Query 023171
Match_columns 286
No_of_seqs 197 out of 1152
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:58:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023171.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023171hhsearch_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 99.3 9.8E-12 2.1E-16 89.9 8.1 58 22-79 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.1 2.1E-10 4.6E-15 86.9 8.6 65 19-83 2-70 (71)
3 KOG1603 Copper chaperone [Inor 99.1 7.7E-10 1.7E-14 84.1 7.9 67 17-83 3-70 (73)
4 KOG4656 Copper chaperone for s 98.7 6.7E-08 1.4E-12 88.2 7.7 69 19-87 7-75 (247)
5 PLN02957 copper, zinc superoxi 98.2 9.3E-06 2E-10 74.5 9.6 72 16-87 3-74 (238)
6 PRK10671 copA copper exporting 98.1 8E-06 1.7E-10 86.3 8.3 64 19-84 3-67 (834)
7 TIGR00003 copper ion binding p 97.9 0.00016 3.4E-09 47.4 9.0 61 20-80 3-67 (68)
8 COG2217 ZntA Cation transport 97.7 7.2E-05 1.6E-09 78.7 7.9 63 19-82 2-69 (713)
9 PRK10671 copA copper exporting 96.8 0.0044 9.6E-08 65.8 8.6 64 20-83 100-164 (834)
10 KOG0207 Cation transport ATPas 96.4 0.0066 1.4E-07 65.4 7.0 66 19-84 146-215 (951)
11 KOG0207 Cation transport ATPas 96.3 0.0076 1.6E-07 65.0 6.8 67 20-86 70-140 (951)
12 PRK11033 zntA zinc/cadmium/mer 96.3 0.019 4E-07 60.7 9.5 66 16-82 50-118 (741)
13 TIGR02052 MerP mercuric transp 94.0 0.71 1.5E-05 33.4 8.9 63 20-82 24-90 (92)
14 cd00371 HMA Heavy-metal-associ 91.0 2 4.2E-05 24.9 8.1 56 24-79 3-61 (63)
15 PRK13748 putative mercuric red 84.0 5.4 0.00012 40.1 8.7 64 22-85 3-69 (561)
16 PF02680 DUF211: Uncharacteriz 70.4 27 0.00058 28.7 7.3 65 17-82 3-76 (95)
17 PF01883 DUF59: Domain of unkn 64.0 12 0.00025 27.6 3.9 33 19-51 34-72 (72)
18 PRK14054 methionine sulfoxide 61.4 25 0.00053 31.4 6.1 45 30-74 10-76 (172)
19 COG1888 Uncharacterized protei 61.1 42 0.00092 27.6 6.8 66 18-83 5-79 (97)
20 PRK10553 assembly protein for 54.5 47 0.001 26.5 6.0 44 32-75 18-62 (87)
21 PF03927 NapD: NapD protein; 50.5 75 0.0016 24.6 6.5 44 32-76 16-60 (79)
22 PRK05528 methionine sulfoxide 42.2 51 0.0011 29.0 4.9 45 30-74 8-69 (156)
23 KOG2236 Uncharacterized conser 40.6 1.4E+02 0.003 31.0 8.3 10 194-203 413-422 (483)
24 PRK13014 methionine sulfoxide 38.3 40 0.00086 30.6 3.7 51 19-74 9-81 (186)
25 PF14437 MafB19-deam: MafB19-l 37.0 70 0.0015 28.1 4.9 42 18-60 99-142 (146)
26 PF01206 TusA: Sulfurtransfera 36.6 59 0.0013 23.6 3.8 51 22-81 2-55 (70)
27 PRK00058 methionine sulfoxide 36.3 58 0.0012 30.2 4.5 45 30-74 52-118 (213)
28 PF15377 DUF4604: Domain of un 35.2 1.9E+02 0.0042 25.0 7.4 14 62-75 63-76 (158)
29 TIGR03406 FeS_long_SufT probab 34.6 52 0.0011 29.4 3.8 35 20-54 114-154 (174)
30 PRK05550 bifunctional methioni 33.9 1E+02 0.0022 29.8 5.8 44 30-73 134-199 (283)
31 PF13732 DUF4162: Domain of un 33.7 1E+02 0.0022 22.9 4.7 43 40-83 26-69 (84)
32 PF01625 PMSR: Peptide methion 32.0 1.1E+02 0.0023 26.8 5.3 46 30-75 7-74 (155)
33 cd04883 ACT_AcuB C-terminal AC 31.1 1.9E+02 0.0042 20.4 7.2 59 22-80 3-68 (72)
34 PF06495 Transformer: Fruit fl 29.0 61 0.0013 29.5 3.3 17 197-214 127-143 (182)
35 PF05046 Img2: Mitochondrial l 28.8 2.7E+02 0.0059 21.9 6.6 58 20-78 29-87 (87)
36 TIGR02945 SUF_assoc FeS assemb 28.1 79 0.0017 24.7 3.5 21 34-54 58-78 (99)
37 KOG3598 Thyroid hormone recept 27.4 1.2E+02 0.0026 35.9 5.8 19 27-45 1685-1703(2220)
38 PF09580 Spore_YhcN_YlaJ: Spor 27.0 1.6E+02 0.0035 25.2 5.5 33 29-61 73-105 (177)
39 cd04888 ACT_PheB-BS C-terminal 26.0 2E+02 0.0044 20.4 5.1 33 19-51 41-74 (76)
40 KOG2573 Ribosome biogenesis pr 24.2 71 0.0015 32.8 3.1 6 148-153 488-493 (498)
41 PRK07334 threonine dehydratase 22.0 2.9E+02 0.0062 27.2 6.8 63 21-83 327-402 (403)
42 PF04972 BON: BON domain; Int 21.8 55 0.0012 23.2 1.3 30 35-65 3-35 (64)
43 PF10262 Rdx: Rdx family; Int 21.2 3.4E+02 0.0074 20.3 5.7 12 64-75 64-75 (76)
44 PF03529 TF_Otx: Otx1 transcri 21.1 57 0.0012 26.5 1.4 10 239-248 57-66 (88)
45 PF08712 Nfu_N: Scaffold prote 20.9 2.5E+02 0.0054 22.1 5.0 40 34-75 37-78 (87)
46 PRK11670 antiporter inner memb 20.9 2E+02 0.0044 28.2 5.5 68 20-87 48-146 (369)
