Query 033867
Match_columns 110
No_of_seqs 54 out of 56
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 07:12:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033867.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033867hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13668 hypothetical protein; 75.9 2.4 5.3E-05 35.0 2.6 44 47-90 8-53 (267)
2 smart00391 MBD Methyl-CpG bind 68.3 11 0.00025 25.2 4.1 29 29-57 26-54 (77)
3 PF07927 YcfA: YcfA-like prote 63.6 13 0.00028 22.3 3.3 16 46-61 1-16 (56)
4 PF03816 LytR_cpsA_psr: Cell e 60.0 6.1 0.00013 28.5 1.7 18 68-85 7-25 (149)
5 cd00122 MBD MeCP2, MBD1, MBD2, 58.1 21 0.00046 22.5 3.7 29 29-57 23-51 (62)
6 KOG0675 Calnexin [Posttranslat 55.7 11 0.00025 34.3 2.9 26 83-108 197-225 (558)
7 PF14056 DUF4250: Domain of un 54.2 7.7 0.00017 25.3 1.2 22 46-71 34-55 (55)
8 cd01396 MeCP2_MBD MeCP2, MBD1, 53.6 29 0.00063 23.3 4.0 29 29-57 24-52 (77)
9 TIGR00350 lytR_cpsA_psr cell e 51.2 11 0.00023 27.6 1.8 18 69-86 9-27 (152)
10 PF02589 DUF162: Uncharacteris 44.9 39 0.00084 24.4 3.8 46 9-55 98-143 (189)
11 smart00359 PUA Putative RNA-bi 44.1 33 0.00071 21.0 2.9 33 2-43 15-47 (77)
12 PF07723 LRR_2: Leucine Rich R 42.2 14 0.0003 20.2 0.9 19 88-106 1-19 (26)
13 PF13590 DUF4136: Domain of un 41.3 34 0.00074 23.3 2.9 28 46-74 41-69 (151)
14 PF15590 Imm15: Immunity prote 41.1 8.4 0.00018 26.6 -0.1 11 56-67 23-33 (69)
15 COG4004 Uncharacterized protei 40.8 18 0.00039 26.4 1.5 22 44-65 12-33 (96)
16 PF07404 TEBP_beta: Telomere-b 40.7 3.4 7.3E-05 35.4 -2.6 23 36-58 98-120 (379)
17 TIGR01436 glu_cys_lig_pln glut 39.6 37 0.0008 29.6 3.5 49 31-82 29-83 (446)
18 smart00850 LytTR LytTr DNA-bin 39.1 52 0.0011 20.6 3.3 37 31-75 19-55 (96)
19 PF11629 Mst1_SARAH: C termina 38.8 18 0.00039 23.5 1.2 13 45-57 9-21 (49)
20 PF01429 MBD: Methyl-CpG bindi 37.2 80 0.0017 20.7 4.1 29 29-57 29-57 (77)
21 PRK09379 membrane-bound transc 35.4 25 0.00054 28.7 1.8 19 68-86 83-102 (303)
22 KOG3606 Cell polarity protein 35.0 19 0.00041 31.2 1.1 30 72-101 129-158 (358)
23 PF09664 DUF2399: Protein of u 34.5 40 0.00087 25.1 2.6 55 10-65 18-74 (152)
24 PF08259 Periviscerokin: Periv 33.0 19 0.00041 17.3 0.4 9 76-84 2-10 (11)
25 PF07285 DUF1444: Protein of u 32.8 39 0.00084 27.1 2.4 44 47-90 8-53 (265)
26 cd07245 Glo_EDI_BRP_like_9 Thi 31.9 1.2E+02 0.0025 18.1 6.3 52 3-60 36-89 (114)
27 PF13382 Adenine_deam_C: Adeni 31.8 12 0.00026 28.7 -0.6 22 38-59 116-137 (171)
28 cd06410 PB1_UP2 Uncharacterize 30.2 1.5E+02 0.0033 20.7 4.8 46 32-85 24-72 (97)
29 PF04841 Vps16_N: Vps16, N-ter 30.2 47 0.001 27.7 2.6 51 30-86 59-112 (410)
30 PF03607 DCX: Doublecortin; I 29.8 28 0.00062 21.9 1.0 17 35-51 31-47 (60)
31 PRK05298 excinuclease ABC subu 29.7 85 0.0018 28.1 4.2 50 31-82 155-205 (652)
32 PF14067 LssY_C: LssY C-termin 27.3 43 0.00094 25.7 1.8 20 42-61 30-49 (192)
33 cd01617 DCX Ubiquitin-like dom 27.2 39 0.00085 22.2 1.3 17 35-51 49-66 (80)
34 cd05563 PTS_IIB_ascorbate PTS_ 27.1 81 0.0018 20.0 2.8 31 32-62 1-33 (86)
35 KOG0855 Alkyl hydroperoxide re 26.9 51 0.0011 26.9 2.1 17 4-20 178-194 (211)
36 cd01518 RHOD_YceA Member of th 26.9 73 0.0016 20.4 2.5 29 31-62 62-90 (101)
37 PF04466 Terminase_3: Phage te 26.8 21 0.00046 29.5 0.0 54 44-98 47-102 (387)
38 PF00397 WW: WW domain; Inter 26.3 65 0.0014 17.8 1.9 20 56-75 3-23 (31)
39 PF01954 DUF104: Protein of un 26.2 82 0.0018 20.5 2.7 29 6-41 8-36 (60)
40 PF12690 BsuPI: Intracellular 26.1 39 0.00085 22.7 1.2 17 88-104 19-35 (82)
41 PRK11783 rlmL 23S rRNA m(2)G24 26.0 60 0.0013 29.2 2.6 33 30-63 54-86 (702)
42 smart00456 WW Domain with 2 co 25.5 1.2E+02 0.0025 16.1 3.0 21 56-76 3-23 (32)
43 TIGR02981 phageshock_pspE phag 24.7 97 0.0021 21.0 3.0 31 30-63 58-88 (101)
44 smart00537 DCX Domain in the D 24.3 51 0.0011 22.2 1.5 17 35-51 55-71 (89)
45 PF08842 Mfa2: Fimbrillin-A as 23.6 32 0.00069 25.4 0.4 9 4-12 33-41 (283)
46 TIGR02254 YjjG/YfnB HAD superf 23.4 47 0.001 23.6 1.2 28 33-63 113-140 (224)
47 CHL00193 ycf35 Ycf35; Provisio 23.4 2.7E+02 0.0058 20.5 5.2 18 42-59 10-27 (128)
48 PLN02891 IMP cyclohydrolase 23.4 1.2E+02 0.0025 28.0 3.9 32 29-63 21-52 (547)
49 cd08968 MeNeil2_N N-terminal d 23.3 1.5E+02 0.0033 22.0 3.9 39 1-44 78-117 (126)
50 cd01395 HMT_MBD Methyl-CpG bin 23.2 89 0.0019 20.5 2.4 28 29-56 22-49 (60)
51 PF07727 RVT_2: Reverse transc 23.2 27 0.00058 27.4 -0.1 35 46-81 132-166 (246)
52 PF04397 LytTR: LytTr DNA-bind 23.2 2.1E+02 0.0045 18.1 5.9 37 30-74 18-54 (98)
53 PF14090 HTH_39: Helix-turn-he 23.1 13 0.00028 23.9 -1.6 29 31-59 4-43 (70)
54 PLN02611 glutamate--cysteine l 22.8 93 0.002 27.6 3.2 47 32-82 76-126 (482)
55 PF13950 Epimerase_Csub: UDP-g 22.6 44 0.00094 21.4 0.8 23 39-61 19-41 (62)
56 PF07453 NUMOD1: NUMOD1 domain 22.0 97 0.0021 17.3 2.2 28 32-59 2-29 (37)
57 TIGR00354 polC DNA polymerase, 21.7 64 0.0014 31.9 2.1 53 3-72 704-761 (1095)
58 COG3076 Uncharacterized protei 20.9 48 0.001 25.4 0.9 36 31-67 69-116 (135)
59 PF10163 EnY2: Transcription f 20.7 59 0.0013 21.9 1.2 21 39-59 13-33 (86)
60 KOG3368 Transport protein part 20.3 54 0.0012 25.3 1.1 15 3-17 5-19 (140)
No 1
>PRK13668 hypothetical protein; Provisional
Probab=75.86 E-value=2.4 Score=35.01 Aligned_cols=44 Identities=18% Similarity=0.435 Sum_probs=34.1
Q ss_pred HHHHHHHhhccceeeecCCCCceEEeec-Cceee-Eeccccccccc
Q 033867 47 SSLEQILTGLGWERYYGGDPDLFQFHKH-SSIDL-ISLPRDFSKFN 90 (110)
Q Consensus 47 ~~LE~~L~~LGWeRYy~~d~~l~QfHkr-~svdL-ISLPrdF~~fk 90 (110)
+.||++|...||...|+-+.+.+++-++ ..--. |+||.-++++.
