Query 033957
Match_columns 107
No_of_seqs 54 out of 56
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 08:10:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033957.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033957hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13668 hypothetical protein; 78.3 2 4.3E-05 35.3 2.7 44 44-87 7-53 (267)
2 PF07927 YcfA: YcfA-like prote 69.1 8.1 0.00018 23.0 3.2 16 44-59 1-16 (56)
3 smart00391 MBD Methyl-CpG bind 66.9 11 0.00025 25.1 3.9 29 27-55 26-54 (77)
4 PF15590 Imm15: Immunity prote 64.1 2.6 5.6E-05 29.0 0.3 13 53-65 22-34 (69)
5 PF03816 LytR_cpsA_psr: Cell e 62.8 5.7 0.00012 28.5 1.9 18 65-82 7-25 (149)
6 cd00122 MBD MeCP2, MBD1, MBD2, 60.7 20 0.00043 22.5 3.9 29 27-55 23-51 (62)
7 KOG0675 Calnexin [Posttranslat 55.4 11 0.00024 34.3 2.8 26 80-105 197-225 (558)
8 smart00359 PUA Putative RNA-bi 54.4 17 0.00036 22.2 2.7 33 2-41 15-47 (77)
9 TIGR00350 lytR_cpsA_psr cell e 54.2 10 0.00022 27.7 2.0 18 66-83 9-27 (152)
10 cd01396 MeCP2_MBD MeCP2, MBD1, 52.8 33 0.00071 23.0 4.1 29 27-55 24-52 (77)
11 COG5123 TOA2 Transcription ini 50.7 11 0.00024 28.0 1.8 16 2-17 71-88 (113)
12 smart00850 LytTR LytTr DNA-bin 47.2 40 0.00086 21.1 3.7 35 29-72 19-55 (96)
13 TIGR01436 glu_cys_lig_pln glut 47.1 23 0.00049 30.7 3.3 49 29-79 29-83 (446)
14 COG4004 Uncharacterized protei 44.2 16 0.00034 26.6 1.6 16 42-57 12-27 (96)
15 TIGR00354 polC DNA polymerase, 43.5 20 0.00044 35.0 2.7 53 3-70 704-762 (1095)
16 PF04841 Vps16_N: Vps16, N-ter 42.8 18 0.00038 30.1 1.9 51 28-83 59-112 (410)
17 PF11629 Mst1_SARAH: C termina 42.6 16 0.00034 23.7 1.3 13 43-55 9-21 (49)
18 PF07723 LRR_2: Leucine Rich R 42.5 13 0.00028 20.2 0.8 19 85-103 1-19 (26)
19 PF14056 DUF4250: Domain of un 41.0 17 0.00038 23.6 1.3 14 44-57 34-47 (55)
20 PRK04023 DNA polymerase II lar 40.8 24 0.00052 34.6 2.7 54 2-70 728-787 (1121)
21 cd06410 PB1_UP2 Uncharacterize 40.3 94 0.002 21.7 5.0 45 30-82 24-72 (97)
22 PF07404 TEBP_beta: Telomere-b 39.3 2.8 6.2E-05 35.7 -3.2 23 34-56 98-120 (379)
23 PRK09379 membrane-bound transc 38.2 23 0.0005 28.8 2.0 19 65-83 83-102 (303)
24 PF02589 DUF162: Uncharacteris 38.1 60 0.0013 23.3 3.9 45 8-53 98-143 (189)
25 PRK14714 DNA polymerase II lar 38.0 28 0.00062 34.7 2.8 54 2-70 775-834 (1337)
26 PF13382 Adenine_deam_C: Adeni 37.9 11 0.00023 28.8 -0.1 27 36-64 116-142 (171)
27 COG3076 Uncharacterized protei 37.4 16 0.00035 27.8 0.8 37 29-65 69-117 (135)
28 PF06415 iPGM_N: BPG-independe 36.9 32 0.00069 27.5 2.5 36 29-64 61-111 (223)
29 PF01429 MBD: Methyl-CpG bindi 36.1 85 0.0018 20.5 4.1 29 27-55 29-57 (77)
30 cd05563 PTS_IIB_ascorbate PTS_ 35.7 49 0.0011 20.9 2.8 47 30-77 1-49 (86)
31 KOG3606 Cell polarity protein 35.6 18 0.0004 31.2 1.0 30 69-98 129-158 (358)
32 PRK05752 uroporphyrinogen-III 33.8 48 0.001 25.1 2.9 26 29-58 4-29 (255)
33 PRK05298 excinuclease ABC subu 33.5 71 0.0015 28.4 4.3 66 29-95 155-230 (652)
34 CHL00193 ycf35 Ycf35; Provisio 33.1 1.5E+02 0.0032 21.8 5.3 30 40-70 10-39 (128)
35 PF08259 Periviscerokin: Periv 32.7 19 0.00041 17.2 0.4 9 73-81 2-10 (11)
36 PF07727 RVT_2: Reverse transc 32.7 14 0.00031 28.8 -0.1 35 44-78 132-166 (246)
37 PF13783 DUF4177: Domain of un 32.4 1.2E+02 0.0027 18.6 4.6 15 43-57 18-35 (61)
38 PLN02611 glutamate--cysteine l 32.0 54 0.0012 28.9 3.3 47 30-79 76-126 (482)
39 PF01954 DUF104: Protein of un 31.9 57 0.0012 21.1 2.7 28 6-39 8-36 (60)
40 PF13119 DUF3973: Domain of un 31.4 15 0.00032 23.2 -0.2 9 4-12 18-26 (41)
41 PF07285 DUF1444: Protein of u 30.5 47 0.001 26.5 2.5 44 45-88 8-54 (265)
42 PF03833 PolC_DP2: DNA polymer 30.3 17 0.00037 34.8 0.0 49 3-69 758-815 (900)
43 PF14067 LssY_C: LssY C-termin 29.3 40 0.00086 25.8 1.9 20 40-59 30-49 (192)
44 PF11767 SET_assoc: Histone ly 29.0 49 0.0011 21.8 2.0 23 42-64 12-34 (66)
45 cd01617 DCX Ubiquitin-like dom 28.8 36 0.00079 22.3 1.4 17 33-49 49-66 (80)
46 PF13590 DUF4136: Domain of un 28.7 76 0.0016 21.5 3.0 28 44-71 41-69 (151)
47 cd01518 RHOD_YceA Member of th 28.2 69 0.0015 20.4 2.6 29 29-60 62-90 (101)
48 PF12690 BsuPI: Intracellular 28.0 36 0.00079 22.7 1.3 17 85-101 19-35 (82)
49 cd00133 PTS_IIB PTS_IIB: subun 27.8 84 0.0018 18.4 2.8 31 30-60 1-33 (84)
50 TIGR02981 phageshock_pspE phag 27.1 86 0.0019 21.2 3.0 31 28-61 58-88 (101)
51 PRK11783 rlmL 23S rRNA m(2)G24 26.9 59 0.0013 29.1 2.7 34 28-62 54-87 (702)
52 cd01395 HMT_MBD Methyl-CpG bin 26.6 74 0.0016 20.8 2.5 27 27-53 22-48 (60)
53 PF04466 Terminase_3: Phage te 25.8 23 0.0005 29.2 0.0 53 42-95 47-102 (387)
54 KOG3061 Proteasome maturation 25.5 30 0.00065 26.4 0.6 24 42-65 93-116 (137)
55 PF00585 Thr_dehydrat_C: C-ter 25.3 35 0.00075 23.0 0.8 37 29-69 50-90 (91)
56 PF03607 DCX: Doublecortin; I 25.1 26 0.00056 22.0 0.2 17 33-49 31-47 (60)
57 PF11379 DUF3182: Protein of u 25.1 85 0.0018 27.3 3.3 36 8-56 135-170 (355)
58 smart00537 DCX Domain in the D 25.1 47 0.001 22.3 1.5 17 33-49 55-71 (89)
59 PF14090 HTH_39: Helix-turn-he 24.9 13 0.00028 23.8 -1.2 29 29-57 4-43 (70)
60 TIGR02254 YjjG/YfnB HAD superf 24.7 41 0.0009 23.7 1.2 28 31-61 113-140 (224)
61 PRK05928 hemD uroporphyrinogen 24.6 1.1E+02 0.0024 21.9 3.4 27 29-59 2-28 (249)
62 PRK11697 putative two-componen 24.0 82 0.0018 22.3 2.6 35 28-74 159-195 (238)
63 TIGR00631 uvrb excinuclease AB 23.7 1.2E+02 0.0025 27.4 4.0 51 29-80 152-203 (655)
64 PRK14715 DNA polymerase II lar 23.0 83 0.0018 32.2 3.2 53 2-69 752-810 (1627)
65 cd04906 ACT_ThrD-I_1 First of 23.0 27 0.00059 22.6 -0.1 35 34-71 47-83 (85)
66 PF13420 Acetyltransf_4: Acety 22.9 53 0.0012 21.7 1.4 54 42-96 96-155 (155)
67 PF10163 EnY2: Transcription f 22.9 35 0.00075 22.9 0.4 22 36-57 12-33 (86)
68 TIGR00318 cyaB adenylyl cyclas 22.8 75 0.0016 23.3 2.2 23 42-64 11-42 (174)
69 PF10382 DUF2439: Protein of u 22.6 1.6E+02 0.0034 19.7 3.6 26 8-43 20-45 (83)
70 cd05566 PTS_IIB_galactitol PTS 22.0 89 0.0019 19.8 2.2 32 29-60 1-34 (89)
71 PRK13958 N-(5'-phosphoribosyl) 21.6 1.5E+02 0.0033 22.6 3.8 35 29-75 54-88 (207)
72 PF09992 DUF2233: Predicted pe 21.2 3E+02 0.0066 19.3 5.5 59 3-61 69-135 (170)
73 COG1391 GlnE Glutamine synthet 21.1 42 0.00091 32.5 0.8 23 37-59 249-273 (963)
74 PF10394 Hat1_N: Histone acety 20.7 16 0.00035 27.1 -1.6 10 62-71 142-151 (161)
75 PF13950 Epimerase_Csub: UDP-g 20.7 39 0.00085 21.5 0.3 24 37-60 19-42 (62)
76 cd05567 PTS_IIB_mannitol PTS_I 20.5 1.2E+02 0.0027 19.5 2.7 52 30-83 2-55 (87)
77 cd01580 AcnA_IRP_Swivel Aconit 20.4 85 0.0018 24.7 2.2 20 31-50 72-91 (171)
78 PF14173 ComGG: ComG operon pr 20.3 2.2E+02 0.0047 19.1 4.0 13 2-14 41-53 (95)
79 COG0766 MurA UDP-N-acetylgluco 20.1 60 0.0013 28.8 1.4 15 42-56 399-413 (421)
80 PF10620 MdcG: Phosphoribosyl- 20.0 2.4E+02 0.0052 21.8 4.6 60 25-84 66-152 (213)
No 1
>PRK13668 hypothetical protein; Provisional
Probab=78.29 E-value=2 Score=35.34 Aligned_cols=44 Identities=27% Similarity=0.507 Sum_probs=33.3
Q ss_pred HHHHHHHHhhccceeecC-CCceeeeee-cCceeE-Eeccccccccc
Q 033957 44 YAVLERKLSSLGWERYYD-DPELLQFHK-RSTVHL-ISLPKDFNKFK 87 (107)
Q Consensus 44 y~~LE~kL~~LGWeRYy~-d~~l~QfHk-r~sv~L-ISLPrdF~~fk 87 (107)
-+.||++|...||...|+ +.+.|++-+ ...--. |+||.-++++.
