Query psy12287
Match_columns 76
No_of_seqs 22 out of 24
Neff 1.9
Searched_HMMs 46136
Date Fri Aug 16 23:28:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12287hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13820 Nucleic_acid_bd: Puta 99.9 4.6E-27 1E-31 165.2 4.8 66 4-71 26-91 (149)
2 PF01402 RHH_1: Ribbon-helix-h 95.6 0.015 3.2E-07 30.9 2.7 25 29-53 1-25 (39)
3 PF11130 TraC_F_IV: F pilus as 91.4 0.85 1.8E-05 31.4 5.8 69 2-74 99-175 (235)
4 PF12651 RHH_3: Ribbon-helix-h 91.0 0.42 9.2E-06 27.3 3.3 25 26-50 1-25 (44)
5 PHA01623 hypothetical protein 87.7 1 2.2E-05 27.1 3.4 27 26-52 12-38 (56)
6 PF01883 DUF59: Domain of unkn 87.2 1.2 2.6E-05 25.9 3.5 50 13-63 22-72 (72)
7 PHA00617 ribbon-helix-helix do 85.2 2.1 4.6E-05 27.9 4.2 36 14-51 28-63 (80)
8 TIGR02945 SUF_assoc FeS assemb 81.5 1.2 2.6E-05 27.5 1.9 39 26-64 37-76 (99)
9 TIGR02793 nikR nickel-responsi 80.0 2.5 5.3E-05 29.0 3.2 21 28-48 1-21 (129)
10 cd04888 ACT_PheB-BS C-terminal 78.6 9.4 0.0002 21.3 5.3 39 22-64 35-75 (76)
11 TIGR02159 PA_CoA_Oxy4 phenylac 78.2 3.2 6.9E-05 28.9 3.3 39 26-64 25-63 (146)
12 PHA01748 hypothetical protein 77.9 4.2 9.2E-05 24.4 3.4 24 28-51 3-26 (60)
13 PF03869 Arc: Arc-like DNA bin 75.6 5.9 0.00013 23.1 3.5 27 29-55 6-32 (50)
14 PRK13721 conjugal transfer ATP 74.3 5.3 0.00011 33.6 4.2 49 27-75 129-182 (844)
15 TIGR01911 HesB_rel_seleno HesB 74.2 5.4 0.00012 25.4 3.3 32 31-66 3-35 (92)
16 PRK09502 iscA iron-sulfur clus 72.7 6.9 0.00015 25.0 3.6 32 31-66 2-33 (107)
17 PRK01002 nickel responsive reg 72.1 6.2 0.00014 27.1 3.5 23 27-49 4-26 (141)
18 PHA01474 nonstructural protein 71.6 1.7 3.8E-05 27.1 0.6 15 22-37 27-41 (52)
19 PRK04460 nickel responsive reg 70.7 7.1 0.00015 27.0 3.5 24 27-50 2-25 (137)
20 PRK02967 nickel responsive reg 66.2 9.7 0.00021 26.4 3.5 23 28-50 2-24 (139)
21 PF10038 DUF2274: Protein of u 65.1 12 0.00026 23.9 3.5 33 16-48 3-35 (69)
22 COG4829 CatC1 Muconolactone de 64.7 5 0.00011 27.8 1.8 33 27-59 8-40 (98)
23 PF09274 ParG: ParG; InterPro 62.5 11 0.00025 24.6 3.1 30 26-55 33-62 (76)
24 PF02834 LigT_PEase: LigT like 62.1 6.3 0.00014 23.1 1.7 27 32-58 1-27 (87)
25 PF06568 DUF1127: Domain of un 61.9 7.6 0.00016 21.5 1.9 20 40-59 15-34 (40)
26 TIGR01997 sufA_proteo FeS asse 61.6 16 0.00035 23.2 3.6 32 31-66 2-33 (107)
27 TIGR02746 TraC-F-type type-IV 60.3 13 0.00027 30.2 3.6 46 30-75 116-166 (797)
28 PF09981 DUF2218: Uncharacteri 60.1 13 0.00029 23.6 3.0 28 2-33 12-39 (89)
29 PF02120 Flg_hook: Flagellar h 58.4 21 0.00046 20.9 3.5 46 16-63 28-74 (85)
30 PRK00630 nickel responsive reg 56.7 17 0.00038 25.5 3.4 24 26-49 9-32 (148)
31 KOG2415|consensus 55.7 6.2 0.00014 34.2 1.2 18 37-54 90-107 (621)
32 TIGR02011 IscA iron-sulfur clu 54.5 19 0.00041 22.8 3.1 30 32-65 1-30 (105)
33 PF15320 RAM: mRNA cap methyla 51.2 12 0.00025 24.5 1.7 19 5-27 19-37 (81)
34 PF01521 Fe-S_biosyn: Iron-sul 49.8 14 0.00031 22.8 1.9 22 31-52 2-23 (112)
35 PF14319 Zn_Tnp_IS91: Transpos 46.5 21 0.00047 23.5 2.4 24 26-53 86-109 (111)
36 TIGR00406 prmA ribosomal prote 46.1 45 0.00098 24.2 4.3 30 29-65 3-32 (288)
37 cd04819 PA_2 PA_2: Protease-as 46.1 24 0.00053 22.9 2.6 21 31-51 102-122 (127)
38 PF04699 P16-Arc: ARP2/3 compl 45.8 7.1 0.00015 27.7 0.1 15 1-15 107-121 (152)
39 PRK13623 iron-sulfur cluster i 45.5 17 0.00038 23.2 1.9 20 30-49 8-27 (115)
40 PRK09504 sufA iron-sulfur clus 45.4 30 0.00066 22.8 3.0 32 32-67 18-49 (122)
41 PF11020 DUF2610: Domain of un 43.0 23 0.0005 23.8 2.2 21 36-56 51-71 (82)
42 TIGR03744 traC_PFL_4706 conjug 42.7 40 0.00086 28.9 4.0 38 37-74 171-208 (893)
43 PF12404 DUF3663: Peptidase ; 42.4 13 0.00027 24.4 0.8 17 51-67 45-61 (77)
44 PF05509 TraY: TraY domain; I 41.9 30 0.00064 20.5 2.3 23 30-52 1-23 (49)
45 TIGR03341 YhgI_GntY IscR-regul 41.8 36 0.00078 24.4 3.2 32 32-67 1-32 (190)
46 TIGR03406 FeS_long_SufT probab 41.4 23 0.0005 25.3 2.2 38 27-64 114-152 (174)
47 PF10723 RepB-RCR_reg: Replica 41.1 51 0.0011 21.2 3.5 23 28-50 42-64 (84)
48 PRK09256 hypothetical protein; 41.0 72 0.0016 22.1 4.5 51 10-65 21-76 (138)
49 COG0864 NikR Predicted transcr 40.6 47 0.001 23.2 3.5 22 26-47 3-24 (136)
50 PF12089 DUF3566: Transmembran 39.5 3.3 7.2E-05 28.7 -2.3 21 15-35 4-24 (119)
51 PRK11675 LexA regulated protei 39.4 52 0.0011 22.0 3.5 26 27-52 50-75 (90)
52 COG5457 Uncharacterized conser 39.4 17 0.00036 22.9 1.0 22 43-64 33-54 (63)
53 PF00398 RrnaAD: Ribosomal RNA 38.9 18 0.00039 25.8 1.3 30 24-55 122-151 (262)
54 cd04480 RPA1_DBD_A_like RPA1_D 38.7 28 0.00062 20.8 2.0 22 29-50 32-53 (86)
55 COG4006 Uncharacterized protei 38.4 15 0.00032 29.3 0.9 36 15-50 238-273 (278)
56 PF03861 ANTAR: ANTAR domain; 37.0 36 0.00078 19.5 2.1 22 35-56 30-51 (56)
57 COG0316 sufA Fe-S cluster asse 36.4 27 0.00058 23.6 1.7 19 31-49 4-22 (110)
58 TIGR02508 type_III_yscG type I 36.2 35 0.00077 24.2 2.4 21 36-56 85-105 (115)
59 cd04922 ACT_AKi-HSDH-ThrA_2 AC 36.0 72 0.0016 17.1 3.2 17 26-42 40-56 (66)
60 COG5639 Uncharacterized conser 35.5 67 0.0015 21.5 3.5 32 16-47 3-34 (77)
61 PF02426 MIase: Muconolactone 34.6 72 0.0016 20.9 3.5 33 27-59 4-40 (91)
62 PF14310 Fn3-like: Fibronectin 34.4 56 0.0012 19.1 2.7 18 21-38 28-45 (71)
63 PF11871 DUF3391: Domain of un 34.0 87 0.0019 19.4 3.7 43 15-67 12-58 (128)
64 cd03567 VHS_GGA VHS domain fam 33.6 28 0.0006 23.8 1.5 28 33-60 34-63 (139)
65 PRK11670 antiporter inner memb 33.0 43 0.00093 25.8 2.6 43 21-64 43-86 (369)
66 PF12535 Nudix_N: Hydrolase of 32.5 31 0.00068 20.9 1.4 14 37-50 6-19 (58)
67 PF02022 Integrase_Zn: Integra 31.7 3.6 7.7E-05 23.6 -2.7 19 25-43 12-30 (40)
68 KOG3380|consensus 31.6 21 0.00045 26.2 0.6 14 1-14 107-120 (152)
69 PLN03082 Iron-sulfur cluster a 31.4 69 0.0015 22.7 3.2 32 31-65 54-86 (163)
70 PF13062 DUF3924: Protein of u 31.3 62 0.0013 20.8 2.7 19 30-48 4-22 (62)
71 PF10604 Polyketide_cyc2: Poly 30.9 1E+02 0.0022 18.0 3.5 39 27-65 3-41 (139)
72 PF13182 DUF4007: Protein of u 30.2 1.1E+02 0.0024 22.9 4.3 70 4-74 204-284 (286)
73 COG3609 Predicted transcriptio 30.1 73 0.0016 20.2 2.9 23 27-49 2-24 (89)
74 cd00078 HECTc HECT domain; C-t 29.8 47 0.001 24.8 2.2 36 33-70 4-41 (352)
75 PF05534 HicB: HicB family; I 29.5 75 0.0016 18.5 2.7 29 28-56 18-46 (51)
76 COG5573 Predicted nucleic-acid 29.3 42 0.0009 24.6 1.9 27 35-71 25-54 (142)
77 TIGR00049 Iron-sulfur cluster 28.7 38 0.00082 20.8 1.4 18 33-50 1-18 (105)
78 cd04916 ACT_AKiii-YclM-BS_2 AC 28.3 95 0.002 16.6 2.8 17 27-43 41-57 (66)
79 PRK11190 Fe/S biogenesis prote 28.2 84 0.0018 22.7 3.3 31 32-66 2-32 (192)
80 PF05856 ARPC4: ARP2/3 complex 27.5 40 0.00087 25.1 1.5 12 25-36 69-80 (170)
81 PHA01486 nonstructural protein 26.8 28 0.00061 19.9 0.5 19 36-54 12-30 (32)
82 PF10236 DAP3: Mitochondrial r 26.7 94 0.002 23.2 3.4 46 30-75 78-131 (309)
83 cd04891 ACT_AK-LysC-DapG-like_ 26.1 1E+02 0.0022 15.6 3.0 16 28-43 42-57 (61)
84 PF07684 NODP: NOTCH protein; 25.7 1E+02 0.0022 18.9 2.9 34 32-66 24-57 (63)
85 TIGR00690 rpoZ DNA-directed RN 25.7 51 0.0011 19.7 1.5 22 32-53 16-37 (59)
86 cd04868 ACT_AK-like ACT domain 25.2 1E+02 0.0022 15.2 3.0 17 27-43 40-56 (60)
87 PF09477 Type_III_YscG: Bacter 25.1 48 0.001 23.5 1.5 21 36-56 86-106 (116)
88 PF09838 DUF2065: Uncharacteri 24.8 27 0.00059 21.0 0.2 23 39-61 24-46 (57)
89 cd04913 ACT_AKii-LysC-BS-like_ 24.6 1.2E+02 0.0027 16.0 2.9 20 27-46 42-61 (75)
90 smart00853 MutL_C MutL C termi 24.5 1.1E+02 0.0024 19.0 3.0 27 29-59 56-82 (136)
91 COG1985 RibD Pyrimidine reduct 24.5 64 0.0014 23.5 2.1 19 52-70 137-155 (218)
92 cd03561 VHS VHS domain family; 24.3 50 0.0011 21.6 1.4 27 33-59 33-61 (133)
93 PF01390 SEA: SEA domain; Int 23.9 95 0.0021 18.4 2.5 45 12-58 51-104 (107)
94 TIGR03455 HisG_C-term ATP phos 23.7 1E+02 0.0022 20.1 2.8 43 26-68 28-76 (100)
95 PRK03564 formate dehydrogenase 23.7 50 0.0011 25.9 1.5 15 36-51 35-49 (309)
96 PF10548 P22_AR_C: P22AR C-ter 23.6 71 0.0015 20.1 1.9 22 36-57 20-41 (74)
97 PRK11688 hypothetical protein; 23.4 1.1E+02 0.0024 20.2 2.9 36 32-67 3-38 (154)
98 cd09030 DUF1425 Putative perip 23.2 53 0.0011 20.5 1.3 18 13-30 58-76 (101)
99 cd04933 ACT_AK1-AT_1 ACT domai 23.2 1E+02 0.0023 19.1 2.6 24 15-39 28-51 (78)
100 PF02518 HATPase_c: Histidine 23.1 1.1E+02 0.0024 17.9 2.6 22 15-37 90-111 (111)
101 KOG0816|consensus 22.9 30 0.00066 26.8 0.2 27 30-59 133-159 (223)
102 PHA00276 phage lambda Rz-like 22.8 84 0.0018 22.8 2.4 27 31-57 108-134 (144)
103 TIGR03221 muco_delta muconolac 22.3 1.5E+02 0.0033 19.8 3.4 11 27-37 3-13 (90)
104 TIGR00209 galT_1 galactose-1-p 22.2 46 0.00099 25.8 1.0 19 28-46 321-339 (347)
105 TIGR01562 FdhE formate dehydro 22.2 51 0.0011 25.7 1.3 14 37-51 32-45 (305)
106 cd02130 PA_ScAPY_like PA_ScAPY 22.2 1.2E+02 0.0025 19.2 2.7 21 31-51 97-117 (122)
107 PF10469 AKAP7_NLS: AKAP7 2'5' 21.7 1.4E+02 0.003 20.4 3.2 51 13-63 80-136 (209)
108 PF13893 RRM_5: RNA recognitio 21.7 1.5E+02 0.0032 15.8 3.6 41 4-45 1-41 (56)
109 PTZ00278 ARP2/3 complex subuni 21.6 57 0.0012 24.5 1.4 15 22-36 67-82 (174)
110 smart00837 DPBB_1 Rare lipopro 21.4 1.2E+02 0.0025 19.3 2.6 25 29-62 62-86 (87)
111 cd07377 WHTH_GntR Winged helix 21.3 90 0.0019 16.5 1.8 16 32-47 35-51 (66)
112 TIGR00755 ksgA dimethyladenosi 21.1 44 0.00095 23.5 0.7 22 28-51 121-142 (253)
113 PF09650 PHA_gran_rgn: Putativ 21.0 84 0.0018 19.9 1.9 17 21-38 52-68 (87)
114 KOG1119|consensus 20.8 1.4E+02 0.003 22.9 3.4 32 30-67 92-123 (199)
115 PF00705 PCNA_N: Proliferating 20.8 1E+02 0.0022 20.4 2.3 27 14-40 32-58 (127)
116 cd00063 FN3 Fibronectin type 3 20.7 1.4E+02 0.003 15.1 2.6 21 15-36 5-25 (93)
117 PRK07777 aminotransferase; Val 20.2 1.2E+02 0.0026 22.0 2.8 22 26-47 360-385 (387)
118 PRK05114 hypothetical protein; 20.1 97 0.0021 19.8 2.0 20 36-55 14-33 (59)
119 COG4063 MtrA Tetrahydromethano 20.0 67 0.0015 25.2 1.5 14 32-45 115-128 (238)
120 cd04924 ACT_AK-Arch_2 ACT doma 20.0 1.6E+02 0.0034 15.6 2.8 17 26-42 40-56 (66)
No 1
>PF13820 Nucleic_acid_bd: Putative nucleic acid-binding region
Probab=99.93 E-value=4.6e-27 Score=165.23 Aligned_cols=66 Identities=59% Similarity=0.830 Sum_probs=59.7
Q ss_pred hHHHhhcCCCCcCeeeeeecCCceeEEEEeccHHHHHHHHHHHHhCChhhhhcceeEEEecchhHHHH
Q psy12287 4 LYKVCFNLGGTEGINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDELILT 71 (76)
Q Consensus 4 ~~~~c~~~~~~~~l~v~kvEPWnSVRVTf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~~I~l 71 (76)
|-++|.- ..+.++++++||||||||||+||||||++||+||+++|++|++|||+|||+|||++|++
T Consensus 26 l~~L~~~--~~~~l~~~~~~~~~sv~V~f~ipreaa~~Lr~LA~~~~~~L~~lgI~SVQIe~e~~I~l 91 (149)
T PF13820_consen 26 LASLYKP--RISDLKVRKVEPWNSVRVTFSIPREAATRLRQLAQHSNPRLRYLGILSVQIEGEEPIGL 91 (149)
T ss_pred HHHHHhc--ccccceeeccccCceEEEEEechHHHHHHHHHHhhcCCcceeeeceEEEEEcCcceeEe
Confidence 4455543 55789999999999999999999999999999999999999999999999999999964
No 2
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=95.63 E-value=0.015 Score=30.88 Aligned_cols=25 Identities=32% Similarity=0.464 Sum_probs=22.1
Q ss_pred EEEEeccHHHHHHHHHHHHhCChhh
Q psy12287 29 RVTFTIPKEAAVRLRQLAQQGNATL 53 (76)
Q Consensus 29 RVTf~IPreAA~rLr~LA~~g~~~L 53 (76)
|+||++|.+-.++|.++|...+..-
T Consensus 1 Riti~l~~~~~~~l~~~a~~~g~s~ 25 (39)
T PF01402_consen 1 RITIRLPDELYERLDELAKELGRSR 25 (39)
T ss_dssp EEEEEEEHHHHHHHHHHHHHHTSSH
T ss_pred CeEEEeCHHHHHHHHHHHHHHCcCH
Confidence 8999999999999999999876543
No 3
>PF11130 TraC_F_IV: F pilus assembly Type-IV secretion system for plasmid transfer
Probab=91.38 E-value=0.85 Score=31.39 Aligned_cols=69 Identities=19% Similarity=0.314 Sum_probs=50.1
Q ss_pred hhhHHHhhcCC---CCcCeeeeeecCCceeEEEEecc-----HHHHHHHHHHHHhCChhhhhcceeEEEecchhHHHHhh
Q psy12287 2 KYLYKVCFNLG---GTEGINLRKVEPWNSVRVTFTIP-----KEAAVRLRQLAQQGNATLLQLGILSVQVEGDELILTLH 73 (76)
Q Consensus 2 ~~~~~~c~~~~---~~~~l~v~kvEPWnSVRVTf~IP-----reAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~~I~l~~ 73 (76)
+|+.+-..+.. ++..+.+.++ .+=|++++| .++.+.|.++...=..+|+..||-...++++..|.++.
