Query 043962
Match_columns 200
No_of_seqs 266 out of 1620
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 10:03:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043962.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043962hhsearch_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 99.5 4.9E-14 1.1E-18 96.0 8.1 59 3-61 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.4 1.6E-12 3.4E-17 92.0 8.2 64 2-65 4-70 (71)
3 KOG1603 Copper chaperone [Inor 98.9 9.5E-09 2.1E-13 72.9 7.7 63 2-65 7-70 (73)
4 COG2217 ZntA Cation transport 98.7 1.8E-08 4E-13 98.3 5.4 63 1-64 3-69 (713)
5 KOG0207 Cation transport ATPas 98.6 5.4E-08 1.2E-12 95.9 6.5 104 1-137 70-176 (951)
6 KOG4656 Copper chaperone for s 98.6 2.5E-07 5.5E-12 77.9 8.1 69 2-71 9-77 (247)
7 PRK10671 copA copper exporting 98.5 1.8E-07 3.8E-12 92.8 7.2 64 1-66 4-67 (834)
8 KOG0207 Cation transport ATPas 98.4 2.1E-07 4.5E-12 91.9 5.2 101 1-117 147-254 (951)
9 PLN02957 copper, zinc superoxi 98.4 2.5E-06 5.4E-11 73.3 9.2 67 2-69 8-74 (238)
10 TIGR00003 copper ion binding p 98.1 1.7E-05 3.8E-10 49.9 7.6 61 2-62 4-67 (68)
11 PRK10671 copA copper exporting 98.1 5.8E-06 1.3E-10 82.1 6.7 65 2-66 101-165 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.4 0.00053 1.2E-08 67.6 8.0 64 2-65 55-119 (741)
13 TIGR02052 MerP mercuric transp 95.6 0.13 2.7E-06 35.3 8.1 63 2-64 25-90 (92)
14 cd00371 HMA Heavy-metal-associ 93.6 0.55 1.2E-05 26.2 6.5 57 4-60 2-60 (63)
15 PRK13748 putative mercuric red 91.6 1.1 2.3E-05 42.4 8.8 66 2-67 2-69 (561)
16 COG1888 Uncharacterized protei 87.9 2 4.4E-05 32.0 5.8 49 18-66 24-80 (97)
17 PF02680 DUF211: Uncharacteriz 87.7 1.5 3.2E-05 32.9 5.0 49 17-65 21-77 (95)
18 PF01206 TusA: Sulfurtransfera 86.7 2.5 5.4E-05 28.8 5.5 54 3-65 2-57 (70)
19 cd03421 SirA_like_N SirA_like_ 74.8 12 0.00025 25.3 5.5 51 4-64 2-54 (67)
20 PRK11018 hypothetical protein; 74.3 21 0.00046 25.2 6.9 55 2-65 9-65 (78)
21 PF05046 Img2: Mitochondrial l 63.5 32 0.00069 25.0 6.1 57 2-60 30-87 (87)
22 PF09580 Spore_YhcN_YlaJ: Spor 63.5 20 0.00043 28.7 5.5 30 14-43 76-105 (177)
23 PF01883 DUF59: Domain of unkn 61.2 13 0.00028 25.3 3.5 19 15-33 54-72 (72)
24 PRK10553 assembly protein for 60.5 34 0.00074 25.0 5.7 42 15-56 19-61 (87)
25 cd00291 SirA_YedF_YeeD SirA, Y 57.9 49 0.0011 21.9 5.9 53 4-65 2-56 (69)
26 PRK14054 methionine sulfoxide 57.8 23 0.0005 29.2 4.9 45 12-56 10-76 (172)
27 COG1094 Predicted RNA-binding 57.1 25 0.00055 29.6 5.1 27 17-44 28-54 (194)
28 cd03420 SirA_RHOD_Pry_redox Si 56.9 49 0.0011 22.5 5.8 53 4-65 2-56 (69)
29 KOG1924 RhoA GTPase effector D 56.8 12 0.00026 37.9 3.6 9 46-54 454-462 (1102)
30 PF03927 NapD: NapD protein; 53.7 58 0.0013 23.1 5.9 42 15-57 17-59 (79)
31 cd02410 archeal_CPSF_KH The ar 53.3 95 0.0021 25.0 7.6 56 15-70 55-117 (145)
32 cd03422 YedF YedF is a bacteri 52.6 65 0.0014 22.0 5.9 53 4-65 2-56 (69)
33 cd03423 SirA SirA (also known 51.9 70 0.0015 21.7 5.9 53 4-65 2-56 (69)
34 PF13732 DUF4162: Domain of un 50.3 63 0.0014 22.2 5.6 44 22-67 26-71 (84)
35 KOG2391 Vacuolar sorting prote 49.7 33 0.00072 31.4 4.9 15 180-194 180-194 (365)
36 cd04883 ACT_AcuB C-terminal AC 47.1 81 0.0017 20.7 7.5 61 3-63 3-69 (72)
37 PF08777 RRM_3: RNA binding mo 44.2 1.2E+02 0.0026 22.7 6.6 57 2-58 2-60 (105)
38 PRK00058 methionine sulfoxide 44.2 41 0.0009 28.7 4.5 44 12-55 52-117 (213)
39 PRK07334 threonine dehydratase 43.5 1.1E+02 0.0023 28.1 7.4 64 2-65 327-402 (403)
40 PRK05528 methionine sulfoxide 43.3 60 0.0013 26.3 5.1 45 12-56 8-69 (156)
41 TIGR03527 selenium_YedF seleni 42.9 69 0.0015 26.7 5.6 54 5-65 2-55 (194)
42 TIGR02898 spore_YhcN_YlaJ spor 41.5 72 0.0016 25.9 5.4 31 13-43 54-84 (158)
43 PF06495 Transformer: Fruit fl 41.0 40 0.00087 28.1 3.8 10 154-163 143-152 (182)
44 PRK00299 sulfur transfer prote 40.7 1.3E+02 0.0028 21.2 7.1 54 2-64 10-65 (81)
45 PF01106 NifU: NifU-like domai 39.2 46 0.00099 23.0 3.4 29 2-31 29-65 (68)
46 PRK13014 methionine sulfoxide 38.5 50 0.0011 27.6 4.1 45 12-56 15-81 (186)
47 TIGR02945 SUF_assoc FeS assemb 38.4 50 0.0011 23.9 3.7 21 16-36 58-78 (99)
48 PF04972 BON: BON domain; Int 37.9 21 0.00045 23.5 1.4 31 16-47 2-35 (64)
49 PRK09577 multidrug efflux prot 36.1 87 0.0019 32.5 6.2 46 15-60 158-211 (1032)
50 PRK10555 aminoglycoside/multid 34.4 91 0.002 32.4 6.0 44 15-58 159-210 (1037)
51 PF13740 ACT_6: ACT domain; PD 34.3 1.1E+02 0.0025 20.9 4.9 56 2-57 3-64 (76)
52 PF03150 CCP_MauG: Di-haem cyt 32.2 11 0.00024 30.4 -0.8 9 116-124 23-31 (159)
53 PF13192 Thioredoxin_3: Thiore 30.4 99 0.0021 21.1 4.0 15 3-17 2-16 (76)
54 cd04909 ACT_PDH-BS C-terminal 30.4 1.6E+02 0.0034 19.2 6.1 58 4-61 4-68 (69)
55 PF09626 DHC: Dihaem cytochrom 30.3 22 0.00048 27.6 0.6 7 118-124 5-11 (120)
56 TIGR03675 arCOG00543 arCOG0054 30.0 2.1E+02 0.0045 28.2 7.5 55 14-68 71-132 (630)
57 PRK14719 bifunctional RNAse/5- 29.6 2.2E+02 0.0047 26.1 7.0 53 3-63 47-99 (360)
58 cd04908 ACT_Bt0572_1 N-termina 28.8 1.7E+02 0.0037 19.1 7.2 53 11-63 11-65 (66)
59 COG0425 SirA Predicted redox p 28.7 2.1E+02 0.0046 20.2 7.1 54 2-64 6-62 (78)
60 COG0694 Thioredoxin-like prote 28.2 68 0.0015 23.9 2.9 32 2-34 45-84 (93)
61 TIGR00915 2A0602 The (Largely 27.9 1.3E+02 0.0029 31.2 6.0 43 16-58 160-210 (1044)
62 PRK11023 outer membrane lipopr 27.8 1.1E+02 0.0024 25.2 4.5 43 15-57 51-96 (191)
63 cd04888 ACT_PheB-BS C-terminal 27.4 67 0.0015 21.3 2.7 20 14-33 55-74 (76)
64 TIGR00268 conserved hypothetic 26.6 1.5E+02 0.0033 25.2 5.2 49 15-64 187-243 (252)
65 COG4004 Uncharacterized protei 26.5 96 0.0021 23.2 3.4 23 22-44 36-58 (96)
66 PRK15127 multidrug efflux syst 26.3 1.5E+02 0.0033 30.8 6.1 43 16-58 160-210 (1049)
67 TIGR03791 TTQ_mauG tryptophan 26.1 27 0.00058 31.0 0.5 9 116-124 24-32 (291)
68 PF11491 DUF3213: Protein of u 26.0 1E+02 0.0022 22.7 3.4 48 15-62 13-63 (88)
69 PF04312 DUF460: Protein of un 25.5 3.5E+02 0.0076 21.6 6.7 37 31-67 46-84 (138)
70 PF01514 YscJ_FliF: Secretory 25.3 68 0.0015 26.9 2.8 21 15-35 117-137 (206)
71 TIGR00489 aEF-1_beta translati 25.1 70 0.0015 23.5 2.5 22 13-34 62-83 (88)
72 PRK05550 bifunctional methioni 25.1 1.4E+02 0.0029 26.7 4.7 45 11-55 133-199 (283)
73 KOG0333 U5 snRNP-like RNA heli 24.3 3.8E+02 0.0082 26.6 7.7 69 6-84 496-566 (673)
74 TIGR02571 ComEB ComE operon pr 24.2 3.2E+02 0.0069 21.8 6.4 52 2-66 88-139 (151)
75 KOG4730 D-arabinono-1, 4-lacto 23.9 91 0.002 29.9 3.5 52 6-62 85-136 (518)
76 cd04886 ACT_ThrD-II-like C-ter 23.5 2E+02 0.0044 18.1 5.3 52 12-63 9-72 (73)
77 PF01625 PMSR: Peptide methion 23.4 80 0.0017 25.4 2.8 45 12-56 7-73 (155)
78 PF09158 MotCF: Bacteriophage 23.1 2.3E+02 0.005 21.5 5.0 40 24-64 39-78 (103)
79 COG1782 Predicted metal-depend 22.9 3.6E+02 0.0078 26.5 7.3 55 15-69 78-139 (637)
80 PF11513 TA0956: Thermoplasma 22.8 1.9E+02 0.0041 21.8 4.4 38 27-64 64-108 (110)
81 COG2092 EFB1 Translation elong 21.7 1.4E+02 0.0031 22.0 3.6 23 12-34 61-83 (88)
82 PF08002 DUF1697: Protein of u 21.7 3.1E+02 0.0066 21.4 5.7 48 17-65 23-75 (137)
83 TIGR02159 PA_CoA_Oxy4 phenylac 21.5 1.4E+02 0.003 23.8 3.8 12 49-60 46-57 (146)
84 TIGR01676 GLDHase galactonolac 21.5 1.5E+02 0.0033 28.8 4.7 39 22-62 110-148 (541)
85 PF13193 AMP-binding_C: AMP-bi 21.4 93 0.002 20.8 2.4 16 18-33 2-17 (73)
86 COG2151 PaaD Predicted metal-s 21.1 92 0.002 23.9 2.5 21 15-35 69-89 (111)
87 PF00034 Cytochrom_C: Cytochro 21.0 30 0.00066 23.0 -0.1 8 116-123 10-17 (91)
88 TIGR03027 pepcterm_export puta 21.0 1.9E+02 0.004 23.0 4.5 57 3-59 38-109 (165)
89 TIGR00401 msrA methionine-S-su 20.8 83 0.0018 25.2 2.3 27 12-38 7-33 (149)
90 PHA02588 cd deoxycytidylate de 20.6 3.5E+02 0.0076 21.9 6.1 52 2-65 102-153 (168)
91 COG0277 GlcD FAD/FMN-containin 20.3 1.1E+02 0.0024 27.7 3.4 39 23-63 82-120 (459)
92 PRK11198 LysM domain/BON super 20.3 1.7E+02 0.0037 23.0 4.0 42 15-56 28-70 (147)
