Query 046169
Match_columns 253
No_of_seqs 222 out of 1301
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:22:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046169.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046169hhsearch_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 2.7E-11 5.8E-16 85.9 8.0 59 11-69 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.1 4.5E-10 9.8E-15 82.9 9.2 66 8-73 2-70 (71)
3 KOG1603 Copper chaperone [Inor 98.7 6.7E-08 1.5E-12 71.5 8.3 67 7-74 4-71 (73)
4 KOG4656 Copper chaperone for s 98.4 1E-06 2.3E-11 77.6 9.0 76 1-78 1-76 (247)
5 PLN02957 copper, zinc superoxi 97.9 6.3E-05 1.4E-09 67.6 9.9 70 8-78 6-75 (238)
6 PRK10671 copA copper exporting 97.9 2.8E-05 6E-10 80.9 7.9 65 8-74 3-67 (834)
7 COG2217 ZntA Cation transport 97.8 6.9E-05 1.5E-09 77.0 7.9 63 9-72 3-69 (713)
8 TIGR00003 copper ion binding p 97.7 0.00036 7.8E-09 45.5 8.5 62 9-70 3-67 (68)
9 KOG0207 Cation transport ATPas 97.1 0.0013 2.9E-08 68.6 7.2 67 8-74 146-215 (951)
10 PRK10671 copA copper exporting 96.7 0.0054 1.2E-07 64.0 8.4 64 9-72 100-163 (834)
11 KOG0207 Cation transport ATPas 96.6 0.0046 9.9E-08 64.7 7.0 69 9-77 70-141 (951)
12 PRK11033 zntA zinc/cadmium/mer 96.2 0.016 3.4E-07 60.1 7.9 63 8-71 53-117 (741)
13 TIGR02052 MerP mercuric transp 92.6 1.6 3.6E-05 30.9 9.0 64 9-72 24-90 (92)
14 cd00371 HMA Heavy-metal-associ 86.6 4.3 9.3E-05 23.2 7.0 57 12-68 2-60 (63)
15 COG1888 Uncharacterized protei 86.5 4.8 0.0001 31.5 7.5 69 6-74 4-80 (97)
16 PRK13748 putative mercuric red 84.1 6.1 0.00013 39.1 9.0 66 11-76 3-70 (561)
17 PF02680 DUF211: Uncharacteriz 82.8 4 8.7E-05 32.1 5.6 67 7-74 4-78 (95)
18 PF01206 TusA: Sulfurtransfera 72.0 17 0.00037 25.8 6.0 54 11-73 2-57 (70)
19 cd03421 SirA_like_N SirA_like_ 46.2 74 0.0016 22.3 5.5 52 12-73 2-55 (67)
20 PRK11018 hypothetical protein; 46.2 1.1E+02 0.0024 22.5 6.6 56 9-73 8-65 (78)
21 PF13732 DUF4162: Domain of un 43.6 77 0.0017 22.8 5.5 47 30-77 26-73 (84)
22 PRK14054 methionine sulfoxide 43.2 54 0.0012 28.3 5.1 46 20-65 10-77 (172)
23 PF01883 DUF59: Domain of unkn 38.0 59 0.0013 23.1 4.0 19 23-41 54-72 (72)
24 PF05046 Img2: Mitochondrial l 38.0 1.8E+02 0.0039 22.1 7.0 59 8-68 28-87 (87)
25 PF08777 RRM_3: RNA binding mo 37.1 1.2E+02 0.0027 23.7 5.9 56 11-66 3-60 (105)
26 PRK10553 assembly protein for 36.0 1.2E+02 0.0026 23.2 5.6 44 21-64 17-61 (87)
27 PF14437 MafB19-deam: MafB19-l 34.8 92 0.002 26.3 5.1 42 8-50 100-142 (146)
28 PF03927 NapD: NapD protein; 30.6 1.7E+02 0.0037 21.7 5.5 42 23-65 17-59 (79)