T Consensus 7 ~~~l~~rL~~~~~~~~~~r~~d~Lri~~~~~~kgvti~L~~~~aky~ 53 (267)
T PRK13668 7 RDKLKKRLSHPDWDFSFDREKETLRIERKDNKKGVTISLPPIVAKWE 53 (267)
T ss_pred HHHHHHHHhCCCCeeEeccCCceEEEEEccCCCceEEEcHHHHHHHH
Confidence 368999999999999997 777777733 333333 88998887764
No 2
>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=69.14 E-value=8.1 Score=23.02 Aligned_cols=16 Identities=25% Similarity=0.412 Sum_probs=12.5
Q ss_pred HHHHHHHHhhccceee
Q 033957 44 YAVLERKLSSLGWERY 59 (107)
Q Consensus 44 y~~LE~kL~~LGWeRY 59 (107)
|++|++.|.++||+--
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 5789999999999955
No 3
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=66.93 E-value=11 Score=25.11 Aligned_cols=29 Identities=24% Similarity=0.243 Sum_probs=25.7
Q ss_pred CcceEEEEccCCceeehHHHHHHHHhhcc
Q 033957 27 TRRKVLVHVPTNEVMTSYAVLERKLSSLG 55 (107)
Q Consensus 27 ~rrKvLvh~ps~Evi~Sy~~LE~kL~~LG 55 (107)
++.-|.-+.|+|.-++|+.++.+-|.+-|
T Consensus 26 ~~~dV~Y~sP~GkklRs~~ev~~YL~~~~ 54 (77)
T smart00391 26 GKFDVYYISPCGKKLRSKSELARYLHKNG 54 (77)
T ss_pred CcccEEEECCCCCeeeCHHHHHHHHHhCC
Confidence 35689999999999999999999998765
No 4
>PF15590 Imm15: Immunity protein 15
Probab=64.08 E-value=2.6 Score=29.00 Aligned_cols=13 Identities=46% Similarity=0.974 Sum_probs=10.3
Q ss_pred hccceeecCCCce
Q 033957 53 SLGWERYYDDPEL 65 (107)
Q Consensus 53 ~LGWeRYy~d~~l 65 (107)
.-|||++|.||.=
T Consensus 22 ~d~We~~y~DP~D 34 (69)
T PF15590_consen 22 PDGWETLYQDPRD 34 (69)
T ss_pred CcchhhhccCCCC
Confidence 3499999998853
No 5
>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=62.79 E-value=5.7 Score=28.49 Aligned_cols=18 Identities=33% Similarity=0.698 Sum_probs=13.8
Q ss_pred eeeeeec-CceeEEecccc
Q 033957 65 LLQFHKR-STVHLISLPKD 82 (107)
Q Consensus 65 l~QfHkr-~sv~LISLPrd 82 (107)
|+.++.. .++.+||+|||
T Consensus 7 l~~~~~~~~~~~~vsIPRD 25 (149)
T PF03816_consen 7 LVSINPDTKKVTLVSIPRD 25 (149)
T ss_dssp EEEEETTTTEEEEEEE-TT
T ss_pred EEEEcCCCCEEEEEEEcCc
Confidence 4567774 89999999997
No 6
>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=60.68 E-value=20 Score=22.54 Aligned_cols=29 Identities=21% Similarity=0.258 Sum_probs=25.6
Q ss_pred CcceEEEEccCCceeehHHHHHHHHhhcc
Q 033957 27 TRRKVLVHVPTNEVMTSYAVLERKLSSLG 55 (107)
Q Consensus 27 ~rrKvLvh~ps~Evi~Sy~~LE~kL~~LG 55 (107)
++.-|.-+.|+|+.++|..++++-|.+-|
T Consensus 23 ~k~dv~Y~sP~Gk~~Rs~~ev~~yL~~~~ 51 (62)
T cd00122 23 GKGDVYYYSPCGKKLRSKPEVARYLEKTG 51 (62)
T ss_pred CcceEEEECCCCceecCHHHHHHHHHhCC
Confidence 35678889999999999999999998765
No 7
>KOG0675 consensus Calnexin [Posttranslational modification, protein turnover, chaperones]
Probab=55.44 E-value=11 Score=34.25 Aligned_cols=26 Identities=38% Similarity=0.682 Sum_probs=22.2
Q ss_pred cccccccc---eeeeEEEEEecCCeeEEe
Q 033957 80 PKDFNKFK---SMHMYDIVVKNRNVFEVR 105 (107)
Q Consensus 80 PrdF~~fk---s~HMYDIVVKnrn~F~Vr 105 (107)
|.++.++- .+|||-.|||+-|.|+||
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 8
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=54.36 E-value=17 Score=22.23 Aligned_cols=33 Identities=24% Similarity=0.338 Sum_probs=21.1
Q ss_pred ceeEEEeCceEEeeCCCccCCCCCCCcceEEEEccCCcee
Q 033957 2 SGVWVFKNGVVRLENPGAEACSNSNTRRKVLVHVPTNEVM 41 (107)
Q Consensus 2 sGVWvFknGV~rlenp~~~~~~~~~~rrKvLvh~ps~Evi 41 (107)
.|-|+|.+||.+.+...++ | --|.|+...|+.+
T Consensus 15 ~g~~v~~~~v~~~~~~~~~---g----~~V~v~~~~g~~v 47 (77)
T smart00359 15 NGASLLAPGVVRVDGGIKE---G----DVVVIVDEKGEPL 47 (77)
T ss_pred cCCCcccceeEEEeCCcCC---C----CEEEEEcCCCCEE
Confidence 4679999999887321111 1 2677777777754
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=54.19 E-value=10 Score=27.67 Aligned_cols=18 Identities=22% Similarity=0.551 Sum_probs=13.8
Q ss_pred eeeeec-CceeEEeccccc
Q 033957 66 LQFHKR-STVHLISLPKDF 83 (107)
Q Consensus 66 ~QfHkr-~sv~LISLPrdF 83 (107)
+-+.+. .++.+||+|||-
T Consensus 9 ~~i~~~~~~~~lisIPRDt 27 (152)
T TIGR00350 9 VTLDPKRKTAVVVSIPRDT 27 (152)
T ss_pred EEEcCCCCEEEEEEecCCc
Confidence 445554 789999999985
No 10
>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=52.82 E-value=33 Score=22.98 Aligned_cols=29 Identities=28% Similarity=0.257 Sum_probs=25.8
Q ss_pred CcceEEEEccCCceeehHHHHHHHHhhcc
Q 033957 27 TRRKVLVHVPTNEVMTSYAVLERKLSSLG 55 (107)
Q Consensus 27 ~rrKvLvh~ps~Evi~Sy~~LE~kL~~LG 55 (107)
++.-|.-+.|+|+-++|..+|++-|.+-|
T Consensus 24 ~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~ 52 (77)
T cd01396 24 GKFDVYYISPTGKKFRSKVELARYLEKNG 52 (77)
T ss_pred CcceEEEECCCCCEEECHHHHHHHHHhCC
Confidence 35578889999999999999999999877
No 11
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=50.73 E-value=11 Score=27.98 Aligned_cols=16 Identities=56% Similarity=0.968 Sum_probs=13.9
Q ss_pred ceeEEE--eCceEEeeCC
Q 033957 2 SGVWVF--KNGVVRLENP 17 (107)
Q Consensus 2 sGVWvF--knGV~rlenp 17 (107)
-|||-| ||=+++++|.
T Consensus 71 D~VWtFi~kn~~~s~~n~ 88 (113)
T COG5123 71 DGVWTFITKNFVMSLNNE 88 (113)
T ss_pred cceeEEEecCeEEEeccc
Confidence 389999 8999999875
No 12
>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=47.15 E-value=40 Score=21.06 Aligned_cols=35 Identities=20% Similarity=0.374 Sum_probs=22.7
Q ss_pred ceEEEEccCCceee--hHHHHHHHHhhccceeecCCCceeeeeecC
Q 033957 29 RKVLVHVPTNEVMT--SYAVLERKLSSLGWERYYDDPELLQFHKRS 72 (107)
Q Consensus 29 rKvLvh~ps~Evi~--Sy~~LE~kL~~LGWeRYy~d~~l~QfHkr~ 72 (107)
+++.+|+.+++... |...+|.+|. ++..+|-|++.
