Query psy3841
Match_columns 73
No_of_seqs 100 out of 272
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 18:47:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0708|consensus 99.9 4.3E-23 9.3E-28 155.6 5.5 64 3-66 240-303 (359)
2 KOG0609|consensus 99.8 6.7E-21 1.4E-25 149.1 5.3 65 4-68 411-475 (542)
3 PF00625 Guanylate_kin: Guanyl 99.7 5.2E-17 1.1E-21 109.2 5.0 60 4-63 73-132 (183)
4 smart00072 GuKc Guanylate kina 99.6 6.1E-16 1.3E-20 104.5 5.9 62 3-64 72-133 (184)
5 PRK14737 gmk guanylate kinase; 99.5 5.5E-14 1.2E-18 96.5 5.5 56 4-61 74-132 (186)
6 PLN02772 guanylate kinase 99.3 3.9E-12 8.5E-17 97.4 5.6 58 4-61 206-263 (398)
7 KOG3580|consensus 99.3 1.8E-12 4E-17 104.7 2.9 54 13-66 676-729 (1027)
8 PRK14738 gmk guanylate kinase; 99.0 8.2E-10 1.8E-14 76.2 5.5 57 4-60 83-139 (206)
9 cd00071 GMPK Guanosine monopho 99.0 8.7E-10 1.9E-14 72.1 4.4 51 4-54 70-120 (137)
10 COG0194 Gmk Guanylate kinase [ 99.0 1.3E-09 2.8E-14 77.0 5.5 58 4-61 73-130 (191)
11 KOG0707|consensus 98.9 7.5E-10 1.6E-14 80.0 4.0 58 4-61 108-165 (231)
12 TIGR03263 guanyl_kin guanylate 98.7 3.9E-08 8.4E-13 65.0 5.7 58 4-61 71-128 (180)
13 PRK00300 gmk guanylate kinase; 98.4 6.1E-07 1.3E-11 60.4 5.8 57 5-61 76-132 (205)
14 PRK10078 ribose 1,5-bisphospho 97.1 0.0014 3.1E-08 44.0 5.0 58 4-62 70-128 (186)
15 TIGR02322 phosphon_PhnN phosph 96.5 0.0086 1.9E-07 39.5 5.4 60 4-64 71-130 (179)
16 cd00227 CPT Chloramphenicol (C 89.8 0.35 7.6E-06 32.0 2.7 48 8-55 69-121 (175)
17 PRK08356 hypothetical protein; 82.4 0.72 1.6E-05 31.1 1.2 53 7-63 75-133 (195)
18 COG1105 FruK Fructose-1-phosph 77.1 5.5 0.00012 30.1 4.5 41 17-62 152-192 (310)
19 COG1889 NOP1 Fibrillarin-like 65.0 7.5 0.00016 28.5 2.8 42 7-48 84-130 (231)
20 PF14695 LINES_C: Lines C-term 60.1 3.5 7.7E-05 22.5 0.3 14 34-47 11-24 (39)
21 KOG4777|consensus 58.6 3.4 7.3E-05 31.7 0.1 30 3-32 309-339 (361)
22 PHA02757 hypothetical protein; 58.1 13 0.00027 22.8 2.5 26 13-38 34-59 (75)
23 COG1618 Predicted nucleotide k 57.9 23 0.0005 25.1 4.2 44 14-59 120-167 (179)
24 COG4990 Uncharacterized protei 54.9 13 0.00029 26.6 2.6 26 8-33 117-142 (195)
25 cd00430 PLPDE_III_AR Type III 53.8 40 0.00087 24.7 5.1 57 6-62 33-90 (367)
26 PRK13340 alanine racemase; Rev 53.7 35 0.00075 25.9 4.9 58 6-63 72-130 (406)
27 PF05274 Baculo_E25: Occlusion 52.4 18 0.00039 25.7 2.9 36 25-61 125-161 (182)
28 PF02254 TrkA_N: TrkA-N domain 51.3 46 0.001 19.9 4.4 48 15-64 12-60 (116)
29 KOG3812|consensus 47.6 47 0.001 26.4 4.8 51 14-64 252-303 (475)
30 PF00752 XPG_N: XPG N-terminal 45.9 13 0.00028 22.5 1.2 29 36-64 65-93 (101)
31 PF07045 DUF1330: Protein of u 45.1 48 0.001 18.7 3.6 48 15-65 9-58 (65)
32 PF01269 Fibrillarin: Fibrilla 44.6 26 0.00057 25.6 2.9 44 5-48 79-128 (229)
33 PF06200 tify: tify domain; I 44.1 14 0.00029 19.7 1.0 17 23-39 13-30 (36)
34 PF08445 FR47: FR47-like prote 41.9 36 0.00077 20.2 2.8 45 2-46 30-79 (86)
35 COG3412 Uncharacterized protei 41.8 37 0.0008 22.9 3.0 29 6-34 38-71 (129)
36 PF02550 AcetylCoA_hydro: Acet 39.5 23 0.00051 24.2 1.9 30 6-35 136-168 (198)
37 PRK11377 dihydroxyacetone kina 37.3 40 0.00088 26.7 3.1 27 8-34 43-74 (473)
38 TIGR02867 spore_II_P stage II 36.5 25 0.00054 24.8 1.7 32 8-39 64-97 (196)
39 PF13508 Acetyltransf_7: Acety 34.4 43 0.00093 18.7 2.2 42 2-44 35-77 (79)
40 PF01885 PTS_2-RNA: RNA 2'-pho 33.8 60 0.0013 22.5 3.2 44 9-53 109-159 (186)
41 TIGR00090 iojap_ybeB iojap-lik 33.4 1.1E+02 0.0024 18.9 4.1 35 24-65 15-49 (99)
42 PF02410 Oligomerisation: Olig 32.4 1.2E+02 0.0027 18.6 4.6 34 24-64 15-48 (100)
43 PF06741 LsmAD: LsmAD domain; 32.2 16 0.00034 22.2 0.1 14 3-16 5-18 (72)
44 PF07299 FBP: Fibronectin-bind 31.9 19 0.00042 25.8 0.5 25 42-66 73-97 (208)
45 PF13899 Thioredoxin_7: Thiore 30.7 1.1E+02 0.0024 17.4 3.9 39 15-53 43-82 (82)
46 PF00581 Rhodanese: Rhodanese- 30.3 68 0.0015 18.5 2.7 23 14-36 2-24 (113)
47 KOG2227|consensus 29.8 37 0.00079 27.8 1.8 40 24-63 287-334 (529)
48 PRK00053 alr alanine racemase; 29.7 1.9E+02 0.004 21.3 5.4 57 6-62 35-93 (363)
49 TIGR00492 alr alanine racemase 29.0 1.8E+02 0.0038 21.4 5.2 57 6-62 34-91 (367)
50 COG3467 Predicted flavin-nucle 28.8 1.2E+02 0.0026 20.6 4.0 22 13-34 12-33 (166)
51 cd06826 PLPDE_III_AR2 Type III 28.8 1.6E+02 0.0035 21.9 5.0 59 6-64 33-92 (365)
52 PRK06762 hypothetical protein; 28.7 1.6E+02 0.0035 18.7 4.9 46 16-61 60-112 (166)
53 smart00485 XPGN Xeroderma pigm 28.7 45 0.00098 20.0 1.7 17 37-53 64-80 (99)
54 PF01479 S4: S4 domain; Inter 28.6 92 0.002 16.1 2.8 21 8-28 10-30 (48)
55 PF01300 Sua5_yciO_yrdC: Telom 27.9 1.3E+02 0.0028 20.1 4.0 42 20-63 2-58 (179)
56 COG4588 AcfC Accessory coloniz 26.6 52 0.0011 24.4 2.0 50 7-62 69-118 (252)
57 cd01519 RHOD_HSP67B2 Member of 26.4 76 0.0016 18.5 2.4 22 13-34 2-24 (106)
58 KOG1530|consensus 26.3 92 0.002 21.2 3.0 36 13-52 26-62 (136)
59 PRK06842 fumarate hydratase; P 26.2 9.4 0.0002 27.0 -1.9 30 25-55 140-169 (185)
60 PF02969 TAF: TATA box binding 25.3 41 0.0009 19.9 1.1 26 13-40 5-30 (66)
61 cd01212 JIP JNK-interacting pr 25.2 40 0.00086 22.7 1.1 31 10-40 19-60 (148)
62 PRK02821 hypothetical protein; 24.5 1E+02 0.0022 18.7 2.7 21 11-31 50-72 (77)
63 PF01740 STAS: STAS domain; I 24.5 53 0.0012 19.7 1.5 30 4-33 14-57 (117)
64 COG2874 FlaH Predicted ATPases 24.5 85 0.0018 23.2 2.7 23 16-38 150-172 (235)
65 PRK00468 hypothetical protein; 24.2 85 0.0018 18.9 2.3 21 11-31 49-74 (75)
66 PRK11070 ssDNA exonuclease Rec 24.1 1.6E+02 0.0035 24.0 4.5 36 3-39 107-144 (575)
67 PF01408 GFO_IDH_MocA: Oxidore 24.0 1E+02 0.0022 18.3 2.7 18 13-30 75-92 (120)
68 cd01449 TST_Repeat_2 Thiosulfa 23.5 82 0.0018 18.8 2.2 23 13-35 2-24 (118)
69 PRK11036 putative S-adenosyl-L 23.4 39 0.00084 23.5 0.8 16 3-18 11-26 (255)
70 PTZ00330 acetyltransferase; Pr 23.2 70 0.0015 19.4 1.9 46 2-47 91-139 (147)
71 PF02964 MeMO_Hyd_G: Methane m 23.0 55 0.0012 22.9 1.5 14 6-19 139-152 (161)
72 PRK11538 ribosome-associated p 22.6 2.1E+02 0.0045 18.1 4.0 34 24-64 20-53 (105)
73 cd00852 NifB NifB belongs to a 22.5 1.6E+02 0.0035 17.7 3.4 34 14-47 53-90 (106)
74 cd01447 Polysulfide_ST Polysul 22.1 1.3E+02 0.0029 17.2 2.9 22 13-34 2-23 (103)
75 PF09391 DUF2000: Protein of u 21.8 79 0.0017 20.9 2.0 22 44-67 53-74 (133)
76 PF13671 AAA_33: AAA domain; P 21.3 2E+02 0.0044 17.4 3.9 41 15-55 61-108 (143)
77 PF06952 PsiA: PsiA protein; 21.1 68 0.0015 23.7 1.7 33 15-52 81-114 (238)
78 PF13529 Peptidase_C39_2: Pept 21.1 1.2E+02 0.0025 18.0 2.6 21 12-32 87-107 (144)
79 cd08633 PI-PLCc_eta2 Catalytic 20.7 95 0.0021 23.0 2.4 23 9-31 26-50 (254)
80 COG0290 InfC Translation initi 20.5 69 0.0015 22.7 1.6 35 1-35 95-129 (176)
81 COG2738 Predicted Zn-dependent 20.5 44 0.00096 24.5 0.6 43 7-50 83-125 (226)
82 PRK05928 hemD uroporphyrinogen 20.3 1.5E+02 0.0032 19.8 3.1 37 12-48 59-104 (249)
83 PRK02228 V-type ATP synthase s 20.2 2.3E+02 0.0049 17.5 4.4 37 15-51 34-77 (100)
84 PF07454 SpoIIP: Stage II spor 20.2 64 0.0014 23.8 1.4 29 9-37 142-172 (268)
85 TIGR01764 excise DNA binding d 20.2 81 0.0018 15.6 1.5 17 9-25 10-26 (49)
86 cd06825 PLPDE_III_VanT Type II 20.1 3.5E+02 0.0075 20.3 5.4 57 6-63 33-91 (368)
87 PF12728 HTH_17: Helix-turn-he 20.1 79 0.0017 16.5 1.5 17 9-25 10-26 (51)
88 PRK11640 putative transcriptio 20.1 49 0.0011 22.2 0.7 17 5-21 14-31 (191)
89 COG1504 Uncharacterized conser 20.1 1.3E+02 0.0028 20.1 2.7 35 9-43 42-89 (121)
90 TIGR01858 tag_bisphos_ald clas 20.0 1.7E+02 0.0037 21.7 3.6 49 12-61 24-90 (282)
91 cd08596 PI-PLCc_epsilon Cataly 20.0 1E+02 0.0022 22.8 2.4 24 9-32 26-51 (254)
No 1
>KOG0708|consensus
Probab=99.88 E-value=4.3e-23 Score=155.60 Aligned_cols=64 Identities=30% Similarity=0.420 Sum_probs=61.3
Q ss_pred ccccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhccc
Q psy3841 3 PRFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKENC 66 (73)
Q Consensus 3 ~~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~~~ 66 (73)
.+||+|+||||++||++|++||+||||||+++|+++|+.++||||||||+|+|.+++++++...
T Consensus 240 ~q~~~~~~~tsv~si~~va~k~~HCiLdv~~~ai~rLq~~~IyPIvIfIr~ks~~~i~e~~~~~ 303 (359)
T KOG0708|consen 240 GQRSNGLYGTSVASIREVAEKGKHCLLDVGGDAIRRLQRNQIYPIVIFIRVKSKKQIKERNLKI 303 (359)
T ss_pred cccCCCcceehHHHHHHHhcCCCceEEecCcchHHHHHhcceeceEEEEEechHHHHHHHhccc
Confidence 5899999999999999999999999999999999999999999999999999999999998544
No 2
>KOG0609|consensus
Probab=99.82 E-value=6.7e-21 Score=149.14 Aligned_cols=65 Identities=12% Similarity=0.200 Sum_probs=62.1
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhccccc
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKENCRF 68 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~~~~~ 68 (73)
-|.+|+||||++||+.|+++||+||||+.|++++.|++++|.||||||+||+.+.++++|+....
