Query psy4372
Match_columns 50
No_of_seqs 113 out of 525
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 23:50:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4372.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4372hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0170|consensus 99.5 2.7E-14 5.7E-19 100.0 2.9 46 1-50 468-513 (621)
2 COG5021 HUL4 Ubiquitin-protein 99.4 6E-14 1.3E-18 101.8 2.8 46 1-50 721-766 (872)
3 cd00078 HECTc HECT domain; C-t 99.4 1.3E-13 2.7E-18 90.6 3.2 45 1-50 208-252 (352)
4 smart00119 HECTc Domain Homolo 99.4 1.7E-13 3.7E-18 90.1 3.1 45 1-50 190-234 (336)
5 KOG0942|consensus 99.4 1.1E-13 2.4E-18 100.9 0.4 45 2-50 855-899 (1001)
6 PF00632 HECT: HECT-domain (ub 99.3 2.5E-12 5.3E-17 82.6 2.3 46 1-50 168-213 (317)
7 KOG4427|consensus 99.2 3.7E-12 8E-17 92.6 2.9 45 2-50 925-969 (1096)
8 KOG0939|consensus 99.2 7.8E-12 1.7E-16 89.4 1.7 45 1-50 569-613 (720)
9 KOG0941|consensus 99.1 3.8E-11 8.3E-16 87.0 3.1 45 1-50 706-750 (850)
10 KOG0940|consensus 97.8 1.6E-05 3.4E-10 53.8 3.0 43 2-49 218-260 (358)
11 KOG0943|consensus 95.9 0.0034 7.4E-08 49.4 1.3 44 1-49 2867-2910(3015)
12 PF08069 Ribosomal_S13_N: Ribo 85.3 0.7 1.5E-05 24.4 1.7 21 12-33 21-41 (60)
13 COG2334 Putative homoserine ki 71.3 3.9 8.4E-05 27.5 2.2 22 1-28 253-274 (331)
14 PF04604 L_biotic_typeA: Type- 68.0 2.7 5.9E-05 21.6 0.8 19 15-33 10-28 (51)
15 cd00926 Cyt_c_Oxidase_VIb Cyto 62.5 1.9 4.2E-05 23.4 -0.5 23 2-24 45-67 (75)
16 PRK08561 rps15p 30S ribosomal 59.9 8.4 0.00018 23.7 2.0 20 12-32 21-40 (151)
17 PRK11768 serine/threonine prot 52.4 15 0.00032 24.0 2.3 21 2-28 247-267 (325)
18 PTZ00072 40S ribosomal protein 52.0 13 0.00027 22.9 1.8 19 12-31 18-36 (148)
19 PRK03430 hypothetical protein; 51.8 8.2 0.00018 23.7 1.0 13 16-28 69-81 (157)
20 PF14769 CLAMP: Flagellar C1a 51.7 15 0.00033 20.3 2.0 18 12-29 56-73 (101)
21 PF02297 COX6B: Cytochrome oxi 50.4 2.8 6.1E-05 22.4 -1.1 22 2-23 43-64 (76)
22 PHA02652 hypothetical protein; 45.7 11 0.00023 20.1 0.7 12 22-33 13-24 (70)
23 PF01346 FKBP_N: Domain amino 45.6 23 0.0005 19.8 2.2 28 2-30 48-75 (124)
24 PF04361 DUF494: Protein of un 41.6 16 0.00034 22.2 1.1 16 13-28 64-79 (155)
25 PF10244 MRP-L51: Mitochondria 39.3 17 0.00037 20.8 1.0 18 13-30 39-56 (94)
26 PF12644 DUF3782: Protein of u 39.2 13 0.00029 18.7 0.5 11 2-12 49-59 (64)
27 KOG4143|consensus 38.4 16 0.00035 23.5 0.9 27 3-29 12-41 (218)
28 TIGR02216 phage_TIGR02216 phag 37.6 65 0.0014 16.9 3.4 44 3-46 7-51 (60)
29 COG5494 Predicted thioredoxin/ 37.1 38 0.00083 22.5 2.4 28 18-48 73-100 (265)
30 KOG0919|consensus 34.4 24 0.00053 24.0 1.2 17 16-32 286-302 (338)
31 PF09550 DUF2376: Conserved hy 34.3 63 0.0014 15.8 3.1 26 20-47 11-36 (43)
32 PF02603 Hpr_kinase_N: HPr Ser 33.6 18 0.0004 20.8 0.5 24 5-28 39-62 (127)
33 PF05361 PP1_inhibitor: PKC-ac 33.5 31 0.00068 21.1 1.5 26 22-47 56-81 (144)
34 PF06569 DUF1128: Protein of u 33.5 34 0.00074 18.6 1.5 13 18-30 52-64 (71)
35 cd00050 MH2 MH2 domain; C term 33.1 52 0.0011 20.5 2.5 39 9-49 107-145 (176)
36 PF13833 EF-hand_8: EF-hand do 32.5 62 0.0013 15.1 3.5 29 20-48 22-50 (54)
37 PF08640 U3_assoc_6: U3 small 32.2 41 0.00088 18.4 1.7 16 15-30 12-27 (83)
38 PF13873 Myb_DNA-bind_5: Myb/S 30.1 42 0.00092 17.2 1.5 13 19-31 4-16 (78)
39 TIGR02906 spore_CotS spore coa 30.1 56 0.0012 20.3 2.3 21 2-28 243-263 (313)
40 COG2922 Smg Uncharacterized pr 30.1 25 0.00053 21.8 0.7 15 14-28 67-81 (157)
41 KOG4045|consensus 29.6 31 0.00068 21.5 1.1 18 14-31 109-126 (168)
42 PF09832 DUF2059: Uncharacteri 29.3 44 0.00095 16.6 1.5 13 17-29 14-26 (64)
43 COG4840 Uncharacterized protei 28.8 42 0.00092 18.2 1.4 10 19-28 53-62 (71)
44 PRK10353 3-methyl-adenine DNA 28.8 55 0.0012 20.6 2.1 30 2-32 54-83 (187)
45 KOG2091|consensus 28.8 48 0.001 23.2 2.0 15 16-30 237-251 (392)
46 PRK14657 acpS 4'-phosphopantet 27.8 44 0.00096 19.1 1.5 12 18-29 29-40 (123)
47 PF12639 Colicin-DNase: DNase/ 27.6 34 0.00073 19.6 0.9 32 1-32 43-77 (110)
48 PF07723 LRR_2: Leucine Rich R 27.5 50 0.0011 14.1 1.3 17 17-33 10-26 (26)
49 TIGR00624 tag DNA-3-methyladen 26.2 66 0.0014 20.1 2.1 29 3-32 54-82 (179)
50 PF11737 DUF3300: Protein of u 26.2 45 0.00097 21.9 1.4 13 20-32 1-13 (237)
51 TIGR01639 P_fal_TIGR01639 Plas 25.9 1E+02 0.0023 15.7 2.7 26 18-47 8-33 (61)
52 COG2818 Tag 3-methyladenine DN 25.8 67 0.0014 20.5 2.1 31 2-33 55-85 (188)
53 PF03047 ComC: COMC family; I 25.5 23 0.0005 16.3 0.0 19 15-33 9-27 (32)
54 PRK12413 phosphomethylpyrimidi 25.1 1.7E+02 0.0038 17.9 3.9 29 4-33 119-147 (253)
55 PF01342 SAND: SAND domain; I 24.5 26 0.00056 19.1 0.1 16 17-33 41-56 (82)
56 PF04844 Ovate: Transcriptiona 24.4 56 0.0012 17.0 1.3 26 3-30 7-32 (59)
57 KOG0030|consensus 24.2 1.5E+02 0.0032 18.4 3.3 30 19-49 120-149 (152)
58 PF01648 ACPS: 4'-phosphopante 23.9 38 0.00082 18.1 0.7 15 18-32 23-37 (115)
59 COG2947 Uncharacterized conser 23.7 56 0.0012 20.3 1.4 46 3-49 101-147 (156)
60 PRK10902 FKBP-type peptidyl-pr 23.6 96 0.0021 20.4 2.6 28 2-31 77-104 (269)
61 PRK06148 hypothetical protein; 23.0 93 0.002 23.9 2.7 21 2-28 262-282 (1013)
62 PF10548 P22_AR_C: P22AR C-ter 22.9 67 0.0015 17.2 1.5 11 19-29 7-17 (74)
63 PRK14658 acpS 4'-phosphopantet 22.8 60 0.0013 18.7 1.4 13 18-30 25-37 (115)
64 TIGR01847 bacteriocin_sig bact 22.8 63 0.0014 14.3 1.2 15 19-33 3-17 (26)
65 PRK14660 acpS 4'-phosphopantet 22.7 56 0.0012 18.7 1.3 12 18-29 29-40 (125)
66 PRK11570 peptidyl-prolyl cis-t 22.6 1.1E+02 0.0023 19.2 2.6 28 2-30 36-63 (206)
67 KOG1994|consensus 22.5 38 0.00083 22.6 0.6 17 28-49 243-259 (268)
68 PF01387 Synuclein: Synuclein; 22.5 38 0.00083 20.5 0.5 10 1-10 1-10 (131)
69 COG2378 Predicted transcriptio 22.4 64 0.0014 21.3 1.6 27 7-33 61-89 (311)
70 PRK14662 acpS 4'-phosphopantet 21.4 83 0.0018 18.1 1.8 13 18-30 29-41 (120)
71 smart00755 Grip golgin-97, Ran 21.3 82 0.0018 15.4 1.5 14 17-30 32-45 (46)
72 smart00760 Bac_DnaA_C Bacteria 21.2 1E+02 0.0022 15.2 2.0 23 21-48 1-23 (60)
73 smart00524 DWB Domain B in dwa 21.0 71 0.0015 19.9 1.5 23 10-32 103-125 (171)
74 PRK14659 acpS 4'-phosphopantet 21.0 69 0.0015 18.2 1.4 13 18-30 29-41 (122)
75 COG4023 SBH1 Preprotein transl 21.0 14 0.00031 19.4 -1.4 22 5-26 7-28 (57)
76 PF14793 DUF4478: Domain of un 20.9 1.2E+02 0.0026 17.9 2.4 34 10-49 4-37 (112)
77 smart00717 SANT SANT SWI3, AD 20.9 77 0.0017 13.8 1.3 16 19-34 3-18 (49)
78 PF13453 zf-TFIIB: Transcripti 20.5 82 0.0018 14.5 1.4 11 19-29 29-39 (41)
79 COG5126 FRQ1 Ca2+-binding prot 20.1 1.6E+02 0.0036 18.0 3.0 30 19-48 124-153 (160)
80 PRK06149 hypothetical protein; 20.1 1.2E+02 0.0025 23.2 2.7 21 2-28 269-289 (972)
81 PF10256 Erf4: Golgin subfamil 20.0 82 0.0018 17.6 1.6 28 6-33 16-43 (118)
82 TIGR00938 thrB_alt homoserine 20.0 1.4E+02 0.0029 19.0 2.7 21 2-28 245-265 (307)
No 1
>KOG0170|consensus
Probab=99.46 E-value=2.7e-14 Score=99.97 Aligned_cols=46 Identities=39% Similarity=0.773 Sum_probs=43.6
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
++||++||++|||.++|++|+|+||+.|+||..+ +|+.++|++||+
T Consensus 468 leAFr~GF~~VF~~~~Lqif~p~EL~~llcg~~e----~ws~~TL~~~i~ 513 (621)
T KOG0170|consen 468 LEAFRSGFSSVFPYEHLQIFTPEELVTLLCGVEE----DWSMATLMEHIK 513 (621)
T ss_pred HHHHHhhhhhccchhheeecCHHHHHHHhccchh----hccHHHHHHhcc
Confidence 4799999999999999999999999999999876 999999999985
No 2
>COG5021 HUL4 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.43 E-value=6e-14 Score=101.82 Aligned_cols=46 Identities=22% Similarity=0.343 Sum_probs=43.2
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
+.||..||++|||..||.||++.|||+||||.++ ++|++||++||.
