Query 015975
Match_columns 397
No_of_seqs 309 out of 1440
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:39:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015975.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015975hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4656 Copper chaperone for s 99.5 1.3E-13 2.7E-18 129.8 7.5 103 12-119 6-110 (247)
2 PF00403 HMA: Heavy-metal-asso 99.2 3.7E-11 8E-16 91.0 8.2 58 16-73 1-62 (62)
3 COG2608 CopZ Copper chaperone 99.1 5.3E-10 1.1E-14 88.6 8.6 65 13-77 2-70 (71)
4 KOG1603 Copper chaperone [Inor 99.0 2.6E-09 5.7E-14 84.9 8.4 68 11-78 3-71 (73)
5 PLN02957 copper, zinc superoxi 98.6 2.5E-07 5.4E-12 88.8 11.0 99 10-113 3-102 (238)
6 PRK10671 copA copper exporting 97.9 1.9E-05 4E-10 87.8 7.9 64 13-78 3-67 (834)
7 COG2217 ZntA Cation transport 97.6 0.00012 2.5E-09 80.7 7.7 63 13-76 2-69 (713)
8 TIGR00003 copper ion binding p 97.6 0.0007 1.5E-08 46.7 8.8 61 14-74 3-67 (68)
9 KOG0207 Cation transport ATPas 96.8 0.0029 6.3E-08 71.0 7.5 67 13-79 146-216 (951)
10 KOG0207 Cation transport ATPas 96.6 0.0043 9.3E-08 69.7 7.2 70 12-81 68-141 (951)
11 PRK10671 copA copper exporting 96.5 0.0067 1.5E-07 67.8 8.1 65 14-78 100-165 (834)
12 PRK11033 zntA zinc/cadmium/mer 96.2 0.013 2.8E-07 64.9 7.7 67 11-77 51-119 (741)
13 TIGR02052 MerP mercuric transp 92.9 1.4 3E-05 33.6 9.4 63 14-76 24-90 (92)
14 cd00371 HMA Heavy-metal-associ 88.4 4.1 8.8E-05 24.9 7.4 54 19-72 4-60 (63)
15 PRK13748 putative mercuric red 83.3 5.9 0.00013 42.0 9.1 64 16-79 3-69 (561)
16 COG1888 Uncharacterized protei 71.2 22 0.00048 30.5 7.2 68 11-78 4-80 (97)
17 PF02680 DUF211: Uncharacteriz 68.8 29 0.00062 29.8 7.5 65 12-77 4-77 (95)
18 PF01883 DUF59: Domain of unkn 67.4 8.4 0.00018 29.9 3.8 33 13-45 34-72 (72)
19 PF14437 MafB19-deam: MafB19-l 59.9 15 0.00032 33.8 4.4 42 12-54 99-142 (146)
20 PF01206 TusA: Sulfurtransfera 54.9 32 0.00069 26.4 5.1 55 16-77 2-57 (70)
21 PRK10553 assembly protein for 41.8 87 0.0019 26.2 6.0 47 24-70 16-63 (87)
22 PF13732 DUF4162: Domain of un 36.3 98 0.0021 24.2 5.3 44 34-78 26-70 (84)
23 TIGR03406 FeS_long_SufT probab 36.2 43 0.00094 31.3 3.7 34 14-47 114-153 (174)
24 PF09580 Spore_YhcN_YlaJ: Spor 32.7 1.1E+02 0.0024 27.6 5.7 48 22-69 72-124 (177)
25 PF05046 Img2: Mitochondrial l 32.1 2.4E+02 0.0052 23.3 7.1 59 13-72 28-87 (87)
26 PF03927 NapD: NapD protein; 31.2 1.8E+02 0.0039 23.6 6.1 45 26-71 16-61 (79)
27 cd04888 ACT_PheB-BS C-terminal 30.6 1.4E+02 0.003 22.4 5.2 33 13-45 41-74 (76)
28 TIGR02945 SUF_assoc FeS assemb 30.5 51 0.0011 27.1 2.9 21 28-48 58-78 (99)
29 cd02987 Phd_like_Phd Phosducin 28.5 16 0.00036 33.6 -0.4 47 101-158 7-53 (175)
30 PRK14054 methionine sulfoxide 27.3 1E+02 0.0022 28.9 4.6 44 24-67 10-75 (172)
31 PRK11018 hypothetical protein; 27.2 2E+02 0.0044 23.0 5.8 56 15-77 9-65 (78)
32 COG5180 PBP1 Protein interacti 25.8 23 0.00051 38.3 0.1 19 332-351 550-568 (654)
33 cd03421 SirA_like_N SirA_like_ 25.1 1.7E+02 0.0038 22.2 4.8 52 18-77 3-55 (67)
34 cd04883 ACT_AcuB C-terminal AC 22.7 3.2E+02 0.007 20.2 7.3 59 17-75 4-69 (72)
35 PF14492 EFG_II: Elongation Fa 20.5 4.3E+02 0.0094 20.8 7.0 60 15-75 6-72 (75)
36 PF13291 ACT_4: ACT domain; PD 20.2 2.9E+02 0.0064 21.3 5.4 33 12-44 47-79 (80)
No 1
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.45 E-value=1.3e-13 Score=129.75 Aligned_cols=103 Identities=21% Similarity=0.331 Sum_probs=88.4