T Consensus 411 Ey~~nlYGTs~dsVr~v~~~gKicvLdv~Pqalk~lRt~Ef~PyVIFI~pP~~~~~r~~r~~~~~ 475 (542)
T KOG0609|consen 411 EYEGNLYGTSLDSVRNVIASGKICVLDVEPQALKVLRTAEFKPYVIFIAPPSLEELRALRKVAVM 475 (542)
T ss_pred cchhccccchHHHHHHHHHhCCEEEEecCHHHhhhhhhhcccceEEEecCCCchhHHHHhhhccc
Confidence 38899999999999999999999999999999999999999999999999999999999988753
No 3
>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2.7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....
Probab=99.68 E-value=5.2e-17 Score=109.20 Aligned_cols=60 Identities=25% Similarity=0.342 Sum_probs=57.5
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhh
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIK 63 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r 63 (73)
+|++|+||||.++|++++++|+|||||+++++++.|+...++|++|||+|+|.+.|++..
T Consensus 73 ~~~g~~YGt~~~~i~~~~~~gk~~il~~~~~g~~~L~~~~~~~~~IfI~~~s~~~l~~~l 132 (183)
T PF00625_consen 73 EYDGNYYGTSKSAIDKVLEEGKHCILDVDPEGVKQLKKAGFNPIVIFIKPPSPEVLKRRL 132 (183)
T ss_dssp EETTEEEEEEHHHHHHHHHTTTEEEEEETHHHHHHHHHCTTTEEEEEEEESSHHHHHHHH
T ss_pred eecchhhhhccchhhHhhhcCCcEEEEccHHHHHHHHhcccCceEEEEEccchHHHHHHH
Confidence 589999999999999999999999999999999999999999999999999999998764
No 4
>smart00072 GuKc Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
Probab=99.63 E-value=6.1e-16 Score=104.47 Aligned_cols=62 Identities=19% Similarity=0.387 Sum_probs=57.7
Q ss_pred ccccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 3 PRFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 3 ~~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
.+|++|+||||+++|++++++|++||||+++++++.|+...+.|++|||.|||.+.|++...
T Consensus 72 ~~~~g~~YGt~~~~i~~~~~~~~~~ild~~~~~~~~l~~~~~~~~vIfi~~~s~~~l~~rl~ 133 (184)
T smart00072 72 GEYSGNYYGTSKETIRQVAEQGKHCLLDIDPQGVKQLRKAQLYPIVIFIAPPSSEELERRLR 133 (184)
T ss_pred EEEcCcCcccCHHHHHHHHHcCCeEEEEECHHHHHHHHHhCCCcEEEEEeCcCHHHHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999998886543
No 5
>PRK14737 gmk guanylate kinase; Provisional
Probab=99.48 E-value=5.5e-14 Score=96.54 Aligned_cols=56 Identities=13% Similarity=0.278 Sum_probs=51.6
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCcccc---EEEEeecCCHHHHHH
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYP---IVLLIKFKSTKQIKE 61 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~P---iVIfIkp~s~~~lke 61 (73)
.|++|+||||.++|++++++|++||||+++++++.|+.. +| ++|||.|||.+.+++
T Consensus 74 ~~~g~~YGt~~~~i~~~~~~g~~~i~d~~~~g~~~l~~~--~~~~~~~Ifi~pps~e~l~~ 132 (186)
T PRK14737 74 EVHDNYYGTPKAFIEDAFKEGRSAIMDIDVQGAKIIKEK--FPERIVTIFIEPPSEEEWEE 132 (186)
T ss_pred EECCeeecCcHHHHHHHHHcCCeEEEEcCHHHHHHHHHh--CCCCeEEEEEECCCHHHHHH
Confidence 689999999999999999999999999999999999864 66 899999999887765
No 6
>PLN02772 guanylate kinase
Probab=99.30 E-value=3.9e-12 Score=97.41 Aligned_cols=58 Identities=12% Similarity=0.181 Sum_probs=55.1
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHH
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKE 61 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke 61 (73)
.|.+|+||||.++|++++++|++||||+.+++.+.|+...+.|++||+.|+|.+.|++
T Consensus 206 e~~Gn~YGTsk~~V~~vl~~Gk~vILdLD~qGar~Lr~~~l~~v~IFI~PPSlEeLe~ 263 (398)
T PLN02772 206 SVHGNLYGTSIEAVEVVTDSGKRCILDIDVQGARSVRASSLEAIFIFICPPSMEELEK 263 (398)
T ss_pred eecCccccccHHHHHHHHHhCCcEEEeCCHHHHHHHHHhcCCeEEEEEeCCCHHHHHH
Confidence 6889999999999999999999999999999999999988899999999999888775
No 7
>KOG3580|consensus
Probab=99.27 E-value=1.8e-12 Score=104.72 Aligned_cols=54 Identities=24% Similarity=0.393 Sum_probs=51.9
Q ss_pred chhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhccc
Q psy3841 13 EEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKENC 66 (73)
Q Consensus 13 si~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~~~ 66 (73)
.+++|++|++|.||++|||.|.||++|+..++||||||+.|.|...+|.||.+.
T Consensus 676 rL~TvrqiieqDKHALLDVTP~AvdrLNY~QwypIVvff~PdSrqgvktmRqrL 729 (1027)
T KOG3580|consen 676 RLNTVRQIIEQDKHALLDVTPKAVDRLNYTQWYPIVVFFNPDSRQGVKTMRQRL 729 (1027)
T ss_pred EehhhHHHHhcccchhhccCHHHHhhhccceeeeEEEEeCCcchHHHHHHHHHh
Confidence 378999999999999999999999999999999999999999999999999876
No 8
>PRK14738 gmk guanylate kinase; Provisional
Probab=99.00 E-value=8.2e-10 Score=76.17 Aligned_cols=57 Identities=11% Similarity=0.151 Sum_probs=48.7
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHH
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIK 60 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lk 60 (73)
+|.+|+||||.++|++++++|++||||++.+++..|+....-.++||+.|+|.+.+.
T Consensus 83 ~~~g~~YGt~~~~i~~~~~~g~~vi~~~~~~g~~~l~~~~pd~~~if~~pps~e~l~ 139 (206)
T PRK14738 83 EVYGNYYGVPKAPVRQALASGRDVIVKVDVQGAASIKRLVPEAVFIFLAPPSMDELT 139 (206)
T ss_pred EEcCceecCCHHHHHHHHHcCCcEEEEcCHHHHHHHHHhCCCeEEEEEeCCCHHHHH
Confidence 578999999999999999999999999999999998764333378899999976544
No 9
>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
Probab=98.96 E-value=8.7e-10 Score=72.11 Aligned_cols=51 Identities=12% Similarity=0.210 Sum_probs=49.1
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecC
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFK 54 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~ 54 (73)
.|++|.||++.++|++++++|+.||||+++++++.|+.....|++||+.||
T Consensus 70 ~~~~~~yg~~~~~i~~~~~~g~~~il~~~~~~~~~l~~~~~~~~~I~i~~~ 120 (137)
T cd00071 70 EFHGNYYGTSKAAVEEALAEGKIVILEIDVQGARQVKKSYPDAVSIFILPP 120 (137)
T ss_pred EEcCEEecCcHHHHHHHHhCCCeEEEEecHHHHHHHHHcCCCeEEEEEECC
Confidence 478999999999999999999999999999999999999999999999998
No 10
>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]
Probab=98.96 E-value=1.3e-09 Score=76.99 Aligned_cols=58 Identities=12% Similarity=0.229 Sum_probs=52.1
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHH
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKE 61 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke 61 (73)
.|.+|+||||.+.|++.+.+|+.+|||+..|....++..-=--+.|||.|||.+.|++
T Consensus 73 ~~~gnyYGT~~~~ve~~~~~G~~vildId~qGa~qvk~~~p~~v~IFi~pPs~eeL~~ 130 (191)
T COG0194 73 EYHGNYYGTSREPVEQALAEGKDVILDIDVQGALQVKKKMPNAVSIFILPPSLEELER 130 (191)
T ss_pred EEcCCcccCcHHHHHHHHhcCCeEEEEEehHHHHHHHHhCCCeEEEEEcCCCHHHHHH
Confidence 4789999999999999999999999999999999998764356788999999999874
No 11
>KOG0707|consensus
Probab=98.95 E-value=7.5e-10 Score=80.05 Aligned_cols=58 Identities=22% Similarity=0.316 Sum_probs=54.5
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHH
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKE 61 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke 61 (73)
+|.+|+||||+++|+++...|+.|+||+..+.+...+...+-++.||++|||.+.+.+
T Consensus 108 ~~~gn~yGtsi~av~~~~~~gk~~ildId~qg~~~i~~~~~~~i~i~~~pps~~~~e~ 165 (231)
T KOG0707|consen 108 TFSGNKYGTSIAAVQRLMLSGKVCILDIDLQGVQPIRATSLDAIYIFIKPPSIKILEE 165 (231)
T ss_pred hhhcccCCchHHHHHHHHhcCCcceeehhhcCceeeecCCCceEEEEecCCcchhHHH
Confidence 6899999999999999999999999999999999999999999999999999776653
No 12
>TIGR03263 guanyl_kin guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.
Probab=98.71 E-value=3.9e-08 Score=64.95 Aligned_cols=58 Identities=9% Similarity=0.198 Sum_probs=52.1
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHH
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKE 61 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke 61 (73)
.|.+|.||++.++|++++++|+.||||+++++++.+......|..||+-+++.+.+++
T Consensus 71 ~~~~~~y~~~~~~i~~~~~~g~~vi~d~~~~~~~~~~~~~~~~~~i~~~~~~~e~~~~ 128 (180)
T TIGR03263 71 EVHGNYYGTPKSPVEEALAAGKDVLLEIDVQGARQVKKKFPDAVSIFILPPSLEELER 128 (180)
T ss_pred EECCeeeCCcHHHHHHHHHCCCeEEEECCHHHHHHHHHhCCCcEEEEEECCCHHHHHH
Confidence 4788999999999999999999999999999999998887778999998888777654
No 13
>PRK00300 gmk guanylate kinase; Provisional
Probab=98.43 E-value=6.1e-07 Score=60.43 Aligned_cols=57 Identities=9% Similarity=0.148 Sum_probs=50.2
Q ss_pred ccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHH
Q psy3841 5 FNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKE 61 (73)
Q Consensus 5 ~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke 61 (73)
+.+|.||++.++|++++++|+.||+|+++++...|......+++||+-+++.+.+++
T Consensus 76 ~~~~~y~~~~~~i~~~l~~g~~vi~dl~~~g~~~l~~~~~~~~~I~i~~~s~~~l~~ 132 (205)
T PRK00300 76 VFGNYYGTPRSPVEEALAAGKDVLLEIDWQGARQVKKKMPDAVSIFILPPSLEELER 132 (205)
T ss_pred ECCccccCcHHHHHHHHHcCCeEEEeCCHHHHHHHHHhCCCcEEEEEECcCHHHHHH
Confidence 568899999999999999999999999999999988876678999999888766553
No 14
>PRK10078 ribose 1,5-bisphosphokinase; Provisional
Probab=97.07 E-value=0.0014 Score=44.04 Aligned_cols=58 Identities=7% Similarity=-0.093 Sum_probs=39.1
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCc-cccEEEEeecCCHHHHHHh
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQH-VYPIVLLIKFKSTKQIKEI 62 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~-l~PiVIfIkp~s~~~lke~ 62 (73)
++.+|+|||+. +++..+++|+++|+|-.....+.+.... -...||++.++.....+.+
T Consensus 70 ~~~g~~yg~~~-~~~~~l~~g~~VI~~G~~~~~~~~~~~~~~~~~vi~l~~s~e~l~~RL 128 (186)
T PRK10078 70 HANGLYYGVGI-EIDLWLHAGFDVLVNGSRAHLPQARARYQSALLPVCLQVSPEILRQRL 128 (186)
T ss_pred HHhCCccCCcH-HHHHHHhCCCEEEEeChHHHHHHHHHHcCCCEEEEEEeCCHHHHHHHH
Confidence 46789999998 6999999999999987765555454431 1234567766543333334
No 15
>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN. Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.
Probab=96.50 E-value=0.0086 Score=39.47 Aligned_cols=60 Identities=8% Similarity=-0.046 Sum_probs=42.6
Q ss_pred cccccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 4 RFNHHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
++.++.||++. .+...+++|..+|+|.+......++...-.-++||+.++.....+.++.
T Consensus 71 ~~~~~~~g~~~-~i~~~~~~g~~vv~~g~~~~~~~~~~~~~~~~~i~l~~~~~~~~~Rl~~ 130 (179)
T TIGR02322 71 QAHGLSYGIPA-EIDQWLEAGDVVVVNGSRAVLPEARQRYPNLLVVNITASPDVLAQRLAA 130 (179)
T ss_pred eecCccccChH-HHHHHHhcCCEEEEECCHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHH
Confidence 45667999998 4888899999999999988777665432233788998655444444443
No 16
>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.