T Consensus 721 ~~AF~~GF~~ii~~~~i~iF~e~ELe~LI~G~~e----~iDidd~K~~T~ 766 (872)
T COG5021 721 FSAFKSGFSEIIPPDLLQIFDESELELLIGGIPE----DIDIDDWKSNTA 766 (872)
T ss_pred HHHHHhhHHHhcCHHHHhhcCHHHHHHHHCCCCc----cccHHHHhhccc
Confidence 4799999999999999999999999999999995 599999999974
No 3
>cd00078 HECTc HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
Probab=99.41 E-value=1.3e-13 Score=90.58 Aligned_cols=45 Identities=40% Similarity=0.699 Sum_probs=42.4
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
++||++||++|+|.++|++|+|+||+.|+||.+ .||+++|++|++
T Consensus 208 ~~afr~Gf~~vip~~~l~~f~~~eL~~lvcG~~-----~id~~~l~~~~~ 252 (352)
T cd00078 208 VEAFRDGFSEVIPEELLSLFTPEELELLICGSE-----DIDLEDLKKNTE 252 (352)
T ss_pred HHHHHHHHHHHcCHHhhhCCCHHHHHHHhCCCC-----CCCHHHHHhceE
Confidence 479999999999999999999999999999997 799999999874
No 4
>smart00119 HECTc Domain Homologous to E6-AP Carboxyl Terminus with. E3 ubiquitin-protein ligases. Can bind to E2 enzymes.
Probab=99.40 E-value=1.7e-13 Score=90.15 Aligned_cols=45 Identities=40% Similarity=0.686 Sum_probs=42.4
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
++||++||++|+|.++|++|+|+||+.|+||.+ .||+++|++|++
T Consensus 190 ~~afr~Gf~~vip~~~l~~f~~~eL~~licG~~-----~i~~~~l~~~~~ 234 (336)
T smart00119 190 LEAFREGFSEVIPENLLRLFTPEELELLICGSP-----EIDVDDLKSNTE 234 (336)
T ss_pred HHHHHHHHHHHcCHHHhhCCCHHHHHHHhCCCC-----CCCHHHHhhheE
Confidence 479999999999999999999999999999998 699999999874
No 5
>KOG0942|consensus
Probab=99.36 E-value=1.1e-13 Score=100.86 Aligned_cols=45 Identities=20% Similarity=0.319 Sum_probs=43.2
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
.||++||+.|||++||+||+++|||.||+|.++ .+|++||++||.
T Consensus 855 ~AFr~Gls~II~~eWl~MF~~~ELQiLIsG~~~----pidldDLr~~te 899 (1001)
T KOG0942|consen 855 SAFRKGLSQIISPEWLRMFNEHELQILISGAED----PIDLDDLRKNTE 899 (1001)
T ss_pred HHHhcchhhcCCHHHHHhhChhheeeeecCCcC----cccHHHHHhhcc
Confidence 699999999999999999999999999999997 899999999984
No 6
>PF00632 HECT: HECT-domain (ubiquitin-transferase); InterPro: IPR000569 The name HECT comes from 'Homologous to the E6-AP Carboxyl Terminus' []. Proteins containing this domain at the C terminus include ubiquitin-protein ligase, which regulates ubiquitination of CDC25. Ubiquitin-protein ligase accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester, and then directly transfers the ubiquitin to targeted substrates. A cysteine residue is required for ubiquitin-thiolester formation. Human thyroid receptor interacting protein 12, which also contains this domain, is a component of an ATP-dependent multisubunit protein that interacts with the ligand binding domain of the thyroid hormone receptor. It could be an E3 ubiquitin-protein ligase. Human ubiquitin-protein ligase E3A interacts with the E6 protein of the cancer-associated Human papillomavirus type 16 and Human papillomavirus type 18. The E6/E6-AP complex binds to and targets the P53 tumour-suppressor protein for ubiquitin-mediated proteolysis.; GO: 0016881 acid-amino acid ligase activity, 0006464 protein modification process, 0005622 intracellular; PDB: 3TUG_A 1ZVD_A 1C4Z_C 1D5F_B 1ND7_A 2XBB_A 2XBF_A 3PT3_A 3G1N_B 3H1D_A ....
Probab=99.26 E-value=2.5e-12 Score=82.61 Aligned_cols=46 Identities=41% Similarity=0.676 Sum_probs=40.0
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
++||++||.+|+|.+.|++|+|+||+.++||.++ .||+++|+++++
T Consensus 168 ~~~~r~Gf~~vi~~~~l~~f~~~eL~~l~~G~~~----~i~~~~l~~~~~ 213 (317)
T PF00632_consen 168 LEAFRKGFYSVIPLELLSLFSPEELERLLCGSPE----PIDVEDLKSNTR 213 (317)
T ss_dssp HHHHHHHHHHHSSHHHHTTSSHHHHHHHHHCBSS-------HHHHHHTEE
T ss_pred HHHHhcchhhcchhHHHHcCCHHHHHHHhcCccc----cCCHHHHHhccc
Confidence 4799999999999999999999999999999982 399999999874
No 7
>KOG4427|consensus
Probab=99.25 E-value=3.7e-12 Score=92.57 Aligned_cols=45 Identities=22% Similarity=0.383 Sum_probs=42.8
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
.||.+||.+++.++||++|+|.||+.||+|... ++|++||++|++
T Consensus 925 ~Af~rG~rsii~P~WlslFs~~elq~LiSG~ns----diDl~DLkrnt~ 969 (1096)
T KOG4427|consen 925 NAFYRGFRSIISPEWLSLFSPPELQRLISGDNS----DIDLDDLKRNTK 969 (1096)
T ss_pred HHHHHHHHHhcCHHHHHccCcHHHHHHhcCCCC----CCCHHHHHhcCE
Confidence 699999999999999999999999999999986 899999999974
No 8
>KOG0939|consensus
Probab=99.18 E-value=7.8e-12 Score=89.36 Aligned_cols=45 Identities=22% Similarity=0.399 Sum_probs=42.4
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
++||++||++++|...+++|++.|||+||||.+ ++|++||++|++
T Consensus 569 l~afl~Gl~~iip~~li~if~E~ELELLisGlp-----eidvdd~k~nt~ 613 (720)
T KOG0939|consen 569 LDAFLAGLHEIIPKVLLSIFDEQELELLISGLP-----EIDVDDLKANTE 613 (720)
T ss_pred HHHHHHHHHHhhHHHHHHHhhhHHHHHHHcCCC-----cccHHHHHhhhh
Confidence 479999999999999999999999999999999 699999999874
No 9
>KOG0941|consensus
Probab=99.12 E-value=3.8e-11 Score=87.05 Aligned_cols=45 Identities=36% Similarity=0.522 Sum_probs=42.3
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhhC
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHCQ 50 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~~ 50 (50)
++||++||++|+..+.|++|+|+||+.||||+. ++|++.|+++|+
T Consensus 706 ~~aF~~GF~~v~~~~~l~lf~peEl~~li~G~~-----~~Dw~~l~~~~~ 750 (850)
T KOG0941|consen 706 FEAFRRGFYKVCDENLLRLFQPEELEKLICGSE-----DYDWKALEETTE 750 (850)
T ss_pred HHHHHHHHHHHhchhhhhhcCHHHHHHHHhCCC-----ccCHHHHhhhce
Confidence 479999999999999999999999999999999 699999999874
No 10
>KOG0940|consensus
Probab=97.83 E-value=1.6e-05 Score=53.84 Aligned_cols=43 Identities=21% Similarity=0.380 Sum_probs=39.7
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhh
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHC 49 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~ 49 (50)
.||.+||..+.|..++++|.+.|++.++||.. .+|+++|.+++
T Consensus 218 ~~l~~~~~~~~p~~~~~~~~e~~~e~~~~~~~-----~~~~~d~~~~t 260 (358)
T KOG0940|consen 218 KALLQGFNELLPQSLLRIFDEMELELALSGDP-----EIDVNDWKQNT 260 (358)
T ss_pred HHHhccccccCCcccccccchhhHHHHhcCCc-----ccchhHHhhhc
Confidence 68999999999999999999999999999999 68888888765
No 11
>KOG0943|consensus
Probab=95.94 E-value=0.0034 Score=49.41 Aligned_cols=44 Identities=23% Similarity=0.430 Sum_probs=39.3
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhh
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHC 49 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~ 49 (50)
++|.++|.-.|+|.+.|.=.+++.+.++|||.. ..++..|.+++
T Consensus 2867 feAiReGiLDViPenmL~~LT~EDfRLiicG~e-----eVniqmL~e~T 2910 (3015)
T KOG0943|consen 2867 FEAIREGILDVIPENMLEDLTAEDFRLIICGCE-----EVNIQMLIEFT 2910 (3015)
T ss_pred HHHHHHhHHhhcchhhhcccCHhHheeeeeccc-----ceehhHhhhhc
Confidence 479999999999999999999999999999998 47777777654
No 12
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 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 [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=85.35 E-value=0.7 Score=24.44 Aligned_cols=21 Identities=29% Similarity=0.314 Sum_probs=13.4
Q ss_pred CCcccccCCCHHHHHHHHhcCC
Q psy4372 12 FPLAQLSMFYPEELEYVFCGSD 33 (50)
Q Consensus 12 ~p~~~L~~F~~~ELe~LicG~~ 33 (50)
-|++|+++ +++|++.+||-..
