Query psy2245
Match_columns 88
No_of_seqs 27 out of 29
Neff 2.2
Searched_HMMs 46136
Date Fri Aug 16 19:51:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2245hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01465 GRIP: GRIP domain; I 99.5 1.8E-14 3.9E-19 86.2 5.2 43 34-76 2-46 (46)
2 smart00755 Grip golgin-97, Ran 99.4 8.1E-13 1.8E-17 80.0 4.9 44 34-77 1-45 (46)
3 PF08349 DUF1722: Protein of u 94.2 0.42 9.2E-06 32.1 7.3 63 16-78 10-77 (117)
4 PRK10167 hypothetical protein; 85.0 7.1 0.00015 28.8 7.4 59 17-75 51-115 (169)
5 PF12844 HTH_19: Helix-turn-he 84.1 2.9 6.3E-05 24.1 4.1 53 19-71 2-57 (64)
6 cd07321 Extradiol_Dioxygenase_ 82.7 2.8 6.1E-05 27.0 4.0 38 41-78 6-46 (77)
7 PF09228 Prok-TraM: Prokaryoti 82.0 1.3 2.7E-05 31.1 2.3 53 13-70 35-101 (102)
8 PF13443 HTH_26: Cro/C1-type H 75.3 6.5 0.00014 22.5 3.6 34 38-71 21-56 (63)
9 PHA01976 helix-turn-helix prot 74.9 11 0.00024 21.8 4.6 55 18-72 4-61 (67)
10 PF01381 HTH_3: Helix-turn-hel 69.8 10 0.00023 21.0 3.5 37 35-71 17-54 (55)
11 PF05952 ComX: Bacillus compet 68.1 2.8 6.1E-05 26.7 1.0 39 40-78 2-40 (57)
12 PRK00465 rpmJ 50S ribosomal pr 66.0 2.4 5.3E-05 25.2 0.4 9 5-13 25-33 (37)
13 PF10410 DnaB_bind: DnaB-helic 65.1 17 0.00037 20.7 3.9 51 21-71 6-58 (59)
14 PF13560 HTH_31: Helix-turn-he 61.3 26 0.00055 20.4 4.2 55 20-74 5-63 (64)
15 PF02093 Gag_p30: Gag P30 core 57.7 20 0.00044 28.0 4.2 46 30-80 21-66 (211)
16 cd07922 CarBa CarBa is the A s 56.1 12 0.00026 24.9 2.4 25 46-77 22-46 (81)
17 PF05119 Terminase_4: Phage te 53.0 14 0.00029 23.0 2.2 24 55-78 70-93 (100)
18 PF07051 OCIA: Ovarian carcino 51.5 11 0.00024 26.8 1.8 26 61-86 20-45 (111)
19 PF08784 RPA_C: Replication pr 49.9 31 0.00068 21.9 3.5 41 36-76 44-86 (102)
20 PF11940 DUF3458: Domain of un 49.0 68 0.0015 26.1 6.1 69 14-84 195-280 (367)
21 PF00444 Ribosomal_L36: Riboso 45.3 7.6 0.00016 23.0 0.1 9 5-13 25-34 (38)
22 cd07921 PCA_45_Doxase_A_like S 44.4 45 0.00098 23.5 3.9 39 39-77 14-55 (106)
23 TIGR01022 rpmJ_bact ribosomal 41.3 11 0.00023 22.5 0.4 9 5-13 25-33 (37)
24 TIGR01558 sm_term_P27 phage te 39.5 36 0.00078 22.5 2.7 23 54-76 78-100 (116)
25 cd07923 Gallate_dioxygenase_C 39.3 51 0.0011 22.8 3.5 32 47-78 14-48 (94)
26 PF07746 LigA: Aromatic-ring-o 38.8 18 0.00039 24.2 1.2 29 49-77 9-40 (88)
27 KOG1567|consensus 38.5 64 0.0014 27.1 4.5 58 3-64 93-155 (344)
28 PRK09210 RNA polymerase sigma 35.9 2E+02 0.0044 22.7 6.8 29 52-80 229-257 (367)
29 KOG0161|consensus 35.9 39 0.00084 33.6 3.3 27 54-80 321-347 (1930)
30 PF14338 Mrr_N: Mrr N-terminal 35.8 96 0.0021 19.6 4.2 35 42-76 7-44 (92)
31 PF06945 DUF1289: Protein of u 35.7 55 0.0012 19.5 2.9 27 53-79 19-45 (51)
32 COG4840 Uncharacterized protei 34.8 84 0.0018 21.2 3.9 36 27-76 24-63 (71)
33 cd07925 LigA_like_1 The A subu 34.6 91 0.002 22.1 4.2 39 39-77 14-55 (106)
34 PRK09706 transcriptional repre 34.3 1.3E+02 0.0027 20.1 4.7 52 19-70 8-62 (135)
35 cd07377 WHTH_GntR Winged helix 33.9 85 0.0018 17.2 4.9 48 35-82 5-53 (66)
36 PF00248 Aldo_ket_red: Aldo/ke 33.8 27 0.00058 24.8 1.5 62 16-78 216-281 (283)
37 PF07499 RuvA_C: RuvA, C-termi 33.6 43 0.00094 19.3 2.1 22 56-78 5-26 (47)
38 PRK00831 rpmJ 50S ribosomal pr 32.9 18 0.00038 22.0 0.4 9 5-13 28-37 (41)
39 TIGR03830 CxxCG_CxxCG_HTH puta 32.5 1.1E+02 0.0024 19.5 4.1 34 40-73 91-124 (127)
40 COG3313 Predicted Fe-S protein 32.2 60 0.0013 21.8 2.8 26 53-78 24-49 (74)
41 cd07650 F-BAR_Syp1p_like The F 32.0 65 0.0014 23.9 3.3 36 36-71 173-213 (228)
42 PF09252 Feld-I_B: Allergen Fe 31.0 76 0.0016 21.0 3.1 29 52-80 13-41 (67)
43 PRK09943 DNA-binding transcrip 30.7 1.6E+02 0.0035 20.4 5.0 57 16-72 7-66 (185)
44 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 30.5 36 0.00077 20.9 1.5 14 40-53 33-46 (50)
45 TIGR02414 pepN_proteo aminopep 29.7 1.7E+02 0.0037 26.4 6.0 54 31-84 664-734 (863)
46 TIGR02263 benz_CoA_red_C benzo 29.6 1.5E+02 0.0033 23.5 5.2 77 3-79 95-182 (380)
47 PF08278 DnaG_DnaB_bind: DNA p 29.3 1.6E+02 0.0035 19.0 5.4 44 32-77 79-125 (127)
48 TIGR03643 conserved hypothetic 29.0 73 0.0016 21.4 2.9 24 57-80 15-38 (72)
49 PF00636 Ribonuclease_3: Ribon 28.4 1.2E+02 0.0026 19.0 3.7 30 36-65 2-38 (114)
50 PF12123 Amidase02_C: N-acetyl 28.2 46 0.001 20.2 1.6 8 80-87 38-45 (45)
51 PF11855 DUF3375: Protein of u 28.1 96 0.0021 25.6 4.0 35 42-76 243-283 (478)
52 PF13936 HTH_38: Helix-turn-he 27.4 28 0.0006 19.8 0.5 15 66-80 4-18 (44)
53 COG0055 AtpD F0F1-type ATP syn 27.3 62 0.0013 28.2 2.8 25 56-80 374-401 (468)
54 PF04802 SMK-1: Component of I 27.2 61 0.0013 24.2 2.5 40 29-72 89-136 (193)
55 cd07924 PCA_45_Doxase_A The A 26.2 1.2E+02 0.0026 22.0 3.8 47 31-77 13-63 (121)
56 PRK13379 protocatechuate 4,5-d 26.2 1.2E+02 0.0026 22.0 3.7 40 39-78 26-68 (119)
57 KOG4369|consensus 26.0 34 0.00074 34.0 1.2 25 48-72 418-444 (2131)
58 KOG2050|consensus 25.9 2.9E+02 0.0062 25.2 6.7 41 35-78 341-381 (652)
59 TIGR02792 PCA_ligA protocatech 25.8 1.2E+02 0.0027 21.8 3.8 39 39-77 19-60 (117)
60 KOG4075|consensus 25.7 46 0.00099 25.3 1.6 29 52-87 48-85 (167)
61 cd07930 bacterial_phosphagen_k 25.7 18 0.00038 27.5 -0.6 45 5-54 104-149 (232)
62 PF11698 V-ATPase_H_C: V-ATPas 25.5 67 0.0015 22.7 2.3 26 40-65 87-114 (119)
63 PRK13378 protocatechuate 4,5-d 25.2 1.6E+02 0.0035 21.2 4.3 49 30-78 15-67 (117)
64 PF01325 Fe_dep_repress: Iron 25.1 1.7E+02 0.0036 17.7 4.3 39 35-76 5-43 (60)
65 PF07813 LTXXQ: LTXXQ motif fa 25.0 20 0.00043 21.7 -0.4 26 55-80 3-28 (100)
66 COG1519 KdtA 3-deoxy-D-manno-o 24.9 1.3E+02 0.0028 25.6 4.2 53 11-67 351-403 (419)
67 PHA02566 alt ADP-ribosyltransf 24.7 73 0.0016 28.9 2.9 48 35-82 393-440 (684)
68 PF14403 CP_ATPgrasp_2: Circul 24.6 1.3E+02 0.0028 25.5 4.1 37 35-79 64-100 (445)
69 PF07138 DUF1386: Protein of u 24.2 64 0.0014 26.9 2.3 40 36-86 133-172 (324)
70 cd06199 SiR Cytochrome p450- l 24.0 1.3E+02 0.0027 23.4 3.8 39 5-43 311-349 (360)
71 PRK14015 pepN aminopeptidase N 23.8 2.6E+02 0.0057 25.3 6.1 54 31-84 674-744 (875)
72 PF10985 DUF2805: Protein of u 23.7 1E+02 0.0023 20.7 2.8 24 57-80 14-37 (73)
73 PRK09726 antitoxin HipB; Provi 23.2 2E+02 0.0043 17.9 4.3 57 15-71 11-70 (88)
74 PRK09390 fixJ response regulat 23.1 2E+02 0.0043 17.8 4.9 32 31-62 85-116 (202)
75 PF06719 AraC_N: AraC-type tra 22.9 2.6E+02 0.0056 19.2 4.8 48 4-53 104-152 (155)
76 PRK11172 dkgB 2,5-diketo-D-glu 22.8 2.1E+02 0.0046 20.9 4.6 58 21-80 192-252 (267)
77 PF05974 DUF892: Domain of unk 22.8 66 0.0014 22.6 1.9 34 40-73 36-69 (159)
78 PRK13377 protocatechuate 4,5-d 22.8 1.5E+02 0.0033 21.8 3.7 48 30-77 15-66 (129)
79 PF03705 CheR_N: CheR methyltr 22.7 79 0.0017 17.8 1.9 38 3-42 16-53 (57)
80 TIGR03330 SAM_DCase_Bsu S-aden 22.2 88 0.0019 21.2 2.3 16 29-44 84-99 (112)
81 cd02639 R3H_RRM R3H domain of 22.2 73 0.0016 19.9 1.8 14 66-79 25-38 (60)
82 PF09537 DUF2383: Domain of un 21.9 87 0.0019 19.9 2.2 61 14-85 16-76 (111)
83 PRK13671 hypothetical protein; 21.7 38 0.00083 27.0 0.5 17 61-77 245-261 (298)
84 PF04539 Sigma70_r3: Sigma-70 21.7 1.4E+02 0.0031 17.6 3.0 33 48-80 13-45 (78)
85 PF04695 Pex14_N: Peroxisomal 21.7 1.6E+02 0.0034 20.4 3.5 33 46-78 11-46 (136)
86 KOG0639|consensus 21.7 54 0.0012 29.7 1.5 72 8-80 50-126 (705)
87 COG0708 XthA Exonuclease III [ 21.6 68 0.0015 25.3 1.9 22 62-83 168-189 (261)
88 cd01383 MYSc_type_VIII Myosin 21.6 75 0.0016 27.8 2.3 25 55-80 239-263 (677)
89 TIGR01931 cysJ sulfite reducta 21.6 1.5E+02 0.0032 25.1 3.9 39 5-43 548-586 (597)
90 PF04225 OapA: Opacity-associa 21.6 1.5E+02 0.0032 19.2 3.2 25 55-79 10-34 (85)
91 PRK07571 bidirectional hydroge 21.4 3.4E+02 0.0073 19.9 5.4 52 20-77 23-76 (169)
92 PF11729 Capsid-VNN: nodavirus 21.3 46 0.001 27.9 1.0 30 46-86 126-155 (340)
93 PF06441 EHN: Epoxide hydrolas 21.3 87 0.0019 21.3 2.2 50 10-59 8-66 (112)
94 PF07540 NOC3p: Nucleolar comp 20.8 1.8E+02 0.004 19.6 3.6 20 31-51 17-36 (95)
95 smart00418 HTH_ARSR helix_turn 20.7 1.5E+02 0.0032 15.5 3.5 23 54-76 9-31 (66)
96 PF11220 DUF3015: Protein of u 20.7 1.3E+02 0.0028 21.9 3.0 26 52-77 80-105 (144)
97 PRK07921 RNA polymerase sigma 20.5 4.3E+02 0.0093 20.8 6.8 26 53-78 187-212 (324)
98 PHA00617 ribbon-helix-helix do 20.4 94 0.002 20.8 2.1 55 9-70 10-66 (80)
99 PF15002 ERK-JNK_inhib: ERK an 20.4 1E+02 0.0022 23.6 2.6 21 54-74 30-50 (207)
100 PRK15321 putative type III sec 20.3 1.2E+02 0.0026 22.1 2.8 20 36-55 34-56 (120)
101 TIGR02400 trehalose_OtsA alpha 20.1 1.2E+02 0.0026 24.7 3.1 32 46-77 401-432 (456)
102 KOG2659|consensus 20.1 1.8E+02 0.0039 22.9 3.9 63 8-73 97-159 (228)
No 1
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=99.53 E-value=1.8e-14 Score=86.16 Aligned_cols=43 Identities=26% Similarity=0.600 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHHHHhc--CccchhhhHHHHHHHhCCCHHHHHHHH
Q psy2245 34 EMTLQFLKSAIFYFLT--DPVNAQGHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 34 EanLefLKnaIy~fLT--D~~~~q~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
++++|||||+|+.||+ |+..+++++.||.+||+|||+|++.|.
