Query psy11263
Match_columns 80
No_of_seqs 100 out of 149
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 22:24:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11263hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03153 TFIIA: Transcription 100.0 8.7E-39 1.9E-43 242.9 7.2 62 19-80 308-375 (375)
2 KOG2652|consensus 100.0 3.4E-35 7.4E-40 230.7 6.5 67 14-80 276-348 (348)
3 COG5149 TOA1 Transcription ini 99.9 3.3E-28 7.1E-33 186.8 6.8 67 14-80 220-292 (293)
4 PF09211 DUF1958: Domain of un 86.0 0.82 1.8E-05 29.1 2.5 29 42-70 23-52 (65)
5 COG5013 NarG Nitrate reductase 85.9 0.52 1.1E-05 43.0 2.1 27 41-67 41-75 (1227)
6 PF03153 TFIIA: Transcription 72.6 1.2 2.5E-05 34.4 0.0 14 3-16 269-282 (375)
7 PF04584 Pox_A28: Poxvirus A28 68.8 2.4 5.3E-05 30.6 0.9 18 44-61 63-80 (140)
8 PRK09719 hypothetical protein; 63.4 1.9 4.2E-05 28.7 -0.4 12 39-50 57-68 (89)
9 smart00456 WW Domain with 2 co 57.9 8.2 0.00018 19.6 1.5 16 65-80 12-27 (32)
10 cd06477 ACD_HspB3_Like Alpha c 49.9 10 0.00022 24.2 1.3 32 37-68 46-83 (83)
11 PF01473 CW_binding_1: Putativ 49.8 24 0.00051 16.5 2.3 17 60-77 2-18 (19)
12 PF12139 APS-reductase_C: Aden 49.0 17 0.00036 24.3 2.2 17 52-72 24-40 (83)
13 COG4847 Uncharacterized protei 48.9 15 0.00033 25.4 2.1 27 51-79 5-31 (103)
14 PF00397 WW: WW domain; Inter 48.5 14 0.0003 19.3 1.5 16 65-80 13-28 (31)
15 PF14480 DNA_pol3_a_NI: DNA po 48.0 16 0.00035 21.8 1.9 13 46-58 31-43 (76)
16 cd00201 WW Two conserved trypt 47.0 16 0.00035 18.1 1.5 16 65-80 11-26 (31)
17 KOG2345|consensus 43.7 22 0.00047 28.6 2.5 19 59-77 13-31 (302)
18 PF09038 53-BP1_Tudor: Tumour 42.0 26 0.00057 24.7 2.5 25 47-71 27-52 (122)
19 COG4079 Uncharacterized protei 40.1 18 0.00039 28.9 1.5 20 50-69 263-282 (293)
20 PTZ00486 apyrase Superfamily; 39.1 37 0.00081 27.7 3.2 31 38-68 59-91 (352)
21 PF13691 Lactamase_B_4: tRNase 38.3 27 0.00058 21.6 1.8 13 61-73 16-28 (63)
22 PF01491 Frataxin_Cyay: Fratax 35.8 39 0.00084 22.4 2.4 22 53-74 32-56 (109)
23 PF10382 DUF2439: Protein of u 35.8 62 0.0014 20.5 3.3 30 40-73 5-38 (83)
24 KOG0284|consensus 35.4 32 0.0007 29.1 2.4 44 36-79 77-121 (464)
25 TIGR03421 FeS_CyaY iron donor 34.3 43 0.00094 22.2 2.5 20 55-74 29-51 (102)
26 PF14267 DUF4357: Domain of un 33.9 25 0.00054 21.2 1.2 17 57-73 5-21 (55)
27 cd06497 ACD_alphaA-crystallin_ 33.6 33 0.00072 21.6 1.8 16 50-65 67-83 (86)
28 cd06471 ACD_LpsHSP_like Group 33.2 34 0.00073 21.1 1.7 13 52-64 77-89 (93)
29 PRK01379 cyaY frataxin-like pr 32.9 46 0.00099 22.4 2.4 15 58-73 35-52 (103)
30 KOG3259|consensus 32.8 17 0.00037 26.9 0.3 16 65-80 19-34 (163)
31 CHL00114 psbX photosystem II p 32.8 27 0.00058 20.4 1.1 12 38-49 28-39 (39)
32 PF10974 DUF2804: Protein of u 32.1 81 0.0018 24.3 4.0 43 34-80 147-197 (333)
33 PF14249 Tocopherol_cycl: Toco 31.4 46 0.00099 26.7 2.6 21 59-79 169-189 (336)
34 PF06079 Apyrase: Apyrase; In 30.6 36 0.00078 27.0 1.9 21 49-69 10-30 (291)
35 PRK00446 cyaY frataxin-like pr 30.4 55 0.0012 21.9 2.5 21 55-75 31-54 (105)
36 PF09943 DUF2175: Uncharacteri 29.6 54 0.0012 22.4 2.4 25 52-78 2-26 (101)
37 TIGR03422 mito_frataxin fratax 28.5 42 0.00092 22.2 1.7 21 54-74 30-53 (97)
38 PHA02095 hypothetical protein 28.1 59 0.0013 21.6 2.3 19 49-67 31-49 (84)
39 PF14864 Alkyl_sulf_C: Alkyl s 28.0 48 0.0011 21.8 1.9 19 46-64 40-58 (125)
40 PF11008 DUF2846: Protein of u 27.4 78 0.0017 20.6 2.8 39 36-80 24-62 (117)
41 cd06479 ACD_HspB7_like Alpha c 27.0 50 0.0011 20.8 1.8 14 52-65 64-78 (81)
42 PF07873 YabP: YabP family; I 26.6 77 0.0017 19.1 2.5 28 49-76 24-51 (66)
43 PF06097 DUF945: Bacterial pro 26.5 55 0.0012 25.2 2.2 17 54-70 440-456 (460)
44 PF13738 Pyr_redox_3: Pyridine 26.3 1.1E+02 0.0024 20.3 3.4 20 41-60 103-122 (203)
45 PF00011 HSP20: Hsp20/alpha cr 25.7 57 0.0012 20.0 1.8 24 42-65 56-84 (102)
46 smart00400 ZnF_CHCC zinc finge 25.6 53 0.0012 18.8 1.6 13 45-57 16-28 (55)
47 COG3250 LacZ Beta-galactosidas 24.6 1.2E+02 0.0026 27.0 4.2 31 45-75 276-306 (808)
48 PF04076 BOF: Bacterial OB fol 24.3 56 0.0012 21.8 1.7 26 54-79 36-62 (103)
49 COG1965 CyaY Protein implicate 24.2 79 0.0017 21.8 2.4 20 55-74 32-54 (106)
50 cd06472 ACD_ScHsp26_like Alpha 24.2 60 0.0013 20.0 1.7 13 52-64 76-88 (92)
51 PF14527 LAGLIDADG_WhiA: WhiA 23.9 65 0.0014 20.8 1.9 16 45-60 49-64 (93)
52 PF12276 DUF3617: Protein of u 23.4 66 0.0014 21.6 1.9 21 37-57 89-109 (162)
53 cd06478 ACD_HspB4-5-6 Alpha-cr 22.9 68 0.0015 19.9 1.8 15 51-65 65-80 (83)
54 PF00070 Pyr_redox: Pyridine n 22.9 1.2E+02 0.0025 17.9 2.8 21 40-60 60-80 (80)
55 cd06464 ACD_sHsps-like Alpha-c 22.7 70 0.0015 18.5 1.7 13 52-64 72-84 (88)
56 COG0071 IbpA Molecular chapero 22.3 61 0.0013 21.9 1.6 13 52-64 116-128 (146)
57 PF03941 INCENP_ARK-bind: Inne 22.0 30 0.00065 20.5 0.0 12 18-29 1-12 (57)
58 cd00503 Frataxin Frataxin is a 22.0 82 0.0018 20.9 2.1 21 54-74 31-54 (105)
59 PF15603 Imm45: Immunity prote 21.9 1.5E+02 0.0033 19.2 3.3 23 45-67 2-25 (82)
60 cd06498 ACD_alphaB-crystallin_ 21.6 74 0.0016 19.9 1.8 16 50-65 64-80 (84)
61 cd06476 ACD_HspB2_like Alpha c 20.9 77 0.0017 19.9 1.7 15 51-65 65-80 (83)
62 PF04985 Phage_tube: Phage tai 20.9 2.5E+02 0.0054 19.3 4.4 38 33-70 120-158 (167)
63 smart00564 PQQ beta-propeller 20.9 93 0.002 15.2 1.8 17 64-80 14-30 (33)
No 1
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=100.00 E-value=8.7e-39 Score=242.92 Aligned_cols=62 Identities=61% Similarity=1.085 Sum_probs=45.7
Q ss_pred CCCCCCCCCCC-----c-CCCCCCCEEEEEEeeeeecCCeeEEEecceeEEECCeeeEeeeceeeeeC
Q psy11263 19 LNSSDDVSEED-----P-ALFDTDNIVVCQYDKITRSRNKWKFYLKDGIMNLNGKDFVFLKANGDADW 80 (80)
Q Consensus 19 lnSddD~sd~d-----~-e~~~~~nvilC~ydKV~R~KnKWKc~LKdGim~ingkDyvF~ka~GE~eW 80 (80)
+|||+|+|++| . ++++++|+||||||||+|+||||||+|||||||||||||||+||+|||||