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~R~~----rl~is~~~p~~~~~~~~~~~l~~~~~~~~~~L~~~gi~~~~~~~~~l~~~l~ 174 (235)
T PF11130_consen 99 EFLRRGAWKGLGGLDDSPTPLRNF----RLFISVKVPGSKPSEEEIEELNELRERLESSLRSAGIPPRRLDPEDLISWLR 174 (235)
T ss_pred HHHHHHhhcCCCcccCCCceeEEE----EEEEEEEecCCcCCccHHHHHHHHHHHHHHHHHHCCCccEEcCHHHHHHHHH
Confidence 45555555332 3344444443 344677788 56777888888888899999999999999999999987
Q ss_pred h
Q psy12287 74 Q 74 (76)
Q Consensus 74 ~ 74 (76)
.
T Consensus 175 ~ 175 (235)
T PF11130_consen 175 R 175 (235)
T ss_pred H
Confidence 5
No 4
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=90.96 E-value=0.42 Score=27.26 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=21.9
Q ss_pred ceeEEEEeccHHHHHHHHHHHHhCC
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQQGN 50 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~~g~ 50 (76)
|-.|+|++||.|=.++|..||.+-.
T Consensus 1 ~r~r~t~~l~~el~~~L~~ls~~t~ 25 (44)
T PF12651_consen 1 NRKRFTFSLDKELYEKLKELSEETG 25 (44)
T ss_pred CceEEEEecCHHHHHHHHHHHHHHC
Confidence 4579999999999999999998643
No 5
>PHA01623 hypothetical protein
Probab=87.71 E-value=1 Score=27.08 Aligned_cols=27 Identities=15% Similarity=0.222 Sum_probs=24.4
Q ss_pred ceeEEEEeccHHHHHHHHHHHHhCChh
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQQGNAT 52 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~~g~~~ 52 (76)
..||++|+||.+=.++|..+|.+++-.
T Consensus 12 k~~r~sVrldeel~~~Ld~y~~~~g~~ 38 (56)
T PHA01623 12 QKAVFGIYMDKDLKTRLKVYCAKNNLQ 38 (56)
T ss_pred cceeEEEEeCHHHHHHHHHHHHHcCCC
Confidence 479999999999999999999988755
No 6
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=87.24 E-value=1.2 Score=25.94 Aligned_cols=50 Identities=24% Similarity=0.287 Sum_probs=35.2
Q ss_pred CCcCeeeeeecCCceeEEEEeccHHHHHHHHHHHHhCChhhhhc-ceeEEEe
Q psy12287 13 GTEGINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQQGNATLLQL-GILSVQV 63 (76)
Q Consensus 13 ~~~~l~v~kvEPWnSVRVTf~IPreAA~rLr~LA~~g~~~Lr~L-GILSVQ~ 63 (76)
+.+.++==.++. +.|+|++++|..+...-..|+++=-..|+++ |+-+|++
T Consensus 22 ~~g~V~~i~i~~-~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 22 ELGMVRDISIEG-GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp TTTSEEEEEECT-CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred HcCCeeEEEEEC-CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 344455556677 8999999999877777777888777888877 7777764
No 7
>PHA00617 ribbon-helix-helix domain containing protein
Probab=85.20 E-value=2.1 Score=27.94 Aligned_cols=36 Identities=25% Similarity=0.360 Sum_probs=28.3
Q ss_pred CcCeeeeeecCCceeEEEEeccHHHHHHHHHHHHhCCh
Q psy12287 14 TEGINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQQGNA 51 (76)
Q Consensus 14 ~~~l~v~kvEPWnSVRVTf~IPreAA~rLr~LA~~g~~ 51 (76)
...+.++=.|| ..++||++|.|=.+||..||..-+-
T Consensus 28 ~~~~~~~~~~~--m~~iSVrLp~eL~erLD~LA~~~Gr 63 (80)
T PHA00617 28 GDTIELTLTET--MDVISFKLPPELNAKLEQVAIKMKK 63 (80)
T ss_pred CCccccccCCC--ceEEEEECCHHHHHHHHHHHHHhCc
Confidence 34555555556 8999999999999999999987543
No 8
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=81.52 E-value=1.2 Score=27.50 Aligned_cols=39 Identities=18% Similarity=0.239 Sum_probs=31.2
Q ss_pred ceeEEEEeccHHHHHHHHHHHHhCChhhhhc-ceeEEEec
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQQGNATLLQL-GILSVQVE 64 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~~g~~~Lr~L-GILSVQ~E 64 (76)
+.|+|++++|..++.-..+|.+.-...|.++ |+-+|.++
T Consensus 37 ~~v~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~ 76 (99)
T TIGR02945 37 GHVDIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVE 76 (99)
T ss_pred CeEEEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEE
Confidence 4799999999888777777877777888885 88777764
No 9
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=79.99 E-value=2.5 Score=28.95 Aligned_cols=21 Identities=29% Similarity=0.368 Sum_probs=18.9
Q ss_pred eEEEEeccHHHHHHHHHHHHh
Q psy12287 28 VRVTFTIPKEAAVRLRQLAQQ 48 (76)
Q Consensus 28 VRVTf~IPreAA~rLr~LA~~ 48 (76)
.|+++++|.+-...|-++++.
T Consensus 1 ~risvslp~~ll~~lD~~~~~ 21 (129)
T TIGR02793 1 QRVTITLDDDLLETLDRLIAR 21 (129)
T ss_pred CEEEEEcCHHHHHHHHHHHHH
Confidence 489999999999999998874
No 10
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=78.58 E-value=9.4 Score=21.33 Aligned_cols=39 Identities=18% Similarity=0.310 Sum_probs=28.1
Q ss_pred ecCCceeEEEEeccHHHHH-HHHHHHHhCChhhhhc-ceeEEEec
Q psy12287 22 VEPWNSVRVTFTIPKEAAV-RLRQLAQQGNATLLQL-GILSVQVE 64 (76)
Q Consensus 22 vEPWnSVRVTf~IPreAA~-rLr~LA~~g~~~Lr~L-GILSVQ~E 64 (76)
..|++..++.|+++-.-.+ .|.++.. +|+++ |+.+|.+-
T Consensus 35 ~~~~~~~~i~~~v~v~~~~~~l~~l~~----~L~~i~~V~~v~~~ 75 (76)
T cd04888 35 IPIHGRANVTISIDTSTMNGDIDELLE----ELREIDGVEKVELV 75 (76)
T ss_pred CCCCCeEEEEEEEEcCchHHHHHHHHH----HHhcCCCeEEEEEe
Confidence 3478888999999876666 8888875 35554 77777653
No 11
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=78.25 E-value=3.2 Score=28.88 Aligned_cols=39 Identities=26% Similarity=0.277 Sum_probs=33.1
Q ss_pred ceeEEEEeccHHHHHHHHHHHHhCChhhhhcceeEEEec
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVE 64 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~E 64 (76)
+.|+|+++++-.++.-...|++.=-.+|+++|+-+|.++
T Consensus 25 d~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~Gv~~V~V~ 63 (146)
T TIGR02159 25 GGVVVKFTPTYSGCPALEVIRQDIRDAVRALGVEVVEVS 63 (146)
T ss_pred CEEEEEEEeCCCCCchHHHHHHHHHHHHHhcCCCeEEEe
Confidence 579999999988888888888888889999999777764
No 12
>PHA01748 hypothetical protein
Probab=77.91 E-value=4.2 Score=24.45 Aligned_cols=24 Identities=21% Similarity=0.209 Sum_probs=21.2
Q ss_pred eEEEEeccHHHHHHHHHHHHhCCh
Q psy12287 28 VRVTFTIPKEAAVRLRQLAQQGNA 51 (76)
Q Consensus 28 VRVTf~IPreAA~rLr~LA~~g~~ 51 (76)
.+++|+||.+=.++|..+|+..+-
T Consensus 3 ~~iSvrLp~el~~eld~~a~~~g~ 26 (60)
T PHA01748 3 KVITFKIEEDLLELLDRYAIKHGL 26 (60)
T ss_pred eEEEEECCHHHHHHHHHHHHHhCC
Confidence 489999999999999999987664
No 13
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=75.57 E-value=5.9 Score=23.11 Aligned_cols=27 Identities=15% Similarity=0.396 Sum_probs=23.6
Q ss_pred EEEEeccHHHHHHHHHHHHhCChhhhh
Q psy12287 29 RVTFTIPKEAAVRLRQLAQQGNATLLQ 55 (76)
Q Consensus 29 RVTf~IPreAA~rLr~LA~~g~~~Lr~ 55 (76)
+.++.||.+=.++|+..|..+...+.+
T Consensus 6 ~f~lRlP~~l~~~lk~~A~~~gRS~Ns 32 (50)
T PF03869_consen 6 QFNLRLPEELKEKLKERAEENGRSMNS 32 (50)
T ss_dssp EEEEECEHHHHHHHHHHHHHTTS-HHH
T ss_pred ceeeECCHHHHHHHHHHHHHhCCChHH
Confidence 688999999999999999999888764
No 14
>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional
Probab=74.26 E-value=5.3 Score=33.56 Aligned_cols=49 Identities=18% Similarity=0.302 Sum_probs=40.3
Q ss_pred eeEEEEeccH----HH-HHHHHHHHHhCChhhhhcceeEEEecchhHHHHhhhh
Q psy12287 27 SVRVTFTIPK----EA-AVRLRQLAQQGNATLLQLGILSVQVEGDELILTLHQA 75 (76)
Q Consensus 27 SVRVTf~IPr----eA-A~rLr~LA~~g~~~Lr~LGILSVQ~EGd~~I~l~~~~ 75 (76)
.|=|||++|. +| -.+|.++...=-..|+.+|+-...++++..|++++..
T Consensus 129 r~~~s~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~g~~~~~l~~~~ll~~~~~~ 182 (844)
T PRK13721 129 RVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFISIVREM 182 (844)
T ss_pred EEEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHCCCCceeCCHHHHHHHHHHH
Confidence 3456888884 23 3478888888889999999999999999999999853
No 15
>TIGR01911 HesB_rel_seleno HesB-like selenoprotein. This model represents a family of small proteins related to HesB and its close homologs, which are likely to be invovlved in iron-sulfur cluster assembly (See TIGR00049 and pfam01521). Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain. A variable Cys/Ser/Gly-rich C-terminal region is not included in the seed alignment and model.
Probab=74.17 E-value=5.4 Score=25.37 Aligned_cols=32 Identities=6% Similarity=0.164 Sum_probs=21.0
Q ss_pred EEeccHHHHHHHHHHHHhC-ChhhhhcceeEEEecch
Q psy12287 31 TFTIPKEAAVRLRQLAQQG-NATLLQLGILSVQVEGD 66 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g-~~~Lr~LGILSVQ~EGd 66 (76)
.++|...||+|++.|.++. ++. .| |.|-++|.
T Consensus 3 ~i~lT~~A~~~i~~ll~~~~~~~---~~-LRi~v~~g 35 (92)
T TIGR01911 3 IVAMSDDAYEEFKDFLKENDIDN---DV-IRIHFAGM 35 (92)
T ss_pred ceEECHHHHHHHHHHHHhCCCCC---ce-EEEEEeCC
Confidence 4678899999999976543 333 23 55655543
No 16
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=72.73 E-value=6.9 Score=24.98 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=22.7
Q ss_pred EEeccHHHHHHHHHHHHhCChhhhhcceeEEEecch
Q psy12287 31 TFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGD 66 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd 66 (76)
+++|...|+++|+++.+..++ ..| |.|.+++.