T Consensus 8 ~~l~~rL~~~~~~~~~~r~~d~Lri~~~~~~kgvti~L~~~~aky~ 53 (267)
T PRK13668 8 DKLKKRLSHPDWDFSFDREKETLRIERKDNKKGVTISLPPIVAKWE 53 (267)
T ss_pred HHHHHHHhCCCCeeEeccCCceEEEEEccCCCceEEEcHHHHHHHH
Confidence 6799999999999999878888887443 33333 88998777764
No 2
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=68.33 E-value=11 Score=25.24 Aligned_cols=29 Identities=28% Similarity=0.308 Sum_probs=25.7
Q ss_pred CcceEEEEccCCceeechHHHHHHHhhcc
Q 033867 29 SRRKVLVHLPTGEVVSSYSSLEQILTGLG 57 (110)
Q Consensus 29 ~rrKvLvh~ps~Evi~Sy~~LE~~L~~LG 57 (110)
++.-|.-+.|+|.-++|+.++.+-|.+-|
T Consensus 26 ~~~dV~Y~sP~GkklRs~~ev~~YL~~~~ 54 (77)
T smart00391 26 GKFDVYYISPCGKKLRSKSELARYLHKNG 54 (77)
T ss_pred CcccEEEECCCCCeeeCHHHHHHHHHhCC
Confidence 45689999999999999999999998765
No 3
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=63.59 E-value=13 Score=22.25 Aligned_cols=16 Identities=25% Similarity=0.509 Sum_probs=12.6
Q ss_pred hHHHHHHHhhccceee
Q 033867 46 YSSLEQILTGLGWERY 61 (110)
Q Consensus 46 y~~LE~~L~~LGWeRY 61 (110)
|.+|++.|.++||+.-
T Consensus 1 ~~el~k~L~~~G~~~~ 16 (56)
T PF07927_consen 1 WRELIKLLEKAGFEEV 16 (56)
T ss_dssp -HHHHHHHHHTT-EEE
T ss_pred ChHHHHHHHHCCCEEe
Confidence 5789999999999866
No 4
>PF03816 LytR_cpsA_psr: Cell envelope-related transcriptional attenuator domain; InterPro: IPR004474 This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.; PDB: 3PE5_B 3QFI_A 3NRO_B 3OKZ_B 3OWQ_C 3MEJ_A 4DE9_A 3TEP_A 3TEL_A 3TFL_A ....
Probab=60.01 E-value=6.1 Score=28.45 Aligned_cols=18 Identities=33% Similarity=0.717 Sum_probs=13.7
Q ss_pred ceEEeec-CceeeEecccc
Q 033867 68 LFQFHKH-SSIDLISLPRD 85 (110)
Q Consensus 68 l~QfHkr-~svdLISLPrd 85 (110)
|+.++.. .++.+||+|||
T Consensus 7 l~~~~~~~~~~~~vsIPRD 25 (149)
T PF03816_consen 7 LVSINPDTKKVTLVSIPRD 25 (149)
T ss_dssp EEEEETTTTEEEEEEE-TT
T ss_pred EEEEcCCCCEEEEEEEcCc
Confidence 4567764 89999999997
No 5
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=58.08 E-value=21 Score=22.54 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=25.7
Q ss_pred CcceEEEEccCCceeechHHHHHHHhhcc
Q 033867 29 SRRKVLVHLPTGEVVSSYSSLEQILTGLG 57 (110)
Q Consensus 29 ~rrKvLvh~ps~Evi~Sy~~LE~~L~~LG 57 (110)
++.-|.-+.|+|+.++|+.++++-|.+-|
T Consensus 23 ~k~dv~Y~sP~Gk~~Rs~~ev~~yL~~~~ 51 (62)
T cd00122 23 GKGDVYYYSPCGKKLRSKPEVARYLEKTG 51 (62)
T ss_pred CcceEEEECCCCceecCHHHHHHHHHhCC
Confidence 45678889999999999999999998866
No 6
>KOG0675 consensus Calnexin [Posttranslational modification, protein turnover, chaperones]
Probab=55.68 E-value=11 Score=34.34 Aligned_cols=26 Identities=31% Similarity=0.542 Sum_probs=22.3
Q ss_pred cccccccc---eeeeEEEEEeCCCeeEEe
Q 033867 83 PRDFSKFN---SVYMYDIVIKNPNVFHVR 108 (110)
Q Consensus 83 PrdF~~fk---s~HMYDIVVKnrn~F~Vr 108 (110)
|.++.++- .+|||-.|||+-|.|+||
T Consensus 197 p~~l~~~~~d~~tHLYTLvl~pd~sfeI~ 225 (558)
T KOG0675|consen 197 PSSLKKPFDDKLTHLYTLVLKPDNTFEIR 225 (558)
T ss_pred CcccccccccCCceeEEEEecCCCeEEEE
Confidence 56666665 899999999999999997
No 7
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=54.20 E-value=7.7 Score=25.33 Aligned_cols=22 Identities=41% Similarity=0.717 Sum_probs=16.8
Q ss_pred hHHHHHHHhhccceeeecCCCCceEE
Q 033867 46 YSSLEQILTGLGWERYYGGDPDLFQF 71 (110)
Q Consensus 46 y~~LE~~L~~LGWeRYy~~d~~l~Qf 71 (110)
=+.|++||.+.|.+ | ||..-||
T Consensus 34 ~~~l~~kL~~~Gy~-Y---~~~~NQF 55 (55)
T PF14056_consen 34 KEELEEKLASIGYE-Y---DEEQNQF 55 (55)
T ss_pred HHHHHHHHHHcCCe-E---chhhCCC
Confidence 36899999999987 5 5665555
No 8
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=53.63 E-value=29 Score=23.33 Aligned_cols=29 Identities=28% Similarity=0.289 Sum_probs=25.9
Q ss_pred CcceEEEEccCCceeechHHHHHHHhhcc
Q 033867 29 SRRKVLVHLPTGEVVSSYSSLEQILTGLG 57 (110)
Q Consensus 29 ~rrKvLvh~ps~Evi~Sy~~LE~~L~~LG 57 (110)
++.-|.-+.|+|+-++|..+|++-|.+-|
T Consensus 24 ~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~ 52 (77)
T cd01396 24 GKFDVYYISPTGKKFRSKVELARYLEKNG 52 (77)
T ss_pred CcceEEEECCCCCEEECHHHHHHHHHhCC
Confidence 35578889999999999999999999887
No 9
>TIGR00350 lytR_cpsA_psr cell envelope-related function transcriptional attenuator common domain. This model describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is proteins psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. Besides the region of strong similarily represented by this model, these proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.
Probab=51.18 E-value=11 Score=27.62 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=13.8
Q ss_pred eEEeec-CceeeEeccccc
Q 033867 69 FQFHKH-SSIDLISLPRDF 86 (110)
Q Consensus 69 ~QfHkr-~svdLISLPrdF 86 (110)
+-+.+. .++.+||+|||-
T Consensus 9 ~~i~~~~~~~~lisIPRDt 27 (152)
T TIGR00350 9 VTLDPKRKTAVVVSIPRDT 27 (152)
T ss_pred EEEcCCCCEEEEEEecCCc
Confidence 445554 789999999985
No 10
>PF02589 DUF162: Uncharacterised ACR, YkgG family COG1556; InterPro: IPR003741 This entry represents a domain found in lactate utilization proteins B (LutB) and C (LutC), as well as several uncharacterised proteins. Lactate utilization proteins B and C are involved in L-lactate degradation and allows cells to grow with lactate as the sole carbon source. LutB probably has a role as an electron transporter during oxidation of L-lactate.; PDB: 2G40_A.
Probab=44.85 E-value=39 Score=24.43 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=33.3
Q ss_pred eCCEEEEeeCCCcccCCCCCCcceEEEEccCCceeechHHHHHHHhh
Q 033867 9 TNGVIRLIENPQAESQGSSSSRRKVLVHLPTGEVVSSYSSLEQILTG 55 (110)
Q Consensus 9 knGV~rlvenp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~~L~~ 55 (110)
.+|-+=+.++++... .-+-.+++.++.++.++++.++++.-+++..