T Consensus 19 ~~~~i~~~~~~~~~~~~l~~~~~~L~---------~~~F~r~hrs~ 55 (96)
T smart00850 19 NYVTIHTKDGTYLVRGTLKELEEKLD---------PTNFFRIHRSY 55 (96)
T ss_pred CEEEEEECCcEEEehhhHHHHHhhCC---------CCceEEechhH
Confidence 58899998776443 4445555442 34678888874
No 13
>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=47.06 E-value=23 Score=30.68 Aligned_cols=49 Identities=18% Similarity=0.304 Sum_probs=34.9
Q ss_pred ceEEEEccCCceeehHH--HHHHHHh----hccceeecCCCceeeeeecCceeEEec
Q 033957 29 RKVLVHVPTNEVMTSYA--VLERKLS----SLGWERYYDDPELLQFHKRSTVHLISL 79 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~--~LE~kL~----~LGWeRYy~d~~l~QfHkr~sv~LISL 79 (107)
-|..++.++++-++-+. .++..|. ..|||.++++.+++++-+.+ .-|||
T Consensus 29 E~f~~~~~~~~~~~y~~~~gi~~~l~~l~~~~g~~~~~e~g~~i~l~~~~--~~itl 83 (446)
T TIGR01436 29 EKFGFEKNTLRPMKYEQKGGIAELLNGIAERFGWQKVMEGDKIIGLKQDK--QSISL 83 (446)
T ss_pred eeeeeecCCCCCCCCCCchhHHHHHHHHHhhcCCceeccCCceeeecCCC--CeEEE
Confidence 37777888888776553 2444444 56999999999999996633 55665
No 14
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=44.24 E-value=16 Score=26.62 Aligned_cols=16 Identities=38% Similarity=0.640 Sum_probs=14.4
Q ss_pred ehHHHHHHHHhhccce
Q 033957 42 TSYAVLERKLSSLGWE 57 (107)
Q Consensus 42 ~Sy~~LE~kL~~LGWe 57 (107)
..++.|+|.|.+|||+
T Consensus 12 ~~~dri~~~l~e~g~~ 27 (96)
T COG4004 12 PDPDRIMRGLSELGWT 27 (96)
T ss_pred CCHHHHHHHHHHhCee
Confidence 3589999999999998
No 15
>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=43.55 E-value=20 Score=34.96 Aligned_cols=53 Identities=32% Similarity=0.655 Sum_probs=34.6
Q ss_pred eeEEEeCceEEeeCCCccCCCCCCCcceEEEEccCCceeehHHHHHHHHhhccceee-cC-----CCceeeeee
Q 033957 3 GVWVFKNGVVRLENPGAEACSNSNTRRKVLVHVPTNEVMTSYAVLERKLSSLGWERY-YD-----DPELLQFHK 70 (107)
Q Consensus 3 GVWvFknGV~rlenp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRY-y~-----d~~l~QfHk 70 (107)
||.|||||-+|-.--..| |-|.-..|+=.|. .||++||.++= |+ |..++++..
T Consensus 704 ~v~vFKDGTiRfD~tD~P-----------lTHfrp~Eigvsv----eklreLGY~~Di~G~pL~~~dQivELk~ 762 (1095)
T TIGR00354 704 GVYVFKDGTARFDATDLP-----------ITHFKPAEIGVSV----EKLRELGYERDYYGAELKDENQIVELKP 762 (1095)
T ss_pred CeeEecCCceeccCcCCC-----------cccccHHHcCCCH----HHHHHcCCccccCCCCCCCccceEEeec
Confidence 899999999999211111 3355556666665 47899999875 44 345666643
No 16
>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=42.79 E-value=18 Score=30.10 Aligned_cols=51 Identities=20% Similarity=0.499 Sum_probs=38.6
Q ss_pred cce-EEEEccCCceeeh--HHHHHHHHhhccceeecCCCceeeeeecCceeEEeccccc
Q 033957 28 RRK-VLVHVPTNEVMTS--YAVLERKLSSLGWERYYDDPELLQFHKRSTVHLISLPKDF 83 (107)
Q Consensus 28 rrK-vLvh~ps~Evi~S--y~~LE~kL~~LGWeRYy~d~~l~QfHkr~sv~LISLPrdF 83 (107)
+++ +-+|.++|+.++| ++. .++-.+||.. +.+|+=.-+.+++...++.-.|
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 454 9999999999998 566 7999999975 5677766666777777664444
No 17
>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=42.60 E-value=16 Score=23.69 Aligned_cols=13 Identities=46% Similarity=0.754 Sum_probs=10.5
Q ss_pred hHHHHHHHHhhcc
Q 033957 43 SYAVLERKLSSLG 55 (107)
Q Consensus 43 Sy~~LE~kL~~LG 55 (107)
||+.|+++|.+|-
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 8999999998874
No 18
>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=42.51 E-value=13 Score=20.23 Aligned_cols=19 Identities=21% Similarity=0.566 Sum_probs=15.5
Q ss_pred ccceeeeEEEEEecCCeeE
Q 033957 85 KFKSMHMYDIVVKNRNVFE 103 (107)
Q Consensus 85 ~fks~HMYDIVVKnrn~F~ 103 (107)
.+|+.|..+|...|...|+
T Consensus 1 sLKtL~L~~v~f~~~~~l~ 19 (26)
T PF07723_consen 1 SLKTLHLDSVVFSDEDSLE 19 (26)
T ss_pred CCeEEEeeEEEECChhHHH
Confidence 3689999999998887664
No 19
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=41.01 E-value=17 Score=23.56 Aligned_cols=14 Identities=50% Similarity=0.752 Sum_probs=12.2
Q ss_pred HHHHHHHHhhccce
Q 033957 44 YAVLERKLSSLGWE 57 (107)
Q Consensus 44 y~~LE~kL~~LGWe 57 (107)
=+.|++||.+.|.+
T Consensus 34 ~~~l~~kL~~~Gy~ 47 (55)
T PF14056_consen 34 KEELEEKLASIGYE 47 (55)
T ss_pred HHHHHHHHHHcCCe
Confidence 36899999999987
No 20
>PRK04023 DNA polymerase II large subunit; Validated
Probab=40.83 E-value=24 Score=34.61 Aligned_cols=54 Identities=30% Similarity=0.554 Sum_probs=35.0
Q ss_pred ceeEEEeCceEEeeCCCccCCCCCCCcceEEEEccCCceeehHHHHHHHHhhccceee-cC-----CCceeeeee
Q 033957 2 SGVWVFKNGVVRLENPGAEACSNSNTRRKVLVHVPTNEVMTSYAVLERKLSSLGWERY-YD-----DPELLQFHK 70 (107)
Q Consensus 2 sGVWvFknGV~rlenp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRY-y~-----d~~l~QfHk 70 (107)
-||.|||||-+|-.--..| |-|.-..|+=+|. .||++||.+.= |+ |..++++..
T Consensus 728 ~~v~vFKDGTiR~D~tD~P-----------lTHfrp~Eigvsv----eklreLGY~~Di~G~pL~~~dQivELk~ 787 (1121)
T PRK04023 728 HDVYVFKDGTVRYDMTDLP-----------LTHFRPREIGVSV----EKLRELGYTHDIYGNPLESEDQIVELKV 787 (1121)
T ss_pred cCeeEecCcceeccCcCCC-----------cccccHHHcCCCH----HHHHHcCCccccCCCCCCCccceEEeec
Confidence 3899999999999211111 3345555666665 47899999884 44 445677643
No 21
>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=40.28 E-value=94 Score=21.66 Aligned_cols=45 Identities=29% Similarity=0.420 Sum_probs=31.2
Q ss_pred eEEEEccCCceeehHHHHHHHHhhccceeecCCC--ceeeeeec-Ccee-EEecccc
Q 033957 30 KVLVHVPTNEVMTSYAVLERKLSSLGWERYYDDP--ELLQFHKR-STVH-LISLPKD 82 (107)
Q Consensus 30 KvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy~d~--~l~QfHkr-~sv~-LISLPrd 82 (107)
.-.++++-+ .||++|-+||.++ ++-+ -.++++.. ...| ||||--|
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 446788888 4999999999987 3322 24566554 5556 8888654
No 22
>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=39.35 E-value=2.8 Score=35.72 Aligned_cols=23 Identities=43% Similarity=0.560 Sum_probs=15.4
Q ss_pred EccCCceeehHHHHHHHHhhccc
Q 033957 34 HVPTNEVMTSYAVLERKLSSLGW 56 (107)
Q Consensus 34 h~ps~Evi~Sy~~LE~kL~~LGW 56 (107)
-+.|-||.|||+-||.||.-.-+
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 47899999999999999865433
No 23
>PRK09379 membrane-bound transcriptional regulator LytR; Provisional
Probab=38.20 E-value=23 Score=28.78 Aligned_cols=19 Identities=16% Similarity=0.670 Sum_probs=15.1
Q ss_pred eeeeeec-CceeEEeccccc
Q 033957 65 LLQFHKR-STVHLISLPKDF 83 (107)
Q Consensus 65 l~QfHkr-~sv~LISLPrdF 83 (107)
|+.+.+. .++.+||+|||=
T Consensus 83 l~~in~~~~~~~~iSIPRDt 102 (303)
T PRK09379 83 VMTLNPKTNSMKMVSIPRDT 102 (303)
T ss_pred EEEEcCCCCeEEEEEecCcc
Confidence 4666654 799999999984
No 24
>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=38.12 E-value=60 Score=23.33 Aligned_cols=45 Identities=18% Similarity=0.254 Sum_probs=32.0
Q ss_pred eCceEEe-eCCCccCCCCCCCcceEEEEccCCceeehHHHHHHHHhh
Q 033957 8 KNGVVRL-ENPGAEACSNSNTRRKVLVHVPTNEVMTSYAVLERKLSS 53 (107)
Q Consensus 8 knGV~rl-enp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~kL~~ 53 (107)
.+|-+=+ ++++... .-+-.+++.++.++.++++.++++.-+++..
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 4676666 6654331 1122378999999999999999999999988
No 25
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=38.03 E-value=28 Score=34.68 Aligned_cols=54 Identities=26% Similarity=0.478 Sum_probs=34.9
Q ss_pred ceeEEEeCceEEeeCCCccCCCCCCCcceEEEEccCCceeehHHHHHHHHhhccceee-cC-----CCceeeeee
Q 033957 2 SGVWVFKNGVVRLENPGAEACSNSNTRRKVLVHVPTNEVMTSYAVLERKLSSLGWERY-YD-----DPELLQFHK 70 (107)
Q Consensus 2 sGVWvFknGV~rlenp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRY-y~-----d~~l~QfHk 70 (107)
-||.|||||-+|-.--..| |-|.-..|+=.|. .||++||.+.= |+ |..++++..
