Query psy11172
Match_columns 75
No_of_seqs 116 out of 542
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 19:52:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11172hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1959|consensus 100.0 1.1E-35 2.3E-40 237.5 5.0 74 1-74 100-176 (996)
2 PLN02701 alpha-mannosidase 100.0 3.4E-33 7.3E-38 227.6 4.7 74 1-74 95-169 (1050)
3 KOG1958|consensus 100.0 5.2E-31 1.1E-35 211.8 5.1 75 1-75 218-293 (1129)
4 PF01074 Glyco_hydro_38: Glyco 99.9 2.5E-27 5.5E-32 167.0 4.4 72 3-74 55-127 (275)
5 PRK09819 alpha-mannosidase; Pr 99.9 3E-23 6.6E-28 166.3 5.3 68 4-74 62-131 (875)
6 KOG4342|consensus 99.7 2E-17 4.3E-22 131.6 5.3 74 1-74 334-408 (1078)
7 COG0383 AMS1 Alpha-mannosidase 99.1 1E-11 2.2E-16 101.6 0.8 71 3-74 253-323 (943)
8 PF03065 Glyco_hydro_57: Glyco 98.7 2.9E-08 6.4E-13 73.0 4.8 61 8-68 110-172 (360)
9 PF01522 Polysacc_deac_1: Poly 97.3 0.00045 9.7E-09 42.4 4.3 52 11-63 47-99 (123)
10 TIGR02764 spore_ybaN_pdaB poly 96.6 0.012 2.6E-07 39.4 6.8 59 11-72 48-107 (191)
11 TIGR02873 spore_ylxY probable 96.4 0.017 3.7E-07 41.6 6.6 59 11-72 127-186 (268)
12 TIGR02884 spore_pdaA delta-lac 95.7 0.054 1.2E-06 37.6 6.5 59 11-72 79-139 (224)
13 COG1449 Alpha-amylase/alpha-ma 95.1 0.041 9E-07 44.1 4.6 60 8-67 179-243 (615)
14 TIGR03006 pepcterm_polyde poly 94.6 0.19 4.1E-06 36.3 6.7 55 11-67 57-112 (265)
15 COG1543 Uncharacterized conser 94.1 0.05 1.1E-06 42.9 3.1 61 7-67 122-184 (504)
16 TIGR03212 uraD_N-term-dom puta 93.8 0.2 4.4E-06 36.7 5.5 54 11-66 106-160 (297)
17 PF08672 APC2: Anaphase promot 88.7 0.28 6.1E-06 28.3 1.4 20 10-29 38-58 (60)
18 PRK15394 4-deoxy-4-formamido-L 85.4 2.2 4.8E-05 31.4 4.9 51 11-63 91-146 (296)
19 PRK14581 hmsF outer membrane N 85.3 2.5 5.4E-05 34.6 5.5 59 12-72 168-254 (672)
20 COG0383 AMS1 Alpha-mannosidase 82.9 0.24 5.3E-06 41.6 -1.1 65 7-73 65-130 (943)
21 PRK14582 pgaB outer membrane N 78.4 6.7 0.00015 32.2 5.6 59 12-72 168-254 (671)
22 PHA02100 hypothetical protein 72.4 2.9 6.3E-05 26.8 1.8 17 50-74 64-80 (112)
23 PF10720 DUF2515: Protein of u 58.4 6.1 0.00013 29.7 1.4 28 26-53 45-72 (308)
24 PRK10148 hypothetical protein; 55.9 6 0.00013 25.9 0.9 13 61-73 123-135 (147)
25 PF06526 DUF1107: Protein of u 55.1 16 0.00034 21.5 2.5 31 19-49 29-59 (64)
26 PF04567 RNA_pol_Rpb2_5: RNA p 47.7 18 0.00039 19.6 1.9 14 14-27 2-15 (48)
27 COG0726 CDA1 Predicted xylanas 47.6 44 0.00096 22.1 4.2 48 14-62 111-158 (267)
28 PF13249 Prenyltrans_2: Prenyl 47.5 22 0.00048 20.9 2.5 24 49-74 47-70 (113)
29 PF12395 DUF3658: Protein of u 47.1 17 0.00036 22.8 1.9 18 14-31 89-106 (111)
30 cd04693 Nudix_Hydrolase_34 Mem 44.2 17 0.00037 22.2 1.6 34 18-61 26-59 (127)
31 KOG2165|consensus 43.2 17 0.00038 30.4 1.9 19 11-29 742-761 (765)
32 KOG0402|consensus 42.7 21 0.00045 22.4 1.8 26 23-48 63-88 (92)
33 PRK15472 nucleoside triphospha 42.3 19 0.00042 22.5 1.7 27 18-47 29-55 (141)
34 PF11625 DUF3253: Protein of u 40.8 13 0.00028 22.9 0.7 28 3-30 39-67 (83)
35 TIGR03826 YvyF flagellar opero 40.5 20 0.00042 23.9 1.6 16 12-27 62-77 (137)
36 PF08557 Lipid_DES: Sphingolip 40.3 54 0.0012 17.4 3.0 32 29-63 8-39 (39)
37 COG2317 Zn-dependent carboxype 36.9 33 0.00071 27.5 2.5 26 50-75 385-419 (497)
38 cd04672 Nudix_Hydrolase_14 Mem 35.4 30 0.00064 21.0 1.7 33 19-61 23-55 (123)
39 cd03428 Ap4A_hydrolase_human_l 35.2 23 0.0005 21.5 1.2 25 20-47 27-51 (130)
40 PF00538 Linker_histone: linke 35.0 44 0.00096 19.3 2.4 16 11-26 49-65 (77)
41 PF04424 DUF544: Protein of un 35.0 26 0.00056 22.4 1.4 19 53-71 81-99 (121)
42 smart00526 H15 Domain in histo 32.9 38 0.00081 18.9 1.8 17 11-27 49-66 (66)
43 PF05005 Ocnus: Janus/Ocnus fa 32.9 40 0.00086 21.5 2.0 23 14-36 52-75 (108)
44 PF08220 HTH_DeoR: DeoR-like h 32.6 77 0.0017 17.3 3.0 24 11-34 33-56 (57)
45 COG4002 Predicted phosphotrans 31.4 82 0.0018 23.0 3.6 31 33-65 112-142 (256)
46 TIGR01322 scrB_fam sucrose-6-p 31.3 22 0.00048 27.0 0.8 19 54-72 14-32 (445)
47 cd04697 Nudix_Hydrolase_38 Mem 31.3 36 0.00078 20.9 1.6 36 18-62 26-61 (126)
48 COG0280 Pta Phosphotransacetyl 31.1 1.9E+02 0.004 21.9 5.6 47 26-72 159-208 (327)
49 COG2994 HlyC ACP:hemolysin acy 31.0 20 0.00043 24.4 0.4 12 14-25 46-57 (148)
50 PRK12862 malic enzyme; Reviewe 30.4 1.2E+02 0.0027 25.3 4.9 31 35-66 607-637 (763)
51 PF02082 Rrf2: Transcriptional 30.1 91 0.002 18.0 3.2 25 11-35 43-71 (83)
52 PF09999 DUF2240: Uncharacteri 29.3 1.1E+02 0.0025 20.4 3.8 53 11-63 40-124 (144)
53 PF02074 Peptidase_M32: Carbox 28.9 26 0.00056 27.8 0.8 24 51-74 385-417 (494)
54 cd06588 PhnB_like Escherichia 27.8 34 0.00074 20.9 1.1 12 62-73 113-124 (128)
55 PF02187 GAS2: Growth-Arrest-S 27.5 24 0.00052 21.2 0.3 17 18-34 45-61 (73)
56 cd04677 Nudix_Hydrolase_18 Mem 27.2 66 0.0014 19.4 2.3 34 19-62 29-62 (132)
57 PF05677 DUF818: Chlamydia CHL 27.2 91 0.002 24.1 3.4 50 22-74 174-224 (365)
58 PF00530 SRCR: Scavenger recep 26.6 33 0.00072 19.8 0.8 14 18-31 7-22 (99)
59 COG1621 SacC Beta-fructosidase 26.3 27 0.00059 27.7 0.5 20 53-72 28-47 (486)
60 cd04696 Nudix_Hydrolase_37 Mem 26.2 56 0.0012 19.7 1.9 33 19-61 25-57 (125)
61 PF08218 Citrate_ly_lig: Citra 25.7 31 0.00067 24.2 0.6 11 46-56 11-21 (182)
62 COG1347 NqrD Na+-transporting 25.4 41 0.00089 23.7 1.2 40 14-53 152-201 (208)
63 cd03427 MTH1 MutT homolog-1 (M 25.4 64 0.0014 19.7 2.0 28 18-48 24-51 (137)
64 PRK01816 hypothetical protein; 25.0 1.5E+02 0.0033 20.0 3.8 40 11-57 99-139 (143)
65 PRK05632 phosphate acetyltrans 24.4 1.8E+02 0.004 23.6 4.9 42 27-69 521-565 (684)
66 cd04681 Nudix_Hydrolase_22 Mem 24.3 73 0.0016 19.2 2.1 33 19-61 26-58 (130)
67 KOG1290|consensus 24.1 79 0.0017 25.8 2.7 27 37-63 187-218 (590)
68 PRK01909 pdxA 4-hydroxythreoni 23.9 1.1E+02 0.0023 23.2 3.3 27 38-64 175-202 (329)
69 PF15007 CEP44: Centrosomal sp 23.8 57 0.0012 21.6 1.6 15 49-63 73-87 (131)
70 cd04670 Nudix_Hydrolase_12 Mem 23.8 63 0.0014 19.5 1.7 34 18-61 25-58 (127)
71 PF04217 DUF412: Protein of un 23.5 2.4E+02 0.0052 19.0 4.6 40 11-57 100-140 (143)
72 cd04684 Nudix_Hydrolase_25 Con 23.1 68 0.0015 19.0 1.8 26 18-46 23-48 (128)
73 PRK05331 putative phosphate ac 23.0 2E+02 0.0044 21.4 4.6 40 27-66 137-180 (334)
74 COG0657 Aes Esterase/lipase [L 22.6 1.3E+02 0.0029 21.1 3.4 41 22-62 83-152 (312)
75 PF06422 PDR_CDR: CDR ABC tran 22.6 50 0.0011 20.4 1.1 23 45-67 29-51 (103)
76 smart00419 HTH_CRP helix_turn_ 22.3 1E+02 0.0022 15.2 2.1 21 11-31 26-47 (48)
77 PF14177 YkyB: YkyB-like prote 22.0 71 0.0015 21.5 1.8 18 11-28 30-48 (140)
78 PRK13272 treA trehalase; Provi 21.9 77 0.0017 25.5 2.3 36 29-64 168-203 (542)
79 PF06819 Arc_PepC: Archaeal Pe 21.5 50 0.0011 21.3 1.0 16 8-23 89-105 (110)
80 TIGR02836 spore_IV_A stage IV 21.5 74 0.0016 25.5 2.1 32 44-75 419-450 (492)
81 COG3811 Uncharacterized protei 21.5 54 0.0012 20.2 1.1 31 11-41 9-53 (85)
82 cd04682 Nudix_Hydrolase_23 Mem 21.4 80 0.0017 19.0 1.9 34 18-61 27-60 (122)
83 KOG1515|consensus 21.4 1.2E+02 0.0027 22.7 3.2 26 22-47 94-119 (336)
84 PRK13270 treF trehalase; Provi 21.3 77 0.0017 25.6 2.1 36 29-64 179-214 (549)
85 PRK08629 coproporphyrinogen II 21.3 2.1E+02 0.0045 22.0 4.4 45 14-58 381-425 (433)
86 PF03755 YicC_N: YicC-like fam 20.9 2.6E+02 0.0055 18.3 4.9 53 8-60 46-101 (159)
87 PF08679 DsrD: Dissimilatory s 20.8 76 0.0017 18.8 1.6 16 11-26 38-54 (67)
88 cd04683 Nudix_Hydrolase_24 Mem 20.6 85 0.0018 18.6 1.9 35 18-62 24-58 (120)
89 PRK13271 treA trehalase; Provi 20.4 81 0.0018 25.5 2.1 36 29-64 167-202 (569)
90 PF14528 LAGLIDADG_3: LAGLIDAD 20.3 20 0.00044 20.2 -1.0 22 42-63 29-50 (77)
91 COG1462 CsgG Uncharacterized p 20.2 1.6E+02 0.0034 21.7 3.4 54 16-71 182-240 (252)
No 1
>KOG1959|consensus
Probab=100.00 E-value=1.1e-35 Score=237.46 Aligned_cols=74 Identities=34% Similarity=0.552 Sum_probs=72.8
Q ss_pred CCCCCCCCChhhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhC--CCCCceeecCCCCCCC
Q psy11172 1 MSWSGEIPNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIG--VKPRYLHNNSRTISSP 74 (75)
Q Consensus 1 ~Ww~~~~~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg--~~P~~~W~~D~Fg~s~ 74 (75)
|||++|+++.|.+ |+||++|||||+||||||||||++||.|+|||+|.||+||+++|| .+|++||+|||||||.