93 KOG0339 ATP-dependent RNA heli 20.1 2.7E+02 0.0057 27.6 5.8 68 11-84 448-517 (731)
94 KOG4034 Uncharacterized conser 20.1 1.9E+02 0.0042 23.7 4.3 57 2-60 112-169 (169)
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=99.53 E-value=4.9e-14 Score=95.99 Aligned_cols=59 Identities=36% Similarity=0.495 Sum_probs=55.2
Q ss_pred EEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEecc---CCHHHHHHHHHhcCCc
Q 043962 3 VLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGL---LDPAIIMQTIGKLGVE 61 (200)
Q Consensus 3 ~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~---v~~~~I~~aI~k~Gy~ 61 (200)
+|+|.||+|++|+++|+++|++++||.++++|+.+++++|.++ ++.++|+++|+++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 6899999999999999999999999999999999999999854 5679999999999994
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.40 E-value=1.6e-12 Score=92.04 Aligned_cols=64 Identities=31% Similarity=0.512 Sum_probs=58.0
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEe--c-cCCHHHHHHHHHhcCCcEEEc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVT--G-LLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~--~-~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
.+|+|+||+|.+|+++|+++|.+++||.+++||+..+++.|+ + .++.++|+++|+++||.+..+
T Consensus 4 ~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 4 TTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred EEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 579999999999999999999999999999999999777765 4 589999999999999987653
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.88 E-value=9.5e-09 Score=72.88 Aligned_cols=63 Identities=38% Similarity=0.691 Sum_probs=56.3
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcC-CcEEEc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLG-VEAELL 65 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~G-y~a~~~ 65 (200)
++++++. +|.+|+.+|++.|.+++||.++++|...++++|.+.+++..|++.|++.| .++..+
T Consensus 7 ~v~kv~~-~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 7 VVLKVNM-HCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred EEEEECc-ccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 4566666 59999999999999999999999999999999999999999999999988 666554
No 4
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.69 E-value=1.8e-08 Score=98.32 Aligned_cols=63 Identities=32% Similarity=0.449 Sum_probs=56.9
Q ss_pred CEEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEec---cCC-HHHHHHHHHhcCCcEEE
Q 043962 1 ICVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTG---LLD-PAIIMQTIGKLGVEAEL 64 (200)
Q Consensus 1 ~v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~---~v~-~~~I~~aI~k~Gy~a~~ 64 (200)
+.+|.|+||+|++|+++|| +|++++||.++.||+.++++.|.. ..+ .+++.+++++.||.+..
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 3579999999999999999 999999999999999999999974 245 68999999999998865
No 5
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.62 E-value=5.4e-08 Score=95.91 Aligned_cols=104 Identities=23% Similarity=0.333 Sum_probs=85.2
Q ss_pred CEEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEec---cCCHHHHHHHHHhcCCcEEEcccCCChHHHHHH
Q 043962 1 ICVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTG---LLDPAIIMQTIGKLGVEAELLAYEKDPKKAKKK 77 (200)
Q Consensus 1 ~v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~---~v~~~~I~~aI~k~Gy~a~~~~~~~~~~~~~~~ 77 (200)
++.|+|.||||++|++.||+.|++++||.++.|.+.+++.+|.. ..+.+.+.+.++++||.+++.......
T Consensus 70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~~~------ 143 (951)
T KOG0207|consen 70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVNGN------ 143 (951)
T ss_pred eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcccCC------
Confidence 46899999999999999999999999999999999999999963 478899999999999998876432111
Q ss_pred HHHHHhccccCCcCccccccCCCCCCcccccccceecCCCcccCCCCCCCCcccCCCcCC
Q 043962 78 LDHFLKGNSKDNKRNLEEIDDHDHDDRGGYEYDARYAMPNCTSCHHPNYGTRRVLPGFPR 137 (200)
Q Consensus 78 ~~~~~~~~~~~n~~~~~~~~~~~~~~s~~~~~pl~~~~m~CasC~~~~~~~~~~lp~~~~ 137 (200)
+. -.+-|.+.+|.|+||....++....++++..
T Consensus 144 --------------------------~~-~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~ 176 (951)
T KOG0207|consen 144 --------------------------SN-QKIYLDVLGMTCASCVSKIESILERLRGVKS 176 (951)
T ss_pred --------------------------CC-CcEEEEeecccccchhhhhHHHHhhccCeeE
Confidence 00 2345788999999999866666677777665
No 6
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.57 E-value=2.5e-07 Score=77.94 Aligned_cols=69 Identities=25% Similarity=0.445 Sum_probs=63.5
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEEcccCCCh
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAELLAYEKDP 71 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~~~~~~~~ 71 (200)
.+|.|.+. |++|++.|++.|..++||++++||+..+.+.|.+.....+|.++|+..|.+|.+.......
T Consensus 9 ~efaV~M~-cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~ps 77 (247)
T KOG4656|consen 9 AEFAVQMT-CESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPS 77 (247)
T ss_pred EEEEEech-hHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchh
Confidence 57888875 9999999999999999999999999999999999999999999999999999998776543
No 7
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.53 E-value=1.8e-07 Score=92.78 Aligned_cols=64 Identities=19% Similarity=0.306 Sum_probs=57.4
Q ss_pred CEEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEEcc
Q 043962 1 ICVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAELLA 66 (200)
Q Consensus 1 ~v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~~~ 66 (200)
+++++|+||+|.+|+.+|+++|++++||.+++||+. +.+|++..+.+++.++++++||.++...
T Consensus 4 ~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 4 TIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred EEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 468999999999999999999999999999999994 5566667889999999999999998753
No 8
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.44 E-value=2.1e-07 Score=91.85 Aligned_cols=101 Identities=23% Similarity=0.333 Sum_probs=82.5
Q ss_pred CEEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEec---cCCHHHHHHHHHhcCCcEEEcccCCChHH----
Q 043962 1 ICVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTG---LLDPAIIMQTIGKLGVEAELLAYEKDPKK---- 73 (200)
Q Consensus 1 ~v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~---~v~~~~I~~aI~k~Gy~a~~~~~~~~~~~---- 73 (200)
++.|.|.||+|++|+.+||+.|.+++||.++++++.++++.|.. .+.+-+|++.|+..||.+..........+
T Consensus 147 ~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~~~~~~~~l~ 226 (951)
T KOG0207|consen 147 KIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYGDTTFKNSLK 226 (951)
T ss_pred cEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeeccccchhhhhh
Confidence 36899999999999999999999999999999999999999963 47889999999999999876542222211
Q ss_pred HHHHHHHHHhccccCCcCccccccCCCCCCcccccccceecCCC
Q 043962 74 AKKKLDHFLKGNSKDNKRNLEEIDDHDHDDRGGYEYDARYAMPN 117 (200)
Q Consensus 74 ~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~s~~~~~pl~~~~m~ 117 (200)
.+.+++..++.|+ .+.+|++|++++++.
T Consensus 227 ~~~ei~~w~~~fl----------------~s~~~~~~v~~~~~~ 254 (951)
T KOG0207|consen 227 HKEEIRKWKRPFL----------------ISLGFSLPVSFAMII 254 (951)
T ss_pred hhhHHHhcchHHH----------------HHHHHHHHHHHHHHH
Confidence 3455565566666 488899999999998
No 9
>PLN02957 copper, zinc superoxide dismutase
Probab=98.36 E-value=2.5e-06 Score=73.29 Aligned_cols=67 Identities=22% Similarity=0.380 Sum_probs=60.0
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEEcccCC
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAELLAYEK 69 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~~~~~~ 69 (200)
++|.| +|+|..|+.+|++.|++++||..+.+|+..++++|....+.++|.++|+++||.++++....