T Consensus 775 ~~v~vFKDGTiR~D~td~P-----------lThfrp~Eigvs~----eklreLGY~~Di~G~pL~~~dQivELk~ 834 (1337)
T PRK14714 775 HDVYVFKDGTVRYDMTDLP-----------VTHFRPREIGVSV----EKLRELGYTQDIHGDPLVHEDQVVELKV 834 (1337)
T ss_pred cCeeEecCCceeccCcCCc-----------cccccHHHcCCCH----HHHHHcCCccccCCCCCCCccceEEeec
Confidence 3899999999999211111 3355556666665 47899999875 44 335666643
No 26
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=37.92 E-value=11 Score=28.82 Aligned_cols=27 Identities=41% Similarity=0.647 Sum_probs=21.1
Q ss_pred cCCceeehHHHHHHHHhhccceeecCCCc
Q 033957 36 PTNEVMTSYAVLERKLSSLGWERYYDDPE 64 (107)
Q Consensus 36 ps~Evi~Sy~~LE~kL~~LGWeRYy~d~~ 64 (107)
|..||+..++.|++.|+++||. ++||-
T Consensus 116 ~~eev~~~~~~l~~~~~~lG~~--~~~p~ 142 (171)
T PF13382_consen 116 PAEEVARQLEELEEALRELGCP--FDDPF 142 (171)
T ss_dssp -HHHHHHHHHHHHHHHHTTS-B--TTTBS
T ss_pred CHHHHHHHHHHHHHHHHHcCCC--CCCHH
Confidence 5678999999999999999998 34554
No 27
>COG3076 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.38 E-value=16 Score=27.81 Aligned_cols=37 Identities=22% Similarity=0.495 Sum_probs=24.0
Q ss_pred ceEEEEccCCceeehHHHHHHHHhh------------ccceeecCCCce
Q 033957 29 RKVLVHVPTNEVMTSYAVLERKLSS------------LGWERYYDDPEL 65 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~kL~~------------LGWeRYy~d~~l 65 (107)
.+++.+-...||--.-+.+...-.+ -||.-||+||+-
T Consensus 69 ~~i~C~Diisev~L~aeiIDaQ~e~l~~L~Ek~~~~YDGWGTY~EdpnA 117 (135)
T COG3076 69 DIVICCDIISEVALNAELIDAQVEQLMPLAEKFDVEYDGWGTYFEDPNA 117 (135)
T ss_pred CEEEEeehhhhhhcCHHHHHHHHHHHHHHHHHhCceecCceeeccCCCc
Confidence 3777777777766555444332222 299999999864
No 28
>PF06415 iPGM_N: BPG-independent PGAM N-terminus (iPGM_N); InterPro: IPR011258 This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (5.4.2.1 from EC). The family is found in conjunction with Metalloenzyme (located in the C-terminal region of the protein). ; GO: 0004619 phosphoglycerate mutase activity, 0030145 manganese ion binding, 0006007 glucose catabolic process, 0005737 cytoplasm; PDB: 1EQJ_A 1EJJ_A 1O99_A 1O98_A 3IGZ_B 3IGY_B 3NVL_A 2IFY_A.
Probab=36.93 E-value=32 Score=27.53 Aligned_cols=36 Identities=39% Similarity=0.708 Sum_probs=26.5
Q ss_pred ceEEEEc-------cCCceeehHHHHHHHHhhccc-------eeecC-CCc
Q 033957 29 RKVLVHV-------PTNEVMTSYAVLERKLSSLGW-------ERYYD-DPE 64 (107)
Q Consensus 29 rKvLvh~-------ps~Evi~Sy~~LE~kL~~LGW-------eRYy~-d~~ 64 (107)
++|.||. |-.--+...+.||.+|.++|. -|||. |+|
T Consensus 61 ~~V~vH~f~DGRDt~P~S~~~yl~~l~~~l~~~~~g~IAsv~GRyyaMDRD 111 (223)
T PF06415_consen 61 KKVYVHAFTDGRDTPPKSALKYLEELEEKLAEIGIGRIASVSGRYYAMDRD 111 (223)
T ss_dssp SEEEEEEEE-SSSS-TTTHHHHHHHHHHHHHHHTCTEEEEEEECCCCT--T
T ss_pred CEEEEEEecCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeceeeeeccc
Confidence 4788884 445566778999999999998 79997 553
No 29
>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=36.13 E-value=85 Score=20.47 Aligned_cols=29 Identities=17% Similarity=0.140 Sum_probs=25.2
Q ss_pred CcceEEEEccCCceeehHHHHHHHHhhcc
Q 033957 27 TRRKVLVHVPTNEVMTSYAVLERKLSSLG 55 (107)
Q Consensus 27 ~rrKvLvh~ps~Evi~Sy~~LE~kL~~LG 55 (107)
++.-|.-+.|+|+-++|..++.+-|.+.+
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 35678888999999999999999998765
No 30
>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=35.72 E-value=49 Score=20.90 Aligned_cols=47 Identities=23% Similarity=0.237 Sum_probs=29.6
Q ss_pred eEEEEccCCceeehH--HHHHHHHhhccceeecCCCceeeeeecCceeEE
Q 033957 30 KVLVHVPTNEVMTSY--AVLERKLSSLGWERYYDDPELLQFHKRSTVHLI 77 (107)
Q Consensus 30 KvLvh~ps~Evi~Sy--~~LE~kL~~LGWeRYy~d~~l~QfHkr~sv~LI 77 (107)
|+||-.|+|-..+.. +.||+.+.++|..-=+...++-|. .-...|||
T Consensus 1 kilvvC~~G~~tS~ll~~kl~~~f~~~~i~~~~~~~~~~~~-~~~~~DlI 49 (86)
T cd05563 1 KILAVCGSGLGSSLMLKMNVEKVLKELGIEAEVEHTDLGSA-KASSADII 49 (86)
T ss_pred CEEEECCCCccHHHHHHHHHHHHHHHCCCcEEEEEeccccc-CCCCCCEE
Confidence 588999999876664 468899999998644333333332 12344555
No 31
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=35.56 E-value=18 Score=31.16 Aligned_cols=30 Identities=40% Similarity=0.491 Sum_probs=24.8
Q ss_pred eecCceeEEeccccccccceeeeEEEEEec
Q 033957 69 HKRSTVHLISLPKDFNKFKSMHMYDIVVKN 98 (107)
Q Consensus 69 Hkr~sv~LISLPrdF~~fks~HMYDIVVKn 98 (107)
||+-..-.||||.||..-.++=--|||-.+
T Consensus 129 p~rr~~~~Is~P~DFRqVSsIIDVDivPEt 158 (358)
T KOG3606|consen 129 PKRRPHLSISLPQDFRQVSSIIDVDIVPET 158 (358)
T ss_pred CccCCCccccCccccceeceeeeecccchh
Confidence 445456789999999999999999998654
No 32
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=33.77 E-value=48 Score=25.14 Aligned_cols=26 Identities=27% Similarity=0.385 Sum_probs=21.8
Q ss_pred ceEEEEccCCceeehHHHHHHHHhhcccee
Q 033957 29 RKVLVHVPTNEVMTSYAVLERKLSSLGWER 58 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~kL~~LGWeR 58 (107)
++|||=-|..+- +.|-++|.++||+=
T Consensus 4 ~~vlvTRp~~~~----~~l~~~l~~~G~~~ 29 (255)
T PRK05752 4 WRLLLTRPAEEC----AALAASLAEAGIFS 29 (255)
T ss_pred CEEEECCcHHHH----HHHHHHHHHcCCCE
Confidence 589998888864 78889999999983
No 33
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=33.46 E-value=71 Score=28.42 Aligned_cols=66 Identities=18% Similarity=0.309 Sum_probs=48.1
Q ss_pred ceEEEEccCCceeehHHHHHHHHhhccceeecCCCceeeeeec-CceeEEec-ccc------c--cccceeeeEEEE
Q 033957 29 RKVLVHVPTNEVMTSYAVLERKLSSLGWERYYDDPELLQFHKR-STVHLISL-PKD------F--NKFKSMHMYDIV 95 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy~d~~l~QfHkr-~sv~LISL-Prd------F--~~fks~HMYDIV 95 (107)
.+.-+++-.|+.|. .+.|.++|.++|.+|----..-=||-.| +-+|+.+. -.+ | ...-|++-+|+.
T Consensus 155 ~~~~~~l~~G~~i~-~~~l~~~L~~~GY~r~~~v~~~GeFsvRG~IiDIfp~~~~~~PvRIeffgdeIesIr~Fd~~ 230 (652)
T PRK05298 155 LKMVLSLRVGQEID-RRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEERAIRIEFFGDEIERISEFDPL 230 (652)
T ss_pred HhceEEEeCCCCcC-HHHHHHHHHHcCCcccCccCCCceEEEECCEEEEeCCCCCCccEEEEEECCEEeEEEEECCC
Confidence 35667888888876 8999999999999998655566789999 56688877 222 1 234566666643
No 34
>CHL00193 ycf35 Ycf35; Provisional
Probab=33.13 E-value=1.5e+02 Score=21.77 Aligned_cols=30 Identities=13% Similarity=0.318 Sum_probs=21.2
Q ss_pred eeehHHHHHHHHhhccceeecCCCceeeeee
Q 033957 40 VMTSYAVLERKLSSLGWERYYDDPELLQFHK 70 (107)
Q Consensus 40 vi~Sy~~LE~kL~~LGWeRYy~d~~l~QfHk 70 (107)
.|+.-+.|++-|..||.. +...+..++-..
T Consensus 10 ~i~d~~~L~~AL~dLg~~-~~~~~~~vrgy~ 39 (128)
T CHL00193 10 SIQNLNLLKKALNDLNIE-WKKENQVIKGYN 39 (128)
T ss_pred EEcCHHHHHHHHHHcCCC-ceeCCceeeccC
Confidence 578999999999999987 333344444333
No 35
>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=32.70 E-value=19 Score=17.20 Aligned_cols=9 Identities=33% Similarity=0.733 Sum_probs=6.9
Q ss_pred ceeEEeccc
Q 033957 73 TVHLISLPK 81 (107)
Q Consensus 73 sv~LISLPr 81 (107)
+.-|||.||
T Consensus 2 ssGlI~fpR 10 (11)
T PF08259_consen 2 SSGLIPFPR 10 (11)
T ss_pred CccccccCC
Confidence 456899887
No 36
>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=32.68 E-value=14 Score=28.79 Aligned_cols=35 Identities=26% Similarity=0.402 Sum_probs=26.8
Q ss_pred HHHHHHHHhhccceeecCCCceeeeeecCceeEEe
Q 033957 44 YAVLERKLSSLGWERYYDDPELLQFHKRSTVHLIS 78 (107)
Q Consensus 44 y~~LE~kL~~LGWeRYy~d~~l~QfHkr~sv~LIS 78 (107)
|+.|-..|.++|+++.-.||||+--+..+..-+|.