T Consensus 98 etGtlvl~~~~~~~r-~~s~lP~~hi~vv~~~kIv~~l~ea~~~~~~ 143 (189)
T PF02589_consen 98 ETGTLVLSSGPGNRR-AVSLLPPVHIVVVGASKIVPNLEEALERLRN 143 (189)
T ss_dssp TTTEEEE---TTT-G-GGGTSSSEEEEEEEGGGEESSHHHHHHHHHH
T ss_pred hCCeEEEeCCCCChh-hhhhCCCeEEEEEcHHHcCCCHHHHHHHHHh
Confidence 577777888765431 1123478999999999999999999999988
No 11
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=44.08 E-value=33 Score=20.99 Aligned_cols=33 Identities=24% Similarity=0.367 Sum_probs=21.5
Q ss_pred cceEEEeeCCEEEEeeCCCcccCCCCCCcceEEEEccCCcee
Q 033867 2 SGVWVFNTNGVIRLIENPQAESQGSSSSRRKVLVHLPTGEVV 43 (110)
Q Consensus 2 sGVWvF~knGV~rlvenp~~~~~~~~~~rrKvLvh~ps~Evi 43 (110)
.|-|+| .+||.+...+.. ++ --|.|+...|+.+
T Consensus 15 ~g~~v~-~~~v~~~~~~~~-~g-------~~V~v~~~~g~~v 47 (77)
T smart00359 15 NGASLL-APGVVRVDGGIK-EG-------DVVVIVDEKGEPL 47 (77)
T ss_pred cCCCcc-cceeEEEeCCcC-CC-------CEEEEEcCCCCEE
Confidence 467999 999987644321 11 2677887777754
No 12
>PF07723 LRR_2: Leucine Rich Repeat; InterPro: IPR013101 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by IPR001611 from INTERPRO [, ].
Probab=42.21 E-value=14 Score=20.20 Aligned_cols=19 Identities=5% Similarity=0.307 Sum_probs=15.6
Q ss_pred ccceeeeEEEEEeCCCeeE
Q 033867 88 KFNSVYMYDIVIKNPNVFH 106 (110)
Q Consensus 88 ~fks~HMYDIVVKnrn~F~ 106 (110)
.+|+.|..+|...|...|+
T Consensus 1 sLKtL~L~~v~f~~~~~l~ 19 (26)
T PF07723_consen 1 SLKTLHLDSVVFSDEDSLE 19 (26)
T ss_pred CCeEEEeeEEEECChhHHH
Confidence 3689999999998887664
No 13
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=41.25 E-value=34 Score=23.29 Aligned_cols=28 Identities=29% Similarity=0.488 Sum_probs=22.7
Q ss_pred hHHHHHHHhhccceeeecCCCCc-eEEeec
Q 033867 46 YSSLEQILTGLGWERYYGGDPDL-FQFHKH 74 (110)
Q Consensus 46 y~~LE~~L~~LGWeRYy~~d~~l-~QfHkr 74 (110)
-+.+|+.|.+.|+.+- ...||+ ++||-.
T Consensus 41 ~~~v~~~L~~~G~~~~-~~~aDl~V~~~~~ 69 (151)
T PF13590_consen 41 QDAVEQELAAKGYRRV-PENADLLVSYHYS 69 (151)
T ss_pred HHHHHHHHHHCCCeec-ccCCCEEEEEEEE
Confidence 3578999999999998 558886 788765
No 14
>PF15590 Imm15: Immunity protein 15
Probab=41.12 E-value=8.4 Score=26.62 Aligned_cols=11 Identities=55% Similarity=1.180 Sum_probs=9.1
Q ss_pred ccceeeecCCCC
Q 033867 56 LGWERYYGGDPD 67 (110)
Q Consensus 56 LGWeRYy~~d~~ 67 (110)
-|||++|. ||.
T Consensus 23 d~We~~y~-DP~ 33 (69)
T PF15590_consen 23 DGWETLYQ-DPR 33 (69)
T ss_pred cchhhhcc-CCC
Confidence 49999999 774
No 15
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.80 E-value=18 Score=26.42 Aligned_cols=22 Identities=27% Similarity=0.444 Sum_probs=17.5
Q ss_pred echHHHHHHHhhccceeeecCC
Q 033867 44 SSYSSLEQILTGLGWERYYGGD 65 (110)
Q Consensus 44 ~Sy~~LE~~L~~LGWeRYy~~d 65 (110)
..++.|+|.|.+|||+=--+||
T Consensus 12 ~~~dri~~~l~e~g~~v~~eGD 33 (96)
T COG4004 12 PDPDRIMRGLSELGWTVSEEGD 33 (96)
T ss_pred CCHHHHHHHHHHhCeeEeeccc
Confidence 3589999999999998554554
No 16
>PF07404 TEBP_beta: Telomere-binding protein beta subunit (TEBP beta); InterPro: IPR010874 Telomeres are specialised protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognise and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes []. This family consists of several telomere-binding protein beta subunits, which appear to be specific to the Oxytrichidae. ; GO: 0042162 telomeric DNA binding, 0000781 chromosome, telomeric region; PDB: 1PH5_B 1PH1_B 1PH8_B 1PH4_B 1PH2_B 1OTC_B 2I0Q_B 1PH6_B 1PH3_B 1PH9_B ....
Probab=40.66 E-value=3.4 Score=35.44 Aligned_cols=23 Identities=30% Similarity=0.455 Sum_probs=15.7
Q ss_pred EccCCceeechHHHHHHHhhccc
Q 033867 36 HLPTGEVVSSYSSLEQILTGLGW 58 (110)
Q Consensus 36 h~ps~Evi~Sy~~LE~~L~~LGW 58 (110)
-+.|-||.|||+-||.||.-.-+
T Consensus 98 rvnsaevftsyanlearlivhsf 120 (379)
T PF07404_consen 98 RVNSAEVFTSYANLEARLIVHSF 120 (379)
T ss_dssp E--TTT-SS-BTTEEEEEEEEEE
T ss_pred ecchHhHhHhhhchhhheehhhc
Confidence 47899999999999999875443
No 17
>TIGR01436 glu_cys_lig_pln glutamate--cysteine ligase, plant type. This model represents one of two highly dissimilar forms of glutamate--cysteine ligase (gamma-glutamylcysteine synthetase), an enzyme of glutathione biosynthesis. The other type is modeled by TIGR01434. This type is found in plants (with a probable transit peptide), root nodule and other bacteria, but not E. coli and closely related species.
Probab=39.62 E-value=37 Score=29.56 Aligned_cols=49 Identities=16% Similarity=0.297 Sum_probs=34.3
Q ss_pred ceEEEEccCCceeechH--HHHHHHh----hccceeeecCCCCceEEeecCceeeEec
Q 033867 31 RKVLVHLPTGEVVSSYS--SLEQILT----GLGWERYYGGDPDLFQFHKHSSIDLISL 82 (110)
Q Consensus 31 rKvLvh~ps~Evi~Sy~--~LE~~L~----~LGWeRYy~~d~~l~QfHkr~svdLISL 82 (110)
-|..++.++++-++-+. .++..|. ..|||.+++ +.+++++-+.+ .-|||
T Consensus 29 E~f~~~~~~~~~~~y~~~~gi~~~l~~l~~~~g~~~~~e-~g~~i~l~~~~--~~itl 83 (446)
T TIGR01436 29 EKFGFEKNTLRPMKYEQKGGIAELLNGIAERFGWQKVME-GDKIIGLKQDK--QSISL 83 (446)
T ss_pred eeeeeecCCCCCCCCCCchhHHHHHHHHHhhcCCceecc-CCceeeecCCC--CeEEE
Confidence 37778888888876553 2555554 559999998 77888886632 55665
No 18
>smart00850 LytTR LytTr DNA-binding domain. This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern.
Probab=39.09 E-value=52 Score=20.61 Aligned_cols=37 Identities=19% Similarity=0.391 Sum_probs=22.4
Q ss_pred ceEEEEccCCceeechHHHHHHHhhccceeeecCCCCceEEeecC
Q 033867 31 RKVLVHLPTGEVVSSYSSLEQILTGLGWERYYGGDPDLFQFHKHS 75 (110)
Q Consensus 31 rKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~~d~~l~QfHkr~ 75 (110)
+++.+|+.+++... +..|.+....|. ++..+|-|++.
