Query 024212
Match_columns 271
No_of_seqs 94 out of 102
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 02:54:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024212.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024212hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03098 LPA1 LOW PSII ACCUMUL 100.0 1.4E-60 3.1E-65 461.6 19.0 194 78-271 181-397 (453)
2 PF11998 DUF3493: Protein of u 100.0 9.2E-30 2E-34 196.1 8.4 74 78-158 2-75 (75)
3 PF06305 DUF1049: Protein of u 86.9 2.9 6.4E-05 30.2 6.2 44 96-170 20-63 (68)
4 PF13778 DUF4174: Domain of un 84.0 3.7 8E-05 33.6 6.2 54 187-240 2-58 (118)
5 PF10066 DUF2304: Uncharacteri 69.5 29 0.00062 28.2 7.4 73 97-174 32-105 (115)
6 PF12666 PrgI: PrgI family pro 65.7 25 0.00054 27.1 6.1 67 88-166 12-78 (93)
7 PF00578 AhpC-TSA: AhpC/TSA fa 65.6 43 0.00092 25.5 7.4 54 181-234 13-68 (124)
8 PF08534 Redoxin: Redoxin; In 65.0 54 0.0012 26.1 8.1 64 175-238 8-75 (146)
9 PF10003 DUF2244: Integral mem 64.7 17 0.00036 30.6 5.3 56 93-161 9-64 (140)
10 PF00255 GSHPx: Glutathione pe 60.6 68 0.0015 26.3 8.1 74 176-251 4-78 (108)
11 PRK09437 bcp thioredoxin-depen 60.0 20 0.00043 29.1 4.9 63 172-234 9-73 (154)
12 cd02968 SCO SCO (an acronym fo 56.5 77 0.0017 24.8 7.6 59 178-236 7-70 (142)
13 PLN02412 probable glutathione 56.0 30 0.00066 29.2 5.5 60 175-234 11-71 (167)
14 TIGR00739 yajC preprotein tran 55.7 15 0.00033 28.8 3.4 45 145-189 12-58 (84)
15 PF10399 UCR_Fe-S_N: Ubiquitin 55.6 26 0.00057 24.5 4.2 27 96-122 11-37 (41)
16 PRK05585 yajC preprotein trans 54.1 22 0.00047 29.2 4.1 45 145-189 27-73 (106)
17 PRK06280 hypothetical protein; 51.4 36 0.00079 26.6 4.8 46 102-155 25-71 (77)
18 cd03017 PRX_BCP Peroxiredoxin 50.8 48 0.001 25.9 5.5 58 176-234 6-66 (140)
19 cd03015 PRX_Typ2cys Peroxiredo 49.7 36 0.00078 28.5 4.9 51 184-235 20-73 (173)
20 PF10960 DUF2762: Protein of u 49.7 22 0.00048 27.5 3.3 36 139-174 9-45 (71)
21 PRK03147 thiol-disulfide oxido 49.0 1.4E+02 0.0031 24.2 8.3 69 167-235 35-104 (173)
22 PRK15051 4-amino-4-deoxy-L-ara 48.0 72 0.0016 25.7 6.2 63 92-161 30-92 (111)
23 cd02970 PRX_like2 Peroxiredoxi 45.2 68 0.0015 25.1 5.6 54 182-235 11-67 (149)
24 PF00406 ADK: Adenylate kinase 44.6 8.1 0.00018 31.4 0.2 11 10-20 1-11 (151)
25 PRK05886 yajC preprotein trans 44.5 40 0.00087 28.1 4.3 46 144-189 12-59 (109)
26 PF04995 CcmD: Heme exporter p 44.3 47 0.001 23.2 4.0 35 137-171 9-43 (46)
27 PRK11476 DNA-binding transcrip 44.2 6.4 0.00014 33.0 -0.4 18 7-25 27-57 (113)
28 TIGR03141 cytochro_ccmD heme e 43.6 48 0.001 23.1 4.0 34 137-170 10-43 (45)
29 cd02964 TryX_like_family Trypa 42.5 79 0.0017 25.1 5.7 57 180-236 4-63 (132)
30 cd03018 PRX_AhpE_like Peroxire 41.9 90 0.0019 24.7 5.9 60 175-234 9-71 (149)
31 cd00340 GSH_Peroxidase Glutath 39.5 58 0.0013 26.7 4.6 53 181-234 10-63 (152)
32 PTZ00253 tryparedoxin peroxida 36.9 71 0.0015 27.7 4.9 53 182-235 25-80 (199)
33 PF04434 SWIM: SWIM zinc finge 36.7 15 0.00032 24.2 0.5 23 14-36 10-34 (40)
34 PF02630 SCO1-SenC: SCO1/SenC; 35.8 2.2E+02 0.0048 24.3 7.7 68 169-236 28-99 (174)
35 TIGR01205 D_ala_D_alaTIGR D-al 34.5 36 0.00077 30.8 2.8 40 196-235 1-41 (315)
36 COG5488 Integral membrane prot 34.3 1.6E+02 0.0035 26.5 6.7 63 88-159 18-81 (164)
37 PF02699 YajC: Preprotein tran 33.3 41 0.00089 26.1 2.6 43 143-193 9-51 (82)
38 PF10011 DUF2254: Predicted me 32.8 1.5E+02 0.0032 28.8 6.8 69 94-163 83-154 (371)
39 cd03012 TlpA_like_DipZ_like Tl 32.3 82 0.0018 24.7 4.2 52 182-233 12-64 (126)
40 PF13244 DUF4040: Domain of un 32.3 1.2E+02 0.0025 23.1 4.8 46 101-154 18-64 (70)
41 PF10686 DUF2493: Protein of u 32.1 1.3E+02 0.0029 22.8 5.1 67 195-271 3-69 (71)
42 PF11286 DUF3087: Protein of u 32.1 3.8E+02 0.0081 24.1 8.7 35 96-132 15-49 (165)
43 PTZ00056 glutathione peroxidas 30.8 3E+02 0.0065 24.1 7.9 61 172-234 18-81 (199)
44 PF12597 DUF3767: Protein of u 30.4 2.2E+02 0.0049 23.8 6.7 41 78-118 16-62 (118)
45 PTZ00256 glutathione peroxidas 30.3 1.5E+02 0.0034 25.2 5.9 65 170-234 17-83 (183)
46 COG0811 TolQ Biopolymer transp 29.4 2.1E+02 0.0045 25.8 6.8 65 104-168 126-199 (216)
47 PRK10606 btuE putative glutath 29.4 1.2E+02 0.0027 26.6 5.3 56 176-234 8-66 (183)
48 PF03210 Paramyx_P_V_C: Paramy 29.3 18 0.00039 31.4 0.0 56 168-223 33-91 (155)
49 PF01618 MotA_ExbB: MotA/TolQ/ 28.7 3.3E+02 0.0072 22.4 9.4 36 88-124 50-85 (139)
50 PRK06531 yajC preprotein trans 28.3 83 0.0018 26.4 3.7 20 151-170 17-36 (113)
51 COG0563 Adk Adenylate kinase a 27.4 27 0.00059 30.4 0.8 12 9-20 4-15 (178)
52 cd02966 TlpA_like_family TlpA- 27.2 2.2E+02 0.0049 20.2 5.5 55 182-236 8-63 (116)
53 PF04418 DUF543: Domain of unk 27.1 17 0.00038 28.4 -0.4 14 13-26 60-73 (75)
54 PF04156 IncA: IncA protein; 25.6 3.5E+02 0.0076 23.1 7.2 15 138-152 43-57 (191)
55 KOG1533 Predicted GTPase [Gene 25.5 32 0.0007 33.1 0.9 15 9-23 6-21 (290)
56 PF01313 Bac_export_3: Bacteri 25.4 2.3E+02 0.0049 22.2 5.5 21 104-124 22-42 (76)
57 KOG2733 Uncharacterized membra 25.4 84 0.0018 31.9 3.8 105 104-229 11-141 (423)
58 PF07535 zf-DBF: DBF zinc fing 24.7 39 0.00085 24.5 1.0 19 17-35 4-23 (49)
59 PF12732 YtxH: YtxH-like prote 24.7 64 0.0014 24.1 2.2 35 100-140 1-35 (74)
60 KOG3078 Adenylate kinase [Nucl 23.5 63 0.0014 30.3 2.4 12 9-20 19-30 (235)
61 TIGR00174 miaA tRNA isopenteny 23.5 58 0.0013 30.9 2.2 41 9-58 3-43 (287)
62 cd03009 TryX_like_TryX_NRX Try 23.4 2.4E+02 0.0053 22.0 5.5 55 182-236 7-64 (131)
63 cd03014 PRX_Atyp2cys Peroxired 23.4 2.3E+02 0.0049 22.4 5.4 53 181-235 14-68 (143)
64 PF06699 PIG-F: GPI biosynthes 23.4 29 0.00063 31.2 0.2 20 224-265 152-171 (190)
65 PF14015 DUF4231: Protein of u 23.1 3.6E+02 0.0077 20.8 6.8 38 80-117 5-42 (112)
66 PF12576 DUF3754: Protein of u 21.8 4.5E+02 0.0098 22.2 7.1 25 97-121 60-84 (141)
67 cd02971 PRX_family Peroxiredox 21.8 2.2E+02 0.0048 22.1 4.9 53 182-234 11-65 (140)
68 COG1585 Membrane protein impli 21.5 3.8E+02 0.0083 22.9 6.6 26 175-200 101-128 (140)
69 PRK08475 F0F1 ATP synthase sub 21.4 1.5E+02 0.0032 25.6 4.1 14 99-112 2-15 (167)
70 TIGR01359 UMP_CMP_kin_fam UMP- 21.2 42 0.0009 27.8 0.7 12 9-20 3-14 (183)
71 TIGR00907 2A0304 amino acid pe 21.1 4.2E+02 0.0092 25.7 7.6 42 78-119 232-273 (482)
72 TIGR02540 gpx7 putative glutat 20.7 2.8E+02 0.006 22.6 5.5 52 181-233 10-63 (153)
73 cd00209 DHFR Dihydrofolate red 20.0 1E+02 0.0022 25.9 2.8 39 188-233 84-122 (158)
No 1
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=100.00 E-value=1.4e-60 Score=461.63 Aligned_cols=194 Identities=28% Similarity=0.499 Sum_probs=180.2
Q ss_pred ccchHHHHHHHHhCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHh
Q 024212 78 EISSAARIRNEVLSPFRSVRMFFYLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSREN 157 (271)
Q Consensus 78 ~~~~~~rLraEa~APFR~lR~Ffy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~ 157 (271)
....++|||+|+++|||++|+|||+||+|||+||+||+++|++++++|++++|+|+++++|||||+|+|++|+|||+||+
T Consensus 181 ~~~~~~kL~~E~~aPfR~~R~f~y~a~~asa~ig~~i~~~rl~~a~aG~~~ap~l~~~~~nlaI~igav~~f~~L~~~e~ 260 (453)
T PLN03098 181 SFRRDLKLISEVQAPFRGVRKFFYVAFTAAAGISTFFTVPRLIRAIQGGDGAPDVLETAGNAAINIGGIVAFVSLFLWEN 260 (453)
T ss_pred chhhHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccHhHhhcccchHHHHHHHHHHHHHHHh
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHhhhhhcccceeEecCCceeehhhhcCcceEEEEeCCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeCCCC
Q 024212 158 KAKNAQLARLSREESLSNLKLRVDEKKIISVNNLRGIARLVICSGPASYIMESFKRSEPFTESLLERGVLVVSFTTDGNI 237 (271)
Q Consensus 158 k~~~~qlari~REe~L~rL~Vrl~~~r~v~L~~LRg~aRvVIvAG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg~s 237 (271)
|++|+||+||+|||+||||+|+++++|+|+|+||||++|||||||++|||+++|+.||+|+++|.+||||||||+|+++.