T Consensus 21 ~~P~W~~~-~~~eVe~~I~kla 41 (60)
T PF08069_consen 21 SPPSWLKY-SPEEVEELIVKLA 41 (60)
T ss_dssp S--TT--S--HHHHHHHHHHHC
T ss_pred CCCCCcCC-CHHHHHHHHHHHH
Confidence 46899995 9999999999754
No 13
>COG2334 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]
Probab=71.25 E-value=3.9 Score=27.46 Aligned_cols=22 Identities=41% Similarity=0.689 Sum_probs=17.6
Q ss_pred ChHHHHHHhccCCcccccCCCHHHHHHH
Q psy4372 1 MESFREGFECVFPLAQLSMFYPEELEYV 28 (50)
Q Consensus 1 ~~AF~~GF~~V~p~~~L~~F~~~ELe~L 28 (50)
+.||.+|+++|.| |++.|++.|
T Consensus 253 ~~a~l~GY~~v~p------l~~~El~~L 274 (331)
T COG2334 253 IAAFLEGYEEVRP------LTAAELELL 274 (331)
T ss_pred HHHHHHHHHhcCC------CCHHHHHHH
Confidence 3689999999988 577777754
No 14
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=67.99 E-value=2.7 Score=21.59 Aligned_cols=19 Identities=26% Similarity=0.399 Sum_probs=15.4
Q ss_pred ccccCCCHHHHHHHHhcCC
Q psy4372 15 AQLSMFYPEELEYVFCGSD 33 (50)
Q Consensus 15 ~~L~~F~~~ELe~LicG~~ 33 (50)
..|+-.+.+||+++++|..
T Consensus 10 ~~lqevs~eELd~ilGg~g 28 (51)
T PF04604_consen 10 NSLQEVSDEELDQILGGAG 28 (51)
T ss_pred HHHHhcCHHHHHHHhCCCC
Confidence 3567789999999999943
No 15
>cd00926 Cyt_c_Oxidase_VIb Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex.
Probab=62.45 E-value=1.9 Score=23.37 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=19.5
Q ss_pred hHHHHHHhccCCcccccCCCHHH
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEE 24 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~E 24 (50)
..|+..|.+.+|.+|+..|+..-
T Consensus 45 ~~~~~~~es~Cp~~Wve~w~ekR 67 (75)
T cd00926 45 KKFRRVYESLCPQEWLEKWDEQR 67 (75)
T ss_pred HHHHHHHHHhCcHHHHHHHHHHH
Confidence 36889999999999999988653
No 16
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=59.85 E-value=8.4 Score=23.74 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=16.6
Q ss_pred CCcccccCCCHHHHHHHHhcC
Q psy4372 12 FPLAQLSMFYPEELEYVFCGS 32 (50)
Q Consensus 12 ~p~~~L~~F~~~ELe~LicG~ 32 (50)
-|++|+++ +++|++.+||-.
T Consensus 21 ~~P~W~~~-~~eeve~~I~~l 40 (151)
T PRK08561 21 EPPEWVDY-SPEEIEELVVEL 40 (151)
T ss_pred CCCccccC-CHHHHHHHHHHH
Confidence 47889885 999999999853
No 17
>PRK11768 serine/threonine protein kinase; Provisional
Probab=52.39 E-value=15 Score=23.99 Aligned_cols=21 Identities=38% Similarity=0.675 Sum_probs=16.3
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHH
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYV 28 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~L 28 (50)
.||.+|..++.| |++.|+..|
T Consensus 247 ~~~l~GY~~~r~------l~~~e~~~l 267 (325)
T PRK11768 247 ETLLEGYEEFCE------FDPRELALI 267 (325)
T ss_pred HHHHHHhhccCC------CCHHHHHHH
Confidence 578889888877 788877654
No 18
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=51.96 E-value=13 Score=22.94 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=16.1
Q ss_pred CCcccccCCCHHHHHHHHhc
Q psy4372 12 FPLAQLSMFYPEELEYVFCG 31 (50)
Q Consensus 12 ~p~~~L~~F~~~ELe~LicG 31 (50)
-|++|+++ +++|++.+||-
T Consensus 18 ~~P~w~~~-~~eeVe~~I~k 36 (148)
T PTZ00072 18 KPPSWLKL-SSSEVEDQICK 36 (148)
T ss_pred CCCchhcC-CHHHHHHHHHH
Confidence 46888885 99999999984
No 19
>PRK03430 hypothetical protein; Validated
Probab=51.82 E-value=8.2 Score=23.74 Aligned_cols=13 Identities=31% Similarity=0.651 Sum_probs=11.6
Q ss_pred cccCCCHHHHHHH
Q psy4372 16 QLSMFYPEELEYV 28 (50)
Q Consensus 16 ~L~~F~~~ELe~L 28 (50)
.+|+|+++|.+.|
T Consensus 69 s~RIYt~~E~~~L 81 (157)
T PRK03430 69 SMRIYTPEECERL 81 (157)
T ss_pred ceeeeCHHHHHhC
Confidence 6999999999875
No 20
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=51.65 E-value=15 Score=20.31 Aligned_cols=18 Identities=11% Similarity=0.340 Sum_probs=15.5
Q ss_pred CCcccccCCCHHHHHHHH
Q psy4372 12 FPLAQLSMFYPEELEYVF 29 (50)
Q Consensus 12 ~p~~~L~~F~~~ELe~Li 29 (50)
-|+..+.+|+++++..++
T Consensus 56 rpp~~~~iFs~~~~~~i~ 73 (101)
T PF14769_consen 56 RPPFSIGIFSVDQVKAII 73 (101)
T ss_pred CCCcccCcCCHHHHHHHH
Confidence 378889999999999875
No 21
>PF02297 COX6B: Cytochrome oxidase c subunit VIb; InterPro: IPR003213 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex that is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptide subunits. One of these subunits is the potentially haem-binding subunit, VIb, which is encoded in the nucleus []. ; GO: 0004129 cytochrome-c oxidase activity, 0005739 mitochondrion; PDB: 1OCC_U 1OCR_U 2DYS_H 3ASO_H 3AG3_U 2EIL_H 2EIJ_U 3AG2_U 3ABM_U 2EIN_U ....
Probab=50.36 E-value=2.8 Score=22.40 Aligned_cols=22 Identities=23% Similarity=0.439 Sum_probs=17.7
Q ss_pred hHHHHHHhccCCcccccCCCHH
Q psy4372 2 ESFREGFECVFPLAQLSMFYPE 23 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ 23 (50)
..|+..|.+.+|.+|++.|+..
T Consensus 43 ~~~~~~ye~~Cp~sWv~~f~~~ 64 (76)
T PF02297_consen 43 KYFRKNYESNCPSSWVKYFDEK 64 (76)
T ss_dssp HHHHHHHHHHS-HHHHHHHHHH
T ss_pred HHHHHHHHHhCcHHHHHHHHHH
Confidence 3688899999999999988764
No 22
>PHA02652 hypothetical protein; Provisional
Probab=45.66 E-value=11 Score=20.09 Aligned_cols=12 Identities=42% Similarity=1.016 Sum_probs=10.7
Q ss_pred HHHHHHHHhcCC
Q psy4372 22 PEELEYVFCGSD 33 (50)
Q Consensus 22 ~~ELe~LicG~~ 33 (50)
..||..|+||.+
T Consensus 13 sneldkllcgdd 24 (70)
T PHA02652 13 SNELDKLLCGDD 24 (70)
T ss_pred cHHHHHHhcccH
Confidence 579999999987
No 23
>PF01346 FKBP_N: Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; InterPro: IPR000774 Peptidyl-prolyl cis-trans isomerase (PPIase) catalyses the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides [, ]. This alpha helical domain is found at the N terminus of proteins belonging to the FKBP-type peptidyl-prolyl cis-trans isomerase(IPR001179 from INTERPRO) family. Peptidyl-prolyl cis-trans isomerase has been shown to accelerate the refolding of several proteins in vitro [, , ]; the FKPB-type enzymes probably act in the folding of extracytoplasmic proteins.; GO: 0006457 protein folding; PDB: 1FD9_A 2VCD_A 3OE2_A 2UZ5_A 3B09_A 1Q6H_B 1Q6I_B 1Q6U_A.
Probab=45.59 E-value=23 Score=19.76 Aligned_cols=28 Identities=14% Similarity=0.155 Sum_probs=18.5
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHh
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFC 30 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~Lic 30 (50)
++|..||.+.+-.... .++++|++..+-
T Consensus 48 ~~~~~Gi~dal~~~~~-~l~~~e~~~~l~ 75 (124)
T PF01346_consen 48 DAFLAGIRDALAGKKP-KLSDEEAQEALQ 75 (124)
T ss_dssp HHHHHHHHHHHCTT---SS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCc-CCCHHHHHHHHH
Confidence 5789999999844444 458888877653
No 24
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=41.56 E-value=16 Score=22.20 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=12.7
Q ss_pred CcccccCCCHHHHHHH
Q psy4372 13 PLAQLSMFYPEELEYV 28 (50)
Q Consensus 13 p~~~L~~F~~~ELe~L 28 (50)
..+.+|+|+++|...|
T Consensus 64 ~~~s~Riyt~~E~~~L 79 (155)
T PF04361_consen 64 SPRSMRIYTPEEQEKL 79 (155)
T ss_pred CCCceEecCHHHHHHC
Confidence 4667899999998765
No 25
>PF10244 MRP-L51: Mitochondrial ribosomal subunit; InterPro: IPR019373 MRP-L51 is a family of small proteins from the intact 55 S mitochondrial ribosome []. It has otherwise been referred to as bMRP-64 []. The exact function of this family is not known.