T Consensus 19 ~~~~i~~~~~~~~~-~~~l~~~~~~L~-------~~~F~r~hrs~ 55 (96)
T smart00850 19 NYVTIHTKDGTYLV-RGTLKELEEKLD-------PTNFFRIHRSY 55 (96)
T ss_pred CEEEEEECCcEEEe-hhhHHHHHhhCC-------CCceEEechhH
Confidence 58899998776443 444444433331 34577888874
No 19
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=38.83 E-value=18 Score=23.48 Aligned_cols=13 Identities=46% Similarity=0.654 Sum_probs=10.5
Q ss_pred chHHHHHHHhhcc
Q 033867 45 SYSSLEQILTGLG 57 (110)
Q Consensus 45 Sy~~LE~~L~~LG 57 (110)
||+.|+++|.+|-
T Consensus 9 s~~eL~~rl~~LD 21 (49)
T PF11629_consen 9 SYEELQQRLASLD 21 (49)
T ss_dssp -HHHHHHHHHHHH
T ss_pred CHHHHHHHHHhCC
Confidence 8999999999873
No 20
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
Probab=37.24 E-value=80 Score=20.67 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=25.3
Q ss_pred CcceEEEEccCCceeechHHHHHHHhhcc
Q 033867 29 SRRKVLVHLPTGEVVSSYSSLEQILTGLG 57 (110)
Q Consensus 29 ~rrKvLvh~ps~Evi~Sy~~LE~~L~~LG 57 (110)
++.-|.-+.|+|+-++|..++.+-|.+.+
T Consensus 29 ~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~ 57 (77)
T PF01429_consen 29 GKKDVYYYSPCGKRFRSKKEVVRYLKENP 57 (77)
T ss_dssp TSEEEEEEETTSEEESSHHHHHHHHTTSS
T ss_pred CceEEEEECCCCCEEeCHHHHHHHHHhCC
Confidence 45678888999999999999999998765
No 21
>PRK09379 membrane-bound transcriptional regulator LytR; Provisional
Probab=35.42 E-value=25 Score=28.72 Aligned_cols=19 Identities=26% Similarity=0.674 Sum_probs=15.2
Q ss_pred ceEEeec-CceeeEeccccc
Q 033867 68 LFQFHKH-SSIDLISLPRDF 86 (110)
Q Consensus 68 l~QfHkr-~svdLISLPrdF 86 (110)
|+.+.+. .++.+||+|||=
T Consensus 83 l~~in~~~~~~~~iSIPRDt 102 (303)
T PRK09379 83 VMTLNPKTNSMKMVSIPRDT 102 (303)
T ss_pred EEEEcCCCCeEEEEEecCcc
Confidence 4667664 799999999984
No 22
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=35.05 E-value=19 Score=31.20 Aligned_cols=30 Identities=37% Similarity=0.441 Sum_probs=24.7
Q ss_pred eecCceeeEeccccccccceeeeEEEEEeC
Q 033867 72 HKHSSIDLISLPRDFSKFNSVYMYDIVIKN 101 (110)
Q Consensus 72 Hkr~svdLISLPrdF~~fks~HMYDIVVKn 101 (110)
||+-..-.||||.||..-.++=--|||=.+
T Consensus 129 p~rr~~~~Is~P~DFRqVSsIIDVDivPEt 158 (358)
T KOG3606|consen 129 PKRRPHLSISLPQDFRQVSSIIDVDIVPET 158 (358)
T ss_pred CccCCCccccCccccceeceeeeecccchh
Confidence 445456789999999999999999998654
No 23
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=34.53 E-value=40 Score=25.05 Aligned_cols=55 Identities=25% Similarity=0.373 Sum_probs=36.0
Q ss_pred CCEEEEeeCC--CcccCCCCCCcceEEEEccCCceeechHHHHHHHhhccceeeecCC
Q 033867 10 NGVIRLIENP--QAESQGSSSSRRKVLVHLPTGEVVSSYSSLEQILTGLGWERYYGGD 65 (110)
Q Consensus 10 nGV~rlvenp--~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~~d 65 (110)
.+.+.++||| .+..-..-+.+...||-+ +|+.=++--.|=++|.+-|..=||.||
T Consensus 18 ~~~V~VvENp~Vf~~~~~~~~~~~~pLVCt-~G~p~~A~~~LL~~L~~~g~~l~y~GD 74 (152)
T PF09664_consen 18 SGRVYVVENPAVFSALADELGASCPPLVCT-SGQPSAAARRLLDRLAAAGARLYYSGD 74 (152)
T ss_pred CCEEEEEecHHHHHHHHHhcCCCCCeEEEc-CCcHHHHHHHHHHHHHhCCCEEEEecC
Confidence 3447789998 111100001133566666 888877777788888999999999884
No 24
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=33.02 E-value=19 Score=17.27 Aligned_cols=9 Identities=56% Similarity=0.859 Sum_probs=6.9
Q ss_pred ceeeEeccc
Q 033867 76 SIDLISLPR 84 (110)
Q Consensus 76 svdLISLPr 84 (110)
+.-||+.||
T Consensus 2 ssGlI~fpR 10 (11)
T PF08259_consen 2 SSGLIPFPR 10 (11)
T ss_pred CccccccCC
Confidence 456899887
No 25
>PF07285 DUF1444: Protein of unknown function (DUF1444); InterPro: IPR010838 This family contains several hypothetical bacterial proteins of unknown function that are approximately 250 residues long.
Probab=32.80 E-value=39 Score=27.06 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=32.8
Q ss_pred HHHHHHHhhccceeeecCCCCceEEeec-Cce-eeEeccccccccc
Q 033867 47 SSLEQILTGLGWERYYGGDPDLFQFHKH-SSI-DLISLPRDFSKFN 90 (110)
Q Consensus 47 ~~LE~~L~~LGWeRYy~~d~~l~QfHkr-~sv-dLISLPrdF~~fk 90 (110)
+.||++|.+.+|.--|+-+.+.+.++.+ ..- --|+||.-++++.
T Consensus 8 ~~l~~~L~~~~~~~~~~~~~~~l~i~~~~~~~~vti~L~~ly~~y~ 53 (265)
T PF07285_consen 8 EKLEERLKHENVTFSFDREKDTLRIEHKDNGKGVTINLDNLYAKYQ 53 (265)
T ss_pred HHHHHHhCcCCCeEEEecCCCEEEEEEecCCCeEEEEhHHHHHHHH
Confidence 5799999999999988777777777544 222 2388988777654
No 26
>cd07245 Glo_EDI_BRP_like_9 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases.
Probab=31.87 E-value=1.2e+02 Score=18.13 Aligned_cols=52 Identities=15% Similarity=0.402 Sum_probs=30.1
Q ss_pred ceEEEeeCC-EEEEeeCCCcccCC-CCCCcceEEEEccCCceeechHHHHHHHhhcccee
Q 033867 3 GVWVFNTNG-VIRLIENPQAESQG-SSSSRRKVLVHLPTGEVVSSYSSLEQILTGLGWER 60 (110)
Q Consensus 3 GVWvF~knG-V~rlvenp~~~~~~-~~~~rrKvLvh~ps~Evi~Sy~~LE~~L~~LGWeR 60 (110)
+.|....++ .+.+..+|...... ..++...+-+.+ .+.+.+.++|.++|.+-
T Consensus 36 ~~~~~~~~~~~i~l~~~~~~~~~~~~~~~~~~~~~~v------~d~~~~~~~l~~~g~~~ 89 (114)
T cd07245 36 GAWLYAGDGPQLHLIEEDPPDALPEGPGRDDHIAFRV------DDLDAFRARLKAAGVPY 89 (114)
T ss_pred ceEEEeCCCcEEEEEecCCCccccCCCcccceEEEEe------CCHHHHHHHHHHcCCCc
Confidence 467553455 77787776433211 011112333433 35899999999999973
No 27
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=31.84 E-value=12 Score=28.69 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=18.4
Q ss_pred cCCceeechHHHHHHHhhccce
Q 033867 38 PTGEVVSSYSSLEQILTGLGWE 59 (110)
Q Consensus 38 ps~Evi~Sy~~LE~~L~~LGWe 59 (110)
|..||+..++.|++.|+++||.