29 PRK05528 methionine sulfoxide 29.9 1.3E+02 0.0029 25.5 5.3 46 20-65 8-70 (156)
30 PRK00058 methionine sulfoxide 26.8 1.1E+02 0.0024 27.4 4.5 46 20-65 52-119 (213)
31 KOG4661 Hsp27-ERE-TATA-binding 26.7 2.7E+02 0.0058 29.1 7.5 67 11-77 407-481 (940)
32 PRK13014 methionine sulfoxide 26.2 1E+02 0.0023 26.9 4.2 46 20-65 15-82 (186)
33 cd03420 SirA_RHOD_Pry_redox Si 23.5 2.8E+02 0.006 19.7 5.8 53 12-73 2-56 (69)
34 cd04906 ACT_ThrD-I_1 First of 23.3 3.1E+02 0.0066 20.1 7.0 64 12-76 4-75 (85)
35 PF09580 Spore_YhcN_YlaJ: Spor 23.0 2E+02 0.0044 23.9 5.3 32 20-51 74-105 (177)
36 cd04908 ACT_Bt0572_1 N-termina 20.1 3E+02 0.0065 18.8 7.6 61 9-71 3-65 (66)
37 cd08032 LARP_7 La RNA-binding 20.0 34 0.00073 26.1 -0.1 10 238-247 13-22 (82)
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=99.26 E-value=2.7e-11 Score=85.90 Aligned_cols=59 Identities=32% Similarity=0.499 Sum_probs=54.7
Q ss_pred EEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecCC---CCHHHHHHHHHHcCCc
Q 046169 11 ELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATGN---VDPKVLIKKLLKAGKQ 69 (253)
Q Consensus 11 ~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g~---~d~~~I~~aL~kaGy~ 69 (253)
+|+|.+|+|.+|+.+|+++|.+++||.++.+|+.+++++|... +++++|.++|+++||+
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 5899999999999999999999999999999999999999843 5679999999999984
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.12 E-value=4.5e-10 Score=82.94 Aligned_cols=66 Identities=32% Similarity=0.457 Sum_probs=59.1
Q ss_pred eEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--C-CCCHHHHHHHHHHcCCceEEc
Q 046169 8 KKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--G-NVDPKVLIKKLLKAGKQAELW 73 (253)
Q Consensus 8 ~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g-~~d~~~I~~aL~kaGy~a~i~ 73 (253)
.+..|+|.+|+|.+|+..|+++|..++||.++.+|+..+++.|. + .++.++|+.+|..+||.+..+
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 45789999999999999999999999999999999999666665 4 589999999999999987654
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.73 E-value=6.7e-08 Score=71.55 Aligned_cols=67 Identities=51% Similarity=0.861 Sum_probs=60.4
Q ss_pred ceEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecCCCCHHHHHHHHHHcC-CceEEcC
Q 046169 7 TKKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATGNVDPKVLIKKLLKAG-KQAELWD 74 (253)
Q Consensus 7 ~~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g~~d~~~I~~aL~kaG-y~a~i~~ 74 (253)
++..++.+++ ||.+|..+|++.|..+.||.++.+|...++++|.+.+++..|++.|.+.| ..+.+|.
