Query 033730
Match_columns 112
No_of_seqs 102 out of 122
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 05:38:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033730.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033730hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07904 Eaf7: Chromatin modif 100.0 1.2E-38 2.7E-43 220.9 6.8 82 25-109 1-91 (91)
2 KOG4051 Uncharacterized conser 99.9 6.3E-24 1.4E-28 167.0 5.0 85 21-109 34-119 (214)
3 PF04504 DUF573: Protein of un 96.7 0.0029 6.3E-08 44.3 4.3 66 18-85 3-71 (98)
4 PF06374 NDUF_C2: NADH-ubiquin 80.2 1.9 4.1E-05 31.7 2.8 32 27-58 37-68 (117)
5 smart00426 TEA TEA domain. 72.4 6.3 0.00014 26.6 3.5 52 20-74 4-64 (68)
6 PF13592 HTH_33: Winged helix- 69.1 5.1 0.00011 25.1 2.4 27 52-78 8-34 (60)
7 cd07977 TFIIE_beta_winged_heli 69.0 9.2 0.0002 25.5 3.7 34 44-77 4-37 (75)
8 PF02186 TFIIE_beta: TFIIE bet 64.2 10 0.00022 24.8 3.2 29 50-81 6-34 (65)
9 PF12776 Myb_DNA-bind_3: Myb/S 58.4 48 0.001 21.5 6.5 59 22-80 2-66 (96)
10 PF01285 TEA: TEA/ATTS domain 56.7 32 0.0007 30.0 5.8 54 20-77 50-111 (431)
11 cd07153 Fur_like Ferric uptake 50.1 26 0.00056 23.6 3.4 39 46-85 14-52 (116)
12 PF13551 HTH_29: Winged helix- 48.1 75 0.0016 20.6 5.7 52 22-77 58-110 (112)
13 PF01475 FUR: Ferric uptake re 47.0 20 0.00044 24.5 2.5 23 53-76 12-34 (120)
14 PF14244 UBN2_3: gag-polypepti 46.3 14 0.00031 26.5 1.7 30 53-82 69-98 (152)
15 PF12921 ATP13: Mitochondrial 44.4 39 0.00084 24.3 3.7 43 28-76 52-95 (126)
16 TIGR01157 pufL photosynthetic 43.5 17 0.00036 29.8 1.9 49 13-62 163-213 (239)
17 PF14223 UBN2: gag-polypeptide 42.8 15 0.00032 24.9 1.3 17 67-83 2-18 (119)
18 PRK09462 fur ferric uptake reg 41.3 43 0.00092 24.0 3.6 37 48-85 33-69 (148)
19 PF00249 Myb_DNA-binding: Myb- 40.6 37 0.0008 19.8 2.7 22 19-40 1-22 (48)
20 PF13565 HTH_32: Homeodomain-l 39.7 86 0.0019 19.4 4.5 44 23-75 32-77 (77)
21 PF14227 UBN2_2: gag-polypepti 39.1 20 0.00043 24.3 1.5 19 66-84 2-20 (119)
22 PF08914 Myb_DNA-bind_2: Rap1 35.7 76 0.0017 20.6 3.8 35 23-79 6-40 (65)
23 smart00515 eIF5C Domain at the 32.3 1.2E+02 0.0026 19.7 4.4 20 67-86 31-50 (83)
24 smart00430 HOLI Ligand binding 28.8 1.6E+02 0.0034 19.8 4.6 18 23-40 94-111 (163)
25 PF07106 TBPIP: Tat binding pr 28.2 77 0.0017 23.3 3.2 28 52-80 4-31 (169)
26 PRK14506 photosynthetic reacti 27.7 42 0.00092 28.1 1.9 48 13-61 197-246 (276)
27 PRK11639 zinc uptake transcrip 27.6 91 0.002 23.2 3.5 38 47-85 40-77 (169)
28 smart00550 Zalpha Z-DNA-bindin 26.7 76 0.0017 20.2 2.6 22 54-75 11-32 (68)
29 KOG4545 Uncharacterized conser 25.7 62 0.0013 25.8 2.4 28 54-81 9-36 (197)
30 TIGR01557 myb_SHAQKYF myb-like 25.1 80 0.0017 20.0 2.5 54 18-80 2-55 (57)
31 KOG0457 Histone acetyltransfer 22.9 1.3E+02 0.0027 26.9 4.0 47 2-48 52-101 (438)
32 cd06843 PLPDE_III_PvsE_like Ty 22.7 1.4E+02 0.003 24.3 4.0 32 19-50 143-174 (377)
33 PF07818 HCNGP: HCNGP-like pro 22.7 2.7E+02 0.0059 19.3 6.4 43 63-109 37-79 (96)
34 PF11793 FANCL_C: FANCL C-term 22.1 21 0.00046 23.2 -0.7 18 44-61 27-44 (70)
35 PF01282 Ribosomal_S24e: Ribos 22.1 66 0.0014 21.8 1.7 18 64-81 11-28 (84)
36 COG3433 Aryl carrier domain [S 21.8 1.1E+02 0.0023 21.1 2.7 37 28-77 32-68 (74)
37 COG3697 CitX Phosphoribosyl-de 20.9 48 0.001 26.3 0.9 26 75-104 116-141 (182)
38 PF13797 Post_transc_reg: Post 20.1 1.4E+02 0.0029 20.5 3.0 17 63-79 25-41 (87)
No 1
>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=100.00 E-value=1.2e-38 Score=220.91 Aligned_cols=82 Identities=34% Similarity=0.691 Sum_probs=77.7
Q ss_pred HHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhh-----cCCCCChHHHHHHHHhhcCccCCCCCccccccCCCCC-
Q 033730 25 ELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRR-----FDRHFAPDEVLQLLDRFYNLDMLKPDDEEMEILNHEE- 98 (112)
Q Consensus 25 e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~-----~~r~~~~~~IW~kL~t~YnL~~Lde~~E~~~~~~~e~- 98 (112)
|+|++||+||++|||| ||||||||+||+++|++. ++++||+++||+||+|+|||++||+.++..++++.+.
