Query 042635
Match_columns 121
No_of_seqs 122 out of 692
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 08:07:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042635.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042635hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1724 SCF ubiquitin ligase, 100.0 2.9E-38 6.3E-43 230.4 11.7 111 3-113 3-162 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 4.1E-35 9E-40 206.1 11.2 109 5-113 2-157 (158)
3 PF01466 Skp1: Skp1 family, di 99.8 1.1E-19 2.4E-24 118.1 7.7 68 38-113 10-78 (78)
4 PF03931 Skp1_POZ: Skp1 family 99.8 2E-19 4.4E-24 112.0 4.0 51 6-56 2-62 (62)
5 smart00512 Skp1 Found in Skp1 99.7 2.4E-16 5.2E-21 106.8 7.3 56 5-60 2-70 (104)
6 KOG3473 RNA polymerase II tran 98.8 4.4E-09 9.5E-14 71.1 3.8 53 4-56 16-82 (112)
7 PF00651 BTB: BTB/POZ domain; 94.0 0.27 5.9E-06 31.9 6.2 52 5-56 11-76 (111)
8 KOG3433 Protein involved in me 93.4 0.096 2.1E-06 39.3 3.3 31 63-98 170-200 (203)
9 COG5124 Protein predicted to b 93.0 0.098 2.1E-06 39.2 2.8 28 66-98 177-204 (209)
10 PHA02713 hypothetical protein; 92.7 0.59 1.3E-05 40.0 7.7 81 6-89 27-133 (557)
11 smart00225 BTB Broad-Complex, 87.4 0.81 1.7E-05 27.7 3.1 45 11-55 5-62 (90)
12 PF03962 Mnd1: Mnd1 family; I 78.9 2.7 5.9E-05 31.3 3.4 31 63-98 157-187 (188)
13 PHA03098 kelch-like protein; P 75.5 10 0.00022 31.7 6.3 76 7-83 12-109 (534)
14 PHA02790 Kelch-like protein; P 63.1 20 0.00043 30.0 5.4 46 8-53 24-83 (480)
15 cd00167 SANT 'SWI3, ADA2, N-Co 62.6 8.2 0.00018 20.4 2.2 20 73-92 23-42 (45)
16 PF08671 SinI: Anti-repressor 62.2 9.9 0.00021 20.2 2.3 13 80-92 15-27 (30)
17 PF00249 Myb_DNA-binding: Myb- 61.8 10 0.00022 21.5 2.5 20 72-91 24-44 (48)
18 PF12674 Zn_ribbon_2: Putative 61.4 22 0.00047 23.0 4.3 43 49-92 27-71 (81)
19 smart00717 SANT SANT SWI3, AD 60.6 9.5 0.00021 20.5 2.2 20 73-92 25-44 (49)
20 PF12556 CobS_N: Cobaltochelat 58.5 5.9 0.00013 22.0 1.0 12 87-98 14-25 (36)
21 KOG4441 Proteins containing BT 57.3 27 0.00059 30.2 5.4 69 11-79 42-134 (571)
22 PF13798 PCYCGC: Protein of un 54.4 19 0.00041 26.4 3.4 25 66-90 116-140 (158)
23 PF03656 Pam16: Pam16; InterP 52.3 9.3 0.0002 26.9 1.5 35 77-113 50-84 (127)
24 TIGR01999 iscU FeS cluster ass 50.9 19 0.0004 24.8 2.8 27 66-92 62-88 (124)
25 PRK11325 scaffold protein; Pro 50.2 19 0.00041 24.9 2.8 27 66-92 64-90 (127)
26 PRK06402 rpl12p 50S ribosomal 50.0 57 0.0012 22.3 5.0 49 45-93 2-59 (106)
27 TIGR03419 NifU_clost FeS clust 49.9 21 0.00046 24.4 3.0 27 66-92 58-84 (121)
28 PF01592 NifU_N: NifU-like N t 47.6 27 0.00058 24.0 3.2 24 66-89 62-85 (126)
29 PRK10219 DNA-binding transcrip 47.1 27 0.00058 22.8 3.1 20 41-60 4-23 (107)
30 PF13518 HTH_28: Helix-turn-he 45.9 34 0.00074 19.0 3.0 22 73-94 4-25 (52)
31 TIGR03147 cyt_nit_nrfF cytochr 44.9 23 0.00049 25.0 2.5 20 72-91 63-83 (126)
32 PRK13379 protocatechuate 4,5-d 44.4 37 0.0008 23.8 3.5 23 72-94 94-116 (119)
33 PTZ00373 60S Acidic ribosomal 44.3 78 0.0017 21.8 5.1 46 44-89 3-58 (112)
34 cd05833 Ribosomal_P2 Ribosomal 42.5 70 0.0015 21.8 4.6 47 44-90 1-57 (109)
35 PRK11511 DNA-binding transcrip 41.6 54 0.0012 22.3 4.0 23 38-60 5-27 (127)
36 PF03918 CcmH: Cytochrome C bi 41.0 25 0.00054 25.3 2.3 18 74-91 65-83 (148)
37 PF13384 HTH_23: Homeodomain-l 40.4 32 0.0007 19.1 2.3 17 78-94 14-30 (50)
38 COG4565 CitB Response regulato 40.1 53 0.0011 25.4 4.0 24 32-56 147-171 (224)
39 PF11338 DUF3140: Protein of u 39.7 28 0.00061 23.3 2.2 24 34-57 52-75 (92)
40 PRK13503 transcriptional activ 38.6 61 0.0013 24.3 4.3 22 39-60 168-189 (278)
41 cd06664 IscU_like Iron-sulfur 38.5 54 0.0012 22.0 3.6 27 66-92 59-85 (123)
42 PF13921 Myb_DNA-bind_6: Myb-l 37.7 30 0.00066 20.1 2.0 31 73-103 21-58 (60)
43 COG0822 IscU NifU homolog invo 37.6 54 0.0012 23.5 3.6 26 66-91 65-90 (150)
44 PF14098 SSPI: Small, acid-sol 37.0 38 0.00082 21.2 2.4 19 73-91 5-23 (65)
45 PRK10240 undecaprenyl pyrophos 36.8 50 0.0011 25.4 3.5 38 41-78 23-72 (229)
46 PLN00138 large subunit ribosom 36.7 97 0.0021 21.3 4.6 46 44-89 1-56 (113)
47 cd07921 PCA_45_Doxase_A_like S 36.6 55 0.0012 22.4 3.3 21 72-92 82-102 (106)
48 cd07925 LigA_like_1 The A subu 36.4 52 0.0011 22.6 3.1 21 72-92 82-102 (106)
49 PF05321 HHA: Haemolysin expre 36.4 1E+02 0.0022 18.8 4.2 42 40-85 8-49 (57)
50 TIGR03685 L21P_arch 50S riboso 35.8 1.1E+02 0.0024 20.7 4.8 49 44-92 1-58 (105)
51 PF08667 BetR: BetR domain; I 35.5 77 0.0017 22.9 4.1 57 39-95 2-65 (147)
52 PRK10144 formate-dependent nit 35.4 39 0.00085 23.8 2.5 19 73-91 64-83 (126)
53 KOG3442 Uncharacterized conser 35.4 35 0.00076 24.2 2.2 25 78-102 52-76 (132)
54 TIGR01994 SUF_scaf_2 SUF syste 34.9 50 0.0011 23.1 3.0 27 66-92 62-88 (137)
55 COG4957 Predicted transcriptio 34.5 36 0.00077 24.6 2.2 18 81-98 98-115 (148)
56 PRK09296 cysteine desufuration 34.1 74 0.0016 22.6 3.8 34 67-100 77-118 (138)
57 PRK09393 ftrA transcriptional 34.0 83 0.0018 24.5 4.5 25 36-60 212-236 (322)
58 TIGR02792 PCA_ligA protocatech 33.6 57 0.0012 22.8 3.1 20 72-91 87-106 (117)
59 PF05443 ROS_MUCR: ROS/MUCR tr 33.1 20 0.00044 25.4 0.8 18 81-98 94-111 (132)
60 cd04411 Ribosomal_P1_P2_L12p R 33.1 1.2E+02 0.0026 20.5 4.6 46 45-90 2-56 (105)
61 PF11399 DUF3192: Protein of u 32.9 43 0.00093 22.8 2.3 36 63-99 16-51 (102)
62 PF13725 tRNA_bind_2: Possible 32.9 1.3E+02 0.0029 19.3 4.7 57 38-94 28-96 (101)
63 PF05920 Homeobox_KN: Homeobox 32.9 75 0.0016 17.6 3.0 33 50-91 1-34 (40)
64 COG2996 Predicted RNA-bindinin 31.7 28 0.0006 27.9 1.4 13 83-95 248-260 (287)
65 PRK15019 CsdA-binding activato 31.6 78 0.0017 22.7 3.6 35 66-100 86-128 (147)
66 PRK14842 undecaprenyl pyrophos 31.5 64 0.0014 25.1 3.4 39 41-79 38-88 (241)
67 PRK13378 protocatechuate 4,5-d 31.5 62 0.0013 22.6 2.9 20 72-91 93-112 (117)
68 PRK13377 protocatechuate 4,5-d 31.3 64 0.0014 22.9 3.0 20 72-91 93-112 (129)
69 cd00068 GGL G protein gamma su 31.3 50 0.0011 19.7 2.2 16 41-56 23-38 (57)
70 PF15063 TC1: Thyroid cancer p 31.1 48 0.001 21.5 2.2 31 73-103 28-58 (79)
71 PF00196 GerE: Bacterial regul 31.1 70 0.0015 18.5 2.8 23 72-94 9-31 (58)
72 TIGR03391 FeS_syn_CsdE cystein 30.4 86 0.0019 22.2 3.7 34 67-100 82-123 (138)
73 cd05832 Ribosomal_L12p Ribosom 30.0 1.6E+02 0.0035 20.1 4.8 50 44-93 1-59 (106)
74 PF09382 RQC: RQC domain; Int 30.0 40 0.00086 21.9 1.8 34 70-103 20-60 (106)
75 PRK14981 DNA-directed RNA poly 29.8 1.2E+02 0.0026 20.6 4.2 64 42-105 32-104 (112)
76 PF01476 LysM: LysM domain; I 29.6 45 0.00098 17.8 1.7 23 71-94 8-31 (44)
77 PRK14833 undecaprenyl pyrophos 29.6 74 0.0016 24.5 3.4 38 41-78 34-83 (233)
78 smart00421 HTH_LUXR helix_turn 29.6 81 0.0018 17.1 2.9 17 78-94 15-31 (58)
79 PF09384 UTP15_C: UTP15 C term 29.5 98 0.0021 21.9 3.9 25 36-60 68-92 (148)
80 COG4680 Uncharacterized protei 29.5 37 0.00079 22.9 1.5 47 40-97 5-51 (98)
81 cd07924 PCA_45_Doxase_A The A 29.5 77 0.0017 22.3 3.1 20 72-91 90-109 (121)
82 PF05871 ESCRT-II: ESCRT-II co 29.4 37 0.00081 24.2 1.6 13 45-57 27-39 (139)
83 PF11103 DUF2887: Protein of u 29.3 74 0.0016 24.1 3.3 26 66-91 175-200 (200)
84 cd00475 CIS_IPPS Cis (Z)-Isopr 29.3 80 0.0017 24.1 3.5 39 41-79 30-80 (221)
85 PF03883 DUF328: Protein of un 29.2 52 0.0011 25.2 2.5 35 66-100 25-59 (237)
86 COG1710 Uncharacterized protei 28.8 39 0.00085 23.9 1.6 20 75-94 102-122 (139)
87 COG2066 GlsA Glutaminase [Amin 28.6 51 0.0011 26.7 2.4 23 64-86 112-134 (309)
88 PF03750 DUF310: Protein of un 28.2 76 0.0017 21.7 3.0 31 65-96 11-43 (119)
89 PF08006 DUF1700: Protein of u 27.6 2.2E+02 0.0049 20.4 5.6 33 62-94 20-53 (181)
90 PRK14839 undecaprenyl pyrophos 27.5 87 0.0019 24.4 3.5 38 41-78 39-88 (239)
91 PF02796 HTH_7: Helix-turn-hel 27.5 86 0.0019 17.4 2.7 16 79-94 19-34 (45)
92 TIGR00055 uppS undecaprenyl di 27.5 85 0.0018 24.1 3.4 37 41-77 29-77 (226)
93 TIGR02603 CxxCH_TIGR02603 puta 27.4 2.1E+02 0.0045 19.6 5.8 49 4-52 79-131 (133)
94 PF13010 pRN1_helical: Primase 27.4 32 0.00069 24.4 1.0 14 77-90 24-37 (135)
95 PF02657 SufE: Fe-S metabolism 27.3 1.2E+02 0.0026 20.9 3.9 31 66-100 71-108 (125)
96 PRK15121 right oriC-binding tr 27.1 1.1E+02 0.0023 23.6 4.0 20 41-60 4-23 (289)
97 COG4049 Uncharacterized protei 26.9 55 0.0012 20.1 1.8 16 4-19 4-19 (65)
98 KOG1602 Cis-prenyltransferase 26.9 52 0.0011 26.1 2.1 58 40-97 65-135 (271)
99 PF13315 DUF4085: Protein of u 26.4 2.6E+02 0.0057 21.3 5.8 53 30-92 68-123 (208)
100 PRK14840 undecaprenyl pyrophos 26.3 88 0.0019 24.5 3.4 38 41-78 52-101 (250)
101 TIGR02000 NifU_proper Fe-S clu 26.0 76 0.0016 25.2 3.0 26 66-91 63-88 (290)
102 TIGR01044 rplV_bact ribosomal 26.0 77 0.0017 21.2 2.6 22 72-93 13-34 (103)
103 PF01255 Prenyltransf: Putativ 25.7 90 0.0019 23.6 3.3 40 41-80 24-75 (223)
104 cd04479 RPA3 RPA3: A subfamily 25.4 1.4E+02 0.0029 19.7 3.7 52 5-56 30-99 (101)
105 PF11543 UN_NPL4: Nuclear pore 25.3 46 0.001 21.2 1.4 20 1-20 1-21 (80)
106 PF15628 RRM_DME: RRM in Demet 25.2 61 0.0013 22.1 2.0 20 73-92 57-76 (103)
107 PRK11566 hdeB acid-resistance 25.2 34 0.00075 23.3 0.8 25 32-56 62-86 (102)
108 KOG4244 Failed axon connection 25.1 74 0.0016 25.4 2.7 22 84-105 111-133 (281)
109 KOG3449 60S acidic ribosomal p 25.0 2.1E+02 0.0047 19.7 4.7 44 46-89 3-56 (112)
110 PF07928 Vps54: Vps54-like pro 25.0 24 0.00052 24.9 0.0 44 13-56 1-48 (135)
111 PLN03212 Transcription repress 24.8 1E+02 0.0022 24.3 3.4 38 74-111 50-101 (249)
112 PRK10945 gene expression modul 24.8 1.6E+02 0.0035 18.8 3.7 42 40-85 20-61 (72)
113 PRK14830 undecaprenyl pyrophos 24.8 1E+02 0.0022 24.0 3.4 39 41-79 52-102 (251)
114 PF08281 Sigma70_r4_2: Sigma-7 24.6 52 0.0011 18.6 1.4 17 78-94 23-39 (54)
115 PF06289 FlbD: Flagellar prote 24.5 1.1E+02 0.0024 18.7 2.9 47 6-52 1-56 (60)
116 PF15120 DUF4561: Domain of un 24.3 1.9E+02 0.0041 21.5 4.6 18 42-59 44-61 (171)
117 PF01726 LexA_DNA_bind: LexA D 24.0 1.3E+02 0.0029 18.3 3.3 29 66-94 10-38 (65)
118 PRK14829 undecaprenyl pyrophos 23.8 1.1E+02 0.0024 23.7 3.5 37 41-77 44-92 (243)
119 PF04355 SmpA_OmlA: SmpA / Oml 23.4 41 0.0009 20.4 0.9 22 74-95 8-29 (71)
120 COG2058 RPP1A Ribosomal protei 23.2 2.6E+02 0.0056 19.3 4.8 49 45-93 2-59 (109)
121 PRK14837 undecaprenyl pyrophos 23.0 1.2E+02 0.0025 23.5 3.4 38 41-78 36-85 (230)
122 PF11460 DUF3007: Protein of u 23.0 76 0.0016 21.7 2.1 23 82-107 78-101 (104)
123 PF02697 DUF217: Uncharacteriz 23.0 1.4E+02 0.003 18.8 3.2 31 80-110 34-66 (71)
124 PRK13372 pcmA protocatechuate 22.7 70 0.0015 27.2 2.3 20 72-91 93-112 (444)
125 smart00224 GGL G protein gamma 22.7 81 0.0018 19.2 2.1 17 41-57 23-39 (63)
126 KOG0183 20S proteasome, regula 22.4 87 0.0019 24.4 2.6 20 4-23 5-24 (249)
127 PRK03094 hypothetical protein; 22.3 57 0.0012 21.2 1.4 12 80-91 64-75 (80)
128 PF05397 Med15_fungi: Mediator 22.0 90 0.0019 21.4 2.4 16 92-107 24-40 (115)
129 cd06170 LuxR_C_like C-terminal 21.8 1.4E+02 0.003 16.2 2.9 17 78-94 12-28 (57)
130 PF08299 Bac_DnaA_C: Bacterial 21.8 1.2E+02 0.0026 18.6 2.7 24 71-94 35-58 (70)
131 PRK13500 transcriptional activ 21.5 1.2E+02 0.0027 23.6 3.4 19 41-59 205-223 (312)
132 KOG2716 Polymerase delta-inter 21.4 3.9E+02 0.0085 20.7 7.6 79 2-82 2-108 (230)
133 PRK14841 undecaprenyl pyrophos 21.3 1.3E+02 0.0029 23.2 3.5 37 41-77 33-81 (233)
134 TIGR02297 HpaA 4-hydroxyphenyl 21.1 1.3E+02 0.0028 22.6 3.4 16 43-58 187-202 (287)
135 PF05225 HTH_psq: helix-turn-h 21.0 1.3E+02 0.0028 16.9 2.6 21 74-94 8-29 (45)
136 PF09883 DUF2110: Uncharacteri 20.9 74 0.0016 24.6 1.9 17 82-98 112-128 (225)
137 PF11116 DUF2624: Protein of u 20.3 2.6E+02 0.0057 18.3 4.2 32 43-83 16-47 (85)
138 PRK14832 undecaprenyl pyrophos 20.2 1.4E+02 0.0031 23.4 3.4 37 41-77 48-96 (253)
139 PRK13367 protocatechuate 4,5-d 20.1 1E+02 0.0023 26.0 2.8 23 72-94 387-409 (420)
140 PRK14834 undecaprenyl pyrophos 20.0 1.4E+02 0.0031 23.2 3.4 37 41-77 44-92 (249)
141 PF02631 RecX: RecX family; I 20.0 2.3E+02 0.0049 18.8 4.1 19 38-56 5-23 (121)
142 TIGR01038 L22_arch ribosomal p 20.0 1.1E+02 0.0024 22.1 2.6 21 72-92 26-46 (150)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.9e-38 Score=230.41 Aligned_cols=111 Identities=43% Similarity=0.677 Sum_probs=98.9
Q ss_pred CCCcEEEEeCCCCeEEecHHHHhhcC-cC---------CC--cccCCCCChhHHHHHHHHHHhhhcCCCCC---------
Q 042635 3 HSKKISLKRADGQLFEVEEPVAMDFE-IE---------DT--VVPLPNVSTEPLSYIIEFCKAHVEFSKQR--------- 61 (121)
Q Consensus 3 s~~~i~L~SsDG~~f~V~~~~a~~S~-ie---------d~--~Ipl~~V~s~~L~kVie~c~~h~~~~~~~--------- 61 (121)
+.++|+|+||||++|+|+.++|++|. |. ++ +||||+|+|.||++||+||+||+.+++..