T Consensus 116 ~~eev~~~~~~l~~~~~~lG~~ 137 (171)
T PF13382_consen 116 PAEEVARQLEELEEALRELGCP 137 (171)
T ss_dssp -HHHHHHHHHHHHHHHHTTS-B
T ss_pred CHHHHHHHHHHHHHHHHHcCCC
Confidence 5678888999999999999988
No 28
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=30.23 E-value=1.5e+02 Score=20.72 Aligned_cols=46 Identities=24% Similarity=0.426 Sum_probs=31.3
Q ss_pred eEEEEccCCceeechHHHHHHHhhccceeeecCCC-CceEEeec-Ccee-eEecccc
Q 033867 32 KVLVHLPTGEVVSSYSSLEQILTGLGWERYYGGDP-DLFQFHKH-SSID-LISLPRD 85 (110)
Q Consensus 32 KvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~~d~-~l~QfHkr-~svd-LISLPrd 85 (110)
.-.++++-+ .||+.|-+||.++ ++... -.++++.. ...| ||||--|
T Consensus 24 tr~i~V~r~---~s~~el~~kl~~~-----~~~~~~~~lky~Lp~edld~Lisv~~D 72 (97)
T cd06410 24 TRIVSVDRS---ISFKELVSKLSEL-----FGAGVVVTLKYQLPDEDLDALISVSND 72 (97)
T ss_pred eEEEEEcCC---CCHHHHHHHHHHH-----hCCCCceEEEEEcCCCCcceeEEecCc
Confidence 456788888 4999999999987 33222 24555544 5556 8888654
No 29
>PF04841 Vps16_N: Vps16, N-terminal region; InterPro: IPR006926 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=30.15 E-value=47 Score=27.73 Aligned_cols=51 Identities=22% Similarity=0.544 Sum_probs=36.8
Q ss_pred cce-EEEEccCCceeec--hHHHHHHHhhccceeeecCCCCceEEeecCceeeEeccccc
Q 033867 30 RRK-VLVHLPTGEVVSS--YSSLEQILTGLGWERYYGGDPDLFQFHKHSSIDLISLPRDF 86 (110)
Q Consensus 30 rrK-vLvh~ps~Evi~S--y~~LE~~L~~LGWeRYy~~d~~l~QfHkr~svdLISLPrdF 86 (110)
+++ +-+|.++|+.++| ++. .++..+||.. +.+|+=.-+.+++...++.-.|
T Consensus 59 ~p~~I~iys~sG~ll~~i~w~~--~~iv~~~wt~----~e~LvvV~~dG~v~vy~~~G~~ 112 (410)
T PF04841_consen 59 KPNSIQIYSSSGKLLSSIPWDS--GRIVGMGWTD----DEELVVVQSDGTVRVYDLFGEF 112 (410)
T ss_pred CCcEEEEECCCCCEeEEEEECC--CCEEEEEECC----CCeEEEEEcCCEEEEEeCCCce
Confidence 444 9999999999998 666 7999999974 4556655566666666553333
No 30
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=29.79 E-value=28 Score=21.86 Aligned_cols=17 Identities=29% Similarity=0.329 Sum_probs=14.5
Q ss_pred EEccCCceeechHHHHH
Q 033867 35 VHLPTGEVVSSYSSLEQ 51 (110)
Q Consensus 35 vh~ps~Evi~Sy~~LE~ 51 (110)
+|+|+|.-|.|.+.||.
T Consensus 31 lyt~~G~~V~~l~~l~d 47 (60)
T PF03607_consen 31 LYTLDGKRVKSLDELED 47 (60)
T ss_dssp EEETTSSEESSGGGS-T
T ss_pred EECCCCCEeCCHHHHCC
Confidence 69999999999999874
No 31
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=29.73 E-value=85 Score=28.09 Aligned_cols=50 Identities=22% Similarity=0.258 Sum_probs=40.0
Q ss_pred ceEEEEccCCceeechHHHHHHHhhccceeeecCCCCceEEeec-CceeeEec
Q 033867 31 RKVLVHLPTGEVVSSYSSLEQILTGLGWERYYGGDPDLFQFHKH-SSIDLISL 82 (110)
Q Consensus 31 rKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~~d~~l~QfHkr-~svdLISL 82 (110)
.+.-+++-.|+.+. .+.|.++|.++|.+|.-- -..-=||-.| +-+|+.+.
T Consensus 155 ~~~~~~l~~G~~i~-~~~l~~~L~~~GY~r~~~-v~~~GeFsvRG~IiDIfp~ 205 (652)
T PRK05298 155 LKMVLSLRVGQEID-RRELLRRLVDLQYERNDI-DFQRGTFRVRGDVIEIFPA 205 (652)
T ss_pred HhceEEEeCCCCcC-HHHHHHHHHHcCCcccCc-cCCCceEEEECCEEEEeCC
Confidence 35667888888875 899999999999999843 4456789999 55688877
No 32
>PF14067 LssY_C: LssY C-terminus
Probab=27.25 E-value=43 Score=25.67 Aligned_cols=20 Identities=30% Similarity=0.567 Sum_probs=17.1
Q ss_pred eeechHHHHHHHhhccceee
Q 033867 42 VVSSYSSLEQILTGLGWERY 61 (110)
Q Consensus 42 vi~Sy~~LE~~L~~LGWeRY 61 (110)
.+.+-+.|.+.|.++||.+.
T Consensus 30 ~~G~~~~l~~~l~~~GW~~a 49 (192)
T PF14067_consen 30 LIGSLDQLRQALEAAGWIEA 49 (192)
T ss_pred EecCHHHHHHHHHHcCCccC
Confidence 45677899999999999976
No 33
>cd01617 DCX Ubiquitin-like domain of DCX. DCX The ubiquitin-like DCX domain is present in tandem within the N-terminal half of the doublecortin protein. Doublecortin is expressed in migrating neurons. Mutations in the gene encoding doublecortin cause lissencephaly in males and 'double-cortex syndrome' in females.
Probab=27.24 E-value=39 Score=22.25 Aligned_cols=17 Identities=29% Similarity=0.270 Sum_probs=15.4
Q ss_pred EEccCC-ceeechHHHHH
Q 033867 35 VHLPTG-EVVSSYSSLEQ 51 (110)
Q Consensus 35 vh~ps~-Evi~Sy~~LE~ 51 (110)
+|+|.| ..|++.+.||.
T Consensus 49 lyt~~g~~~v~~~~~l~~ 66 (80)
T cd01617 49 LYTLDGGHRVSLLDELED 66 (80)
T ss_pred EEcCCCCeEeccHHHhcC
Confidence 799999 99999999984
No 34
>cd05563 PTS_IIB_ascorbate PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a transmembrane channel IIC subunit. Subunits IIA, IIB, and IIC are encoded by the sgaA, sgaB, and sgaT genes of the E. coli sgaTBA operon. In some bacteria, the IIB (SgaB) domain is fused C-terminal to the IIA (SgaT) domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include ascorbate, chitobiose/lichenan, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=27.15 E-value=81 Score=19.96 Aligned_cols=31 Identities=29% Similarity=0.292 Sum_probs=23.6
Q ss_pred eEEEEccCCceeech--HHHHHHHhhccceeee
Q 033867 32 KVLVHLPTGEVVSSY--SSLEQILTGLGWERYY 62 (110)
Q Consensus 32 KvLvh~ps~Evi~Sy--~~LE~~L~~LGWeRYy 62 (110)
|+||-.|+|-..+.. +.||+.+.++|..--+
T Consensus 1 kilvvC~~G~~tS~ll~~kl~~~f~~~~i~~~~ 33 (86)
T cd05563 1 KILAVCGSGLGSSLMLKMNVEKVLKELGIEAEV 33 (86)
T ss_pred CEEEECCCCccHHHHHHHHHHHHHHHCCCcEEE
Confidence 588999999876663 4588999999986443
No 35
>KOG0855 consensus Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=26.91 E-value=51 Score=26.91 Aligned_cols=17 Identities=41% Similarity=0.767 Sum_probs=14.7
Q ss_pred eEEEeeCCEEEEeeCCC
Q 033867 4 VWVFNTNGVIRLIENPQ 20 (110)
Q Consensus 4 VWvF~knGV~rlvenp~ 20 (110)
-|+|+|+||..++-|-.
T Consensus 178 h~if~kg~~k~~ik~~~ 194 (211)
T KOG0855|consen 178 HYIFDKGGVKQLIKNNQ 194 (211)
T ss_pred EEEEecCCeEEEEEecc
Confidence 59999999999998754
No 36
>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.
