Query psy12148
Match_columns 116
No_of_seqs 118 out of 474
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 19:57:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12148.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12148hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1314|consensus 99.9 3E-23 6.5E-28 165.7 6.5 96 1-100 15-143 (414)
2 KOG1313|consensus 99.8 5.4E-21 1.2E-25 148.7 0.3 97 1-97 31-151 (309)
3 KOG1315|consensus 99.8 2E-19 4.4E-24 142.4 1.6 64 34-97 43-158 (307)
4 KOG1311|consensus 99.6 7.1E-16 1.5E-20 120.7 8.0 24 76-99 141-164 (299)
5 PF01529 zf-DHHC: DHHC palmito 99.5 1.4E-15 3E-20 109.5 -0.4 22 76-97 76-97 (174)
6 COG5273 Uncharacterized protei 99.5 3.7E-14 8E-19 112.6 4.6 54 44-97 63-158 (309)
7 KOG1312|consensus 99.1 2.3E-10 5E-15 90.2 5.8 22 76-97 176-197 (341)
8 KOG0509|consensus 99.0 3.2E-10 7E-15 96.2 4.6 22 76-97 448-469 (600)
9 PF07010 Endomucin: Endomucin; 70.7 13 0.00029 29.0 5.4 34 36-69 193-226 (259)
10 PF08098 ATX_III: Anemonia sul 40.5 12 0.00025 19.3 0.4 8 78-85 14-21 (27)
11 PF06024 DUF912: Nucleopolyhed 31.6 49 0.0011 22.0 2.4 16 11-26 73-88 (101)
12 TIGR00540 hemY_coli hemY prote 30.7 1.7E+02 0.0038 23.5 5.9 43 23-65 30-72 (409)
13 PRK10747 putative protoheme IX 29.7 2.1E+02 0.0045 23.1 6.2 42 24-65 31-72 (398)
14 PF07219 HemY_N: HemY protein 27.5 1.8E+02 0.0038 19.2 4.6 43 23-65 5-47 (108)
15 PF14283 DUF4366: Domain of un 26.6 38 0.00082 25.9 1.3 26 1-26 160-185 (218)
16 PF08370 PDR_assoc: Plant PDR 23.7 1.7E+02 0.0036 18.2 3.6 28 38-65 33-60 (65)
17 KOG2765|consensus 23.2 61 0.0013 27.2 2.0 89 5-94 246-334 (416)
18 TIGR03630 arch_S17P archaeal r 22.1 63 0.0014 22.0 1.6 15 70-84 8-22 (102)
No 1
>KOG1314|consensus
Probab=99.88 E-value=3e-23 Score=165.67 Aligned_cols=96 Identities=17% Similarity=0.095 Sum_probs=73.9
Q ss_pred CCcchhhHHHHHHHHhhhee-EEEeccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCC-----
Q psy12148 1 MSPAFVVLVVTLTSFVVFLS-YWIGVPFYWHKSPALTCVLIVVGNWILLNYVFHYYMGVTTMPGYPPQGGLIPEA----- 74 (116)
Q Consensus 1 ~Gp~fV~~vi~Li~~i~~~~-y~vvLP~~~~~~s~~~~~~li~~~~l~~~il~nY~~ai~tdPG~vP~~~~~~~~----- 74 (116)
+||.+.+.++..+++.+... -....| .++..+..+-+.+.+...|+++||++|++|.||+||.+|.....
