Query 031429
Match_columns 159
No_of_seqs 158 out of 706
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 13:58:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031429hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3088 CcmH Uncharacterized p 100.0 2.1E-51 4.5E-56 324.2 14.1 132 2-142 22-153 (153)
2 PRK10144 formate-dependent nit 100.0 3.5E-47 7.6E-52 293.1 12.2 101 4-104 20-120 (126)
3 TIGR03147 cyt_nit_nrfF cytochr 100.0 9E-47 1.9E-51 290.9 12.2 101 4-104 20-120 (126)
4 PF03918 CcmH: Cytochrome C bi 100.0 4.9E-47 1.1E-51 298.2 7.3 123 8-140 25-148 (148)
5 PRK09458 pspB phage shock prot 92.7 0.24 5.3E-06 35.6 4.5 16 125-140 34-49 (75)
6 TIGR02976 phageshock_pspB phag 91.3 0.58 1.3E-05 33.4 5.1 14 125-138 34-47 (75)
7 PF06667 PspB: Phage shock pro 91.2 0.6 1.3E-05 33.4 5.1 15 125-139 34-48 (75)
8 PF12273 RCR: Chitin synthesis 86.6 0.56 1.2E-05 35.6 2.4 10 86-95 2-11 (130)
9 smart00831 Cation_ATPase_N Cat 84.9 5.5 0.00012 25.9 6.3 41 55-96 8-51 (64)
10 PF13798 PCYCGC: Protein of un 84.9 6.9 0.00015 31.8 8.0 62 13-74 64-148 (158)
11 PF08671 SinI: Anti-repressor 83.7 2.3 5E-05 25.5 3.6 25 44-68 3-27 (30)
12 PF00690 Cation_ATPase_N: Cati 81.6 3.3 7.1E-05 27.7 4.3 44 54-98 17-63 (69)
13 PF14420 Clr5: Clr5 domain 79.7 4.2 9.1E-05 26.7 4.2 31 45-75 7-38 (54)
14 PF05402 PqqD: Coenzyme PQQ sy 76.9 3.6 7.7E-05 27.1 3.2 27 47-73 19-45 (68)
15 PF03461 TRCF: TRCF domain; I 74.8 5.4 0.00012 29.1 4.0 31 44-74 16-49 (101)
16 COG3763 Uncharacterized protei 73.2 12 0.00025 26.8 5.1 39 88-134 8-46 (71)
17 PRK06266 transcription initiat 72.8 5.2 0.00011 32.4 3.8 33 21-53 133-165 (178)
18 PF05184 SapB_1: Saposin-like 71.2 10 0.00022 22.4 4.0 29 41-69 5-33 (39)
19 KOG2878 Predicted kinase [Gene 70.3 4.3 9.4E-05 35.1 2.9 24 48-72 223-246 (282)
20 PRK11712 ribonuclease G; Provi 70.2 8.9 0.00019 35.9 5.2 55 25-79 403-475 (489)
21 PF14002 YniB: YniB-like prote 69.5 15 0.00033 30.1 5.8 50 44-100 102-158 (166)
22 PF06755 DUF1219: Protein of u 68.2 7.7 0.00017 30.0 3.6 34 48-81 47-80 (114)
23 PRK08207 coproporphyrinogen II 65.5 7 0.00015 36.2 3.5 25 48-72 112-136 (488)
24 PRK07668 hypothetical protein; 64.9 18 0.00039 31.2 5.7 75 14-93 6-81 (254)
25 cd00922 Cyt_c_Oxidase_IV Cytoc 63.9 64 0.0014 25.2 8.1 75 57-141 46-122 (136)
26 PF14353 CpXC: CpXC protein 63.5 2.3 4.9E-05 31.9 -0.0 34 24-57 1-34 (128)
27 PF07508 Recombinase: Recombin 63.1 15 0.00032 25.5 4.1 29 44-72 4-32 (102)
28 PRK00523 hypothetical protein; 62.4 23 0.0005 25.3 4.9 13 123-135 36-48 (72)
29 PF13565 HTH_32: Homeodomain-l 62.3 19 0.0004 24.0 4.3 33 43-75 32-66 (77)
30 PRK01844 hypothetical protein; 62.2 24 0.00052 25.2 4.9 13 123-135 35-47 (72)
31 COG4640 Predicted membrane pro 62.0 20 0.00043 33.4 5.6 60 78-141 44-103 (465)
32 COG1740 HyaA Ni,Fe-hydrogenase 61.4 8.1 0.00018 35.0 3.0 52 25-77 57-116 (355)
33 PF01102 Glycophorin_A: Glycop 61.4 13 0.00029 28.7 3.9 6 105-110 88-93 (122)
34 PF04233 Phage_Mu_F: Phage Mu 61.1 16 0.00035 25.9 4.0 28 45-72 2-29 (112)
35 PF04423 Rad50_zn_hook: Rad50 61.0 8.8 0.00019 24.9 2.4 40 13-52 8-48 (54)
36 TIGR00373 conserved hypothetic 59.4 11 0.00024 29.8 3.2 33 20-52 124-156 (158)
37 PF12273 RCR: Chitin synthesis 59.3 14 0.0003 28.0 3.6 13 86-98 5-17 (130)
38 COG3677 Transposase and inacti 57.2 25 0.00055 27.1 4.8 60 23-82 52-124 (129)
39 PF08069 Ribosomal_S13_N: Ribo 57.0 10 0.00023 26.1 2.3 31 42-72 29-59 (60)
40 TIGR03370 PEPCTERM_Roseo varia 56.3 17 0.00036 21.3 2.7 9 94-102 10-18 (26)
41 COG1725 Predicted transcriptio 55.8 25 0.00054 27.4 4.5 32 42-73 91-122 (125)
42 PRK02079 pyrroloquinoline quin 54.3 15 0.00033 26.6 3.0 28 47-74 38-65 (88)
43 PF09905 DUF2132: Uncharacteri 54.0 10 0.00022 26.6 1.9 21 56-76 7-27 (64)
44 PF08004 DUF1699: Protein of u 53.2 17 0.00038 28.7 3.3 28 42-69 89-116 (131)
45 TIGR03853 matur_matur probable 52.7 25 0.00054 25.4 3.8 30 50-79 8-39 (77)
46 COG3105 Uncharacterized protei 52.3 20 0.00043 28.5 3.5 23 84-106 3-27 (138)
47 PF08542 Rep_fac_C: Replicatio 52.1 29 0.00063 23.7 4.0 31 44-74 21-51 (89)
48 TIGR01167 LPXTG_anchor LPXTG-m 52.0 19 0.0004 20.8 2.6 9 84-92 10-18 (34)
49 TIGR01432 QOXA cytochrome aa3 51.7 95 0.0021 25.5 7.6 70 29-98 2-81 (217)
50 TIGR03521 GldG gliding-associa 51.6 18 0.00039 33.8 3.7 20 89-108 529-549 (552)
51 PF11293 DUF3094: Protein of u 51.1 15 0.00033 25.0 2.3 21 125-145 2-22 (55)
52 PF02936 COX4: Cytochrome c ox 50.7 68 0.0015 25.2 6.3 20 57-76 46-65 (142)
53 PF13936 HTH_38: Helix-turn-he 50.5 11 0.00025 23.4 1.6 28 40-67 3-30 (44)
54 PF08006 DUF1700: Protein of u 50.5 23 0.00049 28.0 3.6 27 41-67 24-50 (181)
55 KOG3908 Queuine-tRNA ribosyltr 49.7 8.4 0.00018 34.8 1.2 67 8-74 293-376 (396)
56 COG2442 Uncharacterized conser 49.5 17 0.00037 26.1 2.5 20 48-67 34-53 (79)
57 PF14410 GH-E: HNH/ENDO VII su 49.5 45 0.00097 23.2 4.6 44 24-68 5-51 (70)
58 PRK05585 yajC preprotein trans 49.3 32 0.00069 25.8 4.1 14 85-98 16-29 (106)
59 PRK10525 cytochrome o ubiquino 49.1 33 0.00071 30.5 4.8 70 29-98 23-102 (315)
60 PF15361 RIC3: Resistance to i 49.0 24 0.00053 28.0 3.6 64 78-141 73-142 (152)
61 COG1644 RPB10 DNA-directed RNA 48.9 33 0.00071 24.0 3.7 38 25-71 5-43 (63)
62 PF15652 Tox-SHH: HNH/Endo VII 48.6 44 0.00095 25.3 4.7 34 38-71 63-96 (100)
63 TIGR01641 phageSPP1_gp7 phage 48.4 24 0.00052 25.3 3.3 26 47-72 2-27 (108)
64 PF01194 RNA_pol_N: RNA polyme 47.9 31 0.00068 23.8 3.5 34 25-67 5-38 (60)
65 PF12298 Bot1p: Eukaryotic mit 47.8 16 0.00035 29.7 2.4 33 37-73 12-45 (172)
66 PHA02591 hypothetical protein; 47.1 30 0.00065 25.4 3.5 24 44-67 46-69 (83)
67 cd00194 UBA Ubiquitin Associat 46.7 45 0.00097 19.5 3.7 28 47-74 2-29 (38)
68 PF07553 Lipoprotein_Ltp: Host 46.7 17 0.00036 23.8 1.9 20 55-74 16-35 (48)
69 PF13584 BatD: Oxygen toleranc 46.5 41 0.00088 30.3 5.0 9 131-139 471-479 (484)
70 TIGR00430 Q_tRNA_tgt tRNA-guan 45.5 33 0.00071 30.8 4.3 54 21-75 296-367 (368)
71 PF09524 Phg_2220_C: Conserved 44.7 45 0.00098 23.7 4.1 45 42-86 16-63 (74)
72 PRK05886 yajC preprotein trans 44.2 39 0.00085 25.7 3.9 6 91-96 8-13 (109)
73 TIGR02230 ATPase_gene1 F0F1-AT 43.5 92 0.002 23.4 5.8 32 36-67 10-42 (100)
74 PF02796 HTH_7: Helix-turn-hel 43.5 25 0.00055 21.8 2.4 22 46-67 10-31 (45)
75 PF05545 FixQ: Cbb3-type cytoc 43.5 30 0.00065 22.0 2.8 13 98-110 23-35 (49)
76 TIGR03859 PQQ_PqqD coenzyme PQ 42.9 30 0.00066 24.2 3.0 27 47-73 33-59 (81)
77 PF03849 Tfb2: Transcription f 42.7 29 0.00062 31.1 3.4 24 47-70 340-363 (366)
78 PF04341 DUF485: Protein of un 42.7 95 0.0021 22.2 5.6 42 68-109 35-77 (91)
79 PF15217 TSC21: TSC21 family 41.9 19 0.00041 29.5 1.9 27 125-151 34-60 (180)
80 TIGR02595 PEP_exosort PEP-CTER 41.6 31 0.00067 19.6 2.3 10 100-109 14-23 (26)
81 TIGR00449 tgt_general tRNA-gua 41.6 40 0.00086 30.2 4.2 55 19-74 293-365 (367)
82 PF12091 DUF3567: Protein of u 41.3 55 0.0012 24.1 4.2 31 41-72 45-75 (85)
83 PF11239 DUF3040: Protein of u 41.3 20 0.00042 25.2 1.8 13 126-138 2-14 (82)
84 smart00025 Pumilio Pumilio-lik 41.2 14 0.00031 20.4 0.9 17 60-76 3-19 (36)
85 cd02029 PRK_like Phosphoribulo 40.7 34 0.00074 30.0 3.5 41 46-86 156-197 (277)
86 PRK15453 phosphoribulokinase; 40.6 37 0.00079 30.0 3.7 39 46-84 162-201 (290)
87 PRK14562 haloacid dehalogenase 40.5 40 0.00088 27.7 3.8 42 41-82 120-163 (204)
88 cd01301 rDP_like renal dipepti 39.8 42 0.0009 29.3 3.9 30 43-75 278-307 (309)
89 PF11569 Homez: Homeodomain le 39.8 26 0.00056 23.9 2.1 19 55-73 34-52 (56)
90 PF14257 DUF4349: Domain of un 39.6 27 0.00058 29.1 2.6 20 45-64 146-165 (262)
91 PF00046 Homeobox: Homeobox do 39.6 40 0.00086 21.2 2.9 26 43-70 26-51 (57)
92 PRK07429 phosphoribulokinase; 39.4 15 0.00031 32.4 1.1 45 49-93 143-188 (327)
93 cd00131 PAX Paired Box domain 38.7 37 0.00079 25.8 3.1 29 37-65 13-41 (128)
94 PRK06393 rpoE DNA-directed RNA 38.6 22 0.00047 24.9 1.6 27 22-48 15-52 (64)
95 PRK11677 hypothetical protein; 38.2 54 0.0012 25.7 4.0 16 89-104 3-20 (134)
96 PRK10573 type IV pilin biogene 38.0 20 0.00044 31.5 1.7 81 9-98 293-376 (399)
97 PF04255 DUF433: Protein of un 37.9 31 0.00067 22.6 2.2 18 49-66 23-40 (56)
98 PRK10807 paraquat-inducible pr 37.8 32 0.00069 32.5 3.1 16 86-101 18-33 (547)
99 PF13584 BatD: Oxygen toleranc 37.7 40 0.00087 30.3 3.6 7 131-137 468-474 (484)
100 PF01466 Skp1: Skp1 family, di 37.3 36 0.00078 23.6 2.6 12 56-67 44-55 (78)
101 PRK08351 DNA-directed RNA poly 37.0 26 0.00056 24.2 1.8 16 24-39 15-30 (61)
102 PF10678 DUF2492: Protein of u 36.7 52 0.0011 23.8 3.4 29 50-78 9-40 (78)
103 COG2771 CsgD DNA-binding HTH d 36.3 51 0.0011 20.6 3.0 20 48-67 10-29 (65)
104 COG3008 PqiB Paraquat-inducibl 35.8 33 0.00072 32.9 2.9 16 87-102 22-37 (553)
105 PF05337 CSF-1: Macrophage col 35.6 12 0.00027 33.0 0.0 10 125-134 271-280 (285)
106 KOG4403 Cell surface glycoprot 35.6 38 0.00083 32.1 3.1 48 59-106 185-235 (575)
107 PF10112 Halogen_Hydrol: 5-bro 34.9 54 0.0012 26.3 3.6 18 124-141 62-79 (199)
108 PF08693 SKG6: Transmembrane a 34.8 23 0.0005 22.6 1.1 8 91-98 19-26 (40)
109 TIGR02531 yecD_yerC TrpR-relat 34.7 54 0.0012 23.8 3.2 24 44-67 37-60 (88)
110 PRK13533 7-cyano-7-deazaguanin 34.7 28 0.00062 32.5 2.2 36 24-59 274-324 (487)
111 COG1202 Superfamily II helicas 34.7 1.1E+02 0.0024 30.4 6.1 72 11-94 725-797 (830)
112 PF13384 HTH_23: Homeodomain-l 34.4 39 0.00085 20.7 2.2 25 43-67 3-27 (50)
113 PF04814 HNF-1_N: Hepatocyte n 33.3 67 0.0015 26.6 4.0 29 41-69 4-32 (180)
114 COG3415 Transposase and inacti 33.3 2.1E+02 0.0045 22.5 6.6 29 40-72 3-32 (138)
115 PF07095 IgaA: Intracellular g 33.2 1E+02 0.0022 30.5 5.7 15 126-140 45-59 (705)
116 PF01402 RHH_1: Ribbon-helix-h 32.9 1E+02 0.0023 17.9 3.9 28 44-71 8-36 (39)
117 PRK10811 rne ribonuclease E; R 32.4 60 0.0013 33.5 4.1 35 26-60 403-437 (1068)
118 COG1862 YajC Preprotein transl 32.4 87 0.0019 23.3 4.1 8 89-96 11-18 (97)
119 PF11985 DUF3486: Protein of u 32.2 80 0.0017 25.1 4.2 28 44-71 12-40 (180)
120 PF09889 DUF2116: Uncharacteri 32.1 1.7E+02 0.0036 20.0 5.7 14 26-40 5-18 (59)
121 PF08996 zf-DNA_Pol: DNA Polym 32.1 37 0.00079 27.4 2.2 30 23-55 44-73 (188)
122 PF03672 UPF0154: Uncharacteri 31.6 93 0.002 21.7 3.9 12 124-135 29-40 (64)
123 PF12677 DUF3797: Domain of un 31.6 24 0.00051 23.6 0.9 19 24-42 13-31 (49)
124 PF14163 SieB: Superinfection 31.2 75 0.0016 24.4 3.8 21 125-145 77-97 (151)
125 PF04246 RseC_MucC: Positive r 31.0 78 0.0017 23.8 3.7 29 67-95 50-81 (135)
126 TIGR00778 ahpD_dom alkylhydrop 30.0 1.3E+02 0.0029 18.2 4.3 41 15-70 9-49 (50)
127 PF00627 UBA: UBA/TS-N domain; 29.9 92 0.002 18.4 3.2 27 48-74 4-30 (37)
128 KOG2629 Peroxisomal membrane a 29.3 3E+02 0.0065 24.6 7.5 21 49-69 25-45 (300)
129 PRK10862 SoxR reducing system 29.0 86 0.0019 24.7 3.8 25 70-94 60-87 (154)
130 PF09753 Use1: Membrane fusion 28.6 64 0.0014 26.9 3.2 15 86-100 228-242 (251)
131 smart00165 UBA Ubiquitin assoc 28.6 1.2E+02 0.0027 17.4 3.7 26 48-73 3-28 (37)
132 PF14076 DUF4258: Domain of un 28.6 30 0.00065 22.5 1.0 30 49-80 6-35 (73)
133 PRK00415 rps27e 30S ribosomal 28.6 23 0.00049 24.4 0.4 18 23-40 10-27 (59)
134 PRK06547 hypothetical protein; 28.5 3.4 7.3E-05 32.8 -4.3 28 126-157 123-150 (172)
135 PLN00083 photosystem II subuni 28.3 17 0.00037 27.3 -0.3 30 67-96 45-87 (101)
136 PRK00398 rpoP DNA-directed RNA 28.2 9.6 0.00021 23.9 -1.4 23 24-46 21-43 (46)
137 PRK08561 rps15p 30S ribosomal 28.1 88 0.0019 25.3 3.7 31 42-72 29-59 (151)
138 PF12575 DUF3753: Protein of u 27.9 1.5E+02 0.0032 21.2 4.5 30 63-94 27-56 (72)
139 PLN00032 DNA-directed RNA poly 27.9 1.1E+02 0.0023 21.9 3.7 38 25-71 5-43 (71)
140 cd00569 HTH_Hin_like Helix-tur 27.9 93 0.002 15.7 3.1 24 44-67 8-31 (42)
141 PF04564 U-box: U-box domain; 27.8 48 0.001 22.6 1.9 33 23-56 38-70 (73)
142 smart00389 HOX Homeodomain. DN 27.7 1.2E+02 0.0027 18.5 3.7 24 45-70 28-51 (56)
143 PRK10856 cytoskeletal protein 27.7 3.3E+02 0.0071 24.1 7.6 15 57-71 73-87 (331)
144 TIGR00391 hydA hydrogenase (Ni 27.7 29 0.00063 31.6 1.0 50 27-77 61-118 (365)
145 TIGR00625 tfb2 Transcription f 27.5 70 0.0015 29.9 3.5 30 47-76 335-364 (448)
146 PF13411 MerR_1: MerR HTH fami 27.5 1.1E+02 0.0024 19.6 3.6 29 41-69 40-68 (69)
147 TIGR00432 arcsn_tRNA_tgt tRNA- 27.4 45 0.00098 31.7 2.3 60 24-83 172-259 (540)
148 PF01997 Translin: Translin fa 27.2 79 0.0017 25.6 3.4 63 20-82 96-167 (200)
149 cd04764 HTH_MlrA-like_sg1 Heli 27.1 85 0.0018 20.4 3.0 25 43-67 42-66 (67)
150 COG3225 GldG ABC-type uncharac 27.0 63 0.0014 30.9 3.1 24 85-108 513-537 (538)
151 PHA02975 hypothetical protein; 26.9 1.3E+02 0.0027 21.5 3.9 18 79-96 37-54 (69)
152 KOG3970 Predicted E3 ubiquitin 26.8 65 0.0014 28.2 2.9 30 23-52 93-124 (299)
153 PF04189 Gcd10p: Gcd10p family 26.7 72 0.0016 28.0 3.3 52 28-81 92-166 (299)
154 PRK10715 flk flagella biosynth 26.6 91 0.002 28.2 3.9 83 42-140 93-175 (335)
155 PRK04016 DNA-directed RNA poly 26.6 1.2E+02 0.0026 21.1 3.7 34 25-67 5-38 (62)
156 cd02026 PRK Phosphoribulokinas 26.5 30 0.00065 29.4 0.9 48 46-93 130-179 (273)
157 PRK01294 lipase chaperone; Pro 26.0 86 0.0019 27.9 3.6 65 8-76 202-266 (336)
158 PF10821 DUF2567: Protein of u 25.9 1E+02 0.0022 25.2 3.8 41 69-109 27-73 (167)
159 PF09925 DUF2157: Predicted me 25.8 2.4E+02 0.0053 21.3 5.8 22 51-72 2-23 (145)
160 PF07937 DUF1686: Protein of u 25.7 2.1E+02 0.0046 23.9 5.6 54 50-103 82-143 (185)
161 PF00196 GerE: Bacterial regul 25.6 90 0.0019 19.9 2.8 20 48-67 9-28 (58)
162 PF03280 Lipase_chap: Proteoba 25.5 60 0.0013 26.3 2.4 37 38-74 102-138 (195)
163 PF11208 DUF2992: Protein of u 25.4 46 0.001 26.0 1.7 25 59-84 34-58 (132)
164 PF13719 zinc_ribbon_5: zinc-r 25.3 25 0.00054 21.4 0.1 16 17-32 18-33 (37)
165 PF09986 DUF2225: Uncharacteri 25.1 30 0.00065 28.6 0.6 11 23-33 4-14 (214)
166 PF13625 Helicase_C_3: Helicas 25.1 1.1E+02 0.0024 22.7 3.6 26 47-72 44-69 (129)
167 PF10045 DUF2280: Uncharacteri 24.9 1.3E+02 0.0027 23.0 3.8 46 40-85 2-53 (104)
168 PF02657 SufE: Fe-S metabolism 24.9 66 0.0014 24.5 2.4 31 35-66 61-91 (125)
169 KOG3471 RNA polymerase II tran 24.9 83 0.0018 29.6 3.4 28 46-73 348-375 (465)
170 cd02028 UMPK_like Uridine mono 24.9 95 0.0021 24.3 3.4 39 44-82 132-170 (179)
171 TIGR02425 decarb_PcaC 4-carbox 24.8 1.4E+02 0.0031 22.6 4.2 25 44-68 73-97 (123)
172 TIGR02501 type_III_yscE type I 24.7 1.7E+02 0.0036 20.3 4.2 18 45-62 24-41 (67)
173 cd01104 HTH_MlrA-CarA Helix-Tu 24.5 1E+02 0.0022 19.8 3.0 25 43-67 43-67 (68)
174 TIGR03068 srtB_sig_NPQTN sorta 24.5 1.4E+02 0.0029 18.5 3.2 17 79-95 2-19 (33)
175 PF11446 DUF2897: Protein of u 24.5 1E+02 0.0023 20.7 3.0 17 85-101 2-18 (55)
176 PF04282 DUF438: Family of unk 24.2 1.2E+02 0.0026 21.4 3.4 27 48-74 3-29 (71)
177 PF12169 DNA_pol3_gamma3: DNA 24.0 1.1E+02 0.0023 22.7 3.3 39 43-81 30-68 (143)
178 smart00035 CLa CLUSTERIN alpha 24.0 28 0.00061 29.6 0.2 43 26-75 74-118 (216)
179 TIGR02837 spore_II_R stage II 23.9 1.6E+02 0.0035 24.1 4.6 34 34-67 44-85 (168)
180 PF09420 Nop16: Ribosome bioge 23.9 56 0.0012 25.8 1.9 16 60-75 121-136 (164)
181 PF03908 Sec20: Sec20; InterP 23.6 1E+02 0.0022 21.9 3.1 10 85-94 70-79 (92)
182 PRK14740 kdbF potassium-transp 23.6 1.8E+02 0.0038 17.5 3.5 14 85-98 2-15 (29)
183 PF04108 APG17: Autophagy prot 23.6 1.1E+02 0.0024 27.6 4.0 32 41-75 367-398 (412)
184 PTZ00072 40S ribosomal protein 23.6 89 0.0019 25.2 3.0 30 42-71 26-55 (148)
185 COG3357 Predicted transcriptio 23.5 33 0.00073 25.8 0.5 17 21-37 73-89 (97)
186 TIGR00762 DegV EDD domain prot 23.5 1.1E+02 0.0024 25.7 3.7 34 43-76 121-154 (275)
187 PF05462 Dicty_CAR: Slime mold 23.4 2E+02 0.0043 25.1 5.4 26 70-95 141-166 (303)
188 PF09892 DUF2119: Uncharacteri 23.3 1.2E+02 0.0026 25.5 3.8 48 29-76 134-181 (193)
189 PRK13685 hypothetical protein; 23.3 97 0.0021 26.7 3.4 8 86-93 10-17 (326)
190 PRK11677 hypothetical protein; 23.2 1E+02 0.0022 24.2 3.2 18 86-103 3-23 (134)
191 PLN02417 dihydrodipicolinate s 23.0 1.9E+02 0.0041 24.4 5.1 50 35-84 74-139 (280)
192 COG4736 CcoQ Cbb3-type cytochr 22.9 1.9E+02 0.0041 19.9 4.1 16 96-111 21-36 (60)
193 PF04478 Mid2: Mid2 like cell 22.8 21 0.00045 28.9 -0.7 10 91-100 60-69 (154)
194 PF03698 UPF0180: Uncharacteri 22.5 71 0.0015 23.0 2.0 17 55-71 63-79 (80)
195 PHA03240 envelope glycoprotein 22.5 87 0.0019 27.2 2.9 34 69-103 196-229 (258)
196 PF08776 VASP_tetra: VASP tetr 22.5 2E+02 0.0044 18.4 3.9 24 42-71 12-35 (40)
197 PF09551 Spore_II_R: Stage II 22.4 1.9E+02 0.0041 22.7 4.6 20 35-54 10-29 (130)
198 PF12979 DUF3863: Domain of Un 22.3 55 0.0012 29.2 1.7 27 54-80 68-98 (351)
199 PF14256 YwiC: YwiC-like prote 22.3 1.2E+02 0.0025 23.3 3.4 25 86-110 82-106 (129)
200 PF03701 UPF0181: Uncharacteri 22.1 1.5E+02 0.0032 20.0 3.3 25 46-70 16-40 (51)
201 smart00351 PAX Paired Box doma 22.0 1.1E+02 0.0023 23.0 3.0 27 39-65 15-41 (125)
202 PF02758 PYRIN: PAAD/DAPIN/Pyr 21.8 47 0.001 23.2 1.0 18 57-74 42-59 (83)
203 PF00482 T2SF: Type II secreti 21.7 68 0.0015 21.8 1.8 65 11-76 28-92 (124)
204 cd00086 homeodomain Homeodomai 21.4 2E+02 0.0043 17.6 3.8 14 57-70 38-51 (59)
205 PF03457 HA: Helicase associat 21.3 1.9E+02 0.0041 18.9 3.9 13 126-138 53-65 (68)
206 COG1307 DegV Uncharacterized p 21.3 1.4E+02 0.0031 25.7 4.0 40 46-85 127-166 (282)
207 PF12555 TPPK_C: Thiamine pyro 21.2 1.6E+02 0.0034 19.3 3.3 15 76-90 6-20 (53)
208 TIGR02220 phg_TIGR02220 phage 21.1 1.5E+02 0.0033 21.1 3.5 30 44-73 21-53 (77)
209 TIGR03180 UraD_2 OHCU decarbox 21.0 86 0.0019 24.9 2.4 19 56-74 116-134 (158)
210 PF14829 GPAT_N: Glycerol-3-ph 20.9 1.5E+02 0.0032 21.5 3.4 36 40-75 8-43 (77)
211 PRK15019 CsdA-binding activato 20.8 2.1E+02 0.0045 22.7 4.6 30 36-66 81-110 (147)
212 PRK13534 7-cyano-7-deazaguanin 20.8 71 0.0015 30.9 2.3 38 24-61 271-323 (639)
213 PF04117 Mpv17_PMP22: Mpv17 / 20.8 87 0.0019 20.8 2.1 30 54-90 3-32 (68)
214 TIGR00739 yajC preprotein tran 20.8 1.5E+02 0.0034 21.1 3.5 6 91-96 7-12 (84)
215 cd04763 HTH_MlrA-like Helix-Tu 20.7 1.3E+02 0.0029 19.5 3.0 22 46-67 46-67 (68)
216 PTZ00382 Variant-specific surf 20.6 38 0.00083 24.8 0.3 12 27-38 22-33 (96)
217 PF10954 DUF2755: Protein of u 20.6 1.2E+02 0.0027 22.8 3.0 6 90-95 77-82 (100)
218 PF01244 Peptidase_M19: Membra 20.5 62 0.0013 28.2 1.7 30 43-75 286-315 (320)
219 PF10642 Tom5: Mitochondrial i 20.4 70 0.0015 21.1 1.5 11 85-95 32-42 (49)
220 PF14316 DUF4381: Domain of un 20.4 1.8E+02 0.0039 22.2 4.1 13 129-141 67-79 (146)
221 PRK09174 F0F1 ATP synthase sub 20.3 1.2E+02 0.0027 24.9 3.3 14 78-91 44-60 (204)
222 PHA03029 hypothetical protein; 20.3 1.4E+02 0.003 21.9 3.2 14 85-98 57-70 (92)
223 PF11044 TMEMspv1-c74-12: Plec 20.2 2.1E+02 0.0046 18.9 3.7 11 85-95 3-13 (49)
224 PF10515 APP_amyloid: beta-amy 20.2 1.2E+02 0.0026 20.4 2.6 10 124-133 25-34 (52)
No 1
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-51 Score=324.24 Aligned_cols=132 Identities=30% Similarity=0.450 Sum_probs=116.5
Q ss_pred CCCchHhhhcHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCC
Q 031429 2 ASNDDELKKKQMADARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKF 81 (159)
Q Consensus 2 ~~~~~~~~~d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~ 81 (159)
+..|++.|.||++|+||++|+++||||+||||||+||||+||.|||.+||++|.+|+||+||+||||+||||||+|+||+
T Consensus 22 a~~d~~~f~~~~qe~ra~~Lt~~LRCp~CQNqsIadSnA~IA~DlR~~V~e~l~eGkS~~qIid~mVaRYG~FVly~Pp~ 101 (153)
T COG3088 22 ATIDTEQFADPAQEQRARALTEELRCPQCQNQSIADSNAPIARDLRHQVYELLQEGKSDQQIIDYMVARYGEFVLYKPPL 101 (153)
T ss_pred hcCCcccCCCHHHHHHHHHHHHhcCCCcCCCCChhhhccHHHHHHHHHHHHHHHcCCcHHHHHHHHHHhhcceeeecCCC
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHhhccchhhHhhhhccCCCCCCHHHHHHHHhhcCCC
Q 031429 82 DLQTAALWLSPLLVAGAAAGIWAYNRHRQKTNVHIMALNLVRGVPLTPKEKETMLDLLTPP 142 (159)
Q Consensus 82 ~~~t~lLW~~P~l~~~~~~~~~~~~rrr~~~~~~~~~~~~~~~~~Ls~eE~~rl~~lL~~~ 142 (159)
++.||+||++|++++++|+++++.+.||+... ....||++|.+|+.+||++.