T Consensus 2 ~i~iT~~A~~~i~~l~~~~~~---~~~-LRi~v~~~ 33 (107)
T PRK09502 2 SITLSDSAAARVNTFLANRGK---GFG-LRLGVRTS 33 (107)
T ss_pred eEEECHHHHHHHHHHHhCcCC---Cce-EEEEEECC
Confidence 477889999999999865443 333 66766654
No 17
>PRK01002 nickel responsive regulator; Provisional
Probab=72.10 E-value=6.2 Score=27.07 Aligned_cols=23 Identities=9% Similarity=0.387 Sum_probs=20.3
Q ss_pred eeEEEEeccHHHHHHHHHHHHhC
Q psy12287 27 SVRVTFTIPKEAAVRLRQLAQQG 49 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA~~g 49 (76)
-+|++++||.+-++.|.+++++.
T Consensus 4 ~~risislp~~ll~~lD~~~~~~ 26 (141)
T PRK01002 4 MMRISISLPDKLLGEFDEIIEER 26 (141)
T ss_pred cEEEEEEeCHHHHHHHHHHHHHc
Confidence 57999999999999999987755
No 18
>PHA01474 nonstructural protein
Probab=71.55 E-value=1.7 Score=27.06 Aligned_cols=15 Identities=47% Similarity=0.982 Sum_probs=11.2
Q ss_pred ecCCceeEEEEeccHH
Q psy12287 22 VEPWNSVRVTFTIPKE 37 (76)
Q Consensus 22 vEPWnSVRVTf~IPre 37 (76)
+.||||.| +|.|.|.
T Consensus 27 lspwnsfr-sfriswr 41 (52)
T PHA01474 27 LSPWNSFR-SFRISWR 41 (52)
T ss_pred eCccccce-eEEEEEe
Confidence 57999998 5777653
No 19
>PRK04460 nickel responsive regulator; Provisional
Probab=70.73 E-value=7.1 Score=27.02 Aligned_cols=24 Identities=8% Similarity=0.314 Sum_probs=20.3
Q ss_pred eeEEEEeccHHHHHHHHHHHHhCC
Q psy12287 27 SVRVTFTIPKEAAVRLRQLAQQGN 50 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA~~g~ 50 (76)
-+|++++||.+-++.|-+++++..
T Consensus 2 ~~Risvslp~~ll~~lD~~~~~~g 25 (137)
T PRK04460 2 TIRFGVSLDSDLLEKFDELIEEKG 25 (137)
T ss_pred eEEEEEEeCHHHHHHHHHHHHHcC
Confidence 379999999999999998877643
No 20
>PRK02967 nickel responsive regulator; Provisional
Probab=66.18 E-value=9.7 Score=26.40 Aligned_cols=23 Identities=26% Similarity=0.309 Sum_probs=19.9
Q ss_pred eEEEEeccHHHHHHHHHHHHhCC
Q psy12287 28 VRVTFTIPKEAAVRLRQLAQQGN 50 (76)
Q Consensus 28 VRVTf~IPreAA~rLr~LA~~g~ 50 (76)
+|+|+++|.+-.+.|.+++++..
T Consensus 2 ~risvslp~~ll~~lD~~~~~~g 24 (139)
T PRK02967 2 QRVTITLDDDLLETLDSLIARRG 24 (139)
T ss_pred eEEEEEcCHHHHHHHHHHHHHcC
Confidence 69999999999999998887643
No 21
>PF10038 DUF2274: Protein of unknown function (DUF2274); InterPro: IPR018733 Members of this family of hypothetical bacterial proteins have no known function.
Probab=65.11 E-value=12 Score=23.86 Aligned_cols=33 Identities=18% Similarity=0.248 Sum_probs=25.6
Q ss_pred CeeeeeecCCceeEEEEeccHHHHHHHHHHHHh
Q psy12287 16 GINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQQ 48 (76)
Q Consensus 16 ~l~v~kvEPWnSVRVTf~IPreAA~rLr~LA~~ 48 (76)
+|++-.++.=..|++||++|-+-...|..-|+-
T Consensus 3 kLklg~lpd~kPVKlti~lpa~l~rdL~~Ya~~ 35 (69)
T PF10038_consen 3 KLKLGPLPDDKPVKLTIELPASLHRDLVAYAEA 35 (69)
T ss_pred CCCCCCCCCCCCeeEEEeCCHHHHHHHHHHHHH
Confidence 456666666677999999999998888776653
No 22
>COG4829 CatC1 Muconolactone delta-isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=64.66 E-value=5 Score=27.79 Aligned_cols=33 Identities=27% Similarity=0.337 Sum_probs=26.0
Q ss_pred eeEEEEeccHHHHHHHHHHHHhCChhhhhccee
Q psy12287 27 SVRVTFTIPKEAAVRLRQLAQQGNATLLQLGIL 59 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA~~g~~~Lr~LGIL 59 (76)
.|||-.+.|.+|++|+|.=-.+-++.|.+-|++
T Consensus 8 tv~~PdsMdad~~er~~A~Eka~s~~Lq~~G~~ 40 (98)
T COG4829 8 TVRVPDSMDADAVERVRAREKARSRELQAQGKL 40 (98)
T ss_pred EEEcCCCCCHHHHHHHHHHHHHHHHHHHhcchH
Confidence 366667788999999998777778888777764
No 23
>PF09274 ParG: ParG; InterPro: IPR015354 This entry represents plasmid partition proteins; it adopts a ribbon-helix-helix fold, with a core of four alpha-helices. The proteins are an essential component of the DNA partition complex of the multi drug resistance plasmid TP228 []. ; PDB: 1P94_B.
Probab=62.45 E-value=11 Score=24.56 Aligned_cols=30 Identities=20% Similarity=0.321 Sum_probs=22.6
Q ss_pred ceeEEEEeccHHHHHHHHHHHHhCChhhhh
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQQGNATLLQ 55 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~~g~~~Lr~ 55 (76)
..+||||+||.|-=.||...|+...-...|
T Consensus 33 k~Krvtv~i~EelH~r~K~~ca~~G~sisd 62 (76)
T PF09274_consen 33 KTKRVTVNIDEELHRRFKAACAKQGTSISD 62 (76)
T ss_dssp TEEEE-EEEEHHHHHHHHHHHHHHT--HHH
T ss_pred ceEEEEEecCHHHHHHHHHHHHHcCCcHHH
Confidence 379999999999999999988876655443
No 24
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=62.12 E-value=6.3 Score=23.06 Aligned_cols=27 Identities=33% Similarity=0.507 Sum_probs=22.3
Q ss_pred EeccHHHHHHHHHHHHhCChhhhhcce
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATLLQLGI 58 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~Lr~LGI 58 (76)
+.+|.++++.|.+|++.-.+.+...|+
T Consensus 1 i~~p~~~~~~L~~l~~~l~~~~~~~~~ 27 (87)
T PF02834_consen 1 IDLPEEIKEQLNQLQERLRQALPPLGI 27 (87)
T ss_dssp EE-THHHHHHHHHHHHHHHHHCCSCTE
T ss_pred CCCCHHHHHHHHHHHHHHhhhccccCC
Confidence 457999999999999988877777777
No 25
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=61.94 E-value=7.6 Score=21.50 Aligned_cols=20 Identities=25% Similarity=0.420 Sum_probs=17.0
Q ss_pred HHHHHHHHhCChhhhhccee
Q psy12287 40 VRLRQLAQQGNATLLQLGIL 59 (76)
Q Consensus 40 ~rLr~LA~~g~~~Lr~LGIL 59 (76)
.-.++|++=.+.+|.|+||-
T Consensus 15 rtr~~L~~Lsd~~L~DIGl~ 34 (40)
T PF06568_consen 15 RTRRELAELSDRQLADIGLT 34 (40)
T ss_pred HHHHHHccCCHHHHHHcCCC
Confidence 44588999999999999984
No 26
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=61.63 E-value=16 Score=23.20 Aligned_cols=32 Identities=22% Similarity=0.451 Sum_probs=22.0
Q ss_pred EEeccHHHHHHHHHHHHhCChhhhhcceeEEEecch
Q psy12287 31 TFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGD 66 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd 66 (76)
.++|-..||++++++.+.... .+| |.|-+++.
T Consensus 2 ~i~iT~~A~~~i~~l~~~~~~---~~~-lRi~v~~~ 33 (107)
T TIGR01997 2 VITLTDAAAIHIRELVAKRPE---AVG-IRLGVKKT 33 (107)
T ss_pred eEEECHHHHHHHHHHHhcCCC---CcE-EEEEEECC
Confidence 367889999999998876543 233 56666543
No 27
>TIGR02746 TraC-F-type type-IV secretion system protein TraC. The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.
Probab=60.30 E-value=13 Score=30.19 Aligned_cols=46 Identities=22% Similarity=0.378 Sum_probs=38.8
Q ss_pred EEEeccH-----HHHHHHHHHHHhCChhhhhcceeEEEecchhHHHHhhhh
Q psy12287 30 VTFTIPK-----EAAVRLRQLAQQGNATLLQLGILSVQVEGDELILTLHQA 75 (76)
Q Consensus 30 VTf~IPr-----eAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~~I~l~~~~ 75 (76)
|++++|. ++.+.|.++..+=-..|+..|+-...+.++.+++++|..
T Consensus 116 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~g~~~~~l~~~e~l~~l~~~ 166 (797)
T TIGR02746 116 LSVSIPFKSPNEDVIQELRSLRERIESTLRSAGFGCRRVDAEDLLSLVREM 166 (797)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHHhCCCCceecCHHHHHHHHHHH
Confidence 3455663 677888999888899999999999999999999999864
No 28
>PF09981 DUF2218: Uncharacterized protein conserved in bacteria (DUF2218); InterPro: IPR014543 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2JPI_A.
Probab=60.11 E-value=13 Score=23.64 Aligned_cols=28 Identities=29% Similarity=0.522 Sum_probs=19.7
Q ss_pred hhhHHHhhcCCCCcCeeeeeecCCceeEEEEe
Q psy12287 2 KYLYKVCFNLGGTEGINLRKVEPWNSVRVTFT 33 (76)
Q Consensus 2 ~~~~~~c~~~~~~~~l~v~kvEPWnSVRVTf~ 33 (76)
+||.+||.|.+ .++.|.--+- +-+|+|.
T Consensus 12 ryl~qLc~Hf~--hk~~v~~d~~--~g~i~f~ 39 (89)
T PF09981_consen 12 RYLKQLCKHFA--HKFEVEWDED--SGRITFP 39 (89)
T ss_dssp HHHHHHHHHTT--TSSEEEE-SS--EEEEE-S
T ss_pred HHHHHHHHHhc--CCCceEEcCC--ceEEEeC
Confidence 79999999997 5666665443 6777765
No 29
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=58.36 E-value=21 Score=20.85 Aligned_cols=46 Identities=24% Similarity=0.318 Sum_probs=31.7
Q ss_pred CeeeeeecCCceeEEEEeccH-HHHHHHHHHHHhCChhhhhcceeEEEe
Q psy12287 16 GINLRKVEPWNSVRVTFTIPK-EAAVRLRQLAQQGNATLLQLGILSVQV 63 (76)
Q Consensus 16 ~l~v~kvEPWnSVRVTf~IPr-eAA~rLr~LA~~g~~~Lr~LGILSVQ~ 63 (76)
.+++ ++.+ +.++|.|.... ++++.|++-..+=...|++.|+-.+++
T Consensus 28 ~v~l-~~~~-~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~ 74 (85)
T PF02120_consen 28 EVKL-RLQG-GNLSVQFTAENPETKELLRQNLPELKERLQAQGLEVVNL 74 (85)
T ss_dssp EEEE-EEET-TEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-EEEEE
T ss_pred EEEE-EEeC-CEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCeEEE
Confidence 3344 3344 58888888855 788889988888888999999865544
No 30
>PRK00630 nickel responsive regulator; Provisional
Probab=56.72 E-value=17 Score=25.51 Aligned_cols=24 Identities=8% Similarity=0.163 Sum_probs=20.5
Q ss_pred ceeEEEEeccHHHHHHHHHHHHhC
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQQG 49 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~~g 49 (76)
.-+|+++|+|.+-..++.++++++
T Consensus 9 ~~~risVslp~~Ll~~lD~~~~~~ 32 (148)
T PRK00630 9 SIIRFSVSLQQNLLDELDNRIIKN 32 (148)
T ss_pred CeEEEEEEcCHHHHHHHHHHHHHc
Confidence 368999999999999999986654
No 31
>KOG2415|consensus
Probab=55.67 E-value=6.2 Score=34.16 Aligned_cols=18 Identities=50% Similarity=0.660 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHhCChhhh
Q psy12287 37 EAAVRLRQLAQQGNATLL 54 (76)
Q Consensus 37 eAA~rLr~LA~~g~~~Lr 54 (76)
.||-||+|||++-|.+||
T Consensus 90 saAIrlKQla~~~~~dlr 107 (621)
T KOG2415|consen 90 SAAIRLKQLAAKANKDLR 107 (621)
T ss_pred HHHHHHHHHHHhcCCceE
Confidence 489999999999999876
No 32
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=54.46 E-value=19 Score=22.80 Aligned_cols=30 Identities=23% Similarity=0.388 Sum_probs=20.4
Q ss_pred EeccHHHHHHHHHHHHhCChhhhhcceeEEEecc
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEG 65 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EG 65 (76)
++|...|+++++++..+... .+| |.|.+++
T Consensus 1 I~iT~~A~~~i~~~~~~~~~---~~~-lRi~v~~ 30 (105)
T TIGR02011 1 ITLTDSAAARVNTFLANRGK---GFG-LRLGVKT 30 (105)
T ss_pred CEECHHHHHHHHHHHhccCC---Cce-EEEEEeC
Confidence 46778999999998865432 333 5666654
No 33
>PF15320 RAM: mRNA cap methylation, RNMT-activating mini protein
Probab=51.16 E-value=12 Score=24.46 Aligned_cols=19 Identities=42% Similarity=0.634 Sum_probs=13.7
Q ss_pred HHHhhcCCCCcCeeeeeecCCce
Q psy12287 5 YKVCFNLGGTEGINLRKVEPWNS 27 (76)
Q Consensus 5 ~~~c~~~~~~~~l~v~kvEPWnS 27 (76)
-|+|..+.++-.+ ||||+|
T Consensus 19 ~~~~~~~~~~PPI----V~~W~~ 37 (81)
T PF15320_consen 19 MEYCKRPFPPPPI----VEPWNS 37 (81)
T ss_pred HHHHhCCCCCCCE----ecCccc
Confidence 4677777775544 899987
No 34
>PF01521 Fe-S_biosyn: Iron-sulphur cluster biosynthesis; InterPro: IPR000361 The proteins in this entry are variously annotated as iron-sulphur cluster insertion protein or Fe/S biogenesis protein. They appear to be involved in Fe-S cluster biogenesis. This family includes IscA, HesB, YadR and YfhF-like proteins. The hesB gene is expressed only under nitrogen fixation conditions []. IscA, an 11 kDa member of the hesB family of proteins, binds iron and [2Fe-2S] clusters, and participates in the biosynthesis of iron-sulphur proteins. IscA is able to bind at least 2 iron ions per dimer []. Other members of this family include various hypothetical proteins that also contain the NifU-like domain (IPR001075 from INTERPRO) suggesting that they too are able to bind iron and are involved in Fe-S cluster biogenesis. The HesB family are found in species as divergent as Homo sapiens (Human) and Haemophilus influenzae suggesting that these proteins are involved in basic cellular functions []. ; PDB: 2D2A_A 1X0G_D 1NWB_A 2K4Z_A 1R94_B 1R95_A 1S98_B 2P2E_A 2QGO_A 2APN_A.