T Consensus 3 ~~~~ikL~SsDG~~f~ve~~~a~~s~~i~~~~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~ 82 (162)
T KOG1724|consen 3 SKKKIKLESSDGEIFEVEEEVARQSQTISAHMIEDGCADENDPIPLPNVTSKILKKVIEWCKKHKDDDPANPEDKELPEE 82 (162)
T ss_pred CCCeEEEEccCCceeehhHHHHHHhHHHHHHHHHcCCCccCCccccCccCHHHHHHHHHHHHHccccccccccccccccc
Confidence 35689999999999999999999999 21 14 89999999999999999999999875421
Q ss_pred ---chh------------------------hhHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCCHHHHH-HHhhcccccC
Q 042635 62 ---SPK------------------------QEMLDYWTETLANRIKNKSVQYVGKFFGIENNFTPKEEV-ARTQYEWAFE 113 (121)
Q Consensus 62 ---~~~------------------------~~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t~eEe~-ir~e~~w~~~ 113 (121)
.+| ++||++||++||+|++||||+|||.+|||++|||++|++ +|++|.|+|+
T Consensus 83 ~~i~~WD~~Flk~d~~tLfdli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~~e~~~~~~ 162 (162)
T KOG1724|consen 83 TDIPEWDAEFLKVDQGTLFDLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIRKENEWAFE 162 (162)
T ss_pred CCccHHHHHHHhcCHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHhhccccccC
Confidence 123 399999999999999999999999999999999999988 9999999985
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.1e-35 Score=206.07 Aligned_cols=109 Identities=32% Similarity=0.494 Sum_probs=97.4
Q ss_pred CcEEEEeCCCCeEEecHHHHhhcC-----cCC-----CcccCCCCChhHHHHHHHHHHhhhcCCCCC------------c
Q 042635 5 KKISLKRADGQLFEVEEPVAMDFE-----IED-----TVVPLPNVSTEPLSYIIEFCKAHVEFSKQR------------S 62 (121)
Q Consensus 5 ~~i~L~SsDG~~f~V~~~~a~~S~-----ied-----~~Ipl~~V~s~~L~kVie~c~~h~~~~~~~------------~ 62 (121)
.+|.|.|.||++|.|+..+|..|- +.+ -+||+|+|.|.+|.+|++||+||+....+. +
T Consensus 2 s~i~l~s~dge~F~vd~~iAerSiLikN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D 81 (158)
T COG5201 2 SMIELESIDGEIFRVDENIAERSILIKNMLCDSTACNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSD 81 (158)
T ss_pred CceEEEecCCcEEEehHHHHHHHHHHHHHhccccccCCCCcccchhHHHHHHHHHHHHhccccCCCccChHhhhccCCcc
Confidence 379999999999999999999998 333 588999999999999999999999854322 1
Q ss_pred ------------------------hhhhHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCCHHHHH-HHhhcccccC
Q 042635 63 ------------------------PKQEMLDYWTETLANRIKNKSVQYVGKFFGIENNFTPKEEV-ARTQYEWAFE 113 (121)
Q Consensus 63 ------------------------~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t~eEe~-ir~e~~w~~~ 113 (121)
++++||++||+.||+||+||||+|||++|||++||||||++ ||+||.|+.+
T Consensus 82 ~wdr~Fm~vDqemL~eI~laaNYL~ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnEWaed 157 (158)
T COG5201 82 FWDRFFMEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWAED 157 (158)
T ss_pred HHHHHHHHhhHHHHHHHHHhhccccchHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhcccccc
Confidence 12499999999999999999999999999999999999999 9999999875
No 3
>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=99.81 E-value=1.1e-19 Score=118.06 Aligned_cols=68 Identities=38% Similarity=0.611 Sum_probs=52.4
Q ss_pred CCChhHHHHHHHHHHhhhcCCCCCchhhhHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCCHHHHH-HHhhcccccC
Q 042635 38 NVSTEPLSYIIEFCKAHVEFSKQRSPKQEMLDYWTETLANRIKNKSVQYVGKFFGIENNFTPKEEV-ARTQYEWAFE 113 (121)
Q Consensus 38 ~V~s~~L~kVie~c~~h~~~~~~~~~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t~eEe~-ir~e~~w~~~ 113 (121)
+++...|-.++.=+.|- ++++|+++||++||++|+||||+|||++|||++|+|+||++ +|++|+|+|+
T Consensus 10 ~~~~~~L~~l~~AA~yL--------~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~~ 78 (78)
T PF01466_consen 10 DVDNDELFDLLNAANYL--------DIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAFE 78 (78)
T ss_dssp -S-HHHHHHHHHHHHHH--------T-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB-
T ss_pred HcCHHHHHHHHHHHHHH--------cchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhcC
Confidence 45555666666555553 46799999999999999999999999999999999999999 9999999985
No 4
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 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 POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=99.77 E-value=2e-19 Score=112.05 Aligned_cols=51 Identities=41% Similarity=0.677 Sum_probs=45.4
Q ss_pred cEEEEeCCCCeEEecHHHHhhcC-----cCC-----CcccCCCCChhHHHHHHHHHHhhhc
Q 042635 6 KISLKRADGQLFEVEEPVAMDFE-----IED-----TVVPLPNVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 6 ~i~L~SsDG~~f~V~~~~a~~S~-----ied-----~~Ipl~~V~s~~L~kVie~c~~h~~ 56 (121)
+|+|+|+||++|.|++++|++|+ +++ .+||||+|++.+|+||++||+||++
T Consensus 2 ~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~~H~~ 62 (62)
T PF03931_consen 2 YVKLVSSDGQEFEVSREAAKQSKTIKNMLEDLGDEDEPIPLPNVSSRILKKVIEWCEHHKN 62 (62)
T ss_dssp EEEEEETTSEEEEEEHHHHTTSHHHHHHHHCTCCCGTEEEETTS-HHHHHHHHHHHHHHHH
T ss_pred EEEEEcCCCCEEEeeHHHHHHhHHHHHHHhhhcccccccccCccCHHHHHHHHHHHHhcCC
Confidence 69999999999999999999999 333 4699999999999999999999974
No 5
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.66 E-value=2.4e-16 Score=106.80 Aligned_cols=56 Identities=46% Similarity=0.745 Sum_probs=50.1
Q ss_pred CcEEEEeCCCCeEEecHHHHhhcC-----cCC--------CcccCCCCChhHHHHHHHHHHhhhcCCCC
Q 042635 5 KKISLKRADGQLFEVEEPVAMDFE-----IED--------TVVPLPNVSTEPLSYIIEFCKAHVEFSKQ 60 (121)
Q Consensus 5 ~~i~L~SsDG~~f~V~~~~a~~S~-----ied--------~~Ipl~~V~s~~L~kVie~c~~h~~~~~~ 60 (121)
.+|+|+|+||++|.|++++|++|+ |++ .+||||+|++.+|++|++||+||+.++.+
T Consensus 2 ~~v~L~S~Dg~~f~v~~~~a~~S~~i~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~~h~~~~~~ 70 (104)
T smart00512 2 KYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVDDPPS 70 (104)
T ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHHHcccCCCC
Confidence 479999999999999999999999 332 38999999999999999999999987654
No 6
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=98.81 E-value=4.4e-09 Score=71.14 Aligned_cols=53 Identities=19% Similarity=0.248 Sum_probs=46.6
Q ss_pred CCcEEEEeCCCCeEEecHHHHhhcC-----cCC---------CcccCCCCChhHHHHHHHHHHhhhc
Q 042635 4 SKKISLKRADGQLFEVEEPVAMDFE-----IED---------TVVPLPNVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 4 ~~~i~L~SsDG~~f~V~~~~a~~S~-----ied---------~~Ipl~~V~s~~L~kVie~c~~h~~ 56 (121)
+..|+|+|+||++|.+.+++|+.|+ |.+ +.+-++++++.+|+||++|+.|...
T Consensus 16 ~~yVkLvS~Ddhefiikre~AmtSgTiraml~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~r 82 (112)
T KOG3473|consen 16 SMYVKLVSSDDHEFIIKREHAMTSGTIRAMLSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVR 82 (112)
T ss_pred hhheEeecCCCcEEEEeehhhhhhhHHHHHHcCCccccccccceEEeccchHHHHHHHHHHhhheee
Confidence 5689999999999999999999999 332 6788999999999999999987544
No 7
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=94.05 E-value=0.27 Score=31.94 Aligned_cols=52 Identities=21% Similarity=0.390 Sum_probs=39.2
Q ss_pred CcEEEEeCCCCeEEecHHHHh-hcC-----cCC--------CcccCCCCChhHHHHHHHHHHhhhc
Q 042635 5 KKISLKRADGQLFEVEEPVAM-DFE-----IED--------TVVPLPNVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 5 ~~i~L~SsDG~~f~V~~~~a~-~S~-----ied--------~~Ipl~~V~s~~L~kVie~c~~h~~ 56 (121)
..++|+..||+.|.|.+.+.. +|+ +.. ..|++++++...+..+++||+....
T Consensus 11 ~D~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~~~ 76 (111)
T PF00651_consen 11 SDVTIRVGDGKTFYVHKNILAARSPYFRNLFEGSKFKESTVPEISLPDVSPEAFEAFLEYMYTGEI 76 (111)
T ss_dssp --EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTTTSTTSSEEEEEETTSCHHHHHHHHHHHHHSEE
T ss_pred CCEEEEECCCEEEeechhhhhccchhhhhcccccccccccccccccccccccccccccccccCCcc
Confidence 458889999999999999986 455 221 2578899999999999999965433
No 8
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.39 E-value=0.096 Score=39.35 Aligned_cols=31 Identities=23% Similarity=0.367 Sum_probs=26.4
Q ss_pred hhhhHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCC
Q 042635 63 PKQEMLDYWTETLANRIKNKSVQYVGKFFGIENNFT 98 (121)
Q Consensus 63 ~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t 98 (121)
++--|.+++|+.. |.-+.+||+.|||+.||.
T Consensus 170 nI~il~dy~~rkf-----~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 170 NIFILIDYLYRKF-----GLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred hHHHHHHHHHHhc-----CCCHHHHhHhcCCCcccc
Confidence 4457888888875 999999999999999984
No 9
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=92.97 E-value=0.098 Score=39.20 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=24.3
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCC
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFGIENNFT 98 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t 98 (121)
-|.++-|+.. |.-|+|||+.|||+.||.
T Consensus 177 ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 177 ILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred HHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 7778778775 899999999999999874
No 10
>PHA02713 hypothetical protein; Provisional
Probab=92.73 E-value=0.59 Score=39.99 Aligned_cols=81 Identities=9% Similarity=0.146 Sum_probs=58.7
Q ss_pred cEEEEeCCCCeEEecHHHHh-hcC---------cCC----CcccCCCCChhHHHHHHHHHHhhhcCCCCCc---------
Q 042635 6 KISLKRADGQLFEVEEPVAM-DFE---------IED----TVVPLPNVSTEPLSYIIEFCKAHVEFSKQRS--------- 62 (121)
Q Consensus 6 ~i~L~SsDG~~f~V~~~~a~-~S~---------ied----~~Ipl~~V~s~~L~kVie~c~~h~~~~~~~~--------- 62 (121)
-|+|...+|+.|.+-+.+.. .|. +.. ..|.|.+|+..+|+.|++|++... ...+
T Consensus 27 DV~L~v~~~~~f~~Hr~vLaa~S~YF~amF~~~~~e~~~~~~v~l~~v~~~~~~~ll~y~Yt~~---i~~~nv~~ll~aA 103 (557)
T PHA02713 27 DVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMIIRDLVTRVNLQMFDKDAVKNIVQYLYNRH---ISSMNVIDVLKCA 103 (557)
T ss_pred CEEEEeCCCCEEeehHHHHhhcCHHHHHHhcCCchhhccCceEEeccCCHHHHHHHHHHhcCCC---CCHHHHHHHHHHH
Confidence 47888877999999999887 444 221 458899999999999999998864 2221
Q ss_pred ---hhhhHHHHHHHHHHHHHhCCCHHHHHh
Q 042635 63 ---PKQEMLDYWTETLANRIKNKSVQYVGK 89 (121)
Q Consensus 63 ---~~~~Ll~~~c~~vA~~ikgkt~eeiR~ 89 (121)
-+..|.++||..+...+.-.+--+|+.
T Consensus 104 ~~lqi~~l~~~C~~~l~~~l~~~NCl~i~~ 133 (557)
T PHA02713 104 DYLLIDDLVTDCESYIKDYTNHDTCIYMYH 133 (557)
T ss_pred HHHCHHHHHHHHHHHHHhhCCccchHHHHH
Confidence 234778888888777666655555554
No 11
>smart00225 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
Probab=87.36 E-value=0.81 Score=27.68 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=36.1
Q ss_pred eCCCCeEEecHHHHhhcC------cCC-------CcccCCCCChhHHHHHHHHHHhhh
Q 042635 11 RADGQLFEVEEPVAMDFE------IED-------TVVPLPNVSTEPLSYIIEFCKAHV 55 (121)
Q Consensus 11 SsDG~~f~V~~~~a~~S~------ied-------~~Ipl~~V~s~~L~kVie~c~~h~ 55 (121)
..+|+.|.|.+.++..+. +.. ..|++++++...++.+++||+...
T Consensus 5 ~v~~~~~~~h~~iL~~~s~~f~~~~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly~~~ 62 (90)
T smart00225 5 VVGGKKFKAHKAVLAACSPYFKALFSGDFKESKKSEIYLDDVSPEDFRALLEFLYTGK 62 (90)
T ss_pred EECCEEEehHHHHHhhcCHHHHHHHcCCCccCCCCEEEecCCCHHHHHHHHHeecCce
Confidence 557899999999887654 221 567899999999999999998754
No 12
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=78.90 E-value=2.7 Score=31.29 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=23.7
Q ss_pred hhhhHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCC
Q 042635 63 PKQEMLDYWTETLANRIKNKSVQYVGKFFGIENNFT 98 (121)
Q Consensus 63 ~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t 98 (121)
++-.|..++++. .|.+.++||+.|||+.||.