T Consensus 1 e~Ei~Lf~a~~~~KPv---Gi~KHF~M~~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~YdL~~lde~E~~~~~~~~~~~ 77 (91)
T PF07904_consen 1 EDEIRLFRAMCRYKPV---GIHKHFHMICIVERLNNPGFDPKLNKHFTIDDIWKKLRTLYDLEALDELEDEIPFPNSEDT 77 (91)
T ss_pred ChHHHHHHHHHhcCCC---ccchHHHHHHHHHHHhccccCCccCCcCCHHHHHHHHHHhcCHHHhcccccccCCcccccc
Confidence 5899999999999999 999999999999999999 9999999999999999999999998555789998877
Q ss_pred ---CccCChhhhcc
Q 033730 99 ---DFCLPQSYFDK 109 (112)
Q Consensus 99 ---dF~LP~~e~~~ 109 (112)
||+||+++||+
T Consensus 78 ~~~eF~LP~~~~ge 91 (91)
T PF07904_consen 78 QYREFSLPEDEYGE 91 (91)
T ss_pred CCCCCcCCHHHhcc
Confidence 99999999985
No 2
>KOG4051 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.89 E-value=6.3e-24 Score=167.01 Aligned_cols=85 Identities=28% Similarity=0.371 Sum_probs=80.8
Q ss_pred cccHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhhcCCCCChHHHHHHHHhhcCccCCCCCccccccCCCCCC-
Q 033730 21 QSQVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRRFDRHFAPDEVLQLLDRFYNLDMLKPDDEEMEILNHEED- 99 (112)
Q Consensus 21 ~~~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t~YnL~~Lde~~E~~~~~~~e~d- 99 (112)
.|.+..|++||.||+++||| |||||||||||+++|++.++|.+++++||++|+|+|+|.+|++ .|..+|++.+++
T Consensus 34 ~Ws~~eE~~L~~ai~g~kPv---GiNkhF~mi~I~~~~~k~~~re~pse~iwn~lnt~y~~~e~~e-lE~~~~pe~e~~p 109 (214)
T KOG4051|consen 34 FWSPLEELGLLHAICGLKPV---GINKHFHMIGIMNEKSKTIPRESPSEDIWNHLNTMYKLKELKE-LELPGFPEEERDP 109 (214)
T ss_pred cccHHHHHHHHHHHHccCCC---CcccchhhhhhHHHHhhcccccchHHHHHHhhhHHHHHHHHHH-HhcCCCCccccCc
Confidence 47899999999999999999 9999999999999999999999999999999999999999995 888999999988
Q ss_pred ccCChhhhcc
Q 033730 100 FCLPQSYFDK 109 (112)
Q Consensus 100 F~LP~~e~~~ 109 (112)
|.||...+++
T Consensus 110 ~~l~~~~ik~ 119 (214)
T KOG4051|consen 110 KDLPEPDIKE 119 (214)
T ss_pred cccccccHHH
Confidence 9999887764
No 3
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=96.70 E-value=0.0029 Score=44.25 Aligned_cols=66 Identities=14% Similarity=0.212 Sum_probs=53.2
Q ss_pred CcccccHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhhcCCCCChHHHHHHHHhh---cCccCCC
Q 033730 18 PKEQSQVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRRFDRHFAPDEVLQLLDRF---YNLDMLK 85 (112)
Q Consensus 18 ~k~~~~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t~---YnL~~Ld 85 (112)
...+|+.|+|+.||+||+.|+=. .|..-+=.|-++.++++..+..+++..++-+|++++ |+..+..
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~--~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k 71 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAK--TGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK 71 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHh--cCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh
Confidence 34689999999999999999533 466555589999999999999999999999998775 5554444
No 4
>PF06374 NDUF_C2: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2); InterPro: IPR009423 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006120 mitochondrial electron transport, NADH to ubiquinone, 0005743 mitochondrial inner membrane
Probab=80.24 E-value=1.9 Score=31.66 Aligned_cols=32 Identities=28% Similarity=0.313 Sum_probs=25.3
Q ss_pred HHHHHHHHhhCCCCCCCCchhHHHHHHHHHHH
Q 033730 27 ELRLLEALEVYPPVKLRGIHRHFVLYGLMEFL 58 (112)
Q Consensus 27 E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l 58 (112)
=+.|+...+..||+-..|||||+-.++|--.+
T Consensus 37 ~~~ll~N~~~rRP~~~sGihr~ll~~t~g~~~ 68 (117)
T PF06374_consen 37 CTALLDNAINRRPPLKSGIHRQLLLATIGWFI 68 (117)
T ss_pred HHHHHHHHHhcCCchhhccHHHHHHHHHHHHH
Confidence 35678888999999669999998877765444
No 5
>smart00426 TEA TEA domain.