T Consensus 2 ~~~~eYLKNvl~~fl~~~~~~~~~~llpvi~tlL~fs~~e~~~i~ 46 (46)
T PF01465_consen 2 GINLEYLKNVLLQFLESREPSEREQLLPVIATLLKFSPEEKQKIL 46 (46)
T ss_dssp -HHHHHHHHHHHHHHTTSS---HHHHHHHHHHHTT--HHHHHHHH
T ss_pred chhHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHCCCHHHHHhhC
Confidence 4799999999999999 445899999999999999999999874
No 2
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=99.38 E-value=8.1e-13 Score=80.00 Aligned_cols=44 Identities=20% Similarity=0.401 Sum_probs=39.0
Q ss_pred hhHHHHHHHHHHHHhcCccc-hhhhHHHHHHHhCCCHHHHHHHHh
Q psy2245 34 EMTLQFLKSAIFYFLTDPVN-AQGHLTALLSILGYSDAQKENIMK 77 (88)
Q Consensus 34 EanLefLKnaIy~fLTD~~~-~q~hLtAI~sIL~FSp~Ek~~V~k 77 (88)
++|+|||||+++.||+-++. +++.+.||.++|+|||+|.+.++.
T Consensus 1 ~~n~eYLKNVll~fl~~~e~~r~~ll~vi~tlL~fs~~e~~~~~~ 45 (46)
T smart00755 1 EANFEYLKNVLLQFLTLRESERETLLKVISTVLQLSPEEMQKLLE 45 (46)
T ss_pred CccHHHHHHHHHHHhccCcchHHHHHHHHHHHhCCCHHHHHHHHh
Confidence 36899999999999994444 899999999999999999998864
No 3
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=94.18 E-value=0.42 Score=32.07 Aligned_cols=63 Identities=19% Similarity=0.313 Sum_probs=52.1
Q ss_pred HHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCC-----CHHHHHHHHhh
Q psy2245 16 RHKRRYDALKDTKPPNDAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGY-----SDAQKENIMKT 78 (88)
Q Consensus 16 ~~~~r~~~~~~~k~~~D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~F-----Sp~Ek~~V~k~ 78 (88)
.+|+-+.+.-.+....+.+..++-....+..-|.-+..+..|.+|++-|.|+ |++||+.....
T Consensus 10 ~~y~~lg~~va~~~~~~~~~~~~~Y~~~l~~al~~~~~~~~~~Nvl~Hi~Gyfk~~ls~~EK~~~~~~ 77 (117)
T PF08349_consen 10 KIYRELGRLVANAGKRPLEEVFEEYEELLMEALSKPPTRGSHINVLQHIFGYFKKKLSSEEKQHFLDL 77 (117)
T ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 4677777777777777788777777888888888888899999999999986 89999877654
No 4
>PRK10167 hypothetical protein; Provisional
Probab=84.98 E-value=7.1 Score=28.80 Aligned_cols=59 Identities=14% Similarity=0.337 Sum_probs=45.1
Q ss_pred HHHHHHHHHhCCCCC-ChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCC-----CHHHHHHH
Q psy2245 17 HKRRYDALKDTKPPN-DAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGY-----SDAQKENI 75 (88)
Q Consensus 17 ~~~r~~~~~~~k~~~-D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~F-----Sp~Ek~~V 75 (88)
+||.+...-.+.... +.+.-++=-...+..-|.-+..+..|.|+++-|.|| |++||+..
T Consensus 51 ~yr~LG~lva~~~~~~~~~~~~~~Y~~~lm~al~~~~t~~~~~NvL~Hi~GYFKk~Ls~~EKq~l 115 (169)
T PRK10167 51 EYRKLGPFVADIHQWQSLDDFYNQYRQRVIVLLSHPANVRDHTNVLMHVQGYFRPHIDSTERQQL 115 (169)
T ss_pred HHHHHHHHHhcCCcCCCHHHHHHHHHHHHHHHHcCCCCcchhHHHHHHHHHHHHhhCCHHHHHHH
Confidence 466666665665554 677666555677788888888899999999999997 99998876
No 5
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=84.07 E-value=2.9 Score=24.09 Aligned_cols=53 Identities=19% Similarity=0.231 Sum_probs=35.0
Q ss_pred HHHHHHHhCCCCCChhh--HHHHHHHHHHHHhc-CccchhhhHHHHHHHhCCCHHH
Q psy2245 19 RRYDALKDTKPPNDAEM--TLQFLKSAIFYFLT-DPVNAQGHLTALLSILGYSDAQ 71 (88)
Q Consensus 19 ~r~~~~~~~k~~~D~Ea--nLefLKnaIy~fLT-D~~~~q~hLtAI~sIL~FSp~E 71 (88)
.|+.+++.+++....+. .+..=++.|+.+.. ...-+-.+|.+|..+|+.|+++
T Consensus 2 ~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~ 57 (64)
T PF12844_consen 2 ERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLDE 57 (64)
T ss_dssp HHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHHH
Confidence 46777777776654442 23333888999998 4455679999999999999986
No 6
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=82.70 E-value=2.8 Score=26.99 Aligned_cols=38 Identities=16% Similarity=0.255 Sum_probs=28.9
Q ss_pred HHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHhh
Q psy2245 41 KSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 41 KnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k~ 78 (88)
.+.|...+.||++++.-+ .|.+.=-++|||||++|+.-
T Consensus 6 ~~~~~~~~~~~~~re~f~~dp~a~~~~~~Lt~eE~~al~~r 46 (77)
T cd07321 6 EKLLEQLLVKPEVKERFKADPEAVLAEYGLTPEEKAALLAR 46 (77)
T ss_pred HHHHHHHhcCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHcC
Confidence 667777777887766554 46777789999999999753
No 7
>PF09228 Prok-TraM: Prokaryotic Transcriptional repressor TraM; InterPro: IPR015309 Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a globular head and an elongated tail, and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation []. ; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Q0O_D 2HJD_D 1UPG_A 1US6_B 1RFY_B.
Probab=81.98 E-value=1.3 Score=31.11 Aligned_cols=53 Identities=28% Similarity=0.490 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHHh----C----------CCCCChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHH
Q psy2245 13 NLIRHKRRYDALKD----T----------KPPNDAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDA 70 (88)
Q Consensus 13 ~~~~~~~r~~~~~~----~----------k~~~D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~ 70 (88)
+-||-+||+.++-+ + .+....+..++|+.-.+ -.++.|.-|+.|++||||.|+
T Consensus 35 ~AIRehR~lv~~ae~~~eew~~~~~d~~~~~~~~~~~~~eY~~~~~-----e~hAQ~~~lstli~~LGyvPk 101 (102)
T PF09228_consen 35 SAIREHRRLVEAAERLFEEWIRLPEDPKISPAVLGELQLEYIERQI-----EMHAQQSALSTLIDILGYVPK 101 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHCHHHSCHHHHTTSCHHSHHHHHHHHHHH-----HHHHHHHHHHHHHHHHTSEE-
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCccCcccchHHHHHHHHHHH-----HhHHHHHHHHHHHHHhCCCCC
Confidence 46899999987644 1 12233347788887654 346678889999999999985
No 8
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=75.33 E-value=6.5 Score=22.54 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhcCc--cchhhhHHHHHHHhCCCHHH
Q psy2245 38 QFLKSAIFYFLTDP--VNAQGHLTALLSILGYSDAQ 71 (88)
Q Consensus 38 efLKnaIy~fLTD~--~~~q~hLtAI~sIL~FSp~E 71 (88)
..=++.|+.++..+ .-+.++|.+|...||-+|+|
T Consensus 21 gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 21 GISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp T--HHHHHHHHTTT-----HHHHHHHHHHHT--HHH
T ss_pred CcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHHH
Confidence 33457788888854 56789999999999999987
No 9
>PHA01976 helix-turn-helix protein
Probab=74.87 E-value=11 Score=21.78 Aligned_cols=55 Identities=16% Similarity=0.135 Sum_probs=40.7
Q ss_pred HHHHHHHHhCCCCCChhhH--HHHHHHHHHHHhcC-ccchhhhHHHHHHHhCCCHHHH
Q psy2245 18 KRRYDALKDTKPPNDAEMT--LQFLKSAIFYFLTD-PVNAQGHLTALLSILGYSDAQK 72 (88)
Q Consensus 18 ~~r~~~~~~~k~~~D~Ean--LefLKnaIy~fLTD-~~~~q~hLtAI~sIL~FSp~Ek 72 (88)
-.|+.++++.++....+.+ +.-=++.|..+... ..-....|.+|..+|+.|+++-
T Consensus 4 ~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~~l 61 (67)
T PHA01976 4 AIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWL 61 (67)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHH
Confidence 4677888888887766632 33346888888884 3446789999999999999864
No 10
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=69.76 E-value=10 Score=21.00 Aligned_cols=37 Identities=19% Similarity=0.118 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHHHhcC-ccchhhhHHHHHHHhCCCHHH
Q psy2245 35 MTLQFLKSAIFYFLTD-PVNAQGHLTALLSILGYSDAQ 71 (88)
Q Consensus 35 anLefLKnaIy~fLTD-~~~~q~hLtAI~sIL~FSp~E 71 (88)
..+..=++.|.+++.+ ..-..+++.+|...||.|+++
T Consensus 17 ~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~~ 54 (55)
T PF01381_consen 17 EKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPEY 54 (55)
T ss_dssp HHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHHH
T ss_pred HHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHHH
Confidence 3444557888899984 567789999999999999876
No 11
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 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 []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=68.10 E-value=2.8 Score=26.72 Aligned_cols=39 Identities=13% Similarity=0.289 Sum_probs=31.0
Q ss_pred HHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhh
Q psy2245 40 LKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 40 LKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~ 78 (88)
+.++|.|++-.|+.-.+--+-=+|++|+++.|.++|..+
T Consensus 2 ~Q~iV~YLv~nPevl~kl~~g~asLIGv~~~e~~aIi~~ 40 (57)
T PF05952_consen 2 KQEIVNYLVQNPEVLEKLKEGEASLIGVDKDEQKAIIDA 40 (57)
T ss_pred hHHHHHHHHHChHHHHHHHcCCeeEecCCHHHHHHHHHH
Confidence 457788887788876666666689999999999998765
No 12
>PRK00465 rpmJ 50S ribosomal protein L36; Reviewed
Probab=66.01 E-value=2.4 Score=25.19 Aligned_cols=9 Identities=56% Similarity=1.394 Sum_probs=7.6
Q ss_pred ccccCCcch
Q psy2245 5 LVCTNPKHN 13 (88)
Q Consensus 5 ~~~~~~~~~ 13 (88)
++|+||+|.
T Consensus 25 Vic~nprhK 33 (37)
T PRK00465 25 VICENPKHK 33 (37)
T ss_pred EEcCCCCcc
Confidence 479999996
No 13
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=65.12 E-value=17 Score=20.66 Aligned_cols=51 Identities=18% Similarity=0.206 Sum_probs=39.1
Q ss_pred HHHHHhCCCCCChhhHHHHHHHHHHHHhc--CccchhhhHHHHHHHhCCCHHH
Q psy2245 21 YDALKDTKPPNDAEMTLQFLKSAIFYFLT--DPVNAQGHLTALLSILGYSDAQ 71 (88)
Q Consensus 21 ~~~~~~~k~~~D~EanLefLKnaIy~fLT--D~~~~q~hLtAI~sIL~FSp~E 71 (88)
+..+.++.+..+||--.+|++.+.=..-. |+.-++..++.+...+|.++++
T Consensus 6 ~~~l~~~~dl~~~egk~~~~~~~~~~i~~i~~~i~r~~y~~~la~~~~i~~~~ 58 (59)
T PF10410_consen 6 IERLSKGYDLDTPEGKAEAVREAAPLIAQIPDPIERELYIRELAERLGISEDA 58 (59)
T ss_dssp HHHHGGGS-TTSHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHCT-SSTT
T ss_pred HHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCcCccc
Confidence 45667778889999999999887644433 8888999999999999988753
No 14
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=61.27 E-value=26 Score=20.44 Aligned_cols=55 Identities=16% Similarity=0.179 Sum_probs=34.8
Q ss_pred HHHHHHhCCCCCChh--hHHHHHHHHHHHHhc-Cc-cchhhhHHHHHHHhCCCHHHHHH
Q psy2245 20 RYDALKDTKPPNDAE--MTLQFLKSAIFYFLT-DP-VNAQGHLTALLSILGYSDAQKEN 74 (88)
Q Consensus 20 r~~~~~~~k~~~D~E--anLefLKnaIy~fLT-D~-~~~q~hLtAI~sIL~FSp~Ek~~ 74 (88)
++.+++..++..-.+ ..+.+=++.|-++.+ +. .-....+.+|..+|+.+++|...
T Consensus 5 ~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~~~~~~~~ 63 (64)
T PF13560_consen 5 RLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGVPPDERAE 63 (64)
T ss_dssp HHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT--HHHHHC
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCcCHHHHcc
Confidence 344444444443333 456667788888888 44 36788999999999999999763
No 15
>PF02093 Gag_p30: Gag P30 core shell protein; InterPro: IPR003036 P30 is essential for viral assembly []. Cleavage of P70 in vitro can be accompanied by a shift from a concentrically coiled internal strand ("immature") to a collapsed ("mature") form of the virus core [].; GO: 0019068 virion assembly; PDB: 3BP9_U 1U7K_D 2Y4Z_A 1BM4_A.
Probab=57.68 E-value=20 Score=27.95 Aligned_cols=46 Identities=17% Similarity=0.294 Sum_probs=30.1
Q ss_pred CCChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 30 PNDAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 30 ~~D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
.-||++-..-|.++++-+--+=.++|+ ++.+| ||+|||..|+....