T Consensus 261 k~~e~q~~ri~Ree~L~rL~v~l~~~~~v~l~~LRg~~RvvIvAG~~e~v~~al~~ae~~r~~L~~r~VlvVPv~~~~~~ 340 (453)
T PLN03098 261 KKEEEQMSQITRDETLSRLPVRLSTNRIVELVQLRDITRPVILAGTKESVTLAMQKAERYRTELLKRGVLLIPVVWGENK 340 (453)
T ss_pred cccHHHHHHHHhhhhhccceEeccCCCEEeHHHhcCcceEEEEECCHHHHHHHHHHhHHHHHHHHHcCcEEEEEecCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998776
Q ss_pred CCC----Cccc-------------------hHHHHHhhhhhccceeeeecccCccCC
Q 024212 238 PSF----EFEE-------------------SEEMKEFTRKRKRLWQLTPVYVSEWSK 271 (271)
Q Consensus 238 ~~~----~f~~-------------------~~~~~~~~~~~~rrw~a~Pv~~~eW~~ 271 (271)
+.. .||. ++.+.+...++++||++|||+++||++
T Consensus 341 ~~~~~~~gfg~~s~~a~~~p~~~~~~~~~~~~~~~~~~~~~~kr~~a~pv~~~~W~~ 397 (453)
T PLN03098 341 DPQPKKKGFGRSSKAAASLPSIGDDFEKRAQSAAAKSVLKGEKRFKAEVVSPAEWER 397 (453)
T ss_pred ccccccccccccchhhhcCCCccchhhhhhHHHHHHHhhhcccceEEeecchHHHHH
Confidence 632 3551 112444556788999999999999973
No 2
>PF11998 DUF3493: Protein of unknown function (DUF3493); InterPro: IPR021883 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 79 to 331 amino acids in length.
Probab=99.96 E-value=9.2e-30 Score=196.08 Aligned_cols=74 Identities=43% Similarity=0.702 Sum_probs=72.3
Q ss_pred ccchHHHHHHHHhCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHh
Q 024212 78 EISSAARIRNEVLSPFRSVRMFFYLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSREN 157 (271)
Q Consensus 78 ~~~~~~rLraEa~APFR~lR~Ffy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~ 157 (271)
+|++++|||+|+++|||++|+|||+||+|||+||++|+++|+++ |++|+|+++||+||+|+|++|+|||+||+
T Consensus 2 ~~~~~~rLraE~~aPfR~lR~f~y~a~~aSa~iG~~i~~~rl~a-------~~~l~~~l~nlaI~igava~~~~L~~~d~ 74 (75)
T PF11998_consen 2 DPEQYARLRAEAQAPFRGLRRFFYGAFGASAGIGLFIFLFRLIA-------GPDLNEALPNLAIQIGAVALFAFLFRWDR 74 (75)
T ss_pred CHHHHHHHHHHHHCchHHHHHHHHHHHHHHHHHHHHHHHHHHHc-------CccHHHHhhhHhHHHHHHHHHHHHHHHhc
Confidence 68899999999999999999999999999999999999999999 79999999999999999999999999998
Q ss_pred h
Q 024212 158 K 158 (271)
Q Consensus 158 k 158 (271)
|
T Consensus 75 k 75 (75)
T PF11998_consen 75 K 75 (75)
T ss_pred C
Confidence 6
No 3
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=86.87 E-value=2.9 Score=30.22 Aligned_cols=44 Identities=20% Similarity=0.424 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhhHHHHHHHHhhh
Q 024212 96 VRMFFYLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKAKNAQLARLSRE 170 (271)
Q Consensus 96 lR~Ffy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~~qlari~RE 170 (271)
+=..+.++|+.++.+|.+++++..+. .+++.++.+++++++.+|
T Consensus 20 l~l~il~~f~~G~llg~l~~~~~~~~-------------------------------~r~~~~~~~k~l~~le~e 63 (68)
T PF06305_consen 20 LGLLILIAFLLGALLGWLLSLPSRLR-------------------------------LRRRIRRLRKELKKLEKE 63 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-------------------------------HHHHHHHHHHHHHHHHHH
Confidence 33567777888888888888877777 677788888888877655
No 4
>PF13778 DUF4174: Domain of unknown function (DUF4174)
Probab=83.99 E-value=3.7 Score=33.62 Aligned_cols=54 Identities=20% Similarity=0.277 Sum_probs=39.2
Q ss_pred ehhhhcCcceEEEEeCC---HhHHHHHHhhchhhHHHHhhcCcEEEEEeeCCCCCCC
Q 024212 187 SVNNLRGIARLVICSGP---ASYIMESFKRSEPFTESLLERGVLVVSFTTDGNIPSF 240 (271)
Q Consensus 187 ~L~~LRg~aRvVIvAG~---~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg~s~~~ 240 (271)
+|.+++...|++||..| ..+...-++.-+.-+..|.+|+|+|+.+.-++.....
T Consensus 2 ~L~~~~w~~R~lvv~aps~~d~~~~~q~~~L~~~~~~l~eRdi~v~~i~~~~~~~~~ 58 (118)
T PF13778_consen 2 PLDQFRWKNRLLVVFAPSADDPRYQQQLEELQNNRCGLDERDIVVIVITGDGARSPG 58 (118)
T ss_pred ChhHhcCcCceEEEECCCCCCHHHHHHHHHHHhhhhccccCceEEEEEeCCcccccc
Confidence 58899999999999886 2233444444445678999999999999665555433
No 5
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=69.49 E-value=29 Score=28.22 Aligned_cols=73 Identities=14% Similarity=0.172 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhhHHHHHHHHhhhhhcc
Q 024212 97 RMFFYLAFVASGSL-GGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKAKNAQLARLSREESLS 174 (271)
Q Consensus 97 R~Ffy~Af~ASA~I-G~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~~qlari~REe~L~ 174 (271)
..++|..++....+ +.+=-+...+|.+-|-..++++- +.+-+.++.+..+-.....++.|+++.+++||-+|-
T Consensus 32 ~~l~Wl~~~i~~l~~~ifP~~~~~vA~~lGi~~~~n~l-----f~~~i~~ll~~~~~l~~~is~le~~i~~L~qeiAl~ 105 (115)
T PF10066_consen 32 YSLLWLVFSIILLILSIFPNILDWVAKLLGIGRPPNLL-----FYLGILFLLVIIFSLYVRISRLEEKIKRLAQEIALL 105 (115)
T ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHHHHHCCCchhHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666655433 33334445556566766665542 233333344444555566778889999999988775
No 6
>PF12666 PrgI: PrgI family protein; InterPro: IPR024414 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Probab=65.69 E-value=25 Score=27.08 Aligned_cols=67 Identities=16% Similarity=0.256 Sum_probs=40.5
Q ss_pred HHhCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhhHHHHHHH
Q 024212 88 EVLSPFRSVRMFFYLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKAKNAQLAR 166 (271)
Q Consensus 88 Ea~APFR~lR~Ffy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~~qlar 166 (271)
.+--.+ +.|++++.+.++..++|.+..+...+. .+..-=+.+=+.+...+..+++.|.-.-|+-+..
T Consensus 12 ki~~Gl-T~RQl~~l~~~~~~~~~~~~~~~~~l~-----------~~~~~~~~i~~~~p~~~~g~~k~~gl~~e~~l~~ 78 (93)
T PF12666_consen 12 KIFFGL-TLRQLICLAIGALVGVGVYLLLWFFLG-----------PDIASWIMIPIALPFAFLGFFKKDGLPLEKYLKY 78 (93)
T ss_pred hhccCC-CHHHHHHHHHHHHHHHHHHHHHHHhcc-----------HHHHHHHHHHHHHHHHHhHhhhhcCCCHHHHHHH
Confidence 345577 999999999999999887777654442 2222233343444444555555555445554443
No 7
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=65.63 E-value=43 Score=25.49 Aligned_cols=54 Identities=17% Similarity=0.355 Sum_probs=43.4
Q ss_pred cCCceeehhhhcCcceEEEEeCC--HhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 181 DEKKIISVNNLRGIARLVICSGP--ASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 181 ~~~r~v~L~~LRg~aRvVIvAG~--~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
.+++.++|.+|+|..-++....+ -.++.+.+..-+.+.+++.+.||-||-|.+|
T Consensus 13 ~~g~~~~l~~l~gk~~vl~f~~~~~c~~c~~~l~~l~~~~~~~~~~~~~vi~is~d 68 (124)
T PF00578_consen 13 SDGKTVSLSDLKGKPVVLFFWPTAWCPFCQAELPELNELYKKYKDKGVQVIGISTD 68 (124)
T ss_dssp TTSEEEEGGGGTTSEEEEEEESTTTSHHHHHHHHHHHHHHHHHHTTTEEEEEEESS
T ss_pred CCCCEEEHHHHCCCcEEEEEeCccCccccccchhHHHHHhhhhccceEEeeecccc
Confidence 35789999999885554444444 5788888888888889999999999999985
No 8
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=64.97 E-value=54 Score=26.08 Aligned_cols=64 Identities=19% Similarity=0.287 Sum_probs=49.3
Q ss_pred cceeEe--cCCceeehhhhcCcceEEEEeCC--HhHHHHHHhhchhhHHHHhhcCcEEEEEeeCCCCC
Q 024212 175 NLKLRV--DEKKIISVNNLRGIARLVICSGP--ASYIMESFKRSEPFTESLLERGVLVVSFTTDGNIP 238 (271)
Q Consensus 175 rL~Vrl--~~~r~v~L~~LRg~aRvVIvAG~--~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg~s~ 238 (271)
.+.+.. .+|+.++|++++|..-||..-++ =..+...+..-+.+.+...+.||-+|-|..+.+..
T Consensus 8 ~~~~~~~~~~g~~~~l~~~~gk~~vv~f~~~~~Cp~C~~~~p~l~~l~~~~~~~~v~~v~v~~~~~~~ 75 (146)
T PF08534_consen 8 DFSLKDLDLDGKPVSLSDFKGKPVVVNFWASAWCPPCRKELPYLNELQEKYKDKGVDVVGVSSDDDPP 75 (146)
T ss_dssp CCEEEEEETTSEEEEGGGGTTSEEEEEEESTTTSHHHHHHHHHHHHHHHHHHTTTCEEEEEEESSSHH
T ss_pred CeEEEeecCCCCEecHHHhCCCeEEEEEEccCCCCcchhhhhhHHhhhhhhccCceEEEEecccCCHH
Confidence 445544 67899999999999977666665 67777777777778888899999999998854433
No 9
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=64.74 E-value=17 Score=30.65 Aligned_cols=56 Identities=13% Similarity=-0.004 Sum_probs=36.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhhHH
Q 024212 93 FRSVRMFFYLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKAKN 161 (271)
Q Consensus 93 FR~lR~Ffy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~ 161 (271)
.|++..|+-+-.+.+..+++.+...-.- =.++.++++++++......++++....|
T Consensus 9 ~~g~~~~~~~~~~~~~~~a~~f~~~GaW-------------~Vl~F~glev~~l~~a~~~~~r~~~~~E 64 (140)
T PF10003_consen 9 PRGFLIFIAILAAVSLIIAIAFLLMGAW-------------PVLPFAGLEVLALWYAFRRNYRHARDYE 64 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhchH-------------HHHHHHHHHHHHHHHHHHHHHhhCcCcE
Confidence 4555555555555555555554443322 2689999999999988888887665443
No 10
>PF00255 GSHPx: Glutathione peroxidase; InterPro: IPR000889 Glutathione peroxidase (GSHPx) (1.11.1.9 from EC) is an enzyme that catalyses the reduction of hydroxyperoxides by glutathione [, ]. Its main function is to protect against the damaging effect of endogenously formed hydroxyperoxides. In higher vertebrates, several forms of GSHPx are known, including a ubiquitous cytosolic form (GSHPx-1), a gastrointestinal cytosolic form (GSHPx-GI), a plasma secreted form (GSHPx-P), and an epididymal secretory form (GSHPx-EP). In addition to these characterised forms, the sequence of a protein of unknown function [] has been shown to be evolutionary related to those of GSHPx's. In filarial nematode parasites, the major soluble cuticular protein (gp29) is a secreted GSHPx, which may provide a mechanism of resistance to the immune reaction of the mammalian host by neutralising the products of the oxidative burst of leukocytes []. The Escherichia coli protein btuE, a periplasmic protein involved in vitamin B12 transport, is evolutionarily related to GSHPxs, although the significance of this relationship is unclear. The structure of bovine seleno-glutathione peroxidase has been determined []. The protein belongs to the alpha-beta class, with a 3 layer(aba) sandwich architecture. The catalyic site of GSHPx contains a conserved residue which is either a cysteine or, in many eukaryotic GSHPx, a selenocysteine []. ; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 3E0U_A 2VUP_A 2RM5_A 2RM6_A 3DWV_B 2P31_B 2R37_B 1GP1_B 2F8A_B 3KIJ_C ....