T Consensus 100 rWW~~qS~~~k~~Vk~LV~~GrLEFi~Ggw~MnDEA~~hY~dvIDQ~TlGlrfL~~tFG~cgrPrvgWqIDPFGHSr 176 (996)
T KOG1959|consen 100 RWWNEQSETQKEQVKKLVNEGRLEFIGGGWSMNDEATTHYQDVIDQFTLGLRFLKDTFGECGRPRVGWQIDPFGHSR 176 (996)
T ss_pred HHHHhcCHHHHHHHHHHHhcCCEEEecCeeeecchhhhhHHHHHHHHHHHHHHHHHHhcccCCcceeeeeCCCCcch
Confidence 6999999999999 999999999999999999999999999999999999999999999 9999999999999995
No 2
>PLN02701 alpha-mannosidase
Probab=99.97 E-value=3.4e-33 Score=227.59 Aligned_cols=74 Identities=47% Similarity=0.784 Sum_probs=72.7
Q ss_pred CCCCCCCCChhhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCCCC
Q psy11172 1 MSWSGEIPNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTISSP 74 (75)
Q Consensus 1 ~Ww~~~~~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s~ 74 (75)
+||++++|+++++ |+||++||||||||||||||||+++|+++|+||++||+||+++||+.|++||+|||||||+
T Consensus 95 ~Ww~~~~pe~~~~vk~LV~~GrLE~vgGgwvm~DEa~~~~esiI~Ql~~G~~~l~~~fG~~P~~~W~iDpFGhs~ 169 (1050)
T PLN02701 95 RWWRDASPSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITEGNMWLNDTIGVAPKNSWAIDPFGYSS 169 (1050)
T ss_pred HHHHhcCHHHHHHHHHHHHcCCEEEECCceecccccccCHHHHHHHHHhhhHHHHhhcCCCCCcCccCCCCCCCH
Confidence 5999999999999 9999999999999999999999999999999999999999999999999999999999996
No 3
>KOG1958|consensus
Probab=99.96 E-value=5.2e-31 Score=211.84 Aligned_cols=75 Identities=52% Similarity=0.797 Sum_probs=73.5
Q ss_pred CCCCCCCCChhhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCCCCC
Q psy11172 1 MSWSGEIPNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTISSPH 75 (75)
Q Consensus 1 ~Ww~~~~~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s~~ 75 (75)
+||++++++.++. |+||++||||||+|||||||||++||.++|+|+++||+||+++.|++|+++|+||||||||.
T Consensus 218 ~ww~~~~~~kk~a~k~lv~~GqlEIvtGGWVMpDEAn~Hy~~~i~qliEGh~Wl~~~igv~P~s~WaiDPFG~S~T 293 (1129)
T KOG1958|consen 218 RWWDDASPTKKNAVKRLVKNGQLEIVTGGWVMPDEANSHYFAMIDQLIEGHQWLKNNIGVTPQSGWAIDPFGYSST 293 (1129)
T ss_pred HhhhhcChHHHHHHHHHHhcCcEEEEeCccccCcccchhHHHHHHHHhhhhhHHhccCCCCCCcccccCCCCCCcc
Confidence 6999999999999 99999999999999999999999999999999999999999999999999999999999983
No 4
>PF01074 Glyco_hydro_38: Glycosyl hydrolases family 38 N-terminal domain; InterPro: IPR000602 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 38 GH38 from CAZY comprises enzymes with only one known activity; alpha-mannosidase (3.2.1.24 from EC) (3.2.1.114 from EC). Lysosomal alpha-mannosidase is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. The enzyme catalyses the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides, and can cleave all known types of alpha-mannosidic linkages. Defects in the gene cause lysosomal alpha-mannosidosis (AM), a lysosomal storage disease characterised by the accumulation of unbranched oligo-saccharide chains.; GO: 0004559 alpha-mannosidase activity, 0005975 carbohydrate metabolic process; PDB: 2WYI_A 2WYH_A 1O7D_A 3CZN_A 2FYV_A 3D50_A 3EJU_A 3EJS_A 3DX3_A 3BVX_A ....
Probab=99.94 E-value=2.5e-27 Score=167.00 Aligned_cols=72 Identities=31% Similarity=0.417 Sum_probs=61.5
Q ss_pred CCCCCCChhhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCCCC
Q psy11172 3 WSGEIPNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTISSP 74 (75)
Q Consensus 3 w~~~~~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s~ 74 (75)
|.+..|+.+++ |+||++||||||||+|||+|++++++|++|+||+.|++|++++||++|+++|++|+||||+
T Consensus 55 ~~~~~p~~~~~~~~lv~~Gri~~vgg~~~~~D~~l~~~Eslirql~~G~~~~~~~fg~~~~~~~~~D~FG~~~ 127 (275)
T PF01074_consen 55 YLEDAPEEFKRIKKLVKEGRIEIVGGWYVQPDENLPSGESLIRQLLYGHKYLRKEFGVRPKVAWQPDSFGHSA 127 (275)
T ss_dssp HHHCSGHHHHHHHHHHHTTSEEESSSBSS-B-SSSS-HHHHHHHHHHHHHHHHHHHTG--SEEEESSSSSB-T
T ss_pred HHHhCCHHHHHHHHHHHhceeEEeCceeeeccccCCCHHHHHHHHhhhHHHHHHhcCCCCCeEEeCCCCCCch
Confidence 33446777777 9999999999999999999999999999999999999999999999999999999999997
No 5
>PRK09819 alpha-mannosidase; Provisional
Probab=99.88 E-value=3e-23 Score=166.30 Aligned_cols=68 Identities=22% Similarity=0.206 Sum_probs=63.0
Q ss_pred CCCCCChhhh-HHHHhcCceEEEccee-eeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCCCC
Q psy11172 4 SGEIPNHKPI-VSLVKSGQLEIVTGGW-VMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTISSP 74 (75)
Q Consensus 4 ~~~~~~~k~~-k~lV~~GqlE~v~GgW-v~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s~ 74 (75)
.+..|+.+++ |+||++||| +.||| ||+|++++++||+||||+.|++|+ ++||..|++||+|||||||+
T Consensus 62 ~~~~Pe~~~~ik~lV~~Grl--~~G~W~v~~D~~l~sgEsliRqll~G~~~~-~~fG~~~~vgwlpD~FG~s~ 131 (875)
T PRK09819 62 LAVKPEDKERVKKLVQAGKL--IIGPWYTQTDQLVVSGESIVRNLLYGIRDC-REFGEPMKIGYLPDSFGQSG 131 (875)
T ss_pred HHhChHHHHHHHHHHHcCCE--eECcEEeecccccCCHHHHHHHHHHHHHHH-HHcCCCCceeeecCCCCCcH
Confidence 3678999999 999999999 34777 899999999999999999999999 79999999999999999996
No 6
>KOG4342|consensus
Probab=99.69 E-value=2e-17 Score=131.63 Aligned_cols=74 Identities=20% Similarity=0.194 Sum_probs=71.8
Q ss_pred CCCCCCCCChhhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCCCC
Q psy11172 1 MSWSGEIPNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTISSP 74 (75)
Q Consensus 1 ~Ww~~~~~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s~ 74 (75)
+|..+.+|+...+ +..+..||+-.|||.||++|.+.|++|++++|+..|+.|+.++||++++.-|++|+||||.
T Consensus 334 ~WlkedhP~~f~kl~e~~~q~qF~pvGGtWVE~DtNiPsGEslvRQFl~GQ~FFlkeFG~~c~~FWLPDTFGYSs 408 (1078)
T KOG4342|consen 334 EWLKEDHPGLFSKLQEFACQGQFVPVGGTWVEMDTNIPSGESLVRQFLQGQNFFLKEFGKMCSEFWLPDTFGYSS 408 (1078)
T ss_pred HHHhhhChhHHHHHHHHHhcCceeeccceEEecCCCCCChHHHHHHHHhhhhHHHHHhhhhhcceeccccccccc
Confidence 4888999999999 9999999999999999999999999999999999999999999999999999999999995
No 7
>COG0383 AMS1 Alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=99.13 E-value=1e-11 Score=101.61 Aligned_cols=71 Identities=24% Similarity=0.244 Sum_probs=63.5
Q ss_pred CCCCCCChhhhHHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCCCC
Q psy11172 3 WSGEIPNHKPIVSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTISSP 74 (75)
Q Consensus 3 w~~~~~~~k~~k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s~ 74 (75)
.....|..... ++|+.+++++++|+||++|.+++++|++++|+..|++|+.+.|+...|+.|.+|+||.|.
T Consensus 253 l~~d~p~l~~~-~~v~~~~~~~~~g~~ve~d~n~~sGEslsrq~~~gq~~~~~~f~~ssri~w~pd~fg~s~ 323 (943)
T COG0383 253 LKPDVPFLFSR-PAVEFEQWEIVGGMWVEEDLNTPSGESLSRQFLYGQRFFTEKFGASSRIYWKPDSFGFSG 323 (943)
T ss_pred hcCccHHHhhc-ccccccceEEeecccccccCCccccchhhhhhhccceeeecccCccceeEeehhccccch
Confidence 33444444333 899999999999999999999999999999999999999999999999999999999985
No 8
>PF03065 Glyco_hydro_57: Glycosyl hydrolase family 57; InterPro: IPR004300 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 57 GH57 from CAZY comprises enzymes with two known activities; alpha-amylase (3.2.1.1 from EC) and 4-alpha-glucanotransferase (2.4.1 from EC).; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process; PDB: 1K1X_B 1K1W_A 1K1Y_A 3N98_A 3N8T_A 3N92_A 1UFA_A 3P0B_A.
Probab=98.67 E-value=2.9e-08 Score=72.97 Aligned_cols=61 Identities=16% Similarity=0.201 Sum_probs=50.4
Q ss_pred CChhhh-HHHHhcCceEEEcceeeeeccCCCCH-HHHHHHHHHHHHHHHhhhCCCCCceeecC
Q psy11172 8 PNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHY-YSMIQQLTHGQQWLLTNIGVKPRYLHNNS 68 (75)
Q Consensus 8 ~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~-~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D 68 (75)
.+.-+. |+|+++|++|++++++..+-..+..- +++..||..|.+.+++.||++|++.|.+.
T Consensus 110 ~~ii~~~~~l~~~G~iEll~~~~~h~ilpl~~~~~d~~~Qi~~~~~~~~~~FG~~P~G~W~pE 172 (360)
T PF03065_consen 110 GDIIEAFRELAERGQIELLTSPYYHPILPLLPDPEDFRAQIEMGREYFKKHFGRRPRGFWLPE 172 (360)
T ss_dssp T-HHHHHHHHHHTTSEEEEEE-TT-B-GGGSSHHHHHHHHHHHHHHHHHHHHSS--SBEE-GG
T ss_pred hhhHHHHHHHHHCCCEEEEeCchHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCCceECcc
Confidence 344567 99999999999999999999999999 99999999999999999999999999874
No 9
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=97.32 E-value=0.00045 Score=42.44 Aligned_cols=52 Identities=17% Similarity=0.234 Sum_probs=44.9
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCc
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRY 63 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~ 63 (75)
.+. +.++++| .||.+.||..++....+.+++.++|....+.|++.+|..|+.
T Consensus 47 ~~~l~~l~~~G-~ei~~H~~~H~~~~~~~~~~~~~ei~~~~~~l~~~~g~~~~~ 99 (123)
T PF01522_consen 47 PDQLRELAAAG-HEIGNHGWSHPNLSTLSPEELRREIERSREILEEITGRPPKG 99 (123)
T ss_dssp HHHHHHHHHTT--EEEEE-SSSSCGGGS-HHHHHHHHHHHHHHHHHHHSSEESE
T ss_pred cccchhHHHHH-HHHHhcCCcccccccCCHHHHHHHHHHHHHHHHHHhCCCCcE
Confidence 355 9999999 999999999999999999999999999999999999995554
No 10
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=96.63 E-value=0.012 Score=39.39 Aligned_cols=59 Identities=17% Similarity=0.217 Sum_probs=50.3
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCC
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTIS 72 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~ 72 (75)
.+. ++++++|. ||.+.+|..++....+.+.+..+|..+.+.|++..|..|+. -.-|+|.