Probab=72.43 E-value=6.3 Score=26.60 Aligned_cols=52 Identities=21% Similarity=0.370 Sum_probs=38.8
Q ss_pred ccccHHHHHHHHHHHhhCCCCCCCCchh-----HHHHH----HHHHHHHhhcCCCCChHHHHHH
Q 033730 20 EQSQVELELRLLEALEVYPPVKLRGIHR-----HFVLY----GLMEFLRRRFDRHFAPDEVLQL 74 (112)
Q Consensus 20 ~~~~~e~E~~Lf~a~~~~kPv~~~GihK-----HF~M~----~I~e~l~~~~~r~~~~~~IW~k 74 (112)
..|.++.|.++..|+..+.|- |-.| +..|. -|++++-..+|+.=+-+.|=.|
T Consensus 4 ~vWp~~lE~Af~~aL~~~~~~---g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsSh 64 (68)
T smart00426 4 GVWSPDIEQAFQEALAIYPPC---GRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSH 64 (68)
T ss_pred CcCcHHHHHHHHHHHHHcCcc---CcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcch
Confidence 468899999999999999999 7764 44443 4888888877766555555333
No 6
>PF13592 HTH_33: Winged helix-turn helix
Probab=69.06 E-value=5.1 Score=25.07 Aligned_cols=27 Identities=22% Similarity=0.588 Sum_probs=24.0
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHhh
Q 033730 52 YGLMEFLRRRFDRHFAPDEVLQLLDRF 78 (112)
Q Consensus 52 ~~I~e~l~~~~~r~~~~~~IW~kL~t~ 78 (112)
--|+.++.+.+|..++...||+.|.++
T Consensus 8 ~~i~~~I~~~fgv~ys~~~v~~lL~r~ 34 (60)
T PF13592_consen 8 KEIAAYIEEEFGVKYSPSGVYRLLKRL 34 (60)
T ss_pred HHHHHHHHHHHCCEEcHHHHHHHHHHc
Confidence 358889999999999999999999874
No 7
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=69.05 E-value=9.2 Score=25.54 Aligned_cols=34 Identities=24% Similarity=0.503 Sum_probs=30.7
Q ss_pred CchhHHHHHHHHHHHHhhcCCCCChHHHHHHHHh
Q 033730 44 GIHRHFVLYGLMEFLRRRFDRHFAPDEVLQLLDR 77 (112)
Q Consensus 44 GihKHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t 77 (112)
|-|+=-+|.-|.++|+++-+..++.++|-++|+.
T Consensus 4 g~~~~t~l~~aV~ymK~r~~~Plt~~EIl~~ls~ 37 (75)
T cd07977 4 GTHVFTQLAKIVDYMKKRHQHPLTLDEILDYLSL 37 (75)
T ss_pred CcchhhhHHHHHHHHHhcCCCCccHHHHHHHHhc
Confidence 7888889999999999886588999999999995
No 8
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=64.22 E-value=10 Score=24.78 Aligned_cols=29 Identities=24% Similarity=0.570 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhhcCCCCChHHHHHHHHhhcCc
Q 033730 50 VLYGLMEFLRRRFDRHFAPDEVLQLLDRFYNL 81 (112)
Q Consensus 50 ~M~~I~e~l~~~~~r~~~~~~IW~kL~t~YnL 81 (112)
+|.-|.|+|+++ +..+++++|-+.|+ .|+
T Consensus 6 ql~~~VeymK~r-~~Plt~~eI~d~l~--~d~ 34 (65)
T PF02186_consen 6 QLAKAVEYMKKR-DHPLTLEEILDYLS--LDI 34 (65)
T ss_dssp HHHHHHHHHHHH--S-B-HHHHHHHHT--SSS
T ss_pred HHHHHHHHHHhc-CCCcCHHHHHHHHc--CCC
Confidence 577899999988 89999999999988 554
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=58.42 E-value=48 Score=21.46 Aligned_cols=59 Identities=14% Similarity=0.111 Sum_probs=38.5
Q ss_pred ccHHHHHHHHHHHhhC--CCCCC-CCchhHHHHHHHHHHHHhhcCCCCChHHH---HHHHHhhcC
Q 033730 22 SQVELELRLLEALEVY--PPVKL-RGIHRHFVLYGLMEFLRRRFDRHFAPDEV---LQLLDRFYN 80 (112)
Q Consensus 22 ~~~e~E~~Lf~a~~~~--kPv~~-~GihKHF~M~~I~e~l~~~~~r~~~~~~I---W~kL~t~Yn 80 (112)
||++.+..|+..++.. +.-.. .|.-+=-..-.|++.|+..+|..++.+.| |+.|.+.|.