Probab=26.90 E-value=73 Score=20.43 Aligned_cols=29 Identities=24% Similarity=0.403 Sum_probs=22.5
Q ss_pred ceEEEEccCCceeechHHHHHHHhhccceeee
Q 033867 31 RKVLVHLPTGEVVSSYSSLEQILTGLGWERYY 62 (110)
Q Consensus 31 rKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy 62 (110)
++++||..+| .+|....+ .|..+|.++.|
T Consensus 62 ~~ivvyC~~G--~rs~~a~~-~L~~~G~~~v~ 90 (101)
T cd01518 62 KKVLMYCTGG--IRCEKASA-YLKERGFKNVY 90 (101)
T ss_pred CEEEEECCCc--hhHHHHHH-HHHHhCCccee
Confidence 5899999988 56666655 68999988654
No 37
>PF04466 Terminase_3: Phage terminase large subunit; InterPro: IPR006701 Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit. This region is found on the large subunit and possesses an endonuclease and ATPase activity that requires Mg2+ and a neutral or slightly basic reaction. This region is also found in bacterial sequences [, ].; GO: 0006323 DNA packaging; PDB: 2WBN_A 2WC9_A.
Probab=26.79 E-value=21 Score=29.52 Aligned_cols=54 Identities=28% Similarity=0.356 Sum_probs=0.0
Q ss_pred echHHHHHHHhhccceeeecCCCCceEEeec--CceeeEeccccccccceeeeEEEE
Q 033867 44 SSYSSLEQILTGLGWERYYGGDPDLFQFHKH--SSIDLISLPRDFSKFNSVYMYDIV 98 (110)
Q Consensus 44 ~Sy~~LE~~L~~LGWeRYy~~d~~l~QfHkr--~svdLISLPrdF~~fks~HMYDIV 98 (110)
|.|+.|...|..||.+-+|.-...-+..|+. +.+-+-.| .|-.+.||++-+|++
T Consensus 47 Sv~~~l~~~i~~~gl~~~f~~~~s~~~i~~~~Gs~i~F~Gl-d~~~kiKS~~~~~~~ 102 (387)
T PF04466_consen 47 SVYAQLKWAIDRLGLSDYFKINKSPIEIYKPNGSKIIFRGL-DDPEKIKSIKGIDII 102 (387)
T ss_dssp ---------------------------------------------------------
T ss_pred HHHHHHHHHHHhcCCCceEEEcCCCceEEccCCCEEEEeCC-CChhhcCCcccccEE
Confidence 6799999999999999988754444444665 56666677 789999999866665
No 38
>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....
Probab=26.28 E-value=65 Score=17.76 Aligned_cols=20 Identities=25% Similarity=0.776 Sum_probs=13.3
Q ss_pred ccceeeecCC-CCceEEeecC
Q 033867 56 LGWERYYGGD-PDLFQFHKHS 75 (110)
Q Consensus 56 LGWeRYy~~d-~~l~QfHkr~ 75 (110)
-||+++++.+ ...+.+|...
T Consensus 3 ~gW~~~~~~~~g~~YY~N~~t 23 (31)
T PF00397_consen 3 PGWEEYFDPDSGRPYYYNHET 23 (31)
T ss_dssp TTEEEEEETTTSEEEEEETTT
T ss_pred cCCEEEEcCCCCCEEEEeCCC
Confidence 3899999644 4556666653
No 39
>PF01954 DUF104: Protein of unknown function DUF104; InterPro: IPR008203 This family includes short archaebacterial proteins of unknown function. Archaeoglobus fulgidus has twelve copies of this protein, with several being clustered together in the genome.; PDB: 2NWT_A.
Probab=26.15 E-value=82 Score=20.48 Aligned_cols=29 Identities=21% Similarity=0.453 Sum_probs=14.7
Q ss_pred EEeeCCEEEEeeCCCcccCCCCCCcceEEEEccCCc
Q 033867 6 VFNTNGVIRLIENPQAESQGSSSSRRKVLVHLPTGE 41 (110)
Q Consensus 6 vF~knGV~rlvenp~~~~~~~~~~rrKvLvh~ps~E 41 (110)
+| +|||++..+...-+- | .+|.|.+.+.+
T Consensus 8 iY-e~GvlkPl~~~~L~E--g----~~V~i~I~~~~ 36 (60)
T PF01954_consen 8 IY-ENGVLKPLEPVDLPE--G----EEVKITIEEEE 36 (60)
T ss_dssp EE-ETTEEEECS-----T--T----EEEEEEE----
T ss_pred EE-ECCEEEECCCCCCCC--C----CEEEEEEecch
Confidence 57 899999998743221 1 36777766654
No 40
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=26.11 E-value=39 Score=22.66 Aligned_cols=17 Identities=35% Similarity=0.501 Sum_probs=11.1
Q ss_pred ccceeeeEEEEEeCCCe
Q 033867 88 KFNSVYMYDIVIKNPNV 104 (110)
Q Consensus 88 ~fks~HMYDIVVKnrn~ 104 (110)
.|.|-+-||++|+|++-
T Consensus 19 ~f~sgq~~D~~v~d~~g 35 (82)
T PF12690_consen 19 QFPSGQRYDFVVKDKEG 35 (82)
T ss_dssp EESSS--EEEEEE-TT-
T ss_pred EeCCCCEEEEEEECCCC
Confidence 47888999999998764
No 41
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=26.02 E-value=60 Score=29.24 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=29.6
Q ss_pred cceEEEEccCCceeechHHHHHHHhhccceeeec
Q 033867 30 RRKVLVHLPTGEVVSSYSSLEQILTGLGWERYYG 63 (110)
Q Consensus 30 rrKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~ 63 (110)
-.+||+.+.+.++ .+++.|.+.+.++-|++|+.
T Consensus 54 A~RVll~l~~f~a-~~~~~Ly~~v~~i~W~~~l~ 86 (702)
T PRK11783 54 ASRILLPLAEFKV-YSDLDLYLGVQAIDWTEHFS 86 (702)
T ss_pred hhheEEEeeeeec-CCHHHHHHHHHcCCHHHhCC
Confidence 4589999998886 48999999999999999987
No 42
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=25.54 E-value=1.2e+02 Score=16.09 Aligned_cols=21 Identities=19% Similarity=0.475 Sum_probs=13.3
Q ss_pred ccceeeecCCCCceEEeecCc
Q 033867 56 LGWERYYGGDPDLFQFHKHSS 76 (110)
Q Consensus 56 LGWeRYy~~d~~l~QfHkr~s 76 (110)
.||+.+++.+...+.++..+.
T Consensus 3 ~gW~~~~~~~g~~yy~n~~t~ 23 (32)
T smart00456 3 PGWEERKDPDGRPYYYNHETK 23 (32)
T ss_pred CCCEEEECCCCCEEEEECCCC
Confidence 589988875544555555444
No 43
>TIGR02981 phageshock_pspE phage shock operon rhodanese PspE. Members of this very narrowly defined protein family are proteins active as rhodanese (EC 2.8.1.1) and found in the extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species. Note that the designation phage shock protein PspE has been applied, incorrectly, in many instances where the genome lacks the phage shock regulon entirely.
Probab=24.68 E-value=97 Score=21.04 Aligned_cols=31 Identities=19% Similarity=0.210 Sum_probs=23.8
Q ss_pred cceEEEEccCCceeechHHHHHHHhhccceeeec
Q 033867 30 RRKVLVHLPTGEVVSSYSSLEQILTGLGWERYYG 63 (110)
Q Consensus 30 rrKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~ 63 (110)
.++++||..+|. +|.... +.|.++|.++++.
T Consensus 58 ~~~vvlyC~~G~--rS~~aa-~~L~~~G~~~v~~ 88 (101)
T TIGR02981 58 NDTVKLYCNAGR--QSGMAK-DILLDMGYTHAEN 88 (101)
T ss_pred CCeEEEEeCCCH--HHHHHH-HHHHHcCCCeEEe
Confidence 468999999996 555554 5888999998764
No 44
>smart00537 DCX Domain in the Doublecortin (DCX) gene product. Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects.
Probab=24.25 E-value=51 Score=22.25 Aligned_cols=17 Identities=29% Similarity=0.362 Sum_probs=15.5
Q ss_pred EEccCCceeechHHHHH
Q 033867 35 VHLPTGEVVSSYSSLEQ 51 (110)
Q Consensus 35 vh~ps~Evi~Sy~~LE~ 51 (110)
+|+|+|.-|+|.+.||.