T Consensus 132 ~~~l~~~L~~~GF~~~~~D~clfi~~~~~~~~ii~ 166 (246)
T PF07727_consen 132 YKTLDKFLKKLGFKQSKADPCLFIKKSGDGFIIIL 166 (246)
T ss_pred hhhcccccchhhhhccccccccccccccccccccc
Confidence 88999999999999999999997444334443333
No 37
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=32.40 E-value=1.2e+02 Score=18.59 Aligned_cols=15 Identities=40% Similarity=0.603 Sum_probs=11.0
Q ss_pred hHHHHHHHHhh---ccce
Q 033957 43 SYAVLERKLSS---LGWE 57 (107)
Q Consensus 43 Sy~~LE~kL~~---LGWe 57 (107)
+.+.+|+.|.+ -|||
T Consensus 18 ~~~~~~~~Ln~~g~eGWe 35 (61)
T PF13783_consen 18 DPEDLEEILNEYGKEGWE 35 (61)
T ss_pred CHHHHHHHHHHHHhCCcE
Confidence 66778877655 5898
No 38
>PLN02611 glutamate--cysteine ligase
Probab=32.05 E-value=54 Score=28.94 Aligned_cols=47 Identities=21% Similarity=0.428 Sum_probs=32.4
Q ss_pred eEEEEccCCceeehHHHHHHHHhhc----cceeecCCCceeeeeecCceeEEec
Q 033957 30 KVLVHVPTNEVMTSYAVLERKLSSL----GWERYYDDPELLQFHKRSTVHLISL 79 (107)
Q Consensus 30 KvLvh~ps~Evi~Sy~~LE~kL~~L----GWeRYy~d~~l~QfHkr~sv~LISL 79 (107)
|..++..+.+ =.+|+.+...|.+| |||.++++.+++++-+. + .-|||
T Consensus 76 ~f~~~~~~~~-pv~y~~i~~lL~~l~~~~gw~~~~e~g~iIgl~~~-g-~~ITl 126 (482)
T PLN02611 76 KFGFELATLR-PMKYDQIAQLLEGLAERFGWEKIMEGDNIIGLKQD-G-QSVSL 126 (482)
T ss_pred eeeccCCCCC-CCCHHHHHHHHHHHHHhcCCceeccCCceecccCC-C-CceEe
Confidence 5555566554 34677777766655 99999999999998553 2 45555
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=31.93 E-value=57 Score=21.14 Aligned_cols=28 Identities=21% Similarity=0.453 Sum_probs=13.7
Q ss_pred EEeCceEEe-eCCCccCCCCCCCcceEEEEccCCc
Q 033957 6 VFKNGVVRL-ENPGAEACSNSNTRRKVLVHVPTNE 39 (107)
Q Consensus 6 vFknGV~rl-enp~~~~~~~~~~rrKvLvh~ps~E 39 (107)
+|+|||++. +...-+ .| .+|.|.+.+.+
T Consensus 8 iYe~GvlkPl~~~~L~--Eg----~~V~i~I~~~~ 36 (60)
T PF01954_consen 8 IYENGVLKPLEPVDLP--EG----EEVKITIEEEE 36 (60)
T ss_dssp EEETTEEEECS-------TT----EEEEEEE----
T ss_pred EEECCEEEECCCCCCC--CC----CEEEEEEecch
Confidence 579999999 653211 11 36777766654
No 40
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=31.38 E-value=15 Score=23.19 Aligned_cols=9 Identities=44% Similarity=0.604 Sum_probs=7.4
Q ss_pred eEEEeCceE
Q 033957 4 VWVFKNGVV 12 (107)
Q Consensus 4 VWvFknGV~ 12 (107)
-|+||||+-
T Consensus 18 ~~iF~ngfY 26 (41)
T PF13119_consen 18 DKIFKNGFY 26 (41)
T ss_pred hhhhhCcee
Confidence 489999975
No 41
>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=30.49 E-value=47 Score=26.46 Aligned_cols=44 Identities=18% Similarity=0.304 Sum_probs=31.6
Q ss_pred HHHHHHHhhccceeecC-CCceeeeeec--CceeEEeccccccccce
Q 033957 45 AVLERKLSSLGWERYYD-DPELLQFHKR--STVHLISLPKDFNKFKS 88 (107)
Q Consensus 45 ~~LE~kL~~LGWeRYy~-d~~l~QfHkr--~sv~LISLPrdF~~fks 88 (107)
+.||++|.+.+|.--|+ +.+.+..+.+ ..---|+||.-+++...
T Consensus 8 ~~l~~~L~~~~~~~~~~~~~~~l~i~~~~~~~~vti~L~~ly~~y~~ 54 (265)
T PF07285_consen 8 EKLEERLKHENVTFSFDREKDTLRIEHKDNGKGVTINLDNLYAKYQE 54 (265)
T ss_pred HHHHHHhCcCCCeEEEecCCCEEEEEEecCCCeEEEEhHHHHHHHHh
Confidence 57999999999998886 6666777543 22223889988877653
No 42
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised 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. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=30.27 E-value=17 Score=34.80 Aligned_cols=49 Identities=39% Similarity=0.753 Sum_probs=0.0
Q ss_pred eeEEEeCceEEe--eC-CCccCCCCCCCcceEEEEccCCceeehHHHHHHHHhhccceee-cC-----CCceeeee
Q 033957 3 GVWVFKNGVVRL--EN-PGAEACSNSNTRRKVLVHVPTNEVMTSYAVLERKLSSLGWERY-YD-----DPELLQFH 69 (107)
Q Consensus 3 GVWvFknGV~rl--en-p~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRY-y~-----d~~l~QfH 69 (107)
||.|||||-+|- .+ | |-|.--.|+=+|. .||++||.+.= |+ |..++++.
T Consensus 758 ~v~vFKDGTvRyD~tD~P--------------lTHfrP~EIgvsv----EkLrELGY~~Di~G~pL~~~dQivELk 815 (900)
T PF03833_consen 758 GVYVFKDGTVRYDMTDLP--------------LTHFRPREIGVSV----EKLRELGYTHDIYGKPLESDDQIVELK 815 (900)
T ss_dssp ----------------------------------------------------------------------------
T ss_pred CeeEecCcceeeccccCc--------------cccccHHhcCCCH----HHHHHhCccccccCCccCCccceeEee
Confidence 899999999999 33 2 2344445665665 47899999874 44 33466664
No 43
>PF14067 LssY_C: LssY C-terminus
Probab=29.35 E-value=40 Score=25.75 Aligned_cols=20 Identities=25% Similarity=0.493 Sum_probs=17.1
Q ss_pred eeehHHHHHHHHhhccceee
Q 033957 40 VMTSYAVLERKLSSLGWERY 59 (107)
Q Consensus 40 vi~Sy~~LE~kL~~LGWeRY 59 (107)
.+.+-+.|.+.|.++||.+.
T Consensus 30 ~~G~~~~l~~~l~~~GW~~a 49 (192)
T PF14067_consen 30 LIGSLDQLRQALEAAGWIEA 49 (192)
T ss_pred EecCHHHHHHHHHHcCCccC
Confidence 45677899999999999976
No 44
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=28.96 E-value=49 Score=21.81 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=20.0
Q ss_pred ehHHHHHHHHhhccceeecCCCc
Q 033957 42 TSYAVLERKLSSLGWERYYDDPE 64 (107)
Q Consensus 42 ~Sy~~LE~kL~~LGWeRYy~d~~ 64 (107)
++.+.+..+|+.-+|+|-..|+.
T Consensus 12 ~~v~d~K~~Lr~y~~~~I~~d~t 34 (66)
T PF11767_consen 12 VTVEDFKKRLRKYRWDRIRDDRT 34 (66)
T ss_pred ccHHHHHHHHhcCCcceEEecCC
Confidence 46789999999999999987764
No 45
>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=28.82 E-value=36 Score=22.31 Aligned_cols=17 Identities=12% Similarity=0.045 Sum_probs=15.5
Q ss_pred EEccCC-ceeehHHHHHH
Q 033957 33 VHVPTN-EVMTSYAVLER 49 (107)
Q Consensus 33 vh~ps~-Evi~Sy~~LE~ 49 (107)
+|+|.| ..|++.+.||.
T Consensus 49 lyt~~g~~~v~~~~~l~~ 66 (80)
T cd01617 49 LYTLDGGHRVSLLDELED 66 (80)
T ss_pred EEcCCCCeEeccHHHhcC
Confidence 799999 99999999984
No 46
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=28.67 E-value=76 Score=21.45 Aligned_cols=28 Identities=21% Similarity=0.532 Sum_probs=22.5
Q ss_pred HHHHHHHHhhccceeecCCCce-eeeeec
Q 033957 44 YAVLERKLSSLGWERYYDDPEL-LQFHKR 71 (107)
Q Consensus 44 y~~LE~kL~~LGWeRYy~d~~l-~QfHkr 71 (107)
-+.+|+.|.+.|+.+-=+.||+ ++||-.
T Consensus 41 ~~~v~~~L~~~G~~~~~~~aDl~V~~~~~ 69 (151)
T PF13590_consen 41 QDAVEQELAAKGYRRVPENADLLVSYHYS 69 (151)
T ss_pred HHHHHHHHHHCCCeecccCCCEEEEEEEE
Confidence 3678999999999987457886 778765
No 47
>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.
Probab=28.18 E-value=69 Score=20.44 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=22.2
Q ss_pred ceEEEEccCCceeehHHHHHHHHhhccceeec
Q 033957 29 RKVLVHVPTNEVMTSYAVLERKLSSLGWERYY 60 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy 60 (107)
++++||..+| .+|....+ .|..+|.++.|
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 68999987654
No 48
>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=27.99 E-value=36 Score=22.71 Aligned_cols=17 Identities=41% Similarity=0.630 Sum_probs=11.1
Q ss_pred ccceeeeEEEEEecCCe
Q 033957 85 KFKSMHMYDIVVKNRNV 101 (107)
Q Consensus 85 ~fks~HMYDIVVKnrn~ 101 (107)
.|.|-+-||++|||++-
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 57888999999998764
No 49
>cd00133 PTS_IIB PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC 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 chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby r
Probab=27.84 E-value=84 Score=18.45 Aligned_cols=31 Identities=29% Similarity=0.245 Sum_probs=24.0
Q ss_pred eEEEEccCCceeehH--HHHHHHHhhccceeec
Q 033957 30 KVLVHVPTNEVMTSY--AVLERKLSSLGWERYY 60 (107)
Q Consensus 30 KvLvh~ps~Evi~Sy--~~LE~kL~~LGWeRYy 60 (107)
|+|+-.++|.-.+.. +.|++.+.+.|..--+
T Consensus 1 ~il~vc~~G~~~s~~l~~~l~~~~~~~~~~~~~ 33 (84)
T cd00133 1 KILVVCGSGIGSSSMLAEKLEKAAKELGIEVKV 33 (84)
T ss_pred CEEEECCCcHhHHHHHHHHHHHHHHHCCCeEEE
Confidence 578888888777766 7899999999986443
No 50
>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=27.05 E-value=86 Score=21.19 Aligned_cols=31 Identities=13% Similarity=0.091 Sum_probs=23.6
Q ss_pred cceEEEEccCCceeehHHHHHHHHhhccceeecC
Q 033957 28 RRKVLVHVPTNEVMTSYAVLERKLSSLGWERYYD 61 (107)
Q Consensus 28 rrKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy~ 61 (107)
.++++||..+|. +|.... +.|.++|.++.+.