T Consensus 102 ~~~T~lLW~~Pv~llllG~~~~~~~~rrr~~~---------~~~~Ls~ee~~rl~~ll~~~ 153 (153)
T COG3088 102 TGQTLLLWGLPVVLLLLGGVLLVRRARRRVRE---------PPQTLSAEEEARLARLLRGD 153 (153)
T ss_pred chhHHHHHHhHHHHHHHHHHHHHHHHhhhhcc---------CCCCCChhHHHHHHHHhcCC
Confidence 99999999999887766655544333332211 24579999999999999863
No 2
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=100.00 E-value=3.5e-47 Score=293.13 Aligned_cols=101 Identities=26% Similarity=0.422 Sum_probs=93.7
Q ss_pred CchHhhhcHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCCCc
Q 031429 4 NDDELKKKQMADARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFDL 83 (159)
Q Consensus 4 ~~~~~~~d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~ 83 (159)
.+.+.|+||++|+|+++|+++||||+||||||+||||++|+|||.+||+||++|+||+||++|||+||||||||+||+++
T Consensus 20 ~~~~~~~~~~~e~r~~~L~~~LRC~vCqnqsiadSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~Pp~~~ 99 (126)
T PRK10144 20 VDTWQFANPQQQQQALNIASQLRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRYNPPLTG 99 (126)
T ss_pred CCcccCCCHHHHHHHHHHHHcCCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCc
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHH
Q 031429 84 QTAALWLSPLLVAGAAAGIWA 104 (159)
Q Consensus 84 ~t~lLW~~P~l~~~~~~~~~~ 104 (159)
.||+||++|++++++|+++++
T Consensus 100 ~t~~LW~~P~~lll~g~~~~~ 120 (126)
T PRK10144 100 QTLVLWALPVVLLLLMALILW 120 (126)
T ss_pred chHHHHHHHHHHHHHHHHHHH
Confidence 999999999886655544433
No 3
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=100.00 E-value=9e-47 Score=290.86 Aligned_cols=101 Identities=29% Similarity=0.486 Sum_probs=94.3
Q ss_pred CchHhhhcHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCCCc
Q 031429 4 NDDELKKKQMADARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFDL 83 (159)
Q Consensus 4 ~~~~~~~d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~ 83 (159)
.+++.|+|+++|+|+++|+++|||||||||||+||||++|+|||++||+||++|+||+||++|||+||||||||+||+++
T Consensus 20 ~~~~~f~~~~~e~r~~~L~~~LRC~vCqnqsiadS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly~Pp~~~ 99 (126)
T TIGR03147 20 VDTYQFHNPEQRTRAVALAKSLRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFVLYNPPFKW 99 (126)
T ss_pred CCcccCCCHHHHHHHHHHHHhCCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCc
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHH
Q 031429 84 QTAALWLSPLLVAGAAAGIWA 104 (159)
Q Consensus 84 ~t~lLW~~P~l~~~~~~~~~~ 104 (159)
.||+||++|++++++|+++++
T Consensus 100 ~t~~LW~~P~lll~~G~~~~~ 120 (126)
T TIGR03147 100 QTLLLWLLPVLLLLLAFVLLW 120 (126)
T ss_pred chHHHHHHHHHHHHHHHHHHH
Confidence 999999999987766554443
No 4
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=100.00 E-value=4.9e-47 Score=298.17 Aligned_cols=123 Identities=33% Similarity=0.514 Sum_probs=61.8
Q ss_pred hhhcHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCCCchhHH
Q 031429 8 LKKKQMADARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAA 87 (159)
Q Consensus 8 ~~~d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~l 87 (159)
.+ |+++++|+++|+++|||||||||||+|||+++|+|||++|+++|++|+|++||++|||+||||+|||+||++|+||+
T Consensus 25 ~~-~~~~e~r~~~l~~~LrCp~Cq~qsi~~s~a~~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG~~Vl~~Pp~~~~~~~ 103 (148)
T PF03918_consen 25 EF-DPEQEARARELAKELRCPVCQNQSIADSNAPIARDMRREIREMLAEGKSDEEIIDYFVERYGEFVLYEPPFKGFTWL 103 (148)
T ss_dssp ---SHHHHHHHHHHHHCCE-TTTTS-CTTT--SHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTT-EES--S------
T ss_pred cC-ChhHHHHHHHHHhcccCCCCCCCchhhcCcHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCcceeecCCCCccHHH
Confidence 44 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHH-HHhhccchhhHhhhhccCCCCCCHHHHHHHHhhcC
Q 031429 88 LWLSPLLVAGAAAGIWAY-NRHRQKTNVHIMALNLVRGVPLTPKEKETMLDLLT 140 (159)
Q Consensus 88 LW~~P~l~~~~~~~~~~~-~rrr~~~~~~~~~~~~~~~~~Ls~eE~~rl~~lL~ 140 (159)
||++|++++++|++++++ .||+++.. ...+||++|++||+++||
T Consensus 104 lW~~P~~~l~~g~~~~~~~~rr~~~~~---------~~~~ls~~e~~rl~~ll~ 148 (148)
T PF03918_consen 104 LWLGPFLLLLLGGALLFRRLRRWRRRA---------AQEELSEEERRRLDALLK 148 (148)
T ss_dssp ------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCC---------CCCCCCHHHHHHHHHHhC
Confidence 999999876665444333 33332221 125799999999999986
No 5
>PRK09458 pspB phage shock protein B; Provisional
Probab=92.71 E-value=0.24 Score=35.60 Aligned_cols=16 Identities=19% Similarity=0.316 Sum_probs=12.1
Q ss_pred CCCCHHHHHHHHhhcC
Q 031429 125 VPLTPKEKETMLDLLT 140 (159)
Q Consensus 125 ~~Ls~eE~~rl~~lL~ 140 (159)
..||++|+++|++|.+
T Consensus 34 ~~Ls~~d~~~L~~L~~ 49 (75)
T PRK09458 34 QGLSQEEQQRLAQLTE 49 (75)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 4699999888876543
No 6
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=91.33 E-value=0.58 Score=33.44 Aligned_cols=14 Identities=14% Similarity=0.415 Sum_probs=10.3
Q ss_pred CCCCHHHHHHHHhh
Q 031429 125 VPLTPKEKETMLDL 138 (159)
Q Consensus 125 ~~Ls~eE~~rl~~l 138 (159)
..||++|.++|++|
T Consensus 34 ~~ls~~d~~~L~~L 47 (75)
T TIGR02976 34 ASLSTDDQALLQEL 47 (75)
T ss_pred CCCCHHHHHHHHHH
Confidence 35888888877664
No 7
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=91.17 E-value=0.6 Score=33.41 Aligned_cols=15 Identities=13% Similarity=0.366 Sum_probs=11.4
Q ss_pred CCCCHHHHHHHHhhc
Q 031429 125 VPLTPKEKETMLDLL 139 (159)
Q Consensus 125 ~~Ls~eE~~rl~~lL 139 (159)
..||++|+++|++|.
T Consensus 34 ~gLs~~d~~~L~~L~ 48 (75)
T PF06667_consen 34 QGLSEEDEQRLQELY 48 (75)
T ss_pred CCCCHHHHHHHHHHH
Confidence 469999998776654
No 8
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=86.56 E-value=0.56 Score=35.62 Aligned_cols=10 Identities=10% Similarity=0.109 Sum_probs=6.2
Q ss_pred HHHHHHHHHH
Q 031429 86 AALWLSPLLV 95 (159)
Q Consensus 86 ~lLW~~P~l~ 95 (159)
|+||++=+++
T Consensus 2 W~l~~iii~~ 11 (130)
T PF12273_consen 2 WVLFAIIIVA 11 (130)
T ss_pred eeeHHHHHHH
Confidence 6777665543
No 9
>smart00831 Cation_ATPase_N Cation transporter/ATPase, N-terminus. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+, Na+, Ca2+, Na+/K+, and H+/K+. In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases PUBMED:12480547, PUBMED:12529322.
Probab=84.91 E-value=5.5 Score=25.93 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=29.8
Q ss_pred HcCCChHHHHHHHHHhhcccccccCCCCchhHHHH---HHHHHHH
Q 031429 55 QAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAALW---LSPLLVA 96 (159)
Q Consensus 55 ~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW---~~P~l~~ 96 (159)
..|.|++|+ +...++||.=.+-.|+.+..-..+| .-|++++
T Consensus 8 ~~GLs~~~v-~~r~~~~G~N~l~~~~~~s~~~~~l~~~~~p~~~i 51 (64)
T smart00831 8 ESGLSSEEA-ARRLERYGPNELPPPKKRSPLLRFLRQFHNPLIYI 51 (64)
T ss_pred ccCCCHHHH-HHHHHHhCCCCCCCCCCCCHHHHHHHHHHhHHHHH
Confidence 459999995 5778899999998887666655555 2476543
No 10
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=84.89 E-value=6.9 Score=31.77 Aligned_cols=62 Identities=16% Similarity=0.242 Sum_probs=50.4
Q ss_pred HHHHHHHHHHhcccCCCCCCCC-----cccc---------------C---cHHHHHHHHHHHHHHHcCCChHHHHHHHHH
Q 031429 13 MADARARNISRNVRCTDCGSQS-----IEDS---------------Q---ADIAILLRKLIRDEIQAGKTDKEVYKKLED 69 (159)
Q Consensus 13 ~~e~r~~~l~~~LRCpvCqnqs-----iadS---------------n---a~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~ 69 (159)
.......+|-+.+-|=+.++++ ..+| . ..+..+.-.+-..|.++|+|..||++++-+
T Consensus 64 ~~A~~~~~~L~~iPCYCGCges~gH~Sn~~Cfi~e~~~dG~Vvwd~Hg~~C~vCl~ia~~a~~~~~~Gks~~eIR~~ID~ 143 (158)
T PF13798_consen 64 QMAAKHPELLEYIPCYCGCGESAGHKSNLDCFIDEIKEDGSVVWDDHGTRCGVCLDIAVQAVQMYQEGKSPKEIRQYIDE 143 (158)
T ss_pred HHHHHhHHHHHcCCcccCCCCCCCCccccccceeeccCCCceeecccccccHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4556778899999999888862 2222 2 267888889999999999999999999999
Q ss_pred hhccc
Q 031429 70 DFGET 74 (159)
Q Consensus 70 RYGd~ 74 (159)
.|.+-
T Consensus 144 kYk~g 148 (158)
T PF13798_consen 144 KYKEG 148 (158)
T ss_pred HHHhC
Confidence 99874
No 11
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=83.70 E-value=2.3 Score=25.52 Aligned_cols=25 Identities=24% Similarity=0.337 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHHH
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKLE 68 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~v 68 (159)
.+-...|.+....|.|.+||.+|+.
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3556789999999999999999985
No 12
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=81.60 E-value=3.3 Score=27.71 Aligned_cols=44 Identities=18% Similarity=0.262 Sum_probs=32.9
Q ss_pred HHcCCChHHHHHHHHHhhcccccccCCCCchhHHHHH---HHHHHHHH
Q 031429 54 IQAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAALWL---SPLLVAGA 98 (159)
Q Consensus 54 l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW~---~P~l~~~~ 98 (159)
...|.|++|+.+. .++||.=.+-.++.++.-..+|- -|++++.+
T Consensus 17 ~~~GLs~~ev~~r-~~~~G~N~l~~~~~~s~~~~~~~~f~~~~~~lL~ 63 (69)
T PF00690_consen 17 SSQGLSSEEVEER-RKKYGPNELPEPKKKSLWRIFLKQFKNPFIILLL 63 (69)
T ss_dssp TSSBBTHHHHHHH-HHHHSSSSTTTTTSSSHHHHHHHHTTSHHHHHHH
T ss_pred CCCCCCHHHHHHH-HHhcccccccccccCcHHHHHHHHHHhHHHHHHH
Confidence 3689999888765 48999999988888887777773 46654433
No 13
>PF14420 Clr5: Clr5 domain
Probab=79.75 E-value=4.2 Score=26.73 Aligned_cols=31 Identities=19% Similarity=0.215 Sum_probs=26.3
Q ss_pred HHHHHHHHHH-HcCCChHHHHHHHHHhhcccc
Q 031429 45 LLRKLIRDEI-QAGKTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 45 dmR~~Ir~~l-~~G~Sd~eI~~~~v~RYGd~V 75 (159)
..|..|.++= .+|+|-+||+++|.+.||=.+
T Consensus 7 ~~K~~I~~LY~~e~~tl~~v~~~M~~~~~F~a 38 (54)
T PF14420_consen 7 PHKEEIERLYIDENKTLEEVMEIMKEEHGFKA 38 (54)
T ss_pred HHHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Confidence 5678888876 799999999999999999443
No 14
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=76.95 E-value=3.6 Score=27.12 Aligned_cols=27 Identities=15% Similarity=0.345 Sum_probs=20.3
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhhcc
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDDFGE 73 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~RYGd 73 (159)
=..|-+++..+.|-+||++.+.++|+.
T Consensus 19 a~~Iw~~~~g~~t~~ei~~~l~~~y~~ 45 (68)
T PF05402_consen 19 AAFIWELLDGPRTVEEIVDALAEEYDV 45 (68)
T ss_dssp HHHHHHH--SSS-HHHHHHHHHHHTT-
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHcCC
Confidence 356788888889999999999999975
No 15
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=74.84 E-value=5.4 Score=29.13 Aligned_cols=31 Identities=19% Similarity=0.266 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHcCCChHHH---HHHHHHhhccc
Q 031429 44 ILLRKLIRDEIQAGKTDKEV---YKKLEDDFGET 74 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI---~~~~v~RYGd~ 74 (159)
.+.|-.+|++|..-.|.+|| .+.|++|||+.
T Consensus 16 ~~~Rl~~Yrrl~~~~~~~el~~l~~El~DRFG~~ 49 (101)
T PF03461_consen 16 DDERLELYRRLASAESEEELEDLREELIDRFGPL 49 (101)
T ss_dssp HHHHHHHHHHHHC--SHHHHHHHHHHHHHHH-S-
T ss_pred hHHHHHHHHHHhhCCCHHHHHHHHHHHHHHcCCC
Confidence 46899999999999999876 56799999974
No 16
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.22 E-value=12 Score=26.82 Aligned_cols=39 Identities=21% Similarity=0.334 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccchhhHhhhhccCCCCCCHHHHHH
Q 031429 88 LWLSPLLVAGAAAGIWAYNRHRQKTNVHIMALNLVRGVPLTPKEKET 134 (159)
Q Consensus 88 LW~~P~l~~~~~~~~~~~~rrr~~~~~~~~~~~~~~~~~Ls~eE~~r 134 (159)
||++=.+++|+++|+++.++--.+ .....++++++--+-
T Consensus 8 l~ivl~ll~G~~~G~fiark~~~k--------~lk~NPpine~~iR~ 46 (71)
T COG3763 8 LLIVLALLAGLIGGFFIARKQMKK--------QLKDNPPINEEMIRM 46 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--------HHhhCCCCCHHHHHH
Confidence 444333455555565544432211 234456898876553
No 17
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.77 E-value=5.2 Score=32.41 Aligned_cols=33 Identities=21% Similarity=0.475 Sum_probs=28.3
Q ss_pred HHhcccCCCCCCCCccccCcHHHHHHHHHHHHH
Q 031429 21 ISRNVRCTDCGSQSIEDSQADIAILLRKLIRDE 53 (159)
Q Consensus 21 l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~ 53 (159)
+...+.||.|.++=...=|+.+...|+..|.++
T Consensus 133 ~~~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I~~l 165 (178)
T PRK06266 133 MEYGFRCPQCGEMLEEYDNSELIKELKEQIKEL 165 (178)
T ss_pred hhcCCcCCCCCCCCeecccHHHHHHHHHHHHHH
Confidence 346899999999988888999999998888665
No 18
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=71.25 E-value=10 Score=22.37 Aligned_cols=29 Identities=34% Similarity=0.471 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHH
Q 031429 41 DIAILLRKLIRDEIQAGKTDKEVYKKLED 69 (159)
Q Consensus 41 ~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~ 69 (159)
++-..+-..|..+|.++.|.++|++++..
T Consensus 5 ~~C~~~v~~i~~~l~~~~t~~~I~~~l~~ 33 (39)
T PF05184_consen 5 DICKFVVKEIEKLLKNNKTEEEIKKALEK 33 (39)
T ss_dssp HHHHHHHHHHHHHHHSTCHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcCccHHHHHHHHHH
Confidence 46677888999999999999999999864
No 19
>KOG2878 consensus Predicted kinase [General function prediction only]
Probab=70.26 E-value=4.3 Score=35.12 Aligned_cols=24 Identities=25% Similarity=0.403 Sum_probs=18.9
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 48 KLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
..++..+..|+||+|+.+ ||+||=
T Consensus 223 hal~~~~~kGMsDEeV~~-FV~rYm 246 (282)
T KOG2878|consen 223 HALRQDGQKGMSDEEVND-FVSRYM 246 (282)
T ss_pred HHHHHhhccCCCHHHHHH-HHHhhh
Confidence 346677899999999876 578874
No 20
>PRK11712 ribonuclease G; Provisional
Probab=70.15 E-value=8.9 Score=35.87 Aligned_cols=55 Identities=15% Similarity=0.172 Sum_probs=41.7
Q ss_pred ccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCC------------------hHHHHHHHHHhhcccccccC
Q 031429 25 VRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKT------------------DKEVYKKLEDDFGETVLYAP 79 (159)
Q Consensus 25 LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~S------------------d~eI~~~~v~RYGd~VL~~P 79 (159)
-.||+|.|.----|...+|.++.++|++....... ..+++..+..+||-.|.+.+
T Consensus 403 ~~Cp~C~G~G~v~s~e~~~~~i~r~i~~~~~~~~~~~~~~~~~p~v~~~l~~~~~~~~~~le~~~g~~i~i~~ 475 (489)
T PRK11712 403 GECPTCHGRGTVKTVETVCYEIMREIVRVHHAYDSDRFLVYASPAVAEALKGEESHALAELEIFVGKQVKVQI 475 (489)
T ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHHHHHHhhCCCceEEEEECHHHHHHHHccchHHHHHHHHHhCCeEEEEE
Confidence 46999999988889999999999999888764432 22455677777777776653
No 21
>PF14002 YniB: YniB-like protein
Probab=69.53 E-value=15 Score=30.05 Aligned_cols=50 Identities=24% Similarity=0.399 Sum_probs=31.0
Q ss_pred HHHHHHHHHHH-------HcCCChHHHHHHHHHhhcccccccCCCCchhHHHHHHHHHHHHHHH
Q 031429 44 ILLRKLIRDEI-------QAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAALWLSPLLVAGAAA 100 (159)
Q Consensus 44 ~dmR~~Ir~~l-------~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW~~P~l~~~~~~ 100 (159)
+.+|+.|.+++ .+|+|.+||-+-. ++=++..=.....|+++|+++.++|.
T Consensus 102 k~ire~IEdqlIlE~akG~~g~treqlE~~i-------~vPrhtif~Q~f~LYi~Piiv~vigy 158 (166)
T PF14002_consen 102 KFIREGIEDQLILEQAKGSEGRTREQLEERI-------VVPRHTIFLQFFPLYILPIIVAVIGY 158 (166)
T ss_pred HHHHHhHHHHHHHHHhcCCccccHHHHHhcc-------cCCCcchHHHHHHHHHHHHHHHHHHH
Confidence 34455555444 4789999998754 33333333456688999987665543
No 22
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=68.16 E-value=7.7 Score=29.99 Aligned_cols=34 Identities=18% Similarity=0.306 Sum_probs=27.8
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhhcccccccCCC
Q 031429 48 KLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKF 81 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~ 81 (159)
..|.+.|..|-|--+-++++|++|.=.-+=.+.|
T Consensus 47 ~vI~~hidaGIs~~~AVN~LVeKY~LvRiD~~gF 80 (114)
T PF06755_consen 47 TVIQEHIDAGISPADAVNFLVEKYELVRIDRNGF 80 (114)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHhhhhcCCccc
Confidence 6799999999999999999999997444444444
No 23
>PRK08207 coproporphyrinogen III oxidase; Provisional
Probab=65.54 E-value=7 Score=36.23 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 48 KLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
+.++++|.+|+|++||.++|.+.|.
T Consensus 112 k~~~~~~~~g~~~~~~~~~~~~~y~ 136 (488)
T PRK08207 112 KILHKLLDEGLSKEEIHKELKEEYL 136 (488)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 4568899999999999999999996
No 24
>PRK07668 hypothetical protein; Validated
Probab=64.90 E-value=18 Score=31.22 Aligned_cols=75 Identities=7% Similarity=0.088 Sum_probs=54.4
Q ss_pred HHHHHHHHHhcccCCCCCCCCccccCc-HHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCCCchhHHHHHHH
Q 031429 14 ADARARNISRNVRCTDCGSQSIEDSQA-DIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAALWLSP 92 (159)
Q Consensus 14 ~e~r~~~l~~~LRCpvCqnqsiadSna-~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW~~P 92 (159)
-++=+.++...||.- | +.+.+. ++-.|+...+.+.-++|+|.+||..-=...|.+.++-.++.+...+.-|+.=
T Consensus 6 Neefl~~L~~yL~~~---g--lseeeieeiL~Ei~~hLlEgQk~GkTA~~IfG~sPk~yA~EL~~~~~~~~~~~~~~l~~ 80 (254)
T PRK07668 6 GRKFLDDTRVYLIAK---G--IKEEDIESFLEDAELHLIEGEKDGKTVEDIFGDSPKEYANELVKEMEVDRKENIKLILF 80 (254)
T ss_pred HHHHHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHHHHcCCcHHHHhCCCHHHHHHHHhcccCCCcchHHHHHHH
Confidence 344455566666542 2 333322 5778888999999999999999999878889999999888887777766644
Q ss_pred H
Q 031429 93 L 93 (159)
Q Consensus 93 ~ 93 (159)
+
T Consensus 81 ~ 81 (254)
T PRK07668 81 I 81 (254)
T ss_pred H
Confidence 3
No 25
>cd00922 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform.
Probab=63.93 E-value=64 Score=25.15 Aligned_cols=75 Identities=15% Similarity=0.015 Sum_probs=44.5
Q ss_pred CCChHHHHHHHHHhhcccccccCCCCchhHHHHHHHH-HHHHHHHHHHHHHHhhccchhhHhhhhccCCCCCCHH-HHHH
Q 031429 57 GKTDKEVYKKLEDDFGETVLYAPKFDLQTAALWLSPL-LVAGAAAGIWAYNRHRQKTNVHIMALNLVRGVPLTPK-EKET 134 (159)
Q Consensus 57 G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW~~P~-l~~~~~~~~~~~~rrr~~~~~~~~~~~~~~~~~Ls~e-E~~r 134 (159)
-.|.+|-+....-.||++--=.+..+| -|...++.. ++++++++++++.|.-.-. ..+..+|.| ..+.