T Consensus 55 lyt~~G~~v~~l~~l~~ 71 (89)
T smart00537 55 LYTLDGKKVTSLDELED 71 (89)
T ss_pred EEcCCCCEECCHHHhCc
Confidence 78999999999999984
No 45
>PF08842 Mfa2: Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; InterPro: IPR014941 This family of proteins may be lipoproteins principally from bacilli. They are between 300 and 400 residues. Many Bacteroides-like bacterial species, including Porphyromonas gingivalis, the causal agent of periodontal infection, carry at least two types of fimbriae, namely FimA and Mfa1 fimbriae, following the names of their major subunit proteins []. Normally, FimA fimbriae are long filaments that are easily detached from cells, whereas Mfa1 fimbriae are short filaments that are tightly bound to cells; however, in the absence of Mfa2 protein, the Mfa1 fimbriae are also very long and are not attached. Mfa2 and Mfa1 are associated with each other in whole P. gingivalis cells to the extent that Mfa2 is located on the cell surface and probably associated with Mfa1 fimbriae in such a way that it anchors the Mfa1 fimbriae to the cell surface and regulates Mfa1 filament length [].; PDB: 3PAY_C 3GF8_A.
Probab=23.62 E-value=32 Score=25.36 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=7.3
Q ss_pred eEEEeeCCE
Q 033867 4 VWVFNTNGV 12 (110)
Q Consensus 4 VWvF~knGV 12 (110)
|++||+||.
T Consensus 33 lyvFd~~g~ 41 (283)
T PF08842_consen 33 LYVFDEDGK 41 (283)
T ss_dssp EEEE-TTSB
T ss_pred EEEEeCCCe
Confidence 799998998
No 46
>TIGR02254 YjjG/YfnB HAD superfamily (subfamily IA) hydrolase, TIGR02254. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549). Most likely, these enzymes are phosphatases.
Probab=23.44 E-value=47 Score=23.57 Aligned_cols=28 Identities=11% Similarity=0.077 Sum_probs=21.3
Q ss_pred EEEEccCCceeechHHHHHHHhhccceeeec
Q 033867 33 VLVHLPTGEVVSSYSSLEQILTGLGWERYYG 63 (110)
Q Consensus 33 vLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~ 63 (110)
..+.+-||- +.+.++.+|..+||.+|++
T Consensus 113 ~~~~i~Sn~---~~~~~~~~l~~~~l~~~fd 140 (224)
T TIGR02254 113 FRLYIVTNG---VRETQYKRLRKSGLFPFFD 140 (224)
T ss_pred CcEEEEeCC---chHHHHHHHHHCCcHhhcC
Confidence 445555553 4688899999999999986
No 47
>CHL00193 ycf35 Ycf35; Provisional
Probab=23.38 E-value=2.7e+02 Score=20.48 Aligned_cols=18 Identities=22% Similarity=0.348 Sum_probs=16.4
Q ss_pred eeechHHHHHHHhhccce
Q 033867 42 VVSSYSSLEQILTGLGWE 59 (110)
Q Consensus 42 vi~Sy~~LE~~L~~LGWe 59 (110)
.|+..+.|++-|..||..
T Consensus 10 ~i~d~~~L~~AL~dLg~~ 27 (128)
T CHL00193 10 SIQNLNLLKKALNDLNIE 27 (128)
T ss_pred EEcCHHHHHHHHHHcCCC
Confidence 578999999999999987
No 48
>PLN02891 IMP cyclohydrolase
Probab=23.36 E-value=1.2e+02 Score=27.95 Aligned_cols=32 Identities=19% Similarity=0.315 Sum_probs=25.3
Q ss_pred CcceEEEEccCCceeechHHHHHHHhhccceeeec
Q 033867 29 SRRKVLVHLPTGEVVSSYSSLEQILTGLGWERYYG 63 (110)
Q Consensus 29 ~rrKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~ 63 (110)
+.|++|+=|-.- |....|=+.|.++|||=+-.
T Consensus 21 ~~krALISVsDK---tgi~~fAk~L~~~gveIiST 52 (547)
T PLN02891 21 GKKQALISLSDK---TDLALLANGLQELGYTIVST 52 (547)
T ss_pred cccEEEEEEecc---cCHHHHHHHHHHCCCEEEEc
Confidence 467899877654 56788899999999997754
No 49
>cd08968 MeNeil2_N N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2). This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of
Probab=23.28 E-value=1.5e+02 Score=22.02 Aligned_cols=39 Identities=15% Similarity=0.285 Sum_probs=22.3
Q ss_pred CcceEEEeeCCEEEEeeCCCcccCC-CCCCcceEEEEccCCceee
Q 033867 1 MSGVWVFNTNGVIRLIENPQAESQG-SSSSRRKVLVHLPTGEVVS 44 (110)
Q Consensus 1 MsGVWvF~knGV~rlvenp~~~~~~-~~~~rrKvLvh~ps~Evi~ 44 (110)
|.|.|.++.-+ .+|.+...+ -..+..|+.++.++|+-+.
T Consensus 78 M~Gs~~~~~~~-----~~~~~~~~~~~~~~~~~l~l~f~~~~~l~ 117 (126)
T cd08968 78 LFGSVRANEFS-----RAKKANKRGDWKDPNPRLVLHFESGGFLV 117 (126)
T ss_pred CEEEEEEcccc-----cCcccccccCCCCCCCeEEEEeCCCcEEE
Confidence 77888883323 223222221 0113469999999998554
No 50
>cd01395 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.
Probab=23.23 E-value=89 Score=20.55 Aligned_cols=28 Identities=18% Similarity=0.382 Sum_probs=23.8
Q ss_pred CcceEEEEccCCceeechHHHHHHHhhc
Q 033867 29 SRRKVLVHLPTGEVVSSYSSLEQILTGL 56 (110)
Q Consensus 29 ~rrKvLvh~ps~Evi~Sy~~LE~~L~~L 56 (110)
.++-|.-..|.|...++|++.++-|.+-
T Consensus 22 ~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t 49 (60)
T cd01395 22 VKKHVIYKAPCGRSLRNMSEVHRYLRET 49 (60)
T ss_pred cccceEEECCcchhhhcHHHHHHHHHhc
Confidence 3556888899999999999999988753
No 51
>PF07727 RVT_2: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR013103 A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This entry includes reverse transcriptases not recognised by IPR000477 from INTERPRO [].
Probab=23.23 E-value=27 Score=27.44 Aligned_cols=35 Identities=29% Similarity=0.496 Sum_probs=25.9
Q ss_pred hHHHHHHHhhccceeeecCCCCceEEeecCceeeEe
Q 033867 46 YSSLEQILTGLGWERYYGGDPDLFQFHKHSSIDLIS 81 (110)
Q Consensus 46 y~~LE~~L~~LGWeRYy~~d~~l~QfHkr~svdLIS 81 (110)
|+.|-..|.++|+++.-. ||||+--+..+..-+|.
T Consensus 132 ~~~l~~~L~~~GF~~~~~-D~clfi~~~~~~~~ii~ 166 (246)
T PF07727_consen 132 YKTLDKFLKKLGFKQSKA-DPCLFIKKSGDGFIIIL 166 (246)
T ss_pred hhhcccccchhhhhcccc-ccccccccccccccccc
Confidence 789999999999999976 99996443334443333
No 52
>PF04397 LytTR: LytTr DNA-binding domain; InterPro: IPR007492 The LytTr domain is a DNA-binding, potential winged helix-turn-helix domain (~100 residues) present in a variety of bacterial transcriptional regulators of the algR/agrA/lytR family. It is named after the lytR response regulators involved in the regulation of cell autolysis. The LytTr domain binds to a specific DNA sequence pattern in the upstream regions of target genes []. The N-terminal of the protein contains a response regulator receiver domain (IPR001789 from INTERPRO).; PDB: 3BS1_A 3D6W_B.