Probab=60.65 E-value=68 Score=26.31 Aligned_cols=74 Identities=20% Similarity=0.393 Sum_probs=47.5
Q ss_pred ceeEecCCceeehhhhcCcceEEE-EeCCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeCCCCCCCCccchHHHHHh
Q 024212 176 LKLRVDEKKIISVNNLRGIARLVI-CSGPASYIMESFKRSEPFTESLLERGVLVVSFTTDGNIPSFEFEESEEMKEF 251 (271)
Q Consensus 176 L~Vrl~~~r~v~L~~LRg~aRvVI-vAG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg~s~~~~f~~~~~~~~~ 251 (271)
+.+.--+|+.++|+++||..=+|+ +|---.+.. -....+.+.+...++|..|+.++-+. -+..|.+..++.++.
T Consensus 4 f~~~~~~G~~v~l~~y~Gkv~LIVNvAs~Cg~t~-qy~~L~~L~~ky~~~gl~ILaFPcnq-Fg~QEp~~~~ei~~~ 78 (108)
T PF00255_consen 4 FSAKDIDGKPVSLSKYKGKVLLIVNVASKCGYTK-QYKQLNELYEKYKDKGLEILAFPCNQ-FGNQEPGSNEEIKEF 78 (108)
T ss_dssp SEEEBTTSSEEEGGGGTTSEEEEEEEESSSTTHH-HHHHHHHHHHHHGGGTEEEEEEEBST-TTTTTSSCHHHHHHH
T ss_pred eeeeCCCCCEECHHHcCCCEEEEEecccccCCcc-ccHHHHHHHHHHhcCCeEEEeeehHH-hccccCCCHHHHHHH
Confidence 344445689999999999664333 332223333 66777889999999999999999731 122344544444443
No 11
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=60.05 E-value=20 Score=29.09 Aligned_cols=63 Identities=17% Similarity=0.179 Sum_probs=44.0
Q ss_pred hcccceeEecCCceeehhhhcCcceEEEEeCC--HhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 172 SLSNLKLRVDEKKIISVNNLRGIARLVICSGP--ASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 172 ~L~rL~Vrl~~~r~v~L~~LRg~aRvVIvAG~--~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
..-.+.+.--+|+.+++.+++|..-+|..-.+ -..+...+...+...++|.+.||.||.|..|
T Consensus 9 ~~p~f~l~~~~G~~~~l~~~~gk~~ll~f~~~~~~p~C~~~~~~l~~~~~~~~~~~v~vi~Is~d 73 (154)
T PRK09437 9 IAPKFSLPDQDGEQVSLTDFQGQRVLVYFYPKAMTPGCTVQACGLRDNMDELKKAGVVVLGISTD 73 (154)
T ss_pred cCCCcEeeCCCCCEEeHHHhCCCCEEEEEECCCCCCchHHHHHHHHHHHHHHHHCCCEEEEEcCC
Confidence 33444444345789999999997655555432 3456666666677888899999999999875
No 12
>cd02968 SCO SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properti
Probab=56.48 E-value=77 Score=24.81 Aligned_cols=59 Identities=19% Similarity=0.201 Sum_probs=43.6
Q ss_pred eEecCCceeehhhhcCcceEEEEeC-CHhH-HHHHHhhchhhHHHHhhcC---cEEEEEeeCCC
Q 024212 178 LRVDEKKIISVNNLRGIARLVICSG-PASY-IMESFKRSEPFTESLLERG---VLVVSFTTDGN 236 (271)
Q Consensus 178 Vrl~~~r~v~L~~LRg~aRvVIvAG-~~e~-V~~al~~Ae~~~~~L~~rg---VLVVPV~~dg~ 236 (271)
+.-.+|+.+++.+++|..-+++..+ .-.. +.+.+...+.+.+++.+.+ |-||-|..|..
T Consensus 7 l~~~~g~~~~l~~~~gk~~vl~f~~~~C~~~C~~~l~~l~~~~~~~~~~~~~~v~~v~vs~d~~ 70 (142)
T cd02968 7 LTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGGDDVQVVFISVDPE 70 (142)
T ss_pred EEcCCCCEEchHHhCCCEEEEEEEcCCCcccCHHHHHHHHHHHHHhhHhhcCceEEEEEEECCC
Confidence 3334678999999988765555433 3333 7778888888999999876 99999998754
No 13
>PLN02412 probable glutathione peroxidase
Probab=56.03 E-value=30 Score=29.21 Aligned_cols=60 Identities=15% Similarity=0.295 Sum_probs=41.2
Q ss_pred cceeEecCCceeehhhhcCcceEEEE-eCCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 175 NLKLRVDEKKIISVNNLRGIARLVIC-SGPASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 175 rL~Vrl~~~r~v~L~~LRg~aRvVIv-AG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
.+.+.-.+|+.++|++++|..-||.. |-.-..+..-+..-+.+.+.+.+.|+.||-|..+
T Consensus 11 df~l~d~~G~~v~l~~~~gk~vlv~f~a~~C~~c~~e~~~l~~l~~~~~~~g~~vvgv~~~ 71 (167)
T PLN02412 11 DFTVKDIGGNDVSLNQYKGKVLLIVNVASKCGLTDSNYKELNVLYEKYKEQGFEILAFPCN 71 (167)
T ss_pred ceEEECCCCCEEeHHHhCCCEEEEEEeCCCCCChHHHHHHHHHHHHHHhhCCcEEEEeccc
Confidence 34444346889999999984333322 4444445545666678888999999999999874
No 14
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=55.66 E-value=15 Score=28.82 Aligned_cols=45 Identities=13% Similarity=0.229 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHhhhhhcccceeEecC--Cceeehh
Q 024212 145 AVSLFAFLYSRENKAKNAQLARLSREESLSNLKLRVDE--KKIISVN 189 (271)
Q Consensus 145 avalf~~L~~~E~k~~~~qlari~REe~L~rL~Vrl~~--~r~v~L~ 189 (271)
.+++|-|+..+.+++++|+.+.+-.+-.-|.=.+..++ |+++.+.
T Consensus 12 ~~~i~yf~~~rpqkK~~k~~~~m~~~L~~Gd~VvT~gGi~G~V~~i~ 58 (84)
T TIGR00739 12 IFLIFYFLIIRPQRKRRKAHKKLIESLKKGDKVLTIGGIIGTVTKIA 58 (84)
T ss_pred HHHHHHHheechHHHHHHHHHHHHHhCCCCCEEEECCCeEEEEEEEe
Confidence 44566666667777777776655544444443444443 4555554
No 15
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=55.64 E-value=26 Score=24.49 Aligned_cols=27 Identities=26% Similarity=0.363 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024212 96 VRMFFYLAFVASGSLGGLIAITQLIGA 122 (271)
Q Consensus 96 lR~Ffy~Af~ASA~IG~~i~l~rliaa 122 (271)
=|.|++.+.++-|++|+..++.=++..
T Consensus 11 RRdFL~~at~~~gavG~~~~a~Pfv~s 37 (41)
T PF10399_consen 11 RRDFLTIATSAVGAVGAAAAAWPFVSS 37 (41)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 489999999999999998887777764
No 16
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=54.15 E-value=22 Score=29.21 Aligned_cols=45 Identities=13% Similarity=0.215 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHhhhhhcccceeEecC--Cceeehh
Q 024212 145 AVSLFAFLYSRENKAKNAQLARLSREESLSNLKLRVDE--KKIISVN 189 (271)
Q Consensus 145 avalf~~L~~~E~k~~~~qlari~REe~L~rL~Vrl~~--~r~v~L~ 189 (271)
.+++|-|+..+.+|+++++.+++-.+-.-|.=.+..++ |+++.+.
T Consensus 27 i~~i~yf~~~RpqkK~~k~~~~~~~~Lk~Gd~VvT~gGi~G~Vv~i~ 73 (106)
T PRK05585 27 FFAIFYFLIIRPQQKRQKEHKKMLSSLAKGDEVVTNGGIIGKVTKVS 73 (106)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHHHhcCCCCEEEECCCeEEEEEEEe
Confidence 34445555556777777666554444333333333333 4555544
No 17
>PRK06280 hypothetical protein; Provisional
Probab=51.44 E-value=36 Score=26.62 Aligned_cols=46 Identities=24% Similarity=0.200 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHH-HHHHHHHHH
Q 024212 102 LAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAV-SLFAFLYSR 155 (271)
Q Consensus 102 ~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGav-alf~~L~~~ 155 (271)
.+....+..|+.+++.=++-+ |||+ ++..+++..|.+ ++|.+-+++
T Consensus 25 ~avi~~g~~gl~~al~f~~l~------APDv--AlTq~~Ve~~~~t~lfl~~l~~ 71 (77)
T PRK06280 25 KCAILTGFGGLGLAYLYQLLL------APDV--ALTEAILGGAILPAFFAFTVRR 71 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHhC------CcHH--HHHHHHHHHHHHHHHHHHHHHH
Confidence 455667777777776555542 7999 799999999988 777766655
No 18
>cd03017 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), w
Probab=50.84 E-value=48 Score=25.93 Aligned_cols=58 Identities=19% Similarity=0.283 Sum_probs=40.8
Q ss_pred ceeEecCCceeehhhhcCcceEEEEeCC---HhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 176 LKLRVDEKKIISVNNLRGIARLVICSGP---ASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 176 L~Vrl~~~r~v~L~~LRg~aRvVIvAG~---~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
+.+.-.+|+.+++.+++|.. ++|.-.+ -..+...+.......+.|.+.|+.||.|..|
T Consensus 6 f~l~~~~g~~~~l~~~~gk~-~ll~f~~~~~cp~C~~~~~~l~~~~~~~~~~~~~vv~is~d 66 (140)
T cd03017 6 FTLPDQDGETVSLSDLRGKP-VVLYFYPKDDTPGCTKEACDFRDLYEEFKALGAVVIGVSPD 66 (140)
T ss_pred ccccCCCCCEEeHHHhCCCc-EEEEEeCCCCCCchHHHHHHHHHHHHHHHHCCCEEEEEcCC
Confidence 33433458999999999743 3333332 2456667777777888899999999999875
No 19
>cd03015 PRX_Typ2cys Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric
Probab=49.72 E-value=36 Score=28.51 Aligned_cols=51 Identities=18% Similarity=0.102 Sum_probs=38.7
Q ss_pred ceeehhhhcCcceEEEEeC--C-HhHHHHHHhhchhhHHHHhhcCcEEEEEeeCC
Q 024212 184 KIISVNNLRGIARLVICSG--P-ASYIMESFKRSEPFTESLLERGVLVVSFTTDG 235 (271)
Q Consensus 184 r~v~L~~LRg~aRvVIvAG--~-~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg 235 (271)
+.++|.+++|. .+||..- + -..+...+..-+.+.+++.+.||-||-|..|.
T Consensus 20 ~~~~l~~~~Gk-~vvl~F~~~~~c~~C~~~l~~l~~~~~~~~~~~v~vv~Is~d~ 73 (173)
T cd03015 20 KEISLSDYKGK-WVVLFFYPLDFTFVCPTEIIAFSDRYEEFKKLNAEVLGVSTDS 73 (173)
T ss_pred eEEehHHhCCC-EEEEEEECCCCCCcCHHHHHHHHHHHHHHHHCCCEEEEEecCC
Confidence 89999999984 3444442 2 34667778888888999999999999998753
No 20
>PF10960 DUF2762: Protein of unknown function (DUF2762); InterPro: IPR024405 BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis [, ] and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity [, ].