T Consensus 308 ~~~~~~~~~dd~~~~~~~~~~~~~~~~~c~~~kv~r~k~~wk~~lk~g~~~~~~~d~~f~~~~ge~~w 375 (375)
T PF03153_consen 308 INSDLDDSDDDVSDEDDEDDFDTDNVVLCQYDKVTRVKNKWKCTLKDGIMHINGKDYVFQKATGEFEW 375 (375)
T ss_dssp ------------B-------STTS-EEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEEEE-
T ss_pred ccCCcCCccccccccccccccCcCCEEEEEeeccccccceeEEEeeeeEEEECCeEEEEeeeeeeecC
Confidence 78877776543 2 66899999999999999999999999999999999999999999999999
No 2
>KOG2652|consensus
Probab=100.00 E-value=3.4e-35 Score=230.69 Aligned_cols=67 Identities=61% Similarity=1.106 Sum_probs=56.3
Q ss_pred CCCCCCCCCCCCC-CCCc-----CCCCCCCEEEEEEeeeeecCCeeEEEecceeEEECCeeeEeeeceeeeeC
Q psy11263 14 IEDEPLNSSDDVS-EEDP-----ALFDTDNIVVCQYDKITRSRNKWKFYLKDGIMNLNGKDFVFLKANGDADW 80 (80)
Q Consensus 14 ~~ed~lnSddD~s-d~d~-----e~~~~~nvilC~ydKV~R~KnKWKc~LKdGim~ingkDyvF~ka~GE~eW 80 (80)
++++.+|||++|. ++++ +..+|+|+||||||||+|+||||||+|||||||||||||||+||+|||||
T Consensus 276 ~dee~~n~Dd~D~~EeeplnsedDvsdt~nvVvCqyDKV~RsKnKWKc~LKDGIM~ingkDY~F~KA~GeaEW 348 (348)
T KOG2652|consen 276 EDEELGNSDDDDGVEEEPLNSEDDVSDTQNVVVCQYDKVNRSKNKWKCYLKDGVMHINGKDYVFQKAQGEAEW 348 (348)
T ss_pred hhhhcccccccCccccccccCcccccccceeEEEeeeeeccccceeeEEeecceEEeCCceeEeeecccccCC
Confidence 3566677777664 3332 12347899999999999999999999999999999999999999999999
No 3
>COG5149 TOA1 Transcription initiation factor IIA, large chain [Transcription]
Probab=99.95 E-value=3.3e-28 Score=186.80 Aligned_cols=67 Identities=39% Similarity=0.740 Sum_probs=59.7
Q ss_pred CCCCCCCCCCCCCCCCc---CC---CCCCCEEEEEEeeeeecCCeeEEEecceeEEECCeeeEeeeceeeeeC
Q psy11263 14 IEDEPLNSSDDVSEEDP---AL---FDTDNIVVCQYDKITRSRNKWKFYLKDGIMNLNGKDFVFLKANGDADW 80 (80)
Q Consensus 14 ~~ed~lnSddD~sd~d~---e~---~~~~nvilC~ydKV~R~KnKWKc~LKdGim~ingkDyvF~ka~GE~eW 80 (80)
.-++.++||+|+||+|. +. ....|+|||+||||+|+|+||||+|||||+.|||+||+|+||+|||||
T Consensus 220 ~~De~~~sdlddsD~d~~~se~egt~~~~n~mlCLYdKVn~~K~kWKCtfkdGvV~In~~Dy~F~kAqgE~EW 292 (293)
T COG5149 220 AKDEGMFSDLDDSDVDSGDSEIEGTKGSTNCMLCLYDKVNMSKGKWKCTFKDGVVSINNIDYVFNKAQGELEW 292 (293)
T ss_pred ccCcccccccCCccccccccccccCCCCceEEEEEeeecccccceeeEEeecceEEecCceeEEeeccceEee
Confidence 35678899999998866 22 234599999999999999999999999999999999999999999999
No 4
>PF09211 DUF1958: Domain of unknown function (DUF1958); InterPro: IPR015294 Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. Penicillin-binding protein 4 (PBP4) functions as a transpeptidase, and belongs to MEROPS peptidase family S11 (clan SE). PBP4 acts co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents []. This entry represents the C-terminal domain PBP4.; PDB: 1TVF_A 3HUN_A 3HUM_B.
Probab=85.99 E-value=0.82 Score=29.05 Aligned_cols=29 Identities=28% Similarity=0.713 Sum_probs=20.6
Q ss_pred EEeeeeecCCeeEEEecceeEEE-CCeeeE
Q psy11263 42 QYDKITRSRNKWKFYLKDGIMNL-NGKDFV 70 (80)
Q Consensus 42 ~ydKV~R~KnKWKc~LKdGim~i-ngkDyv 70 (80)
+|+=|-+-+++|++.++||.+++ +++.|+
T Consensus 23 lYd~VpK~~~~~~~~v~dg~v~vd~~r~fl 52 (65)
T PF09211_consen 23 LYDVVPKGKKPYKLKVKDGKVHVDYGRQFL 52 (65)
T ss_dssp EEEEEETT--GSEEEEETTEEEEE-S--BS
T ss_pred hhhhccCCCccceEEEeCCEEEEeCCcccC
Confidence 57778888888999999999999 666654
No 5
>COG5013 NarG Nitrate reductase alpha subunit [Energy production and conversion]
Probab=85.85 E-value=0.52 Score=43.02 Aligned_cols=27 Identities=37% Similarity=0.764 Sum_probs=23.1
Q ss_pred EEEeeeeec--------CCeeEEEecceeEEECCe
Q psy11263 41 CQYDKITRS--------RNKWKFYLKDGIMNLNGK 67 (80)
Q Consensus 41 C~ydKV~R~--------KnKWKc~LKdGim~ingk 67 (80)
=|||||-|| ...||+..||||++-..+
T Consensus 41 WqhDKvVRSTHGVNCTGSCSWkIYVKdGiITWEtQ 75 (1227)
T COG5013 41 WQHDKVVRSTHGVNCTGSCSWKIYVKNGLITWETQ 75 (1227)
T ss_pred hcccceeeccCCccccceeeEEEEEeCCEEEEeec
Confidence 379999998 458999999999997665
No 6
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=72.60 E-value=1.2 Score=34.39 Aligned_cols=14 Identities=29% Similarity=0.273 Sum_probs=0.0
Q ss_pred ccccccccccCCCC
Q psy11263 3 LIPTLAQVVCGIED 16 (80)
Q Consensus 3 ~~~~l~~~~~~~~e 16 (80)
.|||++++....++
T Consensus 269 ~~~Q~DG~~d~~~~ 282 (375)
T PF03153_consen 269 RIPQLDGAGDDSDD 282 (375)
T ss_dssp --------------
T ss_pred ccccccCCCCCccc
Confidence 47888888555544
No 7
>PF04584 Pox_A28: Poxvirus A28 family; InterPro: IPR007664 The poxvirus A28 protein is expressed at late times during the virus replication cycle and is a membrane component of the intracellular mature virion. Repression of A28 inhibits cell-to-cell spread, suggesting that all poxviruses use a common A28-dependent mechanism of cell penetration []. An N-terminal hydrophobic sequence, present in all poxvirus A28 orthologues, anchors the protein in the virion surface membrane so that most of it is exposed to the cytoplasm [].; GO: 0016032 viral reproduction, 0019031 viral envelope
Probab=68.85 E-value=2.4 Score=30.61 Aligned_cols=18 Identities=17% Similarity=0.536 Sum_probs=14.0
Q ss_pred eeeeecCCeeEEEeccee
Q psy11263 44 DKITRSRNKWKFYLKDGI 61 (80)
Q Consensus 44 dKV~R~KnKWKc~LKdGi 61 (80)
|-|.-+|.||||.+.+++
T Consensus 63 D~~~DvkqKWRCv~~~~~ 80 (140)
T PF04584_consen 63 DEVYDVKQKWRCVKYNNV 80 (140)
T ss_pred CcccChhhceEEEeeCCe
Confidence 345668999999998865
No 8
>PRK09719 hypothetical protein; Provisional
Probab=63.44 E-value=1.9 Score=28.65 Aligned_cols=12 Identities=50% Similarity=0.850 Sum_probs=10.1
Q ss_pred EEEEEeeeeecC
Q psy11263 39 VVCQYDKITRSR 50 (80)
Q Consensus 39 ilC~ydKV~R~K 50 (80)
--|||||.+|+-
T Consensus 57 wrcqydklhrvp 68 (89)
T PRK09719 57 WRCQYDKLHRVP 68 (89)
T ss_pred hhcchhhhhccc
Confidence 469999999974
No 9
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=57.95 E-value=8.2 Score=19.61 Aligned_cols=16 Identities=13% Similarity=0.736 Sum_probs=14.3
Q ss_pred CCeeeEeeeceeeeeC
Q psy11263 65 NGKDFVFLKANGDADW 80 (80)
Q Consensus 65 ngkDyvF~ka~GE~eW 80 (80)
