Query 039056
Match_columns 110
No_of_seqs 110 out of 1123
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 05:54:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039056.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039056hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.6 2.1E-15 4.5E-20 90.4 8.8 61 24-87 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.6 4.5E-14 9.8E-19 87.7 8.9 66 22-90 3-69 (71)
3 KOG4656 Copper chaperone for s 99.4 1.7E-12 3.7E-17 95.3 9.3 80 21-106 7-89 (247)
4 KOG1603 Copper chaperone [Inor 99.3 2E-11 4.4E-16 76.0 8.5 66 20-91 4-70 (73)
5 PRK10671 copA copper exporting 98.8 4.5E-08 9.8E-13 83.9 9.3 62 21-90 3-65 (834)
6 PLN02957 copper, zinc superoxi 98.7 2.6E-07 5.6E-12 69.2 9.8 79 21-105 6-87 (238)
7 COG2217 ZntA Cation transport 98.6 1.2E-07 2.7E-12 80.5 7.7 64 22-89 3-68 (713)
8 KOG0207 Cation transport ATPas 98.2 5.1E-06 1.1E-10 71.8 7.0 72 28-103 2-85 (951)
9 TIGR00003 copper ion binding p 98.2 4.3E-05 9.4E-10 42.3 8.6 63 22-87 3-66 (68)
10 KOG0207 Cation transport ATPas 98.1 1.5E-05 3.1E-10 69.1 7.7 73 21-96 146-219 (951)
11 PRK11033 zntA zinc/cadmium/mer 97.6 0.00031 6.6E-09 60.1 8.8 63 21-88 53-116 (741)
12 PRK10671 copA copper exporting 97.6 0.00023 5E-09 61.4 7.8 62 22-89 100-162 (834)
13 PRK13748 putative mercuric red 95.3 0.32 7E-06 39.9 10.8 41 24-64 3-44 (561)
14 PF01206 TusA: Sulfurtransfera 95.0 0.21 4.6E-06 29.9 6.8 54 24-90 2-56 (70)
15 TIGR02052 MerP mercuric transp 94.0 0.75 1.6E-05 27.4 9.3 63 22-87 24-87 (92)
16 PRK11018 hypothetical protein; 91.7 2.1 4.4E-05 26.6 7.4 55 22-89 8-63 (78)
17 cd03420 SirA_RHOD_Pry_redox Si 91.5 1.5 3.3E-05 26.4 6.5 54 25-91 2-56 (69)
18 PRK00299 sulfur transfer prote 90.4 3 6.4E-05 26.0 7.5 55 22-89 9-64 (81)
19 COG0425 SirA Predicted redox p 90.3 2.4 5.3E-05 26.4 6.8 51 22-85 5-56 (78)
20 COG1888 Uncharacterized protei 89.7 3.3 7.2E-05 27.0 7.0 61 21-86 6-74 (97)
21 cd00291 SirA_YedF_YeeD SirA, Y 89.6 2.8 6.1E-05 24.6 6.6 52 25-89 2-54 (69)
22 cd03421 SirA_like_N SirA_like_ 88.9 2.6 5.7E-05 24.9 5.9 52 25-90 2-54 (67)
23 cd03423 SirA SirA (also known 88.9 3.5 7.6E-05 24.7 6.9 53 25-90 2-55 (69)
24 cd03422 YedF YedF is a bacteri 88.6 3.6 7.8E-05 24.7 6.4 53 25-90 2-55 (69)
25 cd00371 HMA Heavy-metal-associ 87.1 2.3 4.9E-05 20.5 5.2 38 28-65 6-43 (63)
26 PF02680 DUF211: Uncharacteriz 86.2 6.6 0.00014 25.7 6.9 61 20-86 4-72 (95)
27 PF01883 DUF59: Domain of unkn 81.1 3.8 8.2E-05 24.5 4.0 32 22-53 35-72 (72)
28 PRK14054 methionine sulfoxide 80.9 3.7 8E-05 29.5 4.5 47 32-81 10-75 (172)
29 TIGR03527 selenium_YedF seleni 77.6 12 0.00025 27.3 6.3 49 28-89 5-53 (194)
30 PRK13014 methionine sulfoxide 75.5 8.9 0.00019 28.0 5.2 54 20-81 8-80 (186)
31 PRK05528 methionine sulfoxide 70.7 12 0.00026 26.5 4.8 47 32-81 8-68 (156)
32 PRK00058 methionine sulfoxide 65.6 13 0.00029 27.6 4.3 47 32-81 52-117 (213)
33 PF01625 PMSR: Peptide methion 61.5 52 0.0011 23.1 6.6 47 32-81 7-72 (155)
34 PF13740 ACT_6: ACT domain; PD 59.7 28 0.00061 20.9 4.4 62 22-84 2-65 (76)
35 TIGR03406 FeS_long_SufT probab 59.5 15 0.00032 26.4 3.6 33 23-55 115-153 (174)
36 PF09580 Spore_YhcN_YlaJ: Spor 58.2 41 0.00089 23.4 5.6 38 30-67 72-109 (177)
37 TIGR02945 SUF_assoc FeS assemb 54.8 16 0.00035 23.1 2.9 21 36-56 58-78 (99)
38 PRK05550 bifunctional methioni 49.6 33 0.00072 26.6 4.3 47 32-81 134-199 (283)
39 COG2151 PaaD Predicted metal-s 49.6 34 0.00073 22.9 3.8 31 25-55 53-89 (111)
40 PRK11152 ilvM acetolactate syn 46.4 67 0.0015 19.9 4.6 34 18-53 42-75 (76)
41 COG0225 MsrA Peptide methionin 45.5 50 0.0011 23.9 4.4 53 21-81 7-78 (174)
42 cd04888 ACT_PheB-BS C-terminal 43.3 65 0.0014 18.6 4.6 32 22-53 42-74 (76)
43 PRK10553 assembly protein for 41.0 94 0.002 19.8 5.9 34 32-65 16-49 (87)
44 PRK09577 multidrug efflux prot 40.1 54 0.0012 29.6 4.7 51 35-85 158-210 (1032)
45 KOG4034 Uncharacterized conser 38.3 64 0.0014 23.2 4.0 53 27-86 116-169 (169)
46 KOG2990 C2C2-type Zn-finger pr 36.5 23 0.00049 27.8 1.5 20 23-42 45-66 (317)
47 COG1166 SpeA Arginine decarbox 35.0 1.3E+02 0.0029 25.9 5.9 54 52-106 45-105 (652)
48 PF14437 MafB19-deam: MafB19-l 34.6 1.3E+02 0.0029 21.1 5.1 40 21-61 100-141 (146)
49 PF08777 RRM_3: RNA binding mo 33.4 1.4E+02 0.003 19.4 6.5 57 24-84 3-60 (105)
50 PF11491 DUF3213: Protein of u 32.8 94 0.002 20.0 3.7 50 35-87 13-62 (88)
51 PRK10555 aminoglycoside/multid 32.2 1.1E+02 0.0023 27.8 5.2 51 34-84 158-210 (1037)
52 TIGR00915 2A0602 The (Largely 31.2 84 0.0018 28.4 4.5 50 35-84 159-210 (1044)
53 PF03927 NapD: NapD protein; 30.6 1.3E+02 0.0029 18.4 5.9 46 32-83 14-59 (79)
54 TIGR00268 conserved hypothetic 30.6 1.7E+02 0.0036 21.7 5.4 62 35-97 187-250 (252)
55 PF04723 GRDA: Glycine reducta 30.1 79 0.0017 22.3 3.3 72 28-103 12-83 (150)
56 PF15643 Tox-PL-2: Papain fold 29.9 46 0.001 22.0 2.0 29 28-64 18-46 (100)
57 PRK14719 bifunctional RNAse/5- 29.9 2.1E+02 0.0045 22.8 6.1 50 24-87 47-97 (360)
58 PF00289 CPSase_L_chain: Carba 29.3 1.7E+02 0.0036 19.1 6.3 68 35-104 14-93 (110)
59 PRK14018 trifunctional thiored 28.9 1.1E+02 0.0024 25.8 4.5 47 32-81 205-269 (521)
60 PRK10509 bacterioferritin-asso 28.7 32 0.0007 20.5 1.1 21 24-44 32-52 (64)
61 PF05046 Img2: Mitochondrial l 28.7 1.5E+02 0.0034 18.5 5.4 56 24-86 31-87 (87)
62 PF13192 Thioredoxin_3: Thiore 28.2 63 0.0014 19.2 2.3 15 23-38 3-17 (76)
63 COG0277 GlcD FAD/FMN-containin 27.4 80 0.0017 24.9 3.4 42 52-99 89-137 (459)
64 COG4669 EscJ Type III secretor 27.3 2.1E+02 0.0046 21.9 5.4 22 33-54 109-130 (246)
65 PRK10503 multidrug efflux syst 27.1 1.3E+02 0.0027 27.4 4.8 56 28-83 62-123 (1040)
66 TIGR02830 spore_III_AG stage I 26.7 61 0.0013 23.6 2.4 31 32-62 60-92 (186)
67 PF01514 YscJ_FliF: Secretory 26.3 72 0.0016 23.3 2.7 22 34-55 116-137 (206)
68 TIGR00489 aEF-1_beta translati 26.2 74 0.0016 20.3 2.5 22 33-54 62-83 (88)
69 COG2177 FtsX Cell division pro 25.3 1.4E+02 0.0031 23.2 4.3 30 23-53 63-92 (297)
70 cd02973 TRX_GRX_like Thioredox 25.2 1.3E+02 0.0029 16.7 3.3 17 28-45 8-24 (67)
71 PF04972 BON: BON domain; Int 25.1 77 0.0017 17.9 2.3 29 37-66 3-34 (64)
72 TIGR02196 GlrX_YruB Glutaredox 25.0 1.3E+02 0.0027 16.6 3.2 16 28-44 7-22 (74)
73 COG0602 NrdG Organic radical a 24.8 75 0.0016 23.3 2.6 36 56-92 71-106 (212)
74 COG2092 EFB1 Translation elong 24.8 75 0.0016 20.5 2.2 25 30-54 59-83 (88)
75 COG4545 Glutaredoxin-related p 24.7 41 0.00088 21.4 1.0 17 28-45 9-25 (85)
76 TIGR00401 msrA methionine-S-su 24.7 58 0.0013 22.8 1.9 47 32-81 7-72 (149)
77 PF08534 Redoxin: Redoxin; In 24.7 1.5E+02 0.0033 19.3 3.9 17 23-39 31-49 (146)
78 PF13732 DUF4162: Domain of un 24.4 1.6E+02 0.0036 17.4 4.2 40 42-86 26-65 (84)
79 COG2100 Predicted Fe-S oxidore 24.1 1.8E+02 0.0038 23.7 4.6 59 23-95 161-224 (414)
80 PRK10614 multidrug efflux syst 23.9 1.7E+02 0.0036 26.5 5.0 56 28-83 53-114 (1025)
81 TIGR02898 spore_YhcN_YlaJ spor 23.6 2.7E+02 0.0059 19.6 5.5 34 33-66 54-87 (158)
82 COG4004 Uncharacterized protei 23.0 1.9E+02 0.0041 18.9 3.8 23 42-64 36-58 (96)
83 PF04805 Pox_E10: E10-like pro 22.7 72 0.0016 19.7 1.8 27 28-54 15-41 (70)
84 PF13193 AMP-binding_C: AMP-bi 22.7 90 0.0019 18.2 2.3 15 38-52 2-16 (73)
85 PRK15127 multidrug efflux syst 22.4 2.1E+02 0.0045 26.1 5.3 49 36-84 160-210 (1049)
86 PF10934 DUF2634: Protein of u 22.2 1.7E+02 0.0037 19.2 3.7 35 31-65 67-104 (112)
87 COG0841 AcrB Cation/multidrug 21.8 1.6E+02 0.0035 26.8 4.5 49 35-83 157-208 (1009)
88 PRK11023 outer membrane lipopr 21.8 2.9E+02 0.0063 19.7 5.1 37 29-65 45-84 (191)
89 TIGR00736 nifR3_rel_arch TIM-b 21.5 3.5E+02 0.0076 20.2 6.1 34 58-92 135-168 (231)
90 COG2331 Uncharacterized protei 21.2 51 0.0011 20.9 0.9 17 29-45 34-50 (82)
91 PRK13265 glycine/sarcosine/bet 21.0 1.3E+02 0.0029 21.2 3.1 71 28-102 13-83 (154)
92 COG1856 Uncharacterized homolo 20.9 1.5E+02 0.0032 22.8 3.5 14 29-42 23-36 (275)
93 PF13291 ACT_4: ACT domain; PD 20.8 1.9E+02 0.0042 16.9 4.4 31 22-52 49-79 (80)
94 COG1432 Uncharacterized conser 20.7 1.2E+02 0.0026 21.5 2.9 40 54-99 109-148 (181)
95 PF13510 Fer2_4: 2Fe-2S iron-s 20.3 1.8E+02 0.004 17.8 3.4 29 50-87 3-31 (82)
96 cd02957 Phd_like Phosducin (Ph 20.2 2.4E+02 0.0052 17.8 4.2 32 23-54 27-62 (113)
97 TIGR02544 III_secr_YscJ type I 20.1 1.1E+02 0.0023 22.2 2.6 22 34-55 108-129 (193)
No 1
>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=99.64 E-value=2.1e-15 Score=90.44 Aligned_cols=61 Identities=26% Similarity=0.403 Sum_probs=56.3
Q ss_pred EEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc
Q 039056 24 VVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY 87 (110)