Probab=89.81 E-value=0.35 Score=31.99 Aligned_cols=48 Identities=13% Similarity=-0.040 Sum_probs=32.1
Q ss_pred cccccchhHHHHHHhCCCEEEEecCcchhhhh----hc-CccccEEEEeecCC
Q psy3841 8 HGLNREEPGKKTNNINNAHVILDVSLAGVERL----HR-QHVYPIVLLIKFKS 55 (73)
Q Consensus 8 ~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L----~~-~~l~PiVIfIkp~s 55 (73)
+.||+..+.++..+++|..||+|......+.+ +. ...-.+.|++.++.
T Consensus 69 ~~y~~~~~~~~~~l~~G~~VIvD~~~~~~~~~r~~~~~~~~~~~~~v~l~~~~ 121 (175)
T cd00227 69 LLEGAWYEAVAAMARAGANVIADDVFLGRAALQDCWRSFVGLDVLWVGVRCPG 121 (175)
T ss_pred HHHHHHHHHHHHHHhCCCcEEEeeeccCCHHHHHHHHHhcCCCEEEEEEECCH
Confidence 58999999999999999999999643321222 11 11123566777664
No 17
>PRK08356 hypothetical protein; Provisional
Probab=82.42 E-value=0.72 Score=31.12 Aligned_cols=53 Identities=8% Similarity=0.126 Sum_probs=27.4
Q ss_pred ccccccchhHHHHHHhC---CCEEEEecCcchhhh---hhcCccccEEEEeecCCHHHHHHhh
Q psy3841 7 HHGLNREEPGKKTNNIN---NAHVILDVSLAGVER---LHRQHVYPIVLLIKFKSTKQIKEIK 63 (73)
Q Consensus 7 ~~~ygtsi~sVr~V~ek---gkhCILdv~~~avk~---L~~~~l~PiVIfIkp~s~~~lke~r 63 (73)
.|.|||++ .++.++++ +...++| +...++. |.. .-..+|++.++....++.++
T Consensus 75 ~~~yG~~~-~~~~~~~~~~~~~~ivid-G~r~~~q~~~l~~--~~~~vi~l~~~~~~~~~Rl~ 133 (195)
T PRK08356 75 KEKYGEDI-LIRLAVDKKRNCKNIAID-GVRSRGEVEAIKR--MGGKVIYVEAKPEIRFERLR 133 (195)
T ss_pred HHhcCcHH-HHHHHHHHhccCCeEEEc-CcCCHHHHHHHHh--cCCEEEEEECCHHHHHHHHH
Confidence 47899985 33333333 3345555 2233322 222 12478899887655455443
No 18
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=77.06 E-value=5.5 Score=30.14 Aligned_cols=41 Identities=24% Similarity=0.275 Sum_probs=28.8
Q ss_pred HHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHh
Q psy3841 17 KKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEI 62 (73)
Q Consensus 17 Vr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~ 62 (73)
++.+-++|..++||.+++++...-... |. +||| +.+.|.++
T Consensus 152 i~~~~~~g~~vilD~Sg~~L~~~L~~~--P~--lIKP-N~~EL~~~ 192 (310)
T COG1105 152 IRILRQQGAKVILDTSGEALLAALEAK--PW--LIKP-NREELEAL 192 (310)
T ss_pred HHHHHhcCCeEEEECChHHHHHHHccC--Cc--EEec-CHHHHHHH
Confidence 344445699999999999997766554 76 5676 44555544
No 19
>COG1889 NOP1 Fibrillarin-like rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=64.99 E-value=7.5 Score=28.54 Aligned_cols=42 Identities=12% Similarity=0.059 Sum_probs=35.8
Q ss_pred ccccccchhHHHHHHhCCCEEEEecCcchhhhhh-----cCccccEE
Q psy3841 7 HHGLNREEPGKKTNNINNAHVILDVSLAGVERLH-----RQHVYPIV 48 (73)
Q Consensus 7 ~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~-----~~~l~PiV 48 (73)
+--=||+++.|-+|+..|..--...+|.....|. +..++||+
T Consensus 84 GAasGTTvSHVSDIv~~G~iYaVEfs~R~~reLl~~a~~R~Ni~PIL 130 (231)
T COG1889 84 GAASGTTVSHVSDIVGEGRIYAVEFSPRPMRELLDVAEKRPNIIPIL 130 (231)
T ss_pred eccCCCcHhHHHhccCCCcEEEEEecchhHHHHHHHHHhCCCceeee
Confidence 3345899999999999999999999999988775 57899984
No 20
>PF14695 LINES_C: Lines C-terminus
Probab=60.05 E-value=3.5 Score=22.50 Aligned_cols=14 Identities=36% Similarity=0.807 Sum_probs=12.6
Q ss_pred chhhhhhcCccccE
Q psy3841 34 AGVERLHRQHVYPI 47 (73)
Q Consensus 34 ~avk~L~~~~l~Pi 47 (73)
.++++|++..+|||
T Consensus 11 ~aI~rL~~k~LFPY 24 (39)
T PF14695_consen 11 LAIERLVRKNLFPY 24 (39)
T ss_pred HHHHHHHHCCCCCC
Confidence 37899999999998
No 21
>KOG4777|consensus
Probab=58.56 E-value=3.4 Score=31.66 Aligned_cols=30 Identities=17% Similarity=0.189 Sum_probs=25.3
Q ss_pred ccccccccccchhHHH-HHHhCCCEEEEecC
Q psy3841 3 PRFNHHGLNREEPGKK-TNNINNAHVILDVS 32 (73)
Q Consensus 3 ~~~~~~~ygtsi~sVr-~V~ekgkhCILdv~ 32 (73)
||=+|++||-|+.-|| ++..-|+..+||..
T Consensus 309 drN~d~gy~VsVGRIR~D~~~D~kfv~L~hn 339 (361)
T KOG4777|consen 309 DRNKDDGYGVSVGRIRRDVSQDGKFVVLDHN 339 (361)
T ss_pred ccccCCCceeeeeeeecccccccceEEEEee
Confidence 6789999999999886 56667999999863
No 22
>PHA02757 hypothetical protein; Provisional
Probab=58.13 E-value=13 Score=22.80 Aligned_cols=26 Identities=4% Similarity=-0.020 Sum_probs=21.4
Q ss_pred chhHHHHHHhCCCEEEEecCcchhhh
Q psy3841 13 EEPGKKTNNINNAHVILDVSLAGVER 38 (73)
Q Consensus 13 si~sVr~V~ekgkhCILdv~~~avk~ 38 (73)
.-+.+++++++.|.||+++.+.+=..
T Consensus 34 ~Qe~~~eildkdK~CiiE~de~sGml 59 (75)
T PHA02757 34 DQEKANEILDKDKACIIEIDEDSGML 59 (75)
T ss_pred cHHHHHHHhcccceEEEEEcCCCCcE
Confidence 44788999999999999999875433
No 23
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=57.88 E-value=23 Score=25.10 Aligned_cols=44 Identities=9% Similarity=0.111 Sum_probs=33.1
Q ss_pred hhHHHHHHhCCCEEEEecCcc----hhhhhhcCccccEEEEeecCCHHHH
Q psy3841 14 EPGKKTNNINNAHVILDVSLA----GVERLHRQHVYPIVLLIKFKSTKQI 59 (73)
Q Consensus 14 i~sVr~V~ekgkhCILdv~~~----avk~L~~~~l~PiVIfIkp~s~~~l 59 (73)
.++|+++++.++..|.-++-. .+++++ .+.++++|+.|.+++.|
T Consensus 120 ~~~ve~vl~~~kpliatlHrrsr~P~v~~ik--~~~~v~v~lt~~NR~~i 167 (179)
T COG1618 120 REAVEEVLKSGKPLIATLHRRSRHPLVQRIK--KLGGVYVFLTPENRNRI 167 (179)
T ss_pred HHHHHHHhcCCCcEEEEEecccCChHHHHhh--hcCCEEEEEccchhhHH
Confidence 367899999999988888877 555554 44688888999887643
No 24
>COG4990 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.94 E-value=13 Score=26.62 Aligned_cols=26 Identities=12% Similarity=0.024 Sum_probs=23.4
Q ss_pred cccccchhHHHHHHhCCCEEEEecCc
Q psy3841 8 HGLNREEPGKKTNNINNAHVILDVSL 33 (73)
Q Consensus 8 ~~ygtsi~sVr~V~ekgkhCILdv~~ 33 (73)
++=|+|+..|+.++++|+.++..++.
T Consensus 117 d~tGksl~~ik~ql~kg~PV~iw~T~ 142 (195)
T COG4990 117 DLTGKSLSDIKGQLLKGRPVVIWVTN 142 (195)
T ss_pred cCcCCcHHHHHHHHhcCCcEEEEEec
Confidence 57799999999999999999998765
No 25
>cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with activ
Probab=53.77 E-value=40 Score=24.70 Aligned_cols=57 Identities=11% Similarity=0.069 Sum_probs=39.1
Q ss_pred cccccccchhHH-HHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHh
Q psy3841 6 NHHGLNREEPGK-KTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEI 62 (73)
Q Consensus 6 ~~~~ygtsi~sV-r~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~ 62 (73)
+-|.||-....| +...+.|...+-..+++....++...+-+-++++.++..+.+++.
T Consensus 33 Kan~yGhg~~~i~~~l~~~G~~~~~vas~~Ea~~~~~~g~~~~i~~~~~~~~~~~~~~ 90 (367)
T cd00430 33 KADAYGHGAVEVAKALEEAGADYFAVATLEEALELREAGITAPILVLGGTPPEEAEEA 90 (367)
T ss_pred eeccccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhcCCCCCEEEEeCCCHHHHHHH
Confidence 457888877777 445566766666678888888888776644456666666666655
No 26
>PRK13340 alanine racemase; Reviewed
Probab=53.70 E-value=35 Score=25.85 Aligned_cols=58 Identities=14% Similarity=0.003 Sum_probs=41.7
Q ss_pred cccccccc-hhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhh
Q psy3841 6 NHHGLNRE-EPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIK 63 (73)
Q Consensus 6 ~~~~ygts-i~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r 63 (73)
+.|.||-- .+-.+...+.|.-++-..++.....|+...+-+.++.+.+++.+.+++.-
T Consensus 72 KAnaYG~G~~~va~~l~~~G~~~~~Vas~~Ea~~lr~~G~~~~ilvl~~~~~~el~~~~ 130 (406)
T PRK13340 72 KADAYGHGIELLMPSIIKANVPCIGIASNEEARRVRELGFTGQLLRVRSASPAEIEQAL 130 (406)
T ss_pred ccccccccHHHHHHHHHHCCCCEEEEccHHHHHHHHhCCCCCCEEEECCCCHHHHHHHH
Confidence 56788874 34446666778777777789999999988877766666776777776543
No 27
>PF05274 Baculo_E25: Occlusion-derived virus envelope protein E25; InterPro: IPR007938 This family consists of several nucleopolyhedrovirus occlusion-derived virus envelope E25 proteins. The N terminus of this protein is extremely hydrophobic, studies suggest that this defined hydrophobic domain is sufficient to direct the protein to induced membrane microvesicles within a baculovirus-infected cell nucleus and the viral envelope. In addition, movement of the protein into the nuclear envelope may initiate through cytoplasmic membranes, such as endoplasmic reticulum, and that transport into the nucleus may be mediated through the outer and inner nuclear membrane [].; GO: 0019031 viral envelope, 0042025 host cell nucleus
Probab=52.39 E-value=18 Score=25.71 Aligned_cols=36 Identities=25% Similarity=0.387 Sum_probs=28.4
Q ss_pred CEEEEecCcchhhhhhcCccccEEEEeecCCHHH-HHH
Q psy3841 25 AHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQ-IKE 61 (73)
Q Consensus 25 khCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~-lke 61 (73)
-.|++|-+-..+..|+.- =|||+++..-.+..+ |||
T Consensus 125 vy~LIDas~st~peLRdv-sypi~VyT~Ns~aQl~LkE 161 (182)
T PF05274_consen 125 VYCLIDASNSTLPELRDV-SYPITVYTNNSSAQLKLKE 161 (182)
T ss_pred EEEEECCCCCCCchhhcc-cccEEEEEcChHHhHHHHh
Confidence 469999999999988776 499999998777554 444
No 28
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=51.31 E-value=46 Score=19.87 Aligned_cols=48 Identities=13% Similarity=0.070 Sum_probs=36.5
Q ss_pred hHHHHHHhCC-CEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 15 PGKKTNNINN-AHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 15 ~sVr~V~ekg-khCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
.-++...+.+ +..++|-.++.++.+.... ++ +++-.+.+.+-|++.+-
T Consensus 12 ~i~~~L~~~~~~vvvid~d~~~~~~~~~~~-~~-~i~gd~~~~~~l~~a~i 60 (116)
T PF02254_consen 12 EIAEQLKEGGIDVVVIDRDPERVEELREEG-VE-VIYGDATDPEVLERAGI 60 (116)
T ss_dssp HHHHHHHHTTSEEEEEESSHHHHHHHHHTT-SE-EEES-TTSHHHHHHTTG
T ss_pred HHHHHHHhCCCEEEEEECCcHHHHHHHhcc-cc-cccccchhhhHHhhcCc
Confidence 4456666777 6999999999999998776 44 57788888888887643
No 29
>KOG3812|consensus
Probab=47.60 E-value=47 Score=26.40 Aligned_cols=51 Identities=20% Similarity=0.237 Sum_probs=33.4
Q ss_pred hhHHHHHHhCCCEEEEecC-cchhhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 14 EPGKKTNNINNAHVILDVS-LAGVERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 14 i~sVr~V~ekgkhCILdv~-~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
|+-|-+.+.+=.-.+||.. -+-=..|....|-||++|||..|.|.|..+=+
T Consensus 252 iErIfelarsLqLvvlDadtInhPaql~ktsLaPI~v~ikvSspKvLqrLir 303 (475)
T KOG3812|consen 252 IERIFELARSLQLVVLDADTINHPAQLAKTSLAPIIVYIKVSSPKVLQRLIR 303 (475)
T ss_pred HHHHHHHHhhceEEEecCCcCCCHHHhccCCCcceEEEEEeCCHHHHHHHHH
Confidence 3334444445556677742 22233566778899999999999998876543
No 30
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=45.93 E-value=13 Score=22.50 Aligned_cols=29 Identities=17% Similarity=0.218 Sum_probs=18.3
Q ss_pred hhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 36 VERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 36 vk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
+..|....+.||+||=..+...+.++..+
T Consensus 65 ~~~L~~~gI~PifVFDG~~~~~K~~~~~~ 93 (101)
T PF00752_consen 65 LCRLLEHGIKPIFVFDGKPPPLKRETIQK 93 (101)
T ss_dssp HHHHHHTTEEEEEEE--STTGGCHHHHHH
T ss_pred HHHHHHCCCEEEEEECCCCchhhHHHHHH
Confidence 44578899999999976554455554443
No 31
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=45.12 E-value=48 Score=18.71 Aligned_cols=48 Identities=13% Similarity=-0.025 Sum_probs=31.8
Q ss_pred hHHHHHHhC--CCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhcc
Q psy3841 15 PGKKTNNIN--NAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKEN 65 (73)
Q Consensus 15 ~sVr~V~ek--gkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~~ 65 (73)
+.+..++++ |+....+-.+..++- ..-...++.|.+||.+..+++-.+
T Consensus 9 ~~~~~~l~~~GG~~l~~~~~~~~leG---~~~~~~~viieFPs~~aa~~~~~s 58 (65)
T PF07045_consen 9 EAVPPILEKYGGRVLARGGEPEVLEG---DWDPDRVVIIEFPSMEAAKAWYNS 58 (65)
T ss_dssp HHHHHHHHHTT-EEEEECEEEEEEES---T-SSSEEEEEEESSHHHHHHHHCS
T ss_pred HHHHHHHHHcCCEEEEECCceeEEec---CCCCCeEEEEECCCHHHHHHHHCC
Confidence 456666666 676666566665555 233478899999999998876443
No 32
>PF01269 Fibrillarin: Fibrillarin; InterPro: IPR000692 Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [, ]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [] and is similar to the yeast NOP1 protein []. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.; GO: 0003723 RNA binding, 0008168 methyltransferase activity, 0006364 rRNA processing, 0008033 tRNA processing; PDB: 3PLA_E 3ID6_C 3ID5_B 1NT2_A 3NVK_J 2NNW_B 3NVM_B 3NMU_J 1PRY_A 1G8A_A ....