T Consensus 2 Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~ 66 (96)
T PF12776_consen 2 WTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYR 66 (96)
T ss_pred CChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHH
Confidence 6788888888888544 22210 14434444456889999999999988766 455555554
No 10
>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=56.67 E-value=32 Score=29.98 Aligned_cols=54 Identities=19% Similarity=0.370 Sum_probs=32.3
Q ss_pred ccccHHHHHHHHHHHhhCCCCCCCCchhHHHHH----H----HHHHHHhhcCCCCChHHHHHHHHh
Q 033730 20 EQSQVELELRLLEALEVYPPVKLRGIHRHFVLY----G----LMEFLRRRFDRHFAPDEVLQLLDR 77 (112)
Q Consensus 20 ~~~~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~----~----I~e~l~~~~~r~~~~~~IW~kL~t 77 (112)
..|.++.|.++.+|+..|.|- |-.| ..+- + |++++...+|+.=+-+.|=-|+.-
T Consensus 50 ~vw~~~~e~af~~al~~~~~~---g~~k-~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqv 111 (431)
T PF01285_consen 50 GVWPPDIEQAFQEALAIYPPC---GRRK-LSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQV 111 (431)
T ss_dssp --S-HHHHHHHHHHHHHS-SS---S----HHHH-----THHHHHHHHHHHHS----SHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhCCCC---CCcc-cccccccccchhHHHHHHHHHhCcccchhHHHHHHHH
Confidence 588999999999999999999 8888 5533 2 888888877776555554444433
No 11
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=50.08 E-value=26 Score=23.59 Aligned_cols=39 Identities=15% Similarity=0.281 Sum_probs=22.6
Q ss_pred hhHHHHHHHHHHHHhhcCCCCChHHHHHHHHhhcCccCCC
Q 033730 46 HRHFVLYGLMEFLRRRFDRHFAPDEVLQLLDRFYNLDMLK 85 (112)
Q Consensus 46 hKHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t~YnL~~Ld 85 (112)
++||..--|.+.|++. +..++..-|.+-|+.|=+...+.
T Consensus 14 ~~~~sa~ei~~~l~~~-~~~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 14 DGHLTAEEIYERLRKK-GPSISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred CCCCCHHHHHHHHHhc-CCCCCHHHHHHHHHHHHhCCCEE
Confidence 3455666666666544 34566666666666655555554
No 12
>PF13551 HTH_29: Winged helix-turn helix
Probab=48.11 E-value=75 Score=20.61 Aligned_cols=52 Identities=29% Similarity=0.485 Sum_probs=37.3
Q ss_pred ccHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHH-HhhcCCCCChHHHHHHHHh
Q 033730 22 SQVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFL-RRRFDRHFAPDEVLQLLDR 77 (112)
Q Consensus 22 ~~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l-~~~~~r~~~~~~IW~kL~t 77 (112)
-+++++..|.+.+....+- |. -+...--|.+.| .+..+..++...||+.|..
T Consensus 58 l~~~~~~~l~~~~~~~p~~---g~-~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPE---GR-SRWTLEELAEWLIEEEFGIDVSPSTIRRILKR 110 (112)
T ss_pred CCHHHHHHHHHHHHHCCCC---CC-CcccHHHHHHHHHHhccCccCCHHHHHHHHHH
Confidence 3566666666666665555 66 445556788876 7788999999999998875
No 13
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=47.05 E-value=20 Score=24.51 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=12.4
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHH
Q 033730 53 GLMEFLRRRFDRHFAPDEVLQLLD 76 (112)
Q Consensus 53 ~I~e~l~~~~~r~~~~~~IW~kL~ 76 (112)
.|.+.|.+.-+ ++|+++||+.|.
T Consensus 12 ~Il~~l~~~~~-~~ta~ei~~~l~ 34 (120)
T PF01475_consen 12 AILELLKESPE-HLTAEEIYDKLR 34 (120)
T ss_dssp HHHHHHHHHSS-SEEHHHHHHHHH
T ss_pred HHHHHHHcCCC-CCCHHHHHHHhh
Confidence 34455544433 666666666664
No 14
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=46.26 E-value=14 Score=26.47 Aligned_cols=30 Identities=7% Similarity=-0.003 Sum_probs=20.5
Q ss_pred HHHHHHHhhcCCCCChHHHHHHHHhhcCcc
Q 033730 53 GLMEFLRRRFDRHFAPDEVLQLLDRFYNLD 82 (112)
Q Consensus 53 ~I~e~l~~~~~r~~~~~~IW~kL~t~YnL~ 82 (112)
.|.+.+...+...-++.+||+.|...|.-.
T Consensus 69 sis~~i~~~i~~~~tak~~W~~L~~~f~~~ 98 (152)
T PF14244_consen 69 SISPDILSTIIFCETAKEIWDALKERFSQK 98 (152)
T ss_pred hhcHHHHhhhHhhhhHHHHHHHHHHHhhcc
Confidence 344455545555668899999999988543
No 15
>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].