+|+-|.|+..|++..|
T Consensus 12 ~g~~yy~n~~t~~s~W 27 (32)
T smart00456 12 DGRPYYYNHETKETQW 27 (32)
T ss_pred CCCEEEEECCCCCEEc
Confidence 4899999999999887
No 10
>cd06477 ACD_HspB3_Like Alpha crystallin domain (ACD) found in mammalian HspB3, also known as heat-shock protein 27-like protein (HSPL27, 17-kDa) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB3 is expressed in adult skeletal muscle, smooth muscle, and heart, and in several other fetal tissues. In muscle cells HspB3 forms an oligomeric 150 kDa complex with myotonic dystrophy protein kinase-binding protein (MKBP/ HspB2), this complex may comprise one of two independent muscle-cell specific chaperone systems. The expression of HspB3 is induced during muscle differentiation controlled by the myogenic factor MyoD. HspB3 may also interact with Hsp22 (HspB8).
Probab=49.89 E-value=10 Score=24.15 Aligned_cols=32 Identities=19% Similarity=0.352 Sum_probs=20.8
Q ss_pred CEEEEEEeeeeec-----CCeeEEEe-cceeEEECCee
Q psy11263 37 NIVVCQYDKITRS-----RNKWKFYL-KDGIMNLNGKD 68 (80)
Q Consensus 37 nvilC~ydKV~R~-----KnKWKc~L-KdGim~ingkD 68 (80)
+++-..|-+.-+- -++=+..| ++||++|.++|
T Consensus 46 ~~~~r~F~R~~~LP~~Vd~~~v~A~~~~dGvL~I~~~~ 83 (83)
T cd06477 46 GFISRSFTRQYQLPDGVEHKDLSAMLCHDGILVVETKD 83 (83)
T ss_pred CEEEEEEEEEEECCCCcchheEEEEEcCCCEEEEEecC
Confidence 4444444443332 45677887 89999998875
No 11
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=49.77 E-value=24 Score=16.52 Aligned_cols=17 Identities=29% Similarity=0.544 Sum_probs=11.7
Q ss_pred eeEEECCeeeEeeeceee
Q psy11263 60 GIMNLNGKDFVFLKANGD 77 (80)
Q Consensus 60 Gim~ingkDyvF~ka~GE 77 (80)
|-++++|+=|.| +.+|.
T Consensus 2 ~W~~~~~~wYy~-~~~G~ 18 (19)
T PF01473_consen 2 GWVQDNGNWYYF-DSDGY 18 (19)
T ss_dssp EEEEETTEEEEE-TTTSB
T ss_pred cCEEECCEEEEe-CCCcc
Confidence 567778888877 55554
No 12
>PF12139 APS-reductase_C: Adenosine-5'-phosphosulfate reductase beta subunit; InterPro: IPR022738 This domain is found in bacteria and archaea and is typically between 112 to 142 amino acids in length. It is found in association with PF00037 from PFAM, and has a conserved FPIRTT sequence motif. The whole beta subunit has the enzymic properties of 1.8.99.2 from EC. ; PDB: 1JNZ_B 2FJE_D 2FJD_B 1JNR_D 2FJB_B 2FJA_B 3GYX_J.
Probab=49.02 E-value=17 Score=24.31 Aligned_cols=17 Identities=29% Similarity=0.768 Sum_probs=12.2
Q ss_pred eeEEEecceeEEECCeeeEee
Q psy11263 52 KWKFYLKDGIMNLNGKDFVFL 72 (80)
Q Consensus 52 KWKc~LKdGim~ingkDyvF~ 72 (80)
-|+|+|+||.+ |+|.|.
T Consensus 24 mWtikFRnG~~----KrFkfP 40 (83)
T PF12139_consen 24 MWTIKFRNGTV----KRFKFP 40 (83)
T ss_dssp EEEEE-TTS-E----EEEEEE
T ss_pred EEEEEecCCce----eeeecc
Confidence 49999999965 677775
No 13
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=48.87 E-value=15 Score=25.35 Aligned_cols=27 Identities=33% Similarity=0.871 Sum_probs=21.8
Q ss_pred CeeEEEecceeEEECCeeeEeeeceeeee
Q psy11263 51 NKWKFYLKDGIMNLNGKDFVFLKANGDAD 79 (80)
Q Consensus 51 nKWKc~LKdGim~ingkDyvF~ka~GE~e 79 (80)
-+|||....|-+ +-|.-|.|.| +|-.-
T Consensus 5 kewkC~VCg~~i-ieGqkFTF~~-kGsVH 31 (103)
T COG4847 5 KEWKCYVCGGTI-IEGQKFTFTK-KGSVH 31 (103)
T ss_pred ceeeEeeeCCEe-eeccEEEEee-CCcch
Confidence 479999999976 6788899988 66543
No 14
>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=48.50 E-value=14 Score=19.28 Aligned_cols=16 Identities=19% Similarity=0.879 Sum_probs=14.5
Q ss_pred CCeeeEeeeceeeeeC
Q psy11263 65 NGKDFVFLKANGDADW 80 (80)
Q Consensus 65 ngkDyvF~ka~GE~eW 80 (80)
.|+-|.|+..||+..|
T Consensus 13 ~g~~YY~N~~t~~s~W 28 (31)
T PF00397_consen 13 SGRPYYYNHETGESQW 28 (31)
T ss_dssp TSEEEEEETTTTEEES
T ss_pred CCCEEEEeCCCCCEEe
Confidence 4899999999999888
No 15
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=47.95 E-value=16 Score=21.84 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=10.8
Q ss_pred eeecCCeeEEEec
Q psy11263 46 ITRSRNKWKFYLK 58 (80)
Q Consensus 46 V~R~KnKWKc~LK 58 (80)
|+|.+++|++.|+
T Consensus 31 v~k~~~~w~f~l~ 43 (76)
T PF14480_consen 31 VHKKSRKWRFHLS 43 (76)
T ss_pred EEccCCEEEEEEE
Confidence 5678889999886
No 16
>cd00201 WW Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Probab=46.95 E-value=16 Score=18.09 Aligned_cols=16 Identities=13% Similarity=0.684 Sum_probs=14.0
Q ss_pred CCeeeEeeeceeeeeC
Q psy11263 65 NGKDFVFLKANGDADW 80 (80)
Q Consensus 65 ngkDyvF~ka~GE~eW 80 (80)
+|+-|.++..+++..|
T Consensus 11 ~g~~yy~n~~t~~s~W 26 (31)
T cd00201 11 DGRVYYYNHNTKETQW 26 (31)
T ss_pred CCCEEEEECCCCCEeC
Confidence 3899999999998877
No 17
>KOG2345|consensus
Probab=43.70 E-value=22 Score=28.59 Aligned_cols=19 Identities=21% Similarity=0.434 Sum_probs=17.7
Q ss_pred ceeEEECCeeeEeeeceee
Q psy11263 59 DGIMNLNGKDFVFLKANGD 77 (80)
Q Consensus 59 dGim~ingkDyvF~ka~GE 77 (80)
+|.+.||++.|.|.+.-||
T Consensus 13 ~~tv~In~~Ryri~~~Lge 31 (302)
T KOG2345|consen 13 RGTVIINNKRYRIQRLLGE 31 (302)
T ss_pred CCcEEEcCceEEEeeeecC
Confidence 8999999999999998876
No 18
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=42.04 E-value=26 Score=24.72 Aligned_cols=25 Identities=36% Similarity=0.659 Sum_probs=21.0
Q ss_pred eecCCeeEEEecceeE-EECCeeeEe
Q psy11263 47 TRSRNKWKFYLKDGIM-NLNGKDFVF 71 (80)
Q Consensus 47 ~R~KnKWKc~LKdGim-~ingkDyvF 71 (80)
.+.++|.|+.|-||-. .|.++|++-
T Consensus 27 ~~~~~kykv~FdDG~~~~v~~~div~ 52 (122)
T PF09038_consen 27 DKGKNKYKVLFDDGYECRVLGKDIVV 52 (122)
T ss_dssp EETTTEEEEEETTS-EEEEECCCEEE
T ss_pred cCCCCeEEEEecCCccceeccCcEEE
Confidence 4679999999999988 599999875
No 19
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.06 E-value=18 Score=28.87 Aligned_cols=20 Identities=35% Similarity=0.682 Sum_probs=16.5
Q ss_pred CCeeEEEecceeEEECCeee
Q psy11263 50 RNKWKFYLKDGIMNLNGKDF 69 (80)
Q Consensus 50 KnKWKc~LKdGim~ingkDy 69 (80)
+--=++..|||+|.|.|+|.