T Consensus 48 ~~~~~~i~~~Gh-eig~Ht~~H~~~~~~~~~~~~~ei~~~~~~l~~~~g~~~~~--fr~P~G~ 107 (191)
T TIGR02764 48 PELVKEIVKDGH-EIGSHGYRHKNYTTLEDEKIKKDILRAQEIIEKLTGKKPTL--FRPPSGA 107 (191)
T ss_pred HHHHHHHHhCCC-EEEECCcCCCCcccCCHHHHHHHHHHHHHHHHHHhCCCCCE--EECCCcC
Confidence 356 99999995 99999999999998999999999999999999999987763 3445553
No 11
>TIGR02873 spore_ylxY probable sporulation protein, polysaccharide deacetylase family. Members of this protein family are most closely related to TIGR02764, a subset of polysaccharide deacetylase family proteins found in a species if and only if the species forms endospores like those of Bacillus subtilis or Clostridium tetani. This family is likewise restricted to spore-formers, but is not universal among them in having sequences with full-length matches to the model.
Probab=96.36 E-value=0.017 Score=41.62 Aligned_cols=59 Identities=20% Similarity=0.254 Sum_probs=52.3
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCC
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTIS 72 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~ 72 (75)
.+. |+++++| .||.+.+|..++...-+.+.+.++|....+.|++..|..|+ |-.-|+|.
T Consensus 127 p~l~k~i~~~G-heIGnHT~sH~~l~~ls~~~~~~Ei~~~~~~i~~~~G~~p~--~fRpP~G~ 186 (268)
T TIGR02873 127 SQLAKMIVEQG-HEIGNHAYNHPDMATLSKEEIYDQINQTNEIIEATIGVTPK--WFAPPSGS 186 (268)
T ss_pred HHHHHHHHHCC-CEEEecCCcCCCcccCCHHHHHHHHHHHHHHHHHHhCCCCC--EEECCCCC
Confidence 456 8999999 59999999999999999999999999999999999999887 56667775
No 12
>TIGR02884 spore_pdaA delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production.
Probab=95.71 E-value=0.054 Score=37.64 Aligned_cols=59 Identities=10% Similarity=-0.036 Sum_probs=50.5
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCC-CCceeecCCCCC
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVK-PRYLHNNSRTIS 72 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~-P~~~W~~D~Fg~ 72 (75)
.+. ++++++| .||.+.+|..++....+.+.+.++|....+.|.+..|.. |+ |---|+|.
T Consensus 79 p~~ir~i~~~G-heIgnHt~~H~~~~~ls~~~~~~ei~~~~~~i~~~~G~~~~~--~fR~P~G~ 139 (224)
T TIGR02884 79 PDLIKRMVDEG-HIVGNHSVHHPSLTAVNDEKFKEELTGVEEEFKKVTGQKEMK--YFRPPRGV 139 (224)
T ss_pred HHHHHHHHHcC-CEeeecCccCcCcccCCHHHHHHHHHHHHHHHHHHhCCCCCC--EEeCCCCC
Confidence 456 9999999 599999999999999999999999999999999999977 43 45556664
No 13
>COG1449 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=95.05 E-value=0.041 Score=44.10 Aligned_cols=60 Identities=17% Similarity=0.155 Sum_probs=52.6
Q ss_pred CChhhh-HHHHhcCceEEEcceeeeeccCCCCHH----HHHHHHHHHHHHHHhhhCCCCCceeec
Q psy11172 8 PNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHYY----SMIQQLTHGQQWLLTNIGVKPRYLHNN 67 (75)
Q Consensus 8 ~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~----~~i~Q~~~G~~fl~~~fg~~P~~~W~~ 67 (75)
+..-+. |+++++|+.|++.--+..+=.++..-. ++++|+..+....++.||+.|++.|.+
T Consensus 179 ~~vl~~~r~l~e~g~~e~~~~pyyHsl~pl~~d~gw~~d~~~qv~~~~~~~~elfG~~p~~~~~t 243 (615)
T COG1449 179 PRVLEAFRELAESGKVELTASPYYHSLIPLLADDGWYEDFKEQVMMSRELYKELFGVWPSGFWNT 243 (615)
T ss_pred hhhHHHHHHHHhcCceEEEecccccccchhcccCCchHHHHHHHHHHHHHHHHHhCCCCccccCh
Confidence 345567 899999999999999998877666655 999999999999999999999999975
No 14
>TIGR03006 pepcterm_polyde polysaccharide deactylase family protein, PEP-CTERM locus subfamily. Members of this protein family belong to the family of polysaccharide deacetylases (pfam01522). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. The highest scoring homologs below the trusted cutoff for this model are found in several species of Methanosarcina, an archaeal genus.
Probab=94.62 E-value=0.19 Score=36.26 Aligned_cols=55 Identities=13% Similarity=0.118 Sum_probs=48.0
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeec
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNN 67 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~ 67 (75)
.+. ++++++| .||.+.||...+....+-+.+.++|....+.|++..|..|+ +|..
T Consensus 57 p~lir~i~~~G-hEIgsHg~sH~~l~~ls~ee~~~eI~~s~~~Le~itG~~~~-gfRa 112 (265)
T TIGR03006 57 PELVRRIVAAG-HELASHGYGHERVTTQTPEAFRADIRRSKALLEDLSGQPVR-GYRA 112 (265)
T ss_pred HHHHHHHHHcC-CEeeeccccCcCchhCCHHHHHHHHHHHHHHHHHHhCCCce-EEEC
Confidence 456 9999999 59999999999888888899999999999999999998876 4543
No 15
>COG1543 Uncharacterized conserved protein [Function unknown]
Probab=94.13 E-value=0.05 Score=42.91 Aligned_cols=61 Identities=18% Similarity=0.099 Sum_probs=50.3
Q ss_pred CCChhhh-HHHHhcCceEEEcceeeeeccCCCCH-HHHHHHHHHHHHHHHhhhCCCCCceeec
Q psy11172 7 IPNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHY-YSMIQQLTHGQQWLLTNIGVKPRYLHNN 67 (75)
Q Consensus 7 ~~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~-~~~i~Q~~~G~~fl~~~fg~~P~~~W~~ 67 (75)
+.+.-.. |++.++|.+||++.+-+.-=...--. +++=.|+..|.+=-.++||..|+.-|.+
T Consensus 122 d~~ll~~f~~~~~~g~ieilts~athg~lPll~~peAi~AQi~~g~~~ye~~fg~~P~GiWlP 184 (504)
T COG1543 122 DGNLLEAFKELQRSGGIEILTSAATHGYLPLLGGPEAIEAQILTGIELYEEHFGLAPKGIWLP 184 (504)
T ss_pred hHHHHHHHHHHHHcCCceeeeehhhheehhhcCCchhhHHHHHHHHHHHHHHhCCCCCceech
Confidence 3445667 99999999999988776654444444 7888999999999999999999999987
No 16
>TIGR03212 uraD_N-term-dom putative urate catabolism protein. This model represents a protein that is predominantly found just upstream of the UraD protein (OHCU decarboxylase) and in a number of instances as a N-terminal fusion with it. UraD itself catalyzes the last step in the catabolism of urate to allantoate. The function of this protein is presently unknown. It shows homology with the pfam01522 polysaccharide deacetylase domain family.
Probab=93.77 E-value=0.2 Score=36.70 Aligned_cols=54 Identities=13% Similarity=0.118 Sum_probs=47.3
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceee
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHN 66 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~ 66 (75)
-++ ++++++| .||.+.||...+...-+.+...++|....+-|++..|.+|. ||.
T Consensus 106 P~~v~~i~~~G-HEIg~Hg~~H~~~~~ls~~~e~~~i~~s~~~i~~~tG~~P~-G~~ 160 (297)
T TIGR03212 106 PEAVAAMKEAG-WEIASHGLRWIDYQDMDEAQEREHIAEAIRLHTEVTGERPL-GWY 160 (297)
T ss_pred HHHHHHHHHcC-CEEeeccccCcccccCCHHHHHHHHHHHHHHHHHHhCCCCc-eEE
Confidence 456 8899999 99999999998888888899999999999999999998765 454
No 17
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=88.69 E-value=0.28 Score=28.29 Aligned_cols=20 Identities=30% Similarity=0.491 Sum_probs=15.0
Q ss_pred hhhh-HHHHhcCceEEEccee
Q psy11172 10 HKPI-VSLVKSGQLEIVTGGW 29 (75)
Q Consensus 10 ~k~~-k~lV~~GqlE~v~GgW 29 (75)
.++- .++|++|++|++||-|
T Consensus 38 L~~fL~~lv~e~~L~~~~G~Y 58 (60)
T PF08672_consen 38 LQEFLDRLVEEGKLECSGGSY 58 (60)
T ss_dssp HHHHHHHHHHTTSEE--TTEE
T ss_pred HHHHHHHHHHCCcEEecCCEE
Confidence 4566 8999999999998876
No 18
>PRK15394 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional
Probab=85.40 E-value=2.2 Score=31.38 Aligned_cols=51 Identities=20% Similarity=0.176 Sum_probs=42.3
Q ss_pred hhh-HHHHhcCceEEEcceeeeec----cCCCCHHHHHHHHHHHHHHHHhhhCCCCCc
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTD----EANSHYYSMIQQLTHGQQWLLTNIGVKPRY 63 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~D----ea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~ 63 (75)
-++ ++.+++ -||.+.||.... ...-+-+.+.++|..+.+-|++..|.+|+.
T Consensus 91 P~lvr~i~~~--HEIG~Hg~~H~~wq~~~~~ls~~e~~~eI~ra~~~Le~itG~~p~g 146 (296)
T PRK15394 91 ADIIREAAKA--HEVGLHAWDHHAWQAWSGVWSRQQLIEQIARGVDALEEIIGQPVTC 146 (296)
T ss_pred HHHHHHHHhc--CEehhcccCccchhcccccCCHHHHHHHHHHHHHHHHHHhCCCCCE
Confidence 455 777777 999999999873 455677889999999999999999988753
No 19
>PRK14581 hmsF outer membrane N-deacetylase; Provisional
Probab=85.29 E-value=2.5 Score=34.63 Aligned_cols=59 Identities=19% Similarity=0.154 Sum_probs=44.4
Q ss_pred hh-HHHHhcCceEEEcceeeeeccC--------------------CCCHH-------HHHHHHHHHHHHHHhhhCCCCCc
Q psy11172 12 PI-VSLVKSGQLEIVTGGWVMTDEA--------------------NSHYY-------SMIQQLTHGQQWLLTNIGVKPRY 63 (75)
Q Consensus 12 ~~-k~lV~~GqlE~v~GgWv~~Dea--------------------~~~~~-------~~i~Q~~~G~~fl~~~fg~~P~~ 63 (75)
+. |+++++|-+||.+.++..+... +..|+ .+.+.+....+.|++..|..|+.
T Consensus 168 ~qIrEM~~sGLvEIGSHT~sHh~~~~~np~g~~~pa~~~~~y~~~~~~yEs~~~~~~rl~~Di~~s~~~Ie~~lG~~p~~ 247 (672)
T PRK14581 168 KQITEMSKSGLVEIGAHTYASHYGVIANPQGNTEPAAANLQYDPKTKQYETVEAFKQRMEKDVALITQRIVQATGKQPRV 247 (672)
T ss_pred HHHHHHHHCCCcEEEcCCcccccccccCccccccchhhhccccccccccccHHHHHHHHHHHHHHHHHHHHHHhCCCCCE
Confidence 35 9999999999999999887421 11233 25567888999999999998885
Q ss_pred eeecCCCCC
Q psy11172 64 LHNNSRTIS 72 (75)
Q Consensus 64 ~W~~D~Fg~ 72 (75)
-+=|||.
T Consensus 248 --FayPyG~ 254 (672)
T PRK14581 248 --WVWPYGA 254 (672)
T ss_pred --EEcCCCC
Confidence 4466775
No 20
>COG0383 AMS1 Alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=82.93 E-value=0.24 Score=41.57 Aligned_cols=65 Identities=18% Similarity=-0.059 Sum_probs=58.4
Q ss_pred CCChhhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCceeecCCCCCC
Q psy11172 7 IPNHKPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSRTISS 73 (75)
Q Consensus 7 ~~~~k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s 73 (75)
.|+.+++ +.+++.|++.+.-. +...|.+.++.++.++.+..|..+..+.. ..-+.|+.+|+||+.
