Query 043718
Match_columns 228
No_of_seqs 145 out of 1146
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:40:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043718.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043718hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.5 2.4E-14 5.3E-19 105.2 8.6 68 4-75 3-70 (73)
2 PF00403 HMA: Heavy-metal-asso 99.4 1.7E-12 3.6E-17 90.7 7.9 57 9-65 1-60 (62)
3 COG2608 CopZ Copper chaperone 99.3 2.5E-11 5.3E-16 89.1 8.1 63 5-67 1-66 (71)
4 KOG4656 Copper chaperone for s 98.9 4.6E-09 9.9E-14 93.2 9.0 77 1-82 1-78 (247)
5 PLN02957 copper, zinc superoxi 98.2 1.6E-05 3.4E-10 70.4 10.2 71 6-81 6-76 (238)
6 PRK10671 copA copper exporting 98.1 6.4E-06 1.4E-10 83.7 7.9 64 6-76 3-67 (834)
7 TIGR00003 copper ion binding p 97.6 0.00077 1.7E-08 42.2 8.5 57 6-62 2-61 (68)
8 COG2217 ZntA Cation transport 97.0 0.0016 3.5E-08 66.5 7.4 61 6-67 2-66 (713)
9 PRK10671 copA copper exporting 96.2 0.014 3E-07 59.8 7.8 56 7-63 100-156 (834)
10 KOG0207 Cation transport ATPas 95.9 0.017 3.7E-07 60.6 6.7 61 6-66 146-209 (951)
11 COG1888 Uncharacterized protei 95.7 0.045 9.7E-07 43.4 6.7 78 1-79 1-86 (97)
12 PRK11033 zntA zinc/cadmium/mer 95.3 0.061 1.3E-06 54.8 8.0 58 6-63 53-111 (741)
13 KOG0207 Cation transport ATPas 94.7 0.059 1.3E-06 56.7 5.9 64 13-80 2-66 (951)
14 PF02680 DUF211: Uncharacteriz 93.3 0.16 3.4E-06 40.4 4.6 74 5-79 4-84 (95)
15 TIGR02052 MerP mercuric transp 87.6 2.9 6.4E-05 28.9 6.4 56 7-62 24-82 (92)
16 cd00371 HMA Heavy-metal-associ 85.7 4.3 9.3E-05 22.3 5.4 36 13-48 6-41 (63)
17 PF01883 DUF59: Domain of unkn 77.7 4.3 9.3E-05 28.9 4.1 32 7-38 35-72 (72)
18 PF13732 DUF4162: Domain of un 75.6 9.7 0.00021 27.5 5.5 48 27-77 26-74 (84)
19 PF04972 BON: BON domain; Int 73.6 3.5 7.5E-05 28.5 2.6 40 21-62 2-44 (64)
20 PRK11198 LysM domain/BON super 69.4 11 0.00024 31.2 5.1 46 20-66 28-74 (147)
21 PRK13748 putative mercuric red 68.1 12 0.00026 36.2 5.8 55 8-62 2-58 (561)
22 PF03927 NapD: NapD protein; 64.3 37 0.00081 25.4 6.7 43 19-62 16-58 (79)
23 PF14535 AMP-binding_C_2: AMP- 64.0 24 0.00051 26.7 5.6 59 21-80 7-82 (96)
24 PF09580 Spore_YhcN_YlaJ: Spor 61.3 8.4 0.00018 31.9 3.0 33 18-50 75-107 (177)
25 PF08260 Kinin: Insect kinin p 58.4 5.2 0.00011 18.7 0.7 8 197-204 1-8 (8)
26 PRK06418 transcription elongat 58.3 34 0.00073 29.6 6.2 69 8-79 8-100 (166)
27 PF14492 EFG_II: Elongation Fa 57.4 52 0.0011 24.1 6.3 56 10-66 8-68 (75)
28 PF08777 RRM_3: RNA binding mo 57.3 30 0.00065 27.2 5.3 56 8-64 2-60 (105)
29 PRK10553 assembly protein for 55.9 94 0.002 24.0 8.4 43 20-62 19-61 (87)
30 PF14437 MafB19-deam: MafB19-l 53.9 31 0.00067 29.4 5.1 41 6-47 100-142 (146)
31 PRK11023 outer membrane lipopr 52.9 30 0.00065 29.7 5.1 45 18-63 49-96 (191)
32 cd04888 ACT_PheB-BS C-terminal 51.8 44 0.00094 23.1 5.0 31 8-38 43-74 (76)
33 PF13740 ACT_6: ACT domain; PD 50.4 89 0.0019 22.5 6.5 59 6-64 1-65 (76)
34 PF05046 Img2: Mitochondrial l 48.3 91 0.002 23.8 6.5 59 5-65 27-86 (87)
35 PF13192 Thioredoxin_3: Thiore 47.2 29 0.00062 24.9 3.5 22 8-30 3-27 (76)
36 PF03958 Secretin_N: Bacterial 46.9 38 0.00081 24.2 4.1 27 35-61 47-73 (82)
37 COG3643 Glutamate formiminotra 46.2 22 0.00048 33.2 3.3 65 13-81 10-79 (302)
38 smart00362 RRM_2 RNA recogniti 44.7 80 0.0017 20.0 7.7 52 10-63 2-58 (72)
39 cd04920 ACT_AKiii-DAPDC_2 ACT 44.3 1.1E+02 0.0023 21.3 6.9 52 13-65 9-61 (63)
40 TIGR03406 FeS_long_SufT probab 43.9 30 0.00066 29.8 3.7 34 7-40 114-153 (174)
41 smart00749 BON bacterial OsmY 43.4 90 0.0019 20.2 6.8 42 21-62 2-45 (62)
42 PF13291 ACT_4: ACT domain; PD 42.8 66 0.0014 22.9 4.8 33 5-37 47-79 (80)
43 COG2177 FtsX Cell division pro 42.8 77 0.0017 29.6 6.4 47 7-67 62-108 (297)
44 PF07837 FTCD_N: Formiminotran 41.8 33 0.00072 30.0 3.6 47 20-67 18-66 (178)
45 TIGR02945 SUF_assoc FeS assemb 41.4 35 0.00077 25.7 3.4 21 21-41 58-78 (99)
46 KOG4034 Uncharacterized conser 40.4 62 0.0013 28.3 5.0 59 5-65 109-168 (169)
47 PRK10568 periplasmic protein; 38.7 66 0.0014 27.9 5.0 38 15-53 57-96 (203)
48 cd04883 ACT_AcuB C-terminal AC 38.2 1.3E+02 0.0028 20.5 6.9 59 9-67 3-67 (72)
49 PRK11023 outer membrane lipopr 38.1 87 0.0019 26.9 5.6 38 19-57 128-167 (191)
50 cd02410 archeal_CPSF_KH The ar 37.8 97 0.0021 26.4 5.7 57 18-77 53-114 (145)
51 PF08821 CGGC: CGGC domain; I 36.8 14 0.00031 29.4 0.6 52 13-66 43-99 (107)
52 COG2151 PaaD Predicted metal-s 36.7 62 0.0013 26.2 4.2 33 8-40 51-89 (111)
53 COG3062 NapD Uncharacterized p 35.1 1.1E+02 0.0024 24.5 5.2 45 18-63 18-62 (94)
54 PF04459 DUF512: Protein of un 34.4 96 0.0021 27.4 5.4 50 23-76 115-168 (204)
55 PRK10555 aminoglycoside/multid 33.5 63 0.0014 34.6 4.8 45 20-64 159-210 (1037)
56 PF05258 DUF721: Protein of un 31.6 92 0.002 22.1 4.1 37 38-74 44-89 (89)
57 cd04879 ACT_3PGDH-like ACT_3PG 28.7 1.1E+02 0.0024 19.9 3.9 15 22-36 54-68 (71)
58 PRK15127 multidrug efflux syst 28.7 87 0.0019 33.7 4.9 44 21-64 160-210 (1049)
59 TIGR02024 FtcD glutamate formi 28.4 74 0.0016 30.0 3.8 64 13-80 10-78 (298)
60 PF02983 Pro_Al_protease: Alph 27.8 1.4E+02 0.003 21.3 4.4 21 30-50 22-42 (62)
61 PRK09577 multidrug efflux prot 27.7 98 0.0021 33.2 5.1 45 20-64 158-209 (1032)
62 PF08002 DUF1697: Protein of u 27.5 2.3E+02 0.005 23.1 6.2 46 20-67 21-70 (137)
63 TIGR00915 2A0602 The (Largely 27.4 1E+02 0.0022 33.2 5.1 44 20-63 159-209 (1044)
64 PF01849 NAC: NAC domain; Int 26.9 66 0.0014 22.5 2.5 28 21-48 2-34 (58)
65 TIGR02898 spore_YhcN_YlaJ spor 26.5 2.2E+02 0.0048 24.3 6.1 31 18-48 54-84 (158)
66 PRK13763 putative RNA-processi 26.4 1.3E+02 0.0029 25.6 4.8 37 21-60 22-61 (180)
67 TIGR00914 2A0601 heavy metal e 26.3 88 0.0019 33.5 4.4 50 18-67 698-756 (1051)
68 PRK00378 nucleoid-associated p 25.8 74 0.0016 29.3 3.3 30 34-66 303-332 (334)
69 PF04468 PSP1: PSP1 C-terminal 25.6 2E+02 0.0043 21.8 5.2 39 33-75 44-86 (88)
70 PF12685 SpoIIIAH: SpoIIIAH-li 24.7 3.1E+02 0.0068 23.5 6.8 53 21-74 138-195 (196)
71 PRK10819 transport protein Ton 24.2 1.2E+02 0.0025 27.5 4.3 8 71-78 49-56 (246)
72 PF09843 DUF2070: Predicted me 23.9 1.9E+02 0.0041 24.5 5.3 48 31-79 61-111 (179)
73 PF00679 EFG_C: Elongation fac 23.6 3.1E+02 0.0066 20.2 8.2 49 17-67 15-67 (89)
74 PF01206 TusA: Sulfurtransfera 23.5 1.7E+02 0.0036 20.4 4.2 49 9-66 2-52 (70)
75 cd04878 ACT_AHAS N-terminal AC 23.0 1.8E+02 0.0038 19.0 4.0 29 7-36 43-71 (72)
76 PF05137 PilN: Fimbrial assemb 22.9 2.7E+02 0.0059 19.4 5.9 47 31-77 12-59 (78)
77 PF00873 ACR_tran: AcrB/AcrD/A 22.9 1.3E+02 0.0029 31.8 5.0 51 17-67 686-745 (1021)
78 cd02393 PNPase_KH Polynucleoti 22.7 1.9E+02 0.0042 20.2 4.3 37 22-62 22-58 (61)
79 KOG3432 Vacuolar H+-ATPase V1 22.5 1.5E+02 0.0033 24.5 4.2 43 30-75 24-66 (121)
80 PF10934 DUF2634: Protein of u 22.5 1.3E+02 0.0029 23.8 3.8 32 19-50 70-104 (112)
81 PTZ00449 104 kDa microneme/rho 22.3 3.6E+02 0.0077 28.4 7.5 19 59-77 486-504 (943)
82 PRK10509 bacterioferritin-asso 22.3 45 0.00097 24.2 1.0 22 9-30 32-53 (64)
83 PRK15317 alkyl hydroperoxide r 21.6 2.2E+02 0.0048 27.6 5.9 71 8-79 120-221 (517)
84 COG0425 SirA Predicted redox p 21.6 3.5E+02 0.0076 20.2 6.6 51 7-66 5-57 (78)
85 TIGR00489 aEF-1_beta translati 20.8 95 0.0021 24.1 2.6 22 18-39 62-83 (88)
86 cd04902 ACT_3PGDH-xct C-termin 20.6 1.9E+02 0.004 19.5 3.8 16 22-37 54-69 (73)
87 PRK09579 multidrug efflux prot 20.4 1.7E+02 0.0037 31.4 5.2 39 20-60 158-196 (1017)
88 PRK04435 hypothetical protein; 20.3 4.9E+02 0.011 21.4 8.8 70 6-77 68-146 (147)
89 PRK15078 polysaccharide export 20.1 1.9E+02 0.0041 27.6 5.0 59 9-67 133-204 (379)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.55 E-value=2.4e-14 Score=105.22 Aligned_cols=68 Identities=35% Similarity=0.514 Sum_probs=61.8
Q ss_pred CceEEEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEe
Q 043718 4 KVTTMVLKVDLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIK 75 (228)
Q Consensus 4 k~~tvvLKV~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIV 75 (228)
.+++.+|+|+|||++|+.+|++.|+.++||.++.+|.++++|||.|. +|+..|+++|++++++ .++++
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~-~~p~~vl~~l~k~~~k---~~~~~ 70 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN-VDPVKLLKKLKKTGGK---RAELW 70 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe-cCHHHHHHHHHhcCCC---ceEEe
Confidence 35788999999999999999999999999999999999999999999 9999999999986644 56555
No 2
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.39 E-value=1.7e-12 Score=90.69 Aligned_cols=57 Identities=33% Similarity=0.473 Sum_probs=51.0
Q ss_pred EEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeec--cCHHHHHHHHHHhc
Q 043718 9 VLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVC--CCPEKMRDKICCKG 65 (228)
Q Consensus 9 vLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~--vDPekLv~aL~kK~ 65 (228)
+|+| +|+|.+|+++|+++|.+++||.++.+|+.+++|+|++.. ++.++|+++|++.|
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~G 60 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAG 60 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTT
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhC
Confidence 6899 999999999999999999999999999999999999761 34599999999543
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.26 E-value=2.5e-11 Score=89.08 Aligned_cols=63 Identities=22% Similarity=0.288 Sum_probs=54.8
Q ss_pred ceEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEE--EeeccCHHHHHHHHHHhcCC
Q 043718 5 VTTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTI--KVVCCCPEKMRDKICCKGDG 67 (228)
Q Consensus 5 ~~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV--~G~~vDPekLv~aL~kK~gK 67 (228)
|+++.|+| +|+|+||+++|+++|.+++||.+|.+|+.+++++| ++..++.++|+++|...++.