T Consensus 15 wGpi~alsiit~i~~~~~~~n~lww~p----~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~~~ 90 (414)
T KOG1314|consen 15 WGPITALSIITIITSTTGYMNSLWWFP----LSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKDEMF 90 (414)
T ss_pred cccHHHHHHHHHHHHHHHHhhhhhhcc----ccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChhHHH
Confidence 69999998886666544332 223233 44555667767777778999999999999999999999976322
Q ss_pred ---------------------------CcccccccCCccccCCceeeehhhhh
Q psy12148 75 ---------------------------MVPVAYFLNTTTTTYNSALECRVSTA 100 (116)
Q Consensus 75 ---------------------------~~HHCpWinNCVG~~N~ryf~~~~~~ 100 (116)
|||||||||||||+.||.||.|+-+-
T Consensus 91 lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf 143 (414)
T KOG1314|consen 91 LQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLF 143 (414)
T ss_pred HHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHH
Confidence 47999999999999999999998654
No 2
>KOG1313|consensus
Probab=99.80 E-value=5.4e-21 Score=148.68 Aligned_cols=97 Identities=21% Similarity=0.173 Sum_probs=74.8
Q ss_pred CCcchhhHHHHHHHHhhheeEEEeccccccccchHHHHHH-HHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCC-------
Q psy12148 1 MSPAFVVLVVTLTSFVVFLSYWIGVPFYWHKSPALTCVLI-VVGNWILLNYVFHYYMGVTTMPGYPPQGGLIP------- 72 (116)
Q Consensus 1 ~Gp~fV~~vi~Li~~i~~~~y~vvLP~~~~~~s~~~~~~l-i~~~~l~~~il~nY~~ai~tdPG~vP~~~~~~------- 72 (116)
+||++|.+|...-...+.+.+++..|++.....+...+.+ ..+.+++.+++++|+||..++|-..|....++
T Consensus 31 ~g~~~~~~V~~~~~~~~~t~~fi~~~f~~~~~~~~~~f~~~~l~i~~l~nvi~hy~ka~t~pPvgn~~~~~~SfC~KC~~ 110 (309)
T KOG1313|consen 31 FGPFLVGAVTNQNTVRVETKSFILRPFRDVILAVFMLFLLATLAIYLLSNVIFHYYKARTKPPVGNPGLENDSFCNKCNY 110 (309)
T ss_pred CCCeEEEEEEeeccchhhhhhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhheeecccCCcCCCCCccccHHhhcCC
Confidence 5899999999999999999999999988755544433333 33468999999999999988874444333221
Q ss_pred ---C-------------CCcccccccCCccccCCceeeehh
Q psy12148 73 ---E-------------AMVPVAYFLNTTTTTYNSALECRV 97 (116)
Q Consensus 73 ---~-------------~~~HHCpWinNCVG~~N~ryf~~~ 97 (116)
+ .|||||||||||||+.|||||.-+
T Consensus 111 pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlF 151 (309)
T KOG1313|consen 111 PKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLF 151 (309)
T ss_pred CCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHH
Confidence 1 168999999999999999999764
No 3
>KOG1315|consensus
Probab=99.75 E-value=2e-19 Score=142.43 Aligned_cols=64 Identities=17% Similarity=0.212 Sum_probs=54.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCC---------------------------------------
Q psy12148 34 ALTCVLIVVGNWILLNYVFHYYMGVTTMPGYPPQGGLIPEA--------------------------------------- 74 (116)
Q Consensus 34 ~~~~~~li~~~~l~~~il~nY~~ai~tdPG~vP~~~~~~~~--------------------------------------- 74 (116)
....+.++.++.+++|..|+|+++++||||+||..+.....
T Consensus 43 ~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdR 122 (307)
T KOG1315|consen 43 IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGSDNERDLPGYTRTSDGAVRYCDKCKCIKPDR 122 (307)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccCcccccceeeEecCCCCceeecccccccCCc
Confidence 56788888999999999999999999999999987743100
Q ss_pred -------------CcccccccCCccccCCceeeehh
Q psy12148 75 -------------MVPVAYFLNTTTTTYNSALECRV 97 (116)
Q Consensus 75 -------------~~HHCpWinNCVG~~N~ryf~~~ 97 (116)
|||||||+|||||+.|||||.-+
T Consensus 123 aHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lf 158 (307)
T KOG1315|consen 123 AHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLF 158 (307)
T ss_pred cccchhhhhhhhccccCCcceeceecccchHHHHHH
Confidence 26999999999999999999754
No 4
>KOG1311|consensus
Probab=99.63 E-value=7.1e-16 Score=120.72 Aligned_cols=24 Identities=13% Similarity=-0.133 Sum_probs=21.8
Q ss_pred cccccccCCccccCCceeeehhhh
Q psy12148 76 VPVAYFLNTTTTTYNSALECRVST 99 (116)
Q Consensus 76 ~HHCpWinNCVG~~N~ryf~~~~~ 99 (116)
||||||+|||||++|||||.++-.