T Consensus 8 ~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~ 74 (238)
T PLN02957 8 TEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGD 74 (238)
T ss_pred EEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCC
Confidence 56788 69999999999999999999999999999999999877788899999999999998775543
No 10
>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=98.15 E-value=1.7e-05 Score=49.88 Aligned_cols=61 Identities=23% Similarity=0.325 Sum_probs=52.4
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEec---cCCHHHHHHHHHhcCCcE
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTG---LLDPAIIMQTIGKLGVEA 62 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~---~v~~~~I~~aI~k~Gy~a 62 (200)
..+.|+|++|..|+.+|++.+.+.+++..+.+++..+++.+.. ..+...+...+...||.+
T Consensus 4 ~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 4 FTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 5688999999999999999999999999999999999988863 346777777788888753
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.09 E-value=5.8e-06 Score=82.10 Aligned_cols=65 Identities=25% Similarity=0.419 Sum_probs=58.0
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEEcc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAELLA 66 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~~~ 66 (200)
+.+.|.||+|++|+.+|++.+.+++||.++.+|+.++++.+....+.+++.+.+++.||.+....
T Consensus 101 ~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 101 QQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred EEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 46889999999999999999999999999999999999888766778889899999999876543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.39 E-value=0.00053 Score=67.63 Aligned_cols=64 Identities=17% Similarity=0.207 Sum_probs=54.1
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEecc-CCHHHHHHHHHhcCCcEEEc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGL-LDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~-v~~~~I~~aI~k~Gy~a~~~ 65 (200)
+.++|.||+|.+|+.+|++.+.+++||.++.+++.++++.+..+ ...+++.+.+++.||.+...
T Consensus 55 ~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 55 YSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred EEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 46889999999999999999999999999999999999888632 12277888899999987543
No 13
>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=95.55 E-value=0.13 Score=35.34 Aligned_cols=63 Identities=24% Similarity=0.367 Sum_probs=49.0
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEec---cCCHHHHHHHHHhcCCcEEE
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTG---LLDPAIIMQTIGKLGVEAEL 64 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~---~v~~~~I~~aI~k~Gy~a~~ 64 (200)
+.+.+.++.|..|..+++..+...+|+....++....+..+.. ..+...+...+++.|+.+++
T Consensus 25 ~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 25 VTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 4567889999999999999999999998888888888766641 24556666667778887554
No 14
>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=93.63 E-value=0.55 Score=26.18 Aligned_cols=57 Identities=33% Similarity=0.547 Sum_probs=38.9
Q ss_pred EEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEecc--CCHHHHHHHHHhcCC
Q 043962 4 LKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGL--LDPAIIMQTIGKLGV 60 (200)
Q Consensus 4 l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~--v~~~~I~~aI~k~Gy 60 (200)
+.+.++.|..|...++..+....|+....+++......+... .+...+...++..|+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (63)
T cd00371 2 LSVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGY 60 (63)
T ss_pred eeECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCC
Confidence 446788899999999999988899887777877766555422 234444334444443
No 15
>PRK13748 putative mercuric reductase; Provisional
Probab=91.59 E-value=1.1 Score=42.42 Aligned_cols=66 Identities=23% Similarity=0.390 Sum_probs=53.6
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEec--cCCHHHHHHHHHhcCCcEEEccc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTG--LLDPAIIMQTIGKLGVEAELLAY 67 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~--~v~~~~I~~aI~k~Gy~a~~~~~ 67 (200)
+.+.+.++.|..|..+++..+...+++....+++..+++.+.. ..+...+...+++.|+..+....
T Consensus 2 ~~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 2 TTLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred EEEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCc
Confidence 4678899999999999999999999999999999888877752 24566677777889988766544
No 16
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=87.86 E-value=2 Score=32.03 Aligned_cols=49 Identities=29% Similarity=0.447 Sum_probs=34.9
Q ss_pred HHHHhhccCCceEEEEe-----cCCC--eEEEec-cCCHHHHHHHHHhcCCcEEEcc
Q 043962 18 MNKKLLKIQGVQGIHID-----TEEG--LVIVTG-LLDPAIIMQTIGKLGVEAELLA 66 (200)
Q Consensus 18 IekaL~kl~GV~~v~Vn-----l~~~--kvtV~~-~v~~~~I~~aI~k~Gy~a~~~~ 66 (200)
+-+.|++++||+.|++. ..+. +++|+| .++-++|.+.|++.|-.++.+.
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiD 80 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSID 80 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehh
Confidence 34567788887766543 3333 455565 4899999999999998877653
No 17
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=87.66 E-value=1.5 Score=32.94 Aligned_cols=49 Identities=27% Similarity=0.413 Sum_probs=34.6
Q ss_pred HHHHHhhccCCceEEEEec-----CCCeEE--Eecc-CCHHHHHHHHHhcCCcEEEc
Q 043962 17 KMNKKLLKIQGVQGIHIDT-----EEGLVI--VTGL-LDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 17 kIekaL~kl~GV~~v~Vnl-----~~~kvt--V~~~-v~~~~I~~aI~k~Gy~a~~~ 65 (200)
.+-+.|.+++||..+++.+ .++.+. |+|. ++.++|.++|++.|-.++.+
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 3556789999988776543 444444 4564 99999999999999887654
No 18
>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=86.65 E-value=2.5 Score=28.79 Aligned_cols=54 Identities=17% Similarity=0.037 Sum_probs=40.6
Q ss_pred EEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEe--ccCCHHHHHHHHHhcCCcEEEc
Q 043962 3 VLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVT--GLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 3 ~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~--~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
++.+.|..|....-++.++|.+++.= +.+.|. .....++|.+.+++.|+....+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 67888999999999999999997432 234443 3456789999999999985544
No 19
>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=74.82 E-value=12 Score=25.31 Aligned_cols=51 Identities=16% Similarity=0.180 Sum_probs=37.7
Q ss_pred EEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEE--eccCCHHHHHHHHHhcCCcEEE
Q 043962 4 LKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIV--TGLLDPAIIMQTIGKLGVEAEL 64 (200)
Q Consensus 4 l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV--~~~v~~~~I~~aI~k~Gy~a~~ 64 (200)
+.+.|..|..=.-+++++| ++..- +.+.| +...+.+.|.+.+++.||..+.
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~~~G~~~~~ 54 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAESRGYEVSV 54 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHHHcCCEEEE
Confidence 5678999999999999999 65322 23333 2335568899999999999854
No 20
>PRK11018 hypothetical protein; Provisional
Probab=74.33 E-value=21 Score=25.16 Aligned_cols=55 Identities=11% Similarity=-0.026 Sum_probs=41.8
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEE--eccCCHHHHHHHHHhcCCcEEEc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIV--TGLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV--~~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
.++.+.|..|..=.-+.+++|.+++.-+ .+.| +...+.+.|...+++.|+.+...
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~---------~L~V~~d~~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKGE---------ILEVVSDCPQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCCC---------EEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 3677889999999999999999885322 2333 23456788999999999987543
No 21
>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=63.55 E-value=32 Score=24.97 Aligned_cols=57 Identities=14% Similarity=0.085 Sum_probs=42.7
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCC-ceEEEEecCCCeEEEeccCCHHHHHHHHHhcCC
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQG-VQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGV 60 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~G-V~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy 60 (200)
+.=+|+|- =.++..-+.+.|....+ -..+.|+..++++.|.|.. .++|.+.|.+.||
T Consensus 30 ~IrkI~GD-~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 30 VIRKIEGD-IWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLLEKGF 87 (87)
T ss_pred EEEeecCC-HHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHHHCcC
Confidence 34467775 57777777777765443 2367899999999999875 6788999988887
No 22
>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=63.49 E-value=20 Score=28.74 Aligned_cols=30 Identities=13% Similarity=0.307 Sum_probs=26.6
Q ss_pred hHHHHHHHhhccCCceEEEEecCCCeEEEe
Q 043962 14 CPSKMNKKLLKIQGVQGIHIDTEEGLVIVT 43 (200)
Q Consensus 14 Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~ 43 (200)
=+.+|++.+.+++||+++.|=...+.+.|-
T Consensus 76 ~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 76 LADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 367899999999999999999999999884
No 23
>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=61.15 E-value=13 Score=25.31 Aligned_cols=19 Identities=16% Similarity=0.473 Sum_probs=14.9
Q ss_pred HHHHHHHhhccCCceEEEE
Q 043962 15 PSKMNKKLLKIQGVQGIHI 33 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~V 33 (200)
...|+++|+.++||.+|+|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 4678888999999998875
No 24
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=60.48 E-value=34 Score=25.04 Aligned_cols=42 Identities=26% Similarity=0.298 Sum_probs=29.4
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEec-cCCHHHHHHHHH
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVTG-LLDPAIIMQTIG 56 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~~-~v~~~~I~~aI~ 56 (200)
...|.+.|..++|++-...|..++|+.|+- ..+..++.+.+.
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 567889999999998666777788888752 234444444444
No 25
>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=57.86 E-value=49 Score=21.95 Aligned_cols=53 Identities=19% Similarity=0.034 Sum_probs=38.5
Q ss_pred EEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEe--ccCCHHHHHHHHHhcCCcEEEc
Q 043962 4 LKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVT--GLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 4 l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~--~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
+.+.|+.|..=.-++.++|+++.. .+.+.|. ......+|.+.+++.||.....
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~ 56 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAKETGHEVLEV 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHHHcCCEEEEE
Confidence 566788898888888888888653 2333443 2356789999999999987543
No 26
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=57.79 E-value=23 Score=29.17 Aligned_cols=45 Identities=16% Similarity=0.249 Sum_probs=35.3
Q ss_pred hhhHHHHHHHhhccCCceEEEEecCCCe-------------------EEEe---ccCCHHHHHHHHH
Q 043962 12 EACPSKMNKKLLKIQGVQGIHIDTEEGL-------------------VIVT---GLLDPAIIMQTIG 56 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~GV~~v~Vnl~~~k-------------------vtV~---~~v~~~~I~~aI~ 56 (200)
.+|-+.+|..+.+++||.++.+-.+.+. |.|+ ..++.++|++..-
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 5788889999999999999999877664 4454 3478888887653
No 27
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=57.06 E-value=25 Score=29.64 Aligned_cols=27 Identities=26% Similarity=0.473 Sum_probs=21.1
Q ss_pred HHHHHhhccCCceEEEEecCCCeEEEec
Q 043962 17 KMNKKLLKIQGVQGIHIDTEEGLVIVTG 44 (200)
Q Consensus 17 kIekaL~kl~GV~~v~Vnl~~~kvtV~~ 44 (200)
.+.+.|.+..|| ++.+|..++.++|..