Probab=44.61 E-value=26 Score=25.61 Aligned_cols=44 Identities=11% Similarity=0.118 Sum_probs=36.3
Q ss_pred ccccccccchhHHHHHHh-CCCEEEEecCcchhhhh-----hcCccccEE
Q psy3841 5 FNHHGLNREEPGKKTNNI-NNAHVILDVSLAGVERL-----HRQHVYPIV 48 (73)
Q Consensus 5 ~~~~~ygtsi~sVr~V~e-kgkhCILdv~~~avk~L-----~~~~l~PiV 48 (73)
|.+.-=||+++-|-|++. .|..--++.+|.+.+.| ++..+.||+
T Consensus 79 YLGAasGTTVSHvSDIvg~~G~VYaVEfs~r~~rdL~~la~~R~NIiPIl 128 (229)
T PF01269_consen 79 YLGAASGTTVSHVSDIVGPDGVVYAVEFSPRSMRDLLNLAKKRPNIIPIL 128 (229)
T ss_dssp EETTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHSTTEEEEE
T ss_pred EecccCCCccchhhhccCCCCcEEEEEecchhHHHHHHHhccCCceeeee
Confidence 345556899999999999 89999999999998887 357788874
No 33
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=44.12 E-value=14 Score=19.68 Aligned_cols=17 Identities=12% Similarity=0.266 Sum_probs=13.4
Q ss_pred CCCEEEEe-cCcchhhhh
Q psy3841 23 NNAHVILD-VSLAGVERL 39 (73)
Q Consensus 23 kgkhCILd-v~~~avk~L 39 (73)
.|+.||+| ++++-.+.+
T Consensus 13 ~G~V~Vfd~v~~~Ka~~i 30 (36)
T PF06200_consen 13 GGQVCVFDDVPPDKAQEI 30 (36)
T ss_pred CCEEEEeCCCCHHHHHHH
Confidence 48999999 888876654
No 34
>PF08445 FR47: FR47-like protein; InterPro: IPR013653 Proteins in this entry have a conserved region similar to the C-terminal region of the Drosophila melanogaster (Fruit fly) hypothetical protein FR47 (Q9VR51 from SWISSPROT). This protein has been found to consist of two N-acyltransferase-like domains swapped with the C-terminal strands. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups; PDB: 1SQH_A 3EC4_B.
Probab=41.86 E-value=36 Score=20.22 Aligned_cols=45 Identities=11% Similarity=0.075 Sum_probs=29.6
Q ss_pred CccccccccccchhH--HHHHHhCCCEEEEecCcc---hhhhhhcCcccc
Q psy3841 2 RPRFNHHGLNREEPG--KKTNNINNAHVILDVSLA---GVERLHRQHVYP 46 (73)
Q Consensus 2 ~~~~~~~~ygtsi~s--Vr~V~ekgkhCILdv~~~---avk~L~~~~l~P 46 (73)
.|.|...+||+.+-+ +++++++|..+.|-+..+ |..-.++..|.+
T Consensus 30 ~p~~RrrGlg~~lv~~l~~~~~~~g~~~~l~v~~~N~~s~~ly~klGf~~ 79 (86)
T PF08445_consen 30 LPEHRRRGLGSALVAALARELLERGKTPFLYVDADNEASIRLYEKLGFRE 79 (86)
T ss_dssp -GGGTTSSHHHHHHHHHHHHHHHTTSEEEEEEETT-HHHHHHHHHCT-EE
T ss_pred CHHHcCCCHHHHHHHHHHHHHHhCCCcEEEEEECCCHHHHHHHHHcCCEE
Confidence 478889999987643 588888999988876433 444444444443
No 35
>COG3412 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.79 E-value=37 Score=22.93 Aligned_cols=29 Identities=10% Similarity=0.006 Sum_probs=23.0
Q ss_pred cccccccchhHHHHHHhC-----CCEEEEecCcc
Q psy3841 6 NHHGLNREEPGKKTNNIN-----NAHVILDVSLA 34 (73)
Q Consensus 6 ~~~~ygtsi~sVr~V~ek-----gkhCILdv~~~ 34 (73)
.|..-|||.+.|++.+++ +--|..|++..
T Consensus 38 ddg~iGTs~~~I~~aI~~~~~ad~~lif~DlGSA 71 (129)
T COG3412 38 DDGQIGTSFEKIMEAIEKANEADHVLVFYDLGSA 71 (129)
T ss_pred CCCCcCcCHHHHHHHHHhccccCceEEEEecchh
Confidence 356789999999999994 66788888644
No 36
>PF02550 AcetylCoA_hydro: Acetyl-CoA hydrolase/transferase N-terminal domain; InterPro: IPR003702 This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase 3.1.2.1 from EC from yeast catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) 2.8.3 from EC produces succinyl-CoA, and acetate-CoA transferase 2.8.3.8 from EC utilises acyl-CoA and acetate to form acetyl-CoA.; GO: 0003824 catalytic activity, 0006084 acetyl-CoA metabolic process; PDB: 2NVV_C 2G39_A 3D3U_A 3S8D_B 3QLI_B 3QLK_B 3GK7_B 3QDQ_A 3EH7_A 2OAS_A ....
Probab=39.45 E-value=23 Score=24.17 Aligned_cols=30 Identities=20% Similarity=0.200 Sum_probs=25.0
Q ss_pred ccccc---ccchhHHHHHHhCCCEEEEecCcch
Q psy3841 6 NHHGL---NREEPGKKTNNINNAHVILDVSLAG 35 (73)
Q Consensus 6 ~~~~y---gtsi~sVr~V~ekgkhCILdv~~~a 35 (73)
++|+| |+|.+.-+.+++..+..|+.|+++.
T Consensus 136 De~Gy~slG~s~~~~~~~ie~A~~vI~eVN~~~ 168 (198)
T PF02550_consen 136 DEHGYFSLGTSVDYTKAAIEQAKKVIVEVNPNM 168 (198)
T ss_dssp -TTSEEECTTBHBTHHHHHHHTSEEEEEEETTS
T ss_pred CCCCCEeecHHHHhHHHHHhcCCeEEEEcCCCC
Confidence 34554 8999999999999999999998764
No 37
>PRK11377 dihydroxyacetone kinase subunit M; Provisional
Probab=37.30 E-value=40 Score=26.71 Aligned_cols=27 Identities=11% Similarity=0.118 Sum_probs=23.0
Q ss_pred cccccchhHHHHHHhC-----CCEEEEecCcc
Q psy3841 8 HGLNREEPGKKTNNIN-----NAHVILDVSLA 34 (73)
Q Consensus 8 ~~ygtsi~sVr~V~ek-----gkhCILdv~~~ 34 (73)
+.+|||.+.|.+.+++ |-.++.|++-.
T Consensus 43 ~~~Gt~~~~i~~ai~~~~~~~gv~v~~DlGSa 74 (473)
T PRK11377 43 NPIGTDAVKVMEAIESVADADHVLVMMDMGSA 74 (473)
T ss_pred CCCCCCHHHHHHHHHhccCCCCEEEEEecchH
Confidence 8899999999999986 67788888654
No 38
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=36.51 E-value=25 Score=24.78 Aligned_cols=32 Identities=22% Similarity=0.261 Sum_probs=27.6
Q ss_pred cccccchhHHHHHHhCCC--EEEEecCcchhhhh
Q psy3841 8 HGLNREEPGKKTNNINNA--HVILDVSLAGVERL 39 (73)
Q Consensus 8 ~~ygtsi~sVr~V~ekgk--hCILdv~~~avk~L 39 (73)
.-|..|-++|++.++++. -.++|++-+++.+-
T Consensus 64 ~sY~~Sr~tv~~~l~~~p~i~~viDiHRDs~~~~ 97 (196)
T TIGR02867 64 QSYDRSRETVKKALKENKDLKYIIDLHRDSVRRK 97 (196)
T ss_pred HHHHHHHHHHHHHHHHCCCceEEEEeecCCCCCC
Confidence 347789999999999987 89999999998653
No 39
>PF13508 Acetyltransf_7: Acetyltransferase (GNAT) domain; PDB: 3EY5_A 3FRM_B 3D8P_B 3GY9_A 3GYA_A 3S6F_A 2Q7B_A 1CM0_B 1XEB_B 1Y7R_A ....
Probab=34.41 E-value=43 Score=18.69 Aligned_cols=42 Identities=10% Similarity=0.160 Sum_probs=24.0
Q ss_pred Cccccccccccch-hHHHHHHhCCCEEEEecCcchhhhhhcCcc
Q psy3841 2 RPRFNHHGLNREE-PGKKTNNINNAHVILDVSLAGVERLHRQHV 44 (73)
Q Consensus 2 ~~~~~~~~ygtsi-~sVr~V~ekgkhCILdv~~~avk~L~~~~l 44 (73)
.|.|.+.+||+.+ +.+.+.+ +.+.+.|..++.+++-..+..+
T Consensus 35 ~~~~rg~Gig~~ll~~~~~~~-~~~~i~l~~~~~~~~fY~~~GF 77 (79)
T PF13508_consen 35 DPEYRGKGIGSKLLNYLLEKA-KSKKIFLFTNPAAIKFYEKLGF 77 (79)
T ss_dssp -GGGTTSSHHHHHHHHHHHHH-TCSEEEEEEEHHHHHHHHHTTE
T ss_pred CHHHcCCCHHHHHHHHHHHHc-CCCcEEEEEcHHHHHHHHHCcC
Confidence 4788899999764 3344444 3455555556655554444443
No 40
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.
Probab=33.83 E-value=60 Score=22.46 Aligned_cols=44 Identities=16% Similarity=0.072 Sum_probs=26.0
Q ss_pred ccccchhHHHHHHhCC------CEEEEecC-cchhhhhhcCccccEEEEeec
Q psy3841 9 GLNREEPGKKTNNINN------AHVILDVS-LAGVERLHRQHVYPIVLLIKF 53 (73)
Q Consensus 9 ~ygtsi~sVr~V~ekg------khCILdv~-~~avk~L~~~~l~PiVIfIkp 53 (73)
+|||+.++...|.++| .|.-|-.+ ..++..-.+. =-|++|+|..