T Consensus 4 ~~~~v~kv~~-~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 4 IKTVVLKVNM-HCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred ccEEEEEECc-ccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 4567788887 99999999999999999999999999999999999999999999999977 6666653
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.44 E-value=1e-06 Score=77.60 Aligned_cols=76 Identities=32% Similarity=0.534 Sum_probs=69.2
Q ss_pred CCCcCCceEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecCCCCHHHHHHHHHHcCCceEEcCCCCc
Q 046169 1 MAKEADTKKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATGNVDPKVLIKKLLKAGKQAELWDNGNQ 78 (253)
Q Consensus 1 Ma~~~~~~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g~~d~~~I~~aL~kaGy~a~i~~~~~~ 78 (253)
|+.. ..-+++|.|+| +|++|+..|+..|..++||.++++|+..+.|.|.+...+..|...|+.+|.++.+...+.+
T Consensus 1 mtSd-~~~~~efaV~M-~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~p 76 (247)
T KOG4656|consen 1 MTSD-DTYEAEFAVQM-TCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKP 76 (247)
T ss_pred CCcC-CceeEEEEEec-hhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCch
Confidence 5554 34568899998 9999999999999999999999999999999999999999999999999999999987765
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=97.94 E-value=6.3e-05 Score=67.55 Aligned_cols=70 Identities=30% Similarity=0.456 Sum_probs=61.9
Q ss_pred eEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecCCCCHHHHHHHHHHcCCceEEcCCCCc
Q 046169 8 KKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATGNVDPKVLIKKLLKAGKQAELWDNGNQ 78 (253)
Q Consensus 8 ~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g~~d~~~I~~aL~kaGy~a~i~~~~~~ 78 (253)
.++.|.+ +|+|..|+.+|++.|.+++||..+.+++...+++|........|...|+++||.++++....+
T Consensus 6 ~~~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~ 75 (238)
T PLN02957 6 LLTEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDP 75 (238)
T ss_pred EEEEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCc
Confidence 3567888 689999999999999999999999999999999998667888899999999999988876553
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.91 E-value=2.8e-05 Score=80.87 Aligned_cols=65 Identities=23% Similarity=0.390 Sum_probs=57.7
Q ss_pred eEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecCCCCHHHHHHHHHHcCCceEEcC
Q 046169 8 KKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATGNVDPKVLIKKLLKAGKQAELWD 74 (253)
Q Consensus 8 ~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g~~d~~~I~~aL~kaGy~a~i~~ 74 (253)
.+++|.|+||+|.+|+.+|+++|.+++||..+.+|+. +.+|....+.+.|.+.|+++||.+.+..
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 3688999999999999999999999999999999994 5556666788999999999999998764
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.76 E-value=6.9e-05 Score=76.99 Aligned_cols=63 Identities=27% Similarity=0.423 Sum_probs=56.9
Q ss_pred EEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecC---CCC-HHHHHHHHHHcCCceEE
Q 046169 9 KIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATG---NVD-PKVLIKKLLKAGKQAEL 72 (253)
Q Consensus 9 ~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g---~~d-~~~I~~aL~kaGy~a~i 72 (253)
+..|.|.||+|.+|+++|+ +|.+++||..+.+|+.+.++.|.. ..+ .+.+...++..||.+..
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 5789999999999999999 999999999999999999999872 345 78999999999998766
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=97.73 E-value=0.00036 Score=45.47 Aligned_cols=62 Identities=23% Similarity=0.402 Sum_probs=51.9
Q ss_pred EEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecC---CCCHHHHHHHHHHcCCce
Q 046169 9 KIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATG---NVDPKVLIKKLLKAGKQA 70 (253)
Q Consensus 9 ~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g---~~d~~~I~~aL~kaGy~a 70 (253)
+..+.|.+++|..|...|++.+..+.++..+.+++....+.|.. ..+...+...+...||.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 46799999999999999999999999999999999999888762 346677777777777753
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.07 E-value=0.0013 Score=68.57 Aligned_cols=67 Identities=22% Similarity=0.367 Sum_probs=61.7
Q ss_pred eEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec---CCCCHHHHHHHHHHcCCceEEcC
Q 046169 8 KKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT---GNVDPKVLIKKLLKAGKQAELWD 74 (253)
Q Consensus 8 ~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~---g~~d~~~I~~aL~kaGy~a~i~~ 74 (253)
.++.|.|.||.|.+|+.+|+..|.+++||.++++++.++++.|. ..+.+.+|++.|+.+|+.+.+..
