sum_probs=44.0
Q ss_pred HHHHHHHHhhcccCCC--HHHHHHHHHHHHHHHHhhhcccccCCCCCCCCChhHHHHHHHHhhhc
Q 036050 196 QGFYDYIKNSLHVDVS--KAQLVDKIRRLKKKFENNLGKGKKKGEDRTFSKPHEQKAYDLSKKFW 258 (393)
Q Consensus 196 ~af~d~ik~sl~~~~s--~~QL~~KiRrLKkKY~~~~~K~~k~G~~p~f~~~HD~~~feLSk~IW 258 (393)
+.+...|+..+..+++ ..-|.++|+.|..+|...+.+. +.-.+..+..=|=|+||+..-.|-
T Consensus 3 GtYl~~i~E~~~~~~~~el~~l~~rl~~m~~~yeeav~~V-ke~~nqe~~Df~ARRLvEMa~~ii 66 (114)
T PF12186_consen 3 GTYLAIIREYEQAEVSPELQPLKERLKKMTEKYEEAVAKV-KEAKNQELQDFHARRLVEMAAHII 66 (114)
T ss_dssp THHHHHHHTGGGS---GGGHHHHHHHHHHHHHHHHHHHHH-HTT--HHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHHHH-HhhcChHHHHHHHHHHHHHHHHHH
Confidence 3466778887776664 5689999999999999999887 433444556667788998887764
No 22
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=25.15 E-value=67 Score=29.31 Aligned_cols=22 Identities=36% Similarity=0.742 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHhhhcccccCC
Q 036050 214 QLVDKIRRLKKKFENNLGKGKKKG 237 (393)
Q Consensus 214 QL~~KiRrLKkKY~~~~~K~~k~G 237 (393)
-+.-|++||++||.... ++ ..|
T Consensus 20 ~~~~kl~kl~r~Y~~lm-~g-~~~ 41 (151)
T PF14584_consen 20 ILNIKLRKLKRRYDALM-RG-KDG 41 (151)
T ss_pred HHHHHHHHHHHHHHHHh-CC-CCc
Confidence 46789999999999997 55 455
No 23
>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=24.84 E-value=1.1e+02 Score=21.70 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHhhCCCCccchHHHHHHHHhhcccCCCHHHHHHHHHHHH
Q 036050 174 IVVLKGMTDYSTKKGLDPNQDMQGFYDYIKNSLHVDVSKAQLVDKIRRLK 223 (393)
Q Consensus 174 I~IL~gli~~~~~~G~~P~~D~~af~d~ik~sl~~~~s~~QL~~KiRrLK 223 (393)
..||+.|- ..|..|+..++.- .++|...+...|++|+
T Consensus 6 ~~Il~~Lq----~d~r~s~~~la~~---------lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 6 RKILRLLQ----EDGRRSYAELAEE---------LGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHH----H-TTS-HHHHHHH---------HTS-HHHHHHHHHHHH
T ss_pred HHHHHHHH----HcCCccHHHHHHH---------HCcCHHHHHHHHHHhC
Confidence 45555554 4477777666533 6789999999999986
No 24
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=24.72 E-value=5.1e+02 Score=26.03 Aligned_cols=64 Identities=22% Similarity=0.367 Sum_probs=43.1
Q ss_pred ccCCCchhHHHHHHHHHH--HHHhhCCCCccchHHHHHHHHh---hcccCCCHHHHHHHHHHHHHHHHhhhcc
Q 036050 165 QRLWSEDDEIVVLKGMTD--YSTKKGLDPNQDMQGFYDYIKN---SLHVDVSKAQLVDKIRRLKKKFENNLGK 232 (393)
Q Consensus 165 qR~WS~eDEI~IL~gli~--~~~~~G~~P~~D~~af~d~ik~---sl~~~~s~~QL~~KiRrLKkKY~~~~~K 232 (393)
.+.|+.+.=+.||+..-+ +.-..|++=. .+|+.|-. ...+.-|-.|+..||..|++||+....+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~----~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~ 122 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKG----PLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAK 122 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcc----cHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 678999888888866543 2223443322 23344433 2357779999999999999999998654