47 cd04908 ACT_Bt0572_1 N-termina 20.6 3.2E+02 0.007 19.3 7.0 58 23-81 4-65 (66)
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=99.31 E-value=9.8e-12 Score=89.87 Aligned_cols=58 Identities=34% Similarity=0.582 Sum_probs=54.1
Q ss_pred EEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEec---CCHHHHHHHHHHcCCC
Q 023171 22 VLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIGN---VDAETLIKKLLRSGKH 79 (286)
Q Consensus 22 ~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg~---vd~eeIikaIrKaGY~ 79 (286)
+|+|. |+|.+|+++|+++|.+++||.++.+|+.+++|+|... ++.++|.++|+++||+
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 58998 9999999999999999999999999999999999965 5669999999999994
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.15 E-value=2.1e-10 Score=86.89 Aligned_cols=65 Identities=31% Similarity=0.456 Sum_probs=58.1
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--e-cCCHHHHHHHHHHcCCCCccC
Q 023171 19 QTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVI--G-NVDAETLIKKLLRSGKHAELW 83 (286)
Q Consensus 19 ~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVt--g-~vd~eeIikaIrKaGY~Aeil 83 (286)
.+..|+|. |+|.+|+.+|+++|..++||.++.||+..+++.|. + .++.++|+++|.++||.+..+
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 45789999 99999999999999999999999999999766665 4 589999999999999987643
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.05 E-value=7.7e-10 Score=84.06 Aligned_cols=67 Identities=52% Similarity=0.878 Sum_probs=61.6
Q ss_pred CceEEEEEEeecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcC-CCCccC
Q 023171 17 QFQTWVLKVLIHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIGNVDAETLIKKLLRSG-KHAELW 83 (286)
Q Consensus 17 k~~tv~fkV~M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg~vd~eeIikaIrKaG-Y~Aeil 83 (286)
..++.+++|.|+|.+|..+|++.|+.+.||.++.+|..+++|+|.+.+++..|++.|++.| .++.+|
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 4567889999999999999999999999999999999999999999999999999999988 666655
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.66 E-value=6.7e-08 Score=88.16 Aligned_cols=69 Identities=28% Similarity=0.417 Sum_probs=64.5
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCCCccCCccc
Q 023171 19 QTWVLKVLIHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIGNVDAETLIKKLLRSGKHAELWPEKK 87 (286)
Q Consensus 19 ~tv~fkV~M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg~vd~eeIikaIrKaGY~Aeil~~ee 87 (286)
-+.+|.|+|+|++|+..|+..|..++||.+|.||+.++.|.|.+...+.+|..+|+.+|.++.+.....
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~ 75 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGK 75 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCc
Confidence 457899999999999999999999999999999999999999999999999999999999998876653
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.19 E-value=9.3e-06 Score=74.45 Aligned_cols=72 Identities=26% Similarity=0.409 Sum_probs=63.5
Q ss_pred CCceEEEEEEeecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCCCccCCccc
Q 023171 16 LQFQTWVLKVLIHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIGNVDAETLIKKLLRSGKHAELWPEKK 87 (286)
Q Consensus 16 ~k~~tv~fkV~M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg~vd~eeIikaIrKaGY~Aeil~~ee 87 (286)
+..+++.|.|.|+|..|+.+|+++|.+++||..+.+++..++++|........|+..|+++||.++++....
T Consensus 3 ~~~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~ 74 (238)
T PLN02957 3 LPELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGD 74 (238)
T ss_pred CCcEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCC
Confidence 345667788889999999999999999999999999999999999877788999999999999987775543
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.10 E-value=8e-06 Score=86.29 Aligned_cols=64 Identities=28% Similarity=0.376 Sum_probs=57.7
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCCCccCC
Q 023171 19 QTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIGNVDAETLIKKLLRSGKHAELWP 84 (286)
Q Consensus 19 ~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg~vd~eeIikaIrKaGY~Aeil~ 84 (286)
++++|.|+ |+|.+|+.+|+++|.+++||..+.||+. +.+|....+.+.|...|+++||.+++..