Probab=49.71 E-value=22 Score=27.54 Aligned_cols=36 Identities=19% Similarity=0.103 Sum_probs=20.5
Q ss_pred cchhHHHHHHHHHHHHHHhhhHHHHHH-HHhhhhhcc
Q 024212 139 LSIDVSAVSLFAFLYSRENKAKNAQLA-RLSREESLS 174 (271)
Q Consensus 139 laIqiGavalf~~L~~~E~k~~~~qla-ri~REe~L~ 174 (271)
+.-|....++|+||+..-.|..++.-. ...||+.+-
T Consensus 9 ~~sQG~fA~LFv~Ll~yvlK~~~~re~~~~~RE~kyq 45 (71)
T PF10960_consen 9 ALSQGIFAVLFVWLLFYVLKENKKREEKQEEREEKYQ 45 (71)
T ss_pred HHHcCcHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHH
Confidence 334455667899998866555332221 226777653
No 21
>PRK03147 thiol-disulfide oxidoreductase; Provisional
Probab=49.01 E-value=1.4e+02 Score=24.17 Aligned_cols=69 Identities=16% Similarity=0.169 Sum_probs=45.5
Q ss_pred HhhhhhcccceeEecCCceeehhhhcCcceEEEE-eCCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeCC
Q 024212 167 LSREESLSNLKLRVDEKKIISVNNLRGIARLVIC-SGPASYIMESFKRSEPFTESLLERGVLVVSFTTDG 235 (271)
Q Consensus 167 i~REe~L~rL~Vrl~~~r~v~L~~LRg~aRvVIv-AG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg 235 (271)
+.-......+.+.--+|+.++++++.+..-++.. +-.-..+...+..-..+.+++.++++-||-|..|.
T Consensus 35 ~~~g~~~p~~~~~~~~g~~~~l~~~~~k~~~l~f~a~~C~~C~~~~~~l~~~~~~~~~~~~~vi~i~~d~ 104 (173)
T PRK03147 35 VQVGKEAPNFVLTDLEGKKIELKDLKGKGVFLNFWGTWCKPCEKEMPYMNELYPKYKEKGVEIIAVNVDE 104 (173)
T ss_pred cCCCCCCCCcEeecCCCCEEeHHHcCCCEEEEEEECCcCHHHHHHHHHHHHHHHHhhcCCeEEEEEEcCC
Confidence 3344445556655556889999999875533333 32334566666666777888888889888888764
No 22
>PRK15051 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; Provisional
Probab=47.97 E-value=72 Score=25.73 Aligned_cols=63 Identities=14% Similarity=0.060 Sum_probs=46.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhhHH
Q 024212 92 PFRSVRMFFYLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKAKN 161 (271)
Q Consensus 92 PFR~lR~Ffy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~ 161 (271)
|+...+.+++.+++.......++.....+. .-|+..+.+-..+..-.++++++++..|+-.-.
T Consensus 30 ~~~~~~~l~~~~~~~~~~~l~~~~~~~al~-------~iplg~Ay~~~~l~~v~~~~~~~l~f~E~ls~~ 92 (111)
T PRK15051 30 GKRRKHIVLWLGLALACLGLAMVLWLLVLQ-------NVPVGIAYPMLSLNFVWVTLAAVKLWHEPVSPR 92 (111)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHHHHh-------hCChHHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence 555556667777665555556677777777 478888999999888899999999988865443
No 23
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=45.17 E-value=68 Score=25.09 Aligned_cols=54 Identities=17% Similarity=0.260 Sum_probs=39.8
Q ss_pred CCceeehhhhcCcceEEEEe--C-CHhHHHHHHhhchhhHHHHhhcCcEEEEEeeCC
Q 024212 182 EKKIISVNNLRGIARLVICS--G-PASYIMESFKRSEPFTESLLERGVLVVSFTTDG 235 (271)
Q Consensus 182 ~~r~v~L~~LRg~aRvVIvA--G-~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg 235 (271)
+|+.+++.++++...+||+- + .=..+.+-+..-+.+.+++.+.||-||-|..|.
T Consensus 11 ~g~~~~l~~~~~~~~~vl~f~~~~~Cp~C~~~~~~l~~~~~~~~~~~v~vv~V~~~~ 67 (149)
T cd02970 11 GGETVTLSALLGEGPVVVVFYRGFGCPFCREYLRALSKLLPELDALGVELVAVGPES 67 (149)
T ss_pred CCCEEchHHHhcCCCEEEEEECCCCChhHHHHHHHHHHHHHHHHhcCeEEEEEeCCC
Confidence 47889999997644444432 2 345667777777888899999999999998753
No 24
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=44.55 E-value=8.1 Score=31.45 Aligned_cols=11 Identities=73% Similarity=1.307 Sum_probs=9.7
Q ss_pred eecccCCCCcc
Q 024212 10 ILGPVGSGRGY 20 (271)
Q Consensus 10 ~~~~~~~~~~~ 20 (271)
|+||+|||++.
T Consensus 1 i~G~PgsGK~t 11 (151)
T PF00406_consen 1 ILGPPGSGKGT 11 (151)
T ss_dssp EEESTTSSHHH
T ss_pred CcCCCCCChHH
Confidence 68999999985
No 25
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=44.49 E-value=40 Score=28.10 Aligned_cols=46 Identities=11% Similarity=0.128 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHhhhhhcccceeEecC--Cceeehh
Q 024212 144 SAVSLFAFLYSRENKAKNAQLARLSREESLSNLKLRVDE--KKIISVN 189 (271)
Q Consensus 144 Gavalf~~L~~~E~k~~~~qlari~REe~L~rL~Vrl~~--~r~v~L~ 189 (271)
..+++|-||..+-+++++|+.+++-.+-.-|-=.+..++ |+++.+.
T Consensus 12 ~i~~i~yF~~iRPQkKr~K~~~~m~~~Lk~GD~VvT~gGi~G~V~~I~ 59 (109)
T PRK05886 12 LIMGGFMYFASRRQRKAMQATIDLHESLQPGDRVHTTSGLQATIVGIT 59 (109)
T ss_pred HHHHHHHHHHccHHHHHHHHHHHHHHhcCCCCEEEECCCeEEEEEEEe
Confidence 344555666666666666665544333333332333333 4555544
No 26
>PF04995 CcmD: Heme exporter protein D (CcmD); InterPro: IPR007078 The CcmD protein is part of a C-type cytochrome biogenesis operon []. The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation []. This protein is found fused to CcmE in P52224 from SWISSPROT. These proteins contain a predicted transmembrane helix.; GO: 0006810 transport, 0016021 integral to membrane
Probab=44.29 E-value=47 Score=23.18 Aligned_cols=35 Identities=14% Similarity=0.193 Sum_probs=26.0
Q ss_pred hccchhHHHHHHHHHHHHHHhhhHHHHHHHHhhhh
Q 024212 137 KGLSIDVSAVSLFAFLYSRENKAKNAQLARLSREE 171 (271)
Q Consensus 137 ~NlaIqiGavalf~~L~~~E~k~~~~qlari~REe 171 (271)
...|+-+.+++.+.+...++.++-.+++++..+.|
T Consensus 9 ~sYg~t~~~l~~l~~~~~~~~r~~~~~l~~~~~r~ 43 (46)
T PF04995_consen 9 SSYGVTALVLAGLIVWSLRRRRRLRKELKRLEARE 43 (46)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 34567777788888888888888888887765443
No 27
>PRK11476 DNA-binding transcriptional activator CaiF; Provisional
Probab=44.20 E-value=6.4 Score=33.05 Aligned_cols=18 Identities=61% Similarity=1.200 Sum_probs=14.4
Q ss_pred eeeeecccC-------------CCCcccccch
Q 024212 7 FSYILGPVG-------------SGRGYCNCQY 25 (271)
Q Consensus 7 ~~~~~~~~~-------------~~~~~~~~~~ 25 (271)
.||||..|| .||| |.||-
T Consensus 27 vSYILS~V~EI~CetK~iPNqLeGRG-CQCQR 57 (113)
T PRK11476 27 LSYILSEVTEISCEVKMIPNQLEGRG-CQCQR 57 (113)
T ss_pred HHHHHhccceeEeecccCcchhccCC-cceee
Confidence 589998887 5887 99984
No 28
>TIGR03141 cytochro_ccmD heme exporter protein CcmD. The model for this protein family describes a small, hydrophobic, and only moderately well-conserved protein, tricky to identify accurately for all of these reasons. However, members are found as part of large operons involved in heme export across the inner membrane for assembly of c-type cytochromes in a large number of bacteria. The gray zone between the trusted cutoff (13.0) and noise cutoff (4.75) includes both low-scoring examples and false-positive matches to hydrophobic domains of longer proteins.
Probab=43.63 E-value=48 Score=23.13 Aligned_cols=34 Identities=12% Similarity=0.089 Sum_probs=24.2
Q ss_pred hccchhHHHHHHHHHHHHHHhhhHHHHHHHHhhh
Q 024212 137 KGLSIDVSAVSLFAFLYSRENKAKNAQLARLSRE 170 (271)
Q Consensus 137 ~NlaIqiGavalf~~L~~~E~k~~~~qlari~RE 170 (271)
...|+-+.+++..++...++.++..+++++..+.
T Consensus 10 ~sYg~t~l~l~~li~~~~~~~r~~~~~l~~~~~r 43 (45)
T TIGR03141 10 LAYGITALVLAGLILWSLLDRRRLLRELRRLEAR 43 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3456666777777777888888888888765543
No 29
>cd02964 TryX_like_family Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX.
Probab=42.53 E-value=79 Score=25.10 Aligned_cols=57 Identities=19% Similarity=0.161 Sum_probs=38.2
Q ss_pred ecCCceeehhhhcCcceEEEEeC-CHhHHHHHHhhchhhHHHHhhc--CcEEEEEeeCCC
Q 024212 180 VDEKKIISVNNLRGIARLVICSG-PASYIMESFKRSEPFTESLLER--GVLVVSFTTDGN 236 (271)
Q Consensus 180 l~~~r~v~L~~LRg~aRvVIvAG-~~e~V~~al~~Ae~~~~~L~~r--gVLVVPV~~dg~ 236 (271)
++++++++|.+++|..=+|..-+ .=..+.+.+...+.+.+++.+. ++-||.|..|..
T Consensus 4 ~~~~~~v~l~~~~Gk~vll~F~atwC~~C~~~~p~l~~l~~~~~~~~~~v~vi~Vs~d~~ 63 (132)
T cd02964 4 LDGEGVVPVSALEGKTVGLYFSASWCPPCRAFTPKLVEFYEKLKEEGKNFEIVFVSRDRS 63 (132)
T ss_pred ccCCccccHHHhCCCEEEEEEECCCCchHHHHHHHHHHHHHHHhhcCCCeEEEEEecCCC
Confidence 35558999999999554444433 2445666666666666777765 788888887654
No 30
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=41.86 E-value=90 Score=24.72 Aligned_cols=60 Identities=12% Similarity=0.139 Sum_probs=41.3
Q ss_pred cceeEecCCceeehhhhcCcce-EEEEe-C-CHhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 175 NLKLRVDEKKIISVNNLRGIAR-LVICS-G-PASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 175 rL~Vrl~~~r~v~L~~LRg~aR-vVIvA-G-~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
.+.+.=.+|+.+++++++|... +++.. + --..+...+..-+...+++.+.||-||-|..|
T Consensus 9 ~~~l~~~~g~~v~l~~~~g~k~~vl~f~~~~~c~~C~~~~~~l~~~~~~~~~~~v~vi~vs~d 71 (149)
T cd03018 9 DFELPDQNGQEVRLSEFRGRKPVVLVFFPLAFTPVCTKELCALRDSLELFEAAGAEVLGISVD 71 (149)
T ss_pred CcEecCCCCCEEeHHHHcCCCeEEEEEeCCCCCccHHHHHHHHHHHHHHHHhCCCEEEEecCC
Confidence 3334334589999999999433 33332 2 24567777777777888888899999888764
No 31
>cd00340 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
Probab=39.55 E-value=58 Score=26.66 Aligned_cols=53 Identities=17% Similarity=0.374 Sum_probs=36.8
Q ss_pred cCCceeehhhhcCcceEEEEe-CCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 181 DEKKIISVNNLRGIARLVICS-GPASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 181 ~~~r~v~L~~LRg~aRvVIvA-G~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
-+|+.++|++++|..-++..- -.-. +...+..-+.+.+++.+.|+.||.|..+
T Consensus 10 ~~G~~v~l~~~~Gk~vvl~fwatwC~-C~~e~p~l~~l~~~~~~~~~~vv~v~~~ 63 (152)
T cd00340 10 IDGEPVSLSKYKGKVLLIVNVASKCG-FTPQYEGLEALYEKYKDRGLVVLGFPCN 63 (152)
T ss_pred CCCCEEeHHHhCCCEEEEEEEcCCCC-chHHHHHHHHHHHHhcCCCEEEEEeccC
Confidence 357899999999854333222 2222 5566666677788888899999999864
No 32
>PTZ00253 tryparedoxin peroxidase; Provisional
Probab=36.90 E-value=71 Score=27.70 Aligned_cols=53 Identities=17% Similarity=0.125 Sum_probs=39.6
Q ss_pred CCceeehhhhcCcceEEEEeCC---HhHHHHHHhhchhhHHHHhhcCcEEEEEeeCC
Q 024212 182 EKKIISVNNLRGIARLVICSGP---ASYIMESFKRSEPFTESLLERGVLVVSFTTDG 235 (271)
Q Consensus 182 ~~r~v~L~~LRg~aRvVIvAG~---~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg 235 (271)
+++.++|++++|. .+++.-.+ -..+...+.....+.++|.++|+-||-|..|.