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 5888999988753
No 51
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=26.88 E-value=59 Score=29.14 Aligned_cols=34 Identities=15% Similarity=0.291 Sum_probs=30.0
Q ss_pred cceEEEEccCCceeehHHHHHHHHhhccceeecCC
Q 033957 28 RRKVLVHVPTNEVMTSYAVLERKLSSLGWERYYDD 62 (107)
Q Consensus 28 rrKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy~d 62 (107)
-.+||+.+.+.++- +++.|.+.+.++-|++|+..
T Consensus 54 A~RVll~l~~f~a~-~~~~Ly~~v~~i~W~~~l~~ 87 (702)
T PRK11783 54 ASRILLPLAEFKVY-SDLDLYLGVQAIDWTEHFSP 87 (702)
T ss_pred hhheEEEeeeeecC-CHHHHHHHHHcCCHHHhCCC
Confidence 35899999998864 89999999999999999864
No 52
>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=26.64 E-value=74 Score=20.85 Aligned_cols=27 Identities=15% Similarity=0.372 Sum_probs=23.5
Q ss_pred CcceEEEEccCCceeehHHHHHHHHhh
Q 033957 27 TRRKVLVHVPTNEVMTSYAVLERKLSS 53 (107)
Q Consensus 27 ~rrKvLvh~ps~Evi~Sy~~LE~kL~~ 53 (107)
.++-|.-..|.|+..++|++.++-|.+
T Consensus 22 ~k~~V~Y~aPCGr~Lr~~~EV~~YL~~ 48 (60)
T cd01395 22 VKKHVIYKAPCGRSLRNMSEVHRYLRE 48 (60)
T ss_pred cccceEEECCcchhhhcHHHHHHHHHh
Confidence 456788889999999999999998875
No 53
>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=25.76 E-value=23 Score=29.20 Aligned_cols=53 Identities=28% Similarity=0.464 Sum_probs=0.0
Q ss_pred ehHHHHHHHHhhccceeecC-CCceeeeeec--CceeEEeccccccccceeeeEEEE
Q 033957 42 TSYAVLERKLSSLGWERYYD-DPELLQFHKR--STVHLISLPKDFNKFKSMHMYDIV 95 (107)
Q Consensus 42 ~Sy~~LE~kL~~LGWeRYy~-d~~l~QfHkr--~sv~LISLPrdF~~fks~HMYDIV 95 (107)
|.|+.|...|..||.+-+|. ...-+..|+. +.+-+-.| .|-.+.||++-+|++
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 67999999999999999887 2333333665 56666677 789999999866665
No 54
>KOG3061 consensus Proteasome maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=25.47 E-value=30 Score=26.38 Aligned_cols=24 Identities=29% Similarity=0.569 Sum_probs=20.2
Q ss_pred ehHHHHHHHHhhccceeecCCCce
Q 033957 42 TSYAVLERKLSSLGWERYYDDPEL 65 (107)
Q Consensus 42 ~Sy~~LE~kL~~LGWeRYy~d~~l 65 (107)
...+.|=-+....|||=||+||.+
T Consensus 93 ~~ldvL~g~~~~ig~ED~~ndp~~ 116 (137)
T KOG3061|consen 93 LGLDVLTGREDNIGFEDILNDPRL 116 (137)
T ss_pred hhhHHHhcccccCCchhccCCccc
Confidence 345677778889999999999987
No 55
>PF00585 Thr_dehydrat_C: C-terminal regulatory domain of Threonine dehydratase; InterPro: IPR001721 Threonine dehydratases including Serine/threonine dehydratase (see IPR001926 from INTERPRO) contain a common C-terminal region that may have a regulatory role. Some members contain two copies of this region [].; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process; PDB: 1TDJ_A 3IAU_A.
Probab=25.35 E-value=35 Score=22.98 Aligned_cols=37 Identities=43% Similarity=0.700 Sum_probs=22.6
Q ss_pred ceEEEE--ccCCceeehHHHHHHHHhhccceeecC--CCceeeee
Q 033957 29 RKVLVH--VPTNEVMTSYAVLERKLSSLGWERYYD--DPELLQFH 69 (107)
Q Consensus 29 rKvLvh--~ps~Evi~Sy~~LE~kL~~LGWeRYy~--d~~l~QfH 69 (107)
-.|||= +|+.+ ..+.|.++|.++|++ |-+ |..+.|.|
T Consensus 50 a~vlvgi~v~~~~---~~~~l~~~L~~~gy~-~~dls~ne~~k~h 90 (91)
T PF00585_consen 50 ARVLVGIEVPDAE---DLEELIERLKALGYP-YEDLSDNELAKLH 90 (91)
T ss_dssp SEEEEEEE-SSTH---HHHHHHHHHTSSS-E-EECTTT-HHHHHC
T ss_pred eeEEEEEEeCCHH---HHHHHHHHHHHcCCC-eEECCCCHHHHhh
Confidence 367764 45443 379999999999987 433 55555544
No 56
>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=25.11 E-value=26 Score=21.96 Aligned_cols=17 Identities=18% Similarity=0.118 Sum_probs=14.3
Q ss_pred EEccCCceeehHHHHHH
Q 033957 33 VHVPTNEVMTSYAVLER 49 (107)
Q Consensus 33 vh~ps~Evi~Sy~~LE~ 49 (107)
+|+++|.-|.|.++||.
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 79999999999998864
No 57
>PF11379 DUF3182: Protein of unknown function (DUF3182); InterPro: IPR021519 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=25.10 E-value=85 Score=27.28 Aligned_cols=36 Identities=25% Similarity=0.324 Sum_probs=25.4
Q ss_pred eCceEEeeCCCccCCCCCCCcceEEEEccCCceeehHHHHHHHHhhccc
Q 033957 8 KNGVVRLENPGAEACSNSNTRRKVLVHVPTNEVMTSYAVLERKLSSLGW 56 (107)
Q Consensus 8 knGV~rlenp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~kL~~LGW 56 (107)
++|-+||..|.+.++-| -+||++-++||+-|.++.=
T Consensus 135 ~~G~VRlKp~~a~gG~G-------------Q~vv~~~~~Ld~~L~~~~~ 170 (355)
T PF11379_consen 135 RDGPVRLKPVHATGGRG-------------QQVVADADELDAALAALDD 170 (355)
T ss_pred ccCCeeeccCcccCCCC-------------ceEecCHHHHHHHHHcCCH
Confidence 57889996664332211 2578999999999988763
No 58
>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=25.10 E-value=47 Score=22.30 Aligned_cols=17 Identities=24% Similarity=0.171 Sum_probs=15.5
Q ss_pred EEccCCceeehHHHHHH
Q 033957 33 VHVPTNEVMTSYAVLER 49 (107)
Q Consensus 33 vh~ps~Evi~Sy~~LE~ 49 (107)
+|+|+|.-|+|.++||.
T Consensus 55 lyt~~G~~v~~l~~l~~ 71 (89)
T smart00537 55 LYTLDGKKVTSLDELED 71 (89)
T ss_pred EEcCCCCEECCHHHhCc
Confidence 79999999999999984
No 59
>PF14090 HTH_39: Helix-turn-helix domain
Probab=24.94 E-value=13 Score=23.78 Aligned_cols=29 Identities=14% Similarity=0.340 Sum_probs=22.8
Q ss_pred ceEEEEccCCceeehHHHHHH-----------HHhhccce
Q 033957 29 RKVLVHVPTNEVMTSYAVLER-----------KLSSLGWE 57 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~-----------kL~~LGWe 57 (107)
.++|=|+-.|..||+++.+++ .|++.||.
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 57888885
No 60
>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=24.74 E-value=41 Score=23.72 Aligned_cols=28 Identities=18% Similarity=0.245 Sum_probs=21.4
Q ss_pred EEEEccCCceeehHHHHHHHHhhccceeecC
Q 033957 31 VLVHVPTNEVMTSYAVLERKLSSLGWERYYD 61 (107)
Q Consensus 31 vLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy~ 61 (107)
..+.+-||- +.+.++.+|..+||.+|++
T Consensus 113 ~~~~i~Sn~---~~~~~~~~l~~~~l~~~fd 140 (224)
T TIGR02254 113 FRLYIVTNG---VRETQYKRLRKSGLFPFFD 140 (224)
T ss_pred CcEEEEeCC---chHHHHHHHHHCCcHhhcC
Confidence 445555663 4688899999999999975
No 61
>PRK05928 hemD uroporphyrinogen-III synthase; Reviewed
Probab=24.57 E-value=1.1e+02 Score=21.88 Aligned_cols=27 Identities=30% Similarity=0.385 Sum_probs=19.8
Q ss_pred ceEEEEccCCceeehHHHHHHHHhhccceee
Q 033957 29 RKVLVHVPTNEVMTSYAVLERKLSSLGWERY 59 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRY 59 (107)
.|+|+=-|+.+ -+.|-++|.++|++=+
T Consensus 2 ~~ilitr~~~~----~~~l~~~l~~~G~~v~ 28 (249)
T PRK05928 2 MKILVTRPSPK----AEELVELLRELGFVAL 28 (249)
T ss_pred CEEEEeCCHHH----HHHHHHHHHHcCCCEE
Confidence 46777777664 3678899999998833
No 62
>PRK11697 putative two-component response-regulatory protein YehT; Provisional
Probab=24.05 E-value=82 Score=22.33 Aligned_cols=35 Identities=29% Similarity=0.293 Sum_probs=24.0
Q ss_pred cceEEEEccCCceee--hHHHHHHHHhhccceeecCCCceeeeeecCce
Q 033957 28 RRKVLVHVPTNEVMT--SYAVLERKLSSLGWERYYDDPELLQFHKRSTV 74 (107)
Q Consensus 28 rrKvLvh~ps~Evi~--Sy~~LE~kL~~LGWeRYy~d~~l~QfHkr~sv 74 (107)
.+++-+|+.+|+... +...||++| ..+|-|++.=|
T Consensus 159 ~~~~~i~~~~~~~~~~~~l~~~~~~~------------~F~r~hrs~iV 195 (238)
T PRK11697 159 LSGVHVVSAEGKGFTELTLKTLEEKT------------PLLRCHRQYLV 195 (238)
T ss_pred CCcEEEEEcCCEEEecccHHHHHhcc------------CeEEechhHeE
Confidence 357889998887554 667777754 26777877544
No 63
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=23.67 E-value=1.2e+02 Score=27.44 Aligned_cols=51 Identities=24% Similarity=0.281 Sum_probs=41.2
Q ss_pred ceEEEEccCCceeehHHHHHHHHhhccceeecCCCceeeeeec-CceeEEecc
Q 033957 29 RKVLVHVPTNEVMTSYAVLERKLSSLGWERYYDDPELLQFHKR-STVHLISLP 80 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy~d~~l~QfHkr-~sv~LISLP 80 (107)
++..+++-.|+.| +.+.|.++|.++|.+|---...-=||-.| +.+|+.+.-
T Consensus 152 ~~~~~~l~~G~~i-~~~~l~~~Lv~~gY~r~~~v~~~G~F~vRG~iiDIfp~~ 203 (655)
T TIGR00631 152 LKMVLHLEVGKEI-DRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAY 203 (655)
T ss_pred HhccEEEeCCCCc-CHHHHHHHHHHcCCcccCccCCCceEEEECCEEEEecCC
Confidence 3567788888887 48999999999999998666677899999 566887754
No 64
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=23.03 E-value=83 Score=32.18 Aligned_cols=53 Identities=28% Similarity=0.613 Sum_probs=33.9
Q ss_pred ceeEEEeCceEEeeCCCccCCCCCCCcceEEEEccCCceeehHHHHHHHHhhccceeec-C-----CCceeeee
Q 033957 2 SGVWVFKNGVVRLENPGAEACSNSNTRRKVLVHVPTNEVMTSYAVLERKLSSLGWERYY-D-----DPELLQFH 69 (107)
Q Consensus 2 sGVWvFknGV~rlenp~~~~~~~~~~rrKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy-~-----d~~l~QfH 69 (107)
-||.|||||-+|-.--..| |-|.-..|+=.|- .||++||.+.=+ + |..++.+.