T Consensus 263 ~pGd~vvv~dg~mki~G~d~ 282 (293)
T COG4079 263 EPGDRVVVKDGVMKIDGKDL 282 (293)
T ss_pred CCCCEEEEecCceEeccccc
Confidence 33457889999999999986
No 20
>PTZ00486 apyrase Superfamily; Provisional
Probab=39.14 E-value=37 Score=27.68 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=24.7
Q ss_pred EEEEEEeeeee--cCCeeEEEecceeEEECCee
Q psy11263 38 IVVCQYDKITR--SRNKWKFYLKDGIMNLNGKD 68 (80)
Q Consensus 38 vilC~ydKV~R--~KnKWKc~LKdGim~ingkD 68 (80)
.|+.=-||-+| .+|+|++.|+-|.+...+..
T Consensus 59 aiIaDlD~~S~~~~~~~w~S~~~~G~L~~~~~~ 91 (352)
T PTZ00486 59 ALVADLDKASKDKEGKKWRSKVIKGTIFRQGNG 91 (352)
T ss_pred EEEecCchhccccCCCceEEEEEEEEEEEcCCC
Confidence 35566688888 58999999999999887754
No 21
>PF13691 Lactamase_B_4: tRNase Z endonuclease
Probab=38.26 E-value=27 Score=21.60 Aligned_cols=13 Identities=8% Similarity=0.508 Sum_probs=10.6
Q ss_pred eEEECCeeeEeee
Q psy11263 61 IMNLNGKDFVFLK 73 (80)
Q Consensus 61 im~ingkDyvF~k 73 (80)
+++.+.+.|+|.+
T Consensus 16 ~l~~d~~rYlFGn 28 (63)
T PF13691_consen 16 LLFFDSRRYLFGN 28 (63)
T ss_pred EEEeCCceEEecc
Confidence 5788999999943
No 22
>PF01491 Frataxin_Cyay: Frataxin-like domain; InterPro: IPR002908 The eukaryotic proteins in this entry include frataxin, the protein that is mutated in Friedreich's ataxia [], and related sequences. Friedreich's ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [, , ]. The bacterial proteins in this entry are iron-sulphur cluster (FeS) metabolism CyaY proteins hmologous to eukaryotic frataxin. Partial Phylogenetic Profiling [] suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species [, ]. ; PDB: 1EW4_A 2P1X_A 1SOY_A 2EFF_A 3T3T_B 3S4M_A 3T3K_A 3S5D_A 1LY7_A 3T3X_B ....
Probab=35.83 E-value=39 Score=22.43 Aligned_cols=22 Identities=18% Similarity=0.406 Sum_probs=17.4
Q ss_pred eEEEecceeEEEC---CeeeEeeec
Q psy11263 53 WKFYLKDGIMNLN---GKDFVFLKA 74 (80)
Q Consensus 53 WKc~LKdGim~in---gkDyvF~ka 74 (80)
.-|.+.+|||+|. |.-||++|-
T Consensus 32 ~d~e~~~gVLti~~~~~~~~VINkQ 56 (109)
T PF01491_consen 32 IDVERSGGVLTIEFPDGGQYVINKQ 56 (109)
T ss_dssp EEEEEETTEEEEEETTSEEEEEEEE
T ss_pred eEEEccCCEEEEEECCCCEEEEeCC
Confidence 4577888999884 889999874
No 23
>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=35.80 E-value=62 Score=20.52 Aligned_cols=30 Identities=23% Similarity=0.639 Sum_probs=20.4
Q ss_pred EEEEeeeeecCCe-eEEEecceeEEEC---CeeeEeee
Q psy11263 40 VCQYDKITRSRNK-WKFYLKDGIMNLN---GKDFVFLK 73 (80)
Q Consensus 40 lC~ydKV~R~KnK-WKc~LKdGim~in---gkDyvF~k 73 (80)
-|||-+=.|.|.| | .||++.+. +|=.|+.-
T Consensus 5 ~~lYT~q~~kK~K~W----~DG~l~~~~~~~kv~Lyde 38 (83)
T PF10382_consen 5 ECLYTHQKTKKRKKW----HDGFLKYHSFNKKVMLYDE 38 (83)
T ss_pred EEEEEccccccceee----ECCEEEEEeCCCEEEEEcC
Confidence 5899877776664 6 49999875 44555543
No 24
>KOG0284|consensus
Probab=35.44 E-value=32 Score=29.10 Aligned_cols=44 Identities=16% Similarity=0.110 Sum_probs=37.0
Q ss_pred CCEEEEEEeeeeecC-CeeEEEecceeEEECCeeeEeeeceeeee
Q psy11263 36 DNIVVCQYDKITRSR-NKWKFYLKDGIMNLNGKDFVFLKANGDAD 79 (80)
Q Consensus 36 ~nvilC~ydKV~R~K-nKWKc~LKdGim~ingkDyvF~ka~GE~e 79 (80)
.|.+.|.-.|..|+. ||=||..-.=-=+=.||..+-...+|||+
T Consensus 77 ~dp~~~~~tKf~h~s~NKvkc~V~~v~WtPeGRRLltgs~SGEFt 121 (464)
T KOG0284|consen 77 DDPSSAFTTKFVHTSSNKVKCPVNVVRWTPEGRRLLTGSQSGEFT 121 (464)
T ss_pred CCcccccccceEeccccccccceeeEEEcCCCceeEeecccccEE
Confidence 578888999999987 99888766555556899999999999997
No 25
>TIGR03421 FeS_CyaY iron donor protein CyaY. Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. Although the trusted cutoff is set low enough to include eukaryotic frataxin sequences, a narrower, exception-type model (TIGR03421) identifies identifies members of that specific set.