Q ss_pred eeEEEEEEeeccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhCCceEEcCCCCccccccCccc
Q 015975 12 IQTCVLKVNIHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGKHAELWSQKSNQNQNQKNNC 91 (397)
Q Consensus 12 ~~tv~LkVdM~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy~ael~~~~~~~~~~~aav~ 91 (397)
.-+++|.|+|+|++|+..|++.|..++||.+|+||+.++.|.|.+...+++|+.+|+.+|+++.+++.+.. .++.
T Consensus 6 ~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~p-----sava 80 (247)
T KOG4656|consen 6 TYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKP-----SAVA 80 (247)
T ss_pred ceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCch-----hHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999988654 2344
Q ss_pred cccCccC--CCCCCCcceeeeccCcCCCCC
Q 015975 92 IKDDKNN--NKGQKQGLMKGFEPLKNQQKF 119 (397)
Q Consensus 92 ile~~~~--~~~~v~GLVR~Vqv~~n~~~~ 119 (397)
++++..+ .+.+|+|||||+|++++...+
T Consensus 81 l~at~a~~~~~~~v~GvvRf~qvt~ek~li 110 (247)
T KOG4656|consen 81 LLATVAKYTGPQAVQGVVRFVQVTEEKTLI 110 (247)
T ss_pred HHHHHHHhcCCccceeEEEEEEeccccEEE
Confidence 4444321 256999999999998887544
No 2
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.24 E-value=3.7e-11 Score=90.99 Aligned_cols=58 Identities=34% Similarity=0.638 Sum_probs=53.9
Q ss_pred EEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEecc---CCHHHHHHHHHHhCCc
Q 015975 16 VLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGS---VDSATLIKKLVRAGKH 73 (397)
Q Consensus 16 ~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~---vd~eeIi~aIekaGy~ 73 (397)
+|+|+ |+|.+|+.+|+++|.+++||.++++|+.+++|+|..+ +++++|+++|+++||+
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 58997 9999999999999999999999999999999999853 5679999999999995
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.08 E-value=5.3e-10 Score=88.62 Aligned_cols=65 Identities=32% Similarity=0.547 Sum_probs=58.2
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEe--c-cCCHHHHHHHHHHhCCceEEc
Q 015975 13 QTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVS--G-SVDSATLIKKLVRAGKHAELW 77 (397)
Q Consensus 13 ~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~--g-~vd~eeIi~aIekaGy~ael~ 77 (397)
.+.+|+|+ |+|.+|+.+|+++|.+++||.+++|++..++++|. . .++.++|+++|+++||.+..+
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 46789998 99999999999999999999999999999666665 4 589999999999999998754
No 4
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.97 E-value=2.6e-09 Score=84.87 Aligned_cols=68 Identities=57% Similarity=0.997 Sum_probs=62.3
Q ss_pred ceeEEEEEEeeccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhC-CceEEcC
Q 015975 11 KIQTCVLKVNIHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAG-KHAELWS 78 (397)
Q Consensus 11 k~~tv~LkVdM~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaG-y~ael~~ 78 (397)
..++.+++|+|+|.+|+.+|++.|..++||.++++|...++|+|.+.+++..|++.|++.+ .+..+|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 4567889999999999999999999999999999999999999999999999999999988 7666653
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.62 E-value=2.5e-07 Score=88.84 Aligned_cols=99 Identities=24% Similarity=0.319 Sum_probs=79.6
Q ss_pred cceeEEEEEEeeccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhCCceEEcCCCCccc-cccC
Q 015975 10 LKIQTCVLKVNIHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGKHAELWSQKSNQN-QNQK 88 (397)
Q Consensus 10 ~k~~tv~LkVdM~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy~ael~~~~~~~~-~~~a 88 (397)
+..++++|.|.|+|..|+.+|++.|.+++||..+.+++..++++|.......+|+++|++.||.++++.....+. ...+
T Consensus 3 ~~~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~~~~~~~ 82 (238)
T PLN02957 3 LPELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPEDFLVSA 82 (238)
T ss_pred CCcEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCccccccce
Confidence 345667788899999999999999999999999999999999999877788999999999999998887744331 1233
Q ss_pred ccccccCccCCCCCCCcceeeeccC
Q 015975 89 NNCIKDDKNNNKGQKQGLMKGFEPL 113 (397)
Q Consensus 89 av~ile~~~~~~~~v~GLVR~Vqv~ 113 (397)
+++.+. ...+.|+|||.|..
T Consensus 83 av~~~~-----g~~v~G~v~~~~~~ 102 (238)
T PLN02957 83 AVAEFK-----GPDIFGVVRFAQVS 102 (238)
T ss_pred EEEEec-----CCceEEEEEEEEcC
Confidence 444432 23588999998874
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.94 E-value=1.9e-05 Score=87.79 Aligned_cols=64 Identities=27% Similarity=0.475 Sum_probs=57.3
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhCCceEEcC
Q 015975 13 QTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGKHAELWS 78 (397)
Q Consensus 13 ~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy~ael~~ 78 (397)
++++|+|+ |+|.+|+.+|+++|++++||..++|++. +++|+...+++.+.++|+++||++++..
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 56889999 9999999999999999999999999994 5566666799999999999999998754
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.63 E-value=0.00012 Score=80.75 Aligned_cols=63 Identities=25% Similarity=0.531 Sum_probs=56.6
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEec---cCC-HHHHHHHHHHhCCceEE
Q 015975 13 QTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSG---SVD-SATLIKKLVRAGKHAEL 76 (397)
Q Consensus 13 ~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g---~vd-~eeIi~aIekaGy~ael 76 (397)
.+++|.|+ |+|..|+.+|| +|++++||.++.|++.+++++|.. ..+ .+++.+++++.||.++.
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 45789999 99999999999 999999999999999999999974 244 78999999999998765
No 8
>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=97.60 E-value=0.0007 Score=46.66 Aligned_cols=61 Identities=23% Similarity=0.464 Sum_probs=51.5
Q ss_pred EEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEec---cCCHHHHHHHHHHhCCce
Q 015975 14 TCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSG---SVDSATLIKKLVRAGKHA 74 (397)
Q Consensus 14 tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g---~vd~eeIi~aIekaGy~a 74 (397)
+..+.|. ++|..|+..|++.+...+++..+.+++...++.|.. ......+...++..||.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 4568898 999999999999999999999999999999988874 346777777778888753
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.80 E-value=0.0029 Score=70.96 Aligned_cols=67 Identities=22% Similarity=0.392 Sum_probs=61.2
Q ss_pred eEEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEec---cCCHHHHHHHHHHhCCceEEcCC
Q 015975 13 QTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSG---SVDSATLIKKLVRAGKHAELWSQ 79 (397)
Q Consensus 13 ~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g---~vd~eeIi~aIekaGy~ael~~~ 79 (397)
.+++|.|. |+|.+|+.+|++.|.+++||.++.+++.++++.|.. .+.+-.+++.|+..|+.+.....