T Consensus 25 ~~~~v~l~d~~Gk-~~lL~F~p~~~~~~C~~e~~~l~~~~~~f~~~g~~vv~IS~d~ 80 (199)
T PTZ00253 25 SFKKISLSSYKGK-WVVLFFYPLDFTFVCPTEIIQFSDSVKRFNELNCEVLACSMDS 80 (199)
T ss_pred CCcEEeHHHHCCC-EEEEEEEcCCCCCcCHHHHHHHHHHHHHHHHcCCEEEEEeCCC
Confidence 4588999999985 45556665 23455555666778899999999999999863
No 33
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=36.66 E-value=15 Score=24.21 Aligned_cols=23 Identities=26% Similarity=0.704 Sum_probs=18.1
Q ss_pred cCCCCcccccchh--hhHHhHHHHh
Q 024212 14 VGSGRGYCNCQYH--ASRFCRQILN 36 (271)
Q Consensus 14 ~~~~~~~~~~~~~--~~~~~~~~~~ 36 (271)
+.....+|+|++. ..-.|+|++.
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~a 34 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVA 34 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHH
Confidence 4667889999976 4678898875
No 34
>PF02630 SCO1-SenC: SCO1/SenC; InterPro: IPR003782 This family is involved in biogenesis of respiratory and photosynthetic systems. In yeast the SCO1 protein is specifically required for a post-translational step in the accumulation of subunits 1 and 2 of cytochrome c oxidase (COXI and COX-II) []. It is a mitochondrion-associated cytochrome c oxidase assembly factor. The purple nonsulphur photosynthetic eubacterium Rhodobacter capsulatus is a versatile organism that can obtain cellular energy by several means, including the capture of light energy for photosynthesis as well as the use of light-independent respiration, in which molecular oxygen serves as a terminal electron acceptor. The SenC protein is required for optimal cytochrome c oxidase activity in aerobically grown R. capsulatus cells and is involved in the induction of structural polypeptides of the light-harvesting and reaction centre complexes [].; PDB: 2K6V_A 3ME8_A 3ME7_A 2GT6_A 2GQL_A 2GQK_A 2GGT_B 1WP0_C 2HRN_A 2GQM_A ....
Probab=35.84 E-value=2.2e+02 Score=24.30 Aligned_cols=68 Identities=16% Similarity=0.226 Sum_probs=43.7
Q ss_pred hhhhcccceeEecCCceeehhhhcCcceEEEE--eCCHhHHHHHHhhchhhHHHHhhc--CcEEEEEeeCCC
Q 024212 169 REESLSNLKLRVDEKKIISVNNLRGIARLVIC--SGPASYIMESFKRSEPFTESLLER--GVLVVSFTTDGN 236 (271)
Q Consensus 169 REe~L~rL~Vrl~~~r~v~L~~LRg~aRvVIv--AG~~e~V~~al~~Ae~~~~~L~~r--gVLVVPV~~dg~ 236 (271)
.........+.=.+|+++++.+|+|...+|-. ..-.+.+-..+..-....+.|.+. .|-+|-|.+|-+
T Consensus 28 ~~~~~~~f~L~d~~G~~~~~~~~~Gk~~lv~F~yT~CpdvCp~~l~~l~~~~~~l~~~~~~v~~v~ISvDP~ 99 (174)
T PF02630_consen 28 NPRIVPDFTLTDQDGKTVTLDDLKGKWVLVFFGYTRCPDVCPTTLANLSQLQKQLGEEGKDVQFVFISVDPE 99 (174)
T ss_dssp TSCSSST-EEEETTSSEEEGGGGTTSEEEEEEE-TTSSSHHHHHHHHHHHHHHHHHHTTTTEEEEEEESSTT
T ss_pred CCccCCCcEEEcCCCCEecHHHhCCCeEEEEEEEcCCCccCHHHHHHHHHHHHHhhhccCceEEEEEEeCCC
Confidence 34444455554467999999999996554332 244556677777666666777764 677777777633
No 35
>TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase. but a number of antibiotic resistance proteins score above the trusted cutoff of this model.
Probab=34.53 E-value=36 Score=30.80 Aligned_cols=40 Identities=23% Similarity=0.202 Sum_probs=35.1
Q ss_pred eEEEEeCCHhHHHH-HHhhchhhHHHHhhcCcEEEEEeeCC
Q 024212 196 RLVICSGPASYIME-SFKRSEPFTESLLERGVLVVSFTTDG 235 (271)
Q Consensus 196 RvVIvAG~~e~V~~-al~~Ae~~~~~L~~rgVLVVPV~~dg 235 (271)
||.|++|+.+.=.+ |+..+....++|.++|.=|+++..+.
T Consensus 1 ~~~~~~gg~s~e~~~s~~s~~~i~~al~~~g~~v~~i~~~~ 41 (315)
T TIGR01205 1 RVAVLFGGKSAEHEISLVSAAAVLKALRDLGYDVYPVDIDK 41 (315)
T ss_pred CEEEEeCCCCCCeeeeHHHHHHHHHHHhhcCCEEEEEeecC
Confidence 68899999888887 79999999999999999998888865
No 36
>COG5488 Integral membrane protein [Function unknown]
Probab=34.27 E-value=1.6e+02 Score=26.46 Aligned_cols=63 Identities=25% Similarity=0.178 Sum_probs=34.7
Q ss_pred HHhCchhhHHHHHHHHHHHHHHH-HHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhh
Q 024212 88 EVLSPFRSVRMFFYLAFVASGSL-GGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKA 159 (271)
Q Consensus 88 Ea~APFR~lR~Ffy~Af~ASA~I-G~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~ 159 (271)
-..+|+|++=.==+.-|+++.++ .+++..+=+.- ++.++ ++.+|+|+-++-+--..+++--++
T Consensus 18 all~p~rSlg~rgf~~lm~~~~~~~~~v~~ff~~i------gAwpV---~~FfGLDvlal~~Afr~nyraAra 81 (164)
T COG5488 18 ALLTPHRSLGPRGFGVLMLALGILSLVVAIFFLVI------GAWPV---LPFFGLDVLALYLAFRANYRAARA 81 (164)
T ss_pred HHhCcccccChhhHHHHHHHHHHHHHHHHHHHHHh------ccCce---eccchHHHHHHHHHHHHHHHHhhh
Confidence 36789998733222223333333 33333333332 25666 899999998876555555554444
No 37
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=33.26 E-value=41 Score=26.10 Aligned_cols=43 Identities=26% Similarity=0.491 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHhhhhhcccceeEecCCceeehhhhcC
Q 024212 143 VSAVSLFAFLYSRENKAKNAQLARLSREESLSNLKLRVDEKKIISVNNLRG 193 (271)
Q Consensus 143 iGavalf~~L~~~E~k~~~~qlari~REe~L~rL~Vrl~~~r~v~L~~LRg 193 (271)
+..+++|-|+..+.+++++|+ +.+-++.|++ ++++++-+-+-|
T Consensus 9 v~~~~i~yf~~~rpqkk~~k~-----~~~m~~~Lk~---Gd~VvT~gGi~G 51 (82)
T PF02699_consen 9 VIIFVIFYFLMIRPQKKQQKE-----HQEMLASLKP---GDEVVTIGGIYG 51 (82)
T ss_dssp HHHHHHHHHHTHHHHHHHHHH-----HTTGGG-------------------
T ss_pred HHHHHHHhhheecHHHHHHHH-----HHHHHHcCCC---CCEEEECCcEEE
Confidence 455666777777777766664 3445566654 234444444444
No 38
>PF10011 DUF2254: Predicted membrane protein (DUF2254); InterPro: IPR018723 Members of this family of proteins comprises various hypothetical and putative membrane proteins. Their exact function, has not, as yet, been defined.
Probab=32.76 E-value=1.5e+02 Score=28.79 Aligned_cols=69 Identities=17% Similarity=0.250 Sum_probs=42.0
Q ss_pred hhHHHHHHH---HHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhhHHHH
Q 024212 94 RSVRMFFYL---AFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKAKNAQ 163 (271)
Q Consensus 94 R~lR~Ffy~---Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~~q 163 (271)
|-+|.|+-= =...+.+||.|++..=.+-++.+..++. .......+++=++.+.++.|+++...-.+--|
T Consensus 83 R~l~~f~~d~~~q~vLg~Figtfvy~l~~l~~i~~~~~~~-~p~~~~~~a~~l~i~~v~~li~fI~~i~~~iq 154 (371)
T PF10011_consen 83 RLLRNFMRDRVTQVVLGTFIGTFVYSLLVLIAIRSGDYGS-VPRLSVFIALALAILSVVLLIYFIHHIARSIQ 154 (371)
T ss_pred HHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHcccccccc-CcchHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 445555432 2566788999998888888887655522 22223555666666667777777665444433
No 39
>cd03012 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
Probab=32.28 E-value=82 Score=24.73 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=38.6
Q ss_pred CCceeehhhhcCcceEEEEeC-CHhHHHHHHhhchhhHHHHhhcCcEEEEEee
Q 024212 182 EKKIISVNNLRGIARLVICSG-PASYIMESFKRSEPFTESLLERGVLVVSFTT 233 (271)
Q Consensus 182 ~~r~v~L~~LRg~aRvVIvAG-~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~ 233 (271)
+++.++|.+++|..-++..-+ .-..+.+.+..-+.+.+++.++|+-||.|..