Q Consensus 24 ~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~ 87 (110)
+|.+ ||+|++|+++|+++|.+++||.++.+|+.+++++|.++.+ .+++++|.++|+++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~---~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPD---KTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTT---TSCHHHHHHHHHHTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecC---CCCHHHHHHHHHHhCcC
Confidence 4788 9999999999999999999999999999999999999843 36789999999999985
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.55 E-value=4.5e-14 Score=87.74 Aligned_cols=66 Identities=18% Similarity=0.248 Sum_probs=59.8
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEE
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFF 90 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~ 90 (110)
...|.+ ||+|++|+++|+++|.+++||.++++|+..+++.|.++. ..++.++|.++++.+||....
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~---~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDS---NKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcC---CcCCHHHHHHHHHHcCCCeee
Confidence 468899 999999999999999999999999999999999999883 357899999999999998654
No 3
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.41 E-value=1.7e-12 Score=95.30 Aligned_cols=80 Identities=16% Similarity=0.267 Sum_probs=70.6
Q ss_pred eEEEEEeeccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCChhHH-
Q 039056 21 QVIVVTANMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSGLFAS- 99 (110)
Q Consensus 21 ~~~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g~~~~- 99 (110)
.+.+|.|.|+|++|++.|++.|..++||.+++||+..+.+.|.+. .++.+|...|+.+|.++++.+.++-.+.
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts------~p~s~i~~~le~tGr~Avl~G~G~psava 80 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETS------VPPSEIQNTLENTGRDAVLRGAGKPSAVA 80 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEcc------CChHHHHHHHHhhChheEEecCCchhHHH
Confidence 457899999999999999999999999999999999999999976 7889999999999999999887755443
Q ss_pred --HHHHhhh
Q 039056 100 --AAFLRFK 106 (110)
Q Consensus 100 --a~~~~~~ 106 (110)
|++++|.
T Consensus 81 l~at~a~~~ 89 (247)
T KOG4656|consen 81 LLATVAKYT 89 (247)
T ss_pred HHHHHHHhc
Confidence 6666654
No 4
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.31 E-value=2e-11 Score=76.02 Aligned_cols=66 Identities=27% Similarity=0.498 Sum_probs=59.5
Q ss_pred eeEEEEEeeccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcC-CceEEE
Q 039056 20 FQVIVVTANMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISG-CYQFFI 91 (110)
Q Consensus 20 ~~~~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G-~~~~~~ 91 (110)
.+..++.++|||.+|..+|++.|+.++||+++++|..+++++|.+. .+|..+.+.+.+.| ..+.+|
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~------~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN------VDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe------cCHHHHHHHHHhcCCCceEEe
Confidence 4567888899999999999999999999999999999999999997 67899999999988 555554
No 5
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.76 E-value=4.5e-08 Score=83.95 Aligned_cols=62 Identities=19% Similarity=0.313 Sum_probs=53.0
Q ss_pred eEEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEE
Q 039056 21 QVIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFF 90 (110)
Q Consensus 21 ~~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~ 90 (110)
+++++.| ||+|++|+.+|+++|++++||.+++||+. +.++.++ .+++.+.+++++.||....
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~------~~~~~i~~~i~~~Gy~~~~ 65 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGT------ASAEALIETIKQAGYDASV 65 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEec------CCHHHHHHHHHhcCCcccc
Confidence 4689999 99999999999999999999999999994 4555544 4678999999999997543
No 6
>PLN02957 copper, zinc superoxide dismutase
Probab=98.66 E-value=2.6e-07 Score=69.16 Aligned_cols=79 Identities=22% Similarity=0.283 Sum_probs=65.4
Q ss_pred eEEEEEeeccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCChh---
Q 039056 21 QVIVVTANMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSGLF--- 97 (110)
Q Consensus 21 ~~~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g~~--- 97 (110)
+++.|.++|+|++|+.+|++.|++++||..+.+|+..++++|.++ ..++.+.+.+++.||...+++...-.
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~------~~~~~I~~aIe~~Gy~a~~~~~~~~~~~~ 79 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS------SPVKAMTAALEQTGRKARLIGQGDPEDFL 79 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec------CCHHHHHHHHHHcCCcEEEecCCCccccc
Confidence 457788899999999999999999999999999999999999874 46788999999999998777765443
Q ss_pred HHHHHHhh
Q 039056 98 ASAAFLRF 105 (110)
Q Consensus 98 ~~a~~~~~ 105 (110)
+.+|++.+
T Consensus 80 ~~~av~~~ 87 (238)
T PLN02957 80 VSAAVAEF 87 (238)
T ss_pred cceEEEEe
Confidence 24454443
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.62 E-value=1.2e-07 Score=80.46 Aligned_cols=64 Identities=27% Similarity=0.403 Sum_probs=56.7
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCC-hHHHHHHHHhcCCceE
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVK-DDPTRSRVKISGCYQF 89 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~-~~~I~~~i~~~G~~~~ 89 (110)
+..|.+ ||+|..|+.+|| .|++++||.++.||+.++++.+.++.. ..+ ++++...+++.||+..
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~---~~~~~~~~~~~v~~~gy~~~ 68 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPE---EVDLPADIVAAVEKAGYSAR 68 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEeccc---ccccHHHHHHHHHhcCcccc
Confidence 468899 999999999999 999999999999999999999999842 234 7899999999999654
No 8
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.17 E-value=5.1e-06 Score=71.77 Aligned_cols=72 Identities=22% Similarity=0.447 Sum_probs=64.6
Q ss_pred eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceE------------EEeeCC
Q 039056 28 NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQF------------FISVSG 95 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~------------~~~~~g 95 (110)
||+|..|.+.|++++.+.+|+.++.|++.+++.+|.++ ...+++.+.+.+++.|++.. .+.+.|
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~----~~~~~~~i~~~ied~gf~~~~~~~~~~~~~~~~l~v~G 77 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYD----NIVSPESIKETIEDMGFEASLLSDSEITASKCYLSVNG 77 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEe----eccCHHHHHHHhhcccceeeecccCccccceeEEEecC
Confidence 89999999999999999999999999999999999998 35899999999999999854 456779
Q ss_pred hhHHHHHH
Q 039056 96 LFASAAFL 103 (110)
Q Consensus 96 ~~~~a~~~ 103 (110)
|+|..|..
T Consensus 78 mtC~scv~ 85 (951)
T KOG0207|consen 78 MTCASCVA 85 (951)
T ss_pred ceeHHHHH
Confidence 98887764
No 9
>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=98.16 E-value=4.3e-05 Score=42.31 Aligned_cols=63 Identities=17% Similarity=0.331 Sum_probs=51.2
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY 87 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~ 87 (110)
+..+.+ +++|..|...+++.+++.+++....+++...++.+.++. .......+...+...||.
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDA---PQATEICIAEAILDAGYE 66 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCC---CCCCHHHHHHHHHHcCCC
Confidence 356888 999999999999999999999999999999999998752 123556666667777763
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.07 E-value=1.5e-05 Score=69.06 Aligned_cols=73 Identities=16% Similarity=0.286 Sum_probs=65.8
Q ss_pred eEEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCCh
Q 039056 21 QVIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSGL 96 (110)
Q Consensus 21 ~~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g~ 96 (110)
++++|.+ ||.|.+|..+|++.|.+++||.++.+++.++++.|.++. ....|-.+.+.++..|+.+.+.+..+.
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~---~~~~pr~i~k~ie~~~~~~~~~~~~~~ 219 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDP---EITGPRDIIKAIEETGFEASVRPYGDT 219 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecc---cccChHHHHHHHHhhcccceeeecccc
Confidence 5789999 999999999999999999999999999999999999984 457889999999999999877775543
No 11
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.65 E-value=0.00031 Score=60.14 Aligned_cols=63 Identities=21% Similarity=0.375 Sum_probs=53.6
Q ss_pred eEEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCce
Q 039056 21 QVIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQ 88 (110)
Q Consensus 21 ~~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~ 88 (110)
++..+.+ ||+|++|..++++.+.+++|+..+.+++.++++.+.++.+ .. +++.+.+++.||..