T Consensus 109 yHGT~~~~~~~I~~~GL~~m~R~hVHls~~~~~a~~sG~R~-~~~V~i~Id~ 159 (186)
T PF01885_consen 109 YHGTYRKAWPSILEEGLKPMGRNHVHLSTGPETAVISGMRR-SCPVLIYIDA 159 (186)
T ss_dssp EE--BGGGHHHHHHH-B---SSSSEEEES-HHHHHHHHTTS-SSBEEEEEEH
T ss_pred EEccchhhHHHHHHhCCCCCCCCEEEEeeccCCceeecCCC-CCeEEEEEcH
Confidence 5789999999988886 45555554 3334433333 4688888865
No 41
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=33.41 E-value=1.1e+02 Score=18.94 Aligned_cols=35 Identities=23% Similarity=0.331 Sum_probs=27.3
Q ss_pred CCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhcc
Q psy3841 24 NAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKEN 65 (73)
Q Consensus 24 gkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~~ 65 (73)
.-+++||++..+ .+..+.|.....|..+++.+-+.
T Consensus 15 ~dI~vldv~~~~-------~~~dy~VI~Tg~S~rh~~aia~~ 49 (99)
T TIGR00090 15 EDIVVLDVRGKS-------SIADYFVIASGTSSRHVKAIADN 49 (99)
T ss_pred CCEEEEECCCCC-------cccCEEEEEEeCCHHHHHHHHHH
Confidence 557999998643 57789999999999998866543
No 42
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=32.36 E-value=1.2e+02 Score=18.55 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=26.0
Q ss_pred CCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 24 NAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 24 gkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
--++++|++. .+.+..+.|.....|..+++.+-+
T Consensus 15 ~dI~v~dv~~-------~~~~~dy~II~T~~S~rh~~aia~ 48 (100)
T PF02410_consen 15 EDIVVLDVRE-------KSSWADYFIIATGRSERHVRAIAD 48 (100)
T ss_dssp EEEEEEEGCT-------TBSS-SEEEEEEESSHHHHHHHHH
T ss_pred CCeEEEECCC-------CCcccCEEEEEEcCCHHHHHHHHH
Confidence 3478999988 457789999999999988886543
No 43
>PF06741 LsmAD: LsmAD domain; InterPro: IPR009604 This entry represents a conserved region approximately 250 residues long located on eukaryotic ataxin-2 []. Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder []. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death []. Ataxin-2 is predicted to consist of mostly non-globular domains [].
Probab=32.22 E-value=16 Score=22.16 Aligned_cols=14 Identities=0% Similarity=0.003 Sum_probs=11.0
Q ss_pred ccccccccccchhH
Q psy3841 3 PRFNHHGLNREEPG 16 (73)
Q Consensus 3 ~~~~~~~ygtsi~s 16 (73)
.-|++|||=|.++.
T Consensus 5 stydE~lYTT~Ld~ 18 (72)
T PF06741_consen 5 STYDENLYTTPLDR 18 (72)
T ss_pred CccCchhceeeccC
Confidence 45999999988764
No 44
>PF07299 FBP: Fibronectin-binding protein (FBP); InterPro: IPR010841 This entry consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species [,].; PDB: 4ADO_B 4ADN_B 2YB5_F.
Probab=31.94 E-value=19 Score=25.77 Aligned_cols=25 Identities=24% Similarity=0.309 Sum_probs=14.8
Q ss_pred CccccEEEEeecCCHHHHHHhhccc
Q psy3841 42 QHVYPIVLLIKFKSTKQIKEIKENC 66 (73)
Q Consensus 42 ~~l~PiVIfIkp~s~~~lke~r~~~ 66 (73)
.+|.|||+-+.++|.++|+++-+..
T Consensus 73 ~~L~~yV~pF~~~t~~qi~kLF~K~ 97 (208)
T PF07299_consen 73 EELKPYVIPFPPITEKQIKKLFPKA 97 (208)
T ss_dssp HHHHCCB-------HHHHHHHTTTS
T ss_pred HHHHHHhcCCCCCCHHHHHHHhhhh
Confidence 4689999999999999999886654
No 45
>PF13899 Thioredoxin_7: Thioredoxin-like; PDB: 2LST_A 3PH9_A 1UC7_A 2JU5_A 1VRS_D 2FWG_A 2FWF_A 2FWH_A 2FWE_A 3FK8_A ....
Probab=30.73 E-value=1.1e+02 Score=17.44 Aligned_cols=39 Identities=15% Similarity=0.227 Sum_probs=18.3
Q ss_pred hHHHHHHhCCCEEE-EecCcchhhhhhcCccccEEEEeec
Q psy3841 15 PGKKTNNINNAHVI-LDVSLAGVERLHRQHVYPIVLLIKF 53 (73)
Q Consensus 15 ~sVr~V~ekgkhCI-Ldv~~~avk~L~~~~l~PiVIfIkp 53 (73)
+.|++.++++-+.+ +|++...-+..-....+|-++|+.|
T Consensus 43 ~~v~~~~~~~fv~v~vd~~~~~~~~~~~~~~~P~~~~ldp 82 (82)
T PF13899_consen 43 PEVQEALNKNFVLVKVDVDDEDPNAQFDRQGYPTFFFLDP 82 (82)
T ss_dssp HHHHHHHHHCSEEEEEETTTHHHHHHHHHCSSSEEEEEET
T ss_pred HHHHHHHHCCEEEEEEEcCCCChhHHhCCccCCEEEEeCC
Confidence 45666444444333 3554332222111255777777765
No 46
>PF00581 Rhodanese: Rhodanese-like domain This Prosite entry represents a subset of this family.; InterPro: IPR001763 Rhodanese, a sulphurtransferase involved in cyanide detoxification (see IPR001307 from INTERPRO) shares evolutionary relationship with a large family of proteins [], including Cdc25 phosphatase catalytic domain. non-catalytic domains of eukaryotic dual-specificity MAPK-phosphatases. non-catalytic domains of yeast PTP-type MAPK-phosphatases. non-catalytic domains of yeast Ubp4, Ubp5, Ubp7. non-catalytic domains of mammalian Ubp-Y. Drosophila heat shock protein HSP-67BB. several bacterial cold-shock and phage shock proteins. plant senescence associated proteins. catalytic and non-catalytic domains of rhodanese (see IPR001307 from INTERPRO). Rhodanese has an internal duplication. This domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases [].; PDB: 2J6P_D 2FSX_A 1UAR_A 1OKG_A 1GMX_A 1GN0_A 3NTD_B 3NTA_B 3NT6_A 1C25_A ....
Probab=30.29 E-value=68 Score=18.48 Aligned_cols=23 Identities=17% Similarity=0.088 Sum_probs=17.0
Q ss_pred hhHHHHHHhCCCEEEEecCcchh
Q psy3841 14 EPGKKTNNINNAHVILDVSLAGV 36 (73)
Q Consensus 14 i~sVr~V~ekgkhCILdv~~~av 36 (73)
.+-+++.++.++..|+|+.+...
T Consensus 2 ~~el~~~l~~~~~~liD~R~~~~ 24 (113)
T PF00581_consen 2 PEELKEMLENESVLLIDVRSPEE 24 (113)
T ss_dssp HHHHHHHHTTTTEEEEEESSHHH
T ss_pred HHHHHhhhhCCCeEEEEeCCHHH
Confidence 34456667889999999986554
No 47
>KOG2227|consensus
Probab=29.76 E-value=37 Score=27.76 Aligned_cols=40 Identities=30% Similarity=0.360 Sum_probs=30.8
Q ss_pred CCEEEE-------ecCcchhhhhhc-CccccEEEEeecCCHHHHHHhh
Q psy3841 24 NAHVIL-------DVSLAGVERLHR-QHVYPIVLLIKFKSTKQIKEIK 63 (73)
Q Consensus 24 gkhCIL-------dv~~~avk~L~~-~~l~PiVIfIkp~s~~~lke~r 63 (73)
+.+||| |..-..+-+|+. ..+.|-+++++|.+.++|-++-
T Consensus 287 ~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il 334 (529)
T KOG2227|consen 287 NSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEIL 334 (529)
T ss_pred cceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHH
Confidence 555655 455556667887 8999999999999999987653
No 48
>PRK00053 alr alanine racemase; Reviewed
Probab=29.66 E-value=1.9e+02 Score=21.34 Aligned_cols=57 Identities=14% Similarity=0.103 Sum_probs=37.6
Q ss_pred cccccccchhHHHHHH-hCCCEEEEecCcchhhhhhcCccc-cEEEEeecCCHHHHHHh
Q psy3841 6 NHHGLNREEPGKKTNN-INNAHVILDVSLAGVERLHRQHVY-PIVLLIKFKSTKQIKEI 62 (73)
Q Consensus 6 ~~~~ygtsi~sVr~V~-ekgkhCILdv~~~avk~L~~~~l~-PiVIfIkp~s~~~lke~ 62 (73)
+-|.||-....|-..+ +.|...+-..+++....++...+. ||+++-...+.+.+++.
T Consensus 35 KanaYghg~~~i~~~l~~~G~~~~~vas~~Ea~~l~~~G~~~~il~l~~~~~~~e~~~~ 93 (363)
T PRK00053 35 KANAYGHGAVEVAKTLLEAGADGFGVATLEEALELREAGITAPILILGGFFPAEDLPLI 93 (363)
T ss_pred eeccccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHH
Confidence 4577887777777766 567656666788888888887665 55444232455556554
No 49
>TIGR00492 alr alanine racemase. This enzyme interconverts L-alanine and D-alanine. Its primary function is to generate D-alanine for cell wall formation. With D-alanine-D-alanine ligase, it makes up the D-alanine branch of the peptidoglycan biosynthetic route. It is a monomer with one pyridoxal phosphate per subunit. In E. coli, the ortholog is duplicated so that a second isozyme, DadX, is present. DadX, a paralog of the biosynthetic Alr, is induced by D- or L-alanine and is involved in catabolism.
Probab=29.01 E-value=1.8e+02 Score=21.45 Aligned_cols=57 Identities=14% Similarity=0.024 Sum_probs=36.6
Q ss_pred cccccccchhHH-HHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHh
Q psy3841 6 NHHGLNREEPGK-KTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEI 62 (73)
Q Consensus 6 ~~~~ygtsi~sV-r~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~ 62 (73)
+-|.||-....| +...+.|.-.+-..+++-...|+...+-+-++++.+...+.+...
T Consensus 34 KAnaYGhg~~~i~~~l~~~G~~~~~vas~~Ea~~lr~~G~~~~ilvl~~~~~~~~~~~ 91 (367)
T TIGR00492 34 KANAYGHGLIEVAKTLLQAGADYFGVANLEEAITLRKAGITAPILLLGGFFAEDLKIL 91 (367)
T ss_pred EcCCccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhcCCCCCEEEEeCCCHHHHHHH
Confidence 457788776655 555677855555568888888888777643455555545555543
No 50
>COG3467 Predicted flavin-nucleotide-binding protein [General function prediction only]
Probab=28.84 E-value=1.2e+02 Score=20.56 Aligned_cols=22 Identities=5% Similarity=-0.209 Sum_probs=19.2
Q ss_pred chhHHHHHHhCCCEEEEecCcc
Q psy3841 13 EEPGKKTNNINNAHVILDVSLA 34 (73)
Q Consensus 13 si~sVr~V~ekgkhCILdv~~~ 34 (73)
|-+-|.+++..|..|.|-...+
T Consensus 12 ~~~~i~~~l~~~~~~~La~~~~ 33 (166)
T COG3467 12 SDEEIDAILAAGRVGRLAFAGD 33 (166)
T ss_pred CHHHHHHHHhhCCEEEEEEcCC
Confidence 7789999999999999987543
No 51
>cd06826 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2. This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=28.76 E-value=1.6e+02 Score=21.88 Aligned_cols=59 Identities=7% Similarity=-0.033 Sum_probs=39.8
Q ss_pred cccccccchhHH-HHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 6 NHHGLNREEPGK-KTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 6 ~~~~ygtsi~sV-r~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
+.|-||--...| +...+.|--.+-..++.-...|+...+-+.++.+.+++.+.+++.-+
T Consensus 33 KAnAYGhG~~~va~~l~~~g~~~f~Vas~~Ea~~lr~~Gi~~~ilvl~~~~~~e~~~~i~ 92 (365)
T cd06826 33 KADAYGHGIALVMPSIIAQNIPCVGITSNEEARVVREAGFTGKILRVRTATPSEIEDALA 92 (365)
T ss_pred EeccccccHHHHHHHHHHCCCCEEEEccHHHHHHHHhcCCCCCEEEEeCCCHHHHHHHHH
Confidence 567788765554 45567777666667888888898887775555556666666665533
No 52
>PRK06762 hypothetical protein; Provisional
Probab=28.71 E-value=1.6e+02 Score=18.69 Aligned_cols=46 Identities=11% Similarity=0.034 Sum_probs=27.1
Q ss_pred HHHHHHhCCCEEEEecCcch------hhhhhcCcccc-EEEEeecCCHHHHHH
Q psy3841 16 GKKTNNINNAHVILDVSLAG------VERLHRQHVYP-IVLLIKFKSTKQIKE 61 (73)
Q Consensus 16 sVr~V~ekgkhCILdv~~~a------vk~L~~~~l~P-iVIfIkp~s~~~lke 61 (73)
.++..++.|..+|+|-.... ++.|....-.| .+|++..|-...++.