T Consensus 46 ~LT~~EKkAlY~isfg~~~~e~~~~~~-ewk~v~~~~~~~i~~s~~~~~~~r~~~~~---------~~P~T~t~Ewqea~ 115 (136)
T cd00922 46 QLTLEEKKALYRISFGETGPEMNAPTG-EWKTVFGGVLAFIGITGVIFGLQRAFVYG---------PKPHTFTEEWQEAQ 115 (136)
T ss_pred hCCHHHHhhHhhhhhccccccccCCCc-cHHHHHHHHHHHHHHHHHHHHHHHHhccC---------CCCCCcCHHHHHHH
Confidence 479999999999999998765555555 566666554 3445544444444432211 123467776 3344
Q ss_pred HHhhcCC
Q 031429 135 MLDLLTP 141 (159)
Q Consensus 135 l~~lL~~ 141 (159)
++.+++.
T Consensus 116 ~er~~~~ 122 (136)
T cd00922 116 LERMLDM 122 (136)
T ss_pred HHHHHHh
Confidence 5555543
No 26
>PF14353 CpXC: CpXC protein
Probab=63.55 E-value=2.3 Score=31.87 Aligned_cols=34 Identities=18% Similarity=0.360 Sum_probs=24.3
Q ss_pred cccCCCCCCCCccccCcHHHHHHHHHHHHHHHcC
Q 031429 24 NVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAG 57 (159)
Q Consensus 24 ~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G 57 (159)
++.||.|....-.+...-+-.+..-++++.|.+|
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g 34 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDG 34 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcC
Confidence 5789999987666665556666666677777765
No 27
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=63.10 E-value=15 Score=25.54 Aligned_cols=29 Identities=10% Similarity=0.050 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
..+-..|++++.+|+|-.+|..+|.+++.
T Consensus 4 a~vVr~if~~~~~g~s~~~I~~~ln~~gi 32 (102)
T PF07508_consen 4 AEVVREIFELYLEGYSLRQIARELNEKGI 32 (102)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhcCC
Confidence 45567788888899999999999999876
No 28
>PRK00523 hypothetical protein; Provisional
Probab=62.44 E-value=23 Score=25.33 Aligned_cols=13 Identities=23% Similarity=0.345 Sum_probs=8.0
Q ss_pred CCCCCCHHHHHHH
Q 031429 123 RGVPLTPKEKETM 135 (159)
Q Consensus 123 ~~~~Ls~eE~~rl 135 (159)
..+++|++--+.+
T Consensus 36 ~NPpine~mir~M 48 (72)
T PRK00523 36 ENPPITENMIRAM 48 (72)
T ss_pred HCcCCCHHHHHHH
Confidence 3467888765543
No 29
>PF13565 HTH_32: Homeodomain-like domain
Probab=62.27 E-value=19 Score=23.98 Aligned_cols=33 Identities=30% Similarity=0.331 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHcC--CChHHHHHHHHHhhcccc
Q 031429 43 AILLRKLIRDEIQAG--KTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G--~Sd~eI~~~~v~RYGd~V 75 (159)
..+++..|.+++.+. .|-.+|.+++.++||-.+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC
Confidence 467888888888775 899999999999999876
No 30
>PRK01844 hypothetical protein; Provisional
Probab=62.16 E-value=24 Score=25.25 Aligned_cols=13 Identities=15% Similarity=0.360 Sum_probs=7.9
Q ss_pred CCCCCCHHHHHHH
Q 031429 123 RGVPLTPKEKETM 135 (159)
Q Consensus 123 ~~~~Ls~eE~~rl 135 (159)
..+++|++--+..
T Consensus 35 ~NPpine~mir~M 47 (72)
T PRK01844 35 KNPPINEQMLKMM 47 (72)
T ss_pred HCCCCCHHHHHHH
Confidence 3457888765543
No 31
>COG4640 Predicted membrane protein [Function unknown]
Probab=62.04 E-value=20 Score=33.45 Aligned_cols=60 Identities=12% Similarity=0.190 Sum_probs=32.0
Q ss_pred cCCCCchhHHHHHHHHHHHHHHHHHHHHHHhhccchhhHhhhhccCCCCCCHHHHHHHHhhcCC
Q 031429 78 APKFDLQTAALWLSPLLVAGAAAGIWAYNRHRQKTNVHIMALNLVRGVPLTPKEKETMLDLLTP 141 (159)
Q Consensus 78 ~Pp~~~~t~lLW~~P~l~~~~~~~~~~~~rrr~~~~~~~~~~~~~~~~~Ls~eE~~rl~~lL~~ 141 (159)
+-+....+.++|..-++++.++++++++.+--.. + ++.-..+ ...++..+++.++.||..
T Consensus 44 rkniskK~ii~was~a~~lIlii~~~~fgk~fss-p-~~~vk~l--e~Ai~~~Dk~kvatLl~~ 103 (465)
T COG4640 44 RKNISKKKIIPWASGAFILILIIILFFFGKNFSS-P-EAQVKIL--ENAIENNDKQKVATLLSP 103 (465)
T ss_pred ccCCccceeehhHHHHHHHHHHHHHHHHhhccCC-H-HHHHHHH--HHHHhcccHHHHHHHhcc
Confidence 6677888999998776554444433333332211 1 1111111 123566677777777763
No 32
>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]
Probab=61.44 E-value=8.1 Score=35.00 Aligned_cols=52 Identities=21% Similarity=0.312 Sum_probs=42.7
Q ss_pred ccCCCCCCCCccccCcHHHHHHHHHHHH-------HHHcCCChHHHHHHHHHhh-cccccc
Q 031429 25 VRCTDCGSQSIEDSQADIAILLRKLIRD-------EIQAGKTDKEVYKKLEDDF-GETVLY 77 (159)
Q Consensus 25 LRCpvCqnqsiadSna~~A~dmR~~Ir~-------~l~~G~Sd~eI~~~~v~RY-Gd~VL~ 77 (159)
+-|..| .+|+..|..|.+.++-.++-. |.++|.--+|.+..-+..| |++||.
T Consensus 57 ~eCTGc-teSfLrs~~P~~~~li~~~IsL~Yhetlmaa~G~~aee~l~~~i~~~kg~yILv 116 (355)
T COG1740 57 LECTGC-TESFLRSEHPTANDLILELISLEYHETLMAASGTQAEELLEDAILKYKGKYILV 116 (355)
T ss_pred ccccCc-hHHHhccCCCCHHHHHHHHHhhhhhhhhhhhcchhHHHHHHHHHHhcCCceEEE
Confidence 346666 799999999999998888732 5688988889888888888 899996
No 33
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=61.42 E-value=13 Score=28.71 Aligned_cols=6 Identities=33% Similarity=0.479 Sum_probs=2.0
Q ss_pred HHHhhc
Q 031429 105 YNRHRQ 110 (159)
Q Consensus 105 ~~rrr~ 110 (159)
.+|+++
T Consensus 88 irR~~K 93 (122)
T PF01102_consen 88 IRRLRK 93 (122)
T ss_dssp HHHHS-
T ss_pred HHHHhc
Confidence 344433
No 34
>PF04233 Phage_Mu_F: Phage Mu protein F like protein; InterPro: IPR006528 This domain is found exclusively in phage-related proteins, internally or toward the C terminus. Some of these proteins have been identified as being involved in phage head morphogenesis [, ].
Probab=61.07 E-value=16 Score=25.89 Aligned_cols=28 Identities=32% Similarity=0.553 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 45 LLRKLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 45 dmR~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
++++.|.+-|..|+|.++|...|.++++
T Consensus 2 ~i~~~v~~~i~~G~~~~~~~~~l~~~~~ 29 (112)
T PF04233_consen 2 RIRQAVTQGIERGKSPQEIAKRLRDRGG 29 (112)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 6899999999999999999999999943
No 35
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=60.96 E-value=8.8 Score=24.86 Aligned_cols=40 Identities=13% Similarity=0.244 Sum_probs=19.2
Q ss_pred HHHHHHHHHHhcc-cCCCCCCCCccccCcHHHHHHHHHHHH
Q 031429 13 MADARARNISRNV-RCTDCGSQSIEDSQADIAILLRKLIRD 52 (159)
Q Consensus 13 ~~e~r~~~l~~~L-RCpvCqnqsiadSna~~A~dmR~~Ir~ 52 (159)
.++..+..|...= .||+|+..-=.+....+..+++.+|..
T Consensus 8 ~~~k~i~~l~~~~~~CPlC~r~l~~e~~~~li~~~~~~i~~ 48 (54)
T PF04423_consen 8 ELKKYIEELKEAKGCCPLCGRPLDEEHRQELIKKYKSEIEE 48 (54)
T ss_dssp HHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCcCCCCCCCCCHHHHHHHHHHHHHHHHh
Confidence 4455666666555 999996542223333455555555443
No 36
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=59.38 E-value=11 Score=29.79 Aligned_cols=33 Identities=18% Similarity=0.260 Sum_probs=26.8
Q ss_pred HHHhcccCCCCCCCCccccCcHHHHHHHHHHHH
Q 031429 20 NISRNVRCTDCGSQSIEDSQADIAILLRKLIRD 52 (159)
Q Consensus 20 ~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~ 52 (159)
++.....||.|.++-...=|+.+-..|+..|..
T Consensus 124 A~~~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i~~ 156 (158)
T TIGR00373 124 AMELNFTCPRCGAMLDYLDNSEAIEKLEEQIKF 156 (158)
T ss_pred HHHcCCcCCCCCCEeeeccCHHHHHHHHHHHHh
Confidence 345689999999988888888888888888764
No 37
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=59.33 E-value=14 Score=27.98 Aligned_cols=13 Identities=15% Similarity=0.074 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHH
Q 031429 86 AALWLSPLLVAGA 98 (159)
Q Consensus 86 ~lLW~~P~l~~~~ 98 (159)
+++-++.++++++
T Consensus 5 ~~iii~~i~l~~~ 17 (130)
T PF12273_consen 5 FAIIIVAILLFLF 17 (130)
T ss_pred HHHHHHHHHHHHH
Confidence 4455555554433
No 38
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.19 E-value=25 Score=27.11 Aligned_cols=60 Identities=13% Similarity=0.226 Sum_probs=42.9
Q ss_pred hcccCCCCCCCCccccCcHHHH---HHHHHHHHHHHcCCChH----------HHHHHHHHhhcccccccCCCC
Q 031429 23 RNVRCTDCGSQSIEDSQADIAI---LLRKLIRDEIQAGKTDK----------EVYKKLEDDFGETVLYAPKFD 82 (159)
Q Consensus 23 ~~LRCpvCqnqsiadSna~~A~---dmR~~Ir~~l~~G~Sd~----------eI~~~~v~RYGd~VL~~Pp~~ 82 (159)
...+|+.|.-+-.....+++.+ ++...++.++..|.+-- +....+..|.|..|...|+..
T Consensus 52 qRyrC~~C~~tf~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~~~~~~ 124 (129)
T COG3677 52 QRYKCKSCGSTFTVETGSPLSKALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEGLRLLT 124 (129)
T ss_pred cccccCCcCcceeeeccCcccccchHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhccCCCc
Confidence 3457777877767777777765 88899999999887743 345566777777777666644
No 39
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=56.99 E-value=10 Score=26.10 Aligned_cols=31 Identities=23% Similarity=0.276 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 42 IAILLRKLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
-+.++-+.|-++-++|.|..||=-.|.+.||
T Consensus 29 ~~~eVe~~I~klakkG~tpSqIG~iLRD~~G 59 (60)
T PF08069_consen 29 SPEEVEELIVKLAKKGLTPSQIGVILRDQYG 59 (60)
T ss_dssp -HHHHHHHHHHHCCTTHCHHHHHHHHHHSCT
T ss_pred CHHHHHHHHHHHHHcCCCHHHhhhhhhhccC
Confidence 4688899999999999999999999999998
No 40
>TIGR03370 PEPCTERM_Roseo variant PEP-CTERM putative exosortase signal, Roseobacter type. A probable protein export sorting signal, PEP-CTERM, was described by Haft, et al. (PubMed:16930487). It is predicted to interact with a putative transpeptidase we designate exosortase. Most examples of this signal are recognized by model TIGR02595, but some unusual clades require different models. This model describes a variant with conserved motif VPLPA, rather than VPEP. This variant is found prominently in two members of the Rhodobacterales, namely Jannaschia sp. CCS1 and Roseobacter denitrificans OCh 114. One interesting member protein has a full-length duplication and therefore two copies of this putative sorting domain.
Probab=56.34 E-value=17 Score=21.30 Aligned_cols=9 Identities=33% Similarity=0.213 Sum_probs=3.6
Q ss_pred HHHHHHHHH
Q 031429 94 LVAGAAAGI 102 (159)
Q Consensus 94 l~~~~~~~~ 102 (159)
++.|++++.
T Consensus 10 Ll~gLggl~ 18 (26)
T TIGR03370 10 LLAGLGGLG 18 (26)
T ss_pred HHHHHHHHH
Confidence 344444333
No 41
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=55.84 E-value=25 Score=27.35 Aligned_cols=32 Identities=19% Similarity=0.271 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHhhcc
Q 031429 42 IAILLRKLIRDEIQAGKTDKEVYKKLEDDFGE 73 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd 73 (159)
....+...|-++...|.|.+||++++.+.|-+
T Consensus 91 ~~~~l~~~I~~~~~~G~s~eei~~~~~~~~~~ 122 (125)
T COG1725 91 AEEELEEFIEEAKALGLSLEEILELLKEIYEE 122 (125)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhc
Confidence 45567779999999999999999999988754
No 42
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=54.28 E-value=15 Score=26.56 Aligned_cols=28 Identities=18% Similarity=0.235 Sum_probs=24.3
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhhccc
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~RYGd~ 74 (159)
=..|-+++...+|-++|++.|.++||+.
T Consensus 38 g~~Iw~~~DG~~tv~eIi~~L~~~y~~~ 65 (88)
T PRK02079 38 AGEILGLIDGKRTVAAIIAELQQQFPDV 65 (88)
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHccch
Confidence 3567888888999999999999999874
No 43
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=53.98 E-value=10 Score=26.56 Aligned_cols=21 Identities=24% Similarity=0.362 Sum_probs=15.0
Q ss_pred cCCChHHHHHHHHHhhccccc
Q 031429 56 AGKTDKEVYKKLEDDFGETVL 76 (159)
Q Consensus 56 ~G~Sd~eI~~~~v~RYGd~VL 76 (159)
-|.+-+.|+..+|+.||=..|
T Consensus 7 HGvtLe~il~~Lv~~yGW~~L 27 (64)
T PF09905_consen 7 HGVTLETILTELVEHYGWEEL 27 (64)
T ss_dssp SS--HHHHHHHHHHHT-HHHH
T ss_pred cchhHHHHHHHHHHHhCHHHH
Confidence 488999999999999995444
No 44
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=53.18 E-value=17 Score=28.69 Aligned_cols=28 Identities=21% Similarity=0.351 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHH
Q 031429 42 IAILLRKLIRDEIQAGKTDKEVYKKLED 69 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~ 69 (159)
+....-+.|.++..+|+|++||.+-+..
T Consensus 89 i~~~vi~~I~el~~eG~s~eei~~ki~~ 116 (131)
T PF08004_consen 89 IPESVIERIKELKSEGKSEEEIAEKISR 116 (131)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4556778999999999999999998764
No 45
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=52.75 E-value=25 Score=25.43 Aligned_cols=30 Identities=20% Similarity=0.391 Sum_probs=23.4
Q ss_pred HHHHHHcC--CChHHHHHHHHHhhcccccccC
Q 031429 50 IRDEIQAG--KTDKEVYKKLEDDFGETVLYAP 79 (159)
Q Consensus 50 Ir~~l~~G--~Sd~eI~~~~v~RYGd~VL~~P 79 (159)
+.-||+.| +|.++.++.+.++||+.+.|--
T Consensus 8 L~mml~~~~~~t~~~L~~~i~~~FG~~arFhT 39 (77)
T TIGR03853 8 LNLMLASGEPYTRESLKAAIEQKFGEDARFHT 39 (77)
T ss_pred HHHHHHcCCCcCHHHHHHHHHHHhCCCceEee
Confidence 33455566 5699999999999999998754
No 46
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.34 E-value=20 Score=28.53 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=14.3
Q ss_pred hhHHHHHHHHH--HHHHHHHHHHHH
Q 031429 84 QTAALWLSPLL--VAGAAAGIWAYN 106 (159)
Q Consensus 84 ~t~lLW~~P~l--~~~~~~~~~~~~ 106 (159)
.|...|+.|++ ++|+++|+++.|
T Consensus 3 wt~~~W~~a~igLvvGi~IG~li~R 27 (138)
T COG3105 3 WTFMTWEYALIGLVVGIIIGALIAR 27 (138)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678999976 445555554443
No 47
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=52.10 E-value=29 Score=23.74 Aligned_cols=31 Identities=19% Similarity=0.283 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHHHHhhccc
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~ 74 (159)
.+.|..+++++.+|.|-.+|+.-|.+..-..
T Consensus 21 ~~~~~~~~~l~~~G~s~~~Il~~l~~~l~~~ 51 (89)
T PF08542_consen 21 KEARKKLYELLVEGYSASDILKQLHEVLVES 51 (89)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 5689999999999999999999999887665
No 48
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=52.04 E-value=19 Score=20.80 Aligned_cols=9 Identities=22% Similarity=0.195 Sum_probs=4.2
Q ss_pred hhHHHHHHH
Q 031429 84 QTAALWLSP 92 (159)
Q Consensus 84 ~t~lLW~~P 92 (159)
.+++.|++=
T Consensus 10 ~~~~~~~G~ 18 (34)
T TIGR01167 10 NSLLLLLGL 18 (34)
T ss_pred cHHHHHHHH
Confidence 344555543
No 49
>TIGR01432 QOXA cytochrome aa3 quinol oxidase, subunit II. This enzyme catalyzes the oxidation of quinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. This subunit contains two transmembrane helices and a large external domain responsible for the binding and oxidation of quinol. QuoX is (presently) only found in gram positive bacteria of the Bacillus/Staphylococcus group. Like CyoA, the ubiquinol oxidase found in proteobacteria, the residues responsible for the ligation of Cu(a) and cytochrome c (found in the related cyt. c oxidases) are absent. Unlike CyoA, QoxA is in complex with a subunit I which contains cytochromes a similar to the cyt. c oxidases (as opposed to cytochromes b).
Probab=51.67 E-value=95 Score=25.51 Aligned_cols=70 Identities=14% Similarity=0.172 Sum_probs=39.7
Q ss_pred CCCCCCccccCcHHHHHHHHHHHHHHHcCCC----hHHHHHHHHHhhccc---ccccCCCCchhH--HH-HHHHHHHHHH
Q 031429 29 DCGSQSIEDSQADIAILLRKLIRDEIQAGKT----DKEVYKKLEDDFGET---VLYAPKFDLQTA--AL-WLSPLLVAGA 98 (159)
Q Consensus 29 vCqnqsiadSna~~A~dmR~~Ir~~l~~G~S----d~eI~~~~v~RYGd~---VL~~Pp~~~~t~--lL-W~~P~l~~~~ 98 (159)
.|..+++-|.++|.|.++....--++.-..= --=++-|+.-||-.. --+.|+..+.+. +. |++|.+++++
T Consensus 2 g~~~~~~ldp~gp~a~~i~~L~~~~~~i~~iI~lvv~~lli~~~~kyr~r~~~~~~~~~~~~n~~LEiiWTiIP~lIl~~ 81 (217)
T TIGR01432 2 GCSNIEVLNPKGPVASSQSDLILYSIVFMLVIVFVVFVLFTIFLVKYRYRKDNGAYSPKMHGNAILETIWTVIPIIIVIA 81 (217)
T ss_pred CCCcccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCccccCcchhhHHHHHHHHHHHHH
Confidence 5777899999999999999865333221100 001444555555321 124466666543 33 5789765433
No 50
>TIGR03521 GldG gliding-associated putative ABC transporter substrate-binding component GldG. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldG is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldG abolish the gliding phenotype. GldG, along with GldA and GldF are believed to compose an ABC transporter and are observed as an operon. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=51.63 E-value=18 Score=33.78 Aligned_cols=20 Identities=15% Similarity=-0.012 Sum_probs=9.7
Q ss_pred HHHH-HHHHHHHHHHHHHHHh
Q 031429 89 WLSP-LLVAGAAAGIWAYNRH 108 (159)
Q Consensus 89 W~~P-~l~~~~~~~~~~~~rr 108 (159)
-++| ++++++|+++|++|||
T Consensus 529 i~~pp~~~l~~G~~~~~~Rrr 549 (552)
T TIGR03521 529 IGLPILLLLLFGLSFTYIRKR 549 (552)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 4556 4444455555544443
No 51
>PF11293 DUF3094: Protein of unknown function (DUF3094); InterPro: IPR021444 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=51.09 E-value=15 Score=25.04 Aligned_cols=21 Identities=19% Similarity=0.321 Sum_probs=17.9
Q ss_pred CCCCHHHHHHHHhhcCCCCCC
Q 031429 125 VPLTPKEKETMLDLLTPPPPQ 145 (159)
Q Consensus 125 ~~Ls~eE~~rl~~lL~~~~~~ 145 (159)
..|++|++++.++.|+.+.|+
T Consensus 2 ~rL~pEDQ~~Vd~yL~a~~~~ 22 (55)
T PF11293_consen 2 SRLNPEDQQRVDEYLQAGVNQ 22 (55)
T ss_pred CCCCHHHHHHHHHHHhCCCCc
Confidence 359999999999999976664
No 52
>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1.9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....
Probab=50.74 E-value=68 Score=25.18 Aligned_cols=20 Identities=20% Similarity=0.037 Sum_probs=14.8
Q ss_pred CCChHHHHHHHHHhhccccc
Q 031429 57 GKTDKEVYKKLEDDFGETVL 76 (159)
Q Consensus 57 G~Sd~eI~~~~v~RYGd~VL 76 (159)
..|.+|-++.+---||+.-=
T Consensus 46 ~LS~eEKkalY~isFg~~g~ 65 (142)
T PF02936_consen 46 KLSLEEKKALYRISFGQTGP 65 (142)
T ss_dssp GS-HHHHHHHHHHH-SS-HH
T ss_pred hCCHHHHHHHHHhhhcCccc
Confidence 48999999999999999764
No 53
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=50.52 E-value=11 Score=23.45 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=13.8
Q ss_pred cHHHHHHHHHHHHHHHcCCChHHHHHHH
Q 031429 40 ADIAILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 40 a~~A~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
..+..+-|.+|..+..+|+|-.+|-+.|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~s~~~IA~~l 30 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGMSIREIAKRL 30 (44)
T ss_dssp ---------HHHHHHCS---HHHHHHHT
T ss_pred cchhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 3466677899999999999999987654
No 54
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=50.50 E-value=23 Score=27.96 Aligned_cols=27 Identities=22% Similarity=0.409 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHH
Q 031429 41 DIAILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 41 ~~A~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
++-.+-++-+.+..++|+|++||++.|
T Consensus 24 e~l~~Y~e~f~d~~~~G~sEeeii~~L 50 (181)
T PF08006_consen 24 EILEYYEEYFDDAGEEGKSEEEIIAEL 50 (181)
T ss_pred HHHHHHHHHHHHhhhCCCCHHHHHHHc
Confidence 456677888888889999999998764
No 55
>KOG3908 consensus Queuine-tRNA ribosyltransferase [RNA processing and modification]
Probab=49.69 E-value=8.4 Score=34.82 Aligned_cols=67 Identities=16% Similarity=0.264 Sum_probs=49.3
Q ss_pred hhhcHHHHHHHHHHHhcccCCCCCCCCcc------c--cC-------cHHHH--HHHHHHHHHHHcCCChHHHHHHHHHh
Q 031429 8 LKKKQMADARARNISRNVRCTDCGSQSIE------D--SQ-------ADIAI--LLRKLIRDEIQAGKTDKEVYKKLEDD 70 (159)
Q Consensus 8 ~~~d~~~e~r~~~l~~~LRCpvCqnqsia------d--Sn-------a~~A~--dmR~~Ir~~l~~G~Sd~eI~~~~v~R 70 (159)
.+..+..+.-+.-|-++--|+.|++-+=+ . +. .-++. +|-+.||+.|.+..=.+=|.+||.++
T Consensus 293 ~l~~~k~k~D~~pid~~C~C~tC~~ytRaylh~l~~~etv~~~lltiHNi~yql~Lmr~vResI~~d~fp~Fvk~Fm~~~ 372 (396)
T KOG3908|consen 293 QLRQKKYKSDFGPIDETCGCPTCKKYTRAYLHALVGKETVGCHLLTIHNIAYQLQLMRDVRESIQEDRFPQFVKNFMASR 372 (396)
T ss_pred eecchhhhhcccCCCCCCCCchhhhHHHHHHHHHccccccceeeeehhhHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 45566777778888899999999974321 1 11 12343 45577899999988899999999999
Q ss_pred hccc
Q 031429 71 FGET 74 (159)
Q Consensus 71 YGd~ 74 (159)
|||.