T Consensus 21 Se~P~~li~lle~i~~Th~pTWdDcqq----LL~~L-fT~EEr~rI~~~Ar 66 (211)
T PF02093_consen 21 SENPQALISLLESIFQTHQPTWDDCQQ----LLQTL-FTTEERERILQEAR 66 (211)
T ss_dssp TTSHHHHHHHHHHHHHHT---HHHHHH----HHHHH-S-HHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHhcCCCHHHHHH----HHHHH-cCHHHHHHHHHHHH
Confidence 468888888888887755433344455 44455 99999999987654
No 16
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=56.10 E-value=12 Score=24.92 Aligned_cols=25 Identities=24% Similarity=0.465 Sum_probs=19.2
Q ss_pred HHhcCccchhhhHHHHHHHhCCCHHHHHHHHh
Q psy2245 46 YFLTDPVNAQGHLTALLSILGYSDAQKENIMK 77 (88)
Q Consensus 46 ~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k 77 (88)
+|+.||+ |.+.=.+.|+||++.|+.
T Consensus 22 rF~~DPe-------a~~~~~gLt~eE~~aL~~ 46 (81)
T cd07922 22 RFQDDPS-------AVFEEYGLTPAERAALRE 46 (81)
T ss_pred HHHHCHH-------HHHHHcCCCHHHHHHHHc
Confidence 4555665 577778999999999965
No 17
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=53.02 E-value=14 Score=23.05 Aligned_cols=24 Identities=21% Similarity=0.322 Sum_probs=20.1
Q ss_pred hhhHHHHHHHhCCCHHHHHHHHhh
Q psy2245 55 QGHLTALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 55 q~hLtAI~sIL~FSp~Ek~~V~k~ 78 (88)
...+.++++-|||||.-|..+...
T Consensus 70 ~~~~~~l~~~lGLtP~sR~kl~~~ 93 (100)
T PF05119_consen 70 MKQMRSLASELGLTPASRAKLAVP 93 (100)
T ss_pred HHHHHHHHHHcCCCHHHHhhccCC
Confidence 456889999999999999987543
No 18
>PF07051 OCIA: Ovarian carcinoma immunoreactive antigen (OCIA); InterPro: IPR009764 This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown [,].
Probab=51.47 E-value=11 Score=26.79 Aligned_cols=26 Identities=4% Similarity=0.100 Sum_probs=21.2
Q ss_pred HHHHhCCCHHHHHHHHhhhhhccccc
Q psy2245 61 LLSILGYSDAQKENIMKTQAHAWKYS 86 (88)
Q Consensus 61 I~sIL~FSp~Ek~~V~k~~~~~Ww~~ 86 (88)
...-..|||||++.+..-+..+.||-
T Consensus 20 ~~~~~~~T~EE~kvlrEC~~ESFwyR 45 (111)
T PF07051_consen 20 PGMPYQLTEEERKVLRECNEESFWYR 45 (111)
T ss_pred CCcCccCCHHHHHHHHHHHHhhhHhc
Confidence 33456899999999999999888873
No 19
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=49.93 E-value=31 Score=21.93 Aligned_cols=41 Identities=20% Similarity=0.408 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhcC-ccchh-hhHHHHHHHhCCCHHHHHHHH
Q psy2245 36 TLQFLKSAIFYFLTD-PVNAQ-GHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 36 nLefLKnaIy~fLTD-~~~~q-~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
.|.-++..||.||.. +...+ =|+..|..-|+++..|...+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al 86 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKAL 86 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHH
Confidence 588899999999996 32222 489999999999998865544
No 20
>PF11940 DUF3458: Domain of unknown function (DUF3458); InterPro: IPR024601 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain, which contains a conserved FSAPV sequence motif, is found in the C-terminal of alanyl aminopeptidases that belong to MEROPS peptidase family M1 (aminopeptidase N, clan MA). ; PDB: 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A 3PUU_A 3B37_A 3B2P_A 3B3B_A ....
Probab=49.04 E-value=68 Score=26.05 Aligned_cols=69 Identities=22% Similarity=0.308 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHhCCCCCChh-hHHHHHHHHHHHHhc--Ccc--------------chhhhHHHHHHHhCCCHHHHHHHH
Q psy2245 14 LIRHKRRYDALKDTKPPNDAE-MTLQFLKSAIFYFLT--DPV--------------NAQGHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 14 ~~~~~~r~~~~~~~k~~~D~E-anLefLKnaIy~fLT--D~~--------------~~q~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
+..+|.++. ..+....|+| +.-+=|||+++.||+ |.. |=..-+.|+..+.+-+..+|..++
T Consensus 195 l~~~y~~~~--~~~~y~~~~~~~g~RaLkn~~L~yL~~~~~~~~~~la~~qy~~A~nMTD~laAL~~l~~~~~~~r~~~L 272 (367)
T PF11940_consen 195 LLALYQALA--ATGPYSPDAEAAGRRALKNLCLSYLAAADDPEAAELAQEQYKSADNMTDRLAALSALVNSDSPEREEAL 272 (367)
T ss_dssp HHHHHHHTH--HTTTTT-SHHHHHHHHHHHHHHHHHHHCTCTHHHHHHHHHHHHSSSHHHHHHHHHHHCCTTSTTHHHHH
T ss_pred HHHHHHHcc--cCCCCCCCHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHhCCChhHHHHHHHHHHhCCCHHHHHHH
Confidence 445555552 2345556776 889999999999999 332 334557788888888888998888
Q ss_pred hhhhhccc
Q psy2245 77 KTQAHAWK 84 (88)
Q Consensus 77 k~~~~~Ww 84 (88)
..=...|.
T Consensus 273 ~~Fy~~w~ 280 (367)
T PF11940_consen 273 EDFYERWK 280 (367)
T ss_dssp HHHHHHHT
T ss_pred HHHHHHHc
Confidence 76666664
No 21
>PF00444 Ribosomal_L36: Ribosomal protein L36; InterPro: IPR000473 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 [, ]. Ribosomal protein L36 is the smallest protein from the large subunit of the prokaryotic ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [] can be grouped into: bacterial L36; algal and plant chloroplast L36; Cyanelle L36. L36 is a small basic and cysteine-rich protein of 37 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_6 2HGU_8 2HGJ_8 1DGZ_A 1DFE_A 2HGQ_8 1VSP_b 1VSA_b 3PIP_4 1VOU_6 ....
Probab=45.31 E-value=7.6 Score=22.98 Aligned_cols=9 Identities=44% Similarity=1.383 Sum_probs=7.4
Q ss_pred ccc-cCCcch
Q psy2245 5 LVC-TNPKHN 13 (88)
Q Consensus 5 ~~~-~~~~~~ 13 (88)
++| +||+|.
T Consensus 25 Vick~nprhK 34 (38)
T PF00444_consen 25 VICKKNPRHK 34 (38)
T ss_dssp EEESSSGGGC
T ss_pred EECCCCCchh
Confidence 578 999996
No 22
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=44.44 E-value=45 Score=23.49 Aligned_cols=39 Identities=15% Similarity=0.286 Sum_probs=28.7
Q ss_pred HHHHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHh
Q psy2245 39 FLKSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMK 77 (88)
Q Consensus 39 fLKnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k 77 (88)
|--|-+..=|.|+++++.-+ .|.+.=-+.|+|||++|+.
T Consensus 14 y~LN~f~~sL~~a~~Re~F~aD~eAy~~~~gLTeEe~~AV~~ 55 (106)
T cd07921 14 YALNKMCMSLNKAENREAFKADEEAYCDKFGLTEEQKQAVLD 55 (106)
T ss_pred hhHHHHHHHHCCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHh
Confidence 44455555566888777665 4778888999999999975
No 23
>TIGR01022 rpmJ_bact ribosomal protein L36, bacterial type. Proteins found by this model occur exclusively in bacteria and organelles.
Probab=41.33 E-value=11 Score=22.46 Aligned_cols=9 Identities=56% Similarity=1.401 Sum_probs=7.6
Q ss_pred ccccCCcch
Q psy2245 5 LVCTNPKHN 13 (88)
Q Consensus 5 ~~~~~~~~~ 13 (88)
++|.||+|.
T Consensus 25 Vick~prhK 33 (37)
T TIGR01022 25 VICKNPKHK 33 (37)
T ss_pred EEeCCCCcc
Confidence 579999996
No 24
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=39.54 E-value=36 Score=22.49 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=20.1
Q ss_pred hhhhHHHHHHHhCCCHHHHHHHH
Q psy2245 54 AQGHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 54 ~q~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
....+.++.+-||+||.-|..+.
T Consensus 78 a~~~~~~l~~elGLtP~sR~kl~ 100 (116)
T TIGR01558 78 AFKQLRSIGSALGLTPSSRSRLV 100 (116)
T ss_pred HHHHHHHHHHHcCCCHHHHHHhc
Confidence 36678899999999999999986
No 25
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=39.31 E-value=51 Score=22.76 Aligned_cols=32 Identities=22% Similarity=0.373 Sum_probs=22.2
Q ss_pred HhcCccchhhhH---HHHHHHhCCCHHHHHHHHhh
Q psy2245 47 FLTDPVNAQGHL---TALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 47 fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k~ 78 (88)
=|.|+++++.-+ .|.+.=-+.|||||+.|+.-
T Consensus 14 sL~~a~~RerF~~D~ea~~~e~gLt~Ee~~av~~r 48 (94)
T cd07923 14 RLIEPAHRERFLEDPEALFDEAGLTEEERTLIRNR 48 (94)
T ss_pred HHCCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHcc
Confidence 344666665544 36777779999999999653
No 26
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=38.75 E-value=18 Score=24.18 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=17.3
Q ss_pred cCccchhhhH---HHHHHHhCCCHHHHHHHHh
Q psy2245 49 TDPVNAQGHL---TALLSILGYSDAQKENIMK 77 (88)
Q Consensus 49 TD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k 77 (88)
.||++++.-+ .|.+.=.+.|+|||+.|..
T Consensus 9 ~~~~~r~~F~~D~~a~~~~~~Lt~eer~av~~ 40 (88)
T PF07746_consen 9 NDPENRERFLADPEAYLDEYGLTEEERQAVLD 40 (88)
T ss_dssp GSHHHHHHHHH-HHHHHHCCT--HHHHHHHHC
T ss_pred cCHHHHHHHHHCHHHHHHHcCCCHHHHHHHHc
Confidence 4454444433 2566677899999999854
No 27
>KOG1567|consensus
Probab=38.45 E-value=64 Score=27.12 Aligned_cols=58 Identities=17% Similarity=0.295 Sum_probs=43.0
Q ss_pred CcccccCCcchHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHhc-----CccchhhhHHHHHHH
Q psy2245 3 SGLVCTNPKHNLIRHKRRYDALKDTKPPNDAEMTLQFLKSAIFYFLT-----DPVNAQGHLTALLSI 64 (88)
Q Consensus 3 ~~~~~~~~~~~~~~~~~r~~~~~~~k~~~D~EanLefLKnaIy~fLT-----D~~~~q~hLtAI~sI 64 (88)
.|+||- ||+.-+.--.+.-.-|..-+-.+++|=.-|-.|-.|. ||.-++-..+||.||
T Consensus 93 dGivne----nl~Erfs~evqv~ear~fygfqIaiENIHSEmYSlLidtyIrD~ker~~LFnAI~t~ 155 (344)
T KOG1567|consen 93 DGIVNE----NLVERFSQEVQVPEARCFYGFQIAIENIHSEMYSLLIDTYIRDPKEREFLFNAIETI 155 (344)
T ss_pred ccchhH----HHHHHHHHHhhcccccchhhhHHHHHHHHHHHHHHHHHHHhcChhhhhHHHHHHHhh
Confidence 477775 4555444444444456666777899999999998887 888789999999998
No 28
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=35.91 E-value=2e+02 Score=22.67 Aligned_cols=29 Identities=7% Similarity=0.124 Sum_probs=22.7
Q ss_pred cchhhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 52 VNAQGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 52 ~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
.|+.-+...|...||.|+++...+++...
T Consensus 229 lgr~pt~~EiA~~l~~~~~~v~~~~~~~~ 257 (367)
T PRK09210 229 LGREPTPEEIAEEMDMPPEKVREILKIAQ 257 (367)
T ss_pred hCCCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence 34556677889999999999999887643
No 29
>KOG0161|consensus
Probab=35.89 E-value=39 Score=33.62 Aligned_cols=27 Identities=22% Similarity=0.404 Sum_probs=22.0
Q ss_pred hhhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 54 AQGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 54 ~q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
.-+.+.+.+.|||||++|+..|.+.-+
T Consensus 321 ef~~t~~a~~ilgfs~~E~~~~~~i~s 347 (1930)
T KOG0161|consen 321 EFQETDEAMDILGFSEEEKISIFRIVS 347 (1930)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 456677888999999999999877654
No 30
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=35.76 E-value=96 Score=19.56 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=26.6
Q ss_pred HHHHHHhcC---ccchhhhHHHHHHHhCCCHHHHHHHH
Q psy2245 42 SAIFYFLTD---PVNAQGHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 42 naIy~fLTD---~~~~q~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
..|...|-| +..+.+-..+|...+++|++|+..-.
T Consensus 7 ~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~ 44 (92)
T PF14338_consen 7 PPILEALKDLGGSASRKEIYERVAERFGLSDEERNERL 44 (92)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHc
Confidence 345555554 56678889999999999999988653
No 31
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=35.68 E-value=55 Score=19.52 Aligned_cols=27 Identities=15% Similarity=0.196 Sum_probs=22.3
Q ss_pred chhhhHHHHHHHhCCCHHHHHHHHhhh
Q psy2245 53 NAQGHLTALLSILGYSDAQKENIMKTQ 79 (88)
Q Consensus 53 ~~q~hLtAI~sIL~FSp~Ek~~V~k~~ 79 (88)
|.--|+.-|..--.+|++||..|++.-
T Consensus 19 GC~RT~dEI~~W~~~s~~er~~i~~~l 45 (51)
T PF06945_consen 19 GCGRTLDEIRDWKSMSDDERRAILARL 45 (51)
T ss_pred CCCCcHHHHHHHhhCCHHHHHHHHHHH
Confidence 455678889999999999999998753
No 32
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.77 E-value=84 Score=21.22 Aligned_cols=36 Identities=17% Similarity=0.211 Sum_probs=21.9
Q ss_pred CCCCCChh----hHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHH
Q psy2245 27 TKPPNDAE----MTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 27 ~k~~~D~E----anLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
|.++.||| ++-+=|.+ ||.+..-+ =+|||-|-++|-
T Consensus 24 N~gvl~~e~~d~~~~edLtd-iy~mvkkk-------------enfSpsEmqaiA 63 (71)
T COG4840 24 NVGVLDPEKYDNANYEDLTD-IYDMVKKK-------------ENFSPSEMQAIA 63 (71)
T ss_pred hhhccCHHhcccccHHHHHH-HHHHHHHh-------------ccCCHHHHHHHH
Confidence 67788887 33333332 34444333 369999999884
No 33
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=34.64 E-value=91 Score=22.08 Aligned_cols=39 Identities=18% Similarity=0.352 Sum_probs=30.4
Q ss_pred HHHHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHh
Q psy2245 39 FLKSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMK 77 (88)
Q Consensus 39 fLKnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k 77 (88)
|--|-+.+=|.++++|+.-+ .|.+.=.+.|+|||++|..