Probab=44.37 E-value=39 Score=24.26 Aligned_cols=43 Identities=23% Similarity=0.279 Sum_probs=32.5
Q ss_pred HHHHHHHhhCCCCCCCCchhHHHHH-HHHHHHHhhcCCCCChHHHHHHHH
Q 033730 28 LRLLEALEVYPPVKLRGIHRHFVLY-GLMEFLRRRFDRHFAPDEVLQLLD 76 (112)
Q Consensus 28 ~~Lf~a~~~~kPv~~~GihKHF~M~-~I~e~l~~~~~r~~~~~~IW~kL~ 76 (112)
.+||.||+-- .|-|.+|... -+.+++.+..+-.++ +.+|..|=
T Consensus 52 ~~lL~AIv~s-----f~~n~~i~~al~~vd~fs~~Y~I~i~-~~~W~~Ll 95 (126)
T PF12921_consen 52 SRLLIAIVHS-----FGYNGDIFSALKLVDFFSRKYPIPIP-KEFWRRLL 95 (126)
T ss_pred HHHHHHHHHH-----HHhcccHHHHHHHHHHHHHHcCCCCC-HHHHHHHH
Confidence 3567777532 2788888887 599999999987777 88998763
No 16
>TIGR01157 pufL photosynthetic reaction center L subunit. This model describes the photosynthetic reaction center L subunit in non-oxygenic photosynthetic bacteria. Reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reaction center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in form of NADH. Ultimately the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is some organic acid and not water. Much of our current functional understanding of photosynthesis comes from the structural determination, spectroscopic studies
Probab=43.46 E-value=17 Score=29.84 Aligned_cols=49 Identities=29% Similarity=0.253 Sum_probs=36.0
Q ss_pred CCCCCCc--ccccHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhhc
Q 033730 13 SASSLPK--EQSQVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRRF 62 (112)
Q Consensus 13 s~ss~~k--~~~~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~~ 62 (112)
|++...+ +..|+|.|-..||..++|- +...||||==--+++.--+-..+
T Consensus 163 s~~~~g~~~e~~~~e~~~~f~R~~~Gys-~~~~gIHR~g~~~A~~~~~~~ai 213 (239)
T TIGR01157 163 SAANPGKGEEVKTPEHEDTYFRDLVGYS-VGTLGIHRVGLFLALSAVFWSAI 213 (239)
T ss_pred eeccCCCCccccchHHHHHHHHHHhccc-chHHHHHHHHHHHHHHHHHHhhe
Confidence 4555544 4668999999999999998 66789999766666665555543
No 17
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=42.84 E-value=15 Score=24.95 Aligned_cols=17 Identities=18% Similarity=0.235 Sum_probs=13.7
Q ss_pred ChHHHHHHHHhhcCccC
Q 033730 67 APDEVLQLLDRFYNLDM 83 (112)
Q Consensus 67 ~~~~IW~kL~t~YnL~~ 83 (112)
|+.++|+.|..+|.=..
T Consensus 2 tA~e~W~~L~~~y~~~~ 18 (119)
T PF14223_consen 2 TAKEAWDALKKRYEGQS 18 (119)
T ss_pred hHHHHHHHHHHHHcCCc
Confidence 67899999999997433
No 18
>PRK09462 fur ferric uptake regulator; Provisional
Probab=41.28 E-value=43 Score=24.04 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHhhcCCCCChHHHHHHHHhhcCccCCC
Q 033730 48 HFVLYGLMEFLRRRFDRHFAPDEVLQLLDRFYNLDMLK 85 (112)
Q Consensus 48 HF~M~~I~e~l~~~~~r~~~~~~IW~kL~t~YnL~~Ld 85 (112)
||..--|.++|++. +..++..-|.+-|..|-+...+.
T Consensus 33 h~sa~eI~~~l~~~-~~~i~~aTVYR~L~~L~e~Gli~ 69 (148)
T PRK09462 33 HVSAEDLYKRLIDM-GEEIGLATVYRVLNQFDDAGIVT 69 (148)
T ss_pred CCCHHHHHHHHHhh-CCCCCHHHHHHHHHHHHHCCCEE
Confidence 44445555555433 24455555555555555544443
No 19
>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=40.62 E-value=37 Score=19.84 Aligned_cols=22 Identities=27% Similarity=0.273 Sum_probs=16.5
Q ss_pred cccccHHHHHHHHHHHhhCCCC
Q 033730 19 KEQSQVELELRLLEALEVYPPV 40 (112)
Q Consensus 19 k~~~~~e~E~~Lf~a~~~~kPv 40 (112)
|..||.|.+..|++++..+.+-
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~ 22 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD 22 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT
T ss_pred CCCCCHHHHHHHHHHHHHhCCc
Confidence 3468999999999999988643
No 20
>PF13565 HTH_32: Homeodomain-like domain
Probab=39.71 E-value=86 Score=19.43 Aligned_cols=44 Identities=23% Similarity=0.314 Sum_probs=30.7
Q ss_pred cHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhhcCCCC--ChHHHHHHH
Q 033730 23 QVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRRFDRHF--APDEVLQLL 75 (112)
Q Consensus 23 ~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~~~r~~--~~~~IW~kL 75 (112)
++|++.. +.+++.-.| .+..--|+++|...+|..+ +..-||+.|
T Consensus 32 ~~e~~~~-i~~~~~~~p--------~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 32 DPEQRER-IIALIEEHP--------RWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred cHHHHHH-HHHHHHhCC--------CCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 5566544 445544555 3556689999999988866 988898765
No 21
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=39.13 E-value=20 Score=24.33 Aligned_cols=19 Identities=16% Similarity=0.230 Sum_probs=14.4
Q ss_pred CChHHHHHHHHhhcCccCC
Q 033730 66 FAPDEVLQLLDRFYNLDML 84 (112)
Q Consensus 66 ~~~~~IW~kL~t~YnL~~L 84 (112)
-++.++|++|..+|.-...