T Consensus 141 DHHC~WvnnCVG~rNyr~F~~f~~ 164 (299)
T KOG1311|consen 141 DHHCPWLNNCIGERNYRYFVLFLF 164 (299)
T ss_pred CCCCCCccceECCCchHHHHHHHH
Confidence 799999999999999999996643
No 5
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=99.52 E-value=1.4e-15 Score=109.54 Aligned_cols=22 Identities=9% Similarity=-0.130 Sum_probs=20.3
Q ss_pred cccccccCCccccCCceeeehh
Q psy12148 76 VPVAYFLNTTTTTYNSALECRV 97 (116)
Q Consensus 76 ~HHCpWinNCVG~~N~ryf~~~ 97 (116)
||||||+|||||.+|||||..+
T Consensus 76 DHHC~w~~~cIG~~N~~~F~~f 97 (174)
T PF01529_consen 76 DHHCPWLGNCIGRRNHRYFLLF 97 (174)
T ss_pred cccchhhccccccccHHHHHHH
Confidence 6999999999999999999754
No 6
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=99.47 E-value=3.7e-14 Score=112.60 Aligned_cols=54 Identities=17% Similarity=0.165 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCCCCCCCC------------------------------------------CCcccccc
Q psy12148 44 NWILLNYVFHYYMGVTTMPGYPPQGGLIPE------------------------------------------AMVPVAYF 81 (116)
Q Consensus 44 ~~l~~~il~nY~~ai~tdPG~vP~~~~~~~------------------------------------------~~~HHCpW 81 (116)
.+++......|++.+.+|||+++++....+ .+||||||
T Consensus 63 ~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~W 142 (309)
T COG5273 63 IVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPW 142 (309)
T ss_pred hhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhhccCccCcc
Confidence 345667788999999999999985532110 02799999
Q ss_pred cCCccccCCceeeehh
Q psy12148 82 LNTTTTTYNSALECRV 97 (116)
Q Consensus 82 inNCVG~~N~ryf~~~ 97 (116)
+|||||.+|||+|..+
T Consensus 143 i~nCVG~~N~r~F~~F 158 (309)
T COG5273 143 INNCVGFRNYRFFYQF 158 (309)
T ss_pred cccccCcchHHHHHHH
Confidence 9999999999999875
No 7
>KOG1312|consensus
Probab=99.07 E-value=2.3e-10 Score=90.22 Aligned_cols=22 Identities=9% Similarity=0.016 Sum_probs=20.2
Q ss_pred cccccccCCccccCCceeeehh
Q psy12148 76 VPVAYFLNTTTTTYNSALECRV 97 (116)
Q Consensus 76 ~HHCpWinNCVG~~N~ryf~~~ 97 (116)
||||.|+|||||.+|.|||.-+
T Consensus 176 DHHCiWiNNCIG~~N~ryF~lF 197 (341)
T KOG1312|consen 176 DHHCIWINNCIGAWNIRYFLLF 197 (341)
T ss_pred ccceEeeecccccchHHHHHHH
Confidence 6999999999999999999754
No 8
>KOG0509|consensus
Probab=99.01 E-value=3.2e-10 Score=96.18 Aligned_cols=22 Identities=9% Similarity=-0.093 Sum_probs=19.9
Q ss_pred cccccccCCccccCCceeeehh
Q psy12148 76 VPVAYFLNTTTTTYNSALECRV 97 (116)
Q Consensus 76 ~HHCpWinNCVG~~N~ryf~~~ 97 (116)
|||||||+||||..|||+|.-+
T Consensus 448 DHhCPwi~ncVG~kNh~~F~~F 469 (600)
T KOG0509|consen 448 DHHCPWIGNCVGLKNHRLFVFF 469 (600)
T ss_pred ccCCCccccccCccchHHHHHH
Confidence 6999999999999999998643
No 9
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=70.69 E-value=13 Score=28.97 Aligned_cols=34 Identities=26% Similarity=0.351 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCC
Q psy12148 36 TCVLIVVGNWILLNYVFHYYMGVTTMPGYPPQGG 69 (116)
Q Consensus 36 ~~~~li~~~~l~~~il~nY~~ai~tdPG~vP~~~ 69 (116)
..+.+++...+.|.++.-|.+|-.+|||++-.+.