Probab=39.28 E-value=17 Score=20.83 Aligned_cols=18 Identities=22% Similarity=0.139 Sum_probs=15.9
Q ss_pred CcccccCCCHHHHHHHHh
Q psy4372 13 PLAQLSMFYPEELEYVFC 30 (50)
Q Consensus 13 p~~~L~~F~~~ELe~Lic 30 (50)
.+.||+=|.-.|++.||-
T Consensus 39 ~P~WlRG~~GNE~q~liR 56 (94)
T PF10244_consen 39 GPSWLRGFRGNELQRLIR 56 (94)
T ss_pred CcHHHhcCCchHHHHHHH
Confidence 488999999999999864
No 26
>PF12644 DUF3782: Protein of unknown function (DUF3782); InterPro: IPR024271 This functionally uncharacterised family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length.
Probab=39.19 E-value=13 Score=18.68 Aligned_cols=11 Identities=45% Similarity=0.836 Sum_probs=8.7
Q ss_pred hHHHHHHhccC
Q psy4372 2 ESFREGFECVF 12 (50)
Q Consensus 2 ~AF~~GF~~V~ 12 (50)
.||+.||..++
T Consensus 49 ~afr~G~~d~l 59 (64)
T PF12644_consen 49 EAFRQGFRDGL 59 (64)
T ss_pred HHHHHHHHHHH
Confidence 48999998764
No 27
>KOG4143|consensus
Probab=38.37 E-value=16 Score=23.49 Aligned_cols=27 Identities=30% Similarity=0.261 Sum_probs=20.8
Q ss_pred HHHHHHhccCCccccc---CCCHHHHHHHH
Q psy4372 3 SFREGFECVFPLAQLS---MFYPEELEYVF 29 (50)
Q Consensus 3 AF~~GF~~V~p~~~L~---~F~~~ELe~Li 29 (50)
|+..++..|+-.-+|. +|+|+||..|-
T Consensus 12 ~v~a~l~~vv~~~~l~~~y~Fdp~~l~el~ 41 (218)
T KOG4143|consen 12 AVAAVLTQVVWLWLLTQSYVFDPEELAELA 41 (218)
T ss_pred HHHHHHHHHHHHHHcccceeeCHHHHHHHH
Confidence 5667777777766664 89999999874
No 28
>TIGR02216 phage_TIGR02216 phage conserved hypothetical protein. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA.
Probab=37.61 E-value=65 Score=16.94 Aligned_cols=44 Identities=14% Similarity=0.214 Sum_probs=24.9
Q ss_pred HHHHHHhcc-CCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHH
Q psy4372 3 SFREGFECV-FPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFF 46 (50)
Q Consensus 3 AF~~GF~~V-~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~ 46 (50)
+.+-||... .+++..=--+|.||..++...........+...|.
T Consensus 7 lmr~G~~~L~L~P~~FW~lTP~EL~~~lg~~~~~~~apl~Ra~Ld 51 (60)
T TIGR02216 7 AMQAGLGGLRLPPDAFWRLTPAELAAAIAGLQGAAAAPLDRAALD 51 (60)
T ss_pred HHHHHHhhcCCCHHHHHhCCHHHHHHHhCCccCCCCCCCCHHHHH
Confidence 345565544 34444445699999998884332112356665554
No 29
>COG5494 Predicted thioredoxin/glutaredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=37.10 E-value=38 Score=22.47 Aligned_cols=28 Identities=21% Similarity=0.276 Sum_probs=22.7
Q ss_pred cCCCHHHHHHHHhcCCCCCCCCCCHHHHHhh
Q psy4372 18 SMFYPEELEYVFCGSDFTSCPQETACTFFIH 48 (50)
Q Consensus 18 ~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~ 48 (50)
..-+|+|++.++.|.-+ ..+|+.++-++
T Consensus 73 dpVdp~~ies~~~G~~~---~~iDv~~~Ve~ 100 (265)
T COG5494 73 DPVDPEEIESILSGQVT---KQIDVASLVEK 100 (265)
T ss_pred CCCCHHHHHHHHcCccc---cccchhhHHHH
Confidence 57899999999999753 46999887664
No 30
>KOG0919|consensus
Probab=34.38 E-value=24 Score=24.00 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=13.8
Q ss_pred cccCCCHHHHHHHHhcC
Q psy4372 16 QLSMFYPEELEYVFCGS 32 (50)
Q Consensus 16 ~L~~F~~~ELe~LicG~ 32 (50)
.|+.|+|.|+..|++=-
T Consensus 286 ~LRYFTprEvArLmgFP 302 (338)
T KOG0919|consen 286 RLRYFTPREVARLMGFP 302 (338)
T ss_pred HhhccCHHHHHHHcCCC
Confidence 47899999999987543
No 31
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376); InterPro: IPR019056 Gene transfer agents belong to a group of unusual genetic exchange elements []. GTAs are unusual in the sense they have the structure of a small tailed phage, which do not possess typical phage traits such as host cell lysis and infectious transmission of the GTA genes. In the Rhodobacter capsulatus GTA the GTA particles contain random 4.5 kb DNA fragments of the R.capsulatus genome. These DNA fragments can be transmitted to other cells where allelic conversion may occur via homologous recombination. The genes coding for the GTA particles are of two distinct types: the first is a cluster of genes reminiscent of a cryptyic prophage, where a number of the genes have similarity to known phage structural genes; the second type consists of two genes coding for a cellular two-component signal transduction system, which regulates the transcription of the GTA structural gene cluster in a growth phase dependent manner []. This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in ]. The function is not known.
Probab=34.33 E-value=63 Score=15.79 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=16.8
Q ss_pred CCHHHHHHHHhcCCCCCCCCCCHHHHHh
Q psy4372 20 FYPEELEYVFCGSDFTSCPQETACTFFI 47 (50)
Q Consensus 20 F~~~ELe~LicG~~~~~~~~~d~~~L~~ 47 (50)
-+|.|| .++.|... .....|...|.+
T Consensus 11 lTP~El-~a~~g~~~-~~~pl~R~~L~~ 36 (43)
T PF09550_consen 11 LTPAEL-RAMLGADA-GAAPLDRAELDA 36 (43)
T ss_pred cCHHHH-HHhcCccc-CCCCCCHHHHHH
Confidence 489999 66677653 234677766643
No 32
>PF02603 Hpr_kinase_N: HPr Serine kinase N terminus; InterPro: IPR011126 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria []. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes []. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains []. ; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1KNX_B 1KO7_A.
Probab=33.56 E-value=18 Score=20.78 Aligned_cols=24 Identities=21% Similarity=0.307 Sum_probs=19.5
Q ss_pred HHHHhccCCcccccCCCHHHHHHH
Q psy4372 5 REGFECVFPLAQLSMFYPEELEYV 28 (50)
Q Consensus 5 ~~GF~~V~p~~~L~~F~~~ELe~L 28 (50)
+.||.+.++++.++++-..|+..|
T Consensus 39 L~G~~~~~~~~RIQiiG~~E~~yl 62 (127)
T PF02603_consen 39 LAGFFNYFHPNRIQIIGNTESAYL 62 (127)
T ss_dssp HTTS-TTTTTCSEEEE-HHHHHHH
T ss_pred hcCccccCCCCeEEEEcHHHHHHH
Confidence 468999999999999999999876
No 33
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=33.55 E-value=31 Score=21.11 Aligned_cols=26 Identities=8% Similarity=-0.027 Sum_probs=18.7
Q ss_pred HHHHHHHHhcCCCCCCCCCCHHHHHh
Q psy4372 22 PEELEYVFCGSDFTSCPQETACTFFI 47 (50)
Q Consensus 22 ~~ELe~LicG~~~~~~~~~d~~~L~~ 47 (50)
-++|+.|..|..+...+++|+++|.+
T Consensus 56 d~qL~eLy~~~e~~~p~EIDIDeLLD 81 (144)
T PF05361_consen 56 DEQLQELYDCQEDEMPEEIDIDELLD 81 (144)
T ss_dssp HHHHHHCSSSSSTTS-SSSHHHHHHC
T ss_pred HHHHHHHhcCCCCCCCCcccHHHHhc
Confidence 35788888887753334799999875
No 34
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=33.52 E-value=34 Score=18.58 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=10.4
Q ss_pred cCCCHHHHHHHHh
Q psy4372 18 SMFYPEELEYVFC 30 (50)
Q Consensus 18 ~~F~~~ELe~Lic 30 (50)
.-|+|.|++.++.
T Consensus 52 ~~fS~sEm~aI~~ 64 (71)
T PF06569_consen 52 DSFSPSEMQAIAE 64 (71)
T ss_pred cCCCHHHHHHHHH
Confidence 3699999998764
No 35
>cd00050 MH2 MH2 domain; C terminal domain of SMAD family proteins, responsible for receptor interaction, transactivation, and homo- and heterooligomerisation; also known as Domain B in dwarfin family proteins
Probab=33.10 E-value=52 Score=20.55 Aligned_cols=39 Identities=18% Similarity=0.133 Sum_probs=27.3
Q ss_pred hccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhh
Q psy4372 9 ECVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHC 49 (50)
Q Consensus 9 ~~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~ 49 (50)
.+|-|...|++|+-++...++.-+.. ...-++.+|.+.|
T Consensus 107 ~Kv~pg~~lKvFd~~~f~~~l~~~~~--~~~~~~~~l~~~c 145 (176)
T cd00050 107 HKVPPGYSLKVFDFEQFEQLLRQAAG--STFDGVYDLRRMC 145 (176)
T ss_pred EEeCCCCEEEEeCHHHHHHHHHhhhc--ccCccHHHHHhhc
Confidence 46778889999999999998876442 1234566665543
No 36
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=32.49 E-value=62 Score=15.12 Aligned_cols=29 Identities=17% Similarity=0.083 Sum_probs=21.7
Q ss_pred CCHHHHHHHHhcCCCCCCCCCCHHHHHhh
Q psy4372 20 FYPEELEYVFCGSDFTSCPQETACTFFIH 48 (50)
Q Consensus 20 F~~~ELe~LicG~~~~~~~~~d~~~L~~~ 48 (50)
++++|++.|+.-.+......++.+++.+.