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 57899999999999999999999999999999999999999987 34789999999999999877665
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.71 E-value=0.0054 Score=64.02 Aligned_cols=64 Identities=27% Similarity=0.430 Sum_probs=56.7
Q ss_pred EEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecCCCCHHHHHHHHHHcCCceEE
Q 046169 9 KIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATGNVDPKVLIKKLLKAGKQAEL 72 (253)
Q Consensus 9 ~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g~~d~~~I~~aL~kaGy~a~i 72 (253)
++.+.|.||+|.+|+..|++.|..++||.++.+++.+.++.|....+...+...+.+.||.+.+
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~ 163 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEA 163 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccc
Confidence 5678999999999999999999999999999999999998887556778888888899997643
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.63 E-value=0.0046 Score=64.69 Aligned_cols=69 Identities=25% Similarity=0.338 Sum_probs=61.9
Q ss_pred EEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec---CCCCHHHHHHHHHHcCCceEEcCCCC
Q 046169 9 KIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT---GNVDPKVLIKKLLKAGKQAELWDNGN 77 (253)
Q Consensus 9 ~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~---g~~d~~~I~~aL~kaGy~a~i~~~~~ 77 (253)
+-.|+|+||+|.+|...|++.|+.++||.++.+.+...+..|. ..+..+.+.+.+++.||.+.++....
T Consensus 70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~ 141 (951)
T KOG0207|consen 70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVN 141 (951)
T ss_pred eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhccc
Confidence 5579999999999999999999999999999999999999986 34789999999999999998876443
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.18 E-value=0.016 Score=60.07 Aligned_cols=63 Identities=22% Similarity=0.342 Sum_probs=52.9
Q ss_pred eEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--CCCCHHHHHHHHHHcCCceE
Q 046169 8 KKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--GNVDPKVLIKKLLKAGKQAE 71 (253)
Q Consensus 8 ~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g~~d~~~I~~aL~kaGy~a~ 71 (253)
.++.+.|.+|+|.+|+.+|++.|..++||..+.+++.+.++.|. .... ..+...+...||.+.
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~-~~I~~aI~~~Gy~a~ 117 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIR-AQVESAVQKAGFSLR 117 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccch-HHHHHHHHhcccccc
Confidence 46678999999999999999999999999999999999998876 2223 667777888888654
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=92.59 E-value=1.6 Score=30.93 Aligned_cols=64 Identities=28% Similarity=0.346 Sum_probs=48.7
Q ss_pred EEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--C-CCCHHHHHHHHHHcCCceEE
Q 046169 9 KIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--G-NVDPKVLIKKLLKAGKQAEL 72 (253)
Q Consensus 9 ~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g-~~d~~~I~~aL~kaGy~a~i 72 (253)
++.+.+.++.|..|...++..+....++....+++....+.+. . ..+...+...+...|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 4567899999999999999999999998888888877776654 2 24555565666677776543
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=86.63 E-value=4.3 Score=23.22 Aligned_cols=57 Identities=35% Similarity=0.511 Sum_probs=38.6
Q ss_pred EEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEecCC--CCHHHHHHHHHHcCC
Q 046169 12 LRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTATGN--VDPKVLIKKLLKAGK 68 (253)
Q Consensus 12 lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~g~--~d~~~I~~aL~kaGy 68 (253)
+.+.++.|..|...++..+....++....+++....+.+... .+...+...+...++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (63)
T cd00371 2 LSVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGY 60 (63)
T ss_pred eeECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCC
Confidence 346778899999999999989999887777777666555421 244444444444443
No 15
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=86.52 E-value=4.8 Score=31.52 Aligned_cols=69 Identities=19% Similarity=0.202 Sum_probs=48.0
Q ss_pred CceEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeC-------CCCeEEecCC-CCHHHHHHHHHHcCCceEEcC
Q 046169 6 DTKKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDP-------LQPKVTATGN-VDPKVLIKKLLKAGKQAELWD 74 (253)
Q Consensus 6 ~~~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~-------~t~kVtV~g~-~d~~~I~~aL~kaGy~a~i~~ 74 (253)