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~ 216 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPY 216 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeec
Confidence 67899998 999999999999999999999999999999999974 47899999999999998776553
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.62 E-value=0.0043 Score=69.66 Aligned_cols=70 Identities=24% Similarity=0.416 Sum_probs=62.7
Q ss_pred eeEEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEec---cCCHHHHHHHHHHhCCceEEcCCCC
Q 015975 12 IQTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSG---SVDSATLIKKLVRAGKHAELWSQKS 81 (397)
Q Consensus 12 ~~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g---~vd~eeIi~aIekaGy~ael~~~~~ 81 (397)
..+..|.|. |+|.+|+..|++.|++++||.++.|.+...+..|.. .++++.+.+.++++||.+.+++...
T Consensus 68 ~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~ 141 (951)
T KOG0207|consen 68 ASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVN 141 (951)
T ss_pred cceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhccc
Confidence 346789999 999999999999999999999999999999999873 5789999999999999999876643
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.53 E-value=0.0067 Score=67.75 Aligned_cols=65 Identities=26% Similarity=0.467 Sum_probs=57.7
Q ss_pred EEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhCCceEEcC
Q 015975 14 TCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGKHAELWS 78 (397)
Q Consensus 14 tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy~ael~~ 78 (397)
++++.|. |+|..|+.+|++.+.+++||.++.+++.++++.|....+++++.+.+++.||.+.++.
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 5678898 9999999999999999999999999999999888766788889899999999876543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.16 E-value=0.013 Score=64.95 Aligned_cols=67 Identities=22% Similarity=0.300 Sum_probs=55.6
Q ss_pred ceeEEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEecc-CCHHHHHHHHHHhCCceEEc
Q 015975 11 KIQTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGS-VDSATLIKKLVRAGKHAELW 77 (397)
Q Consensus 11 k~~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~-vd~eeIi~aIekaGy~ael~ 77 (397)
...++.+.|. |+|.+|+.+|++.+.+++||..+.+++.++++.|..+ ...+++.+.+++.||.+...
T Consensus 51 ~~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 51 SGTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 3456778898 9999999999999999999999999999999888632 12267778889999987654
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=92.86 E-value=1.4 Score=33.60 Aligned_cols=63 Identities=24% Similarity=0.405 Sum_probs=48.3
Q ss_pred EEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEec---cCCHHHHHHHHHHhCCceEE
Q 015975 14 TCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSG---SVDSATLIKKLVRAGKHAEL 76 (397)
Q Consensus 14 tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g---~vd~eeIi~aIekaGy~ael 76 (397)
++.+.+. +.|..|...++..+...++|..+.+.....++.+.. ......+...+++.|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 4566777 999999999999999999998888888888766652 24566666666777877544
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=88.42 E-value=4.1 Score=24.88 Aligned_cols=54 Identities=35% Similarity=0.622 Sum_probs=37.0
Q ss_pred Ee-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEecc--CCHHHHHHHHHHhCC
Q 015975 19 VN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGS--VDSATLIKKLVRAGK 72 (397)
Q Consensus 19 Vd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~--vd~eeIi~aIekaGy 72 (397)
+. +.|..|...++..+...+++....+.+....+.+... .....+...++..++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (63)
T cd00371 4 VEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGY 60 (63)
T ss_pred ECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCC
Confidence 45 8899999999999999999877777777766655532 244444344444443
No 15
>PRK13748 putative mercuric reductase; Provisional
Probab=83.29 E-value=5.9 Score=41.97 Aligned_cols=64 Identities=22% Similarity=0.422 Sum_probs=51.4
Q ss_pred EEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEec--cCCHHHHHHHHHHhCCceEEcCC
Q 015975 16 VLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSG--SVDSATLIKKLVRAGKHAELWSQ 79 (397)
Q Consensus 16 ~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g--~vd~eeIi~aIekaGy~ael~~~ 79 (397)
.+.+. ++|..|..+++..+...+++....+++....+.+.. ..+...+...+++.++..++...