T Consensus 193 vvIaliVitl~vf~LvgLyr~C~k~dPg~p~~g~ 226 (259)
T PF07010_consen 193 VVIALIVITLSVFTLVGLYRMCWKTDPGTPENGP 226 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCCCcccCC
Confidence 4444555666677777789999999999875554
No 10
>PF08098 ATX_III: Anemonia sulcata toxin III family; InterPro: IPR012509 This entry occurs within the Anemonia sulcata toxin III (ATX III) neurotoxin family. ATX III is a neurotoxin that is produced by sea anemone; it adopts a compact structure containing four reverse turns and two other chain reversals, but no regular alpha-helix or beta-sheet. A hydrophobic patch found on the surface of the peptide may constitute part of the sodium channel binding surface [].; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0042151 nematocyst; PDB: 1ANS_A.
Probab=40.45 E-value=12 Score=19.35 Aligned_cols=8 Identities=0% Similarity=-0.247 Sum_probs=4.6
Q ss_pred cccccCCc
Q psy12148 78 VAYFLNTT 85 (116)
Q Consensus 78 HCpWinNC 85 (116)
-|||..||
T Consensus 14 gC~WGQ~~ 21 (27)
T PF08098_consen 14 GCPWGQNC 21 (27)
T ss_dssp T-SSS-SS
T ss_pred CCcccccc
Confidence 48888887
No 11
>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins.
Probab=31.57 E-value=49 Score=22.03 Aligned_cols=16 Identities=6% Similarity=0.235 Sum_probs=9.3
Q ss_pred HHHHHhhheeEEEecc
Q psy12148 11 TLTSFVVFLSYWIGVP 26 (116)
Q Consensus 11 ~Li~~i~~~~y~vvLP 26 (116)
+++..+..++||+++.
T Consensus 73 ~IlVily~IyYFVILR 88 (101)
T PF06024_consen 73 CILVILYAIYYFVILR 88 (101)
T ss_pred HHHHHHhhheEEEEEe
Confidence 3344445567777774
No 12
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=30.71 E-value=1.7e+02 Score=23.53 Aligned_cols=43 Identities=2% Similarity=-0.171 Sum_probs=24.7
Q ss_pred EeccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Q psy12148 23 IGVPFYWHKSPALTCVLIVVGNWILLNYVFHYYMGVTTMPGYP 65 (116)
Q Consensus 23 vvLP~~~~~~s~~~~~~li~~~~l~~~il~nY~~ai~tdPG~v 65 (116)
+.++.|-.+.|+.....+++..++++.++|..++.++.-|+..
T Consensus 30 i~~~~~~ie~s~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ 72 (409)
T TIGR00540 30 IETANRIIEMSITGLAIFFIIALAIIFAFEWGLRRFFRLGAHS 72 (409)
T ss_pred EEECCEEEEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHH
Confidence 3446665566655444444444444445666777777777764
No 13
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=29.75 E-value=2.1e+02 Score=23.06 Aligned_cols=42 Identities=7% Similarity=-0.004 Sum_probs=24.2
Q ss_pred eccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Q psy12148 24 GVPFYWHKSPALTCVLIVVGNWILLNYVFHYYMGVTTMPGYP 65 (116)
Q Consensus 24 vLP~~~~~~s~~~~~~li~~~~l~~~il~nY~~ai~tdPG~v 65 (116)
.++.|..+.|+.....+++..++++.+++.....++.-|+..
T Consensus 31 ~~~~~~ie~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~ 72 (398)
T PRK10747 31 QTDNYNIETSVTGLAIILILAMVVLFAIEWLLRRIFRTGART 72 (398)
T ss_pred EECCEEEEehHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhh
Confidence 345555565555444444444444455566777777777765
No 14
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=27.49 E-value=1.8e+02 Score=19.21 Aligned_cols=43 Identities=9% Similarity=0.206 Sum_probs=28.4
Q ss_pred EeccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Q psy12148 23 IGVPFYWHKSPALTCVLIVVGNWILLNYVFHYYMGVTTMPGYP 65 (116)
Q Consensus 23 vvLP~~~~~~s~~~~~~li~~~~l~~~il~nY~~ai~tdPG~v 65 (116)
+.++.+..+.+......+++..++.+.+++..++.++..|+..