T Consensus 14 y~LN~fc~sl~~~~nRe~F~aD~~Ay~~~~~Lteeqr~av~~ 55 (106)
T cd07925 14 YALNKMCFSFNDAANREAFLADEEAYCEKFGLTPEQKQAVRN 55 (106)
T ss_pred hHHHHHHHHHCCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHH
Confidence 55566667777888887766 4778888999999999964
No 34
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=34.30 E-value=1.3e+02 Score=20.05 Aligned_cols=52 Identities=15% Similarity=0.090 Sum_probs=22.1
Q ss_pred HHHHHHHhCCCCCChh--hHHHHHHHHHHHHhcCc-cchhhhHHHHHHHhCCCHH
Q psy2245 19 RRYDALKDTKPPNDAE--MTLQFLKSAIFYFLTDP-VNAQGHLTALLSILGYSDA 70 (88)
Q Consensus 19 ~r~~~~~~~k~~~D~E--anLefLKnaIy~fLTD~-~~~q~hLtAI~sIL~FSp~ 70 (88)
.|+.++++.++....+ ..+..=.+.|..+.... .-....|.+|..+||.|+.
T Consensus 8 ~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~ 62 (135)
T PRK09706 8 QRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPT 62 (135)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence 4455555544444333 12222234444444421 2233445555555555544
No 35
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=33.92 E-value=85 Score=17.19 Aligned_cols=48 Identities=19% Similarity=0.124 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHH-HHhhhhhc
Q psy2245 35 MTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKEN-IMKTQAHA 82 (88)
Q Consensus 35 anLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~-V~k~~~~~ 82 (88)
...+++++.+....-.+...-...+.|...++.|++.-.. +.++...+
T Consensus 5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G 53 (66)
T cd07377 5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEG 53 (66)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4456666666655332222233578899999999887444 44444333
No 36
>PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A ....
Probab=33.80 E-value=27 Score=24.85 Aligned_cols=62 Identities=13% Similarity=0.213 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhCCCCCChhhHHHHHH--HHHHHHhcCccchhhhHHHHHHHh--CCCHHHHHHHHhh
Q psy2245 16 RHKRRYDALKDTKPPNDAEMTLQFLK--SAIFYFLTDPVNAQGHLTALLSIL--GYSDAQKENIMKT 78 (88)
Q Consensus 16 ~~~~r~~~~~~~k~~~D~EanLefLK--naIy~fLTD~~~~q~hLtAI~sIL--~FSp~Ek~~V~k~ 78 (88)
...+.+.++-+.....-++.+|.|+- ..+---+.-.+ .-+||...+.++ .+|++|.+.|++.
T Consensus 216 ~~~~~l~~~a~~~g~s~~q~al~~~l~~~~~~~~i~g~~-~~~~l~en~~a~~~~L~~~~~~~i~~~ 281 (283)
T PF00248_consen 216 ELADALRELAEEHGVSPAQLALRWVLSHPGVASVIVGAS-SPEHLEENLAALDFPLTEEELAEIDQI 281 (283)
T ss_dssp GGHHHHHHHHHHHTSSHHHHHHHHHHTSHTTEEEEEB-S-SHHHHHHHHGGSSSG--HHHHHHHHTT
T ss_pred hhhhhhhhhhhhcccccchhhhhhhhhccccccccCCCC-CHHHHHHHHHHhCCCCCHHHHHHHHhh
Confidence 44455666655566666778999987 44443343444 467788777776 7899999988764
No 37
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=33.60 E-value=43 Score=19.29 Aligned_cols=22 Identities=36% Similarity=0.521 Sum_probs=13.8
Q ss_pred hhHHHHHHHhCCCHHHHHHHHhh
Q psy2245 56 GHLTALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 56 ~hLtAI~sIL~FSp~Ek~~V~k~ 78 (88)
+-+.|+ .-||||++|-..+.+.
T Consensus 5 d~~~AL-~~LGy~~~e~~~av~~ 26 (47)
T PF07499_consen 5 DALEAL-ISLGYSKAEAQKAVSK 26 (47)
T ss_dssp HHHHHH-HHTTS-HHHHHHHHHH
T ss_pred HHHHHH-HHcCCCHHHHHHHHHH
Confidence 334444 4599999998776553
No 38
>PRK00831 rpmJ 50S ribosomal protein L36; Validated
Probab=32.94 E-value=18 Score=21.99 Aligned_cols=9 Identities=22% Similarity=0.667 Sum_probs=7.1
Q ss_pred ccc-cCCcch
Q psy2245 5 LVC-TNPKHN 13 (88)
Q Consensus 5 ~~~-~~~~~~ 13 (88)
++| +||+|.
T Consensus 28 Vick~nprhK 37 (41)
T PRK00831 28 VINKKNPRFK 37 (41)
T ss_pred EEcCCCCccc
Confidence 478 599985
No 39
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=32.49 E-value=1.1e+02 Score=19.52 Aligned_cols=34 Identities=21% Similarity=0.128 Sum_probs=19.9
Q ss_pred HHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHH
Q psy2245 40 LKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKE 73 (88)
Q Consensus 40 LKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~ 73 (88)
=++.|-+|..+...-...+..++.+|+.+|+...
T Consensus 91 ~~~tis~~e~g~~~p~~~~~~l~~~l~~~p~~l~ 124 (127)
T TIGR03830 91 GVNAFSRYERGEVRPSKALDKLLRLLDKHPELLE 124 (127)
T ss_pred CHHHHHHHHCCCCCCCHHHHHHHHHHHHChHHHH
Confidence 4566667766444223345666677777776554
No 40
>COG3313 Predicted Fe-S protein [General function prediction only]
Probab=32.19 E-value=60 Score=21.81 Aligned_cols=26 Identities=8% Similarity=0.217 Sum_probs=21.5
Q ss_pred chhhhHHHHHHHhCCCHHHHHHHHhh
Q psy2245 53 NAQGHLTALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 53 ~~q~hLtAI~sIL~FSp~Ek~~V~k~ 78 (88)
|..-++.-|..-...|+.||.+|++.
T Consensus 24 GC~Rt~~Ei~~W~~msd~Er~aVl~~ 49 (74)
T COG3313 24 GCGRTRDEIFNWSSMSDDERRAVLRL 49 (74)
T ss_pred cccccHHHHHHHhhCCHHHHHHHHHH
Confidence 45567778888899999999999875
No 41
>cd07650 F-BAR_Syp1p_like The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of yeast Syp1 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Syp1p is associated with septins, a family of GTP-binding proteins that serve as elements of septin filaments, which are required for cell morphogenesis and division. Syp1p regulates cell-cycle dependent septin cytoskeletal dynamics in yeast. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCH domain Only (FCHO) proteins and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=31.97 E-value=65 Score=23.87 Aligned_cols=36 Identities=19% Similarity=0.328 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhc---Cc--cchhhhHHHHHHHhCCCHHH
Q psy2245 36 TLQFLKSAIFYFLT---DP--VNAQGHLTALLSILGYSDAQ 71 (88)
Q Consensus 36 nLefLKnaIy~fLT---D~--~~~q~hLtAI~sIL~FSp~E 71 (88)
=|.|||+++..|-| |. ...+.+=.-..++++|+|++
T Consensus 173 Rl~~lk~~l~~y~~~~sd~~~~~~~~~E~~~~~l~~~~~e~ 213 (228)
T cd07650 173 RLNHLKDVLLQFQTHESDYALRTTESAEECMNQLLEFDTED 213 (228)
T ss_pred HHHHHHHHHHHHHhHhhHHHHHhhHHHHHHHHHHhCCChHH
Confidence 47899999999998 32 12234445567788999875
No 42
>PF09252 Feld-I_B: Allergen Fel d I-B chain; InterPro: IPR015332 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans. The nomenclature system uses the first three letters of the genus, followed by the first letter of the species name, followed by a number (additional letters can be added to the name as required to discriminate between similar designations). Fel d 1 is allergen 1 from Felis silvestris catus (Cat), which is an important agent in human allergic reactions []. The protein is expressed in saliva and sebaceous glands. The complete primary structure of Fel d 1 has been determined []. The allergen is tetrameric glycoprotein consisting of two disulphide-linked heterodimers of chains 1 and 2, which have been shown to be encoded by different genes. Fel d 1 chains 1 and 2 share structural similarity with uteroglobin, a secretoglobin superfamily member; chain 2 is a glycoprotein with N-linked oligosaccharides. This entry represents Fel d 1 chain 2.; GO: 0005615 extracellular space; PDB: 1ZKR_B 1PUO_B 2EJN_B.
Probab=30.98 E-value=76 Score=20.96 Aligned_cols=29 Identities=28% Similarity=0.274 Sum_probs=23.0
Q ss_pred cchhhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 52 VNAQGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 52 ~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
.|+..-|++-++-.+=|++||.+..|.|.
T Consensus 13 ~g~k~~L~~~L~~~naT~~E~~AfeKIQd 41 (67)
T PF09252_consen 13 SGSKTWLNHELSKFNATDEEKEAFEKIQD 41 (67)
T ss_dssp TT-HHHHHHHHHHTT--HHHHHHHHHHHH
T ss_pred hcchhHHHHHHHHhcCChHHHHHHHHHHH
Confidence 45677899999999999999999999885
No 43
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=30.67 E-value=1.6e+02 Score=20.37 Aligned_cols=57 Identities=19% Similarity=0.187 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhCCCCCChhhH--HHHHHHHHHHHhcC-ccchhhhHHHHHHHhCCCHHHH
Q psy2245 16 RHKRRYDALKDTKPPNDAEMT--LQFLKSAIFYFLTD-PVNAQGHLTALLSILGYSDAQK 72 (88)
Q Consensus 16 ~~~~r~~~~~~~k~~~D~Ean--LefLKnaIy~fLTD-~~~~q~hLtAI~sIL~FSp~Ek 72 (88)
.+-.|+.+++++++....|.+ +.-=++.|-.+... ..-...+|.+|...|+.++.+-
T Consensus 7 ~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l 66 (185)
T PRK09943 7 APGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEF 66 (185)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHH
Confidence 456788888888887766632 22346667777763 3445789999999999998764
No 44
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=30.49 E-value=36 Score=20.91 Aligned_cols=14 Identities=43% Similarity=0.721 Sum_probs=11.7
Q ss_pred HHHHHHHHhcCccc
Q psy2245 40 LKSAIFYFLTDPVN 53 (88)
Q Consensus 40 LKnaIy~fLTD~~~ 53 (88)
-+++|-.||.||.+
T Consensus 33 Sr~~Ir~yl~dP~~ 46 (50)
T PF11427_consen 33 SRTCIRRYLKDPVN 46 (50)
T ss_dssp -HHHHHHHHHSCCC
T ss_pred cHHHHHHHhcChhh
Confidence 47899999999986
No 45
>TIGR02414 pepN_proteo aminopeptidase N, Escherichia coli type. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile. This family consists of all aminopeptidases closely related to E. coli PepN and presumed to have similar (not identical) function. Nearly all are found in Proteobacteria, but members are found also in Cyanobacteria, plants, and apicomplexan parasites. This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (TIGR02412), from the membrane bound aminopeptidase N family in animals, etc.
Probab=29.73 E-value=1.7e+02 Score=26.39 Aligned_cols=54 Identities=22% Similarity=0.389 Sum_probs=39.6
Q ss_pred CChh-hHHHHHHHHHHHHhc--C-cc-------------chhhhHHHHHHHhCCCHHHHHHHHhhhhhccc
Q psy2245 31 NDAE-MTLQFLKSAIFYFLT--D-PV-------------NAQGHLTALLSILGYSDAQKENIMKTQAHAWK 84 (88)
Q Consensus 31 ~D~E-anLefLKnaIy~fLT--D-~~-------------~~q~hLtAI~sIL~FSp~Ek~~V~k~~~~~Ww 84 (88)
.|++ +..+=|||+.+.||. | ++ |-.+.+.|+-.+++.+..||..++..=...|.
T Consensus 664 ~~~~~~~~R~l~n~~l~~l~~~~~~~~~~~~~~~~~~a~~mtd~~~al~~l~~~~~~~~~~~l~~f~~~~~ 734 (863)
T TIGR02414 664 VDPAAAGRRALRNACLSYLSAADDAEIRNLALEQFKSADNMTDRLAALSALVHFESDFRERALAAFYQKWK 734 (863)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHhCCCHHHHHHHHHHHhcCCChhHHHHHHHHHHHHC
Confidence 5555 788999999999997 3 22 22345778888888777889887776666674
No 46
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=29.57 E-value=1.5e+02 Score=23.45 Aligned_cols=77 Identities=9% Similarity=0.068 Sum_probs=48.5
Q ss_pred CcccccCCcchHHHHHHHHHHHHhCC-------C-CCChhhHHHHHHHHHHHHhc---CccchhhhHHHHHHHhCCCHHH
Q psy2245 3 SGLVCTNPKHNLIRHKRRYDALKDTK-------P-PNDAEMTLQFLKSAIFYFLT---DPVNAQGHLTALLSILGYSDAQ 71 (88)
Q Consensus 3 ~~~~~~~~~~~~~~~~~r~~~~~~~k-------~-~~D~EanLefLKnaIy~fLT---D~~~~q~hLtAI~sIL~FSp~E 71 (88)
+|+|.++.=..+.+.|..+......+ + ..|.+++++|+++-+..|-. ...|+.=+-.++.....-+.+.