Probab=34.27 E-value=43 Score=22.24 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=14.2
Q ss_pred EEecceeEEE---CCeeeEeeec
Q psy11263 55 FYLKDGIMNL---NGKDFVFLKA 74 (80)
Q Consensus 55 c~LKdGim~i---ngkDyvF~ka 74 (80)
|.+.+|||+| ||.-||++|-
T Consensus 29 ~e~~~gVLti~f~~~~~~VINkQ 51 (102)
T TIGR03421 29 CERAGGVLTLTFENGSQIIINKQ 51 (102)
T ss_pred eecCCCEEEEEECCCCEEEEeCC
Confidence 4556778777 5778888774
No 26
>PF14267 DUF4357: Domain of unknown function (DUF4357)
Probab=33.95 E-value=25 Score=21.16 Aligned_cols=17 Identities=29% Similarity=0.720 Sum_probs=13.3
Q ss_pred ecceeEEECCeeeEeee
Q psy11263 57 LKDGIMNLNGKDFVFLK 73 (80)
Q Consensus 57 LKdGim~ingkDyvF~k 73 (80)
+.+|+|...|..|+|.+
T Consensus 5 i~~G~l~~~~~~~~f~~ 21 (55)
T PF14267_consen 5 IEDGVLVPDGGRLVFTQ 21 (55)
T ss_pred HhCCCEEecCCcEEEec
Confidence 46889988888888765
No 27
>cd06497 ACD_alphaA-crystallin_HspB4 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaA-crystallin (HspB4, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 does not belong to this group. Mutations inHspB4 have been associated with Autosomal Dominant Congenital Cataract (ADCC). The chaperone-like functions of HspB4 are considered important for maintaining lens transparency and preventing cataract.
Probab=33.61 E-value=33 Score=21.56 Aligned_cols=16 Identities=19% Similarity=0.443 Sum_probs=12.8
Q ss_pred CCeeEEEe-cceeEEEC
Q psy11263 50 RNKWKFYL-KDGIMNLN 65 (80)
Q Consensus 50 KnKWKc~L-KdGim~in 65 (80)
..+=++.| +|||++|.
T Consensus 67 ~~~i~A~~~~dGvL~I~ 83 (86)
T cd06497 67 QSAITCSLSADGMLTFS 83 (86)
T ss_pred hHHeEEEeCCCCEEEEE
Confidence 44678999 89999984
No 28
>cd06471 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic me
Probab=33.23 E-value=34 Score=21.06 Aligned_cols=13 Identities=15% Similarity=0.455 Sum_probs=10.9
Q ss_pred eeEEEecceeEEE
Q psy11263 52 KWKFYLKDGIMNL 64 (80)
Q Consensus 52 KWKc~LKdGim~i 64 (80)
+=+..|+|||++|
T Consensus 77 ~i~A~~~dGvL~I 89 (93)
T cd06471 77 EIKAKYENGVLKI 89 (93)
T ss_pred HCEEEEECCEEEE
Confidence 4578889999987
No 29
>PRK01379 cyaY frataxin-like protein; Provisional
Probab=32.92 E-value=46 Score=22.42 Aligned_cols=15 Identities=40% Similarity=0.696 Sum_probs=8.0
Q ss_pred cceeEEE---CCeeeEeee
Q psy11263 58 KDGIMNL---NGKDFVFLK 73 (80)
Q Consensus 58 KdGim~i---ngkDyvF~k 73 (80)
-+|||+| +|. ||.+|
T Consensus 35 ~~gVLtl~~~~gt-~VINk 52 (103)
T PRK01379 35 QGDILNLDTDKGI-YVINK 52 (103)
T ss_pred cCCEEEEEeCCcE-EEEeC
Confidence 3455554 344 66665
No 30
>KOG3259|consensus
Probab=32.83 E-value=17 Score=26.91 Aligned_cols=16 Identities=19% Similarity=0.779 Sum_probs=14.9
Q ss_pred CCeeeEeeeceeeeeC
Q psy11263 65 NGKDFVFLKANGDADW 80 (80)
Q Consensus 65 ngkDyvF~ka~GE~eW 80 (80)
.|+.|.|+..|++.+|
T Consensus 19 ~gr~YyfN~~T~~SqW 34 (163)
T KOG3259|consen 19 SGRPYYFNTETNESQW 34 (163)
T ss_pred CCCcceeccccchhhc
Confidence 6899999999999988
No 31
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=32.78 E-value=27 Score=20.37 Aligned_cols=12 Identities=42% Similarity=0.609 Sum_probs=10.1
Q ss_pred EEEEEEeeeeec
Q psy11263 38 IVVCQYDKITRS 49 (80)
Q Consensus 38 vilC~ydKV~R~ 49 (80)
+.+.|-|||+|+
T Consensus 28 ifvSq~D~v~R~ 39 (39)
T CHL00114 28 LFVSQKDRTTRN 39 (39)
T ss_pred EEEeccceeccC
Confidence 678899999984
No 32
>PF10974 DUF2804: Protein of unknown function (DUF2804); InterPro: IPR021243 This is a family of proteins with unknown function.
Probab=32.07 E-value=81 Score=24.29 Aligned_cols=43 Identities=26% Similarity=0.435 Sum_probs=29.5
Q ss_pred CCCCEEEEEEeeeeecCCeeEEEec------ceeEEECCeeeEee--eceeeeeC
Q psy11263 34 DTDNIVVCQYDKITRSRNKWKFYLK------DGIMNLNGKDFVFL--KANGDADW 80 (80)
Q Consensus 34 ~~~nvilC~ydKV~R~KnKWKc~LK------dGim~ingkDyvF~--ka~GE~eW 80 (80)
..+.+.+|.==. .++|-.+-| .|.|.++|+.|.|+ .+.|=+.|
T Consensus 147 ~~e~L~vv~P~~----~~~f~yt~K~~~~pv~G~v~~g~~~~~~~~~~~~a~lD~ 197 (333)
T PF10974_consen 147 GHEPLNVVTPWG----ENRFYYTQKQNGLPVSGSVRLGGKEYSFDPENAFAVLDW 197 (333)
T ss_pred CCCCEEEEeecC----CCCEEEEEEecCcceEEEEEECCEEEecCCCCcEEEEEc
Confidence 445566654322 344666666 49999999999999 67776665
No 33
>PF14249 Tocopherol_cycl: Tocopherol cyclase
Probab=31.36 E-value=46 Score=26.65 Aligned_cols=21 Identities=29% Similarity=0.531 Sum_probs=18.4
Q ss_pred ceeEEECCeeeEeeeceeeee
Q psy11263 59 DGIMNLNGKDFVFLKANGDAD 79 (80)
Q Consensus 59 dGim~ingkDyvF~ka~GE~e 79 (80)
.|-+.+||+.|-|..+.|-.|
T Consensus 169 sG~i~~nG~~~~F~~g~gY~E 189 (336)
T PF14249_consen 169 SGWIEWNGKRYDFTGGPGYIE 189 (336)
T ss_pred EEEEEECCEEEEECCCceeec
Confidence 488899999999999988665
No 34
>PF06079 Apyrase: Apyrase; InterPro: IPR009283 This family consists of several eukaryotic apyrase (or adenosine diphosphatase) proteins (3.6.1.5 from EC), and related nucleoside diphosphatases (3.6.1.6 from EC). The salivary apyrases of blood-feeding arthropods are nucleotide hydrolysing enzymes implicated in the inhibition of host platelet aggregation through the hydrolysis of extracellular adenosine diphosphate [].; GO: 0005509 calcium ion binding, 0016462 pyrophosphatase activity; PDB: 2H2N_A 1S18_A 2H2U_A 1S1D_B.
Probab=30.61 E-value=36 Score=27.04 Aligned_cols=21 Identities=33% Similarity=0.975 Sum_probs=16.4
Q ss_pred cCCeeEEEecceeEEECCeee
Q psy11263 49 SRNKWKFYLKDGIMNLNGKDF 69 (80)
Q Consensus 49 ~KnKWKc~LKdGim~ingkDy 69 (80)
.++.|++.||-|.+++++.-+
T Consensus 10 ~~~~w~S~~~~G~L~~~~~~~ 30 (291)
T PF06079_consen 10 DKNTWRSYLKKGYLTFSGDKY 30 (291)
T ss_dssp -TT-EEEEEEEEEEEEETTSS
T ss_pred CCCcEEEEEEEeEEEECCCcc
Confidence 358899999999999988654
No 35
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=30.38 E-value=55 Score=21.91 Aligned_cols=21 Identities=19% Similarity=0.457 Sum_probs=14.7
Q ss_pred EEecceeEEE---CCeeeEeeece
Q psy11263 55 FYLKDGIMNL---NGKDFVFLKAN 75 (80)
Q Consensus 55 c~LKdGim~i---ngkDyvF~ka~ 75 (80)
|.+.+||++| ||.-||.+|-+
T Consensus 31 ~e~~~gVLti~f~~~~~~VINkQ~ 54 (105)
T PRK00446 31 CERNGGVLTLTFENGSKIIINRQE 54 (105)
T ss_pred eeccCCEEEEEECCCCEEEEeCCC
Confidence 5556788877 47778888743
No 36
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=29.57 E-value=54 Score=22.40 Aligned_cols=25 Identities=36% Similarity=0.707 Sum_probs=19.3
Q ss_pred eeEEEecceeEEECCeeeEeeeceeee
Q psy11263 52 KWKFYLKDGIMNLNGKDFVFLKANGDA 78 (80)
Q Consensus 52 KWKc~LKdGim~ingkDyvF~ka~GE~ 78 (80)
||||.+..+=+ +.|.-|-|.+- |-.