T Consensus 60 ~~~~~~~~g~~vild~~~~~~~~~~~~~~l~~~~~~~~~~v~Ldap~e~~~~R 112 (166)
T PRK06762 60 LVRYGLGHCEFVILEGILNSDRYGPMLKELIHLFRGNAYTYYFDLSFEETLRR 112 (166)
T ss_pred HHHHHHhCCCEEEEchhhccHhHHHHHHHHHHhcCCCeEEEEEeCCHHHHHHH
Confidence 34455778999999865322 44454432234 677888765444443
No 53
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=28.70 E-value=45 Score=20.04 Aligned_cols=17 Identities=24% Similarity=0.169 Sum_probs=12.9
Q ss_pred hhhhcCccccEEEEeec
Q psy3841 37 ERLHRQHVYPIVLLIKF 53 (73)
Q Consensus 37 k~L~~~~l~PiVIfIkp 53 (73)
..|....+.|++||=.+
T Consensus 64 ~~L~~~~I~PifVFDG~ 80 (99)
T smart00485 64 CRLLEFGIKPIFVFDGK 80 (99)
T ss_pred HHHHHCCCeEEEEECCC
Confidence 34778999999999433
No 54
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=28.60 E-value=92 Score=16.08 Aligned_cols=21 Identities=10% Similarity=0.042 Sum_probs=17.2
Q ss_pred cccccchhHHHHHHhCCCEEE
Q psy3841 8 HGLNREEPGKKTNNINNAHVI 28 (73)
Q Consensus 8 ~~ygtsi~sVr~V~ekgkhCI 28 (73)
-+++.|..-+++.+++|...|
T Consensus 10 ~~~~~sr~~a~~~I~~g~V~V 30 (48)
T PF01479_consen 10 LGLASSRSEARRLIKQGRVKV 30 (48)
T ss_dssp TTSSSSHHHHHHHHHTTTEEE
T ss_pred cCCcCCHHHHHHhcCCCEEEE
Confidence 467788999999999998643
No 55
>PF01300 Sua5_yciO_yrdC: Telomere recombination; InterPro: IPR006070 The YrdC family of hypothetical proteins are widely distributed in eukaryotes and prokaryotes and occur as: (i) independent proteins, (ii) with C-terminal extensions, and (iii) as domains in larger proteins, some of which are implicated in regulation []. The YrdC protein, which consists solely of this domain, forms an alpha/beta twisted open-sheet structure composed of seven alpha helices and seven beta strands []. YrdC from Escherichia coli preferentially binds to double-stranded RNA and DNA. YrdC is predicted to be an rRNA maturation factor, as deletions in its gene lead to immature ribosomal 30S subunits and, consequently, fewer translating ribosomes []. Therefore, YrdC may function by keeping an rRNA structure needed for proper processing of 16S rRNA, especially at lower temperatures. Sua5 is an example of a multi-domain protein that contains an N-terminal YrdC-like domain and a C-terminal Sua5 domain. Sua5 was identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a translation initiation defect in the cytochrome c gene and is required for normal growth in yeast; however its exact function remains unknown []. HypF is involved in the synthesis of the active site of [NiFe]-hydrogenases [].; PDB: 3L7V_A 1KK9_A 1K7J_A 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A 2EQA_A ....
Probab=27.91 E-value=1.3e+02 Score=20.11 Aligned_cols=42 Identities=29% Similarity=0.359 Sum_probs=22.4
Q ss_pred HHhCCCEEEEe-----------cCcchhhhhh----cCccccEEEEeecCCHHHHHHhh
Q psy3841 20 NNINNAHVILD-----------VSLAGVERLH----RQHVYPIVLLIKFKSTKQIKEIK 63 (73)
Q Consensus 20 V~ekgkhCILd-----------v~~~avk~L~----~~~l~PiVIfIkp~s~~~lke~r 63 (73)
++++|..+++- .+++|+++|. +..=+|+++++ .|.+++++.-
T Consensus 2 ~Lk~G~vvi~PTdT~ygl~~~~~n~~av~ri~~iK~R~~~Kpl~ll~--~~~~~l~~~~ 58 (179)
T PF01300_consen 2 ILKAGGVVIYPTDTVYGLGCDAFNPEAVERIYKIKQRPKNKPLILLV--SSIEQLEEYV 58 (179)
T ss_dssp HHHTT-EEEEEESSSEEEEEETTSHHHHHHHHHHHTSSTTS--EEEE--SSHHHHHHHE
T ss_pred ccccCCEEEEECCCEEEEEEecCCHHHHHHHHHhhcccCCCCEEEEE--CCHHHHHHHh
Confidence 45566665543 2566777765 23367887774 4566666543
No 56
>COG4588 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [General function prediction only]
Probab=26.63 E-value=52 Score=24.38 Aligned_cols=50 Identities=14% Similarity=0.176 Sum_probs=32.8
Q ss_pred ccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHh
Q psy3841 7 HHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEI 62 (73)
Q Consensus 7 ~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~ 62 (73)
|-++|+|-||--++++.-+- +. +.+.++-..+-|-+|.+++-+.+.||.+
T Consensus 69 Dilfgaseqsalaia~~~~~---~f---s~~~i~ply~R~aiIlvkkgNPknIk~~ 118 (252)
T COG4588 69 DILFGASEQSALAIAEDHKD---SF---SEKNIQPLYLRPAIILVKKGNPKNIKGF 118 (252)
T ss_pred ceeecccHHHHHHHHHhccc---cc---cccccceeeeeceEEEecCCCccccccH
Confidence 45899999999999987431 12 2333333455688899986665555533
No 57
>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily. This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.
Probab=26.36 E-value=76 Score=18.50 Aligned_cols=22 Identities=18% Similarity=0.083 Sum_probs=16.7
Q ss_pred chhHHHHHHh-CCCEEEEecCcc
Q psy3841 13 EEPGKKTNNI-NNAHVILDVSLA 34 (73)
Q Consensus 13 si~sVr~V~e-kgkhCILdv~~~ 34 (73)
|.+.+++.++ ++...|||+.+.
T Consensus 2 ~~~~~~~~l~~~~~~~iiDvR~~ 24 (106)
T cd01519 2 SFEEVKNLPNPHPNKVLIDVREP 24 (106)
T ss_pred cHHHHHHhcCCCCCEEEEECCCH
Confidence 5567777777 667899999865
No 58
>KOG1530|consensus
Probab=26.28 E-value=92 Score=21.21 Aligned_cols=36 Identities=22% Similarity=0.191 Sum_probs=25.9
Q ss_pred chhHHHHHHhCCCEEEEecC-cchhhhhhcCccccEEEEee
Q psy3841 13 EEPGKKTNNINNAHVILDVS-LAGVERLHRQHVYPIVLLIK 52 (73)
Q Consensus 13 si~sVr~V~ekgkhCILdv~-~~avk~L~~~~l~PiVIfIk 52 (73)
|.+-++++.+.|-+.+|||. |+..+.-+ + |-.|.|.
T Consensus 26 ~~~qvk~L~~~~~~~llDVRepeEfk~gh---~-~~siNiP 62 (136)
T KOG1530|consen 26 SVEQVKNLLQHPDVVLLDVREPEEFKQGH---I-PASINIP 62 (136)
T ss_pred EHHHHHHHhcCCCEEEEeecCHHHhhccC---C-cceEecc
Confidence 56778999999999999994 44444443 3 6666663
No 59
>PRK06842 fumarate hydratase; Provisional
Probab=26.25 E-value=9.4 Score=27.04 Aligned_cols=30 Identities=17% Similarity=0.371 Sum_probs=24.4
Q ss_pred CEEEEecCcchhhhhhcCccccEEEEeecCC
Q psy3841 25 AHVILDVSLAGVERLHRQHVYPIVLLIKFKS 55 (73)
Q Consensus 25 khCILdv~~~avk~L~~~~l~PiVIfIkp~s 55 (73)
.....|+.|+|+-.|.-.+| |-+|-+....
T Consensus 140 ~v~~~dLG~EAi~~l~V~df-P~iV~iD~~G 169 (185)
T PRK06842 140 VIAYEDLGAEAIRKLEVKDF-PVVVIIDSEG 169 (185)
T ss_pred EEeccccCccEEEEEEEecC-CEEEEEeCCC
Confidence 34578899999999998998 9998886543
No 60
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=25.30 E-value=41 Score=19.88 Aligned_cols=26 Identities=15% Similarity=0.059 Sum_probs=15.8
Q ss_pred chhHHHHHHhCCCEEEEecCcchhhhhh
Q psy3841 13 EEPGKKTNNINNAHVILDVSLAGVERLH 40 (73)
Q Consensus 13 si~sVr~V~ekgkhCILdv~~~avk~L~ 40 (73)
|.+||+.++|+-- |-+++.++.+.|-
T Consensus 5 ~~esvk~iAes~G--i~~l~de~a~~La 30 (66)
T PF02969_consen 5 SQESVKDIAESLG--ISNLSDEAAKALA 30 (66)
T ss_dssp -HHHHHHHHHHTT-----B-HHHHHHHH
T ss_pred CHHHHHHHHHHcC--CCCCCHHHHHHHH
Confidence 5689999999832 4567777777653
No 61
>cd01212 JIP JNK-interacting protein (JIP) Phosphotyrosine-binding (PTB) domain. JNK-interacting protein (JIP) Phosphotyrosine-binding (PTB) domain. JIP is a mitogen-activated protein kinase scaffold protein. JIP consists of a C-terminal SH3 domain, followed by a PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=25.21 E-value=40 Score=22.72 Aligned_cols=31 Identities=13% Similarity=0.091 Sum_probs=22.5
Q ss_pred cccch--hHHHHHHhC---------CCEEEEecCcchhhhhh
Q psy3841 10 LNREE--PGKKTNNIN---------NAHVILDVSLAGVERLH 40 (73)
Q Consensus 10 ygtsi--~sVr~V~ek---------gkhCILdv~~~avk~L~ 40 (73)
-|+.+ +|++.+... ..-|+|.|++++|+-.-
T Consensus 19 kG~~v~~~A~rki~~~~k~~~~~~~~~~v~L~VS~~Girl~D 60 (148)
T cd01212 19 KGNGVLCQAMRKIVGEYKNSEESPTPQTCILEISDRGLRMVD 60 (148)
T ss_pred CCcHHHHHHHHHHHHHHHhhccCCCCcEEEEEEecCcEEEEe
Confidence 34555 888888643 24699999999998763
No 62
>PRK02821 hypothetical protein; Provisional
Probab=24.49 E-value=1e+02 Score=18.68 Aligned_cols=21 Identities=24% Similarity=0.211 Sum_probs=17.0
Q ss_pred ccchhHHHHHHh--CCCEEEEec
Q psy3841 11 NREEPGKKTNNI--NNAHVILDV 31 (73)
Q Consensus 11 gtsi~sVr~V~e--kgkhCILdv 31 (73)
|.-++|||.++. .|+.+-|++
T Consensus 50 Gr~i~AIRtlv~a~~~~~v~leI 72 (77)
T PRK02821 50 GRTATALRTVVAAIGGRGVRVDV 72 (77)
T ss_pred CchHHHHHHHHHHhcCCeEEEEE
Confidence 678899999988 677777765
No 63
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=24.49 E-value=53 Score=19.73 Aligned_cols=30 Identities=20% Similarity=0.155 Sum_probs=21.0
Q ss_pred cccccccccchhHHHHHHh----CC----------CEEEEecCc
Q psy3841 4 RFNHHGLNREEPGKKTNNI----NN----------AHVILDVSL 33 (73)
Q Consensus 4 ~~~~~~ygtsi~sVr~V~e----kg----------khCILdv~~ 33 (73)
|+++.++-.+.+.+++.+. .+ ++.|||++.
T Consensus 14 ~~~g~l~f~~~~~~~~~i~~~~~~~~~~~~~~~~~~~vIlD~s~ 57 (117)
T PF01740_consen 14 RLDGPLFFANAEEFRDRIRKLIDEDPERIKKRQTIKNVILDMSG 57 (117)
T ss_dssp EEESEESHHHHHHHHHHHHHHHCCSSS--HTSSSSSEEEEEETT
T ss_pred EEeeEEEHHHHHHHHHHHHHhhhcccccccccccceEEEEEEEe
Confidence 5667777777777766654 35 799999853
No 64
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=24.47 E-value=85 Score=23.17 Aligned_cols=23 Identities=13% Similarity=0.047 Sum_probs=19.1
Q ss_pred HHHHHHhCCCEEEEecCcchhhh
Q psy3841 16 GKKTNNINNAHVILDVSLAGVER 38 (73)
Q Consensus 16 sVr~V~ekgkhCILdv~~~avk~ 38 (73)
-+|...++||..||.++|.++..
