Query 045648
Match_columns 142
No_of_seqs 152 out of 453
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 04:03:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045648.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045648hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.1 1.5E-10 3.3E-15 79.0 5.5 64 7-84 6-70 (73)
2 PF00403 HMA: Heavy-metal-asso 98.0 5E-06 1.1E-10 53.5 3.0 52 13-78 6-60 (62)
3 KOG4656 Copper chaperone for s 94.9 0.039 8.4E-07 46.9 4.4 62 11-86 12-74 (247)
4 COG2608 CopZ Copper chaperone 93.6 0.14 3E-06 34.7 4.2 56 12-78 6-64 (71)
5 PLN02957 copper, zinc superoxi 93.1 0.2 4.4E-06 41.0 5.1 63 13-89 13-76 (238)
6 PRK10671 copA copper exporting 77.9 2.1 4.6E-05 40.6 3.2 61 11-84 6-67 (834)
7 PF09846 DUF2073: Uncharacteri 44.7 33 0.00072 26.1 3.5 41 33-76 48-94 (104)
8 PF02680 DUF211: Uncharacteriz 40.6 40 0.00087 25.2 3.4 42 30-78 24-71 (95)
9 KOG2872 Uroporphyrinogen decar 38.9 18 0.00039 32.5 1.5 33 36-71 271-307 (359)
10 COG1888 Uncharacterized protei 36.0 47 0.001 25.1 3.1 42 30-78 26-73 (97)
11 TIGR00156 conserved hypothetic 34.6 73 0.0016 24.7 4.1 35 32-66 77-111 (126)
12 COG2217 ZntA Cation transport 32.2 53 0.0011 31.8 3.6 60 11-82 5-69 (713)
13 PF04076 BOF: Bacterial OB fol 30.6 86 0.0019 23.2 3.8 36 31-66 53-88 (103)
14 PF07744 SPOC: SPOC domain; I 30.1 96 0.0021 21.7 3.9 32 56-87 38-72 (119)
15 PF05193 Peptidase_M16_C: Pept 29.9 59 0.0013 22.7 2.7 21 57-77 20-40 (184)
16 PF03927 NapD: NapD protein; 29.6 19 0.00041 25.1 0.1 33 10-43 39-71 (79)
17 PF02107 FlgH: Flagellar L-rin 26.6 60 0.0013 25.8 2.5 44 34-86 110-157 (179)
18 PF14485 DUF4431: Domain of un 25.9 51 0.0011 21.3 1.7 23 43-65 6-28 (48)
19 PF05359 DUF748: Domain of Unk 24.0 57 0.0012 23.7 1.8 65 4-69 7-72 (151)
20 KOG0582 Ste20-like serine/thre 22.1 27 0.00059 32.9 -0.3 27 60-86 189-219 (516)
21 cd02958 UAS UAS family; UAS is 21.9 86 0.0019 21.9 2.3 24 55-78 87-111 (114)
22 PRK10671 copA copper exporting 21.2 95 0.0021 29.7 3.1 59 12-81 103-162 (834)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.10 E-value=1.5e-10 Score=78.95 Aligned_cols=64 Identities=20% Similarity=0.311 Sum_probs=56.3
Q ss_pred eeeeeeeeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEEEeecHHHHHHHHHhhc-ceEEEE
Q 045648 7 VIDGTLKFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVDPVNVMSKWRKYW-PADIIL 84 (142)
Q Consensus 7 ~~~~~l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vDpv~vv~klRK~~-~A~Ivs 84 (142)
..-.++.|.|+.|..++. +.+.++.||.++.+|.++ +++||.|++||..|+.+|+|.+ .+..+.