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~ 66 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYK 66 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCC
Confidence 46789999 99999999999999999999999999999955555 45237999999999977774
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.93 E-value=4.6e-09 Score=93.20 Aligned_cols=77 Identities=17% Similarity=0.328 Sum_probs=68.3
Q ss_pred CCCC-ceEEEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEeCCCC
Q 043718 1 MPDK-VTTMVLKVDLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIKSPDD 79 (228)
Q Consensus 1 MAek-~~tvvLKV~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIVsp~~ 79 (228)
|+.. .-+++|.|.|+|++|++.|++.|..+.||.+|+||+.++.|.|.++ +.+..|.++|+ .+|+ ++.|++.+.
T Consensus 1 mtSd~~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts-~p~s~i~~~le-~tGr---~Avl~G~G~ 75 (247)
T KOG4656|consen 1 MTSDDTYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETS-VPPSEIQNTLE-NTGR---DAVLRGAGK 75 (247)
T ss_pred CCcCCceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEcc-CChHHHHHHHH-hhCh---heEEecCCc
Confidence 4443 3468899999999999999999999999999999999999999998 89999999998 6776 899999988
Q ss_pred CCC
Q 043718 80 QKK 82 (228)
Q Consensus 80 pk~ 82 (228)
+..
T Consensus 76 psa 78 (247)
T KOG4656|consen 76 PSA 78 (247)
T ss_pred hhH
Confidence 744
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.16 E-value=1.6e-05 Score=70.44 Aligned_cols=71 Identities=15% Similarity=0.192 Sum_probs=61.2
Q ss_pred eEEEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEeCCCCCC
Q 043718 6 TTMVLKVDLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIKSPDDQK 81 (228)
Q Consensus 6 ~tvvLKV~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIVsp~~pk 81 (228)
+++.|.|+|+|.+|+.+|+++|.+++||.++.+|+.+++++|... .+...|+++|++ .|. .+++++...+.
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~-~~~~~I~~aIe~-~Gy---~a~~~~~~~~~ 76 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS-SPVKAMTAALEQ-TGR---KARLIGQGDPE 76 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec-CCHHHHHHHHHH-cCC---cEEEecCCCcc
Confidence 467788899999999999999999999999999999999999876 788889999984 443 58888776554
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.13 E-value=6.4e-06 Score=83.75 Aligned_cols=64 Identities=20% Similarity=0.370 Sum_probs=55.0
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEeC
Q 043718 6 TTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIKS 76 (228)
Q Consensus 6 ~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIVs 76 (228)
++++|+| +|+|.+|+++|+++|.+++||.++.+|++ +++|++. ++.+.|.++|.+.+. ++++++
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~-~~~~~i~~~i~~~Gy----~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGT-ASAEALIETIKQAGY----DASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEec-CCHHHHHHHHHhcCC----cccccc
Confidence 5789999 99999999999999999999999999994 5667776 799999999995555 566654
No 7
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.63 E-value=0.00077 Score=42.21 Aligned_cols=57 Identities=12% Similarity=0.314 Sum_probs=47.4
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEe--eccCHHHHHHHHH
Q 043718 6 TTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKV--VCCCPEKMRDKIC 62 (228)
Q Consensus 6 ~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G--~~vDPekLv~aL~ 62 (228)
+++.|.| +|+|..|...|.+.|..+.++..+.+++..+++.|.. ...+...+...|.
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL 61 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH
Confidence 4677999 9999999999999999999999999999999988863 1135666666665
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.04 E-value=0.0016 Score=66.48 Aligned_cols=61 Identities=16% Similarity=0.346 Sum_probs=52.1
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEee--ccC-HHHHHHHHHHhcCC
Q 043718 6 TTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVV--CCC-PEKMRDKICCKGDG 67 (228)
Q Consensus 6 ~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~--~vD-PekLv~aL~kK~gK 67 (228)
.++.|.| +|||..|+.+|+ +|.+++||.++.+|+.+++++|... ..+ .+.+..+++..+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~ 66 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYS 66 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCcc
Confidence 4678999 999999999999 9999999999999999999999742 145 67888888866553
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.24 E-value=0.014 Score=59.79 Aligned_cols=56 Identities=13% Similarity=0.329 Sum_probs=50.1
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHH
Q 043718 7 TMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICC 63 (228)
Q Consensus 7 tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~k 63 (228)
++.|.| +|+|.+|+..|++.|..++||.++.+|+.++++.|.+. .+.+.+.+.+..
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~-~s~~~I~~~I~~ 156 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGS-ASPQDLVQAVEK 156 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEcc-CCHHHHHHHHHh
Confidence 567889 99999999999999999999999999999999998765 688888888774
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=95.94 E-value=0.017 Score=60.58 Aligned_cols=61 Identities=15% Similarity=0.305 Sum_probs=52.2
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEe--eccCHHHHHHHHHHhcC
Q 043718 6 TTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKV--VCCCPEKMRDKICCKGD 66 (228)
Q Consensus 6 ~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G--~~vDPekLv~aL~kK~g 66 (228)
.+++|.| +|.|..|..+|++.|.+++||+++++|+.+++++|.- ....+.++++.|...+-
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~ 209 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGF 209 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcc
Confidence 4789999 9999999999999999999999999999999999962 12467888888885433
No 11
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=95.69 E-value=0.045 Score=43.43 Aligned_cols=78 Identities=21% Similarity=0.175 Sum_probs=55.7
Q ss_pred CCCCceEEEEEE-eccChhhHHHHHHHHhcCCCceeEEE-----Ec--CCCEEEEEeeccCHHHHHHHHHHhcCCccccE
Q 043718 1 MPDKVTTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIY-----DE--KQNKVTIKVVCCCPEKMRDKICCKGDGVIKSI 72 (228)
Q Consensus 1 MAek~~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~v-----D~--k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~a 72 (228)
|+..++.++|-| -=|-+-=.-.+-+.|++|+||+.|.+ |. .+=++||.|+.+|.+.|.+.|.+ .|.+|.+|
T Consensus 1 ~~~~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~-~Gg~IHSi 79 (97)
T COG1888 1 MMKGIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEE-LGGAIHSI 79 (97)
T ss_pred CCccceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHH-cCCeeeeh
Confidence 566777788877 44444445567788999999877743 32 45567888988999999999995 55567777
Q ss_pred EEeCCCC
Q 043718 73 EIKSPDD 79 (228)
Q Consensus 73 EIVsp~~ 79 (228)
.-|-.++
T Consensus 80 DevvaGk 86 (97)
T COG1888 80 DEVVAGK 86 (97)
T ss_pred hhhhhcc
Confidence 6665554
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=95.30 E-value=0.061 Score=54.83 Aligned_cols=58 Identities=14% Similarity=0.237 Sum_probs=45.8
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHH
Q 043718 6 TTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICC 63 (228)
Q Consensus 6 ~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~k 63 (228)
+++.|+| +|+|.+|..+|+++|.+++||.++.+++.++++.|.......+.+.+.+..
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~ 111 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQK 111 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHh
Confidence 3567889 999999999999999999999999999999998886321112555555553
No 13
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=94.66 E-value=0.059 Score=56.68 Aligned_cols=64 Identities=20% Similarity=0.365 Sum_probs=54.3
Q ss_pred eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEe-eccCHHHHHHHHHHhcCCccccEEEeCCCCC
Q 043718 13 DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKV-VCCCPEKMRDKICCKGDGVIKSIEIKSPDDQ 80 (228)
Q Consensus 13 ~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G-~~vDPekLv~aL~kK~gK~IK~aEIVsp~~p 80 (228)
+|+|..|.+.|.++|++.+||.++.+++.+++.+|.- ..++++.|+++|...+. ++++++....
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf----~~~~~~~~~~ 66 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGF----EASLLSDSEI 66 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccc----eeeecccCcc
Confidence 7999999999999999999999999999888877752 33799999999997665 6888876543
No 14
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=93.31 E-value=0.16 Score=40.42 Aligned_cols=74 Identities=20% Similarity=0.212 Sum_probs=48.8
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCCceeEEE-----EcCCCE--EEEEeeccCHHHHHHHHHHhcCCccccEEEeCC
Q 043718 5 VTTMVLKVDLQCSKCYKKVKKVLSKFPQIQDQIY-----DEKQNK--VTIKVVCCCPEKMRDKICCKGDGVIKSIEIKSP 77 (228)
Q Consensus 5 ~~tvvLKV~M~C~gCakKIkKaL~kl~GV~sV~v-----D~k~~k--VtV~G~~vDPekLv~aL~kK~gK~IK~aEIVsp 77 (228)
++.++|-|---=+==.-.+-++|++++||..|.+ |.++.. +||+|..+|.+.|.++|. ..|.+|.||.-|..