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 35677 999999999999999999999899999888877763 34566677777888888766655
No 16
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=71.17 E-value=22 Score=30.46 Aligned_cols=68 Identities=28% Similarity=0.330 Sum_probs=43.0
Q ss_pred ceeEEEEEEe-eccHhHHHHHHHHHhccCCeeEEE-----EecC--CCEEEEec-cCCHHHHHHHHHHhCCceEEcC
Q 015975 11 KIQTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVN-----IDAE--QQKVTVSG-SVDSATLIKKLVRAGKHAELWS 78 (397)
Q Consensus 11 k~~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~-----VDla--tqkVtV~g-~vd~eeIi~aIekaGy~ael~~ 78 (397)
...+++|.|- -+-.--.-.+.+.|.+++||.-|. +|.+ .-+++|.+ .++.++|.+.|++.|-....+.
T Consensus 4 ~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiD 80 (97)
T COG1888 4 GIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSID 80 (97)
T ss_pred cceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehh
Confidence 3455666664 332223334566778888875443 3333 44455565 7999999999999997665443
No 17
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=68.79 E-value=29 Score=29.85 Aligned_cols=65 Identities=26% Similarity=0.357 Sum_probs=42.9
Q ss_pred eeEEEEEEe-eccHhHHHHHHHHHhccCCeeEEE-----EecCCCEEEE--ec-cCCHHHHHHHHHHhCCceEEc
Q 015975 12 IQTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVN-----IDAEQQKVTV--SG-SVDSATLIKKLVRAGKHAELW 77 (397)
Q Consensus 12 ~~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~-----VDlatqkVtV--~g-~vd~eeIi~aIekaGy~ael~ 77 (397)
.++++|.|- -+-++ .-.+-+.|.+++||..|. +|..+..+.| ++ .++.++|.++|++.|-.+..+
T Consensus 4 irRlVLDVlKP~~p~-i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPS-IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp EEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred eeEEEEEeecCCCCC-HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 456777775 43333 446778899999987654 4555555544 45 599999999999999766544
No 18
>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=67.44 E-value=8.4 Score=29.89 Aligned_cols=33 Identities=15% Similarity=0.465 Sum_probs=22.4
Q ss_pred eEEEEEEeeccHhHH------HHHHHHHhccCCeeEEEE
Q 015975 13 QTCVLKVNIHCDGCK------QKVKKLLQRIEGVYQVNI 45 (397)
Q Consensus 13 ~tv~LkVdM~C~sCa------~kIEKAL~kL~GV~sV~V 45 (397)
.++.+.+.+.++.|. ..|+++|..++||.+|+|
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 445666666665554 778899999999998875
No 19
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=59.91 E-value=15 Score=33.81 Aligned_cols=42 Identities=17% Similarity=0.339 Sum_probs=35.2
Q ss_pred eeEEEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecC-CCEEEE
Q 015975 12 IQTCVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAE-QQKVTV 54 (397)
Q Consensus 12 ~~tv~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDla-tqkVtV 54 (397)
-..+++.|+ -.|..|..-|....+++ |+.++.|... ++++.+
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 566889998 88999999999998887 9999988877 776554
No 20
>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=54.94 E-value=32 Score=26.39 Aligned_cols=55 Identities=16% Similarity=0.118 Sum_probs=38.5
Q ss_pred EEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhCCceEEc
Q 015975 16 VLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGKHAELW 77 (397)
Q Consensus 16 ~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy~ael~ 77 (397)
++.+. +.|+...-+++++|.+++.=..++ |.++.......|...+++.|+++..+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G~~l~-------v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPGEVLE-------VLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT-EEE-------EEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCCCEEE-------EEECCccHHHHHHHHHHHCCCEEEEE
Confidence 35555 899999999999999984332221 12234566788999999999986554
No 21
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=41.76 E-value=87 Score=26.21 Aligned_cols=47 Identities=19% Similarity=0.206 Sum_probs=33.5
Q ss_pred HhHHHHHHHHHhccCCeeEEEEecCCCEEEEe-ccCCHHHHHHHHHHh
Q 015975 24 DGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVS-GSVDSATLIKKLVRA 70 (397)
Q Consensus 24 ~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~-g~vd~eeIi~aIeka 70 (397)
+.=...|++.|..++|+.-.-.|...+|+.|+ ...+..++.+.|+.+
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~I 63 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIESV 63 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHHH
Confidence 33477899999999999866677777887776 345566666666553
No 22
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=36.25 E-value=98 Score=24.20 Aligned_cols=44 Identities=18% Similarity=0.403 Sum_probs=32.5
Q ss_pred HhccCCeeEEEEecCC-CEEEEeccCCHHHHHHHHHHhCCceEEcC
Q 015975 34 LQRIEGVYQVNIDAEQ-QKVTVSGSVDSATLIKKLVRAGKHAELWS 78 (397)
Q Consensus 34 L~kL~GV~sV~VDlat-qkVtV~g~vd~eeIi~aIekaGy~ael~~ 78 (397)
|..+++|..+...-.. -++.|....+..+|++.|.+.|. +.-+.