T Consensus 150 ~~r~l~d~gKvIilTvhp~~l~e 172 (235)
T COG2874 150 FLRKLSDLGKVIILTVHPSALDE 172 (235)
T ss_pred HHHHHHhCCCEEEEEeChhhcCH
Confidence 34666778999999999999874
No 65
>PRK00468 hypothetical protein; Provisional
Probab=24.24 E-value=85 Score=18.85 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=16.3
Q ss_pred ccchhHHHHHHh-----CCCEEEEec
Q psy3841 11 NREEPGKKTNNI-----NNAHVILDV 31 (73)
Q Consensus 11 gtsi~sVr~V~e-----kgkhCILdv 31 (73)
|.-++|||.++. .|+.+.||+
T Consensus 49 Gr~i~AIRtvv~aaa~k~~~rv~leI 74 (75)
T PRK00468 49 GRIAKAIRTVVKAAAIKENKRVVVEI 74 (75)
T ss_pred ChhHHHHHHHHHHHHhcCCCEEEEEE
Confidence 577899999887 377777775
No 66
>PRK11070 ssDNA exonuclease RecJ; Provisional
Probab=24.13 E-value=1.6e+02 Score=23.98 Aligned_cols=36 Identities=14% Similarity=0.179 Sum_probs=26.9
Q ss_pred ccccccccccchhHHHHHHhCC--CEEEEecCcchhhhh
Q psy3841 3 PRFNHHGLNREEPGKKTNNINN--AHVILDVSLAGVERL 39 (73)
Q Consensus 3 ~~~~~~~ygtsi~sVr~V~ekg--khCILdv~~~avk~L 39 (73)
+|| +.+||-|.++|+++.++| -....|++-.+.+.+
T Consensus 107 ~R~-~eGYGl~~~~i~~~~~~~~~LiItvD~Gi~~~e~i 144 (575)
T PRK11070 107 NRF-EDGYGLSPEVVDQAHARGAQLIVTVDNGISSHAGV 144 (575)
T ss_pred CCC-cCCCCCCHHHHHHHHhcCCCEEEEEcCCcCCHHHH
Confidence 344 457999999999999886 455567777776665
No 67
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=23.99 E-value=1e+02 Score=18.30 Aligned_cols=18 Identities=17% Similarity=0.163 Sum_probs=13.6
Q ss_pred chhHHHHHHhCCCEEEEe
Q psy3841 13 EEPGKKTNNINNAHVILD 30 (73)
Q Consensus 13 si~sVr~V~ekgkhCILd 30 (73)
..+.++..++.|+|++++
T Consensus 75 h~~~~~~~l~~g~~v~~E 92 (120)
T PF01408_consen 75 HAEIAKKALEAGKHVLVE 92 (120)
T ss_dssp HHHHHHHHHHTTSEEEEE
T ss_pred hHHHHHHHHHcCCEEEEE
Confidence 446677888888888877
No 68
>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.
Probab=23.52 E-value=82 Score=18.80 Aligned_cols=23 Identities=9% Similarity=-0.048 Sum_probs=17.0
Q ss_pred chhHHHHHHhCCCEEEEecCcch
Q psy3841 13 EEPGKKTNNINNAHVILDVSLAG 35 (73)
Q Consensus 13 si~sVr~V~ekgkhCILdv~~~a 35 (73)
|.+.+++.++++...|||+.+..
T Consensus 2 s~~~l~~~l~~~~~~iiDvR~~~ 24 (118)
T cd01449 2 TAEEVLANLDSGDVQLVDARSPE 24 (118)
T ss_pred CHHHHHHhcCCCCcEEEeCCCHH
Confidence 55667777777778899997743
No 69
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=23.36 E-value=39 Score=23.53 Aligned_cols=16 Identities=6% Similarity=0.142 Sum_probs=12.3
Q ss_pred ccccccccccchhHHH
Q psy3841 3 PRFNHHGLNREEPGKK 18 (73)
Q Consensus 3 ~~~~~~~ygtsi~sVr 18 (73)
++|.++.|||....++
T Consensus 11 ~~f~~~~y~~~~g~~r 26 (255)
T PRK11036 11 EKFSRNIYGTTKGQIR 26 (255)
T ss_pred HHHHHhccCCCccHHH
Confidence 5788899999865555
No 70
>PTZ00330 acetyltransferase; Provisional
Probab=23.18 E-value=70 Score=19.42 Aligned_cols=46 Identities=20% Similarity=0.199 Sum_probs=28.1
Q ss_pred Cccccccccccch-hHHHHHH-hCCC-EEEEecCcchhhhhhcCccccE
Q psy3841 2 RPRFNHHGLNREE-PGKKTNN-INNA-HVILDVSLAGVERLHRQHVYPI 47 (73)
Q Consensus 2 ~~~~~~~~ygtsi-~sVr~V~-ekgk-hCILdv~~~avk~L~~~~l~Pi 47 (73)
.|.|.+.++|+.+ +.+.+.+ ++|. ..+|+.+..|++-..+..|.+.
T Consensus 91 ~~~~rg~Gig~~l~~~~~~~a~~~~~~~l~l~~n~~a~~~y~k~GF~~~ 139 (147)
T PTZ00330 91 DPSYRGQGLGRALISDLCEIARSSGCYKVILDCTEDMVAFYKKLGFRAC 139 (147)
T ss_pred CHHHcCCCHHHHHHHHHHHHHHHCCCCEEEEecChHHHHHHHHCCCEEe
Confidence 4678888888643 3333333 3343 3468888877777766666543
No 71
>PF02964 MeMO_Hyd_G: Methane monooxygenase, hydrolase gamma chain; InterPro: IPR004222 Methane monooxygenases (1.14.13.25 from EC) catalyse the oxidation of methane to methanol in the presence of oxygen and NADH in methanotrophs. It has a broad specificity, hydroxylating many alkanes, and converting alkenes into the corresponding epoxides. In additional reactions, CO is oxidized to CO2, ammonia is oxidized to hydroxylamine, and some aromatic compounds and cyclic alkanes can also be hydroxylated, although more slowly. In Methylococcus capsulatus there are two forms of the enzyme, a soluble and a membrane-bound type. The soluble form consists of 3 components, A, B and C. Protein A is made up of 3 chains, alpha, beta and gamma. This entry represents the gamma chain of methane monooxygenases. Structurally, the gamma chain contains two domains, each consisting of a three helices arranged in an open bundle topology [, ]. ; GO: 0015049 methane monooxygenase activity, 0015947 methane metabolic process; PDB: 1FZ1_E 1FZ4_F 1XU3_E 1FZ7_F 1XVB_F 1FZ3_E 1XMG_E 1FZI_F 1XVD_F 1FZ2_E ....
Probab=23.03 E-value=55 Score=22.85 Aligned_cols=14 Identities=7% Similarity=-0.104 Sum_probs=11.2
Q ss_pred cccccccchhHHHH
Q psy3841 6 NHHGLNREEPGKKT 19 (73)
Q Consensus 6 ~~~~ygtsi~sVr~ 19 (73)
|-++||||++-.|+
T Consensus 139 n~dyy~~pLeeLRk 152 (161)
T PF02964_consen 139 NTDYYATPLEELRK 152 (161)
T ss_dssp CTTTTSS-HHHHHH
T ss_pred CcchhcCcHHHHHH
Confidence 56899999998886
No 72
>PRK11538 ribosome-associated protein; Provisional
Probab=22.64 E-value=2.1e+02 Score=18.11 Aligned_cols=34 Identities=15% Similarity=0.240 Sum_probs=26.6
Q ss_pred CCEEEEecCcchhhhhhcCccccEEEEeecCCHHHHHHhhc
Q psy3841 24 NAHVILDVSLAGVERLHRQHVYPIVLLIKFKSTKQIKEIKE 64 (73)
Q Consensus 24 gkhCILdv~~~avk~L~~~~l~PiVIfIkp~s~~~lke~r~ 64 (73)
.-+++||+... +.+..+.|+....|..+++.+-+
T Consensus 20 ~DI~vlDv~~~-------~~~~Dy~VIatg~S~rh~~aia~ 53 (105)
T PRK11538 20 QDIIALDVQGK-------SSITDCMIICTGTSSRHVMSIAD 53 (105)
T ss_pred CCeEEEECCCC-------CcccCEEEEEEeCCHHHHHHHHH
Confidence 45789999864 44778999999999998886543
No 73
>cd00852 NifB NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins.
Probab=22.54 E-value=1.6e+02 Score=17.73 Aligned_cols=34 Identities=15% Similarity=0.095 Sum_probs=27.1
Q ss_pred hhHHHHHHh--CCCEEEEe--cCcchhhhhhcCccccE
Q psy3841 14 EPGKKTNNI--NNAHVILD--VSLAGVERLHRQHVYPI 47 (73)
Q Consensus 14 i~sVr~V~e--kgkhCILd--v~~~avk~L~~~~l~Pi 47 (73)
.+.+..+++ +|.-+|+- +++.|.++|+...+.++
T Consensus 53 ~~~~~~~l~~l~~~~vvi~~~iG~~a~~~L~~~GI~v~ 90 (106)
T cd00852 53 EDRLDAIIKLLSDCDAVLCAKIGDEPKEKLEEAGIEVI 90 (106)
T ss_pred HhHHHHHHHHHcCCcEEeehhhCccHHHHHHHCCCEEE
Confidence 455665665 78888876 89999999999998886
No 74
>cd01447 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.
Probab=22.10 E-value=1.3e+02 Score=17.21 Aligned_cols=22 Identities=9% Similarity=0.015 Sum_probs=16.4
Q ss_pred chhHHHHHHhCCCEEEEecCcc
Q psy3841 13 EEPGKKTNNINNAHVILDVSLA 34 (73)
Q Consensus 13 si~sVr~V~ekgkhCILdv~~~ 34 (73)
|.+.+.+.++++...|||+.+.
T Consensus 2 s~~el~~~~~~~~~~iiDvR~~ 23 (103)
T cd01447 2 SPEDARALLGSPGVLLVDVRDP 23 (103)
T ss_pred CHHHHHHHHhCCCeEEEECCCH
Confidence 4566777777677789999864
No 75
>PF09391 DUF2000: Protein of unknown function (DUF2000); InterPro: IPR018988 This is a family of proteins of unknown function. The structure of one of the proteins in this family has been shown to adopt an alpha beta fold. ; PDB: 2GAX_A.
Probab=21.85 E-value=79 Score=20.89 Aligned_cols=22 Identities=23% Similarity=0.502 Sum_probs=15.7
Q ss_pred cccEEEEeecCCHHHHHHhhcccc
Q psy3841 44 VYPIVLLIKFKSTKQIKEIKENCR 67 (73)
Q Consensus 44 l~PiVIfIkp~s~~~lke~r~~~~ 67 (73)
-+|+.|+-. +.++|++++.++.
T Consensus 53 ~~PipIL~a--~~~~L~~l~~~a~ 74 (133)
T PF09391_consen 53 HIPIPILKA--NSEQLRELRQKAL 74 (133)
T ss_dssp SS-EEEEEE---HHHHHHHHHHHH
T ss_pred CcCeEEEEc--CHHHHHHHHHHHH
Confidence 368887765 7899999998774
No 76
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=21.30 E-value=2e+02 Score=17.36 Aligned_cols=41 Identities=12% Similarity=0.046 Sum_probs=24.7
Q ss_pred hHHHHHHhCCCEEEEecCcc-hh------hhhhcCccccEEEEeecCC
Q psy3841 15 PGKKTNNINNAHVILDVSLA-GV------ERLHRQHVYPIVLLIKFKS 55 (73)
Q Consensus 15 ~sVr~V~ekgkhCILdv~~~-av------k~L~~~~l~PiVIfIkp~s 55 (73)
+.++..++.|..+|+|-..- .. +.++...+...+|++.++.
T Consensus 61 ~~~~~~l~~g~~~vvd~~~~~~~~r~~~~~~~~~~~~~~~~v~l~~~~ 108 (143)
T PF13671_consen 61 AAIRKALRNGNSVVVDNTNLSREERARLRELARKHGYPVRVVYLDAPE 108 (143)
T ss_dssp HHHHHHHHTT-EEEEESS--SHHHHHHHHHHHHHCTEEEEEEEECHHH
T ss_pred HHHHHHHHcCCCceeccCcCCHHHHHHHHHHHHHcCCeEEEEEEECCH
Confidence 56777888999999993322 21 1233455556778887644
No 77
>PF06952 PsiA: PsiA protein; InterPro: IPR009713 This family consists of several Enterobacterial PsiA proteins. The function of PsiA is unknown although it is thought that it may affect the generation of an SOS signal in Escherichia coli [].
Probab=21.14 E-value=68 Score=23.72 Aligned_cols=33 Identities=18% Similarity=0.106 Sum_probs=25.8
Q ss_pred hHHHHHHhC-CCEEEEecCcchhhhhhcCccccEEEEee
Q psy3841 15 PGKKTNNIN-NAHVILDVSLAGVERLHRQHVYPIVLLIK 52 (73)
Q Consensus 15 ~sVr~V~ek-gkhCILdv~~~avk~L~~~~l~PiVIfIk 52 (73)
.++...|+. |..|+|-++.++-.+| ||=|.|-.
T Consensus 81 ~AlD~LIeSrGe~cpLPLs~dv~~~L-----FPev~~~~ 114 (238)
T PF06952_consen 81 RALDRLIESRGEYCPLPLSSDVAARL-----FPEVQFRR 114 (238)
T ss_pred HHHHHHHHcCCceeeccCCHHHHHHh-----CcchhhhH
Confidence 467777775 9999999999887655 89887753
No 78
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=21.09 E-value=1.2e+02 Score=18.02 Aligned_cols=21 Identities=19% Similarity=0.048 Sum_probs=11.4
Q ss_pred cchhHHHHHHhCCCEEEEecC
Q psy3841 12 REEPGKKTNNINNAHVILDVS 32 (73)
Q Consensus 12 tsi~sVr~V~ekgkhCILdv~ 32 (73)
.+.+.|++-+++|+.+|+.+.
