Query psy5411
Match_columns 88
No_of_seqs 101 out of 215
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 16:48:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5411hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3546|consensus 99.9 4E-23 8.8E-28 168.1 4.9 85 1-86 130-214 (1167)
2 smart00210 TSPN Thrombospondin 99.7 5E-17 1.1E-21 113.7 9.3 79 3-86 93-172 (184)
3 KOG3546|consensus 98.9 1.4E-10 3.1E-15 95.5 -2.7 85 1-87 1039-1125(1167)
4 PF02210 Laminin_G_2: Laminin 98.6 4.7E-07 1E-11 57.3 9.1 75 3-81 31-105 (128)
5 smart00282 LamG Laminin G doma 98.4 4E-06 8.6E-11 54.6 8.1 55 24-80 57-111 (135)
6 cd00110 LamG Laminin G domain; 98.3 2.1E-06 4.5E-11 56.0 5.7 54 25-80 76-129 (151)
7 PF13385 Laminin_G_3: Concanav 98.0 1.7E-05 3.8E-10 50.7 5.5 52 24-78 80-131 (157)
8 PF00054 Laminin_G_1: Laminin 97.5 0.00099 2.1E-08 43.8 8.1 71 3-78 31-101 (131)
9 smart00159 PTX Pentraxin / C-r 97.3 0.0014 2.9E-08 46.6 7.1 64 20-86 81-146 (206)
10 cd00152 PTX Pentraxins are pla 97.1 0.0033 7.1E-08 44.3 7.6 57 21-80 82-140 (201)
11 PF00354 Pentaxin: Pentaxin fa 97.1 0.0032 6.8E-08 44.8 6.9 64 20-86 75-140 (195)
12 smart00560 LamGL LamG-like jel 94.5 0.057 1.2E-06 35.4 3.7 41 29-75 61-103 (133)
13 KOG3514|consensus 93.4 0.15 3.2E-06 45.3 4.8 52 24-77 100-151 (1591)
14 PF06439 DUF1080: Domain of Un 91.7 0.24 5.2E-06 33.3 3.4 35 22-56 120-154 (185)
15 PF02057 Glyco_hydro_59: Glyco 88.5 1.9 4E-05 36.5 6.6 41 18-58 600-640 (669)
16 KOG1834|consensus 87.6 0.92 2E-05 38.7 4.3 51 3-54 413-467 (952)
17 KOG3516|consensus 84.5 2.4 5.1E-05 38.1 5.4 50 24-76 441-490 (1306)
18 KOG3516|consensus 84.2 4.5 9.8E-05 36.4 6.9 73 2-77 845-917 (1306)
19 cd02175 GH16_lichenase lichena 78.3 6.3 0.00014 27.7 5.0 41 27-67 136-181 (212)
20 KOG1219|consensus 78.2 3.8 8.3E-05 39.9 4.6 48 27-76 3761-3808(4289)
21 cd08023 GH16_laminarinase_like 77.9 11 0.00025 26.5 6.2 37 20-56 147-185 (235)
22 cd02178 GH16_beta_agarase Beta 77.7 5.9 0.00013 28.8 4.8 53 27-79 177-238 (258)
23 PF07622 DUF1583: Protein of u 73.1 7.2 0.00016 31.1 4.4 36 24-59 85-120 (399)
24 cd00413 Glyco_hydrolase_16 gly 71.1 14 0.00031 25.2 5.2 29 27-55 140-168 (210)
25 PF00722 Glyco_hydro_16: Glyco 66.7 23 0.00049 23.8 5.4 34 26-59 115-148 (185)
26 cd02182 GH16_Strep_laminarinas 62.6 24 0.00053 25.6 5.2 30 27-56 170-204 (259)
27 PF08787 Alginate_lyase2: Algi 61.1 19 0.00041 26.1 4.4 29 27-55 162-190 (236)
28 cd02180 GH16_fungal_KRE6_gluca 58.9 29 0.00062 26.3 5.2 30 27-56 206-240 (295)
29 KOG4495|consensus 58.1 7.8 0.00017 25.5 1.7 22 34-55 3-24 (110)
30 TIGR03436 acidobact_VWFA VWFA- 53.4 25 0.00055 25.6 4.0 27 19-45 259-287 (296)
31 cd01788 ElonginB Ubiquitin-lik 48.1 15 0.00033 24.7 1.9 22 34-55 3-24 (119)
32 cd04508 TUDOR Tudor domains ar 47.9 21 0.00045 18.8 2.2 31 28-58 11-44 (48)
33 cd04467 S1_aIF5A S1_aIF5A: Arc 45.6 56 0.0012 19.1 3.9 35 34-70 7-43 (57)
34 COG2378 Predicted transcriptio 44.1 54 0.0012 24.8 4.6 46 1-46 153-198 (311)
35 PF02973 Sialidase: Sialidase, 41.7 71 0.0015 22.9 4.7 30 27-56 101-132 (190)
36 PF03421 YopJ: YopJ Serine/Thr 40.0 53 0.0012 23.0 3.8 33 20-52 72-108 (177)
37 cd02177 GH16_kappa_carrageenas 39.5 64 0.0014 24.1 4.4 30 27-56 188-217 (269)
38 PRK13442 atpC F0F1 ATP synthas 38.9 63 0.0014 20.0 3.7 22 27-48 57-83 (89)
39 cd02183 GH16_fungal_CRH1_trans 38.6 1.2E+02 0.0026 21.5 5.5 29 28-56 114-142 (203)
40 PF10080 DUF2318: Predicted me 38.4 32 0.00069 22.3 2.3 21 27-47 3-23 (102)
41 PF01436 NHL: NHL repeat; Int 38.1 39 0.00085 16.3 2.1 21 60-80 3-23 (28)
42 PF09008 Head_binding: Head bi 36.6 25 0.00054 23.5 1.6 17 64-80 23-39 (114)
43 PF03633 Glyco_hydro_65C: Glyc 35.9 78 0.0017 17.4 4.3 26 27-52 3-30 (54)
44 PF10102 DUF2341: Domain of un 35.3 51 0.0011 20.6 2.8 32 2-33 45-82 (89)
45 cd08024 GH16_CCF Coelomic cyto 32.5 1.1E+02 0.0023 23.5 4.7 31 27-57 203-233 (330)
46 PF00567 TUDOR: Tudor domain; 31.0 77 0.0017 18.9 3.1 30 26-55 63-95 (121)
47 TIGR03606 non_repeat_PQQ dehyd 31.0 48 0.001 26.8 2.6 29 58-86 229-257 (454)
48 PF04582 Reo_sigmaC: Reovirus 30.8 37 0.00079 26.5 1.9 25 34-58 235-259 (326)
49 PRK07718 fliL flagellar basal 27.7 57 0.0012 21.9 2.2 23 19-41 52-74 (142)
50 PF14099 Polysacc_lyase: Polys 27.4 2.1E+02 0.0044 19.8 5.1 28 25-52 148-180 (224)
51 PF12087 DUF3564: Protein of u 26.7 1.6E+02 0.0034 19.9 4.2 76 1-80 1-95 (121)
52 cd01253 PH_beta_spectrin Beta- 26.7 1.3E+02 0.0029 18.3 3.7 25 27-51 19-43 (104)
53 PF00207 A2M: Alpha-2-macroglo 26.6 1.5E+02 0.0033 17.8 4.0 26 17-42 15-40 (92)
54 KOG3514|consensus 24.9 99 0.0022 28.5 3.6 47 27-75 1142-1189(1591)
55 PF02823 ATP-synt_DE_N: ATP sy 24.5 1.5E+02 0.0033 17.5 3.6 22 27-48 52-78 (80)
56 PRK14736 atpC F0F1 ATP synthas 24.1 1.4E+02 0.003 19.9 3.6 22 27-48 55-81 (133)
57 PRK00539 atpC F0F1 ATP synthas 23.7 1.6E+02 0.0034 19.6 3.8 24 27-50 55-83 (133)
58 cd02179 GH16_beta_GRP beta-1,3 23.1 2E+02 0.0042 22.0 4.6 31 26-56 197-227 (321)
59 PRK01474 atpC F0F1 ATP synthas 22.9 1.7E+02 0.0038 18.7 3.8 21 28-48 59-84 (112)
60 KOG4289|consensus 22.7 2E+02 0.0044 27.7 5.2 33 26-58 1395-1428(2531)
61 PF01149 Fapy_DNA_glyco: Forma 22.6 1.4E+02 0.003 18.8 3.2 29 27-55 87-115 (116)
62 PF09313 DUF1971: Domain of un 22.0 2E+02 0.0043 17.8 3.7 19 27-47 63-81 (82)
63 KOG1653|consensus 21.6 50 0.0011 23.6 1.0 9 29-37 104-112 (175)
64 TIGR03166 alt_F1F0_F1_eps alte 20.8 1.8E+02 0.0039 19.1 3.6 22 27-48 52-78 (122)
65 PF07953 Toxin_R_bind_N: Clost 20.3 3.5E+02 0.0076 19.7 5.3 33 27-59 126-159 (195)
No 1
>KOG3546|consensus
Probab=99.87 E-value=4e-23 Score=168.05 Aligned_cols=85 Identities=29% Similarity=0.488 Sum_probs=82.4
Q ss_pred CceEEEEecCCCCccceeeeEEECCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCC
Q psy5411 1 MNLTLLYTDVTKFSTTQPIASFLIPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPI 80 (88)
Q Consensus 1 ~~i~l~Ytd~~~~~~s~~~asF~v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~ 80 (88)
|+|+||||+++ +..++++|+|++|.|.++|+|||++|++..|+||+|||+.++.++.||.+.|.|++++.||+||||++
T Consensus 130 q~i~l~ytepg-~~~s~~aa~f~~p~~~~~w~~~a~~v~g~~v~l~v~cee~~r~p~~rss~~l~~e~~ag~f~~~ag~~ 208 (1167)
T KOG3546|consen 130 QDISLLYTEPG-AGQTHTAASFRLPAFVGQWTHLALSVAGGFVALYVDCEEFQRMPLARSSRGLELEPGAGLFVAQAGGA 208 (1167)
T ss_pred ceeEEEeccCC-CCccchhheeccchhhchhhheeeeecCceEEEEechHHhcccchhccccceeecCCcceEEeccCCC
Confidence 78999999998 77899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcee
Q psy5411 81 IKGALD 86 (88)
Q Consensus 81 ~~~~f~ 86 (88)
..++|.
T Consensus 209 ~~~~f~ 214 (1167)
T KOG3546|consen 209 DPDKFQ 214 (1167)
T ss_pred ChHhhh
Confidence 999986
No 2
>smart00210 TSPN Thrombospondin N-terminal -like domains. Heparin-binding and cell adhesion domain of thrombospondin
Probab=99.72 E-value=5e-17 Score=113.72 Aligned_cols=79 Identities=29% Similarity=0.418 Sum_probs=58.0
Q ss_pred eEEEEecCCCCccceeeeEEE-CCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCCC
Q psy5411 3 LTLLYTDVTKFSTTQPIASFL-IPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPII 81 (88)
Q Consensus 3 i~l~Ytd~~~~~~s~~~asF~-v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~~ 81 (88)
+.|+|.+.+ + ..+.++|+ ++++||+|||++|+|++++|+||+||+++++++++|..++ .++. ++++++.+....