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~ 70 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI-IRSFE 70 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC-eeEEE
Confidence 7888999988765433 34455566788999999999998 65544
No 23
>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=36.17 E-value=43 Score=31.35 Aligned_cols=34 Identities=15% Similarity=0.406 Sum_probs=24.5
Q ss_pred EEEEEEeeccHhHH------HHHHHHHhccCCeeEEEEec
Q 015975 14 TCVLKVNIHCDGCK------QKVKKLLQRIEGVYQVNIDA 47 (397)
Q Consensus 14 tv~LkVdM~C~sCa------~kIEKAL~kL~GV~sV~VDl 47 (397)
++.+.+.++...|. ..|+.+|..++||.+|+|++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 45555555555554 45889999999999988874
No 24
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=32.72 E-value=1.1e+02 Score=27.63 Aligned_cols=48 Identities=10% Similarity=0.236 Sum_probs=34.8
Q ss_pred ccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEec-----cCCHHHHHHHHHH
Q 015975 22 HCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSG-----SVDSATLIKKLVR 69 (397)
Q Consensus 22 ~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g-----~vd~eeIi~aIek 69 (397)
.=..-+.+|++.+.+++||.++.|=.....+.|-- ....++|.+.|++
T Consensus 72 ~~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~~ 124 (177)
T PF09580_consen 72 DRQQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVEK 124 (177)
T ss_pred hHHHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHHH
Confidence 34556789999999999999999998888887742 2344455554443
No 25
>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=32.06 E-value=2.4e+02 Score=23.34 Aligned_cols=59 Identities=17% Similarity=0.213 Sum_probs=45.0
Q ss_pred eEEEEEEeeccHhHHHHHHHHHhccCC-eeEEEEecCCCEEEEeccCCHHHHHHHHHHhCC
Q 015975 13 QTCVLKVNIHCDGCKQKVKKLLQRIEG-VYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGK 72 (397)
Q Consensus 13 ~tv~LkVdM~C~sCa~kIEKAL~kL~G-V~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy 72 (397)
.|+.=+|+=+=..|...+++.|..... -..+.|+..++.|.|.|. ...+|.+.|.+.||
T Consensus 28 ~T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~-~~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 28 ITVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD-HVEEVKKWLLEKGF 87 (87)
T ss_pred EEEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCc-cHHHHHHHHHHCcC
Confidence 344455666667888888888866544 236889999999999987 48889999998886
No 26
>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=31.21 E-value=1.8e+02 Score=23.60 Aligned_cols=45 Identities=20% Similarity=0.232 Sum_probs=32.2
Q ss_pred HHHHHHHHHhccCCeeEEEEecCCCEEEEe-ccCCHHHHHHHHHHhC
Q 015975 26 CKQKVKKLLQRIEGVYQVNIDAEQQKVTVS-GSVDSATLIKKLVRAG 71 (397)
Q Consensus 26 Ca~kIEKAL~kL~GV~sV~VDlatqkVtV~-g~vd~eeIi~aIekaG 71 (397)
=...|+++|..++|+.-...+.. +|+.|+ ...+..++.+.+.++.