Probab=49.83 E-value=14 Score=22.81 Aligned_cols=22 Identities=36% Similarity=0.457 Sum_probs=17.9
Q ss_pred EEeccHHHHHHHHHHHHhCChh
Q psy12287 31 TFTIPKEAAVRLRQLAQQGNAT 52 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g~~~ 52 (76)
.++|-.+|+++|+++..+.+..
T Consensus 2 ~I~iT~~A~~~l~~~~~~~~~~ 23 (112)
T PF01521_consen 2 KITITDAAAERLKQLLKEDPKK 23 (112)
T ss_dssp EEEE-HHHHHHHHHHHHCTTES
T ss_pred EEEECHHHHHHHHHHHhcCCCE
Confidence 4778899999999999887765
No 35
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=46.55 E-value=21 Score=23.46 Aligned_cols=24 Identities=42% Similarity=0.592 Sum_probs=17.8
Q ss_pred ceeEEEEeccHHHHHHHHHHHHhCChhh
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQQGNATL 53 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~~g~~~L 53 (76)
.=-.|+||||.+ ||.++..+...|
T Consensus 86 ~y~HvVFTlP~~----L~~~~~~n~~~l 109 (111)
T PF14319_consen 86 PYFHVVFTLPHE----LRPLFRQNRRLL 109 (111)
T ss_pred CeEEEEEcCcHH----HHHHHHHCHHHh
Confidence 356799999975 888887765443
No 36
>TIGR00406 prmA ribosomal protein L11 methyltransferase. Ribosomal protein L11 methyltransferase is an S-adenosyl-L-methionine-dependent methyltransferase required for the modification of ribosomal protein L11. This protein is found in bacteria and (with a probable transit peptide) in Arabidopsis.
Probab=46.11 E-value=45 Score=24.23 Aligned_cols=30 Identities=23% Similarity=0.298 Sum_probs=23.2
Q ss_pred EEEEeccHHHHHHHHHHHHhCChhhhhcceeEEEecc
Q psy12287 29 RVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEG 65 (76)
Q Consensus 29 RVTf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EG 65 (76)
.|++..|.|+++.+-. .|-++|+.+|.+|.
T Consensus 3 ~~~~~~~~~~~e~~~~-------~l~~~g~~gv~~~d 32 (288)
T TIGR00406 3 EIRINTTKELAEATSD-------ALEEAGAVGVTFED 32 (288)
T ss_pred EEEEEeCHHHHHHHHH-------HHHhcCCCEEEEEc
Confidence 4566778999986654 47889999999864
No 37
>cd04819 PA_2 PA_2: Protease-associated (PA) domain subgroup 2. A subgroup of PA-domain containing proteins. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuola
Probab=46.10 E-value=24 Score=22.87 Aligned_cols=21 Identities=19% Similarity=0.446 Sum_probs=18.3
Q ss_pred EEeccHHHHHHHHHHHHhCCh
Q psy12287 31 TFTIPKEAAVRLRQLAQQGNA 51 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g~~ 51 (76)
+|+|..+.+++|..+++.|.+
T Consensus 102 ~v~Is~edg~~L~~~l~~g~~ 122 (127)
T cd04819 102 AASVSGEDGLRLARVAERNDT 122 (127)
T ss_pred EEEEeHHHHHHHHHHHhcCCc
Confidence 578999999999999998754
No 38
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=45.83 E-value=7.1 Score=27.69 Aligned_cols=15 Identities=33% Similarity=0.443 Sum_probs=10.6
Q ss_pred ChhhHHHhhcCCCCc
Q psy12287 1 MKYLYKVCFNLGGTE 15 (76)
Q Consensus 1 ~~~~~~~c~~~~~~~ 15 (76)
|||+||--+.+.++.
T Consensus 107 MKYiYkg~~~~~~~s 121 (152)
T PF04699_consen 107 MKYIYKGMESPSENS 121 (152)
T ss_dssp HHHHHHHTTS--TTH
T ss_pred HHHHHHhccCccCcc
Confidence 899999888777643
No 39
>PRK13623 iron-sulfur cluster insertion protein ErpA; Provisional
Probab=45.47 E-value=17 Score=23.24 Aligned_cols=20 Identities=15% Similarity=0.419 Sum_probs=16.4
Q ss_pred EEEeccHHHHHHHHHHHHhC
Q psy12287 30 VTFTIPKEAAVRLRQLAQQG 49 (76)
Q Consensus 30 VTf~IPreAA~rLr~LA~~g 49 (76)
..++|-..|+++++++.+..
T Consensus 8 ~~i~iT~~A~~~i~~~~~~~ 27 (115)
T PRK13623 8 LPLVFTDAAAAKVKELIEEE 27 (115)
T ss_pred cceEECHHHHHHHHHHHhhC
Confidence 45788999999999988653
No 40
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=45.36 E-value=30 Score=22.83 Aligned_cols=32 Identities=22% Similarity=0.349 Sum_probs=22.2
Q ss_pred EeccHHHHHHHHHHHHhCChhhhhcceeEEEecchh
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDE 67 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~ 67 (76)
++|-..|+.++++|.+.... .+| |.|.+++.+
T Consensus 18 I~iT~~A~~~i~~l~~~~~~---~~~-LRi~v~~gG 49 (122)
T PRK09504 18 LTLTPAAAAHIRELMAKQPG---MKG-VRLGVKQTG 49 (122)
T ss_pred EEECHHHHHHHHHHHhcCCC---Cce-EEEEEECCC
Confidence 56678999999999865332 233 778887653
No 41
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=42.96 E-value=23 Score=23.79 Aligned_cols=21 Identities=24% Similarity=0.428 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHhCChhhhhc
Q psy12287 36 KEAAVRLRQLAQQGNATLLQL 56 (76)
Q Consensus 36 reAA~rLr~LA~~g~~~Lr~L 56 (76)
.||-.+|.+||++||=.+.+|
T Consensus 51 ~~sl~kL~~La~~N~v~feeL 71 (82)
T PF11020_consen 51 MDSLSKLYKLAKENNVSFEEL 71 (82)
T ss_pred HHHHHHHHHHHHHcCCCHHHH
Confidence 478999999999999887776
No 42
>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family. Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.
Probab=42.67 E-value=40 Score=28.92 Aligned_cols=38 Identities=18% Similarity=0.221 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHhCChhhhhcceeEEEecchhHHHHhhh
Q psy12287 37 EAAVRLRQLAQQGNATLLQLGILSVQVEGDELILTLHQ 74 (76)
Q Consensus 37 eAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~~I~l~~~ 74 (76)
+...+|.++...=...|+.+|+-+..+.|+..+++||.
T Consensus 171 ~~~~~l~~~~~~l~~~L~~~g~~~~~l~~~~~l~~l~~ 208 (893)
T TIGR03744 171 DPIEMLNQVCERLIAALANAGVTARRQNGRQIYEWLLR 208 (893)
T ss_pred CHHHHHHHHHHHHHHHHhhCCceeEEcCHHHHHHHHHH
Confidence 66779999999999999999999999999999999984
No 43
>PF12404 DUF3663: Peptidase ; InterPro: IPR008330 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 family represents the peptidase B group of leucyl aminopeptidases, which are restricted to the gammaproteobacteria. They contain a C-terminal aminopeptidase catalytic domain and an N-terminal domain of unknown function. They are zinc-dependent exopeptidases (3.4.11.1 from EC) and belong to MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF). They selectively release N-terminal amino acid residues from polypeptides and proteins and are involved in the processing, catabolism and degradation of intracellular proteins [, , ]. Leucyl aminopeptidase forms a homohexamer containing two trimers stacked on top of one another []. Each monomer binds two zinc ions. The zinc-binding and catalytic sites are located within the C-terminal catalytic domain []. The same catalytic aminopeptidase domain is found in the other M17 peptidases IPR011356 from INTERPRO. These two groups of aminopeptidases differ by their N-terminal domains. The N-terminal domain in members of IPR011356 from INTERPRO has been implicated in DNA binding [, ] and it is not associated with members of this family which have a different N-terminal domain and therefore are not expected to bind DNA or be involved in transcriptional regulation. In addition, there are related proteins with the same catalytic domain and unique N-terminal sequences unrelated to any of the two N-terminal domains discussed above. For additional information please see [, , , ]. ; GO: 0004177 aminopeptidase activity, 0008235 metalloexopeptidase activity, 0030145 manganese ion binding, 0005737 cytoplasm
Probab=42.40 E-value=13 Score=24.43 Aligned_cols=17 Identities=29% Similarity=0.390 Sum_probs=15.2
Q ss_pred hhhhhcceeEEEecchh
Q psy12287 51 ATLLQLGILSVQVEGDE 67 (76)
Q Consensus 51 ~~Lr~LGILSVQ~EGd~ 67 (76)
..|+..||-+|.+.||+
T Consensus 45 RkLd~qGI~~V~L~G~~ 61 (77)
T PF12404_consen 45 RKLDGQGIKNVALAGEG 61 (77)
T ss_pred HHHhhCCCceEEEecCC
Confidence 57899999999999984
No 44
>PF05509 TraY: TraY domain; InterPro: IPR008876 This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid [].; GO: 0003677 DNA binding, 0000746 conjugation
Probab=41.87 E-value=30 Score=20.54 Aligned_cols=23 Identities=26% Similarity=0.456 Sum_probs=19.8
Q ss_pred EEEeccHHHHHHHHHHHHhCChh
Q psy12287 30 VTFTIPKEAAVRLRQLAQQGNAT 52 (76)
Q Consensus 30 VTf~IPreAA~rLr~LA~~g~~~ 52 (76)
|+|.+|.|.-++|-++|+.....
T Consensus 1 v~~~L~~e~~~~L~~~a~rsGRS 23 (49)
T PF05509_consen 1 VNFRLDEETNQRLEAAAERSGRS 23 (49)
T ss_pred CeEecCHHHHHHHHHHHHHhCCc
Confidence 68999999999999999876554
No 45
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=41.76 E-value=36 Score=24.40 Aligned_cols=32 Identities=28% Similarity=0.306 Sum_probs=21.9
Q ss_pred EeccHHHHHHHHHHHHhCChhhhhcceeEEEecchh
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDE 67 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~ 67 (76)
++|...||.+++.|.+..++ ..| |.|-+++.+
T Consensus 1 I~IT~~A~~~l~~ll~~~~~---~~~-LRv~V~~gG 32 (190)
T TIGR03341 1 ITITEAAQAYLAKLLAKQNE---GTG-IRVFVVNPG 32 (190)
T ss_pred CEECHHHHHHHHHHHhhCCC---Cce-EEEEEECCc
Confidence 46778999999998876442 334 667666543
No 46
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=41.45 E-value=23 Score=25.30 Aligned_cols=38 Identities=18% Similarity=0.217 Sum_probs=29.7
Q ss_pred eeEEEEeccHHHHHHHHHHHHhCChhhhhc-ceeEEEec
Q psy12287 27 SVRVTFTIPKEAAVRLRQLAQQGNATLLQL-GILSVQVE 64 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA~~g~~~Lr~L-GILSVQ~E 64 (76)
.|+|++++|-.++...-.|++.=...|..+ |+-+|+++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~ 152 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVE 152 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEE
Confidence 689999999888777777777767788886 88777764
No 47
>PF10723 RepB-RCR_reg: Replication regulatory protein RepB; InterPro: IPR019661 This family of proteins regulates the replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of the replication of the RCR plasmids occurs mainly at the initiation of leading strand synthesis at the dso, such that concentration of Rep protein controls plasmid replication []. ; PDB: 2KEL_B.
Probab=41.07 E-value=51 Score=21.16 Aligned_cols=23 Identities=30% Similarity=0.507 Sum_probs=19.9
Q ss_pred eEEEEeccHHHHHHHHHHHHhCC
Q psy12287 28 VRVTFTIPKEAAVRLRQLAQQGN 50 (76)
Q Consensus 28 VRVTf~IPreAA~rLr~LA~~g~ 50 (76)
-++.+-||.++.++|.+||....
T Consensus 42 k~i~v~I~~~~K~~L~~lc~~~G 64 (84)
T PF10723_consen 42 KRINVFIPNELKERLEELCKEQG 64 (84)
T ss_dssp EEEEEEEEHHHHHHHHHHHHHS-
T ss_pred CeeEEEECHHHHHHHHHHHHHcC
Confidence 38999999999999999998754
No 48
>PRK09256 hypothetical protein; Provisional
Probab=40.97 E-value=72 Score=22.12 Aligned_cols=51 Identities=25% Similarity=0.453 Sum_probs=36.2
Q ss_pred cCCCCcCeeeeeecCCceeEEEE-----eccHHHHHHHHHHHHhCChhhhhcceeEEEecc
Q psy12287 10 NLGGTEGINLRKVEPWNSVRVTF-----TIPKEAAVRLRQLAQQGNATLLQLGILSVQVEG 65 (76)
Q Consensus 10 ~~~~~~~l~v~kvEPWnSVRVTf-----~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EG 65 (76)
--+++++=.|||++- -|+++| .||.+.-++|.....+. +..=|.|.|+...
T Consensus 21 RSSGPGGQ~VNKt~S--kV~l~~~~~~~~lp~~~~~~l~~~~~~r---~~~~g~l~i~~~~ 76 (138)
T PRK09256 21 RASGPGGQNVNKVST--AVELRFDIAASSLPEFYKERLLALAGHR---ITKDGVIVIKAQE 76 (138)
T ss_pred EcCCCCcccccccce--eeEEEechhhccCCHHHHHHHHHHhcCc---ccCCCcEEEEECC
Confidence 346778889999996 888888 48888778877643332 5556766666543
No 49
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=40.65 E-value=47 Score=23.20 Aligned_cols=22 Identities=23% Similarity=0.492 Sum_probs=19.6
Q ss_pred ceeEEEEeccHHHHHHHHHHHH
Q psy12287 26 NSVRVTFTIPKEAAVRLRQLAQ 47 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~LA~ 47 (76)
+..||++|||.+=.++|-.+.+
T Consensus 3 ~~~RisVSLp~~Ll~elD~~i~ 24 (136)
T COG0864 3 AMMRISVSLPEELLEELDELIE 24 (136)
T ss_pred ceEEEEEECcHHHHHHHHHHHH
Confidence 3579999999999999998888
No 50
>PF12089 DUF3566: Transmembrane domain of unknown function (DUF3566); InterPro: IPR021949 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 136 to 304 amino acids in length. This region represents a transmembrane region found at the C terminus of the proteins.
Probab=39.45 E-value=3.3 Score=28.72 Aligned_cols=21 Identities=24% Similarity=0.863 Sum_probs=17.1
Q ss_pred cCeeeeeecCCceeEEEEecc
Q psy12287 15 EGINLRKVEPWNSVRVTFTIP 35 (76)
Q Consensus 15 ~~l~v~kvEPWnSVRVTf~IP 35 (76)
-++++.+++||+-.|++|-+.