T Consensus 28 ~v~k~ie~~~~~-~~~iD~~~~~V~i~~ 54 (194)
T COG1094 28 EVKKAIEEKTGV-KLRIDSKTGSVTIRT 54 (194)
T ss_pred cchHHHHhhcCe-EEEEECCCCeEEEEe
Confidence 456677777777 489999999999963
No 28
>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=56.92 E-value=49 Score=22.55 Aligned_cols=53 Identities=15% Similarity=-0.069 Sum_probs=40.1
Q ss_pred EEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEe--ccCCHHHHHHHHHhcCCcEEEc
Q 043962 4 LKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVT--GLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 4 l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~--~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
+.+.|..|..=.-+.+++|.++..- +.+.|. .....++|.+..++.|+.....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G---------~~l~V~~d~~~a~~di~~~~~~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDG---------EQLEVKASDPGFARDAQAWCKSTGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 5678999999999999999987522 233443 3466789999999999987654
No 29
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=56.80 E-value=12 Score=37.93 Aligned_cols=9 Identities=11% Similarity=0.349 Sum_probs=3.8
Q ss_pred CCHHHHHHH
Q 043962 46 LDPAIIMQT 54 (200)
Q Consensus 46 v~~~~I~~a 54 (200)
++...|++.
T Consensus 454 id~~~liD~ 462 (1102)
T KOG1924|consen 454 IDLTELIDK 462 (1102)
T ss_pred CcHHHHHHH
Confidence 344444443
No 30
>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=53.74 E-value=58 Score=23.13 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=28.9
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEe-ccCCHHHHHHHHHh
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVT-GLLDPAIIMQTIGK 57 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~-~~v~~~~I~~aI~k 57 (200)
...|.++|..++|++-...+-. +|+.|+ ...+..++.+.+.+
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHH
Confidence 4678899999999965556655 888775 33455566665554
No 31
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=53.32 E-value=95 Score=25.03 Aligned_cols=56 Identities=13% Similarity=0.137 Sum_probs=39.3
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEecc-------CCHHHHHHHHHhcCCcEEEcccCCC
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVTGL-------LDPAIIMQTIGKLGVEAELLAYEKD 70 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~-------v~~~~I~~aI~k~Gy~a~~~~~~~~ 70 (200)
...|++.+-+-.||.++.+|..++.|.|... -....+.+...++|+...++...+-
T Consensus 55 ~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpPi 117 (145)
T cd02410 55 IKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPPI 117 (145)
T ss_pred HHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCCC
Confidence 3455555555579999999999999999632 2334456666789999988755443
No 32
>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=52.59 E-value=65 Score=21.97 Aligned_cols=53 Identities=11% Similarity=-0.004 Sum_probs=39.6
Q ss_pred EEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEE--eccCCHHHHHHHHHhcCCcEEEc
Q 043962 4 LKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIV--TGLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 4 l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV--~~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
+.+.|..|..=.-+.+++|++++.- +.+.| +...+.+.|.+.+++.|+.+...
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G---------~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~ 56 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPG---------EILEVISDCPQSINNIPIDARNHGYKVLAI 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEecCchHHHHHHHHHHHcCCEEEEE
Confidence 4567888999999999999988522 22333 34467789999999999988653
No 33
>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=51.95 E-value=70 Score=21.70 Aligned_cols=53 Identities=21% Similarity=0.105 Sum_probs=39.1
Q ss_pred EEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEE--eccCCHHHHHHHHHhcCCcEEEc
Q 043962 4 LKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIV--TGLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 4 l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV--~~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
+.+.|..|..=.-+.+++|.+++- .+.+.| +...+.++|.+.+++.||.+...
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s~~di~~~~~~~g~~~~~~ 56 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKP---------GDTLLVLATDPSTTRDIPKFCTFLGHELLAQ 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCchHHHHHHHHHHcCCEEEEE
Confidence 456788899988899999988742 123333 33467789999999999987654
No 34
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=50.35 E-value=63 Score=22.24 Aligned_cols=44 Identities=16% Similarity=0.273 Sum_probs=31.9
Q ss_pred hhccCCceEEEEecCCCeEEE--eccCCHHHHHHHHHhcCCcEEEccc
Q 043962 22 LLKIQGVQGIHIDTEEGLVIV--TGLLDPAIIMQTIGKLGVEAELLAY 67 (200)
Q Consensus 22 L~kl~GV~~v~Vnl~~~kvtV--~~~v~~~~I~~aI~k~Gy~a~~~~~ 67 (200)
|..++||..+...- .+.+.| ....+..+|++.+.+.|. +.-...
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~~ 71 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDEETANELLQELIEKGI-IRSFEE 71 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHHhCCC-eeEEEE
Confidence 77889999887643 443444 455778999999999999 665433
No 35
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=49.69 E-value=33 Score=31.44 Aligned_cols=15 Identities=20% Similarity=0.295 Sum_probs=8.0
Q ss_pred CCCCCCCcccCCCCC
Q 043962 180 DVGNAPHHTFSDENV 194 (200)
Q Consensus 180 ~~~~~~~~~fsd~n~ 194 (200)
+.|.++..+-.|+|+
T Consensus 180 ~~gas~~~~~~~d~~ 194 (365)
T KOG2391|consen 180 PGGASALPYMTDDNA 194 (365)
T ss_pred CCccccCcccCCCCC
Confidence 334445556666664
No 36
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=47.08 E-value=81 Score=20.71 Aligned_cols=61 Identities=10% Similarity=0.138 Sum_probs=36.8
Q ss_pred EEEEecCCChhhHHHHHHHhhccCC-ceEEEEecC--CCe--EEEec-cCCHHHHHHHHHhcCCcEE
Q 043962 3 VLKVELQCCEACPSKMNKKLLKIQG-VQGIHIDTE--EGL--VIVTG-LLDPAIIMQTIGKLGVEAE 63 (200)
Q Consensus 3 ~l~V~GmtC~~Ca~kIekaL~kl~G-V~~v~Vnl~--~~k--vtV~~-~v~~~~I~~aI~k~Gy~a~ 63 (200)
.+.|....-.+.-.+|.+.|.+... |.++..... .+. +.|.- ..+.+++.+.|++.||.+.
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v~ 69 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEVL 69 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCeee
Confidence 3445444456777788888876532 445543332 223 33332 2466799999999999753
No 37
>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=44.21 E-value=1.2e+02 Score=22.67 Aligned_cols=57 Identities=9% Similarity=0.060 Sum_probs=34.0
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEec--cCCHHHHHHHHHhc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTG--LLDPAIIMQTIGKL 58 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~--~v~~~~I~~aI~k~ 58 (200)
+.++|.|..=..+...|+..++....|.-|++........|.. ......+++++...
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 4678887655556888999999999999998888788888863 34466777777665
No 38
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=44.20 E-value=41 Score=28.73 Aligned_cols=44 Identities=16% Similarity=0.293 Sum_probs=34.1
Q ss_pred hhhHHHHHHHhhccCCceEEEEecCCC-------------------eEEEe---ccCCHHHHHHHH
Q 043962 12 EACPSKMNKKLLKIQGVQGIHIDTEEG-------------------LVIVT---GLLDPAIIMQTI 55 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~GV~~v~Vnl~~~-------------------kvtV~---~~v~~~~I~~aI 55 (200)
.+|-+.+|..+.+++||.++.|-.+.+ -|.|+ ..++.++|++..
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~F 117 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVF 117 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 578888999999999999999988744 24444 247888888766
No 39
>PRK07334 threonine dehydratase; Provisional
Probab=43.49 E-value=1.1e+02 Score=28.10 Aligned_cols=64 Identities=9% Similarity=0.109 Sum_probs=41.3
Q ss_pred EEEEEecCCChhhHHHHHHHhhccC-CceEEEEecC-----CCeEEEe------ccCCHHHHHHHHHhcCCcEEEc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQ-GVQGIHIDTE-----EGLVIVT------GLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~-GV~~v~Vnl~-----~~kvtV~------~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
+.|.|....=.+=-..|-+.|++.+ .|.+++.... .+.+.+. .....++|+++|++.||.++++
T Consensus 327 v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 327 ARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred EEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 5666766655666788888887653 2455554422 3454432 2234578999999999999875
No 40
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=43.34 E-value=60 Score=26.31 Aligned_cols=45 Identities=13% Similarity=0.133 Sum_probs=33.7
Q ss_pred hhhHHHHHHHhhccCCceEEEEecCCCe--------------EEEe---ccCCHHHHHHHHH
Q 043962 12 EACPSKMNKKLLKIQGVQGIHIDTEEGL--------------VIVT---GLLDPAIIMQTIG 56 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~GV~~v~Vnl~~~k--------------vtV~---~~v~~~~I~~aI~ 56 (200)
.+|=+-+|..+.+++||.++.+-.+.+. |.|+ ..++.++|++..-
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 5788888999999999999999765543 3343 2478888887663
No 41
>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=42.93 E-value=69 Score=26.70 Aligned_cols=54 Identities=19% Similarity=0.104 Sum_probs=39.0
Q ss_pred EEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEEc
Q 043962 5 KVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 5 ~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
.+.|..|..=.-+.+++|.+++.-+.+ ++.++.....+.|.+.+++.||++...
T Consensus 2 D~rGl~CP~Pvi~tKkal~~l~~g~~L-------~VlvD~~~a~~nV~~~~~~~G~~v~~~ 55 (194)
T TIGR03527 2 DARGLACPQPVILTKKALDELGEEGVL-------TVIVDNEAAKENVSKFATSLGYEVEVE 55 (194)
T ss_pred CCCCCCCCHHHHHHHHHHHcCCCCCEE-------EEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 456889999999999999988521111 222334466788999999999988653
No 42
>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=41.52 E-value=72 Score=25.90 Aligned_cols=31 Identities=13% Similarity=0.237 Sum_probs=27.0
Q ss_pred hhHHHHHHHhhccCCceEEEEecCCCeEEEe
Q 043962 13 ACPSKMNKKLLKIQGVQGIHIDTEEGLVIVT 43 (200)
Q Consensus 13 ~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~ 43 (200)
.=+.+|.+.+.+++||.++.+=...+.+.|-
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vg 84 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVG 84 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEE
Confidence 4477899999999999999999999988873
No 43
>PF06495 Transformer: Fruit fly transformer protein; InterPro: IPR010519 This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster [].; GO: 0006397 mRNA processing, 0046660 female sex differentiation, 0005634 nucleus
Probab=41.02 E-value=40 Score=28.07 Aligned_cols=10 Identities=10% Similarity=-0.190 Sum_probs=5.6
Q ss_pred CCCCCCcCCC
Q 043962 154 PPPPRYVRWT 163 (200)
Q Consensus 154 ~p~~~~~~~~ 163 (200)
.++++|+|..