T Consensus 93 ~~~~~~~~~-g--~~~~~~f~~~~l~dg~WH~lal~V~~~~v~LyvDC~~~~~~~l~~~~~~-~~~~-~g~~~~g~~~~~ 167 (184)
T smart00210 93 LLLRYQGVD-G--KQHTVSFRNLPLADGQWHKLALSVSGSSATLYVDCNEIDSRPLDRPGQP-PIDT-DGIEVRGAQAAD 167 (184)
T ss_pred EEEEECCCC-C--cEEEEeecCCccccCCceEEEEEEeCCEEEEEECCccccceecCCcccc-cccc-cceEEEeeccCC
Confidence 556665443 2 45678998 8999999999999999999999999999999999998753 3343 333333343343
Q ss_pred CCcee
Q psy5411 82 KGALD 86 (88)
Q Consensus 82 ~~~f~ 86 (88)
++.|+
T Consensus 168 ~~~f~ 172 (184)
T smart00210 168 RKPFQ 172 (184)
T ss_pred CCcce
Confidence 56665
No 3
>KOG3546|consensus
Probab=98.86 E-value=1.4e-10 Score=95.49 Aligned_cols=85 Identities=19% Similarity=0.166 Sum_probs=76.6
Q ss_pred CceEEEEecCCCCccceeeeEEECCCCCCCceEEEEE--EECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecC
Q psy5411 1 MNLTLLYTDVTKFSTTQPIASFLIPAPTGKYFKFALK--VTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAG 78 (88)
Q Consensus 1 ~~i~l~Ytd~~~~~~s~~~asF~v~~~d~~Whr~als--V~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG 78 (88)
|+++++|+.++ ...-..+++|-|.+|. +|+.|++. +..|+|++|+||+-.++..+.|.|++++++.+|+++|+|||
T Consensus 1039 qdlSlIvrqAd-rnigpivnlkGvalfp-kWnSIfsg~~glsdkvsfiYsfdgRdttlvprwPqklvwhgsSplgirlag 1116 (1167)
T KOG3546|consen 1039 QDLSLIVRQAD-RNIGPIVNLKGVALFP-KWNSIFSGSEGLSDKVSFIYSFDGRDTTLVPRWPQKLVWHGSSPLGIRLAG 1116 (1167)
T ss_pred hhHHHHHHHHh-hhccceeeccceeecc-chHhhhcccccccCCcceeEeecCccccccCCcchhheecCCCccchhhhh
Confidence 56778888887 4445677889888888 99999999 99999999999999999999999999999999999999999
Q ss_pred CCCCCceec
Q psy5411 79 PIIKGALDI 87 (88)
Q Consensus 79 ~~~~~~f~~ 87 (88)
+.+.+.|++
T Consensus 1117 sycegwrtv 1125 (1167)
T KOG3546|consen 1117 SYCEGWRTV 1125 (1167)
T ss_pred ccccceeEe
Confidence 999998874
No 4
>PF02210 Laminin_G_2: Laminin G domain; InterPro: IPR012680 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, including a large number of extracellular proteins. The C terminus of the laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions have been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each have five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012679 from INTERPRO).; PDB: 3POY_A 3QCW_B 3R05_B 3ASI_A 3MW4_B 3MW3_A 1QU0_D 1DYK_A 1OKQ_A 3SH4_A ....
Probab=98.64 E-value=4.7e-07 Score=57.28 Aligned_cols=75 Identities=16% Similarity=0.123 Sum_probs=54.8
Q ss_pred eEEEEecCCCCccceeeeEEECCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCCC
Q psy5411 3 LTLLYTDVTKFSTTQPIASFLIPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPII 81 (88)
Q Consensus 3 i~l~Ytd~~~~~~s~~~asF~v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~~ 81 (88)
+.+.|.-.+ . .........+..|++||++.+...++.++|.+||.+........... ..++....+|||..-+..
T Consensus 31 l~~~~~~g~-~--~~~~~~~~~~~~dg~wh~v~i~~~~~~~~l~Vd~~~~~~~~~~~~~~-~~~~~~~~l~iGg~~~~~ 105 (128)
T PF02210_consen 31 LVVRYNLGG-S--EIVTTFSNSNLNDGQWHKVSISRDGNRVTLTVDGQSVSSESLPSSSS-DSLDPDGSLYIGGLPESN 105 (128)
T ss_dssp EEEEEESSS-S--EEEEEECSSSSTSSSEEEEEEEEETTEEEEEETTSEEEEEESSSTTH-HCBESEEEEEESSTTTTC
T ss_pred EEEEEEccc-c--ceeeeccCccccccceeEEEEEEeeeeEEEEecCccceEEeccccce-ecccCCCCEEEecccCcc
Confidence 455555432 1 22333344577999999999999999999999999998777665442 356667789999987765
No 5
>smart00282 LamG Laminin G domain.
Probab=98.36 E-value=4e-06 Score=54.57 Aligned_cols=55 Identities=22% Similarity=0.228 Sum_probs=41.7
Q ss_pred CCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCC
Q psy5411 24 IPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPI 80 (88)
Q Consensus 24 v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~ 80 (88)
.+..||+||++++...++.++|++|+....+.....+. -.++....+|||.+.+.
T Consensus 57 ~~~~dg~WH~v~i~~~~~~~~l~VD~~~~~~~~~~~~~--~~l~~~~~l~iGG~p~~ 111 (135)
T smart00282 57 TPLNDGQWHRVAVERNGRRVTLSVDGENPVSGESPGGL--TILNLDGPLYLGGLPED 111 (135)
T ss_pred eEeCCCCEEEEEEEEeCCEEEEEECCCccccEECCCCc--eEEecCCCcEEccCCch
Confidence 45689999999999999999999999765444333222 34556788999987654
No 6
>cd00110 LamG Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
Probab=98.29 E-value=2.1e-06 Score=56.05 Aligned_cols=54 Identities=20% Similarity=0.273 Sum_probs=41.3
Q ss_pred CCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCC
Q psy5411 25 PAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPI 80 (88)
Q Consensus 25 ~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~ 80 (88)
+..||+||++++...++.++|++|+....+....... ..++....+|||.....
T Consensus 76 ~v~dg~Wh~v~i~~~~~~~~l~VD~~~~~~~~~~~~~--~~~~~~~~~~iGg~~~~ 129 (151)
T cd00110 76 PLNDGQWHSVSVERNGRSVTLSVDGERVVESGSPGGS--ALLNLDGPLYLGGLPED 129 (151)
T ss_pred ccCCCCEEEEEEEECCCEEEEEECCccEEeeeCCCCc--eeecCCCCeEEcCCCCc
Confidence 4699999999999999999999999854333322221 14677899999998764
No 7
>PF13385 Laminin_G_3: Concanavalin A-like lectin/glucanases superfamily; PDB: 4DQA_A 1N1Y_A 1MZ6_A 1MZ5_A 1N1S_A 2A75_A 1WCS_A 1N1T_A 1N1V_A 2FHR_A ....
Probab=98.01 E-value=1.7e-05 Score=50.73 Aligned_cols=52 Identities=29% Similarity=0.451 Sum_probs=39.5
Q ss_pred CCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecC
Q psy5411 24 IPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAG 78 (88)
Q Consensus 24 v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG 78 (88)
.+..+++||++++.+++++++||+|++...+........ ..+...++||+.+
T Consensus 80 ~~~~~~~W~~l~~~~~~~~~~lyvnG~~~~~~~~~~~~~---~~~~~~~~iG~~~ 131 (157)
T PF13385_consen 80 SNLPDNKWHHLALTYDGSTVTLYVNGELVGSSTIPSNIS---LNSNGPLFIGGSG 131 (157)
T ss_dssp S---TT-EEEEEEEEETTEEEEEETTEEETTCTEESSSS---TTSCCEEEESS-S
T ss_pred cccCCCCEEEEEEEEECCeEEEEECCEEEEeEeccCCcC---CCCcceEEEeecC
Confidence 455689999999999999999999999998877766432 2567799999987
No 8
>PF00054 Laminin_G_1: Laminin G domain; InterPro: IPR012679 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, which includes a large number of extracellular proteins. The C terminus of laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions has been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each has five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012680 from INTERPRO).; PDB: 1OKQ_A 1DYK_A 2C5D_A 1H30_A 1LHW_A 1KDK_A 1LHU_A 1KDM_A 1LHO_A 1D2S_A ....
Probab=97.53 E-value=0.00099 Score=43.85 Aligned_cols=71 Identities=15% Similarity=0.113 Sum_probs=46.4
Q ss_pred eEEEEecCCCCccceeeeEEECCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecC
Q psy5411 3 LTLLYTDVTKFSTTQPIASFLIPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAG 78 (88)
Q Consensus 3 i~l~Ytd~~~~~~s~~~asF~v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG 78 (88)
+.|.|.-.. .+ ....-..+..||+||++.+...+..++|-+|=++..+....-.+. ..++....||||-.-
T Consensus 31 l~~~~~~G~-~~---~~~~~~~~i~dg~wh~v~~~r~~~~~~L~Vd~~~~~~~~s~~~~~-~~l~~~~~lyvGG~p 101 (131)
T PF00054_consen 31 LEFRYNLGS-GP---ASLRSPQKINDGKWHTVSVSRNGRNGSLSVDGEEVVTGESPSGAT-QSLDVDGPLYVGGLP 101 (131)
T ss_dssp EEEEEESSS-EE---EEEEESSETTSSSEEEEEEEEETTEEEEEETTSEEEEEEECSSSS-SSCEECSEEEESSSS
T ss_pred EEEEEeCCC-cc---ceecCCCccCCCcceEEEEEEcCcEEEEEECCccceeeecCCccc-cccccccCEEEccCC
Confidence 556664333 22 122233356899999999999999999999977663333333332 235556779999876
No 9
>smart00159 PTX Pentraxin / C-reactive protein / pentaxin family. This family form a doscoid pentameric structure. Human serum amyloid P demonstrates calcium-mediated ligand-binding.
Probab=97.29 E-value=0.0014 Score=46.58 Aligned_cols=64 Identities=16% Similarity=0.271 Sum_probs=45.0
Q ss_pred eEEECCCCCCCceEEEEEEE--CCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCCCCCcee
Q psy5411 20 ASFLIPAPTGKYFKFALKVT--LDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPIIKGALD 86 (88)
Q Consensus 20 asF~v~~~d~~Whr~alsV~--~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~~~~~f~ 86 (88)
..++++..+++||++++.-. .++++||+|=+......+... -.+.+++.+.|||.-....+.|+
T Consensus 81 ~~~~~~~~~g~W~hvc~tw~~~~g~~~lyvnG~~~~~~~~~~g---~~i~~~G~lvlGq~qd~~gg~f~ 146 (206)
T smart00159 81 VQFPVPESDGKWHHICTTWESSSGIAELWVDGKPGVRKGLAKG---YTVKPGGSIILGQEQDSYGGGFD 146 (206)
T ss_pred EEecccccCCceEEEEEEEECCCCcEEEEECCEEcccccccCC---cEECCCCEEEEEecccCCCCCCC
Confidence 34556678999999999987 567999999887633333221 24677899999997555445453
No 10
>cd00152 PTX Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. "Long" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers.