T Consensus 22 ~s~~e~~~l~~~~D~~~~G~I~~~EF~~~ 50 (54)
T PF13833_consen 22 LSEEEVDRLFREFDTDGDGYISFDEFISM 50 (54)
T ss_dssp SCHHHHHHHHHHHTTSSSSSEEHHHHHHH
T ss_pred CCHHHHHHHHHhcccCCCCCCCHHHHHHH
Confidence 89999999988765434456888887653
No 37
>PF08640 U3_assoc_6: U3 small nucleolar RNA-associated protein 6; InterPro: IPR013949 This entry represents U3 nucleolar RNA-associated proteins which are involved in nucleolar processing of pre-18S ribosomal RNA [].
Probab=32.18 E-value=41 Score=18.36 Aligned_cols=16 Identities=19% Similarity=0.318 Sum_probs=12.8
Q ss_pred ccccCCCHHHHHHHHh
Q psy4372 15 AQLSMFYPEELEYVFC 30 (50)
Q Consensus 15 ~~L~~F~~~ELe~Lic 30 (50)
....+|+++|+..++-
T Consensus 12 ~~~~lFt~~EI~~Ivk 27 (83)
T PF08640_consen 12 ERKGLFTKEEIREIVK 27 (83)
T ss_pred HHhCCCCHHHHHHHHH
Confidence 4457999999998864
No 38
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=30.10 E-value=42 Score=17.18 Aligned_cols=13 Identities=31% Similarity=0.128 Sum_probs=9.4
Q ss_pred CCCHHHHHHHHhc
Q psy4372 19 MFYPEELEYVFCG 31 (50)
Q Consensus 19 ~F~~~ELe~LicG 31 (50)
-|+++|.+.||.=
T Consensus 4 ~fs~~E~~~Lv~~ 16 (78)
T PF13873_consen 4 NFSEEEKEILVEL 16 (78)
T ss_pred CCCHHHHHHHHHH
Confidence 4788888877653
No 39
>TIGR02906 spore_CotS spore coat protein, CotS family. Members of this family include the spore coat proteins CotS and YtaA from Bacillus subtilis and, from other endospore-forming bacteria, homologs that are more closely related to these two than to the spore coat proteins YutH and YsxE. The CotS family is more broadly distributed than YutH or YsxE, but still is not universal among spore-formers.
Probab=30.08 E-value=56 Score=20.34 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=14.2
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHH
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYV 28 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~L 28 (50)
.+|++|+.++.|. +++|++.|
T Consensus 243 ~~~l~gY~~~~~L------~~~e~~~l 263 (313)
T TIGR02906 243 KEIIEAYSSINPL------SKEEKEVL 263 (313)
T ss_pred HHHHHHhhccCCC------CHHHHHHH
Confidence 4788899887763 55555544
No 40
>COG2922 Smg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.07 E-value=25 Score=21.84 Aligned_cols=15 Identities=27% Similarity=0.485 Sum_probs=11.8
Q ss_pred cccccCCCHHHHHHH
Q psy4372 14 LAQLSMFYPEELEYV 28 (50)
Q Consensus 14 ~~~L~~F~~~ELe~L 28 (50)
+..+|+|+++|.+.|
T Consensus 67 ~~~lRIYt~EE~~rL 81 (157)
T COG2922 67 PLALRIYTPEECDRL 81 (157)
T ss_pred CcceEeeCHHHHhcc
Confidence 347899999998764
No 41
>KOG4045|consensus
Probab=29.61 E-value=31 Score=21.46 Aligned_cols=18 Identities=22% Similarity=0.109 Sum_probs=15.7
Q ss_pred cccccCCCHHHHHHHHhc
Q psy4372 14 LAQLSMFYPEELEYVFCG 31 (50)
Q Consensus 14 ~~~L~~F~~~ELe~LicG 31 (50)
+.||+=|.-.||+.||--
T Consensus 109 P~WLRG~~GNElq~lirk 126 (168)
T KOG4045|consen 109 PTWLRGFPGNELQKLIRK 126 (168)
T ss_pred chHhhcCCchHHHHHHHH
Confidence 689999999999999753
No 42
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=29.31 E-value=44 Score=16.62 Aligned_cols=13 Identities=31% Similarity=0.490 Sum_probs=9.5
Q ss_pred ccCCCHHHHHHHH
Q psy4372 17 LSMFYPEELEYVF 29 (50)
Q Consensus 17 L~~F~~~ELe~Li 29 (50)
-+.|+.+||+.++
T Consensus 14 ~~~ft~~El~~i~ 26 (64)
T PF09832_consen 14 AEHFTEEELDAIL 26 (64)
T ss_dssp HHHS-HHHHHHHH
T ss_pred HHHCCHHHHHHHH
Confidence 3568999999885
No 43
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.80 E-value=42 Score=18.24 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=8.1
Q ss_pred CCCHHHHHHH
Q psy4372 19 MFYPEELEYV 28 (50)
Q Consensus 19 ~F~~~ELe~L 28 (50)
-|+|.|++.+
T Consensus 53 nfSpsEmqai 62 (71)
T COG4840 53 NFSPSEMQAI 62 (71)
T ss_pred cCCHHHHHHH
Confidence 5899999865
No 44
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=28.79 E-value=55 Score=20.61 Aligned_cols=30 Identities=17% Similarity=0.315 Sum_probs=21.8
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHhcC
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFCGS 32 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~ 32 (50)
++|++-|... .+..+..|++++++.|+.-.
T Consensus 54 e~fr~aF~~F-d~~~VA~~~e~die~Ll~d~ 83 (187)
T PRK10353 54 ENYRACFHQF-DPVKVAAMQEEDVERLVQDA 83 (187)
T ss_pred HHHHHHHcCC-CHHHHhCCCHHHHHHHhcCc
Confidence 3566666654 56778889999999987643
No 45
>KOG2091|consensus
Probab=28.78 E-value=48 Score=23.23 Aligned_cols=15 Identities=40% Similarity=0.685 Sum_probs=12.2
Q ss_pred cccCCCHHHHHHHHh
Q psy4372 16 QLSMFYPEELEYVFC 30 (50)
Q Consensus 16 ~L~~F~~~ELe~Lic 30 (50)
.+.+|+|+|++.|.-
T Consensus 237 ~~~~ft~ee~~~L~~ 251 (392)
T KOG2091|consen 237 QLKFFTPEEFSKLVA 251 (392)
T ss_pred CcCcCCHHHHHHHHH
Confidence 356799999999864
No 46
>PRK14657 acpS 4'-phosphopantetheinyl transferase; Provisional
Probab=27.78 E-value=44 Score=19.14 Aligned_cols=12 Identities=25% Similarity=0.359 Sum_probs=10.3
Q ss_pred cCCCHHHHHHHH
Q psy4372 18 SMFYPEELEYVF 29 (50)
Q Consensus 18 ~~F~~~ELe~Li 29 (50)
++|+|+|+..+-
T Consensus 29 rift~~E~~~~~ 40 (123)
T PRK14657 29 RILHPAELAAMP 40 (123)
T ss_pred hCCCHHHHHHHH
Confidence 799999999853
No 47
>PF12639 Colicin-DNase: DNase/tRNase domain of colicin-like bacteriocin; InterPro: IPR024622 This entry represents a C-terminal domain with endonuclease activity found in some colicin/pyocin bacteriocins, including colicin E2, E7, E9 and pyocin S1 and S2. The structure of this domain in colicin E7 has been described as a novel alpha/beta fold containing a Zn2+ ion [].; GO: 0004519 endonuclease activity; PDB: 3U43_B 2VLN_B 1V14_A 1V13_A 2GYK_B 1V15_C 2GZJ_F 2VLP_B 1FSJ_C 2GZG_B ....
Probab=27.64 E-value=34 Score=19.60 Aligned_cols=32 Identities=28% Similarity=0.375 Sum_probs=23.3
Q ss_pred ChHHHHHHhccC--CcccccCCCHHHHHHH-HhcC
Q psy4372 1 MESFREGFECVF--PLAQLSMFYPEELEYV-FCGS 32 (50)
Q Consensus 1 ~~AF~~GF~~V~--p~~~L~~F~~~ELe~L-icG~ 32 (50)
|.+|++-|..-+ .+...+-|+++.|+.| -.|.
T Consensus 43 F~~~r~~~w~~V~~dp~l~~qF~~~~l~~i~~~g~ 77 (110)
T PF12639_consen 43 FDEFRKAFWKEVAKDPELSKQFTPENLERIMKGGK 77 (110)
T ss_dssp HHHHHHHHHHHHHHSHHHHTTS-HHHHHHH-HTT-
T ss_pred HHHHHHHHHHHHHhChHHHHhcCHHHHHHHHhcCC
Confidence 467888888877 3555689999999999 6663
No 48
>PF07723 LRR_2: Leucine Rich Repeat; InterPro: IPR013101 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by IPR001611 from INTERPRO [, ].