T Consensus 4 ~~L~l~rIDpwSv~K~sfllS 24 (119)
T PF12089_consen 4 ARLTLTRIDPWSVMKVSFLLS 24 (119)
T ss_pred eEEEEEEeChHHHHHHHHHHH
Confidence 368899999999988887543
No 51
>PRK11675 LexA regulated protein; Provisional
Probab=39.40 E-value=52 Score=22.00 Aligned_cols=26 Identities=23% Similarity=0.300 Sum_probs=23.3
Q ss_pred eeEEEEeccHHHHHHHHHHHHhCChh
Q psy12287 27 SVRVTFTIPKEAAVRLRQLAQQGNAT 52 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA~~g~~~ 52 (76)
-.||+|-|..|.-+.|.++|.+.+-.
T Consensus 50 lKRveVKldedl~ekL~eyAe~~nit 75 (90)
T PRK11675 50 LKRVELKLNADLVDALNELAEARNIS 75 (90)
T ss_pred ceeEEEEECHHHHHHHHHHHHHcCCC
Confidence 47999999999999999999998754
No 52
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=39.39 E-value=17 Score=22.92 Aligned_cols=22 Identities=27% Similarity=0.474 Sum_probs=16.7
Q ss_pred HHHHHhCChhhhhcceeEEEec
Q psy12287 43 RQLAQQGNATLLQLGILSVQVE 64 (76)
Q Consensus 43 r~LA~~g~~~Lr~LGILSVQ~E 64 (76)
++|.+-.+.+|.|+||---|++
T Consensus 33 ~eL~~lsd~~L~DiGisR~d~~ 54 (63)
T COG5457 33 RELLRLSDHLLSDIGISRADIE 54 (63)
T ss_pred HHHHHHhHHHHHHcCCCHHHHH
Confidence 4677778899999999654443
No 53
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=38.91 E-value=18 Score=25.83 Aligned_cols=30 Identities=33% Similarity=0.523 Sum_probs=21.3
Q ss_pred CCceeEEEEeccHHHHHHHHHHHHhCChhhhh
Q psy12287 24 PWNSVRVTFTIPKEAAVRLRQLAQQGNATLLQ 55 (76)
Q Consensus 24 PWnSVRVTf~IPreAA~rLr~LA~~g~~~Lr~ 55 (76)
.|+.++..|-+++|.|+|| +|.-|+..-+.
T Consensus 122 ~~g~~~~~l~vq~e~a~rl--~a~pg~~~~~~ 151 (262)
T PF00398_consen 122 RFGRVRMVLMVQKEVAERL--LAKPGSKRYSR 151 (262)
T ss_dssp GGCEEEEEEEEEHHHHHHH--HTSTTSTTCSH
T ss_pred cccccceEEEEehhhhhhc--cCCCCCCccch
Confidence 4566888999999999887 56666544333
No 54
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=38.71 E-value=28 Score=20.80 Aligned_cols=22 Identities=41% Similarity=0.709 Sum_probs=19.6
Q ss_pred EEEEeccHHHHHHHHHHHHhCC
Q psy12287 29 RVTFTIPKEAAVRLRQLAQQGN 50 (76)
Q Consensus 29 RVTf~IPreAA~rLr~LA~~g~ 50 (76)
++..+||++.+.+.+.+=++|+
T Consensus 32 ~I~a~i~~~~~~~f~~~L~eg~ 53 (86)
T cd04480 32 RIHATIPKRLAAKFRPLLKEGK 53 (86)
T ss_pred EEEEEECHHHHHhhhhhceeCC
Confidence 7889999999999999888874
No 55
>COG4006 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.41 E-value=15 Score=29.29 Aligned_cols=36 Identities=25% Similarity=0.148 Sum_probs=30.4
Q ss_pred cCeeeeeecCCceeEEEEeccHHHHHHHHHHHHhCC
Q psy12287 15 EGINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQQGN 50 (76)
Q Consensus 15 ~~l~v~kvEPWnSVRVTf~IPreAA~rLr~LA~~g~ 50 (76)
+.+..-.++||||-|+-...|+-+|+..+.|+-.++
T Consensus 238 e~~~l~~~~d~~sk~lgp~~~~~lae~~~rl~~~~~ 273 (278)
T COG4006 238 EAMGLASRLDDNSKRLGPARARYLAEYIRRLAFPED 273 (278)
T ss_pred HhcchhhcCCchhhccCcchhHHHHHHHHHHhcchh
Confidence 345667789999999999999999999999986543
No 56
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=36.96 E-value=36 Score=19.46 Aligned_cols=22 Identities=27% Similarity=0.256 Sum_probs=18.0
Q ss_pred cHHHHHHHHHHHHhCChhhhhc
Q psy12287 35 PKEAAVRLRQLAQQGNATLLQL 56 (76)
Q Consensus 35 PreAA~rLr~LA~~g~~~Lr~L 56 (76)
|.+|-+.||..|.+.+-.+.++
T Consensus 30 e~~A~~~Lr~~Am~~~~~l~~v 51 (56)
T PF03861_consen 30 EDEAYRLLRRQAMRRRRSLADV 51 (56)
T ss_dssp HHHHHHHHHHHHHHCTS-HHHH
T ss_pred HHHHHHHHHHHHHHcCCCHHHH
Confidence 6788899999999999887764
No 57
>COG0316 sufA Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]
Probab=36.43 E-value=27 Score=23.57 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=16.6
Q ss_pred EEeccHHHHHHHHHHHHhC
Q psy12287 31 TFTIPKEAAVRLRQLAQQG 49 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g 49 (76)
.++|+..||.|++.|.++.
T Consensus 4 ~itlT~~Aa~~v~~ll~~~ 22 (110)
T COG0316 4 MITLTDAAAARVKALLAKE 22 (110)
T ss_pred ceeeCHHHHHHHHHHHHhc
Confidence 5788999999999998876
No 58
>TIGR02508 type_III_yscG type III secretion protein, YscG family. YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.
Probab=36.21 E-value=35 Score=24.19 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHhCChhhhhc
Q psy12287 36 KEAAVRLRQLAQQGNATLLQL 56 (76)
Q Consensus 36 reAA~rLr~LA~~g~~~Lr~L 56 (76)
..++.||-.||++|+|+|.+.
T Consensus 85 s~l~~rl~rla~sg~p~lq~F 105 (115)
T TIGR02508 85 SALESRLNRLAASGDPRLQTF 105 (115)
T ss_pred HHHHHHHHHHHhCCCHHHHHH
Confidence 456789999999999999764
No 59
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=35.99 E-value=72 Score=17.08 Aligned_cols=17 Identities=12% Similarity=0.247 Sum_probs=12.8
Q ss_pred ceeEEEEeccHHHHHHH
Q psy12287 26 NSVRVTFTIPKEAAVRL 42 (76)
Q Consensus 26 nSVRVTf~IPreAA~rL 42 (76)
+.++++|.+|++...+.
T Consensus 40 s~~~is~~v~~~~~~~~ 56 (66)
T cd04922 40 SERNISAVIDEDDATKA 56 (66)
T ss_pred cccEEEEEEeHHHHHHH
Confidence 45889999998776554
No 60
>COG5639 Uncharacterized conserved small protein [Function unknown]
Probab=35.45 E-value=67 Score=21.46 Aligned_cols=32 Identities=22% Similarity=0.329 Sum_probs=22.0
Q ss_pred CeeeeeecCCceeEEEEeccHHHHHHHHHHHH
Q psy12287 16 GINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQ 47 (76)
Q Consensus 16 ~l~v~kvEPWnSVRVTf~IPreAA~rLr~LA~ 47 (76)
+|++-++--=.+|++||++|-+=-.-|..-|+
T Consensus 3 kLKLg~lpd~~pvKlTv~~pa~L~~~L~~Yaa 34 (77)
T COG5639 3 KLKLGKLPDRTPVKLTVELPASLHRALDDYAA 34 (77)
T ss_pred ccccCCCCCCCceeEEEecChhHHHHHHHHHH
Confidence 34455554456799999999887666665554
No 61
>PF02426 MIase: Muconolactone delta-isomerase; InterPro: IPR003464 This small enzyme forms a homodecameric complex, that catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway (5.3.3.4 from EC). The protein has a ferredoxin-like fold according to SCOP.; GO: 0006725 cellular aromatic compound metabolic process
Probab=34.56 E-value=72 Score=20.94 Aligned_cols=33 Identities=24% Similarity=0.360 Sum_probs=18.7
Q ss_pred eeEEEEeccHH----HHHHHHHHHHhCChhhhhccee
Q psy12287 27 SVRVTFTIPKE----AAVRLRQLAQQGNATLLQLGIL 59 (76)
Q Consensus 27 SVRVTf~IPre----AA~rLr~LA~~g~~~Lr~LGIL 59 (76)
-|++|+++|.+ .+.+++.==++..++|.+=|.+
T Consensus 4 lv~m~v~~P~~~~~~~~~~~~a~E~~~a~eLq~~G~~ 40 (91)
T PF02426_consen 4 LVRMTVNVPPDMPPEEVDRLKAREKARAQELQRQGKW 40 (91)
T ss_pred EEEEEeeCCCCCCHHHHHHHHHHHHHHHHHHHHCCee
Confidence 37888888753 4455544444444555555543
No 62
>PF14310 Fn3-like: Fibronectin type III-like domain; PDB: 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A.
Probab=34.45 E-value=56 Score=19.11 Aligned_cols=18 Identities=39% Similarity=0.634 Sum_probs=13.7
Q ss_pred eecCCceeEEEEeccHHH
Q psy12287 21 KVEPWNSVRVTFTIPKEA 38 (76)
Q Consensus 21 kvEPWnSVRVTf~IPreA 38 (76)
.+.|=.|.+|+|.||.++
T Consensus 28 ~l~pGes~~v~~~l~~~~ 45 (71)
T PF14310_consen 28 SLAPGESKTVSFTLPPED 45 (71)
T ss_dssp EE-TT-EEEEEEEEEHHH
T ss_pred EECCCCEEEEEEEECHHH
Confidence 378889999999999864
No 63
>PF11871 DUF3391: Domain of unknown function (DUF3391); InterPro: IPR021812 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is typically between 122 to 139 amino acids in length. This domain is found associated with PF01966 from PFAM.
Probab=34.03 E-value=87 Score=19.44 Aligned_cols=43 Identities=26% Similarity=0.531 Sum_probs=29.0
Q ss_pred cCeeeeeec-CCceeEE---EEeccHHHHHHHHHHHHhCChhhhhcceeEEEecchh
Q psy12287 15 EGINLRKVE-PWNSVRV---TFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDE 67 (76)
Q Consensus 15 ~~l~v~kvE-PWnSVRV---Tf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~ 67 (76)
-++.|.++. ||..--. .|-|-.++-- ..|+++||..|-++.+-
T Consensus 12 ~GM~V~~~~~~w~~~pfl~~~f~I~s~~~I----------~~L~~~gi~~V~Id~~k 58 (128)
T PF11871_consen 12 PGMYVSRLDRSWLEHPFLFQGFLIKSQADI----------EKLRRLGIQEVYIDPDK 58 (128)
T ss_pred CCcEEEecCCCccCCCeeeeceeECCHHHH----------HHHHHCCCcEEEEECCC
Confidence 357788888 9975433 3666544322 23889999999998653
No 64
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=33.60 E-value=28 Score=23.84 Aligned_cols=28 Identities=25% Similarity=0.201 Sum_probs=23.0
Q ss_pred eccHHHHHHHHHHHHhCCh--hhhhcceeE
Q psy12287 33 TIPKEAAVRLRQLAQQGNA--TLLQLGILS 60 (76)
Q Consensus 33 ~IPreAA~rLr~LA~~g~~--~Lr~LGILS 60 (76)
+-|++|+.-|+.--+.+|| +|++|-+|.
T Consensus 34 ~~~k~a~rai~krl~~~n~~v~l~AL~LLe 63 (139)
T cd03567 34 EGPQLAVRLLAHKIQSPQEKEALQALTVLE 63 (139)
T ss_pred ccHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3499999999998888887 788887664
No 65
>PRK11670 antiporter inner membrane protein; Provisional
Probab=33.01 E-value=43 Score=25.78 Aligned_cols=43 Identities=16% Similarity=0.322 Sum_probs=31.9
Q ss_pred eecCCceeEEEEeccHHHHHHHHHHHHhCChhhhhc-ceeEEEec
Q psy12287 21 KVEPWNSVRVTFTIPKEAAVRLRQLAQQGNATLLQL-GILSVQVE 64 (76)
Q Consensus 21 kvEPWnSVRVTf~IPreAA~rLr~LA~~g~~~Lr~L-GILSVQ~E 64 (76)
.++. +.|+|++.+|..++.....+.++-...|.++ |+-+|.++
T Consensus 43 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (369)
T PRK11670 43 ALLD-DTLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWK 86 (369)
T ss_pred EEeC-CEEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEE
Confidence 3444 6789999998887666666777777888886 88777765
No 66
>PF12535 Nudix_N: Hydrolase of X-linked nucleoside diphosphate N terminal ; PDB: 3Q1P_B 3Q4I_B.
Probab=32.49 E-value=31 Score=20.86 Aligned_cols=14 Identities=50% Similarity=0.529 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHhCC
Q psy12287 37 EAAVRLRQLAQQGN 50 (76)
Q Consensus 37 eAA~rLr~LA~~g~ 50 (76)
+.|.||+.+||.|-
T Consensus 6 ~~a~~lqaiAqtGL 19 (58)
T PF12535_consen 6 EWAKRLQAIAQTGL 19 (58)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhh
Confidence 57899999999873
No 67
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=31.70 E-value=3.6 Score=23.61 Aligned_cols=19 Identities=26% Similarity=0.412 Sum_probs=12.4
Q ss_pred CceeEEEEeccHHHHHHHH
Q psy12287 25 WNSVRVTFTIPKEAAVRLR 43 (76)
Q Consensus 25 WnSVRVTf~IPreAA~rLr 43 (76)
|.+.+-.|.||+..|..+-
T Consensus 12 ~~~L~~~f~ip~~vAk~IV 30 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIV 30 (40)
T ss_dssp HHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHHccCHHHHHHHH
Confidence 4456667999999998764
No 68
>KOG3380|consensus
Probab=31.58 E-value=21 Score=26.19 Aligned_cols=14 Identities=36% Similarity=0.403 Sum_probs=11.3
Q ss_pred ChhhHHHhhcCCCC
Q psy12287 1 MKYLYKVCFNLGGT 14 (76)
Q Consensus 1 ~~~~~~~c~~~~~~ 14 (76)
|||+||--+.|.+.
T Consensus 107 mKYiYkGm~~p~d~ 120 (152)
T KOG3380|consen 107 MKYIYKGMEIPSDN 120 (152)
T ss_pred HHHHHHHhcCcccc
Confidence 89999987777664
No 69
>PLN03082 Iron-sulfur cluster assembly; Provisional
Probab=31.43 E-value=69 Score=22.74 Aligned_cols=32 Identities=22% Similarity=0.281 Sum_probs=20.5
Q ss_pred EEeccHHHHHHHHHHHHhCC-hhhhhcceeEEEecc
Q psy12287 31 TFTIPKEAAVRLRQLAQQGN-ATLLQLGILSVQVEG 65 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g~-~~Lr~LGILSVQ~EG 65 (76)
+++|-..||+|++++-++.+ +. +.| |.|.+++
T Consensus 54 ~I~lTd~A~~~ik~l~~~~~~~~--~~~-LRl~V~~ 86 (163)
T PLN03082 54 AVHMTDNCIRRLKELQTSEPSAE--DKM-LRLSVET 86 (163)
T ss_pred ceEECHHHHHHHHHHHHhCCCCC--Cce-EEEEEec
Confidence 37788999999999865432 21 222 5565554
No 70
>PF13062 DUF3924: Protein of unknown function (DUF3924)
Probab=31.32 E-value=62 Score=20.80 Aligned_cols=19 Identities=42% Similarity=0.604 Sum_probs=16.4
Q ss_pred EEEeccHHHHHHHHHHHHh
Q psy12287 30 VTFTIPKEAAVRLRQLAQQ 48 (76)
Q Consensus 30 VTf~IPreAA~rLr~LA~~ 48 (76)
.|+.+|.|-|++|..|-|.