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~----~~-~~I~~aI~~~Gy~a 116 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADND----IR-AQVESAVQKAGFSL 116 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEeccc----ch-HHHHHHHHhccccc
Confidence 4577889 9999999999999999999999999999999999887632 22 67778888899864
No 12
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.63 E-value=0.00023 Score=61.37 Aligned_cols=62 Identities=16% Similarity=0.275 Sum_probs=53.4
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceE
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQF 89 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~ 89 (110)
++.+.+ ||+|.+|..++++.+.+++|+..+.+|+.+++..+.+. .+++.+.+.+++.||...
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~------~s~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGS------ASPQDLVQAVEKAGYGAE 162 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEcc------CCHHHHHHHHHhcCCCcc
Confidence 467889 99999999999999999999999999999999888643 456778888899998754
No 13
>PRK13748 putative mercuric reductase; Provisional
Probab=95.32 E-value=0.32 Score=39.89 Aligned_cols=41 Identities=20% Similarity=0.445 Sum_probs=35.3
Q ss_pred EEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEe
Q 039056 24 VVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKA 64 (110)
Q Consensus 24 ~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~ 64 (110)
.+.+ +|+|.+|..+++..+...+++....+++..+...+.+
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~ 44 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAI 44 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEE
Confidence 3557 8999999999999999999988888898888877764
No 14
>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=94.98 E-value=0.21 Score=29.90 Aligned_cols=54 Identities=11% Similarity=0.149 Sum_probs=40.9
Q ss_pred EEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEE
Q 039056 24 VVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFF 90 (110)
Q Consensus 24 ~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~ 90 (110)
++.+ |+.||....++.++|.+++ .+..+.|..+ ++.....|...++..|+.-+-
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~---------~G~~l~v~~d----~~~~~~di~~~~~~~g~~~~~ 56 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP---------PGEVLEVLVD----DPAAVEDIPRWCEENGYEVVE 56 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG---------TT-EEEEEES----STTHHHHHHHHHHHHTEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC---------CCCEEEEEEC----CccHHHHHHHHHHHCCCEEEE
Confidence 5777 9999999999999999875 3356667766 345668899999999986333
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=93.96 E-value=0.75 Score=27.38 Aligned_cols=63 Identities=17% Similarity=0.246 Sum_probs=46.1
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY 87 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~ 87 (110)
...+.+ +++|..|...++..+...+++....+++...+..+.... .......+...+...|+.
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~g~~ 87 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDD---EKTNVKALTEATTDAGYP 87 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECC---CCCCHHHHHHHHHhcCCC
Confidence 346667 899999999999999999998888888888887666431 112445555555667765
No 16
>PRK11018 hypothetical protein; Provisional
Probab=91.68 E-value=2.1 Score=26.57 Aligned_cols=55 Identities=9% Similarity=0.020 Sum_probs=43.1
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceE
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQF 89 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~ 89 (110)
..++.+ |+.||...-+.+++|.+++ ..+.+.|..+ ++.....|...+++.|+.-+
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~---------~G~~L~V~~d----~~~a~~di~~~~~~~G~~v~ 63 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLK---------KGEILEVVSD----CPQSINNIPLDARNHGYTVL 63 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCC---------CCCEEEEEeC----CccHHHHHHHHHHHcCCEEE
Confidence 468888 9999999999999998875 3345666655 34566889999999998744
No 17
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=91.48 E-value=1.5 Score=26.39 Aligned_cols=54 Identities=20% Similarity=0.223 Sum_probs=41.6
Q ss_pred EEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEE
Q 039056 25 VTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFI 91 (110)
Q Consensus 25 ~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~ 91 (110)
+.+ |+.||.-.-+.+++|.+++ ..+.+.|..+ ++.....|....+..|+.-+..
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~---------~G~~l~V~~d----~~~a~~di~~~~~~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQ---------DGEQLEVKAS----DPGFARDAQAWCKSTGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEEC----CccHHHHHHHHHHHcCCEEEEE
Confidence 456 8999999999999998875 3355666665 3466788999999999875433
No 18
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=90.40 E-value=3 Score=26.03 Aligned_cols=55 Identities=13% Similarity=0.161 Sum_probs=43.1
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceE
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQF 89 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~ 89 (110)
..++.. |+.||.-.-+.+++|.+++ ..+.+.|..+ ++.....|....+..|++-+
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~---------~G~~l~V~~d----d~~~~~di~~~~~~~G~~~~ 64 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQ---------PGETLLIIAD----DPATTRDIPSFCRFMDHELL 64 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCC---------CCCEEEEEeC----CccHHHHHHHHHHHcCCEEE
Confidence 467888 9999999999999998875 3355666665 34567889999999998644
No 19
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=90.33 E-value=2.4 Score=26.44 Aligned_cols=51 Identities=20% Similarity=0.266 Sum_probs=40.0
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcC
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISG 85 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G 85 (110)
..++.+ |++|+.-...+.++|.+++ ....+.|..+ ++.....|...+++.|
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~---------~Ge~LeV~~d----dp~~~~dIp~~~~~~~ 56 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLK---------PGEILEVIAD----DPAAKEDIPAWAKKEG 56 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCC---------CCCEEEEEec----CcchHHHHHHHHHHcC
Confidence 468889 9999999999999999876 4566677665 3455678888888555
No 20
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=89.65 E-value=3.3 Score=27.04 Aligned_cols=61 Identities=20% Similarity=0.229 Sum_probs=40.3
Q ss_pred eEEEEEe-eccChhHHHHHHHHHhcCCCcceE-------EEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCC
Q 039056 21 QVIVVTA-NMGCTRCRGRVSQIISKLTGLEEY-------IVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGC 86 (110)
Q Consensus 21 ~~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v-------~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~ 86 (110)
..+++.+ --|-+.-.-.+.+.|.+++||+.+ +++..+-++++.+. .++.++|.+.+++.|.
T Consensus 6 RRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~-----~ldydei~~~iE~~Gg 74 (97)
T COG1888 6 RRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGT-----NLDYDEIEEVIEELGG 74 (97)
T ss_pred eeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcC-----CCCHHHHHHHHHHcCC
Confidence 4456666 333333344555668888888764 33334556777765 5899999999999995
No 21
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=89.58 E-value=2.8 Score=24.59 Aligned_cols=52 Identities=13% Similarity=0.134 Sum_probs=40.0
Q ss_pred EEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceE
Q 039056 25 VTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQF 89 (110)
Q Consensus 25 ~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~ 89 (110)
+.+ |+.||.-..++.++|.+++ ....+.|..+ .+.....|...++..||.-+
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~---------~g~~l~v~~d----~~~~~~~i~~~~~~~g~~~~ 54 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLK---------SGEVLEVLLD----DPGAVEDIPAWAKETGHEVL 54 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCC---------CCCEEEEEec----CCcHHHHHHHHHHHcCCEEE
Confidence 455 8999999999999998864 3455666665 23567889999999998744
No 22
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=88.87 E-value=2.6 Score=24.91 Aligned_cols=52 Identities=13% Similarity=0.227 Sum_probs=37.9
Q ss_pred EEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEE
Q 039056 25 VTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFF 90 (110)
Q Consensus 25 ~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~ 90 (110)
+.+ |+.||...-+.+++| ++. .++.+.|..+ .+.....|...+++.||.-..
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~---------~g~~l~v~~d----~~~s~~~i~~~~~~~G~~~~~ 54 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELE---------AGGEIEVLVD----NEVAKENVSRFAESRGYEVSV 54 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcC---------CCCEEEEEEc----ChhHHHHHHHHHHHcCCEEEE
Confidence 456 899999999999999 543 2345566554 234567899999999987533
No 23
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=88.87 E-value=3.5 Score=24.71 Aligned_cols=53 Identities=11% Similarity=0.138 Sum_probs=40.5
Q ss_pred EEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEE
Q 039056 25 VTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFF 90 (110)
Q Consensus 25 ~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~ 90 (110)
+.+ |..||.-.-+.+++|.+++ ..+.+.|..+ ++.....|...+++.||.-+.
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~---------~G~~l~V~~d----d~~s~~di~~~~~~~g~~~~~ 55 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK---------PGDTLLVLAT----DPSTTRDIPKFCTFLGHELLA 55 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC---------CCCEEEEEeC----CCchHHHHHHHHHHcCCEEEE
Confidence 345 8999999999999998864 3345666665 346778899999999987543
No 24
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=88.63 E-value=3.6 Score=24.75 Aligned_cols=53 Identities=11% Similarity=0.071 Sum_probs=40.7
Q ss_pred EEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEE
Q 039056 25 VTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFF 90 (110)
Q Consensus 25 ~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~ 90 (110)
+.+ |..||.-.-+.+++|++++ ....+.|..+ ++.....|.+.++..|+.-+.
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~---------~G~~l~V~~d----~~~s~~ni~~~~~~~g~~v~~ 55 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLK---------PGEILEVISD----CPQSINNIPIDARNHGYKVLA 55 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEec----CchHHHHHHHHHHHcCCEEEE
Confidence 345 8999999999999999875 3355666665 346778899999999987543
No 25
>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=87.12 E-value=2.3 Score=20.52 Aligned_cols=38 Identities=32% Similarity=0.625 Sum_probs=30.6
Q ss_pred eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEec
Q 039056 28 NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKAD 65 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~ 65 (110)
++.|..|...++..+...+++.....++......+.++
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 43 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYD 43 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEEC
Confidence 78999999999999888888777777777776666543
No 26
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=86.19 E-value=6.6 Score=25.73 Aligned_cols=61 Identities=18% Similarity=0.324 Sum_probs=39.7
Q ss_pred eeEEEEEe-eccChhHHHHHHHHHhcCCCcceEE-----EeCCCC--EEEEEecCCCCCCCChHHHHHHHHhcCC
Q 039056 20 FQVIVVTA-NMGCTRCRGRVSQIISKLTGLEEYI-----VDVPNK--RVTVKADFGLNKNVKDDPTRSRVKISGC 86 (110)
Q Consensus 20 ~~~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~-----Vdl~~~--kv~V~~~~~~~~~~~~~~I~~~i~~~G~ 86 (110)
...++|.| --|-+. .-.+.+.|.+++||+.+. +|..+. ++++.|+ .++.++|.+++++.|.
T Consensus 4 irRlVLDVlKP~~p~-i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~-----~id~d~i~~~Ie~~Gg 72 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPS-IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGD-----DIDFDEIKEAIEELGG 72 (95)
T ss_dssp EEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEES-----SE-HHHHHHHHHHTT-
T ss_pred eeEEEEEeecCCCCC-HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeC-----CCCHHHHHHHHHHcCC
Confidence 34567777 335444 445666799999988753 444544 4555564 5899999999999994
No 27
>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=81.09 E-value=3.8 Score=24.49 Aligned_cols=32 Identities=16% Similarity=0.374 Sum_probs=21.3
Q ss_pred EEEEEeeccChhHH------HHHHHHHhcCCCcceEEE
Q 039056 22 VIVVTANMGCTRCR------GRVSQIISKLTGLEEYIV 53 (110)
Q Consensus 22 ~~~~~Vgm~C~~C~------~~Vek~L~~i~GV~~v~V 53 (110)
++.+.+.+..++|. ..|+++|..++|+.+++|
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 45566655555554 678888999999988875
No 28
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=80.89 E-value=3.7 Score=29.53 Aligned_cols=47 Identities=11% Similarity=0.053 Sum_probs=37.9
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCCE-------------------EEEEecCCCCCCCChHHHHHHH
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNKR-------------------VTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~k-------------------v~V~~~~~~~~~~~~~~I~~~i 81 (110)
++|=+-++..+.+++||.++.+-+.++. |.|.+|+ ..++.++|.+..