T Consensus 157 NI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 157 NIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred hHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 334666666554 3999999999999999984
No 13
>PHA03098 kelch-like protein; Provisional
Probab=75.46 E-value=10 Score=31.73 Aligned_cols=76 Identities=9% Similarity=0.122 Sum_probs=50.0
Q ss_pred EEEE-eCCCCeEEecHHHHhh-cC-----cCC----CcccCCCCChhHHHHHHHHHHhhhcCCCCC--c---------hh
Q 042635 7 ISLK-RADGQLFEVEEPVAMD-FE-----IED----TVVPLPNVSTEPLSYIIEFCKAHVEFSKQR--S---------PK 64 (121)
Q Consensus 7 i~L~-SsDG~~f~V~~~~a~~-S~-----ied----~~Ipl~~V~s~~L~kVie~c~~h~~~~~~~--~---------~~ 64 (121)
|+|. +.+|+.|.+.+.++.. |. +.. ..|.|+. +..+|+.|++|++...-.-... . .+
T Consensus 12 v~l~~~~~~~~~~~Hk~vLaa~S~yF~~mf~~~~~~~~i~l~~-~~~~~~~~l~y~Ytg~~~i~~~~~~~ll~~A~~l~~ 90 (534)
T PHA03098 12 ESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLNI-DYDSFNEVIKYIYTGKINITSNNVKDILSIANYLII 90 (534)
T ss_pred EEEEEEcCCEEEEeHHHHHHhhhHHHHHHHhCCCCCceEEecC-CHHHHHHHHHHhcCCceEEcHHHHHHHHHHHHHhCc
Confidence 4555 5789999999999764 55 222 6688888 9999999999998754321111 0 12
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q 042635 65 QEMLDYWTETLANRIKNKS 83 (121)
Q Consensus 65 ~~Ll~~~c~~vA~~ikgkt 83 (121)
..|.++|++.+...+.-.+
T Consensus 91 ~~l~~~C~~~l~~~l~~~n 109 (534)
T PHA03098 91 DFLINLCINYIIKIIDDNN 109 (534)
T ss_pred HHHHHHHHHHHHHhCCHhH
Confidence 3666666666655554333
No 14
>PHA02790 Kelch-like protein; Provisional
Probab=63.06 E-value=20 Score=30.04 Aligned_cols=46 Identities=13% Similarity=0.098 Sum_probs=31.9
Q ss_pred EEEeCCCCeEEecHHHHh-hcC---------cCC--CcccC--CCCChhHHHHHHHHHHh
Q 042635 8 SLKRADGQLFEVEEPVAM-DFE---------IED--TVVPL--PNVSTEPLSYIIEFCKA 53 (121)
Q Consensus 8 ~L~SsDG~~f~V~~~~a~-~S~---------ied--~~Ipl--~~V~s~~L~kVie~c~~ 53 (121)
.+.---|+.|.+-+.+.. .|. +.+ ..|.+ .+|+..+|+.|++|++-
T Consensus 24 ~~~~~~~~~~~~HR~VLAa~S~YFraMF~~~~~Es~~~v~~~~~~v~~~~l~~lldy~YT 83 (480)
T PHA02790 24 TIIEAIGGNIIVNSTILKKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSYT 83 (480)
T ss_pred eEEEEcCcEEeeehhhhhhcCHHHHHHhcCCccccccceEEEecCcCHHHHHHHHHhhee
Confidence 344456889999999854 454 211 33433 38999999999999854
No 15
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=62.57 E-value=8.2 Score=20.43 Aligned_cols=20 Identities=10% Similarity=0.243 Sum_probs=16.5
Q ss_pred HHHHHHHhCCCHHHHHhhcC
Q 042635 73 ETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 73 ~~vA~~ikgkt~eeiR~~f~ 92 (121)
..||..+.++|+.+++..|.
T Consensus 23 ~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 23 EKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHhHcCCCCHHHHHHHHH
Confidence 46788888899999998764
No 16
>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=62.23 E-value=9.9 Score=20.20 Aligned_cols=13 Identities=15% Similarity=0.243 Sum_probs=9.3
Q ss_pred hCCCHHHHHhhcC
Q 042635 80 KNKSVQYVGKFFG 92 (121)
Q Consensus 80 kgkt~eeiR~~f~ 92 (121)
.|-|.+|||+++.
T Consensus 15 ~Gls~eeir~FL~ 27 (30)
T PF08671_consen 15 SGLSKEEIREFLE 27 (30)
T ss_dssp TT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHH
Confidence 4999999999874
No 17
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=61.84 E-value=10 Score=21.45 Aligned_cols=20 Identities=10% Similarity=0.267 Sum_probs=16.8
Q ss_pred HHHHHHHHh-CCCHHHHHhhc
Q 042635 72 TETLANRIK-NKSVQYVGKFF 91 (121)
Q Consensus 72 c~~vA~~ik-gkt~eeiR~~f 91 (121)
=..||..+. |+|+.++|..|
T Consensus 24 W~~Ia~~~~~~Rt~~qc~~~~ 44 (48)
T PF00249_consen 24 WKKIAKRMPGGRTAKQCRSRY 44 (48)
T ss_dssp HHHHHHHHSSSSTHHHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHH
Confidence 347888888 99999999876
No 18
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=61.38 E-value=22 Score=23.02 Aligned_cols=43 Identities=9% Similarity=0.208 Sum_probs=31.6
Q ss_pred HHHHhhhcCCCCCc--hhhhHHHHHHHHHHHHHhCCCHHHHHhhcC
Q 042635 49 EFCKAHVEFSKQRS--PKQEMLDYWTETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 49 e~c~~h~~~~~~~~--~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f~ 92 (121)
+||.|-..+...+. .++.+++.+.+.++..- +.+++++|+++.
T Consensus 27 ~YC~yCy~~G~Ft~~~t~eemie~~~~~~~~~~-~~~~~~a~~~~~ 71 (81)
T PF12674_consen 27 DYCSYCYQNGEFTQDITMEEMIEFCVPFMDEFN-GMTPEEARKMMP 71 (81)
T ss_pred hHHHHHhcCCceeecCCHHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence 67777666554443 56789998888887763 389999998863
No 19
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=60.60 E-value=9.5 Score=20.47 Aligned_cols=20 Identities=10% Similarity=0.302 Sum_probs=16.5
Q ss_pred HHHHHHHhCCCHHHHHhhcC
Q 042635 73 ETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 73 ~~vA~~ikgkt~eeiR~~f~ 92 (121)
..||..+.++|+.+++..|.
T Consensus 25 ~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 25 EKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHcCCCCHHHHHHHHH
Confidence 46788888999999998764
No 20
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=58.48 E-value=5.9 Score=22.01 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=10.4
Q ss_pred HHhhcCCCCCCC
Q 042635 87 VGKFFGIENNFT 98 (121)
Q Consensus 87 iR~~f~I~~d~t 98 (121)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 689999999875
No 21
>KOG4441 consensus Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms; General function prediction only]
Probab=57.27 E-value=27 Score=30.19 Aligned_cols=69 Identities=14% Similarity=0.217 Sum_probs=45.6
Q ss_pred eCCCCeEEecHHHHhhcC----------cCC---CcccCCCCChhHHHHHHHHHHhhhcCCCCC--c---------hhhh
Q 042635 11 RADGQLFEVEEPVAMDFE----------IED---TVVPLPNVSTEPLSYIIEFCKAHVEFSKQR--S---------PKQE 66 (121)
Q Consensus 11 SsDG~~f~V~~~~a~~S~----------ied---~~Ipl~~V~s~~L~kVie~c~~h~~~~~~~--~---------~~~~ 66 (121)
.-+|+.|..-+-+...+. +.. ..|.|..|++.+|..+++|++...-.-... . .+..
T Consensus 42 ~v~~~~~~aHR~VLAa~S~YFraMFt~~l~e~~~~~i~l~~v~~~~l~~ll~y~Yt~~i~i~~~nVq~ll~aA~~lQi~~ 121 (571)
T KOG4441|consen 42 LVGDREFPAHRVVLAACSPYFRAMFTSGLKESKQKEINLEGVDPETLELLLDYAYTGKLEISEDNVQELLEAASLLQIPE 121 (571)
T ss_pred EECCeeechHHHHHHhccHHHHHHhcCCcccccceEEEEecCCHHHHHHHHHHhhcceEEechHhHHHHHHHHHHhhhHH
Confidence 344588888887775443 222 788899999999999999998765432211 1 1346
Q ss_pred HHHHHHHHHHHHH
Q 042635 67 MLDYWTETLANRI 79 (121)
Q Consensus 67 Ll~~~c~~vA~~i 79 (121)
+.+.||..+...+
T Consensus 122 v~~~C~~fL~~~l 134 (571)
T KOG4441|consen 122 VVDACCEFLESQL 134 (571)
T ss_pred HHHHHHHHHHhcC
Confidence 6677766655443
No 22
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=54.36 E-value=19 Score=26.43 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhh
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKF 90 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~ 90 (121)
-=|+.+-..+...=+|||+.|||++
T Consensus 116 vCl~ia~~a~~~~~~Gks~~eIR~~ 140 (158)
T PF13798_consen 116 VCLDIAVQAVQMYQEGKSPKEIRQY 140 (158)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 4455566666666679999999986
No 23
>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.
Probab=52.33 E-value=9.3 Score=26.92 Aligned_cols=35 Identities=11% Similarity=0.364 Sum_probs=16.6
Q ss_pred HHHhCCCHHHHHhhcCCCCCCCHHHHHHHhhcccccC
Q 042635 77 NRIKNKSVQYVGKFFGIENNFTPKEEVARTQYEWAFE 113 (121)
Q Consensus 77 ~~ikgkt~eeiR~~f~I~~d~t~eEe~ir~e~~w~~~ 113 (121)
...+|.|.+|-|+++|+++..+.|+ |.+.+.-.|+
T Consensus 50 ~~~~~Mtl~EA~~ILnv~~~~~~ee--I~k~y~~Lf~ 84 (127)
T PF03656_consen 50 SNSKGMTLDEARQILNVKEELSREE--IQKRYKHLFK 84 (127)
T ss_dssp -------HHHHHHHHT--G--SHHH--HHHHHHHHHH
T ss_pred hhcCCCCHHHHHHHcCCCCccCHHH--HHHHHHHHHh
Confidence 3456999999999999998777644 4454444443
No 24
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=50.88 E-value=19 Score=24.81 Aligned_cols=27 Identities=19% Similarity=-0.039 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcC
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~ 92 (121)
..--.++..++.+++|||.+|.+.+-+
T Consensus 62 ~~s~Asas~~~e~i~Gktl~ea~~i~~ 88 (124)
T TIGR01999 62 GSAIASSSLATELIKGKSLEEALKIKN 88 (124)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHhccH
Confidence 444555567799999999999987644
No 25
>PRK11325 scaffold protein; Provisional
Probab=50.16 E-value=19 Score=24.94 Aligned_cols=27 Identities=7% Similarity=-0.069 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcC
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~ 92 (121)
..--.++..++.+++|||.+|.+.+-+
T Consensus 64 ~is~Asas~~~e~~~Gktl~ea~~i~~ 90 (127)
T PRK11325 64 GSAIASSSLVTEWVKGKTLDEALAIKN 90 (127)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHhcCH
Confidence 444455557799999999999987744
No 26
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=49.96 E-value=57 Score=22.29 Aligned_cols=49 Identities=12% Similarity=0.083 Sum_probs=33.9
Q ss_pred HHHHHHHHhhhcCCCCC-chhhhHHHHH--------HHHHHHHHhCCCHHHHHhhcCC
Q 042635 45 SYIIEFCKAHVEFSKQR-SPKQEMLDYW--------TETLANRIKNKSVQYVGKFFGI 93 (121)
Q Consensus 45 ~kVie~c~~h~~~~~~~-~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~~f~I 93 (121)
+.|..|+--|.....++ ++++.+|+.+ -+.++..++|+++++++.-.+.
T Consensus 2 ~yiyAaLLL~~~g~~it~e~I~~IL~AAGveVee~~~k~~v~aL~GkdIeElI~~a~~ 59 (106)
T PRK06402 2 EYIYAALLLHSAGKEINEDNLKKVLEAAGVEVDEARVKALVAALEDVNIEEAIKKAAA 59 (106)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 45566666665554333 6777776553 5667888899999999977665
No 27
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=49.91 E-value=21 Score=24.44 Aligned_cols=27 Identities=11% Similarity=-0.018 Sum_probs=20.4
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcC
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~ 92 (121)
.+--.++..++.+++|||.+|..++..
T Consensus 58 ~is~Asas~~~e~i~Gk~l~ea~~i~~ 84 (121)
T TIGR03419 58 GAAIASSSMATEMIKGKTLEEAWELTN 84 (121)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHhhh
Confidence 455555667799999999999887643
No 28
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=47.56 E-value=27 Score=23.97 Aligned_cols=24 Identities=17% Similarity=0.076 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHh
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGK 89 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~ 89 (121)
.+.-.++..++.+++|||.+|+.+
T Consensus 62 ~~~~Asas~~~~~i~gk~l~ea~~ 85 (126)
T PF01592_consen 62 AISIASASMMCELIKGKTLEEALK 85 (126)
T ss_dssp HHHHHHHHHHHHHHTTSBHHHHHC
T ss_pred hHHHHHHHHHHHHHcCCCHHHHHH
Confidence 677777778899999999999864
No 29
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=47.12 E-value=27 Score=22.76 Aligned_cols=20 Identities=10% Similarity=0.297 Sum_probs=15.1
Q ss_pred hhHHHHHHHHHHhhhcCCCC
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ 60 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~ 60 (121)
..++.+|+.|+..|...+..
T Consensus 4 ~~~~~~~~~~i~~~~~~~~~ 23 (107)
T PRK10219 4 QKIIQTLIAWIDEHIDQPLN 23 (107)
T ss_pred HHHHHHHHHHHHHhcCCCCC
Confidence 46788999999988765543
No 30
>PF13518 HTH_28: Helix-turn-helix domain
Probab=45.92 E-value=34 Score=18.97 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCHHHHHhhcCCC
Q 042635 73 ETLANRIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 73 ~~vA~~ikgkt~eeiR~~f~I~ 94 (121)
+.|.....|.|..++.+.|||.
T Consensus 4 ~iv~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 4 QIVELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHHHcCCCHHHHHHHHCCC
Confidence 3455566799999999999995
No 31
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=44.94 E-value=23 Score=25.01 Aligned_cols=20 Identities=20% Similarity=0.253 Sum_probs=15.0
Q ss_pred HHHHHHHHh-CCCHHHHHhhc
Q 042635 72 TETLANRIK-NKSVQYVGKFF 91 (121)
Q Consensus 72 c~~vA~~ik-gkt~eeiR~~f 91 (121)
-+.|..++. |+|-+||+.+|
T Consensus 63 R~~Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 63 RHEVYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHH
Confidence 345666555 89999999885
No 32
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=44.42 E-value=37 Score=23.77 Aligned_cols=23 Identities=0% Similarity=-0.051 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCCHHHHHhhcCCC
Q 042635 72 TETLANRIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f~I~ 94 (121)
-+.|+..++|.|.||.+++=|++
T Consensus 94 ~q~i~a~mtG~t~eeF~~tr~~~ 116 (119)
T PRK13379 94 NLQVYAIMRGETFEEFMQTRRVP 116 (119)
T ss_pred HHHHHHHhcCCcHHHHHHHccCC
Confidence 56788888999999999987776
No 33
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=44.28 E-value=78 Score=21.81 Aligned_cols=46 Identities=7% Similarity=0.127 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhhcCC-CCC-chhhhHHHHH--------HHHHHHHHhCCCHHHHHh
Q 042635 44 LSYIIEFCKAHVEFS-KQR-SPKQEMLDYW--------TETLANRIKNKSVQYVGK 89 (121)
Q Consensus 44 L~kVie~c~~h~~~~-~~~-~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~ 89 (121)
|+.|-.|+--+.... .++ ++++.+|+.+ -..++..++||+.+|+-.