T Consensus 95 d~vv~~~tCD~~k~l~~~~~~~~~~~~~~~ldlP~~~~~~~~~~Y~~~el~~l~~~LE~~~G~~it~e~L~~aI~~~N~~ 174 (380)
T TIGR02263 95 DGMLFPSICDVIRNLSGMWKLMFPGKGARYFDLPHNFDDDLGGEFYTAELNELCEGLEHLSGKKITDDAIRASIAVFNDN 174 (380)
T ss_pred cEEEEeccchhHHHHHHHHHHhCCCCcEEEEeCCCCCCcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 34555555555666666555444322 2 24778889999999877654 5555555666666666777777
Q ss_pred HHHHHhhh
Q psy2245 72 KENIMKTQ 79 (88)
Q Consensus 72 k~~V~k~~ 79 (88)
|+...+..
T Consensus 175 R~~~~~l~ 182 (380)
T TIGR02263 175 RKLIQALY 182 (380)
T ss_pred HHHHHHHH
Confidence 77776643
No 47
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB []. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 2HAJ_A 1T3W_B.
Probab=29.27 E-value=1.6e+02 Score=18.98 Aligned_cols=44 Identities=16% Similarity=0.193 Sum_probs=27.5
Q ss_pred ChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhC---CCHHHHHHHHh
Q psy2245 32 DAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILG---YSDAQKENIMK 77 (88)
Q Consensus 32 D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~---FSp~Ek~~V~k 77 (88)
|++..-+++.+++-++.-.. ..+.+..+.+-.. .|++||+...+
T Consensus 79 ~~~~~~~ef~d~l~~L~~~~--~~~~i~~L~~k~~~~~Lt~eEk~el~~ 125 (127)
T PF08278_consen 79 DEEDIEQEFQDALARLQEQA--LERRIEELKAKPRRGGLTDEEKQELRR 125 (127)
T ss_dssp HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHTTT---HHHHHHHHH
T ss_pred CchhHHHHHHHHHHHHHHHH--HHHHHHHHHHhhccCCcCHHHHHHHHH
Confidence 66666666677766665543 3556666666666 89999887654
No 48
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=29.02 E-value=73 Score=21.38 Aligned_cols=24 Identities=17% Similarity=0.307 Sum_probs=21.9
Q ss_pred hHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 57 HLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 57 hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
.+.||..-.|+|+.|.-.+||...
T Consensus 15 pFeaI~~~fGL~E~eVi~lMR~~l 38 (72)
T TIGR03643 15 PFEAIEQQFGLSEKEVIKLMRQNL 38 (72)
T ss_pred CHHHHHHHHCCCHHHHHHHHHhhc
Confidence 478999999999999999999876
No 49
>PF00636 Ribonuclease_3: Ribonuclease III domain; InterPro: IPR000999 Prokaryotic ribonuclease III (3.1.26.3 from EC) (gene rnc) [] is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs. RNase III is evolutionary related to a number of proteins including []: Saccharomyces cerevisiae (Baker's yeast) protein pac1, a ribonuclease that probably inhibits mating and meiosis by degrading a specific mRNA required for sexual development yeast ribonuclease III (gene RNT1), a dsRNA-specific nuclease that cleaves eukaryotic preribosomal RNA at various sites Caenorhabditis elegans hypothetical protein F26E4.13 Paramecium bursaria Chlorella virus 1 (PBCV-1) 1 protein A464R Synechocystis sp. (strain PCC 6803) hypothetical protein slr0346 yeast hypothetical protein SpAC8A4.08c, a protein with a N-terminal helicase domain and a C-terminal RNase III domain C. elegans hypothetical protein K12H4.8, a protein with the same structure as SpAC8A4.08c ; GO: 0003723 RNA binding, 0004525 ribonuclease III activity, 0006396 RNA processing; PDB: 2GSL_A 2NUE_B 1YYO_A 2NUF_A 1YZ9_A 1JFZ_A 1YYW_C 1RC5_B 1YYK_B 1RC7_A ....
Probab=28.41 E-value=1.2e+02 Score=18.98 Aligned_cols=30 Identities=40% Similarity=0.549 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHhc-------CccchhhhHHHHHHHh
Q psy2245 36 TLQFLKSAIFYFLT-------DPVNAQGHLTALLSIL 65 (88)
Q Consensus 36 nLefLKnaIy~fLT-------D~~~~q~hLtAI~sIL 65 (88)
-||||=++|..|++ -|.-..+.|+.+-+.+
T Consensus 2 rLefLGDavL~~~v~~~l~~~~p~~~~~~L~~~r~~~ 38 (114)
T PF00636_consen 2 RLEFLGDAVLKLLVSEYLFEKYPNLNEGQLTKLRSAL 38 (114)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTTSSHHHHHHHHHHH
T ss_pred cHhHhHHHHHHHHHHHHHHHHCCCCChhHHHHHHHHH
Confidence 47888888877766 2444456666554443
No 50
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=28.18 E-value=46 Score=20.20 Aligned_cols=8 Identities=25% Similarity=0.779 Sum_probs=3.9
Q ss_pred hhcccccc
Q psy2245 80 AHAWKYSY 87 (88)
Q Consensus 80 ~~~Ww~~~ 87 (88)
+.+|||-|
T Consensus 38 ~rgWwYe~ 45 (45)
T PF12123_consen 38 ERGWWYEV 45 (45)
T ss_dssp HTT--EEE
T ss_pred hcCcEEeC
Confidence 46899964
No 51
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=28.07 E-value=96 Score=25.64 Aligned_cols=35 Identities=23% Similarity=0.260 Sum_probs=27.1
Q ss_pred HHHHHHhcCccchhhhHHHHHHHhC------CCHHHHHHHH
Q psy2245 42 SAIFYFLTDPVNAQGHLTALLSILG------YSDAQKENIM 76 (88)
Q Consensus 42 naIy~fLTD~~~~q~hLtAI~sIL~------FSp~Ek~~V~ 76 (88)
+++|.||.||+.....=..|.+||. .+|.+|..+.
T Consensus 243 ~aF~~~L~d~~~~~~l~~~l~~Vl~~~~~~~L~~~~r~~Lr 283 (478)
T PF11855_consen 243 RAFWDFLLDPERQAELDELLDQVLARPFARDLDPDQRRFLR 283 (478)
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHcCcccccCCHHHHHHHH
Confidence 5799999999987777777888886 6677775443
No 52
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=27.38 E-value=28 Score=19.81 Aligned_cols=15 Identities=7% Similarity=0.093 Sum_probs=4.0
Q ss_pred CCCHHHHHHHHhhhh
Q psy2245 66 GYSDAQKENIMKTQA 80 (88)
Q Consensus 66 ~FSp~Ek~~V~k~~~ 80 (88)
++|++||..|.....
T Consensus 4 ~Lt~~eR~~I~~l~~ 18 (44)
T PF13936_consen 4 HLTPEERNQIEALLE 18 (44)
T ss_dssp --------HHHHHHC
T ss_pred chhhhHHHHHHHHHH
Confidence 467777777765543
No 53
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=27.32 E-value=62 Score=28.20 Aligned_cols=25 Identities=24% Similarity=0.502 Sum_probs=20.5
Q ss_pred hhHHHHHHHhCC---CHHHHHHHHhhhh
Q psy2245 56 GHLTALLSILGY---SDAQKENIMKTQA 80 (88)
Q Consensus 56 ~hLtAI~sIL~F---Sp~Ek~~V~k~~~ 80 (88)
.-|.-|.+|||| |+|.|..|.||+.
T Consensus 374 keLqDIIaILGmdELseedk~~V~rArk 401 (468)
T COG0055 374 KELQDIIAILGMDELSEEDKLTVARARK 401 (468)
T ss_pred HHHHHHHHHhCchhcChhHHHHHHHHHH
Confidence 346778888875 8999999999876
No 54
>PF04802 SMK-1: Component of IIS longevity pathway SMK-1; InterPro: IPR006887 This is a conserved region which characterises a number of eukaryotic proteins of unknown function.
Probab=27.22 E-value=61 Score=24.18 Aligned_cols=40 Identities=23% Similarity=0.413 Sum_probs=26.9
Q ss_pred CCCChhh--------HHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHH
Q psy2245 29 PPNDAEM--------TLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQK 72 (88)
Q Consensus 29 ~~~D~Ea--------nLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek 72 (88)
++.||+. -|+|||++|.-=.- -+++++.|-|+..|+..|-
T Consensus 89 pi~~~~l~~kIhqtyRlqYLkDvvL~r~l----Dd~~~s~L~s~I~~n~~~I 136 (193)
T PF04802_consen 89 PIPDPELLSKIHQTYRLQYLKDVVLPRFL----DDNTFSTLNSLIFFNQVEI 136 (193)
T ss_pred ecCCHHHHHHHHHHHhHHHHHHHHccccc----ccHHHHHHHHHHHHhHHHH
Confidence 4556763 68999999986222 2556777777777766554
No 55
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=26.17 E-value=1.2e+02 Score=21.98 Aligned_cols=47 Identities=19% Similarity=0.182 Sum_probs=32.5
Q ss_pred CChhhHH-HHHHHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHh
Q psy2245 31 NDAEMTL-QFLKSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMK 77 (88)
Q Consensus 31 ~D~EanL-efLKnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k 77 (88)
-|.|.+. -|=-|-+..=|.++++|+.-+ .|.+.=.+.|+|||++|..
T Consensus 13 Fd~~~srkgy~LN~fc~sl~~~~nRerF~ade~Ay~~~~~Lteeqr~aV~~ 63 (121)
T cd07924 13 FDAERARKGYHLNQFCMSLMKAENRERFKADERAYLDKWPMTEEQKQAVLA 63 (121)
T ss_pred cCHHHHHHHHHHHHHHHHhCCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHH
Confidence 3444332 244466666677888877666 4777888999999999964
No 56
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=26.17 E-value=1.2e+02 Score=21.96 Aligned_cols=40 Identities=20% Similarity=0.278 Sum_probs=29.7
Q ss_pred HHHHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHhh
Q psy2245 39 FLKSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 39 fLKnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k~ 78 (88)
|=-|-+..=|.++++|+.-+ .|.+.=-+.|+|||+.|..-
T Consensus 26 y~LN~fc~sl~~~~~RerF~aDe~ay~~~~~Lt~eqk~aV~~R 68 (119)
T PRK13379 26 LRLNRFFWHMIRAPWRDRFLQDAEALMQEAGLTEQEKELIRAR 68 (119)
T ss_pred HHHHHHHHHHccHHHHHHHHhCHHHHHHHcCCCHHHHHHHHhc
Confidence 44455666677888877665 47788889999999999653
No 57
>KOG4369|consensus
Probab=25.98 E-value=34 Score=34.04 Aligned_cols=25 Identities=20% Similarity=0.319 Sum_probs=19.0
Q ss_pred hcCccc--hhhhHHHHHHHhCCCHHHH
Q psy2245 48 LTDPVN--AQGHLTALLSILGYSDAQK 72 (88)
Q Consensus 48 LTD~~~--~q~hLtAI~sIL~FSp~Ek 72 (88)
+||.|- -++||+||+++++||+|.-
T Consensus 418 ~~e~e~~~ikk~~~~~~s~~~ft~e~~ 444 (2131)
T KOG4369|consen 418 STETETAEIKKVLRAIESVYGFTSEPP 444 (2131)
T ss_pred cchhhHHHHHHHHhhhHhhcCCCCCch
Confidence 445432 4789999999999998753
No 58
>KOG2050|consensus
Probab=25.88 E-value=2.9e+02 Score=25.22 Aligned_cols=41 Identities=17% Similarity=0.195 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhh
Q psy2245 35 MTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 35 anLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~ 78 (88)
.-|+-|+..|++|+--+.|.+ -|+..|-+=||.||+.|.|+
T Consensus 341 e~l~ll~elv~e~vHT~dGS~---vAm~li~~a~aKeRK~IiK~ 381 (652)
T KOG2050|consen 341 ELLELLKELVPEMVHTRDGSR---VAMKLIWHATAKERKLIIKN 381 (652)
T ss_pred HHHHHHHHHHHHHhcCCchHH---HHHHHHhhCCHHHHHHHHHH
Confidence 445667888999988776654 58889999999999999876
No 59
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=25.85 E-value=1.2e+02 Score=21.85 Aligned_cols=39 Identities=18% Similarity=0.201 Sum_probs=29.3
Q ss_pred HHHHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHh
Q psy2245 39 FLKSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMK 77 (88)
Q Consensus 39 fLKnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k 77 (88)
|=-|-+..=|.+++||+.-+ .|-+.=-+.|+|||+.|..
T Consensus 19 y~LN~fc~sl~~~~nRerF~ade~Ay~d~~~Lt~eqk~av~~ 60 (117)
T TIGR02792 19 YNLNQFCMSLMKAENRERFKADESAYLDEWNLTPAQKQAVLA 60 (117)
T ss_pred HHHHHHHHHhcCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHh
Confidence 44466666677888877665 4777788999999999964
No 60
>KOG4075|consensus
Probab=25.74 E-value=46 Score=25.35 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=21.6
Q ss_pred cchhhhHHHHHHHh---------CCCHHHHHHHHhhhhhcccccc
Q psy2245 52 VNAQGHLTALLSIL---------GYSDAQKENIMKTQAHAWKYSY 87 (88)
Q Consensus 52 ~~~q~hLtAI~sIL---------~FSp~Ek~~V~k~~~~~Ww~~~ 87 (88)
..+.-+++++++-| ..|.+||+++ ||+||
T Consensus 48 ~~~~~e~~~~~~aL~eKek~~Wk~LS~~EKkal-------YrisF 85 (167)
T KOG4075|consen 48 AIRFRELSAEIKALREKEKAPWKQLSTEEKKAL-------YRISF 85 (167)
T ss_pred chhhhcccHHHHHHHHHhcCChhhcCHHHHHHH-------HHHHh
Confidence 45677778877766 6899999888 66665
No 61
>cd07930 bacterial_phosphagen_kinase Phosphagen (guanidino) kinases found in bacteria. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, such as phosphocreatine (PCr) or phosphoarginine, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. This subfamily is specific to bacteria and lacks an N-terminal domain, which otherwise forms part of the substrate binding site. Most of the catalytic residues are found in the larger C-terminal domain, however, which appears conserved in these bacterial proteins. Their functions have not been characterized.