T Consensus 373 ~~D~ 376 (396)
T KOG3908|consen 373 FKDS 376 (396)
T ss_pred hCCC
Confidence 9965
No 56
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=49.52 E-value=17 Score=26.07 Aligned_cols=20 Identities=20% Similarity=0.227 Sum_probs=16.8
Q ss_pred HHHHHHHHcCCChHHHHHHH
Q 031429 48 KLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
..|-+++++|.|++||.+.|
T Consensus 34 ~~Il~~l~~G~s~eeil~dy 53 (79)
T COG2442 34 WDILEMLAAGESIEEILADY 53 (79)
T ss_pred HHHHHHHHCCCCHHHHHHhC
Confidence 35778999999999998764
No 57
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=49.47 E-value=45 Score=23.20 Aligned_cols=44 Identities=20% Similarity=0.187 Sum_probs=33.8
Q ss_pred cccCCCCCCCCc---cccCcHHHHHHHHHHHHHHHcCCChHHHHHHHH
Q 031429 24 NVRCTDCGSQSI---EDSQADIAILLRKLIRDEIQAGKTDKEVYKKLE 68 (159)
Q Consensus 24 ~LRCpvCqnqsi---adSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v 68 (159)
+++|+.| ++.| .|=..--+.+-|+.+.....-|.|.+|+++||-
T Consensus 5 ~~~~~~~-~~~i~~~~dmgH~~~~e~~~~~~~~~~~~~t~ke~~d~~n 51 (70)
T PF14410_consen 5 KVRDPNT-GYPIEGPWDMGHKPGVEYWRLVGRAEEGGITRKEFLDWYN 51 (70)
T ss_pred eEecCCC-CCCCCCCCCccCchHHHHHHHHHHHHhcCCCHHHHHHHHh
Confidence 5678777 5556 222222388999999999999999999999997
No 58
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=49.34 E-value=32 Score=25.79 Aligned_cols=14 Identities=36% Similarity=0.216 Sum_probs=7.9
Q ss_pred hHHHHHHHHHHHHH
Q 031429 85 TAALWLSPLLVAGA 98 (159)
Q Consensus 85 t~lLW~~P~l~~~~ 98 (159)
+.+.+++|++++.+
T Consensus 16 ~~~~~ll~lvii~~ 29 (106)
T PRK05585 16 SGLSSLLPLVVFFA 29 (106)
T ss_pred CcHHHHHHHHHHHH
Confidence 34566667765533
No 59
>PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional
Probab=49.12 E-value=33 Score=30.47 Aligned_cols=70 Identities=14% Similarity=0.212 Sum_probs=40.1
Q ss_pred CCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHH----HHHHHHhh---cccccccCCCCchhH---HHHHHHHHHHHH
Q 031429 29 DCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEV----YKKLEDDF---GETVLYAPKFDLQTA---ALWLSPLLVAGA 98 (159)
Q Consensus 29 vCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI----~~~~v~RY---Gd~VL~~Pp~~~~t~---lLW~~P~l~~~~ 98 (159)
.||++++-+-..++|.+.+..|.-.+.-..=--=+ .-+|+=|| ++..-|.|.....+. +.|.+|++++++
T Consensus 23 ~gc~~~~l~P~G~~a~~~~~Li~~~~~~~liv~i~V~~l~~~f~~ryR~~~~~a~y~p~~~~s~~lE~v~W~iP~lIl~~ 102 (315)
T PRK10525 23 SGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIF 102 (315)
T ss_pred cCCCccccCCCChhHHHHHHHHHHHHHHHHhhHHHHHHHHheeEEEEecCCCcCCCCCcccCCceehhHHHHHHHHHHHH
Confidence 34488999999999999999886554321110000 11222233 233456675544432 359999876544
No 60
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=49.01 E-value=24 Score=28.02 Aligned_cols=64 Identities=13% Similarity=0.083 Sum_probs=32.2
Q ss_pred cCCCCchhHHHHHHHHHHHHHHHHH-H-HHH-HhhccchhhHh-h--hhccCCCCCCHHHHHHHHhhcCC
Q 031429 78 APKFDLQTAALWLSPLLVAGAAAGI-W-AYN-RHRQKTNVHIM-A--LNLVRGVPLTPKEKETMLDLLTP 141 (159)
Q Consensus 78 ~Pp~~~~t~lLW~~P~l~~~~~~~~-~-~~~-rrr~~~~~~~~-~--~~~~~~~~Ls~eE~~rl~~lL~~ 141 (159)
.|.-++.+++.|++|+-.+|+++.+ + ++. .+++....+.. . ........+++.|..+|.+-|.+
T Consensus 73 ~~~g~~~g~~~~imPlYtiGI~~f~lY~l~Ki~~~k~~~~~~~~~~~~~~~~~~~~~~~eL~qLq~rL~q 142 (152)
T PF15361_consen 73 QPGGSGKGLMGQIMPLYTIGIVLFILYTLFKIKKKKDSPRERKSSTERKGNTKRKITDYELAQLQERLAQ 142 (152)
T ss_pred CCCCCCCchhhhHhHHHHHHHHHHHHHHHHHHHhcCCccccccccccccccccccchHHHHHHHHHHHHH
Confidence 4455688899999998766554322 2 222 11111100000 0 00112235777777777766654
No 61
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=48.86 E-value=33 Score=24.01 Aligned_cols=38 Identities=26% Similarity=0.529 Sum_probs=28.0
Q ss_pred ccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHH-HHhh
Q 031429 25 VRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKL-EDDF 71 (159)
Q Consensus 25 LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~-v~RY 71 (159)
+||-.|.+. ++ +.=.+-.+++++|++..+++|.| ++||
T Consensus 5 iRCFsCGkv--------i~-~~w~~y~~rv~~ge~p~~vLDdLGv~RY 43 (63)
T COG1644 5 VRCFSCGKV--------IG-HKWEEYKRRVEEGEDPGEVLDDLGVKRY 43 (63)
T ss_pred eEeecCCCC--------HH-HHHHHHHHHHHcCCCHHHHHHHhCcHHH
Confidence 578777543 33 34566778999999999999987 5555
No 62
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=48.59 E-value=44 Score=25.32 Aligned_cols=34 Identities=15% Similarity=0.191 Sum_probs=29.8
Q ss_pred cCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhh
Q 031429 38 SQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDF 71 (159)
Q Consensus 38 Sna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RY 71 (159)
=++.+=++|-...++|+.+|-+++.+..+|.+-|
T Consensus 63 w~t~~~~Ef~~~~~eM~dAGV~~~~~~~~l~~~Y 96 (100)
T PF15652_consen 63 WSTTLQEEFNNSYREMFDAGVSKECRKKALKAQY 96 (100)
T ss_pred ccchHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3456778888889999999999999999999977
No 63
>TIGR01641 phageSPP1_gp7 phage putative head morphogenesis protein, SPP1 gp7 family. This model describes a region of about 110 amino acids found exclusively in phage-related proteins, internally or toward the C-terminus. One member, gp7 of phage SPP1, appears involved in head morphogenesis.
Probab=48.45 E-value=24 Score=25.31 Aligned_cols=26 Identities=27% Similarity=0.562 Sum_probs=23.6
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
...|.+-|.+|+|.++|.+.+.++||
T Consensus 2 ~~~l~~gi~~G~~~~~iak~i~~~~~ 27 (108)
T TIGR01641 2 EDILADGVQRGLGPNELAKRLRKELG 27 (108)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHC
Confidence 35788999999999999999999996
No 64
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=47.94 E-value=31 Score=23.77 Aligned_cols=34 Identities=24% Similarity=0.469 Sum_probs=23.5
Q ss_pred ccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHH
Q 031429 25 VRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 25 LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
+||..|.. -|+ +.-++-.+.+++|.+..+++|.+
T Consensus 5 VRCFTCGk-vi~--------~~~e~y~~~~~~~~~~~~~Ld~L 38 (60)
T PF01194_consen 5 VRCFTCGK-VIG--------NKWEEYLERLENGEDPGDALDDL 38 (60)
T ss_dssp SS-STTTS-BTC--------GHHHHHHHHHHTTS-HHHHHHHT
T ss_pred eecCCCCC-Chh--------HhHHHHHHHHHcCCCHHHHHHHh
Confidence 68999954 344 34566677888899999999875
No 65
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=47.76 E-value=16 Score=29.69 Aligned_cols=33 Identities=30% Similarity=0.491 Sum_probs=25.6
Q ss_pred ccCcHHHHHHHHHHHHHH-HcCCChHHHHHHHHHhhcc
Q 031429 37 DSQADIAILLRKLIRDEI-QAGKTDKEVYKKLEDDFGE 73 (159)
Q Consensus 37 dSna~~A~dmR~~Ir~~l-~~G~Sd~eI~~~~v~RYGd 73 (159)
-+|.+++.++|.+|++++ .+|+|-.+| ...||=
T Consensus 12 ~~~~~lse~~r~~Iy~~~~~~~~sv~~v----S~~ygi 45 (172)
T PF12298_consen 12 RSNPVLSEELREQIYEDVMQDGKSVREV----SQKYGI 45 (172)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCHHHH----HHHhCC
Confidence 468889999999999999 667766554 556663
No 66
>PHA02591 hypothetical protein; Provisional
Probab=47.07 E-value=30 Score=25.39 Aligned_cols=24 Identities=17% Similarity=0.059 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHH
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
.|++...+++.+.|.|-+||-+.+
T Consensus 46 dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 46 DDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred chHHHHHHHHHHcCCCHHHHHHHh
Confidence 478899999999999999997764
No 67
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=46.73 E-value=45 Score=19.47 Aligned_cols=28 Identities=14% Similarity=0.208 Sum_probs=24.1
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhhccc
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~RYGd~ 74 (159)
...|..++..|.+.++++..|..-.||.
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~ 29 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRATNNNV 29 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCH
Confidence 3567888899999999999999988874
No 68
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=46.66 E-value=17 Score=23.83 Aligned_cols=20 Identities=20% Similarity=0.536 Sum_probs=17.6
Q ss_pred HcCCChHHHHHHHHHhhccc
Q 031429 55 QAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 55 ~~G~Sd~eI~~~~v~RYGd~ 74 (159)
..++|++.|++.|+..||+-
T Consensus 16 ~~~~Sk~~l~~QL~se~ge~ 35 (48)
T PF07553_consen 16 TMHMSKQGLYDQLTSEYGEG 35 (48)
T ss_pred hccCCHHHHHHHHHhhcccC
Confidence 36799999999999999984
No 69
>PF13584 BatD: Oxygen tolerance
Probab=46.49 E-value=41 Score=30.28 Aligned_cols=9 Identities=11% Similarity=0.006 Sum_probs=3.9
Q ss_pred HHHHHHhhc
Q 031429 131 EKETMLDLL 139 (159)
Q Consensus 131 E~~rl~~lL 139 (159)
..+.+++.+
T Consensus 471 ~l~~~~~a~ 479 (484)
T PF13584_consen 471 SLKAAEQAL 479 (484)
T ss_pred HHHHHHHHh
Confidence 334444444
No 70
>TIGR00430 Q_tRNA_tgt tRNA-guanine transglycosylase, queuosine-34-forming. This tRNA-guanine transglycosylase (tgt) catalyzes an exchange for the guanine base at position 34 of many tRNAs; this nucleotide is subsequently modified to queuosine. The Archaea have a closely related enzyme that catalyzes a base exchange for guanine at position 15 in some tRNAs, a site that is subsequently converted to the archaeal-specific modified base archaeosine (7-formamidino-7-deazaguanosine), while Archaeoglobus fulgidus has both enzymes.
Probab=45.48 E-value=33 Score=30.81 Aligned_cols=54 Identities=19% Similarity=0.307 Sum_probs=37.2
Q ss_pred HHhcccCCCCCCCCccc------c------------CcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccc
Q 031429 21 ISRNVRCTDCGSQSIED------S------------QADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 21 l~~~LRCpvCqnqsiad------S------------na~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~V 75 (159)
|...=-|++|++-|-+. + |--.-..+-+.||+.|.+|. -+|.++.|...|++.+
T Consensus 296 i~~~C~C~tC~~~traYLhHL~~~~E~l~~~LLt~HNl~~~~~l~~~iR~aI~~g~-~~e~~~~~~~~~~~~~ 367 (368)
T TIGR00430 296 LDEECDCYTCKNYSRAYLRHLIRCNELLGARLATLHNLHFYLRLMEKIRQAILEDR-FLSFRTEFLERYGEEV 367 (368)
T ss_pred CCCCCCCccccccCHHHHHhhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-HHHHHHHHHHHhcccC
Confidence 44566799998754332 2 22334556678999999997 6677777778898764
No 71
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=44.67 E-value=45 Score=23.71 Aligned_cols=45 Identities=16% Similarity=0.144 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHcCCChHH---HHHHHHHhhcccccccCCCCchhH
Q 031429 42 IAILLRKLIRDEIQAGKTDKE---VYKKLEDDFGETVLYAPKFDLQTA 86 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~e---I~~~~v~RYGd~VL~~Pp~~~~t~ 86 (159)
.+..-+..|+.++.+|.|.++ |+|+.++..++---+..=..+.|+
T Consensus 16 ~~~~~~~~I~aRl~eG~t~edf~~VID~k~~~W~~~~~m~~YLRP~TL 63 (74)
T PF09524_consen 16 NTKSTKKLIKARLNEGYTLEDFKKVIDNKVAEWKGDPKMEKYLRPETL 63 (74)
T ss_pred CcHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHhcCchhh
Confidence 455678899999999999987 578888887765544444444443
No 72
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=44.21 E-value=39 Score=25.67 Aligned_cols=6 Identities=33% Similarity=0.694 Sum_probs=3.1
Q ss_pred HHHHHH
Q 031429 91 SPLLVA 96 (159)
Q Consensus 91 ~P~l~~ 96 (159)
+|++++
T Consensus 8 l~lv~i 13 (109)
T PRK05886 8 LPFLLI 13 (109)
T ss_pred HHHHHH
Confidence 465544
No 73
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=43.53 E-value=92 Score=23.36 Aligned_cols=32 Identities=9% Similarity=0.181 Sum_probs=22.5
Q ss_pred cccCcHHHHHHHHHHHHHHHcCC-ChHHHHHHH
Q 031429 36 EDSQADIAILLRKLIRDEIQAGK-TDKEVYKKL 67 (159)
Q Consensus 36 adSna~~A~dmR~~Ir~~l~~G~-Sd~eI~~~~ 67 (159)
.+++.+++++.++...+++.+.+ .+..+...|
T Consensus 10 ~~~~~~~~~~v~~~~~R~~~a~r~~~~~~~~~l 42 (100)
T TIGR02230 10 SAKDKPLEKRVGDKELRKLRARKNATRSIWEGL 42 (100)
T ss_pred CcccchHHHHHHHHHHHHHHHHhcCCCcHHHHH
Confidence 45566899999999988887776 454454433
No 74
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=43.53 E-value=25 Score=21.79 Aligned_cols=22 Identities=18% Similarity=0.211 Sum_probs=16.2
Q ss_pred HHHHHHHHHHcCCChHHHHHHH
Q 031429 46 LRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 46 mR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
..++|.+|+++|+|..||-..|
T Consensus 10 ~~~~i~~l~~~G~si~~IA~~~ 31 (45)
T PF02796_consen 10 QIEEIKELYAEGMSIAEIAKQF 31 (45)
T ss_dssp CHHHHHHHHHTT--HHHHHHHT
T ss_pred HHHHHHHHHHCCCCHHHHHHHH
Confidence 3678999999999999987643
No 75
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=43.45 E-value=30 Score=22.00 Aligned_cols=13 Identities=31% Similarity=0.662 Sum_probs=7.3
Q ss_pred HHHHHHHHHHhhc
Q 031429 98 AAAGIWAYNRHRQ 110 (159)
Q Consensus 98 ~~~~~~~~~rrr~ 110 (159)
+|+++|.++++++
T Consensus 23 ~gi~~w~~~~~~k 35 (49)
T PF05545_consen 23 IGIVIWAYRPRNK 35 (49)
T ss_pred HHHHHHHHcccch
Confidence 3555666665543
No 76
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=42.91 E-value=30 Score=24.20 Aligned_cols=27 Identities=15% Similarity=0.186 Sum_probs=24.0
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhhcc
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDDFGE 73 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~RYGd 73 (159)
=..|-+++...+|-++|.+.|.++|+.
T Consensus 33 g~~Iw~lldg~~tv~eI~~~L~~~Y~~ 59 (81)
T TIGR03859 33 AGEILELCDGKRSLAEIIQELAQRFPA 59 (81)
T ss_pred HHHHHHHccCCCcHHHHHHHHHHHcCC
Confidence 356888999999999999999999985
No 77
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=42.73 E-value=29 Score=31.12 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=21.8
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHh
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDD 70 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~R 70 (159)
|+-|++.+..|-|-+||+.|+..+
T Consensus 340 r~Sv~~A~~~GIta~qIi~fL~~~ 363 (366)
T PF03849_consen 340 RESVRRALKNGITADQIISFLRSH 363 (366)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhc
Confidence 778999999999999999999753
No 78
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=42.71 E-value=95 Score=22.22 Aligned_cols=42 Identities=21% Similarity=0.214 Sum_probs=26.6
Q ss_pred HHhhcccccccCCCCc-hhHHHHHHHHHHHHHHHHHHHHHHhh
Q 031429 68 EDDFGETVLYAPKFDL-QTAALWLSPLLVAGAAAGIWAYNRHR 109 (159)
Q Consensus 68 v~RYGd~VL~~Pp~~~-~t~lLW~~P~l~~~~~~~~~~~~rrr 109 (159)
..-|-+..+..|-..| .|+.+|++=++++...++.++|.++.
T Consensus 35 l~a~~p~~m~~~v~~G~~t~g~~~g~~~~~~~~~l~~~Yv~~A 77 (91)
T PF04341_consen 35 LSAFAPELMATPVFPGSLTLGIVLGLGQIVFAWVLTWLYVRRA 77 (91)
T ss_pred HHHHCHHHHcCcccCCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677788888856 88878877655444434445555544
No 79
>PF15217 TSC21: TSC21 family
Probab=41.95 E-value=19 Score=29.48 Aligned_cols=27 Identities=30% Similarity=0.385 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHHhhcCCCCCCCCCCcc
Q 031429 125 VPLTPKEKETMLDLLTPPPPQRPSPSS 151 (159)
Q Consensus 125 ~~Ls~eE~~rl~~lL~~~~~~~~~~~~ 151 (159)
+.+|++|+.+|+.-|...++-||.||.
T Consensus 34 srvtpqEQ~Kld~QLr~kEfyrp~P~p 60 (180)
T PF15217_consen 34 SRVTPQEQAKLDTQLRDKEFYRPIPSP 60 (180)
T ss_pred cccCHHHHHHHHHHhhhhhhcccCCCC
Confidence 358999999999999999999999875
No 80
>TIGR02595 PEP_exosort PEP-CTERM putative exosortase interaction domain. This model describes a 25-residue domain that includes a near-invariant Pro-Glu-Pro (PEP) motif, a thirteen residue strongly hydrophobic sequence likely to span the membrane, and a five-residue strongly basic motif that often contains four Arg residues. In nearly every case, this motif is found within nine residues, and usually within five residues, of the extreme C-terminus of the protein. Proteins with this motif typically have signal sequences at the N-terminus. This region appears many times per genome or not at all, and co-occurs in genomes with a proposed protein-sorting integral membrane protein we designate exosortase (see TIGR02602). PEP-CTERM proteins frequently are poorly conserved, Ser/Thr-rich proteins and may become extensively modified proteinaceous constituents of extracellular material in bacterial biofilms.
Probab=41.64 E-value=31 Score=19.63 Aligned_cols=10 Identities=30% Similarity=0.494 Sum_probs=4.0
Q ss_pred HHHHHHHHhh
Q 031429 100 AGIWAYNRHR 109 (159)
Q Consensus 100 ~~~~~~~rrr 109 (159)
++++..+||+
T Consensus 14 ~~~~~~rrrk 23 (26)
T TIGR02595 14 LGFLLLRRRR 23 (26)
T ss_pred HHHHHHhhcc
Confidence 3344444443
No 81
>TIGR00449 tgt_general tRNA-guanine transglycosylases, various specificities. Different tRNA-guanine transglycosylases catalyze different tRNA base modifications. Two guanine base substitutions by different enzymes described by the model are involved in generating queuosine at position 34 in bacterial tRNAs and archaeosine at position 15 in archaeal tRNAs. This model is designed for fragment searching, so the superfamily is used loosely.
Probab=41.58 E-value=40 Score=30.25 Aligned_cols=55 Identities=16% Similarity=0.283 Sum_probs=36.5
Q ss_pred HHHHhcccCCCCCCCCcc------cc------------CcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhccc
Q 031429 19 RNISRNVRCTDCGSQSIE------DS------------QADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 19 ~~l~~~LRCpvCqnqsia------dS------------na~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~ 74 (159)
.-|...=-|++|++-|-+ .+ |--.-..+-+.||+.|.+|. -.|.++.+..+|+..
T Consensus 293 ~Pi~~~C~C~~C~~~sraYlhhL~~~~E~l~~~Ll~~HNl~~~~~~~~~iR~aI~~g~-~~e~~~~~~~~~~~~ 365 (367)
T TIGR00449 293 RPLDEPCDCYVCKNYSRAYLRHLIRCNELLGARLATEHNLHFSFRLIEKIRQAILEDR-LLSFVEEFLEAYGRL 365 (367)
T ss_pred CCCCCCCCCccccccCHHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-HHHHHHHHHHhcccc
Confidence 334556679999975422 22 33344566678999999996 667777777777653
No 82
>PF12091 DUF3567: Protein of unknown function (DUF3567); InterPro: IPR021951 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif.
Probab=41.33 E-value=55 Score=24.10 Aligned_cols=31 Identities=23% Similarity=0.276 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 41 DIAILLRKLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 41 ~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
..|...|+.|...+++.-|.+||=+|+ +.|.
T Consensus 45 ~~Ae~Fr~~V~~li~~~Pt~EevDdfL-~~y~ 75 (85)
T PF12091_consen 45 SWAEMFREDVQALIASEPTQEEVDDFL-GGYD 75 (85)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHH-HHHH
Confidence 699999999999999999988887665 4453
No 83
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=41.31 E-value=20 Score=25.24 Aligned_cols=13 Identities=23% Similarity=0.616 Sum_probs=11.1
Q ss_pred CCCHHHHHHHHhh
Q 031429 126 PLTPKEKETMLDL 138 (159)
Q Consensus 126 ~Ls~eE~~rl~~l 138 (159)
+||++||++|+++
T Consensus 2 ~LSe~E~r~L~ei 14 (82)
T PF11239_consen 2 PLSEHEQRRLEEI 14 (82)
T ss_pred CCCHHHHHHHHHH
Confidence 5999999988765
No 84
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=41.16 E-value=14 Score=20.42 Aligned_cols=17 Identities=18% Similarity=0.452 Sum_probs=14.4
Q ss_pred hHHHHHHHHHhhccccc
Q 031429 60 DKEVYKKLEDDFGETVL 76 (159)
Q Consensus 60 d~eI~~~~v~RYGd~VL 76 (159)
...+.+...++||.+|+
T Consensus 3 ~~~~~~l~~~~~g~~vi 19 (36)
T smart00025 3 KGHLLELSKDQYGNRVV 19 (36)
T ss_pred hHHHHHHHhcchhhHHH
Confidence 46788899999999987
No 85
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=40.70 E-value=34 Score=30.00 Aligned_cols=41 Identities=20% Similarity=0.413 Sum_probs=32.6
Q ss_pred HHHHHHHHHHcCCChHHHHHHHHHhhcccccc-cCCCCchhH
Q 031429 46 LRKLIRDEIQAGKTDKEVYKKLEDDFGETVLY-APKFDLQTA 86 (159)
Q Consensus 46 mR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~-~Pp~~~~t~ 86 (159)
+|+..|..-+.|+|-++|++-+..|--+++.| .|.++-...
T Consensus 156 irRI~RD~~ERGrs~EsVi~qilrrmpdy~~yI~PQ~~~tDI 197 (277)
T cd02029 156 IQKIHRDTAERGYSAEAVMDTILRRMPDYINYICPQFSRTDI 197 (277)
T ss_pred HHHHHhhhHhhCCCHHHHHHHHHHhCchHHhhCCcccccCcE
Confidence 34566666678999999999999999999999 666655433
No 86
>PRK15453 phosphoribulokinase; Provisional
Probab=40.63 E-value=37 Score=29.97 Aligned_cols=39 Identities=21% Similarity=0.433 Sum_probs=31.0
Q ss_pred HHHHHHHHHHcCCChHHHHHHHHHhhcccccc-cCCCCch
Q 031429 46 LRKLIRDEIQAGKTDKEVYKKLEDDFGETVLY-APKFDLQ 84 (159)
Q Consensus 46 mR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~-~Pp~~~~ 84 (159)
+|+..|..-+.|+|.++|++-+..|--+++.| .|.++-.
T Consensus 162 irRI~RD~~ERGrs~EsVi~qilrrmPdy~~yI~PQ~~~t 201 (290)
T PRK15453 162 IQKIHRDTSERGYSREAVMDTILRRMPDYINYITPQFSRT 201 (290)
T ss_pred HHHHHhhhHhhCCCHHHHHHHHHHhCChHhhhCCCCcccC
Confidence 34555666678999999999999999999999 6665543
No 87
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=40.55 E-value=40 Score=27.73 Aligned_cols=42 Identities=14% Similarity=0.137 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHcCCC--hHHHHHHHHHhhcccccccCCCC
Q 031429 41 DIAILLRKLIRDEIQAGKT--DKEVYKKLEDDFGETVLYAPKFD 82 (159)
Q Consensus 41 ~~A~dmR~~Ir~~l~~G~S--d~eI~~~~v~RYGd~VL~~Pp~~ 82 (159)
+++.+|++.+-..+..|.. ..+|.++|.+-|+.|.+++.|-.
T Consensus 120 Dl~GEL~R~al~~l~~gd~~~~~~i~~fm~~ly~~~~~l~~~~~ 163 (204)
T PRK14562 120 DAIGELRRHILELLRKGEIEEAEKLLEIMEEIYEFLMTLDYPDA 163 (204)
T ss_pred HHHhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence 6899999999999999987 45699999999999999998844
No 88
>cd01301 rDP_like renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. Although the biological function of the enzyme is still unknown, it has been suggested to play a role in the renal glutathione metabolism.
Probab=39.84 E-value=42 Score=29.27 Aligned_cols=30 Identities=20% Similarity=0.230 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHHHHhhcccc
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~V 75 (159)
+.+|...+.++++.|.|+++|...+ |||+.
T Consensus 278 ~~~~~~l~~~L~~rG~s~~~i~~i~---g~N~l 307 (309)
T cd01301 278 VSDLPNLTAELLERGYSEEEIEKIA---GGNFL 307 (309)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH---hhchh
Confidence 7899999999999999999999887 66654
No 89
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=39.77 E-value=26 Score=23.86 Aligned_cols=19 Identities=11% Similarity=0.165 Sum_probs=13.8
Q ss_pred HcCCChHHHHHHHHHhhcc
Q 031429 55 QAGKTDKEVYKKLEDDFGE 73 (159)
Q Consensus 55 ~~G~Sd~eI~~~~v~RYGd 73 (159)
+.|+|-+||++||.++=++
T Consensus 34 kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 34 KSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp HTT--HHHHHHHHHHHS--
T ss_pred HHCCCHHHHHHHHHHhccc
Confidence 6899999999999998665
No 90
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=39.61 E-value=27 Score=29.14 Aligned_cols=20 Identities=10% Similarity=0.152 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHcCCChHHHH
Q 031429 45 LLRKLIRDEIQAGKTDKEVY 64 (159)
Q Consensus 45 dmR~~Ir~~l~~G~Sd~eI~ 64 (159)
..+..+.+++.+-++-++|+
T Consensus 146 ~~~~rl~~ll~ka~~~~d~l 165 (262)
T PF14257_consen 146 AEEERLLELLEKAKTVEDLL 165 (262)
T ss_pred HHHHHHHHHHHhcCCHHHHH
Confidence 34455556665555655444
No 91
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=39.58 E-value=40 Score=21.17 Aligned_cols=26 Identities=19% Similarity=0.308 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHHHHh
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKLEDD 70 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~v~R 70 (159)
..+.+..|...+ |.|..+|..||..+
T Consensus 26 ~~~~~~~la~~l--~l~~~~V~~WF~nr 51 (57)
T PF00046_consen 26 SKEEREELAKEL--GLTERQVKNWFQNR 51 (57)
T ss_dssp HHHHHHHHHHHH--TSSHHHHHHHHHHH
T ss_pred cccccccccccc--cccccccccCHHHh
Confidence 344555666555 99999999999764
No 92
>PRK07429 phosphoribulokinase; Provisional
Probab=39.42 E-value=15 Score=32.40 Aligned_cols=45 Identities=20% Similarity=0.294 Sum_probs=36.5
Q ss_pred HHHHHHHcCCChHHHHHHHHHhhcccccc-cCCCCchhHHHHHHHH
Q 031429 49 LIRDEIQAGKTDKEVYKKLEDDFGETVLY-APKFDLQTAALWLSPL 93 (159)
Q Consensus 49 ~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~-~Pp~~~~t~lLW~~P~ 93 (159)
.-|.+...|.|.++|.+.+..+.-++..| .|..+....++++.|.