T Consensus 4 irRlVLDVlKP~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSIDeVva 82 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSIDEVVA 82 (95)
T ss_dssp EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEEEEEEE
T ss_pred eeEEEEEeecCCCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEeeeeeee
Confidence 4566676622233345567889999999888854 333333 555687789999999999 56667888877655
Q ss_pred CC
Q 043718 78 DD 79 (228)
Q Consensus 78 ~~ 79 (228)
++
T Consensus 83 G~ 84 (95)
T PF02680_consen 83 GK 84 (95)
T ss_dssp ES
T ss_pred cc
Confidence 44
No 15
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=87.59 E-value=2.9 Score=28.87 Aligned_cols=56 Identities=16% Similarity=0.238 Sum_probs=41.6
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEe--eccCHHHHHHHHH
Q 043718 7 TMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKV--VCCCPEKMRDKIC 62 (228)
Q Consensus 7 tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G--~~vDPekLv~aL~ 62 (228)
++.+.+ +++|.+|...++..+....||....++....++.+.. ...+...+...+.
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT 82 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH
Confidence 456777 9999999999999999999999898888888766642 1134444544444
No 16
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=85.70 E-value=4.3 Score=22.33 Aligned_cols=36 Identities=28% Similarity=0.605 Sum_probs=30.7
Q ss_pred eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEE
Q 043718 13 DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIK 48 (228)
Q Consensus 13 ~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~ 48 (228)
+++|..|...+...+..+.|+....+++....+.+.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVE 41 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEE
Confidence 889999999999999999998888888777766665
No 17
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=77.69 E-value=4.3 Score=28.95 Aligned_cols=32 Identities=13% Similarity=0.428 Sum_probs=22.8
Q ss_pred EEEEEEeccChhhH------HHHHHHHhcCCCceeEEE
Q 043718 7 TMVLKVDLQCSKCY------KKVKKVLSKFPQIQDQIY 38 (228)
Q Consensus 7 tvvLKV~M~C~gCa------kKIkKaL~kl~GV~sV~v 38 (228)
++.|.+.+...+|. ..|+++|..++||.+|+|
T Consensus 35 ~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 56677766665554 789999999999999875
No 18
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=75.61 E-value=9.7 Score=27.49 Aligned_cols=48 Identities=17% Similarity=0.264 Sum_probs=33.7
Q ss_pred HhcCCCceeEEEEcCC-CEEEEEeeccCHHHHHHHHHHhcCCccccEEEeCC
Q 043718 27 LSKFPQIQDQIYDEKQ-NKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIKSP 77 (228)
Q Consensus 27 L~kl~GV~sV~vD~k~-~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIVsp 77 (228)
|..++||.++..+... -++.|... .+...|++.|..+ |- |.+.++..|
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~-~~~~~ll~~l~~~-g~-I~~f~~~~P 74 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDE-ETANELLQELIEK-GI-IRSFEEEEP 74 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCc-ccHHHHHHHHHhC-CC-eeEEEEcCC
Confidence 8889999999876433 34555554 5778899999855 43 777776544
No 19
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=73.56 E-value=3.5 Score=28.47 Aligned_cols=40 Identities=20% Similarity=0.217 Sum_probs=20.8
Q ss_pred HHHHHHHhc---CCCceeEEEEcCCCEEEEEeeccCHHHHHHHHH
Q 043718 21 KKVKKVLSK---FPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKIC 62 (228)
Q Consensus 21 kKIkKaL~k---l~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~ 62 (228)
.+|+.+|.. +++- ++.+...++.|+++|. ++-...++++.
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~-v~s~~~~~~a~ 44 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGE-VPSQEQRDAAE 44 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEE-ESSCHHHHHHH
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEee-CcHHHHHHhHH
Confidence 467788877 4455 7889999999999998 64333333333
No 20
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=69.41 E-value=11 Score=31.17 Aligned_cols=46 Identities=17% Similarity=0.106 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCC-CceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcC
Q 043718 20 YKKVKKVLSKFP-QIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGD 66 (228)
Q Consensus 20 akKIkKaL~kl~-GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~g 66 (228)
+++|.++|.+.. ++..+.|...++.|++.|. +.-+..+.+|....+
T Consensus 28 ~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~-v~s~~~~~~~~~aa~ 74 (147)
T PRK11198 28 ADALKEHISKQGLGDADVNVQVEDGKATVSGD-AASQEAKEKILLAVG 74 (147)
T ss_pred HHHHHHHHHhcCCCcCCceEEEeCCEEEEEEE-eCCHHHHHHHHHHhc
Confidence 466777776632 4666777888999999999 777777778776665
No 21
>PRK13748 putative mercuric reductase; Provisional
Probab=68.06 E-value=12 Score=36.16 Aligned_cols=55 Identities=20% Similarity=0.441 Sum_probs=42.4
Q ss_pred EEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEee-ccCHHHHHHHHH
Q 043718 8 MVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVV-CCCPEKMRDKIC 62 (228)
Q Consensus 8 vvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~-~vDPekLv~aL~ 62 (228)
+.|.+ +|+|.+|..+++..+..++++....+++..+.+.+... ..+...+...+.
T Consensus 2 ~~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~ 58 (561)
T PRK13748 2 TTLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA 58 (561)
T ss_pred EEEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH
Confidence 34667 99999999999999999999999999998888777631 134455555554
No 22
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=64.26 E-value=37 Score=25.41 Aligned_cols=43 Identities=21% Similarity=0.312 Sum_probs=30.6
Q ss_pred hHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHH
Q 043718 19 CYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKIC 62 (228)
Q Consensus 19 CakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~ 62 (228)
=...|+++|..++||+=...|.+ +++.|+-..-+...+.+.|.
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 35789999999999966677766 66666432236677777666
No 23
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=63.96 E-value=24 Score=26.73 Aligned_cols=59 Identities=15% Similarity=0.338 Sum_probs=35.8
Q ss_pred HHHHHHHhcCCCce-eE--EEE--cCCCEEEEEee---cc-C--------HHHHHHHHHHhcCCccccEEEeCCCCC
Q 043718 21 KKVKKVLSKFPQIQ-DQ--IYD--EKQNKVTIKVV---CC-C--------PEKMRDKICCKGDGVIKSIEIKSPDDQ 80 (228)
Q Consensus 21 kKIkKaL~kl~GV~-sV--~vD--~k~~kVtV~G~---~v-D--------PekLv~aL~kK~gK~IK~aEIVsp~~p 80 (228)
..|..+|.+++|+. .. .++ ...+.++|... .+ + .+.|.++|+.+.|-.. .|+|+.++.=
T Consensus 7 ~~Ie~vl~~~~~~~~~y~i~v~~~~~~D~l~v~vE~~~~~~~~~~~~~~l~~~i~~~lk~~lgv~~-~V~lv~~gtL 82 (96)
T PF14535_consen 7 SQIEEVLREFPEVSPEYQIVVTREGGLDELTVRVELRPGFSDDAEDLEALAERIAERLKERLGVRP-EVELVPPGTL 82 (96)
T ss_dssp HHHHHHHCTSTTEEEEEEEEEEEETTEEEEEEEEEESTTCCTTHHHHHHHHHHHHHHHHHHHSS-E-EEEEE-TT-S
T ss_pred HHHHHHHHhCcCCCCcEEEEEEcCCCCcEEEEEEEECCccCcchHHHHHHHHHHHHHHHhhcCceE-EEEEECCCCc
Confidence 46899999999987 33 333 24445555422 01 1 2467777777877544 8888988653
No 24
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=61.35 E-value=8.4 Score=31.95 Aligned_cols=33 Identities=12% Similarity=0.229 Sum_probs=28.0
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCEEEEEee
Q 043718 18 KCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVV 50 (228)
Q Consensus 18 gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~ 50 (228)
.=+.+|.+.|.+++||.++.+=..++.+.|...
T Consensus 75 ~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~ 107 (177)
T PF09580_consen 75 QLADRIANRVKKVPGVEDATVVVTDDNAYVAVD 107 (177)
T ss_pred HHHHHHHHHHhcCCCceEEEEEEECCEEEEEEE
Confidence 346889999999999999999998898888543
No 25
>PF08260 Kinin: Insect kinin peptide; InterPro: IPR013202 This entry represents neuropeptides that are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. Insect kinins also mediate visceral muscle contractile activity (myotropic activity) []. These peptides have lengths ranging from 6 to 14 amino acids [].
Probab=58.36 E-value=5.2 Score=18.74 Aligned_cols=8 Identities=50% Similarity=1.568 Sum_probs=6.0
Q ss_pred CCCccCCC
Q 043718 197 RPVYDSWG 204 (228)
Q Consensus 197 ~p~yd~~g 204 (228)
+|+|.|||
T Consensus 1 ~pafnswg 8 (8)
T PF08260_consen 1 DPAFNSWG 8 (8)
T ss_pred CccccccC
Confidence 36788887
No 26
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=58.33 E-value=34 Score=29.58 Aligned_cols=69 Identities=19% Similarity=0.275 Sum_probs=43.0
Q ss_pred EEEEEeccChhhHHHH------------HHHHhcC------CCceeEEEEcCCCEEEEEeeccC------HHHHHHHHHH
Q 043718 8 MVLKVDLQCSKCYKKV------------KKVLSKF------PQIQDQIYDEKQNKVTIKVVCCC------PEKMRDKICC 63 (228)
Q Consensus 8 vvLKV~M~C~gCakKI------------kKaL~kl------~GV~sV~vD~k~~kVtV~G~~vD------PekLv~aL~k 63 (228)
+=+|-++-|.+|.++| .++|.+| .++.-...=..+++|++....-| --..+++|++
T Consensus 8 ~c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l~~ 87 (166)
T PRK06418 8 VCVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKALSR 87 (166)
T ss_pred EEeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHHHH
Confidence 3355599999999875 5788887 33333332223466665321011 1357889999
Q ss_pred hcCCccccEEEeCCCC
Q 043718 64 KGDGVIKSIEIKSPDD 79 (228)
Q Consensus 64 K~gK~IK~aEIVsp~~ 79 (228)
+.|+ +|+||.-..