T Consensus 3 MkyvaAYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa 58 (112)
T PTZ00373 3 MKYVAAYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIA 58 (112)
T ss_pred hHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHH
Confidence 677778877665533 233 6777777553 556778888999888865
No 34
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=42.53 E-value=70 Score=21.83 Aligned_cols=47 Identities=11% Similarity=0.157 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhhcCC-CCC-chhhhHHHHH--------HHHHHHHHhCCCHHHHHhh
Q 042635 44 LSYIIEFCKAHVEFS-KQR-SPKQEMLDYW--------TETLANRIKNKSVQYVGKF 90 (121)
Q Consensus 44 L~kVie~c~~h~~~~-~~~-~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~~ 90 (121)
|+.|-.|+--+.... .++ ++++.+|+.+ -..+++.++||+.+++-.-
T Consensus 1 MkyvaAylL~~l~g~~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~ 57 (109)
T cd05833 1 MKYVAAYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAA 57 (109)
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHH
Confidence 356677776665533 333 7777777654 4567788899999988653
No 35
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=41.59 E-value=54 Score=22.31 Aligned_cols=23 Identities=13% Similarity=0.265 Sum_probs=17.1
Q ss_pred CCChhHHHHHHHHHHhhhcCCCC
Q 042635 38 NVSTEPLSYIIEFCKAHVEFSKQ 60 (121)
Q Consensus 38 ~V~s~~L~kVie~c~~h~~~~~~ 60 (121)
+-+...+.+|++|...|...+..
T Consensus 5 ~~~~~~i~~~~~~I~~~~~~~~s 27 (127)
T PRK11511 5 NTDAITIHSILDWIEDNLESPLS 27 (127)
T ss_pred cccHHHHHHHHHHHHHhcCCCCC
Confidence 34566788999999998776543
No 36
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=41.03 E-value=25 Score=25.26 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=11.0
Q ss_pred HHHHHH-hCCCHHHHHhhc
Q 042635 74 TLANRI-KNKSVQYVGKFF 91 (121)
Q Consensus 74 ~vA~~i-kgkt~eeiR~~f 91 (121)
.|..++ .|+|.+||+++|
T Consensus 65 ~I~~~l~~G~s~~eI~~~~ 83 (148)
T PF03918_consen 65 EIREMLAEGKSDEEIIDYF 83 (148)
T ss_dssp HHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 344443 499999999884
No 37
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=40.37 E-value=32 Score=19.12 Aligned_cols=17 Identities=18% Similarity=0.259 Sum_probs=11.8
Q ss_pred HHhCCCHHHHHhhcCCC
Q 042635 78 RIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 78 ~ikgkt~eeiR~~f~I~ 94 (121)
...|+|..+|-+.||++
T Consensus 14 ~~~G~s~~~ia~~lgvs 30 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVS 30 (50)
T ss_dssp HHHT--HHHHHHHHTS-
T ss_pred HHCCCCHHHHHHHHCcC
Confidence 33499999999999987
No 38
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=40.06 E-value=53 Score=25.43 Aligned_cols=24 Identities=21% Similarity=0.187 Sum_probs=19.1
Q ss_pred CcccCC-CCChhHHHHHHHHHHhhhc
Q 042635 32 TVVPLP-NVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 32 ~~Ipl~-~V~s~~L~kVie~c~~h~~ 56 (121)
.+.+|| .++..||++|.+|.+ +..
T Consensus 147 ~~~~LPkGi~~~Tl~~i~~~~~-~~~ 171 (224)
T COG4565 147 PPDDLPKGLDELTLQKVREALK-EPD 171 (224)
T ss_pred CcccCCCCcCHHHHHHHHHHHh-CcC
Confidence 456677 799999999999988 443
No 39
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=39.68 E-value=28 Score=23.26 Aligned_cols=24 Identities=17% Similarity=0.315 Sum_probs=19.4
Q ss_pred ccCCCCChhHHHHHHHHHHhhhcC
Q 042635 34 VPLPNVSTEPLSYIIEFCKAHVEF 57 (121)
Q Consensus 34 Ipl~~V~s~~L~kVie~c~~h~~~ 57 (121)
--|..=+-..|++|+.||..|...
T Consensus 52 ~dltddD~~hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 52 TDLTDDDYEHMRKVVGYVKRHLAQ 75 (92)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHhc
Confidence 335556668899999999999887
No 40
>PRK13503 transcriptional activator RhaS; Provisional
Probab=38.63 E-value=61 Score=24.31 Aligned_cols=22 Identities=14% Similarity=0.188 Sum_probs=15.5
Q ss_pred CChhHHHHHHHHHHhhhcCCCC
Q 042635 39 VSTEPLSYIIEFCKAHVEFSKQ 60 (121)
Q Consensus 39 V~s~~L~kVie~c~~h~~~~~~ 60 (121)
.....++++++|.+.|...+..
T Consensus 168 ~~~~~i~~~~~~I~~~~~~~~t 189 (278)
T PRK13503 168 NSDARLNQLLAWLEDHFAEEVN 189 (278)
T ss_pred ccHHHHHHHHHHHHHhhcCCCC
Confidence 3456688888888888765543
No 41
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=38.47 E-value=54 Score=22.05 Aligned_cols=27 Identities=19% Similarity=0.119 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcC
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~ 92 (121)
.+.-.++..++.+++|||.+|+..+.+
T Consensus 59 ~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 59 AISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 555666667899999999999998753
No 42
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=37.75 E-value=30 Score=20.11 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCHHHHHhhcCC------C-CCCCHHHHH
Q 042635 73 ETLANRIKNKSVQYVGKFFGI------E-NNFTPKEEV 103 (121)
Q Consensus 73 ~~vA~~ikgkt~eeiR~~f~I------~-~d~t~eEe~ 103 (121)
..||..+..+|+.+++..|.- . ..+|++|++
T Consensus 21 ~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~ 58 (60)
T PF13921_consen 21 KKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQ 58 (60)
T ss_dssp HHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHH
T ss_pred HHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHh
Confidence 468888844999999988642 1 246777664
No 43
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=37.64 E-value=54 Score=23.52 Aligned_cols=26 Identities=12% Similarity=0.046 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhc
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f 91 (121)
++.-.....++.+++|||.+|+.++-
T Consensus 65 ~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 65 AISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 56666677789999999999998875
No 44
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=37.03 E-value=38 Score=21.24 Aligned_cols=19 Identities=11% Similarity=0.214 Sum_probs=15.7
Q ss_pred HHHHHHHhCCCHHHHHhhc
Q 042635 73 ETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 73 ~~vA~~ikgkt~eeiR~~f 91 (121)
++|-..++|+|.+|++.+-
T Consensus 5 ~AI~~nv~g~s~~el~~~I 23 (65)
T PF14098_consen 5 QAIIHNVKGSSKEELKDTI 23 (65)
T ss_pred HHHHHHccCCCHHHHHHHH
Confidence 4667778999999999874
No 45
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.83 E-value=50 Score=25.42 Aligned_cols=38 Identities=5% Similarity=0.114 Sum_probs=26.0
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANR 78 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~ 78 (121)
...|..|++||..+.-.... . .+++.||++.+.++...
T Consensus 23 ~~~l~~i~~~c~~~GI~~lT~yaFS~eN~~R~~~Ev~~Lm~l~~~~l~~~ 72 (229)
T PRK10240 23 AKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSE 72 (229)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEeeehhhcCcCHHHHHHHHHHHHHHHHHH
Confidence 46789999999977432211 1 35679999988876543
No 46
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=36.74 E-value=97 Score=21.32 Aligned_cols=46 Identities=13% Similarity=0.139 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhhcCC--CCCchhhhHHHHH--------HHHHHHHHhCCCHHHHHh
Q 042635 44 LSYIIEFCKAHVEFS--KQRSPKQEMLDYW--------TETLANRIKNKSVQYVGK 89 (121)
Q Consensus 44 L~kVie~c~~h~~~~--~~~~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~ 89 (121)
|+.|-.|+--..... +..++|+.+|+.+ -..++..++||+.+++-.
T Consensus 1 mkyvaAyll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~L~gK~i~eLIa 56 (113)
T PLN00138 1 MKVVAAYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEVKGKDITELIA 56 (113)
T ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHHH
Confidence 456677776554432 3337787777654 456788889999999984
No 47
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=36.61 E-value=55 Score=22.44 Aligned_cols=21 Identities=0% Similarity=0.072 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCHHHHHhhcC
Q 042635 72 TETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f~ 92 (121)
-+.|...++|.|.||.+++..
T Consensus 82 ~~~~~a~mtG~t~eef~~~~~ 102 (106)
T cd07921 82 MQDIGAQMTGMTEEEFRAMMV 102 (106)
T ss_pred HHHHHHHhcCCCHHHHHHHHH
Confidence 567888889999999888754
No 48
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=36.45 E-value=52 Score=22.59 Aligned_cols=21 Identities=5% Similarity=0.001 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCHHHHHhhcC
Q 042635 72 TETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f~ 92 (121)
-+.|...++|.|.||.+++..
T Consensus 82 ~q~i~a~mtG~t~eef~~~~~ 102 (106)
T cd07925 82 MQDIGGLQTGMSTEEFKAMLV 102 (106)
T ss_pred HHHHHHHhcCCCHHHHHHHHH
Confidence 567888889999999888754
No 49
>PF05321 HHA: Haemolysin expression modulating protein; InterPro: IPR007985 This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of the Hha/YmoA/RmoA family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer []. Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature []. YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. RmoA is a plasmid R100 modulator involved in plasmid transfer []. The HHA family of proteins display striking similarity to the oligomerization domain of the H-NS proteins.; PDB: 1JW2_A 2K5S_A 2JQT_A.
Probab=36.44 E-value=1e+02 Score=18.81 Aligned_cols=42 Identities=14% Similarity=0.036 Sum_probs=28.0
Q ss_pred ChhHHHHHHHHHHhhhcCCCCCchhhhHHHHHHHHHHHHHhCCCHH
Q 042635 40 STEPLSYIIEFCKAHVEFSKQRSPKQEMLDYWTETLANRIKNKSVQ 85 (121)
Q Consensus 40 ~s~~L~kVie~c~~h~~~~~~~~~~~~Ll~~~c~~vA~~ikgkt~e 85 (121)
+.++|+||++...+...+ +++..+..++=...|.++.||-..
T Consensus 8 s~dtLEkv~e~~~~~L~~----~e~~~f~~AaDHR~AEL~~~klyD 49 (57)
T PF05321_consen 8 SLDTLEKVIEHNRYKLTD----DELEAFNSAADHRRAELTMGKLYD 49 (57)
T ss_dssp -HHHHHHHHHHHHHHS-H----HHHHHHHHHHHHHHHHHHTTS--S
T ss_pred CHhhHHHHHHHhhCcCCH----HHHHHHHHHHHHHHHHHHHhhhhh
Confidence 357999999988775322 455566666666788888887644
No 50
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=35.84 E-value=1.1e+02 Score=20.65 Aligned_cols=49 Identities=12% Similarity=0.085 Sum_probs=32.6
Q ss_pred HHHHHHHHHhhhcCCCCC-chhhhHHHHH--------HHHHHHHHhCCCHHHHHhhcC
Q 042635 44 LSYIIEFCKAHVEFSKQR-SPKQEMLDYW--------TETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 44 L~kVie~c~~h~~~~~~~-~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~~f~ 92 (121)
|+.|..|+--|.....++ ++++.||..+ -..++..++||+++++-.-..
T Consensus 1 M~yvyA~Lll~~~g~~iT~e~I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~~~~ 58 (105)
T TIGR03685 1 MEYIYAALLLHSAGKEINEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKKAA 58 (105)
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhhh
Confidence 345666666666554433 6777777654 356788999999888775443
No 51
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=35.54 E-value=77 Score=22.89 Aligned_cols=57 Identities=14% Similarity=0.172 Sum_probs=38.8
Q ss_pred CChhHHHHHHHHHHhhhcCCCCC-chhhhHHHHHHHHHHHHHhCCC---HHHHHhh---cCCCC
Q 042635 39 VSTEPLSYIIEFCKAHVEFSKQR-SPKQEMLDYWTETLANRIKNKS---VQYVGKF---FGIEN 95 (121)
Q Consensus 39 V~s~~L~kVie~c~~h~~~~~~~-~~~~~Ll~~~c~~vA~~ikgkt---~eeiR~~---f~I~~ 95 (121)
.+..+..+|-+=|..+.-..... ..+-.+|++.-..+-.+++|++ .+||++. ||++-
T Consensus 2 ~~~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~ 65 (147)
T PF08667_consen 2 DDQAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSP 65 (147)
T ss_pred hhHHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCH
Confidence 34567778888777765433221 4566888888888889999985 5666544 77663
No 52
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=35.39 E-value=39 Score=23.81 Aligned_cols=19 Identities=11% Similarity=0.078 Sum_probs=14.3
Q ss_pred HHHHHHHh-CCCHHHHHhhc
Q 042635 73 ETLANRIK-NKSVQYVGKFF 91 (121)
Q Consensus 73 ~~vA~~ik-gkt~eeiR~~f 91 (121)
..|..++. |+|.+||+.+|
T Consensus 64 ~~Vr~~i~~G~sd~eI~~~~ 83 (126)
T PRK10144 64 HQVYSMVAEGKSEVEIIGWM 83 (126)
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 45555555 89999999885
No 53
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.38 E-value=35 Score=24.19 Aligned_cols=25 Identities=8% Similarity=0.134 Sum_probs=19.6
Q ss_pred HHhCCCHHHHHhhcCCCCCCCHHHH
Q 042635 78 RIKNKSVQYVGKFFGIENNFTPKEE 102 (121)
Q Consensus 78 ~ikgkt~eeiR~~f~I~~d~t~eEe 102 (121)
...|.|.+|-++++||.++++.+|-
T Consensus 52 ~~~~iTlqEa~qILnV~~~ln~eei 76 (132)
T KOG3442|consen 52 SNGKITLQEAQQILNVKEPLNREEI 76 (132)
T ss_pred ccccccHHHHhhHhCCCCCCCHHHH
Confidence 3346799999999999988776543
No 54
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=34.89 E-value=50 Score=23.07 Aligned_cols=27 Identities=15% Similarity=0.127 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcC
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~ 92 (121)
.+--.++..++.+++|||.+|+..+.+
T Consensus 62 ais~Asas~~~e~i~Gk~~~ea~~l~~ 88 (137)
T TIGR01994 62 SISQASASMMTELIKGKTVEEALSLVE 88 (137)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 444455567799999999999987753
No 55
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=34.49 E-value=36 Score=24.56 Aligned_cols=18 Identities=6% Similarity=0.176 Sum_probs=17.0
Q ss_pred CCCHHHHHhhcCCCCCCC
Q 042635 81 NKSVQYVGKFFGIENNFT 98 (121)
Q Consensus 81 gkt~eeiR~~f~I~~d~t 98 (121)
|.||+|-|.-+|++.|+.
T Consensus 98 gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 98 GLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred CCCHHHHHHhcCCCCCCC
Confidence 899999999999999985
No 56
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=34.05 E-value=74 Score=22.55 Aligned_cols=34 Identities=12% Similarity=0.204 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhh--------cCCCCCCCHH
Q 042635 67 MLDYWTETLANRIKNKSVQYVGKF--------FGIENNFTPK 100 (121)
Q Consensus 67 Ll~~~c~~vA~~ikgkt~eeiR~~--------f~I~~d~t~e 100 (121)
+..--+..+...+.|+||+||.++ +|+..-+||-
T Consensus 77 ivkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 118 (138)
T PRK09296 77 IVKGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTPS 118 (138)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCcc
Confidence 333335556667799999998853 5677667664
No 57
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=34.02 E-value=83 Score=24.55 Aligned_cols=25 Identities=16% Similarity=0.375 Sum_probs=18.6
Q ss_pred CCCCChhHHHHHHHHHHhhhcCCCC
Q 042635 36 LPNVSTEPLSYIIEFCKAHVEFSKQ 60 (121)
Q Consensus 36 l~~V~s~~L~kVie~c~~h~~~~~~ 60 (121)
++......+.++++|...|...+..
T Consensus 212 ~~~~~~~~~~~~~~~i~~~~~~~~s 236 (322)
T PRK09393 212 VASRESDRLGPLIDWMRAHLAEPHT 236 (322)
T ss_pred ccccchHHHHHHHHHHHhccCCCCC
Confidence 4445567899999999998776544
No 58
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=33.63 E-value=57 Score=22.75 Aligned_cols=20 Identities=5% Similarity=0.130 Sum_probs=15.1
Q ss_pred HHHHHHHHhCCCHHHHHhhc
Q 042635 72 TETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f 91 (121)
-+.|+..++|.|.||.+++.
T Consensus 87 ~q~i~a~mtG~t~eef~~mm 106 (117)
T TIGR02792 87 FQQMAGSMTGMTEEEYRQMM 106 (117)
T ss_pred HHHHHHHhcCCCHHHHHHHH
Confidence 56677778888888887763
No 59
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=33.12 E-value=20 Score=25.39 Aligned_cols=18 Identities=6% Similarity=0.222 Sum_probs=12.6
Q ss_pred CCCHHHHHhhcCCCCCCC
Q 042635 81 NKSVQYVGKFFGIENNFT 98 (121)
Q Consensus 81 gkt~eeiR~~f~I~~d~t 98 (121)
|.||+|=|+.||++.|+.