T Consensus 65 ~~~~~~~~~~~~~~~~l~ig~~-~~~~~~~~~~~e~~~rn~l~~~~~~~~~~-~~~~~g~~~d~~g~~ 130 (943)
T COG0383 65 PPELKDRVKLLIASGKLGIGPW-YTQTDTFILSGESNVRNLLIGEFDAERFG-KAMKLGYFPDTFGNL 130 (943)
T ss_pred cccchhhHHHHHhhcCccccCC-CCeeEEEEeccccceeeeecchHHHHHhh-hhhccccccccchhh
Confidence 4566678 99999999998877 99999999999999999999999988877 889999999999974
No 21
>PRK14582 pgaB outer membrane N-deacetylase; Provisional
Probab=78.36 E-value=6.7 Score=32.16 Aligned_cols=59 Identities=19% Similarity=0.190 Sum_probs=43.9
Q ss_pred hh-HHHHhcCceEEEcceeeeecc--CC------------------CCH-------HHHHHHHHHHHHHHHhhhCCCCCc
Q psy11172 12 PI-VSLVKSGQLEIVTGGWVMTDE--AN------------------SHY-------YSMIQQLTHGQQWLLTNIGVKPRY 63 (75)
Q Consensus 12 ~~-k~lV~~GqlE~v~GgWv~~De--a~------------------~~~-------~~~i~Q~~~G~~fl~~~fg~~P~~ 63 (75)
+. |+++++|-+||-+.++-.|.. ++ ..| +.+.+.|....+.|++..|..|+.
T Consensus 168 eqIreM~~sGlvEIGSHT~~sH~~l~anp~g~~~pa~~~r~~~~~~~~yEs~~e~~~ri~~DL~~s~~~Ie~~tG~~p~~ 247 (671)
T PRK14582 168 QQVREVARSRLVEIASHTWNSHYGIQANPQGSLLPAAVNRAYFTDHARYETAAEYRERIRLDAVKMTEYIRTKAGKNPRV 247 (671)
T ss_pred HHHHHHHhCCCeEEEcCCchhccccccccccccccchhcccccccccccccHHHHHHHHHHHHHHHHHHHHHHhCCCCcE
Confidence 45 999999999999999964431 11 122 225678999999999999999886
Q ss_pred eeecCCCCC
Q psy11172 64 LHNNSRTIS 72 (75)
Q Consensus 64 ~W~~D~Fg~ 72 (75)
-.=|||.
T Consensus 248 --FayPyG~ 254 (671)
T PRK14582 248 --WVWPYGE 254 (671)
T ss_pred --EecCCCC
Confidence 4556764
No 22
>PHA02100 hypothetical protein
Probab=72.41 E-value=2.9 Score=26.76 Aligned_cols=17 Identities=18% Similarity=0.362 Sum_probs=14.3
Q ss_pred HHHHHhhhCCCCCceeecCCCCCCC
Q psy11172 50 QQWLLTNIGVKPRYLHNNSRTISSP 74 (75)
Q Consensus 50 ~~fl~~~fg~~P~~~W~~D~Fg~s~ 74 (75)
.|||.++||+. +|||.|
T Consensus 64 VQYIl~EFd~q--------AfGhtp 80 (112)
T PHA02100 64 VQYISEEFGTQ--------ALGHTP 80 (112)
T ss_pred HHHHHHHhCcc--------ccCCCC
Confidence 58999999975 588887
No 23
>PF10720 DUF2515: Protein of unknown function (DUF2515); InterPro: IPR019658 This family is conserved in Firmicutes. Several members are annotated as YppC. The function is not known.
Probab=58.43 E-value=6.1 Score=29.72 Aligned_cols=28 Identities=21% Similarity=0.370 Sum_probs=22.3
Q ss_pred cceeeeeccCCCCHHHHHHHHHHHHHHH
Q psy11172 26 TGGWVMTDEANSHYYSMIQQLTHGQQWL 53 (75)
Q Consensus 26 ~GgWv~~Dea~~~~~~~i~Q~~~G~~fl 53 (75)
||||-|+|....-+..++..-..-.-|+
T Consensus 45 N~GWnMTDL~g~~~~~lL~~~~~~~~F~ 72 (308)
T PF10720_consen 45 NAGWNMTDLKGELLPRLLSEEEREWLFL 72 (308)
T ss_pred cCCccchhcCcchhhhhcCHHHHHHHHH
Confidence 8999999999999988887665544443
No 24
>PRK10148 hypothetical protein; Provisional
Probab=55.86 E-value=6 Score=25.85 Aligned_cols=13 Identities=0% Similarity=-0.166 Sum_probs=11.6
Q ss_pred CCceeecCCCCCC
Q psy11172 61 PRYLHNNSRTISS 73 (75)
Q Consensus 61 P~~~W~~D~Fg~s 73 (75)
++.||..|+||++
T Consensus 123 ~~~g~v~D~fGi~ 135 (147)
T PRK10148 123 HGFGKVTDKFGVP 135 (147)
T ss_pred hccEEEECCCCCE
Confidence 5889999999985
No 25
>PF06526 DUF1107: Protein of unknown function (DUF1107); InterPro: IPR009491 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2JRO_A.
Probab=55.13 E-value=16 Score=21.53 Aligned_cols=31 Identities=16% Similarity=0.366 Sum_probs=22.1
Q ss_pred cCceEEEcceeeeeccCCCCHHHHHHHHHHH
Q psy11172 19 SGQLEIVTGGWVMTDEANSHYYSMIQQLTHG 49 (75)
Q Consensus 19 ~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G 49 (75)
-|.+||-+|--++|+.+.+-..+++.++-.-
T Consensus 29 ~G~feFd~Gkillp~~~~~~~~~~~~EiN~~ 59 (64)
T PF06526_consen 29 IGAFEFDNGKILLPKKADKRHLSVMSEINQE 59 (64)
T ss_dssp TEEEEEETTEE---SS--HHHHHHHHHHHHH
T ss_pred cccEEEcCCEEeCCccccHHHHHHHHHHHHH
Confidence 5889999999999999999998888877543
No 26
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=47.71 E-value=18 Score=19.57 Aligned_cols=14 Identities=29% Similarity=0.482 Sum_probs=11.5
Q ss_pred HHHHhcCceEEEcc
Q psy11172 14 VSLVKSGQLEIVTG 27 (75)
Q Consensus 14 k~lV~~GqlE~v~G 27 (75)
..||++|-+|+|+-
T Consensus 2 ~~ll~~G~vE~id~ 15 (48)
T PF04567_consen 2 DDLLKEGVVEYIDA 15 (48)
T ss_dssp HHHHHTTSEEEEET
T ss_pred hhHhhCCCEEEecc
Confidence 36899999999863
No 27
>COG0726 CDA1 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]
Probab=47.59 E-value=44 Score=22.10 Aligned_cols=48 Identities=17% Similarity=0.213 Sum_probs=40.9
Q ss_pred HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCC
Q psy11172 14 VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62 (75)
Q Consensus 14 k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~ 62 (75)
++.++ .-.|+.+.+|-..+....+...+..+|...+..|.+..|.+|+
T Consensus 111 ~~~~~-~Gheig~H~~~h~~~~~~~~~~~~~~i~~~~~~l~~~~g~~~~ 158 (267)
T COG0726 111 KRIAE-AGHEIGNHGYDHPDLQDLSLEELGAEIARAHDILKKITGGRPR 158 (267)
T ss_pred HHHHh-ccCeehhCcccCCCcccCCHHHHHHHHHHHHHHHHHHhCCCCc
Confidence 44444 4468999999999999999999999999999999999998643
No 28
>PF13249 Prenyltrans_2: Prenyltransferase-like; PDB: 1O6R_B 1O6Q_B 1H35_C 1H3A_C 1SQC_A 1UMP_A 1O6H_C 1O79_B 1GSZ_C 1H37_C ....
Probab=47.53 E-value=22 Score=20.93 Aligned_cols=24 Identities=21% Similarity=0.375 Sum_probs=19.3
Q ss_pred HHHHHHhhhCCCCCceeecCCCCCCC
Q psy11172 49 GQQWLLTNIGVKPRYLHNNSRTISSP 74 (75)
Q Consensus 49 G~~fl~~~fg~~P~~~W~~D~Fg~s~ 74 (75)
|.+||.+... |..+|...++|+.+
T Consensus 47 ~~~~L~~~q~--~dGg~~~~~~~~~~ 70 (113)
T PF13249_consen 47 AVEWLLSQQN--PDGGWGSNPDGGPP 70 (113)
T ss_dssp HHHHHHHHB---TTSGBBSSTTTT-B
T ss_pred HHHHHHHhCC--CCCCccCCCCCCCc
Confidence 6999999776 99999999988765
No 29
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=47.09 E-value=17 Score=22.83 Aligned_cols=18 Identities=33% Similarity=0.296 Sum_probs=14.8
Q ss_pred HHHHhcCceEEEcceeee
Q psy11172 14 VSLVKSGQLEIVTGGWVM 31 (75)
Q Consensus 14 k~lV~~GqlE~v~GgWv~ 31 (75)
+.||++|+||+.|-.=-|
T Consensus 89 ~~Li~~G~le~~g~~~~m 106 (111)
T PF12395_consen 89 RELISQGVLEIKGDPKDM 106 (111)
T ss_pred HHHHHCCCEEEecCCCcc
Confidence 899999999998755444
No 30
>cd04693 Nudix_Hydrolase_34 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=44.22 E-value=17 Score=22.21 Aligned_cols=34 Identities=18% Similarity=0.359 Sum_probs=25.9
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCC
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P 61 (75)
.-|.+++..||.+.+.|.. ++.++.+ +++.|+.+
T Consensus 26 ~pg~w~~p~GG~ve~gE~~---~aa~REl-------~EEtGl~~ 59 (127)
T cd04693 26 WPGMWDLSVGGHVQAGETS---TAAEREV-------KEELGLEL 59 (127)
T ss_pred CCCcccccCCCcCCCCCCH---HHHHHHH-------HHHhCCCc
Confidence 3489999879999999975 8887776 66677654
No 31
>KOG2165|consensus
Probab=43.24 E-value=17 Score=30.36 Aligned_cols=19 Identities=26% Similarity=0.613 Sum_probs=16.5
Q ss_pred hhh-HHHHhcCceEEEccee
Q psy11172 11 KPI-VSLVKSGQLEIVTGGW 29 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgW 29 (75)
+.- +++|++|+|+|++|.|
T Consensus 742 ~~fLq~kV~e~kL~f~~G~Y 761 (765)
T KOG2165|consen 742 QGFLQRKVREGKLEFIAGSY 761 (765)
T ss_pred HHHHHHHhhccceEEeccee
Confidence 444 7999999999999987
No 32
>KOG0402|consensus
Probab=42.65 E-value=21 Score=22.36 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=23.0
Q ss_pred EEEcceeeeeccCCCCHHHHHHHHHH
Q psy11172 23 EIVTGGWVMTDEANSHYYSMIQQLTH 48 (75)
Q Consensus 23 E~v~GgWv~~Dea~~~~~~~i~Q~~~ 48 (75)
-+.||.|+.+-.|..+..+.|+++.+
T Consensus 63 v~agga~~~~t~aa~t~rs~irrlre 88 (92)
T KOG0402|consen 63 VVAGGAYTVTTAAAATVRSTIRRLRE 88 (92)
T ss_pred eeccceEEeccchhHHHHHHHHHHHH
Confidence 46899999999999999999999865
No 33
>PRK15472 nucleoside triphosphatase NudI; Provisional
Probab=42.26 E-value=19 Score=22.46 Aligned_cols=27 Identities=22% Similarity=0.297 Sum_probs=19.9
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHHH
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQLT 47 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~ 47 (75)
-.|.|++.||+ |+++|. .-+++++.+.
T Consensus 29 ~~g~W~lPgG~-ve~gEs--~~~aa~REl~ 55 (141)
T PRK15472 29 FPGQWALSGGG-VEPGER--IEEALRREIR 55 (141)
T ss_pred CCCceeCCccc-CCCCCC--HHHHHHHHHH
Confidence 35999999755 999984 5577777663
No 34
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=40.79 E-value=13 Score=22.90 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=20.4
Q ss_pred CCCCCCChhhh-HHHHhcCceEEEcceee
Q psy11172 3 WSGEIPNHKPI-VSLVKSGQLEIVTGGWV 30 (75)
Q Consensus 3 w~~~~~~~k~~-k~lV~~GqlE~v~GgWv 30 (75)
|.+.-+..++. ..|+++|+++|.=+|=+
T Consensus 39 WR~lm~~vR~~A~~L~~~G~i~I~qkG~~ 67 (83)
T PF11625_consen 39 WRDLMPPVRAAARRLARAGRIEITQKGKP 67 (83)
T ss_dssp -GGGHHHHHHHHHHHHHTTSEEEEETTEE
T ss_pred hHHHHHHHHHHHHHHHHCCcEEEEECCEe
Confidence 33444455677 89999999999877754
No 35
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=40.55 E-value=20 Score=23.85 Aligned_cols=16 Identities=19% Similarity=0.438 Sum_probs=13.5
Q ss_pred hhHHHHhcCceEEEcc
Q psy11172 12 PIVSLVKSGQLEIVTG 27 (75)
Q Consensus 12 ~~k~lV~~GqlE~v~G 27 (75)
.+.++|++|||++...