T Consensus 2 kWkC~iCg~~I-~~gqlFTF~~k-G~V 26 (101)
T PF09943_consen 2 KWKCYICGKPI-YEGQLFTFTKK-GPV 26 (101)
T ss_pred ceEEEecCCee-eecceEEEecC-CcE
Confidence 89999988765 57788888776 543
No 37
>TIGR03422 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately.
Probab=28.52 E-value=42 Score=22.18 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=14.7
Q ss_pred EEEecceeEEEC---CeeeEeeec
Q psy11263 54 KFYLKDGIMNLN---GKDFVFLKA 74 (80)
Q Consensus 54 Kc~LKdGim~in---gkDyvF~ka 74 (80)
-|.+.+|||+|. |.-||++|-
T Consensus 30 D~e~~~gVLti~~~~~~~~VINkQ 53 (97)
T TIGR03422 30 DVEYSSGVLTLELPSVGTYVINKQ 53 (97)
T ss_pred ccccCCCEEEEEECCCCEEEEeCC
Confidence 345567888874 668888874
No 38
>PHA02095 hypothetical protein
Probab=28.09 E-value=59 Score=21.63 Aligned_cols=19 Identities=32% Similarity=0.784 Sum_probs=16.8
Q ss_pred cCCeeEEEecceeEEECCe
Q psy11263 49 SRNKWKFYLKDGIMNLNGK 67 (80)
Q Consensus 49 ~KnKWKc~LKdGim~ingk 67 (80)
..+.|.|.--|||++|.|-
T Consensus 31 ~ng~wefsrvdgilciegd 49 (84)
T PHA02095 31 ENGSWEFSRVDGILCIEGD 49 (84)
T ss_pred ecCcEEEEeccEEEEecCC
Confidence 3778999999999999884
No 39
>PF14864 Alkyl_sulf_C: Alkyl sulfatase C-terminal; PDB: 2CG2_A 2CG3_A 2CFU_A 2CFZ_A 2YHE_C.
Probab=28.03 E-value=48 Score=21.81 Aligned_cols=19 Identities=21% Similarity=0.611 Sum_probs=15.7
Q ss_pred eeecCCeeEEEecceeEEE
Q psy11263 46 ITRSRNKWKFYLKDGIMNL 64 (80)
Q Consensus 46 V~R~KnKWKc~LKdGim~i 64 (80)
+.-++-+|.+.|++||++.
T Consensus 40 ~~D~~e~~~l~l~NgvL~~ 58 (125)
T PF14864_consen 40 FTDTGEQYTLELRNGVLNY 58 (125)
T ss_dssp ETTTTEEEEEEEETTEEEE
T ss_pred EcCCCCeEEEEEECCEEEe
Confidence 3445679999999999998
No 40
>PF11008 DUF2846: Protein of unknown function (DUF2846); InterPro: IPR022548 Some members in this group of proteins with unknown function are annotated as lipoproteins. However this cannot be confirmed.
Probab=27.37 E-value=78 Score=20.56 Aligned_cols=39 Identities=15% Similarity=0.236 Sum_probs=28.4
Q ss_pred CCEEEEEEeeeeecCCeeEEEecceeEEECCeeeEeeeceeeeeC
Q psy11263 36 DNIVVCQYDKITRSRNKWKFYLKDGIMNLNGKDFVFLKANGDADW 80 (80)
Q Consensus 36 ~nvilC~ydKV~R~KnKWKc~LKdGim~ingkDyvF~ka~GE~eW 80 (80)
++-.|..| |.++.|-..++--| .|||+ +++..++|.|.|
T Consensus 24 ~~a~IYvY----R~~~~~g~~~~~~v-~vdg~-~ig~l~~g~y~~ 62 (117)
T PF11008_consen 24 GKARIYVY----RPSSFFGSAVKPDV-YVDGE-LIGELKNGGYFY 62 (117)
T ss_pred CcEEEEEE----EECCccCccccceE-EECCE-EEEEeCCCeEEE
Confidence 56777777 88888876555555 88884 567777777754
No 41
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=27.05 E-value=50 Score=20.82 Aligned_cols=14 Identities=21% Similarity=0.375 Sum_probs=10.6
Q ss_pred eeEEEe-cceeEEEC
Q psy11263 52 KWKFYL-KDGIMNLN 65 (80)
Q Consensus 52 KWKc~L-KdGim~in 65 (80)
+=++.| ++|||+|.
T Consensus 64 ~v~A~l~~~GvL~I~ 78 (81)
T cd06479 64 SVSSSLGEDGTLTIK 78 (81)
T ss_pred HeEEEecCCCEEEEE
Confidence 456676 99999984
No 42
>PF07873 YabP: YabP family; InterPro: IPR022476 Members of this protein family are the YabP and YqfC proteins of the bacterial sporulation program, as found in Bacillus subtilis, Clostridium tetani, and other spore-forming members of the Firmicutes. ; PDB: 2KYI_B 3IPF_B 2KS0_A.
Probab=26.63 E-value=77 Score=19.07 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=22.8
Q ss_pred cCCeeEEEecceeEEECCeeeEeeecee
Q psy11263 49 SRNKWKFYLKDGIMNLNGKDFVFLKANG 76 (80)
Q Consensus 49 ~KnKWKc~LKdGim~ingkDyvF~ka~G 76 (80)
+-++=++..+.|.+.|.|++..-...+.
T Consensus 24 ~~~~I~l~t~~g~l~I~G~~L~I~~l~~ 51 (66)
T PF07873_consen 24 DDEEIRLNTKKGKLTIKGEGLVIKYLNL 51 (66)
T ss_dssp ETTEEEEEETTEEEEEEEEEEEEEECET
T ss_pred CCCEEEEEeCCEEEEEECceEEEeEeec
Confidence 3567788999999999999988776554
No 43
>PF06097 DUF945: Bacterial protein of unknown function (DUF945); InterPro: IPR010352 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.49 E-value=55 Score=25.15 Aligned_cols=17 Identities=35% Similarity=0.653 Sum_probs=14.6
Q ss_pred EEEecceeEEECCeeeE
Q psy11263 54 KFYLKDGIMNLNGKDFV 70 (80)
Q Consensus 54 Kc~LKdGim~ingkDyv 70 (80)
.+.+++|-+.||||.+.
T Consensus 440 ~~~~~~g~l~lNG~~ip 456 (460)
T PF06097_consen 440 ELQLKNGQLTLNGQPIP 456 (460)
T ss_pred EEEEECCEEEECCeECc
Confidence 46789999999999874
No 44
>PF13738 Pyr_redox_3: Pyridine nucleotide-disulphide oxidoreductase; PDB: 3D1C_A 4A9W_B 2YLX_A 2YM2_A 2YLW_A 2YLR_A 2YM1_A 2YLS_A 1W4X_A 2YLT_A ....
Probab=26.27 E-value=1.1e+02 Score=20.26 Aligned_cols=20 Identities=20% Similarity=0.602 Sum_probs=16.9
Q ss_pred EEEeeeeecCCeeEEEecce
Q psy11263 41 CQYDKITRSRNKWKFYLKDG 60 (80)
Q Consensus 41 C~ydKV~R~KnKWKc~LKdG 60 (80)
+...+|.|..++|.+++++|
T Consensus 103 ~~V~~v~~~~~~w~v~~~~~ 122 (203)
T PF13738_consen 103 TRVESVRRDGDGWTVTTRDG 122 (203)
T ss_dssp --EEEEEEETTTEEEEETTS
T ss_pred CEEEEEEEeccEEEEEEEec
Confidence 66789999999999999999
No 45
>PF00011 HSP20: Hsp20/alpha crystallin family This prints entry is a subset of the Pfam entry.; InterPro: IPR002068 Prokaryotic and eukaryotic organisms respond to heat shock or other environmental stress by inducing the synthesis of proteins collectively known as heat-shock proteins (hsp) []. Amongst them is a family of proteins with an average molecular weight of 20 Kd, known as the hsp20 proteins []. These seem to act as chaperones that can protect other proteins against heat-induced denaturation and aggregation. Hsp20 proteins seem to form large heterooligomeric aggregates. Structurally, this family is characterised by the presence of a conserved C-terminal domain of about 100 residues.; PDB: 2BOL_B 3N3E_B 2H50_P 2H53_F 2BYU_L 1GME_D 3VQM_J 3VQK_E 3VQL_A 3AAC_A ....