T Consensus 88 ~lgk---~VevVE~s~ 100 (166)
T PRK06418 88 KLGK---KVRVVEKTN 100 (166)
T ss_pred HhCC---cEEEEEcCC
Confidence 9997 888887543
No 27
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=57.37 E-value=52 Score=24.06 Aligned_cols=56 Identities=11% Similarity=0.078 Sum_probs=39.7
Q ss_pred EEEeccChhhHHHHHHHHhcC---CCceeEEEEcCCCEEEEEe--eccCHHHHHHHHHHhcC
Q 043718 10 LKVDLQCSKCYKKVKKVLSKF---PQIQDQIYDEKQNKVTIKV--VCCCPEKMRDKICCKGD 66 (228)
Q Consensus 10 LKV~M~C~gCakKIkKaL~kl---~GV~sV~vD~k~~kVtV~G--~~vDPekLv~aL~kK~g 66 (228)
+.|.-.=.+=..++.++|.+| +---.+..|.+++.+.|.| . +--+.++++|++++|
T Consensus 8 ~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Ge-lhlev~~~~L~~~~~ 68 (75)
T PF14492_consen 8 VAIEPKNKEDEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGE-LHLEVLLERLKRRFG 68 (75)
T ss_dssp EEEEESSHHHHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSH-HHHHHHHHHHHHTTC
T ss_pred EEEEECCHhHHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCH-HHHHHHHHHHHHHHC
Confidence 334333345566777777776 3455889999999999985 4 566889999998887
No 28
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=57.29 E-value=30 Score=27.21 Aligned_cols=56 Identities=14% Similarity=0.204 Sum_probs=32.9
Q ss_pred EEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEE--eeccCHHHHHHHHHHh
Q 043718 8 MVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIK--VVCCCPEKMRDKICCK 64 (228)
Q Consensus 8 vvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~--G~~vDPekLv~aL~kK 64 (228)
++|+| +++=+-....|+.+|+.+..|.-|.+...+..-.|. .. -+...+++++...
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~-~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTP-EAAQKALEKLKEA 60 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS----HHHHHHHHHHT
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCc-chHHHHHHHHHhc
Confidence 35677 576666699999999999999999988877776664 32 3567788888755
No 29
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=55.85 E-value=94 Score=24.04 Aligned_cols=43 Identities=16% Similarity=0.233 Sum_probs=31.7
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHH
Q 043718 20 YKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKIC 62 (228)
Q Consensus 20 akKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~ 62 (228)
...|.++|..++|++=...|..+++++|+-..-+...+++.|.
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 7889999999999988888887787766532125565555555
No 30
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=53.91 E-value=31 Score=29.41 Aligned_cols=41 Identities=20% Similarity=0.310 Sum_probs=32.8
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcC-CCEEEE
Q 043718 6 TTMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEK-QNKVTI 47 (228)
Q Consensus 6 ~tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k-~~kVtV 47 (228)
..++|.| .-.|..|...|.....++ |+.+++|-.. ++++.+
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVYY 142 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEEE
Confidence 3678888 667999999998888777 8888888776 776665
No 31
>PRK11023 outer membrane lipoprotein; Provisional
Probab=52.93 E-value=30 Score=29.75 Aligned_cols=45 Identities=20% Similarity=0.090 Sum_probs=34.5
Q ss_pred hhHHHHHHHHhcCCCce---eEEEEcCCCEEEEEeeccCHHHHHHHHHH
Q 043718 18 KCYKKVKKVLSKFPQIQ---DQIYDEKQNKVTIKVVCCCPEKMRDKICC 63 (228)
Q Consensus 18 gCakKIkKaL~kl~GV~---sV~vD~k~~kVtV~G~~vDPekLv~aL~k 63 (228)
.=..+|+.+|..-+++. ++.++..++.|+++|. ++-+..+.+..+
T Consensus 49 ~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~-V~~~~~k~~A~~ 96 (191)
T PRK11023 49 TLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQ-SPNAELSERAKQ 96 (191)
T ss_pred HHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEE-eCCHHHHHHHHH
Confidence 44678889998877774 5888889999999999 766665555553
No 32
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=51.85 E-value=44 Score=23.11 Aligned_cols=31 Identities=6% Similarity=0.134 Sum_probs=20.5
Q ss_pred EEEEEeccChh-hHHHHHHHHhcCCCceeEEE
Q 043718 8 MVLKVDLQCSK-CYKKVKKVLSKFPQIQDQIY 38 (228)
Q Consensus 8 vvLKV~M~C~g-CakKIkKaL~kl~GV~sV~v 38 (228)
+.|.|..+-.. =-+.|.+.|++++||.+|.+
T Consensus 43 i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 43 VTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 44445444443 66778888888888887764
No 33
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=50.44 E-value=89 Score=22.46 Aligned_cols=59 Identities=15% Similarity=0.104 Sum_probs=40.9
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCC-ceeEEEEcCCCEEEEE----eeccCHHHHHHHHHHh
Q 043718 6 TTMVLKV-DLQCSKCYKKVKKVLSKFPQ-IQDQIYDEKQNKVTIK----VVCCCPEKMRDKICCK 64 (228)
Q Consensus 6 ~tvvLKV-~M~C~gCakKIkKaL~kl~G-V~sV~vD~k~~kVtV~----G~~vDPekLv~aL~kK 64 (228)
+.+++.| +.+..|-...|.++|.+..+ |.+++...-.+..+.. +..-+.+.|.+.|...
T Consensus 1 ~~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~l 65 (76)
T PF13740_consen 1 EQLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEEL 65 (76)
T ss_dssp EEEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHHH
T ss_pred CEEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHHH
Confidence 3578888 99999999999999999987 7777777766665543 3212455677777654
No 34
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=48.32 E-value=91 Score=23.79 Aligned_cols=59 Identities=22% Similarity=0.218 Sum_probs=43.9
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCC-ceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhc
Q 043718 5 VTTMVLKVDLQCSKCYKKVKKVLSKFPQ-IQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKG 65 (228)
Q Consensus 5 ~~tvvLKV~M~C~gCakKIkKaL~kl~G-V~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~ 65 (228)
..|++=+|.=+=....+.+.+.|....+ -..+.++.-+++|.|.|. -.+.|.+.|..++
T Consensus 27 ~~T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~--~~~~Vk~wL~~~G 86 (87)
T PF05046_consen 27 KITVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD--HVEEVKKWLLEKG 86 (87)
T ss_pred eEEEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCc--cHHHHHHHHHHCc
Confidence 4466666755557788888888876655 347789999999999997 3577888887654
No 35
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=47.18 E-value=29 Score=24.94 Aligned_cols=22 Identities=14% Similarity=0.391 Sum_probs=13.4
Q ss_pred EEEEEeccChhhHH---HHHHHHhcC
Q 043718 8 MVLKVDLQCSKCYK---KVKKVLSKF 30 (228)
Q Consensus 8 vvLKV~M~C~gCak---KIkKaL~kl 30 (228)
+.+ ++.+|..|.. .++.++..+
T Consensus 3 I~v-~~~~C~~C~~~~~~~~~~~~~~ 27 (76)
T PF13192_consen 3 IKV-FSPGCPYCPELVQLLKEAAEEL 27 (76)
T ss_dssp EEE-ECSSCTTHHHHHHHHHHHHHHT
T ss_pred EEE-eCCCCCCcHHHHHHHHHHHHhc
Confidence 344 5888999983 333444444
No 36
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=46.89 E-value=38 Score=24.16 Aligned_cols=27 Identities=22% Similarity=0.281 Sum_probs=19.6
Q ss_pred eEEEEcCCCEEEEEeeccCHHHHHHHH
Q 043718 35 DQIYDEKQNKVTIKVVCCCPEKMRDKI 61 (228)
Q Consensus 35 sV~vD~k~~kVtV~G~~vDPekLv~aL 61 (228)
.|.+|..+|.|+|.|+.-+.+.|.+.|
T Consensus 47 ~i~~d~~tNsliv~g~~~~~~~i~~li 73 (82)
T PF03958_consen 47 RIVADERTNSLIVRGTPEDLEQIRELI 73 (82)
T ss_dssp EEEEECTTTEEEEEEEHHHHHHHHHHH
T ss_pred EEEEECCCCEEEEEeCHHHHHHHHHHH
Confidence 899999999999999833334444443
No 37
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=46.21 E-value=22 Score=33.22 Aligned_cols=65 Identities=14% Similarity=0.187 Sum_probs=42.9
Q ss_pred eccChhhH---HHHHHHHhcCCCceeEEEE--cCCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEeCCCCCC
Q 043718 13 DLQCSKCY---KKVKKVLSKFPQIQDQIYD--EKQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIKSPDDQK 81 (228)
Q Consensus 13 ~M~C~gCa---kKIkKaL~kl~GV~sV~vD--~k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIVsp~~pk 81 (228)
|.+=++=. .+|..++.++++|.-++++ .+-|+-.|+-. .|++++++++..-.+. .+++|+-...+
T Consensus 10 NfSEG~~~~~ie~i~a~~~~~~~v~ildve~danhNRsViT~v-gdp~~~~~A~f~~ik~---AaelIDM~~H~ 79 (302)
T COG3643 10 NFSEGRDLEKIEKIVAAAKSIPTVKILDVEMDANHNRSVITLV-GDPSKVVNAAFALIKK---AAELIDMRNHK 79 (302)
T ss_pred CccccccHHHHHHHHHHHhcCCceEEEEeccCCCCCceEEEEe-cChHHHHHHHHHHHHH---HHHhhchhccC
Confidence 55555444 4555666677886655554 46666666666 5899999999876665 56777665443
No 38
>smart00362 RRM_2 RNA recognition motif.
Probab=44.73 E-value=80 Score=20.03 Aligned_cols=52 Identities=19% Similarity=0.196 Sum_probs=38.7
Q ss_pred EEE-eccChhhHHHHHHHHhcCCCceeEEEEcCC----CEEEEEeeccCHHHHHHHHHH
Q 043718 10 LKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQ----NKVTIKVVCCCPEKMRDKICC 63 (228)
Q Consensus 10 LKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~----~kVtV~G~~vDPekLv~aL~k 63 (228)
|.| ++...--...|++.|..+..|..+.+-... +.+.|+-. +.+....+|..
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~--~~~~a~~a~~~ 58 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFE--SEEDAEKAIEA 58 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeC--CHHHHHHHHHH
Confidence 445 777777889999999999999998888765 66777643 55666666654
No 39
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=44.27 E-value=1.1e+02 Score=21.33 Aligned_cols=52 Identities=8% Similarity=-0.042 Sum_probs=37.6
Q ss_pred ec-cChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhc
Q 043718 13 DL-QCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKG 65 (228)
Q Consensus 13 ~M-~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~ 65 (228)
+| ...+...++-++|.+. +|.-+.....+..+++-...-|.++++++|++++
T Consensus 9 g~~~~~gv~~~~~~~L~~~-~i~~i~~~~s~~~is~vv~~~d~~~av~~LH~~f 61 (63)
T cd04920 9 GIRSLLHKLGPALEVFGKK-PVHLVSQAANDLNLTFVVDEDQADGLCARLHFQL 61 (63)
T ss_pred CcccCccHHHHHHHHHhcC-CceEEEEeCCCCeEEEEEeHHHHHHHHHHHHHHH
Confidence 66 5788999999999775 8888888887777765322135566777777543
No 40
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=43.89 E-value=30 Score=29.84 Aligned_cols=34 Identities=12% Similarity=0.291 Sum_probs=25.0
Q ss_pred EEEEEEeccChhhH------HHHHHHHhcCCCceeEEEEc
Q 043718 7 TMVLKVDLQCSKCY------KKVKKVLSKFPQIQDQIYDE 40 (228)
Q Consensus 7 tvvLKV~M~C~gCa------kKIkKaL~kl~GV~sV~vD~ 40 (228)
.+.|.+.|+-.+|. ..|+++|..++||.+|.+++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 45566655555554 56899999999999998874
No 41
>smart00749 BON bacterial OsmY and nodulation domain.