T Consensus 12 ~~~~v~l~~~~gk~vvl~F~a~~C~~C~~~~p~l~~l~~~~~~~~~~vi~i~~ 64 (126)
T cd03012 12 TDKPLSLAQLRGKVVLLDFWTYCCINCLHTLPYLTDLEQKYKDDGLVVIGVHS 64 (126)
T ss_pred CCCccCHHHhCCCEEEEEEECCCCccHHHHHHHHHHHHHHcCcCCeEEEEecc
Confidence 367899999988554444333 3345667777888888999999999998865
No 40
>PF13244 DUF4040: Domain of unknown function (DUF4040)
Probab=32.26 E-value=1.2e+02 Score=23.11 Aligned_cols=46 Identities=28% Similarity=0.354 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHH-HHHHHHHH
Q 024212 101 YLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAV-SLFAFLYS 154 (271)
Q Consensus 101 y~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGav-alf~~L~~ 154 (271)
..+....+.+|..+++.=+.-+ |||+ ++..++|..|.. ++|.+.++
T Consensus 18 l~avi~~~~~g~~~al~f~~l~------APDV--AlTe~~Vg~gl~~~l~~~al~ 64 (70)
T PF13244_consen 18 LAAVIALGVFGFLIALLFVLLG------APDV--ALTEAAVGTGLTTVLFLLALR 64 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC------CcHH--HHHHHHHHHhHHHHHHHHHHH
Confidence 3455666777777776666653 7998 788888888543 34444333
No 41
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=32.07 E-value=1.3e+02 Score=22.80 Aligned_cols=67 Identities=10% Similarity=0.210 Sum_probs=33.3
Q ss_pred ceEEEEeCCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeCCCCCCCCccchHHHHHhhhhhccceeeeecccCccCC
Q 024212 195 ARLVICSGPASYIMESFKRSEPFTESLLERGVLVVSFTTDGNIPSFEFEESEEMKEFTRKRKRLWQLTPVYVSEWSK 271 (271)
Q Consensus 195 aRvVIvAG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg~s~~~~f~~~~~~~~~~~~~~rrw~a~Pv~~~eW~~ 271 (271)
...||++|++++-+..+-.+. +-+.+.+....+ ++.. .+|.+ -...++.. +.++.+... +++.+|++
T Consensus 3 g~rVli~GgR~~~D~~~i~~~-Ld~~~~~~~~~~--lvhG-ga~~G---aD~iA~~w--A~~~gv~~~-~~~adW~~ 69 (71)
T PF10686_consen 3 GMRVLITGGRDWTDHELIWAA-LDKVHARHPDMV--LVHG-GAPKG---ADRIAARW--ARERGVPVI-RFPADWQR 69 (71)
T ss_pred CCEEEEEECCccccHHHHHHH-HHHHHHhCCCEE--EEEC-CCCCC---HHHHHHHH--HHHCCCeeE-EeCcChhh
Confidence 356888898888654443222 233444455544 4444 44321 11223333 344455554 46777764
No 42
>PF11286 DUF3087: Protein of unknown function (DUF3087); InterPro: IPR021438 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=32.06 E-value=3.8e+02 Score=24.11 Aligned_cols=35 Identities=26% Similarity=0.193 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCh
Q 024212 96 VRMFFYLAFVASGSLGGLIAITQLIGALANPARAADV 132 (271)
Q Consensus 96 lR~Ffy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L 132 (271)
+|++ -+++.++=.+.++.+ .+++=++.|++++.++
T Consensus 15 ~n~v-~~~~v~~lai~sl~~-s~llI~lFg~~~~~nf 49 (165)
T PF11286_consen 15 LNRV-IVACVASLAILSLAF-SQLLIALFGGESGGNF 49 (165)
T ss_pred HHHH-HHHHHHHHHHHHHHH-HHHHHHHcCCCCCCce
Confidence 4444 445555555555444 4455558887777766
No 43
>PTZ00056 glutathione peroxidase; Provisional
Probab=30.77 E-value=3e+02 Score=24.14 Aligned_cols=61 Identities=11% Similarity=0.267 Sum_probs=40.7
Q ss_pred hcccceeEecCCceeehhhhcCcceEEEEeCCH---hHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 172 SLSNLKLRVDEKKIISVNNLRGIARLVICSGPA---SYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 172 ~L~rL~Vrl~~~r~v~L~~LRg~aRvVIvAG~~---e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
.+-.+.+.--+|+.++|+++||. ||++.=.+ ..+.+-+..-+.+.+.+.+.|+.||-|..+
T Consensus 18 ~~pdf~l~d~~G~~vsL~~~kGk--vvlv~fwAswC~~C~~e~p~L~~l~~~~~~~g~~vvgv~~~ 81 (199)
T PTZ00056 18 SIYDYTVKTLEGTTVPMSSLKNK--VLMITNSASKCGLTKKHVDQMNRLHSVFNPLGLEILAFPTS 81 (199)
T ss_pred CCCceEEECCCCCEEeHHHhCCC--EEEEEEECCCCCChHHHHHHHHHHHHHHhcCceEEEEecch
Confidence 45555555456899999999985 44442122 233444555667777888899999998764
No 44
>PF12597 DUF3767: Protein of unknown function (DUF3767); InterPro: IPR022533 This group of proteins includes mitochodrial cytochrome c oxidase proteins [], and some transmembrane domain-containing proteins of unknown function known as FAM36A. Proteins in this family are typically between 112 and 199 amino acids in length.
Probab=30.39 E-value=2.2e+02 Score=23.77 Aligned_cols=41 Identities=20% Similarity=0.257 Sum_probs=26.1
Q ss_pred ccchHHHHHHHHhCchhh------HHHHHHHHHHHHHHHHHHHHHHH
Q 024212 78 EISSAARIRNEVLSPFRS------VRMFFYLAFVASGSLGGLIAITQ 118 (271)
Q Consensus 78 ~~~~~~rLraEa~APFR~------lR~Ffy~Af~ASA~IG~~i~l~r 118 (271)
.++..+.+++=-...|+. +|--|..++++++++|++.++..
T Consensus 16 ~~t~~~A~ksi~~~df~~~~~iPCfR~slL~Gi~~G~~vG~~~fl~~ 62 (118)
T PF12597_consen 16 RPTLSDAVKSIKLSDFRNVHKIPCFRDSLLYGIAGGFGVGGLRFLFT 62 (118)
T ss_pred CCcHHHHHHhcCHHHHhHHhcCCcHHHHHHHHHHHHHHHHhhhhccc
Confidence 444444444433444443 46678888999999998877654
No 45
>PTZ00256 glutathione peroxidase; Provisional
Probab=30.25 E-value=1.5e+02 Score=25.24 Aligned_cols=65 Identities=6% Similarity=0.257 Sum_probs=44.3
Q ss_pred hhhcccceeEecCCceeehhhhcCcceEEEE--eCCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 170 EESLSNLKLRVDEKKIISVNNLRGIARLVIC--SGPASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 170 Ee~L~rL~Vrl~~~r~v~L~~LRg~aRvVIv--AG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
++.+-.+.+.-.+|+.++|+++||..=|+++ |--=..+.+-+..-+.+.+.+.++||.||-|..+
T Consensus 17 ~~~~p~f~l~d~~G~~vsLs~~~Gk~vvlv~n~atwCp~C~~e~p~l~~l~~~~~~~gv~vv~vs~~ 83 (183)
T PTZ00256 17 TKSFFEFEAIDIDGQLVQLSKFKGKKAIIVVNVACKCGLTSDHYTQLVELYKQYKSQGLEILAFPCN 83 (183)
T ss_pred CCcccceEeEcCCCCEEeHHHhCCCcEEEEEEECCCCCchHHHHHHHHHHHHHHhhCCcEEEEEecc
Confidence 4556666666556899999999986433333 2212345555666667788888999999988754
No 46
>COG0811 TolQ Biopolymer transport proteins [Intracellular trafficking and secretion]
Probab=29.44 E-value=2.1e+02 Score=25.78 Aligned_cols=65 Identities=18% Similarity=0.128 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCC---C--C----CCChHHhhhccchhHHHHHHHHHHHHHHhhhHHHHHHHHh
Q 024212 104 FVASGSLGGLIAITQLIGALANP---A--R----AADVPEILKGLSIDVSAVSLFAFLYSRENKAKNAQLARLS 168 (271)
Q Consensus 104 f~ASA~IG~~i~l~rliaal~G~---~--~----a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~~qlari~ 168 (271)
-..|=+||+|-++.-++-+..|- . + ++.+.|+|..-++-+.+..-..+.|..=+++-++++.++.
T Consensus 126 ~s~aP~lGL~GTV~GIm~aF~~i~~~~~~~~a~vA~GIseAL~aTA~GL~vAIPAvi~yn~l~r~~~~~~~~~e 199 (216)
T COG0811 126 GSIAPFLGLLGTVWGIMPAFIGIGAGGGADLAVVAPGISEALIATAIGLFVAIPAVVAYNVLRRKVEELLAKLE 199 (216)
T ss_pred HHhhhHHHHHHHHHHHHHHHHHHhccCCCCHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445666666665555544331 1 1 2556666666555555444444444444444455555443
No 47
>PRK10606 btuE putative glutathione peroxidase; Provisional
Probab=29.43 E-value=1.2e+02 Score=26.62 Aligned_cols=56 Identities=9% Similarity=0.284 Sum_probs=37.2
Q ss_pred ceeEecCCceeehhhhcCcceEEEEe---CCHhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 176 LKLRVDEKKIISVNNLRGIARLVICS---GPASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 176 L~Vrl~~~r~v~L~~LRg~aRvVIvA---G~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
+.+.--+|+.++|+++||. ||+|. -.-.+.. .+..-+.+.+.+.+.|+.|+-|..+
T Consensus 8 f~~~~~~G~~v~Ls~~~GK--vvLVvf~AS~C~~~~-q~~~L~~L~~~y~~~gl~Vlg~p~n 66 (183)
T PRK10606 8 TVVTTIDGEVTTLEKYAGN--VLLIVNVASKCGLTP-QYEQLENIQKAWADQGFVVLGFPCN 66 (183)
T ss_pred cEeECCCCCEEeHHHhCCC--EEEEEEEeCCCCCcH-HHHHHHHHHHHHhhCCeEEEEeecc
Confidence 4444445789999999994 44332 2112232 3666777888888999988888763
No 48
>PF03210 Paramyx_P_V_C: Paramyxovirus P/V phosphoprotein C-terminal; InterPro: IPR004897 Paramyxoviral P genes are able to generate more than one product, using alternative reading frames and RNA editing. The P gene encodes the structural phosphoprotein P. In addition, it encodes several non-structural proteins present in the infected cell but not in the virus particle. This family includes phosphoprotein P and the non-structural phosphoprotein V from different paramyxoviruses. Phosphoprotein P is a modular protein organised into two moieties that are both functionally and structurally distinct: a well-conserved C-terminal moiety that contains all the regions required for transcription, and a poorly conserved, intrinsically unstructured N-terminal moiety that provides several additional functions required for replication. The N-terminal moiety is responsible for binding to newly synthesized free N(0) (nucleoprotein that has not yet bound RNA), in order to prevent the binding of N(0) to cellular RNA. The C-terminal moiety consists of an oligomerisation domain, an N-RNA (nucleoprotein-RNA)-binding domain and an L polymerase-binding domain [, ]. Phosphoprotein P is essential for the activity of the RNA polymerase complex which it forms with another subunit, L IPR001016 from INTERPRO. Although all the catalytic activities of the polymerase are associated with the L subunit, its function requires specific interactions with phosphoprotein P []. The P and V phosphoproteins are amino co-terminal, but diverge at their C-termini. This difference is generated by an RNA-editing mechanism in which one or two non-templated G residues are inserted into P-gene-derived mRNA. In Measles virus and Sendai virus, one G residue is inserted and the edited transcript encodes the V protein. In Mumps virus, Simian virus 5 and Newcastle disease virus, two G residues are inserted, and the edited transcript codes for the P protein []. Being phosphoproteins, both P and V are rich in serine and threonine residues over their whole lengths. In addition, the V proteins are rich in cysteine residues at the C-termini [].; PDB: 1T6O_A 2K9D_A 1OKS_A 3BBZ_B.
Probab=29.29 E-value=18 Score=31.45 Aligned_cols=56 Identities=18% Similarity=0.234 Sum_probs=0.0
Q ss_pred hhhhhcccceeEe-cCCceeehhhhcCcc--eEEEEeCCHhHHHHHHhhchhhHHHHhh
Q 024212 168 SREESLSNLKLRV-DEKKIISVNNLRGIA--RLVICSGPASYIMESFKRSEPFTESLLE 223 (271)
Q Consensus 168 ~REe~L~rL~Vrl-~~~r~v~L~~LRg~a--RvVIvAG~~e~V~~al~~Ae~~~~~L~~ 223 (271)
+=|..|+-+++=- |.++..+++++|... ++||++|+...-.+.....+.+..+|.+
T Consensus 33 tiEG~l~si~ImdPG~~~~~s~~~~k~~~~~~pVI~~g~g~~~~~v~~~~~I~~d~Lar 91 (155)
T PF03210_consen 33 TIEGQLTSIMIMDPGNGSVSSLNEMKKNPKLKPVIVRGPGRGLKEVTQDGTIDLDELAR 91 (155)
T ss_dssp -----------------------------------------------------------
T ss_pred HHHHHHheeeEecCCCCCCCCHHHHHhCCCcCcEEecCCCCcccccCcCCeecccccCC
Confidence 3566777766544 567889999999976 6999999999888887766666666554
No 49
>PF01618 MotA_ExbB: MotA/TolQ/ExbB proton channel family MotA family only; InterPro: IPR002898 This family groups together integral membrane proteins that appear to be involved in translocation of proteins across a membrane. These proteins are probably proton channels. MotA is an essential component of the flagellar motor that uses a proton gradient to generate rotational motion in the flagellar []. ExbB is part of the TonB-dependent transduction complex. The TonB complex uses the proton gradient across the inner bacterial membrane to transport large molecules across the outer bacterial membrane.; GO: 0008565 protein transporter activity, 0006810 transport, 0016020 membrane
Probab=28.70 E-value=3.3e+02 Score=22.37 Aligned_cols=36 Identities=25% Similarity=0.303 Sum_probs=16.0
Q ss_pred HHhCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 024212 88 EVLSPFRSVRMFFYLAFVASGSLGGLIAITQLIGALA 124 (271)
Q Consensus 88 Ea~APFR~lR~Ffy~Af~ASA~IG~~i~l~rliaal~ 124 (271)
+.+.....++.....+ -.=|.+|.++-+...+.+++
T Consensus 50 ~~~~~~~~l~~i~~~a-P~lGLlGTv~Gmi~~f~~l~ 85 (139)
T PF01618_consen 50 RLERNLSILRTIASIA-PLLGLLGTVIGMIEAFQALA 85 (139)
T ss_pred HHHcchHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHh
Confidence 3344444444444333 22344555555555555554
No 50
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=28.28 E-value=83 Score=26.38 Aligned_cols=20 Identities=15% Similarity=0.270 Sum_probs=11.0
Q ss_pred HHHHHHhhhHHHHHHHHhhh
Q 024212 151 FLYSRENKAKNAQLARLSRE 170 (271)
Q Consensus 151 ~L~~~E~k~~~~qlari~RE 170 (271)
||..+-+++++|+.+.+-..