...+++|.+--.+-.--...+.+.|.+++||..+++.. .+-+++|.|. ++.++|.+.|++.|-.++.++
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 35566676655454444556677888998877665433 3445566654 999999999999998877654
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=84.11 E-value=6.1 Score=39.08 Aligned_cols=66 Identities=26% Similarity=0.361 Sum_probs=51.6
Q ss_pred EEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--CCCCHHHHHHHHHHcCCceEEcCCC
Q 046169 11 ELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--GNVDPKVLIKKLLKAGKQAELWDNG 76 (253)
Q Consensus 11 ~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g~~d~~~I~~aL~kaGy~a~i~~~~ 76 (253)
.+.+.+++|.+|..+++..+..+.++....+++....+.+. ...+...+...+...|+.......+
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~~ 70 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADAP 70 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCcc
Confidence 46789999999999999999999999999999888876665 2245566666677788776666553
No 17
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=82.78 E-value=4 Score=32.09 Aligned_cols=67 Identities=19% Similarity=0.236 Sum_probs=44.9
Q ss_pred ceEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeC-----CCCeEE--ecCC-CCHHHHHHHHHHcCCceEEcC
Q 046169 7 TKKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDP-----LQPKVT--ATGN-VDPKVLIKKLLKAGKQAELWD 74 (253)
Q Consensus 7 ~~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~-----~t~kVt--V~g~-~d~~~I~~aL~kaGy~a~i~~ 74 (253)
+.+++|.|--.|-++ .-.+.+.|..++||..+++.. .+..+. |.|. ++.+.|.++|++.|-.++.++
T Consensus 4 irRlVLDVlKP~~p~-i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSID 78 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPS-IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSID 78 (95)
T ss_dssp EEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEEE
T ss_pred eeEEEEEeecCCCCC-HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEeee
Confidence 566777665543333 346778899999998777543 444443 4454 999999999999998777654
No 18
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=72.03 E-value=17 Score=25.75 Aligned_cols=54 Identities=15% Similarity=-0.003 Sum_probs=39.6
Q ss_pred EEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--CCCCHHHHHHHHHHcCCceEEc
Q 046169 11 ELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--GNVDPKVLIKKLLKAGKQAELW 73 (253)
Q Consensus 11 ~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g~~d~~~I~~aL~kaGy~a~i~ 73 (253)
+|.+.|+.|+....++.++|..++.- +.+.|. ......+|...+...|+.+..+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 57889999999999999999998432 223332 3456788999999999975544
No 19
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=46.21 E-value=74 Score=22.28 Aligned_cols=52 Identities=17% Similarity=0.127 Sum_probs=36.9
Q ss_pred EEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--CCCCHHHHHHHHHHcCCceEEc
Q 046169 12 LRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--GNVDPKVLIKKLLKAGKQAELW 73 (253)
Q Consensus 12 lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g~~d~~~I~~aL~kaGy~a~i~ 73 (253)
|.+.|+.|+.=..+++++| .+.. .+.+.|. .......|...+++.||.+...
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~ 55 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSVE 55 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEEE
Confidence 5678899999999999999 6532 1223332 3355678888899999988543
No 20
>PRK11018 hypothetical protein; Provisional
Probab=46.19 E-value=1.1e+02 Score=22.49 Aligned_cols=56 Identities=9% Similarity=-0.082 Sum_probs=41.7
Q ss_pred EEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--CCCCHHHHHHHHHHcCCceEEc
Q 046169 9 KIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--GNVDPKVLIKKLLKAGKQAELW 73 (253)
Q Consensus 9 ~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g~~d~~~I~~aL~kaGy~a~i~ 73 (253)
..+|.+.|+.|+.=..+.+++|.++..- +.+.|. .......|...++..|+.+...
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 3678999999999999999999998532 222332 3356678888888999987543
No 21
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=43.60 E-value=77 Score=22.85 Aligned_cols=47 Identities=17% Similarity=0.300 Sum_probs=33.4
Q ss_pred HhCCCCeeEEEEeCCC-CeEEecCCCCHHHHHHHHHHcCCceEEcCCCC
Q 046169 30 LRGVEGVLKIEIDPLQ-PKVTATGNVDPKVLIKKLLKAGKQAELWDNGN 77 (253)
Q Consensus 30 L~kl~GV~sv~Vd~~t-~kVtV~g~~d~~~I~~aL~kaGy~a~i~~~~~ 77 (253)
|..++||..+..+-.. -++.|....+..+|+..|...|. +.-+....