Probab=43.43 E-value=90 Score=20.21 Aligned_cols=42 Identities=19% Similarity=0.063 Sum_probs=28.8
Q ss_pred HHHHHHHhcCCCcee--EEEEcCCCEEEEEeeccCHHHHHHHHH
Q 043718 21 KKVKKVLSKFPQIQD--QIYDEKQNKVTIKVVCCCPEKMRDKIC 62 (228)
Q Consensus 21 kKIkKaL~kl~GV~s--V~vD~k~~kVtV~G~~vDPekLv~aL~ 62 (228)
.+|+.+|.....+.. +.+....+.|++.|...+.+.+..+..
T Consensus 2 ~~v~~~l~~~~~~~~~~~~v~~~~~~vvL~g~~~~~~~~~~~~~ 45 (62)
T smart00749 2 EKVKKALAKDGLIKADSIVVVTDGGVVVLLGGVVDNAEAAAAAA 45 (62)
T ss_pred hhHHHHHhhCCCCCcCceEEEEECCEEEEeeecCCHHHHHHHHH
Confidence 578899988887765 677778899998876234444443333
No 42
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=42.79 E-value=66 Score=22.88 Aligned_cols=33 Identities=12% Similarity=0.261 Sum_probs=24.5
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCCceeEE
Q 043718 5 VTTMVLKVDLQCSKCYKKVKKVLSKFPQIQDQI 37 (228)
Q Consensus 5 ~~tvvLKV~M~C~gCakKIkKaL~kl~GV~sV~ 37 (228)
...+.|.|...--.=-+.|.+.|++++||.+|.
T Consensus 47 ~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 47 TARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 345666666666666778888999999998874
No 43
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=42.77 E-value=77 Score=29.56 Aligned_cols=47 Identities=13% Similarity=0.098 Sum_probs=39.5
Q ss_pred EEEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcCC
Q 043718 7 TMVLKVDLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGDG 67 (228)
Q Consensus 7 tvvLKV~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK 67 (228)
++.|+++.+ +.|.+.|++.|..++||+++++- |.++-.+.|+.+.|.
T Consensus 62 ~vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~~-------------sre~~l~~L~~~lg~ 108 (297)
T COG2177 62 TVYLQIDAD-QDDAALVREKIEGIPGVKSVRFI-------------SREEALKELQPWLGF 108 (297)
T ss_pred EEEEecCCC-hHHHHHHHHHHhcCCCcceEEEe-------------CHHHHHHHHHHHcCc
Confidence 455666777 99999999999999999988763 678889999999984
No 44
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=41.76 E-value=33 Score=30.04 Aligned_cols=47 Identities=17% Similarity=0.217 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCCcee--EEEEcCCCEEEEEeeccCHHHHHHHHHHhcCC
Q 043718 20 YKKVKKVLSKFPQIQD--QIYDEKQNKVTIKVVCCCPEKMRDKICCKGDG 67 (228)
Q Consensus 20 akKIkKaL~kl~GV~s--V~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK 67 (228)
..+|.+++++.+||.- +..|.+-|+..|+-. -+++.|.+++.....+
T Consensus 18 ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~v-G~p~~v~~a~~~~~~~ 66 (178)
T PF07837_consen 18 IEAIAKAARNVPGVKLLDVFSDADYNRSVITLV-GEPEAVAEAAFAAIRK 66 (178)
T ss_dssp HHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEE-E-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEe-eChHHHHHHHHHHHHH
Confidence 4566666677777554 456678888777744 3678888888765554
No 45
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=41.43 E-value=35 Score=25.72 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=17.9
Q ss_pred HHHHHHHhcCCCceeEEEEcC
Q 043718 21 KKVKKVLSKFPQIQDQIYDEK 41 (228)
Q Consensus 21 kKIkKaL~kl~GV~sV~vD~k 41 (228)
+.|+.+|..+.||.+|.+++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 568889999999999998864
No 46
>KOG4034 consensus Uncharacterized conserved protein NOF (Neighbor of FAU) [Function unknown]
Probab=40.42 E-value=62 Score=28.27 Aligned_cols=59 Identities=17% Similarity=0.188 Sum_probs=45.5
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCCc-eeEEEEcCCCEEEEEeeccCHHHHHHHHHHhc
Q 043718 5 VTTMVLKVDLQCSKCYKKVKKVLSKFPQI-QDQIYDEKQNKVTIKVVCCCPEKMRDKICCKG 65 (228)
Q Consensus 5 ~~tvvLKV~M~C~gCakKIkKaL~kl~GV-~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~ 65 (228)
..|++=+|.-+=-.|.+.++..|.-+.|= -.-.||.-++++.+.|. -.+.|.+.|.+||
T Consensus 109 ~lT~IRkVeGDi~aLe~DL~s~L~~~~~~s~~t~VnelsgqI~~~g~--~v~~vr~~L~eKG 168 (169)
T KOG4034|consen 109 ILTVIRKVEGDIWALENDLRSTLEMSPKKSYATHVNELSGQIVLKGN--HVDTVREWLQEKG 168 (169)
T ss_pred EEEEEEeecccHHHHHHHHHHHHhhccCCChhhhhhhhcceEEEeCC--hHHHHHHHHHHcc
Confidence 34555667777789999999999998873 33468999999998886 4458999998776
No 47
>PRK10568 periplasmic protein; Provisional
Probab=38.73 E-value=66 Score=27.91 Aligned_cols=38 Identities=26% Similarity=0.176 Sum_probs=29.5
Q ss_pred cChhhHHHHHHHHhcCCCce--eEEEEcCCCEEEEEeeccC
Q 043718 15 QCSKCYKKVKKVLSKFPQIQ--DQIYDEKQNKVTIKVVCCC 53 (228)
Q Consensus 15 ~C~gCakKIkKaL~kl~GV~--sV~vD~k~~kVtV~G~~vD 53 (228)
+-..=..+|+.+|..-+++. ++.+...++.|++.|. ++
T Consensus 57 ~D~~I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~-V~ 96 (203)
T PRK10568 57 DDSAITAKVKAALVDHDNIKSTDISVKTHQKVVTLSGF-VE 96 (203)
T ss_pred cHHHHHHHHHHHHHhCCCCCCCceEEEEECCEEEEEEE-eC
Confidence 34445678888888877764 6778889999999998 65
No 48
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=38.21 E-value=1.3e+02 Score=20.51 Aligned_cols=59 Identities=8% Similarity=0.100 Sum_probs=36.2
Q ss_pred EEEEeccCh-hhHHHHHHHHhcCCC-ceeEEEEcC----CCEEEEEeeccCHHHHHHHHHHhcCC
Q 043718 9 VLKVDLQCS-KCYKKVKKVLSKFPQ-IQDQIYDEK----QNKVTIKVVCCCPEKMRDKICCKGDG 67 (228)
Q Consensus 9 vLKV~M~C~-gCakKIkKaL~kl~G-V~sV~vD~k----~~kVtV~G~~vDPekLv~aL~kK~gK 67 (228)
.|.|.|.-. |--.+|.+.|.+... |.++..... ...|+|.....+.+.+++.|++++.+
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~ 67 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYE 67 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCe
Confidence 445544443 677888888888753 666654432 22344443224778999999977653
No 49
>PRK11023 outer membrane lipoprotein; Provisional
Probab=38.14 E-value=87 Score=26.93 Aligned_cols=38 Identities=11% Similarity=0.088 Sum_probs=29.0
Q ss_pred hHHHHHHHHhcCCCceeE--EEEcCCCEEEEEeeccCHHHH
Q 043718 19 CYKKVKKVLSKFPQIQDQ--IYDEKQNKVTIKVVCCCPEKM 57 (228)
Q Consensus 19 CakKIkKaL~kl~GV~sV--~vD~k~~kVtV~G~~vDPekL 57 (228)
=..+|+.+|..-++|... .+...++.|++.|. ++.+..
T Consensus 128 It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~-v~~~e~ 167 (191)
T PRK11023 128 ITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGL-VTQREA 167 (191)
T ss_pred HHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEE-eCHHHH
Confidence 566899999888877654 55557999999998 776543
No 50
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=37.75 E-value=97 Score=26.42 Aligned_cols=57 Identities=12% Similarity=0.140 Sum_probs=36.3
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCEEEEEee----cc-CHHHHHHHHHHhcCCccccEEEeCC
Q 043718 18 KCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVV----CC-CPEKMRDKICCKGDGVIKSIEIKSP 77 (228)
Q Consensus 18 gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~----~v-DPekLv~aL~kK~gK~IK~aEIVsp 77 (228)
.=.+.|++.+=.-.||+++.||.+++.|+|... .+ -....++.|..++|= ...|+..
T Consensus 53 ~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW---~p~vvRt 114 (145)
T cd02410 53 EAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGW---APKVVRT 114 (145)
T ss_pred HHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCC---eeEEEec
Confidence 344555555555579999999999999999632 01 124455666666664 4555543
No 51
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=36.79 E-value=14 Score=29.43 Aligned_cols=52 Identities=15% Similarity=0.089 Sum_probs=26.4
Q ss_pred eccChhhHH-HHHHHHhc--CCCceeEEEEcCCCEEEEE--eeccCHHHHHHHHHHhcC
Q 043718 13 DLQCSKCYK-KVKKVLSK--FPQIQDQIYDEKQNKVTIK--VVCCCPEKMRDKICCKGD 66 (228)
Q Consensus 13 ~M~C~gCak-KIkKaL~k--l~GV~sV~vD~k~~kVtV~--G~~vDPekLv~aL~kK~g 66 (228)
-++|+||-. +|...+.. ..||+.|.+ .+-.+.=. +.|=..+.|.+.|++++|
T Consensus 43 f~~CgGCpg~~~~~~~~~l~~~~~d~IHl--ssC~~~~~~~~~CP~~~~~~~~I~~~~g 99 (107)
T PF08821_consen 43 FFTCGGCPGRKLVRRIKKLKKNGADVIHL--SSCMVKGNPHGPCPHIDEIKKIIEEKFG 99 (107)
T ss_pred EeeCCCCChhHHHHHHHHHHHCCCCEEEE--cCCEecCCCCCCCCCHHHHHHHHHHHhC
Confidence 449999862 22222222 245553322 22222111 133356889999998876
No 52
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=36.67 E-value=62 Score=26.21 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=24.4
Q ss_pred EEEEEeccChhh------HHHHHHHHhcCCCceeEEEEc
Q 043718 8 MVLKVDLQCSKC------YKKVKKVLSKFPQIQDQIYDE 40 (228)
Q Consensus 8 vvLKV~M~C~gC------akKIkKaL~kl~GV~sV~vD~ 40 (228)
+.+++.++=.+| ...|+++|..+.||+++++++
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 344444444555 688999999999999988873
No 53
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=35.10 E-value=1.1e+02 Score=24.49 Aligned_cols=45 Identities=18% Similarity=0.091 Sum_probs=33.5
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHH
Q 043718 18 KCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICC 63 (228)
Q Consensus 18 gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~k 63 (228)
.=...|+.+|..|+|++--.-|...+.|.|.-. -+.+.|.+.|..