T Consensus 62 ~I~~~IreGRL~~~~~ 77 (137)
T TIGR03826 62 LILKFIREGRLQLKHF 77 (137)
T ss_pred HHHHHHHcCCeeccCC
Confidence 3389999999999864
No 36
>PF08557 Lipid_DES: Sphingolipid Delta4-desaturase (DES); InterPro: IPR013866 Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine []. Some proteins in this entry have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis []. This small protein associates with FA_desaturase IPR005804 from INTERPRO and appears to be specific to sphingolipid delta 4-desaturase. ; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0006633 fatty acid biosynthetic process, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=40.26 E-value=54 Score=17.45 Aligned_cols=32 Identities=25% Similarity=0.337 Sum_probs=24.7
Q ss_pred eeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCc
Q psy11172 29 WVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRY 63 (75)
Q Consensus 29 Wv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~ 63 (75)
||..||. ....-.+|+.-|-=|++-||..|.+
T Consensus 8 W~~~~eP---H~~RRk~IL~k~PeIk~L~G~dp~t 39 (39)
T PF08557_consen 8 WVYTDEP---HASRRKEILKKHPEIKKLMGPDPLT 39 (39)
T ss_pred EeCCCCc---cHHHHHHHHHhChHHHHHhCCCCCC
Confidence 7777774 5667778888888899999988853
No 37
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=36.93 E-value=33 Score=27.49 Aligned_cols=26 Identities=12% Similarity=0.210 Sum_probs=21.5
Q ss_pred HHHHHhhhCCCCCc---------eeecCCCCCCCC
Q psy11172 50 QQWLLTNIGVKPRY---------LHNNSRTISSPH 75 (75)
Q Consensus 50 ~~fl~~~fg~~P~~---------~W~~D~Fg~s~~ 75 (75)
.+-..+.+|++|+. .|+--+|||.|.
T Consensus 385 n~kme~yLGirp~~d~eG~LQDIHWs~GsfGYFPs 419 (497)
T COG2317 385 NDKMEEYLGIRPKNDAEGVLQDIHWSHGSFGYFPT 419 (497)
T ss_pred HHHHHHHcCCCCCCccccccccccccCCCcCcCch
Confidence 35567889999985 899999999983
No 38
>cd04672 Nudix_Hydrolase_14 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=35.41 E-value=30 Score=21.01 Aligned_cols=33 Identities=18% Similarity=0.403 Sum_probs=22.2
Q ss_pred cCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCC
Q psy11172 19 SGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61 (75)
Q Consensus 19 ~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P 61 (75)
.|.+++. ||+|+++| +.-++.++.+ +++.|+..
T Consensus 23 ~~~w~~P-GG~ve~gE--s~~~aa~REl-------~EEtG~~~ 55 (123)
T cd04672 23 DGLWSLP-GGWADVGL--SPAENVVKEV-------KEETGLDV 55 (123)
T ss_pred CCcEeCC-ccccCCCC--CHHHHHHHHH-------HHHhCCee
Confidence 6788887 69999887 4556665554 55555433
No 39
>cd03428 Ap4A_hydrolase_human_like Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one subfamily and fungi/animals/archaea enzymes, represented by this subfamily, fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val) that functions as a metal binding and
Probab=35.21 E-value=23 Score=21.46 Aligned_cols=25 Identities=16% Similarity=0.296 Sum_probs=18.4
Q ss_pred CceEEEcceeeeeccCCCCHHHHHHHHH
Q psy11172 20 GQLEIVTGGWVMTDEANSHYYSMIQQLT 47 (75)
Q Consensus 20 GqlE~v~GgWv~~Dea~~~~~~~i~Q~~ 47 (75)
|++++. ||.++++| +.-++.++.+.
T Consensus 27 ~~w~~P-gG~ve~gE--s~~~aa~REl~ 51 (130)
T cd03428 27 GHWDFP-KGHVEPGE--DDLEAALRETE 51 (130)
T ss_pred CcCcCC-cCCCCCCC--CHHHHHHHHHH
Confidence 899987 66689988 45577777653
No 40
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=35.03 E-value=44 Score=19.32 Aligned_cols=16 Identities=31% Similarity=0.245 Sum_probs=14.1
Q ss_pred hhh-HHHHhcCceEEEc
Q psy11172 11 KPI-VSLVKSGQLEIVT 26 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~ 26 (75)
+.. +++|++|+|+-+.
T Consensus 49 ~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 49 KRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHHHHHCTSEEECS
T ss_pred HHHHHHHHHCCcEEeec
Confidence 455 9999999999998
No 41
>PF04424 DUF544: Protein of unknown function (DUF544) ; InterPro: IPR007518 This is a eukaryotic protein of unknown function.
Probab=34.99 E-value=26 Score=22.38 Aligned_cols=19 Identities=5% Similarity=-0.246 Sum_probs=16.0
Q ss_pred HHhhhCCCCCceeecCCCC
Q psy11172 53 LLTNIGVKPRYLHNNSRTI 71 (75)
Q Consensus 53 l~~~fg~~P~~~W~~D~Fg 71 (75)
|.+-||++-.-||.+||--
T Consensus 81 lFdl~~I~LvHGWl~dp~~ 99 (121)
T PF04424_consen 81 LFDLFNIPLVHGWLVDPQD 99 (121)
T ss_pred hHHhhCCCceeeeccCCCC
Confidence 5778899999999999854
No 42
>smart00526 H15 Domain in histone families 1 and 5.
Probab=32.92 E-value=38 Score=18.94 Aligned_cols=17 Identities=47% Similarity=0.513 Sum_probs=13.7
Q ss_pred hhh-HHHHhcCceEEEcc
Q psy11172 11 KPI-VSLVKSGQLEIVTG 27 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~G 27 (75)
+.. +++|++|.|+-+.|
T Consensus 49 ~~~Lk~~v~~G~l~q~kg 66 (66)
T smart00526 49 KLALKKLVASGKLVQVKG 66 (66)
T ss_pred HHHHHHHHhcCceeecCC
Confidence 345 89999999998765
No 43
>PF05005 Ocnus: Janus/Ocnus family (Ocnus); InterPro: IPR007702 This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster [].; PDB: 2OZX_A 2OZW_A 2NMM_C 2AI6_A 2HW4_A.
Probab=32.88 E-value=40 Score=21.54 Aligned_cols=23 Identities=30% Similarity=0.360 Sum_probs=17.3
Q ss_pred HHHHhcC-ceEEEcceeeeeccCC
Q psy11172 14 VSLVKSG-QLEIVTGGWVMTDEAN 36 (75)
Q Consensus 14 k~lV~~G-qlE~v~GgWv~~Dea~ 36 (75)
+.+-+.| +.|.+|||.+.+|...
T Consensus 52 ~el~~~gl~~~clGGGrI~hd~~~ 75 (108)
T PF05005_consen 52 EELEKLGLCTECLGGGRIEHDPDK 75 (108)
T ss_dssp HHHHHCTEEEEEEEEEEEEEETTT
T ss_pred HHHHHcCCeEEEeCCcEEEeCCCC
Confidence 3444445 7899999999999763
No 44
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=32.55 E-value=77 Score=17.28 Aligned_cols=24 Identities=29% Similarity=0.497 Sum_probs=20.3
Q ss_pred hhhHHHHhcCceEEEcceeeeecc
Q psy11172 11 KPIVSLVKSGQLEIVTGGWVMTDE 34 (75)
Q Consensus 11 k~~k~lV~~GqlE~v~GgWv~~De 34 (75)
++...|.+.|.+.-+-||.+-.|+
T Consensus 33 RDl~~L~~~g~i~r~~GG~~~~~~ 56 (57)
T PF08220_consen 33 RDLNKLEKQGLIKRTHGGAVLNDS 56 (57)
T ss_pred HHHHHHHHCCCEEEEcCEEEeCCC
Confidence 344899999999999999988764
No 45
>COG4002 Predicted phosphotransacetylase [General function prediction only]
Probab=31.43 E-value=82 Score=23.04 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=26.3
Q ss_pred ccCCCCHHHHHHHHHHHHHHHHhhhCCCCCcee
Q psy11172 33 DEANSHYYSMIQQLTHGQQWLLTNIGVKPRYLH 65 (75)
Q Consensus 33 Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W 65 (75)
||-. .-+|.++-+..+-+||++ .|+.|+++=
T Consensus 112 DEg~-ti~dk~ri~~laaeflrr-~~~ep~VaV 142 (256)
T COG4002 112 DEGK-TIKDKIRIIELAAEFLRR-TGIEPKVAV 142 (256)
T ss_pred CCCc-cHHHHHHHHHHHHHHHHH-hCCCcceEE
Confidence 5544 678999999999999998 999999863
No 46
>TIGR01322 scrB_fam sucrose-6-phosphate hydrolase.
Probab=31.33 E-value=22 Score=27.01 Aligned_cols=19 Identities=11% Similarity=-0.036 Sum_probs=16.2
Q ss_pred HhhhCCCCCceeecCCCCC
Q psy11172 54 LTNIGVKPRYLHNNSRTIS 72 (75)
Q Consensus 54 ~~~fg~~P~~~W~~D~Fg~ 72 (75)
+-.|.++|..+|.+||-|.
T Consensus 14 rp~~H~~p~~gw~nDPng~ 32 (445)
T TIGR01322 14 RPTFHIQPQTGLLNDPNGL 32 (445)
T ss_pred CccCccCCCcCCccCCCcc
Confidence 4567789999999999885
No 47
>cd04697 Nudix_Hydrolase_38 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=31.29 E-value=36 Score=20.88 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=25.1
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCC
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~ 62 (75)
..|.+++.-||.++++|. .-++.++. ++++.|+.+.
T Consensus 26 ~~g~w~~~~GG~ve~gE~--~~~aa~RE-------l~EEtGl~~~ 61 (126)
T cd04697 26 CPGYWDIAFGGVVQAGES--YLQNAQRE-------LEEELGIDGV 61 (126)
T ss_pred CCCcccCcCCcccCCCCC--HHHHHHHH-------HHHHHCCCcc
Confidence 468899977999998885 34555555 4667776554
No 48
>COG0280 Pta Phosphotransacetylase [Energy production and conversion]
Probab=31.11 E-value=1.9e+02 Score=21.92 Aligned_cols=47 Identities=13% Similarity=0.087 Sum_probs=33.9
Q ss_pred cceeeeeccCCCCH--HHHHHHHHHHHHHHHhhhCCCCCceeecC-CCCC
Q psy11172 26 TGGWVMTDEANSHY--YSMIQQLTHGQQWLLTNIGVKPRYLHNNS-RTIS 72 (75)
Q Consensus 26 ~GgWv~~Dea~~~~--~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D-~Fg~ 72 (75)
++-.+..|+|+..+ -..+.+|+.----..+.||+.||++-+-- +||+
T Consensus 159 ~~~l~~~D~avn~~PtaeeladIa~~sa~~a~~fgi~PkVAlLS~St~gs 208 (327)
T COG0280 159 DGTLFFADCAVNPDPTAEELADIAENAAETARRFGIEPKVALLSYSTFGS 208 (327)
T ss_pred CceEEEEecccCCCCCHHHHHHHHHHHHHHHHHhCCCCceEEEEeecCCC
Confidence 45677889887544 44556677777778899999999987654 4444
No 49
>COG2994 HlyC ACP:hemolysin acyltransferase (hemolysin-activating protein) [Posttranslational modification, protein turnover, chaperones]
Probab=31.02 E-value=20 Score=24.39 Aligned_cols=12 Identities=25% Similarity=0.470 Sum_probs=8.5
Q ss_pred HHHHhcCceEEE
Q psy11172 14 VSLVKSGQLEIV 25 (75)
Q Consensus 14 k~lV~~GqlE~v 25 (75)
-..+++||+-+.
T Consensus 46 LPalk~~Qf~ly 57 (148)
T COG2994 46 LPALKLGQFALY 57 (148)
T ss_pred hHHHhcCceEEE
Confidence 456788888765
No 50
>PRK12862 malic enzyme; Reviewed
Probab=30.42 E-value=1.2e+02 Score=25.31 Aligned_cols=31 Identities=6% Similarity=0.085 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhhCCCCCceee
Q psy11172 35 ANSHYYSMIQQLTHGQQWLLTNIGVKPRYLHN 66 (75)
Q Consensus 35 a~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~ 66 (75)
..|+-+.+++-...+.+++++ ||+.||++=.