T Consensus 87 ~~~~~i~~~i~~G~Pvi~~~~ 107 (144)
T PF13529_consen 87 ASFDDIKQEIDAGRPVIVSVN 107 (144)
T ss_dssp S-HHHHHHHHHTT--EEEEEE
T ss_pred CcHHHHHHHHHCCCcEEEEEE
Confidence 455666666666666666664
No 79
>cd08633 PI-PLCc_eta2 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta2. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-eta isozyme 2. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-eta represents a class of neuron-speific PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding m
Probab=20.68 E-value=95 Score=23.01 Aligned_cols=23 Identities=4% Similarity=-0.126 Sum_probs=19.6
Q ss_pred ccc-cchhHHHHHHhCCCEEE-Eec
Q psy3841 9 GLN-REEPGKKTNNINNAHVI-LDV 31 (73)
Q Consensus 9 ~yg-tsi~sVr~V~ekgkhCI-Ldv 31 (73)
++| .|+++.++++.+|+-|| ||+
T Consensus 26 l~~~ss~e~y~~aL~~GcRcvElD~ 50 (254)
T cd08633 26 LMSQSRVDMYAWVLQAGCRCVEVDC 50 (254)
T ss_pred cCCccCHHHHHHHHHcCCcEEEEEe
Confidence 556 57999999999999998 676
No 80
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=20.52 E-value=69 Score=22.68 Aligned_cols=35 Identities=14% Similarity=0.337 Sum_probs=30.0
Q ss_pred CCccccccccccchhHHHHHHhCCCEEEEecCcch
Q psy3841 1 MRPRFNHHGLNREEPGKKTNNINNAHVILDVSLAG 35 (73)
Q Consensus 1 ~~~~~~~~~ygtsi~sVr~V~ekgkhCILdv~~~a 35 (73)
|||.-.+|-|-|.+..++.-+++|.++=+.+....
T Consensus 95 ~rp~Id~hD~~~K~k~~~rFLe~GdkVKvtirfrG 129 (176)
T COG0290 95 LRPKIDEHDYETKLKNARRFLEKGDKVKVTIRFRG 129 (176)
T ss_pred eecCcCcchHHHHHHHHHHHHHCCCeEEEEEEEec
Confidence 57888999999999999999999999877774433
No 81
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=20.50 E-value=44 Score=24.45 Aligned_cols=43 Identities=12% Similarity=0.042 Sum_probs=29.4
Q ss_pred ccccccchhHHHHHHhCCCEEEEecCcchhhhhhcCccccEEEE
Q psy3841 7 HHGLNREEPGKKTNNINNAHVILDVSLAGVERLHRQHVYPIVLL 50 (73)
Q Consensus 7 ~~~ygtsi~sVr~V~ekgkhCILdv~~~avk~L~~~~l~PiVIf 50 (73)
.|+||+|+.++--.+-+--|.+=|-.--+-=+++ ..+.|.+.|
T Consensus 83 ~~y~g~Sia~~aVAAHEVGHAiQd~~~Y~~L~~R-~~lvPv~~~ 125 (226)
T COG2738 83 ANYYGPSIAAIAVAAHEVGHAIQDQEDYAFLVLR-HALVPVANF 125 (226)
T ss_pred cccCCccHHHHHHHHHHhhHHHhhhcccHHHHHh-hcccceecc
Confidence 5899999999988777766777665555554554 345565544
No 82
>PRK05928 hemD uroporphyrinogen-III synthase; Reviewed
Probab=20.32 E-value=1.5e+02 Score=19.77 Aligned_cols=37 Identities=3% Similarity=-0.146 Sum_probs=29.2
Q ss_pred cchhHHHHHHhC---------CCEEEEecCcchhhhhhcCccccEE
Q psy3841 12 REEPGKKTNNIN---------NAHVILDVSLAGVERLHRQHVYPIV 48 (73)
Q Consensus 12 tsi~sVr~V~ek---------gkhCILdv~~~avk~L~~~~l~PiV 48 (73)
||-.+|+...+. ...+++-+++..-+.|+...+.+..
T Consensus 59 tS~~av~~~~~~~~~~~~~~~~~~~~~avG~~Ta~~l~~~G~~~~~ 104 (249)
T PRK05928 59 TSKNAVEFLLSALKKKKLKWPKNKKYAAIGEKTALALKKLGGKVVF 104 (249)
T ss_pred ECHHHHHHHHHHHHhcCcCCCCCCEEEEECHHHHHHHHHcCCCccc
Confidence 888888888762 4578889999999999887776653
No 83
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=20.24 E-value=2.3e+02 Score=17.49 Aligned_cols=37 Identities=16% Similarity=0.106 Sum_probs=25.8
Q ss_pred hHHHHHHhCCCEEEEecCcc-------hhhhhhcCccccEEEEe
Q psy3841 15 PGKKTNNINNAHVILDVSLA-------GVERLHRQHVYPIVLLI 51 (73)
Q Consensus 15 ~sVr~V~ekgkhCILdv~~~-------avk~L~~~~l~PiVIfI 51 (73)
+++++++..+...|+=++-+ .++++......|.||.|
T Consensus 34 ~~l~~l~~~~d~gII~Ite~~~~~i~e~i~~~~~~~~~P~ii~I 77 (100)
T PRK02228 34 EAVEEVLEDDDVGILVMHDDDLEKLPRRLRRTLEESVEPTVVTL 77 (100)
T ss_pred HHHHHHhhCCCEEEEEEehhHhHhhHHHHHHHHhcCCCCEEEEE
Confidence 46777766666667666555 34455567889999999
No 84
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=20.20 E-value=64 Score=23.78 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=25.5
Q ss_pred ccccchhHHHHHHhCCCE--EEEecCcchhh
Q psy3841 9 GLNREEPGKKTNNINNAH--VILDVSLAGVE 37 (73)
Q Consensus 9 ~ygtsi~sVr~V~ekgkh--CILdv~~~avk 37 (73)
-|..|.++|++.++++.- .++|++=+++.
T Consensus 142 sY~~Sr~tv~~~l~~~p~i~~~iDiHRDs~~ 172 (268)
T PF07454_consen 142 SYKRSRETVKKALKENPDIKVVIDIHRDSVP 172 (268)
T ss_pred HHHHHHHHHHHHHHHCCCceEEEEecCCCCC
Confidence 477899999999999665 99999999987
No 85
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=20.17 E-value=81 Score=15.63 Aligned_cols=17 Identities=6% Similarity=-0.246 Sum_probs=12.9
Q ss_pred ccccchhHHHHHHhCCC
Q psy3841 9 GLNREEPGKKTNNINNA 25 (73)
Q Consensus 9 ~ygtsi~sVr~V~ekgk 25 (73)
++|.|..+|...+++|.
T Consensus 10 ~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 10 YLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHCCCHHHHHHHHHcCC
Confidence 45778888888887775
No 86
>cd06825 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, VanT and similar proteins. This subfamily is composed of Enterococcus gallinarum VanT and similar proteins. VanT is a membrane-bound serine racemase (EC 5.1.1.18) that is essential for vancomycin resistance in Enterococcus gallinarum. It converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. The C-terminal region of this protein contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, which is homologous to the fold type III PLP-dependent enzyme, bacterial alanine racemase (AR). AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. On the basis of this similarity, it has been suggested that dimer formation of VanT is required for its catalytic activity, and that it catalyzes the racemization of serine in a mechanistically similar manner to that of alanine by
Probab=20.13 E-value=3.5e+02 Score=20.26 Aligned_cols=57 Identities=12% Similarity=0.166 Sum_probs=38.1
Q ss_pred cccccccchhHH-HHHHhCCCEEEEecCcchhhhhhcCccc-cEEEEeecCCHHHHHHhh
Q psy3841 6 NHHGLNREEPGK-KTNNINNAHVILDVSLAGVERLHRQHVY-PIVLLIKFKSTKQIKEIK 63 (73)
Q Consensus 6 ~~~~ygtsi~sV-r~V~ekgkhCILdv~~~avk~L~~~~l~-PiVIfIkp~s~~~lke~r 63 (73)
+.|.||--...| +...+.|-..+-.-+..--..|+...+. ||.++ .++..+.+.++-
T Consensus 33 KanAYGhG~~~va~~l~~~G~~~faVa~~~EA~~Lr~~Gi~~~Ilvl-~~~~~~~~~~~~ 91 (368)
T cd06825 33 KANAYGHGDVEVARVLEQIGIDFFAVATIDEGIRLREAGIKGEILIL-GYTPPVRAKELK 91 (368)
T ss_pred eccccCCCHHHHHHHHHHcCCCEEEEccHHHHHHHHhcCCCCCEEEE-cCCCHHHHHHHH
Confidence 567888765554 4444557777777788888888887776 88775 555555555543
No 87
>PF12728 HTH_17: Helix-turn-helix domain
Probab=20.12 E-value=79 Score=16.53 Aligned_cols=17 Identities=6% Similarity=-0.283 Sum_probs=12.5
Q ss_pred ccccchhHHHHHHhCCC
Q psy3841 9 GLNREEPGKKTNNINNA 25 (73)
Q Consensus 9 ~ygtsi~sVr~V~ekgk 25 (73)
++|.|.++|...+.+|.
T Consensus 10 ~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 10 LLGISRSTVYRWIRQGK 26 (51)
T ss_pred HHCcCHHHHHHHHHcCC
Confidence 46777788888877774
No 88
>PRK11640 putative transcriptional regulator; Provisional
Probab=20.11 E-value=49 Score=22.19 Aligned_cols=17 Identities=18% Similarity=0.161 Sum_probs=10.6
Q ss_pred cccccc-ccchhHHHHHH
Q psy3841 5 FNHHGL-NREEPGKKTNN 21 (73)
Q Consensus 5 ~~~~~y-gtsi~sVr~V~ 21 (73)
|.+++| |||++.|-+-+
T Consensus 14 f~~~Gy~~tsi~~I~~~a 31 (191)
T PRK11640 14 LEQQGLANTTLEMLAERV 31 (191)
T ss_pred HHHhCcccCCHHHHHHHh
Confidence 555666 67777665544
No 89
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=20.07 E-value=1.3e+02 Score=20.09 Aligned_cols=35 Identities=9% Similarity=-0.018 Sum_probs=26.6
Q ss_pred ccccc----hhHHHHHHhC---------CCEEEEecCcchhhhhhcCc
Q psy3841 9 GLNRE----EPGKKTNNIN---------NAHVILDVSLAGVERLHRQH 43 (73)
Q Consensus 9 ~ygts----i~sVr~V~ek---------gkhCILdv~~~avk~L~~~~ 43 (73)
.|||| .+-++.+.+. |.+-.|.+++.|.+-++...
T Consensus 42 K~GTSHkl~~eEle~~lee~~E~ivvGTG~~G~l~l~~ea~e~~r~k~ 89 (121)
T COG1504 42 KYGTSHKLALEELEELLEEGPEVIVVGTGQSGMLELSEEAREFFRKKG 89 (121)
T ss_pred hcCcccccCHHHHHHHHhcCCcEEEEecCceeEEEeCHHHHHHHHhcC
Confidence 57765 5667777765 77788888888888888765
No 90
>TIGR01858 tag_bisphos_ald class II aldolase, tagatose bisphosphate family. This model describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4.
Probab=20.04 E-value=1.7e+02 Score=21.67 Aligned_cols=49 Identities=14% Similarity=0.142 Sum_probs=32.7
Q ss_pred cchhHHHHHHh----CCCEEEEecCcchhhhhh-------------cCccccEEEEee-cCCHHHHHH
Q psy3841 12 REEPGKKTNNI----NNAHVILDVSLAGVERLH-------------RQHVYPIVLLIK-FKSTKQIKE 61 (73)
Q Consensus 12 tsi~sVr~V~e----kgkhCILdv~~~avk~L~-------------~~~l~PiVIfIk-p~s~~~lke 61 (73)
...++++.|++ .+...||.+++.+++... ... .|+++++. -++.+.+++
T Consensus 24 ~n~e~~~avi~AAee~~sPvIlq~s~~~~~~~~~~~~~~~~~~~a~~~~-VPValHLDHg~~~e~i~~ 90 (282)
T TIGR01858 24 HNLETIQAVVETAAEMRSPVILAGTPGTFKHAGTEYIVALCSAASTTYN-MPLALHLDHHESLDDIRQ 90 (282)
T ss_pred CCHHHHHHHHHHHHHhCCCEEEEeCccHHhhCCHHHHHHHHHHHHHHCC-CCEEEECCCCCCHHHHHH
Confidence 34566666665 399999999998876432 222 48888886 456666553
No 91
>cd08596 PI-PLCc_epsilon Catalytic domain of metazoan phosphoinositide-specific phospholipase C-epsilon. This family corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-epsilon isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-epsilon represents a class of mammalian PI-PLC that has an N-terminal CDC25 homology domain with a guanyl-nucleotide exchange factor (GFF) activity, a pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core
Probab=20.02 E-value=1e+02 Score=22.84 Aligned_cols=24 Identities=8% Similarity=-0.092 Sum_probs=19.9
Q ss_pred ccc-cchhHHHHHHhCCCEEE-EecC
Q psy3841 9 GLN-REEPGKKTNNINNAHVI-LDVS 32 (73)
Q Consensus 9 ~yg-tsi~sVr~V~ekgkhCI-Ldv~ 32 (73)
++| .|+++.++++.+|+-|| ||+-
T Consensus 26 l~~~ss~~~y~~aL~~GcRcvElD~w 51 (254)
T cd08596 26 LKGESSVELYSQVLLTGCRCVELDCW 51 (254)
T ss_pred cCCccCHHHHHHHHHcCCcEEEEEee
Confidence 445 56999999999999999 7873
Done!