T Consensus 143 ~~~~~y~~~~ 152 (182)
T PF06495_consen 143 QGAYPYQMPP 152 (182)
T ss_pred ccccccccCC
Confidence 4566666443
No 44
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=40.70 E-value=1.3e+02 Score=21.24 Aligned_cols=54 Identities=11% Similarity=-0.041 Sum_probs=40.4
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEE--eccCCHHHHHHHHHhcCCcEEE
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIV--TGLLDPAIIMQTIGKLGVEAEL 64 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV--~~~v~~~~I~~aI~k~Gy~a~~ 64 (200)
.++.+.|..|..=.-+.+++|++++.- +.+.| +.....++|....++.|++...
T Consensus 10 ~~lD~~Gl~CP~Pll~~kk~l~~l~~G---------~~l~V~~dd~~~~~di~~~~~~~G~~~~~ 65 (81)
T PRK00299 10 HTLDALGLRCPEPVMMVRKTVRNMQPG---------ETLLIIADDPATTRDIPSFCRFMDHELLA 65 (81)
T ss_pred eEEecCCCCCCHHHHHHHHHHHcCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 467788999999999999999988522 22333 2345678899999999998754
No 45
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=39.15 E-value=46 Score=22.96 Aligned_cols=29 Identities=17% Similarity=0.528 Sum_probs=18.7
Q ss_pred EEEEEecCCChhhH-------HHHHHHhh-ccCCceEE
Q 043962 2 CVLKVELQCCEACP-------SKMNKKLL-KIQGVQGI 31 (200)
Q Consensus 2 v~l~V~GmtC~~Ca-------~kIekaL~-kl~GV~~v 31 (200)
+.++..|- |.+|. ..||+.|+ .++.+..|
T Consensus 29 V~V~l~Ga-C~gC~~s~~Tl~~~Ie~~L~~~~~~v~~V 65 (68)
T PF01106_consen 29 VYVRLTGA-CSGCPSSDMTLKQGIEQALREAVPEVKRV 65 (68)
T ss_dssp EEEEEESS-CCSSCCHHHHHHHHHHHHHHHHSTT-SEE
T ss_pred EEEEEEeC-CCCCCCHHHHHHHHHHHHHHHHCCCCceE
Confidence 56788896 99993 55666665 45655544
No 46
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=38.52 E-value=50 Score=27.61 Aligned_cols=45 Identities=16% Similarity=0.161 Sum_probs=34.4
Q ss_pred hhhHHHHHHHhhccCCceEEEEecCCCe-------------------EEEe---ccCCHHHHHHHHH
Q 043962 12 EACPSKMNKKLLKIQGVQGIHIDTEEGL-------------------VIVT---GLLDPAIIMQTIG 56 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~GV~~v~Vnl~~~k-------------------vtV~---~~v~~~~I~~aI~ 56 (200)
.+|-+-+|..+.+++||.++.+-.+.+. |.|. ..++.++|++..-
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff 81 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF 81 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence 5788888999999999999999876664 4443 3478888887663
No 47
>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=38.44 E-value=50 Score=23.88 Aligned_cols=21 Identities=10% Similarity=0.341 Sum_probs=16.2
Q ss_pred HHHHHHhhccCCceEEEEecC
Q 043962 16 SKMNKKLLKIQGVQGIHIDTE 36 (200)
Q Consensus 16 ~kIekaL~kl~GV~~v~Vnl~ 36 (200)
..|+++|.+++|+++++|++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457777888899988888764
No 48
>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=37.94 E-value=21 Score=23.49 Aligned_cols=31 Identities=23% Similarity=0.438 Sum_probs=15.8
Q ss_pred HHHHHHhhc---cCCceEEEEecCCCeEEEeccCC
Q 043962 16 SKMNKKLLK---IQGVQGIHIDTEEGLVIVTGLLD 47 (200)
Q Consensus 16 ~kIekaL~k---l~GV~~v~Vnl~~~kvtV~~~v~ 47 (200)
.+|+++|.+ +++- .+.|....+.+++.|.++
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~ 35 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEVP 35 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEES
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeCc
Confidence 356777776 3344 578888899999998753
No 49
>PRK09577 multidrug efflux protein; Reviewed
Probab=36.15 E-value=87 Score=32.53 Aligned_cols=46 Identities=13% Similarity=0.094 Sum_probs=36.3
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEe--------ccCCHHHHHHHHHhcCC
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVT--------GLLDPAIIMQTIGKLGV 60 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~--------~~v~~~~I~~aI~k~Gy 60 (200)
+.+|+..|++++||.+|+++-...++.|. ..++..+|.++|+..+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~ 211 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNA 211 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCC
Confidence 46799999999999999998765566663 23788999999987554
No 50
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=34.36 E-value=91 Score=32.38 Aligned_cols=44 Identities=14% Similarity=0.122 Sum_probs=34.8
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEe--------ccCCHHHHHHHHHhc
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVT--------GLLDPAIIMQTIGKL 58 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~--------~~v~~~~I~~aI~k~ 58 (200)
+..+++.|++++||.+|+++-...++.|. ..++.++|.++|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 46788999999999999998765656664 237889999999853
No 51
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=34.33 E-value=1.1e+02 Score=20.86 Aligned_cols=56 Identities=7% Similarity=-0.086 Sum_probs=37.8
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCC-ceEEEEecCCCeEEEe----cc-CCHHHHHHHHHh
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQG-VQGIHIDTEEGLVIVT----GL-LDPAIIMQTIGK 57 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~G-V~~v~Vnl~~~kvtV~----~~-v~~~~I~~aI~k 57 (200)
+.+.|-|....+-...|.+.|.+..+ |.+++.....+..+.. .. .+.+++.+++++
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~ 64 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEE 64 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHH
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHH
Confidence 46778899999999999999999866 6677777777766642 21 244566666654
No 52
>PF03150 CCP_MauG: Di-haem cytochrome c peroxidase; InterPro: IPR004852 This is a group of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidizable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site) []. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1IQC_A 2VHD_B 1EB7_A 3RN0_A 3SVW_B 3RMZ_A 3SJL_B 3PXW_A 3SLE_B 3PXS_A ....
Probab=32.16 E-value=11 Score=30.40 Aligned_cols=9 Identities=56% Similarity=1.438 Sum_probs=5.5
Q ss_pred CCcccCCCC
Q 043962 116 PNCTSCHHP 124 (200)
Q Consensus 116 m~CasC~~~ 124 (200)
+.|+|||.+
T Consensus 23 ~SCasCH~~ 31 (159)
T PF03150_consen 23 VSCASCHDP 31 (159)
T ss_dssp --HHHHS-T
T ss_pred cCchhhCCC
Confidence 569999985
No 53
>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=30.45 E-value=99 Score=21.11 Aligned_cols=15 Identities=33% Similarity=0.567 Sum_probs=10.0
Q ss_pred EEEEecCCChhhHHH
Q 043962 3 VLKVELQCCEACPSK 17 (200)
Q Consensus 3 ~l~V~GmtC~~Ca~k 17 (200)
.++|-+.+|..|...
T Consensus 2 ~I~v~~~~C~~C~~~ 16 (76)
T PF13192_consen 2 KIKVFSPGCPYCPEL 16 (76)
T ss_dssp EEEEECSSCTTHHHH
T ss_pred EEEEeCCCCCCcHHH
Confidence 344556679999943
No 54
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=30.37 E-value=1.6e+02 Score=19.19 Aligned_cols=58 Identities=16% Similarity=0.112 Sum_probs=33.7
Q ss_pred EEEecCCChhhHHHHHHHhhccCC-ceEEEEecC----CCeEEEec--cCCHHHHHHHHHhcCCc
Q 043962 4 LKVELQCCEACPSKMNKKLLKIQG-VQGIHIDTE----EGLVIVTG--LLDPAIIMQTIGKLGVE 61 (200)
Q Consensus 4 l~V~GmtC~~Ca~kIekaL~kl~G-V~~v~Vnl~----~~kvtV~~--~v~~~~I~~aI~k~Gy~ 61 (200)
+.|..-.=.+...+|.+.|.+... |.++..... .+.+.+.- ..+.+++.+.|++.||.
T Consensus 4 ~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~L~~~G~~ 68 (69)
T cd04909 4 LYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAGYE 68 (69)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCHHHHHHHHHHHHHcCCc
Confidence 344333336677788888876532 444433321 23333332 23578999999999996
No 55
>PF09626 DHC: Dihaem cytochrome c; InterPro: IPR018588 Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth []. In certain species DHC is found upstream of IPR011577 from INTERPRO. ; PDB: 2FWT_A 2FW5_A.
Probab=30.33 E-value=22 Score=27.61 Aligned_cols=7 Identities=57% Similarity=1.383 Sum_probs=4.9
Q ss_pred cccCCCC
Q 043962 118 CTSCHHP 124 (200)
Q Consensus 118 CasC~~~ 124 (200)
|+||||.
T Consensus 5 CgsCH~a 11 (120)
T PF09626_consen 5 CGSCHMA 11 (120)
T ss_dssp TTSSS--
T ss_pred hhhccCc
Confidence 9999993
No 56
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=30.04 E-value=2.1e+02 Score=28.22 Aligned_cols=55 Identities=15% Similarity=0.206 Sum_probs=40.2
Q ss_pred hHHHHHHHhhccCCceEEEEecCCCeEEEecc-------CCHHHHHHHHHhcCCcEEEcccC
Q 043962 14 CPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGL-------LDPAIIMQTIGKLGVEAELLAYE 68 (200)
Q Consensus 14 Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~-------v~~~~I~~aI~k~Gy~a~~~~~~ 68 (200)
-...|++.+-+-.||.++.++..++.|.|+.. -.-..+.+..+++|+..+++...