T Consensus 94 gltp~eYR~kwGlp~dyp 111 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDYP 111 (132)
T ss_dssp -S-HHHHHHHTT-GGG--
T ss_pred CCCHHHHHHHhCcCCCCc
Confidence 999999999999998863
No 60
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=33.10 E-value=1.2e+02 Score=20.49 Aligned_cols=46 Identities=13% Similarity=0.139 Sum_probs=27.0
Q ss_pred HHHHHHHHhhhcCCCCC-chhhhHHHHH--------HHHHHHHHhCCCHHHHHhh
Q 042635 45 SYIIEFCKAHVEFSKQR-SPKQEMLDYW--------TETLANRIKNKSVQYVGKF 90 (121)
Q Consensus 45 ~kVie~c~~h~~~~~~~-~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~~ 90 (121)
+.|..|+--|-....++ ++|+.+|+.+ -..++..+.||+++++-.-
T Consensus 2 ~~v~A~Lll~~~g~~~ta~~I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~ 56 (105)
T cd04411 2 EYVAAYLLLHKGGKELTEDKIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISK 56 (105)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHH
Confidence 44555665555543333 5666555442 4456677788888877654
No 61
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=32.94 E-value=43 Score=22.80 Aligned_cols=36 Identities=17% Similarity=0.183 Sum_probs=26.8
Q ss_pred hhhhHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCCH
Q 042635 63 PKQEMLDYWTETLANRIKNKSVQYVGKFFGIENNFTP 99 (121)
Q Consensus 63 ~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t~ 99 (121)
+|+.==..--+.||.+--|.|.++++..+|-+ |||+
T Consensus 16 ~W~drq~~Nr~~i~~L~lg~s~~~V~~~lG~p-dfsE 51 (102)
T PF11399_consen 16 DWEDRQAYNRQNIAKLSLGMSKDQVIALLGTP-DFSE 51 (102)
T ss_pred CHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCC-Cchh
Confidence 34433333466788887899999999999988 8874
No 62
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=32.91 E-value=1.3e+02 Score=19.26 Aligned_cols=57 Identities=14% Similarity=0.199 Sum_probs=29.8
Q ss_pred CCChhHHHHHHHHHHhhhcCCCCCchhhhHHHHH------------HHHHHHHHhCCCHHHHHhhcCCC
Q 042635 38 NVSTEPLSYIIEFCKAHVEFSKQRSPKQEMLDYW------------TETLANRIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 38 ~V~s~~L~kVie~c~~h~~~~~~~~~~~~Ll~~~------------c~~vA~~ikgkt~eeiR~~f~I~ 94 (121)
.++..-++++-.||..+.......+-+..|+-.. .--|+.-+.+||.+++-+.||++
T Consensus 28 ~ls~~d~~rL~~ya~g~~~y~~v~~~l~~l~~~~~~~~~~Ls~~q~~lLi~k~LQ~ksw~~~a~~l~l~ 96 (101)
T PF13725_consen 28 SLSPIDLQRLERYARGGRDYESVAPALWRLAFQYFLSPVSLSELQQALLIAKGLQGKSWEEVAKELGLP 96 (101)
T ss_dssp ---HHHHHHHHHHHHS---TCCCHHHHHHHHHH----------S--HHHHHHHCS---HHHHHHHCT-S
T ss_pred cCCHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccccchhhHHHHHHHHHHHHHCCCCHHHHHHHcCCC
Confidence 5677888888889877766443322222222111 22457777899999999999986
No 63
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=32.89 E-value=75 Score=17.58 Aligned_cols=33 Identities=15% Similarity=0.253 Sum_probs=17.1
Q ss_pred HHHhhhcCCCCC-chhhhHHHHHHHHHHHHHhCCCHHHHHhhc
Q 042635 50 FCKAHVEFSKQR-SPKQEMLDYWTETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 50 ~c~~h~~~~~~~-~~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f 91 (121)
|+..|...|-|+ ++...|... .|.|..+|..-|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~---------tgls~~Qi~~WF 34 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQ---------TGLSRKQISNWF 34 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHH---------HTS-HHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHH---------cCCCHHHHHHHH
Confidence 667777777665 333333222 367777776554
No 64
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=31.70 E-value=28 Score=27.88 Aligned_cols=13 Identities=31% Similarity=0.445 Sum_probs=11.8
Q ss_pred CHHHHHhhcCCCC
Q 042635 83 SVQYVGKFFGIEN 95 (121)
Q Consensus 83 t~eeiR~~f~I~~ 95 (121)
|||+|++.|||+.
T Consensus 248 sPEdIk~~FgiSK 260 (287)
T COG2996 248 SPEDIKATFGISK 260 (287)
T ss_pred CHHHHHHHhCcCH
Confidence 6999999999984
No 65
>PRK15019 CsdA-binding activator; Provisional
Probab=31.64 E-value=78 Score=22.75 Aligned_cols=35 Identities=9% Similarity=0.208 Sum_probs=23.3
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhh--------cCCCCCCCHH
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKF--------FGIENNFTPK 100 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~--------f~I~~d~t~e 100 (121)
.++.--+..+...+.|+||+||.++ +|+..-+||-
T Consensus 86 ~IvkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 128 (147)
T PRK15019 86 RIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSAS 128 (147)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCcc
Confidence 3334344555666799999999862 5777777764
No 66
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=31.50 E-value=64 Score=25.07 Aligned_cols=39 Identities=5% Similarity=0.095 Sum_probs=26.8
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANRI 79 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~i 79 (121)
...|..|++||....-.... . ++++.||++.+.++...+
T Consensus 38 ~~~l~~i~~~c~~lgI~~vTvYaFS~eN~~R~~~EV~~Lm~L~~~~l~~~~ 88 (241)
T PRK14842 38 ANAIDRLMDASLEYGLKNISLYAFSTENWKRPITEIRSIFGLLVEFIETRL 88 (241)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 46889999999876432111 1 456799999988876643
No 67
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=31.48 E-value=62 Score=22.58 Aligned_cols=20 Identities=0% Similarity=-0.016 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCHHHHHhhc
Q 042635 72 TETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f 91 (121)
-+.|+..++|.|.||.+++.
T Consensus 93 ~q~i~a~mtG~t~eef~~mm 112 (117)
T PRK13378 93 MQDIGAQQTGMTKEEFKAKL 112 (117)
T ss_pred HHHHHHHhcCCCHHHHHHHH
Confidence 56677788899999888763
No 68
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=31.27 E-value=64 Score=22.89 Aligned_cols=20 Identities=5% Similarity=0.130 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCHHHHHhhc
Q 042635 72 TETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f 91 (121)
-+.|+..++|.|.||.+++.
T Consensus 93 ~q~i~a~mtG~t~eef~~mm 112 (129)
T PRK13377 93 FQQMAGSMTGMTEEEYRQMM 112 (129)
T ss_pred HHHHHHHhcCCCHHHHHHHH
Confidence 56677788888888888764
No 69
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=31.26 E-value=50 Score=19.72 Aligned_cols=16 Identities=13% Similarity=0.615 Sum_probs=12.7
Q ss_pred hhHHHHHHHHHHhhhc
Q 042635 41 TEPLSYIIEFCKAHVE 56 (121)
Q Consensus 41 s~~L~kVie~c~~h~~ 56 (121)
|....-+++||+.|..
T Consensus 23 S~a~~~l~~y~e~~~~ 38 (57)
T cd00068 23 SKAAAELLKYCEQNAE 38 (57)
T ss_pred HHHHHHHHHHHHhcCC
Confidence 5667788999999855
No 70
>PF15063 TC1: Thyroid cancer protein 1
Probab=31.15 E-value=48 Score=21.50 Aligned_cols=31 Identities=16% Similarity=0.263 Sum_probs=27.5
Q ss_pred HHHHHHHhCCCHHHHHhhcCCCCCCCHHHHH
Q 042635 73 ETLANRIKNKSVQYVGKFFGIENNFTPKEEV 103 (121)
Q Consensus 73 ~~vA~~ikgkt~eeiR~~f~I~~d~t~eEe~ 103 (121)
+.+|+.+.+-+-++|+..|.-.-|--.||.+
T Consensus 28 kasaNIFe~vn~~qlqrLF~~sGD~kAEeRA 58 (79)
T PF15063_consen 28 KASANIFENVNLDQLQRLFQKSGDKKAEERA 58 (79)
T ss_pred hhhhhhhhccCHHHHHHHHHHccchhHHHHH
Confidence 4689999999999999999999998888877
No 71
>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=31.11 E-value=70 Score=18.48 Aligned_cols=23 Identities=22% Similarity=0.186 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCHHHHHhhcCCC
Q 042635 72 TETLANRIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f~I~ 94 (121)
...+.-+..|+|+.||-..+||.
T Consensus 9 ~~vl~~l~~G~~~~eIA~~l~is 31 (58)
T PF00196_consen 9 LEVLRLLAQGMSNKEIAEELGIS 31 (58)
T ss_dssp HHHHHHHHTTS-HHHHHHHHTSH
T ss_pred HHHHHHHHhcCCcchhHHhcCcc
Confidence 34556677899999999999886
No 72
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=30.42 E-value=86 Score=22.19 Aligned_cols=34 Identities=9% Similarity=0.186 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhh--------cCCCCCCCHH
Q 042635 67 MLDYWTETLANRIKNKSVQYVGKF--------FGIENNFTPK 100 (121)
Q Consensus 67 Ll~~~c~~vA~~ikgkt~eeiR~~--------f~I~~d~t~e 100 (121)
++.--+..+...+.|+||+||.++ +|+..-+||-
T Consensus 82 IvkGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSps 123 (138)
T TIGR03391 82 IVRGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSAS 123 (138)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCcc
Confidence 333334555666799999999844 4666666653
No 73
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=30.01 E-value=1.6e+02 Score=20.05 Aligned_cols=50 Identities=12% Similarity=0.109 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhhcCCCCC-chhhhHHHHH--------HHHHHHHHhCCCHHHHHhhcCC
Q 042635 44 LSYIIEFCKAHVEFSKQR-SPKQEMLDYW--------TETLANRIKNKSVQYVGKFFGI 93 (121)
Q Consensus 44 L~kVie~c~~h~~~~~~~-~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~~f~I 93 (121)
|+.|..|+--|.....++ ++++.||..+ -+.++..++|++++++-.-.+.
T Consensus 1 M~yvyAaLLL~~~G~eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~~~~ 59 (106)
T cd05832 1 MEYIYAALLLHYAGKEINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKAAV 59 (106)
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 345666776666654433 6777777654 4567888999999998877663
No 74
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=30.00 E-value=40 Score=21.85 Aligned_cols=34 Identities=6% Similarity=0.247 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhCCCHHHHHhh-------cCCCCCCCHHHHH
Q 042635 70 YWTETLANRIKNKSVQYVGKF-------FGIENNFTPKEEV 103 (121)
Q Consensus 70 ~~c~~vA~~ikgkt~eeiR~~-------f~I~~d~t~eEe~ 103 (121)
++-..+++.++|.....|++. ||+-.+++..+.+
T Consensus 20 ~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~ 60 (106)
T PF09382_consen 20 FGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWE 60 (106)
T ss_dssp S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHH
T ss_pred ccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHH
Confidence 467789999999888887765 9999999988776
No 75
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=29.75 E-value=1.2e+02 Score=20.57 Aligned_cols=64 Identities=16% Similarity=0.217 Sum_probs=37.1
Q ss_pred hHHHHHHHHHHhhhcCCCCC-ch-hhhHHHHH--HHHHHHHH---hCCCHHHHHhhcCCC-CCCCHHHHH-HH
Q 042635 42 EPLSYIIEFCKAHVEFSKQR-SP-KQEMLDYW--TETLANRI---KNKSVQYVGKFFGIE-NNFTPKEEV-AR 105 (121)
Q Consensus 42 ~~L~kVie~c~~h~~~~~~~-~~-~~~Ll~~~--c~~vA~~i---kgkt~eeiR~~f~I~-~d~t~eEe~-ir 105 (121)
..+++-++|.+....-.+.. .. .+.|+.+. ....|.+| .=+|++|+|.+|.-. .-+++|+.+ |-
T Consensus 32 ~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~~l~e~~a~~I~nL~P~~~dElrai~~~~~~~~~~e~l~~IL 104 (112)
T PRK14981 32 YELRRTLDYLNRFSKLDPEDAEELVEELLELEKMKEKTAVKIADILPETRDELRAIFAKERYTLSPEELDEIL 104 (112)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccCCCHHHHHHHHhcCCCCHHHHHHHHHHhccCCCHHHHHHHH
Confidence 37777788887765543322 11 12444443 22223333 358999999998755 347788776 54
No 76
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=29.62 E-value=45 Score=17.85 Aligned_cols=23 Identities=22% Similarity=0.147 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCCHHHHHhhc-CCC
Q 042635 71 WTETLANRIKNKSVQYVGKFF-GIE 94 (121)
Q Consensus 71 ~c~~vA~~ikgkt~eeiR~~f-~I~ 94 (121)
+|..||... |-+.++|++.- ++.
T Consensus 8 tl~~IA~~~-~~~~~~l~~~N~~~~ 31 (44)
T PF01476_consen 8 TLWSIAKRY-GISVDELMELNPNID 31 (44)
T ss_dssp -HHHHHHHT-TS-HHHHHHHCCTTH
T ss_pred cHHHHHhhh-hhhHhHHHHhcCCCC
Confidence 467777775 78888888765 443
No 77
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=29.61 E-value=74 Score=24.54 Aligned_cols=38 Identities=16% Similarity=0.185 Sum_probs=26.4
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANR 78 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~ 78 (121)
...|..|++||....-.... . ++++.||++...++...
T Consensus 34 ~~~l~~~~~~c~~~gI~~lTvyaFS~eN~~R~~~Ev~~Lm~L~~~~l~~~ 83 (233)
T PRK14833 34 VKTLREITIWCANHKLECLTLYAFSTENWKRPKSEVDFLMKLLKKYLKDE 83 (233)
T ss_pred HHHHHHHHHHHHHcCCCEEEEeecchhhcCcCHHHHHHHHHHHHHHHHHH
Confidence 46899999999877432211 1 46679999988877553
No 78
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=29.56 E-value=81 Score=17.09 Aligned_cols=17 Identities=12% Similarity=0.178 Sum_probs=14.1
Q ss_pred HHhCCCHHHHHhhcCCC
Q 042635 78 RIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 78 ~ikgkt~eeiR~~f~I~ 94 (121)
...|+|..+|-+.+|++
T Consensus 15 ~~~g~s~~eia~~l~is 31 (58)
T smart00421 15 LAEGLTNKEIAERLGIS 31 (58)
T ss_pred HHcCCCHHHHHHHHCCC
Confidence 45789999999999986
No 79
>PF09384 UTP15_C: UTP15 C terminal; InterPro: IPR018983 This entry represents the C-terminal domain of the U3 small nucleolar RNA-associated protein 15 (UTP15). This protein is involved in nucleolar processing of pre-18S ribosomal RNA, and is required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). UTP15 is a component of the ribosomal small subunit (SSU) processome, which is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome [, ]. This domain is found C-terminal to the WD40 repeat (IPR001680 from INTERPRO). UTP15 associates with U3 snoRNA, which is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA []. ; GO: 0006364 rRNA processing, 0005730 nucleolus
Probab=29.53 E-value=98 Score=21.89 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=21.5
Q ss_pred CCCCChhHHHHHHHHHHhhhcCCCC
Q 042635 36 LPNVSTEPLSYIIEFCKAHVEFSKQ 60 (121)
Q Consensus 36 l~~V~s~~L~kVie~c~~h~~~~~~ 60 (121)
|.+-+...|..|+.|+.+|-.+|-.
T Consensus 68 L~~Rde~~L~piL~Fl~k~i~~pr~ 92 (148)
T PF09384_consen 68 LAGRDEESLEPILKFLIKNITDPRY 92 (148)
T ss_pred HHhCCHHHHHHHHHHHHHhCCCccc
Confidence 6788999999999999999887654
No 80
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.52 E-value=37 Score=22.88 Aligned_cols=47 Identities=11% Similarity=0.093 Sum_probs=28.8
Q ss_pred ChhHHHHHHHHHHhhhcCCCCCchhhhHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCC
Q 042635 40 STEPLSYIIEFCKAHVEFSKQRSPKQEMLDYWTETLANRIKNKSVQYVGKFFGIENNF 97 (121)
Q Consensus 40 ~s~~L~kVie~c~~h~~~~~~~~~~~~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~ 97 (121)
+...|+ ++++.|...+ .+++.|++...+. .=++|++|+.+|+..+++
T Consensus 5 akk~lk---~~~~k~P~ae---~pL~aw~~~v~ka-----~w~~P~diK~~f~~d~~~ 51 (98)
T COG4680 5 AKKALK---DAMEKYPQAE---TPLKAWGNVVSKA-----YWKKPEDIKSVFPLDNFK 51 (98)
T ss_pred hHhHHH---HHHHhCcccc---chHHHHHHHHHhc-----ccCCHHHHHHhcCcccce
Confidence 344454 4455553322 3466666655442 348999999999977664
No 81
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=29.49 E-value=77 Score=22.25 Aligned_cols=20 Identities=10% Similarity=0.134 Sum_probs=14.7
Q ss_pred HHHHHHHHhCCCHHHHHhhc
Q 042635 72 TETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f 91 (121)
-+.|+..++|.|.||-+++.