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp---~~isy~~Ll~~f 75 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDP---AVISYRELLELF 75 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECC---CcCCHHHHHHHH
Confidence 6788888999999999999998877665 8888984 468888887543
No 29
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=77.57 E-value=12 Score=27.34 Aligned_cols=49 Identities=12% Similarity=0.106 Sum_probs=37.2
Q ss_pred eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceE
Q 039056 28 NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQF 89 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~ 89 (110)
|+.||...-+.+++|.+++. .+.+.|..+ ++...+.|.+.++..||+-.
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD----~~~a~~nV~~~~~~~G~~v~ 53 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGE---------EGVLTVIVD----NEAAKENVSKFATSLGYEVE 53 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCC---------CCEEEEEEC----CccHHHHHHHHHHHcCCEEE
Confidence 88999999999999988752 345566555 34566789999999998643
No 30
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=75.50 E-value=8.9 Score=27.96 Aligned_cols=54 Identities=13% Similarity=0.168 Sum_probs=40.1
Q ss_pred eeEEEEEeeccChhHHHHHHHHHhcCCCcceEEEeCCCCE-------------------EEEEecCCCCCCCChHHHHHH
Q 039056 20 FQVIVVTANMGCTRCRGRVSQIISKLTGLEEYIVDVPNKR-------------------VTVKADFGLNKNVKDDPTRSR 80 (110)
Q Consensus 20 ~~~~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~k-------------------v~V~~~~~~~~~~~~~~I~~~ 80 (110)
.+++.|. ++|=.-++..+.+++||.++.+-+.++. |.|.+|+ ..++.++|.+.
T Consensus 8 ~~~a~~a-----gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp---~~iSy~~LL~~ 79 (186)
T PRK13014 8 METATFA-----GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDP---KQVSYENLLQI 79 (186)
T ss_pred ccEEEEe-----cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECC---CcCCHHHHHHH
Confidence 3445554 5677778888999999999988877664 7888884 45788888764
Q ss_pred H
Q 039056 81 V 81 (110)
Q Consensus 81 i 81 (110)
.
T Consensus 80 F 80 (186)
T PRK13014 80 F 80 (186)
T ss_pred H
Confidence 4
No 31
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=70.74 E-value=12 Score=26.52 Aligned_cols=47 Identities=17% Similarity=0.087 Sum_probs=36.1
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCC--------------EEEEEecCCCCCCCChHHHHHHH
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNK--------------RVTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~--------------kv~V~~~~~~~~~~~~~~I~~~i 81 (110)
++|=+-+|..+.+++||.++.+-+.++ .|.|.+|+ ..++.++|++..
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp---~~isy~~LL~~f 68 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDP---RMVSITDLMGYL 68 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECC---CcCCHHHHHHHH
Confidence 677788889999999999988876553 27788884 467888887654
No 32
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=65.61 E-value=13 Score=27.64 Aligned_cols=47 Identities=15% Similarity=0.084 Sum_probs=36.7
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCC-------------------EEEEEecCCCCCCCChHHHHHHH
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNK-------------------RVTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~-------------------kv~V~~~~~~~~~~~~~~I~~~i 81 (110)
++|-+-+|..+.+++||.++.|-+.++ .|.|.+|+ ..++.++|.+..
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp---~~ISy~~LL~~F 117 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDP---AVISYEQLLQVF 117 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECC---ccCCHHHHHHHH
Confidence 677888888999999999999887743 37888884 457888886544
No 33
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=61.52 E-value=52 Score=23.13 Aligned_cols=47 Identities=17% Similarity=0.111 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCC-------------------EEEEEecCCCCCCCChHHHHHHH
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNK-------------------RVTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~-------------------kv~V~~~~~~~~~~~~~~I~~~i 81 (110)
.+|=.-++..+.+++||.++.+-+.++ .|.|.+|+ ..++.++|.+..
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~---~~is~~~Ll~~f 72 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDP---SVISYEELLDVF 72 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEET---TTS-HHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECC---CcccHHHHHHHH
Confidence 567888889999999999998876554 57788884 457778876654
No 34
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=59.73 E-value=28 Score=20.91 Aligned_cols=62 Identities=13% Similarity=0.068 Sum_probs=37.5
Q ss_pred EEEEEe-eccChhHHHHHHHHHhcCCC-cceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhc
Q 039056 22 VIVVTA-NMGCTRCRGRVSQIISKLTG-LEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKIS 84 (110)
Q Consensus 22 ~~~~~V-gm~C~~C~~~Vek~L~~i~G-V~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~ 84 (110)
.+.+.+ |.+.++-...|.+.|.+..+ +.+.+.....+..+...-.+.+ ..+.+++.+.+++.
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~-~~~~~~l~~~L~~l 65 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP-EDSLERLESALEEL 65 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES-HHHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC-cccHHHHHHHHHHH
Confidence 467788 99999999999999998766 5566665555554443221111 12446666666654
No 35
>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=59.47 E-value=15 Score=26.44 Aligned_cols=33 Identities=12% Similarity=0.317 Sum_probs=23.1
Q ss_pred EEEEeeccChhHH------HHHHHHHhcCCCcceEEEeC
Q 039056 23 IVVTANMGCTRCR------GRVSQIISKLTGLEEYIVDV 55 (110)
Q Consensus 23 ~~~~Vgm~C~~C~------~~Vek~L~~i~GV~~v~Vdl 55 (110)
+.+.+-+..++|. ..|+.+|..++|+.+++|++
T Consensus 115 V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 115 VDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 4555555555554 45888999999998887764
No 36
>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=58.22 E-value=41 Score=23.40 Aligned_cols=38 Identities=21% Similarity=0.351 Sum_probs=31.6
Q ss_pred cChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCC
Q 039056 30 GCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFG 67 (110)
Q Consensus 30 ~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~ 67 (110)
.=..=+.+|.+.+.+++||+++.|=.....+.|-.+.+
T Consensus 72 ~~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~ 109 (177)
T PF09580_consen 72 DRQQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLD 109 (177)
T ss_pred hHHHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEec
Confidence 34667889999999999999999888888888876643
No 37
>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=54.81 E-value=16 Score=23.11 Aligned_cols=21 Identities=19% Similarity=0.431 Sum_probs=17.1
Q ss_pred HHHHHHHhcCCCcceEEEeCC
Q 039056 36 GRVSQIISKLTGLEEYIVDVP 56 (110)
Q Consensus 36 ~~Vek~L~~i~GV~~v~Vdl~ 56 (110)
..++.+|..++|+.++++++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457788889999998888864
No 38
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=49.63 E-value=33 Score=26.62 Aligned_cols=47 Identities=17% Similarity=0.104 Sum_probs=36.1
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCC-------------------EEEEEecCCCCCCCChHHHHHHH
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNK-------------------RVTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~-------------------kv~V~~~~~~~~~~~~~~I~~~i 81 (110)
.+|=.-++..+.+++||.++.+-+.++ .|.|.+|+ ..++.++|.+..
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp---~~isy~~LL~~F 199 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDP---AKISYETLLKVF 199 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECC---ccCCHHHHHHHH
Confidence 677788888999999999988876554 37888884 457888877654
No 39
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=49.61 E-value=34 Score=22.90 Aligned_cols=31 Identities=19% Similarity=0.487 Sum_probs=22.8
Q ss_pred EEeeccChhH------HHHHHHHHhcCCCcceEEEeC
Q 039056 25 VTANMGCTRC------RGRVSQIISKLTGLEEYIVDV 55 (110)
Q Consensus 25 ~~Vgm~C~~C------~~~Vek~L~~i~GV~~v~Vdl 55 (110)
+.+.++-++| ...++.+|.+++||++++|++
T Consensus 53 v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 53 VKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 3334444555 678999999999998888875
No 40
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=46.41 E-value=67 Score=19.85 Aligned_cols=34 Identities=18% Similarity=0.114 Sum_probs=25.8
Q ss_pred CceeEEEEEeeccChhHHHHHHHHHhcCCCcceEEE
Q 039056 18 PSFQVIVVTANMGCTRCRGRVSQIISKLTGLEEYIV 53 (110)
Q Consensus 18 ~~~~~~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~V 53 (110)
+....+++.++ -+.....+.+.|+++.+|..+++
T Consensus 42 ~~~sriti~v~--~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 42 AQNINIELTVA--SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred CCEEEEEEEEC--CCchHHHHHHHHhcCcCeEEEEE
Confidence 33445666664 58999999999999999977765
No 41
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=45.50 E-value=50 Score=23.91 Aligned_cols=53 Identities=13% Similarity=0.104 Sum_probs=38.1
Q ss_pred eEEEEEeeccChhHHHHHHHHHhcCCCcceEEEeCCCC-------------------EEEEEecCCCCCCCChHHHHHHH
Q 039056 21 QVIVVTANMGCTRCRGRVSQIISKLTGLEEYIVDVPNK-------------------RVTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 21 ~~~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~-------------------kv~V~~~~~~~~~~~~~~I~~~i 81 (110)
+++.|. ++|=+-+++...+++||.++.+-..++ .|.|.+|+ ..++.++|++..