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~~~~ 73 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI-IRSFEEEE 73 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC-eeEEEEcC
Confidence 7888999998864322 34445555778899999999998 66554433
No 22
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=43.17 E-value=54 Score=28.32 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=35.2
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeCCCCe-------------------EEec---CCCCHHHHHHHHHH
Q 046169 20 DGCKRKVKKALRGVEGVLKIEIDPLQPK-------------------VTAT---GNVDPKVLIKKLLK 65 (253)
Q Consensus 20 ~~Ca~kIekaL~kl~GV~sv~Vd~~t~k-------------------VtV~---g~~d~~~I~~aL~k 65 (253)
.+|-|-++..+.+++||.++.+-...+. |.|. ..++.++|+...-+
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~ 77 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQ 77 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHH
Confidence 4788999999999999999998876664 4444 34777888776643
No 23
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=38.01 E-value=59 Score=23.05 Aligned_cols=19 Identities=21% Similarity=0.660 Sum_probs=15.2
Q ss_pred HHHHHHHHhCCCCeeEEEE
Q 046169 23 KRKVKKALRGVEGVLKIEI 41 (253)
Q Consensus 23 a~kIekaL~kl~GV~sv~V 41 (253)
...|+.+|..++||.+++|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 5778899999999998875
No 24
>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=38.00 E-value=1.8e+02 Score=22.07 Aligned_cols=59 Identities=15% Similarity=0.149 Sum_probs=44.6
Q ss_pred eEEEEEecCCCchhHHHHHHHHHhCCCC-eeEEEEeCCCCeEEecCCCCHHHHHHHHHHcCC
Q 046169 8 KKIELRVFVNCCDGCKRKVKKALRGVEG-VLKIEIDPLQPKVTATGNVDPKVLIKKLLKAGK 68 (253)
Q Consensus 8 ~~v~lkV~GM~C~~Ca~kIekaL~kl~G-V~sv~Vd~~t~kVtV~g~~d~~~I~~aL~kaGy 68 (253)
.|+.=+|+| +=..+...+...|..... -..+.|+..++.|.|.|.. ..+|.+-|...||
T Consensus 28 ~T~IrkI~G-D~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 28 ITVIRKIEG-DIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLLEKGF 87 (87)
T ss_pred EEEEEeecC-CHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHHHCcC
Confidence 455568999 778888888888865543 3467788999999999874 6677777777776
No 25
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=37.09 E-value=1.2e+02 Score=23.70 Aligned_cols=56 Identities=13% Similarity=0.047 Sum_probs=34.5
Q ss_pred EEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--CCCCHHHHHHHHHHc
Q 046169 11 ELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--GNVDPKVLIKKLLKA 66 (253)
Q Consensus 11 ~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g~~d~~~I~~aL~ka 66 (253)
+|+|.|++=..+...|+..|.....|..|.+........|. ....+..++..+...
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 56777766666689999999999999999888877777776 445577788887765
No 26
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=36.02 E-value=1.2e+02 Score=23.23 Aligned_cols=44 Identities=11% Similarity=0.124 Sum_probs=31.4
Q ss_pred hHHHHHHHHHhCCCCeeEEEEeCCCCeEEec-CCCCHHHHHHHHH
Q 046169 21 GCKRKVKKALRGVEGVLKIEIDPLQPKVTAT-GNVDPKVLIKKLL 64 (253)
Q Consensus 21 ~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~-g~~d~~~I~~aL~ 64 (253)
.=...+.+.|..++|+.-.-.|...+++.|+ ...+...+.+.|.