Probab=25.68 E-value=18 Score=27.55 Aligned_cols=45 Identities=27% Similarity=0.356 Sum_probs=35.0
Q ss_pred ccccCCcchHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHhc-Cccch
Q psy2245 5 LVCTNPKHNLIRHKRRYDALKDTKPPNDAEMTLQFLKSAIFYFLT-DPVNA 54 (88)
Q Consensus 5 ~~~~~~~~~~~~~~~r~~~~~~~k~~~D~EanLefLKnaIy~fLT-D~~~~ 54 (88)
+.|..+.-||-..|.|+.++-+.= |..|.|--+-=|.||| +|.|-
T Consensus 104 I~~~~~G~~l~~~~~r~~~~~~~l-----e~~l~fAfd~~lGYLTscPtNl 149 (232)
T cd07930 104 IQCLLPGLQLEEAYERADKIDDLL-----EEKLDYAFDEKLGYLTACPTNV 149 (232)
T ss_pred EEEEeCCCCHHHHHHHHHHHHHHH-----HhhccccccCCceEEeeCCCCC
Confidence 346777889999999997765532 4567899999999999 88763
No 62
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=25.52 E-value=67 Score=22.69 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=19.4
Q ss_pred HHHHHHHHhc--CccchhhhHHHHHHHh
Q psy2245 40 LKSAIFYFLT--DPVNAQGHLTALLSIL 65 (88)
Q Consensus 40 LKnaIy~fLT--D~~~~q~hLtAI~sIL 65 (88)
.|..|+..|+ |++.+-+-|.|++.++
T Consensus 87 ~K~~vM~Lm~h~d~eVr~eAL~avQklm 114 (119)
T PF11698_consen 87 AKERVMELMNHEDPEVRYEALLAVQKLM 114 (119)
T ss_dssp HHHHHHHHTS-SSHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence 3777888888 7777777777777665
No 63
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=25.20 E-value=1.6e+02 Score=21.20 Aligned_cols=49 Identities=22% Similarity=0.289 Sum_probs=36.0
Q ss_pred CCChhhHH-HHHHHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHhh
Q psy2245 30 PNDAEMTL-QFLKSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 30 ~~D~EanL-efLKnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k~ 78 (88)
+-|.|.+. -|--|-+.+=|.++++|+.-+ .|-+.=-+.|+|||+.|..-
T Consensus 15 ~Fd~~~srkgY~LN~fc~sl~~~~nRe~F~ade~Ay~~~~~Lteeqk~aV~~R 67 (117)
T PRK13378 15 IFDGEQARKGYALNKMCFSFNDAANRAAFLADEAAYCRKYGLNEEQKEAIRNR 67 (117)
T ss_pred CcCHHHHHHHHHHHHHHHHhCCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHhh
Confidence 44556333 366677777788888887766 47778889999999999653
No 64
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=25.15 E-value=1.7e+02 Score=17.69 Aligned_cols=39 Identities=15% Similarity=0.223 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHH
Q psy2245 35 MTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 35 anLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
..=.|||- ||..-. ++..=..+.|...|+.||.--....
T Consensus 5 ~~e~YL~~-Iy~l~~--~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 5 SEEDYLKA-IYELSE--EGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp HHHHHHHH-HHHHHH--CTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHH-HHHHHc--CCCCccHHHHHHHHCCChHHHHHHH
Confidence 34468874 555554 4456678999999999998766544
No 65
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=24.99 E-value=20 Score=21.74 Aligned_cols=26 Identities=23% Similarity=0.317 Sum_probs=15.2
Q ss_pred hhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 55 QGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 55 q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
++|+..|..=|++||++++.+.....
T Consensus 3 ~~~~~~l~~~L~LT~eQ~~~~~~i~~ 28 (100)
T PF07813_consen 3 EGRIDRLKEELNLTDEQKAKWRAIRQ 28 (100)
T ss_dssp -----STTTTS--THHHHHHHHHHHH
T ss_pred cchHHHHHhhCCCCHHHHHHHHHHHH
Confidence 35667777889999999998876543
No 66
>COG1519 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]
Probab=24.87 E-value=1.3e+02 Score=25.64 Aligned_cols=53 Identities=21% Similarity=0.127 Sum_probs=43.3
Q ss_pred cchHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCC
Q psy2245 11 KHNLIRHKRRYDALKDTKPPNDAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGY 67 (88)
Q Consensus 11 ~~~~~~~~~r~~~~~~~k~~~D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~F 67 (88)
-+|.-.++++++++..-..+.|. +.|..++.+.+.|+..++++-+|...++..
T Consensus 351 ~~Nf~ei~~~l~~~ga~~~v~~~----~~l~~~v~~l~~~~~~r~~~~~~~~~~v~~ 403 (419)
T COG1519 351 TFNFSDIAERLLQAGAGLQVEDA----DLLAKAVELLLADEDKREAYGRAGLEFLAQ 403 (419)
T ss_pred cccHHHHHHHHHhcCCeEEECCH----HHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 36788899999998887777773 458899999999999899888888777643
No 67
>PHA02566 alt ADP-ribosyltransferase; Provisional
Probab=24.74 E-value=73 Score=28.87 Aligned_cols=48 Identities=19% Similarity=0.192 Sum_probs=36.3
Q ss_pred hHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhhhhhc
Q psy2245 35 MTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKTQAHA 82 (88)
Q Consensus 35 anLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~~~ 82 (88)
+-.+|+++++|.|--+.-..-.-.++=...-+.|++|+.+|.....++
T Consensus 393 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~LT~~E~~AI~dY~~sg 440 (684)
T PHA02566 393 AKTKFLMRAIYKFARESASQMYEITGARDPKKLTPAESRAIREYCASG 440 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccCCHHHHHHHHHHHHhh
Confidence 456999999999988666544444444477889999999998876644
No 68
>PF14403 CP_ATPgrasp_2: Circularly permuted ATP-grasp type 2
Probab=24.58 E-value=1.3e+02 Score=25.49 Aligned_cols=37 Identities=27% Similarity=0.447 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhhh
Q psy2245 35 MTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKTQ 79 (88)
Q Consensus 35 anLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~ 79 (88)
-.++=+..++-+||+|+ ++...++|||+|.+-|+.-+
T Consensus 64 ~l~~i~~kv~~~~l~d~--------~lR~~fg~~~~~e~Li~~dp 100 (445)
T PF14403_consen 64 TLYSILLKVIRRYLRDP--------ELRKLFGFSPEEEELILIDP 100 (445)
T ss_pred HHHHHHHHHHHHHhCCH--------HHHHHhCcCHHHHHHhcCCC
Confidence 45566777888899988 36778999999999887654
No 69
>PF07138 DUF1386: Protein of unknown function (DUF1386); InterPro: IPR009815 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf11; it is a family of uncharacterised viral proteins.
Probab=24.23 E-value=64 Score=26.94 Aligned_cols=40 Identities=18% Similarity=0.365 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhhhhhccccc
Q psy2245 36 TLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKTQAHAWKYS 86 (88)
Q Consensus 36 nLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~~~Ww~~ 86 (88)
...=|+.+|++|+--. +-+-|.++..+ |+|- ....+|||-
T Consensus 133 ~~~~Lq~~i~~F~~f~--~~~~L~~vA~v--F~p~-------~~~~GWWY~ 172 (324)
T PF07138_consen 133 VTDLLQTIIGRFIHFV--RCGKLEHVADV--FNPT-------IDVVGWWYN 172 (324)
T ss_pred HHHHHHHHHHHHHHHh--hhhHHHHHHHh--cCCC-------CCcccchhh
Confidence 4556888999999722 23445555555 5664 123789994
No 70
>cd06199 SiR Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain.
Probab=23.97 E-value=1.3e+02 Score=23.44 Aligned_cols=39 Identities=21% Similarity=0.183 Sum_probs=25.9
Q ss_pred ccccCCcchHHHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q psy2245 5 LVCTNPKHNLIRHKRRYDALKDTKPPNDAEMTLQFLKSA 43 (88)
Q Consensus 5 ~~~~~~~~~~~~~~~r~~~~~~~k~~~D~EanLefLKna 43 (88)
.||-+|+.=.......+.+.-.+....+.|.+.+||++.
T Consensus 311 YvCG~~~~M~~~V~~~L~~i~~~~~~~~~~~a~~~~~~l 349 (360)
T cd06199 311 YVCGDAKRMAKDVDAALLDIIATEGGMDEEEAEAYLKEL 349 (360)
T ss_pred EEECCCccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 368777655555666666666666666777777777763
No 71
>PRK14015 pepN aminopeptidase N; Provisional
Probab=23.78 E-value=2.6e+02 Score=25.29 Aligned_cols=54 Identities=22% Similarity=0.365 Sum_probs=38.8
Q ss_pred CChh-hHHHHHHHHHHHHhc--Cc-c-------------chhhhHHHHHHHhCCCHHHHHHHHhhhhhccc
Q psy2245 31 NDAE-MTLQFLKSAIFYFLT--DP-V-------------NAQGHLTALLSILGYSDAQKENIMKTQAHAWK 84 (88)
Q Consensus 31 ~D~E-anLefLKnaIy~fLT--D~-~-------------~~q~hLtAI~sIL~FSp~Ek~~V~k~~~~~Ww 84 (88)
.|++ +..+-|||+.+.||+ |+ + |-...+.|+-.+++-+.++|..++..=...|.
T Consensus 674 ~~~~~~~~R~l~n~~l~~l~~~~~~~~~~~~~~~~~~a~~mtd~~~al~~l~~~~~~~~~~~l~~f~~~~~ 744 (875)
T PRK14015 674 PDAEAAGRRALRNVCLSYLAAADDEEAAELAEAQFDQADNMTDRLAALSALVNADLPERDEALADFYDRWK 744 (875)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHHHhC
Confidence 4444 889999999999999 32 2 12345678888888777888877766556664
No 72
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=23.75 E-value=1e+02 Score=20.67 Aligned_cols=24 Identities=17% Similarity=0.317 Sum_probs=21.9
Q ss_pred hHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 57 HLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 57 hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
.+.||..-.|+|+.|.-.+||...
T Consensus 14 pFeaI~~qfGl~E~eVi~lMR~~L 37 (73)
T PF10985_consen 14 PFEAIERQFGLSEKEVIKLMRKEL 37 (73)
T ss_pred CHHHHHHHHCCCHHHHHHHHHhhc
Confidence 478999999999999999999876
No 73
>PRK09726 antitoxin HipB; Provisional
Probab=23.21 E-value=2e+02 Score=17.94 Aligned_cols=57 Identities=12% Similarity=0.158 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHhCCCCCChhhH--HHHHHHHHHHHhcCc-cchhhhHHHHHHHhCCCHHH
Q psy2245 15 IRHKRRYDALKDTKPPNDAEMT--LQFLKSAIFYFLTDP-VNAQGHLTALLSILGYSDAQ 71 (88)
Q Consensus 15 ~~~~~r~~~~~~~k~~~D~Ean--LefLKnaIy~fLTD~-~~~q~hLtAI~sIL~FSp~E 71 (88)
.++..|+.++++.++....+.+ +.-=.+.|..+..+. .-.-..|-.|...||.+...
T Consensus 11 ~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~~ 70 (88)
T PRK09726 11 TQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL 70 (88)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcch
Confidence 3566778888887777666633 334567888888854 34568899999999999765
No 74
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=23.11 E-value=2e+02 Score=17.83 Aligned_cols=32 Identities=16% Similarity=0.331 Sum_probs=19.3
Q ss_pred CChhhHHHHHHHHHHHHhcCccchhhhHHHHH
Q psy2245 31 NDAEMTLQFLKSAIFYFLTDPVNAQGHLTALL 62 (88)
Q Consensus 31 ~D~EanLefLKnaIy~fLTD~~~~q~hLtAI~ 62 (88)
.|++..++.++.-+..|+..|...+.-+.+|.
T Consensus 85 ~~~~~~~~~~~~g~~~~l~~p~~~~~l~~~l~ 116 (202)
T PRK09390 85 GDVPLAVEAMKLGAVDFIEKPFEDERLIGAIE 116 (202)
T ss_pred CCHHHHHHHHHcChHHHhhCCCCHHHHHHHHH
Confidence 46666777777777777776655443333333
No 75
>PF06719 AraC_N: AraC-type transcriptional regulator N-terminus; InterPro: IPR009594 This entry represents the N terminus of bacterial ARAC-type transcriptional regulators. In Escherichia coli these regulate the L-arabinose operon through sensing the presence of arabinose, and when the sugar is present, transmitting this information from the arabinose-binding domains to the protein s DNA-binding domains []. This family might represent the N-terminal arm of the protein, which binds to the C-terminal DNA binding domains to hold them in a state where the protein prefers to loop and remain non-activating []. This domain is associated with the IPR000005 from INTERPRO domain.
Probab=22.87 E-value=2.6e+02 Score=19.16 Aligned_cols=48 Identities=19% Similarity=0.337 Sum_probs=34.9
Q ss_pred cccccCCcchHHHHHHHHHHHHhCCCCCChh-hHHHHHHHHHHHHhcCccc
Q psy2245 4 GLVCTNPKHNLIRHKRRYDALKDTKPPNDAE-MTLQFLKSAIFYFLTDPVN 53 (88)
Q Consensus 4 ~~~~~~~~~~~~~~~~r~~~~~~~k~~~D~E-anLefLKnaIy~fLTD~~~ 53 (88)
|+....-..++.....|+.++-++. .|-+ -.=.++|.++|+.|+.+.|
T Consensus 104 ~~~~~~~~~~l~da~~RLl~ll~~p--~d~~~L~pli~rEi~yrLL~~~~G 152 (155)
T PF06719_consen 104 GIFVAPADEELLDALLRLLRLLDDP--EDIPILAPLILREILYRLLQGPQG 152 (155)
T ss_pred ccccccCCHHHHHHHHHHHHHHCCc--hhhHHHHHHHHHHHHHHHHcCCCC
Confidence 5566666788999999999997643 3433 2334778899999987765
No 76
>PRK11172 dkgB 2,5-diketo-D-gluconate reductase B; Provisional
Probab=22.82 E-value=2.1e+02 Score=20.92 Aligned_cols=58 Identities=9% Similarity=0.072 Sum_probs=37.2
Q ss_pred HHHHHhCCCCCChhhHHHHHHHHHHHHhc-CccchhhhHHHHHHHhC--CCHHHHHHHHhhhh
Q psy2245 21 YDALKDTKPPNDAEMTLQFLKSAIFYFLT-DPVNAQGHLTALLSILG--YSDAQKENIMKTQA 80 (88)
Q Consensus 21 ~~~~~~~k~~~D~EanLefLKnaIy~fLT-D~~~~q~hLtAI~sIL~--FSp~Ek~~V~k~~~ 80 (88)
+.++-+..+..-++++|.|+-+-- ... =.....+|+...+.++. +|++|.+.|+++..