T Consensus 7 ~~a~fa-----gGCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp---~~isy~~LL~~f 78 (174)
T COG0225 7 EKAYFA-----GGCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDP---KVISYEELLEVF 78 (174)
T ss_pred EEEEEe-----ccCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCC---ccccHHHHHHHH
Confidence 445554 567777888899999999887765444 36778884 467888887665
No 42
>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=43.29 E-value=65 Score=18.57 Aligned_cols=32 Identities=6% Similarity=0.182 Sum_probs=23.7
Q ss_pred EEEEEeeccChh-HHHHHHHHHhcCCCcceEEE
Q 039056 22 VIVVTANMGCTR-CRGRVSQIISKLTGLEEYIV 53 (110)
Q Consensus 22 ~~~~~Vgm~C~~-C~~~Vek~L~~i~GV~~v~V 53 (110)
.+.|.+..+-.. -..++-+.|++++||.++.+
T Consensus 42 ~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 42 NVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 355555445554 78889999999999988764
No 43
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=40.99 E-value=94 Score=19.76 Aligned_cols=34 Identities=18% Similarity=0.318 Sum_probs=27.4
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEec
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKAD 65 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~ 65 (110)
+.=...|.+.|..+||++-.-.|-..+|+.|+-+
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE 49 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVE 49 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEE
Confidence 4557889999999999977777777788888765
No 44
>PRK09577 multidrug efflux protein; Reviewed
Probab=40.07 E-value=54 Score=29.58 Aligned_cols=51 Identities=12% Similarity=0.060 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCC--CCCCChHHHHHHHHhcC
Q 039056 35 RGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGL--NKNVKDDPTRSRVKISG 85 (110)
Q Consensus 35 ~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~--~~~~~~~~I~~~i~~~G 85 (110)
.+++++.|.+++||.+++++-....+.|..|++. .-.++++++.++++..+
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 4679999999999999998876666666543210 12477888999997765
No 45
>KOG4034 consensus Uncharacterized conserved protein NOF (Neighbor of FAU) [Function unknown]
Probab=38.35 E-value=64 Score=23.15 Aligned_cols=53 Identities=9% Similarity=0.054 Sum_probs=40.5
Q ss_pred eeccChhHHHHHHHHHhcCCCcce-EEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCC
Q 039056 27 ANMGCTRCRGRVSQIISKLTGLEE-YIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGC 86 (110)
Q Consensus 27 Vgm~C~~C~~~Vek~L~~i~GV~~-v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~ 86 (110)
|.=+--.|.+.++..|..++|-.. -.||--++++.+.++ ..+.+.+.+.+.|+
T Consensus 116 VeGDi~aLe~DL~s~L~~~~~~s~~t~VnelsgqI~~~g~-------~v~~vr~~L~eKGF 169 (169)
T KOG4034|consen 116 VEGDIWALENDLRSTLEMSPKKSYATHVNELSGQIVLKGN-------HVDTVREWLQEKGF 169 (169)
T ss_pred ecccHHHHHHHHHHHHhhccCCChhhhhhhhcceEEEeCC-------hHHHHHHHHHHccC
Confidence 433456899999999999888533 358889999998876 23688888888775
No 46
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=36.46 E-value=23 Score=27.80 Aligned_cols=20 Identities=20% Similarity=0.507 Sum_probs=15.7
Q ss_pred EEEEe--eccChhHHHHHHHHH
Q 039056 23 IVVTA--NMGCTRCRGRVSQII 42 (110)
Q Consensus 23 ~~~~V--gm~C~~C~~~Vek~L 42 (110)
+.|.+ +++|.+|.+.|-.-+
T Consensus 45 IRFEMPynIWC~gC~nhIgmGv 66 (317)
T KOG2990|consen 45 IRFEMPYNIWCDGCKNHIGMGV 66 (317)
T ss_pred EEEecccchhhccHHHhhhccc
Confidence 55666 799999999987643
No 47
>COG1166 SpeA Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]
Probab=35.00 E-value=1.3e+02 Score=25.94 Aligned_cols=54 Identities=19% Similarity=0.163 Sum_probs=40.0
Q ss_pred EEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc-eEEEeeCChhHH------HHHHhhh
Q 039056 52 IVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY-QFFISVSGLFAS------AAFLRFK 106 (110)
Q Consensus 52 ~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~-~~~~~~~g~~~~------a~~~~~~ 106 (110)
.+| ..+.++|..+++....++..+|++++++.|+. ++++.+.-+..- +||.+.+
T Consensus 45 ~In-~~G~v~V~P~~~~~~~~dL~elV~~l~~~g~~LPlL~rFp~IL~~Rl~~ln~aF~~Ai 105 (652)
T COG1166 45 DIN-DAGHVTVCPDPDPGARVDLAELVKALRDRGLRLPLLLRFPQILQHRLRSLNAAFARAI 105 (652)
T ss_pred eec-CCccEEEecCCCccccccHHHHHHHHHhcCCCCceEEechHHHHHHHHHHHHHHHHHH
Confidence 443 34888998776655677889999999999987 888887766553 6666554
No 48
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=34.56 E-value=1.3e+02 Score=21.09 Aligned_cols=40 Identities=20% Similarity=0.453 Sum_probs=29.5
Q ss_pred eEEEEEe-eccChhHHHHHHHHHhcCCCcceEEEeCC-CCEEE
Q 039056 21 QVIVVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVP-NKRVT 61 (110)
Q Consensus 21 ~~~~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~-~~kv~ 61 (110)
..+++.| ---|..|...|.....+ -|+.++.|... ++++.
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~-lGl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEK-LGLKSLTIHEPDSGKVY 141 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHH-cCCCeEEEEecCCCcEE
Confidence 3466777 57899999999887766 48888887776 66443
No 49
>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=33.36 E-value=1.4e+02 Score=19.40 Aligned_cols=57 Identities=9% Similarity=0.086 Sum_probs=34.2
Q ss_pred EEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhc
Q 039056 24 VVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKIS 84 (110)
Q Consensus 24 ~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~ 84 (110)
.+.+ |++-+-+...|+..++....|..|++..-.....|.+.. +.......+.+...
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~----~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKT----PEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS-------HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECC----cchHHHHHHHHHhc
Confidence 3455 566666799999999999999999999888899999872 33456666666665
No 50
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=32.85 E-value=94 Score=19.98 Aligned_cols=50 Identities=8% Similarity=-0.130 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc
Q 039056 35 RGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY 87 (110)
Q Consensus 35 ~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~ 87 (110)
+..++=.|+.-++|..+-+|--.+...|.+|. ...+.+++.+.+++.++.
T Consensus 13 A~~~QYeLsk~~~vyRvFiNgYar~g~VifDe---~kl~~e~lL~~le~~kpE 62 (88)
T PF11491_consen 13 AMVKQYELSKNEAVYRVFINGYARNGFVIFDE---SKLSKEELLEMLEEFKPE 62 (88)
T ss_dssp THHHHHTTTTTTTB------TTSS--EEE--B----S-SHHHH---HHHTTT-
T ss_pred HHHHHHHhhcccceeeeeecccccceEEEECc---ccCCHHHHHHHHHhcChh
Confidence 45566678899999999999988888888884 457889999999988864
No 51
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=32.17 E-value=1.1e+02 Score=27.78 Aligned_cols=51 Identities=6% Similarity=0.078 Sum_probs=37.0
Q ss_pred HHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCC--CCCCChHHHHHHHHhc
Q 039056 34 CRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGL--NKNVKDDPTRSRVKIS 84 (110)
Q Consensus 34 C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~--~~~~~~~~I~~~i~~~ 84 (110)
=+..+++.|.+++||.+++++-....+.|..|++. .-.++++++.++++..
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 158 VASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 34678999999999999998865566777655211 1256788888888754
No 52
>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=31.19 E-value=84 Score=28.44 Aligned_cols=50 Identities=12% Similarity=0.092 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCC--CCCCChHHHHHHHHhc
Q 039056 35 RGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGL--NKNVKDDPTRSRVKIS 84 (110)
Q Consensus 35 ~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~--~~~~~~~~I~~~i~~~ 84 (110)
...+++.|.+++||.++++.-....+.|..|++. .-.+++.++.++++..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 3568999999999999998777666777755211 1257788889998873
No 53
>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=30.64 E-value=1.3e+02 Score=18.44 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=31.1
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHh
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKI 83 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~ 83 (110)
+.=...+.+.|..+||++-.-.+-. +|+.|+-+. .+...+.+.+..
T Consensus 14 p~~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~-----~~~~~~~~~~~~ 59 (79)
T PF03927_consen 14 PERLEEVAEALAAIPGVEVHAVDED-GKIVVTIEA-----ESSEEEVDLIDA 59 (79)
T ss_dssp CCCHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEE-----SSHHHHHHHHHH
T ss_pred chhHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEe-----CChHHHHHHHHH
Confidence 3446788899999999966666655 877777652 234555555544
No 54
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=30.63 E-value=1.7e+02 Score=21.69 Aligned_cols=62 Identities=11% Similarity=0.161 Sum_probs=43.2
Q ss_pred HHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCC-CC-ChHHHHHHHHhcCCceEEEeeCChh
Q 039056 35 RGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNK-NV-KDDPTRSRVKISGCYQFFISVSGLF 97 (110)
Q Consensus 35 ~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~-~~-~~~~I~~~i~~~G~~~~~~~~~g~~ 97 (110)
....|+.|..+ |..++.|-.....++|+-+++.-. .. ..+.|...+++.||..+.+-..|..
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~gf~~v~ldl~g~~ 250 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIGFRKVLIDLEGYR 250 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcCCCeEEEccCCcc
Confidence 55667778774 888899998889999986521100 00 1367889999999998877666653
No 55
>PF04723 GRDA: Glycine reductase complex selenoprotein A; InterPro: IPR006812 Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP []. A member of this family may also exist in Treponema denticola [].; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=30.07 E-value=79 Score=22.25 Aligned_cols=72 Identities=13% Similarity=0.011 Sum_probs=35.7
Q ss_pred eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCChhHHHHHH
Q 039056 28 NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSGLFASAAFL 103 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g~~~~a~~~ 103 (110)
|=..+--...++..+... | .+|-|......|-......+..+...|.+..++.|..-+++-.++--+-+|.+
T Consensus 12 GdRDGiPgpAie~c~~~~-g---aevvfs~TeCFVctaagaMDLEnQ~rvk~~aEk~g~enlvVvlG~aeaE~a~l 83 (150)
T PF04723_consen 12 GDRDGIPGPAIEECVKTA-G---AEVVFSSTECFVCTAAGAMDLENQQRVKDLAEKYGAENLVVVLGAAEAEAAGL 83 (150)
T ss_pred ecCCCCCcHHHHHHHHhc-C---ceEEEEeeeEEEecccccccHHHHHHHHHHHHhcCCccEEEEecCCChhhhhh
Confidence 445555556666666543 2 23333333333322211122234455666667777766666666555555444
No 56
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=29.94 E-value=46 Score=21.97 Aligned_cols=29 Identities=21% Similarity=0.603 Sum_probs=20.8
Q ss_pred eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEe
Q 039056 28 NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKA 64 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~ 64 (110)
...|..|+..+++.|.. .|+ ..+.+++..