T Consensus 18 e~l~av~~~L~~ip~~EV~~~d~~GKlVVVie~-~~~~~l~~tie~ 62 (94)
T COG3062 18 ERLSAVKTALLAIPGCEVYGEDAEGKLVVVIEA-EDSETLLETIES 62 (94)
T ss_pred HHHHHHHHHHhcCCCcEeeccCCCceEEEEEEc-CchHHHHHHHHH
Confidence 456789999999999988888877444444322 377889998874
No 54
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=34.44 E-value=96 Score=27.41 Aligned_cols=50 Identities=10% Similarity=0.135 Sum_probs=31.1
Q ss_pred HHHHHhcCCCce----eEEEEcCCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEeC
Q 043718 23 VKKVLSKFPQIQ----DQIYDEKQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIKS 76 (228)
Q Consensus 23 IkKaL~kl~GV~----sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIVs 76 (228)
+-+.|+++.|.. .|.=++=.++|||+|- ++-.+|+++|+.+... +.-||.
T Consensus 115 ~~~~l~~~~~~~v~V~~V~N~fFG~~ItVaGL-LTg~Dii~~L~~~~~~---d~lllP 168 (204)
T PF04459_consen 115 LVEKLNRIPGLEVEVVPVKNRFFGGTITVAGL-LTGQDIIEQLKGKELG---DLLLLP 168 (204)
T ss_pred HHHHHhccCCCeEEEEEeecCCCCCCeEEeeC-ccHHHHHHHhCcCCCC---CEEEEC
Confidence 333444556632 2233344578999998 8999999999853332 455553
No 55
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=33.53 E-value=63 Score=34.64 Aligned_cols=45 Identities=16% Similarity=0.121 Sum_probs=34.8
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCEEEEEe-------eccCHHHHHHHHHHh
Q 043718 20 YKKVKKVLSKFPQIQDQIYDEKQNKVTIKV-------VCCCPEKMRDKICCK 64 (228)
Q Consensus 20 akKIkKaL~kl~GV~sV~vD~k~~kVtV~G-------~~vDPekLv~aL~kK 64 (228)
++.|+..|.+++||.+|+++.....+.|.- ..++..+|.++|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 467999999999999999987666676641 125778888899854
No 56
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=31.56 E-value=92 Score=22.14 Aligned_cols=37 Identities=19% Similarity=0.107 Sum_probs=25.2
Q ss_pred EEcCCCEEEEEee--------ccCHHHHHHHHHHhcC-CccccEEE
Q 043718 38 YDEKQNKVTIKVV--------CCCPEKMRDKICCKGD-GVIKSIEI 74 (228)
Q Consensus 38 vD~k~~kVtV~G~--------~vDPekLv~aL~kK~g-K~IK~aEI 74 (228)
+++++++++|... -+--..|+++|...+| ..|++|+|
T Consensus 44 ~~i~~g~L~i~v~~~~~~~~L~~~~~~il~~l~~~~g~~~i~~I~~ 89 (89)
T PF05258_consen 44 VSIKDGTLVIEVDSSAWAQELRYMKPQILKKLNEFLGFPAIKDIRF 89 (89)
T ss_pred EEEECCEEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCCCccEeeC
Confidence 4446888888643 0123678889998888 67777764
No 57
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=28.72 E-value=1.1e+02 Score=19.89 Aligned_cols=15 Identities=27% Similarity=0.321 Sum_probs=6.5
Q ss_pred HHHHHHhcCCCceeE
Q 043718 22 KVKKVLSKFPQIQDQ 36 (228)
Q Consensus 22 KIkKaL~kl~GV~sV 36 (228)
.|.+.|++++||.+|
T Consensus 54 ~l~~~l~~~~~V~~v 68 (71)
T cd04879 54 EVLEELKALPGIIRV 68 (71)
T ss_pred HHHHHHHcCCCeEEE
Confidence 444444444444443
No 58
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=28.67 E-value=87 Score=33.69 Aligned_cols=44 Identities=16% Similarity=0.110 Sum_probs=33.4
Q ss_pred HHHHHHHhcCCCceeEEEEcCCCEEEEE-------eeccCHHHHHHHHHHh
Q 043718 21 KKVKKVLSKFPQIQDQIYDEKQNKVTIK-------VVCCCPEKMRDKICCK 64 (228)
Q Consensus 21 kKIkKaL~kl~GV~sV~vD~k~~kVtV~-------G~~vDPekLv~aL~kK 64 (228)
+.|+..|.+++||.+|++......+.|. ...++..+|.++|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 5699999999999999998776657764 1125677778888843
No 59
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=28.38 E-value=74 Score=30.04 Aligned_cols=64 Identities=14% Similarity=0.134 Sum_probs=41.5
Q ss_pred eccChhh---HHHHHHHHhcCCCceeEEEEc--CCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEeCCCCC
Q 043718 13 DLQCSKC---YKKVKKVLSKFPQIQDQIYDE--KQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIKSPDDQ 80 (228)
Q Consensus 13 ~M~C~gC---akKIkKaL~kl~GV~sV~vD~--k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIVsp~~p 80 (228)
|.+=++= ..+|.++++..+||.-++++. +-|+..|+-. -+++.|++++..-.++ .+++|+-...
T Consensus 10 nfSEGR~~~vie~I~~a~~~~~gv~lld~~~D~d~NRsv~Tlv-g~pe~v~eaa~~~~~~---A~elIDm~~H 78 (298)
T TIGR02024 10 NFSEGRNKEVIEKIVDAIIKTDNVKLLDVDMDPDHNRSVITFV-GEPECVVNAALKLAKK---AAELIDMRNH 78 (298)
T ss_pred eeccCCCHHHHHHHHHHHhcCCCcEEEeCCCCCCCCceEEEEe-cChHHHHHHHHHHHHH---HHHhcCcccc
Confidence 5554433 456667777788877666554 6677777644 3688999988876665 4555555443
No 60
>PF02983 Pro_Al_protease: Alpha-lytic protease prodomain; InterPro: IPR004236 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The alpha-lytic protease prodomain is associated with serine peptidases, specifically the alpha-lytic endopeptidases and streptogrisin A, B, C, D and E, which are bacterial enzymes and which belong to MEROPS peptidase subfamily S1A (IPR001316 from INTERPRO). The protease precursor in Gram-negative bacterial proteases may be a general property of extracellular bacterial proteases []. The proteases are encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [, ]. The pro region also acts as a potent inhibitor of the mature enzyme []. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0005576 extracellular region; PDB: 3PRO_C 2PRO_B 4PRO_C.
Probab=27.83 E-value=1.4e+02 Score=21.33 Aligned_cols=21 Identities=19% Similarity=0.177 Sum_probs=18.2
Q ss_pred CCCceeEEEEcCCCEEEEEee
Q 043718 30 FPQIQDQIYDEKQNKVTIKVV 50 (228)
Q Consensus 30 l~GV~sV~vD~k~~kVtV~G~ 50 (228)
-.++.+..+|..+|+|+|+..
T Consensus 22 ~~~~~~WyvD~~tn~VVV~a~ 42 (62)
T PF02983_consen 22 PVAVTSWYVDPRTNKVVVTAD 42 (62)
T ss_dssp GGCEEEEEEECCCTEEEEEEE
T ss_pred CCCcceEEEeCCCCeEEEEEC
Confidence 357999999999999999854
No 61
>PRK09577 multidrug efflux protein; Reviewed
Probab=27.71 E-value=98 Score=33.20 Aligned_cols=45 Identities=7% Similarity=0.070 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCEEEEE-------eeccCHHHHHHHHHHh
Q 043718 20 YKKVKKVLSKFPQIQDQIYDEKQNKVTIK-------VVCCCPEKMRDKICCK 64 (228)
Q Consensus 20 akKIkKaL~kl~GV~sV~vD~k~~kVtV~-------G~~vDPekLv~aL~kK 64 (228)
.+.|+..|.+++||.+|+++.....|.|. ...++..+|.++|+..
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~ 209 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAH 209 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 46799999999999999999866666663 1125777888899864
No 62
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=27.54 E-value=2.3e+02 Score=23.14 Aligned_cols=46 Identities=9% Similarity=0.048 Sum_probs=32.8
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHH----HHHhcCC
Q 043718 20 YKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDK----ICCKGDG 67 (228)
Q Consensus 20 akKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~a----L~kK~gK 67 (228)
-..++.+|.++ |-.+|++=+.++-|.++.. .+.+.|..+ |...+|.
T Consensus 21 MaeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~-~~~~~l~~~ie~~l~~~fG~ 70 (137)
T PF08002_consen 21 MAELREALEDL-GFTNVRTYIQSGNVVFESD-RDPAELAAKIEKALEERFGF 70 (137)
T ss_dssp HHHHHHHHHHC-T-EEEEEETTTTEEEEEES-S-HHHHHHHHHHHHHHH-TT
T ss_pred HHHHHHHHHHc-CCCCceEEEeeCCEEEecC-CChHHHHHHHHHHHHHhcCC
Confidence 35677888888 9999999999999999965 677665544 4556664
No 63
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=27.43 E-value=1e+02 Score=33.17 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCEEEEEe-------eccCHHHHHHHHHH
Q 043718 20 YKKVKKVLSKFPQIQDQIYDEKQNKVTIKV-------VCCCPEKMRDKICC 63 (228)
Q Consensus 20 akKIkKaL~kl~GV~sV~vD~k~~kVtV~G-------~~vDPekLv~aL~k 63 (228)
.+.|+..|.+++||.+|+++..+..+.|.- ..++..+|.++|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 357999999999999999998866677751 12577888899986
No 64
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=26.88 E-value=66 Score=22.52 Aligned_cols=28 Identities=29% Similarity=0.463 Sum_probs=18.0
Q ss_pred HHHHHHHhc-----CCCceeEEEEcCCCEEEEE
Q 043718 21 KKVKKVLSK-----FPQIQDQIYDEKQNKVTIK 48 (228)
Q Consensus 21 kKIkKaL~k-----l~GV~sV~vD~k~~kVtV~ 48 (228)
++++++|.+ |+||..|.+-..++++.+.
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~ 34 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVF 34 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEEE
Confidence 355666665 4699999999999888875
No 65
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=26.47 E-value=2.2e+02 Score=24.28 Aligned_cols=31 Identities=10% Similarity=0.059 Sum_probs=27.4
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCEEEEE
Q 043718 18 KCYKKVKKVLSKFPQIQDQIYDEKQNKVTIK 48 (228)
Q Consensus 18 gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~ 48 (228)
.=+.+|.+.+.+++||.++.+=...+.+.|-
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vg 84 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVG 84 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEE
Confidence 5678999999999999999998888888884
No 66
>PRK13763 putative RNA-processing protein; Provisional
Probab=26.43 E-value=1.3e+02 Score=25.63 Aligned_cols=37 Identities=16% Similarity=0.142 Sum_probs=26.6
Q ss_pred HHHHHHHhcCCCceeEEEEcCCCEEEEE---eeccCHHHHHHH
Q 043718 21 KKVKKVLSKFPQIQDQIYDEKQNKVTIK---VVCCCPEKMRDK 60 (228)
Q Consensus 21 kKIkKaL~kl~GV~sV~vD~k~~kVtV~---G~~vDPekLv~a 60 (228)
.++-+.|.+.-|++ +++|.++++|+|. +. |++.+.++
T Consensus 22 Gk~Ik~I~e~tg~~-I~i~~~~g~V~I~~~~~~--d~~~i~kA 61 (180)
T PRK13763 22 GETKKEIEERTGVK-LEIDSETGEVIIEPTDGE--DPLAVLKA 61 (180)
T ss_pred hhHHHHHHHHHCcE-EEEECCCCeEEEEeCCCC--CHHHHHHH
Confidence 56667777777876 8999888999997 43 55555443
No 67
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=26.25 E-value=88 Score=33.49 Aligned_cols=50 Identities=16% Similarity=0.243 Sum_probs=36.2
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCC--CEEEEEe-------eccCHHHHHHHHHHhcCC
Q 043718 18 KCYKKVKKVLSKFPQIQDQIYDEKQ--NKVTIKV-------VCCCPEKMRDKICCKGDG 67 (228)
Q Consensus 18 gCakKIkKaL~kl~GV~sV~vD~k~--~kVtV~G-------~~vDPekLv~aL~kK~gK 67 (228)
.=+++|+..|..++||.+|+.|... ..+.|.- ..++++.|.+.|+...+.