T Consensus 143 i~Rd~~rrG~s~eei~~~i~~r~pd~~~yI~P~k~~ADiVI~~~p~ 188 (327)
T PRK07429 143 IKRDMAKRGHTYEQVLAEIEAREPDFEAYIRPQRQWADVVIQFLPT 188 (327)
T ss_pred HHHHHhhcCCCHHHHHHHHHHhCccHhhhhcccccCCCEEEEcCCC
Confidence 44666678999999999998888888765 6778888888888885
No 93
>cd00131 PAX Paired Box domain
Probab=38.72 E-value=37 Score=25.82 Aligned_cols=29 Identities=14% Similarity=0.140 Sum_probs=25.0
Q ss_pred ccCcHHHHHHHHHHHHHHHcCCChHHHHH
Q 031429 37 DSQADIAILLRKLIRDEIQAGKTDKEVYK 65 (159)
Q Consensus 37 dSna~~A~dmR~~Ir~~l~~G~Sd~eI~~ 65 (159)
.=..|++.|+|..|-.+.++|.|..+|-.
T Consensus 13 ~m~~~lS~d~R~rIv~~~~~G~s~~~iA~ 41 (128)
T cd00131 13 VNGRPLPDSIRQRIVELAQSGIRPCDISR 41 (128)
T ss_pred cCCCcCCHHHHHHHHHHHHcCCCHHHHHH
Confidence 33468999999999999999999999844
No 94
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=38.57 E-value=22 Score=24.86 Aligned_cols=27 Identities=15% Similarity=0.154 Sum_probs=17.9
Q ss_pred HhcccCCCCCCCCcc-----------ccCcHHHHHHHH
Q 031429 22 SRNVRCTDCGSQSIE-----------DSQADIAILLRK 48 (159)
Q Consensus 22 ~~~LRCpvCqnqsia-----------dSna~~A~dmR~ 48 (159)
...-.||+|.+.++. -.+|.+|+-|+-
T Consensus 15 ~~~~~Cp~Cgs~~~S~~w~G~v~i~dPe~S~vAk~~~i 52 (64)
T PRK06393 15 TPEKTCPVHGDEKTTTEWFGFLIITEPEGSAIAKRAGI 52 (64)
T ss_pred cCCCcCCCCCCCcCCcCcceEEEEECCchhHHHHHhCC
Confidence 344589999998743 345667776654
No 95
>PRK11677 hypothetical protein; Provisional
Probab=38.16 E-value=54 Score=25.74 Aligned_cols=16 Identities=38% Similarity=0.623 Sum_probs=6.7
Q ss_pred HHHHHH--HHHHHHHHHH
Q 031429 89 WLSPLL--VAGAAAGIWA 104 (159)
Q Consensus 89 W~~P~l--~~~~~~~~~~ 104 (159)
|+.+++ ++|+++|+++
T Consensus 3 W~~a~i~livG~iiG~~~ 20 (134)
T PRK11677 3 WEYALIGLVVGIIIGAVA 20 (134)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444443 3334444443
No 96
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=37.97 E-value=20 Score=31.47 Aligned_cols=81 Identities=14% Similarity=0.077 Sum_probs=47.8
Q ss_pred hhcHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCC---ChHHHHHHHHHhhcccccccCCCCchh
Q 031429 9 KKKQMADARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGK---TDKEVYKKLEDDFGETVLYAPKFDLQT 85 (159)
Q Consensus 9 ~~d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~---Sd~eI~~~~v~RYGd~VL~~Pp~~~~t 85 (159)
..++.+.++..++...++ +|+++.++=...- ..=..+..++..|. +-+++++.+.+.|-+... .+-..
T Consensus 293 ~~n~~l~~~~~~i~~~v~----~G~sls~al~~~~-~fp~~~~~~i~~GE~sG~L~~~L~~la~~~~~~~~----~~~~~ 363 (399)
T PRK10573 293 LRCPYWQQALTQIQQQIA----QGIPLWLALKNHP-LFPPLCLQLVRVGEESGSLDLMLENLAHWHQEQTQ----ALADN 363 (399)
T ss_pred cCCHHHHHHHHHHHHHHH----CcccHHHHHhhCC-CCcHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHH----HHHHH
Confidence 456777777777777665 5666666422110 12234555665554 456677777777776654 23345
Q ss_pred HHHHHHHHHHHHH
Q 031429 86 AALWLSPLLVAGA 98 (159)
Q Consensus 86 ~lLW~~P~l~~~~ 98 (159)
...++-|++++++
T Consensus 364 ~~~ll~P~~il~i 376 (399)
T PRK10573 364 LAQLLEPLLMIIT 376 (399)
T ss_pred HHHHHHHHHHHHH
Confidence 6779999764433
No 97
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=37.92 E-value=31 Score=22.58 Aligned_cols=18 Identities=28% Similarity=0.385 Sum_probs=13.3
Q ss_pred HHHHHHHcCCChHHHHHH
Q 031429 49 LIRDEIQAGKTDKEVYKK 66 (159)
Q Consensus 49 ~Ir~~l~~G~Sd~eI~~~ 66 (159)
.|.+++++|.|.+||.+.
T Consensus 23 ~i~~~~~~G~s~eeI~~~ 40 (56)
T PF04255_consen 23 DILDLLAAGESPEEIAED 40 (56)
T ss_dssp HHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHH
Confidence 567788999999999875
No 98
>PRK10807 paraquat-inducible protein B; Provisional
Probab=37.85 E-value=32 Score=32.46 Aligned_cols=16 Identities=25% Similarity=0.536 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 031429 86 AALWLSPLLVAGAAAG 101 (159)
Q Consensus 86 ~lLW~~P~l~~~~~~~ 101 (159)
-++|++|++++++|+.
T Consensus 18 s~iWlvP~~a~~i~~~ 33 (547)
T PRK10807 18 SPVWIFPIVTALIGAW 33 (547)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 4799999987766543
No 99
>PF13584 BatD: Oxygen tolerance
Probab=37.72 E-value=40 Score=30.30 Aligned_cols=7 Identities=14% Similarity=0.302 Sum_probs=3.2
Q ss_pred HHHHHHh
Q 031429 131 EKETMLD 137 (159)
Q Consensus 131 E~~rl~~ 137 (159)
.+++|++
T Consensus 468 ~~~~l~~ 474 (484)
T PF13584_consen 468 AKKSLKA 474 (484)
T ss_pred HHHHHHH
Confidence 4444444
No 100
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=37.31 E-value=36 Score=23.55 Aligned_cols=12 Identities=33% Similarity=0.540 Sum_probs=9.8
Q ss_pred cCCChHHHHHHH
Q 031429 56 AGKTDKEVYKKL 67 (159)
Q Consensus 56 ~G~Sd~eI~~~~ 67 (159)
.|+|.+||+++|
T Consensus 44 ~gks~eeir~~f 55 (78)
T PF01466_consen 44 KGKSPEEIRKYF 55 (78)
T ss_dssp TTS-HHHHHHHH
T ss_pred cCCCHHHHHHHc
Confidence 499999999987
No 101
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=37.04 E-value=26 Score=24.18 Aligned_cols=16 Identities=38% Similarity=0.810 Sum_probs=11.6
Q ss_pred cccCCCCCCCCccccC
Q 031429 24 NVRCTDCGSQSIEDSQ 39 (159)
Q Consensus 24 ~LRCpvCqnqsiadSn 39 (159)
.-+||.|.+.++.+..
T Consensus 15 ~~~CP~Cgs~~~T~~W 30 (61)
T PRK08351 15 EDRCPVCGSRDLSDEW 30 (61)
T ss_pred CCcCCCCcCCcccccc
Confidence 3479999998855543
No 102
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=36.66 E-value=52 Score=23.76 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=22.7
Q ss_pred HHHHH-HcC--CChHHHHHHHHHhhccccccc
Q 031429 50 IRDEI-QAG--KTDKEVYKKLEDDFGETVLYA 78 (159)
Q Consensus 50 Ir~~l-~~G--~Sd~eI~~~~v~RYGd~VL~~ 78 (159)
|-.|+ +.| +|.++.++.+.++||+...|-
T Consensus 9 VL~mmi~~~~~~t~~~L~~ai~~~FG~~arFh 40 (78)
T PF10678_consen 9 VLNMMIESGNPYTKEELKAAIIEKFGEDARFH 40 (78)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHHHhCCCceEE
Confidence 44444 444 689999999999999999874
No 103
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=36.34 E-value=51 Score=20.60 Aligned_cols=20 Identities=30% Similarity=0.453 Sum_probs=16.7
Q ss_pred HHHHHHHHcCCChHHHHHHH
Q 031429 48 KLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
.+|..++.+|+|..||-+.+
T Consensus 10 ~~v~~l~~~G~s~~eia~~l 29 (65)
T COG2771 10 REILRLVAQGKSNKEIARIL 29 (65)
T ss_pred HHHHHHHHCCCCHHHHHHHH
Confidence 36788999999999998765
No 104
>COG3008 PqiB Paraquat-inducible protein B [General function prediction only]
Probab=35.82 E-value=33 Score=32.88 Aligned_cols=16 Identities=25% Similarity=0.559 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHH
Q 031429 87 ALWLSPLLVAGAAAGI 102 (159)
Q Consensus 87 lLW~~P~l~~~~~~~~ 102 (159)
..|++|++.+.+|+.+
T Consensus 22 piWllPivAl~igawL 37 (553)
T COG3008 22 PIWLLPIVALLIGAWL 37 (553)
T ss_pred chHHHHHHHHHHHHHH
Confidence 6899999877665433
No 105
>PF05337 CSF-1: Macrophage colony stimulating factor-1 (CSF-1); InterPro: IPR008001 Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility [] and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption [].; GO: 0005125 cytokine activity, 0008083 growth factor activity, 0016021 integral to membrane; PDB: 3EJJ_A.
Probab=35.65 E-value=12 Score=32.96 Aligned_cols=10 Identities=40% Similarity=0.597 Sum_probs=0.0
Q ss_pred CCCCHHHHHH
Q 031429 125 VPLTPKEKET 134 (159)
Q Consensus 125 ~~Ls~eE~~r 134 (159)
.+|+.+|-+.
T Consensus 271 spLtqdedrq 280 (285)
T PF05337_consen 271 SPLTQDEDRQ 280 (285)
T ss_dssp ----------
T ss_pred CCCccCCCcc
Confidence 3565555443
No 106
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=35.56 E-value=38 Score=32.10 Aligned_cols=48 Identities=21% Similarity=0.374 Sum_probs=25.1
Q ss_pred ChHHHHHHHHHhhcccccccCCCCchh-HHH-HHHHHH-HHHHHHHHHHHH
Q 031429 59 TDKEVYKKLEDDFGETVLYAPKFDLQT-AAL-WLSPLL-VAGAAAGIWAYN 106 (159)
Q Consensus 59 Sd~eI~~~~v~RYGd~VL~~Pp~~~~t-~lL-W~~P~l-~~~~~~~~~~~~ 106 (159)
+|---.+-+.=.-=|.|||-||.+..+ |.= .++-++ ++|+|+.++.|+
T Consensus 185 kd~~hrQKlqLkalDvVLFGpp~~~~~n~~KD~iLv~lili~v~gcw~ay~ 235 (575)
T KOG4403|consen 185 KDRSHRQKLQLKALDVVLFGPPYKTNHNWTKDFILVVLILIGVGGCWFAYR 235 (575)
T ss_pred CchHHHHhhhhhhcceEEecCCcCCCcchhhhHHHHHHHHHHhhhhhhhhh
Confidence 333333334444458999999987654 422 344444 334444444443
No 107
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=34.88 E-value=54 Score=26.25 Aligned_cols=18 Identities=22% Similarity=0.327 Sum_probs=13.5
Q ss_pred CCCCCHHHHHHHHhhcCC
Q 031429 124 GVPLTPKEKETMLDLLTP 141 (159)
Q Consensus 124 ~~~Ls~eE~~rl~~lL~~ 141 (159)
...||..|.+.+++.|++
T Consensus 62 ~~gls~~e~~~~~~~l~e 79 (199)
T PF10112_consen 62 EAGLSDREYEYIREILEE 79 (199)
T ss_pred hcCCChhHHHHHHHHHHH
Confidence 357999998887777654
No 108
>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]. This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].
Probab=34.80 E-value=23 Score=22.61 Aligned_cols=8 Identities=25% Similarity=0.056 Sum_probs=4.2
Q ss_pred HHHHHHHH
Q 031429 91 SPLLVAGA 98 (159)
Q Consensus 91 ~P~l~~~~ 98 (159)
.|++++++
T Consensus 19 VPV~vI~~ 26 (40)
T PF08693_consen 19 VPVGVIII 26 (40)
T ss_pred echHHHHH
Confidence 57654444
No 109
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=34.72 E-value=54 Score=23.80 Aligned_cols=24 Identities=17% Similarity=0.256 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHH
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
-.-|.+|.+++.+|+|..||-+.+
T Consensus 37 Ls~R~~I~~ll~~G~S~~eIA~~L 60 (88)
T TIGR02531 37 LAQRLQVAKMLKQGKTYSDIEAET 60 (88)
T ss_pred hhHHHHHHHHHHCCCCHHHHHHHH
Confidence 345699999999999999997654
No 110
>PRK13533 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=34.71 E-value=28 Score=32.53 Aligned_cols=36 Identities=14% Similarity=0.330 Sum_probs=26.8
Q ss_pred cccCCCCCCCCcc---------------ccCcHHHHHHHHHHHHHHHcCCC
Q 031429 24 NVRCTDCGSQSIE---------------DSQADIAILLRKLIRDEIQAGKT 59 (159)
Q Consensus 24 ~LRCpvCqnqsia---------------dSna~~A~dmR~~Ir~~l~~G~S 59 (159)
.-.|++|+|-|-+ .-|--.-.++-++||+.|.+|.=
T Consensus 274 ~C~C~~C~~ysrayL~~L~~~~~~~Ll~~HNl~~~~~~m~~iR~aI~~g~l 324 (487)
T PRK13533 274 PCSCPVCSKYTPKELREMPAEERERLLAEHNLYVTFEEIRRIKQAIKEGRL 324 (487)
T ss_pred CCCChhcCccCHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHHHHcCCH
Confidence 3469999986643 35556667788899999999963
No 111
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=34.65 E-value=1.1e+02 Score=30.43 Aligned_cols=72 Identities=17% Similarity=0.206 Sum_probs=52.0
Q ss_pred cHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHH-HHHHHHHHcCCChHHHHHHHHHhhcccccccCCCCchhHHHH
Q 031429 11 KQMADARARNISRNVRCTDCGSQSIEDSQADIAILLR-KLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAALW 89 (159)
Q Consensus 11 d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR-~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW 89 (159)
||.+.+..-.|..++-|-.|+. | +..|..+- ..|-+.=.+|++.-||...|-.+||=.-. | ...+-|
T Consensus 725 d~k~~e~l~~i~~df~~c~c~d-----~-ce~~~~~lse~ii~lR~~gk~p~~Isr~l~~~Ygi~aY---p---gDif~w 792 (830)
T COG1202 725 DPKLKEKLLLIYMDFLNCTCRD-----C-CECAEQRLSEKIIELRIEGKDPSQISRILEKRYGIQAY---P---GDIFTW 792 (830)
T ss_pred CHHHHHHHHHHHHHHhcCchhh-----h-HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhCeeec---C---hhHHHH
Confidence 7788888889999988776753 3 44555554 66777778999999999999999995432 2 344556
Q ss_pred HHHHH
Q 031429 90 LSPLL 94 (159)
Q Consensus 90 ~~P~l 94 (159)
+=-++
T Consensus 793 Ld~~v 797 (830)
T COG1202 793 LDTLV 797 (830)
T ss_pred HHHHH
Confidence 55544
No 112
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=34.37 E-value=39 Score=20.67 Aligned_cols=25 Identities=24% Similarity=0.226 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHH
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
..+.|.+|-.++.+|+|..+|-..|
T Consensus 3 ~~~~R~~ii~l~~~G~s~~~ia~~l 27 (50)
T PF13384_consen 3 SEERRAQIIRLLREGWSIREIAKRL 27 (50)
T ss_dssp -------HHHHHHHT--HHHHHHHH
T ss_pred chhHHHHHHHHHHCCCCHHHHHHHH
Confidence 3467888889999999999987654
No 113
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=33.35 E-value=67 Score=26.62 Aligned_cols=29 Identities=24% Similarity=0.357 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHH
Q 031429 41 DIAILLRKLIRDEIQAGKTDKEVYKKLED 69 (159)
Q Consensus 41 ~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~ 69 (159)
.+...-+..+..++..|+|+++|+..+-+
T Consensus 4 ~l~~~QieLLqrL~~SG~TK~~ii~ALe~ 32 (180)
T PF04814_consen 4 KLTIEQIELLQRLRRSGMTKEEIIHALET 32 (180)
T ss_dssp HHHHHHHHHHHHHHHCT--HHHHHHHHTT
T ss_pred cccHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 45667788999999999999999999863
No 114
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.29 E-value=2.1e+02 Score=22.50 Aligned_cols=29 Identities=28% Similarity=0.384 Sum_probs=23.8
Q ss_pred cHHHHHHHHHHHHHH-HcCCChHHHHHHHHHhhc
Q 031429 40 ADIAILLRKLIRDEI-QAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 40 a~~A~dmR~~Ir~~l-~~G~Sd~eI~~~~v~RYG 72 (159)
.|.+.|+|..+...+ .+|+|..||-. +||
T Consensus 3 k~~s~~~R~~~~~~~~~~G~S~re~Ak----~~g 32 (138)
T COG3415 3 KPFSNDLRERVVDAVVGEGLSCREAAK----RFG 32 (138)
T ss_pred chhhHHHHHHHHHHHHHcCccHHHHHH----HhC
Confidence 367889999998888 99999999864 566
No 115
>PF07095 IgaA: Intracellular growth attenuator protein IgaA; InterPro: IPR010771 This family consists of several bacterial intracellular growth attenuator (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the Escherichia coli YrfF and Proteus mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in Salmonella enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria [].; GO: 0009276 Gram-negative-bacterium-type cell wall, 0016021 integral to membrane
Probab=33.23 E-value=1e+02 Score=30.52 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=14.3
Q ss_pred CCCHHHHHHHHhhcC
Q 031429 126 PLTPKEKETMLDLLT 140 (159)
Q Consensus 126 ~Ls~eE~~rl~~lL~ 140 (159)
.||+||+..++..|+
T Consensus 45 KLt~eEr~aIe~YL~ 59 (705)
T PF07095_consen 45 KLTAEERQAIEQYLN 59 (705)
T ss_pred CCCHHHHHHHHHHHH
Confidence 799999999999998
No 116
>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=32.89 E-value=1e+02 Score=17.91 Aligned_cols=28 Identities=11% Similarity=0.234 Sum_probs=20.6
Q ss_pred HHHHHHHHHHH-HcCCChHHHHHHHHHhh
Q 031429 44 ILLRKLIRDEI-QAGKTDKEVYKKLEDDF 71 (159)
Q Consensus 44 ~dmR~~Ir~~l-~~G~Sd~eI~~~~v~RY 71 (159)
.++.+.+.++. ..|.|..+++...+..|
T Consensus 8 ~~~~~~l~~~a~~~g~s~s~~ir~ai~~~ 36 (39)
T PF01402_consen 8 DELYERLDELAKELGRSRSELIREAIREY 36 (39)
T ss_dssp HHHHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34555555555 67999999999988876
No 117
>PRK10811 rne ribonuclease E; Reviewed
Probab=32.43 E-value=60 Score=33.48 Aligned_cols=35 Identities=17% Similarity=0.421 Sum_probs=30.6
Q ss_pred cCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCCh
Q 031429 26 RCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTD 60 (159)
Q Consensus 26 RCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd 60 (159)
.||+|.|.----|+.-++..+.++|.+....+.+.
T Consensus 403 ~Cp~C~GtG~v~s~etla~~i~R~I~re~~~~~~~ 437 (1068)
T PRK10811 403 VCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQ 437 (1068)
T ss_pred cCcccCCCcccccHHHHHHHHHHHHHHHHhhcccc
Confidence 79999998888888899999999999988887653
No 118
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=32.40 E-value=87 Score=23.33 Aligned_cols=8 Identities=38% Similarity=0.650 Sum_probs=3.7
Q ss_pred HHHHHHHH
Q 031429 89 WLSPLLVA 96 (159)
Q Consensus 89 W~~P~l~~ 96 (159)
=++|++++
T Consensus 11 ~ll~~vl~ 18 (97)
T COG1862 11 LLLPLVLI 18 (97)
T ss_pred HHHHHHHH
Confidence 34455544
No 119
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.19 E-value=80 Score=25.06 Aligned_cols=28 Identities=14% Similarity=0.287 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHc-CCChHHHHHHHHHhh
Q 031429 44 ILLRKLIRDEIQA-GKTDKEVYKKLEDDF 71 (159)
Q Consensus 44 ~dmR~~Ir~~l~~-G~Sd~eI~~~~v~RY 71 (159)
.++|..+.++|.+ |.|..||++.+.+.-
T Consensus 12 ~eir~~l~~~L~~~~~t~~ei~~~~~~~~ 40 (180)
T PF11985_consen 12 PEIREWLDQMLRDGGFTQYEILAEWLEEL 40 (180)
T ss_pred HHHHHHHHHHHHhCCCChHHHHHHHHHhh
Confidence 5799999998877 689999999999987
No 120
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=32.14 E-value=1.7e+02 Score=19.98 Aligned_cols=14 Identities=21% Similarity=0.695 Sum_probs=10.0
Q ss_pred cCCCCCCCCccccCc
Q 031429 26 RCTDCGSQSIEDSQA 40 (159)
Q Consensus 26 RCpvCqnqsiadSna 40 (159)
.||+| |.+|....+
T Consensus 5 HC~~C-G~~Ip~~~~ 18 (59)
T PF09889_consen 5 HCPVC-GKPIPPDES 18 (59)
T ss_pred cCCcC-CCcCCcchh
Confidence 69999 667766544
No 121
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=32.10 E-value=37 Score=27.40 Aligned_cols=30 Identities=27% Similarity=0.515 Sum_probs=20.3
Q ss_pred hcccCCCCCCCCccccCcHHHHHHHHHHHHHHH
Q 031429 23 RNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQ 55 (159)
Q Consensus 23 ~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~ 55 (159)
..+.|+.|.. ..+.+-++..|...||+.|.
T Consensus 44 ~~~~C~~C~~---~~~~~~l~Nql~l~iR~~i~ 73 (188)
T PF08996_consen 44 SGLQCPNCST---PLSPASLVNQLELQIREHIS 73 (188)
T ss_dssp TEEEETTT-----B--HHHHHHHHHHHHHHHHH
T ss_pred CcCcCCCCCC---cCCHHHHHHHHHHHHHHHHH
Confidence 3577888766 56667788888888888775
No 122
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=31.60 E-value=93 Score=21.70 Aligned_cols=12 Identities=25% Similarity=0.373 Sum_probs=7.6
Q ss_pred CCCCCHHHHHHH
Q 031429 124 GVPLTPKEKETM 135 (159)
Q Consensus 124 ~~~Ls~eE~~rl 135 (159)
.++++++--+.+
T Consensus 29 NPpine~mir~M 40 (64)
T PF03672_consen 29 NPPINEKMIRAM 40 (64)
T ss_pred CCCCCHHHHHHH
Confidence 457887765544
No 123
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=31.60 E-value=24 Score=23.57 Aligned_cols=19 Identities=16% Similarity=0.760 Sum_probs=15.2
Q ss_pred cccCCCCCCCCccccCcHH
Q 031429 24 NVRCTDCGSQSIEDSQADI 42 (159)
Q Consensus 24 ~LRCpvCqnqsiadSna~~ 42 (159)
--.||+|-|+.|.++...+
T Consensus 13 Y~~Cp~CGN~~vGngEG~l 31 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTL 31 (49)
T ss_pred hccCcccCCcEeecCcceE
Confidence 4579999999999887643
No 124
>PF14163 SieB: Superinfection exclusion protein B
Probab=31.21 E-value=75 Score=24.38 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=17.2
Q ss_pred CCCCHHHHHHHHhhcCCCCCC
Q 031429 125 VPLTPKEKETMLDLLTPPPPQ 145 (159)
Q Consensus 125 ~~Ls~eE~~rl~~lL~~~~~~ 145 (159)
..||++|++-|...+..+.+.
T Consensus 77 ~~Lt~~EkavL~~~~~~~~~~ 97 (151)
T PF14163_consen 77 NSLTPEEKAVLREFYIQGNNT 97 (151)
T ss_pred HhCCHHHHHHHHHHHHCCCCe
Confidence 379999999999998877543
No 125
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=31.05 E-value=78 Score=23.78 Aligned_cols=29 Identities=21% Similarity=0.261 Sum_probs=18.9
Q ss_pred HHHhhcccccccCCCCc---hhHHHHHHHHHH
Q 031429 67 LEDDFGETVLYAPKFDL---QTAALWLSPLLV 95 (159)
Q Consensus 67 ~v~RYGd~VL~~Pp~~~---~t~lLW~~P~l~ 95 (159)
.-.+=||.|...=+-+. ...+++++|+++
T Consensus 50 ~~~~~GD~V~v~i~~~~~~~aa~l~Y~lPll~ 81 (135)
T PF04246_consen 50 IGAKVGDRVEVEIPESSLLKAAFLVYLLPLLA 81 (135)
T ss_pred CCCCCCCEEEEEeccchHHHHHHHHHHHHHHH
Confidence 34456888877666554 345778889753
No 126
>TIGR00778 ahpD_dom alkylhydroperoxidase AhpD family core domain. Members of the family include the alkylhydroperoxidase AhpD of Mycobacterium tuberculosis, a macrophage infectivity potentiator peptide of Legionella pneumophila, and an uncharacterized peptide in the tetrachloroethene reductive dehalogenase operon of Dehalospirillum multivorans. We suggest that many peptides containing this domain may have alkylhydroperoxidase or related antioxidant activity.
Probab=29.97 E-value=1.3e+02 Score=18.23 Aligned_cols=41 Identities=24% Similarity=0.250 Sum_probs=26.1
Q ss_pred HHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHh
Q 031429 15 DARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDD 70 (159)
Q Consensus 15 e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~R 70 (159)
|-=...++....|.-| +..-.......|.|++||.+-+.=+
T Consensus 9 eli~l~~s~~~~C~yc---------------~~~H~~~a~~~G~~~~ei~~v~~~~ 49 (50)
T TIGR00778 9 ELIAIAVSQINGCGYC---------------LDAHTKLARKAGVTAEELAEALAWA 49 (50)
T ss_pred HHHHHHHHHHcCCHHH---------------HHHHHHHHHHcCCCHHHHHHHHHhH
Confidence 3334455555666666 3334556678899999999866533
No 127
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=29.90 E-value=92 Score=18.37 Aligned_cols=27 Identities=11% Similarity=0.213 Sum_probs=20.4
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhhccc
Q 031429 48 KLIRDEIQAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~v~RYGd~ 74 (159)
..|.+++..|.+.++.+..|..--||.