Probab=97.13 E-value=0.0033 Score=44.34 Aligned_cols=57 Identities=14% Similarity=0.243 Sum_probs=42.3
Q ss_pred EEECCCCCCCceEEEEEEE--CCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCC
Q psy5411 21 SFLIPAPTGKYFKFALKVT--LDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPI 80 (88)
Q Consensus 21 sF~v~~~d~~Whr~alsV~--~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~ 80 (88)
.+..+..+++||+++++-. .+.++||+|=+++.+..+... ..+.+++.+.|||.-..
T Consensus 82 ~~~~~~~~g~W~hv~~t~d~~~g~~~lyvnG~~~~~~~~~~~---~~~~~~g~l~lG~~q~~ 140 (201)
T cd00152 82 TFKVPESDGAWHHICVTWESTSGIAELWVNGKLSVRKSLKKG---YTVGPGGSIILGQEQDS 140 (201)
T ss_pred EEeccCCCCCEEEEEEEEECCCCcEEEEECCEEeccccccCC---CEECCCCeEEEeecccC
Confidence 4445568999999999987 567999999988866654332 24567889999986433
No 11
>PF00354 Pentaxin: Pentaxin family; InterPro: IPR001759 Pentaxins (or pentraxins) [, ] are a family of proteins which show, under electron microscopy, a discoid arrangement of five noncovalently bound subunits. Proteins of the pentaxin family are involved in acute immunological responses []. Three of the principal members of the pentaxin family are serum proteins: namely, C-reactive protein (CRP) [], serum amyloid P component protein (SAP) [], and female protein (FP) []. CRP is expressed during acute phase response to tissue injury or inflammation in mammals. The protein resembles antibody and performs several functions associated with host defence: it promotes agglutination, bacterial capsular swelling and phagocytosis, and activates the classical complement pathway through its calcium-dependent binding to phosphocholine. CRPs have also been sequenced in an invertebrate, Limulus polyphemus (Atlantic horseshoe crab), where they are a normal constituent of the hemolymph. SAP is a vertebrate protein that is a precursor of amyloid component P. It is found in all types of amyloid deposits, in glomerular basement menbrane and in elastic fibres in blood vessels. SAP binds to various lipoprotein ligands in a calcium-dependent manner, and it has been suggested that, in mammals, this may have important implications in atherosclerosis and amyloidosis. FP is a SAP homologue found in Mesocricetus auratus (Golden hamster). The concentration of this plasma protein is altered by sex steroids and stimuli that elicit an acute phase response. Pentaxin proteins expressed in the nervous system are neural pentaxin I (NPI) and II (NPII) []. NPI and NPII are homologous and can exist within one species. It is suggested that both proteins mediate the uptake of synaptic macromolecules and play a role in synaptic plasticity. Apexin, a sperm acrosomal protein, is a homologue of NPII found in Cavia porcellus (Guinea pig) []. PTX3 (or TSG-14) protein is a cytokine-induced protein that is homologous to CRPs and SAPs, but its function is not yet known.; PDB: 2A3W_F 3KQR_C 3D5O_D 2A3X_G 1SAC_D 2W08_B 1GYK_B 1LGN_A 2A3Y_A 1B09_D ....
Probab=97.05 E-value=0.0032 Score=44.76 Aligned_cols=64 Identities=22% Similarity=0.292 Sum_probs=46.3
Q ss_pred eEEECCCCCCCceEEEEEEE--CCeEEEEECCccceeEEEecCCCceeeecCcEEEEeecCCCCCCcee
Q psy5411 20 ASFLIPAPTGKYFKFALKVT--LDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAGPIIKGALD 86 (88)
Q Consensus 20 asF~v~~~d~~Whr~alsV~--~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqaG~~~~~~f~ 86 (88)
..+..+..+++||++.++=+ .+.+.||+|=....+..+.. ...+.+++++.+||--....|.|+
T Consensus 75 ~~~~~~~~~~~Whh~C~tW~s~~G~~~ly~dG~~~~~~~~~~---g~~i~~gG~~vlGQeQd~~gG~fd 140 (195)
T PF00354_consen 75 VSFSGPIRDGQWHHICVTWDSSTGRWQLYVDGVRLSSTGLAT---GHSIPGGGTLVLGQEQDSYGGGFD 140 (195)
T ss_dssp EEEEECS-TSS-EEEEEEEETTTTEEEEEETTEEEEEEESST---T--B-SSEEEEESS-BSBTTBTCS
T ss_pred eEeccccCCCCcEEEEEEEecCCcEEEEEECCEecccccccC---CceECCCCEEEECccccccCCCcC
Confidence 45666778999999999855 48999999999665554432 245678999999999999888887
No 12
>smart00560 LamGL LamG-like jellyroll fold domain.
Probab=94.54 E-value=0.057 Score=35.44 Aligned_cols=41 Identities=22% Similarity=0.285 Sum_probs=30.3
Q ss_pred CCceEEEEEEEC--CeEEEEECCccceeEEEecCCCceeeecCcEEEEe
Q psy5411 29 GKYFKFALKVTL--DGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLG 75 (88)
Q Consensus 29 ~~Whr~alsV~~--~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iG 75 (88)
++||++++..++ ++++||+|=+++.+.... + ......+.||
T Consensus 61 ~~W~hva~v~d~~~g~~~lYvnG~~~~~~~~~--~----~~~~~~~~iG 103 (133)
T smart00560 61 GVWVHLAGVYDGGAGKLSLYVNGVEVATSETQ--P----SPSSGNLPQG 103 (133)
T ss_pred CCEEEEEEEEECCCCeEEEEECCEEccccccC--C----cccCCceEEe
Confidence 999999999998 899999998887544321 2 1234567777
No 13
>KOG3514|consensus
Probab=93.35 E-value=0.15 Score=45.30 Aligned_cols=52 Identities=12% Similarity=0.032 Sum_probs=42.5
Q ss_pred CCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeec
Q psy5411 24 IPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQA 77 (88)
Q Consensus 24 v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqa 77 (88)
++..|++||++-|-=.-.+++|.+|=.++......|+-+...+ ++-+|||-.
T Consensus 100 ~~i~D~~WH~v~i~r~~e~t~L~vDgv~~~~~~~~~~f~fg~i--asdvfVGGl 151 (1591)
T KOG3514|consen 100 VRIDDDKWHTVTIFRSWENTKLEVDGVLVFKILNQRSFVFGNI--ASDVFVGGL 151 (1591)
T ss_pred ceecCCceeEEEEEeccccceEEechhhhhhhhhcceeeeeee--ehheeecCC
Confidence 5678999999999999999999999988877777776654444 458999854
No 14
>PF06439 DUF1080: Domain of Unknown Function (DUF1080); InterPro: IPR010496 This is a family of proteins of unknown function.; PDB: 3IMM_B 3NMB_A 3S5Q_A 3OSD_A 3HBK_A 3H3L_A 3U1X_A.
Probab=91.73 E-value=0.24 Score=33.32 Aligned_cols=35 Identities=17% Similarity=0.321 Sum_probs=26.9
Q ss_pred EECCCCCCCceEEEEEEECCeEEEEECCccceeEE
Q psy5411 22 FLIPAPTGKYFKFALKVTLDGVTAFVNCEEIESTR 56 (88)
Q Consensus 22 F~v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~ 56 (88)
.......++||++-|.|.+++++.++|=+++....
T Consensus 120 ~~~~~~~~~W~~~~I~~~g~~i~v~vnG~~v~~~~ 154 (185)
T PF06439_consen 120 VNVAIPPGEWNTVRIVVKGNRITVWVNGKPVADFT 154 (185)
T ss_dssp S--S--TTSEEEEEEEEETTEEEEEETTEEEEEEE
T ss_pred ccccCCCCceEEEEEEEECCEEEEEECCEEEEEEE
Confidence 33445789999999999999999999998775544
No 15
>PF02057 Glyco_hydro_59: Glycosyl hydrolase family 59; InterPro: IPR001286 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 59 GH59 from CAZY comprises enzymes with only one known activity; galactocerebrosidase (3.2.1.46 from EC). Globoid cell leukodystrophy (Krabbe disease) is a severe, autosomal recessive disorder that results from deficiency of galactocerebrosidase (GALC) activity [, , ]. GALC is responsible for the lysosomal catabolism of certain galactolipids, including galactosylceramide and psychosine [].; GO: 0004336 galactosylceramidase activity, 0006683 galactosylceramide catabolic process; PDB: 3ZR6_A 3ZR5_A.
Probab=88.50 E-value=1.9 Score=36.46 Aligned_cols=41 Identities=20% Similarity=0.166 Sum_probs=31.1
Q ss_pred eeeEEECCCCCCCceEEEEEEECCeEEEEECCccceeEEEe
Q psy5411 18 PIASFLIPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVV 58 (88)
Q Consensus 18 ~~asF~v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~ 58 (88)
.+++-..+...++||+++|.++++.++=.+|=..+.+....
T Consensus 600 ~l~~G~~~~~~~~WhtltL~~~g~~~ta~lng~~l~~~~~~ 640 (669)
T PF02057_consen 600 TLASGTADIGAGKWHTLTLTISGSTATAMLNGTVLWTDVDS 640 (669)
T ss_dssp EEEEEE-S--TT-EEEEEEEEETTEEEEEETTEEEEEEEE-
T ss_pred EEeeeeecccCCeEEEEEEEEECCEEEEEECCEEeEEeccc
Confidence 45677777888999999999999999999999999765543
No 16
>KOG1834|consensus
Probab=87.60 E-value=0.92 Score=38.72 Aligned_cols=51 Identities=24% Similarity=0.416 Sum_probs=37.0
Q ss_pred eEEEEe-cCCCCccceeeeEEE--CCC-CCCCceEEEEEEECCeEEEEECCcccee
Q psy5411 3 LTLLYT-DVTKFSTTQPIASFL--IPA-PTGKYFKFALKVTLDGVTAFVNCEEIES 54 (88)
Q Consensus 3 i~l~Yt-d~~~~~~s~~~asF~--v~~-~d~~Whr~alsV~~~~VtL~~DC~~~~~ 54 (88)
+.|+|. |++ ...+...|-|. .|. -|+.||..+|-|+.-.||||+|=...+.
T Consensus 413 l~fllr~d~~-~~~~fRpaef~Wkl~qVCD~EWH~Y~ln~efp~VtlyvDG~Sfep 467 (952)
T KOG1834|consen 413 LEFLLRRDAG-ATSDFRPAEFHWKLPQVCDNEWHHYVLNVEFPDVTLYVDGKSFEP 467 (952)
T ss_pred EEEEEccCcc-ccccccchheeccchhhhhhhhheeEEeecCceEEEEEcCcccCC
Confidence 445554 444 33344446665 444 8999999999999999999999987754
No 17
>KOG3516|consensus
Probab=84.46 E-value=2.4 Score=38.09 Aligned_cols=50 Identities=14% Similarity=0.274 Sum_probs=39.2
Q ss_pred CCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEee
Q psy5411 24 IPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQ 76 (88)
Q Consensus 24 v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGq 76 (88)
..+.||+||.++++.+.+...+-+|=.+..-.+... ++...++.+-|+|.