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i~ 61 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAIN 61 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHHC
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHHH
Confidence 45678999999999965566666 666665 4556777777776643
No 27
>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=30.61 E-value=1.4e+02 Score=22.44 Aligned_cols=33 Identities=15% Similarity=0.284 Sum_probs=23.6
Q ss_pred eEEEEEEeeccHh-HHHHHHHHHhccCCeeEEEE
Q 015975 13 QTCVLKVNIHCDG-CKQKVKKLLQRIEGVYQVNI 45 (397)
Q Consensus 13 ~tv~LkVdM~C~s-Ca~kIEKAL~kL~GV~sV~V 45 (397)
..+.|.|+..-.. ....|-+.|++++||.+|.+
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 3355555544443 77888999999999998864
No 28
>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=30.47 E-value=51 Score=27.11 Aligned_cols=21 Identities=19% Similarity=0.358 Sum_probs=17.1
Q ss_pred HHHHHHHhccCCeeEEEEecC
Q 015975 28 QKVKKLLQRIEGVYQVNIDAE 48 (397)
Q Consensus 28 ~kIEKAL~kL~GV~sV~VDla 48 (397)
..|+.+|..++|+.+|+|.+.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457888999999999988864
No 29
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=28.45 E-value=16 Score=33.59 Aligned_cols=47 Identities=19% Similarity=0.362 Sum_probs=24.9
Q ss_pred CCCCcceeeeccCcCCCCCccccCCCCCCCCCCCccchHHHhhhhhhchhhhhhhhHH
Q 015975 101 GQKQGLMKGFEPLKNQQKFPTFISEDDDDYFDDDEEDYEDELSFLKANQLGQLGLLRQ 158 (397)
Q Consensus 101 ~~v~GLVR~Vqv~~n~~~~p~~~s~~~~~~~d~d~~d~~~~l~f~g~~~~~~lg~l~~ 158 (397)
+-+.||+.=-+.++.. .++.+.++ ++|||+|+.|+-++.++ |-.|++
T Consensus 7 tg~kgv~~d~~~~~~~-------~~~~~~~d-~~~~~~e~~l~~~R~~R---~~el~~ 53 (175)
T cd02987 7 TGPKGVINDWRKFKQL-------KESEQEDD-DDDEDKEEFLQQYREQR---MQEMHA 53 (175)
T ss_pred CCCchhHHHHHHHHhh-------hchhhhhh-hhhhhHHHHHHHHHHHH---HHHHHH
Confidence 3455666555554444 22222222 23344467899899888 445544
No 30
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=27.26 E-value=1e+02 Score=28.86 Aligned_cols=44 Identities=16% Similarity=0.370 Sum_probs=33.2
Q ss_pred HhHHHHHHHHHhccCCeeEEEEecCCCE-------------------EEEe---ccCCHHHHHHHH
Q 015975 24 DGCKQKVKKLLQRIEGVYQVNIDAEQQK-------------------VTVS---GSVDSATLIKKL 67 (397)
Q Consensus 24 ~sCa~kIEKAL~kL~GV~sV~VDlatqk-------------------VtV~---g~vd~eeIi~aI 67 (397)
.+|-+.+|..+.+++||.++.+-...+. |.|. ..++.++|++..
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f 75 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELF 75 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHH
Confidence 5677778888999999999998776654 4554 247888888754
No 31
>PRK11018 hypothetical protein; Provisional
Probab=27.19 E-value=2e+02 Score=23.00 Aligned_cols=56 Identities=9% Similarity=-0.061 Sum_probs=40.6
Q ss_pred EEEEEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhCCceEEc
Q 015975 15 CVLKVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGKHAELW 77 (397)
Q Consensus 15 v~LkVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy~ael~ 77 (397)
.++.+. +.|+.-.-+.+++|++++.-..+. |.++...+...|...+++.|+++...
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~~L~-------V~~d~~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKGEILE-------VVSDCPQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCCCEEE-------EEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 456666 999999999999999986332222 12234567788999999999987643
No 32
>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=25.78 E-value=23 Score=38.29 Aligned_cols=19 Identities=42% Similarity=0.630 Sum_probs=14.2
Q ss_pred HHhhcCCcccccCCCCCCCC
Q 015975 332 NRHALQQPQMMYHRSPVVPP 351 (397)
Q Consensus 332 ~~~~~~qp~m~y~~~p~~~p 351 (397)
++-||||| |.||++|+-.|
T Consensus 550 Y~P~~PQ~-~~~~PSP~~~P 568 (654)
T COG5180 550 YMPFQPQP-MFYHPSPQMMP 568 (654)
T ss_pred ccCCCCCc-ccccCCCCCCc
Confidence 55566777 89999988754
No 33
>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=25.10 E-value=1.7e+02 Score=22.19 Aligned_cols=52 Identities=17% Similarity=0.209 Sum_probs=35.5
Q ss_pred EEe-eccHhHHHHHHHHHhccCCeeEEEEecCCCEEEEeccCCHHHHHHHHHHhCCceEEc
Q 015975 18 KVN-IHCDGCKQKVKKLLQRIEGVYQVNIDAEQQKVTVSGSVDSATLIKKLVRAGKHAELW 77 (397)
Q Consensus 18 kVd-M~C~sCa~kIEKAL~kL~GV~sV~VDlatqkVtV~g~vd~eeIi~aIekaGy~ael~ 77 (397)
.+. +.|+.-.-+++++| ++..-..+.| .++...+...|...+++.||.+...