T Consensus 2 ~ta~~~W~~L~~~y~~~~~ 20 (119)
T PF14227_consen 2 KTAKEMWDKLKKKYEKKSF 20 (119)
T ss_pred CCHHHHHHHHHHHHcCCCH
Confidence 3678999999988865443
No 22
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=35.65 E-value=76 Score=20.64 Aligned_cols=35 Identities=11% Similarity=0.083 Sum_probs=21.6
Q ss_pred cHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhhcCCCCChHHHHHHHHhhc
Q 033730 23 QVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRRFDRHFAPDEVLQLLDRFY 79 (112)
Q Consensus 23 ~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t~Y 79 (112)
|.|+...|+++|..+.+- +..++-..||+.|...+
T Consensus 6 T~edD~~l~~~v~~~~~~----------------------~~~~~Gn~iwk~le~~~ 40 (65)
T PF08914_consen 6 TEEDDAALLDYVKENERQ----------------------GGSVSGNKIWKELEEKH 40 (65)
T ss_dssp -HHHHHHHHHHHHHT--S----------------------TTTTTSSHHHHHHHHS-
T ss_pred CHHHHHHHHHHHHHhccC----------------------CCCCchHHHHHHHHHHc
Confidence 678888888888776655 33455666777776544
No 23
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=32.30 E-value=1.2e+02 Score=19.66 Aligned_cols=20 Identities=20% Similarity=0.413 Sum_probs=16.8
Q ss_pred ChHHHHHHHHhhcCccCCCC
Q 033730 67 APDEVLQLLDRFYNLDMLKP 86 (112)
Q Consensus 67 ~~~~IW~kL~t~YnL~~Lde 86 (112)
..+.+=.-|..+||.|.|+|
T Consensus 31 ~~~~~~~il~~LYd~dileE 50 (83)
T smart00515 31 LIKLLPKILKSLYDADILEE 50 (83)
T ss_pred HHHHHHHHHHHHhhhccccH
Confidence 45667778899999999997
No 24
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=28.77 E-value=1.6e+02 Score=19.76 Aligned_cols=18 Identities=28% Similarity=0.440 Sum_probs=15.9
Q ss_pred cHHHHHHHHHHHhhCCCC
Q 033730 23 QVELELRLLEALEVYPPV 40 (112)
Q Consensus 23 ~~e~E~~Lf~a~~~~kPv 40 (112)
-.+.|..+++|++-+.|.
T Consensus 94 l~~~E~~~l~ai~l~~~~ 111 (163)
T smart00430 94 LDDEEYALLKAILLFNPA 111 (163)
T ss_pred CCHHHHHHHHHHHHcChh
Confidence 468899999999999985
No 25
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=28.24 E-value=77 Score=23.26 Aligned_cols=28 Identities=11% Similarity=0.465 Sum_probs=23.6
Q ss_pred HHHHHHHHhhcCCCCChHHHHHHHHhhcC
Q 033730 52 YGLMEFLRRRFDRHFAPDEVLQLLDRFYN 80 (112)
Q Consensus 52 ~~I~e~l~~~~~r~~~~~~IW~kL~t~Yn 80 (112)
-.|.++|.++ +|.+++.+|.+-|..-|.
T Consensus 4 ~~Il~y~~~q-NRPys~~di~~nL~~~~~ 31 (169)
T PF07106_consen 4 DAILEYMKEQ-NRPYSAQDIFDNLHNKVG 31 (169)
T ss_pred HHHHHHHHHc-CCCCcHHHHHHHHHhhcc
Confidence 3688899866 899999999999998764
No 26
>PRK14506 photosynthetic reaction center subunit L; Provisional
Probab=27.69 E-value=42 Score=28.08 Aligned_cols=48 Identities=27% Similarity=0.273 Sum_probs=34.7
Q ss_pred CCCCCCc--ccccHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhh
Q 033730 13 SASSLPK--EQSQVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRR 61 (112)
Q Consensus 13 s~ss~~k--~~~~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~ 61 (112)
|++...+ +..++|.|...||..++|- +..+||||==--+++.--+-..