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 56899999 9999999999999999999999999995 4666667899999999999999998754
No 7
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.91 E-value=0.00016 Score=47.39 Aligned_cols=61 Identities=20% Similarity=0.422 Sum_probs=52.4
Q ss_pred EEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe---cCCHHHHHHHHHHcCCCC
Q 023171 20 TWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIG---NVDAETLIKKLLRSGKHA 80 (286)
Q Consensus 20 tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg---~vd~eeIikaIrKaGY~A 80 (286)
++.|.|. |+|..|..+|++.|..+.++..+.+++...++.|.. ......+...+...||.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 4578999 999999999999999999999999999999988873 356777777788888864
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.75 E-value=7.2e-05 Score=78.67 Aligned_cols=63 Identities=24% Similarity=0.451 Sum_probs=56.7
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe---cCC-HHHHHHHHHHcCCCCcc
Q 023171 19 QTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIG---NVD-AETLIKKLLRSGKHAEL 82 (286)
Q Consensus 19 ~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg---~vd-~eeIikaIrKaGY~Aei 82 (286)
.++.|.|. |+|..|+++|| +|.+++||..+.||+.+++++|.. ..+ .+++...++++||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 35789999 99999999999 999999999999999999999973 345 78999999999998865
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.79 E-value=0.0044 Score=65.82 Aligned_cols=64 Identities=22% Similarity=0.435 Sum_probs=57.0
Q ss_pred EEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEecCCHHHHHHHHHHcCCCCccC
Q 023171 20 TWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIGNVDAETLIKKLLRSGKHAELW 83 (286)
Q Consensus 20 tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg~vd~eeIikaIrKaGY~Aeil 83 (286)
++.|.|. |+|..|+.+|++.|..++||..+.+++..+++.|....+..+|.+.++++||.+.++
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~ 164 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAI 164 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCcccc
Confidence 5678899 999999999999999999999999999999988876677888889999999986543
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.45 E-value=0.0066 Score=65.41 Aligned_cols=66 Identities=26% Similarity=0.457 Sum_probs=60.0
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEE---ecCCHHHHHHHHHHcCCCCccCC
Q 023171 19 QTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVI---GNVDAETLIKKLLRSGKHAELWP 84 (286)
Q Consensus 19 ~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVt---g~vd~eeIikaIrKaGY~Aeil~ 84 (286)
.++.|.|. |+|.+|+.+|++.|.+++||.++.+++.++++.|. ..+.+..|++.|+..||.+....
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 67899999 99999999999999999999999999999999987 34789999999999999875543
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.35 E-value=0.0076 Score=64.98 Aligned_cols=67 Identities=27% Similarity=0.406 Sum_probs=60.9
Q ss_pred EEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEE---ecCCHHHHHHHHHHcCCCCccCCcc
Q 023171 20 TWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVI---GNVDAETLIKKLLRSGKHAELWPEK 86 (286)
Q Consensus 20 tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVt---g~vd~eeIikaIrKaGY~Aeil~~e 86 (286)
+..|+|. |+|..|++.|++.|+.+.||.++.|.+...+..|. ..++.+.+.+.++++||.+.++...
T Consensus 70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~ 140 (951)
T KOG0207|consen 70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESV 140 (951)
T ss_pred eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcc
Confidence 6689999 99999999999999999999999999999999987 4578999999999999999876554
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.33 E-value=0.019 Score=60.73 Aligned_cols=66 Identities=17% Similarity=0.301 Sum_probs=55.3
Q ss_pred CCceEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe--cCCHHHHHHHHHHcCCCCcc
Q 023171 16 LQFQTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIG--NVDAETLIKKLLRSGKHAEL 82 (286)
Q Consensus 16 ~k~~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg--~vd~eeIikaIrKaGY~Aei 82 (286)
....++.|.|. |+|.+|+.+|++.|..++||..+.+++.++++.|.. ... +++...++++||.+..