Probab=27.47 E-value=50 Score=14.09 Aligned_cols=17 Identities=18% Similarity=0.294 Sum_probs=11.4
Q ss_pred ccCCCHHHHHHHHhcCC
Q psy4372 17 LSMFYPEELEYVFCGSD 33 (50)
Q Consensus 17 L~~F~~~ELe~LicG~~ 33 (50)
..+.+..-++.||+|-+
T Consensus 10 v~f~~~~~l~~LlS~CP 26 (26)
T PF07723_consen 10 VVFSDEDSLERLLSGCP 26 (26)
T ss_pred EEECChhHHHHhhccCc
Confidence 34445556899998864
No 49
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.18 E-value=66 Score=20.08 Aligned_cols=29 Identities=10% Similarity=0.336 Sum_probs=21.2
Q ss_pred HHHHHHhccCCcccccCCCHHHHHHHHhcC
Q psy4372 3 SFREGFECVFPLAQLSMFYPEELEYVFCGS 32 (50)
Q Consensus 3 AF~~GF~~V~p~~~L~~F~~~ELe~LicG~ 32 (50)
+|++-|... .+..+..|++++++.|+.-.
T Consensus 54 ~fr~aF~~F-d~~~VA~~~e~~ie~L~~d~ 82 (179)
T TIGR00624 54 NYRRAFSGF-DIVKVARMTDADVERLLQDD 82 (179)
T ss_pred HHHHHHcCC-CHHHHhCCCHHHHHHHhcCc
Confidence 455555554 67778889999999988643
No 50
>PF11737 DUF3300: Protein of unknown function (DUF3300); InterPro: IPR021728 This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.
Probab=26.17 E-value=45 Score=21.92 Aligned_cols=13 Identities=15% Similarity=0.286 Sum_probs=10.3
Q ss_pred CCHHHHHHHHhcC
Q psy4372 20 FYPEELEYVFCGS 32 (50)
Q Consensus 20 F~~~ELe~LicG~ 32 (50)
|+++||++|+.--
T Consensus 1 fs~~qL~qlvAPI 13 (237)
T PF11737_consen 1 FSAAQLDQLVAPI 13 (237)
T ss_pred CCHHHHHHHhcch
Confidence 7888998887654
No 51
>TIGR01639 P_fal_TIGR01639 Plasmodium falciparum uncharacterized domain TIGR01639. This model represents a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not found elsewhere, including closely related species such as Plasmodium yoelii. No member of this family is characterized.
Probab=25.91 E-value=1e+02 Score=15.66 Aligned_cols=26 Identities=19% Similarity=0.143 Sum_probs=20.3
Q ss_pred cCCCHHHHHHHHhcCCCCCCCCCCHHHHHh
Q psy4372 18 SMFYPEELEYVFCGSDFTSCPQETACTFFI 47 (50)
Q Consensus 18 ~~F~~~ELe~LicG~~~~~~~~~d~~~L~~ 47 (50)
+-.|.+||..+|....+ ..+.+|+..
T Consensus 8 ~~lTeEEl~~~i~~L~~----~~~~~dm~~ 33 (61)
T TIGR01639 8 KKLSKEELNELINSLDE----IPNRNDMLI 33 (61)
T ss_pred HHccHHHHHHHHHhhcC----CCCHHHHHH
Confidence 45789999999999986 567777653
No 52
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.78 E-value=67 Score=20.48 Aligned_cols=31 Identities=23% Similarity=0.446 Sum_probs=22.2
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHhcCC
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFCGSD 33 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~LicG~~ 33 (50)
+||++-|... .++.+-.|++++++.|+.-..
T Consensus 55 e~freaF~~F-d~~kVA~~~~~dverLl~d~g 85 (188)
T COG2818 55 EAFREAFHGF-DPEKVAAMTEEDVERLLADAG 85 (188)
T ss_pred HHHHHHHhcC-CHHHHHcCCHHHHHHHHhCcc
Confidence 3566666554 667777889999999986543
No 53
>PF03047 ComC: COMC family; InterPro: IPR004288 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family consists of streptococcal competence stimulating peptide precursors, which are generally up to 50 amino acid residues long. In all the members of this family, the leader sequence is cleaved after two conserved glycine residues; thus the leader sequence is of the double- glycine type []. Competence stimulating peptides (CSP) are small (less than 25 amino acid residues) cationic peptides. The N-terminal amino acid residue is negatively charged, either glutamate or aspartate. The C-terminal end is positively charged. The third residue is also positively charged: a highly conserved arginine []. Some COMC proteins and their precursors (not included in this family) do not fully follow the above description. Functionally, CSP act as pheromones, stimulating competence for genetic transformation in streptococci. In streptococci, the (CSP mediated) competence response requires exponential cell growth at a critical density, a relatively simple requirement when compared to the stationary-phase requirement of Haemophilus, or the late-logarithmic- phase of Bacillus []. All bacteria induced to competence by a particular CSP are said to belong to the same pherotype, because each CSP is recognised by a specific receptor (the signalling domain of a histidine kinase ComD). Pherotypes are not necessarily species-specific. In addition, an organism may change pherotype. There are two possible mechanisms for pherotype switching: horizontal gene transfer, and accumulation of point mutations. The biological significance of pherotypes and pherotype switching is not definitively determined. Pherotype switching occurs frequently enough in naturally competent streptococci to suggest that it may be an important contributor to genetic exchange between different bacterial species []. This entry also includes proteins that form bacteriocin-like propetides with a glycine-glycine cleavage site. The bacteriocin is initially formed as a pre-propeptide and upon cleavage at the glycine-glycine cleavage site, a leader peptide and the propeptide would be formed. The propeptide then undergoes posttranslational modification before becoming functional [].; GO: 0005186 pheromone activity; PDB: 2I2J_A 2I2H_A 2A1C_A.
Probab=25.53 E-value=23 Score=16.35 Aligned_cols=19 Identities=26% Similarity=0.232 Sum_probs=0.0
Q ss_pred ccccCCCHHHHHHHHhcCC
Q psy4372 15 AQLSMFYPEELEYVFCGSD 33 (50)
Q Consensus 15 ~~L~~F~~~ELe~LicG~~ 33 (50)
+..+..+.+||+.+.+|.-
T Consensus 9 ~~F~~lt~~eL~~I~GG~~ 27 (32)
T PF03047_consen 9 EQFEELTEEELQEIQGGDW 27 (32)
T ss_dssp -------------------
T ss_pred HHHhcCCHHHHhhccCCce
Confidence 3445678999999999875
No 54
>PRK12413 phosphomethylpyrimidine kinase; Provisional
Probab=25.09 E-value=1.7e+02 Score=17.91 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=19.5
Q ss_pred HHHHHhccCCcccccCCCHHHHHHHHhcCC
Q psy4372 4 FREGFECVFPLAQLSMFYPEELEYVFCGSD 33 (50)
Q Consensus 4 F~~GF~~V~p~~~L~~F~~~ELe~LicG~~ 33 (50)
+++.+.+++|...+-.-|..|++.| .|.+
T Consensus 119 ~~~~l~~ll~~~dli~pN~~E~~~L-~g~~ 147 (253)
T PRK12413 119 LRQELIQFFPYVTVITPNLVEAELL-SGKE 147 (253)
T ss_pred HHHHHHHHhccCcEECCCHHHHHHH-hCcC
Confidence 3444555677767767799999976 4654
No 55
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=24.55 E-value=26 Score=19.09 Aligned_cols=16 Identities=31% Similarity=0.405 Sum_probs=11.0
Q ss_pred ccCCCHHHHHHHHhcCC
Q psy4372 17 LSMFYPEELEYVFCGSD 33 (50)
Q Consensus 17 L~~F~~~ELe~LicG~~ 33 (50)
=+.|+|.|.|. .+|..
T Consensus 41 g~~~TP~eFE~-~~G~~ 56 (82)
T PF01342_consen 41 GRWFTPSEFER-HGGKG 56 (82)
T ss_dssp TEEE-HHHHHH-HHTTC
T ss_pred CcEECHHHHHh-hcCcc
Confidence 35799999995 55665
No 56
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=24.44 E-value=56 Score=17.01 Aligned_cols=26 Identities=19% Similarity=0.262 Sum_probs=17.4
Q ss_pred HHHHHHhccCCcccccCCCHHHHHHHHh
Q psy4372 3 SFREGFECVFPLAQLSMFYPEELEYVFC 30 (50)
Q Consensus 3 AF~~GF~~V~p~~~L~~F~~~ELe~Lic 30 (50)
-|++...+.|-...++ ++++|+.|+.
T Consensus 7 DFr~SM~EMI~~~~i~--~~~~LeeLL~ 32 (59)
T PF04844_consen 7 DFRESMVEMIEENGIR--DWDDLEELLA 32 (59)
T ss_pred HHHHHHHHHHHHcCCC--CHHHHHHHHH
Confidence 4666666666555554 8888887763
No 57
>KOG0030|consensus
Probab=24.20 E-value=1.5e+02 Score=18.40 Aligned_cols=30 Identities=20% Similarity=0.182 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHhcCCCCCCCCCCHHHHHhhh
Q psy4372 19 MFYPEELEYVFCGSDFTSCPQETACTFFIHC 49 (50)
Q Consensus 19 ~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~ 49 (50)
-.+.+|.+.|+.|..+. ..-++.+++-+++
T Consensus 120 kl~eeEVe~Llag~eD~-nG~i~YE~fVk~i 149 (152)
T KOG0030|consen 120 KLTEEEVEELLAGQEDS-NGCINYEAFVKHI 149 (152)
T ss_pred hccHHHHHHHHcccccc-CCcCcHHHHHHHH
Confidence 35889999999998752 2458888887753
No 58
>PF01648 ACPS: 4'-phosphopantetheinyl transferase superfamily; InterPro: IPR008278 These proteins transfer the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of pp-binding. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP []. This superfamily consists of two subtypes: The ACPS type such as ACPS_ECOLI and the Sfp type such as SFP_BACSU. The structure of the Sfp type is known [], which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion. ; GO: 0000287 magnesium ion binding, 0008897 holo-[acyl-carrier-protein] synthase activity, 0009059 macromolecule biosynthetic process; PDB: 3QMN_S 3GWM_A 3NFD_D 3NE9_C 1FTH_C 1FTE_C 1FTF_B 3HYK_B 2WDY_A 2WDS_A ....
Probab=23.94 E-value=38 Score=18.07 Aligned_cols=15 Identities=40% Similarity=0.616 Sum_probs=10.2
Q ss_pred cCCCHHHHHHHHhcC
Q psy4372 18 SMFYPEELEYVFCGS 32 (50)
Q Consensus 18 ~~F~~~ELe~LicG~ 32 (50)
++|+|+|+..+-.-.