T Consensus 197 a~~~~g~~~ev~~~E~e~~f~R~~~Gys-~g~~gIHR~g~~~A~~~~~~~a 246 (276)
T PRK14506 197 SAANPEKGEEVKTPEHENTFFRDLIGYS-IGTLGIHRLGLFLALSAVFWSA 246 (276)
T ss_pred eeccCCCCccccchhHHHHHHHHHhccc-ccHHHHHHHHHHHHHHHHHHhh
Confidence 3444444 3558999999999999998 6678999975556665555544
No 27
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=27.57 E-value=91 Score=23.19 Aligned_cols=38 Identities=21% Similarity=0.410 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHHhhcCCCCChHHHHHHHHhhcCccCCC
Q 033730 47 RHFVLYGLMEFLRRRFDRHFAPDEVLQLLDRFYNLDMLK 85 (112)
Q Consensus 47 KHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t~YnL~~Ld 85 (112)
+||..--|.++|++. +..++..-|.+-|..|-+...+.
T Consensus 40 ~hlSa~eI~~~L~~~-~~~is~aTVYRtL~~L~e~Glv~ 77 (169)
T PRK11639 40 GAISAYDLLDLLREA-EPQAKPPTVYRALDFLLEQGFVH 77 (169)
T ss_pred CCCCHHHHHHHHHhh-CCCCCcchHHHHHHHHHHCCCEE
Confidence 345555555555433 23445555555555544444443
No 28
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=26.70 E-value=76 Score=20.16 Aligned_cols=22 Identities=23% Similarity=0.292 Sum_probs=11.0
Q ss_pred HHHHHHhhcCCCCChHHHHHHH
Q 033730 54 LMEFLRRRFDRHFAPDEVLQLL 75 (112)
Q Consensus 54 I~e~l~~~~~r~~~~~~IW~kL 75 (112)
|.+.|.++-+..++..+|++.|
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~l 32 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNL 32 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHH
Confidence 3444444433346666666655
No 29
>KOG4545 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.73 E-value=62 Score=25.81 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=23.4
Q ss_pred HHHHHHhhcCCCCChHHHHHHHHhhcCc
Q 033730 54 LMEFLRRRFDRHFAPDEVLQLLDRFYNL 81 (112)
Q Consensus 54 I~e~l~~~~~r~~~~~~IW~kL~t~YnL 81 (112)
-..++++.+...|.+++.|+++.+.||-
T Consensus 9 f~~r~r~~~~~~i~~pe~fkr~g~~~~~ 36 (197)
T KOG4545|consen 9 FITRLRQRLTDRIQMPERFKRWGQYWNG 36 (197)
T ss_pred HHHHHHHhccccccchHHHHHHHHHHHH
Confidence 3456777788899999999999999973
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=25.12 E-value=80 Score=19.97 Aligned_cols=54 Identities=17% Similarity=0.196 Sum_probs=33.8
Q ss_pred CcccccHHHHHHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhhcCCCCChHHHHHHHHhhcC
Q 033730 18 PKEQSQVELELRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRRFDRHFAPDEVLQLLDRFYN 80 (112)
Q Consensus 18 ~k~~~~~e~E~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t~Yn 80 (112)
++..||.|...++++||..+--. +. =.=-.|++.|. ...++...|=.||..+|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g-----~~-a~pk~I~~~~~---~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGP-----DW-ATPKRILELMV---VDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCC-----cc-cchHHHHHHcC---CCCCCHHHHHHHHHHHHc
Confidence 45689999999999999765321 10 00002344443 245688888888877764
No 31
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=22.94 E-value=1.3e+02 Score=26.85 Aligned_cols=47 Identities=21% Similarity=0.180 Sum_probs=29.4
Q ss_pred CCCCCCCC--CCCC-CCCCCcccccHHHHHHHHHHHhhCCCCCCCCchhH
Q 033730 2 SVHSPCKA--PPSS-ASSLPKEQSQVELELRLLEALEVYPPVKLRGIHRH 48 (112)
Q Consensus 2 ~~~~~~~~--~~~s-~ss~~k~~~~~e~E~~Lf~a~~~~kPv~~~GihKH 48 (112)
+.|.|.-+ --++ +..+-...||.+.|+.|++|+..+.=-.-++|-+|
T Consensus 52 ~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~h 101 (438)
T KOG0457|consen 52 GKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADH 101 (438)
T ss_pred CCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHH
Confidence 34555544 2223 23444568999999999999998875433334443
No 32
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=22.68 E-value=1.4e+02 Score=24.32 Aligned_cols=32 Identities=28% Similarity=0.316 Sum_probs=21.7
Q ss_pred cccccHHHHHHHHHHHhhCCCCCCCCchhHHH
Q 033730 19 KEQSQVELELRLLEALEVYPPVKLRGIHRHFV 50 (112)
Q Consensus 19 k~~~~~e~E~~Lf~a~~~~kPv~~~GihKHF~ 50 (112)
|+.-++++-..+++.+...+-+.+.|+|-|+-
T Consensus 143 rfG~~~~~~~~~~~~~~~~~~l~~~Glh~H~g 174 (377)
T cd06843 143 PFGIDEADLPDALELLRDLPNIRLRGFHFHLM 174 (377)
T ss_pred CCCcCHHHHHHHHHHHHhCCCccEEEEEEEcC
Confidence 56556666567777776655556669988873
No 33
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=22.66 E-value=2.7e+02 Score=19.32 Aligned_cols=43 Identities=14% Similarity=0.315 Sum_probs=26.9
Q ss_pred CCCCChHHHHHHHHhhcCccCCCCCccccccCCCCCCccCChhhhcc
Q 033730 63 DRHFAPDEVLQLLDRFYNLDMLKPDDEEMEILNHEEDFCLPQSYFDK 109 (112)
Q Consensus 63 ~r~~~~~~IW~kL~t~YnL~~Lde~~E~~~~~~~e~dF~LP~~e~~~ 109 (112)
.+.|+=+.|.+||-.+.++++.-. ..| +.-.-.-.+|.+.|-+
T Consensus 37 s~~frNP~i~ekLi~~~~Ide~gT---n~p-~~i~dP~~~~~~~y~e 79 (96)
T PF07818_consen 37 SKSFRNPSILEKLIEFFGIDEYGT---NFP-KDIFDPHGFPEEDYYE 79 (96)
T ss_pred ccccCChHHHHHHHHHcCCCcccC---CCC-hhhcCCCCCCHHHHHH
Confidence 577888999999999998877543 332 1111223467665543
No 34
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=22.11 E-value=21 Score=23.17 Aligned_cols=18 Identities=22% Similarity=0.287 Sum_probs=11.5
Q ss_pred CchhHHHHHHHHHHHHhh
Q 033730 44 GIHRHFVLYGLMEFLRRR 61 (112)
Q Consensus 44 GihKHF~M~~I~e~l~~~ 61 (112)
.=++.||+.|+.+.|+..