T Consensus 50 ~~~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~-~~I~~aI~~~Gy~a~~ 118 (741)
T PRK11033 50 VSGTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIR-AQVESAVQKAGFSLRD 118 (741)
T ss_pred CCCceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccch-HHHHHHHHhccccccc
Confidence 34456788999 999999999999999999999999999999988863 223 6777888999998754
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=93.97 E-value=0.71 Score=33.38 Aligned_cols=63 Identities=22% Similarity=0.334 Sum_probs=48.5
Q ss_pred EEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe---cCCHHHHHHHHHHcCCCCcc
Q 023171 20 TWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIG---NVDAETLIKKLLRSGKHAEL 82 (286)
Q Consensus 20 tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg---~vd~eeIikaIrKaGY~Aei 82 (286)
++.+.+. +.|..|...++..+....+|..+.++.....+.+.. ......+...+.+.||.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 3457788 999999999999999999998888888888766652 24556666666778887543
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=90.97 E-value=2 Score=24.91 Aligned_cols=56 Identities=30% Similarity=0.506 Sum_probs=39.1
Q ss_pred EEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEec--CCHHHHHHHHHHcCCC
Q 023171 24 KVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIGN--VDAETLIKKLLRSGKH 79 (286)
Q Consensus 24 kV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg~--vd~eeIikaIrKaGY~ 79 (286)
.+. +.|..|...++..+....++....+++....+.+... .....+...+...++.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGYK 61 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCCC
Confidence 356 8999999999999999999887777877766666532 2444444445555543
No 15
>PRK13748 putative mercuric reductase; Provisional
Probab=83.97 E-value=5.4 Score=40.13 Aligned_cols=64 Identities=20% Similarity=0.347 Sum_probs=51.0
Q ss_pred EEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEEe--cCCHHHHHHHHHHcCCCCccCCc
Q 023171 22 VLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVIG--NVDAETLIKKLLRSGKHAELWPE 85 (286)
Q Consensus 22 ~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVtg--~vd~eeIikaIrKaGY~Aeil~~ 85 (286)
.+.+. |+|..|..+++..+..+.++..+.+++....+.+.. ..+...+...+...|+..++...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCc
Confidence 46678 999999999999999999999999999988877763 24566676777888887655544
No 16
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=70.43 E-value=27 Score=28.73 Aligned_cols=65 Identities=23% Similarity=0.321 Sum_probs=42.2
Q ss_pred CceEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEE-----ecCCcEEE--EEec-CCHHHHHHHHHHcCCCCcc
Q 023171 17 QFQTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVI-----DSQQHKVT--VIGN-VDAETLIKKLLRSGKHAEL 82 (286)
Q Consensus 17 k~~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~V-----Dl~t~kVt--Vtg~-vd~eeIikaIrKaGY~Aei 82 (286)
..++++|.|- -+-. -.--+-+.|.++.||..|.+ |..+..+. |.|. ++.++|.++|++.|-.++-
T Consensus 3 ~irRlVLDVlKP~~p-~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHS 76 (95)
T PF02680_consen 3 GIRRLVLDVLKPHEP-SIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHS 76 (95)
T ss_dssp SEEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEE
T ss_pred ceeEEEEEeecCCCC-CHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEe
Confidence 3456777777 5433 34466778999999887654 33444444 4464 9999999999999976543
No 17
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=64.00 E-value=12 Score=27.63 Aligned_cols=33 Identities=15% Similarity=0.356 Sum_probs=22.4
Q ss_pred eEEEEEEeecChhHH------HHHHHHHhcCCCeeEEEE
Q 023171 19 QTWVLKVLIHCEGCK------KKVTKILKGIEGVYTAVI 51 (286)
Q Consensus 19 ~tv~fkV~M~C~~Ca------~kIEKAL~kI~GV~sV~V 51 (286)
.++.|.+.+...+|. ..|+++|..++||.+|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 355666666665554 678889999999998875
No 18
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=61.40 E-value=25 Score=31.45 Aligned_cols=45 Identities=13% Similarity=0.285 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEecCCcE-------------------EEEE---ecCCHHHHHHHHH
Q 023171 30 EGCKKKVTKILKGIEGVYTAVIDSQQHK-------------------VTVI---GNVDAETLIKKLL 74 (286)
Q Consensus 30 ~~Ca~kIEKAL~kI~GV~sV~VDl~t~k-------------------VtVt---g~vd~eeIikaIr 74 (286)
.+|-+-++..+.+++||.++.+-+..+. |.|+ ..++.++|++..-
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 7899999999999999999999888765 4454 4578888888653
No 19
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=61.10 E-value=42 Score=27.59 Aligned_cols=66 Identities=26% Similarity=0.288 Sum_probs=40.4
Q ss_pred ceEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEE-----ec--CCcEEEEEe-cCCHHHHHHHHHHcCCCCccC
Q 023171 18 FQTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVI-----DS--QQHKVTVIG-NVDAETLIKKLLRSGKHAELW 83 (286)
Q Consensus 18 ~~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~V-----Dl--~t~kVtVtg-~vd~eeIikaIrKaGY~Aeil 83 (286)
..+++|.|- -+=+--.--+-+.|.++.||.-|.+ |. .+-+++|.| +++.++|.+.|++.|-.++-+
T Consensus 5 iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSi 79 (97)
T COG1888 5 IRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSI 79 (97)
T ss_pred ceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeeh
Confidence 445556655 3322223344556777777665433 33 344455565 599999999999999866543
No 20
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=54.53 E-value=47 Score=26.51 Aligned_cols=44 Identities=23% Similarity=0.331 Sum_probs=32.8
Q ss_pred HHHHHHHHHhcCCCeeEEEEecCCcEEEEE-ecCCHHHHHHHHHH
Q 023171 32 CKKKVTKILKGIEGVYTAVIDSQQHKVTVI-GNVDAETLIKKLLR 75 (286)
Q Consensus 32 Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVt-g~vd~eeIikaIrK 75 (286)
=...|.+.|..++|+.-...|...++++|+ ...+..++++.|..
T Consensus 18 ~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~ 62 (87)
T PRK10553 18 RISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIES 62 (87)
T ss_pred HHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHH
Confidence 367899999999999977777888888887 34555655555554
No 21
>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=50.46 E-value=75 Score=24.56 Aligned_cols=44 Identities=20% Similarity=0.233 Sum_probs=32.2
Q ss_pred HHHHHHHHHhcCCCeeEEEEecCCcEEEEE-ecCCHHHHHHHHHHc
Q 023171 32 CKKKVTKILKGIEGVYTAVIDSQQHKVTVI-GNVDAETLIKKLLRS 76 (286)
Q Consensus 32 Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVt-g~vd~eeIikaIrKa 76 (286)
=...|.++|..++|+.-...+-. +++.|+ ...+..++.+.+...