T Consensus 441 ~~lnDG~WHsv~~~ak~n~~~~~iDd~~~~~~~~~~---p~~V~tg~tY~fgg 490 (1306)
T KOG3516|consen 441 LKLNDGAWHSVSFNAKKNRLVLMIDDGEAEIAPDSK---PLQVYTGTTYYFGG 490 (1306)
T ss_pred ccCCCCceEEEEEEeecceeEEEEcCcccccccCCc---cEEEEeCCeeEecc
Confidence 466899999999999999999988877765554443 35567788888884
No 18
>KOG3516|consensus
Probab=84.20 E-value=4.5 Score=36.39 Aligned_cols=73 Identities=8% Similarity=0.028 Sum_probs=49.0
Q ss_pred ceEEEEecCCCCccceeeeEEECCCCCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEeec
Q psy5411 2 NLTLLYTDVTKFSTTQPIASFLIPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQA 77 (88)
Q Consensus 2 ~i~l~Ytd~~~~~~s~~~asF~v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGqa 77 (88)
+++|-|-..+ ++....+ .=+-+.-|++||.++..-...+..|-||=-+...++..=.| ..-++--+.+|||-+
T Consensus 845 ~vtf~~dvgn-Gp~~~~V-~s~t~~nD~qWH~V~~Ern~K~a~LqVD~~~~~~r~sp~~~-~~~L~l~s~l~vGgt 917 (1306)
T KOG3516|consen 845 EVTFAFDVGN-GPSQLTV-RSPTELNDNQWHQVRAERNSKEASLQVDGLPKSIRTSPIPG-TRLLQLYSSLFVGGT 917 (1306)
T ss_pred ceEEEEEcCC-CceeEEE-cCCcccCCCceEEEEEEeccccceEEEcCcccceecCCCCC-EEEEEeccceecccc
Confidence 4566665544 4432222 11235589999999999999999999998777666553323 344666788898863
No 19
>cd02175 GH16_lichenase lichenase, member of glycosyl hydrolase family 16. Lichenase, also known as 1,3-1,4-beta-glucanase, is a member of glycosyl hydrolase family 16, that specifically cleaves 1,4-beta-D-glucosidic bonds in mixed-linked beta glucans that also contain 1,3-beta-D-glucosidic linkages. Natural substrates of beta-glucanase are beta-glucans from grain endosperm cell walls or lichenan from the Islandic moss, Cetraria islandica. This protein is found not only in bacteria but also in anaerobic fungi. This domain includes two seven-stranded antiparallel beta-sheets that are adjacent to one another forming a compact, jellyroll beta-sandwich structure.
Probab=78.34 E-value=6.3 Score=27.74 Aligned_cols=41 Identities=12% Similarity=0.362 Sum_probs=31.6
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeEEE-----ecCCCceeee
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIESTRV-----VRNPQELLFD 67 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~-----~R~p~~l~~~ 67 (88)
..+.||..+|.-..++++.|+|=+++.+..- ...|..+.++
T Consensus 136 ~~~~~H~Y~v~W~~~~i~~yvDg~~v~~~~~~~~~~p~~p~~i~~n 181 (212)
T cd02175 136 ASEGFHTYAFEWEPDSIRWYVDGELVHEATATDPNIPDTPGKIMMN 181 (212)
T ss_pred cccccEEEEEEEeCCEEEEEECCEEEEEEcCccCCCCCCCcEEEEE
Confidence 4679999999999999999999988766643 3445445555
No 20
>KOG1219|consensus
Probab=78.24 E-value=3.8 Score=39.88 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=33.9
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeEEEecCCCceeeecCcEEEEee
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQ 76 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R~p~~l~~~~~~~l~iGq 76 (88)
-||+||+++|+..++...|-+|=.-.++....---.-+ .....||.|-
T Consensus 3761 nDgqWHsialerrr~~irlsvDd~~~~~atvPg~~~tl--n~d~hiy~Ga 3808 (4289)
T KOG1219|consen 3761 NDGQWHSIALERRRNHIRLSVDDDTYDSATVPGMKSTL--NLDTHIYLGA 3808 (4289)
T ss_pred ecCceeEEEeeccCCceEEEEcccCceeeecccceeec--cccceEEEee
Confidence 69999999999999999999998877655433222222 2336666663
No 21
>cd08023 GH16_laminarinase_like Laminarinase, member of the glycosyl hydrolase family 16. Laminarinase, also known as glucan endo-1,3-beta-D-glucosidase, is a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans.
Probab=77.89 E-value=11 Score=26.54 Aligned_cols=37 Identities=19% Similarity=0.347 Sum_probs=30.4
Q ss_pred eEEECC--CCCCCceEEEEEEECCeEEEEECCccceeEE
Q psy5411 20 ASFLIP--APTGKYFKFALKVTLDGVTAFVNCEEIESTR 56 (88)
Q Consensus 20 asF~v~--~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~ 56 (88)
..+..+ ...+.||..++.-..++|++|+|=+++.+..
T Consensus 147 ~~~~~~~~~~~~~fHtY~~~W~p~~i~~yvDG~~v~~~~ 185 (235)
T cd08023 147 GSYTLPTDDLSDDFHTYAVEWTPDKITFYVDGKLYFTYT 185 (235)
T ss_pred ccEECCCCCcCCCcEEEEEEEECCEEEEEECCEEEEEEc
Confidence 445554 4789999999999999999999988886553
No 22
>cd02178 GH16_beta_agarase Beta-agarase, member of glycosyl hydrolase family 16. Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Agarose is a linear chain of galactose units linked by alternating L-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Agarose forms thermo-reversible gels that are widely used in the food industry or as a laboratory medium. While beta-agarases are also found in two other families derived from the sequence-based classification of glycosyl hydrolases (GH50, and GH86) the GH16 members are most abundant. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold.
Probab=77.73 E-value=5.9 Score=28.82 Aligned_cols=53 Identities=8% Similarity=0.224 Sum_probs=37.5
Q ss_pred CCCCceEEEEEEE-CCeEEEEECCccceeEEE--------ecCCCceeeecCcEEEEeecCC
Q psy5411 27 PTGKYFKFALKVT-LDGVTAFVNCEEIESTRV--------VRNPQELLFDSASTLYLGQAGP 79 (88)
Q Consensus 27 ~d~~Whr~alsV~-~~~VtL~~DC~~~~~~~~--------~R~p~~l~~~~~~~l~iGqaG~ 79 (88)
..+.||-.+|.-. .+++++|+|=+++.+..- -..|..|+++-+..=|-|++++
T Consensus 177 ~~~~fHtY~veW~~p~~i~fyvDG~~~~~~~~~~~~~~~~f~~p~~liln~avg~w~g~~~~ 238 (258)
T cd02178 177 LADDFHVYGVYWKDPDTIRFYIDGVLVRTVENSEITDGTGFDQPMYIIIDTETYDWRGEPTD 238 (258)
T ss_pred cccCeEEEEEEEcCCCeEEEEECCEEEEEEcCcccCcCCcCCCCeEEEEEeccccCCCCCCc
Confidence 5689999999999 999999999887755432 1346567777544336564434
No 23
>PF07622 DUF1583: Protein of unknown function (DUF1583); InterPro: IPR011475 Most of the Rhodopirellula baltica hypothetical proteins that have this domain also match PF07619 from PFAM.
Probab=73.05 E-value=7.2 Score=31.15 Aligned_cols=36 Identities=17% Similarity=0.171 Sum_probs=34.2
Q ss_pred CCCCCCCceEEEEEEECCeEEEEECCccceeEEEec
Q psy5411 24 IPAPTGKYFKFALKVTLDGVTAFVNCEEIESTRVVR 59 (88)
Q Consensus 24 v~~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R 59 (88)
+|+.+..|+++-|.-.|++|.|.+|=+.+..+++..
T Consensus 85 ~~l~~~~wN~v~l~~~g~~v~l~LN~~~i~~~~~~~ 120 (399)
T PF07622_consen 85 LPLKVNAWNRVRLQRRGDKVQLHLNGQLIYERPLEP 120 (399)
T ss_pred CCCCccccceEEEEEeCCEEEEEeCCceeEecccCC
Confidence 577999999999999999999999999999999988
No 24
>cd00413 Glyco_hydrolase_16 glycosyl hydrolase family 16. The O-Glycosyl hydrolases 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 glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues.
Probab=71.07 E-value=14 Score=25.25 Aligned_cols=29 Identities=14% Similarity=0.334 Sum_probs=25.8
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeE
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIEST 55 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~ 55 (88)
..+.||..++.-..+.+++|+|=+++.+.
T Consensus 140 ~~~~~H~Y~~~W~~~~i~~yvDG~~~~~~ 168 (210)
T cd00413 140 PADDFHTYRVDWTPGEITFYVDGVLVATI 168 (210)
T ss_pred CccCeEEEEEEEeCCEEEEEECCEEEEEE
Confidence 68999999999999999999998777544
No 25
>PF00722 Glyco_hydro_16: Glycosyl hydrolases family 16; InterPro: IPR000757 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 16 GH16 from CAZY comprises enzymes with a number of known activities; lichenase (3.2.1.73 from EC); xyloglucan xyloglucosyltransferase (2.4.1.207 from EC); agarase (3.2.1.81 from EC); kappa-carrageenase (3.2.1.83 from EC); endo-beta-1,3-glucanase (3.2.1.39 from EC); endo-beta-1,3-1,4-glucanase (3.2.1.6 from EC); endo-beta-galactosidase (3.2.1.103 from EC).; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3DGT_A 2CL2_A 2WLQ_A 2WNE_A 2W39_A 2W52_A 3ILN_A 4DFS_A 1UMZ_A 1UN1_B ....
Probab=66.72 E-value=23 Score=23.79 Aligned_cols=34 Identities=9% Similarity=0.316 Sum_probs=29.4
Q ss_pred CCCCCceEEEEEEECCeEEEEECCccceeEEEec
Q psy5411 26 APTGKYFKFALKVTLDGVTAFVNCEEIESTRVVR 59 (88)
Q Consensus 26 ~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~~R 59 (88)
.....||..++.-..+.|.+|+|=+.+.+..-..
T Consensus 115 ~~~~~~h~y~~~W~~~~i~fyiDg~~~~~~~~~~ 148 (185)
T PF00722_consen 115 DPSTDFHTYGFEWTPDRIRFYIDGKLVRTVTNSD 148 (185)
T ss_dssp TTTTSEEEEEEEEETTEEEEEETTEEEEEEESSG
T ss_pred CcCCCcEEEEEEEecCeEEEEECCEEEEEEeccc
Confidence 3679999999999999999999999987666554
No 26
>cd02182 GH16_Strep_laminarinase_like Streptomyces laminarinase-like, member of glycosyl hydrolase family 16. Proteins similar to Streptomyces sioyaensis beta-1,3-glucanase (laminarinase) present in Actinomycetales as well as Peziomycotina. Laminarinases belong to glycosyl hydrolase family 16 and hydrolyze the glycosidic bond of the 1,3-beta-linked glucan, a major component of fungal and plant cell walls and the structural and storage polysaccharides (laminarin) of marine macro-algae. Members of the GH16 family have a conserved jelly roll fold with an active site channel.
Probab=62.61 E-value=24 Score=25.59 Aligned_cols=30 Identities=3% Similarity=0.201 Sum_probs=25.3
Q ss_pred CCCCceEEEEEEEC-----CeEEEEECCccceeEE
Q psy5411 27 PTGKYFKFALKVTL-----DGVTAFVNCEEIESTR 56 (88)
Q Consensus 27 ~d~~Whr~alsV~~-----~~VtL~~DC~~~~~~~ 56 (88)
.+..||..++.-.. +++++|+|=+++.+..