T Consensus 607 ~~pt~e~La~ia~~aa~~ar~-~GIePRVAvL 637 (763)
T PRK12862 607 EDPTAEELAEITILAAEEVRR-FGIEPKVALL 637 (763)
T ss_pred CCCCHHHHHHHHHHHHHHHHH-cCCCCeEEEE
Confidence 346678888888899999995 9999999876
No 51
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=30.13 E-value=91 Score=18.00 Aligned_cols=25 Identities=28% Similarity=0.494 Sum_probs=19.8
Q ss_pred hhh-HHHHhcCceEEE---cceeeeeccC
Q psy11172 11 KPI-VSLVKSGQLEIV---TGGWVMTDEA 35 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v---~GgWv~~Dea 35 (75)
+.. ++|+++|=++-. +|||.-...+
T Consensus 43 ~kil~~L~~~Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 43 RKILQKLKKAGLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp HHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred HHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence 556 999999999998 7898876544
No 52
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=29.29 E-value=1.1e+02 Score=20.41 Aligned_cols=53 Identities=19% Similarity=0.290 Sum_probs=34.0
Q ss_pred hhh-HHHHhcCceEEEcceeeee--------------c----cCCCCHHHHHHHHHH-----------HHHHHHhhhC--
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMT--------------D----EANSHYYSMIQQLTH-----------GQQWLLTNIG-- 58 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~--------------D----ea~~~~~~~i~Q~~~-----------G~~fl~~~fg-- 58 (75)
+.. ...+++|=++.-+|..+-+ | ..-+.++.+++-++. ...-++++||
T Consensus 40 k~li~~A~~eGLl~~~~~~l~~~Fd~~~v~iP~~FkP~~~~l~e~~~fe~ild~ia~~~g~~~~evv~~in~~q~~~~~~ 119 (144)
T PF09999_consen 40 KRLIDEAIEEGLLEEEGGYLVPNFDPSEVEIPLGFKPDEEILQERDPFERILDYIAAKTGIEKQEVVAEINELQEELGGL 119 (144)
T ss_pred HHHHHHHHHCCCeeecCCEEEEecCccccccCCCCCCcHHHHhcccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcc
Confidence 556 8899999999977777733 3 223455666665554 4445777777
Q ss_pred CCCCc
Q psy11172 59 VKPRY 63 (75)
Q Consensus 59 ~~P~~ 63 (75)
+.|++
T Consensus 120 l~~e~ 124 (144)
T PF09999_consen 120 LDPEA 124 (144)
T ss_pred CCHHH
Confidence 55543
No 53
>PF02074 Peptidase_M32: Carboxypeptidase Taq (M32) metallopeptidase; InterPro: IPR001333 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M32 (carboxypeptidase Taq family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. Carboxypeptidase Taq is a zinc-containing thermostable metallopeptidase. It was originally discovered and purified from Thermus aquaticus; optimal enzymatic activity occurs at 80 celcius. Although very little is known about this enzyme, it is thought either to be associated with a membrane or to be particle bound.; GO: 0004181 metallocarboxypeptidase activity, 0006508 proteolysis; PDB: 1K9X_A 1KA4_A 1KA2_A 3DWC_A 1WGZ_A 3HQ2_A 3HOA_B.
Probab=28.93 E-value=26 Score=27.76 Aligned_cols=24 Identities=13% Similarity=0.147 Sum_probs=15.4
Q ss_pred HHHHhhhCCCCC---------ceeecCCCCCCC
Q psy11172 51 QWLLTNIGVKPR---------YLHNNSRTISSP 74 (75)
Q Consensus 51 ~fl~~~fg~~P~---------~~W~~D~Fg~s~ 74 (75)
+-.++.||++|+ +.|+.-.|||.|
T Consensus 385 ~km~eyLGi~p~~d~eG~LQDvHWs~G~fGYFP 417 (494)
T PF02074_consen 385 EKMEEYLGITPPNDAEGVLQDVHWSSGSFGYFP 417 (494)
T ss_dssp HHHHHHHS---SSCTTTTTS-STTTTT-TS-TH
T ss_pred HHHHHHcCCCCCCCCccccccccccCCccccch
Confidence 456788999887 489999999987
No 54
>cd06588 PhnB_like Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates. The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to
Probab=27.85 E-value=34 Score=20.94 Aligned_cols=12 Identities=17% Similarity=-0.117 Sum_probs=10.6
Q ss_pred CceeecCCCCCC
Q psy11172 62 RYLHNNSRTISS 73 (75)
Q Consensus 62 ~~~W~~D~Fg~s 73 (75)
+.++-.||||+.
T Consensus 113 ~~~~v~Dp~G~~ 124 (128)
T cd06588 113 LFGWVTDRFGVS 124 (128)
T ss_pred ccEEEECCCCCE
Confidence 689999999985
No 55
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=27.51 E-value=24 Score=21.22 Aligned_cols=17 Identities=35% Similarity=0.622 Sum_probs=10.9
Q ss_pred hcCceEEEcceeeeecc
Q psy11172 18 KSGQLEIVTGGWVMTDE 34 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~De 34 (75)
.+-=+--|||||..-++
T Consensus 45 ~~~vMVRVGGGW~tL~~ 61 (73)
T PF02187_consen 45 RSHVMVRVGGGWDTLEE 61 (73)
T ss_dssp TTEEEEEETTEEEEHHH
T ss_pred CCEEEEEeCCcHHHHHH
Confidence 33344569999987443
No 56
>cd04677 Nudix_Hydrolase_18 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=27.16 E-value=66 Score=19.36 Aligned_cols=34 Identities=18% Similarity=0.273 Sum_probs=23.4
Q ss_pred cCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCC
Q psy11172 19 SGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62 (75)
Q Consensus 19 ~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~ 62 (75)
.|+++| -||+|+++|. ..+++++.+ +++.|+.+.
T Consensus 29 ~~~w~~-PgG~v~~gEt--~~~aa~REl-------~EE~Gi~~~ 62 (132)
T cd04677 29 TGDWGL-PGGAMELGES--LEETARREL-------KEETGLEVE 62 (132)
T ss_pred CCcEEC-CeeecCCCCC--HHHHHHHHH-------HHHhCCeee
Confidence 378887 4799999994 566666554 666775443
No 57
>PF05677 DUF818: Chlamydia CHLPS protein (DUF818); InterPro: IPR008536 This family of unknown function includes several Chlamydia CHLPS proteins and Legionella SidB proteins.
Probab=27.16 E-value=91 Score=24.10 Aligned_cols=50 Identities=10% Similarity=-0.017 Sum_probs=37.8
Q ss_pred eEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhh-CCCCCceeecCCCCCCC
Q psy11172 22 LEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNI-GVKPRYLHNNSRTISSP 74 (75)
Q Consensus 22 lE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~f-g~~P~~~W~~D~Fg~s~ 74 (75)
+-+.|--=|++-...++.++++.-.....+||+++. |+.|+. |=.+|||.
T Consensus 174 vl~fNYpGVg~S~G~~s~~dLv~~~~a~v~yL~d~~~G~ka~~---Ii~yG~SL 224 (365)
T PF05677_consen 174 VLVFNYPGVGSSTGPPSRKDLVKDYQACVRYLRDEEQGPKAKN---IILYGHSL 224 (365)
T ss_pred EEEECCCccccCCCCCCHHHHHHHHHHHHHHHHhcccCCChhe---EEEeeccc
Confidence 334444447777888889999999999999999877 778874 55677773
No 58
>PF00530 SRCR: Scavenger receptor cysteine-rich domain; InterPro: IPR001190 The egg peptide speract receptor is a transmembrane glycoprotein []. Other members of this family include the macrophage scavenger receptor type I (a membrane glycoprotein implicated in the pathologic deposition of cholesterol in arterial walls during artherogenesis), an enteropeptidase and T-cell surface glycoprotein CD5 (may act as a receptor in regulating T-cell proliferation).; GO: 0005044 scavenger receptor activity, 0016020 membrane; PDB: 2XRC_D 2JP0_A 2JOP_A 2OYA_A 2OY3_A 1BY2_A 2OTT_Y 2JA4_A.
Probab=26.60 E-value=33 Score=19.79 Aligned_cols=14 Identities=29% Similarity=0.760 Sum_probs=10.7
Q ss_pred hcCceEE-E-cceeee
Q psy11172 18 KSGQLEI-V-TGGWVM 31 (75)
Q Consensus 18 ~~GqlE~-v-~GgWv~ 31 (75)
.+|++|+ . +|.|--
T Consensus 7 ~~G~vev~~~~~~W~~ 22 (99)
T PF00530_consen 7 CEGRVEVCFYNGSWGT 22 (99)
T ss_dssp TEEEEEEEEETTEEEE
T ss_pred eeEEEEEEEECCEEEe
Confidence 4799999 6 888853
No 59
>COG1621 SacC Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism]
Probab=26.33 E-value=27 Score=27.71 Aligned_cols=20 Identities=10% Similarity=-0.154 Sum_probs=16.1
Q ss_pred HHhhhCCCCCceeecCCCCC
Q psy11172 53 LLTNIGVKPRYLHNNSRTIS 72 (75)
Q Consensus 53 l~~~fg~~P~~~W~~D~Fg~ 72 (75)
.+-.|.++|..||.+||=|.