T Consensus 6 ~~v~kv~~~C~gc~~kV~-----~~l~~~~GV~~v~id~~~---------~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 6 TVVLKVNMHCEGCARKVK-----RVLQKLKGVESVDIDIKK---------QKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred EEEEEECcccccHHHHHH-----HHhhccCCeEEEEecCCC---------CEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 344578899999999887 999999999999999999 9999999999999999999977 444433
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=98.01 E-value=5e-06 Score=53.46 Aligned_cols=52 Identities=15% Similarity=0.092 Sum_probs=45.6
Q ss_pred eeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEEEeec---HHHHHHHHHhhc
Q 045648 13 KFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVD---PVNVMSKWRKYW 78 (142)
Q Consensus 13 ~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vD---pv~vv~klRK~~ 78 (142)
.|+|..|.++.- ++|..++||.++.+|... ++++|.++-+ +..|.+.|++.|
T Consensus 6 ~m~C~~C~~~v~-----~~l~~~~GV~~v~vd~~~---------~~v~v~~~~~~~~~~~i~~~i~~~G 60 (62)
T PF00403_consen 6 GMTCEGCAKKVE-----KALSKLPGVKSVKVDLET---------KTVTVTYDPDKTSIEKIIEAIEKAG 60 (62)
T ss_dssp STTSHHHHHHHH-----HHHHTSTTEEEEEEETTT---------TEEEEEESTTTSCHHHHHHHHHHTT
T ss_pred CcccHHHHHHHH-----HHHhcCCCCcEEEEECCC---------CEEEEEEecCCCCHHHHHHHHHHhC
Confidence 477888888776 999999999999999999 9999999854 599999999865
No 3
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=94.92 E-value=0.039 Score=46.89 Aligned_cols=62 Identities=13% Similarity=0.134 Sum_probs=51.3
Q ss_pred eeeeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEEEeecHHHHHHHHHhhc-ceEEEEcC
Q 045648 11 TLKFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVDPVNVMSKWRKYW-PADIILVG 86 (142)
Q Consensus 11 ~l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vDpv~vv~klRK~~-~A~Ivsvg 86 (142)
-+.|+|+.|-.- ++..|..++||.++.+|.++ +.|.|-+.+-|..+...|+-++ .|-|.-.|
T Consensus 12 aV~M~cescvna-----vk~~L~~V~Gi~~vevdle~---------q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G 74 (247)
T KOG4656|consen 12 AVQMTCESCVNA-----VKACLKGVPGINSVEVDLEQ---------QIVSVETSVPPSEIQNTLENTGRDAVLRGAG 74 (247)
T ss_pred EEechhHHHHHH-----HHHHhccCCCcceEEEEhhh---------cEEEEEccCChHHHHHHHHhhChheEEecCC
Confidence 356776666432 24789999999999999999 9999999999999999999998 78777655
No 4
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=93.61 E-value=0.14 Score=34.74 Aligned_cols=56 Identities=16% Similarity=0.136 Sum_probs=41.7
Q ss_pred eeeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEE--E-eecHHHHHHHHHhhc
Q 045648 12 LKFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSV--G-TVDPVNVMSKWRKYW 78 (142)
Q Consensus 12 l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVv--G-~vDpv~vv~klRK~~ 78 (142)
+++..|.|...+- .+.++|..+.||.++.+|+.. +..+|. + .++...+...+.+.+
T Consensus 6 l~v~~MtC~~C~~--~V~~al~~v~gv~~v~v~l~~---------~~~~V~~d~~~~~~~~i~~ai~~aG 64 (71)
T COG2608 6 LKVEGMTCGHCVK--TVEKALEEVDGVASVDVDLEK---------GTATVTFDSNKVDIEAIIEAIEDAG 64 (71)
T ss_pred EEECCcCcHHHHH--HHHHHHhcCCCeeEEEEEccc---------CeEEEEEcCCcCCHHHHHHHHHHcC
Confidence 4444555555554 233999999999999999988 666664 4 389999999988877
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=93.08 E-value=0.2 Score=41.03 Aligned_cols=63 Identities=14% Similarity=0.127 Sum_probs=51.4
Q ss_pred eeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEEEeecHHHHHHHHHhhc-ceEEEEcCCCC
Q 045648 13 KFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVDPVNVMSKWRKYW-PADIILVGPTK 89 (142)