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~~~nv 30 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRACNGNV 30 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHTTTSH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCCH
Confidence 456677777999999999998877753
No 128
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.26 E-value=3e+02 Score=24.65 Aligned_cols=21 Identities=14% Similarity=0.096 Sum_probs=16.8
Q ss_pred HHHHHHHcCCChHHHHHHHHH
Q 031429 49 LIRDEIQAGKTDKEVYKKLED 69 (159)
Q Consensus 49 ~Ir~~l~~G~Sd~eI~~~~v~ 69 (159)
.+.=+...|.|++||-..|..
T Consensus 25 kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 25 KREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred HHHHHHhcCCCHHHHHHHHHh
Confidence 334455789999999999986
No 129
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=28.99 E-value=86 Score=24.69 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=18.9
Q ss_pred hhcccccccCCCCc---hhHHHHHHHHH
Q 031429 70 DFGETVLYAPKFDL---QTAALWLSPLL 94 (159)
Q Consensus 70 RYGd~VL~~Pp~~~---~t~lLW~~P~l 94 (159)
+=||.|...=|-+. ...+++++|++
T Consensus 60 ~vGD~V~v~i~e~~llkaa~lvYllPLl 87 (154)
T PRK10862 60 VPGQKVELGIAEGSLLRSALLVYMTPLV 87 (154)
T ss_pred CCCCEEEEecchhhHHHHHHHHHHHHHH
Confidence 55999988877666 35577899975
No 130
>PF09753 Use1: Membrane fusion protein Use1; InterPro: IPR019150 This entry represents a family of proteins, approximately 300 residues in length, involved in vesicle transport. They have a single C-terminal transmembrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport [].
Probab=28.63 E-value=64 Score=26.92 Aligned_cols=15 Identities=20% Similarity=0.195 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHH
Q 031429 86 AALWLSPLLVAGAAA 100 (159)
Q Consensus 86 ~lLW~~P~l~~~~~~ 100 (159)
|++|++=++++++.+
T Consensus 228 ~~~~~~i~~v~~~Fi 242 (251)
T PF09753_consen 228 CWTWLMIFVVIIVFI 242 (251)
T ss_pred HHHHHHHHHHHHHHH
Confidence 899986655444333
No 131
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=28.63 E-value=1.2e+02 Score=17.42 Aligned_cols=26 Identities=23% Similarity=0.323 Sum_probs=22.3
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhhcc
Q 031429 48 KLIRDEIQAGKTDKEVYKKLEDDFGE 73 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~v~RYGd 73 (159)
..|.+++..|.++++++..+..-=||
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~~~d 28 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAANGN 28 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 56778888899999999999887776
No 132
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=28.61 E-value=30 Score=22.51 Aligned_cols=30 Identities=13% Similarity=0.182 Sum_probs=24.0
Q ss_pred HHHHHHHcCCChHHHHHHHHHhhcccccccCC
Q 031429 49 LIRDEIQAGKTDKEVYKKLEDDFGETVLYAPK 80 (159)
Q Consensus 49 ~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp 80 (159)
-+.+|.+.|-|.++|.+.| .+|+.+--.+.
T Consensus 6 a~~rm~eR~Is~~~I~~~l--~~g~i~~~~~~ 35 (73)
T PF14076_consen 6 ARERMQERGISEEDIEDAL--ENGEIIEDYSD 35 (73)
T ss_pred HHHHHHhCCCCHHHHHHHH--hcCeEeeecCC
Confidence 3567889999999999999 56998865443
No 133
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=28.58 E-value=23 Score=24.41 Aligned_cols=18 Identities=39% Similarity=0.822 Sum_probs=13.5
Q ss_pred hcccCCCCCCCCccccCc
Q 031429 23 RNVRCTDCGSQSIEDSQA 40 (159)
Q Consensus 23 ~~LRCpvCqnqsiadSna 40 (159)
-+++||.|.|+.+-=|+|
T Consensus 10 ~~VkCp~C~n~q~vFsha 27 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHA 27 (59)
T ss_pred EEEECCCCCCeEEEEecC
Confidence 357899999987665555
No 134
>PRK06547 hypothetical protein; Provisional
Probab=28.46 E-value=3.4 Score=32.79 Aligned_cols=28 Identities=25% Similarity=0.385 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHhhcCCCCCCCCCCcccccccc
Q 031429 126 PLTPKEKETMLDLLTPPPPQRPSPSSWWRRWR 157 (159)
Q Consensus 126 ~Ls~eE~~rl~~lL~~~~~~~~~~~~~~~~~~ 157 (159)
-|+.....|+.++++.+.+.+| ||.+|-
T Consensus 123 ~ld~~~~vr~~R~~~Rd~~~~~----~~~~w~ 150 (172)
T PRK06547 123 WLDGPEALRKERALARDPDYAP----HWEMWA 150 (172)
T ss_pred EEECCHHHHHHHHHhcCchhhH----HHHHHH
Confidence 4556667778888888877777 999984
No 135
>PLN00083 photosystem II subunit R; Provisional
Probab=28.30 E-value=17 Score=27.33 Aligned_cols=30 Identities=20% Similarity=0.156 Sum_probs=18.6
Q ss_pred HHHhhc--ccccccCCCCch-----------hHHHHHHHHHHH
Q 031429 67 LEDDFG--ETVLYAPKFDLQ-----------TAALWLSPLLVA 96 (159)
Q Consensus 67 ~v~RYG--d~VL~~Pp~~~~-----------t~lLW~~P~l~~ 96 (159)
|+++|| |.==|.|-.+.. .+++|.+-++.+
T Consensus 45 f~~KyGkANVDgYSPIY~p~eWs~sGD~Y~GgL~~WA~tlagl 87 (101)
T PLN00083 45 LGLRNGKANVDEYSPIYTPQEFKTDGDKYEGDLKLAAAAVAGV 87 (101)
T ss_pred ehhccCcccccccCCccChhhcCCCcchhhccHHHHHHHHHHH
Confidence 788999 333455544322 578898776543
No 136
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.20 E-value=9.6 Score=23.94 Aligned_cols=23 Identities=22% Similarity=0.502 Sum_probs=17.5
Q ss_pred cccCCCCCCCCccccCcHHHHHH
Q 031429 24 NVRCTDCGSQSIEDSQADIAILL 46 (159)
Q Consensus 24 ~LRCpvCqnqsiadSna~~A~dm 46 (159)
.++||.|.+.-+...++++.+.+
T Consensus 21 ~~~Cp~CG~~~~~~~~~~~v~~~ 43 (46)
T PRK00398 21 GVRCPYCGYRILFKERPPVVKRV 43 (46)
T ss_pred ceECCCCCCeEEEccCCCcceEe
Confidence 68999998888888777765443
No 137
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=28.10 E-value=88 Score=25.28 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 42 IAILLRKLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
-+.+.-+.|-++-.+|.|..||=-.|.+.||
T Consensus 29 ~~eeve~~I~~lakkG~~pSqIG~~LRD~~g 59 (151)
T PRK08561 29 SPEEIEELVVELAKQGYSPSMIGIILRDQYG 59 (151)
T ss_pred CHHHHHHHHHHHHHCCCCHHHhhhhHhhccC
Confidence 4678889999999999999999999999996
No 138
>PF12575 DUF3753: Protein of unknown function (DUF3753); InterPro: IPR009175 This group represents an uncharacterised conserved protein belonging to poxvirus family I2.
Probab=27.91 E-value=1.5e+02 Score=21.22 Aligned_cols=30 Identities=10% Similarity=-0.037 Sum_probs=15.1
Q ss_pred HHHHHHHhhcccccccCCCCchhHHHHHHHHH
Q 031429 63 VYKKLEDDFGETVLYAPKFDLQTAALWLSPLL 94 (159)
Q Consensus 63 I~~~~v~RYGd~VL~~Pp~~~~t~lLW~~P~l 94 (159)
|+.-|.+...... .-..+++||..|+.-++
T Consensus 27 VksVltdk~~~~~--~~~~~~~~~~~~ii~ii 56 (72)
T PF12575_consen 27 VKSVLTDKKKLKN--NKNNKNFNWIILIISII 56 (72)
T ss_pred HHHHHcCCccccc--cCCCCcchHHHHHHHHH
Confidence 4444555554444 33344566666655544
No 139
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=27.89 E-value=1.1e+02 Score=21.91 Aligned_cols=38 Identities=26% Similarity=0.397 Sum_probs=25.9
Q ss_pred ccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHH-HHhh
Q 031429 25 VRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKL-EDDF 71 (159)
Q Consensus 25 LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~-v~RY 71 (159)
.||-.|.+- | + +.=.+-.+++++|.+..+++|.| +.||
T Consensus 5 VRCFTCGkv-i-------g-~~we~y~~~~~~g~~~~~~LD~LG~~RY 43 (71)
T PLN00032 5 VRCFTCGKV-I-------G-NKWDTYLDLLQADYSEGDALDALGLVRY 43 (71)
T ss_pred eeecCCCCC-c-------H-HHHHHHHHHHhcCCCHHHHHHHhCchhh
Confidence 577777443 2 2 23346677889999999999987 3444
No 140
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=27.89 E-value=93 Score=15.73 Aligned_cols=24 Identities=21% Similarity=0.206 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHH
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
.+.+..|.+++.+|.|..+|-..+
T Consensus 8 ~~~~~~i~~~~~~~~s~~~ia~~~ 31 (42)
T cd00569 8 PEQIEEARRLLAAGESVAEIARRL 31 (42)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 345677888888999888887644
No 141
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=27.76 E-value=48 Score=22.56 Aligned_cols=33 Identities=12% Similarity=-0.034 Sum_probs=24.2
Q ss_pred hcccCCCCCCCCccccCcHHHHHHHHHHHHHHHc
Q 031429 23 RNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQA 56 (159)
Q Consensus 23 ~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~ 56 (159)
....||.| ++.|..++.--...||+.|.+-+++
T Consensus 38 ~~~~~P~t-~~~l~~~~l~pn~~Lk~~I~~~~~~ 70 (73)
T PF04564_consen 38 NGGTDPFT-RQPLSESDLIPNRALKSAIEEWCAE 70 (73)
T ss_dssp TSSB-TTT--SB-SGGGSEE-HHHHHHHHHHHHH
T ss_pred CCCCCCCC-CCcCCcccceECHHHHHHHHHHHHH
Confidence 47899999 8889988777788999999887754
No 142
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=27.71 E-value=1.2e+02 Score=18.52 Aligned_cols=24 Identities=13% Similarity=0.255 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHcCCChHHHHHHHHHh
Q 031429 45 LLRKLIRDEIQAGKTDKEVYKKLEDD 70 (159)
Q Consensus 45 dmR~~Ir~~l~~G~Sd~eI~~~~v~R 70 (159)
+.+..|.+.+ |.|..+|..||..|
T Consensus 28 ~~~~~la~~~--~l~~~qV~~WF~nr 51 (56)
T smart00389 28 EEREELAAKL--GLSERQVKVWFQNR 51 (56)
T ss_pred HHHHHHHHHH--CcCHHHHHHhHHHH
Confidence 3444444444 89999999999875
No 143
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=27.70 E-value=3.3e+02 Score=24.10 Aligned_cols=15 Identities=20% Similarity=0.244 Sum_probs=10.8
Q ss_pred CCChHHHHHHHHHhh
Q 031429 57 GKTDKEVYKKLEDDF 71 (159)
Q Consensus 57 G~Sd~eI~~~~v~RY 71 (159)
|.+.++++..|-..+
T Consensus 73 gv~~~~L~~~~~~~~ 87 (331)
T PRK10856 73 HIPEEELLPGLEKQA 87 (331)
T ss_pred CcCHHHHHHhhhhcC
Confidence 888888877665554
No 144
>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA). Called (hupA/hydA/hupS/hoxK/vhtG) Involved in hydrogenase reactions performing different specific functions in different species eg (EC 1.12.2.1) in Desulfovibrio gigas,(EC 1.12.99.3) in Wolinella succinogenes and (EC 1.18.99.1) in E.coli and a number of other species and (EC 1.12.99.-) in the archea.
Probab=27.66 E-value=29 Score=31.57 Aligned_cols=50 Identities=20% Similarity=0.192 Sum_probs=35.5
Q ss_pred CCCCCCCCccccCcHHHHHHHHHH-------HHHHHcCCChHHHHHHHHHh-hcccccc
Q 031429 27 CTDCGSQSIEDSQADIAILLRKLI-------RDEIQAGKTDKEVYKKLEDD-FGETVLY 77 (159)
Q Consensus 27 CpvCqnqsiadSna~~A~dmR~~I-------r~~l~~G~Sd~eI~~~~v~R-YGd~VL~ 77 (159)
|..| .+|+.++..|...|+-..+ -=|-++|..-+++++-.++. .|.+||.
T Consensus 61 CtGC-s~SlL~s~~P~~~~~ll~~isl~yhptlmaa~G~~ae~~l~~~~~~~~g~~ILv 118 (365)
T TIGR00391 61 CTGC-TESLLRSAHPTVENLILETISLEYHETLMAAFGHQAEENKHDAIEKYKGQYILV 118 (365)
T ss_pred CCCc-HHHHhccCCCCHHHHHhcCceEEechHhHHhhHHHHHHHHHHHHhccCCCeEEE
Confidence 5555 6899999998877665554 22346787788888876655 5888885
No 145
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.49 E-value=70 Score=29.91 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=25.3
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhhccccc
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDDFGETVL 76 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL 76 (159)
|+-|++.+..|-|-+||+.|+...==+.+.
T Consensus 335 r~Sv~~A~~~GITa~qIi~fl~~~ahp~~~ 364 (448)
T TIGR00625 335 RESIRRALANGITAQQIIHYLRTHAHPQMR 364 (448)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCChhhh
Confidence 778999999999999999999976555443
No 146
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=27.48 E-value=1.1e+02 Score=19.64 Aligned_cols=29 Identities=17% Similarity=0.194 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHH
Q 031429 41 DIAILLRKLIRDEIQAGKTDKEVYKKLED 69 (159)
Q Consensus 41 ~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~ 69 (159)
+-..+.-..|+.+...|.|-+||.+++.+
T Consensus 40 ~~dv~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 40 EEDVERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 45566778899999999999999998864
No 147
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=27.45 E-value=45 Score=31.67 Aligned_cols=60 Identities=12% Similarity=0.211 Sum_probs=36.6
Q ss_pred cccCCCCCCCCc---------------cccCcHHHHHHHHHHHHHHHcCCChHHHHH-------------HHHHhhcccc
Q 031429 24 NVRCTDCGSQSI---------------EDSQADIAILLRKLIRDEIQAGKTDKEVYK-------------KLEDDFGETV 75 (159)
Q Consensus 24 ~LRCpvCqnqsi---------------adSna~~A~dmR~~Ir~~l~~G~Sd~eI~~-------------~~v~RYGd~V 75 (159)
.--|++|+|-|- +..|--.-..+-+.||+.|.+|.=.+=+-. .|-+.|...-
T Consensus 172 ~C~C~~C~~ysrayL~hL~~~~~~~Lla~HNL~~~~~~m~~iR~aI~~g~l~e~ve~r~R~hP~l~~~~r~l~~~~~~lE 251 (540)
T TIGR00432 172 PCSCPVCSNYTPEELRRMEKNERERLIAEHNLYVSFQEIETIKQAIKDGSLFELVEERVRAHPNLLEGYRQVKHYWDLIE 251 (540)
T ss_pred CCCCccccccCHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCHHHHHHHHHHHHHHHHHH
Confidence 456889998653 334444556778899999999974432222 2323344455
Q ss_pred cccCCCCc
Q 031429 76 LYAPKFDL 83 (159)
Q Consensus 76 L~~Pp~~~ 83 (159)
-+.|-++.
T Consensus 252 ~~~P~~k~ 259 (540)
T TIGR00432 252 KFDPRKKK 259 (540)
T ss_pred hhCCCccC
Confidence 56666664
No 148
>PF01997 Translin: Translin family; InterPro: IPR002848 Translins are DNA-binding proteins that specifically recognise consensus sequences at the breakpoint junctions in chromosomal translocations, mostly involving immunoglobulin (Ig)/T-cell receptor gene segments. They seem to recognise single-stranded DNA ends generated by staggered breaks occuring at recombination hot spots []. Translin folds into an alpha-alpha superhelix, consisting of two curved layers of alpha/alpha topology [, ].; GO: 0043565 sequence-specific DNA binding; PDB: 3QB5_K 3PJA_L 1J1J_D 3RIU_C 3AXJ_B 4DG7_C 2QVA_C 2QRX_A 1KEY_C.
Probab=27.19 E-value=79 Score=25.56 Aligned_cols=63 Identities=8% Similarity=0.121 Sum_probs=44.7
Q ss_pred HHHhcccCCCCCCCCccccC-------cHHHHHHHHHHHHHHHcCC--ChHHHHHHHHHhhcccccccCCCC
Q 031429 20 NISRNVRCTDCGSQSIEDSQ-------ADIAILLRKLIRDEIQAGK--TDKEVYKKLEDDFGETVLYAPKFD 82 (159)
Q Consensus 20 ~l~~~LRCpvCqnqsiadSn-------a~~A~dmR~~Ir~~l~~G~--Sd~eI~~~~v~RYGd~VL~~Pp~~ 82 (159)
++.+.|-++......+.=+. ++++.+|++..-..+..|. ...+|.+||.+-|..|.++++|..
T Consensus 96 ev~~~l~~~~~~~~~~~v~~~dYL~Gl~DltGEL~R~ai~~v~~gd~~~~~~i~~f~~~l~~~~~~l~~~~~ 167 (200)
T PF01997_consen 96 EVGEILGFSEDDEDRFHVTPEDYLLGLADLTGELMRYAINSVTKGDYERPEKILEFMRELYSGFQLLNLPDA 167 (200)
T ss_dssp HHHHHCTCBSSTSCSSB--HHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHHHHHTSGGTTG
T ss_pred HHHHHHhhccccccceecCHHHHHHHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHHHHHHHHHhCcchhh
Confidence 44455555544433332222 2689999999999999994 568999999999999999998653
No 149
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=27.12 E-value=85 Score=20.40 Aligned_cols=25 Identities=32% Similarity=0.333 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHH
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
.-..-..|+.+...|.|-+||..+|
T Consensus 42 ~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 42 DIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 3344556899999999999999876
No 150
>COG3225 GldG ABC-type uncharacterized transport system involved in gliding motility, auxiliary component [Cell motility and secretion]
Probab=27.03 E-value=63 Score=30.93 Aligned_cols=24 Identities=25% Similarity=0.315 Sum_probs=14.1
Q ss_pred hHHHH-HHHHHHHHHHHHHHHHHHh
Q 031429 85 TAALW-LSPLLVAGAAAGIWAYNRH 108 (159)
Q Consensus 85 t~lLW-~~P~l~~~~~~~~~~~~rr 108 (159)
+|+=| ++|.++++++++-|.++||
T Consensus 513 ~l~n~vilP~L~l~f~l~~w~wRrr 537 (538)
T COG3225 513 KLLNLVILPLLILLFALLRWLWRRR 537 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 56666 4688776555544544443
No 151
>PHA02975 hypothetical protein; Provisional
Probab=26.92 E-value=1.3e+02 Score=21.46 Aligned_cols=18 Identities=11% Similarity=0.174 Sum_probs=12.4
Q ss_pred CCCCchhHHHHHHHHHHH
Q 031429 79 PKFDLQTAALWLSPLLVA 96 (159)
Q Consensus 79 Pp~~~~t~lLW~~P~l~~ 96 (159)
|..++.+|..|+.-++++
T Consensus 37 ~~~~~~~~~~~ii~i~~v 54 (69)
T PHA02975 37 PKKKSSLSIILIIFIIFI 54 (69)
T ss_pred CCcCCchHHHHHHHHHHH
Confidence 555888888887665433
No 152
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.83 E-value=65 Score=28.19 Aligned_cols=30 Identities=17% Similarity=0.401 Sum_probs=21.9
Q ss_pred hcccCCCCCCCCccccC--cHHHHHHHHHHHH
Q 031429 23 RNVRCTDCGSQSIEDSQ--ADIAILLRKLIRD 52 (159)
Q Consensus 23 ~~LRCpvCqnqsiadSn--a~~A~dmR~~Ir~ 52 (159)
...+||+|..+..-.-| +|+|..||+++.+
T Consensus 93 aGyqCP~Cs~eiFPp~NlvsPva~aLre~L~q 124 (299)
T KOG3970|consen 93 AGYQCPCCSQEIFPPINLVSPVAEALREQLKQ 124 (299)
T ss_pred CcccCCCCCCccCCCccccchhHHHHHHHHHh
Confidence 34689999877665555 5888888887764
No 153
>PF04189 Gcd10p: Gcd10p family; InterPro: IPR007316 eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit of eIF3 [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation
Probab=26.72 E-value=72 Score=28.05 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=42.3
Q ss_pred CCCCCCCccccCcHHHHHH-HHHHHHHHHcCCChHHHHHHHHH----------------------hhcccccccCCC
Q 031429 28 TDCGSQSIEDSQADIAILL-RKLIRDEIQAGKTDKEVYKKLED----------------------DFGETVLYAPKF 81 (159)
Q Consensus 28 pvCqnqsiadSna~~A~dm-R~~Ir~~l~~G~Sd~eI~~~~v~----------------------RYGd~VL~~Pp~ 81 (159)
..+-|+.|.|.++ ++.| ..+|.+|=++|.|-+||++-+++ +|...+...||-
T Consensus 92 ~~~dNr~i~D~~~--~QkLt~eeIe~LK~~g~sg~eII~kLiens~tF~~KT~FSqeKYlkrK~kKy~~~ftv~~pt 166 (299)
T PF04189_consen 92 SSRDNRNIIDDNS--SQKLTQEEIEELKKEGVSGEEIIEKLIENSSTFDKKTEFSQEKYLKRKQKKYLKRFTVLRPT 166 (299)
T ss_pred ccccccccccccc--cccCCHHHHHHHHHcCCCHHHHHHHHHHhccchhhhhHHHHHHHHHHHHhhhhceEEEeCCC
Confidence 4678899999887 4444 46788888899999999999987 788888877774
No 154
>PRK10715 flk flagella biosynthesis regulator; Provisional
Probab=26.61 E-value=91 Score=28.21 Aligned_cols=83 Identities=22% Similarity=0.255 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHhhccchhhHhhhhc
Q 031429 42 IAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAALWLSPLLVAGAAAGIWAYNRHRQKTNVHIMALNL 121 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW~~P~l~~~~~~~~~~~~rrr~~~~~~~~~~~~ 121 (159)
..+.+..++-+++.+|...+++-||....||..+|-. +.|-=+- -++-|+-...-.. +.+ ....
T Consensus 93 a~rqLl~qLt~ll~qgnnRQavsdfirqqFG~t~L~~-----------Lt~~QLq--qvl~~Lq~gql~i-Pqp--q~~~ 156 (335)
T PRK10715 93 ATRQLLQQLTELLPQGNNRQAVSDFIRQQFGQTVLSQ-----------LSPEQLK--QVLTLLQNGQLSI-PQP--QQRP 156 (335)
T ss_pred hHHHHHHHHHHHhhccchHHHHHHHHHHHhCcchHhh-----------cCHHHHH--HHHHHHHcCCcCC-CCC--CCCC
Confidence 4567788888999999999999999999999988732 2332111 0111211111011 100 0112
Q ss_pred cCCCCCCHHHHHHHHhhcC
Q 031429 122 VRGVPLTPKEKETMLDLLT 140 (159)
Q Consensus 122 ~~~~~Ls~eE~~rl~~lL~ 140 (159)
..+-+|++.|+.-|++|+.
T Consensus 157 ~tDRPLlPAeh~tLnqLVt 175 (335)
T PRK10715 157 ATDRPLLPAEHNALNQLVT 175 (335)
T ss_pred CCCCCCCHHHHHHHHHHHH
Confidence 3456899999999998865
No 155
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=26.57 E-value=1.2e+02 Score=21.11 Aligned_cols=34 Identities=32% Similarity=0.609 Sum_probs=23.1
Q ss_pred ccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHH
Q 031429 25 VRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 25 LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
+||-.|..- ++. .=.+-.+++++|++..+++|.|
T Consensus 5 vRCFTCGkv--------i~~-~we~y~~~~~~g~~~~~vLd~L 38 (62)
T PRK04016 5 VRCFTCGKV--------IAE-KWEEFKERVEAGEDPGKVLDDL 38 (62)
T ss_pred eEecCCCCC--------hHH-HHHHHHHHHHcCCCHHHHHHHc
Confidence 577777432 332 2344667788999999999965
No 156
>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=26.55 E-value=30 Score=29.43 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=36.8
Q ss_pred HHHHHHHHH-HcCCChHHHHHHHHHhhcccccc-cCCCCchhHHHHHHHH
Q 031429 46 LRKLIRDEI-QAGKTDKEVYKKLEDDFGETVLY-APKFDLQTAALWLSPL 93 (159)
Q Consensus 46 mR~~Ir~~l-~~G~Sd~eI~~~~v~RYGd~VL~-~Pp~~~~t~lLW~~P~ 93 (159)
++..|.+.+ ..|.|.++|.+.+..+.=++..| .|..+-...++++.|-
T Consensus 130 ~~r~i~Rd~~rrG~s~e~v~~~i~~r~~~~~~~I~P~~~~ADvVI~~~p~ 179 (273)
T cd02026 130 FAWKIQRDMAERGHSLEDVLASIEARKPDFEAYIDPQKQYADVVIQVLPT 179 (273)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHhhchhHHHHhccccccCcEEEEccCc
Confidence 444464444 56999999999998888888866 6667778888888885
No 157
>PRK01294 lipase chaperone; Provisional
Probab=25.96 E-value=86 Score=27.89 Aligned_cols=65 Identities=9% Similarity=0.054 Sum_probs=42.1
Q ss_pred hhhcHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhccccc
Q 031429 8 LKKKQMADARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVL 76 (159)
Q Consensus 8 ~~~d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL 76 (159)
..++.+...+..+|..+|-=.. -+.+.. +.-..+++..+.++-.+|.|.++|...-++-||+.+-
T Consensus 202 ~Ls~~qK~~~l~~L~~qLP~~~--~~~~~~--~~~~~~l~~~~~~l~~~g~s~~~~~~~r~~~vG~EaA 266 (336)
T PRK01294 202 SLSDAQKAARLAALEAQLPEDL--RAALQE--SQRQQALLQQLAQLQASGASPQELRLMRAQLVGPEAA 266 (336)
T ss_pred CCCHHHHHHHHHHHHHhCCHhh--HHHHHH--HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcCHHHH
Confidence 3344455556666665543222 222322 2345567788888889999999999999998887653
No 158
>PF10821 DUF2567: Protein of unknown function (DUF2567); InterPro: IPR021213 This is a bacterial family of proteins with unknown function.
Probab=25.86 E-value=1e+02 Score=25.19 Aligned_cols=41 Identities=24% Similarity=0.175 Sum_probs=19.6
Q ss_pred HhhcccccccCCCCc---hhHHHHHHHHH---HHHHHHHHHHHHHhh
Q 031429 69 DDFGETVLYAPKFDL---QTAALWLSPLL---VAGAAAGIWAYNRHR 109 (159)
Q Consensus 69 ~RYGd~VL~~Pp~~~---~t~lLW~~P~l---~~~~~~~~~~~~rrr 109 (159)
.+.|+.|..-+.-++ |....|+.=+. .+..++++|..|++|
T Consensus 27 t~~G~~v~~~l~~e~~~~F~a~a~f~~l~lv~Gvvaav~~W~~R~~R 73 (167)
T PF10821_consen 27 TRSGERVHAYLGGESEHFFDADALFVLLGLVLGVVAAVAVWLWRRRR 73 (167)
T ss_pred cCCCceeeccCCCcchhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 467888754444333 44444444332 222244456655444
No 159
>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function.