T Consensus 170 ~~~~fHtY~veW~~~~~~~~~I~~yvDG~~~~t~~ 204 (259)
T cd02182 170 CDTGFHTYAVEIDRTNGDAESIRWYLDGVVYHTVT 204 (259)
T ss_pred CCCCcEEEEEEEccCCCCCCEEEEEECCEEEEEEe
Confidence 56899999999985 9999999988775543
No 27
>PF08787 Alginate_lyase2: Alginate lyase; InterPro: IPR014895 Alginate lyases are enzymes that degrade the linear polysaccharide alignate. They cleave the glycosidic linkage of alignate through a beta-elimination reaction. This region forms an all beta fold, which is different to the all alpha fold of IPR008397 from INTERPRO. ; PDB: 1VAV_B 1UAI_A 1J1T_A 2Z42_A 2ZAC_A 2ZAB_A 2ZAA_A 2ZA9_A 2CWS_A.
Probab=61.15 E-value=19 Score=26.07 Aligned_cols=29 Identities=24% Similarity=0.496 Sum_probs=24.8
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeE
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIEST 55 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~ 55 (88)
..|+|-++.|.|.++.|+++++++.....
T Consensus 162 ~LG~~F~y~I~v~~~~l~V~ing~~~~~~ 190 (236)
T PF08787_consen 162 PLGEWFSYEIEVSGGTLTVTINGEGKTTV 190 (236)
T ss_dssp ETT-EEEEEEEEETTEEEEEETTEEEEEE
T ss_pred eCCCEEEEEEEEECCEEEEEEECCcceEE
Confidence 45799999999999999999999977655
No 28
>cd02180 GH16_fungal_KRE6_glucanase Saccharomyces cerevisiae KRE6 and related glucanses, member of glycosyl hydrolase family 16. KRE6 is a Saccharomyces cerevisiae glucanase that participates in the synthesis of beta-1,6-glucan, a major structural component of the cell wall. It is a golgi membrane protein required for normal beta-1,6-glucan levels in the cell wall. KRE6 is closely realted to laminarinase, a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans.
Probab=58.86 E-value=29 Score=26.35 Aligned_cols=30 Identities=13% Similarity=0.138 Sum_probs=26.0
Q ss_pred CCCCceEEEEEEEC-----CeEEEEECCccceeEE
Q psy5411 27 PTGKYFKFALKVTL-----DGVTAFVNCEEIESTR 56 (88)
Q Consensus 27 ~d~~Whr~alsV~~-----~~VtL~~DC~~~~~~~ 56 (88)
..+.||..++.... +++++|+|=+...+..
T Consensus 206 ~~~~fHtY~veW~~~~~~~~~I~wyvDg~~~~~~~ 240 (295)
T cd02180 206 NGNEFQTYGFEYRPDDEDDGYITWFVDDEPTWTIY 240 (295)
T ss_pred cCCCcEEEEEEEecCCCCCCEEEEEECCEEEEEEe
Confidence 47889999999999 8999999998775544
No 29
>KOG4495|consensus
Probab=58.08 E-value=7.8 Score=25.52 Aligned_cols=22 Identities=23% Similarity=0.318 Sum_probs=19.3
Q ss_pred EEEEEECCeEEEEECCccceeE
Q psy5411 34 FALKVTLDGVTAFVNCEEIEST 55 (88)
Q Consensus 34 ~alsV~~~~VtL~~DC~~~~~~ 55 (88)
+-|.|...+-|.|.||++-.++
T Consensus 3 ~f~~VrR~kttif~da~es~tV 24 (110)
T KOG4495|consen 3 VFLRVRRHKTTIFTDAKESSTV 24 (110)
T ss_pred eeeeeeecceeEEeecCccccH
Confidence 4678999999999999998775
No 30
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=53.35 E-value=25 Score=25.58 Aligned_cols=27 Identities=26% Similarity=0.546 Sum_probs=19.6
Q ss_pred eeEEEC--CCCCCCceEEEEEEECCeEEE
Q psy5411 19 IASFLI--PAPTGKYFKFALKVTLDGVTA 45 (88)
Q Consensus 19 ~asF~v--~~~d~~Whr~alsV~~~~VtL 45 (88)
..+|.- +..||+||++.+.|....+++
T Consensus 259 ~l~y~~~~~~~dg~~~~i~V~~~~~~~~~ 287 (296)
T TIGR03436 259 LIGYYPPNPAHDGKFRKIKVRVKRKGLKV 287 (296)
T ss_pred EEEEcCCCCCCCCceeEEEEEEeCCCceE
Confidence 456653 336899999999998765544
No 31
>cd01788 ElonginB Ubiquitin-like domain of Elongin B. Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.
Probab=48.11 E-value=15 Score=24.71 Aligned_cols=22 Identities=18% Similarity=0.247 Sum_probs=18.9
Q ss_pred EEEEEECCeEEEEECCccceeE
Q psy5411 34 FALKVTLDGVTAFVNCEEIEST 55 (88)
Q Consensus 34 ~alsV~~~~VtL~~DC~~~~~~ 55 (88)
+-|.|...+.|.|.||++-.++
T Consensus 3 vFlmIrR~KTTiF~dakes~tV 24 (119)
T cd01788 3 VFLMIRRHKTTIFTDAKESTTV 24 (119)
T ss_pred eEEEEEecceEEEeecCCcccH
Confidence 4578999999999999998765
No 32
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=47.89 E-value=21 Score=18.81 Aligned_cols=31 Identities=16% Similarity=0.285 Sum_probs=20.4
Q ss_pred CCCceEEEE-EEE-CC-eEEEEECCccceeEEEe
Q psy5411 28 TGKYFKFAL-KVT-LD-GVTAFVNCEEIESTRVV 58 (88)
Q Consensus 28 d~~Whr~al-sV~-~~-~VtL~~DC~~~~~~~~~ 58 (88)
|++|.|--+ ++. ++ -..+|+|....+..+..
T Consensus 11 d~~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~ 44 (48)
T cd04508 11 DGKWYRAKITSILSDGKVEVFFVDYGNTEVVPLS 44 (48)
T ss_pred CCeEEEEEEEEECCCCcEEEEEEcCCCcEEEeHH
Confidence 799999554 333 33 35569998887766543
No 33
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=45.56 E-value=56 Score=19.08 Aligned_cols=35 Identities=23% Similarity=0.225 Sum_probs=25.9
Q ss_pred EEEEEECCeEEEEECCccceeEEEecCCCc--eeeecCc
Q psy5411 34 FALKVTLDGVTAFVNCEEIESTRVVRNPQE--LLFDSAS 70 (88)
Q Consensus 34 ~alsV~~~~VtL~~DC~~~~~~~~~R~p~~--l~~~~~~ 70 (88)
.-+|+.|+.|.|- |=+-.++..+.+ |.. ..+++|.
T Consensus 7 qVisi~g~~vQlM-D~eTYeT~ev~~-p~~~~~~i~~G~ 43 (57)
T cd04467 7 QVLSIMGDVVQLM-DLETYETFEVPI-PEEIKDKLEPGK 43 (57)
T ss_pred EEEEEcCCEEEEe-ccccceeEEEec-chhhcccCCCCC
Confidence 4578999988776 999999999888 434 3455554
No 34
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=44.13 E-value=54 Score=24.80 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=35.1
Q ss_pred CceEEEEecCCCCccceeeeEEECCCCCCCceEEEEEEECCeEEEE
Q psy5411 1 MNLTLLYTDVTKFSTTQPIASFLIPAPTGKYFKFALKVTLDGVTAF 46 (88)
Q Consensus 1 ~~i~l~Ytd~~~~~~s~~~asF~v~~~d~~Whr~alsV~~~~VtL~ 46 (88)
+.+.|.|.+.++....+.+..+.+-...+.|+=+|..-..+.+..|
T Consensus 153 ~~l~~~Y~~~~g~~t~R~V~P~~l~~~~~~wylva~c~~r~~~R~F 198 (311)
T COG2378 153 KVLSFDYRDSSGEETERIVEPLGLVFKGGHWYLVAWCELRQDFRTF 198 (311)
T ss_pred CeEEEEEECCCCCceeEEEeeeEEEEECCEEEEEeeecccCceeEE
Confidence 4578999988755556666777766689999999998888876553
No 35
>PF02973 Sialidase: Sialidase, N-terminal domain; InterPro: IPR004124 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. Sialidases (GH33 from CAZY) hydrolyse alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. Sialidases may act as pathogenic factors in microbial infections []. The 1.8 A structure of trans-sialidase from leech (Macrobdella decora, Q27701 from SWISSPROT) in complex with 2-deoxy-2, 3-didehydro-NeuAc was solved. The refined model comprising residues 81-769 has a catalytic beta-propeller domain, a N-terminal lectin-like domain and an irregular beta-stranded domain inserted into the catalytic domain [].; GO: 0004308 exo-alpha-sialidase activity, 0005975 carbohydrate metabolic process; PDB: 2JKB_A 2VW2_A 2VW0_A 2VW1_A 2V73_B 2V72_A 1SLI_A 1SLL_A 2SLI_A 4SLI_A ....
Probab=41.68 E-value=71 Score=22.90 Aligned_cols=30 Identities=17% Similarity=0.199 Sum_probs=24.6
Q ss_pred CCCCceEEEEEEE--CCeEEEEECCccceeEE
Q psy5411 27 PTGKYFKFALKVT--LDGVTAFVNCEEIESTR 56 (88)
Q Consensus 27 ~d~~Whr~alsV~--~~~VtL~~DC~~~~~~~ 56 (88)
.+..||.+|+..+ +..+.||+|=+.+.+..
T Consensus 101 ~~~~~~tva~~ad~~~~~ykly~NG~~v~~~~ 132 (190)
T PF02973_consen 101 NNVTFNTVAFVADSKNKGYKLYVNGELVSTLS 132 (190)
T ss_dssp TEES-EEEEEEEETTTTEEEEEETTCEEEEEE
T ss_pred CCceEEEEEEEEecCCCeEEEEeCCeeEEEec
Confidence 5567999999997 99999999998876553
No 36
>PF03421 YopJ: YopJ Serine/Threonine acetyltransferase; InterPro: IPR005083 The infection of mammalian host cells by Yersinia sp. causes a rapid induction of the mitogen-activated protein kinase (MAPK; including the ERK, JNK and p38 pathways) and nuclear factor kappaB (NF-kappaB) signalling pathways that would typically result in cytokine production and initiation of the innate immune response. However, these pathways are rapidly inhibited promoting apoptosis. YopJ has been shown to block phosphorylation of active site residues []. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate []. Serine and threonine acetylation is yet another complication to the control of signalling pathways and may be a may be a widespread mode of biochemical regulation of endogenous processes in eukaryotic cells. It has been shown that YopJ is a serine/threonine acetyltransferase []. It acetylates the serine and threonine residues in the phosphorylation sites of MAPK kinases and nuclear factor kappaB, preventing their activation by phosphorylation and the inhibition of these signalling pathways []. This entry contains YopJ and related proteins.