Q Consensus 13 ~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vDpv~vv~klRK~~-~A~Ivsvgp~k 89 (142)
.|.|+.|..+.- +.+..++||.++.+|... ++++|.+.+++..+...+++.+ .+.+++.++.+
T Consensus 13 gMsC~~Ca~~Ie-----k~L~~~~GV~~v~vn~~~---------~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 13 DMKCEGCVAAVK-----NKLETLEGVKAVEVDLSN---------QVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred CccCHHHHHHHH-----HHHhcCCCeEEEEEEcCC---------CEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 477777755543 778899999999999998 8999999889999999999877 67788776554
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=77.95 E-value=2.1 Score=40.60 Aligned_cols=61 Identities=11% Similarity=0.046 Sum_probs=46.2
Q ss_pred eeeeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEEEeecHHHHHHHHHhhc-ceEEEE
Q 045648 11 TLKFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVDPVNVMSKWRKYW-PADIIL 84 (142)
Q Consensus 11 ~l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vDpv~vv~klRK~~-~A~Ivs 84 (142)
++.+.+|.|.+++-+ +.+++..++||..+.+|.+. .+|.+.+++..+...++..+ .+.+.+
T Consensus 6 ~l~V~gmtC~~C~~~--i~~al~~~~gv~~v~v~~~~-----------~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 6 DLTLDGLSCGHCVKR--VKESLEQRPDVEQADVSITE-----------AHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred EEEECCcccHHHHHH--HHHHHhcCCCcceEEEeeeE-----------EEEEecCCHHHHHHHHHhcCCcccccc
Confidence 455556666666542 44999999999999999854 35667889999999999877 777754
No 7
>PF09846 DUF2073: Uncharacterized protein conserved in archaea (DUF2073); InterPro: IPR012017 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=44.65 E-value=33 Score=26.14 Aligned_cols=41 Identities=24% Similarity=0.467 Sum_probs=29.2
Q ss_pred eccCcceEEEecccc--ccccc----cCCCCeEEEEEeecHHHHHHHHHh
Q 045648 33 HFISGVVVASLDRRR--YRFIS----NVAGEEIDSVGTVDPVNVMSKWRK 76 (142)
Q Consensus 33 ~~i~GV~svs~D~k~--~~~~~----~~~~~kvtVvG~vDpv~vv~klRK 76 (142)
..++||+--+...+. --|+. .-.+.++||+| |.+++..|+|
T Consensus 48 d~F~GIEiesyp~~~~~~~f~~rl~gk~~~~rlTVIG---PAn~mktlkK 94 (104)
T PF09846_consen 48 DEFSGIEIESYPSKEADKSFLGRLLGKKSRERLTVIG---PANQMKTLKK 94 (104)
T ss_pred cccCceEEEecCcccccccHHHHHhCCCCCCCeEEEc---cHHHHHHHhc
Confidence 578899888876655 34444 44445999998 6777888877
No 8
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=40.63 E-value=40 Score=25.22 Aligned_cols=42 Identities=17% Similarity=0.160 Sum_probs=31.7
Q ss_pred ceeeccCcceEEEe-----ccccccccccCCCCeEEEEEe-ecHHHHHHHHHhhc
Q 045648 30 RLLHFISGVVVASL-----DRRRYRFISNVAGEEIDSVGT-VDPVNVMSKWRKYW 78 (142)
Q Consensus 30 k~v~~i~GV~svs~-----D~k~~~~~~~~~~~kvtVvG~-vDpv~vv~klRK~~ 78 (142)
+.|+.++||..+.+ |... -+=+||+.|+ +|-..+.+.+.+++
T Consensus 24 ~~l~~~~gV~gVnitv~EvD~et-------e~lkitiEG~~id~d~i~~~Ie~~G 71 (95)
T PF02680_consen 24 KALSELEGVDGVNITVVEVDVET-------ENLKITIEGDDIDFDEIKEAIEELG 71 (95)
T ss_dssp HHHHTSTTEEEEEEEEEEE-SSE-------EEEEEEEEESSE-HHHHHHHHHHTT
T ss_pred HHHHhCCCcceEEEEEEEeeccc-------cEEEEEEEeCCCCHHHHHHHHHHcC
Confidence 67889999987765 4433 2357889997 99999999999877
No 9
>KOG2872 consensus Uroporphyrinogen decarboxylase [Coenzyme transport and metabolism]
Probab=38.86 E-value=18 Score=32.53 Aligned_cols=33 Identities=24% Similarity=0.382 Sum_probs=24.3
Q ss_pred CcceEEEec----cccccccccCCCCeEEEEEeecHHHHH
Q 045648 36 SGVVVASLD----RRRYRFISNVAGEEIDSVGTVDPVNVM 71 (142)
Q Consensus 36 ~GV~svs~D----~k~~~~~~~~~~~kvtVvG~vDpv~vv 71 (142)
.|.+.|++| +++ -.+..|++||+.|++||..|.