T Consensus 71 ~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 71 AIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred HHHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 34566666666689999999999999999632 13455566777899999886543
No 57
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=29.56 E-value=2.2e+02 Score=26.11 Aligned_cols=53 Identities=11% Similarity=0.128 Sum_probs=34.6
Q ss_pred EEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEE
Q 043962 3 VLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAE 63 (200)
Q Consensus 3 ~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~ 63 (200)
++.|.+-.|..|+..|.++ ||.+|-+-..-+. .|.....++++.++.+|..+.
T Consensus 47 ~i~~s~~p~~~cad~ii~~-----gi~rVVi~~D~d~---~G~~~~~~~~~~L~~aGi~V~ 99 (360)
T PRK14719 47 FITVSNTPVFQIADDLIAE-----NISEVILLTDFDR---AGRVYAKNIMEEFQSRGIKVN 99 (360)
T ss_pred EEEEeCCchHHHHHHHHHc-----CCCEEEEEECCCC---CCCccchHHHHHHHHCCCEEE
Confidence 4677888899999998764 4444333221111 333445578999999999884
No 58
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=28.83 E-value=1.7e+02 Score=19.12 Aligned_cols=53 Identities=11% Similarity=0.136 Sum_probs=33.1
Q ss_pred ChhhHHHHHHHhhccCC-ceEEEEecCCCeEEEe-ccCCHHHHHHHHHhcCCcEE
Q 043962 11 CEACPSKMNKKLLKIQG-VQGIHIDTEEGLVIVT-GLLDPAIIMQTIGKLGVEAE 63 (200)
Q Consensus 11 C~~Ca~kIekaL~kl~G-V~~v~Vnl~~~kvtV~-~~v~~~~I~~aI~k~Gy~a~ 63 (200)
-.+=-.+|-+.|.+... |.++-+....+++.+. ...+.+.+.+.|++.||.+.
T Consensus 11 ~pG~La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 11 KPGRLAAVTEILSEAGINIRALSIADTSEFGILRLIVSDPDKAKEALKEAGFAVK 65 (66)
T ss_pred CCChHHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEECCHHHHHHHHHHCCCEEE
Confidence 46666777777766533 4455443333344433 12556789999999999864
No 59
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=28.67 E-value=2.1e+02 Score=20.17 Aligned_cols=54 Identities=20% Similarity=0.067 Sum_probs=39.3
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEe--ccCCHHHHHHHHHhcC-CcEEE
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVT--GLLDPAIIMQTIGKLG-VEAEL 64 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~--~~v~~~~I~~aI~k~G-y~a~~ 64 (200)
.+|.+.|..|..=.-.+.++|++++- .+.+.|. ......+|...+++.| +....
T Consensus 6 ~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~~~~~~ll~ 62 (78)
T COG0425 6 KVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKKEGGHELLE 62 (78)
T ss_pred eEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHHcCCcEEEE
Confidence 47889999999999999999999853 3344553 2355688888888555 65433
No 60
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=28.15 E-value=68 Score=23.88 Aligned_cols=32 Identities=25% Similarity=0.531 Sum_probs=21.8
Q ss_pred EEEEEecCCChhhHH-------HHHHHhhc-cCCceEEEEe
Q 043962 2 CVLKVELQCCEACPS-------KMNKKLLK-IQGVQGIHID 34 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~-------kIekaL~k-l~GV~~v~Vn 34 (200)
|.++..|- |.+|.. -||+.|+. +++|..|...
T Consensus 45 V~l~l~Ga-C~gC~sS~~TLk~gIE~~L~~~i~ev~~V~~v 84 (93)
T COG0694 45 VYLRLGGA-CSGCPSSTVTLKNGIERQLKEEIPEVKEVEQV 84 (93)
T ss_pred EEEEeCCc-CCCCcccHHHHHHHHHHHHHHhCCccceEEEc
Confidence 56777886 999964 47777763 5666665443
No 61
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=27.85 E-value=1.3e+02 Score=31.20 Aligned_cols=43 Identities=19% Similarity=0.242 Sum_probs=34.8
Q ss_pred HHHHHHhhccCCceEEEEecCCCeEEEe--------ccCCHHHHHHHHHhc
Q 043962 16 SKMNKKLLKIQGVQGIHIDTEEGLVIVT--------GLLDPAIIMQTIGKL 58 (200)
Q Consensus 16 ~kIekaL~kl~GV~~v~Vnl~~~kvtV~--------~~v~~~~I~~aI~k~ 58 (200)
..|+..|++++||.+|++.-..+++.|+ ..++..+|.++|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 160 SNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 5688999999999999998775566664 247889999999863
No 62
>PRK11023 outer membrane lipoprotein; Provisional
Probab=27.76 E-value=1.1e+02 Score=25.16 Aligned_cols=43 Identities=21% Similarity=0.295 Sum_probs=30.9
Q ss_pred HHHHHHHhhccCCce---EEEEecCCCeEEEeccCCHHHHHHHHHh
Q 043962 15 PSKMNKKLLKIQGVQ---GIHIDTEEGLVIVTGLLDPAIIMQTIGK 57 (200)
Q Consensus 15 a~kIekaL~kl~GV~---~v~Vnl~~~kvtV~~~v~~~~I~~aI~k 57 (200)
..+|+.+|.+-+++. .++|....+.+++.|.++.++.....++
T Consensus 51 ~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A~~ 96 (191)
T PRK11023 51 ELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAKQ 96 (191)
T ss_pred HHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHHHH
Confidence 567888887766663 5788889999999988766555544443
No 63
>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=27.44 E-value=67 Score=21.30 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=17.0
Q ss_pred hHHHHHHHhhccCCceEEEE
Q 043962 14 CPSKMNKKLLKIQGVQGIHI 33 (200)
Q Consensus 14 Ca~kIekaL~kl~GV~~v~V 33 (200)
--.+|-+.|++++||.+|.+
T Consensus 55 ~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 55 DIDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHHhcCCCeEEEEE
Confidence 66788889999999998864
No 64
>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=26.56 E-value=1.5e+02 Score=25.21 Aligned_cols=49 Identities=14% Similarity=0.274 Sum_probs=35.2
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEecc-------C-CHHHHHHHHHhcCCcEEE
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVTGL-------L-DPAIIMQTIGKLGVEAEL 64 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~-------v-~~~~I~~aI~k~Gy~a~~ 64 (200)
..+.|+.|..+ |...+.|-...+.+.|+-. . ..++|.+.++++||.-..
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~gf~~v~ 243 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIGFRKVL 243 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcCCCeEE
Confidence 34566677774 8888999888888888621 1 247788899999997543
No 65
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.52 E-value=96 Score=23.23 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=19.5
Q ss_pred hhccCCceEEEEecCCCeEEEec
Q 043962 22 LLKIQGVQGIHIDTEEGLVIVTG 44 (200)
Q Consensus 22 L~kl~GV~~v~Vnl~~~kvtV~~ 44 (200)
+...+|++.++++..++++.|++
T Consensus 36 vas~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 36 VASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EEecCCceEEEEecccceEEEec
Confidence 34568999999999999999975
No 66
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=26.29 E-value=1.5e+02 Score=30.83 Aligned_cols=43 Identities=14% Similarity=0.195 Sum_probs=34.4
Q ss_pred HHHHHHhhccCCceEEEEecCCCeEEEe--------ccCCHHHHHHHHHhc
Q 043962 16 SKMNKKLLKIQGVQGIHIDTEEGLVIVT--------GLLDPAIIMQTIGKL 58 (200)
Q Consensus 16 ~kIekaL~kl~GV~~v~Vnl~~~kvtV~--------~~v~~~~I~~aI~k~ 58 (200)
+.|+..|++++||.++++.-..+++.|. ..++..+|.++|+..
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 5688999999999999987665657764 237889999999854
No 67
>TIGR03791 TTQ_mauG tryptophan tryptophylquinone biosynthesis enzyme MauG. Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain.
Probab=26.06 E-value=27 Score=31.04 Aligned_cols=9 Identities=44% Similarity=1.420 Sum_probs=7.7
Q ss_pred CCcccCCCC
Q 043962 116 PNCTSCHHP 124 (200)
Q Consensus 116 m~CasC~~~ 124 (200)
+.|+|||.+
T Consensus 24 ~SCasCH~p 32 (291)
T TIGR03791 24 MSCATCHNP 32 (291)
T ss_pred cCchhcCCc
Confidence 569999995
No 68
>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=25.99 E-value=1e+02 Score=22.72 Aligned_cols=48 Identities=15% Similarity=0.106 Sum_probs=26.6
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEe---ccCCHHHHHHHHHhcCCcE
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVT---GLLDPAIIMQTIGKLGVEA 62 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~---~~v~~~~I~~aI~k~Gy~a 62 (200)
+..++=.|++.++|-.|-+|--++...|. ...+.++|++.+++.+..+
T Consensus 13 A~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEV 63 (88)
T PF11491_consen 13 AMVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLEEFKPEV 63 (88)
T ss_dssp THHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HHHTTT-S
T ss_pred HHHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHHhcChhh
Confidence 44566678999999999999877777764 3578999999999988754
No 69
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=25.52 E-value=3.5e+02 Score=21.61 Aligned_cols=37 Identities=11% Similarity=0.146 Sum_probs=29.4
Q ss_pred EEEecCCCeEEEec--cCCHHHHHHHHHhcCCcEEEccc
Q 043962 31 IHIDTEEGLVIVTG--LLDPAIIMQTIGKLGVEAELLAY 67 (200)
Q Consensus 31 v~Vnl~~~kvtV~~--~v~~~~I~~aI~k~Gy~a~~~~~ 67 (200)
+-+|+..+-+.+.+ ..+.++|++.|.+.|..+-+..+
T Consensus 46 AildL~G~~l~l~S~R~~~~~evi~~I~~~G~PviVAtD 84 (138)
T PF04312_consen 46 AILDLDGELLDLKSSRNMSRSEVIEWISEYGKPVIVATD 84 (138)
T ss_pred EEEecCCcEEEEEeecCCCHHHHHHHHHHcCCEEEEEec
Confidence 45677777777764 48999999999999998876544
No 70
>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=25.29 E-value=68 Score=26.87 Aligned_cols=21 Identities=14% Similarity=0.425 Sum_probs=18.2
Q ss_pred HHHHHHHhhccCCceEEEEec
Q 043962 15 PSKMNKKLLKIQGVQGIHIDT 35 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl 35 (200)
...+++.|+.++||++++|.+
T Consensus 117 e~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEEE
Confidence 457889999999999999885
No 71
>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=25.15 E-value=70 Score=23.48 Aligned_cols=22 Identities=18% Similarity=0.382 Sum_probs=18.6
Q ss_pred hhHHHHHHHhhccCCceEEEEe
Q 043962 13 ACPSKMNKKLLKIQGVQGIHID 34 (200)
Q Consensus 13 ~Ca~kIekaL~kl~GV~~v~Vn 34 (200)
.-...||.++++++||++++|-
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 3358999999999999998875
No 72
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=25.05 E-value=1.4e+02 Score=26.69 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=34.3
Q ss_pred ChhhHHHHHHHhhccCCceEEEEecCCCe-------------------EEEe---ccCCHHHHHHHH
Q 043962 11 CEACPSKMNKKLLKIQGVQGIHIDTEEGL-------------------VIVT---GLLDPAIIMQTI 55 (200)
Q Consensus 11 C~~Ca~kIekaL~kl~GV~~v~Vnl~~~k-------------------vtV~---~~v~~~~I~~aI 55 (200)
-.+|=+.+|..+.+++||.++.+-.+.+. |.|+ ..++.++|++..