Probab=39.96 E-value=53 Score=23.05 Aligned_cols=33 Identities=9% Similarity=-0.021 Sum_probs=24.6
Q ss_pred eEEECCCCCCCceEEEEEEE---CCeEEE-EECCccc
Q psy5411 20 ASFLIPAPTGKYFKFALKVT---LDGVTA-FVNCEEI 52 (88)
Q Consensus 20 asF~v~~~d~~Whr~alsV~---~~~VtL-~~DC~~~ 52 (88)
..|-|+.-.+.+|.+|+.|+ ++.+|+ .+++-..
T Consensus 72 ~R~Iv~~~~~~~H~~a~Dvr~~~~~k~SlI~~Epa~~ 108 (177)
T PF03421_consen 72 WRAIVNLGGDGIHHVALDVRHTPNGKPSLIVFEPASF 108 (177)
T ss_pred eEEEEeCCCCCCcEEEEEEeecCCCCceEEEEccccc
Confidence 44556778899999999998 777777 5566543
No 37
>cd02177 GH16_kappa_carrageenase Kappa-carrageenase, member of glycosyl hydrolase family 16. Kappa-carrageenase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of kappa-carrageenans, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Carrageenans are linear chains of galactose units linked by alternating D-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Depending on the position and number of sulfate ester modifications they are subdivided into kappa-, iota-, and lambda-carrageenases, kappa being modified once. Carrageenans form thermo-reversible gels widely used for industrial applications. Kappa-carrageenases exist in bacteria belonging to at least three phylogenetically distant branches, including pseudoalteromonas, planctomycetes, and baceroidetes. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to
Probab=39.47 E-value=64 Score=24.10 Aligned_cols=30 Identities=17% Similarity=0.393 Sum_probs=26.4
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeEE
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIESTR 56 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~~ 56 (88)
..+.||..+|.-..+++++|||=+.+.+.+
T Consensus 188 ~~~~fH~y~v~W~~~~i~~yvDg~~~~~~~ 217 (269)
T cd02177 188 PSKDFHTYGCNVNQDEIIWYVDGVEVGRKP 217 (269)
T ss_pred CccCcEEEEEEEeCCEEEEEECCEEEEEEc
Confidence 568899999999999999999999886554
No 38
>PRK13442 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=38.87 E-value=63 Score=19.97 Aligned_cols=22 Identities=18% Similarity=0.351 Sum_probs=17.1
Q ss_pred CCCCceEEE-----EEEECCeEEEEEC
Q psy5411 27 PTGKYFKFA-----LKVTLDGVTAFVN 48 (88)
Q Consensus 27 ~d~~Whr~a-----lsV~~~~VtL~~D 48 (88)
.+++|.+++ +.|++|+|++..|
T Consensus 57 ~~~~~~~~~v~gG~~~v~~n~v~Il~~ 83 (89)
T PRK13442 57 PGGERISAAVDGGFISFDSNKLTVLAE 83 (89)
T ss_pred CCCcEEEEEEccEEEEEECCEEEEEEe
Confidence 478899988 4688888888765
No 39
>cd02183 GH16_fungal_CRH1_transglycosylase glycosylphosphatidylinositol-glucanosyltransferase. Group of fungal GH16 members related to Saccharomyces cerevisiae Crh1p. Chr1p and Crh2p are transglycosylases that are required for the linkage of chitin to beta(1-3)glucose branches of beta(1-6)glucan, an important step in the assembly of new cell wall. Both have been shown to be glycosylphosphatidylinositol (GPI)-anchored. A third homologous protein, Crr1p, functions in the formation of the spore wall. They belongs to the family 16 of glycosyl hydrolases that includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues.
Probab=38.65 E-value=1.2e+02 Score=21.52 Aligned_cols=29 Identities=14% Similarity=0.366 Sum_probs=25.4
Q ss_pred CCCceEEEEEEECCeEEEEECCccceeEE
Q psy5411 28 TGKYFKFALKVTLDGVTAFVNCEEIESTR 56 (88)
Q Consensus 28 d~~Whr~alsV~~~~VtL~~DC~~~~~~~ 56 (88)
...||..+|.=..+.+++|+|=+++.+..
T Consensus 114 ~~dFHtY~veWtpd~I~~yVDG~~v~~~~ 142 (203)
T cd02183 114 TEEFHTYTIDWTKDRITWYIDGKVVRTLT 142 (203)
T ss_pred CcCcEEEEEEEecCEEEEEECCEEEEEEe
Confidence 37899999999999999999998875543
No 40
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=38.41 E-value=32 Score=22.33 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=17.5
Q ss_pred CCCCceEEEEEEECCeEEEEE
Q psy5411 27 PTGKYFKFALKVTLDGVTAFV 47 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~ 47 (88)
.|++-||++++..|.+|.+++
T Consensus 3 ~Dgklh~y~y~~~G~~vrff~ 23 (102)
T PF10080_consen 3 KDGKLHRYAYTDDGKEVRFFA 23 (102)
T ss_pred cCCcEEEEEEcCCCEEEEEEE
Confidence 578889999988888888876
No 41
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=38.12 E-value=39 Score=16.30 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=16.5
Q ss_pred CCCceeeecCcEEEEeecCCC
Q psy5411 60 NPQELLFDSASTLYLGQAGPI 80 (88)
Q Consensus 60 ~p~~l~~~~~~~l~iGqaG~~ 80 (88)
.|..+..++.+.|||+..+..
T Consensus 3 ~P~gvav~~~g~i~VaD~~n~ 23 (28)
T PF01436_consen 3 YPHGVAVDSDGNIYVADSGNH 23 (28)
T ss_dssp SEEEEEEETTSEEEEEECCCT
T ss_pred CCcEEEEeCCCCEEEEECCCC
Confidence 466788888999999887653
No 42
>PF09008 Head_binding: Head binding; InterPro: IPR009093 This entry represents the N-terminal domain of the Bacteriophage P22, Gp9, tailspike protein (TSP). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The tailspike protein of Salmonella bacteriophage P22 is a viral adhesion protein that mediates attachment of the viral protein to host cell-surface lipopolysaccharide. The tailspike protein displays both receptor binding and destroying properties, inactivating the receptor by endoglycosidase activity. The N-terminal, head-binding domain mediates the non-covalent attachment of the six homotrimeric tailspike molecules to the DNA injection apparatus []. The N-terminal domain of the P22 tailspike protein shows significant sequence similarity to the N-terminal domain of the Shigella phage Sf6 tailspike protein [].; GO: 0009405 pathogenesis; PDB: 2XC1_C 1LKT_D 2VFQ_A 2VFO_A 2VFN_A 2VFP_A 2VKY_B 2VFM_A 2VNL_A 2VBK_A ....
Probab=36.63 E-value=25 Score=23.48 Aligned_cols=17 Identities=24% Similarity=0.499 Sum_probs=12.0
Q ss_pred eeeecCcEEEEeecCCC
Q psy5411 64 LLFDSASTLYLGQAGPI 80 (88)
Q Consensus 64 l~~~~~~~l~iGqaG~~ 80 (88)
+--...+.||||++|.-
T Consensus 23 F~~~~~GKiYIGk~~tD 39 (114)
T PF09008_consen 23 FWANFNGKIYIGKAGTD 39 (114)
T ss_dssp SSB-TTEEEEEESTTS-
T ss_pred HhhhcCCcEEEecCCCC
Confidence 33456889999999964
No 43
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 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. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=35.91 E-value=78 Score=17.36 Aligned_cols=26 Identities=4% Similarity=0.119 Sum_probs=12.9
Q ss_pred CCCCceEEEEEEE--CCeEEEEECCccc
Q psy5411 27 PTGKYFKFALKVT--LDGVTAFVNCEEI 52 (88)
Q Consensus 27 ~d~~Whr~alsV~--~~~VtL~~DC~~~ 52 (88)
...+|.++++++. |..+.+-++-+.+
T Consensus 3 LP~~w~~l~F~~~~rg~~l~v~i~~~~v 30 (54)
T PF03633_consen 3 LPKQWSSLSFRLRYRGHWLEVEITHEKV 30 (54)
T ss_dssp --TT-SEEEEEEEETTEEEEEEEETTEE
T ss_pred CCCccCEeEEEEEECCEEEEEEEECCEE
Confidence 4567777776663 4444444554444
No 44
>PF10102 DUF2341: Domain of unknown function (DUF2341); InterPro: IPR018765 This domain of unknown function is found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins.
Probab=35.33 E-value=51 Score=20.58 Aligned_cols=32 Identities=22% Similarity=0.243 Sum_probs=19.0
Q ss_pred ceEEEEecCCCCccceeeeEEEC-CCCCC-----CceE
Q psy5411 2 NLTLLYTDVTKFSTTQPIASFLI-PAPTG-----KYFK 33 (88)
Q Consensus 2 ~i~l~Ytd~~~~~~s~~~asF~v-~~~d~-----~Whr 33 (88)
.|.+||..+.....+...++|.. +.|.+ +||-
T Consensus 45 ~i~lyyGn~~a~~~sn~~~vF~ffDdf~~~~~~~~W~~ 82 (89)
T PF10102_consen 45 TIYLYYGNPSATSASNGDAVFEFFDDFEGSLDTTKWHF 82 (89)
T ss_pred EEEEEECCCCCccCCCcccEEEEecCCCCccccceEeE
Confidence 47788887663333444477653 44555 8873
No 45
>cd08024 GH16_CCF Coelomic cytolytic factor, member of glycosyl hydrolase family 16. Subgroup of glucanases of unknown function that are related to beta-GRP (beta-1,3-glucan recognition protein), but contain active site residues. Beta-GRPs are one group of pattern recognition receptors (PRRs), also referred to as biosensor proteins, that complexes with pathogen-associated beta-1,3-glucans and then transduces signals necessary for activation of an appropriate innate immune response. Beta-GRPs are present in insects and lack all catalytic residues. This subgroup contains related proteins that still contain the active site and are widely distributed in eukaryotes. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic residues, like those of other glycosyl hydrolase family 16 members.
Probab=32.47 E-value=1.1e+02 Score=23.48 Aligned_cols=31 Identities=19% Similarity=0.256 Sum_probs=27.1
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeEEE
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIESTRV 57 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~~~ 57 (88)
+.+.||..+|.=..+.+++|+|=+++.+...
T Consensus 203 ~~~~FHtY~veWtpd~I~fyVDG~~~~~v~~ 233 (330)
T cd08024 203 FADDFHTYGLDWTPDHIRFYVDDRLILTLDV 233 (330)
T ss_pred cccCCEEEEEEEeCCEEEEEECCEEEEEEec
Confidence 6788999999999999999999888766654
No 46
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=31.02 E-value=77 Score=18.95 Aligned_cols=30 Identities=7% Similarity=0.373 Sum_probs=20.1
Q ss_pred CCCCCceEEEE--EEECCeEEE-EECCccceeE
Q psy5411 26 APTGKYFKFAL--KVTLDGVTA-FVNCEEIEST 55 (88)
Q Consensus 26 ~~d~~Whr~al--sV~~~~VtL-~~DC~~~~~~ 55 (88)
..+++|+|--+ ....+.+.+ |+|=-...+.