T Consensus 271 tG~DVvgLDWTvdp~e---ar~~~g~~VtlQGNlDP~~ly 307 (359)
T KOG2872|consen 271 TGYDVVGLDWTVDPAE---ARRRVGNRVTLQGNLDPGVLY 307 (359)
T ss_pred cCCcEEeecccccHHH---HHHhhCCceEEecCCChHHhc
Confidence 589999885 433 224457889999999997653
No 10
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.01 E-value=47 Score=25.07 Aligned_cols=42 Identities=19% Similarity=0.121 Sum_probs=31.8
Q ss_pred ceeeccCcceEEEe-----ccccccccccCCCCeEEEEEe-ecHHHHHHHHHhhc
Q 045648 30 RLLHFISGVVVASL-----DRRRYRFISNVAGEEIDSVGT-VDPVNVMSKWRKYW 78 (142)
Q Consensus 30 k~v~~i~GV~svs~-----D~k~~~~~~~~~~~kvtVvG~-vDpv~vv~klRK~~ 78 (142)
+.|++++||+.|.+ |.+. -+=++|+-|+ +|=..+...|-+++
T Consensus 26 ~~lskl~gVegVNItv~eiD~et-------~~~~itIeG~~ldydei~~~iE~~G 73 (97)
T COG1888 26 LELSKLEGVEGVNITVTEIDVET-------ENLKITIEGTNLDYDEIEEVIEELG 73 (97)
T ss_pred HHHhhcCCcceEEEEEEEeeehh-------cceEEEEEcCCCCHHHHHHHHHHcC
Confidence 56778888876654 4443 3468899996 99999999998877
No 11
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=34.59 E-value=73 Score=24.66 Aligned_cols=35 Identities=11% Similarity=0.117 Sum_probs=29.5
Q ss_pred eeccCcceEEEeccccccccccCCCCeEEEEEeec
Q 045648 32 LHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVD 66 (142)
Q Consensus 32 v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vD 66 (142)
...-.|--.|.+|.+.++-..--.+.+|.+.|.||
T Consensus 77 F~D~TG~I~VeId~~~w~G~~v~p~d~V~I~GeVD 111 (126)
T TIGR00156 77 FRDKSGEINVVIPAAVWNGREVQPKDMVNISGSLD 111 (126)
T ss_pred EECCCCCEEEEECHHHcCCCcCCCCCEEEEEEEEC
Confidence 45567888889999888877777899999999999
No 12
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=32.22 E-value=53 Score=31.81 Aligned_cols=60 Identities=23% Similarity=0.238 Sum_probs=46.9
Q ss_pred eeeeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEEEe---ec-HHHHHHHHHhhc-ceEE
Q 045648 11 TLKFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSVGT---VD-PVNVMSKWRKYW-PADI 82 (142)
Q Consensus 11 ~l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~---vD-pv~vv~klRK~~-~A~I 82 (142)
++.+..|.|-+++..+. .|.+++||..+.++... ++++|..+ .+ +..+...+++.+ .+..