Probab=25.65 E-value=57 Score=20.03 Aligned_cols=24 Identities=17% Similarity=0.450 Sum_probs=14.9
Q ss_pred EEeeeeec-----CCeeEEEecceeEEEC
Q psy11263 42 QYDKITRS-----RNKWKFYLKDGIMNLN 65 (80)
Q Consensus 42 ~ydKV~R~-----KnKWKc~LKdGim~in 65 (80)
.|.+.-+- -++=++.+++|+|+|.
T Consensus 56 ~f~r~~~lP~~vd~~~i~a~~~~GvL~I~ 84 (102)
T PF00011_consen 56 SFERSIRLPEDVDPDKIKASYENGVLTIT 84 (102)
T ss_dssp EEEEEEE-STTB-GGG-EEEETTSEEEEE
T ss_pred eEEEEEcCCCcCCcceEEEEecCCEEEEE
Confidence 45554443 3455788899999883
No 46
>smart00400 ZnF_CHCC zinc finger.
Probab=25.62 E-value=53 Score=18.81 Aligned_cols=13 Identities=0% Similarity=0.220 Sum_probs=9.7
Q ss_pred eeeecCCeeEEEe
Q psy11263 45 KITRSRNKWKFYL 57 (80)
Q Consensus 45 KV~R~KnKWKc~L 57 (80)
+|...||.|+|-=
T Consensus 16 ~v~~~kn~~~Cf~ 28 (55)
T smart00400 16 SVSPDKQFFHCFG 28 (55)
T ss_pred EEECCCCEEEEeC
Confidence 4566789999974
No 47
>COG3250 LacZ Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]
Probab=24.61 E-value=1.2e+02 Score=27.01 Aligned_cols=31 Identities=23% Similarity=0.250 Sum_probs=24.1
Q ss_pred eeeecCCeeEEEecceeEEECCeeeEeeece
Q psy11263 45 KITRSRNKWKFYLKDGIMNLNGKDFVFLKAN 75 (80)
Q Consensus 45 KV~R~KnKWKc~LKdGim~ingkDyvF~ka~ 75 (80)
.+.+.=+=.++.+++|.+.||||..+|.-++
T Consensus 276 ~~~~~iGfR~iei~~~~~~iNGkpvf~kGvn 306 (808)
T COG3250 276 AEALRIGFRTVEIKDGLLLINGKPVFIRGVN 306 (808)
T ss_pred EEEeeeccEEEEEECCeEEECCeEEEEeeee
Confidence 4444445678999999999999999886543
No 48
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=24.30 E-value=56 Score=21.82 Aligned_cols=26 Identities=23% Similarity=0.532 Sum_probs=19.8
Q ss_pred EEEecceeE-EECCeeeEeeeceeeee
Q psy11263 54 KFYLKDGIM-NLNGKDFVFLKANGDAD 79 (80)
Q Consensus 54 Kc~LKdGim-~ingkDyvF~ka~GE~e 79 (80)
.++|..=|+ +|++-.|+|.=+||+..
T Consensus 36 ~V~L~G~Iv~~l~~d~Y~F~D~TG~I~ 62 (103)
T PF04076_consen 36 PVTLEGNIVKQLGDDKYLFRDATGEIE 62 (103)
T ss_dssp EEEEEEEEEEEEETTEEEEEETTEEEE
T ss_pred eEEEEEEEEEEecCCEEEEECCCCcEE
Confidence 456665544 68889999999999864
No 49
>COG1965 CyaY Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism]
Probab=24.23 E-value=79 Score=21.81 Aligned_cols=20 Identities=25% Similarity=0.574 Sum_probs=12.8
Q ss_pred EEecceeEEE---CCeeeEeeec
Q psy11263 55 FYLKDGIMNL---NGKDFVFLKA 74 (80)
Q Consensus 55 c~LKdGim~i---ngkDyvF~ka 74 (80)
|-+.+|||+| ||--|+++|-
T Consensus 32 ~d~qg~VlTl~f~ngs~iiINkQ 54 (106)
T COG1965 32 CEIQGGVLTLTFDNGSQIIINKQ 54 (106)
T ss_pred eecCCCEEEEEECCCcEEEEeCC
Confidence 3445777776 5667777764
No 50
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=24.16 E-value=60 Score=20.04 Aligned_cols=13 Identities=23% Similarity=0.687 Sum_probs=10.3
Q ss_pred eeEEEecceeEEE
Q psy11263 52 KWKFYLKDGIMNL 64 (80)
Q Consensus 52 KWKc~LKdGim~i 64 (80)
+=+..|+|||++|
T Consensus 76 ~i~A~~~nGvL~I 88 (92)
T cd06472 76 EVKAFLENGVLTV 88 (92)
T ss_pred HCEEEEECCEEEE
Confidence 4467889999987
No 51
>PF14527 LAGLIDADG_WhiA: WhiA LAGLIDADG-like domain; PDB: 3HYI_A 3HYJ_D.
Probab=23.90 E-value=65 Score=20.76 Aligned_cols=16 Identities=50% Similarity=0.862 Sum_probs=12.0
Q ss_pred eeeecCCeeEEEecce
Q psy11263 45 KITRSRNKWKFYLKDG 60 (80)
Q Consensus 45 KV~R~KnKWKc~LKdG 60 (80)
|+.+.|+++.+++|++
T Consensus 49 k~~~r~~~~~vYlK~~ 64 (93)
T PF14527_consen 49 KIIKRKNKYVVYLKDS 64 (93)
T ss_dssp EEEEESSEEEEEE--H
T ss_pred eeeeecCceEEEEcCH
Confidence 6778899999999985
No 52
>PF12276 DUF3617: Protein of unknown function (DUF3617); InterPro: IPR022061 This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Probab=23.41 E-value=66 Score=21.57 Aligned_cols=21 Identities=24% Similarity=0.476 Sum_probs=17.5
Q ss_pred CEEEEEEeeeeecCCeeEEEe
Q psy11263 37 NIVVCQYDKITRSRNKWKFYL 57 (80)
Q Consensus 37 nvilC~ydKV~R~KnKWKc~L 57 (80)
+--=|.|..+.|+.++|++.+
T Consensus 89 ~~~~C~~~~~~~~~~~~~~~~ 109 (162)
T PF12276_consen 89 ENQDCTYTDVSRSGGTVTFTM 109 (162)
T ss_pred CCCCCCEeeEEEeCCEEEEEE
Confidence 333499999999999998887
No 53
>cd06478 ACD_HspB4-5-6 Alpha-crystallin domain found in alphaA-crystallin (HspB4), alphaB-crystallin (HspB5), and the small heat shock protein (sHsp) HspB6, also known as Hsp20. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 on the other hand is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. HspB5's functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its ol
Probab=22.89 E-value=68 Score=19.88 Aligned_cols=15 Identities=20% Similarity=0.399 Sum_probs=11.4
Q ss_pred CeeEEEe-cceeEEEC
Q psy11263 51 NKWKFYL-KDGIMNLN 65 (80)
Q Consensus 51 nKWKc~L-KdGim~in 65 (80)
.+=++.| +|||++|.
T Consensus 65 ~~i~A~~~~dGvL~I~ 80 (83)
T cd06478 65 AAITSSLSADGVLTIS 80 (83)
T ss_pred HHeEEEECCCCEEEEE
Confidence 3567888 69999874
No 54
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR023753 from INTERPRO. It is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZKQ_A 3DGZ_A 1ZDL_A 2R9Z_B 2RAB_A 2A87_B 1M6I_A 2YVG_A 2GR1_A 2GQW_A ....