T Consensus 28 ~Rp~yHftP~~G~mNDPNG~ 47 (486)
T COG1621 28 YRPQYHFTPPTGWLNDPNGL 47 (486)
T ss_pred CCceeeecCCcCceECCCce
Confidence 34556689999999999883
No 60
>cd04696 Nudix_Hydrolase_37 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=26.24 E-value=56 Score=19.74 Aligned_cols=33 Identities=21% Similarity=0.239 Sum_probs=23.1
Q ss_pred cCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCC
Q psy11172 19 SGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61 (75)
Q Consensus 19 ~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P 61 (75)
.|++++. ||.+.++|. ..++.++.+ +++.|+.+
T Consensus 25 ~~~w~lP-GG~ve~gEs--~~~aa~REl-------~EEtGl~~ 57 (125)
T cd04696 25 RGLWGVP-GGKVEWGET--LEEALKREF-------REETGLKL 57 (125)
T ss_pred CCcEeCC-ceeccCCCC--HHHHHHHHH-------HHHhCCcc
Confidence 5889975 888999884 567776665 55666543
No 61
>PF08218 Citrate_ly_lig: Citrate lyase ligase C-terminal domain; InterPro: IPR013166 [Citrate (pro-3S)-lyase] ligase (6.2.1.22 from EC), also known as citrate lyase ligase, is responsible for acetylation of the prosthetic group (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase. It converts the inactive thiol form of the enzyme to the active form. In Clostridium sphenoides, citrate lyase ligase actively degrades citrate. In Clostridium sporosphaeroides and Lactococcus lactis, however, the enzyme is under stringent regulatory control. The enzyme's activity in anaerobic bacteria is modulated by phosphorylation and dephosphorylation []. The proteins in this entry represent the C-terminal domain of citrate lyase ligase.; GO: 0008771 [citrate (pro-3S)-lyase] ligase activity
Probab=25.75 E-value=31 Score=24.17 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=9.4
Q ss_pred HHHHHHHHHhh
Q psy11172 46 LTHGQQWLLTN 56 (75)
Q Consensus 46 ~~~G~~fl~~~ 56 (75)
+|.||+||-++
T Consensus 11 FT~GH~yLiE~ 21 (182)
T PF08218_consen 11 FTLGHRYLIEQ 21 (182)
T ss_pred CccHHHHHHHH
Confidence 68999999875
No 62
>COG1347 NqrD Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD [Energy production and conversion]
Probab=25.37 E-value=41 Score=23.74 Aligned_cols=40 Identities=25% Similarity=0.421 Sum_probs=30.2
Q ss_pred HHHHhcCce-------EEEcceeeeeccC---CCCHHHHHHHHHHHHHHH
Q psy11172 14 VSLVKSGQL-------EIVTGGWVMTDEA---NSHYYSMIQQLTHGQQWL 53 (75)
Q Consensus 14 k~lV~~Gql-------E~v~GgWv~~Dea---~~~~~~~i~Q~~~G~~fl 53 (75)
|+|+-.|.+ ++.+|||.+||-. .|+-.=+|.=|..|.+-+
T Consensus 152 REL~G~Gkl~G~~v~~~i~~ggwy~pnGL~lLaPSAFFliG~~IW~~rt~ 201 (208)
T COG1347 152 RELFGSGKLFGFTVFPTIQDGGWYQPNGLFLLAPSAFFLIGFMIWGLRTW 201 (208)
T ss_pred HHHhccCceeeEEeeeeeccCcccCCCceEEeCchHHHHHHHHHHHHhcc
Confidence 788888876 6889999999964 466666777777776543
No 63
>cd03427 MTH1 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved nudix motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a m
Probab=25.35 E-value=64 Score=19.66 Aligned_cols=28 Identities=25% Similarity=0.194 Sum_probs=20.4
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHHHH
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQLTH 48 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~ 48 (75)
..|.+++. ||.|+.+| +.-+++++.+.+
T Consensus 24 ~~~~w~~P-gG~ve~gE--s~~~aa~RE~~E 51 (137)
T cd03427 24 GWGGWNGP-GGKVEPGE--TPEECAIRELKE 51 (137)
T ss_pred CCCeEeCC-ceeCCCCC--CHHHHHHHHHHH
Confidence 36778876 67888888 666777777643
No 64
>PRK01816 hypothetical protein; Provisional
Probab=24.97 E-value=1.5e+02 Score=19.98 Aligned_cols=40 Identities=18% Similarity=0.222 Sum_probs=29.6
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhh
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNI 57 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~f 57 (75)
.++ .+++++|.- +.+-++.|+|.++.+=+-.-.+-|-++|
T Consensus 99 ~el~~Kl~~~g~~-------~~p~~~~P~Y~dLA~lLk~Af~~ld~~f 139 (143)
T PRK01816 99 YEVREKLQEAGQA-------LAPVEGKPTYQALADLLKRAFKQLDKTF 139 (143)
T ss_pred HHHHHHHHHcCCc-------cCCCCCCCCHHHHHHHHHHHHHHcCHHH
Confidence 567 888888732 6778899999999988776665554444
No 65
>PRK05632 phosphate acetyltransferase; Reviewed
Probab=24.44 E-value=1.8e+02 Score=23.61 Aligned_cols=42 Identities=14% Similarity=0.059 Sum_probs=31.5
Q ss_pred ceeeeeccCC---CCHHHHHHHHHHHHHHHHhhhCCCCCceeecCC
Q psy11172 27 GGWVMTDEAN---SHYYSMIQQLTHGQQWLLTNIGVKPRYLHNNSR 69 (75)
Q Consensus 27 GgWv~~Dea~---~~~~~~i~Q~~~G~~fl~~~fg~~P~~~W~~D~ 69 (75)
+-.++.|++. |+-+.+++-...+-.+.+ .||+.||++-+.-+
T Consensus 521 ~~~~~~D~gvn~~P~~e~l~~ia~~aa~~a~-~~GiePkVAlLs~s 565 (684)
T PRK05632 521 QVLVYGDCAVNPDPTAEQLAEIAIQSADSAA-AFGIEPRVAMLSYS 565 (684)
T ss_pred ceEEEecCeeeCCCCHHHHHHHHHHHHHHHH-HhCCCCeEEEEecC
Confidence 3345556554 566888888888888888 89999999988543
No 66
>cd04681 Nudix_Hydrolase_22 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=24.30 E-value=73 Score=19.21 Aligned_cols=33 Identities=27% Similarity=0.526 Sum_probs=22.1
Q ss_pred cCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCC
Q psy11172 19 SGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61 (75)
Q Consensus 19 ~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P 61 (75)
.|.+++. ||.|+++|. .-++.++.+ +++.|+.+
T Consensus 26 ~~~w~~P-gG~ve~gEs--~~~aa~RE~-------~EEtGl~~ 58 (130)
T cd04681 26 KGTLDLP-GGFVDPGES--AEEALIREI-------REETGLKV 58 (130)
T ss_pred CCcEeCC-ceeecCCCC--HHHHHHHHH-------HHHhCCcc
Confidence 5889986 789999984 455555554 55556544
No 67
>KOG1290|consensus
Probab=24.08 E-value=79 Score=25.85 Aligned_cols=27 Identities=26% Similarity=0.432 Sum_probs=22.5
Q ss_pred CCHHHHHHHHHHHHHHHHhhhCC-----CCCc
Q psy11172 37 SHYYSMIQQLTHGQQWLLTNIGV-----KPRY 63 (75)
Q Consensus 37 ~~~~~~i~Q~~~G~~fl~~~fg~-----~P~~ 63 (75)
+.-..++.|+..|+.||.++.|+ +|..
T Consensus 187 ~~VK~I~~qvL~GLdYLH~ecgIIHTDlKPEN 218 (590)
T KOG1290|consen 187 SCVKEICRQVLTGLDYLHRECGIIHTDLKPEN 218 (590)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCccccCCCcce
Confidence 34578999999999999999994 6655
No 68
>PRK01909 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Validated
Probab=23.90 E-value=1.1e+02 Score=23.15 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=20.9
Q ss_pred CHHHHHHHHHHHHHHHHhhhCC-CCCce
Q psy11172 38 HYYSMIQQLTHGQQWLLTNIGV-KPRYL 64 (75)
Q Consensus 38 ~~~~~i~Q~~~G~~fl~~~fg~-~P~~~ 64 (75)
+-+.+++.+..-++.|++.||+ +||++
T Consensus 175 t~e~i~~~i~l~~~~l~~~~gi~~PrIa 202 (329)
T PRK01909 175 TIDGLVETLAIIDRDLRRDFGLAAPRIL 202 (329)
T ss_pred CHHHHHHHHHHHHHHHHHHhCCCCCCEE
Confidence 3466667777888999999996 89864
No 69
>PF15007 CEP44: Centrosomal spindle body, CEP44
Probab=23.78 E-value=57 Score=21.59 Aligned_cols=15 Identities=20% Similarity=0.211 Sum_probs=12.6
Q ss_pred HHHHHHhhhCCCCCc
Q psy11172 49 GQQWLLTNIGVKPRY 63 (75)
Q Consensus 49 G~~fl~~~fg~~P~~ 63 (75)
=-+.|++.||++|..
T Consensus 73 vyk~LRdef~YkP~l 87 (131)
T PF15007_consen 73 VYKLLRDEFNYKPSL 87 (131)
T ss_pred HHHHHHHHhCCCCCC
Confidence 357899999999975
No 70
>cd04670 Nudix_Hydrolase_12 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=23.77 E-value=63 Score=19.54 Aligned_cols=34 Identities=18% Similarity=0.403 Sum_probs=23.2
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCC
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P 61 (75)
..|.+++- ||.|+++| +.-++.++.+ +++.|+..
T Consensus 25 ~~~~w~~P-GG~ve~gE--t~~~aa~RE~-------~EE~Gl~~ 58 (127)
T cd04670 25 TPNGWKLP-GGLVDPGE--DIFDGAVREV-------LEETGIDT 58 (127)
T ss_pred CCCcEECC-CccCCCCC--CHHHHHHHHH-------HHHHCCCc
Confidence 46889985 88888888 4555666554 56666544
No 71
>PF04217 DUF412: Protein of unknown function, DUF412; InterPro: IPR007334 This family consists of bacterial uncharacterised proteins.
Probab=23.55 E-value=2.4e+02 Score=18.99 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=31.6
Q ss_pred hhh-HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhh
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNI 57 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~f 57 (75)
.++ ++++++|.- +.+-++.|.|.|+.+=+-.-.+-|-+.|
T Consensus 100 ~ei~~Kl~~~g~~-------~~~~~~~P~Y~dLA~lL~~Af~~LDk~f 140 (143)
T PF04217_consen 100 HEIRQKLQEQGIA-------LQPVKSKPRYQDLAELLKRAFKQLDKSF 140 (143)
T ss_pred HHHHHHHHHcCCc-------cCCCCCCCCHHHHHHHHHHHHHHhHHHH
Confidence 567 889988864 6677889999999998877776666655
No 72
>cd04684 Nudix_Hydrolase_25 Contains a crystal structure of the Nudix hydrolase from Enterococcus faecalis, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability
Probab=23.09 E-value=68 Score=19.00 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=18.4
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHH
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQL 46 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~ 46 (75)
..|.+++. ||.|+++| +.-+++++.+
T Consensus 23 ~~~~w~lP-gG~ve~gE--~~~~aa~RE~ 48 (128)
T cd04684 23 YEGRWDLP-GGGIEPGE--SPEEALHREV 48 (128)
T ss_pred CCCeEECC-CcccCCCC--CHHHHHHHHH
Confidence 35889887 67799888 4556666655
No 73
>PRK05331 putative phosphate acyltransferase; Provisional
Probab=22.97 E-value=2e+02 Score=21.43 Aligned_cols=40 Identities=23% Similarity=0.284 Sum_probs=30.3
Q ss_pred ceeeeeccCC---CCHHHHHHHHHHHHHHHHhhhCC-CCCceee
Q psy11172 27 GGWVMTDEAN---SHYYSMIQQLTHGQQWLLTNIGV-KPRYLHN 66 (75)
Q Consensus 27 GgWv~~Dea~---~~~~~~i~Q~~~G~~fl~~~fg~-~P~~~W~ 66 (75)
|-.++.|.+. |+-+.+++-...|..|.+..||+ .||++=+
T Consensus 137 ~~~~l~D~gan~~p~~e~L~~~A~~~a~~a~~~~Gi~~PrVAlL 180 (334)
T PRK05331 137 GGTVLLDLGANVDCKPEHLVQFAVMGSVYAEAVLGIENPRVGLL 180 (334)
T ss_pred CeEEEEeCeEcCCCCHHHHHHHHHHHHHHHHHHcCCCCCeEEEE
Confidence 3445556543 55677787778899999999998 5999987
No 74
>COG0657 Aes Esterase/lipase [Lipid metabolism]
Probab=22.61 E-value=1.3e+02 Score=21.06 Aligned_cols=41 Identities=24% Similarity=0.609 Sum_probs=28.1
Q ss_pred eEEEcceeeeeccCCC--------------------------CHHHHHHHHHHHHHHHHhh---hCCCCC
Q psy11172 22 LEIVTGGWVMTDEANS--------------------------HYYSMIQQLTHGQQWLLTN---IGVKPR 62 (75)
Q Consensus 22 lE~v~GgWv~~Dea~~--------------------------~~~~~i~Q~~~G~~fl~~~---fg~~P~ 62 (75)
+.+=||||++.+...- .|-..++......+|+.++ ||+.|+
T Consensus 83 ly~HGGg~~~g~~~~~~~~~~~~~~~~g~~vv~vdYrlaPe~~~p~~~~d~~~a~~~l~~~~~~~g~dp~ 152 (312)
T COG0657 83 LYLHGGGWVLGSLRTHDALVARLAAAAGAVVVSVDYRLAPEHPFPAALEDAYAAYRWLRANAAELGIDPS 152 (312)
T ss_pred EEEeCCeeeecChhhhHHHHHHHHHHcCCEEEecCCCCCCCCCCCchHHHHHHHHHHHHhhhHhhCCCcc
Confidence 4456788887765544 2456667777788888877 677666
No 75
>PF06422 PDR_CDR: CDR ABC transporter; InterPro: IPR010929 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). In yeast, the PDR and CDR ABC transporters display extensive sequence homology, and confer resistance to several anti-fungal compounds by actively transporting their substrates out of the cell. These transporters have two homologous halves, each with an N-terminal intracellular hydrophilic region that contains an ATP-binding site, followed by a C-terminal membrane-associated region containing six transmembrane segments []. This entry represents a domain of the PDR/CDR ABC transporter comprising extracellular loop 3, transmembrane segment 6 and a linker region.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane
Probab=22.57 E-value=50 Score=20.40 Aligned_cols=23 Identities=17% Similarity=0.216 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhhhCCCCCceeec
Q psy11172 45 QLTHGQQWLLTNIGVKPRYLHNN 67 (75)
Q Consensus 45 Q~~~G~~fl~~~fg~~P~~~W~~ 67 (75)
.++.|-+||...||+....-|.+
T Consensus 29 ~~V~G~~YL~~~y~y~~sh~WRN 51 (103)
T PF06422_consen 29 TYVSGDDYLEESYGYSYSHRWRN 51 (103)
T ss_pred cEEeHHHHHhhhccccccchhhh
Confidence 35679999999999999999873
No 76
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=22.31 E-value=1e+02 Score=15.18 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=16.5
Q ss_pred hhh-HHHHhcCceEEEcceeee
Q psy11172 11 KPI-VSLVKSGQLEIVTGGWVM 31 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~GgWv~ 31 (75)
... ++|.++|-++..+|.++-
T Consensus 26 ~~~l~~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 26 SRTLKRLEKEGLISREGGRIVI 47 (48)
T ss_pred HHHHHHHHHCCCEEEeCCEEEE
Confidence 455 899999999988876653
No 77
>PF14177 YkyB: YkyB-like protein
Probab=21.95 E-value=71 Score=21.52 Aligned_cols=18 Identities=17% Similarity=0.183 Sum_probs=14.5
Q ss_pred hhh-HHHHhcCceEEEcce
Q psy11172 11 KPI-VSLVKSGQLEIVTGG 28 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~Gg 28 (75)
+.. .+||++|+.+.||=-
T Consensus 30 k~aL~Kll~E~kA~kiGlH 48 (140)
T PF14177_consen 30 KKALQKLLEEGKAKKIGLH 48 (140)
T ss_pred HHHHHHHHHcCcceEEEEe
Confidence 344 899999999999744
No 78
>PRK13272 treA trehalase; Provisional
Probab=21.90 E-value=77 Score=25.53 Aligned_cols=36 Identities=17% Similarity=0.208 Sum_probs=30.0
Q ss_pred eeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCce
Q psy11172 29 WVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYL 64 (75)
Q Consensus 29 Wv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~ 64 (75)
|++-=...+...++++.|+...-++-+++|..|..+
T Consensus 168 ~i~~GLl~s~~~~~a~~mi~Nf~~~i~~yGfIPNG~ 203 (542)
T PRK13272 168 FTMLGLVKSGQTTLSRQMLDNFAYLIDTYGHIPNGN 203 (542)
T ss_pred HHHHhhhhcCcHHHHHHHHHHHHHHHHHcCcCcCCc
Confidence 555556667778999999999999999999999764
No 79
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=21.54 E-value=50 Score=21.32 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=11.8
Q ss_pred CChhhh-HHHHhcCceE
Q psy11172 8 PNHKPI-VSLVKSGQLE 23 (75)
Q Consensus 8 ~~~k~~-k~lV~~GqlE 23 (75)
.+.-+. |+||++|.++
T Consensus 89 ~E~IE~Lk~Lv~eGKi~ 105 (110)
T PF06819_consen 89 KEDIEKLKKLVEEGKIE 105 (110)
T ss_pred HHHHHHHHHHHHcCCCc
Confidence 344455 9999999985
No 80
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=21.51 E-value=74 Score=25.51 Aligned_cols=32 Identities=16% Similarity=0.077 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhhhCCCCCceeecCCCCCCCC
Q psy11172 44 QQLTHGQQWLLTNIGVKPRYLHNNSRTISSPH 75 (75)
Q Consensus 44 ~Q~~~G~~fl~~~fg~~P~~~W~~D~Fg~s~~ 75 (75)
.|--.-.+||.+.|.-.|..-|..+=||-|.|
T Consensus 419 kQseeLv~yl~~~fe~~p~~iW~sniFGKsl~ 450 (492)
T TIGR02836 419 KQSEELVKYLLEQFEDDPLKIWESNIFGKSLS 450 (492)
T ss_pred HHHHHHHHHHHHHhhcChhheecccccCccHH
Confidence 34455568999999999999999999998864
No 81
>COG3811 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.50 E-value=54 Score=20.20 Aligned_cols=31 Identities=23% Similarity=0.587 Sum_probs=22.9
Q ss_pred hhhHHHHhcCceEEEc--------------ceeeeeccCCCCHHH
Q psy11172 11 KPIVSLVKSGQLEIVT--------------GGWVMTDEANSHYYS 41 (75)
Q Consensus 11 k~~k~lV~~GqlE~v~--------------GgWv~~Dea~~~~~~ 41 (75)
+-++.|.+-||+||.- -||+-+|+.+.-+..