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 34688999999999976666666 777766 456677777777654
No 22
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=42.21 E-value=51 Score=29.04 Aligned_cols=45 Identities=22% Similarity=0.298 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEecCCcE--------------EEEE---ecCCHHHHHHHHH
Q 023171 30 EGCKKKVTKILKGIEGVYTAVIDSQQHK--------------VTVI---GNVDAETLIKKLL 74 (286)
Q Consensus 30 ~~Ca~kIEKAL~kI~GV~sV~VDl~t~k--------------VtVt---g~vd~eeIikaIr 74 (286)
.+|-+-++..+.+++||.++.+-+..+. |.|+ ..++.++|++..-
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 6889999999999999999999877643 3333 3477888888663
No 23
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.61 E-value=1.4e+02 Score=30.96 Aligned_cols=10 Identities=50% Similarity=1.006 Sum_probs=6.6
Q ss_pred CCCCCCCCCC
Q 023171 194 PRHQQQYPSP 203 (286)
Q Consensus 194 p~~~~~~p~~ 203 (286)
.+.|+.||+|
T Consensus 413 ~pq~qNyppp 422 (483)
T KOG2236|consen 413 SPQQQNYPPP 422 (483)
T ss_pred CcccCCCCCC
Confidence 5566677665
No 24
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=38.30 E-value=40 Score=30.59 Aligned_cols=51 Identities=22% Similarity=0.340 Sum_probs=38.6
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCCeeEEEEecCCcE-------------------EEEE---ecCCHHHHHHHHH
Q 023171 19 QTWVLKVLIHCEGCKKKVTKILKGIEGVYTAVIDSQQHK-------------------VTVI---GNVDAETLIKKLL 74 (286)
Q Consensus 19 ~tv~fkV~M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~k-------------------VtVt---g~vd~eeIikaIr 74 (286)
.++.|. .+|-+-++..+.+++||.++.+-+..+. |.|. ..++.++|++..-
T Consensus 9 ~~a~~a-----gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff 81 (186)
T PRK13014 9 ETATFA-----GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF 81 (186)
T ss_pred cEEEEe-----cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence 445555 7888889999999999999999888764 3444 3478888887663
No 25
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=37.05 E-value=70 Score=28.15 Aligned_cols=42 Identities=17% Similarity=0.228 Sum_probs=33.0
Q ss_pred ceEEEEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecC-CcEEEE
Q 023171 18 FQTWVLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQ-QHKVTV 60 (286)
Q Consensus 18 ~~tv~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~-t~kVtV 60 (286)
-..+++.|+ -.|..|..-|.....++ |+.++.|-.. ++++.+
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVYY 142 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEEE
Confidence 456789999 99999999888877765 8888877766 665554
No 26
>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=36.57 E-value=59 Score=23.61 Aligned_cols=51 Identities=18% Similarity=0.167 Sum_probs=36.5
Q ss_pred EEEEe-ecChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHHcCCCCc
Q 023171 22 VLKVL-IHCEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVI--GNVDAETLIKKLLRSGKHAE 81 (286)
Q Consensus 22 ~fkV~-M~C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVt--g~vd~eeIikaIrKaGY~Ae 81 (286)
+|.+. +.|....-+++++|.+++.= ..+.|. .......|...++..||.+.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~ 55 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVV 55 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEE
Confidence 45666 89999999999999997322 224443 23556889999999999743
No 27
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=36.30 E-value=58 Score=30.22 Aligned_cols=45 Identities=20% Similarity=0.379 Sum_probs=35.3
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEecCCcE-------------------EEEE---ecCCHHHHHHHHH
Q 023171 30 EGCKKKVTKILKGIEGVYTAVIDSQQHK-------------------VTVI---GNVDAETLIKKLL 74 (286)
Q Consensus 30 ~~Ca~kIEKAL~kI~GV~sV~VDl~t~k-------------------VtVt---g~vd~eeIikaIr 74 (286)
.+|-+-++..+.+++||.++.|-+..+. |.|+ ..++.++|++..-
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 7899999999999999999999888542 3343 3478888887663
No 28
>PF15377 DUF4604: Domain of unknown function (DUF4604)
Probab=35.25 E-value=1.9e+02 Score=24.99 Aligned_cols=14 Identities=21% Similarity=0.230 Sum_probs=9.5
Q ss_pred ecCCHHHHHHHHHH
Q 023171 62 GNVDAETLIKKLLR 75 (286)
Q Consensus 62 g~vd~eeIikaIrK 75 (286)
+.++.+++...++.
T Consensus 63 ~~lt~eE~~~~~~~ 76 (158)
T PF15377_consen 63 GDLTAEEAEAEKKE 76 (158)
T ss_pred CcccHHHHHHHHHh
Confidence 45677777777666
No 29
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=34.59 E-value=52 Score=29.37 Aligned_cols=35 Identities=11% Similarity=0.246 Sum_probs=24.6
Q ss_pred EEEEEEeecChhHH------HHHHHHHhcCCCeeEEEEecC
Q 023171 20 TWVLKVLIHCEGCK------KKVTKILKGIEGVYTAVIDSQ 54 (286)
Q Consensus 20 tv~fkV~M~C~~Ca------~kIEKAL~kI~GV~sV~VDl~ 54 (286)
++.|.+.+...+|. ..|+.+|..++||.+|.|++.