Probab=22.89 E-value=1.2e+02 Score=17.87 Aligned_cols=21 Identities=19% Similarity=0.317 Sum_probs=16.2
Q ss_pred EEEEeeeeecCCeeEEEecce
Q psy11263 40 VCQYDKITRSRNKWKFYLKDG 60 (80)
Q Consensus 40 lC~ydKV~R~KnKWKc~LKdG 60 (80)
-|+..+|....++.+++|+||
T Consensus 60 ~~~v~~i~~~~~~~~V~~~~g 80 (80)
T PF00070_consen 60 NTKVKEIEKDGDGVEVTLEDG 80 (80)
T ss_dssp SEEEEEEEEETTSEEEEEETS
T ss_pred CCEEEEEEEeCCEEEEEEecC
Confidence 366777777777777999987
No 55
>cd06464 ACD_sHsps-like Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=22.71 E-value=70 Score=18.48 Aligned_cols=13 Identities=31% Similarity=0.606 Sum_probs=9.7
Q ss_pred eeEEEecceeEEE
Q psy11263 52 KWKFYLKDGIMNL 64 (80)
Q Consensus 52 KWKc~LKdGim~i 64 (80)
+=++.+++|++.|
T Consensus 72 ~i~a~~~~G~L~I 84 (88)
T cd06464 72 KIKASLENGVLTI 84 (88)
T ss_pred HcEEEEeCCEEEE
Confidence 4567788888887
No 56
>COG0071 IbpA Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.29 E-value=61 Score=21.89 Aligned_cols=13 Identities=23% Similarity=0.391 Sum_probs=11.3
Q ss_pred eeEEEecceeEEE
Q psy11263 52 KWKFYLKDGIMNL 64 (80)
Q Consensus 52 KWKc~LKdGim~i 64 (80)
+=+..|++||++|
T Consensus 116 ~~~A~~~nGvL~I 128 (146)
T COG0071 116 VIKAKYKNGLLTV 128 (146)
T ss_pred ceeeEeeCcEEEE
Confidence 4678999999998
No 57
>PF03941 INCENP_ARK-bind: Inner centromere protein, ARK binding region; InterPro: IPR005635 This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregation with cell division in yeast [].; PDB: 2BFX_C 2BFY_C 3ZTX_D 2VGO_D 2VGP_D 2VRX_D 4AF3_D.
Probab=22.02 E-value=30 Score=20.53 Aligned_cols=12 Identities=42% Similarity=0.689 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCC
Q psy11263 18 PLNSSDDVSEED 29 (80)
Q Consensus 18 ~lnSddD~sd~d 29 (80)
+|+||+++++++
T Consensus 1 ei~SD~eddd~~ 12 (57)
T PF03941_consen 1 EINSDDEDDDED 12 (57)
T ss_dssp ------------
T ss_pred CCCCcccccccc
Confidence 367776555443
No 58
>cd00503 Frataxin Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet.
Probab=21.96 E-value=82 Score=20.90 Aligned_cols=21 Identities=19% Similarity=0.434 Sum_probs=14.4
Q ss_pred EEEecceeEEEC---CeeeEeeec
Q psy11263 54 KFYLKDGIMNLN---GKDFVFLKA 74 (80)
Q Consensus 54 Kc~LKdGim~in---gkDyvF~ka 74 (80)
-|.+.+|||+|. |.-||++|-
T Consensus 31 D~e~~~gVLti~f~~~~~~VINkQ 54 (105)
T cd00503 31 DVETQGGVLTLTFGNGSTIVINRQ 54 (105)
T ss_pred eeeccCCEEEEEECCCCEEEEeCC
Confidence 355567777773 777888774
No 59
>PF15603 Imm45: Immunity protein 45
Probab=21.90 E-value=1.5e+02 Score=19.23 Aligned_cols=23 Identities=35% Similarity=0.505 Sum_probs=17.9
Q ss_pred eeeecCCeeEEEecce-eEEECCe
Q psy11263 45 KITRSRNKWKFYLKDG-IMNLNGK 67 (80)
Q Consensus 45 KV~R~KnKWKc~LKdG-im~ingk 67 (80)
|++++.+.=++.|.+| ++.+.|.
T Consensus 2 ki~~t~s~i~~el~~G~~~~~~GE 25 (82)
T PF15603_consen 2 KITGTRSYITFELEEGARRKAQGE 25 (82)
T ss_pred EEEecCCceEEEecCCEEEEEeee
Confidence 7889999999999988 5555443
No 60
>cd06498 ACD_alphaB-crystallin_HspB5 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaB-crystallin (HspB5, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. HspB4 does not belong to this group. HspB5 shows increased synthesis in response to stress. HspB5 is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. Its functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its oligomerization and anti-apoptotic activ
Probab=21.62 E-value=74 Score=19.91 Aligned_cols=16 Identities=19% Similarity=0.243 Sum_probs=12.1
Q ss_pred CCeeEEEec-ceeEEEC
Q psy11263 50 RNKWKFYLK-DGIMNLN 65 (80)
Q Consensus 50 KnKWKc~LK-dGim~in 65 (80)
..+=++.|+ |||++|.
T Consensus 64 ~~~i~A~~~~dGvL~I~ 80 (84)
T cd06498 64 PLTITSSLSPDGVLTVC 80 (84)
T ss_pred hHHcEEEeCCCCEEEEE
Confidence 346788895 9999874
No 61
>cd06476 ACD_HspB2_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB2/heat shock 27kDa protein 2 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB2 is preferentially and constitutively expressed in skeletal muscle and heart. HspB2 shows homooligomeric activity and forms aggregates in muscle cytosol. Although its expression is not induced by heat shock, it redistributes to the insoluble fraction in response to heat shock. In the mouse heart, HspB2 plays a role in maintaining energetic balance, by protecting cardiac energetics during ischemia/reperfusion, and allowing for increased work during acute inotropic challenge. hHspB2 [previously also known as myotonic dystrophy protein kinase (DMPK) binding protein (MKBP)] is selectively up-regulated in skeletal muscles from myotonic dystrophy patients.
Probab=20.93 E-value=77 Score=19.90 Aligned_cols=15 Identities=27% Similarity=0.328 Sum_probs=11.9
Q ss_pred CeeEEEec-ceeEEEC
Q psy11263 51 NKWKFYLK-DGIMNLN 65 (80)
Q Consensus 51 nKWKc~LK-dGim~in 65 (80)
.+=+..|. |||++|.
T Consensus 65 ~~v~A~~~~dGvL~I~ 80 (83)
T cd06476 65 LLVRASLSHDGILCIQ 80 (83)
T ss_pred hhEEEEecCCCEEEEE
Confidence 46788895 9999883
No 62
>PF04985 Phage_tube: Phage tail tube protein FII; InterPro: IPR006498 This entry is represented by Bacteriophage P2, FII, the major tail tube protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The tails of some phage are contractile. These sequences represent the tail tube, or tail core, protein of the contractile tail of phage P2, and homologous proteins from other phage.
Probab=20.89 E-value=2.5e+02 Score=19.28 Aligned_cols=38 Identities=18% Similarity=0.196 Sum_probs=30.1
Q ss_pred CCCCCEEEEEEeeeeec-CCeeEEEecceeEEECCeeeE
Q psy11263 33 FDTDNIVVCQYDKITRS-RNKWKFYLKDGIMNLNGKDFV 70 (80)
Q Consensus 33 ~~~~nvilC~ydKV~R~-KnKWKc~LKdGim~ingkDyv 70 (80)
.+++.-+=|.|=|.... +-.+.+-..+.|..|||.|++
T Consensus 120 ~~~~~~~~v~yyk~~idG~~~~eiD~~n~i~~vnGvD~l 158 (167)
T PF04985_consen 120 TETSIEFSVTYYKLEIDGKEIIEIDKLNNIYRVNGVDQL 158 (167)
T ss_pred ccceEEEEEEEEEEEECCEEEEEEECccCEEEECCEEhh
Confidence 45666677888777765 557999999999999999984
No 63
>smart00564 PQQ beta-propeller repeat. Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases.
Probab=20.88 E-value=93 Score=15.15 Aligned_cols=17 Identities=18% Similarity=0.495 Sum_probs=13.1
Q ss_pred ECCeeeEeeeceeeeeC
Q psy11263 64 LNGKDFVFLKANGDADW 80 (80)
Q Consensus 64 ingkDyvF~ka~GE~eW 80 (80)
.+|+=|.++..+|+..|
T Consensus 14 ~~g~l~a~d~~~G~~~W 30 (33)
T smart00564 14 TDGTLYALDAKTGEILW 30 (33)
T ss_pred CCCEEEEEEcccCcEEE
Confidence 35677888888888877
Done!