T Consensus 90 ~q~i~a~mtG~s~eef~~mm 109 (121)
T cd07924 90 FQQAAGSMTGMSMEEYRQMM 109 (121)
T ss_pred HHHHHHHhcCCCHHHHHHHH
Confidence 55677777888888877653
No 82
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=29.36 E-value=37 Score=24.16 Aligned_cols=13 Identities=31% Similarity=0.950 Sum_probs=9.8
Q ss_pred HHHHHHHHhhhcC
Q 042635 45 SYIIEFCKAHVEF 57 (121)
Q Consensus 45 ~kVie~c~~h~~~ 57 (121)
..|+.||.||+-.
T Consensus 27 ~lIl~y~~~~k~~ 39 (139)
T PF05871_consen 27 DLILDYCRHHKIF 39 (139)
T ss_dssp HHHHHHHHHTT-S
T ss_pred HHHHHHHHHhcee
Confidence 3589999999874
No 83
>PF11103 DUF2887: Protein of unknown function (DUF2887); InterPro: IPR022573 This bacterial group of proteins has no known function.
Probab=29.31 E-value=74 Score=24.07 Aligned_cols=26 Identities=15% Similarity=0.253 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhc
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f 91 (121)
.|+++.-..+..++..+|-+||.+||
T Consensus 175 ~lleLIEtIlvyKfp~lSreEIeaMl 200 (200)
T PF11103_consen 175 ELLELIETILVYKFPQLSREEIEAML 200 (200)
T ss_pred HHHHHHHHHHHHHccccCHHHHHHhC
Confidence 88888888999999999999999987
No 84
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=29.27 E-value=80 Score=24.13 Aligned_cols=39 Identities=13% Similarity=0.226 Sum_probs=26.0
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANRI 79 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~i 79 (121)
...|..|++||..+.-.... . .+++.||++....+...+
T Consensus 30 ~~~~~~i~~~~~~~gI~~lTvyaFS~eN~~R~~~EV~~Lm~l~~~~l~~~~ 80 (221)
T cd00475 30 AEKLRDILRWCLELGVKEVTLYAFSTENWKRPKEEVDFLMELFRDVLRRIL 80 (221)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEeechhhhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999987432111 1 356688888887765543
No 85
>PF03883 DUF328: Protein of unknown function (DUF328); InterPro: IPR005583 The members of this family are functionally uncharacterised. They are about 250 amino acids in length.
Probab=29.16 E-value=52 Score=25.20 Aligned_cols=35 Identities=20% Similarity=0.187 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcCCCCCCCHH
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFGIENNFTPK 100 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~~d~t~e 100 (121)
+.+.-..+.++..++..|++|+++.|+|...+..+
T Consensus 25 p~f~~~~~~l~~~L~~~s~~el~~l~~is~~la~~ 59 (237)
T PF03883_consen 25 PEFLEKTEELLEALKSLSEEELKKLMKISDKLAEE 59 (237)
T ss_pred cChHHHHHHHHHHHHhcCHHHHHHHHCCCHHHHHH
Confidence 44444567788888999999999999999665443
No 86
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.85 E-value=39 Score=23.90 Aligned_cols=20 Identities=20% Similarity=0.390 Sum_probs=16.2
Q ss_pred HHHHHh-CCCHHHHHhhcCCC
Q 042635 75 LANRIK-NKSVQYVGKFFGIE 94 (121)
Q Consensus 75 vA~~ik-gkt~eeiR~~f~I~ 94 (121)
|-.|++ ||+|.||-+.+||+
T Consensus 102 i~emlr~gk~preIsk~lGIp 122 (139)
T COG1710 102 IREMLRNGKTPREISKDLGIP 122 (139)
T ss_pred HHHHHHcCCCHHHHHHhhCCc
Confidence 344444 89999999999997
No 87
>COG2066 GlsA Glutaminase [Amino acid transport and metabolism]
Probab=28.60 E-value=51 Score=26.68 Aligned_cols=23 Identities=9% Similarity=0.183 Sum_probs=19.8
Q ss_pred hhhHHHHHHHHHHHHHhCCCHHH
Q 042635 64 KQEMLDYWTETLANRIKNKSVQY 86 (121)
Q Consensus 64 ~~~Ll~~~c~~vA~~ikgkt~ee 86 (121)
..++++.+.-.|++++.|.++++
T Consensus 112 ~NPmINAGAI~v~~li~g~~~~~ 134 (309)
T COG2066 112 RNPMINAGAIAVASLLPGRTADE 134 (309)
T ss_pred CCccccccHHHHHhhccCCCcHH
Confidence 35899999999999999988655
No 88
>PF03750 DUF310: Protein of unknown function (DUF310); InterPro: IPR010149 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents the C-terminal domain of a minor family of CRISPR-associated proteins. These proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element.
Probab=28.23 E-value=76 Score=21.67 Aligned_cols=31 Identities=19% Similarity=0.402 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHHHHh--CCCHHHHHhhcCCCCC
Q 042635 65 QEMLDYWTETLANRIK--NKSVQYVGKFFGIENN 96 (121)
Q Consensus 65 ~~Ll~~~c~~vA~~ik--gkt~eeiR~~f~I~~d 96 (121)
+.|.+.+.+ +|..++ +-|+.|||++|+--..
T Consensus 11 ~~~~~~Ae~-~~k~l~~~~lttsQlRkf~~~v~~ 43 (119)
T PF03750_consen 11 ELLVDYAEK-IAKELKKNKLTTSQLRKFYDEVKR 43 (119)
T ss_pred HHHHHHHHH-HHHHHHhCCCCHHHHHHHHHHHHH
Confidence 345555544 455555 4799999999985443
No 89
>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=27.62 E-value=2.2e+02 Score=20.35 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=24.3
Q ss_pred chhhhHHHHHHHHHHHHH-hCCCHHHHHhhcCCC
Q 042635 62 SPKQEMLDYWTETLANRI-KNKSVQYVGKFFGIE 94 (121)
Q Consensus 62 ~~~~~Ll~~~c~~vA~~i-kgkt~eeiR~~f~I~ 94 (121)
++.+..++.-..++.+.. .|+|.+|+-+-+|=+
T Consensus 20 ~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P 53 (181)
T PF08006_consen 20 EEREEILEYYEEYFDDAGEEGKSEEEIIAELGSP 53 (181)
T ss_pred HHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCH
Confidence 556677777777776654 489999999999833
No 90
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=27.50 E-value=87 Score=24.37 Aligned_cols=38 Identities=11% Similarity=0.047 Sum_probs=25.5
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANR 78 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~ 78 (121)
...|..|++||....-.... . ++++.|+++.+.++...
T Consensus 39 ~~~l~~i~~~c~~~GI~~lTvYaFS~EN~~R~~~EV~~Lm~L~~~~l~~~ 88 (239)
T PRK14839 39 VEAIRRVVEAAPDLGIGTLTLYAFSSDNWRRPAAEVGGLMRLLRAYLRNE 88 (239)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEechhhcCCCHHHHHHHHHHHHHHHHHH
Confidence 46789999999976432111 1 35668998888776543
No 91
>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=27.49 E-value=86 Score=17.40 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=11.3
Q ss_pred HhCCCHHHHHhhcCCC
Q 042635 79 IKNKSVQYVGKFFGIE 94 (121)
Q Consensus 79 ikgkt~eeiR~~f~I~ 94 (121)
-.|.|..+|-+.|||.
T Consensus 19 ~~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVS 34 (45)
T ss_dssp HTT--HHHHHHHTTS-
T ss_pred HCCCCHHHHHHHHCcC
Confidence 3589999999999986
No 92
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=27.48 E-value=85 Score=24.14 Aligned_cols=37 Identities=11% Similarity=0.221 Sum_probs=25.3
Q ss_pred hhHHHHHHHHHHhhhcCCC-----CC-------chhhhHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSK-----QR-------SPKQEMLDYWTETLAN 77 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~-----~~-------~~~~~Ll~~~c~~vA~ 77 (121)
...|+.|++||....-... +. ++++.||++...++..
T Consensus 29 ~~~~~~v~~~c~~~GI~~lT~yaFStEN~~Rp~~EV~~Lm~L~~~~l~~ 77 (226)
T TIGR00055 29 VKSLRRILRWCANLGVECLTLYAFSTENWKRPKEEVDFLMELFEKKLDR 77 (226)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEeehhhcCcCHHHHHHHHHHHHHHHHH
Confidence 4689999999987643211 11 3566899988877754
No 93
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=27.43 E-value=2.1e+02 Score=19.61 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=33.0
Q ss_pred CCcEEEEeCCCCeEEecHHHHhhcC-cCCCccc---CCCCChhHHHHHHHHHH
Q 042635 4 SKKISLKRADGQLFEVEEPVAMDFE-IEDTVVP---LPNVSTEPLSYIIEFCK 52 (121)
Q Consensus 4 ~~~i~L~SsDG~~f~V~~~~a~~S~-ied~~Ip---l~~V~s~~L~kVie~c~ 52 (121)
...++|+..+|+.+.|.++-+..-. ......| +..++..-|.-++.|+.
T Consensus 79 ~~~~~l~~~~g~~~~i~~~~I~~~~~~~~S~MP~gl~~~Lt~~e~~dL~aYL~ 131 (133)
T TIGR02603 79 ADGVTVKMPGGVEQSVPREEIKSREALPVSLMPEGLEMGLSDQDLADLVAYLK 131 (133)
T ss_pred CCeEEEEcCCCcEEEEEHHHHHHhhcCCCCcCCchhhccCCHHHHHHHHHHHh
Confidence 3568888899999999886654322 2212233 23578888888999874
No 94
>PF13010 pRN1_helical: Primase helical domain; PDB: 1RO0_A 1RNI_A 1RO2_A 3M1M_A.
Probab=27.42 E-value=32 Score=24.38 Aligned_cols=14 Identities=29% Similarity=0.442 Sum_probs=5.8
Q ss_pred HHHhCCCHHHHHhh
Q 042635 77 NRIKNKSVQYVGKF 90 (121)
Q Consensus 77 ~~ikgkt~eeiR~~ 90 (121)
+.++|||+|.||.-
T Consensus 24 drfkGKtveair~e 37 (135)
T PF13010_consen 24 DRFKGKTVEAIREE 37 (135)
T ss_dssp -------HHHHHHH
T ss_pred ccccCchHHHHHHH
Confidence 56789999999963
No 95
>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=27.33 E-value=1.2e+02 Score=20.91 Aligned_cols=31 Identities=13% Similarity=0.397 Sum_probs=22.2
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhh-------cCCCCCCCHH
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKF-------FGIENNFTPK 100 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~-------f~I~~d~t~e 100 (121)
||+-+.+ ..+.|+||+||..+ +|+.+-+||-
T Consensus 71 Gl~all~----~~~~g~t~~eI~~~~~~fl~~lgl~~~Ls~s 108 (125)
T PF02657_consen 71 GLLALLL----EVLNGQTPEEILAFDPDFLEQLGLSQHLSPS 108 (125)
T ss_dssp HHHHHHH----HHTTT-BHHHHHHS-THHHHHHTSCCCSTHH
T ss_pred HHHHHHH----HHHcCCCHHHHHhCCHHHHHHcCcccccCch
Confidence 5555444 45699999999876 7888888875
No 96
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=27.08 E-value=1.1e+02 Score=23.58 Aligned_cols=20 Identities=5% Similarity=0.170 Sum_probs=15.8
Q ss_pred hhHHHHHHHHHHhhhcCCCC
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ 60 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~ 60 (121)
...+.++++|.+.|...+..
T Consensus 4 ~~~i~~~~~~i~~~~~~~~~ 23 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQPLS 23 (289)
T ss_pred HHHHHHHHHHHHhcccCCCC
Confidence 46788999999999776544
No 97
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=26.91 E-value=55 Score=20.15 Aligned_cols=16 Identities=31% Similarity=0.434 Sum_probs=12.8
Q ss_pred CCcEEEEeCCCCeEEe
Q 042635 4 SKKISLKRADGQLFEV 19 (121)
Q Consensus 4 ~~~i~L~SsDG~~f~V 19 (121)
-+.+++.|.||++|--
T Consensus 4 ~KA~Kv~~RDGE~~lr 19 (65)
T COG4049 4 LKAIKVRDRDGEEFLR 19 (65)
T ss_pred ceeeEeeccCCceeee
Confidence 4568999999998864
No 98
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=26.87 E-value=52 Score=26.14 Aligned_cols=58 Identities=16% Similarity=0.178 Sum_probs=37.2
Q ss_pred ChhHHHHHHHHHHhhhcCCCCC------------chhhhHHHHHHHHHHH-HHhCCCHHHHHhhcCCCCCC
Q 042635 40 STEPLSYIIEFCKAHVEFSKQR------------SPKQEMLDYWTETLAN-RIKNKSVQYVGKFFGIENNF 97 (121)
Q Consensus 40 ~s~~L~kVie~c~~h~~~~~~~------------~~~~~Ll~~~c~~vA~-~ikgkt~eeiR~~f~I~~d~ 97 (121)
-...|..+++||....-..+.. .++++||+++-+++-. ..+|....+.+-.+-|--|+
T Consensus 65 Gf~~l~~ile~C~~lGI~~vT~fAFSieNFkRs~eEVd~LM~L~~~k~~~~~~~~~~~~~~gvririiGdl 135 (271)
T KOG1602|consen 65 GFEALKEILELCKELGIKEVTVFAFSIENFKRSPEEVDGLMDLALEKIERLLEQGEKLDKYGVRIRVIGDL 135 (271)
T ss_pred HHHHHHHHHHHHHHcCCcEEEEEEEehhhhCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCeEEEEEcch
Confidence 3467899999998765433221 4678999999998866 33455555544445444454
No 99
>PF13315 DUF4085: Protein of unknown function (DUF4085)
Probab=26.39 E-value=2.6e+02 Score=21.35 Aligned_cols=53 Identities=25% Similarity=0.263 Sum_probs=35.9
Q ss_pred CCCcccCCCCChhHHHHHHHHHHhhhcCCCCCchhhhHHHHHHHHHH---HHHhCCCHHHHHhhcC
Q 042635 30 EDTVVPLPNVSTEPLSYIIEFCKAHVEFSKQRSPKQEMLDYWTETLA---NRIKNKSVQYVGKFFG 92 (121)
Q Consensus 30 ed~~Ipl~~V~s~~L~kVie~c~~h~~~~~~~~~~~~Ll~~~c~~vA---~~ikgkt~eeiR~~f~ 92 (121)
.|..+.+.-.+.++.+.+.+||+... ..+.-.|+.-- +.|+++=|.-+++.|+
T Consensus 68 ~d~~~~~~~~s~~l~~~~~ew~~~~~----------~~~~~~~~~Y~e~~~sI~~~lp~~v~ql~~ 123 (208)
T PF13315_consen 68 ADIRFNLDYPSEKLKKAITEWCEDYE----------KRVKRLCQAYYEYYNSIKEKLPQNVQQLFN 123 (208)
T ss_pred ccCcccCCCCcHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHhhhHHHHHHhh
Confidence 34457777788999999999998753 44444444332 2367777888888664
No 100
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=26.35 E-value=88 Score=24.47 Aligned_cols=38 Identities=11% Similarity=0.108 Sum_probs=25.9
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANR 78 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~ 78 (121)
...|..|++||....-.... . ++++.||++.+.++...
T Consensus 52 ~~~l~~v~~~c~~~GIk~lTvYaFS~EN~~R~~~EV~~Lm~L~~~~l~~~ 101 (250)
T PRK14840 52 AKSLPQIVDTALHLGIEVLTLFAFSTENFSRSKEEVAELFSLFNSQLDSQ 101 (250)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHHHHHHHH
Confidence 46899999999876432111 1 35668898888877654
No 101
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=26.01 E-value=76 Score=25.22 Aligned_cols=26 Identities=15% Similarity=-0.041 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhc
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f 91 (121)
..--.++..++.+++|||++|..++.
T Consensus 63 ais~ASAs~~~eli~Gktv~ea~~i~ 88 (290)
T TIGR02000 63 GSAIASSSALTEMIKGLTLDEALKVS 88 (290)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHhh
Confidence 44555566789999999999977664
No 102
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=25.95 E-value=77 Score=21.15 Aligned_cols=22 Identities=23% Similarity=0.267 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCCHHHHHhhcCC
Q 042635 72 TETLANRIKNKSVQYVGKFFGI 93 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f~I 93 (121)
+..||+.|+|+++++-..++..