Probab=23.19 E-value=2.1e+02 Score=18.11 Aligned_cols=37 Identities=16% Similarity=0.301 Sum_probs=22.5
Q ss_pred cceEEEEccCCceeechHHHHHHHhhccceeeecCCCCceEEeec
Q 033867 30 RRKVLVHLPTGEVVSSYSSLEQILTGLGWERYYGGDPDLFQFHKH 74 (110)
Q Consensus 30 rrKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~~d~~l~QfHkr 74 (110)
.+.+.+|+. ++..+....|.+....| . ++.++|-|++
T Consensus 18 ~~~~~i~~~-~~~~~~~~tl~~~~~~l------~-~~~F~r~hrs 54 (98)
T PF04397_consen 18 GHYVRIHTK-NGSYEIRGTLKELEEQL------P-PPNFIRIHRS 54 (98)
T ss_dssp TTEEEEEES-S-EEEECS-HHHHHHHS--------TTTEEEEETT
T ss_pred CCEEEEEEC-CcEEEEeCCHHHHhhhh------c-ccccccccce
Confidence 368999999 55555455555544443 2 4677888887
No 53
>PF14090 HTH_39: Helix-turn-helix domain
Probab=23.14 E-value=13 Score=23.94 Aligned_cols=29 Identities=17% Similarity=0.402 Sum_probs=22.6
Q ss_pred ceEEEEccCCceeechHHHHH-----------HHhhccce
Q 033867 31 RKVLVHLPTGEVVSSYSSLEQ-----------ILTGLGWE 59 (110)
Q Consensus 31 rKvLvh~ps~Evi~Sy~~LE~-----------~L~~LGWe 59 (110)
.++|=|+-.|..||+++++++ .|++.||.
T Consensus 4 ~rIL~~L~~~~~it~~ea~~~~gi~~~~aRI~eLR~~G~~ 43 (70)
T PF14090_consen 4 KRILAALRRGGSITTLEARRELGIMRLAARISELRKKGYP 43 (70)
T ss_pred HHHHHHHHcCCCcCHHHHHHHcCCCCHHHHHHHHHHcCCe
Confidence 466777878888999998865 57788884
No 54
>PLN02611 glutamate--cysteine ligase
Probab=22.76 E-value=93 Score=27.63 Aligned_cols=47 Identities=28% Similarity=0.520 Sum_probs=31.5
Q ss_pred eEEEEccCCceeechHHHHHHHhhc----cceeeecCCCCceEEeecCceeeEec
Q 033867 32 KVLVHLPTGEVVSSYSSLEQILTGL----GWERYYGGDPDLFQFHKHSSIDLISL 82 (110)
Q Consensus 32 KvLvh~ps~Evi~Sy~~LE~~L~~L----GWeRYy~~d~~l~QfHkr~svdLISL 82 (110)
|..++..+.+ =.+|+.+...|.+| ||+.+++ +.+++++-+. + .-|||
T Consensus 76 ~f~~~~~~~~-pv~y~~i~~lL~~l~~~~gw~~~~e-~g~iIgl~~~-g-~~ITl 126 (482)
T PLN02611 76 KFGFELATLR-PMKYDQIAQLLEGLAERFGWEKIME-GDNIIGLKQD-G-QSVSL 126 (482)
T ss_pred eeeccCCCCC-CCCHHHHHHHHHHHHHhcCCceecc-CCceecccCC-C-CceEe
Confidence 5556666554 34677777776655 9999998 7788887542 2 45555
No 55
>PF13950 Epimerase_Csub: UDP-glucose 4-epimerase C-term subunit; PDB: 1EK5_A 1I3K_B 1I3M_B 1HZJ_A 1EK6_A 1I3N_A 1I3L_A 2CNB_B 1GY8_D 1NAI_A ....
Probab=22.56 E-value=44 Score=21.38 Aligned_cols=23 Identities=17% Similarity=0.429 Sum_probs=12.5
Q ss_pred CCceeechHHHHHHHhhccceee
Q 033867 39 TGEVVSSYSSLEQILTGLGWERY 61 (110)
Q Consensus 39 s~Evi~Sy~~LE~~L~~LGWeRY 61 (110)
.|.+-.+|+.-++.-..|||+=-
T Consensus 19 ~GD~~~~~Ad~~kA~~~LgW~p~ 41 (62)
T PF13950_consen 19 PGDPAHLVADISKAREELGWKPK 41 (62)
T ss_dssp TT--SEE-B--HHHHHHC----S
T ss_pred CCchhhhhCCHHHHHHHhCCCcC
Confidence 68899999999999999999843
No 56
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=21.98 E-value=97 Score=17.28 Aligned_cols=28 Identities=21% Similarity=0.204 Sum_probs=21.4
Q ss_pred eEEEEccCCceeechHHHHHHHhhccce
Q 033867 32 KVLVHLPTGEVVSSYSSLEQILTGLGWE 59 (110)
Q Consensus 32 KvLvh~ps~Evi~Sy~~LE~~L~~LGWe 59 (110)
+|.+|--.+.-+.+|.++-+--..||..
T Consensus 2 ~V~~yd~~~~~i~~F~Si~eAa~~l~i~ 29 (37)
T PF07453_consen 2 PVYVYDLNTNEIKSFDSIREAARYLGIS 29 (37)
T ss_pred eEEEEECCCCeEEEEcCHHHHHHHhCCC
Confidence 6777866666689999888888877765
No 57
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=21.68 E-value=64 Score=31.90 Aligned_cols=53 Identities=30% Similarity=0.543 Sum_probs=36.3
Q ss_pred ceEEEeeCCEEEEeeCCCcccCCCCCCcceEEEEccCCceeechHHHHHHHhhccceeeecCCC-----CceEEe
Q 033867 3 GVWVFNTNGVIRLIENPQAESQGSSSSRRKVLVHLPTGEVVSSYSSLEQILTGLGWERYYGGDP-----DLFQFH 72 (110)
Q Consensus 3 GVWvF~knGV~rlvenp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~~L~~LGWeRYy~~d~-----~l~QfH 72 (110)
||.|| |||-+|---.. --|-|.-..|+=.|. .||++||.++=+.|+| .++++.
T Consensus 704 ~v~vF-KDGTiRfD~tD------------~PlTHfrp~Eigvsv----eklreLGY~~Di~G~pL~~~dQivELk 761 (1095)
T TIGR00354 704 GVYVF-KDGTARFDATD------------LPITHFKPAEIGVSV----EKLRELGYERDYYGAELKDENQIVELK 761 (1095)
T ss_pred CeeEe-cCCceeccCcC------------CCcccccHHHcCCCH----HHHHHcCCccccCCCCCCCccceEEee
Confidence 89999 99999974321 113455566766665 4789999998776644 566654
No 58
>COG3076 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.85 E-value=48 Score=25.40 Aligned_cols=36 Identities=22% Similarity=0.409 Sum_probs=22.6
Q ss_pred ceEEEEccCCceeechHHHHHHHhh------------ccceeeecCCCC
Q 033867 31 RKVLVHLPTGEVVSSYSSLEQILTG------------LGWERYYGGDPD 67 (110)
Q Consensus 31 rKvLvh~ps~Evi~Sy~~LE~~L~~------------LGWeRYy~~d~~ 67 (110)
.+++.+-...||--.-+.+...-.+ -||.-||+ ||+
T Consensus 69 ~~i~C~Diisev~L~aeiIDaQ~e~l~~L~Ek~~~~YDGWGTY~E-dpn 116 (135)
T COG3076 69 DIVICCDIISEVALNAELIDAQVEQLMPLAEKFDVEYDGWGTYFE-DPN 116 (135)
T ss_pred CEEEEeehhhhhhcCHHHHHHHHHHHHHHHHHhCceecCceeecc-CCC
Confidence 3777777777766555444332222 29999999 664
No 59
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=20.71 E-value=59 Score=21.88 Aligned_cols=21 Identities=33% Similarity=0.468 Sum_probs=15.3
Q ss_pred CCceeechHHHHHHHhhccce
Q 033867 39 TGEVVSSYSSLEQILTGLGWE 59 (110)
Q Consensus 39 s~Evi~Sy~~LE~~L~~LGWe 59 (110)
|||--.=-+.|.++|.+.||.
T Consensus 13 sGe~~~L~~~L~~rL~e~GW~ 33 (86)
T PF10163_consen 13 SGEYERLKELLRQRLIECGWR 33 (86)
T ss_dssp CTHHHHHHHHHHHHHHHTTHH
T ss_pred cCcHHHHHHHHHHHHHHCChH
Confidence 444444456789999999996
No 60
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.27 E-value=54 Score=25.33 Aligned_cols=15 Identities=27% Similarity=0.642 Sum_probs=12.0
Q ss_pred ceEEEeeCCEEEEee
Q 033867 3 GVWVFNTNGVIRLIE 17 (110)
Q Consensus 3 GVWvF~knGV~rlve 17 (110)
++|+||++|+--.-.
T Consensus 5 ~~yIFdR~g~Cl~y~ 19 (140)
T KOG3368|consen 5 NFYIFDRNGVCLFYR 19 (140)
T ss_pred EEEEEcCCccEEEeh
Confidence 789999999975543
Done!