T Consensus 698 ~~a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~~~~~g 756 (1051)
T TIGR00914 698 ATAEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVATAVGG 756 (1051)
T ss_pred HHHHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHHhCC
Confidence 4467899999999999999998754 4455531 125778888899865543
No 68
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=25.76 E-value=74 Score=29.32 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=24.7
Q ss_pred eeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcC
Q 043718 34 QDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGD 66 (228)
Q Consensus 34 ~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~g 66 (228)
+.|.+|..++++||.|. |..|++.|.+..+
T Consensus 303 ~~i~yd~~~~~ltI~~~---p~~l~~ql~r~~~ 332 (334)
T PRK00378 303 ERIFYDPATDTLTIKGT---PPNLRDQLQRRLK 332 (334)
T ss_pred CceEEcCCCCEEEEeCC---CHHHHHHHHHHhc
Confidence 48899999999999986 4788888886554
No 69
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=25.60 E-value=2e+02 Score=21.82 Aligned_cols=39 Identities=15% Similarity=0.131 Sum_probs=31.4
Q ss_pred ceeEEEEcCCCEEEEE----eeccCHHHHHHHHHHhcCCccccEEEe
Q 043718 33 IQDQIYDEKQNKVTIK----VVCCCPEKMRDKICCKGDGVIKSIEIK 75 (228)
Q Consensus 33 V~sV~vD~k~~kVtV~----G~~vDPekLv~aL~kK~gK~IK~aEIV 75 (228)
+.++.+.++.++|+|- +. +|-..|+..|.+..+- .|++.
T Consensus 44 lvd~e~~~D~~k~~fyy~a~~r-vDFR~Lvr~L~~~f~~---RIem~ 86 (88)
T PF04468_consen 44 LVDVEYQFDGSKLTFYYTAESR-VDFRELVRDLAREFKT---RIEMR 86 (88)
T ss_pred EEEEEEEcCCCEEEEEEEeCCc-CcHHHHHHHHHHHhCc---eEEEE
Confidence 6677888899999993 55 7999999999987764 67764
No 70
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=24.66 E-value=3.1e+02 Score=23.49 Aligned_cols=53 Identities=13% Similarity=0.152 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCCceeEEEEcCCCEEEEEee--cc---CHHHHHHHHHHhcCCccccEEE
Q 043718 21 KKVKKVLSKFPQIQDQIYDEKQNKVTIKVV--CC---CPEKMRDKICCKGDGVIKSIEI 74 (228)
Q Consensus 21 kKIkKaL~kl~GV~sV~vD~k~~kVtV~G~--~v---DPekLv~aL~kK~gK~IK~aEI 74 (228)
..|...| +-.|-.++.+.+.+++|+|... .+ +..+|.+.+.+.+|-....|.|
T Consensus 138 ~~iE~ll-kakGf~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 138 MEIENLL-KAKGFEDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp HHHHHHH-HTTS-SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred HHHHHHH-HhCCCCceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 3454444 4459999999999999999743 12 3466888888888743334443
No 71
>PRK10819 transport protein TonB; Provisional
Probab=24.25 E-value=1.2e+02 Score=27.50 Aligned_cols=8 Identities=25% Similarity=0.600 Sum_probs=4.6
Q ss_pred cEEEeCCC
Q 043718 71 SIEIKSPD 78 (228)
Q Consensus 71 ~aEIVsp~ 78 (228)
+|++|.+.
T Consensus 49 sV~mv~pa 56 (246)
T PRK10819 49 SVTMVAPA 56 (246)
T ss_pred EEEEeccc
Confidence 56666553
No 72
>PF09843 DUF2070: Predicted membrane protein (DUF2070); InterPro: IPR019204 This domain of unknown function is found in various bacterial and archael hypothetical proteins, as well as in prokaryotic polyketide synthase.
Probab=23.88 E-value=1.9e+02 Score=24.52 Aligned_cols=48 Identities=15% Similarity=0.180 Sum_probs=32.8
Q ss_pred CCceeEEEEcCCCEEEE---EeeccCHHHHHHHHHHhcCCccccEEEeCCCC
Q 043718 31 PQIQDQIYDEKQNKVTI---KVVCCCPEKMRDKICCKGDGVIKSIEIKSPDD 79 (228)
Q Consensus 31 ~GV~sV~vD~k~~kVtV---~G~~vDPekLv~aL~kK~gK~IK~aEIVsp~~ 79 (228)
-||....++...++..+ .|..++ ..|+++|++..+..+..+||++...
T Consensus 61 ~gi~~~~v~~~g~~~~lv~~DsNNm~-~~lr~~i~~~~~~~~d~~ev~TTDt 111 (179)
T PF09843_consen 61 GGISALVVEVGGQRSALVLADSNNME-PGLREKIREALGDVVDEVEVMTTDT 111 (179)
T ss_pred cccEEEEEEeCCcEEEEEEEECCCCC-HHHHHHHHHHHhhhcceeEEecCcc
Confidence 36778888886666444 455344 5577777777777677899887643
No 73
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=23.59 E-value=3.1e+02 Score=20.23 Aligned_cols=49 Identities=20% Similarity=0.055 Sum_probs=33.4
Q ss_pred hhhHHHHHHHHhcCCC-ceeEEEEcCCCEEEEEeeccC---HHHHHHHHHHhcCC
Q 043718 17 SKCYKKVKKVLSKFPQ-IQDQIYDEKQNKVTIKVVCCC---PEKMRDKICCKGDG 67 (228)
Q Consensus 17 ~gCakKIkKaL~kl~G-V~sV~vD~k~~kVtV~G~~vD---PekLv~aL~kK~gK 67 (228)
.....+|...|.+..| |.+...+ .++.++|++. +. ...+...|+..+..
T Consensus 15 ~~~~g~v~~~l~~r~g~i~~~~~~-~~~~~~i~~~-iP~~~~~gf~~~Lr~~T~G 67 (89)
T PF00679_consen 15 EEYLGKVISDLSKRRGEILSMDPI-GGDRVVIEAE-IPVRELFGFRSELRSLTSG 67 (89)
T ss_dssp GGGHHHHHHHHHHTT-EEEEEEEE-STTEEEEEEE-EEGGGHTTHHHHHHHHTTT
T ss_pred HHHHHHHHHHhcccccEEEechhh-hhhheeEEEE-EChhhhhhHHHHhhccCCC
Confidence 6889999999999888 4455555 6889999876 32 33455666655543
No 74
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=23.48 E-value=1.7e+02 Score=20.41 Aligned_cols=49 Identities=22% Similarity=0.232 Sum_probs=31.7
Q ss_pred EEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEee-ccCHHHHHHHHHHhcC
Q 043718 9 VLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVV-CCCPEKMRDKICCKGD 66 (228)
Q Consensus 9 vLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~-~vDPekLv~aL~kK~g 66 (228)
+|.+ ++.|....-+++++|.+++.= +.+.|... ....+.|...+...+.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~ 52 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGY 52 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCC
Confidence 5667 999999999999999998532 33444332 1234667777775444
No 75
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=22.99 E-value=1.8e+02 Score=19.03 Aligned_cols=29 Identities=14% Similarity=0.252 Sum_probs=15.7
Q ss_pred EEEEEEeccChhhHHHHHHHHhcCCCceeE
Q 043718 7 TMVLKVDLQCSKCYKKVKKVLSKFPQIQDQ 36 (228)
Q Consensus 7 tvvLKV~M~C~gCakKIkKaL~kl~GV~sV 36 (228)
.+.|.++.. +.=...+.+.|.+++||.+|
T Consensus 43 ~~~~~~~~~-~~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 43 RITIVVEGD-DDVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred EEEEEEECC-HHHHHHHHHHHhCCccEEEe
Confidence 345555432 13355566666667776665
No 76
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=22.91 E-value=2.7e+02 Score=19.36 Aligned_cols=47 Identities=6% Similarity=-0.046 Sum_probs=30.0
Q ss_pred CCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHh-cCCccccEEEeCC
Q 043718 31 PQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCK-GDGVIKSIEIKSP 77 (228)
Q Consensus 31 ~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK-~gK~IK~aEIVsp 77 (228)
+||.=-++....++|+|+|...+...|.+.+..- .-..+..+.|.+.
T Consensus 12 ~~v~l~~l~~~~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~ 59 (78)
T PF05137_consen 12 EGVWLTSLSINGNTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSI 59 (78)
T ss_pred CCEEEEEEEEeCCEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEE
Confidence 5777777778899999999744666555555431 1223456666654
No 77
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=22.86 E-value=1.3e+02 Score=31.81 Aligned_cols=51 Identities=20% Similarity=0.266 Sum_probs=38.4
Q ss_pred hhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEee---------ccCHHHHHHHHHHhcCC
Q 043718 17 SKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVV---------CCCPEKMRDKICCKGDG 67 (228)
Q Consensus 17 ~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~---------~vDPekLv~aL~kK~gK 67 (228)
..=+++|++.|++++|+.+|..|...++-.+.-. .++.+.|.+.|+...+.
T Consensus 686 ~~~a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~~a~~G 745 (1021)
T PF00873_consen 686 RKAAEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLRTAFSG 745 (1021)
T ss_dssp HHHHHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHHHHHS-
T ss_pred HHHHHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHHHHhcc
Confidence 3567899999999999999999998887666422 24677788888866554
No 78
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=22.70 E-value=1.9e+02 Score=20.18 Aligned_cols=37 Identities=14% Similarity=0.034 Sum_probs=23.4
Q ss_pred HHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHHHH
Q 043718 22 KVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKIC 62 (228)
Q Consensus 22 KIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~ 62 (228)
...+.|..--|++ +.++. +++|+|.|. +.+.+..++.