T Consensus 4 ltielpke~aekl~llkqa 22 (62)
T PF13062_consen 4 LTIELPKETAEKLDLLKQA 22 (62)
T ss_pred eeEeccHHHHHHHHHHHHH
Confidence 6889999999999888764
No 71
>PF10604 Polyketide_cyc2: Polyketide cyclase / dehydrase and lipid transport; InterPro: IPR019587 This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily []. ; PDB: 3QRZ_C 3CNW_A 3P9V_A 3OQU_B 3NEF_B 3JRQ_B 3KAY_A 3JRS_A 3KDJ_A 3NMN_C ....
Probab=30.95 E-value=1e+02 Score=18.01 Aligned_cols=39 Identities=21% Similarity=0.233 Sum_probs=28.4
Q ss_pred eeEEEEeccHHHHHHHHHHHHhCChhhhhcceeEEEecc
Q psy12287 27 SVRVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEG 65 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EG 65 (76)
.+.+++.||..+.+=.+.++.-.+-.-+.-++.++++.+
T Consensus 3 ~~~~~~~v~a~~e~V~~~l~d~~~~~~w~~~~~~~~~~~ 41 (139)
T PF10604_consen 3 KVEVSIEVPAPPEAVWDLLSDPENWPRWWPGVKSVELLS 41 (139)
T ss_dssp EEEEEEEESS-HHHHHHHHTTTTGGGGTSTTEEEEEEEE
T ss_pred EEEEEEEECCCHHHHHHHHhChhhhhhhhhceEEEEEcc
Confidence 356777777777777777877677766777899998765
No 72
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=30.18 E-value=1.1e+02 Score=22.87 Aligned_cols=70 Identities=27% Similarity=0.330 Sum_probs=49.6
Q ss_pred hHHHhh----cCCCCcCeeeeee--cCCceeEEEEeccHHH-HHHHHHHHHh-CChhh-hhcceeEEEecc--hhHHHHh
Q psy12287 4 LYKVCF----NLGGTEGINLRKV--EPWNSVRVTFTIPKEA-AVRLRQLAQQ-GNATL-LQLGILSVQVEG--DELILTL 72 (76)
Q Consensus 4 ~~~~c~----~~~~~~~l~v~kv--EPWnSVRVTf~IPreA-A~rLr~LA~~-g~~~L-r~LGILSVQ~EG--d~~I~l~ 72 (76)
+|-+.+ +..+...+.+..+ +| .|.---|.|++++ +++|++|++. |.=.+ +-.|+-.|++.. ....++|
T Consensus 204 ~YaL~~~~~~~~~~~~sis~~~L~~~~-~sPGriF~L~~~~l~~~L~~l~~~~g~i~~~~TaGl~qv~~~~~~~~~~~~L 282 (286)
T PF13182_consen 204 LYALLDFAERESPGRNSISFDELLNEP-GSPGRIFKLDEESLAERLEQLEEIYGFISWSDTAGLDQVYLKDEELDAWDVL 282 (286)
T ss_pred HHHHHHHHHHhCCCCcEEEHHHHhcCC-CCcceEeccCHHHHHHHHHHHHhhcCcEEEEEcCCCeEEEeccccCCHHHHH
Confidence 444444 4457788888887 46 7888889999887 6789999988 44333 346888888876 5555666
Q ss_pred hh
Q psy12287 73 HQ 74 (76)
Q Consensus 73 ~~ 74 (76)
.+
T Consensus 283 ~~ 284 (286)
T PF13182_consen 283 KQ 284 (286)
T ss_pred HH
Confidence 54
No 73
>COG3609 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]
Probab=30.08 E-value=73 Score=20.16 Aligned_cols=23 Identities=13% Similarity=0.407 Sum_probs=19.9
Q ss_pred eeEEEEeccHHHHHHHHHHHHhC
Q psy12287 27 SVRVTFTIPKEAAVRLRQLAQQG 49 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA~~g 49 (76)
..++||+||.+=...++.|-+.|
T Consensus 2 ~~~isV~lp~~~~~~i~~lV~~G 24 (89)
T COG3609 2 MKKISVRLPEQLVEFIDELVESG 24 (89)
T ss_pred CcceeEeCCHHHHHHHHHHHHcC
Confidence 45789999999999999998876
No 74
>cd00078 HECTc HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains.
Probab=29.79 E-value=47 Score=24.77 Aligned_cols=36 Identities=31% Similarity=0.434 Sum_probs=25.0
Q ss_pred eccHH--HHHHHHHHHHhCChhhhhcceeEEEecchhHHH
Q psy12287 33 TIPKE--AAVRLRQLAQQGNATLLQLGILSVQVEGDELIL 70 (76)
Q Consensus 33 ~IPre--AA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~~I~ 70 (76)
+|.|+ -.+-+++|+.-++..|+. .+.|+++||..|.
T Consensus 4 ~v~R~~i~~~~~~~l~~~~~~~l~~--~l~V~F~gE~g~D 41 (352)
T cd00078 4 TVRRDRILEDALRQLSKVSSSDLKK--VLEVEFVGEEGID 41 (352)
T ss_pred EEECCcHHHHHHHHHHhcCHHHhcC--ceEEEECCCCccC
Confidence 44444 234466666666667775 9999999998775
No 75
>PF05534 HicB: HicB family; InterPro: IPR008651 This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches [].
Probab=29.54 E-value=75 Score=18.45 Aligned_cols=29 Identities=24% Similarity=0.253 Sum_probs=24.7
Q ss_pred eEEEEeccHHHHHHHHHHHHhCChhhhhc
Q psy12287 28 VRVTFTIPKEAAVRLRQLAQQGNATLLQL 56 (76)
Q Consensus 28 VRVTf~IPreAA~rLr~LA~~g~~~Lr~L 56 (76)
=++++.||.+-=.++...|+..+-.|.++
T Consensus 18 g~~~lRi~~~Lh~~l~~~A~~~gvSlN~~ 46 (51)
T PF05534_consen 18 GKFNLRIPPELHRALAEAAAAEGVSLNQW 46 (51)
T ss_pred CceeeeCCHHHHHHHHHHHHHhCCCHHHH
Confidence 47899999999999999999887777654
No 76
>COG5573 Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]
Probab=29.34 E-value=42 Score=24.55 Aligned_cols=27 Identities=33% Similarity=0.421 Sum_probs=20.2
Q ss_pred cHHHHHHHHHHHHhCChhhhhcc---eeEEEecchhHHHH
Q psy12287 35 PKEAAVRLRQLAQQGNATLLQLG---ILSVQVEGDELILT 71 (76)
Q Consensus 35 PreAA~rLr~LA~~g~~~Lr~LG---ILSVQ~EGd~~I~l 71 (76)
-|+||++|- +++| |.|||+=+|..-.+
T Consensus 25 kr~~a~~L~----------~a~~~~~VVs~QVl~Et~~vl 54 (142)
T COG5573 25 KRDAAEVLE----------QALGHTYVVSVQVLNETCYVL 54 (142)
T ss_pred HHHHHHHHH----------HhcCceEEEehHHHHHHHHHH
Confidence 477888774 5778 99999988865444
No 77
>TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.
Probab=28.73 E-value=38 Score=20.82 Aligned_cols=18 Identities=28% Similarity=0.379 Sum_probs=14.4
Q ss_pred eccHHHHHHHHHHHHhCC
Q psy12287 33 TIPKEAAVRLRQLAQQGN 50 (76)
Q Consensus 33 ~IPreAA~rLr~LA~~g~ 50 (76)
+|...|+++|+++.+..+
T Consensus 1 ~iT~~A~~~l~~~~~~~~ 18 (105)
T TIGR00049 1 TLTDSAAKRIKALLAGEG 18 (105)
T ss_pred CcCHHHHHHHHHHHhcCC
Confidence 467899999999886654
No 78
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.25 E-value=95 Score=16.59 Aligned_cols=17 Identities=12% Similarity=0.210 Sum_probs=13.1
Q ss_pred eeEEEEeccHHHHHHHH
Q psy12287 27 SVRVTFTIPKEAAVRLR 43 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr 43 (76)
...++|.||++-..+..
T Consensus 41 ~~~isf~v~~~d~~~~~ 57 (66)
T cd04916 41 EISIMIGVHNEDADKAV 57 (66)
T ss_pred ccEEEEEEeHHHHHHHH
Confidence 58899999997765543
No 79
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=28.20 E-value=84 Score=22.68 Aligned_cols=31 Identities=19% Similarity=0.194 Sum_probs=20.7
Q ss_pred EeccHHHHHHHHHHHHhCChhhhhcceeEEEecch
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGD 66 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd 66 (76)
++|-..||.|++.|.++... ..| |.|-+++.
T Consensus 2 i~iTd~A~~~i~~ll~~~~~---~~~-LRI~V~~g 32 (192)
T PRK11190 2 ITISDAAQAHFAKLLANQEE---GTQ-IRVFVINP 32 (192)
T ss_pred cEECHHHHHHHHHHHhcCCC---Cce-EEEEEECC
Confidence 56788999999998765432 233 56666543
No 80
>PF05856 ARPC4: ARP2/3 complex 20 kDa subunit (ARPC4); InterPro: IPR008384 This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion [].; GO: 0030041 actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_K 1K8K_F 1U2V_F 2P9S_F 2P9U_F 2P9N_F 3DXK_F 1TYQ_F 3RSE_F 2P9I_F ....
Probab=27.48 E-value=40 Score=25.10 Aligned_cols=12 Identities=50% Similarity=0.645 Sum_probs=8.3
Q ss_pred CceeEEEEeccH
Q psy12287 25 WNSVRVTFTIPK 36 (76)
Q Consensus 25 WnSVRVTf~IPr 36 (76)
-|||||+|.|-.
T Consensus 69 iNSvRvSi~ikq 80 (170)
T PF05856_consen 69 INSVRVSIKIKQ 80 (170)
T ss_dssp SSEEEEEEE---
T ss_pred cceEEEEEEecc
Confidence 599999999975
No 81
>PHA01486 nonstructural protein
Probab=26.76 E-value=28 Score=19.91 Aligned_cols=19 Identities=32% Similarity=0.545 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHhCChhhh
Q psy12287 36 KEAAVRLRQLAQQGNATLL 54 (76)
Q Consensus 36 reAA~rLr~LA~~g~~~Lr 54 (76)
|.-|-|||.|-++.++-|.
T Consensus 12 rsiairlrklpassdqmlq 30 (32)
T PHA01486 12 RSIAIRLRKLPASSDQMLQ 30 (32)
T ss_pred HHHHHHHHhCCCcHHHHHh
Confidence 4568899999888887664
No 82
>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=26.71 E-value=94 Score=23.22 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=35.0
Q ss_pred EEEeccHHHHHHHHHHHHhCChhhhhcce--------eEEEecchhHHHHhhhh
Q psy12287 30 VTFTIPKEAAVRLRQLAQQGNATLLQLGI--------LSVQVEGDELILTLHQA 75 (76)
Q Consensus 30 VTf~IPreAA~rLr~LA~~g~~~Lr~LGI--------LSVQ~EGd~~I~l~~~~ 75 (76)
-.|.-|..|++-|+++.+.|.+.|..+-+ .....+|..+.+++.+.
T Consensus 78 ~~~~qP~~a~~~L~~~~~~N~~~L~~i~~s~~~~~~~~~~~~~g~tL~dLv~~g 131 (309)
T PF10236_consen 78 GLYDQPMYAAKWLKKFLKANEELLKKIKLSKDYKWSKRESTPKGSTLLDLVEQG 131 (309)
T ss_pred CeeecHHHHHHHHHHHHHHhHHHHHhccccccccccccccCCCCCCHHHHHHhh
Confidence 56889999999999999999999988653 12344566666666543
No 83
>cd04891 ACT_AK-LysC-DapG-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the first and third, of four, ACT domains present in cyanobacteria AK. Also included are the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (Bacillus subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.09 E-value=1e+02 Score=15.59 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=13.0
Q ss_pred eEEEEeccHHHHHHHH
Q psy12287 28 VRVTFTIPKEAAVRLR 43 (76)
Q Consensus 28 VRVTf~IPreAA~rLr 43 (76)
+.++|.++.+...+..
T Consensus 42 ~~is~~v~~~~~~~~~ 57 (61)
T cd04891 42 TDISFTVPKSDLEKAL 57 (61)
T ss_pred EEEEEEEeHHHHHHHH
Confidence 8999999998776653
No 84
>PF07684 NODP: NOTCH protein; InterPro: IPR011656 NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals []. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be elucidated.; GO: 0007219 Notch signaling pathway, 0007275 multicellular organismal development, 0030154 cell differentiation, 0016021 integral to membrane; PDB: 3ETO_A 3I08_D 3L95_X 2OO4_A.
Probab=25.73 E-value=1e+02 Score=18.88 Aligned_cols=34 Identities=29% Similarity=0.355 Sum_probs=25.2
Q ss_pred EeccHHHHHHHHHHHHhCChhhhhcceeEEEecch
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGD 66 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd 66 (76)
|.=+.+||.-|-.+|+.++-.. .+-|-||+.+..
T Consensus 24 F~~a~~aA~fLaA~aa~~~L~~-~~PI~~v~~~~~ 57 (63)
T PF07684_consen 24 FSSADSAADFLAAMAAKGTLNF-PFPIYSVRSEPP 57 (63)
T ss_dssp -SBHHHHHHHHHHHHHCT---S-SSEEEEEEEES-
T ss_pred cCCHHHHHHHHHHHHhhccCCC-CCceEEEEeecC
Confidence 5667899999999999987766 888999998754
No 85
>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit. The trusted cutoff excludes archaeal homologs but captures some organellar sequences.
Probab=25.72 E-value=51 Score=19.66 Aligned_cols=22 Identities=32% Similarity=0.443 Sum_probs=17.1
Q ss_pred EeccHHHHHHHHHHHHhCChhh
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATL 53 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~L 53 (76)
|.+---||.|-|||...+.+.+
T Consensus 16 Y~Lv~~aakRArqL~~~~~~~~ 37 (59)
T TIGR00690 16 YDLVLVAARRARQLQLKGTDPI 37 (59)
T ss_pred hHHHHHHHHHHHHHHhCCCCCc
Confidence 5566679999999998776654
No 86
>cd04868 ACT_AK-like ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes each of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). Typically, AK consists of two ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Aspartokinase is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of aspartokinase with different repressors and allosteric inhibitors. Pairs of ACT domains are proposed to specifically bind am
Probab=25.25 E-value=1e+02 Score=15.24 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=13.2
Q ss_pred eeEEEEeccHHHHHHHH
Q psy12287 27 SVRVTFTIPKEAAVRLR 43 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr 43 (76)
+..++|.+|.+-..++.