T Consensus 9 RtLH~LAqGGrIe~~rd~~grI~~v~C~tRdGw~l~dctlavF~k 53 (85)
T COG3811 9 RTLHALAQGGRIEIERDASGRITSVECYTRDGWLLPDCTLAVFRK 53 (85)
T ss_pred HHHHHHhcCCeEEEEecCCCcEEEEEEecccccccCCccHHHHHH
Confidence 3338999999999975 488888887654443
No 82
>cd04682 Nudix_Hydrolase_23 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=21.43 E-value=80 Score=19.02 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=23.5
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCC
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKP 61 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P 61 (75)
-.|++++. ||-|+.+| +.-+++++.+ +++.|+.+
T Consensus 27 ~~g~w~~P-gG~ve~gE--~~~~aa~RE~-------~EE~Gl~~ 60 (122)
T cd04682 27 YPGHWDLP-GGHREGGE--TPLECVLREL-------LEEIGLTL 60 (122)
T ss_pred CCCcEeCC-CccccCCC--CHHHHHHHHH-------HHHhCCcc
Confidence 35899987 57788887 4667777766 45556554
No 83
>KOG1515|consensus
Probab=21.39 E-value=1.2e+02 Score=22.69 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=22.6
Q ss_pred eEEEcceeeeeccCCCCHHHHHHHHH
Q psy11172 22 LEIVTGGWVMTDEANSHYYSMIQQLT 47 (75)
Q Consensus 22 lE~v~GgWv~~Dea~~~~~~~i~Q~~ 47 (75)
+-|=|||||+---+.+.|..+..++.
T Consensus 94 vyfHGGGf~~~S~~~~~y~~~~~~~a 119 (336)
T KOG1515|consen 94 VYFHGGGFCLGSANSPAYDSFCTRLA 119 (336)
T ss_pred EEEeCCccEeCCCCCchhHHHHHHHH
Confidence 55779999999999999999988874
No 84
>PRK13270 treF trehalase; Provisional
Probab=21.32 E-value=77 Score=25.57 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=29.8
Q ss_pred eeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCce
Q psy11172 29 WVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYL 64 (75)
Q Consensus 29 Wv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~ 64 (75)
|++-=...+...++++.|+....+|-++||..|..+
T Consensus 179 wi~~GLl~sg~~~~a~~mi~Nf~~li~~yGfIPNG~ 214 (549)
T PRK13270 179 FTMLGLAESGREDLLKCMADNFAWMIENYGHIPNGN 214 (549)
T ss_pred HHHHHhhhcCcHHHHHHHHHHHHHHHHHcCcCcCCc
Confidence 455555666778999999999999999999999764
No 85
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=21.27 E-value=2.1e+02 Score=22.00 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=39.8
Q ss_pred HHHHhcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhC
Q psy11172 14 VSLVKSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIG 58 (75)
Q Consensus 14 k~lV~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg 58 (75)
..|++.|-++.-++-+..++....-...++.++..|.+-+++.+-
T Consensus 381 ~~l~~~Gll~~~~~~l~lT~~G~~~~d~i~~~f~~g~~~~r~~~~ 425 (433)
T PRK08629 381 LLLKLIGAIKNDPGDLIVTDFGKYLGVVMMKEFYTGMDNVRAQFR 425 (433)
T ss_pred HHHHHCCCEEEECCEEEECcchhHHHHHHHHHHHhChHHHHHHHH
Confidence 789999999988888999999998889999999999888887764
No 86
>PF03755 YicC_N: YicC-like family, N-terminal region ; InterPro: IPR013527 Proteins in this entry are homologues of YicC (P23839 from SWISSPROT) from Escherichia coli. Although it is relatively poorly characterised YicC has been shown to be important for cells in the stationary phase, and essential for growth at high temperatures []. This domain is found at the N-terminal region of these proteins.
Probab=20.89 E-value=2.6e+02 Score=18.33 Aligned_cols=53 Identities=9% Similarity=0.119 Sum_probs=36.5
Q ss_pred CChhhh-HHHHhcCceEEE-cceeee-eccCCCCHHHHHHHHHHHHHHHHhhhCCC
Q psy11172 8 PNHKPI-VSLVKSGQLEIV-TGGWVM-TDEANSHYYSMIQQLTHGQQWLLTNIGVK 60 (75)
Q Consensus 8 ~~~k~~-k~lV~~GqlE~v-~GgWv~-~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~ 60 (75)
+..++. ++.|+.|++++. .=-... ......-=..++.++..-.+-|.+.+|..
T Consensus 46 ~~ir~~i~~~l~RGkV~v~i~~~~~~~~~~~~~in~~l~~~y~~~l~~l~~~~~~~ 101 (159)
T PF03755_consen 46 PEIRKLIRKKLSRGKVEVSIRVERSSESAVELRINEELAKAYYEALKELAEELGLA 101 (159)
T ss_pred HHHHHHHHHhcccceEEEEEEEEECcccCCCcccCHHHHHHHHHHHHHHHHHcCCC
Confidence 345777 999999999984 211111 11222234789999999999999999864
No 87
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=20.78 E-value=76 Score=18.83 Aligned_cols=16 Identities=44% Similarity=0.561 Sum_probs=12.8
Q ss_pred hhh-HHHHhcCceEEEc
Q psy11172 11 KPI-VSLVKSGQLEIVT 26 (75)
Q Consensus 11 k~~-k~lV~~GqlE~v~ 26 (75)
+.+ ..||++|.+|+-.
T Consensus 38 KKi~~~LV~Eg~l~yWS 54 (67)
T PF08679_consen 38 KKIVNELVNEGKLEYWS 54 (67)
T ss_dssp HHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHhhCeEEEEc
Confidence 455 7899999999854
No 88
>cd04683 Nudix_Hydrolase_24 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=20.64 E-value=85 Score=18.62 Aligned_cols=35 Identities=20% Similarity=0.231 Sum_probs=23.0
Q ss_pred hcCceEEEcceeeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCC
Q psy11172 18 KSGQLEIVTGGWVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPR 62 (75)
Q Consensus 18 ~~GqlE~v~GgWv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~ 62 (75)
..|.+++. ||.|+++|. .-++.++ =++++.|+..+
T Consensus 24 ~~~~w~lP-gG~ve~gE~--~~~aa~R-------El~EEtGl~v~ 58 (120)
T cd04683 24 MDGQWALP-AGHLEKGED--AVTAAVR-------EAREEIGVTLD 58 (120)
T ss_pred CCCeEeCC-ccccCCCCC--HHHHHHH-------HHHHHHCCccC
Confidence 46889987 777888873 3445554 45677776543
No 89
>PRK13271 treA trehalase; Provisional
Probab=20.38 E-value=81 Score=25.53 Aligned_cols=36 Identities=14% Similarity=0.129 Sum_probs=29.3
Q ss_pred eeeeccCCCCHHHHHHHHHHHHHHHHhhhCCCCCce
Q psy11172 29 WVMTDEANSHYYSMIQQLTHGQQWLLTNIGVKPRYL 64 (75)
Q Consensus 29 Wv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg~~P~~~ 64 (75)
|++-=...+...++++.|+...-++-++||..|..+
T Consensus 167 ~i~~GLl~s~~~~~a~~mi~Nf~~~i~~yG~IPNg~ 202 (569)
T PRK13271 167 FTMLGLAESGHWDKVADMVANFAHEIDTWGHIPNGN 202 (569)
T ss_pred HHHHhhHhcCCHHHHHHHHHHHHHHHHHhCcCcCCc
Confidence 444455566778899999999999999999999764
No 90
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=20.27 E-value=20 Score=20.20 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHhhhCCCCCc
Q psy11172 42 MIQQLTHGQQWLLTNIGVKPRY 63 (75)
Q Consensus 42 ~i~Q~~~G~~fl~~~fg~~P~~ 63 (75)
.-..+.+..+.|..+||+.|++
T Consensus 29 ~s~~ll~~v~~lL~~lGi~~~i 50 (77)
T PF14528_consen 29 KSKELLEDVQKLLLRLGIKASI 50 (77)
T ss_dssp S-HHHHHHHHHHHHHTT--EEE
T ss_pred CCHHHHHHHHHHHHHCCCeeEE
Confidence 3345666667778899998865
No 91
>COG1462 CsgG Uncharacterized protein involved in formation of curli polymers [Cell envelope biogenesis, outer membrane]
Probab=20.17 E-value=1.6e+02 Score=21.69 Aligned_cols=54 Identities=7% Similarity=0.071 Sum_probs=40.6
Q ss_pred HHhcCceEEEcce----eeeeccCCCCHHHHHHHHHHHHHHHHhhhC-CCCCceeecCCCC
Q psy11172 16 LVKSGQLEIVTGG----WVMTDEANSHYYSMIQQLTHGQQWLLTNIG-VKPRYLHNNSRTI 71 (75)
Q Consensus 16 lV~~GqlE~v~Gg----Wv~~Dea~~~~~~~i~Q~~~G~~fl~~~fg-~~P~~~W~~D~Fg 71 (75)
-+..|.++|+|.| +-..=...+........|.+-. ...-.+ .-|..+|.+++++
T Consensus 182 e~~ag~~~v~G~~~~~~~~~s~~s~~~~ka~~~~i~ea~--v~~lv~~~~~~~a~~~~~~~ 240 (252)
T COG1462 182 EVSAGNFEVIGFGRLGGGTVSYDSTPNGKALRLAIIEAT--VAQLVNLAIDSGAWQPVNAA 240 (252)
T ss_pred eeccCCceEeccccccccccccccCchHHHHHHHHHHHH--HHHhhccCCcccccCchhhh
Confidence 4677899999988 8888888888888888887763 222334 6788888888764
Done!