T Consensus 18 ~~qC~~cA~Al~~~L~~-~gI-------~Gk~i~l~T 46 (100)
T PF15643_consen 18 IFQCVECASALKQFLKQ-AGI-------PGKIIRLYT 46 (100)
T ss_pred ceehHHHHHHHHHHHHH-CCC-------CceEEEEEe
Confidence 56899999999999975 233 445555554
No 57
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=29.91 E-value=2.1e+02 Score=22.82 Aligned_cols=50 Identities=14% Similarity=0.129 Sum_probs=0.0
Q ss_pred EEEe-eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc
Q 039056 24 VVTA-NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY 87 (110)
Q Consensus 24 ~~~V-gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~ 87 (110)
.+.+ .-.|.+|+..|-+. |+ ++|.+-.|+++........+.+.++.+|.+
T Consensus 47 ~i~~s~~p~~~cad~ii~~-----gi---------~rVVi~~D~d~~G~~~~~~~~~~L~~aGi~ 97 (360)
T PRK14719 47 FITVSNTPVFQIADDLIAE-----NI---------SEVILLTDFDRAGRVYAKNIMEEFQSRGIK 97 (360)
T ss_pred EEEEeCCchHHHHHHHHHc-----CC---------CEEEEEECCCCCCCccchHHHHHHHHCCCE
No 58
>PF00289 CPSase_L_chain: Carbamoyl-phosphate synthase L chain, N-terminal domain; InterPro: IPR005481 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the large subunit of carbamoyl phosphate synthase. This domain can also be found in certain other related proteins. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VA7_A 3OUU_A 3OUZ_B 1W96_B 1W93_A 1ULZ_A 3HB9_C 3HO8_A 3BG5_C 3HBL_A ....
Probab=29.27 E-value=1.7e+02 Score=19.12 Aligned_cols=68 Identities=13% Similarity=0.180 Sum_probs=40.5
Q ss_pred HHHHHHHHhcCCCcceEEEeC-----------CCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCChhHH-HHH
Q 039056 35 RGRVSQIISKLTGLEEYIVDV-----------PNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSGLFAS-AAF 102 (110)
Q Consensus 35 ~~~Vek~L~~i~GV~~v~Vdl-----------~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g~~~~-a~~ 102 (110)
+-++-++++++ |++.+-++- .++.+.+..........+.+.|.+.+++.|.+++. +..|+++- +.|
T Consensus 14 a~r~~ra~r~~-Gi~tv~v~s~~d~~s~~~~~ad~~~~~~~~~~~~~yl~~e~I~~ia~~~g~~~i~-pGyg~lse~~~f 91 (110)
T PF00289_consen 14 AVRIIRALREL-GIETVAVNSNPDTVSTHVDMADEAYFEPPGPSPESYLNIEAIIDIARKEGADAIH-PGYGFLSENAEF 91 (110)
T ss_dssp HHHHHHHHHHT-TSEEEEEEEGGGTTGHHHHHSSEEEEEESSSGGGTTTSHHHHHHHHHHTTESEEE-STSSTTTTHHHH
T ss_pred HHHHHHHHHHh-CCcceeccCchhcccccccccccceecCcchhhhhhccHHHHhhHhhhhcCcccc-cccchhHHHHHH
Confidence 34455555554 777776663 33334443222222347889999999999987766 55555543 555
Q ss_pred Hh
Q 039056 103 LR 104 (110)
Q Consensus 103 ~~ 104 (110)
++
T Consensus 92 a~ 93 (110)
T PF00289_consen 92 AE 93 (110)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 59
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=28.89 E-value=1.1e+02 Score=25.82 Aligned_cols=47 Identities=15% Similarity=0.183 Sum_probs=36.2
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCCC------------------EEEEEecCCCCCCCChHHHHHHH
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPNK------------------RVTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~~------------------kv~V~~~~~~~~~~~~~~I~~~i 81 (110)
++|=.-+|..+.+++||.++.+-+.++ .|.|.+|+ ..++.++|.+..
T Consensus 205 gGCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp---~~is~~~Ll~~f 269 (521)
T PRK14018 205 GGCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDA---DKLSLDTILQYY 269 (521)
T ss_pred cCCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECC---CcCcHHHHHHHH
Confidence 677788888999999999988877555 26778884 457888876654
No 60
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=28.73 E-value=32 Score=20.51 Aligned_cols=21 Identities=14% Similarity=0.468 Sum_probs=17.4
Q ss_pred EEEeeccChhHHHHHHHHHhc
Q 039056 24 VVTANMGCTRCRGRVSQIISK 44 (110)
Q Consensus 24 ~~~Vgm~C~~C~~~Vek~L~~ 44 (110)
.+.+|-.|+.|...+++.|..
T Consensus 32 ~~~~g~~CG~C~~~i~~il~~ 52 (64)
T PRK10509 32 FVPVGNQCGKCIRAAREVMQD 52 (64)
T ss_pred hcCCCCCccchHHHHHHHHHH
Confidence 356688999999999998864
No 61
>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=28.70 E-value=1.5e+02 Score=18.54 Aligned_cols=56 Identities=7% Similarity=0.071 Sum_probs=40.0
Q ss_pred EEEeeccChhHHHHHHHHHhcCCC-cceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCC
Q 039056 24 VVTANMGCTRCRGRVSQIISKLTG-LEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGC 86 (110)
Q Consensus 24 ~~~Vgm~C~~C~~~Vek~L~~i~G-V~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~ 86 (110)
.=+|.=+=..+...+.+.|....+ -..+.|+-.++.+.|.|+. ..++.+.|...|+
T Consensus 31 IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-------~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 31 IRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-------VEEVKKWLLEKGF 87 (87)
T ss_pred EEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-------HHHHHHHHHHCcC
Confidence 334422346778888888865544 2368899999999999972 3778888888875
No 62
>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=28.16 E-value=63 Score=19.24 Aligned_cols=15 Identities=40% Similarity=0.651 Sum_probs=10.0
Q ss_pred EEEEeeccChhHHHHH
Q 039056 23 IVVTANMGCTRCRGRV 38 (110)
Q Consensus 23 ~~~~Vgm~C~~C~~~V 38 (110)
+.+ ++..|+.|....
T Consensus 3 I~v-~~~~C~~C~~~~ 17 (76)
T PF13192_consen 3 IKV-FSPGCPYCPELV 17 (76)
T ss_dssp EEE-ECSSCTTHHHHH
T ss_pred EEE-eCCCCCCcHHHH
Confidence 344 577799999433
No 63
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=27.39 E-value=80 Score=24.92 Aligned_cols=42 Identities=19% Similarity=0.225 Sum_probs=31.8
Q ss_pred EEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc------e-EEEeeCChhHH
Q 039056 52 IVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY------Q-FFISVSGLFAS 99 (110)
Q Consensus 52 ~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~------~-~~~~~~g~~~~ 99 (110)
++|..+++++|..- +...++.+.+.+.|+. . ...+++|+.+-
T Consensus 89 ~id~~~~~~~v~aG------v~l~~l~~~l~~~G~~~p~~p~s~~~~tIGG~ia~ 137 (459)
T COG0277 89 EIDPEDGTATVQAG------VTLEDLEKALAPHGLFLPVDPSSSGTATIGGNIAT 137 (459)
T ss_pred ccCcCCCEEEEcCC------ccHHHHHHHHHHcCCccCCCccccccceEccchhc
Confidence 68888999999754 7789999999999965 1 14567776654
No 64
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=27.27 E-value=2.1e+02 Score=21.88 Aligned_cols=22 Identities=23% Similarity=0.270 Sum_probs=17.1
Q ss_pred hHHHHHHHHHhcCCCcceEEEe
Q 039056 33 RCRGRVSQIISKLTGLEEYIVD 54 (110)
Q Consensus 33 ~C~~~Vek~L~~i~GV~~v~Vd 54 (110)
.=..++++.|++++||-+++|.
T Consensus 109 ~~eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 109 AKEQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHHHHHHHHhcCceEEEEEE
Confidence 3467899999999998876543
No 65
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=27.08 E-value=1.3e+02 Score=27.38 Aligned_cols=56 Identities=9% Similarity=0.200 Sum_probs=34.2
Q ss_pred eccChhH----HHHHHHHHhcCCCcceEEEeCCCC--EEEEEecCCCCCCCChHHHHHHHHh
Q 039056 28 NMGCTRC----RGRVSQIISKLTGLEEYIVDVPNK--RVTVKADFGLNKNVKDDPTRSRVKI 83 (110)
Q Consensus 28 gm~C~~C----~~~Vek~L~~i~GV~~v~Vdl~~~--kv~V~~~~~~~~~~~~~~I~~~i~~ 83 (110)
|.+-... ...+|+.|+.++||+.++..-..+ .++|+++.+.+-.....++.+++.+
T Consensus 62 Gas~~~vE~~Vt~piE~~l~~v~gv~~i~S~S~~G~s~i~v~f~~g~d~~~a~~ev~~~i~~ 123 (1040)
T PRK10503 62 GASPDVMTSAVTAPLERQFGQMSGLKQMSSQSSGGASVITLQFQLTLPLDVAEQEVQAAINA 123 (1040)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCccEEEEEecCCeEEEEEEEECCCChHHHHHHHHHHHHH
Confidence 5555553 456788899999999987655555 4555665332112223566666654
No 66
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=26.72 E-value=61 Score=23.60 Aligned_cols=31 Identities=16% Similarity=0.400 Sum_probs=23.1
Q ss_pred hhHHHHHHHHHhcCCCcceEE--EeCCCCEEEE
Q 039056 32 TRCRGRVSQIISKLTGLEEYI--VDVPNKRVTV 62 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~--Vdl~~~kv~V 62 (110)
..-..+++..|.++.|+.+|+ ++|.++.-.|
T Consensus 60 ~~lE~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 60 KQYENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 456788999999999999876 4555554444
No 67
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=26.34 E-value=72 Score=23.25 Aligned_cols=22 Identities=23% Similarity=0.442 Sum_probs=18.5
Q ss_pred HHHHHHHHHhcCCCcceEEEeC
Q 039056 34 CRGRVSQIISKLTGLEEYIVDV 55 (110)
Q Consensus 34 C~~~Vek~L~~i~GV~~v~Vdl 55 (110)
=...+++.|+.++||+++.|++
T Consensus 116 le~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 116 LEGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHHcCCCeeEEEEEE
Confidence 4567889999999999998874
No 68
>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=26.25 E-value=74 Score=20.32 Aligned_cols=22 Identities=18% Similarity=0.214 Sum_probs=19.3
Q ss_pred hHHHHHHHHHhcCCCcceEEEe
Q 039056 33 RCRGRVSQIISKLTGLEEYIVD 54 (110)
Q Consensus 33 ~C~~~Vek~L~~i~GV~~v~Vd 54 (110)
+-...++..+++++||+++++.