T Consensus 13 ~~~va~~IrG~~v~~A~~~L~f 34 (103)
T TIGR01044 13 ARLVADLIRGKSVSQALDILRF 34 (103)
T ss_pred HHHHHHHHcCCcHHHHHHHHhh
Confidence 5678999999999998887763
No 103
>PF01255 Prenyltransf: Putative undecaprenyl diphosphate synthase; InterPro: IPR001441 Synonym(s): Di-trans-poly-cis-undecaprenyl-diphosphate synthase, Undecaprenyl pyrophosphate synthetase, Undecaprenyl pyrophosphate synthase, UPP synthetase Di-trans-poly-cis-decaprenylcistransferase (2.5.1.31 from EC) (UPP synthetase) generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) []. This bacterial enzyme is also found in archaebacteria and in a number of uncharacterised proteins including some from yeasts. This entry also matches related enzymes that transfer alkyl groups, such as dehydrodolichyl diphosphate synthase.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 2D2R_B 2DTN_B 1F75_B 1X07_A 2E9D_A 1JP3_A 3QAS_A 1X09_A 1V7U_B 2E9A_A ....
Probab=25.71 E-value=90 Score=23.60 Aligned_cols=40 Identities=20% Similarity=0.261 Sum_probs=26.5
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHHHh
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANRIK 80 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~ik 80 (121)
...|+.|++||....-.... . .+++.|+++..+.+...+.
T Consensus 24 ~~~l~~i~~~~~~~gI~~lTvYaFS~eN~~R~~~EV~~Lm~l~~~~l~~~~~ 75 (223)
T PF01255_consen 24 AEKLKEIVEWCLELGIKYLTVYAFSTENWKRPKEEVDALMDLFERYLRELID 75 (223)
T ss_dssp HHHHHHHHHHHHHCT-SEEEEEEEETTGGGS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEecchhhcCCHHHHHHHHHHHHHHHHHHhh
Confidence 35789999999876332111 1 3566889888887766554
No 104
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=25.40 E-value=1.4e+02 Score=19.72 Aligned_cols=52 Identities=10% Similarity=0.130 Sum_probs=35.1
Q ss_pred CcEEEEeCCCCeEEecHHH---HhhcC-c------CC-------CcccCC-CCChhHHHHHHHHHHhhhc
Q 042635 5 KKISLKRADGQLFEVEEPV---AMDFE-I------ED-------TVVPLP-NVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 5 ~~i~L~SsDG~~f~V~~~~---a~~S~-i------ed-------~~Ipl~-~V~s~~L~kVie~c~~h~~ 56 (121)
..+.++|+||....|...- +..++ + .+ ..+.+. +++..+..++++++..++.
T Consensus 30 ~~~~~~~~Dg~~v~v~l~~~~~~~~~~~vEViG~V~~~~~I~~~~~~~~g~~~D~~~yn~lv~l~~~~~~ 99 (101)
T cd04479 30 DSLTLISSDGVNVTVELNRPLDLPISGYVEVIGKVSPDLTIRVLSYIDFGDDFDMDLYNELVKLSHKFKN 99 (101)
T ss_pred CeEEEEcCCCCEEEEEeCCCCCcccCCEEEEEEEECCCCeEEEEEEEECCCccCHHHHHHHHHHHhhCcc
Confidence 3689999999777775332 23333 1 11 345554 7999999999999887753
No 105
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=25.30 E-value=46 Score=21.24 Aligned_cols=20 Identities=30% Similarity=0.459 Sum_probs=10.1
Q ss_pred CCCCCcEEEEeCCC-CeEEec
Q 042635 1 MRHSKKISLKRADG-QLFEVE 20 (121)
Q Consensus 1 m~s~~~i~L~SsDG-~~f~V~ 20 (121)
|.++-.|.++|.|| ..++++
T Consensus 1 ~~~~milRvrS~dG~~Rie~~ 21 (80)
T PF11543_consen 1 MASSMILRVRSKDGMKRIEVS 21 (80)
T ss_dssp -----EEEEE-SSEEEEEEE-
T ss_pred CCccEEEEEECCCCCEEEEcC
Confidence 66667899999999 455554
No 106
>PF15628 RRM_DME: RRM in Demeter
Probab=25.20 E-value=61 Score=22.08 Aligned_cols=20 Identities=10% Similarity=0.165 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCHHHHHhhcC
Q 042635 73 ETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 73 ~~vA~~ikgkt~eeiR~~f~ 92 (121)
..|+...||.|.+||...|-
T Consensus 57 tsv~SIfrGls~~eIq~cF~ 76 (103)
T PF15628_consen 57 TSVSSIFRGLSREEIQQCFW 76 (103)
T ss_pred CcHHHHhcccCHHHHHHHHh
Confidence 35788889999999999874
No 107
>PRK11566 hdeB acid-resistance protein; Provisional
Probab=25.17 E-value=34 Score=23.29 Aligned_cols=25 Identities=28% Similarity=0.529 Sum_probs=20.0
Q ss_pred CcccCCCCChhHHHHHHHHHHhhhc
Q 042635 32 TVVPLPNVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 32 ~~Ipl~~V~s~~L~kVie~c~~h~~ 56 (121)
+-+.+.++.-..-.+|++||+.|..
T Consensus 62 D~vd~~e~et~~tPkvie~Ckk~P~ 86 (102)
T PRK11566 62 DYVDLNETDTTQVPKVIEYCKKNPQ 86 (102)
T ss_pred ccccccceeeeechHHHHHHHhCCc
Confidence 4577777777778899999999854
No 108
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=25.11 E-value=74 Score=25.41 Aligned_cols=22 Identities=18% Similarity=0.424 Sum_probs=18.0
Q ss_pred HHHHHhhcCCCCCCCHHHHH-HH
Q 042635 84 VQYVGKFFGIENNFTPKEEV-AR 105 (121)
Q Consensus 84 ~eeiR~~f~I~~d~t~eEe~-ir 105 (121)
...+|+.|++++++++||++ -+
T Consensus 111 ~~~L~~hf~~~~~L~~e~~a~s~ 133 (281)
T KOG4244|consen 111 EDRLRKHFKIPDDLSAEQRAQSR 133 (281)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHH
Confidence 34678999999999999987 44
No 109
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=25.02 E-value=2.1e+02 Score=19.75 Aligned_cols=44 Identities=14% Similarity=0.187 Sum_probs=25.3
Q ss_pred HHHHHHHhhhcCC--CCCchhhhHHHHH--------HHHHHHHHhCCCHHHHHh
Q 042635 46 YIIEFCKAHVEFS--KQRSPKQEMLDYW--------TETLANRIKNKSVQYVGK 89 (121)
Q Consensus 46 kVie~c~~h~~~~--~~~~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~ 89 (121)
.|-.|+-...... |...+++.+|+-. ...|-..++||+.+|+-.
T Consensus 3 yvaAYLL~~lgGn~~psa~DikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA 56 (112)
T KOG3449|consen 3 YVAAYLLAVLGGNASPSASDIKKILESVGAEIDDERINLVLSELKGKDIEELIA 56 (112)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHH
Confidence 3445554433322 2236777666543 445666778999888753
No 110
>PF07928 Vps54: Vps54-like protein; InterPro: IPR012501 This family contains various proteins that are homologues of the yeast Vps54 protein, such as the rat homologue (Q9JMK8 from SWISSPROT), the human homologue (Q86YF7 from SWISSPROT), and the mouse homologue (Q8R3X1 from SWISSPROT). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments []. All Vps54 homologues contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs []. ; GO: 0042147 retrograde transport, endosome to Golgi; PDB: 3N1E_B 3N1B_B.
Probab=25.02 E-value=24 Score=24.89 Aligned_cols=44 Identities=20% Similarity=0.335 Sum_probs=0.0
Q ss_pred CCCeEEecHHHHhhcC-cCC---CcccCCCCChhHHHHHHHHHHhhhc
Q 042635 13 DGQLFEVEEPVAMDFE-IED---TVVPLPNVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 13 DG~~f~V~~~~a~~S~-ied---~~Ipl~~V~s~~L~kVie~c~~h~~ 56 (121)
||+.|.|...+...-+ +.+ -..-+|.+..+++.+++++++....
T Consensus 1 d~e~f~vv~s~l~ll~~l~~Y~~~~~~~P~~a~di~~~l~elLk~fNS 48 (135)
T PF07928_consen 1 DNEKFVVVGSALLLLKMLSDYLQLASNFPSLAPDILSRLLELLKLFNS 48 (135)
T ss_dssp ------------------------------------------------
T ss_pred CCCceecHHHHHHHHHHHHHHHHHHHHCchhHHHHHHHHHHHHHHHHH
Confidence 7888888888887766 554 1123566899999999999876544
No 111
>PLN03212 Transcription repressor MYB5; Provisional
Probab=24.84 E-value=1e+02 Score=24.29 Aligned_cols=38 Identities=16% Similarity=0.196 Sum_probs=28.2
Q ss_pred HHHHHH-hCCCHHHHHhhcC------CCC-CCCHHHHH-HHh-----hcccc
Q 042635 74 TLANRI-KNKSVQYVGKFFG------IEN-NFTPKEEV-ART-----QYEWA 111 (121)
Q Consensus 74 ~vA~~i-kgkt~eeiR~~f~------I~~-d~t~eEe~-ir~-----e~~w~ 111 (121)
.||..+ .|+|+.+.|++|. |.. .+|+||++ |.+ -+.|+
T Consensus 50 ~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnKWs 101 (249)
T PLN03212 50 SLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWS 101 (249)
T ss_pred HHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccccHH
Confidence 477777 4899999999874 665 59999888 544 25665
No 112
>PRK10945 gene expression modulator; Provisional
Probab=24.80 E-value=1.6e+02 Score=18.78 Aligned_cols=42 Identities=19% Similarity=0.090 Sum_probs=25.1
Q ss_pred ChhHHHHHHHHHHhhhcCCCCCchhhhHHHHHHHHHHHHHhCCCHH
Q 042635 40 STEPLSYIIEFCKAHVEFSKQRSPKQEMLDYWTETLANRIKNKSVQ 85 (121)
Q Consensus 40 ~s~~L~kVie~c~~h~~~~~~~~~~~~Ll~~~c~~vA~~ikgkt~e 85 (121)
+.++|+||++-..+. .+.+++..+..++=...|.+..||--.
T Consensus 20 s~eTLEkvie~~~~~----L~~~E~~~f~~AaDHR~AEL~~~KLyD 61 (72)
T PRK10945 20 TIDTLERVIEKNKYE----LSDDELAVFYSAADHRLAELTMNKLYD 61 (72)
T ss_pred cHHHHHHHHHHhhcc----CCHHHHHHHHHHHHHHHHHHHhchhHh
Confidence 457888888744433 222455555555555677777776544
No 113
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=24.77 E-value=1e+02 Score=24.05 Aligned_cols=39 Identities=8% Similarity=-0.034 Sum_probs=26.5
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANRI 79 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~i 79 (121)
...|..|++||....-.... . .+++.|+++...++...+
T Consensus 52 ~~~l~~~l~~c~~~GI~~vTvYaFS~eN~~R~~~Ev~~Lm~l~~~~l~~~~ 102 (251)
T PRK14830 52 MDTVKKITKAASELGVKVLTLYAFSTENWKRPKDEVKFLMNLPVEFLDKFV 102 (251)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEEehhhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 35789999999876432111 1 356789998888776654
No 114
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=24.56 E-value=52 Score=18.57 Aligned_cols=17 Identities=18% Similarity=0.325 Sum_probs=11.3
Q ss_pred HHhCCCHHHHHhhcCCC
Q 042635 78 RIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 78 ~ikgkt~eeiR~~f~I~ 94 (121)
.+.|.|..||-+.+|++
T Consensus 23 ~~~g~s~~eIa~~l~~s 39 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGIS 39 (54)
T ss_dssp HTS---HHHHHHHCTS-
T ss_pred HHHCcCHHHHHHHHCcC
Confidence 56799999999999987
No 115
>PF06289 FlbD: Flagellar protein (FlbD); InterPro: IPR009384 This family consists of several bacterial FlbD flagellar proteins. The exact function of this family is unknown [].
Probab=24.54 E-value=1.1e+02 Score=18.73 Aligned_cols=47 Identities=21% Similarity=0.343 Sum_probs=32.7
Q ss_pred cEEEEeCCCCeEEecHHHHhhcC--------cCC-CcccCCCCChhHHHHHHHHHH
Q 042635 6 KISLKRADGQLFEVEEPVAMDFE--------IED-TVVPLPNVSTEPLSYIIEFCK 52 (121)
Q Consensus 6 ~i~L~SsDG~~f~V~~~~a~~S~--------ied-~~Ipl~~V~s~~L~kVie~c~ 52 (121)
+|.|.--+|+.|.+....+..-. |-+ ..+-+.+=-.+++++|++|-.
T Consensus 1 MI~lTrlng~~f~lN~d~IE~ie~~PDTvItL~~G~k~vV~Es~~eVi~ki~~y~~ 56 (60)
T PF06289_consen 1 MIKLTRLNGEPFYLNPDLIETIEETPDTVITLTNGKKYVVKESVEEVIEKIIEYRR 56 (60)
T ss_pred CeEEEEeCCCEEEEChHHEEEEEEcCCeEEEEeCCCEEEEECCHHHHHHHHHHHHH
Confidence 57888899999999988876543 111 233344556788899998854
No 116
>PF15120 DUF4561: Domain of unknown function (DUF4561)
Probab=24.30 E-value=1.9e+02 Score=21.48 Aligned_cols=18 Identities=11% Similarity=0.277 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHhhhcCCC
Q 042635 42 EPLSYIIEFCKAHVEFSK 59 (121)
Q Consensus 42 ~~L~kVie~c~~h~~~~~ 59 (121)
.++..|-.||+||.....
T Consensus 44 ~tI~QV~~y~eh~~~nst 61 (171)
T PF15120_consen 44 STIGQVQKYMEHHCNNST 61 (171)
T ss_pred ccHHHHHHHHHHHhcccc
Confidence 467889999999876544
No 117
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=24.02 E-value=1.3e+02 Score=18.27 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHhhcCCC
Q 042635 66 EMLDYWTETLANRIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 66 ~Ll~~~c~~vA~~ikgkt~eeiR~~f~I~ 94 (121)
..|++.++++...-..=|..||.+.||+.
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~ 38 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLK 38 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSS
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCC
Confidence 45555566555553334667888888876
No 118
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=23.78 E-value=1.1e+02 Score=23.71 Aligned_cols=37 Identities=3% Similarity=-0.089 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLAN 77 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~ 77 (121)
...|..|++||....-.... . .+++.||++...++..
T Consensus 44 ~~~l~~iv~~c~~~gI~~vTvYaFS~eN~kR~~~Ev~~lm~L~~~~l~~ 92 (243)
T PRK14829 44 EPVLFDVVAGAIEAGVPYLSLYTFSTENWKRSPDEVRFLMGFSRDVIHR 92 (243)
T ss_pred HHHHHHHHHHHHHcCCCEEEEeeecchhhCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999987432111 1 3566888888877654
No 119
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=23.39 E-value=41 Score=20.36 Aligned_cols=22 Identities=18% Similarity=0.172 Sum_probs=15.9
Q ss_pred HHHHHHhCCCHHHHHhhcCCCC
Q 042635 74 TLANRIKNKSVQYVGKFFGIEN 95 (121)
Q Consensus 74 ~vA~~ikgkt~eeiR~~f~I~~ 95 (121)
.++..-.|+|.+|++.+||-+.
T Consensus 8 ~~~~i~~GmTk~qV~~lLG~P~ 29 (71)
T PF04355_consen 8 QLAQIKPGMTKDQVRALLGSPS 29 (71)
T ss_dssp HHTTT-TTSBHHHHHHHHTS-S
T ss_pred HHHhhcCCCCHHHHHHhcCCCC
Confidence 3444556999999999999773
No 120
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=23.18 E-value=2.6e+02 Score=19.26 Aligned_cols=49 Identities=14% Similarity=0.136 Sum_probs=35.5
Q ss_pred HHHHHHHHhhhcCCCCC-chhhhHHHHH--------HHHHHHHHhCCCHHHHHhhcCC
Q 042635 45 SYIIEFCKAHVEFSKQR-SPKQEMLDYW--------TETLANRIKNKSVQYVGKFFGI 93 (121)
Q Consensus 45 ~kVie~c~~h~~~~~~~-~~~~~Ll~~~--------c~~vA~~ikgkt~eeiR~~f~I 93 (121)
+.|..|+-.|..+.-.+ +.++.+|+.+ .+.+..-+.|++.+|+-+-++.