T Consensus 40 ~~~~s~~v~~~~~~~~~ 56 (60)
T cd04868 40 EVNISFTVDESDLEKAV 56 (60)
T ss_pred cEEEEEEEeHHHHHHHH
Confidence 58899999998766553
No 87
>PF09477 Type_III_YscG: Bacterial type II secretion system chaperone protein (type_III_yscG); InterPro: IPR013348 YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia, and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens.; GO: 0009405 pathogenesis; PDB: 3PH0_D 2UWJ_G 2P58_C.
Probab=25.10 E-value=48 Score=23.45 Aligned_cols=21 Identities=29% Similarity=0.423 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHhCChhhhhc
Q psy12287 36 KEAAVRLRQLAQQGNATLLQL 56 (76)
Q Consensus 36 reAA~rLr~LA~~g~~~Lr~L 56 (76)
..+..||..||.+|+|++.+.
T Consensus 86 ~~~e~~l~rla~~g~~~~q~F 106 (116)
T PF09477_consen 86 SALESRLTRLASSGSPELQAF 106 (116)
T ss_dssp HHHHHHHHHHCT-SSHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHH
Confidence 356778999999999998764
No 88
>PF09838 DUF2065: Uncharacterized protein conserved in bacteria (DUF2065); InterPro: IPR019201 This entry represents a protein found in various prokaryotic proteins, and has no known function.
Probab=24.78 E-value=27 Score=21.05 Aligned_cols=23 Identities=39% Similarity=0.518 Sum_probs=19.0
Q ss_pred HHHHHHHHHhCChhhhhcceeEE
Q psy12287 39 AVRLRQLAQQGNATLLQLGILSV 61 (76)
Q Consensus 39 A~rLr~LA~~g~~~Lr~LGILSV 61 (76)
=+-++++++..+.+||..|..|+
T Consensus 24 r~~l~~l~~~p~~~lR~~Gl~~~ 46 (57)
T PF09838_consen 24 RRMLRQLAQLPDRQLRRIGLVSM 46 (57)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH
Confidence 34578999999999999997664
No 89
>cd04913 ACT_AKii-LysC-BS-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is fee
Probab=24.57 E-value=1.2e+02 Score=16.02 Aligned_cols=20 Identities=20% Similarity=0.433 Sum_probs=14.9
Q ss_pred eeEEEEeccHHHHHHHHHHH
Q psy12287 27 SVRVTFTIPKEAAVRLRQLA 46 (76)
Q Consensus 27 SVRVTf~IPreAA~rLr~LA 46 (76)
+..++|.+|.+...+..+.-
T Consensus 42 ~~~is~~v~~~d~~~~~~~l 61 (75)
T cd04913 42 TTDISFTVPKSDLKKALAVL 61 (75)
T ss_pred cEEEEEEecHHHHHHHHHHH
Confidence 47899999988777665543
No 90
>smart00853 MutL_C MutL C terminal dimerisation domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.
Probab=24.50 E-value=1.1e+02 Score=19.00 Aligned_cols=27 Identities=26% Similarity=0.335 Sum_probs=20.7
Q ss_pred EEEEeccHHHHHHHHHHHHhCChhhhhccee
Q psy12287 29 RVTFTIPKEAAVRLRQLAQQGNATLLQLGIL 59 (76)
Q Consensus 29 RVTf~IPreAA~rLr~LA~~g~~~Lr~LGIL 59 (76)
-+++++|.+-+..+++. ...|+++|+-
T Consensus 56 P~~i~l~~~e~~~l~~~----~~~l~~~Gf~ 82 (136)
T smart00853 56 PVILELSPEEAALLEEH----QELLARLGFE 82 (136)
T ss_pred CEEEEcCHHHHHHHHHH----HHHHHHcCeE
Confidence 37788888888877764 4579999974
No 91
>COG1985 RibD Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]
Probab=24.48 E-value=64 Score=23.47 Aligned_cols=19 Identities=42% Similarity=0.457 Sum_probs=14.9
Q ss_pred hhhhcceeEEEecchhHHH
Q psy12287 52 TLLQLGILSVQVEGDELIL 70 (76)
Q Consensus 52 ~Lr~LGILSVQ~EGd~~I~ 70 (76)
+|.+.||.||-+||..-++
T Consensus 137 ~L~~~~i~~vlvEGG~~L~ 155 (218)
T COG1985 137 ELAERGINSVLVEGGATLN 155 (218)
T ss_pred HHHhCCCcEEEEccCHHHH
Confidence 3566679999999988654
No 92
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=24.32 E-value=50 Score=21.56 Aligned_cols=27 Identities=44% Similarity=0.577 Sum_probs=21.1
Q ss_pred eccHHHHHHHHHHHHhCCh--hhhhccee
Q psy12287 33 TIPKEAAVRLRQLAQQGNA--TLLQLGIL 59 (76)
Q Consensus 33 ~IPreAA~rLr~LA~~g~~--~Lr~LGIL 59 (76)
+-|++|+.-||.-=+.+|| +|++|-+|
T Consensus 33 ~~~k~a~raL~krl~~~n~~vql~AL~lL 61 (133)
T cd03561 33 NGPKEAARAIRKKIKYGNPHVQLLALTLL 61 (133)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5689999999988888875 56666555
No 93
>PF01390 SEA: SEA domain; InterPro: IPR000082 SEA is an extracellular domain associated with O-glycosylation []. Proteins found to contain SEA-modules include, agrin, enterokinase, 63 kDa Strongylocentrotus purpuratus (Purple sea urchin) sperm protein, perlecan (heparan sulphate proteoglycan core, mucin 1 and the cell surface antigen, 114/A10, and two functionally uncharacterised, probably extracellular, Caenorhabditis elegans proteins. Despite the functional diversity of these adhesive proteins, a common denominator seems to be their existence in heavily glycosylated environments. In addition, the better characterised proteins all contain O-glycosidic-linked carbohydrates such as heparan sulphate that contribute considerably to their molecular masses. The common module might regulate or assist binding to neighbouring carbohydrate moieties. Enterokinase, the initiator of intestinal digestion, is a mosaic protease composed of a distinctive assortment of domains []. ; PDB: 2ACM_B 1IVZ_A 2E7V_A.
Probab=23.92 E-value=95 Score=18.44 Aligned_cols=45 Identities=29% Similarity=0.467 Sum_probs=28.3
Q ss_pred CCCcCeeeeeecCCceeEEEEec---------cHHHHHHHHHHHHhCChhhhhcce
Q psy12287 12 GGTEGINLRKVEPWNSVRVTFTI---------PKEAAVRLRQLAQQGNATLLQLGI 58 (76)
Q Consensus 12 ~~~~~l~v~kvEPWnSVRVTf~I---------PreAA~rLr~LA~~g~~~Lr~LGI 58 (76)
.+-....|.++.| .||-|.|.+ +.+..+.++.-.++ +.....|+|
T Consensus 51 ~~~~~~~I~~f~~-gsViv~~~~~f~~~~~~~~~~~~~~l~~~l~~-~~~~~~l~i 104 (107)
T PF01390_consen 51 PGFVGVTITSFRP-GSVIVDFDVIFDPPSSAPPADIEEALQNALQQ-TSNIGNLTI 104 (107)
T ss_dssp TTEEEEEEEEEEE-TEEEEEEEEEEETTT-S-HHHHHHHHHHHHCC-HHCCCCCEE
T ss_pred CCcceEEEEEEEC-CCEEEEEEEEEeCCCCCCHHHHHHHHHHHHHh-hcCcccccC
Confidence 3446678889999 999888776 33444555554444 444555554
No 94
>TIGR03455 HisG_C-term ATP phosphoribosyltransferase, C-terminal domain. This domain corresponds to the C-terminal third of the HisG protein. It is absent in many lineages.
Probab=23.69 E-value=1e+02 Score=20.08 Aligned_cols=43 Identities=21% Similarity=0.381 Sum_probs=28.7
Q ss_pred ceeEEEEeccHHHHHHHHH-HHHhCChhhhhc---ceeEEE--ecchhH
Q psy12287 26 NSVRVTFTIPKEAAVRLRQ-LAQQGNATLLQL---GILSVQ--VEGDEL 68 (76)
Q Consensus 26 nSVRVTf~IPreAA~rLr~-LA~~g~~~Lr~L---GILSVQ--~EGd~~ 68 (76)
+++-|++|+|++..+...+ |..-+.|+-..| |-.+|+ ++.+.+
T Consensus 28 ~~~~v~~Nvp~~~l~~v~~ilPg~~~PTVs~l~~~~w~AV~~vv~~~~v 76 (100)
T TIGR03455 28 GKVLLMMNVPRDNLDEVRALLPGLEGPTVSPLADEGWVAVHAVVDEKVV 76 (100)
T ss_pred heeEEEEeCChhhHHHHHHhcCCCCCCCcCcCCCCCeEEEEEEEcHHHH
Confidence 3688999999999887665 455555776666 665555 344443
No 95
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=23.67 E-value=50 Score=25.90 Aligned_cols=15 Identities=53% Similarity=0.663 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHhCCh
Q psy12287 36 KEAAVRLRQLAQQGNA 51 (76)
Q Consensus 36 reAA~rLr~LA~~g~~ 51 (76)
..-|+|||+||+ +||
T Consensus 35 ~~RA~Rl~~LA~-~~p 49 (309)
T PRK03564 35 NRRAERLRQLAE-NNP 49 (309)
T ss_pred HHHHHHHHHHHh-cCC
Confidence 367999999996 455
No 96
>PF10548 P22_AR_C: P22AR C-terminal domain; InterPro: IPR018876 This entry represents the carboxy-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018875 from INTERPRO.
Probab=23.64 E-value=71 Score=20.11 Aligned_cols=22 Identities=41% Similarity=0.391 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHhCChhhhhcc
Q psy12287 36 KEAAVRLRQLAQQGNATLLQLG 57 (76)
Q Consensus 36 reAA~rLr~LA~~g~~~Lr~LG 57 (76)
|-|+.|-+.+.++=-|.|++||
T Consensus 20 w~~~~~m~~~~~~l~p~L~~lg 41 (74)
T PF10548_consen 20 WFAAERMRELCQELYPALKALG 41 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC
Confidence 6789999999999999999998
No 97
>PRK11688 hypothetical protein; Provisional
Probab=23.45 E-value=1.1e+02 Score=20.17 Aligned_cols=36 Identities=17% Similarity=0.005 Sum_probs=29.3
Q ss_pred EeccHHHHHHHHHHHHhCChhhhhcceeEEEecchh
Q psy12287 32 FTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDE 67 (76)
Q Consensus 32 f~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~ 67 (76)
+-=|.|..++++..-.+.+|-.+.||+-=+.++.+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~pf~~~lG~~~~~~~~g~ 38 (154)
T PRK11688 3 VLTQEEALKLVGEIFVYHMPFNRLLGLELERLEPDF 38 (154)
T ss_pred ccCHHHHHHHHHHHHHhcCCHHHHhCcEEEEEeCCE
Confidence 334789999999988888999999999877777654
No 98
>cd09030 DUF1425 Putative periplasmic lipoprotein. This bacterial family of proteins contains members described as putative lipoproteins, some are also known as YcfL. The function of this family is unknown. Family members have also been annotated as predicted periplasmic lipoproteins (COG5633), and appear to contain an N-terminal membrane lipoprotein lipid attachment side (pfam08139), which is not included in this alignment model.
Probab=23.24 E-value=53 Score=20.53 Aligned_cols=18 Identities=28% Similarity=0.816 Sum_probs=14.8
Q ss_pred CCcCeeeeee-cCCceeEE
Q psy12287 13 GTEGINLRKV-EPWNSVRV 30 (76)
Q Consensus 13 ~~~~l~v~kv-EPWnSVRV 30 (76)
|.+++.+... |||.++.+
T Consensus 58 D~~G~~v~~~~~~w~~l~l 76 (101)
T cd09030 58 DAQGLEVEPEQEPWQSLTL 76 (101)
T ss_pred CCCCCCcCCCCCCCEEEEE
Confidence 5678888888 99998865
No 99
>cd04933 ACT_AK1-AT_1 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the first of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine. This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. Like the Escherichia coli AKIII (LysC), Arabidopsis AK1 binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. A loop in common is involved in the binding of both Lys and S-adenosylmethionine providing an explanation for the synergistic inhibition by these effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.21 E-value=1e+02 Score=19.07 Aligned_cols=24 Identities=21% Similarity=0.355 Sum_probs=16.1
Q ss_pred cCeeeeeecCCceeEEEEeccHHHH
Q psy12287 15 EGINLRKVEPWNSVRVTFTIPKEAA 39 (76)
Q Consensus 15 ~~l~v~kvEPWnSVRVTf~IPreAA 39 (76)
..+.+.-+-. ....++|++|++.+
T Consensus 28 ~~InVDmI~q-s~~sISftV~~sd~ 51 (78)
T cd04933 28 LGISVDVVAT-SEVSISLTLDPSKL 51 (78)
T ss_pred cCCcEEEEEe-cCCEEEEEEEhhhh
Confidence 4455555532 34889999998777
No 100
>PF02518 HATPase_c: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; InterPro: IPR003594 This domain is found in several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins. The fold of this domain consists of two layers, alpha/beta, which contains an 8-stranded mixed beta-sheet. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0005524 ATP binding; PDB: 3JZ3_A 3DGE_A 2C2A_A 2BU5_A 2BU8_A 2BU6_A 2BU7_A 2BU2_A 2BTZ_A 3K99_D ....
Probab=23.15 E-value=1.1e+02 Score=17.93 Aligned_cols=22 Identities=32% Similarity=0.478 Sum_probs=16.2
Q ss_pred cCeeeeeecCCceeEEEEeccHH
Q psy12287 15 EGINLRKVEPWNSVRVTFTIPKE 37 (76)
Q Consensus 15 ~~l~v~kvEPWnSVRVTf~IPre 37 (76)
..++++..+ +.-.+|+|.||.|
T Consensus 90 g~l~~~~~~-~~gt~v~~~~p~~ 111 (111)
T PF02518_consen 90 GELTIESSE-GGGTTVTFTLPLE 111 (111)
T ss_dssp EEEEEEEET-TTEEEEEEEEEGS
T ss_pred CEEEEEEcC-CCcEEEEEEEECc
Confidence 346666655 4889999999964
No 101
>KOG0816|consensus
Probab=22.95 E-value=30 Score=26.83 Aligned_cols=27 Identities=37% Similarity=0.455 Sum_probs=22.9
Q ss_pred EEEeccHHHHHHHHHHHHhCChhhhhccee
Q psy12287 30 VTFTIPKEAAVRLRQLAQQGNATLLQLGIL 59 (76)
Q Consensus 30 VTf~IPreAA~rLr~LA~~g~~~Lr~LGIL 59 (76)
-||+||. .-|++-|-+=.|+||.||+=
T Consensus 133 ~Tv~ip~---Gpl~~f~hsmEP~lRklglP 159 (223)
T KOG0816|consen 133 ETVTIPE---GPLEQFAHSMEPQLRKLGLP 159 (223)
T ss_pred ceEeecC---cchhhcccccchhhHhhcCc
Confidence 5889985 56888899999999999974
No 102
>PHA00276 phage lambda Rz-like lysis protein
Probab=22.81 E-value=84 Score=22.80 Aligned_cols=27 Identities=26% Similarity=0.318 Sum_probs=23.1
Q ss_pred EEeccHHHHHHHHHHHHhCChhhhhcc
Q psy12287 31 TFTIPKEAAVRLRQLAQQGNATLLQLG 57 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g~~~Lr~LG 57 (76)
+-.+-.+.|.||-.+++.|+..+|+|-
T Consensus 108 RAeLd~~~A~rii~i~~~gD~~iralq 134 (144)
T PHA00276 108 RAELDERDAKRLIGITQRGDAWIKALQ 134 (144)
T ss_pred ceeeCHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677899999999999999999873
No 103
>TIGR03221 muco_delta muconolactone delta-isomerase. Members of this protein family are muconolactone delta-isomerase (EC 5.3.3.4), the CatC protein of the ortho cleavage pathway for metabolizing aromatic compounds by way of catechol.