Probab=25.81 E-value=2.4e+02 Score=21.35 Aligned_cols=22 Identities=14% Similarity=0.163 Sum_probs=18.7
Q ss_pred HHHHHcCCChHHHHHHHHHhhc
Q 031429 51 RDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 51 r~~l~~G~Sd~eI~~~~v~RYG 72 (159)
.+-+++|.=++|-.+.+.+.|+
T Consensus 2 ~~w~~~GlI~~~q~~~i~~~~~ 23 (145)
T PF09925_consen 2 DRWVEQGLITPEQAEAILAFYG 23 (145)
T ss_pred HhHHHCCCCCHHHHHHHHHHhh
Confidence 4567888888888999999999
No 160
>PF07937 DUF1686: Protein of unknown function (DUF1686); InterPro: IPR012468 The members of this family are all hypothetical proteins of unknown function expressed by the eukaryotic parasite Encephalitozoon cuniculi GB-M1. The region in question is approximately 250 amino acids long.
Probab=25.72 E-value=2.1e+02 Score=23.88 Aligned_cols=54 Identities=7% Similarity=0.056 Sum_probs=38.7
Q ss_pred HHHHHHcCCChHHHHHHHHH------hh--cccccccCCCCchhHHHHHHHHHHHHHHHHHH
Q 031429 50 IRDEIQAGKTDKEVYKKLED------DF--GETVLYAPKFDLQTAALWLSPLLVAGAAAGIW 103 (159)
Q Consensus 50 Ir~~l~~G~Sd~eI~~~~v~------RY--Gd~VL~~Pp~~~~t~lLW~~P~l~~~~~~~~~ 103 (159)
+....+.|+|..|+.-+... -| |+.-++.|-.++.+...+.+++++.++.+++.
T Consensus 82 vQ~l~r~gMs~rq~~v~~~GNivm~~a~~ag~~k~f~p~~~~~~~~i~~g~Vvfa~lLllv~ 143 (185)
T PF07937_consen 82 VQNLVRRGMSWRQMCVFGAGNIVMGAACFAGPVKMFMPGSKGRNHWICVGLVVFAILLLLVS 143 (185)
T ss_pred HHHHHHcCCCHHHHHHHHHhHHHHHHHHHcCCccccCccccCCcceeehHHHHHHHHHHHHH
Confidence 45566779999999988653 33 34556788889999999999987654444333
No 161
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=25.61 E-value=90 Score=19.85 Aligned_cols=20 Identities=20% Similarity=0.307 Sum_probs=16.1
Q ss_pred HHHHHHHHcCCChHHHHHHH
Q 031429 48 KLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
.+|-..+.+|+|..||=+.|
T Consensus 9 ~~vl~~l~~G~~~~eIA~~l 28 (58)
T PF00196_consen 9 LEVLRLLAQGMSNKEIAEEL 28 (58)
T ss_dssp HHHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHhcCCcchhHHhc
Confidence 45888999999999998776
No 162
>PF03280 Lipase_chap: Proteobacterial lipase chaperone protein; InterPro: IPR004961 The proteobacterial lipase chaperone is a lipase helper protein which may be involved in the folding of extracellular lipase during its passage through the periplasm [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016020 membrane; PDB: 2ES4_E.
Probab=25.49 E-value=60 Score=26.31 Aligned_cols=37 Identities=14% Similarity=0.172 Sum_probs=28.2
Q ss_pred cCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhccc
Q 031429 38 SQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 38 Sna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~ 74 (159)
-+.....++...+.++-+.|.|.++|....+..||+.
T Consensus 102 ~~~~~~~~l~~~~~~l~~~g~~~~~~~~~r~~~vg~e 138 (195)
T PF03280_consen 102 RNAQLLQDLQQQTQELQAQGASEQELRAARAQLVGPE 138 (195)
T ss_dssp HHHHHHHHHHHHHHHHHHTT--HHHHHHHHHCCC-HH
T ss_pred HhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCHH
Confidence 3456677888888889999999999999999988854
No 163
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.42 E-value=46 Score=26.03 Aligned_cols=25 Identities=16% Similarity=0.502 Sum_probs=19.9
Q ss_pred ChHHHHHHHHHhhcccccccCCCCch
Q 031429 59 TDKEVYKKLEDDFGETVLYAPKFDLQ 84 (159)
Q Consensus 59 Sd~eI~~~~v~RYGd~VL~~Pp~~~~ 84 (159)
+|.||++|+..+|.. +.+.|+....
T Consensus 34 ~d~Ei~~fi~~~~~~-L~f~~~~~~~ 58 (132)
T PF11208_consen 34 KDPEIYEFILKHWYK-LRFSPAVEVE 58 (132)
T ss_pred CcHHHHHHHHHHHHH-hcCCcccccc
Confidence 689999999999988 6666665543
No 164
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=25.35 E-value=25 Score=21.36 Aligned_cols=16 Identities=38% Similarity=0.829 Sum_probs=11.7
Q ss_pred HHHHHHhcccCCCCCC
Q 031429 17 RARNISRNVRCTDCGS 32 (159)
Q Consensus 17 r~~~l~~~LRCpvCqn 32 (159)
+...-+..+||+.|+.
T Consensus 18 ~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 18 KLPAGGRKVRCPKCGH 33 (37)
T ss_pred HcccCCcEEECCCCCc
Confidence 3445567899999975
No 165
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=25.11 E-value=30 Score=28.57 Aligned_cols=11 Identities=27% Similarity=1.059 Sum_probs=7.8
Q ss_pred hcccCCCCCCC
Q 031429 23 RNVRCTDCGSQ 33 (159)
Q Consensus 23 ~~LRCpvCqnq 33 (159)
+++.||||.++
T Consensus 4 k~~~CPvC~~~ 14 (214)
T PF09986_consen 4 KKITCPVCGKE 14 (214)
T ss_pred CceECCCCCCe
Confidence 56778888663
No 166
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=25.08 E-value=1.1e+02 Score=22.74 Aligned_cols=26 Identities=23% Similarity=0.152 Sum_probs=21.3
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhhc
Q 031429 47 RKLIRDEIQAGKTDKEVYKKLEDDFG 72 (159)
Q Consensus 47 R~~Ir~~l~~G~Sd~eI~~~~v~RYG 72 (159)
+.-+...+..|.|.++|+++|...=+
T Consensus 44 ~~Sl~~A~~~G~~~e~i~~~L~~~S~ 69 (129)
T PF13625_consen 44 PASLWRAASAGLTAEEIIEFLERYSK 69 (129)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHcC
Confidence 34578899999999999999976543
No 167
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.92 E-value=1.3e+02 Score=23.03 Aligned_cols=46 Identities=22% Similarity=0.324 Sum_probs=40.2
Q ss_pred cHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhccccc------ccCCCCchh
Q 031429 40 ADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVL------YAPKFDLQT 85 (159)
Q Consensus 40 a~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL------~~Pp~~~~t 85 (159)
|.+..+++..|-+.|+-=.|..|+.+...+.||=.|- |+|......
T Consensus 2 A~L~~~vK~FIVQ~LAcfdTPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~ 53 (104)
T PF10045_consen 2 AALKKEVKAFIVQSLACFDTPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGR 53 (104)
T ss_pred CCccHHHHHHHHHHHHhhCCHHHHHHHHHHHhCCccCHHHHHHcCchHHHHH
Confidence 3466789999999999999999999999999999998 999876543
No 168
>PF02657 SufE: Fe-S metabolism associated domain; InterPro: IPR003808 This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons [].; PDB: 1MZG_B 1WLO_A 3G0M_A 1NI7_A.
Probab=24.92 E-value=66 Score=24.48 Aligned_cols=31 Identities=29% Similarity=0.308 Sum_probs=25.3
Q ss_pred ccccCcHHHHHHHHHHHHHHHcCCChHHHHHH
Q 031429 35 IEDSQADIAILLRKLIRDEIQAGKTDKEVYKK 66 (159)
Q Consensus 35 iadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~ 66 (159)
.+||+|.+.+-|-..+-+.+ +|+|.+||.++
T Consensus 61 ~adSda~ivkGl~all~~~~-~g~t~~eI~~~ 91 (125)
T PF02657_consen 61 RADSDARIVKGLLALLLEVL-NGQTPEEILAF 91 (125)
T ss_dssp EEEESSHHHHHHHHHHHHHT-TT-BHHHHHHS
T ss_pred EecCccHHHHHHHHHHHHHH-cCCCHHHHHhC
Confidence 46899999999988887754 89999999875
No 169
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=24.87 E-value=83 Score=29.58 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=24.7
Q ss_pred HHHHHHHHHHcCCChHHHHHHHHHhhcc
Q 031429 46 LRKLIRDEIQAGKTDKEVYKKLEDDFGE 73 (159)
Q Consensus 46 mR~~Ir~~l~~G~Sd~eI~~~~v~RYGd 73 (159)
=|+-||..+..|-|.+||+.|+..+=-+
T Consensus 348 TreSVr~Al~~GITa~QII~fLet~ahp 375 (465)
T KOG3471|consen 348 TRESVRRALDNGITAEQIIHFLETHAHP 375 (465)
T ss_pred eHHHHHHHHhcCCcHHHHHHHHHhccCc
Confidence 3788999999999999999999987555
No 170
>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
Probab=24.85 E-value=95 Score=24.35 Aligned_cols=39 Identities=18% Similarity=0.173 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCCC
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFD 82 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~ 82 (159)
+-.|+..|.....|.+.++++......-=....+.||++
T Consensus 132 rl~rri~RD~~~rg~~~~~~i~~~~~~~~~~~~~~~~~~ 170 (179)
T cd02028 132 RLLRRVVRDIQFRGYSAELTILMWPSVPSGEEFIIPPLQ 170 (179)
T ss_pred HHHHHHHHhHHhhCCCHHHHhhhcccccCchhhcCCCch
Confidence 556888888899999999999974433333344555554
No 171
>TIGR02425 decarb_PcaC 4-carboxymuconolactone decarboxylase. Members of this family are 4-carboxymuconolactone decarboxylase, which catalyzes the third step in the catabolism of protocatechuate (and therefore the fourth step in the catabolism of para-hydroxybenzoate, of 3-hydroxybenzoate, of vanillate, etc.). Most members of this family are encoded within protocatechuate catabolism operons. This protein is sometimes found as a fusion protein with other enzymes of the pathway, as in Rhodococcus opacus, Streptomyces avermitilis, and Caulobacter crescentus.
Probab=24.83 E-value=1.4e+02 Score=22.57 Aligned_cols=25 Identities=20% Similarity=0.235 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHcCCChHHHHHHHH
Q 031429 44 ILLRKLIRDEIQAGKTDKEVYKKLE 68 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~eI~~~~v 68 (159)
..++..++..+..|-|.+||++.+.
T Consensus 73 ~~l~~h~~~Al~~G~T~~ei~Evl~ 97 (123)
T TIGR02425 73 EELAMHVRATANTGVTEDDIKEVLL 97 (123)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4699999999999999999998764
No 172
>TIGR02501 type_III_yscE type III secretion system protein, YseE family. Members of this family are found exclusively in type III secretion appparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis. This protein is small (about 70 amino acids) and not well characterized.
Probab=24.68 E-value=1.7e+02 Score=20.34 Aligned_cols=18 Identities=6% Similarity=0.233 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHcCCChHH
Q 031429 45 LLRKLIRDEIQAGKTDKE 62 (159)
Q Consensus 45 dmR~~Ir~~l~~G~Sd~e 62 (159)
+-+..|.+.+..|.|.+|
T Consensus 24 ~a~~~lk~qL~~~~tp~q 41 (67)
T TIGR02501 24 AALAELKEQLSRGGDPQQ 41 (67)
T ss_pred HHHHHHHHHHhCCCCHHH
Confidence 345667777778888776
No 173
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=24.51 E-value=1e+02 Score=19.80 Aligned_cols=25 Identities=16% Similarity=0.082 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHH
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
-...-..|+.+...|.|-++|.+++
T Consensus 43 ~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 43 DVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 3345567888999999999999875
No 174
>TIGR03068 srtB_sig_NPQTN sortase B signal domain, NPQTN class. This model represents one of the boutique (rare) sortase signals, recognized by sortase B (SrtB) rather than by the housekeeping-type SrtA class sortase. This sequence, beginning NPQTN, shows little similarity to several other SrtB substrates.
Probab=24.50 E-value=1.4e+02 Score=18.45 Aligned_cols=17 Identities=24% Similarity=0.407 Sum_probs=10.0
Q ss_pred CCCCchh-HHHHHHHHHH
Q 031429 79 PKFDLQT-AALWLSPLLV 95 (159)
Q Consensus 79 Pp~~~~t-~lLW~~P~l~ 95 (159)
|.-++.+ ..+++.|++.
T Consensus 2 PQTs~gtp~y~y~Ip~v~ 19 (33)
T TIGR03068 2 PQTNAGTPAYIYAIPVAS 19 (33)
T ss_pred CCCCCCCcchhhHHHHHH
Confidence 4444444 3778888764
No 175
>PF11446 DUF2897: Protein of unknown function (DUF2897); InterPro: IPR021550 This is a bacterial family of uncharacterised proteins.
Probab=24.48 E-value=1e+02 Score=20.66 Aligned_cols=17 Identities=35% Similarity=0.561 Sum_probs=11.9
Q ss_pred hHHHHHHHHHHHHHHHH
Q 031429 85 TAALWLSPLLVAGAAAG 101 (159)
Q Consensus 85 t~lLW~~P~l~~~~~~~ 101 (159)
+|-.|+.=++++|+.++
T Consensus 2 ~~~~wlIIviVlgvIig 18 (55)
T PF11446_consen 2 TWNPWLIIVIVLGVIIG 18 (55)
T ss_pred cchhhHHHHHHHHHHHh
Confidence 56788877777766554
No 176
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=24.25 E-value=1.2e+02 Score=21.41 Aligned_cols=27 Identities=22% Similarity=0.400 Sum_probs=22.3
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhhccc
Q 031429 48 KLIRDEIQAGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 48 ~~Ir~~l~~G~Sd~eI~~~~v~RYGd~ 74 (159)
..|-.+|.+|.+.++|..-|.+-+++.
T Consensus 3 K~ii~~Lh~G~~~e~vk~~F~~~~~~V 29 (71)
T PF04282_consen 3 KEIIKRLHEGEDPEEVKEEFKKLFSDV 29 (71)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHCCC
Confidence 355677899999999999999988873
No 177
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=24.02 E-value=1.1e+02 Score=22.66 Aligned_cols=39 Identities=21% Similarity=0.276 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCC
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKF 81 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~ 81 (159)
+.+.-..+.+.+.+|++-.++++-|.+.|-+..+++=-.
T Consensus 30 ~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ll~~k~~~ 68 (143)
T PF12169_consen 30 AAEALELLNELLEQGKDPKQFLDDLIEYLRDLLLYKITG 68 (143)
T ss_dssp HHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHTTSG
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 356677899999999999999999999999988876544
No 178
>smart00035 CLa CLUSTERIN alpha chain.
Probab=24.00 E-value=28 Score=29.62 Aligned_cols=43 Identities=16% Similarity=0.414 Sum_probs=31.6
Q ss_pred cCCCCCC-CCccccC-cHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccc
Q 031429 26 RCTDCGS-QSIEDSQ-ADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 26 RCpvCqn-qsiadSn-a~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~V 75 (159)
.|-+||. ++++.|. -|.-..||.++-+.|+ +.+-+..+|++..
T Consensus 74 qCEKCqeiLsvDCs~~~P~q~~Lr~El~eAL~-------LaE~ftqqYd~lL 118 (216)
T smart00035 74 QCEKCQEILSVDCSTNNPDQPQLRQELDESLQ-------LAERFTQQYDQLL 118 (216)
T ss_pred HHHHHHHHHhhhccCCCcchHHHHHHHHHHHH-------HHHHHHHHHHHHH
Confidence 4889998 5555543 3888899999988874 5677778887654
No 179
>TIGR02837 spore_II_R stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage II sporulation protein R.
Probab=23.87 E-value=1.6e+02 Score=24.12 Aligned_cols=34 Identities=21% Similarity=0.284 Sum_probs=23.1
Q ss_pred CccccCcHHHHHHHHHHHHHH--------HcCCChHHHHHHH
Q 031429 34 SIEDSQADIAILLRKLIRDEI--------QAGKTDKEVYKKL 67 (159)
Q Consensus 34 siadSna~~A~dmR~~Ir~~l--------~~G~Sd~eI~~~~ 67 (159)
-|++|+++--+.++..||..+ .+..|.+|-.++.
T Consensus 44 VlANSDs~~DQ~lKl~VRD~Vl~~~~~~~~~~~s~~ea~~~i 85 (168)
T TIGR02837 44 VLANSDSDEDQALKLKVRDAVLKEIRPWLSGLKSLEEARRVI 85 (168)
T ss_pred EEcCCCCHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHH
Confidence 478999988888888887644 4455555554443
No 180
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=23.86 E-value=56 Score=25.76 Aligned_cols=16 Identities=19% Similarity=0.295 Sum_probs=13.0
Q ss_pred hHHHHHHHHHhhcccc
Q 031429 60 DKEVYKKLEDDFGETV 75 (159)
Q Consensus 60 d~eI~~~~v~RYGd~V 75 (159)
+.+.+.+|+++|||-.
T Consensus 121 e~~~i~~Li~KhGdDy 136 (164)
T PF09420_consen 121 EIEYIEYLIEKHGDDY 136 (164)
T ss_pred HHHHHHHHHHHHCccH
Confidence 4567899999999863
No 181
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=23.63 E-value=1e+02 Score=21.85 Aligned_cols=10 Identities=10% Similarity=0.318 Sum_probs=6.1
Q ss_pred hHHHHHHHHH
Q 031429 85 TAALWLSPLL 94 (159)
Q Consensus 85 t~lLW~~P~l 94 (159)
.+++|++=++
T Consensus 70 ~~li~~~~~~ 79 (92)
T PF03908_consen 70 RILIFFAFLF 79 (92)
T ss_pred HHHHHHHHHH
Confidence 5668876433
No 182
>PRK14740 kdbF potassium-transporting ATPase subunit F; Provisional
Probab=23.59 E-value=1.8e+02 Score=17.47 Aligned_cols=14 Identities=43% Similarity=0.582 Sum_probs=9.9
Q ss_pred hHHHHHHHHHHHHH
Q 031429 85 TAALWLSPLLVAGA 98 (159)
Q Consensus 85 t~lLW~~P~l~~~~ 98 (159)
+|++|+.-.+.+++
T Consensus 2 ~~~~wls~a~a~~L 15 (29)
T PRK14740 2 TVLDWLSLALATGL 15 (29)
T ss_pred cHHHHHHHHHHHHH
Confidence 68999977655444
No 183
>PF04108 APG17: Autophagy protein Apg17 ; InterPro: IPR007240 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Autophagy protein 17 (Apg17) is required for activating Apg1 protein kinases. This entry also contains Autophagy protein 11 which is involved in cytoplasm to vacuole transport (Cvt) and pexophagy. ; GO: 0006914 autophagy
Probab=23.58 E-value=1.1e+02 Score=27.64 Aligned_cols=32 Identities=6% Similarity=0.146 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccc
Q 031429 41 DIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 41 ~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~V 75 (159)
.++.+|+.++..+-.+ |.+=+..|...||+|+
T Consensus 367 ~i~~~~~eeL~~l~ee---E~~~Re~F~~e~GdyL 398 (412)
T PF04108_consen 367 KIIREANEELDKLREE---EQRRREAFLKEYGDYL 398 (412)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHHHHccCcC
Confidence 5777888888888876 8888999999999997
No 184
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=23.57 E-value=89 Score=25.21 Aligned_cols=30 Identities=17% Similarity=0.116 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHhh
Q 031429 42 IAILLRKLIRDEIQAGKTDKEVYKKLEDDF 71 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RY 71 (159)
.+.+.-+.|-++-.+|.+..||=-.|.+.|
T Consensus 26 ~~eeVe~~I~klaKkG~~pSqIG~iLRD~~ 55 (148)
T PTZ00072 26 SSSEVEDQICKLAKKGLTPSQIGVILRDSM 55 (148)
T ss_pred CHHHHHHHHHHHHHCCCCHhHhhhhhhhcc
Confidence 367888999999999999999999999999
No 185
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=23.52 E-value=33 Score=25.79 Aligned_cols=17 Identities=41% Similarity=0.843 Sum_probs=13.4
Q ss_pred HHhcccCCCCCCCCccc
Q 031429 21 ISRNVRCTDCGSQSIED 37 (159)
Q Consensus 21 l~~~LRCpvCqnqsiad 37 (159)
|-.--|||.|-.|.|.+
T Consensus 73 ik~pSRCP~CKSE~Ie~ 89 (97)
T COG3357 73 IKKPSRCPKCKSEWIEE 89 (97)
T ss_pred cCCcccCCcchhhcccC
Confidence 44456999999999876
No 186
>TIGR00762 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity.
Probab=23.48 E-value=1.1e+02 Score=25.65 Aligned_cols=34 Identities=29% Similarity=0.179 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHHHHhhccccc
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVL 76 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL 76 (159)
-..|-.++.+++++|+|-+||++++.+.--....
T Consensus 121 ~g~~v~~a~~~~~~G~s~~eI~~~l~~~~~~~~~ 154 (275)
T TIGR00762 121 LGLLVLEAAKLAEEGKSLEEILAKLEELRERTKL 154 (275)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcEE
Confidence 3456678899999999999999999875444333
No 187
>PF05462 Dicty_CAR: Slime mold cyclic AMP receptor
Probab=23.36 E-value=2e+02 Score=25.09 Aligned_cols=26 Identities=27% Similarity=0.451 Sum_probs=20.3
Q ss_pred hhcccccccCCCCchhHHHHHHHHHH
Q 031429 70 DFGETVLYAPKFDLQTAALWLSPLLV 95 (159)
Q Consensus 70 RYGd~VL~~Pp~~~~t~lLW~~P~l~ 95 (159)
.||++==.+|..+...+.+|.+|+.+
T Consensus 141 ~~G~WCWI~~~~~~~r~~lfY~Pl~i 166 (303)
T PF05462_consen 141 PAGNWCWIKPEWDVWRFALFYIPLWI 166 (303)
T ss_pred CCCCceeecCCCcchHHHHHHHHHHH
Confidence 45666667888888899999999753
No 188
>PF09892 DUF2119: Uncharacterized protein conserved in archaea (DUF2119); InterPro: IPR019218 This entry represents a family of hypothetical archaeal proteins of unknown function.
Probab=23.34 E-value=1.2e+02 Score=25.46 Aligned_cols=48 Identities=19% Similarity=0.186 Sum_probs=38.5
Q ss_pred CCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhccccc
Q 031429 29 DCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVL 76 (159)
Q Consensus 29 vCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL 76 (159)
.|..--+-+-..+.+.+.-.+|-+.+....|.+|++++|..+|=+.+-
T Consensus 134 ~C~TlEvP~~~~~~~~~~~~~iL~~~~~s~~Rde~i~kl~~~YP~q~~ 181 (193)
T PF09892_consen 134 FCMTLEVPNWKSDESKEEVLEILEIIKESKNRDEFIEKLKKKYPEQAK 181 (193)
T ss_pred eEEEEEcCCCccHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhhHHHH
Confidence 354444446667788888889999999999999999999999977653
No 189
>PRK13685 hypothetical protein; Provisional
Probab=23.31 E-value=97 Score=26.69 Aligned_cols=8 Identities=0% Similarity=-0.214 Sum_probs=4.2
Q ss_pred HHHHHHHH
Q 031429 86 AALWLSPL 93 (159)
Q Consensus 86 ~lLW~~P~ 93 (159)
|+||++++
T Consensus 10 ~~l~ll~~ 17 (326)
T PRK13685 10 WFFLFLLV 17 (326)
T ss_pred HHHHHHHH
Confidence 45565544
No 190
>PRK11677 hypothetical protein; Provisional
Probab=23.21 E-value=1e+02 Score=24.17 Aligned_cols=18 Identities=22% Similarity=0.074 Sum_probs=8.4
Q ss_pred HHHHH---HHHHHHHHHHHHH
Q 031429 86 AALWL---SPLLVAGAAAGIW 103 (159)
Q Consensus 86 ~lLW~---~P~l~~~~~~~~~ 103 (159)
|++|+ +=.+++|+.++-+
T Consensus 3 W~~a~i~livG~iiG~~~~R~ 23 (134)
T PRK11677 3 WEYALIGLVVGIIIGAVAMRF 23 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 55552 3344555554443
No 191
>PLN02417 dihydrodipicolinate synthase
Probab=22.95 E-value=1.9e+02 Score=24.42 Aligned_cols=50 Identities=16% Similarity=0.185 Sum_probs=33.5
Q ss_pred ccccCcHHHHHHHHHHHHHHHcCC-------------ChHHHHHHH--HHhhcccccccCCC-Cch
Q 031429 35 IEDSQADIAILLRKLIRDEIQAGK-------------TDKEVYKKL--EDDFGETVLYAPKF-DLQ 84 (159)
Q Consensus 35 iadSna~~A~dmR~~Ir~~l~~G~-------------Sd~eI~~~~--v~RYGd~VL~~Pp~-~~~ 84 (159)
|....+.-..+..+..+..-+.|. |+++|++|| +...++.++|+-|. .|.
T Consensus 74 i~gv~~~~t~~~i~~a~~a~~~Gadav~~~~P~y~~~~~~~i~~~f~~va~~~pi~lYn~P~~tg~ 139 (280)
T PLN02417 74 IGNTGSNSTREAIHATEQGFAVGMHAALHINPYYGKTSQEGLIKHFETVLDMGPTIIYNVPGRTGQ 139 (280)
T ss_pred EEECCCccHHHHHHHHHHHHHcCCCEEEEcCCccCCCCHHHHHHHHHHHHhhCCEEEEEChhHhCc
Confidence 333444444566666776667775 789999999 44566888998873 443
No 192
>COG4736 CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones]
Probab=22.89 E-value=1.9e+02 Score=19.89 Aligned_cols=16 Identities=19% Similarity=0.083 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHhhcc
Q 031429 96 AGAAAGIWAYNRHRQK 111 (159)
Q Consensus 96 ~~~~~~~~~~~rrr~~ 111 (159)
+.++++++.++.+++.
T Consensus 21 ~fiavi~~ayr~~~K~ 36 (60)
T COG4736 21 FFIAVIYFAYRPGKKG 36 (60)
T ss_pred HHHHHHHHHhcccchh
Confidence 3345555666655543
No 193
>PF04478 Mid2: Mid2 like cell wall stress sensor; InterPro: IPR007567 This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway [].