T Consensus 27 ~C~~~fH~~CL~~wf~~~ 44 (70)
T PF11793_consen 27 SCGKKFHLLCLSEWFLSL 44 (70)
T ss_dssp T----B-SGGGHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHc
Confidence 446889999999999875
No 35
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=22.11 E-value=66 Score=21.79 Aligned_cols=18 Identities=17% Similarity=0.189 Sum_probs=14.3
Q ss_pred CCCChHHHHHHHHhhcCc
Q 033730 64 RHFAPDEVLQLLDRFYNL 81 (112)
Q Consensus 64 r~~~~~~IW~kL~t~YnL 81 (112)
...+-.+|+.+|..+||.
T Consensus 11 ~Tpsr~ei~~klA~~~~~ 28 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNV 28 (84)
T ss_dssp SS--HHHHHHHHHHHHTS
T ss_pred CCCCHHHHHHHHHHHhCC
Confidence 456778999999999998
No 36
>COG3433 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.79 E-value=1.1e+02 Score=21.05 Aligned_cols=37 Identities=22% Similarity=0.279 Sum_probs=27.0
Q ss_pred HHHHHHHhhCCCCCCCCchhHHHHHHHHHHHHhhcCCCCChHHHHHHHHh
Q 033730 28 LRLLEALEVYPPVKLRGIHRHFVLYGLMEFLRRRFDRHFAPDEVLQLLDR 77 (112)
Q Consensus 28 ~~Lf~a~~~~kPv~~~GihKHF~M~~I~e~l~~~~~r~~~~~~IW~kL~t 77 (112)
||+.+.+.+||-. |.---|.+++ ++.+++.-|+.|.+
T Consensus 32 iR~M~L~~~wR~~---G~~i~F~~La----------~~PTl~aW~qLl~~ 68 (74)
T COG3433 32 IRMMALLERWRKR---GADIDFAQLA----------ANPTLAAWWQLLST 68 (74)
T ss_pred HHHHHHHHHHHHc---CCcccHHHHH----------hCccHHHHHHHHHh
Confidence 5666667777777 7777776654 67888888888875
No 37
>COG3697 CitX Phosphoribosyl-dephospho-CoA transferase (holo-ACP synthetase) [Coenzyme metabolism / Lipid metabolism]
Probab=20.88 E-value=48 Score=26.26 Aligned_cols=26 Identities=35% Similarity=0.764 Sum_probs=17.3
Q ss_pred HHhhcCccCCCCCccccccCCCCCCccCCh
Q 033730 75 LDRFYNLDMLKPDDEEMEILNHEEDFCLPQ 104 (112)
Q Consensus 75 L~t~YnL~~Lde~~E~~~~~~~e~dF~LP~ 104 (112)
|+++||+|.||.+-+.+. -++|.||.
T Consensus 116 LGRLwDiDVi~~~g~~LS----R~~~~lp~ 141 (182)
T COG3697 116 LGRLWDIDVLDAEGEILS----RRDFGLPP 141 (182)
T ss_pred hhhhccceeeccCCCEee----ccccCCCC
Confidence 678899999996333332 35677774
No 38
>PF13797 Post_transc_reg: Post-transcriptional regulator
Probab=20.07 E-value=1.4e+02 Score=20.49 Aligned_cols=17 Identities=6% Similarity=0.067 Sum_probs=14.8
Q ss_pred CCCCChHHHHHHHHhhc
Q 033730 63 DRHFAPDEVLQLLDRFY 79 (112)
Q Consensus 63 ~r~~~~~~IW~kL~t~Y 79 (112)
=..|+.++||+.|.+.|
T Consensus 25 Y~~vt~~dlw~yl~~~~ 41 (87)
T PF13797_consen 25 YESVTEEDLWSYLTEKK 41 (87)
T ss_pred cCcCCHHHHHHHHHHHH
Confidence 36899999999998876
Done!