T Consensus 5 ~l~v~Gm~Ca~C~~~ie---~l~~~~gV~~~~vn~~t---------~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 5 SLSVEGMTCAACASRIE---ALNKLPGVEEARVNLAT---------ERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred EEeecCcCcHHHHHHHH---HHhcCCCeeEEEeeccc---------ceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 45566677777666434 89999999999999998 89999864 56 789999999877 4544
No 13
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=30.59 E-value=86 Score=23.18 Aligned_cols=36 Identities=19% Similarity=0.314 Sum_probs=23.9
Q ss_pred eeeccCcceEEEeccccccccccCCCCeEEEEEeec
Q 045648 31 LLHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVD 66 (142)
Q Consensus 31 ~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vD 66 (142)
+...-+|-..|.+|.+.++=..--+..+|.+.|.||
T Consensus 53 ~F~D~TG~I~VeId~~~w~g~~vt~~~~Vri~GeVD 88 (103)
T PF04076_consen 53 LFRDATGEIEVEIDDDVWRGQTVTPDDKVRISGEVD 88 (103)
T ss_dssp EEEETTEEEEEE--GGGSTT----TTSEEEEEEEEE
T ss_pred EEECCCCcEEEEEChhhcCCcccCCCCEEEEEEEEe
Confidence 345567888888888876655556778999999999
No 14
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=30.10 E-value=96 Score=21.65 Aligned_cols=32 Identities=28% Similarity=0.396 Sum_probs=22.1
Q ss_pred CCeEEEEEeecHHHHHHHHHhhc--c-eEEEEcCC
Q 045648 56 GEEIDSVGTVDPVNVMSKWRKYW--P-ADIILVGP 87 (142)
Q Consensus 56 ~~kvtVvG~vDpv~vv~klRK~~--~-A~Ivsvgp 87 (142)
-.+|+|.|.+|+..+-+.|++.. + -+|+.+..
T Consensus 38 p~~i~i~gRl~~~~~~~yl~~i~~s~~~~v~v~~~ 72 (119)
T PF07744_consen 38 PKKIDIRGRLDPEKVWDYLRQIRKSRSKDVCVVAL 72 (119)
T ss_dssp -EEE-EEEE-SHHHHHHHHHHTSSTTT-EEEEEEE
T ss_pred CcEEEEEeecCHHHHHHHHHhcccCCCceEEEEEE
Confidence 47999999999999999998854 2 15555544
No 15
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=29.92 E-value=59 Score=22.66 Aligned_cols=21 Identities=29% Similarity=0.427 Sum_probs=18.4
Q ss_pred CeEEEEEeecHHHHHHHHHhh
Q 045648 57 EEIDSVGTVDPVNVMSKWRKY 77 (142)
Q Consensus 57 ~kvtVvG~vDpv~vv~klRK~ 77 (142)
-.+.++|++|+..+...++++
T Consensus 20 ~~l~i~Gd~~~~~~~~~i~~~ 40 (184)
T PF05193_consen 20 MTLVIVGDIDPDELEKLIEKY 40 (184)
T ss_dssp EEEEEEESSGHHHHHHHHHHH
T ss_pred eEEEEEcCccHHHHHHHHHhh
Confidence 578889999999999999874
No 16
>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=29.56 E-value=19 Score=25.10 Aligned_cols=33 Identities=21% Similarity=0.207 Sum_probs=20.7