T Consensus 17 yf~iRPQkKr~Ke~~em~~s 36 (113)
T PRK06531 17 FFMQRQQKKQAQERQNQLNA 36 (113)
T ss_pred HheechHHHHHHHHHHHHHh
Confidence 34456666666666554433
No 51
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=27.42 E-value=27 Score=30.44 Aligned_cols=12 Identities=50% Similarity=0.996 Sum_probs=10.6
Q ss_pred eeecccCCCCcc
Q 024212 9 YILGPVGSGRGY 20 (271)
Q Consensus 9 ~~~~~~~~~~~~ 20 (271)
.|+||+|||.|.
T Consensus 4 iilG~pGaGK~T 15 (178)
T COG0563 4 LILGPPGAGKST 15 (178)
T ss_pred EEECCCCCCHHH
Confidence 589999999985
No 52
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=27.16 E-value=2.2e+02 Score=20.17 Aligned_cols=55 Identities=22% Similarity=0.259 Sum_probs=38.1
Q ss_pred CCceeehhhhcCcceEEEEeC-CHhHHHHHHhhchhhHHHHhhcCcEEEEEeeCCC
Q 024212 182 EKKIISVNNLRGIARLVICSG-PASYIMESFKRSEPFTESLLERGVLVVSFTTDGN 236 (271)
Q Consensus 182 ~~r~v~L~~LRg~aRvVIvAG-~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg~ 236 (271)
+++.+++.++++..=++...+ .-..+...+..-..+.+.+.+.++.++.|.+|.+
T Consensus 8 ~g~~~~~~~~~~k~~ll~f~~~~C~~C~~~~~~l~~~~~~~~~~~~~~~~v~~d~~ 63 (116)
T cd02966 8 DGKPVSLSDLKGKVVLVNFWASWCPPCRAEMPELEALAKEYKDDGVEVVGVNVDDD 63 (116)
T ss_pred CCCEeehHHcCCCEEEEEeecccChhHHHHhHHHHHHHHHhCCCCeEEEEEECCCC
Confidence 468899999986443333333 2245666666666777777778999999999765
No 53
>PF04418 DUF543: Domain of unknown function (DUF543); InterPro: IPR007512 This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. These proteins contain a conserved N-terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.
Probab=27.10 E-value=17 Score=28.39 Aligned_cols=14 Identities=36% Similarity=0.722 Sum_probs=11.9
Q ss_pred ccCCCCcccccchh
Q 024212 13 PVGSGRGYCNCQYH 26 (271)
Q Consensus 13 ~~~~~~~~~~~~~~ 26 (271)
-.|.|.+|.||||.
T Consensus 60 G~G~G~aY~~c~~~ 73 (75)
T PF04418_consen 60 GFGIGMAYSECQRD 73 (75)
T ss_pred ccccchhHHHHHHh
Confidence 36899999999974
No 54
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=25.60 E-value=3.5e+02 Score=23.06 Aligned_cols=15 Identities=20% Similarity=-0.062 Sum_probs=6.1
Q ss_pred ccchhHHHHHHHHHH
Q 024212 138 GLSIDVSAVSLFAFL 152 (271)
Q Consensus 138 NlaIqiGavalf~~L 152 (271)
-..|-+|++.+-+.+
T Consensus 43 ~~~lAlg~vL~~~g~ 57 (191)
T PF04156_consen 43 IALLALGVVLLSLGL 57 (191)
T ss_pred HHHHHHHHHHHHHHH
Confidence 334444444333333
No 55
>KOG1533 consensus Predicted GTPase [General function prediction only]
Probab=25.48 E-value=32 Score=33.13 Aligned_cols=15 Identities=53% Similarity=1.227 Sum_probs=12.4
Q ss_pred eeecccCCCC-ccccc
Q 024212 9 YILGPVGSGR-GYCNC 23 (271)
Q Consensus 9 ~~~~~~~~~~-~~~~~ 23 (271)
-|.||+|||. .||+-
T Consensus 6 vVIGPPgSGKsTYc~g 21 (290)
T KOG1533|consen 6 VVIGPPGSGKSTYCNG 21 (290)
T ss_pred EEEcCCCCCccchhhh
Confidence 4789999997 58974
No 56
>PF01313 Bac_export_3: Bacterial export proteins, family 3; InterPro: IPR002191 The fliL operon of Escherichia coli contains seven genes (including fliO, fliP, fliQ and fliR) involved in the biosynthesis and functioning of the flagellar organelle []. The fliO, fliP, fliQ and fliR genes encode highly hydrophobic polypeptides. The fliQ gene product, a small integral membrane protein that contains two putative transmembrane (TM) regions, is required for the assembly of the rivet at the earliest stage of flagellar biosynthesis. Proteins sharing an evolutionary relationship with FliQ have been found in a range of bacteria: these include Yop translocation protein S from Yersinia pestis []; surface antigen-presentation protein SpaQ from Salmonella typhimurium and Shigella flexneri []; and probable translocation protein Y4YM from Rhizobium sp. (strain NGR234) []. All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways [].; GO: 0009306 protein secretion, 0016020 membrane
Probab=25.44 E-value=2.3e+02 Score=22.22 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhc
Q 024212 104 FVASGSLGGLIAITQLIGALA 124 (271)
Q Consensus 104 f~ASA~IG~~i~l~rliaal~ 124 (271)
+.++..+|+.|+++|.+..++
T Consensus 22 L~~alvvGlvIsi~QA~TqIq 42 (76)
T PF01313_consen 22 LLVALVVGLVISIFQAATQIQ 42 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 566778999999999998544
No 57
>KOG2733 consensus Uncharacterized membrane protein [Function unknown]
Probab=25.42 E-value=84 Score=31.89 Aligned_cols=105 Identities=24% Similarity=0.448 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccchhHHHHHHHHHHHHHHhhhHHHHHHHHhhhh--hcccceeEe-
Q 024212 104 FVASGSLGGLIAITQLIGALANPARAADVPEILKGLSIDVSAVSLFAFLYSRENKAKNAQLARLSREE--SLSNLKLRV- 180 (271)
Q Consensus 104 f~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~NlaIqiGavalf~~L~~~E~k~~~~qlari~REe--~L~rL~Vrl- 180 (271)
+||||+.|.+|.-. ++. .+.+.|+.+-+++ |+.++=++-++.+.+-- .|+.-.+-+
T Consensus 11 yGASGfTG~yivee-~v~-----------~~~~~~~slavAG---------Rn~~KL~~vL~~~~~k~~~~ls~~~i~i~ 69 (423)
T KOG2733|consen 11 YGASGFTGKYIVEE-AVS-----------SQVFEGLSLAVAG---------RNEKKLQEVLEKVGEKTGTDLSSSVILIA 69 (423)
T ss_pred EccccccceeeHHH-Hhh-----------hhcccCceEEEec---------CCHHHHHHHHHHHhhccCCCcccceEEEe
Confidence 68899999888643 222 1245566666655 33333333333333211 255544444
Q ss_pred cCCceeehhhhcCcceEEE-EeCCH----hHHHHHHhhc------------------hhhHHHHhhcCcEEE
Q 024212 181 DEKKIISVNNLRGIARLVI-CSGPA----SYIMESFKRS------------------EPFTESLLERGVLVV 229 (271)
Q Consensus 181 ~~~r~v~L~~LRg~aRvVI-vAG~~----e~V~~al~~A------------------e~~~~~L~~rgVLVV 229 (271)
+.....+|.+|=..+|||| ++||= |-|-.|..++ .+|-+.-.+.||.||
T Consensus 70 D~~n~~Sl~emak~~~vivN~vGPyR~hGE~VVkacienG~~~vDISGEP~f~E~mq~kYhd~A~ekGVYIV 141 (423)
T KOG2733|consen 70 DSANEASLDEMAKQARVIVNCVGPYRFHGEPVVKACIENGTHHVDISGEPQFMERMQLKYHDLAKEKGVYIV 141 (423)
T ss_pred cCCCHHHHHHHHhhhEEEEeccccceecCcHHHHHHHHcCCceeccCCCHHHHHHHHHHHHHHHHhcCeEEE
Confidence 4457788999999999888 55552 2222222211 345666678999997
No 58
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=24.71 E-value=39 Score=24.49 Aligned_cols=19 Identities=32% Similarity=0.723 Sum_probs=13.4
Q ss_pred CCccc-ccchhhhHHhHHHH
Q 024212 17 GRGYC-NCQYHASRFCRQIL 35 (271)
Q Consensus 17 ~~~~~-~~~~~~~~~~~~~~ 35 (271)
-.||| ||+..-..|..|+.
T Consensus 4 k~GYCE~C~~ky~~l~~Hi~ 23 (49)
T PF07535_consen 4 KPGYCENCRVKYDDLEEHIQ 23 (49)
T ss_pred CCccCccccchhhhHHHHhC
Confidence 35899 56776677777764
No 59
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=24.68 E-value=64 Score=24.13 Aligned_cols=35 Identities=26% Similarity=0.466 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHhhhccc
Q 024212 100 FYLAFVASGSLGGLIAITQLIGALANPARAADVPEILKGLS 140 (271)
Q Consensus 100 fy~Af~ASA~IG~~i~l~rliaal~G~~~a~~L~e~l~Nla 140 (271)
|+.+|.+++.+|+.+.++ ++ +..|.++-+-+.+-.