T Consensus 3 D~rG~~CP~P~l~~k~al-~~~~g~~l~v-------~~d~~~s~~~i~~~~~~~G~~~~~~ 55 (67)
T cd03421 3 DARGLACPQPVIKTKKAL-ELEAGGEIEV-------LVDNEVAKENVSRFAESRGYEVSVE 55 (67)
T ss_pred ccCCCCCCHHHHHHHHHH-hcCCCCEEEE-------EEcChhHHHHHHHHHHHcCCEEEEE
Confidence 444 88999999999999 5532222211 1233456688999999999988543
No 34
>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=22.74 E-value=3.2e+02 Score=20.22 Aligned_cols=59 Identities=14% Similarity=0.213 Sum_probs=33.9
Q ss_pred EEEe-eccHhHHHHHHHHHhccC-CeeEEEEecC----CCEEEEec-cCCHHHHHHHHHHhCCceE
Q 015975 17 LKVN-IHCDGCKQKVKKLLQRIE-GVYQVNIDAE----QQKVTVSG-SVDSATLIKKLVRAGKHAE 75 (397)
Q Consensus 17 LkVd-M~C~sCa~kIEKAL~kL~-GV~sV~VDla----tqkVtV~g-~vd~eeIi~aIekaGy~ae 75 (397)
+.|. -+.++...+|.+.|.+.. .|.++..... ...+.|.- ..+.+.+++.|++.||++.
T Consensus 4 ~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v~ 69 (72)
T cd04883 4 IEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEVL 69 (72)
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCeee
Confidence 4444 334456667777776552 2344433332 22244442 2467799999999999764
No 35
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=20.48 E-value=4.3e+02 Score=20.82 Aligned_cols=60 Identities=22% Similarity=0.366 Sum_probs=41.0
Q ss_pred EEEEEeeccHhHHHHHHHHHhcc----CCeeEEEEecCCCEEEEe--ccCCHHHHHHHHHHh-CCceE
Q 015975 15 CVLKVNIHCDGCKQKVKKLLQRI----EGVYQVNIDAEQQKVTVS--GSVDSATLIKKLVRA-GKHAE 75 (397)
Q Consensus 15 v~LkVdM~C~sCa~kIEKAL~kL----~GV~sV~VDlatqkVtV~--g~vd~eeIi~aIeka-Gy~ae 75 (397)
+.+.|.-.=..=..++..+|.++ |.+ .+..|..++.+.|. |.+..+.+++.|++. |.+++
T Consensus 6 ~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l-~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 6 LSVAIEPKNKEDEPKLSEALQKLSEEDPSL-RVERDEETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHH-TTS-EEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred EEEEEEECCHhHHHHHHHHHHHHHhcCCeE-EEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 34455433345556666666655 555 68899999999887 578999999999864 54443
No 36
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=20.18 E-value=2.9e+02 Score=21.28 Aligned_cols=33 Identities=21% Similarity=0.271 Sum_probs=23.9
Q ss_pred eeEEEEEEeeccHhHHHHHHHHHhccCCeeEEE
Q 015975 12 IQTCVLKVNIHCDGCKQKVKKLLQRIEGVYQVN 44 (397)
Q Consensus 12 ~~tv~LkVdM~C~sCa~kIEKAL~kL~GV~sV~ 44 (397)
...+.|.|+..-..=...|-+.|++++||.+|.
T Consensus 47 ~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 47 TARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 445666676555556667778899999998774
Done!