T Consensus 63 ~~~~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~v 95 (121)
T PF00567_consen 63 SEDGRWYRAVITVDIDENQYKVFLIDYGNTEKV 95 (121)
T ss_dssp TTTSEEEEEEEEEEECTTEEEEEETTTTEEEEE
T ss_pred ecCCceeeEEEEEecccceeEEEEEecCceEEE
Confidence 36899999998 555666555 6665554443
No 47
>TIGR03606 non_repeat_PQQ dehydrogenase, PQQ-dependent, s-GDH family. PQQ, or pyrroloquinoline-quinone, serves as a cofactor for a number of sugar and alcohol dehydrogenases in a limited number of bacterial species. Most characterized PQQ-dependent enzymes have multiple repeats of a sequence region described by pfam01011 (PQQ enzyme repeat), but this protein family in unusual in lacking that repeat. Below the noise cutoff are related proteins mostly from species that lack PQQ biosynthesis.
Probab=30.98 E-value=48 Score=26.79 Aligned_cols=29 Identities=41% Similarity=0.664 Sum_probs=23.8
Q ss_pred ecCCCceeeecCcEEEEeecCCCCCCcee
Q psy5411 58 VRNPQELLFDSASTLYLGQAGPIIKGALD 86 (88)
Q Consensus 58 ~R~p~~l~~~~~~~l~iGqaG~~~~~~f~ 86 (88)
.|+|+.|.|++.+.||++..|+...+.+.
T Consensus 229 ~RNp~Gla~dp~G~Lw~~e~Gp~~~DEiN 257 (454)
T TIGR03606 229 HRNPQGLAFTPDGTLYASEQGPNSDDELN 257 (454)
T ss_pred ccccceeEECCCCCEEEEecCCCCCcEEE
Confidence 48898899999899999999987655544
No 48
>PF04582 Reo_sigmaC: Reovirus sigma C capsid protein; InterPro: IPR007662 Protein sigmaC in its native state was shown to be a homotrimer. It was demonstrated that the sigmaC subunits are not covalently bound via disulphide linkages and the formation of an intrachain disulphide bond between the two cysteine residues of the sigmaC polypeptide may have a negative effect on oligomer stability. The susceptibility of the trimer to pH, temperature, ionic strength, chemical denaturants and detergents indicates that hydrophobic interactions contribute much more to oligomer stability than do ionic interactions and hydrogen bonding [].; PDB: 2VRS_C 2JJL_A 2BSF_A 2BT7_A 2BT8_A.
Probab=30.84 E-value=37 Score=26.50 Aligned_cols=25 Identities=20% Similarity=0.147 Sum_probs=18.4
Q ss_pred EEEEEECCeEEEEECCccceeEEEe
Q psy5411 34 FALKVTLDGVTAFVNCEEIESTRVV 58 (88)
Q Consensus 34 ~alsV~~~~VtL~~DC~~~~~~~~~ 58 (88)
-+|.|.++.|+|-+||..+...|.+
T Consensus 235 ~~~Tvt~~~~~L~f~l~~it~~p~D 259 (326)
T PF04582_consen 235 QSLTVTGNSVSLVFDLDYITPPPSD 259 (326)
T ss_dssp SEEEE-SSEEEEEEEGGGEES--S-
T ss_pred CceEecCCcEEEEEEhhhccCCccc
Confidence 3678999999999999999777744
No 49
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=27.68 E-value=57 Score=21.88 Aligned_cols=23 Identities=13% Similarity=0.384 Sum_probs=18.5
Q ss_pred eeEEECCCCCCCceEEEEEEECC
Q psy5411 19 IASFLIPAPTGKYFKFALKVTLD 41 (88)
Q Consensus 19 ~asF~v~~~d~~Whr~alsV~~~ 41 (88)
...|.+++.+++|-|+.++++-+
T Consensus 52 l~~~~vNL~~~~ylk~~i~l~~~ 74 (142)
T PRK07718 52 TPEITTNLKSGNFIRIQFKIETD 74 (142)
T ss_pred cCCeEEEcCCCCEEEEEEEEEEC
Confidence 45788888899999999987643
No 50
>PF14099 Polysacc_lyase: Polysaccharide lyase; PDB: 3ILR_A 3IKW_A 3INA_A 3IMN_A 3IN9_A 2ZZJ_A.
Probab=27.43 E-value=2.1e+02 Score=19.80 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=21.1
Q ss_pred CCCCCCceEEEEEEE-----CCeEEEEECCccc
Q psy5411 25 PAPTGKYFKFALKVT-----LDGVTAFVNCEEI 52 (88)
Q Consensus 25 ~~~d~~Whr~alsV~-----~~~VtL~~DC~~~ 52 (88)
+...|+||++.+.|. .+.+.+++|=+.+
T Consensus 148 ~~~~G~W~~~~i~~~~s~~~~G~~~vw~nG~~v 180 (224)
T PF14099_consen 148 PVERGKWHDFVIHVKWSPDSDGFLEVWLNGKLV 180 (224)
T ss_dssp CS-TTSEEEEEEEEEE-CCCTEEEEEEECCEEC
T ss_pred CcCCCcEEEEEEEEEECCCCCEEEEEEECCEEE
Confidence 445599999999995 4568888887665
No 51
>PF12087 DUF3564: Protein of unknown function (DUF3564); InterPro: IPR021947 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 118 to 142 amino acids in length. This protein has a conserved WSRE sequence motif.
Probab=26.74 E-value=1.6e+02 Score=19.91 Aligned_cols=76 Identities=12% Similarity=0.151 Sum_probs=40.1
Q ss_pred CceEEEEecCCCCccceeeeEEECCCCCCCceEEE-----------EEEECCeEEEEECCccceeEEEec--------CC
Q psy5411 1 MNLTLLYTDVTKFSTTQPIASFLIPAPTGKYFKFA-----------LKVTLDGVTAFVNCEEIESTRVVR--------NP 61 (88)
Q Consensus 1 ~~i~l~Ytd~~~~~~s~~~asF~v~~~d~~Whr~a-----------lsV~~~~VtL~~DC~~~~~~~~~R--------~p 61 (88)
|+|+++-...+ ...+...|.-=++...++|.|-+ |...++.+.| |-.-...++-. .-
T Consensus 1 MRLTI~ld~~d-~~~~~ayAVLWlDtd~r~WSRE~H~GidLP~WG~l~~~~g~~~l---c~~d~~~~lC~L~GL~~~~~~ 76 (121)
T PF12087_consen 1 MRLTIHLDTFD-PTTPHAYAVLWLDTDERRWSREGHQGIDLPAWGKLRDEEGATRL---CAPDSGAPLCVLEGLDLDARQ 76 (121)
T ss_pred CeEEEEecCCC-CCCccceEEEEEEcCCcccccccccCccCCCCcceEecCCcEEE---ecCCCCCceEEEeCccccCCC
Confidence 56666654333 22332333333466889999975 5666676666 55443333322 11
Q ss_pred CceeeecCcEEEEeecCCC
Q psy5411 62 QELLFDSASTLYLGQAGPI 80 (88)
Q Consensus 62 ~~l~~~~~~~l~iGqaG~~ 80 (88)
.+.+-+.|...|..+++..
T Consensus 77 ~p~eg~~G~A~w~~~~~~~ 95 (121)
T PF12087_consen 77 GPFEGEQGRAQWCAHAGRA 95 (121)
T ss_pred CCcccCcccEEEeccCCCC
Confidence 1233344556666666654
No 52
>cd01253 PH_beta_spectrin Beta-spectrin pleckstrin homology (PH) domain. Beta-spectrin pleckstrin homology (PH) domain. Beta spectrin binds actin and functions as a major component of the cytoskeleton underlying cellular membranes. Beta spectrin consists of multiple spectrin repeats followed by a PH domain, which binds to Inositol-1,4,5-Trisphosphate. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. PH domains are often involved in targeting proteins to the plasma membrane via lipid binding. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=26.73 E-value=1.3e+02 Score=18.26 Aligned_cols=25 Identities=0% Similarity=-0.088 Sum_probs=22.6
Q ss_pred CCCCceEEEEEEECCeEEEEECCcc
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEE 51 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~ 51 (88)
..+.|++.-+...++...+|-|...
T Consensus 19 ~~~~Wk~r~~vL~~~~L~~ykd~~~ 43 (104)
T cd01253 19 SNRSWDNVYGVLCGQSLSFYKDEKM 43 (104)
T ss_pred CCCCcceEEEEEeCCEEEEEecCcc
Confidence 5899999999999999999999764
No 53
>PF00207 A2M: Alpha-2-macroglobulin family; InterPro: IPR001599 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0004866 endopeptidase inhibitor activity; PDB: 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 2PN5_A 3FRP_G 3HRZ_B ....
Probab=26.56 E-value=1.5e+02 Score=17.82 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=21.4
Q ss_pred eeeeEEECCCCCCCceEEEEEEECCe
Q psy5411 17 QPIASFLIPAPTGKYFKFALKVTLDG 42 (88)
Q Consensus 17 ~~~asF~v~~~d~~Whr~alsV~~~~ 42 (88)
....+|++|..-++|+=.|+++..+.
T Consensus 15 ~~~~~~~lPd~it~w~v~a~a~s~~~ 40 (92)
T PF00207_consen 15 KATFSFTLPDSITSWRVTAFAVSPTG 40 (92)
T ss_dssp EEEEEEE-SSSSSEEEEEEEEEETTT
T ss_pred EEEEEEECCCCccEEEEEEEEECCCC
Confidence 44578889999999999999999983
No 54
>KOG3514|consensus
Probab=24.86 E-value=99 Score=28.50 Aligned_cols=47 Identities=19% Similarity=0.273 Sum_probs=33.8
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeE-EEecCCCceeeecCcEEEEe
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIEST-RVVRNPQELLFDSASTLYLG 75 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~-~~~R~p~~l~~~~~~~l~iG 75 (88)
.||++|=+-++=.|++.||=+|--++... |-.|. -.+|.+.+.|-||
T Consensus 1142 NDgkYHVVRFtR~GGNATLQVD~wpV~e~yP~grq--lTiFNtqa~I~IG 1189 (1591)
T KOG3514|consen 1142 NDGKYHVVRFTRSGGNATLQVDSWPVNERYPAGRQ--LTIFNSQARISIG 1189 (1591)
T ss_pred cCCceEEEEEEecCCceEEEecccchhhccCCCce--eEEeeccceEEec
Confidence 79999999999999999999998877433 33321 2445555555444
No 55
>PF02823 ATP-synt_DE_N: ATP synthase, Delta/Epsilon chain, beta-sandwich domain; InterPro: IPR020546 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This family represents subunits called delta (in mitochondrial ATPase) or epsilon (in bacteria or chloroplast ATPase). The interaction site of subunit C of the F0 complex with the delta or epsilon subunit of the F1 complex may be important for connecting the rotor of F1 (gamma subunit) to the rotor of F0 (C subunit) []. In bacterial species, the delta subunit is the equivalent of the Oligomycin sensitive subunit (OSCP, IPR000711 from INTERPRO) in metazoans. The C-terminal domain of the epsilon subunit appears to act as an inhibitor of ATPase activity []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0045261 proton-transporting ATP synthase complex, catalytic core F(1); PDB: 2WSS_H 1E79_H 2JDI_H 2W6I_H 2W6H_H 2W6J_H 2CK3_H 2V7Q_H 1H8E_H 2XND_H ....