No 25
>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=22.83 E-value=1.3e+02 Score=23.08 Aligned_cols=19 Identities=21% Similarity=0.424 Sum_probs=17.1
Q ss_pred ccCCCchhHHHHHHHHHHH
Q 036050 165 QRLWSEDDEIVVLKGMTDY 183 (393)
Q Consensus 165 qR~WS~eDEI~IL~gli~~ 183 (393)
...||++....+|+||-.|
T Consensus 3 r~~WT~eeh~~Fl~ai~~~ 21 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKL 21 (57)
T ss_pred CCCCCHHHHHHHHHHHHHh
Confidence 3569999999999999988
No 26
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=20.37 E-value=70 Score=31.61 Aligned_cols=52 Identities=25% Similarity=0.514 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhhCC--C------------Cccch-HHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhh
Q 036050 174 IVVLKGMTDYSTKKGL--D------------PNQDM-QGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENN 229 (393)
Q Consensus 174 I~IL~gli~~~~~~G~--~------------P~~D~-~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~ 229 (393)
++|++||++|+-. |+ . +..|+ .+|+.||.. +..++.=+--||+||++=+.-.
T Consensus 41 Lvi~NaLvSYqLs-~kGEe~W~~Fs~yfs~~~~~~~~~~~~~FL~~---s~~n~r~~~~KikRl~k~~~~~ 107 (246)
T PF09171_consen 41 LVIANALVSYQLS-GKGEEYWWEFSEYFSKRPIEDICEAFIEFLSN---SKYNRRLLEQKIKRLRKFCPFL 107 (246)
T ss_dssp HHHHHHHT-SS-T-T-HHHHHHHHHHHHCTS--SSHHHHHHHHCCC----TTS-TTHHHHHHHHHHHCCHH
T ss_pred HHHHHHHHHHhcC-CchHHHHHHHHHHHhcCCchhHHHHHHHHHhh---CcchHHHHHHHHHHHHHHHHHH
Confidence 6789999999653 32 1 11122 334444433 4567777888999998766544
No 27
>smart00595 MADF subfamily of SANT domain.
Probab=20.31 E-value=1.5e+02 Score=23.38 Aligned_cols=36 Identities=14% Similarity=0.302 Sum_probs=28.8
Q ss_pred HHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhhhccc
Q 036050 196 QGFYDYIKNSLHVDVSKAQLVDKIRRLKKKFENNLGKG 233 (393)
Q Consensus 196 ~af~d~ik~sl~~~~s~~QL~~KiRrLKkKY~~~~~K~ 233 (393)
..++..|-..|.. +..++..|++.||.+|.....|+
T Consensus 27 ~~aW~~Ia~~l~~--~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 27 RKAWEEIAEELGL--SVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHHHHHCc--CHHHHHHHHHHHHHHHHHHHHHH
Confidence 4466777666554 99999999999999999987654
No 28
>PF08031 BBE: Berberine and berberine like ; InterPro: IPR012951 This domain is found in the berberine bridge and berberine bridge-like enzymes, which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyse the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine [].; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 2IPI_A 2Y3S_A 2Y3R_D 2Y08_B 2Y4G_A 3D2H_A 3FW9_A 3FW8_A 3FWA_A 3D2J_A ....
Probab=20.13 E-value=77 Score=22.99 Aligned_cols=13 Identities=31% Similarity=0.820 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHh
Q 036050 216 VDKIRRLKKKFEN 228 (393)
Q Consensus 216 ~~KiRrLKkKY~~ 228 (393)
+++|++||+||.=
T Consensus 24 ~~rL~~iK~~yDP 36 (47)
T PF08031_consen 24 YDRLRAIKRKYDP 36 (47)
T ss_dssp HHHHHHHHHHH-T
T ss_pred HHHHHHHHHHhCc
Confidence 8999999999974
Done!