T Consensus 22 ~~ik~I~~~tg~~-I~i~~-~g~v~I~G~--~~~~v~~A~~ 58 (61)
T cd02393 22 KTIKKIIEETGVK-IDIED-DGTVYIAAS--DKEAAEKAKK 58 (61)
T ss_pred hHHHHHHHHHCCE-EEeCC-CCEEEEEeC--CHHHHHHHHH
Confidence 3444555555665 55554 688999996 6677666654
No 79
>KOG3432 consensus Vacuolar H+-ATPase V1 sector, subunit F [Energy production and conversion]
Probab=22.52 E-value=1.5e+02 Score=24.55 Aligned_cols=43 Identities=12% Similarity=0.115 Sum_probs=34.0
Q ss_pred CCCceeEEEEcCCCEEEEEeeccCHHHHHHHHHHhcCCccccEEEe
Q 043718 30 FPQIQDQIYDEKQNKVTIKVVCCCPEKMRDKICCKGDGVIKSIEIK 75 (228)
Q Consensus 30 l~GV~sV~vD~k~~kVtV~G~~vDPekLv~aL~kK~gK~IK~aEIV 75 (228)
|-||..+.-+-+.|-+.|... .+.+.|.+++..-+.| .+|.||
T Consensus 24 laGvg~v~~~r~~Nf~vv~~~-Tt~~eiedaF~~f~~R--dDIaIi 66 (121)
T KOG3432|consen 24 LAGVGEVNENREPNFLVVDSK-TTVEEIEDAFKSFTAR--DDIAII 66 (121)
T ss_pred eecccccccCCCCCEEEEecc-CCHHHHHHHHHhhccc--cCeEEE
Confidence 468888888889999999876 6889999999876666 455554
No 80
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=22.48 E-value=1.3e+02 Score=23.83 Aligned_cols=32 Identities=3% Similarity=0.233 Sum_probs=24.7
Q ss_pred hHHHHHHHHhc---CCCceeEEEEcCCCEEEEEee
Q 043718 19 CYKKVKKVLSK---FPQIQDQIYDEKQNKVTIKVV 50 (228)
Q Consensus 19 CakKIkKaL~k---l~GV~sV~vD~k~~kVtV~G~ 50 (228)
-.+.|+.||.. +.+|.+++++..++++.|+-+
T Consensus 70 i~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f~ 104 (112)
T PF10934_consen 70 IEREIEEALLQDPRITSVENFSFEWEGDSLYVSFT 104 (112)
T ss_pred HHHHHHHHHhcCCCcceEEEEEEEEECCEEEEEEE
Confidence 35678888855 567888899999999888643
No 81
>PTZ00449 104 kDa microneme/rhoptry antigen; Provisional
Probab=22.35 E-value=3.6e+02 Score=28.41 Aligned_cols=19 Identities=21% Similarity=0.242 Sum_probs=9.1
Q ss_pred HHHHHhcCCccccEEEeCC
Q 043718 59 DKICCKGDGVIKSIEIKSP 77 (228)
Q Consensus 59 ~aL~kK~gK~IK~aEIVsp 77 (228)
++|-++..+....|+--..
T Consensus 486 kklikkskkkl~~i~eeds 504 (943)
T PTZ00449 486 KKLIKKSKKKLAPIEEEDS 504 (943)
T ss_pred HHHHHHhhccCCCcccccc
Confidence 3444456654445554443
No 82
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=22.31 E-value=45 Score=24.19 Aligned_cols=22 Identities=27% Similarity=0.602 Sum_probs=18.6
Q ss_pred EEEEeccChhhHHHHHHHHhcC
Q 043718 9 VLKVDLQCSKCYKKVKKVLSKF 30 (228)
Q Consensus 9 vLKV~M~C~gCakKIkKaL~kl 30 (228)
.++++-.|++|...|++.|...
T Consensus 32 ~~~~g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 32 FVPVGNQCGKCIRAAREVMQDE 53 (64)
T ss_pred hcCCCCCccchHHHHHHHHHHH
Confidence 3677899999999999998654
No 83
>PRK15317 alkyl hydroperoxide reductase subunit F; Provisional
Probab=21.63 E-value=2.2e+02 Score=27.61 Aligned_cols=71 Identities=14% Similarity=0.170 Sum_probs=40.1
Q ss_pred EEEEEeccChhhHHHHH--HHHhcC-CCceeEEEEc-------------------CCCEEEEEeeccCHHHHHHHHHHhc
Q 043718 8 MVLKVDLQCSKCYKKVK--KVLSKF-PQIQDQIYDE-------------------KQNKVTIKVVCCCPEKMRDKICCKG 65 (228)
Q Consensus 8 vvLKV~M~C~gCakKIk--KaL~kl-~GV~sV~vD~-------------------k~~kVtV~G~~vDPekLv~aL~kK~ 65 (228)
+.+-|..+|..|.+.++ ..|... +.|..-.+|. -++.....|. .+.+.|+++|....
T Consensus 120 i~~fv~~~Cp~Cp~~v~~~~~~a~~~~~i~~~~id~~~~~~~~~~~~v~~VP~~~i~~~~~~~g~-~~~~~~~~~~~~~~ 198 (517)
T PRK15317 120 FETYVSLSCHNCPDVVQALNLMAVLNPNITHTMIDGALFQDEVEARNIMAVPTVFLNGEEFGQGR-MTLEEILAKLDTGA 198 (517)
T ss_pred EEEEEcCCCCCcHHHHHHHHHHHHhCCCceEEEEEchhCHhHHHhcCCcccCEEEECCcEEEecC-CCHHHHHHHHhccc
Confidence 44445999999986332 223222 3444444433 2344555676 67788888887542
Q ss_pred C---------CccccEEEeCCCC
Q 043718 66 D---------GVIKSIEIKSPDD 79 (228)
Q Consensus 66 g---------K~IK~aEIVsp~~ 79 (228)
+ ....++.||+-++
T Consensus 199 ~~~~~~~~~~~~~~dvvIIGgGp 221 (517)
T PRK15317 199 AARAAEELNAKDPYDVLVVGGGP 221 (517)
T ss_pred cccchhhcccCCCCCEEEECCCH
Confidence 2 3345677776543
No 84
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=21.59 E-value=3.5e+02 Score=20.17 Aligned_cols=51 Identities=20% Similarity=0.227 Sum_probs=34.9
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCEEEEEee-ccCHHHHHHHHHHhcC
Q 043718 7 TMVLKV-DLQCSKCYKKVKKVLSKFPQIQDQIYDEKQNKVTIKVV-CCCPEKMRDKICCKGD 66 (228)
Q Consensus 7 tvvLKV-~M~C~gCakKIkKaL~kl~GV~sV~vD~k~~kVtV~G~-~vDPekLv~aL~kK~g 66 (228)
+.+|-+ +++|..=.-.++++|.+++- ...+.|..+ .....+|...++..+|
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~~~~ 57 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKKEGG 57 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHHcCC
Confidence 568888 99999999999999999963 233344332 1234566666665554
No 85
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=20.84 E-value=95 Score=24.13 Aligned_cols=22 Identities=9% Similarity=0.031 Sum_probs=19.2
Q ss_pred hhHHHHHHHHhcCCCceeEEEE
Q 043718 18 KCYKKVKKVLSKFPQIQDQIYD 39 (228)
Q Consensus 18 gCakKIkKaL~kl~GV~sV~vD 39 (228)
+=...|..+|++++||+++++.
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 4459999999999999999875
No 86
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=20.63 E-value=1.9e+02 Score=19.54 Aligned_cols=16 Identities=25% Similarity=0.301 Sum_probs=8.1
Q ss_pred HHHHHHhcCCCceeEE
Q 043718 22 KVKKVLSKFPQIQDQI 37 (228)
Q Consensus 22 KIkKaL~kl~GV~sV~ 37 (228)
.+.+.|++++||..+.
T Consensus 54 ~~~~~l~~~~~v~~v~ 69 (73)
T cd04902 54 EVLEELRALPGILSAK 69 (73)
T ss_pred HHHHHHHcCCCccEEE
Confidence 4555555555554443
No 87
>PRK09579 multidrug efflux protein; Reviewed
Probab=20.39 E-value=1.7e+02 Score=31.44 Aligned_cols=39 Identities=13% Similarity=0.156 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCEEEEEeeccCHHHHHHH
Q 043718 20 YKKVKKVLSKFPQIQDQIYDEKQNKVTIKVVCCCPEKMRDK 60 (228)
Q Consensus 20 akKIkKaL~kl~GV~sV~vD~k~~kVtV~G~~vDPekLv~a 60 (228)
.+.|+..|.+++||.+|++...... .|... +|++++...
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~-ei~V~-vd~~kl~~~ 196 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVF-AMRLW-LDPVKLAGF 196 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCce-EEEEE-eCHHHHHHc
No 88
>PRK04435 hypothetical protein; Provisional
Probab=20.28 E-value=4.9e+02 Score=21.39 Aligned_cols=70 Identities=19% Similarity=0.147 Sum_probs=42.9
Q ss_pred eEEEEEEeccC-hhhHHHHHHHHhcCCC-ceeEEEEcC-CCE--EE--EEeec--cCHHHHHHHHHHhcCCccccEEEeC
Q 043718 6 TTMVLKVDLQC-SKCYKKVKKVLSKFPQ-IQDQIYDEK-QNK--VT--IKVVC--CCPEKMRDKICCKGDGVIKSIEIKS 76 (228)
Q Consensus 6 ~tvvLKV~M~C-~gCakKIkKaL~kl~G-V~sV~vD~k-~~k--Vt--V~G~~--vDPekLv~aL~kK~gK~IK~aEIVs 76 (228)
+.++|.+.+.. .|=-.+|.++|++..+ |.++..+.. ++. ++ |.... .+.+.|+++|+.-- -|.+|+|++
T Consensus 68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~~~~L~~Li~~L~~i~--gV~~V~i~~ 145 (147)
T PRK04435 68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSMEGDIDELLEKLRNLD--GVEKVELIG 145 (147)
T ss_pred cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCChHHHHHHHHHHHHcCC--CcEEEEEEe
Confidence 46777875544 5678889999988865 666655443 343 33 32210 13456777777433 367899886
Q ss_pred C
Q 043718 77 P 77 (228)
Q Consensus 77 p 77 (228)
.
T Consensus 146 ~ 146 (147)
T PRK04435 146 M 146 (147)
T ss_pred c
Confidence 4
No 89
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=20.15 E-value=1.9e+02 Score=27.63 Aligned_cols=59 Identities=19% Similarity=0.227 Sum_probs=41.4
Q ss_pred EEEE-eccChhhHHHHHHHHhcC---CCceeEEEEcCCCEEEEEeec-------c-C-HHHHHHHHHHhcCC
Q 043718 9 VLKV-DLQCSKCYKKVKKVLSKF---PQIQDQIYDEKQNKVTIKVVC-------C-C-PEKMRDKICCKGDG 67 (228)
Q Consensus 9 vLKV-~M~C~gCakKIkKaL~kl---~GV~sV~vD~k~~kVtV~G~~-------v-D-PekLv~aL~kK~gK 67 (228)
.++| +|+=..=.+.|++.|.++ +.|.--..+..+++|+|.|.. + + +..|+++|...+|-
T Consensus 133 ~V~vaG~T~~e~~~~I~~~L~~~~~~PqV~V~v~~~~s~~V~V~GeV~~PG~~~l~~~~~tlldaIa~AGG~ 204 (379)
T PRK15078 133 KVHVAGKTVTEIRSDITGRLAKYIESPQVDVNIAAFRSQKAYVTGEVNKSGQQAITNVPLTILDAINAAGGL 204 (379)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEccCCceEEEEEceecCCeEEEecCCCccHHHHHHHccCC
Confidence 3677 899999999999999875 234322334467789998741 1 2 46899999866653
Done!