T Consensus 17 e~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 17 ERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 3367889999999999888787778888876 3344554544444
No 27
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=34.82 E-value=92 Score=26.35 Aligned_cols=42 Identities=17% Similarity=0.290 Sum_probs=32.1
Q ss_pred eEEEEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCC-CCeEEe
Q 046169 8 KKIELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPL-QPKVTA 50 (253)
Q Consensus 8 ~~v~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~-t~kVtV 50 (253)
..+++.|+--.|..|..-|.....++ |+.++.|... ++++.+
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVYY 142 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEEE
Confidence 35778888878999999998887776 8887777665 665544
No 28
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=30.58 E-value=1.7e+02 Score=21.69 Aligned_cols=42 Identities=19% Similarity=0.167 Sum_probs=30.5
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCeEEec-CCCCHHHHHHHHHH
Q 046169 23 KRKVKKALRGVEGVLKIEIDPLQPKVTAT-GNVDPKVLIKKLLK 65 (253)
Q Consensus 23 a~kIekaL~kl~GV~sv~Vd~~t~kVtV~-g~~d~~~I~~aL~k 65 (253)
...+.+.|..++|+.-...+.. +++.|. ...+...+.+.|..
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHH
Confidence 5678899999999977677766 777776 33566666666654
No 29
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=29.86 E-value=1.3e+02 Score=25.52 Aligned_cols=46 Identities=22% Similarity=0.331 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeCCCCe--------------EEec---CCCCHHHHHHHHHH
Q 046169 20 DGCKRKVKKALRGVEGVLKIEIDPLQPK--------------VTAT---GNVDPKVLIKKLLK 65 (253)
Q Consensus 20 ~~Ca~kIekaL~kl~GV~sv~Vd~~t~k--------------VtV~---g~~d~~~I~~aL~k 65 (253)
.+|-|-++..+.+++||.++.+-...+. |.|. ..++.++|+...-+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 4788999999999999999998775533 3333 34677777776644
No 30
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=26.79 E-value=1.1e+02 Score=27.42 Aligned_cols=46 Identities=13% Similarity=0.199 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeCCCCe-------------------EEec---CCCCHHHHHHHHHH
Q 046169 20 DGCKRKVKKALRGVEGVLKIEIDPLQPK-------------------VTAT---GNVDPKVLIKKLLK 65 (253)
Q Consensus 20 ~~Ca~kIekaL~kl~GV~sv~Vd~~t~k-------------------VtV~---g~~d~~~I~~aL~k 65 (253)
.+|-|-++..+.+++||.++.+-+..+. |.|. ..++.++|+...-+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~ 119 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWE 119 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHH
Confidence 5788999999999999999999887442 3443 34777888776643
No 31
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=26.66 E-value=2.7e+02 Score=29.05 Aligned_cols=67 Identities=12% Similarity=0.054 Sum_probs=45.5
Q ss_pred EEEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCC--------eEEecCCCCHHHHHHHHHHcCCceEEcCCCC
Q 046169 11 ELRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQP--------KVTATGNVDPKVLIKKLLKAGKQAELWDNGN 77 (253)
Q Consensus 11 ~lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~--------kVtV~g~~d~~~I~~aL~kaGy~a~i~~~~~ 77 (253)
.|-|.||.-..=+..++.++++..-|.-+.|-..+. -||......+...+..|.++-..-.+++++.