T Consensus 1 F~~g~l~Ga~~Ga~~glL--~a----P~sG~e~R~~l~~~~ 35 (74)
T PF12732_consen 1 FLLGFLAGAAAGAAAGLL--FA----PKSGKETREKLKDKA 35 (74)
T ss_pred CHHHHHHHHHHHHHHHHH--hC----CCCcHHHHHHHHHHH
Confidence 566777888888776653 22 344555554444433
No 60
>KOG3078 consensus Adenylate kinase [Nucleotide transport and metabolism]
Probab=23.54 E-value=63 Score=30.28 Aligned_cols=12 Identities=50% Similarity=0.933 Sum_probs=10.4
Q ss_pred eeecccCCCCcc
Q 024212 9 YILGPVGSGRGY 20 (271)
Q Consensus 9 ~~~~~~~~~~~~ 20 (271)
-++||+|+|.|+
T Consensus 19 v~~G~pg~gkgt 30 (235)
T KOG3078|consen 19 VLLGAPGSGKGT 30 (235)
T ss_pred EEEeCCCCCCCc
Confidence 478999999995
No 61
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=23.46 E-value=58 Score=30.90 Aligned_cols=41 Identities=17% Similarity=0.297 Sum_probs=29.5
Q ss_pred eeecccCCCCcccccchhhhHHhHHHHhhcccCCCCCCcccccccceeec
Q 024212 9 YILGPVGSGRGYCNCQYHASRFCRQILNKYRSRTTPGLSISLPLHSTWTA 58 (271)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~ 58 (271)
.|.||.|||.. .++.++...+.-..+|..+-..|.++.|+-
T Consensus 3 ~i~G~t~~GKs---------~la~~l~~~~~~~iis~Ds~qvY~~l~IgT 43 (287)
T TIGR00174 3 FIMGPTAVGKS---------QLAIQLAKKLNAEIISVDSMQIYKGMDIGT 43 (287)
T ss_pred EEECCCCCCHH---------HHHHHHHHhCCCcEEEechhheeeeccccC
Confidence 68999999974 455555444433578888888888888874
No 62
>cd03009 TryX_like_TryX_NRX Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the
Probab=23.45 E-value=2.4e+02 Score=21.99 Aligned_cols=55 Identities=18% Similarity=0.133 Sum_probs=33.5
Q ss_pred CCceeehhhhcCcceEEEEeCC-HhHHHHHHhhchhhHHHHhhc--CcEEEEEeeCCC
Q 024212 182 EKKIISVNNLRGIARLVICSGP-ASYIMESFKRSEPFTESLLER--GVLVVSFTTDGN 236 (271)
Q Consensus 182 ~~r~v~L~~LRg~aRvVIvAG~-~e~V~~al~~Ae~~~~~L~~r--gVLVVPV~~dg~ 236 (271)
+|+.++|.+++|..-+|..-.+ =..+.+-+..-+.+.+++.+. ++-||.|..|.+
T Consensus 7 ~G~~v~l~~~~gk~vll~Fwa~wC~~C~~~~p~l~~~~~~~~~~~~~~~vv~is~d~~ 64 (131)
T cd03009 7 DGGKVPVSSLEGKTVGLYFSASWCPPCRAFTPKLVEFYEKLKESGKNFEIVFISWDRD 64 (131)
T ss_pred CCCCccHHHhCCcEEEEEEECCCChHHHHHhHHHHHHHHHHHhcCCCEEEEEEECCCC
Confidence 5899999999996544444333 223333333334455666654 677888887654
No 63
>cd03014 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based
Probab=23.43 E-value=2.3e+02 Score=22.45 Aligned_cols=53 Identities=13% Similarity=0.201 Sum_probs=35.4
Q ss_pred cCCceeehhhhcCcceEEEE-eCC-HhHHHHHHhhchhhHHHHhhcCcEEEEEeeCC
Q 024212 181 DEKKIISVNNLRGIARLVIC-SGP-ASYIMESFKRSEPFTESLLERGVLVVSFTTDG 235 (271)
Q Consensus 181 ~~~r~v~L~~LRg~aRvVIv-AG~-~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~dg 235 (271)
.+++.++|++++|..-|+.. ++. -..+...+..-+.+.+++ .|+.||-|..|.
T Consensus 14 ~~g~~~~l~~~~gk~vvl~f~~~~~c~~C~~e~~~l~~~~~~~--~~~~vi~Is~d~ 68 (143)
T cd03014 14 SDLSEVSLADFAGKVKVISVFPSIDTPVCATQTKRFNKEAAKL--DNTVVLTISADL 68 (143)
T ss_pred CCCcEEeHHHhCCCeEEEEEEcCCCCCcCHHHHHHHHHHHHhc--CCCEEEEEECCC
Confidence 45789999999986433332 333 255677676666666665 389999888753
No 64
>PF06699 PIG-F: GPI biosynthesis protein family Pig-F; InterPro: IPR009580 Glycosylphosphatidylinositol anchor biosynthesis protein Pig-F is involved in glycosylphosphatidylinositol (GPI) anchor biosynthesis [, , ]. ; GO: 0006506 GPI anchor biosynthetic process, 0005789 endoplasmic reticulum membrane, 0016021 integral to membrane
Probab=23.41 E-value=29 Score=31.18 Aligned_cols=20 Identities=25% Similarity=0.508 Sum_probs=16.3
Q ss_pred cCcEEEEEeeCCCCCCCCccchHHHHHhhhhhccceeeeecc
Q 024212 224 RGVLVVSFTTDGNIPSFEFEESEEMKEFTRKRKRLWQLTPVY 265 (271)
Q Consensus 224 rgVLVVPV~~dg~s~~~~f~~~~~~~~~~~~~~rrw~a~Pv~ 265 (271)
-|..++|.++ ||-||.||+-
T Consensus 152 lGa~pIPLDW----------------------DRpWQ~WPi~ 171 (190)
T PF06699_consen 152 LGAVPIPLDW----------------------DRPWQAWPIT 171 (190)
T ss_pred HcceeccCCC----------------------CCccccCChH
Confidence 4778888888 5889999985
No 65
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=23.08 E-value=3.6e+02 Score=20.81 Aligned_cols=38 Identities=11% Similarity=0.116 Sum_probs=26.2
Q ss_pred chHHHHHHHHhCchhhHHHHHHHHHHHHHHHHHHHHHH
Q 024212 80 SSAARIRNEVLSPFRSVRMFFYLAFVASGSLGGLIAIT 117 (271)
Q Consensus 80 ~~~~rLraEa~APFR~lR~Ffy~Af~ASA~IG~~i~l~ 117 (271)
..+.+.....|.=|+.+|+.-.+....+|.++.+..+.
T Consensus 5 ~~y~~~a~~~q~~~~~~~~~~i~~~~~~a~i~~l~~~~ 42 (112)
T PF14015_consen 5 DWYDKKARRAQRRYRRLRIASIILSVLGAVIPVLASLS 42 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566666777778888888777777777777644443
No 66
>PF12576 DUF3754: Protein of unknown function (DUF3754); InterPro: IPR022227 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Probab=21.83 E-value=4.5e+02 Score=22.21 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024212 97 RMFFYLAFVASGSLGGLIAITQLIG 121 (271)
Q Consensus 97 R~Ffy~Af~ASA~IG~~i~l~rlia 121 (271)
|.+=+.-+..++.+|++..+.++..
T Consensus 60 ~~~D~~~l~~~~vvg~v~~~~~~~~ 84 (141)
T PF12576_consen 60 RPFDRVKLGVSAVVGGVAVFVKLVG 84 (141)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3444566778888888888888777
No 67
>cd02971 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a
Probab=21.79 E-value=2.2e+02 Score=22.08 Aligned_cols=53 Identities=11% Similarity=0.163 Sum_probs=36.7
Q ss_pred CCceeehhhhcCcceEEEEe-C-CHhHHHHHHhhchhhHHHHhhcCcEEEEEeeC
Q 024212 182 EKKIISVNNLRGIARLVICS-G-PASYIMESFKRSEPFTESLLERGVLVVSFTTD 234 (271)
Q Consensus 182 ~~r~v~L~~LRg~aRvVIvA-G-~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~d 234 (271)
+++.+++.++++..-+|+.- + .-..+...+..-+...+.|.+.++-+|-|..|
T Consensus 11 ~g~~~~l~~~~gk~~ll~f~~~~~c~~C~~~~~~l~~~~~~~~~~~~~~i~is~d 65 (140)
T cd02971 11 DGGEVSLSDFKGKWVVLFFYPKDFTPVCTTELCAFRDLAEEFAKGGAEVLGVSVD 65 (140)
T ss_pred CCcEEehHHhCCCeEEEEEeCCCCCCcCHHHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence 47899999997654444433 2 33455666666677777887889888888764
No 68
>COG1585 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=21.48 E-value=3.8e+02 Score=22.89 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=13.7
Q ss_pred cceeEecCC--ceeehhhhcCcceEEEE
Q 024212 175 NLKLRVDEK--KIISVNNLRGIARLVIC 200 (271)
Q Consensus 175 rL~Vrl~~~--r~v~L~~LRg~aRvVIv 200 (271)
+-+|++++. +..+..++.-..+|.|+
T Consensus 101 ~g~Vkv~g~~Wra~~~~~l~~G~~V~Vv 128 (140)
T COG1585 101 RGRVKVEGESWRARSDEDLPAGDRVEVV 128 (140)
T ss_pred eEEEEECCeEeEEecCCCCCCCCEEEEE
Confidence 344555543 55555666544455554
No 69
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=21.36 E-value=1.5e+02 Score=25.64 Aligned_cols=14 Identities=21% Similarity=0.560 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHH
Q 024212 99 FFYLAFVASGSLGG 112 (271)
Q Consensus 99 Ffy~Af~ASA~IG~ 112 (271)
||++.|.++.+.|+
T Consensus 2 ~~~~~~~~~~a~~~ 15 (167)
T PRK08475 2 FFFLLLLGFYAFAA 15 (167)
T ss_pred hHHHHHHHHHHHHc
Confidence 66666666655544
No 70
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=21.23 E-value=42 Score=27.78 Aligned_cols=12 Identities=50% Similarity=1.060 Sum_probs=10.4
Q ss_pred eeecccCCCCcc
Q 024212 9 YILGPVGSGRGY 20 (271)
Q Consensus 9 ~~~~~~~~~~~~ 20 (271)
.|+||+|||.+.
T Consensus 3 ~i~G~pGsGKst 14 (183)
T TIGR01359 3 FVLGGPGSGKGT 14 (183)
T ss_pred EEECCCCCCHHH
Confidence 589999999974
No 71
>TIGR00907 2A0304 amino acid permease (GABA permease).
Probab=21.11 E-value=4.2e+02 Score=25.68 Aligned_cols=42 Identities=14% Similarity=-0.002 Sum_probs=33.7
Q ss_pred ccchHHHHHHHHhCchhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 024212 78 EISSAARIRNEVLSPFRSVRMFFYLAFVASGSLGGLIAITQL 119 (271)
Q Consensus 78 ~~~~~~rLraEa~APFR~lR~Ffy~Af~ASA~IG~~i~l~rl 119 (271)
+.+.-.-+=+|++.|=|.+-+-+..+...+..++.+..+.-+
T Consensus 232 G~e~~~~~a~E~knP~r~iP~Ai~~s~~i~~~~~~~~~l~~~ 273 (482)
T TIGR00907 232 GYDGTAHMAEEIENPEVVGPRAIIGAVAIGIVTGFCFNIVLF 273 (482)
T ss_pred CcchhhHHHHhcCChhhhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 666778889999999999999999998877777765555433
No 72
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7.
Probab=20.70 E-value=2.8e+02 Score=22.59 Aligned_cols=52 Identities=12% Similarity=0.284 Sum_probs=36.6
Q ss_pred cCCceeehhhhcCcceEEEE--eCCHhHHHHHHhhchhhHHHHhhcCcEEEEEee
Q 024212 181 DEKKIISVNNLRGIARLVIC--SGPASYIMESFKRSEPFTESLLERGVLVVSFTT 233 (271)
Q Consensus 181 ~~~r~v~L~~LRg~aRvVIv--AG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~ 233 (271)
.+|++++|++++|.. +||. |-.=..+...+...+.+.+++...||.||-|..
T Consensus 10 ~~G~~~~l~~~~Gk~-vvv~~~as~C~~c~~~~~~l~~l~~~~~~~~~~v~~i~~ 63 (153)
T TIGR02540 10 ARGRTVSLEKYRGKV-SLVVNVASECGFTDQNYRALQELHRELGPSHFNVLAFPC 63 (153)
T ss_pred CCCCEecHHHhCCCE-EEEEEeCCCCCchhhhHHHHHHHHHHHhhCCeEEEEEec
Confidence 457899999999954 3333 222234556666777888888889999988874
No 73
>cd00209 DHFR Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy. 5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis.
Probab=20.02 E-value=1e+02 Score=25.95 Aligned_cols=39 Identities=5% Similarity=-0.068 Sum_probs=30.1
Q ss_pred hhhhcCcceEEEEeCCHhHHHHHHhhchhhHHHHhhcCcEEEEEee
Q 024212 188 VNNLRGIARLVICSGPASYIMESFKRSEPFTESLLERGVLVVSFTT 233 (271)
Q Consensus 188 L~~LRg~aRvVIvAG~~e~V~~al~~Ae~~~~~L~~rgVLVVPV~~ 233 (271)
+..|+...+-|.|.|+++-+...++. +-+--+.|+|+..
T Consensus 84 v~~lk~~~~~I~v~GG~~l~~~~l~~-------iDe~~l~v~pv~~ 122 (158)
T cd00209 84 LELAENTVEEIFVIGGAEIYKQALPY-------ADRLYLTRIHAEF 122 (158)
T ss_pred HHHHhcCCCeEEEECcHHHHHHHHhh-------CCEEEEEEECCcc
Confidence 45566445678889999988888776 5566789999999
Done!