Q ss_pred eeeeeechhhhhhhccccccceeeccCcceEEEe
Q 045648 10 GTLKFTAMKIEAKHISFCPSRLLHFISGVVVASL 43 (142)
Q Consensus 10 ~~l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~ 43 (142)
|++-++-+--....+ ....+.|..++||-++++
T Consensus 39 GKiVVtiE~~~~~~~-~~~~~~i~~l~GVlsa~l 71 (79)
T PF03927_consen 39 GKIVVTIEAESSEEE-VDLIDAINALPGVLSASL 71 (79)
T ss_dssp TEEEEEEEESSHHHH-HHHHHHHCCSTTEEEEEE
T ss_pred CeEEEEEEeCChHHH-HHHHHHHHcCCCceEEEE
Confidence 666665333332222 123388999999999987
No 17
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=26.64 E-value=60 Score=25.79 Aligned_cols=44 Identities=23% Similarity=0.219 Sum_probs=30.7
Q ss_pred ccCcceEEEeccccccccccCCCCeEEEEEeecHHHHHHH--HH--hhcceEEEEcC
Q 045648 34 FISGVVVASLDRRRYRFISNVAGEEIDSVGTVDPVNVMSK--WR--KYWPADIILVG 86 (142)
Q Consensus 34 ~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vDpv~vv~k--lR--K~~~A~Ivsvg 86 (142)
.|.|=..+.++... +.|.+.|.|.|.++-.- +- +.-.|.|.-.|
T Consensus 110 ~I~G~k~i~vn~e~---------~~i~lsGiVRp~DI~~~NtV~S~~IAda~I~y~G 157 (179)
T PF02107_consen 110 VIEGEKQIRVNGEE---------QYIRLSGIVRPEDIDPDNTVLSSKIADARIEYSG 157 (179)
T ss_pred EEEEEEEEEECCCE---------EEEEEEEEECHHHCCCCCeEchheeEeEEEEEcc
Confidence 36677778888887 99999999999988621 11 23356666554
No 18
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=25.85 E-value=51 Score=21.34 Aligned_cols=23 Identities=17% Similarity=0.600 Sum_probs=17.9
Q ss_pred eccccccccccCCCCeEEEEEee
Q 045648 43 LDRRRYRFISNVAGEEIDSVGTV 65 (142)
Q Consensus 43 ~D~k~~~~~~~~~~~kvtVvG~v 65 (142)
++...|+......|.+|+|+|++
T Consensus 6 l~~~~~~~~~~~~Gk~V~V~G~l 28 (48)
T PF14485_consen 6 LSEEDYSYLKSLLGKRVSVTGKL 28 (48)
T ss_pred eChhhhHHHHHhcCCeEEEEEEE
Confidence 35566677777889999999985
No 19
>PF05359 DUF748: Domain of Unknown Function (DUF748); InterPro: IPR008023 This is a family of proteins of unknown function.
Probab=23.96 E-value=57 Score=23.68 Aligned_cols=65 Identities=14% Similarity=0.258 Sum_probs=32.6
Q ss_pred ccceeeeeeeeechhhhhhhccccccceeeccCcceEEEeccccccccccCCC-CeEEEEEeecHHH
Q 045648 4 RASVIDGTLKFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAG-EEIDSVGTVDPVN 69 (142)
Q Consensus 4 ~~~~~~~~l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~-~kvtVvG~vDpv~ 69 (142)
+.++.+|.+.+++.-... ...+.+..+=-.+.++.+..=..-.|++-.++.+ +.+.+.|.++|..