T Consensus 407 NlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk 481 (940)
T KOG4661|consen 407 NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK 481 (940)
T ss_pred ceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence 578999998888999999999987776555533221 1222233455667778888777777776654
No 32
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=26.23 E-value=1e+02 Score=26.93 Aligned_cols=46 Identities=22% Similarity=0.290 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeCCCCe-------------------EEec---CCCCHHHHHHHHHH
Q 046169 20 DGCKRKVKKALRGVEGVLKIEIDPLQPK-------------------VTAT---GNVDPKVLIKKLLK 65 (253)
Q Consensus 20 ~~Ca~kIekaL~kl~GV~sv~Vd~~t~k-------------------VtV~---g~~d~~~I~~aL~k 65 (253)
.+|-|-++..+.+++||.++.+-...+. |.|. ..++.++|+...-+
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~ 82 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFS 82 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHH
Confidence 4788888999999999999998776654 3343 33677777776643
No 33
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=23.48 E-value=2.8e+02 Score=19.67 Aligned_cols=53 Identities=11% Similarity=0.020 Sum_probs=39.1
Q ss_pred EEecCCCchhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec--CCCCHHHHHHHHHHcCCceEEc
Q 046169 12 LRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT--GNVDPKVLIKKLLKAGKQAELW 73 (253)
Q Consensus 12 lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~--g~~d~~~I~~aL~kaGy~a~i~ 73 (253)
|.+.|+.|+.=..+++++|.++.. .+.+.|. ......+|....+..|+.....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCKSTGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 567888999999999999999852 2223333 3356778888889999987644
No 34
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.31 E-value=3.1e+02 Score=20.12 Aligned_cols=64 Identities=13% Similarity=0.113 Sum_probs=39.0
Q ss_pred EEecCCCchhHHHHHHHHHhCCCCeeEEEEeCC---CCeEEec----C-CCCHHHHHHHHHHcCCceEEcCCC
Q 046169 12 LRVFVNCCDGCKRKVKKALRGVEGVLKIEIDPL---QPKVTAT----G-NVDPKVLIKKLLKAGKQAELWDNG 76 (253)
Q Consensus 12 lkV~GM~C~~Ca~kIekaL~kl~GV~sv~Vd~~---t~kVtV~----g-~~d~~~I~~aL~kaGy~a~i~~~~ 76 (253)
|.|...+=++=-.++-.+|. -.+|..+..+.. ...+.|. + ..+.+.++..|++.||.+......
T Consensus 4 l~v~ipD~PG~L~~ll~~l~-~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~~~~~ 75 (85)
T cd04906 4 LAVTIPERPGSFKKFCELIG-PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVDLSDD 75 (85)
T ss_pred EEEecCCCCcHHHHHHHHhC-CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEECCCC
Confidence 44444444555556666666 346666666552 3334432 2 344778999999999998876544
No 35
>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=23.00 E-value=2e+02 Score=23.92 Aligned_cols=32 Identities=9% Similarity=0.142 Sum_probs=27.4
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeCCCCeEEec
Q 046169 20 DGCKRKVKKALRGVEGVLKIEIDPLQPKVTAT 51 (253)
Q Consensus 20 ~~Ca~kIekaL~kl~GV~sv~Vd~~t~kVtV~ 51 (253)
..=+..|...+.+++||..+.+-.....+.|-
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 34578899999999999999998888888774
No 36
>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=20.11 E-value=3e+02 Score=18.82 Aligned_cols=61 Identities=15% Similarity=0.059 Sum_probs=36.5
Q ss_pred EEEEEecCCCchhHHHHHHHHHhCCC-CeeEEEEeCCCCeEEec-CCCCHHHHHHHHHHcCCceE
Q 046169 9 KIELRVFVNCCDGCKRKVKKALRGVE-GVLKIEIDPLQPKVTAT-GNVDPKVLIKKLLKAGKQAE 71 (253)
Q Consensus 9 ~v~lkV~GM~C~~Ca~kIekaL~kl~-GV~sv~Vd~~t~kVtV~-g~~d~~~I~~aL~kaGy~a~ 71 (253)
++.+.++. -.+=-.+|-..|.+.. .|.++.+....++..+. ...+.+.+.+.|++.||.+.
T Consensus 3 ri~v~v~d--~pG~La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 3 QLSVFLEN--KPGRLAAVTEILSEAGINIRALSIADTSEFGILRLIVSDPDKAKEALKEAGFAVK 65 (66)
T ss_pred EEEEEEcC--CCChHHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEECCHHHHHHHHHHCCCEEE
Confidence 44444444 5556667777775553 34555554433344433 22567789999999999864
No 37
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=20.04 E-value=34 Score=26.10 Aligned_cols=10 Identities=40% Similarity=0.527 Sum_probs=7.5
Q ss_pred ccccccCCCC
Q 046169 238 VGDYFSDENT 247 (253)
Q Consensus 238 ~~~~f~~~n~ 247 (253)
++=||||+|=
T Consensus 13 vEfYFSd~NL 22 (82)
T cd08032 13 VDFWFGDVNL 22 (82)
T ss_pred HHhhcchhhc
Confidence 4559999984
Done!