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 5569999999999999998864
No 69
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=25.28 E-value=1.4e+02 Score=23.17 Aligned_cols=30 Identities=10% Similarity=0.158 Sum_probs=24.3
Q ss_pred EEEEeeccChhHHHHHHHHHhcCCCcceEEE
Q 039056 23 IVVTANMGCTRCRGRVSQIISKLTGLEEYIV 53 (110)
Q Consensus 23 ~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~V 53 (110)
+.+..+.+ ..|.+.+++.+.+.+||.++.+
T Consensus 63 vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~ 92 (297)
T COG2177 63 VYLQIDAD-QDDAALVREKIEGIPGVKSVRF 92 (297)
T ss_pred EEEecCCC-hHHHHHHHHHHhcCCCcceEEE
Confidence 44555555 9999999999999999987764
No 70
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=25.23 E-value=1.3e+02 Score=16.75 Aligned_cols=17 Identities=18% Similarity=0.473 Sum_probs=10.4
Q ss_pred eccChhHHHHHHHHHhcC
Q 039056 28 NMGCTRCRGRVSQIISKL 45 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i 45 (110)
.-+|+.|. .+++.|+.+
T Consensus 8 ~~~C~~C~-~~~~~l~~l 24 (67)
T cd02973 8 SPTCPYCP-DAVQAANRI 24 (67)
T ss_pred CCCCCCcH-HHHHHHHHH
Confidence 45899994 444555544
No 71
>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=25.14 E-value=77 Score=17.91 Aligned_cols=29 Identities=24% Similarity=0.303 Sum_probs=16.1
Q ss_pred HHHHHHhc---CCCcceEEEeCCCCEEEEEecC
Q 039056 37 RVSQIISK---LTGLEEYIVDVPNKRVTVKADF 66 (110)
Q Consensus 37 ~Vek~L~~---i~GV~~v~Vdl~~~kv~V~~~~ 66 (110)
+|+..|.. +++- ++.+...++.+++.|..
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEV 34 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEE
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeC
Confidence 45666665 3444 68888899999999983
No 72
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=25.01 E-value=1.3e+02 Score=16.61 Aligned_cols=16 Identities=13% Similarity=0.476 Sum_probs=11.0
Q ss_pred eccChhHHHHHHHHHhc
Q 039056 28 NMGCTRCRGRVSQIISK 44 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~ 44 (110)
.-+|+.|... .+.|..
T Consensus 7 ~~~C~~C~~~-~~~l~~ 22 (74)
T TIGR02196 7 TPWCPPCKKA-KEYLTS 22 (74)
T ss_pred CCCChhHHHH-HHHHHH
Confidence 3579999864 455655
No 73
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=24.79 E-value=75 Score=23.25 Aligned_cols=36 Identities=8% Similarity=-0.141 Sum_probs=21.3
Q ss_pred CCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEe
Q 039056 56 PNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFIS 92 (110)
Q Consensus 56 ~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~ 92 (110)
..+-++++|-.. -.+.....+.+.+++.||+..+=+
T Consensus 71 ~~~~V~lTGGEP-~~~~~l~~Ll~~l~~~g~~~~lET 106 (212)
T COG0602 71 KARGVSLTGGEP-LLQPNLLELLELLKRLGFRIALET 106 (212)
T ss_pred CcceEEEeCCcC-CCcccHHHHHHHHHhCCceEEecC
Confidence 334677776521 011246778888898887655533
No 74
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=24.75 E-value=75 Score=20.50 Aligned_cols=25 Identities=12% Similarity=0.226 Sum_probs=20.9
Q ss_pred cChhHHHHHHHHHhcCCCcceEEEe
Q 039056 30 GCTRCRGRVSQIISKLTGLEEYIVD 54 (110)
Q Consensus 30 ~C~~C~~~Vek~L~~i~GV~~v~Vd 54 (110)
.-.+-...+++.|+.++||+++++-
T Consensus 59 D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 59 DKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred ccccCcHHHHHHHhhccCcceEEEE
Confidence 3456789999999999999998764
No 75
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=24.71 E-value=41 Score=21.39 Aligned_cols=17 Identities=24% Similarity=0.509 Sum_probs=13.4
Q ss_pred eccChhHHHHHHHHHhcC
Q 039056 28 NMGCTRCRGRVSQIISKL 45 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i 45 (110)
.++|+.|+..++- |.++
T Consensus 9 sn~Cpdca~a~ey-l~rl 25 (85)
T COG4545 9 SNLCPDCAPAVEY-LERL 25 (85)
T ss_pred cccCcchHHHHHH-HHHc
Confidence 5899999999987 4443
No 76
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=24.68 E-value=58 Score=22.76 Aligned_cols=47 Identities=17% Similarity=0.109 Sum_probs=34.3
Q ss_pred hhHHHHHHHHHhcCCCcceEEEeCCC-------------------CEEEEEecCCCCCCCChHHHHHHH
Q 039056 32 TRCRGRVSQIISKLTGLEEYIVDVPN-------------------KRVTVKADFGLNKNVKDDPTRSRV 81 (110)
Q Consensus 32 ~~C~~~Vek~L~~i~GV~~v~Vdl~~-------------------~kv~V~~~~~~~~~~~~~~I~~~i 81 (110)
++|=.-++..+.+++||.++.+-+.+ ..|.|.+|+ ..++.++|.+..
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp---~~is~~~Ll~~f 72 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDP---KVISYEELLDVF 72 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECC---CcCcHHHHHHHH
Confidence 57777888889999999988775433 346677874 457888876644
No 77
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=24.66 E-value=1.5e+02 Score=19.26 Aligned_cols=17 Identities=29% Similarity=0.604 Sum_probs=12.2
Q ss_pred EEEEe-ec-cChhHHHHHH
Q 039056 23 IVVTA-NM-GCTRCRGRVS 39 (110)
Q Consensus 23 ~~~~V-gm-~C~~C~~~Ve 39 (110)
+.+.. .- +|+.|...+.
T Consensus 31 ~vv~f~~~~~Cp~C~~~~p 49 (146)
T PF08534_consen 31 VVVNFWASAWCPPCRKELP 49 (146)
T ss_dssp EEEEEESTTTSHHHHHHHH
T ss_pred EEEEEEccCCCCcchhhhh
Confidence 34444 54 9999998885
No 78
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=24.41 E-value=1.6e+02 Score=17.41 Aligned_cols=40 Identities=15% Similarity=0.228 Sum_probs=29.1
Q ss_pred HhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCC
Q 039056 42 ISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGC 86 (110)
Q Consensus 42 L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~ 86 (110)
|..++||..+..+ ..+.+.+..+. .....+|.+.+.+.|.
T Consensus 26 l~~~~~v~~v~~~-~~~~~~i~l~~----~~~~~~ll~~l~~~g~ 65 (84)
T PF13732_consen 26 LEELPGVESVEQD-GDGKLRIKLED----EETANELLQELIEKGI 65 (84)
T ss_pred HhhCCCeEEEEEe-CCcEEEEEECC----cccHHHHHHHHHhCCC
Confidence 7888999888754 45556666652 2566889999988885
No 79
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=24.11 E-value=1.8e+02 Score=23.69 Aligned_cols=59 Identities=14% Similarity=0.113 Sum_probs=36.6
Q ss_pred EEEEe-ec----cChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCC
Q 039056 23 IVVTA-NM----GCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSG 95 (110)
Q Consensus 23 ~~~~V-gm----~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g 95 (110)
++..+ |+ +-++-..-| ++|..++||+-++. .++-+.+. +++++.++++|.+.+..|+..
T Consensus 161 lEaHlDGqGEP~lYP~l~~lV-qalk~~~~v~vVSm--QTng~~L~-----------~~lv~eLeeAGLdRiNlSv~a 224 (414)
T COG2100 161 LEAHLDGQGEPLLYPHLVDLV-QALKEHKGVEVVSM--QTNGVLLS-----------KKLVDELEEAGLDRINLSVDA 224 (414)
T ss_pred eEEEecCCCCCccchhHHHHH-HHHhcCCCceEEEE--eeCceecc-----------HHHHHHHHHhCCceEEeeccc
Confidence 45555 44 334444433 34677788755544 33333332 668999999999999888753
No 80
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=23.92 E-value=1.7e+02 Score=26.51 Aligned_cols=56 Identities=11% Similarity=0.198 Sum_probs=32.9
Q ss_pred eccChhHH----HHHHHHHhcCCCcceEEEeCCCC--EEEEEecCCCCCCCChHHHHHHHHh
Q 039056 28 NMGCTRCR----GRVSQIISKLTGLEEYIVDVPNK--RVTVKADFGLNKNVKDDPTRSRVKI 83 (110)
Q Consensus 28 gm~C~~C~----~~Vek~L~~i~GV~~v~Vdl~~~--kv~V~~~~~~~~~~~~~~I~~~i~~ 83 (110)
|.+-.... ..+|+.|+.++|++++...-..+ .+.++++.+.+-.....++.+++.+
T Consensus 53 Gas~~~ve~~vt~piE~~l~~i~gv~~i~S~s~~G~s~i~l~f~~~~d~~~a~~~v~~~v~~ 114 (1025)
T PRK10614 53 GASPETMASSVATPLERSLGRIAGVNEMTSSSSLGSTRIILQFDFDRDINGAARDVQAAINA 114 (1025)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECCCChHHHHHHHHHHHHH
Confidence 45544444 56688999999999997554444 5555665332111123455665553
No 81
>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=23.56 E-value=2.7e+02 Score=19.63 Aligned_cols=34 Identities=15% Similarity=0.262 Sum_probs=30.0
Q ss_pred hHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecC
Q 039056 33 RCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADF 66 (110)
Q Consensus 33 ~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~ 66 (110)
.=+.+|.+.+.+++||.++.+=.....+.|-.+.
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv~~ 87 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVGVDL 87 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEEEEc
Confidence 6788999999999999999998888888887764
No 82
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.02 E-value=1.9e+02 Score=18.92 Aligned_cols=23 Identities=17% Similarity=0.367 Sum_probs=20.3
Q ss_pred HhcCCCcceEEEeCCCCEEEEEe
Q 039056 42 ISKLTGLEEYIVDVPNKRVTVKA 64 (110)
Q Consensus 42 L~~i~GV~~v~Vdl~~~kv~V~~ 64 (110)
+...||+..+.++.+++++.|.+
T Consensus 36 vas~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 36 VASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EEecCCceEEEEecccceEEEec
Confidence 45678999999999999999986
No 83
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=22.72 E-value=72 Score=19.67 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=20.2
Q ss_pred eccChhHHHHHHHHHhcCCCcceEEEe
Q 039056 28 NMGCTRCRGRVSQIISKLTGLEEYIVD 54 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i~GV~~v~Vd 54 (110)
.|-|+.|.....+++++-.=+.+-++|
T Consensus 15 tLPC~~Cr~HA~~ai~kNNiMSs~DiN 41 (70)
T PF04805_consen 15 TLPCPECRIHAKEAIQKNNIMSSNDIN 41 (70)
T ss_pred cCCCHHHHHHHHHHHHhcCccccCCcc
Confidence 488999999999999876555444444
No 84
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=22.66 E-value=90 Score=18.15 Aligned_cols=15 Identities=13% Similarity=0.399 Sum_probs=12.9
Q ss_pred HHHHHhcCCCcceEE
Q 039056 38 VSQIISKLTGLEEYI 52 (110)
Q Consensus 38 Vek~L~~i~GV~~v~ 52 (110)
||..|.+++||.++-
T Consensus 2 IE~~l~~~~~V~~~~ 16 (73)
T PF13193_consen 2 IESVLRQHPGVAEAA 16 (73)
T ss_dssp HHHHHHTSTTEEEEE
T ss_pred HHHHHhcCCCccEEE
Confidence 789999999998864
No 85
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=22.39 E-value=2.1e+02 Score=26.06 Aligned_cols=49 Identities=8% Similarity=0.039 Sum_probs=35.7
Q ss_pred HHHHHHHhcCCCcceEEEeCCCCEEEEEecCCC--CCCCChHHHHHHHHhc
Q 039056 36 GRVSQIISKLTGLEEYIVDVPNKRVTVKADFGL--NKNVKDDPTRSRVKIS 84 (110)
Q Consensus 36 ~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~--~~~~~~~~I~~~i~~~ 84 (110)
+.++..|.+++||.++++.-....+.|..|++. .-.+++.++..+++..