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l~ 154 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVELV 154 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEEE
Confidence 45555555555554 448889999999998887653
No 30
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=33.90 E-value=1e+02 Score=29.78 Aligned_cols=44 Identities=27% Similarity=0.331 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEecCCcE-------------------EEEE---ecCCHHHHHHHH
Q 023171 30 EGCKKKVTKILKGIEGVYTAVIDSQQHK-------------------VTVI---GNVDAETLIKKL 73 (286)
Q Consensus 30 ~~Ca~kIEKAL~kI~GV~sV~VDl~t~k-------------------VtVt---g~vd~eeIikaI 73 (286)
.+|-+-++..+.+++||.++.+-+..+. |.|+ ..++.++|++..
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F 199 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVF 199 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 8899999999999999999999887654 3343 347778888765
No 31
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=33.67 E-value=1e+02 Score=22.92 Aligned_cols=43 Identities=19% Similarity=0.347 Sum_probs=30.8
Q ss_pred HhcCCCeeEEEEecCC-cEEEEEecCCHHHHHHHHHHcCCCCccC
Q 023171 40 LKGIEGVYTAVIDSQQ-HKVTVIGNVDAETLIKKLLRSGKHAELW 83 (286)
Q Consensus 40 L~kI~GV~sV~VDl~t-~kVtVtg~vd~eeIikaIrKaGY~Aeil 83 (286)
|..++||..+...-.. -++.|.......+|+..|...|. +.-+
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f 69 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI-IRSF 69 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC-eeEE
Confidence 7888999988764332 23444456778999999999998 6433
No 32
>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=32.03 E-value=1.1e+02 Score=26.80 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=34.5
Q ss_pred hhHHHHHHHHHhcCCCeeEEEEecCCc-------------------EEEEE---ecCCHHHHHHHHHH
Q 023171 30 EGCKKKVTKILKGIEGVYTAVIDSQQH-------------------KVTVI---GNVDAETLIKKLLR 75 (286)
Q Consensus 30 ~~Ca~kIEKAL~kI~GV~sV~VDl~t~-------------------kVtVt---g~vd~eeIikaIrK 75 (286)
.+|-+.++..+.+++||.++.+-+..+ .|.|+ ..++.++|++..-+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~~ 74 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFFR 74 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHHH
Confidence 578899999999999999999987665 23333 34788888887643
No 33
>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=31.09 E-value=1.9e+02 Score=20.37 Aligned_cols=59 Identities=14% Similarity=0.214 Sum_probs=34.2
Q ss_pred EEEEe-ecChhHHHHHHHHHhcC-CCeeEEEEecC----CcEEEEEe-cCCHHHHHHHHHHcCCCC
Q 023171 22 VLKVL-IHCEGCKKKVTKILKGI-EGVYTAVIDSQ----QHKVTVIG-NVDAETLIKKLLRSGKHA 80 (286)
Q Consensus 22 ~fkV~-M~C~~Ca~kIEKAL~kI-~GV~sV~VDl~----t~kVtVtg-~vd~eeIikaIrKaGY~A 80 (286)
+|.|. -+-.+...+|...|.+. -.|..+..... ...++|.- ..+.+.+.+.|++.||++
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v 68 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEV 68 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCee
Confidence 34444 33445666777777654 23444433332 22233432 246679999999999976
No 34
>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=28.99 E-value=61 Score=29.47 Aligned_cols=17 Identities=35% Similarity=0.460 Sum_probs=10.0
Q ss_pred CCCCCCCCCccCCCCCcc
Q 023171 197 QQQYPSPPFMQQEHPPMY 214 (286)
Q Consensus 197 ~~~~p~~~~~~~~~p~~~ 214 (286)
.|+|+|++-.+|-+| ||
T Consensus 127 ~~~y~~~~~~~~~~~-m~ 143 (182)
T PF06495_consen 127 EYAYGWPPPAPQFNP-MQ 143 (182)
T ss_pred ccccCCCCccccccc-cc
Confidence 788888654444443 54
No 35
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=28.76 E-value=2.7e+02 Score=21.86 Aligned_cols=58 Identities=21% Similarity=0.170 Sum_probs=42.7
Q ss_pred EEEEEEeecChhHHHHHHHHHhcCCC-eeEEEEecCCcEEEEEecCCHHHHHHHHHHcCC
Q 023171 20 TWVLKVLIHCEGCKKKVTKILKGIEG-VYTAVIDSQQHKVTVIGNVDAETLIKKLLRSGK 78 (286)
Q Consensus 20 tv~fkV~M~C~~Ca~kIEKAL~kI~G-V~sV~VDl~t~kVtVtg~vd~eeIikaIrKaGY 78 (286)
|+.=+|+-+=..+..-+...|..... -..+.|+..++.|.|.|.. ..+|.+.|...||
T Consensus 29 T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 29 TVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLLEKGF 87 (87)
T ss_pred EEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHHHCcC
Confidence 44445664446777777777765544 2357899999999999885 7888999998887
No 36
>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=28.11 E-value=79 Score=24.68 Aligned_cols=21 Identities=14% Similarity=0.332 Sum_probs=16.9
Q ss_pred HHHHHHHhcCCCeeEEEEecC
Q 023171 34 KKVTKILKGIEGVYTAVIDSQ 54 (286)
Q Consensus 34 ~kIEKAL~kI~GV~sV~VDl~ 54 (286)
..|+.+|..++||.++.|++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457888888999998888765
No 37
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=27.42 E-value=1.2e+02 Score=35.91 Aligned_cols=19 Identities=26% Similarity=0.363 Sum_probs=7.8
Q ss_pred ecChhHHHHHHHHHhcCCC
Q 023171 27 IHCEGCKKKVTKILKGIEG 45 (286)
Q Consensus 27 M~C~~Ca~kIEKAL~kI~G 45 (286)
++|.--...|...=.++.|
T Consensus 1685 Itcep~gslidtkgnkiag 1703 (2220)
T KOG3598|consen 1685 ITCEPYGSLIDTKGNKIAG 1703 (2220)
T ss_pred eeecccccccccccceecc
Confidence 4444444444433333333
No 38
>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=27.05 E-value=1.6e+02 Score=25.17 Aligned_cols=33 Identities=15% Similarity=0.206 Sum_probs=28.1
Q ss_pred ChhHHHHHHHHHhcCCCeeEEEEecCCcEEEEE
Q 023171 29 CEGCKKKVTKILKGIEGVYTAVIDSQQHKVTVI 61 (286)
Q Consensus 29 C~~Ca~kIEKAL~kI~GV~sV~VDl~t~kVtVt 61 (286)
=..=+.+|.+.+.+++||.++.|=.....+.|-
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 355678999999999999999988888888775
No 39
>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=25.97 E-value=2e+02 Score=20.43 Aligned_cols=33 Identities=12% Similarity=0.135 Sum_probs=23.7
Q ss_pred eEEEEEEeecChh-HHHHHHHHHhcCCCeeEEEE
Q 023171 19 QTWVLKVLIHCEG-CKKKVTKILKGIEGVYTAVI 51 (286)
Q Consensus 19 ~tv~fkV~M~C~~-Ca~kIEKAL~kI~GV~sV~V 51 (286)
..+.|.|...=.. -...|-+.|++++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 3455556534343 77889999999999998864
No 40
>KOG2573 consensus Ribosome biogenesis protein - Nop56p/Sik1p [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=24.24 E-value=71 Score=32.77 Aligned_cols=6 Identities=83% Similarity=0.828 Sum_probs=2.2
Q ss_pred ccccCC
Q 023171 148 KKKKKG 153 (286)
Q Consensus 148 kkkkk~ 153 (286)
|||||+
T Consensus 488 kKkkKk 493 (498)
T KOG2573|consen 488 KKKKKK 493 (498)
T ss_pred cccccc
Confidence 333333
No 41
>PRK07334 threonine dehydratase; Provisional
Probab=22.04 E-value=2.9e+02 Score=27.16 Aligned_cols=63 Identities=16% Similarity=0.108 Sum_probs=40.2
Q ss_pred EEEEEe-ecChhHHHHHHHHHhcC-CCeeEEEEecC-----CcEEEEE--e----cCCHHHHHHHHHHcCCCCccC
Q 023171 21 WVLKVL-IHCEGCKKKVTKILKGI-EGVYTAVIDSQ-----QHKVTVI--G----NVDAETLIKKLLRSGKHAELW 83 (286)
Q Consensus 21 v~fkV~-M~C~~Ca~kIEKAL~kI-~GV~sV~VDl~-----t~kVtVt--g----~vd~eeIikaIrKaGY~Aeil 83 (286)
+.|.|. .+=.+=...|-.+|... -.|.++.+... .+.+.|. - ......|++.|++.||.+.++
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 567777 55556677888888765 23555555432 3454443 1 124568899999999998775
No 42
>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=21.75 E-value=55 Score=23.19 Aligned_cols=30 Identities=23% Similarity=0.340 Sum_probs=15.0
Q ss_pred HHHHHHhc---CCCeeEEEEecCCcEEEEEecCC
Q 023171 35 KVTKILKG---IEGVYTAVIDSQQHKVTVIGNVD 65 (286)
Q Consensus 35 kIEKAL~k---I~GV~sV~VDl~t~kVtVtg~vd 65 (286)
+|+.+|.. +++. .+.|...++.|+|.|.++
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~ 35 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEVP 35 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEES
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeCc
Confidence 45666665 3343 467777888888888763
No 43
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=21.24 E-value=3.4e+02 Score=20.32 Aligned_cols=12 Identities=8% Similarity=0.318 Sum_probs=7.9
Q ss_pred CCHHHHHHHHHH
Q 023171 64 VDAETLIKKLLR 75 (286)
Q Consensus 64 vd~eeIikaIrK 75 (286)
-+.++|+++|++
T Consensus 64 P~~~~i~~~I~~ 75 (76)
T PF10262_consen 64 PDPDEIVQLIRD 75 (76)
T ss_dssp S-HHHHHHHHHH
T ss_pred CCHHHHHHHHhc
Confidence 467788887764
No 44