T Consensus 192 l~~~a~~~~~s~aqval~w~l~~~--~~~i~g~~~~~~l~~n~~~~~~~L~~~~~~~i~~~~~ 252 (267)
T PRK11172 192 IARIAAKHNATPAQVILAWAMQLG--YSVIPSSTKRENLASNLLAQDLQLDAEDMAAIAALDR 252 (267)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhCC--CEeecCCCCHHHHHHHHhhcCCCcCHHHHHHHhhhcc
Confidence 344444445555668888876541 111 22334678888888865 59999999998764
No 77
>PF05974 DUF892: Domain of unknown function (DUF892); InterPro: IPR010287 This domain is found in several hypothetical bacterial proteins of unknown function.; PDB: 4ERU_B 3OGH_A 2GS4_B 2GYQ_B 3HIU_A.
Probab=22.81 E-value=66 Score=22.56 Aligned_cols=34 Identities=21% Similarity=0.290 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHH
Q psy2245 40 LKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKE 73 (88)
Q Consensus 40 LKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~ 73 (88)
||+++=..+...+.+...|..|+..||-+|..+.
T Consensus 36 L~~~l~~h~~eT~~q~~rLe~~~~~lg~~p~~~~ 69 (159)
T PF05974_consen 36 LKAALEEHLEETEQQIERLEQIFEALGADPSAEK 69 (159)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTTS-S-CHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccCCCccCc
Confidence 7889889999889899999999999999998766
No 78
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=22.77 E-value=1.5e+02 Score=21.77 Aligned_cols=48 Identities=19% Similarity=0.198 Sum_probs=33.8
Q ss_pred CCChhhHH-HHHHHHHHHHhcCccchhhhH---HHHHHHhCCCHHHHHHHHh
Q psy2245 30 PNDAEMTL-QFLKSAIFYFLTDPVNAQGHL---TALLSILGYSDAQKENIMK 77 (88)
Q Consensus 30 ~~D~EanL-efLKnaIy~fLTD~~~~q~hL---tAI~sIL~FSp~Ek~~V~k 77 (88)
+-|.+.+. -|=-|-+..=|.++++|+.-+ .|.+.=-+.|+|||++|..
T Consensus 15 ~Fd~~~srkgY~LN~fc~sL~~~~nRerF~ade~Ay~de~~Lteeqr~aV~~ 66 (129)
T PRK13377 15 IFDADMSRKGYHLNQFCMSLMKAENRERFKADERAYLDEWPMTEEQKQAVLA 66 (129)
T ss_pred ccCHHHHHHHHHHHHHHHHhCCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHh
Confidence 34555333 355566666677888887766 4777778999999999964
No 79
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=22.72 E-value=79 Score=17.83 Aligned_cols=38 Identities=18% Similarity=0.210 Sum_probs=19.6
Q ss_pred CcccccCCcchHHHHHHHHHHHHhCCCCCChhhHHHHHHH
Q psy2245 3 SGLVCTNPKHNLIRHKRRYDALKDTKPPNDAEMTLQFLKS 42 (88)
Q Consensus 3 ~~~~~~~~~~~~~~~~~r~~~~~~~k~~~D~EanLefLKn 42 (88)
+|+..+.-|..++ .||+...-...+..+.++=+++|++
T Consensus 16 ~Gi~l~~~K~~~l--~rRl~~rm~~~~~~~~~~y~~~L~~ 53 (57)
T PF03705_consen 16 TGIDLSEYKRSLL--ERRLARRMRALGLPSFAEYYELLRS 53 (57)
T ss_dssp H-----GGGHHHH--HHHHHHHHHHHT---HHHHHHHHHH
T ss_pred HCCCCchhhHHHH--HHHHHHHHHHcCCCCHHHHHHHHHh
Confidence 4666666665554 5777777777777777776666654
No 80
>TIGR03330 SAM_DCase_Bsu S-adenosylmethionine decarboxylase proenzyme, Bacillus form. Members of this protein family are the single chain precursor of the two chains of the mature S-adenosylmethionine decarboxylase as found in Methanocaldococcus jannaschii, Bacillus subtilis, and a wide range of other species. It differs substantially in architecture from the form as found in Escherichia coli, and lacks any extended homology to the eukaryotic form (TIGR00535).
Probab=22.19 E-value=88 Score=21.18 Aligned_cols=16 Identities=25% Similarity=0.488 Sum_probs=13.3
Q ss_pred CCCChhhHHHHHHHHH
Q psy2245 29 PPNDAEMTLQFLKSAI 44 (88)
Q Consensus 29 ~~~D~EanLefLKnaI 44 (88)
...||+.+++||++++
T Consensus 84 ~~~~p~~a~~~l~~~f 99 (112)
T TIGR03330 84 DHSDPEKAFEYLVEAL 99 (112)
T ss_pred CCCCHHHHHHHHHHHh
Confidence 3478999999999875
No 81
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=22.16 E-value=73 Score=19.93 Aligned_cols=14 Identities=14% Similarity=0.109 Sum_probs=11.3
Q ss_pred CCCHHHHHHHHhhh
Q psy2245 66 GYSDAQKENIMKTQ 79 (88)
Q Consensus 66 ~FSp~Ek~~V~k~~ 79 (88)
+|||+||..|-...
T Consensus 25 ~ls~~eRriih~la 38 (60)
T cd02639 25 SLSPAERRIVHLLA 38 (60)
T ss_pred CCCHHHHHHHHHHH
Confidence 68999999987653
No 82
>PF09537 DUF2383: Domain of unknown function (DUF2383); InterPro: IPR019052 This entry represents a functionally uncharacterised ferritin like domain.; PDB: 3FSE_B.
Probab=21.94 E-value=87 Score=19.86 Aligned_cols=61 Identities=18% Similarity=0.085 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhhhhhcccc
Q psy2245 14 LIRHKRRYDALKDTKPPNDAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKTQAHAWKY 85 (88)
Q Consensus 14 ~~~~~~r~~~~~~~k~~~D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~~~Ww~ 85 (88)
-+..|+...+.-+ | .-||+.+-.|..+......-|++.+.-||-+|.+.-.++.. .+.+|.
T Consensus 16 ~~~~Y~~a~~~~~-----~-----~~lk~~f~~~~~~~~~~~~~L~~~i~~~Gg~p~~~gs~~g~-~~r~~~ 76 (111)
T PF09537_consen 16 GIEGYEKAAEKAE-----D-----PELKSLFQEFAQERQQHAEELQAEIQELGGEPEESGSFKGA-LHRAWM 76 (111)
T ss_dssp HHHHHHHHHHH-------S-----HHHHHHHHHHHHHHHHHHHHHHHHHHHTT--H----HHCHH-HH-TTT
T ss_pred HHHHHHHHHHHCC-----C-----HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcccCHHHH-HHHHHH
Confidence 3455665554433 3 35888888999998888899999999999999998665433 355553
No 83
>PRK13671 hypothetical protein; Provisional
Probab=21.75 E-value=38 Score=27.00 Aligned_cols=17 Identities=24% Similarity=0.122 Sum_probs=8.3
Q ss_pred HHHHhCCCHHHHHHHHh
Q psy2245 61 LLSILGYSDAQKENIMK 77 (88)
Q Consensus 61 I~sIL~FSp~Ek~~V~k 77 (88)
+..|.++|+.=-.++.+
T Consensus 245 L~~~~~v~eGLenRi~~ 261 (298)
T PRK13671 245 LAKIWLVSEGIENLFKK 261 (298)
T ss_pred HHHHcCCCHHHHHHHHH
Confidence 44555555544444433
No 84
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.74 E-value=1.4e+02 Score=17.62 Aligned_cols=33 Identities=12% Similarity=0.189 Sum_probs=23.3
Q ss_pred hcCccchhhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 48 LTDPVNAQGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 48 LTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
|.-..||.-+..-|...||.|+++...++....
T Consensus 13 L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~ 45 (78)
T PF04539_consen 13 LEQELGREPTDEEIAEELGISVEEVRELLQASR 45 (78)
T ss_dssp HHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHS
T ss_pred HHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCC
Confidence 444556777778889999999999999987654
No 85
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=21.73 E-value=1.6e+02 Score=20.39 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=20.3
Q ss_pred HHhcCccchhhhHHHHHHHh---CCCHHHHHHHHhh
Q psy2245 46 YFLTDPVNAQGHLTALLSIL---GYSDAQKENIMKT 78 (88)
Q Consensus 46 ~fLTD~~~~q~hLtAI~sIL---~FSp~Ek~~V~k~ 78 (88)
.||.|+..++--+.-=...| |.|++|.+..++-
T Consensus 11 ~FL~~p~V~~sp~~~k~~FL~sKGLt~~EI~~al~~ 46 (136)
T PF04695_consen 11 KFLQDPKVRNSPLEKKIAFLESKGLTEEEIDEALGR 46 (136)
T ss_dssp HHHCTTTCCCS-HHHHHHHHHHCT--HHHHHHHHHH
T ss_pred HHhCCcccccCCHHHHHHHHHcCCCCHHHHHHHHHh
Confidence 68888877766654433333 8999998877654
No 86
>KOG0639|consensus
Probab=21.71 E-value=54 Score=29.74 Aligned_cols=72 Identities=19% Similarity=0.205 Sum_probs=50.1
Q ss_pred cCCcchHHHHHHHHHHHHhCCCC--C-ChhhH--HHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 8 TNPKHNLIRHKRRYDALKDTKPP--N-DAEMT--LQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 8 ~~~~~~~~~~~~r~~~~~~~k~~--~-D~Ean--LefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
.|-|.++-|||-+|-|.-..-++ + ..|++ |+=+-.-|.=||+- ++.||-|.|++.-=+.|-.|+.+|..+|+
T Consensus 50 A~EKteMqRhYvmYyEmSygLniemhKq~EI~KRLn~i~aQl~PfLsq-ehQqqvlqAvEraKqvT~~eln~iig~qa 126 (705)
T KOG0639|consen 50 ASEKTEMQRHYVMYYEMSYGLNIEMHKQTEIAKRLNTICAQLIPFLSQ-EHQQQVLQAVERAKQVTMSELNAIIGLQA 126 (705)
T ss_pred hhhhhhhhhheeeeeeeccccchhhHHHHHHHHHHHHHHHHHhhhhhH-HHHHHHHHHHHHHhhcchhhhhhhccccc
Confidence 36788899999998877654332 1 22322 22222336667763 34699999999999999999999998665
No 87
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair]
Probab=21.62 E-value=68 Score=25.35 Aligned_cols=22 Identities=5% Similarity=0.071 Sum_probs=16.5
Q ss_pred HHHhCCCHHHHHHHHhhhhhcc
Q psy2245 62 LSILGYSDAQKENIMKTQAHAW 83 (88)
Q Consensus 62 ~sIL~FSp~Ek~~V~k~~~~~W 83 (88)
...-+|+||||+...++-..+|
T Consensus 168 ~~~~~f~~eeR~~~~~ll~~G~ 189 (261)
T COG0708 168 EGNSGFLPEERAWFRRLLNAGF 189 (261)
T ss_pred CCCCCCCHHHHHHHHHHHHcch
Confidence 3456899999999887766553
No 88
>cd01383 MYSc_type_VIII Myosin motor domain, plant-specific type VIII myosins, a subgroup which has been associated with endocytosis, cytokinesis, cell-to-cell coupling and gating at plasmodesmata. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates f
Probab=21.61 E-value=75 Score=27.75 Aligned_cols=25 Identities=28% Similarity=0.368 Sum_probs=18.6
Q ss_pred hhhHHHHHHHhCCCHHHHHHHHhhhh
Q psy2245 55 QGHLTALLSILGYSDAQKENIMKTQA 80 (88)
Q Consensus 55 q~hLtAI~sIL~FSp~Ek~~V~k~~~ 80 (88)
+..+.| +..||||++|+..|.+.=+
T Consensus 239 ~~~~~a-l~~lG~~~~e~~~I~~iLa 263 (677)
T cd01383 239 HTLVEA-LDIVHISKEDQENVFAMLA 263 (677)
T ss_pred HHHHHH-HHHcCCCHHHHHHHHHHHH
Confidence 334444 8899999999999977543
No 89
>TIGR01931 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component. This model describes an NADPH-dependent sulfite reductase flavoprotein subunit. Most members of this family are found in Cys biosynthesis gene clusters. The closest homologs below the trusted cutoff are designated as subunits nitrate reductase.
Probab=21.58 E-value=1.5e+02 Score=25.14 Aligned_cols=39 Identities=18% Similarity=0.192 Sum_probs=30.9
Q ss_pred ccccCCcchHHHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q psy2245 5 LVCTNPKHNLIRHKRRYDALKDTKPPNDAEMTLQFLKSA 43 (88)
Q Consensus 5 ~~~~~~~~~~~~~~~r~~~~~~~k~~~D~EanLefLKna 43 (88)
.||-+|+.-.....+.+.+.-.+....+.|.+-+||++.
T Consensus 548 YvCG~~~~M~~~V~~~L~~i~~~~g~~s~~~A~~~l~~l 586 (597)
T TIGR01931 548 YVCGDAKKMAKDVHQALLDIIAKEGHLDAEEAEEYLTDL 586 (597)
T ss_pred EEECCCccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 478888776677777788887777888888888998764
No 90
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=21.57 E-value=1.5e+02 Score=19.17 Aligned_cols=25 Identities=12% Similarity=0.267 Sum_probs=19.2
Q ss_pred hhhHHHHHHHhCCCHHHHHHHHhhh
Q psy2245 55 QGHLTALLSILGYSDAQKENIMKTQ 79 (88)
Q Consensus 55 q~hLtAI~sIL~FSp~Ek~~V~k~~ 79 (88)
-++|..|.+=+|+|.++-+.|+.+.