T Consensus 2 eYi~a~llL~~agkei~e~~l~~vl~aaGveve~~r~k~lvaaLeg~~idE~i~~~~~ 59 (109)
T COG2058 2 EYIYAYLLLHLAGKEITEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAE 59 (109)
T ss_pred hHHHHHHHHHHccCcCCHHHHHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcc
Confidence 45667777777665433 6777777654 6677778899999999887765
No 121
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=23.01 E-value=1.2e+02 Score=23.51 Aligned_cols=38 Identities=8% Similarity=-0.045 Sum_probs=25.5
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLANR 78 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~~ 78 (121)
...|+.|++||....-.... . ++++.||++...++...
T Consensus 36 ~~~~~~i~~~c~~~GI~~lT~YaFS~EN~~Rp~~EV~~Lm~L~~~~l~~~ 85 (230)
T PRK14837 36 LKRAKEIVKHSLKLGIKYLSLYVFSTENWNRTDSEIEHLMFLIADYLSSE 85 (230)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHHHHHHHH
Confidence 46789999999976432111 1 35668998888776543
No 122
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=22.97 E-value=76 Score=21.70 Aligned_cols=23 Identities=13% Similarity=0.189 Sum_probs=15.4
Q ss_pred CCHHHHHhhcCCCCCCCHHHHH-HHhh
Q 042635 82 KSVQYVGKFFGIENNFTPKEEV-ARTQ 107 (121)
Q Consensus 82 kt~eeiR~~f~I~~d~t~eEe~-ir~e 107 (121)
.+.+++.+.|. .+||||.+ +..|
T Consensus 78 ~~~~~lqkRle---~l~~eE~~~L~~e 101 (104)
T PF11460_consen 78 LTNEELQKRLE---ELSPEELEALQAE 101 (104)
T ss_pred HhHHHHHHHHH---hCCHHHHHHHHHH
Confidence 34567777775 66888877 6654
No 123
>PF02697 DUF217: Uncharacterized ACR, COG1753; InterPro: IPR003847 This entry is represented by Natrialba phage PhiCh1, Orf96. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.96 E-value=1.4e+02 Score=18.77 Aligned_cols=31 Identities=23% Similarity=0.253 Sum_probs=21.2
Q ss_pred hCCCHHHHHhhcCCCCCCCHHHHH--HHhhccc
Q 042635 80 KNKSVQYVGKFFGIENNFTPKEEV--ARTQYEW 110 (121)
Q Consensus 80 kgkt~eeiR~~f~I~~d~t~eEe~--ir~e~~w 110 (121)
+.+....+..+||+-+|-..++.. +++.-.|
T Consensus 34 ~~~~~~~l~~~~g~l~deea~~~~~~i~e~r~~ 66 (71)
T PF02697_consen 34 KEKKRRDLMDYFGILSDEEADEMEKDIKEEREE 66 (71)
T ss_pred cccchhHHHHHhccCChhhHHHHHHHHHHHHHH
Confidence 468889999999998776544333 5554444
No 124
>PRK13372 pcmA protocatechuate 4,5-dioxygenase; Provisional
Probab=22.72 E-value=70 Score=27.21 Aligned_cols=20 Identities=10% Similarity=0.091 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCHHHHHhhc
Q 042635 72 TETLANRIKNKSVQYVGKFF 91 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f 91 (121)
-+.|+..++|.|.||.|+++
T Consensus 93 ~~~~~a~m~g~t~e~f~~~~ 112 (444)
T PRK13372 93 FQQMAGSMTGLSEAAYRDMM 112 (444)
T ss_pred HHHHHHhhcCCCHHHHHHHH
Confidence 56788889999999999885
No 125
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=22.65 E-value=81 Score=19.18 Aligned_cols=17 Identities=18% Similarity=0.556 Sum_probs=13.1
Q ss_pred hhHHHHHHHHHHhhhcC
Q 042635 41 TEPLSYIIEFCKAHVEF 57 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~ 57 (121)
|.....+++||+.|...
T Consensus 23 S~a~~~li~y~e~~~~~ 39 (63)
T smart00224 23 SKAAEELLAYCEQHAEE 39 (63)
T ss_pred HHHHHHHHHHHHcCCCC
Confidence 56677889999987664
No 126
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=22.44 E-value=87 Score=24.38 Aligned_cols=20 Identities=30% Similarity=0.567 Sum_probs=17.0
Q ss_pred CCcEEEEeCCCCeEEecHHH
Q 042635 4 SKKISLKRADGQLFEVEEPV 23 (121)
Q Consensus 4 ~~~i~L~SsDG~~f~V~~~~ 23 (121)
.+.+++-|.||+.|+|....
T Consensus 5 draltvFSPDGhL~QVEYAq 24 (249)
T KOG0183|consen 5 DRALTVFSPDGHLFQVEYAQ 24 (249)
T ss_pred ccceEEECCCCCEEeeHhHH
Confidence 56799999999999997643
No 127
>PRK03094 hypothetical protein; Provisional
Probab=22.29 E-value=57 Score=21.22 Aligned_cols=12 Identities=0% Similarity=-0.044 Sum_probs=10.0
Q ss_pred hCCCHHHHHhhc
Q 042635 80 KNKSVQYVGKFF 91 (121)
Q Consensus 80 kgkt~eeiR~~f 91 (121)
.|+|+|||.+..
T Consensus 64 ~G~TaeEI~~~v 75 (80)
T PRK03094 64 SGLTADEICQQV 75 (80)
T ss_pred CCCCHHHHHHHH
Confidence 599999998764
No 128
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=21.96 E-value=90 Score=21.38 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=13.1
Q ss_pred CCCCCCCHHHHH-HHhh
Q 042635 92 GIENNFTPKEEV-ARTQ 107 (121)
Q Consensus 92 ~I~~d~t~eEe~-ir~e 107 (121)
.|++++||||.+ |+..
T Consensus 24 ~v~~~ls~eeK~~i~~~ 40 (115)
T PF05397_consen 24 PVTNSLSPEEKAAIRQQ 40 (115)
T ss_pred cccccCCHHHHHHHHHH
Confidence 467889999999 8874
No 129
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=21.82 E-value=1.4e+02 Score=16.22 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=14.1
Q ss_pred HHhCCCHHHHHhhcCCC
Q 042635 78 RIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 78 ~ikgkt~eeiR~~f~I~ 94 (121)
...|.|..+|-+.+|++
T Consensus 12 ~~~~~s~~eia~~l~~s 28 (57)
T cd06170 12 LAEGKTNKEIADILGIS 28 (57)
T ss_pred HHcCCCHHHHHHHHCCC
Confidence 34789999999999986
No 130
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=21.82 E-value=1.2e+02 Score=18.62 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=16.8
Q ss_pred HHHHHHHHHhCCCHHHHHhhcCCC
Q 042635 71 WTETLANRIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 71 ~c~~vA~~ikgkt~eeiR~~f~I~ 94 (121)
.+-+++....|.|..+|-++||--
T Consensus 35 va~yL~r~~~~~sl~~Ig~~fg~r 58 (70)
T PF08299_consen 35 VAMYLARELTGLSLSEIGRYFGGR 58 (70)
T ss_dssp HHHHHHHHHS---HHHHHHHCTSS
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCC
Confidence 455778888899999999999954
No 131
>PRK13500 transcriptional activator RhaR; Provisional
Probab=21.50 E-value=1.2e+02 Score=23.59 Aligned_cols=19 Identities=16% Similarity=0.020 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHHhhhcCCC
Q 042635 41 TEPLSYIIEFCKAHVEFSK 59 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~ 59 (121)
...+.++++|.+.|...+.
T Consensus 205 ~~~l~~i~~yI~~~~~e~i 223 (312)
T PRK13500 205 ETLLDKLITRLAASLKSPF 223 (312)
T ss_pred HHHHHHHHHHHHHcccCCC
Confidence 4567888888888776553
No 132
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=21.42 E-value=3.9e+02 Score=20.67 Aligned_cols=79 Identities=16% Similarity=0.314 Sum_probs=51.4
Q ss_pred CCCCcEEEEeCCCCeEEecHHHHhhcC------cCCCccc---------CCCCChhHHHHHHHHHHhhhcCCCCC-ch--
Q 042635 2 RHSKKISLKRADGQLFEVEEPVAMDFE------IEDTVVP---------LPNVSTEPLSYIIEFCKAHVEFSKQR-SP-- 63 (121)
Q Consensus 2 ~s~~~i~L~SsDG~~f~V~~~~a~~S~------ied~~Ip---------l~~V~s~~L~kVie~c~~h~~~~~~~-~~-- 63 (121)
.++..|+| --.|.+|.-++....... ++ ..|| +-+=+.+=+..|+.|+.--...-|.. .+
T Consensus 2 ~~~~~vkL-nvGG~~F~Tsk~TLtk~dg~fk~m~e-~~i~~~~d~s~~IFIDRSpKHF~~ILNfmRdGdv~LPe~~kel~ 79 (230)
T KOG2716|consen 2 SMSETVKL-NVGGTIFKTSKSTLTKFDGFFKTMLE-TDIPVEKDESGCIFIDRSPKHFDTILNFMRDGDVDLPESEKELK 79 (230)
T ss_pred CccceEEE-ecCCeEEEeehhhhhhhhhHHHHHhh-cCCccccCCcCcEEecCChhHHHHHHHhhhcccccCccchHHHH
Confidence 34455664 456889999888886533 22 2222 22556778999999998433332222 22
Q ss_pred ----------hhhHHHHHHHHHHHHHhCC
Q 042635 64 ----------KQEMLDYWTETLANRIKNK 82 (121)
Q Consensus 64 ----------~~~Ll~~~c~~vA~~ikgk 82 (121)
+++|.++|..+++..+++.
T Consensus 80 El~~EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 80 ELLREAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred HHHHHHHHhhHHHHHHHHHHHhhhcccCc
Confidence 3599999999999998875
No 133
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.33 E-value=1.3e+02 Score=23.15 Aligned_cols=37 Identities=8% Similarity=0.077 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLAN 77 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~ 77 (121)
...|..|++||....-.... . .+++.|+++....+..
T Consensus 33 ~~~l~~i~~~~~~lgIk~lTvYaFS~eN~~R~~~Ev~~Lm~L~~~~l~~ 81 (233)
T PRK14841 33 AEVLHNTVKWSLELGIKYLTAFSFSTENWKRPKEEVEFLMDLFVQMIDR 81 (233)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEeeeHhhcCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999876332111 1 3567999998887754
No 134
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=21.07 E-value=1.3e+02 Score=22.63 Aligned_cols=16 Identities=0% Similarity=-0.128 Sum_probs=9.3
Q ss_pred HHHHHHHHHHhhhcCC
Q 042635 43 PLSYIIEFCKAHVEFS 58 (121)
Q Consensus 43 ~L~kVie~c~~h~~~~ 58 (121)
.+.+++.|...|...+
T Consensus 187 ~~~~~~~~I~~~~~~~ 202 (287)
T TIGR02297 187 LFNRFNFLIEENYKQH 202 (287)
T ss_pred HHHHHHHHHHHhhccC
Confidence 4566666766555443
No 135
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=20.95 E-value=1.3e+02 Score=16.92 Aligned_cols=21 Identities=14% Similarity=0.292 Sum_probs=13.7
Q ss_pred HHHHHHhC-CCHHHHHhhcCCC
Q 042635 74 TLANRIKN-KSVQYVGKFFGIE 94 (121)
Q Consensus 74 ~vA~~ikg-kt~eeiR~~f~I~ 94 (121)
+|...-.| +|..+.-+.|||+
T Consensus 8 Ai~~v~~g~~S~r~AA~~ygVp 29 (45)
T PF05225_consen 8 AIEAVKNGKMSIRKAAKKYGVP 29 (45)
T ss_dssp HHHHHHTTSS-HHHHHHHHT--
T ss_pred HHHHHHhCCCCHHHHHHHHCcC
Confidence 44444577 8999999999998
No 136
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.86 E-value=74 Score=24.62 Aligned_cols=17 Identities=18% Similarity=0.378 Sum_probs=14.9
Q ss_pred CCHHHHHhhcCCCCCCC
Q 042635 82 KSVQYVGKFFGIENNFT 98 (121)
Q Consensus 82 kt~eeiR~~f~I~~d~t 98 (121)
++|.||+..||+-++++
T Consensus 112 g~~~Qi~~rFG~V~hlP 128 (225)
T PF09883_consen 112 GSPRQIRRRFGLVQHLP 128 (225)
T ss_pred CCHHHHHHHhCcccCCc
Confidence 89999999999887664
No 137
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=20.26 E-value=2.6e+02 Score=18.32 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhhhcCCCCCchhhhHHHHHHHHHHHHHhCCC
Q 042635 43 PLSYIIEFCKAHVEFSKQRSPKQEMLDYWTETLANRIKNKS 83 (121)
Q Consensus 43 ~L~kVie~c~~h~~~~~~~~~~~~Ll~~~c~~vA~~ikgkt 83 (121)
+..-.++||..|.- +|-.-=.+.|++.++|++
T Consensus 16 T~~eLlkyskqy~i---------~it~~QA~~I~~~lr~k~ 47 (85)
T PF11116_consen 16 TAKELLKYSKQYNI---------SITKKQAEQIANILRGKN 47 (85)
T ss_pred CHHHHHHHHHHhCC---------CCCHHHHHHHHHHHhcCC
Confidence 44445555555532 233333566777777776
No 138
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.18 E-value=1.4e+02 Score=23.36 Aligned_cols=37 Identities=11% Similarity=0.126 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLAN 77 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~ 77 (121)
...|..|++||....-.... . .+++.|+++.+.++..
T Consensus 48 ~~~l~~i~~~c~~~gI~~lTvyaFS~EN~~Rp~~EV~~Lm~L~~~~l~~ 96 (253)
T PRK14832 48 ARTLKELLRCCKDWGIKALTAYAFSTENWQRPIEEVDFLMLLFERLLRR 96 (253)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999876432111 1 3556888887776644
No 139
>PRK13367 protocatechuate 4,5-dioxygenase; Provisional
Probab=20.12 E-value=1e+02 Score=25.97 Aligned_cols=23 Identities=4% Similarity=0.062 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCHHHHHhhcCCC
Q 042635 72 TETLANRIKNKSVQYVGKFFGIE 94 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f~I~ 94 (121)
-+.|...++|.|.||.+++=|.+
T Consensus 387 ~~~~~a~m~g~s~e~f~~~r~~~ 409 (420)
T PRK13367 387 NLHIYAAMRGQTLEAFQKTRNQQ 409 (420)
T ss_pred HHHHHHhhcCCCHHHHHHHhCCc
Confidence 56678888999999999887655
No 140
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.05 E-value=1.4e+02 Score=23.21 Aligned_cols=37 Identities=8% Similarity=-0.027 Sum_probs=25.3
Q ss_pred hhHHHHHHHHHHhhhcCCCC-----C-------chhhhHHHHHHHHHHH
Q 042635 41 TEPLSYIIEFCKAHVEFSKQ-----R-------SPKQEMLDYWTETLAN 77 (121)
Q Consensus 41 s~~L~kVie~c~~h~~~~~~-----~-------~~~~~Ll~~~c~~vA~ 77 (121)
...|..|++||....-.... . .+++.||++.+..+..
T Consensus 44 ~~~l~~i~~~c~~lgI~~lTvYaFS~eN~~R~~~EV~~Lm~L~~~~l~~ 92 (249)
T PRK14834 44 VEALRRVVRAAGELGIGYLTLFAFSSENWSRPASEVSDLFGLLRLFIRR 92 (249)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEEEeccccCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999876432211 1 3566899988887754
No 141
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=20.05 E-value=2.3e+02 Score=18.85 Aligned_cols=19 Identities=21% Similarity=0.128 Sum_probs=13.8
Q ss_pred CCChhHHHHHHHHHHhhhc
Q 042635 38 NVSTEPLSYIIEFCKAHVE 56 (121)
Q Consensus 38 ~V~s~~L~kVie~c~~h~~ 56 (121)
.++..+...||++|..+..
T Consensus 5 g~~~e~I~~vi~~l~~~gy 23 (121)
T PF02631_consen 5 GFSEEAIEEVIDRLKELGY 23 (121)
T ss_dssp T--HHHHHHHHHHHHHTTS
T ss_pred CCCHHHHHHHHHHHHHcCC
Confidence 4678889999999987644
No 142
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=20.02 E-value=1.1e+02 Score=22.07 Aligned_cols=21 Identities=14% Similarity=0.268 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCHHHHHhhcC
Q 042635 72 TETLANRIKNKSVQYVGKFFG 92 (121)
Q Consensus 72 c~~vA~~ikgkt~eeiR~~f~ 92 (121)
+..||+.|+|++.++-..++.
T Consensus 26 ~r~va~~IrG~~v~~A~~~L~ 46 (150)
T TIGR01038 26 ARETARAIRGMELDKARKYLE 46 (150)
T ss_pred HHHHHHHHcCCcHHHHHHHHH
Confidence 567899999999999888865
Done!