Probab=22.82 E-value=21 Score=28.91 Aligned_cols=10 Identities=30% Similarity=0.421 Sum_probs=4.2
Q ss_pred HHHHHHHHHH
Q 031429 91 SPLLVAGAAA 100 (159)
Q Consensus 91 ~P~l~~~~~~ 100 (159)
+|++++++++
T Consensus 60 g~ill~il~l 69 (154)
T PF04478_consen 60 GPILLGILAL 69 (154)
T ss_pred HHHHHHHHHh
Confidence 3555433333
No 194
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=22.51 E-value=71 Score=23.04 Aligned_cols=17 Identities=24% Similarity=0.528 Sum_probs=14.8
Q ss_pred HcCCChHHHHHHHHHhh
Q 031429 55 QAGKTDKEVYKKLEDDF 71 (159)
Q Consensus 55 ~~G~Sd~eI~~~~v~RY 71 (159)
+.|+|.+||.+-+.+|.
T Consensus 63 A~G~T~eEI~~~v~~rl 79 (80)
T PF03698_consen 63 ASGLTAEEIVQEVEERL 79 (80)
T ss_pred cCCCCHHHHHHHHHHhh
Confidence 68999999999988773
No 195
>PHA03240 envelope glycoprotein M; Provisional
Probab=22.50 E-value=87 Score=27.17 Aligned_cols=34 Identities=12% Similarity=0.146 Sum_probs=18.2
Q ss_pred HhhcccccccCCCCchhHHHHHHHHHHHHHHHHHH
Q 031429 69 DDFGETVLYAPKFDLQTAALWLSPLLVAGAAAGIW 103 (159)
Q Consensus 69 ~RYGd~VL~~Pp~~~~t~lLW~~P~l~~~~~~~~~ 103 (159)
+-|---|-+.+... .+-..|++|++++.++++++
T Consensus 196 ds~agnveaqr~~~-aaH~~WIiilIIiIiIIIL~ 229 (258)
T PHA03240 196 DSFTGNFEAHRSKD-AAHIAWIFIAIIIIIVIILF 229 (258)
T ss_pred cccccceeeecccc-cchHhHHHHHHHHHHHHHHH
Confidence 33433444444332 34568999987664444333
No 196
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=22.47 E-value=2e+02 Score=18.37 Aligned_cols=24 Identities=17% Similarity=0.340 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHhh
Q 031429 42 IAILLRKLIRDEIQAGKTDKEVYKKLEDDF 71 (159)
Q Consensus 42 ~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RY 71 (159)
+-.+||.++..+ ++||++.+++..
T Consensus 12 IL~EvrkEl~K~------K~EIIeA~~~eL 35 (40)
T PF08776_consen 12 ILEEVRKELQKV------KEEIIEAIRQEL 35 (40)
T ss_dssp HHHHHHHHHHHH------HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH------HHHHHHHHHHHH
Confidence 445566666554 788999887643
No 197
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=22.41 E-value=1.9e+02 Score=22.66 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=14.7
Q ss_pred ccccCcHHHHHHHHHHHHHH
Q 031429 35 IEDSQADIAILLRKLIRDEI 54 (159)
Q Consensus 35 iadSna~~A~dmR~~Ir~~l 54 (159)
|+.|+++.-+.++.+||..|
T Consensus 10 lANSDS~~DQ~lKl~VRD~V 29 (130)
T PF09551_consen 10 LANSDSPEDQALKLKVRDAV 29 (130)
T ss_pred EcCCCCHHHHHHHHHHHHHH
Confidence 67888887777777776543
No 198
>PF12979 DUF3863: Domain of Unknown Function with PDB structure (DUF3863); InterPro: IPR024334 This entry represents a functionally uncharacterised domain found in bacterial sequences. The structure of one of the sequences, A6LGL1 from SWISSPROT from Parabacteroides distasonis atcc 8503, has been determined.; PDB: 3LM3_A.
Probab=22.35 E-value=55 Score=29.21 Aligned_cols=27 Identities=19% Similarity=0.541 Sum_probs=15.0
Q ss_pred HHcCCC-hHHHHHHHH---HhhcccccccCC
Q 031429 54 IQAGKT-DKEVYKKLE---DDFGETVLYAPK 80 (159)
Q Consensus 54 l~~G~S-d~eI~~~~v---~RYGd~VL~~Pp 80 (159)
|.+|.. -.||.+|+| +.|||.|.|-|-
T Consensus 68 Led~~~nyr~IR~y~v~c~~k~GDevsyfPG 98 (351)
T PF12979_consen 68 LEDGRPNYRQIRDYVVECQQKYGDEVSYFPG 98 (351)
T ss_dssp HH--SHHHHHHHHHHHHHHHHH--EEEE---
T ss_pred hhcCChhHHHHHHHHHHHHHHhCCceeeccc
Confidence 344433 368999887 589999999996
No 199
>PF14256 YwiC: YwiC-like protein
Probab=22.29 E-value=1.2e+02 Score=23.31 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Q 031429 86 AALWLSPLLVAGAAAGIWAYNRHRQ 110 (159)
Q Consensus 86 ~lLW~~P~l~~~~~~~~~~~~rrr~ 110 (159)
.++|++|+.+..+++-++..+||+.
T Consensus 82 ~ll~~~~~~~pl~~v~~~~~~~~~e 106 (129)
T PF14256_consen 82 RLLWWALLFLPLFAVNLYFAKRKRE 106 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 4566666443333333444444443
No 200
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=22.14 E-value=1.5e+02 Score=19.98 Aligned_cols=25 Identities=12% Similarity=0.206 Sum_probs=19.8
Q ss_pred HHHHHHHHHHcCCChHHHHHHHHHh
Q 031429 46 LRKLIRDEIQAGKTDKEVYKKLEDD 70 (159)
Q Consensus 46 mR~~Ir~~l~~G~Sd~eI~~~~v~R 70 (159)
--..|.+++++|+|-.|-+....+.
T Consensus 16 AvE~Iq~LMaqGmSsgEAI~~VA~~ 40 (51)
T PF03701_consen 16 AVERIQELMAQGMSSGEAIAIVAQE 40 (51)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHHH
Confidence 3468999999999999887766554
No 201
>smart00351 PAX Paired Box domain.
Probab=22.05 E-value=1.1e+02 Score=23.04 Aligned_cols=27 Identities=15% Similarity=0.085 Sum_probs=23.1
Q ss_pred CcHHHHHHHHHHHHHHHcCCChHHHHH
Q 031429 39 QADIAILLRKLIRDEIQAGKTDKEVYK 65 (159)
Q Consensus 39 na~~A~dmR~~Ir~~l~~G~Sd~eI~~ 65 (159)
..+++.|+|..|-.+..+|.|..+|-.
T Consensus 15 ~~~~s~~~R~riv~~~~~G~s~~~iA~ 41 (125)
T smart00351 15 GRPLPDEERQRIVELAQNGVRPCDISR 41 (125)
T ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHH
Confidence 356888999999999999999998843
No 202
>PF02758 PYRIN: PAAD/DAPIN/Pyrin domain; InterPro: IPR004020 Pyrin domain was identified as putative protein-protein interaction domain at the N-terminal region of several proteins thought to function in apoptotic and inflammatory signalling pathways. Using secondary structure prediction and potential-based fold recognition methods, the PYRIN domain is predicted to be a member of the six-helix bundle death domain-fold superfamily that includes death domains (DDs), death effector domains (DEDs), and caspase recruitment domains (CARDs). Members of the death domain-fold superfamily are well established mediators of protein-protein interactions found in many proteins involved in apoptosis and inflammation, indicating further that the PYRIN domains serve a similar function. Comparison of a circular dichroism spectrum of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1 with spectra of several proteins known to adopt the death domain-fold provides experimental support for the structure prediction [] It is found in interferon-inducible proteins, pyrin and myeloid cell nuclear differentiation antigen.; PDB: 2DO9_A 2YU0_A 2KN6_A 1UCP_A 2L6A_A 2KM6_A 1PN5_A 2DBG_A 3QF2_B 2HM2_Q.
Probab=21.81 E-value=47 Score=23.24 Aligned_cols=18 Identities=17% Similarity=0.350 Sum_probs=15.8
Q ss_pred CCChHHHHHHHHHhhccc
Q 031429 57 GKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 57 G~Sd~eI~~~~v~RYGd~ 74 (159)
+.+..++.+.|++.||+.
T Consensus 42 ~ad~~~la~lLv~~y~~~ 59 (83)
T PF02758_consen 42 KADREDLADLLVQHYGEQ 59 (83)
T ss_dssp HSSHHHHHHHHHHHTCHH
T ss_pred hCCHHHHHHHHHHHcCHH
Confidence 477999999999999975
No 203
>PF00482 T2SF: Type II secretion system (T2SS), protein F; InterPro: IPR018076 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) [], have been found to be evolutionary related. These are proteins of about 400 amino acids that are highly hydrophobic and which are thought to be integral protein of the inner membrane. Proteins with this domain form a platform for the type II secretion machinery, as well as the type IV pili and the archaeal flagellae [].; PDB: 2VMA_A 3C1Q_A 2VMB_B 2WHN_B.
Probab=21.72 E-value=68 Score=21.84 Aligned_cols=65 Identities=15% Similarity=0.161 Sum_probs=28.3
Q ss_pred cHHHHHHHHHHHhcccCCCCCCCCccccCcHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhccccc
Q 031429 11 KQMADARARNISRNVRCTDCGSQSIEDSQADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETVL 76 (159)
Q Consensus 11 d~~~e~r~~~l~~~LRCpvCqnqsiadSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL 76 (159)
++.+...++++...++.-.=-.+.+..+++.+ .+.-..+....+.|-+-.++++.+.+.|-+...
T Consensus 28 ~~~l~~~~~~~~~~l~~G~~~~~al~~~~~~~-~~~~~~~~~~~~~g~~~~~~l~~~a~~~~~~~~ 92 (124)
T PF00482_consen 28 SGPLREELQKIRRRLRNGGSLEEALERTGSEF-PDFVASLIQAGESGGDLSEVLEQLADQLRERER 92 (124)
T ss_dssp SHHHHHHHHHHHHHHHTT--HHHHHCTSTTTS--HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHcCCCHHHHHHHhcccC-chHHHHHHHHHhhCCcHHHHHHHHHHHHHHHHH
Confidence 44555555555555544332223333332233 333333333344555555666655555555544
No 204
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=21.39 E-value=2e+02 Score=17.56 Aligned_cols=14 Identities=21% Similarity=0.368 Sum_probs=11.3
Q ss_pred CCChHHHHHHHHHh
Q 031429 57 GKTDKEVYKKLEDD 70 (159)
Q Consensus 57 G~Sd~eI~~~~v~R 70 (159)
|.|..+|..||..|
T Consensus 38 ~l~~~qV~~WF~nr 51 (59)
T cd00086 38 GLTERQVKIWFQNR 51 (59)
T ss_pred CcCHHHHHHHHHHH
Confidence 78888888888765
No 205
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=21.31 E-value=1.9e+02 Score=18.90 Aligned_cols=13 Identities=38% Similarity=0.485 Sum_probs=8.8
Q ss_pred CCCHHHHHHHHhh
Q 031429 126 PLTPKEKETMLDL 138 (159)
Q Consensus 126 ~Ls~eE~~rl~~l 138 (159)
.|+++..++|++|
T Consensus 53 ~L~~er~~~L~~l 65 (68)
T PF03457_consen 53 KLTPERIERLDAL 65 (68)
T ss_dssp ---HHHHHHHHHH
T ss_pred CCCHHHHHHHHcC
Confidence 3999999999875
No 206
>COG1307 DegV Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.30 E-value=1.4e+02 Score=25.70 Aligned_cols=40 Identities=33% Similarity=0.257 Sum_probs=32.4
Q ss_pred HHHHHHHHHHcCCChHHHHHHHHHhhcccccccCCCCchh
Q 031429 46 LRKLIRDEIQAGKTDKEVYKKLEDDFGETVLYAPKFDLQT 85 (159)
Q Consensus 46 mR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t 85 (159)
+-.++.+|+.+|+|.+||++.+.+.....-+|-..-+-.+
T Consensus 127 ~v~~a~~l~~~G~s~~ei~~~l~~~~~~t~~~~~v~~L~~ 166 (282)
T COG1307 127 LVLEAAELAKAGKSFEEILKKLEEIREKTKAYFVVDDLDN 166 (282)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhcEEEEEECchhH
Confidence 4457899999999999999999998888877766655443
No 207
>PF12555 TPPK_C: Thiamine pyrophosphokinase C terminal; InterPro: IPR022215 This domain family is found in bacteria, and is approximately 50 amino acids in length. The proteins in this family catalyses the pyrophosphorylation of thiamine in yeast and synthesizes thiamine pyrophosphate (TPP), a thiamine coenzyme.
Probab=21.21 E-value=1.6e+02 Score=19.31 Aligned_cols=15 Identities=27% Similarity=0.348 Sum_probs=10.8
Q ss_pred cccCCCCchhHHHHH
Q 031429 76 LYAPKFDLQTAALWL 90 (159)
Q Consensus 76 L~~Pp~~~~t~lLW~ 90 (159)
||++..++..+++.+
T Consensus 6 LYrsris~~~~~~lv 20 (53)
T PF12555_consen 6 LYRSRISGWALALLV 20 (53)
T ss_pred HhcCCCchHHHHHHH
Confidence 799999998444443
No 208
>TIGR02220 phg_TIGR02220 phage conserved hypothetical protein, C-terminal domain. This model represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=21.13 E-value=1.5e+02 Score=21.11 Aligned_cols=30 Identities=20% Similarity=0.216 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHcCCChHH---HHHHHHHhhcc
Q 031429 44 ILLRKLIRDEIQAGKTDKE---VYKKLEDDFGE 73 (159)
Q Consensus 44 ~dmR~~Ir~~l~~G~Sd~e---I~~~~v~RYGd 73 (159)
..=+..|+.++.+|.+.++ |+++.+..+++
T Consensus 21 k~~~~lI~aR~~eg~~~~dfk~VId~k~~~W~~ 53 (77)
T TIGR02220 21 AKHKKLIKARWNEGYTLEDFKKVIDNKVSEWLG 53 (77)
T ss_pred HhHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcC
Confidence 4457889999999999865 77888888875
No 209
>TIGR03180 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff.
Probab=20.99 E-value=86 Score=24.90 Aligned_cols=19 Identities=21% Similarity=0.454 Sum_probs=17.5
Q ss_pred cCCChHHHHHHHHHhhccc
Q 031429 56 AGKTDKEVYKKLEDDFGET 74 (159)
Q Consensus 56 ~G~Sd~eI~~~~v~RYGd~ 74 (159)
.|+|.++|++.|..|++|.
T Consensus 116 ~g~s~~~IL~~l~~Rl~n~ 134 (158)
T TIGR03180 116 AGRSAEEMLDALQARLPND 134 (158)
T ss_pred CCCCHHHHHHHHHHHhCCC
Confidence 6999999999999999974
No 210
>PF14829 GPAT_N: Glycerol-3-phosphate acyltransferase N-terminal; PDB: 1IUQ_A 1K30_A.
Probab=20.88 E-value=1.5e+02 Score=21.50 Aligned_cols=36 Identities=25% Similarity=0.239 Sum_probs=29.8
Q ss_pred cHHHHHHHHHHHHHHHcCCChHHHHHHHHHhhcccc
Q 031429 40 ADIAILLRKLIRDEIQAGKTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 40 a~~A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~V 75 (159)
+.--+|+-..|++.+++|+=...|-.-|.+-|.|+-
T Consensus 8 ~~~Eqells~IkkeveaGkLP~~va~gmeelY~NYk 43 (77)
T PF14829_consen 8 ARSEQELLSGIKKEVEAGKLPANVAAGMEELYQNYK 43 (77)
T ss_dssp --SHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHHHcCCCChhHHHHHHHHHHHHH
Confidence 344578999999999999999999999999999873
No 211
>PRK15019 CsdA-binding activator; Provisional
Probab=20.82 E-value=2.1e+02 Score=22.67 Aligned_cols=30 Identities=27% Similarity=0.268 Sum_probs=24.5
Q ss_pred cccCcHHHHHHHHHHHHHHHcCCChHHHHHH
Q 031429 36 EDSQADIAILLRKLIRDEIQAGKTDKEVYKK 66 (159)
Q Consensus 36 adSna~~A~dmR~~Ir~~l~~G~Sd~eI~~~ 66 (159)
+||+|++.+-|-..+.+. -+|+|.+||+++
T Consensus 81 ~dSDA~IvkGl~alL~~~-~~g~tp~eIl~~ 110 (147)
T PRK15019 81 GDSEGRIVRGLLAVLLTA-VEGKTAAELQAQ 110 (147)
T ss_pred eeCccHHHHHHHHHHHHH-HcCCCHHHHHhc
Confidence 359999999988887764 579999999873
No 212
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=20.82 E-value=71 Score=30.93 Aligned_cols=38 Identities=13% Similarity=0.226 Sum_probs=27.7
Q ss_pred cccCCCCCCCCcc---------------ccCcHHHHHHHHHHHHHHHcCCChH
Q 031429 24 NVRCTDCGSQSIE---------------DSQADIAILLRKLIRDEIQAGKTDK 61 (159)
Q Consensus 24 ~LRCpvCqnqsia---------------dSna~~A~dmR~~Ir~~l~~G~Sd~ 61 (159)
.--|++|+|-|-+ ..|--.-..+-+.||+.|.+|.=.+
T Consensus 271 ~C~C~~C~~ytrayL~hL~~~~~~~Ll~~HNl~~~~~~~~~iR~aI~~g~l~e 323 (639)
T PRK13534 271 PCSCPVCSKYTPKELREMPKEERTRLLAEHNLYVIFEEINRIKQAIKEGSLWE 323 (639)
T ss_pred CCCCccccccCHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHcCCHHH
Confidence 3458999986643 3555666778899999999997443
No 213
>PF04117 Mpv17_PMP22: Mpv17 / PMP22 family ; InterPro: IPR007248 The 22 kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information []. Mpv17 is a closely related peroxisomal protein involved in the development of early-onset glomerulosclerosis []. A member of this family found in Saccharomyces cerevisiae (Baker's yeast) is an integral membrane protein of the inner mitochondrial membrane and has been suggested to play a role in mitochondrial function during heat shock [].; GO: 0016021 integral to membrane
Probab=20.80 E-value=87 Score=20.81 Aligned_cols=30 Identities=27% Similarity=0.458 Sum_probs=24.6
Q ss_pred HHcCCChHHHHHHHHHhhcccccccCCCCchhHHHHH
Q 031429 54 IQAGKTDKEVYKKLEDDFGETVLYAPKFDLQTAALWL 90 (159)
Q Consensus 54 l~~G~Sd~eI~~~~v~RYGd~VL~~Pp~~~~t~lLW~ 90 (159)
+.+|+|-++|.+.+.+.|-+... .+|..|.
T Consensus 3 ~l~g~s~~~~~~~l~~~~~~~~~-------~~~~~Wp 32 (68)
T PF04117_consen 3 LLEGKSWEEIKEKLKRDYWPTLK-------ASWKFWP 32 (68)
T ss_pred cccCCCHHHHHHHHHHHHHHHHH-------HHhHhHH
Confidence 45899999999999999988876 4666663
No 214
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=20.76 E-value=1.5e+02 Score=21.09 Aligned_cols=6 Identities=33% Similarity=0.683 Sum_probs=2.5
Q ss_pred HHHHHH
Q 031429 91 SPLLVA 96 (159)
Q Consensus 91 ~P~l~~ 96 (159)
+|++++
T Consensus 7 ~~~vv~ 12 (84)
T TIGR00739 7 LPLVLI 12 (84)
T ss_pred HHHHHH
Confidence 344443
No 215
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=20.73 E-value=1.3e+02 Score=19.55 Aligned_cols=22 Identities=27% Similarity=0.107 Sum_probs=18.3
Q ss_pred HHHHHHHHHHcCCChHHHHHHH
Q 031429 46 LRKLIRDEIQAGKTDKEVYKKL 67 (159)
Q Consensus 46 mR~~Ir~~l~~G~Sd~eI~~~~ 67 (159)
.-..|+.+...|.|-++|..++
T Consensus 46 ~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 46 RILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh
Confidence 3455888999999999999876
No 216
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=20.58 E-value=38 Score=24.84 Aligned_cols=12 Identities=17% Similarity=0.529 Sum_probs=5.6
Q ss_pred CCCCCCCCcccc
Q 031429 27 CTDCGSQSIEDS 38 (159)
Q Consensus 27 CpvCqnqsiadS 38 (159)
|+.|.+++=..|
T Consensus 22 C~~C~~~~C~~C 33 (96)
T PTZ00382 22 CVLCSVGNCKSC 33 (96)
T ss_pred CCcCCCCCCcCC
Confidence 555554333333
No 217
>PF10954 DUF2755: Protein of unknown function (DUF2755); InterPro: IPR020513 This entry contains membrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=20.56 E-value=1.2e+02 Score=22.79 Aligned_cols=6 Identities=50% Similarity=0.883 Sum_probs=4.1
Q ss_pred HHHHHH
Q 031429 90 LSPLLV 95 (159)
Q Consensus 90 ~~P~l~ 95 (159)
+.||++
T Consensus 77 LiPFL~ 82 (100)
T PF10954_consen 77 LIPFLA 82 (100)
T ss_pred HHHHHH
Confidence 568874
No 218
>PF01244 Peptidase_M19: Membrane dipeptidase (Peptidase family M19); InterPro: IPR008257 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 group of peptidases belong to the MEROPS peptidase family M19 (membrane dipeptidase family, clan MJ). The protein fold of the peptidase domain for members of this family resembles that of Klebsiella urease, the type example for clan MJ. Renal dipeptidase (rDP) (3.4.13.19 from EC), also known as microsomal dipeptidase, is a zinc-dependent metalloenzyme that hydrolyzes a wide range of dipeptides. It is involved in renal metabolism of glutathione and its conjugates. It is a homodimeric disulphide-linked glycoprotein attached to the renal brush border microvilli membrane by a GPI-anchor. A glutamate residue has recently been shown [,] to be important for the catalytic activity of rDP. rDP seems to be evolutionary related to hypothetical proteins in the PQQ biosynthesis operons of Acinetobacter calcoaceticus and Klebsiella pneumoniae.; GO: 0008235 metalloexopeptidase activity, 0008239 dipeptidyl-peptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis; PDB: 3NEH_B 2RAG_D 3LU2_A 3B40_A 3LY0_A 3FDG_B 2I5G_B 3S2J_A 3S2N_A 3S2L_A ....
Probab=20.45 E-value=62 Score=28.25 Aligned_cols=30 Identities=20% Similarity=0.288 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHcCCChHHHHHHHHHhhcccc
Q 031429 43 AILLRKLIRDEIQAGKTDKEVYKKLEDDFGETV 75 (159)
Q Consensus 43 A~dmR~~Ir~~l~~G~Sd~eI~~~~v~RYGd~V 75 (159)
+.++-+.+.++++.|.|+++|...| |||+.
T Consensus 286 ~~~~~~l~~~L~~rG~s~~~i~kI~---g~N~l 315 (320)
T PF01244_consen 286 PSDLPNLTEELLKRGYSEEDIEKIL---GGNFL 315 (320)
T ss_dssp GGGHHHHHHHHHHTTS-HHHHHHHH---THHHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHH---hHhHH
Confidence 6788999999999999999999887 56554
No 219
>PF10642 Tom5: Mitochondrial import receptor subunit or translocase; InterPro: IPR019603 This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore []. Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Probab=20.42 E-value=70 Score=21.15 Aligned_cols=11 Identities=45% Similarity=0.836 Sum_probs=8.6
Q ss_pred hHHHHHHHHHH
Q 031429 85 TAALWLSPLLV 95 (159)
Q Consensus 85 t~lLW~~P~l~ 95 (159)
-.+||+.|+++
T Consensus 32 a~~LylsP~~~ 42 (49)
T PF10642_consen 32 AALLYLSPFAI 42 (49)
T ss_pred HHHHHHhHHHH
Confidence 45889999864
No 220
>PF14316 DUF4381: Domain of unknown function (DUF4381)
Probab=20.38 E-value=1.8e+02 Score=22.19 Aligned_cols=13 Identities=15% Similarity=0.141 Sum_probs=7.5
Q ss_pred HHHHHHHHhhcCC
Q 031429 129 PKEKETMLDLLTP 141 (159)
Q Consensus 129 ~eE~~rl~~lL~~ 141 (159)
.+.-..+..|||.
T Consensus 67 ~~~~~~l~~LLKr 79 (146)
T PF14316_consen 67 AEWLAALNELLKR 79 (146)
T ss_pred HHHHHHHHHHHHH
Confidence 3455566666663
No 221
>PRK09174 F0F1 ATP synthase subunit B'; Validated
Probab=20.35 E-value=1.2e+02 Score=24.91 Aligned_cols=14 Identities=43% Similarity=0.807 Sum_probs=9.3
Q ss_pred cCCCCchhH---HHHHH
Q 031429 78 APKFDLQTA---ALWLS 91 (159)
Q Consensus 78 ~Pp~~~~t~---lLW~~ 91 (159)
.|||+..++ ++|++
T Consensus 44 ~p~~~~~~~~~~l~w~~ 60 (204)
T PRK09174 44 FPPFDSTHYASQLLWLA 60 (204)
T ss_pred CCCCcchhccHHHHHHH
Confidence 699988754 45643
No 222
>PHA03029 hypothetical protein; Provisional
Probab=20.29 E-value=1.4e+02 Score=21.93 Aligned_cols=14 Identities=36% Similarity=0.729 Sum_probs=9.4
Q ss_pred hHHHHHHHHHHHHH
Q 031429 85 TAALWLSPLLVAGA 98 (159)
Q Consensus 85 t~lLW~~P~l~~~~ 98 (159)
|.+.|++|+.+.++
T Consensus 57 nf~fwllp~al~a~ 70 (92)
T PHA03029 57 NFLFWLLPFALAAA 70 (92)
T ss_pred HHHHHHHHHHHHHH
Confidence 34569999876543
No 223
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=20.18 E-value=2.1e+02 Score=18.93 Aligned_cols=11 Identities=9% Similarity=0.003 Sum_probs=8.1
Q ss_pred hHHHHHHHHHH
Q 031429 85 TAALWLSPLLV 95 (159)
Q Consensus 85 t~lLW~~P~l~ 95 (159)
||+-|+.-+++
T Consensus 3 ~wlt~iFsvvI 13 (49)
T PF11044_consen 3 TWLTTIFSVVI 13 (49)
T ss_pred hHHHHHHHHHH
Confidence 78888877653
No 224
>PF10515 APP_amyloid: beta-amyloid precursor protein C-terminus; InterPro: IPR019543 This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with IPR008154 from INTERPRO, further towards the N terminus. ; PDB: 2ROZ_A 3DXD_D 1X11_D 2LP1_A 2LOH_A 3MXC_L 3MXY_L 3DXC_B 3DXE_D 3L81_B ....
Probab=20.17 E-value=1.2e+02 Score=20.45 Aligned_cols=10 Identities=40% Similarity=0.574 Sum_probs=4.0
Q ss_pred CCCCCHHHHH
Q 031429 124 GVPLTPKEKE 133 (159)
Q Consensus 124 ~~~Ls~eE~~ 133 (159)
++.+|+||+.
T Consensus 25 D~~~tpEe~h 34 (52)
T PF10515_consen 25 DPCLTPEERH 34 (52)
T ss_dssp -----HHHHH
T ss_pred cCCCChHHHH
Confidence 4568998876
Done!