T Consensus 752 ~~v~vFKDGTiRfD~tD~P-----------iThfkp~Eigvsv----eklreLGY~~Di~G~pL~~~dQivELk 810 (1627)
T PRK14715 752 NDVYVFKDGTIRFDCTDVP-----------ITHFKPSEINVSV----EKLRELGYDKDIEGKPLERDDQILELK 810 (1627)
T ss_pred cCeeEecCCceeccCcCCc-----------cccccHHhcCCCH----HHHHHcCCccccCCCCCCCcceeEEee
Confidence 4899999999999321111 2344455666665 478999998754 3 33566653
No 65
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.01 E-value=27 Score=22.64 Aligned_cols=35 Identities=34% Similarity=0.405 Sum_probs=25.2
Q ss_pred EccCCceeehHHHHHHHHhhccceeec--CCCceeeeeec
Q 033957 34 HVPTNEVMTSYAVLERKLSSLGWERYY--DDPELLQFHKR 71 (107)
Q Consensus 34 h~ps~Evi~Sy~~LE~kL~~LGWeRYy--~d~~l~QfHkr 71 (107)
.++.| ....+.+.+.|.+.|++ +. .|.++.++|-|
T Consensus 47 e~~~~--~~~~~~i~~~L~~~G~~-~~~~~~~~~~~~~l~ 83 (85)
T cd04906 47 SVANG--AEELAELLEDLKSAGYE-VVDLSDDELAKTHLR 83 (85)
T ss_pred EeCCc--HHHHHHHHHHHHHCCCC-eEECCCCHHHHHHhh
Confidence 44443 34578999999999996 43 47778888865
No 66
>PF13420 Acetyltransf_4: Acetyltransferase (GNAT) domain; PDB: 3DR8_A 3DR6_A 2AE6_B 2JLM_C 2J8R_A 1YVO_B 2J8M_A 2J8N_A 2BL1_A 3IWG_A ....
Probab=22.90 E-value=53 Score=21.74 Aligned_cols=54 Identities=20% Similarity=0.207 Sum_probs=42.3
Q ss_pred ehHHHHHHHH-hhccceeecC-----CCceeeeeecCceeEEeccccccccceeeeEEEEE
Q 033957 42 TSYAVLERKL-SSLGWERYYD-----DPELLQFHKRSTVHLISLPKDFNKFKSMHMYDIVV 96 (107)
Q Consensus 42 ~Sy~~LE~kL-~~LGWeRYy~-----d~~l~QfHkr~sv~LISLPrdF~~fks~HMYDIVV 96 (107)
.-++.|++.+ .++|=++-+- ++..++|+++-+-.....=+++-...- +.||+|+
T Consensus 96 ~l~~~l~~~af~~~~~~~i~~~v~~~N~~~i~~~~~~GF~~~g~~~~~~~~~~-~y~D~~~ 155 (155)
T PF13420_consen 96 KLLDELIEYAFKELGIHKIYLEVFSSNEKAINFYKKLGFEEEGELKDHIFING-KYYDVVW 155 (155)
T ss_dssp HHHHHHHHHH-HHTT-CEEEEEEETT-HHHHHHHHHTTEEEEEEEEEEEEETT-EEEEEEE
T ss_pred HHHHHHHHHhhhccCeEEEEEEEecCCHHHHHHHHhCCCEEEEEEecEEEECC-eEEEeEC
Confidence 3578889999 9999998763 777899999988888888788777776 7888764
No 67
>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=22.89 E-value=35 Score=22.89 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=16.3
Q ss_pred cCCceeehHHHHHHHHhhccce
Q 033957 36 PTNEVMTSYAVLERKLSSLGWE 57 (107)
Q Consensus 36 ps~Evi~Sy~~LE~kL~~LGWe 57 (107)
.|||--.=-+.|.++|.+.||.
T Consensus 12 ~sGe~~~L~~~L~~rL~e~GW~ 33 (86)
T PF10163_consen 12 ESGEYERLKELLRQRLIECGWR 33 (86)
T ss_dssp HCTHHHHHHHHHHHHHHHTTHH
T ss_pred HcCcHHHHHHHHHHHHHHCChH
Confidence 3555444457889999999996
No 68
>TIGR00318 cyaB adenylyl cyclase CyaB, putative. The protein CyaB from Aeromonas hydrophila is a second adenylyl cyclase from that species, as demonstrated by complementation in E. coli and by assay of the enzymatic properties of purified recombinant protein. It has no detectable homology to any other protein of known function, and has several unusual properties, including an optimal temperature of 65 degrees and an optimal pH of 9.5. A cluster of uncharaterized archaeal homologs may be orthologous and serve (under certain circumstances) to produce the regulatory metabolite cyclic AMP (cAMP).
Probab=22.75 E-value=75 Score=23.27 Aligned_cols=23 Identities=22% Similarity=0.470 Sum_probs=18.2
Q ss_pred ehHHHHHHHHhhccce---------eecCCCc
Q 033957 42 TSYAVLERKLSSLGWE---------RYYDDPE 64 (107)
Q Consensus 42 ~Sy~~LE~kL~~LGWe---------RYy~d~~ 64 (107)
.+++.++++|.++|.. .||+.|+
T Consensus 11 ~d~~~~~~~L~~~g~~~~~~~~q~D~Yfd~p~ 42 (174)
T TIGR00318 11 PDKEKVVEKLKNKGFKFIKKEFQHDIYFSNPC 42 (174)
T ss_pred CCHHHHHHHHHhcCcccccccceEEEeecCCC
Confidence 4788999999999964 5777664
No 69
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=22.60 E-value=1.6e+02 Score=19.71 Aligned_cols=26 Identities=15% Similarity=0.365 Sum_probs=19.8
Q ss_pred eCceEEeeCCCccCCCCCCCcceEEEEccCCceeeh
Q 033957 8 KNGVVRLENPGAEACSNSNTRRKVLVHVPTNEVMTS 43 (107)
Q Consensus 8 knGV~rlenp~~~~~~~~~~rrKvLvh~ps~Evi~S 43 (107)
.||++++-. ..+|+.+|-..|..|.|
T Consensus 20 ~DG~l~~~~----------~~~kv~Lyde~~~~i~~ 45 (83)
T PF10382_consen 20 HDGFLKYHS----------FNKKVMLYDEDGNLIGS 45 (83)
T ss_pred ECCEEEEEe----------CCCEEEEEcCCCCEEeE
Confidence 599999941 13589999998888765
No 70
>cd05566 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. 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 galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and
Probab=21.97 E-value=89 Score=19.79 Aligned_cols=32 Identities=19% Similarity=0.206 Sum_probs=25.0
Q ss_pred ceEEEEccCCceeeh--HHHHHHHHhhccceeec
Q 033957 29 RKVLVHVPTNEVMTS--YAVLERKLSSLGWERYY 60 (107)
Q Consensus 29 rKvLvh~ps~Evi~S--y~~LE~kL~~LGWeRYy 60 (107)
+|+|+-.|+|--.|. -+.||+.+.++|..-..
T Consensus 1 ~~ilivC~~G~~tS~~l~~~i~~~~~~~~i~~~v 34 (89)
T cd05566 1 KKILVACGTGVATSTVVASKVKELLKENGIDVKV 34 (89)
T ss_pred CEEEEECCCCccHHHHHHHHHHHHHHHCCCceEE
Confidence 479999999976654 56799999999986443
No 71
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=21.60 E-value=1.5e+02 Score=22.58 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=24.5
Q ss_pred ceEEEEccCCceeehHHHHHHHHhhccceeecCCCceeeeeecCcee
Q 033957 29 RKVLVHVPTNEVMTSYAVLERKLSSLGWERYYDDPELLQFHKRSTVH 75 (107)
Q Consensus 29 rKvLvh~ps~Evi~Sy~~LE~kL~~LGWeRYy~d~~l~QfHkr~sv~ 75 (107)
++|.|++.. +-+.+++.+..+| ++.+|+|--.+..