T Consensus 23 ~~~t~~E~~~l~~~~ 37 (115)
T PF01648_consen 23 RFFTPEELEWLRSLP 37 (115)
T ss_dssp HHS-HHHHHHHHCTS
T ss_pred HhCCHHHHHHHHhCC
Confidence 579999999765443
No 59
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=23.69 E-value=56 Score=20.28 Aligned_cols=46 Identities=15% Similarity=0.065 Sum_probs=34.4
Q ss_pred HHHHHHhccCCccccc-CCCHHHHHHHHhcCCCCCCCCCCHHHHHhhh
Q psy4372 3 SFREGFECVFPLAQLS-MFYPEELEYVFCGSDFTSCPQETACTFFIHC 49 (50)
Q Consensus 3 AF~~GF~~V~p~~~L~-~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~ 49 (50)
+|.+-|.+.++++.|+ -+..+|+-.|.-|+.= ++...+-+.|+..|
T Consensus 101 ~~v~~~~~~vtL~~lK~~~~~~~~~~l~~g~RL-SV~PVt~~ew~~i~ 147 (156)
T COG2947 101 RFVRKLPRPVTLKELKANPELAEMSLLVKGNRL-SVQPVTPEEWKEIL 147 (156)
T ss_pred HHHhhcCCCccHHHHhcCcchhhhhhhhccCee-eeeeCCHHHHHHHH
Confidence 5778888999999996 6778888888888862 24466777776654
No 60
>PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=23.57 E-value=96 Score=20.36 Aligned_cols=28 Identities=14% Similarity=0.228 Sum_probs=22.6
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHhc
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFCG 31 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~LicG 31 (50)
++|..||.+.+.... ..+++|++..+-.
T Consensus 77 ~~~~~G~~d~~~~~~--~~~~~e~~~~l~~ 104 (269)
T PRK10902 77 DQLIAGVQDAFADKS--KLSDQEIEQTLQA 104 (269)
T ss_pred HHHHHHHHHHHcCCC--CCCHHHHHHHHHH
Confidence 578999999997764 4799999987754
No 61
>PRK06148 hypothetical protein; Provisional
Probab=23.00 E-value=93 Score=23.91 Aligned_cols=21 Identities=24% Similarity=0.702 Sum_probs=16.1
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHH
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYV 28 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~L 28 (50)
.||++|+.+|.| .++.|++.|
T Consensus 262 ~a~laGY~sv~p------Lt~~E~~~L 282 (1013)
T PRK06148 262 AALVAGYHAVYP------LQAQELDLL 282 (1013)
T ss_pred HHHHHHHhhcCC------CCHHHHHHH
Confidence 479999999988 467776654
No 62
>PF10548 P22_AR_C: P22AR C-terminal domain; InterPro: IPR018876 This entry represents the carboxy-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018875 from INTERPRO.
Probab=22.89 E-value=67 Score=17.21 Aligned_cols=11 Identities=36% Similarity=0.501 Sum_probs=8.6
Q ss_pred CCCHHHHHHHH
Q psy4372 19 MFYPEELEYVF 29 (50)
Q Consensus 19 ~F~~~ELe~Li 29 (50)
=|+.+||+.|.
T Consensus 7 ~fTe~El~~L~ 17 (74)
T PF10548_consen 7 QFTEEELQSLV 17 (74)
T ss_pred ccCHHHHHHHH
Confidence 48899998774
No 63
>PRK14658 acpS 4'-phosphopantetheinyl transferase; Provisional
Probab=22.82 E-value=60 Score=18.68 Aligned_cols=13 Identities=38% Similarity=0.674 Sum_probs=11.0
Q ss_pred cCCCHHHHHHHHh
Q psy4372 18 SMFYPEELEYVFC 30 (50)
Q Consensus 18 ~~F~~~ELe~Lic 30 (50)
|+|+|+|++....
T Consensus 25 Rilt~~E~~~~~~ 37 (115)
T PRK14658 25 RILIDNELEYYFQ 37 (115)
T ss_pred HcCCHHHHHHHHh
Confidence 7999999998653
No 64
>TIGR01847 bacteriocin_sig bacteriocin-type signal sequence. Bacteriocins are bacterial peptide products toxic to closely related bacteria. This model represents the N-terminal region up to the GG cleavage motif. Processing to remove this bacteriocin leader peptide occurs together with export by an ABC transporter. Note: because this model is so small (15 amino acids), it may have many spurious high-scoring matches to unrelated proteins, even with fairly stringent cutoff scores. The most likely true positives are small proteins of Gram-positive bacteria, matching regions that start within the first 15 amino acids, and encoded near bacteriocin transport family proteins (TIGR01000, TIGR01193).
Probab=22.76 E-value=63 Score=14.30 Aligned_cols=15 Identities=20% Similarity=0.324 Sum_probs=12.7
Q ss_pred CCCHHHHHHHHhcCC
Q psy4372 19 MFYPEELEYVFCGSD 33 (50)
Q Consensus 19 ~F~~~ELe~LicG~~ 33 (50)
.-+..||+.++.|..
T Consensus 3 ~Ls~kEL~~I~GG~~ 17 (26)
T TIGR01847 3 ELSEKELAQIIGGXX 17 (26)
T ss_pred cCCHHHHhhccCCcc
Confidence 457899999999987
No 65
>PRK14660 acpS 4'-phosphopantetheinyl transferase; Provisional
Probab=22.71 E-value=56 Score=18.75 Aligned_cols=12 Identities=25% Similarity=0.675 Sum_probs=10.4
Q ss_pred cCCCHHHHHHHH
Q psy4372 18 SMFYPEELEYVF 29 (50)
Q Consensus 18 ~~F~~~ELe~Li 29 (50)
++|+|+|+....
T Consensus 29 rift~~E~~~~~ 40 (125)
T PRK14660 29 RIYTPGEIAYCT 40 (125)
T ss_pred HhCCHHHHHHHH
Confidence 799999999864
No 66
>PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional
Probab=22.59 E-value=1.1e+02 Score=19.20 Aligned_cols=28 Identities=7% Similarity=0.058 Sum_probs=20.8
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHHHh
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYVFC 30 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~Lic 30 (50)
++|..||.+.+..+..++ +++|++..+.
T Consensus 36 ~~~~~G~~d~~~g~~~~~-~~~~~~~~~~ 63 (206)
T PRK11570 36 EALVAGLADALEGKHPAV-PVDVVHRALR 63 (206)
T ss_pred HHHHHHHHHHHcCCCCCC-CHHHHHHHHH
Confidence 578899999887765544 7888776654
No 67
>KOG1994|consensus
Probab=22.51 E-value=38 Score=22.56 Aligned_cols=17 Identities=29% Similarity=0.829 Sum_probs=14.1
Q ss_pred HHhcCCCCCCCCCCHHHHHhhh
Q psy4372 28 VFCGSDFTSCPQETACTFFIHC 49 (50)
Q Consensus 28 LicG~~~~~~~~~d~~~L~~~~ 49 (50)
++||-. -=|-+||.+||
T Consensus 243 ~fCG~~-----y~~~edl~ehC 259 (268)
T KOG1994|consen 243 FFCGIK-----YKDEEDLYEHC 259 (268)
T ss_pred EEeccc-----cCCHHHHHHhC
Confidence 578988 57789999988
No 68
>PF01387 Synuclein: Synuclein; InterPro: IPR001058 Synucleins are small, soluble proteins expressed primarily in neural tissue and in certain tumors [, []. The family includes three known proteins: alpha-synuclein, beta-synuclein, and gamma-synuclein. All synucleins have in common a highly conserved alpha-helical lipid-binding motif with similarity to the class-A2 lipid-binding domains of the exchangeable apolipoproteins []. Synuclein family members are not found outside vertebrates, although they have some conserved structural similarity with plant 'late-embryo-abundant' proteins. The alpha- and beta-synuclein proteins are found primarily in brain tissue, where they are seen mainly in presynaptic terminals [, ]. The gamma-synuclein protein is found primarily in the peripheral nervous system and retina, but its expression in breast tumors is a marker for tumor progression []. Normal cellular functions have not been determined for any of the synuclein proteins, although some data suggest a role in the regulation of membrane stability and/or turnover. Mutations in alpha-synuclein are associated with rare familial cases of early-onset Parkinson's disease, and the protein accumulates abnormally in Parkinson's disease, Alzheimer's disease, and several other neurodegenerative illnesses []. ; PDB: 3Q27_A 3Q28_A 2KKW_A 3Q29_C 3Q25_A 2JN5_A 3Q26_A 1XQ8_A.
Probab=22.48 E-value=38 Score=20.46 Aligned_cols=10 Identities=40% Similarity=0.846 Sum_probs=7.0
Q ss_pred ChHHHHHHhc
Q psy4372 1 MESFREGFEC 10 (50)
Q Consensus 1 ~~AF~~GF~~ 10 (50)
|+.|+.||+.
T Consensus 1 mdvf~kgfs~ 10 (131)
T PF01387_consen 1 MDVFMKGFSM 10 (131)
T ss_dssp HHHHHHHHHH
T ss_pred CcHHHhhhhh
Confidence 5677777764
No 69
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=22.38 E-value=64 Score=21.34 Aligned_cols=27 Identities=30% Similarity=0.200 Sum_probs=21.3
Q ss_pred HHhccCCcccc--cCCCHHHHHHHHhcCC
Q psy4372 7 GFECVFPLAQL--SMFYPEELEYVFCGSD 33 (50)
Q Consensus 7 GF~~V~p~~~L--~~F~~~ELe~LicG~~ 33 (50)
|.+.+.|.-.| .+|+++|+..|+.|..