Probab=22.33 E-value=1.5e+02 Score=19.81 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=8.2
Q ss_pred eeEEEEeccHH
Q psy12287 27 SVRVTFTIPKE 37 (76)
Q Consensus 27 SVRVTf~IPre 37 (76)
-|+.|++||.+
T Consensus 3 lV~m~V~~P~~ 13 (90)
T TIGR03221 3 HVRMDVNLPVD 13 (90)
T ss_pred EEEEEeeCCCC
Confidence 37888888864
No 104
>TIGR00209 galT_1 galactose-1-phosphate uridylyltransferase, family 1. This enzyme is involved in glucose and galactose interconversion. This model describes one of two extremely distantly related branches of the model pfam01087 from PFAM.
Probab=22.22 E-value=46 Score=25.80 Aligned_cols=19 Identities=32% Similarity=0.251 Sum_probs=14.2
Q ss_pred eEEEEeccHHHHHHHHHHH
Q psy12287 28 VRVTFTIPKEAAVRLRQLA 46 (76)
Q Consensus 28 VRVTf~IPreAA~rLr~LA 46 (76)
+-+.=..|-+||++||.+.
T Consensus 321 ~~in~~~PE~aA~~LR~~~ 339 (347)
T TIGR00209 321 ETQRDLTAEQAAERLRALS 339 (347)
T ss_pred CccCCCCHHHHHHHHHhcc
Confidence 3344457999999999983
No 105
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.18 E-value=51 Score=25.68 Aligned_cols=14 Identities=50% Similarity=0.612 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHhCCh
Q psy12287 37 EAAVRLRQLAQQGNA 51 (76)
Q Consensus 37 eAA~rLr~LA~~g~~ 51 (76)
.-|+|||+||+ +||
T Consensus 32 ~RA~RL~~LA~-~~p 45 (305)
T TIGR01562 32 RRAERLLQLAE-GHP 45 (305)
T ss_pred HHHHHHHHHhc-cCC
Confidence 56899999996 444
No 106
>cd02130 PA_ScAPY_like PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY). This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino acid-MCAs or dipeptides is stimulated by Co2+ while the hydrolysis of dipeptidyl-MCAs, tripeptides, and longer peptides is inhibited by Co2+. ScAPY is vacuolar and is activated by proteolytic processing. LAP1 is a secreted leucine aminopeptidase. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stab
Probab=22.16 E-value=1.2e+02 Score=19.21 Aligned_cols=21 Identities=24% Similarity=0.253 Sum_probs=18.1
Q ss_pred EEeccHHHHHHHHHHHHhCCh
Q psy12287 31 TFTIPKEAAVRLRQLAQQGNA 51 (76)
Q Consensus 31 Tf~IPreAA~rLr~LA~~g~~ 51 (76)
.+.|+++.+++|+.+.++|.+
T Consensus 97 ~v~Is~~~G~~L~~~l~~g~~ 117 (122)
T cd02130 97 TVGISQEDGKALVAALANGGE 117 (122)
T ss_pred EEEecHHHHHHHHHHHhcCCc
Confidence 678999999999998888754
No 107
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=21.75 E-value=1.4e+02 Score=20.41 Aligned_cols=51 Identities=24% Similarity=0.324 Sum_probs=42.5
Q ss_pred CCcCeeeeeecCCce----eEEEEeccHHH--HHHHHHHHHhCChhhhhcceeEEEe
Q psy12287 13 GTEGINLRKVEPWNS----VRVTFTIPKEA--AVRLRQLAQQGNATLLQLGILSVQV 63 (76)
Q Consensus 13 ~~~~l~v~kvEPWnS----VRVTf~IPreA--A~rLr~LA~~g~~~Lr~LGILSVQ~ 63 (76)
.+-.++++.++-.+. +||-+-=|.+. ..+|++++..=...+.+.||....-
T Consensus 80 ~~~~i~l~Gl~~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~ 136 (209)
T PF10469_consen 80 PPLKITLKGLGYFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDD 136 (209)
T ss_pred CCceEEeeechhhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccc
Confidence 556788889988888 89998878764 6999999999999999999987543
No 108
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=21.72 E-value=1.5e+02 Score=15.84 Aligned_cols=41 Identities=27% Similarity=0.356 Sum_probs=28.9
Q ss_pred hHHHhhcCCCCcCeeeeeecCCceeEEEEeccHHHHHHHHHH
Q psy12287 4 LYKVCFNLGGTEGINLRKVEPWNSVRVTFTIPKEAAVRLRQL 45 (76)
Q Consensus 4 ~~~~c~~~~~~~~l~v~kvEPWnSVRVTf~IPreAA~rLr~L 45 (76)
||++|..-|+-..+++.+-.+ +.+-|+|.=+.+|..-++.|
T Consensus 1 L~~~f~~fG~V~~i~~~~~~~-~~a~V~f~~~~~A~~a~~~l 41 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIKIFKKKR-GFAFVEFASVEDAQKAIEQL 41 (56)
T ss_dssp HHHHHTTTS-EEEEEEETTST-TEEEEEESSHHHHHHHHHHH
T ss_pred ChHHhCCcccEEEEEEEeCCC-CEEEEEECCHHHHHHHHHHh
Confidence 577777777655555544443 67999999888887777777
No 109
>PTZ00278 ARP2/3 complex subunit; Provisional
Probab=21.58 E-value=57 Score=24.46 Aligned_cols=15 Identities=53% Similarity=0.961 Sum_probs=11.9
Q ss_pred ecC-CceeEEEEeccH
Q psy12287 22 VEP-WNSVRVTFTIPK 36 (76)
Q Consensus 22 vEP-WnSVRVTf~IPr 36 (76)
+|| -|||||+|.|..
T Consensus 67 IE~SiNSvRiSi~ikq 82 (174)
T PTZ00278 67 IEPSINSVRISFSFKK 82 (174)
T ss_pred EEcccceEEEEEEehh
Confidence 344 599999999975
No 110
>smart00837 DPBB_1 Rare lipoprotein A (RlpA)-like double-psi beta-barrel. Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen.
Probab=21.36 E-value=1.2e+02 Score=19.34 Aligned_cols=25 Identities=28% Similarity=0.503 Sum_probs=19.2
Q ss_pred EEEEeccHHHHHHHHHHHHhCChhhhhcceeEEE
Q psy12287 29 RVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQ 62 (76)
Q Consensus 29 RVTf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ 62 (76)
|-.|.+..+|=.+|-+ ++.||+.||
T Consensus 62 ~~hfDLS~~AF~~iA~---------~~~Gvi~v~ 86 (87)
T smart00837 62 RKHFDLSQPAFEKIAQ---------YKAGIVPVK 86 (87)
T ss_pred CcCeEcCHHHHHHHhh---------hcCCEEeeE
Confidence 5568888888877655 477999887
No 111
>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=21.29 E-value=90 Score=16.53 Aligned_cols=16 Identities=19% Similarity=0.424 Sum_probs=9.6
Q ss_pred EeccHHHHHH-HHHHHH
Q psy12287 32 FTIPKEAAVR-LRQLAQ 47 (76)
Q Consensus 32 f~IPreAA~r-Lr~LA~ 47 (76)
|.|++.++.+ |..|++
T Consensus 35 ~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 35 LGVSRTTVREALRELEA 51 (66)
T ss_pred HCCCHHHHHHHHHHHHH
Confidence 5677777655 555544
No 112
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=21.14 E-value=44 Score=23.52 Aligned_cols=22 Identities=32% Similarity=0.392 Sum_probs=14.5
Q ss_pred eEEEEeccHHHHHHHHHHHHhCCh
Q psy12287 28 VRVTFTIPKEAAVRLRQLAQQGNA 51 (76)
Q Consensus 28 VRVTf~IPreAA~rLr~LA~~g~~ 51 (76)
.+..|.+++|.|+|| +|.-|+.
T Consensus 121 ~~~~~~~q~e~a~Rl--~a~pg~~ 142 (253)
T TIGR00755 121 RLAVLMVQKEVAERL--TAKPGSK 142 (253)
T ss_pred ceEEEEehHHHHHHH--ccCCCCC
Confidence 466777777777777 5555554
No 113
>PF09650 PHA_gran_rgn: Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); InterPro: IPR013433 Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been predominantly found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=21.04 E-value=84 Score=19.91 Aligned_cols=17 Identities=18% Similarity=0.180 Sum_probs=14.5
Q ss_pred eecCCceeEEEEeccHHH
Q psy12287 21 KVEPWNSVRVTFTIPKEA 38 (76)
Q Consensus 21 kvEPWnSVRVTf~IPreA 38 (76)
.|.| ++|||.+.+|+=+
T Consensus 52 ~V~~-d~v~l~v~Lg~Ll 68 (87)
T PF09650_consen 52 DVAD-DHVRLEVKLGFLL 68 (87)
T ss_pred EEcC-CEEEEEEEcHHHH
Confidence 4678 8999999999865
No 114
>KOG1119|consensus
Probab=20.84 E-value=1.4e+02 Score=22.91 Aligned_cols=32 Identities=19% Similarity=0.422 Sum_probs=25.2
Q ss_pred EEEeccHHHHHHHHHHHHhCChhhhhcceeEEEecchh
Q psy12287 30 VTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDE 67 (76)
Q Consensus 30 VTf~IPreAA~rLr~LA~~g~~~Lr~LGILSVQ~EGd~ 67 (76)
..+.+..+|-.||++++.++- -.|-|+|||.+
T Consensus 92 ~~~~lsds~~krl~EI~~~~p------e~LRl~VegGG 123 (199)
T KOG1119|consen 92 FNLHLSDSCSKRLKEIYENSP------EFLRLTVEGGG 123 (199)
T ss_pred ceEEehhHHHHHHHHHHhCCc------ceEEEEEecCC
Confidence 345677889999999998775 46779999975
No 115
>PF00705 PCNA_N: Proliferating cell nuclear antigen, N-terminal domain; InterPro: IPR022648 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1U76_E 2ZVK_B 1VYJ_A 1UL1_B 3P87_D 2ZVM_C 2ZVL_A 1AXC_C 3VKX_A 3TBL_B ....
Probab=20.81 E-value=1e+02 Score=20.43 Aligned_cols=27 Identities=30% Similarity=0.538 Sum_probs=21.9
Q ss_pred CcCeeeeeecCCceeEEEEeccHHHHH
Q psy12287 14 TEGINLRKVEPWNSVRVTFTIPKEAAV 40 (76)
Q Consensus 14 ~~~l~v~kvEPWnSVRVTf~IPreAA~ 40 (76)
+++++++-+-|=+-.=|.++||++|=+
T Consensus 32 ~~Gi~~~amD~s~Valv~l~l~~~~F~ 58 (127)
T PF00705_consen 32 EDGISLQAMDPSHVALVDLELPSEAFE 58 (127)
T ss_dssp SSEEEEEEE-TTSSEEEEEEEEGGGSS
T ss_pred cCCEEEEEECCCcEEEEEEEechhcce
Confidence 578999999998888889999998743
No 116
>cd00063 FN3 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
Probab=20.72 E-value=1.4e+02 Score=15.13 Aligned_cols=21 Identities=24% Similarity=0.488 Sum_probs=13.3
Q ss_pred cCeeeeeecCCceeEEEEeccH
Q psy12287 15 EGINLRKVEPWNSVRVTFTIPK 36 (76)
Q Consensus 15 ~~l~v~kvEPWnSVRVTf~IPr 36 (76)
..+++....| ++++|+.+-|.
T Consensus 5 ~~~~~~~~~~-~~~~v~W~~~~ 25 (93)
T cd00063 5 TNLRVTDVTS-TSVTLSWTPPE 25 (93)
T ss_pred CCcEEEEecC-CEEEEEECCCC
Confidence 3456666666 77777776664
No 117
>PRK07777 aminotransferase; Validated
Probab=20.17 E-value=1.2e+02 Score=22.02 Aligned_cols=22 Identities=41% Similarity=0.466 Sum_probs=15.2
Q ss_pred ceeEEEEeccH----HHHHHHHHHHH
Q psy12287 26 NSVRVTFTIPK----EAAVRLRQLAQ 47 (76)
Q Consensus 26 nSVRVTf~IPr----eAA~rLr~LA~ 47 (76)
+.||++|.-|. +|.+||++++-
T Consensus 360 ~~~Ri~~~~~~~~l~~~l~~l~~~~~ 385 (387)
T PRK07777 360 HLVRFAFCKRDDTLDEAIRRLRALRG 385 (387)
T ss_pred CeEEEEecCCHHHHHHHHHHHHHHhc
Confidence 46999999876 34666666553
No 118
>PRK05114 hypothetical protein; Provisional
Probab=20.10 E-value=97 Score=19.77 Aligned_cols=20 Identities=25% Similarity=0.325 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHhCChhhhh
Q psy12287 36 KEAAVRLRQLAQQGNATLLQ 55 (76)
Q Consensus 36 reAA~rLr~LA~~g~~~Lr~ 55 (76)
.+|++|+++|-++|=..=.+
T Consensus 14 Q~AVErIq~LMaqGmSsgEA 33 (59)
T PRK05114 14 QKAVERIQELMAQGMSSGEA 33 (59)
T ss_pred HHHHHHHHHHHHccccHHHH
Confidence 57999999999998654333
No 119
>COG4063 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A [Coenzyme metabolism]
Probab=20.03 E-value=67 Score=25.18 Aligned_cols=14 Identities=43% Similarity=0.529 Sum_probs=12.0
Q ss_pred EeccHHHHHHHHHH
Q psy12287 32 FTIPKEAAVRLRQL 45 (76)
Q Consensus 32 f~IPreAA~rLr~L 45 (76)
=|||+||-+|.||-
T Consensus 115 ENi~~eaveRfqqq 128 (238)
T COG4063 115 ENIPDEAVERFQQQ 128 (238)
T ss_pred hcCCHHHHHHHHHH
Confidence 38999999999963
No 120
>cd04924 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.01 E-value=1.6e+02 Score=15.60 Aligned_cols=17 Identities=6% Similarity=0.296 Sum_probs=12.6
Q ss_pred ceeEEEEeccHHHHHHH
Q psy12287 26 NSVRVTFTIPKEAAVRL 42 (76)
Q Consensus 26 nSVRVTf~IPreAA~rL 42 (76)
...+++|.||++-..++
T Consensus 40 s~~~isf~i~~~~~~~~ 56 (66)
T cd04924 40 SEYNISFVVAEDDGWAA 56 (66)
T ss_pred ccceEEEEEeHHHHHHH
Confidence 35899999998665444
Done!