T Consensus 133 agGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F 199 (283)
T PRK05550 133 AGGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVF 199 (283)
T ss_pred ecCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 36788999999999999999999775553 3343 347778888766
No 73
>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]
Probab=24.30 E-value=3.8e+02 Score=26.56 Aligned_cols=69 Identities=17% Similarity=0.180 Sum_probs=42.5
Q ss_pred EecCCChhhHHHHHHHhhccCCceEEEEecCCCeE--EEeccCCHHHHHHHHHhcCCcEEEcccCCChHHHHHHHHHHHh
Q 043962 6 VELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLV--IVTGLLDPAIIMQTIGKLGVEAELLAYEKDPKKAKKKLDHFLK 83 (200)
Q Consensus 6 V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kv--tV~~~v~~~~I~~aI~k~Gy~a~~~~~~~~~~~~~~~~~~~~~ 83 (200)
|.+|+=..=..++.++|.+. .+..+ .|...-..+.|.+.|+|+||.+..+..+..+++.+..+..++.
T Consensus 496 v~m~~ed~k~kkL~eil~~~----------~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~ 565 (673)
T KOG0333|consen 496 VEMVSEDEKRKKLIEILESN----------FDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFRE 565 (673)
T ss_pred EEEecchHHHHHHHHHHHhC----------CCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHh
Confidence 44444444455666666553 11122 2234456788999999999999988777766666666655544
Q ss_pred c
Q 043962 84 G 84 (200)
Q Consensus 84 ~ 84 (200)
+
T Consensus 566 ~ 566 (673)
T KOG0333|consen 566 G 566 (673)
T ss_pred c
Confidence 3
No 74
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=24.18 E-value=3.2e+02 Score=21.78 Aligned_cols=52 Identities=15% Similarity=0.271 Sum_probs=34.1
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEEcc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAELLA 66 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~~~ 66 (200)
.++-+...-|..|+..|..+ ||..|-+. ....+...-.+.++++|..++-+.
T Consensus 88 ~tlYvT~ePC~~Ca~ai~~a-----gI~~Vvy~--------~~~~~~~~~~~~l~~~gi~v~~~~ 139 (151)
T TIGR02571 88 AEIYVTHFPCLQCTKSIIQA-----GIKKIYYA--------QDYHNHPYAIELFEQAGVELKKVP 139 (151)
T ss_pred cEEEEeCCCcHHHHHHHHHh-----CCCEEEEc--------cCCCCcHHHHHHHHHCCCEEEEeC
Confidence 35677777899999988764 67665432 111122345678889998887663
No 75
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=23.86 E-value=91 Score=29.92 Aligned_cols=52 Identities=21% Similarity=0.249 Sum_probs=36.7
Q ss_pred EecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcE
Q 043962 6 VELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEA 62 (200)
Q Consensus 6 V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a 62 (200)
+.++.|..- .--.+.+++-|. ++|....++||++.+...+|++.+++.||..
T Consensus 85 p~~l~ctdg---~lisl~~lnkVv--~~dpe~~tvTV~aGirlrQLie~~~~~GlsL 136 (518)
T KOG4730|consen 85 PSKLVCTDG---LLISLDKLNKVV--EFDPELKTVTVQAGIRLRQLIEELAKLGLSL 136 (518)
T ss_pred CCcceeccc---cEEEhhhhccce--eeCchhceEEeccCcCHHHHHHHHHhcCccc
Confidence 345555544 222344555554 4577788999998899999999999999974
No 76
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.47 E-value=2e+02 Score=18.11 Aligned_cols=52 Identities=13% Similarity=0.110 Sum_probs=28.9
Q ss_pred hhhHHHHHHHhhccCC-ceEEEEecC-----CCeEEE----ec--cCCHHHHHHHHHhcCCcEE
Q 043962 12 EACPSKMNKKLLKIQG-VQGIHIDTE-----EGLVIV----TG--LLDPAIIMQTIGKLGVEAE 63 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~G-V~~v~Vnl~-----~~kvtV----~~--~v~~~~I~~aI~k~Gy~a~ 63 (200)
.+=-.+|-+.|.+..+ |.++..... .+...+ +. ..+.+++++.|++.||.+.
T Consensus 9 ~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~~~~~l~~l~~~l~~~g~~~~ 72 (73)
T cd04886 9 PGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAALREAGYDVR 72 (73)
T ss_pred CChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeCCHHHHHHHHHHHHHcCCEEe
Confidence 3345566777766543 444443322 233333 22 1334689999999999763
No 77
>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=23.40 E-value=80 Score=25.43 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=33.2
Q ss_pred hhhHHHHHHHhhccCCceEEEEecCCC----------------e---EEEe---ccCCHHHHHHHHH
Q 043962 12 EACPSKMNKKLLKIQGVQGIHIDTEEG----------------L---VIVT---GLLDPAIIMQTIG 56 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~GV~~v~Vnl~~~----------------k---vtV~---~~v~~~~I~~aI~ 56 (200)
.+|-+.+|..+.+++||.++.+-.+.+ - |.|+ ..++.++|++..-
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~ 73 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFF 73 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHH
Confidence 578899999999999999999977554 2 2333 3478888887764
No 78
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=23.13 E-value=2.3e+02 Score=21.54 Aligned_cols=40 Identities=20% Similarity=0.386 Sum_probs=27.3
Q ss_pred ccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEE
Q 043962 24 KIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAEL 64 (200)
Q Consensus 24 kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~ 64 (200)
+..|+...++. ..+..+|-+---.+++++.+.++|..++.
T Consensus 39 Rt~GirqfEi~-n~G~~RI~gYk~se~~~~~f~slG~~~K~ 78 (103)
T PF09158_consen 39 RTKGIRQFEIR-NKGEFRIFGYKMSEEIIKKFTSLGMEVKQ 78 (103)
T ss_dssp EETTEEEEEEE-TTSEEEEEEES--HHHHHHHHHTT-EEEE
T ss_pred ccCceeEEEEe-cCCcEEEEEEcCCHHHHHHHHhcCcEEEE
Confidence 44677766665 45667776555568899999999998876
No 79
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=22.88 E-value=3.6e+02 Score=26.52 Aligned_cols=55 Identities=13% Similarity=0.192 Sum_probs=40.3
Q ss_pred HHHHHHHhhccCCceEEEEecCCCeEEEecc-------CCHHHHHHHHHhcCCcEEEcccCC
Q 043962 15 PSKMNKKLLKIQGVQGIHIDTEEGLVIVTGL-------LDPAIIMQTIGKLGVEAELLAYEK 69 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~-------v~~~~I~~aI~k~Gy~a~~~~~~~ 69 (200)
.+.|++.+-+..||.++.++..++.|.|+.+ -.-+.+....+++|+.++++...+
T Consensus 78 ~~~I~eivP~ea~i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PP 139 (637)
T COG1782 78 RKIILEIVPEEAGITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPP 139 (637)
T ss_pred HHHHHHhCccccCceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCC
Confidence 4566777777789999999999999999632 123455666678999998875543
No 80
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=22.77 E-value=1.9e+02 Score=21.82 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=25.9
Q ss_pred CceEEEEecCCCeEEEec-cCC------HHHHHHHHHhcCCcEEE
Q 043962 27 GVQGIHIDTEEGLVIVTG-LLD------PAIIMQTIGKLGVEAEL 64 (200)
Q Consensus 27 GV~~v~Vnl~~~kvtV~~-~v~------~~~I~~aI~k~Gy~a~~ 64 (200)
-|.-+-+|...+-+.|.. +++ .++|++..++.||+++.
T Consensus 64 TvGFvviN~dKK~mSvsFsdideNmK~~i~ei~kkykd~GykvE~ 108 (110)
T PF11513_consen 64 TVGFVVINKDKKMMSVSFSDIDENMKNSIEEIVKKYKDSGYKVEI 108 (110)
T ss_dssp EEEEEEEETTTTEEEEEE-S--CCHHHHHHHHHHHHHCCS-EEEE
T ss_pred eeEEEEEecCCeEEEEEecchhHHHHHHHHHHHHHhhcCCceeec
Confidence 367788898888888863 222 35667777789998875
No 81
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=21.75 E-value=1.4e+02 Score=22.01 Aligned_cols=23 Identities=17% Similarity=0.514 Sum_probs=19.1
Q ss_pred hhhHHHHHHHhhccCCceEEEEe
Q 043962 12 EACPSKMNKKLLKIQGVQGIHID 34 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~GV~~v~Vn 34 (200)
.+--..+|++|++++||+++++-
T Consensus 61 Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 61 EGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred ccCcHHHHHHHhhccCcceEEEE
Confidence 55677899999999999988764
No 82
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=21.73 E-value=3.1e+02 Score=21.35 Aligned_cols=48 Identities=19% Similarity=0.405 Sum_probs=30.7
Q ss_pred HHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHH-----hcCCcEEEc
Q 043962 17 KMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIG-----KLGVEAELL 65 (200)
Q Consensus 17 kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~-----k~Gy~a~~~ 65 (200)
.+++.|.++ |-.+|+.=+.++.+.++...+.+++..+|+ ..||.+.++
T Consensus 23 eLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 23 ELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp HHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred HHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 445556665 888999999999999987677766666554 478877654
No 83
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=21.49 E-value=1.4e+02 Score=23.82 Aligned_cols=12 Identities=33% Similarity=0.432 Sum_probs=6.0
Q ss_pred HHHHHHHHhcCC
Q 043962 49 AIIMQTIGKLGV 60 (200)
Q Consensus 49 ~~I~~aI~k~Gy 60 (200)
++|.++|+..|+
T Consensus 46 ~~I~~aL~~~Gv 57 (146)
T TIGR02159 46 QDIRDAVRALGV 57 (146)
T ss_pred HHHHHHHHhcCC
Confidence 344455555554
No 84
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=21.48 E-value=1.5e+02 Score=28.75 Aligned_cols=39 Identities=21% Similarity=0.274 Sum_probs=32.0
Q ss_pred hhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcE
Q 043962 22 LLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEA 62 (200)
Q Consensus 22 L~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a 62 (200)
|.++.+|. +||..+++++|.+.+...+|.+++.+.|+..