Probab=24.53 E-value=1.5e+02 Score=17.46 Aligned_cols=22 Identities=32% Similarity=0.425 Sum_probs=17.3
Q ss_pred CCCCceEEEE-----EEECCeEEEEEC
Q psy5411 27 PTGKYFKFAL-----KVTLDGVTAFVN 48 (88)
Q Consensus 27 ~d~~Whr~al-----sV~~~~VtL~~D 48 (88)
.|++|+++++ .|++++|++..|
T Consensus 52 ~~~~~~~~~v~~G~~~v~~n~v~Il~~ 78 (80)
T PF02823_consen 52 ADGEEKKFAVSGGFLEVKDNEVTILAD 78 (80)
T ss_dssp SSSEEEEEEESSEEEEEETSEEEEEES
T ss_pred cCCCEEEEEEcCEEEEEECCEEEEEEc
Confidence 6789999875 588888887765
No 56
>PRK14736 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=24.13 E-value=1.4e+02 Score=19.92 Aligned_cols=22 Identities=18% Similarity=0.249 Sum_probs=17.4
Q ss_pred CCCCceEEEE-----EEECCeEEEEEC
Q psy5411 27 PTGKYFKFAL-----KVTLDGVTAFVN 48 (88)
Q Consensus 27 ~d~~Whr~al-----sV~~~~VtL~~D 48 (88)
.++.|.++++ .|..|+|++..|
T Consensus 55 ~~~~~~~~~v~gGf~eV~~n~v~Ila~ 81 (133)
T PRK14736 55 TTGNGKRIYVRGGFAEIGPTSVTVLAE 81 (133)
T ss_pred CCCcEEEEEEeceEEEEECCEEEEEee
Confidence 4789999884 588888887765
No 57
>PRK00539 atpC F0F1 ATP synthase subunit epsilon; Validated
Probab=23.72 E-value=1.6e+02 Score=19.62 Aligned_cols=24 Identities=4% Similarity=-0.086 Sum_probs=19.0
Q ss_pred CCCCceEEEE-----EEECCeEEEEECCc
Q psy5411 27 PTGKYFKFAL-----KVTLDGVTAFVNCE 50 (88)
Q Consensus 27 ~d~~Whr~al-----sV~~~~VtL~~DC~ 50 (88)
.++.|+.+++ .|.+|+|++..|=-
T Consensus 55 ~~~~~~~~~v~gGf~ev~~n~v~Ilad~a 83 (133)
T PRK00539 55 ADKTKRSAIIGAGLLLIKKTEAKIFTENF 83 (133)
T ss_pred CCCcEEEEEEeeeEEEEECCEEEEEECeE
Confidence 4788988887 58999999988743
No 58
>cd02179 GH16_beta_GRP beta-1,3-glucan recognition protein, member of glycosyl hydrolase family 16. Beta-GRP (beta-1,3-glucan recognition protein) is one of several pattern recognition receptors (PRRs), also referred to as biosensor proteins, that complexes with pathogen-associated beta-1,3-glucans and then transduces signals necessary for activation of an appropriate innate immune response. They are present in insects and lack all catalytic residues. This subgroup also contains related proteins of unknown function that still contain the active site. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic residues, like those of other glycosyl hydrolase family 16 members.
Probab=23.15 E-value=2e+02 Score=22.00 Aligned_cols=31 Identities=23% Similarity=0.344 Sum_probs=27.3
Q ss_pred CCCCCceEEEEEEECCeEEEEECCccceeEE
Q psy5411 26 APTGKYFKFALKVTLDGVTAFVNCEEIESTR 56 (88)
Q Consensus 26 ~~d~~Whr~alsV~~~~VtL~~DC~~~~~~~ 56 (88)
.+...||..+|.=..+.+++|||=+.+.+..
T Consensus 197 ~~~ddFHtY~leWtpd~I~f~VDg~~~~~~~ 227 (321)
T cd02179 197 LWSDDFHVYTLEWKPDGITLMVDGEEYGEIE 227 (321)
T ss_pred ccccCcEEEEEEEeCCEEEEEECCEEEEEEe
Confidence 3678899999999999999999999886665
No 59
>PRK01474 atpC F0F1 ATP synthase subunit epsilon; Validated
Probab=22.86 E-value=1.7e+02 Score=18.74 Aligned_cols=21 Identities=10% Similarity=0.034 Sum_probs=14.5
Q ss_pred CCCceEEEE-----EEECCeEEEEEC
Q psy5411 28 TGKYFKFAL-----KVTLDGVTAFVN 48 (88)
Q Consensus 28 d~~Whr~al-----sV~~~~VtL~~D 48 (88)
++.|.++++ .|.+|+|++..|
T Consensus 59 ~~~~~~~~v~gGf~~v~~n~v~Ila~ 84 (112)
T PRK01474 59 HKSENTYLISGGVTEVTGNYINIATE 84 (112)
T ss_pred CCcEEEEEEcceEEEEECCEEEEEeC
Confidence 467888874 467777777654
No 60
>KOG4289|consensus
Probab=22.70 E-value=2e+02 Score=27.73 Aligned_cols=33 Identities=15% Similarity=0.231 Sum_probs=25.0
Q ss_pred CCCCCceEEEEEEECCeEEEEE-CCccceeEEEe
Q psy5411 26 APTGKYFKFALKVTLDGVTAFV-NCEEIESTRVV 58 (88)
Q Consensus 26 ~~d~~Whr~alsV~~~~VtL~~-DC~~~~~~~~~ 58 (88)
..||+||-++|.-.....++-+ ||+--....+.
T Consensus 1395 vsDGqWHtV~l~YyNK~av~svDdCdt~~al~fg 1428 (2531)
T KOG4289|consen 1395 VSDGQWHTVQLEYYNKVAVVSVDDCDTNVALRFG 1428 (2531)
T ss_pred cccCceeEEEEEEeceEEEEEeccccccceeeec
Confidence 3899999999999988888754 57765444444
No 61
>PF01149 Fapy_DNA_glyco: Formamidopyrimidine-DNA glycosylase N-terminal domain; InterPro: IPR012319 This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006284 base-excision repair; PDB: 1K82_C 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A ....
Probab=22.65 E-value=1.4e+02 Score=18.85 Aligned_cols=29 Identities=14% Similarity=0.071 Sum_probs=22.3
Q ss_pred CCCCceEEEEEEECCeEEEEECCccceeE
Q psy5411 27 PTGKYFKFALKVTLDGVTAFVNCEEIEST 55 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~DC~~~~~~ 55 (88)
...++.|+.|..+++..-.|.|+-...+.
T Consensus 87 ~~~~~~~~~l~~~~g~~L~f~D~R~fg~~ 115 (116)
T PF01149_consen 87 WPPKHTRLRLRFEDGSRLRFVDPRRFGRV 115 (116)
T ss_dssp G-STTEEEEEEETSSEEEEEEETTS--EE
T ss_pred CCCCeEEEEEEECCCCEEEEEcCCCCCCC
Confidence 56888999999999998889998877543
No 62
>PF09313 DUF1971: Domain of unknown function (DUF1971); InterPro: IPR015392 This uncharacterised domain is predominantly found in bacterial Tellurite resistance proteins. ; PDB: 3BB6_C 3M70_A 3DL3_I.
Probab=21.98 E-value=2e+02 Score=17.75 Aligned_cols=19 Identities=5% Similarity=0.081 Sum_probs=10.4
Q ss_pred CCCCceEEEEEEECCeEEEEE
Q psy5411 27 PTGKYFKFALKVTLDGVTAFV 47 (88)
Q Consensus 27 ~d~~Whr~alsV~~~~VtL~~ 47 (88)
....|||+.. .++.+.+++
T Consensus 63 ~Pq~wH~V~p--~s~D~~f~l 81 (82)
T PF09313_consen 63 EPQQWHRVEP--LSDDLRFQL 81 (82)
T ss_dssp -TT-EEEEEE--SSTT-EEEE
T ss_pred CCCceEEEEE--CCCCEEEEe
Confidence 5789999875 344455544
No 63
>KOG1653|consensus
Probab=21.55 E-value=50 Score=23.59 Aligned_cols=9 Identities=0% Similarity=0.253 Sum_probs=7.3
Q ss_pred CCceEEEEE
Q psy5411 29 GKYFKFALK 37 (88)
Q Consensus 29 ~~Whr~als 37 (88)
-+|||+++=
T Consensus 104 tqWHRVsVf 112 (175)
T KOG1653|consen 104 TQWHRVSVF 112 (175)
T ss_pred ceeEEEEee
Confidence 689999873
No 64
>TIGR03166 alt_F1F0_F1_eps alternate F1F0 ATPase, F1 subunit epsilon. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 epsilon subunit of this apparent second ATP synthase.
Probab=20.77 E-value=1.8e+02 Score=19.08 Aligned_cols=22 Identities=18% Similarity=0.022 Sum_probs=16.1
Q ss_pred CCCCceEEEE-----EEECCeEEEEEC
Q psy5411 27 PTGKYFKFAL-----KVTLDGVTAFVN 48 (88)
Q Consensus 27 ~d~~Whr~al-----sV~~~~VtL~~D 48 (88)
.+++|+.+++ .|.+|+|++..|
T Consensus 52 ~~~~~~~~av~gGf~~v~~n~v~Il~~ 78 (122)
T TIGR03166 52 ADGGEHYVAVDQGILVKRGADVEVSVR 78 (122)
T ss_pred CCCcEEEEEEeeeEEEEECCEEEEEec
Confidence 4788988754 578888887765
No 65
>PF07953 Toxin_R_bind_N: Clostridium neurotoxin, N-terminal receptor binding; InterPro: IPR012928 The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (IPR000395 from INTERPRO), the central translocation domain and two receptor binding domains []. This domain is the N-terminal receptor binding domain, which is comprised of two seven-stranded beta-sheets sandwiched together to form a jelly role motif []. The role of this domain in receptor binding appears to be indirect. ; GO: 0004222 metalloendopeptidase activity, 0050827 toxin receptor binding, 0009405 pathogenesis, 0051609 inhibition of neurotransmitter uptake, 0005576 extracellular region; PDB: 3RSJ_B 3FUQ_A 3FFZ_B 1G9B_A 1S0F_A 1Z0H_B 1F31_A 1G9D_A 1S0C_A 1S0D_A ....
Probab=20.30 E-value=3.5e+02 Score=19.69 Aligned_cols=33 Identities=12% Similarity=0.246 Sum_probs=27.5
Q ss_pred CCCCceEEEEEEEC-CeEEEEECCccceeEEEec
Q psy5411 27 PTGKYFKFALKVTL-DGVTAFVNCEEIESTRVVR 59 (88)
Q Consensus 27 ~d~~Whr~alsV~~-~~VtL~~DC~~~~~~~~~R 59 (88)
...+|+=+.+++.. +..-+|++=+.+...+++-
T Consensus 126 yiNkW~fITITnnrL~~~~IyINg~Li~~~~I~~ 159 (195)
T PF07953_consen 126 YINKWFFITITNNRLGNSKIYINGNLIDNESIKN 159 (195)
T ss_dssp STTSEEEEEEEEETTSEEEEEETTEEEEEEE-TT
T ss_pred hcccEEEEEEEcccCccceEEECCEEEcccchhh
Confidence 34899999999987 6669999999998888764
Done!