T Consensus 54 ~~VgVf~~~-----~~~~i~~~~~~~~-------~d~vQLHG~e~~~ 88 (207)
T PRK13958 54 DKVCVVVNP-----DLTTIEHILSNTS-------INTIQLHGTESID 88 (207)
T ss_pred CEEEEEeCC-----CHHHHHHHHHhCC-------CCEEEECCCCCHH
Confidence 578888654 6677777777554 7899999754433
No 72
>PF09992 DUF2233: Predicted periplasmic protein (DUF2233); InterPro: IPR018711 This entry contains proteins that catalyze the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides, this is achieved by removing GlcNAc residues from GlcNAc-alpha-P-mannose moieties, which are formed in the first step.; PDB: 3OHG_A.
Probab=21.24 E-value=3e+02 Score=19.32 Aligned_cols=59 Identities=20% Similarity=0.178 Sum_probs=27.4
Q ss_pred eeEEEeCceEEe-eCCCcc-CCCCC--C--CcceEEEEccCCc--eeehHHHHHHHHhhccceeecC
Q 033957 3 GVWVFKNGVVRL-ENPGAE-ACSNS--N--TRRKVLVHVPTNE--VMTSYAVLERKLSSLGWERYYD 61 (107)
Q Consensus 3 GVWvFknGV~rl-enp~~~-~~~~~--~--~rrKvLvh~ps~E--vi~Sy~~LE~kL~~LGWeRYy~ 61 (107)
|.+..+||-+.. ..+... ..+.+ | ...++++.+-.|. .=.|+.+|-+.|.+||...-.+
T Consensus 69 gp~Lv~nG~~~~~~~~~~~~~~~RtaiG~~~~g~l~l~~vdg~~~~g~tl~ela~~l~~lG~~~Ain 135 (170)
T PF09992_consen 69 GPLLVKNGKIVPNFSDEGWGRHPRTAIGVTADGKLLLIVVDGRQSAGMTLDELAQLLKSLGCVDAIN 135 (170)
T ss_dssp S-EEEETTEE----TTSGGSSB-EEEEEE-TTSEEEEEEE----S--B-HHHHHHHHHHHT-SEEEE
T ss_pred CceEeECCEEccCcccCccccCCEEEEEEeCCCcEEEEEEcCCcCCCCCHHHHHHHHHHcCcCeEEE
Confidence 556668998775 222110 00000 0 0125555554441 2358999999999999997643
No 73
>COG1391 GlnE Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]
Probab=21.07 E-value=42 Score=32.49 Aligned_cols=23 Identities=39% Similarity=0.712 Sum_probs=20.6
Q ss_pred CCceeehHHHHHHHHhhcc--ceee
Q 033957 37 TNEVMTSYAVLERKLSSLG--WERY 59 (107)
Q Consensus 37 s~Evi~Sy~~LE~kL~~LG--WeRY 59 (107)
||..+.|++++|+-..+-| ||||
T Consensus 249 SgpLv~s~~A~e~YYq~~Gr~WER~ 273 (963)
T COG1391 249 SGPLVLSLAALEDYYQEQGRDWERY 273 (963)
T ss_pred CCCccccHHHHHHHHHHhcccHHHH
Confidence 5778899999999998877 9999
No 74
>PF10394 Hat1_N: Histone acetyl transferase HAT1 N-terminus; InterPro: IPR019467 This entry represents the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of IPR000182 from INTERPRO. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyse the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated []. ; GO: 0004402 histone acetyltransferase activity, 0016568 chromatin modification; PDB: 2P0W_A 1BOB_A.
Probab=20.71 E-value=16 Score=27.07 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=6.7
Q ss_pred CCceeeeeec
Q 033957 62 DPELLQFHKR 71 (107)
Q Consensus 62 d~~l~QfHkr 71 (107)
||...++|+|
T Consensus 142 ~~~~~~~h~R 151 (161)
T PF10394_consen 142 DPGFRELHRR 151 (161)
T ss_dssp SCCHHHHHHH
T ss_pred CHHHHHHHHH
Confidence 6666667666
No 75
>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=20.69 E-value=39 Score=21.50 Aligned_cols=24 Identities=21% Similarity=0.432 Sum_probs=12.8
Q ss_pred CCceeehHHHHHHHHhhccceeec
Q 033957 37 TNEVMTSYAVLERKLSSLGWERYY 60 (107)
Q Consensus 37 s~Evi~Sy~~LE~kL~~LGWeRYy 60 (107)
.|.+-.+|+.-++.-..|||+=-|
T Consensus 19 ~GD~~~~~Ad~~kA~~~LgW~p~~ 42 (62)
T PF13950_consen 19 PGDPAHLVADISKAREELGWKPKY 42 (62)
T ss_dssp TT--SEE-B--HHHHHHC----SS
T ss_pred CCchhhhhCCHHHHHHHhCCCcCC
Confidence 688999999999999999998433
No 76
>cd05567 PTS_IIB_mannitol PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIA, IIB, and IIC domains are expressed from the mtlA gene as a single protein, also known as the mannitol PTS permease, the mtl transporter, or MtlA. MtlA is only functional as a dimer with the dimer contacts occuring between the IIC domains. MtlA takes up exogenous mannitol releasing the phosphate ester into the cytoplasm in preparation for oxidation to fructose-6-phosphate by the NAD-dependent mannitol-P dehydrogenase (MtlD). 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 mannitol, chitobiose/lichenan, ascorbate, lactose, galactitol, fructose, and a s
Probab=20.46 E-value=1.2e+02 Score=19.53 Aligned_cols=52 Identities=17% Similarity=0.236 Sum_probs=33.4
Q ss_pred eEEEEccCCceeehH--HHHHHHHhhccceeecCCCceeeeeecCceeEEeccccc
Q 033957 30 KVLVHVPTNEVMTSY--AVLERKLSSLGWERYYDDPELLQFHKRSTVHLISLPKDF 83 (107)
Q Consensus 30 KvLvh~ps~Evi~Sy--~~LE~kL~~LGWeRYy~d~~l~QfHkr~sv~LISLPrdF 83 (107)
|+|+..++|-..+.. ..+++.+.++|..--...-++-++- ...|||=-..++
T Consensus 2 kilvvCg~G~gtS~ml~~ki~~~~~~~~~~~~v~~~~~~~~~--~~~Dliitt~~l 55 (87)
T cd05567 2 KIVFACDAGMGSSAMGASVLRKKLKKAGLEIPVTNSAIDELP--SDADLVVTHASL 55 (87)
T ss_pred EEEEECCCCccHHHHHHHHHHHHHHHCCCceEEEEcchhhCC--CCCCEEEEChHH
Confidence 799999999876654 5588888888887444433333332 445666544444
No 77
>cd01580 AcnA_IRP_Swivel Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.
Probab=20.40 E-value=85 Score=24.70 Aligned_cols=20 Identities=40% Similarity=0.491 Sum_probs=17.1
Q ss_pred EEEEccCCceeehHHHHHHH
Q 033957 31 VLVHVPTNEVMTSYAVLERK 50 (107)
Q Consensus 31 vLvh~ps~Evi~Sy~~LE~k 50 (107)
.-.|.|+||+.+.|+..++-
T Consensus 72 ~t~~~p~g~~~~i~~aA~~Y 91 (171)
T cd01580 72 TTHHPPTGEVMSIYDAAMRY 91 (171)
T ss_pred cEEECCCCcEeeHHHHHHHH
Confidence 45789999999999998864
No 78
>PF14173 ComGG: ComG operon protein 7
Probab=20.31 E-value=2.2e+02 Score=19.05 Aligned_cols=13 Identities=23% Similarity=0.659 Sum_probs=11.6
Q ss_pred ceeEEEeCceEEe
Q 033957 2 SGVWVFKNGVVRL 14 (107)
Q Consensus 2 sGVWvFknGV~rl 14 (107)
.|+|.|.+|.|..
T Consensus 41 ~~~~~y~~G~Vsy 53 (95)
T PF14173_consen 41 TGSFQYPDGTVSY 53 (95)
T ss_pred ceEEEecCCEEEE
Confidence 4889999999998
No 79
>COG0766 MurA UDP-N-acetylglucosamine enolpyruvyl transferase [Cell envelope biogenesis, outer membrane]
Probab=20.10 E-value=60 Score=28.76 Aligned_cols=15 Identities=47% Similarity=0.647 Sum_probs=13.3
Q ss_pred ehHHHHHHHHhhccc
Q 033957 42 TSYAVLERKLSSLGW 56 (107)
Q Consensus 42 ~Sy~~LE~kL~~LGW 56 (107)
+-|+.||.||++||=
T Consensus 399 RGYe~~~~KL~~lGA 413 (421)
T COG0766 399 RGYERLEEKLRALGA 413 (421)
T ss_pred cChhHHHHHHHHcCC
Confidence 569999999999993
No 80
>PF10620 MdcG: Phosphoribosyl-dephospho-CoA transferase MdcG; InterPro: IPR017557 Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61 from EC). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.; GO: 0016779 nucleotidyltransferase activity
Probab=20.03 E-value=2.4e+02 Score=21.78 Aligned_cols=60 Identities=20% Similarity=0.351 Sum_probs=38.8
Q ss_pred CCCcceEEEEccCCceee--------------------hHHHHHHHHhhcccee-ecC------CCceeeeeecCceeEE
Q 033957 25 SNTRRKVLVHVPTNEVMT--------------------SYAVLERKLSSLGWER-YYD------DPELLQFHKRSTVHLI 77 (107)
Q Consensus 25 ~~~rrKvLvh~ps~Evi~--------------------Sy~~LE~kL~~LGWeR-Yy~------d~~l~QfHkr~sv~LI 77 (107)
..+++++-..++.+.|+. .+..|+..+..+||+= .|+ =..+-..|..|.+||+
T Consensus 66 ~~r~qR~a~~v~~~~I~~~~~P~~L~~~~~~~p~~~~~~l~~l~~~~~~~~~~~gv~GS~g~qlaTGl~~l~~~SDLDLl 145 (213)
T PF10620_consen 66 RWRKQRLALWVPPSAIVRVVTPEALAEALPQAPFPWQPALQALRALLDALGLRWGVYGSLGFQLATGLPYLHADSDLDLL 145 (213)
T ss_pred CCCceEEEEEecHHHhhccCCHHHHHhhhhcCCHHHHHHHHHHHHHHHHcCCCEEEehhHHHHHHhCccccCCCCCceEE
Confidence 445668888888887753 4556666666666653 244 2344557888999998
Q ss_pred ecccccc
Q 033957 78 SLPKDFN 84 (107)
Q Consensus 78 SLPrdF~ 84 (107)
-=|.+..
T Consensus 146 i~~~~~~ 152 (213)
T PF10620_consen 146 IRPPSPS 152 (213)
T ss_pred EeCCChh
Confidence 6665544
Done!