>PF03529 TF_Otx: Otx1 transcription factor; InterPro: IPR013851 Otx proteins constitute a class of vertebrate homeodomain-containing transcription factors that have been shown to be essential for anterior head formation, including brain morphogenesis. They are orthologous to the product of the Drosophila head gap gene, orthodenticle (Otd), and appear to play similar roles in both, since the developmental abnormalities caused by disruption of these transcription factors in one, can be recovered by substitution of the factor(s) from the other. Such studies have provided strong evidence that there exists a conserved genetic programme for insect and mammalian brain development, which presumably arose in a more primitive common ancestor [, ]. Two vertebrate orthodenticle-related transcription factors have been indentified, Otx1 and Otx2, which have sizes of 355 and 289 residues respectively. They contain a bicoid-like homeodomain, which features a conserved lysine residue at position 9 of the DNA recognition helix, which is thought to confer high-affinity binding to TAATCC/T elements on DNA []. Otd-like transcription factors have also been found in zebrafish and certain lamprey species. This entry represents a conserved region found in the C-terminal region of these proteins.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0007275 multicellular organismal development, 0005634 nucleus
Probab=21.05 E-value=57 Score=26.52 Aligned_cols=10 Identities=30% Similarity=0.610 Sum_probs=7.0
Q ss_pred cccCcccccc
Q 023171 239 YAPSMHAYYN 248 (286)
Q Consensus 239 y~~~~~~~~~ 248 (286)
|+.|||.+.+
T Consensus 57 YLsPMh~~l~ 66 (88)
T PF03529_consen 57 YLSPMHSQLH 66 (88)
T ss_pred cccccccccC
Confidence 4678988655
No 45
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 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 domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=20.94 E-value=2.5e+02 Score=22.05 Aligned_cols=40 Identities=25% Similarity=0.301 Sum_probs=27.4
Q ss_pred HHHHHHHhcCCCeeEEEEecCCcEEEEE--ecCCHHHHHHHHHH
Q 023171 34 KKVTKILKGIEGVYTAVIDSQQHKVTVI--GNVDAETLIKKLLR 75 (286)
Q Consensus 34 ~kIEKAL~kI~GV~sV~VDl~t~kVtVt--g~vd~eeIikaIrK 75 (286)
.-+-+.|-.++||.+|-+.. +-|+|+ ..++.+.|...|..
T Consensus 37 spLA~~Lf~i~gV~~Vf~~~--dfItVtK~~~~~W~~l~~~I~~ 78 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIGD--DFITVTKNPDADWEDLKPEIRE 78 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEET--TEEEEEE-TTS-HHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEEC--CEEEEeeCCCCCHHHHHHHHHH
Confidence 34445566999999876654 458887 45888888887764
No 46
>PRK11670 antiporter inner membrane protein; Provisional
Probab=20.89 E-value=2e+02 Score=28.21 Aligned_cols=68 Identities=16% Similarity=0.148 Sum_probs=41.9
Q ss_pred EEEEEEeecChhH------HHHHHHHHhcCCCeeEEEEecCC------------------cEEEEE------ec-CCHHH
Q 023171 20 TWVLKVLIHCEGC------KKKVTKILKGIEGVYTAVIDSQQ------------------HKVTVI------GN-VDAET 68 (286)
Q Consensus 20 tv~fkV~M~C~~C------a~kIEKAL~kI~GV~sV~VDl~t------------------~kVtVt------g~-vd~ee 68 (286)
++.|.|.+.-..| ...++.+|..++||.++.|.+.. +.+.|. |. +...-
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avN 127 (369)
T PRK11670 48 TLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVN 127 (369)
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHH
Confidence 3445555433333 35688899999999877654432 223343 22 23455
Q ss_pred HHHHHHHcCCCCccCCccc
Q 023171 69 LIKKLLRSGKHAELWPEKK 87 (286)
Q Consensus 69 IikaIrKaGY~Aeil~~ee 87 (286)
|...|.+.|+++-++..+-
T Consensus 128 LA~aLA~~G~rVlLID~D~ 146 (369)
T PRK11670 128 LALALAAEGAKVGILDADI 146 (369)
T ss_pred HHHHHHHCCCcEEEEeCCC
Confidence 6778889999987776553
No 47
>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=20.55 E-value=3.2e+02 Score=19.35 Aligned_cols=58 Identities=21% Similarity=0.150 Sum_probs=34.1
Q ss_pred EEEe-ecChhHHHHHHHHHhcCCC-eeEEEEecCCcEEE--EEecCCHHHHHHHHHHcCCCCc
Q 023171 23 LKVL-IHCEGCKKKVTKILKGIEG-VYTAVIDSQQHKVT--VIGNVDAETLIKKLLRSGKHAE 81 (286)
Q Consensus 23 fkV~-M~C~~Ca~kIEKAL~kI~G-V~sV~VDl~t~kVt--Vtg~vd~eeIikaIrKaGY~Ae 81 (286)
|.|. -+-.+=..+|-+.|.+... |..+.+.....+++ |.. -+.+.+.+.|++.||++.
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~-~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEFGILRLIV-SDPDKAKEALKEAGFAVK 65 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEE-CCHHHHHHHHHHCCCEEE
Confidence 4444 4455666677777765432 34443322222333 334 557799999999999864
Done!