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 568999999999999998755556777655211 1256778888888854
No 86
>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=22.17 E-value=1.7e+02 Score=19.20 Aligned_cols=35 Identities=9% Similarity=0.235 Sum_probs=27.6
Q ss_pred ChhHHHHHHHHH---hcCCCcceEEEeCCCCEEEEEec
Q 039056 31 CTRCRGRVSQII---SKLTGLEEYIVDVPNKRVTVKAD 65 (110)
Q Consensus 31 C~~C~~~Vek~L---~~i~GV~~v~Vdl~~~kv~V~~~ 65 (110)
..--.+.|+.+| .++.+|++..+.....++.+.++
T Consensus 67 ~sEi~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f~ 104 (112)
T PF10934_consen 67 ESEIEREIEEALLQDPRITSVENFSFEWEGDSLYVSFT 104 (112)
T ss_pred HHHHHHHHHHHHhcCCCcceEEEEEEEEECCEEEEEEE
Confidence 445677888888 46777888889999999988875
No 87
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=21.84 E-value=1.6e+02 Score=26.85 Aligned_cols=49 Identities=10% Similarity=0.095 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCCcceEEEeCC-CCEEEEEecCCCCC--CCChHHHHHHHHh
Q 039056 35 RGRVSQIISKLTGLEEYIVDVP-NKRVTVKADFGLNK--NVKDDPTRSRVKI 83 (110)
Q Consensus 35 ~~~Vek~L~~i~GV~~v~Vdl~-~~kv~V~~~~~~~~--~~~~~~I~~~i~~ 83 (110)
.+.+++.|.+++||.++++.=. ...++|..|++.-. .++++++..+|+.
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~~ 208 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIRA 208 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHHH
No 88
>PRK11023 outer membrane lipoprotein; Provisional
Probab=21.77 E-value=2.9e+02 Score=19.72 Aligned_cols=37 Identities=16% Similarity=0.117 Sum_probs=30.3
Q ss_pred ccChhHHHHHHHHHhcCCCcc---eEEEeCCCCEEEEEec
Q 039056 29 MGCTRCRGRVSQIISKLTGLE---EYIVDVPNKRVTVKAD 65 (110)
Q Consensus 29 m~C~~C~~~Vek~L~~i~GV~---~v~Vdl~~~kv~V~~~ 65 (110)
+....=..+|+..|..-+++. .+.|+..++.+++.|.
T Consensus 45 ~dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~ 84 (191)
T PRK11023 45 VDDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQ 84 (191)
T ss_pred ehhHHHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEE
Confidence 456777889999998777663 5888889999999998
No 89
>TIGR00736 nifR3_rel_arch TIM-barrel protein, putative. Members of this family show a distant relationship by PSI-BLAST to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. At least two closely related but well-separable families among the bacteria, the nifR3/yhdG family and the yjbN family, share a more distant relationship to this family of shorter, exclusively archaeal proteins.
Probab=21.45 E-value=3.5e+02 Score=20.16 Aligned_cols=34 Identities=12% Similarity=-0.010 Sum_probs=21.1
Q ss_pred CEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEe
Q 039056 58 KRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFIS 92 (110)
Q Consensus 58 ~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~ 92 (110)
.-++|+..... ...+.-++.+.++++|.+.+.+-
T Consensus 135 ~PVsvKiR~~~-~~~~~~~~a~~l~~aGad~i~Vd 168 (231)
T TIGR00736 135 KPIFVKIRGNC-IPLDELIDALNLVDDGFDGIHVD 168 (231)
T ss_pred CcEEEEeCCCC-CcchHHHHHHHHHHcCCCEEEEe
Confidence 34666655321 12344578899999998876553
No 90
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.19 E-value=51 Score=20.85 Aligned_cols=17 Identities=18% Similarity=0.727 Sum_probs=14.6
Q ss_pred ccChhHHHHHHHHHhcC
Q 039056 29 MGCTRCRGRVSQIISKL 45 (110)
Q Consensus 29 m~C~~C~~~Vek~L~~i 45 (110)
-.|+.|..++++.|++.
T Consensus 34 t~ce~c~a~~kk~l~~v 50 (82)
T COG2331 34 TTCEECGARLKKLLNAV 50 (82)
T ss_pred ccChhhChHHHHhhccc
Confidence 47999999999998763
No 91
>PRK13265 glycine/sarcosine/betaine reductase complex protein A; Reviewed
Probab=20.95 E-value=1.3e+02 Score=21.15 Aligned_cols=71 Identities=13% Similarity=-0.004 Sum_probs=32.3
Q ss_pred eccChhHHHHHHHHHhcCCCcceEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCChhHHHHH
Q 039056 28 NMGCTRCRGRVSQIISKLTGLEEYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSGLFASAAF 102 (110)
Q Consensus 28 gm~C~~C~~~Vek~L~~i~GV~~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g~~~~a~~ 102 (110)
|=..+--...|+..++. .|. +|-|.+-...|-......+..+...+.+..++.|..-+++-+++.-+-+|.
T Consensus 13 GdRDGiPgpAie~c~k~-~ga---evvfs~TECfVctaAGAMDLEnQ~Rvk~~aEk~g~eNvvVllGaaeaEaag 83 (154)
T PRK13265 13 GDRDGIPGPAIEECVKT-TGA---EVVFSSTECFVUTAAGAMDLENQKRVKDLAEKFGAENVVVILGAAEAEAAG 83 (154)
T ss_pred ecCCCCCcHHHHHHHhc-cCc---eEEEEeeeEEEeecccccchHHHHHHHHHHHhcCCccEEEEecccchhhcc
Confidence 44445555556665544 232 333333333331111111123334455566666666666665555444443
No 92
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=20.87 E-value=1.5e+02 Score=22.84 Aligned_cols=14 Identities=14% Similarity=0.579 Sum_probs=11.8
Q ss_pred ccChhHHHHHHHHH
Q 039056 29 MGCTRCRGRVSQII 42 (110)
Q Consensus 29 m~C~~C~~~Vek~L 42 (110)
+.|++|.+++-...
T Consensus 23 lnC~HCg~~~L~~M 36 (275)
T COG1856 23 LNCPHCGRHYLEHM 36 (275)
T ss_pred ecChHHHHHHHHHh
Confidence 78999999987763
No 93
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=20.80 E-value=1.9e+02 Score=16.93 Aligned_cols=31 Identities=10% Similarity=0.130 Sum_probs=21.7
Q ss_pred EEEEEeeccChhHHHHHHHHHhcCCCcceEE
Q 039056 22 VIVVTANMGCTRCRGRVSQIISKLTGLEEYI 52 (110)
Q Consensus 22 ~~~~~Vgm~C~~C~~~Vek~L~~i~GV~~v~ 52 (110)
.+.|.+...-..=...+-+.|++++||..|.
T Consensus 49 ~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 49 RITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 3555555555566677777899999997763
No 94
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=20.65 E-value=1.2e+02 Score=21.50 Aligned_cols=40 Identities=13% Similarity=-0.017 Sum_probs=28.9
Q ss_pred eCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCceEEEeeCChhHH
Q 039056 54 DVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCYQFFISVSGLFAS 99 (110)
Q Consensus 54 dl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~~~~~~~~g~~~~ 99 (110)
+.....+.+++| -+..-+++.++..|.+..++++.++.+.
T Consensus 109 ~~~D~ivl~SgD------~DF~p~v~~~~~~G~rv~v~~~~~~~s~ 148 (181)
T COG1432 109 KNVDTIVLFSGD------GDFIPLVEAARDKGKRVEVAGIEPMTSS 148 (181)
T ss_pred cCCCEEEEEcCC------ccHHHHHHHHHHcCCEEEEEecCCcCHH
Confidence 344555666666 3445578999999999999999985554
No 95
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=20.31 E-value=1.8e+02 Score=17.75 Aligned_cols=29 Identities=14% Similarity=0.155 Sum_probs=20.7
Q ss_pred eEEEeCCCCEEEEEecCCCCCCCChHHHHHHHHhcCCc
Q 039056 50 EYIVDVPNKRVTVKADFGLNKNVKDDPTRSRVKISGCY 87 (110)
Q Consensus 50 ~v~Vdl~~~kv~V~~~~~~~~~~~~~~I~~~i~~~G~~ 87 (110)
.+++.++.+.+.+... +.|.+++.+.|++
T Consensus 3 ~v~i~idG~~v~~~~G---------~til~al~~~gi~ 31 (82)
T PF13510_consen 3 MVTITIDGKPVEVPPG---------ETILEALLAAGID 31 (82)
T ss_dssp EEEEEETTEEEEEEET----------BHHHHHHHTT--
T ss_pred EEEEEECCEEEEEcCC---------CHHHHHHHHCCCe
Confidence 4677788888887643 6699999999965
No 96
>cd02957 Phd_like Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-te
Probab=20.25 E-value=2.4e+02 Score=17.76 Aligned_cols=32 Identities=19% Similarity=0.356 Sum_probs=17.5
Q ss_pred EEEEe-eccChhHHH---HHHHHHhcCCCcceEEEe
Q 039056 23 IVVTA-NMGCTRCRG---RVSQIISKLTGLEEYIVD 54 (110)
Q Consensus 23 ~~~~V-gm~C~~C~~---~Vek~L~~i~GV~~v~Vd 54 (110)
+.+.. .-+|+.|.. .+++...+.+++.-+++|
T Consensus 27 vvv~F~a~~c~~C~~l~~~l~~la~~~~~v~f~~vd 62 (113)
T cd02957 27 VVVHFYEPGFPRCKILDSHLEELAAKYPETKFVKIN 62 (113)
T ss_pred EEEEEeCCCCCcHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 44445 668999983 344444455554334444
No 97
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=20.07 E-value=1.1e+02 Score=22.20 Aligned_cols=22 Identities=27% Similarity=0.379 Sum_probs=17.8
Q ss_pred HHHHHHHHHhcCCCcceEEEeC
Q 039056 34 CRGRVSQIISKLTGLEEYIVDV 55 (110)
Q Consensus 34 C~~~Vek~L~~i~GV~~v~Vdl 55 (110)
=...+++.|..++||.++.|++
T Consensus 108 le~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 108 IEQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHHhcCCeeeeEEEE
Confidence 4567888999999999887764
Done!