T Consensus 61 ~gy~~~~~~~L~pl~ft~~E~~Al~~~l~ 89 (311)
T COG2378 61 GGYRLRPGFKLPPLMFTEEEAEALLLALR 89 (311)
T ss_pred ccEEEccCCCCCcccCCHHHHHHHHHHHH
Confidence 45666676666 4999999999998876
No 70
>PRK14662 acpS 4'-phosphopantetheinyl transferase; Provisional
Probab=21.38 E-value=83 Score=18.11 Aligned_cols=13 Identities=46% Similarity=0.935 Sum_probs=10.8
Q ss_pred cCCCHHHHHHHHh
Q psy4372 18 SMFYPEELEYVFC 30 (50)
Q Consensus 18 ~~F~~~ELe~Lic 30 (50)
++|+|+|++....
T Consensus 29 Ri~t~~E~~~~~~ 41 (120)
T PRK14662 29 RLFHPEELAYCLA 41 (120)
T ss_pred HcCCHHHHHHHHh
Confidence 7999999997643
No 71
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=21.25 E-value=82 Score=15.44 Aligned_cols=14 Identities=21% Similarity=0.401 Sum_probs=10.3
Q ss_pred ccCCCHHHHHHHHh
Q psy4372 17 LSMFYPEELEYVFC 30 (50)
Q Consensus 17 L~~F~~~ELe~Lic 30 (50)
+-=|+|+|.+.+.+
T Consensus 32 lL~fs~~e~~~~~~ 45 (46)
T smart00755 32 VLQLSPEEMQKLLE 45 (46)
T ss_pred HhCCCHHHHHHHHh
Confidence 44589999887753
No 72
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=21.23 E-value=1e+02 Score=15.18 Aligned_cols=23 Identities=9% Similarity=-0.206 Sum_probs=15.2
Q ss_pred CHHHHHHHHhcCCCCCCCCCCHHHHHhh
Q psy4372 21 YPEELEYVFCGSDFTSCPQETACTFFIH 48 (50)
Q Consensus 21 ~~~ELe~LicG~~~~~~~~~d~~~L~~~ 48 (50)
+++++...+|-.= .++.++|...
T Consensus 1 ~~~~I~~~Va~~~-----~i~~~~i~s~ 23 (60)
T smart00760 1 TIEEIIEAVAEYF-----GVKPEDLKSK 23 (60)
T ss_pred CHHHHHHHHHHHh-----CCCHHHHhcC
Confidence 3567777777665 5777777654
No 73
>smart00524 DWB Domain B in dwarfin family proteins.
Probab=21.04 E-value=71 Score=19.85 Aligned_cols=23 Identities=13% Similarity=0.166 Sum_probs=18.9
Q ss_pred ccCCcccccCCCHHHHHHHHhcC
Q psy4372 10 CVFPLAQLSMFYPEELEYVFCGS 32 (50)
Q Consensus 10 ~V~p~~~L~~F~~~ELe~LicG~ 32 (50)
+|-|...|++|+-++...++.-.
T Consensus 103 Kv~pg~~lKvFd~~~f~~~l~~~ 125 (171)
T smart00524 103 KLPPGYSIKVFDMEKFAQLLARE 125 (171)
T ss_pred EECCCCeEEEeChHHHHHHHHhh
Confidence 45688889999999999988644
No 74
>PRK14659 acpS 4'-phosphopantetheinyl transferase; Provisional
Probab=21.04 E-value=69 Score=18.19 Aligned_cols=13 Identities=23% Similarity=0.324 Sum_probs=10.9
Q ss_pred cCCCHHHHHHHHh
Q psy4372 18 SMFYPEELEYVFC 30 (50)
Q Consensus 18 ~~F~~~ELe~Lic 30 (50)
++|+|+|+..+..
T Consensus 29 r~ft~~E~~~~~~ 41 (122)
T PRK14659 29 RVFSEKEIEDSLK 41 (122)
T ss_pred hcCCHHHHHHHHh
Confidence 7999999998653
No 75
>COG4023 SBH1 Preprotein translocase subunit Sec61beta [Intracellular trafficking and secretion]
Probab=20.98 E-value=14 Score=19.37 Aligned_cols=22 Identities=23% Similarity=0.409 Sum_probs=16.5
Q ss_pred HHHHhccCCcccccCCCHHHHH
Q psy4372 5 REGFECVFPLAQLSMFYPEELE 26 (50)
Q Consensus 5 ~~GF~~V~p~~~L~~F~~~ELe 26 (50)
.+|+.++...-.++.|.++|..
T Consensus 7 ~eg~~~~~~AGLi~f~eEee~~ 28 (57)
T COG4023 7 SEGLQSPAAAGLIRFFEEEEIK 28 (57)
T ss_pred ccccCCccccceeeeecccccC
Confidence 3577776666678999998876
No 76
>PF14793 DUF4478: Domain of unknown function (DUF4478); PDB: 2PMB_D 3GH1_D 3BQ9_B.
Probab=20.94 E-value=1.2e+02 Score=17.87 Aligned_cols=34 Identities=18% Similarity=0.295 Sum_probs=20.3
Q ss_pred ccCCcccccCCCHHHHHHHHhcCCCCCCCCCCHHHHHhhh
Q psy4372 10 CVFPLAQLSMFYPEELEYVFCGSDFTSCPQETACTFFIHC 49 (50)
Q Consensus 10 ~V~p~~~L~~F~~~ELe~LicG~~~~~~~~~d~~~L~~~~ 49 (50)
.|=|...|.+.+..|.+.|--.+. =++-.|.++|
T Consensus 4 ~i~P~gsl~~LSq~Ev~~L~~~s~------~~ly~LfR~C 37 (112)
T PF14793_consen 4 QISPKGSLDLLSQLEVDRLKDSSS------SGLYQLFRNC 37 (112)
T ss_dssp EE--SSCGGG--HHHHHHHCTCCC------CHHHHHHHHH
T ss_pred EECCCchHHHhCHHHHHHHHhccc------ccHHHHHHhh
Confidence 356889999999999998843333 3355555555
No 77
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=20.93 E-value=77 Score=13.78 Aligned_cols=16 Identities=19% Similarity=-0.047 Sum_probs=12.6
Q ss_pred CCCHHHHHHHHhcCCC
Q psy4372 19 MFYPEELEYVFCGSDF 34 (50)
Q Consensus 19 ~F~~~ELe~LicG~~~ 34 (50)
-++++|.+.|+.+...
T Consensus 3 ~Wt~~E~~~l~~~~~~ 18 (49)
T smart00717 3 EWTEEEDELLIELVKK 18 (49)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 4789999999877653
No 78
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.47 E-value=82 Score=14.53 Aligned_cols=11 Identities=36% Similarity=0.474 Sum_probs=8.7
Q ss_pred CCCHHHHHHHH
Q psy4372 19 MFYPEELEYVF 29 (50)
Q Consensus 19 ~F~~~ELe~Li 29 (50)
.|+..|++.++
T Consensus 29 W~d~~el~~~~ 39 (41)
T PF13453_consen 29 WFDAGELEKLL 39 (41)
T ss_pred EccHHHHHHHH
Confidence 57888988875
No 79
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=20.07 E-value=1.6e+02 Score=18.02 Aligned_cols=30 Identities=17% Similarity=-0.039 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHhcCCCCCCCCCCHHHHHhh
Q psy4372 19 MFYPEELEYVFCGSDFTSCPQETACTFFIH 48 (50)
Q Consensus 19 ~F~~~ELe~LicG~~~~~~~~~d~~~L~~~ 48 (50)
-.+.+|++.||-+.+..+...++.++..+.
T Consensus 124 ~~~deev~~ll~~~d~d~dG~i~~~eF~~~ 153 (160)
T COG5126 124 RLSDEEVEKLLKEYDEDGDGEIDYEEFKKL 153 (160)
T ss_pred cCCHHHHHHHHHhcCCCCCceEeHHHHHHH
Confidence 357889999988887655567888887664
No 80
>PRK06149 hypothetical protein; Provisional
Probab=20.06 E-value=1.2e+02 Score=23.20 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=16.2
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHH
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYV 28 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~L 28 (50)
.+|++|+.+|.| +++.|++.|
T Consensus 269 ~~~l~GY~svrp------Lt~~E~~~L 289 (972)
T PRK06149 269 LPAVRAYHAVRP------LSEAELKAL 289 (972)
T ss_pred HHHHHHHHhcCC------CCHHHHHHH
Confidence 478999999987 577777663
No 81
>PF10256 Erf4: Golgin subfamily A member 7/ERF4 family; InterPro: IPR019383 Proteins in this entry include Golgin subfamily A member 7 and the Ras modification protein ERF4.
Probab=20.03 E-value=82 Score=17.56 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=22.6
Q ss_pred HHHhccCCcccccCCCHHHHHHHHhcCC
Q psy4372 6 EGFECVFPLAQLSMFYPEELEYVFCGSD 33 (50)
Q Consensus 6 ~GF~~V~p~~~L~~F~~~ELe~LicG~~ 33 (50)
-+|...+|.+.=...+|+|.+.+|.--.
T Consensus 16 ~~Fs~~~P~~L~~~is~~ef~~iI~~IN 43 (118)
T PF10256_consen 16 PQFSTEYPGELSGYISPEEFEEIINTIN 43 (118)
T ss_pred CccCccCCHhhcCCCCHHHHHHHHHHHH
Confidence 4788889988767899999999886543
No 82
>TIGR00938 thrB_alt homoserine kinase, Neisseria type. Homoserine kinase is required in the biosynthesis of threonine from aspartate.The member of this family from Pseudomonas aeruginosa was shown by direct assay and complementation to act specifically as a homoserine kinase.
Probab=20.02 E-value=1.4e+02 Score=18.97 Aligned_cols=21 Identities=24% Similarity=0.332 Sum_probs=14.3
Q ss_pred hHHHHHHhccCCcccccCCCHHHHHHH
Q psy4372 2 ESFREGFECVFPLAQLSMFYPEELEYV 28 (50)
Q Consensus 2 ~AF~~GF~~V~p~~~L~~F~~~ELe~L 28 (50)
.+|++|..++.|. +++|++.|
T Consensus 245 ~~~l~gY~~~~~L------s~~e~~~l 265 (307)
T TIGR00938 245 KALIKGYHQSRPL------TEEEKAAF 265 (307)
T ss_pred HHHHHHHHhcCCC------CHHHHHHH
Confidence 5788888888663 56665443
Done!