T Consensus 7 ~l~l~~g~i~f~D~~~~~-~~~~~l~~i~~~l~~l~~~~~~~~~~~l~~~~~~~g~l~~~G~~~~~~ 72 (151)
T PF05359_consen 7 HLSLKNGRINFTDQSVPP-PFKLELSDINLTLDNLSTDSNEPAPVSLSASLNGGGTLSASGKLSPFP 72 (151)
T ss_pred EEEEECCEEEEEeCCCCC-CceEEEEEEEEEEEeccCCCCCcEEEEEEEEeCCCCEEEEEEEEEeCC
Confidence 567889999999865543 2211111111222222211111123444444444 6888888877543
No 20
>KOG0582 consensus Ste20-like serine/threonine protein kinase [Signal transduction mechanisms]
Probab=22.14 E-value=27 Score=32.93 Aligned_cols=27 Identities=37% Similarity=0.458 Sum_probs=23.8
Q ss_pred EEEEe---ecHHHHHHHHHhhc-ceEEEEcC
Q 045648 60 DSVGT---VDPVNVMSKWRKYW-PADIILVG 86 (142)
Q Consensus 60 tVvG~---vDpv~vv~klRK~~-~A~Ivsvg 86 (142)
|.+|+ +-|..||..++=|. .|||||+|
T Consensus 189 tfvgtp~wmAPEvl~q~~~GYdfKaDIwSfG 219 (516)
T KOG0582|consen 189 TFVGTPCWMAPEVLMQQLHGYDFKADIWSFG 219 (516)
T ss_pred cccCcccccChHHhhhcccCccchhhhhhhh
Confidence 56775 99999999999887 99999988
No 21
>cd02958 UAS UAS family; UAS is a domain of unknown function. Most members of this family are uncharacterized proteins with similarity to FAS-associated factor 1 (FAF1) and ETEA because of the presence of a UAS domain N-terminal to a ubiquitin-associated UBX domain. FAF1 is a longer protein, compared to the other members of this family, having additional N-terminal domains, a ubiquitin-associated UBA domain and a nuclear targeting domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. ETEA is the protein product of a highly expressed gene in T-cells and eosinophils of atopic dermatitis patients. The presence of the ubiquitin-associated UBX domain in the proteins of this family suggests the possibility of their involvement in ubiquitination. Recently, FAF1 has been shown to interact with valosin-containing protein (VCP),
Probab=21.91 E-value=86 Score=21.89 Aligned_cols=24 Identities=21% Similarity=0.544 Sum_probs=18.6
Q ss_pred CCCeEEE-EEeecHHHHHHHHHhhc
Q 045648 55 AGEEIDS-VGTVDPVNVMSKWRKYW 78 (142)
Q Consensus 55 ~~~kvtV-vG~vDpv~vv~klRK~~ 78 (142)
.|+.+.+ .|.++|..+++.|++..
T Consensus 87 ~g~~l~~~~G~~~~~~f~~~L~~~~ 111 (114)
T cd02958 87 TGEVLKVWSGNITPEDLLSQLIEFL 111 (114)
T ss_pred cCcEeEEEcCCCCHHHHHHHHHHHH
Confidence 3455554 79999999999998753
No 22
>PRK10671 copA copper exporting ATPase; Provisional
Probab=21.24 E-value=95 Score=29.75 Aligned_cols=59 Identities=17% Similarity=0.182 Sum_probs=42.2
Q ss_pred eeeechhhhhhhccccccceeeccCcceEEEeccccccccccCCCCeEEEEEeecHHHHHHHHHhhc-ceE
Q 045648 12 LKFTAMKIEAKHISFCPSRLLHFISGVVVASLDRRRYRFISNVAGEEIDSVGTVDPVNVMSKWRKYW-PAD 81 (142)
Q Consensus 12 l~~~~~k~~~Ka~~~~~~k~v~~i~GV~svs~D~k~~~~~~~~~~~kvtVvG~vDpv~vv~klRK~~-~A~ 81 (142)
+.+..+.|-..+- .+.+.+..++||.++.++... ++..+.+..++..+...++..+ .+.
T Consensus 103 l~V~Gm~Ca~Ca~--~Ie~~L~~~~GV~~a~vnl~t---------~~~~V~~~~s~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 103 LLLSGMSCASCVS--RVQNALQSVPGVTQARVNLAE---------RTALVMGSASPQDLVQAVEKAGYGAE 162 (834)
T ss_pred EEeCCcCcHHHHH--HHHHHHhcCCCceeeeeecCC---------CeEEEEccCCHHHHHHHHHhcCCCcc
Confidence 3344455544443 234788999999999999988 7777777788888888888766 443
Done!