T Consensus 10 GDtLs~iF~~~gls~~dl~~v~~~~ 34 (85)
T PF04225_consen 10 GDTLSTIFRRAGLSASDLYAVLEAD 34 (85)
T ss_dssp T--HHHHHHHTT--HHHHHHHHHHG
T ss_pred CCcHHHHHHHcCCCHHHHHHHHhcc
Confidence 3689999999999999999999876
No 91
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=21.39 E-value=3.4e+02 Score=19.89 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=38.6
Q ss_pred HHHHHHhCCCCCChhhHHHHHHHH--HHHHhcCccchhhhHHHHHHHhCCCHHHHHHHHh
Q psy2245 20 RYDALKDTKPPNDAEMTLQFLKSA--IFYFLTDPVNAQGHLTALLSILGYSDAQKENIMK 77 (88)
Q Consensus 20 r~~~~~~~k~~~D~EanLefLKna--Iy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k 77 (88)
++++..... ..++++-|..|..+ .|.|+. .+.+.+|...|+.++.+.+.|..
T Consensus 23 ~i~~ii~~~-~~~~~~li~~L~~iQ~~~GyIp-----~e~~~~iA~~l~v~~a~V~gVat 76 (169)
T PRK07571 23 VLEATMKRN-QYRQDALIEVLHKAQELFGYLE-----RDLLLYVARQLKLPLSRVYGVAT 76 (169)
T ss_pred HHHHHHHHc-CCCHHHHHHHHHHHHHHcCCCC-----HHHHHHHHHHhCcCHHHHHHHHH
Confidence 444444433 46899999988765 466664 56789999999999999998854
No 92
>PF11729 Capsid-VNN: nodavirus capsid protein ; InterPro: IPR024292 The capsid or coat protein of this family is expressed in Nodaviridae, that are ssRNA positive-strand viruses, with no DNA stage. These viruses are the causative agents of viral nervous necrosis in marine fish [].
Probab=21.34 E-value=46 Score=27.90 Aligned_cols=30 Identities=27% Similarity=0.379 Sum_probs=23.6
Q ss_pred HHhcCccchhhhHHHHHHHhCCCHHHHHHHHhhhhhccccc
Q psy2245 46 YFLTDPVNAQGHLTALLSILGYSDAQKENIMKTQAHAWKYS 86 (88)
Q Consensus 46 ~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k~~~~~Ww~~ 86 (88)
.||-||...+.+++||++. ..++.+-||-|
T Consensus 126 gFl~DPtd~d~t~~Alqat-----------rGa~vaKwWeS 155 (340)
T PF11729_consen 126 GFLPDPTDGDHTFDALQAT-----------RGAVVAKWWES 155 (340)
T ss_pred EEcCCCCcccHHHHHHHHh-----------ccceehhhhhh
Confidence 5888999999999999764 34556788866
No 93
>PF06441 EHN: Epoxide hydrolase N terminus; InterPro: IPR010497 This entry represents the N-terminal region of the eukaryotic epoxide hydrolase protein. Epoxide hydrolases (3.3.2.3 from EC) comprise a group of functionally related enzymes that catalyse the addition of water to oxirane compounds (epoxides), thereby usually generating vicinal trans-diols. EHs have been found in all types of living organisms, including mammals, invertebrates, plants, fungi and bacteria. In animals, the major interest in EH is directed towards their detoxification capacity for epoxides since they are important safeguards against the cytotoxic and genotoxic potential of oxirane derivatives that are often reactive electrophiles because of the high tension of the three-membered ring system and the strong polarisation of the C--O bonds. This is of significant relevance because epoxides are frequent intermediary metabolites, which arise during the biotransformation of foreign compounds []. This domain is often found in conjunction with IPR000073 from INTERPRO.; GO: 0004301 epoxide hydrolase activity, 0009636 response to toxin, 0016020 membrane; PDB: 3G0I_B 3G02_A 1QO7_A.
Probab=21.25 E-value=87 Score=21.33 Aligned_cols=50 Identities=22% Similarity=0.350 Sum_probs=29.9
Q ss_pred CcchHHHHHHHHHHHHhCCCCCChh-------hHHHHHHHHHHHHhc--CccchhhhHH
Q psy2245 10 PKHNLIRHKRRYDALKDTKPPNDAE-------MTLQFLKSAIFYFLT--DPVNAQGHLT 59 (88)
Q Consensus 10 ~~~~~~~~~~r~~~~~~~k~~~D~E-------anLefLKnaIy~fLT--D~~~~q~hLt 59 (88)
|..-|-+..+|+...+--....++. .++.+||.++=|..+ |=...+..||
T Consensus 8 ~~~~l~~l~~rl~~~r~p~~~~~~~~~~w~~G~~~~~l~~L~~yW~~~fDWr~~E~~lN 66 (112)
T PF06441_consen 8 PDEELDDLRQRLRATRLPDEPPEPGQEDWDYGTPLDWLKELVDYWRNEFDWRKHEARLN 66 (112)
T ss_dssp -HHHHHHHHHHHHHS------TGGG-TT-TTSS-HHHHHHHHHHHHHT--HHHHHHHHT
T ss_pred CHHHHHHHHHHHhccCCCCCCcCCCccccccCCCHHHHHHHHHHHhhcCChHHHHHHHH
Confidence 4566778888888887644444443 689999999999997 4444454444
No 94
>PF07540 NOC3p: Nucleolar complex-associated protein; InterPro: IPR011501 Nucleolar complex-associated protein (Noc3p, Q07896 from SWISSPROT) is conserved in eukaryotes and plays essential roles in replication and rRNA processing in Saccharomyces cerevisiae [].
Probab=20.79 E-value=1.8e+02 Score=19.55 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=12.8
Q ss_pred CChhhHHHHHHHHHHHHhcCc
Q psy2245 31 NDAEMTLQFLKSAIFYFLTDP 51 (88)
Q Consensus 31 ~D~EanLefLKnaIy~fLTD~ 51 (88)
-|||.|+.-||. +..+..+.
T Consensus 17 e~PE~ni~~lk~-l~~~~~~~ 36 (95)
T PF07540_consen 17 EDPEENIGSLKR-LLKLCESK 36 (95)
T ss_pred HCHHHHHHHHHH-HHHHHhcc
Confidence 478888777776 44555544
No 95
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.75 E-value=1.5e+02 Score=15.52 Aligned_cols=23 Identities=22% Similarity=0.290 Sum_probs=17.5
Q ss_pred hhhhHHHHHHHhCCCHHHHHHHH
Q psy2245 54 AQGHLTALLSILGYSDAQKENIM 76 (88)
Q Consensus 54 ~q~hLtAI~sIL~FSp~Ek~~V~ 76 (88)
...+++.|..-|++|+..-..+.
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l 31 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHL 31 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHH
Confidence 35688899999999998855444
No 96
>PF11220 DUF3015: Protein of unknown function (DUF3015); InterPro: IPR021383 This bacterial family of proteins has no known function.
Probab=20.70 E-value=1.3e+02 Score=21.92 Aligned_cols=26 Identities=23% Similarity=0.317 Sum_probs=22.2
Q ss_pred cchhhhHHHHHHHhCCCHHHHHHHHh
Q psy2245 52 VNAQGHLTALLSILGYSDAQKENIMK 77 (88)
Q Consensus 52 ~~~q~hLtAI~sIL~FSp~Ek~~V~k 77 (88)
.|.-+||+|+.++|+-+|+.|..+-+
T Consensus 80 ~G~GE~L~ala~llgv~~~d~~~f~~ 105 (144)
T PF11220_consen 80 RGQGEHLDALAELLGVPAEDRAAFGA 105 (144)
T ss_pred cCCcchHHHHHHHhCCCHhhHHHHHH
Confidence 56778999999999999998887644
No 97
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=20.49 E-value=4.3e+02 Score=20.78 Aligned_cols=26 Identities=8% Similarity=0.167 Sum_probs=20.6
Q ss_pred chhhhHHHHHHHhCCCHHHHHHHHhh
Q psy2245 53 NAQGHLTALLSILGYSDAQKENIMKT 78 (88)
Q Consensus 53 ~~q~hLtAI~sIL~FSp~Ek~~V~k~ 78 (88)
|+.-+...|...||.|+++...+++.
T Consensus 187 gr~pt~~EiA~~lgi~~~~v~~~~~~ 212 (324)
T PRK07921 187 GREATDEELAEESGIPEEKIADLLEH 212 (324)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 55556778999999999998888654
No 98
>PHA00617 ribbon-helix-helix domain containing protein
Probab=20.44 E-value=94 Score=20.79 Aligned_cols=55 Identities=16% Similarity=0.225 Sum_probs=35.8
Q ss_pred CCcchHHHHHHHHHHHHhCCCCC--ChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHH
Q psy2245 9 NPKHNLIRHKRRYDALKDTKPPN--DAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDA 70 (88)
Q Consensus 9 ~~~~~~~~~~~r~~~~~~~k~~~--D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~ 70 (88)
-||...-|.||-++++|+++++. =++. ++ ..-+=.|++ -.+-|.++....|.|..
T Consensus 10 ~~~~~~~~~yr~~e~~~~~~~~~~~~~~~-m~-----~iSVrLp~e-L~erLD~LA~~~GrsRS 66 (80)
T PHA00617 10 LPKSSYSRSYRKIEVTRKGDTIELTLTET-MD-----VISFKLPPE-LNAKLEQVAIKMKKSKS 66 (80)
T ss_pred cCCcchhHHHHHHHHHhcCCccccccCCC-ce-----EEEEECCHH-HHHHHHHHHHHhCcCHH
Confidence 48999999999999999977765 2222 21 111111333 36678888888888743
No 99
>PF15002 ERK-JNK_inhib: ERK and JNK pathways, inhibitor
Probab=20.37 E-value=1e+02 Score=23.61 Aligned_cols=21 Identities=29% Similarity=0.417 Sum_probs=17.9
Q ss_pred hhhhHHHHHHHhCCCHHHHHH
Q psy2245 54 AQGHLTALLSILGYSDAQKEN 74 (88)
Q Consensus 54 ~q~hLtAI~sIL~FSp~Ek~~ 74 (88)
|.+|+.||.+|+..-+-+|+.
T Consensus 30 R~eh~~ai~~l~~~~~~~k~~ 50 (207)
T PF15002_consen 30 RKEHLAAIKSLFEIDDYEKRY 50 (207)
T ss_pred HHHHHHHHHHHHhCCcHHHHH
Confidence 789999999999999955543
No 100
>PRK15321 putative type III secretion system effector protein OrgC; Provisional
Probab=20.26 E-value=1.2e+02 Score=22.11 Aligned_cols=20 Identities=25% Similarity=0.449 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHhc---Cccchh
Q psy2245 36 TLQFLKSAIFYFLT---DPVNAQ 55 (88)
Q Consensus 36 nLefLKnaIy~fLT---D~~~~q 55 (88)
.-+=||++||+-|- ||++.+
T Consensus 34 ~S~~~KD~I~q~m~~F~dp~~G~ 56 (120)
T PRK15321 34 SSETLKDSIYQEMNAFKDPNSGD 56 (120)
T ss_pred CcHHHHHHHHHHHHHhCCCCCCC
Confidence 33558999999998 888765
No 101
>TIGR02400 trehalose_OtsA alpha,alpha-trehalose-phosphate synthase [UDP-forming]. This enzyme catalyzes the key, penultimate step in biosynthesis of trehalose, a compatible solute made as an osmoprotectant in some species in all three domains of life. The gene symbol OtsA stands for osmotically regulated trehalose synthesis A. Trehalose helps protect against both osmotic and thermal stresses, and is made from two glucose subunits. This model excludes glucosylglycerol-phosphate synthase, an enzyme of an analogous osmoprotectant system in many cyanobacterial strains. This model does not identify archaeal examples, as they are more divergent than glucosylglycerol-phosphate synthase. Sequences that score in the gray zone between the trusted and noise cutoffs include a number of yeast multidomain proteins in which the N-terminal domain may be functionally equivalent to this family. The gray zone also includes the OtsA of Cornyebacterium glutamicum (and related species), shown to be responsib
Probab=20.11 E-value=1.2e+02 Score=24.68 Aligned_cols=32 Identities=19% Similarity=0.302 Sum_probs=26.6
Q ss_pred HHhcCccchhhhHHHHHHHhCCCHHHHHHHHh
Q psy2245 46 YFLTDPVNAQGHLTALLSILGYSDAQKENIMK 77 (88)
Q Consensus 46 ~fLTD~~~~q~hLtAI~sIL~FSp~Ek~~V~k 77 (88)
.+|.+|.+.++.-.||..+|.-+++||+..++
T Consensus 401 gllVnP~d~~~lA~aI~~aL~~~~~er~~r~~ 432 (456)
T TIGR02400 401 ALLVNPYDIDGMADAIARALTMPLEEREERHR 432 (456)
T ss_pred cEEECCCCHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 45668888888999999999999999876554
No 102
>KOG2659|consensus
Probab=20.09 E-value=1.8e+02 Score=22.86 Aligned_cols=63 Identities=17% Similarity=0.173 Sum_probs=47.4
Q ss_pred cCCcchHHHHHHHHHHHHhCCCCCChhhHHHHHHHHHHHHhcCccchhhhHHHHHHHhCCCHHHHH
Q psy2245 8 TNPKHNLIRHKRRYDALKDTKPPNDAEMTLQFLKSAIFYFLTDPVNAQGHLTALLSILGYSDAQKE 73 (88)
Q Consensus 8 ~~~~~~~~~~~~r~~~~~~~k~~~D~EanLefLKnaIy~fLTD~~~~q~hLtAI~sIL~FSp~Ek~ 73 (88)
||+.-...-.+-++.|+...+. -|.+|+|+++-+.-+=-++.-..++|.-++++|=|-+.+..
T Consensus 97 ~n~~l~F~Lq~q~lIEliR~~~---~eeal~F~q~~LA~~a~e~~~~~~elE~~l~lLvf~~~~~s 159 (228)
T KOG2659|consen 97 TNRELFFHLQQLHLIELIREGK---TEEALEFAQTKLAPFAEENPKKMEELERTLALLVFELSQES 159 (228)
T ss_pred cchhHHHHHHHHHHHHHHHhhh---HHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcCCcccC
Confidence 3433345556667777776655 68999999999988887665689999999999999765543
Done!