T Consensus 110 L~~ln~Vl--~vD~~~~tVtV~AG~~l~~L~~~L~~~Glal 148 (541)
T TIGR01676 110 LALMDKVL--EVDEEKKRVRVQAGIRVQQLVDAIKEYGITL 148 (541)
T ss_pred hhhCCCCE--EEcCCCCEEEEcCCCCHHHHHHHHHHcCCEe
Confidence 44566663 6778889999998899999999999999865
No 85
>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=21.43 E-value=93 Score=20.83 Aligned_cols=16 Identities=19% Similarity=0.277 Sum_probs=13.9
Q ss_pred HHHHhhccCCceEEEE
Q 043962 18 MNKKLLKIQGVQGIHI 33 (200)
Q Consensus 18 IekaL~kl~GV~~v~V 33 (200)
||.+|.+.+||.++.|
T Consensus 2 IE~~l~~~~~V~~~~V 17 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAV 17 (73)
T ss_dssp HHHHHHTSTTEEEEEE
T ss_pred HHHHHhcCCCccEEEE
Confidence 8999999999988755
No 86
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=21.09 E-value=92 Score=23.87 Aligned_cols=21 Identities=19% Similarity=0.477 Sum_probs=18.2
Q ss_pred HHHHHHHhhccCCceEEEEec
Q 043962 15 PSKMNKKLLKIQGVQGIHIDT 35 (200)
Q Consensus 15 a~kIekaL~kl~GV~~v~Vnl 35 (200)
...|+++|.+++||++++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 567899999999999988875
No 87
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=21.04 E-value=30 Score=23.05 Aligned_cols=8 Identities=50% Similarity=1.389 Sum_probs=6.7
Q ss_pred CCcccCCC
Q 043962 116 PNCTSCHH 123 (200)
Q Consensus 116 m~CasC~~ 123 (200)
..|++||-
T Consensus 10 ~~C~~CH~ 17 (91)
T PF00034_consen 10 ANCAACHG 17 (91)
T ss_dssp HHTTTTHB
T ss_pred CcChhcCC
Confidence 36999997
No 88
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=21.02 E-value=1.9e+02 Score=22.98 Aligned_cols=57 Identities=12% Similarity=0.103 Sum_probs=37.8
Q ss_pred EEEEecCCChhhHHHHHHHhhccCCceEEEEecC------CCeEEEeccC---------CHHHHHHHHHhcC
Q 043962 3 VLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTE------EGLVIVTGLL---------DPAIIMQTIGKLG 59 (200)
Q Consensus 3 ~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~------~~kvtV~~~v---------~~~~I~~aI~k~G 59 (200)
.+++.|+|-..=.+.|++.|++.----.+.|.+. ..++.|.|.+ ....|.++|..+|
T Consensus 38 ~v~v~G~T~~e~~~~I~~~l~~~~~~p~v~V~v~~~~~~~~~~V~V~GeV~~PG~y~~~~~~tl~~ai~~AG 109 (165)
T TIGR03027 38 DLVASGKTPTQLARDIEEKLAKYVRNPVVTVIVTGFIGPFSEQIRVVGAAANPQALPYREGMTLLDVMIAVG 109 (165)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEeecccCCCcEEEEEEEeCCCceeeeCCCCcHHHHHHHcC
Confidence 3678999999999999999987421112333332 4678886432 2356788888776
No 89
>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=20.78 E-value=83 Score=25.24 Aligned_cols=27 Identities=22% Similarity=0.297 Sum_probs=22.5
Q ss_pred hhhHHHHHHHhhccCCceEEEEecCCC
Q 043962 12 EACPSKMNKKLLKIQGVQGIHIDTEEG 38 (200)
Q Consensus 12 ~~Ca~kIekaL~kl~GV~~v~Vnl~~~ 38 (200)
.+|=+-+|..+.+++||.++.+-.+.+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 578888899999999999999866544
No 90
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=20.65 E-value=3.5e+02 Score=21.88 Aligned_cols=52 Identities=13% Similarity=0.201 Sum_probs=34.7
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEEEc
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAELL 65 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~~~ 65 (200)
.++-|...-|..|+..|..+ ||..|-+... .+-+...-++.|++.|.+++.+
T Consensus 102 ~tLYvTlePC~~Ca~aI~~~-----gI~rVvy~~~-------~~~~~~~~~~~L~~~Gi~v~~~ 153 (168)
T PHA02588 102 ATMYVTASPCPDCAKAIAQS-----GIKKLVYCEK-------YDRNGPGWDDILRKSGIEVIQI 153 (168)
T ss_pred cEEEEeCCCcHHHHHHHHHh-----CCCEEEEeec-------cCCCcHHHHHHHHHCCCEEEEe
Confidence 46778888899999998664 6665544311 1112334678899999987765
No 91
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=20.27 E-value=1.1e+02 Score=27.68 Aligned_cols=39 Identities=15% Similarity=0.229 Sum_probs=31.0
Q ss_pred hccCCceEEEEecCCCeEEEeccCCHHHHHHHHHhcCCcEE
Q 043962 23 LKIQGVQGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGVEAE 63 (200)
Q Consensus 23 ~kl~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy~a~ 63 (200)
.++.+|. ++|..+++++|..-+...+|.+++++.|+..-
T Consensus 82 ~~mn~i~--~id~~~~~~~v~aGv~l~~l~~~l~~~G~~~p 120 (459)
T COG0277 82 SRLNRIL--EIDPEDGTATVQAGVTLEDLEKALAPHGLFLP 120 (459)
T ss_pred hhhcchh--ccCcCCCEEEEcCCccHHHHHHHHHHcCCccC
Confidence 3445554 68888999999988899999999999888643
No 92
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=20.25 E-value=1.7e+02 Score=23.04 Aligned_cols=42 Identities=17% Similarity=0.249 Sum_probs=26.7
Q ss_pred HHHHHHHhhcc-CCceEEEEecCCCeEEEeccCCHHHHHHHHH
Q 043962 15 PSKMNKKLLKI-QGVQGIHIDTEEGLVIVTGLLDPAIIMQTIG 56 (200)
Q Consensus 15 a~kIekaL~kl-~GV~~v~Vnl~~~kvtV~~~v~~~~I~~aI~ 56 (200)
..+|++.|.+. -+...++|....+.+++.|.+.......++.
T Consensus 28 ~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~ 70 (147)
T PRK11198 28 ADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKIL 70 (147)
T ss_pred HHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHH
Confidence 45677777653 2344566777799999998765544444443
No 93
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=20.13 E-value=2.7e+02 Score=27.56 Aligned_cols=68 Identities=28% Similarity=0.343 Sum_probs=43.0
Q ss_pred ChhhHHHHHHHhhccCCceEEEEecCCCeEE--EeccCCHHHHHHHHHhcCCcEEEcccCCChHHHHHHHHHHHhc
Q 043962 11 CEACPSKMNKKLLKIQGVQGIHIDTEEGLVI--VTGLLDPAIIMQTIGKLGVEAELLAYEKDPKKAKKKLDHFLKG 84 (200)
Q Consensus 11 C~~Ca~kIekaL~kl~GV~~v~Vnl~~~kvt--V~~~v~~~~I~~aI~k~Gy~a~~~~~~~~~~~~~~~~~~~~~~ 84 (200)
|.+-..|+...|+.|.+-. ..++|. |+...+.++|.+.|.--||.+.+......+.+..+.+.+++++
T Consensus 448 ~~s~~~Kl~wl~~~L~~f~------S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk 517 (731)
T KOG0339|consen 448 CPSEEKKLNWLLRHLVEFS------SEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKK 517 (731)
T ss_pred ccCcHHHHHHHHHHhhhhc------cCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhc
Confidence 5666666666666664432 233444 3456889999999999999988876655554444444444333
No 94
>KOG4034 consensus Uncharacterized conserved protein NOF (Neighbor of FAU) [Function unknown]
Probab=20.10 E-value=1.9e+02 Score=23.74 Aligned_cols=57 Identities=16% Similarity=0.162 Sum_probs=42.8
Q ss_pred EEEEEecCCChhhHHHHHHHhhccCCc-eEEEEecCCCeEEEeccCCHHHHHHHHHhcCC
Q 043962 2 CVLKVELQCCEACPSKMNKKLLKIQGV-QGIHIDTEEGLVIVTGLLDPAIIMQTIGKLGV 60 (200)
Q Consensus 2 v~l~V~GmtC~~Ca~kIekaL~kl~GV-~~v~Vnl~~~kvtV~~~v~~~~I~~aI~k~Gy 60 (200)
+.=+|+|- =-+|.+.++..|....|= -...||-.++++.+.+..- +.|.+.+.+-||
T Consensus 112 ~IRkVeGD-i~aLe~DL~s~L~~~~~~s~~t~VnelsgqI~~~g~~v-~~vr~~L~eKGF 169 (169)
T KOG4034|consen 112 VIRKVEGD-IWALENDLRSTLEMSPKKSYATHVNELSGQIVLKGNHV-DTVREWLQEKGF 169 (169)
T ss_pred EEEeeccc-HHHHHHHHHHHHhhccCCChhhhhhhhcceEEEeCChH-HHHHHHHHHccC
Confidence 44468885 789999999999987663 3356898999999776422 278888888776
Done!