T Consensus 5 I~~~~~~ie~sl~~~~~~l~~~~~~l~ll~~ll~~~~~~p~~~ 47 (108)
T PF07219_consen 5 ISWGGYRIETSLWVALILLLLLFVVLYLLLRLLRRLLSLPSRV 47 (108)
T ss_pred EEECCEEEEeeHHHHHHHHHHHHHHHHHHHHHHHHHHhChHHH
Confidence 3445555555655555555566667777788888888888765
No 15
>PF14283 DUF4366: Domain of unknown function (DUF4366)
Probab=26.56 E-value=38 Score=25.91 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=15.6
Q ss_pred CCcchhhHHHHHHHHhhheeEEEecc
Q psy12148 1 MSPAFVVLVVTLTSFVVFLSYWIGVP 26 (116)
Q Consensus 1 ~Gp~fV~~vi~Li~~i~~~~y~vvLP 26 (116)
+|.++++++++|++..++.||.+.-|
T Consensus 160 ~g~ll~lllv~l~gGGa~yYfK~~K~ 185 (218)
T PF14283_consen 160 MGSLLLLLLVALIGGGAYYYFKFYKP 185 (218)
T ss_pred hHHHHHHHHHHHhhcceEEEEEEecc
Confidence 36677777777777755544444333
No 16
>PF08370 PDR_assoc: Plant PDR ABC transporter associated; InterPro: IPR013581 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This domain is found on the C terminus of ABC-2 type transporter domains (IPR013525 from INTERPRO). It seems to be associated with the plant pleiotropic drug resistance (PDR) protein family of ABC transporters. Like in yeast, plant PDR ABC transporters may also play a role in the transport of antifungal agents [] (see also IPR010929 from INTERPRO). The PDR family is characterised by a configuration in which the ABC domain is nearer the N terminus of the protein than the transmembrane domain [].
Probab=23.66 E-value=1.7e+02 Score=18.21 Aligned_cols=28 Identities=21% Similarity=0.263 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCC
Q psy12148 38 VLIVVGNWILLNYVFHYYMGVTTMPGYP 65 (116)
Q Consensus 38 ~~li~~~~l~~~il~nY~~ai~tdPG~v 65 (116)
.-.+++..++||+++....+-+.+||.+
T Consensus 33 vgaL~G~~vlFNil~~laL~yL~p~~k~ 60 (65)
T PF08370_consen 33 VGALLGFIVLFNILFTLALTYLNPLGKS 60 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcCCC
Confidence 4455677788899988888888888776
No 17
>KOG2765|consensus
Probab=23.24 E-value=61 Score=27.24 Aligned_cols=89 Identities=11% Similarity=-0.031 Sum_probs=45.1
Q ss_pred hhhHHHHHHHHhhheeEEEeccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCcccccccCC
Q psy12148 5 FVVLVVTLTSFVVFLSYWIGVPFYWHKSPALTCVLIVVGNWILLNYVFHYYMGVTTMPGYPPQGGLIPEAMVPVAYFLNT 84 (116)
Q Consensus 5 fV~~vi~Li~~i~~~~y~vvLP~~~~~~s~~~~~~li~~~~l~~~il~nY~~ai~tdPG~vP~~~~~~~~~~HHCpWinN 84 (116)
++.-...|.+...|..|.+.+.....+.....-..+.+|..-+++++.-+.-...-|-= .-+.+..+....--|.-+||
T Consensus 246 llG~llaL~sA~~YavY~vllk~~~~~eg~rvdi~lffGfvGLfnllllwP~l~iL~~~-~~e~F~lP~~~q~~~vv~~~ 324 (416)
T KOG2765|consen 246 LLGNLLALLSALLYAVYTVLLKRKIGDEGERVDIQLFFGFVGLFNLLLLWPPLIILDFF-GEERFELPSSTQFSLVVFNN 324 (416)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHHHhHHHHHHHHh-ccCcccCCCCceeEeeeHhh
Confidence 34445678888888888887765544432222222223333233332222111111111 22234555566677889999
Q ss_pred ccccCCceee
Q psy12148 85 TTTTYNSALE 94 (116)
Q Consensus 85 CVG~~N~ryf 94 (116)
|+|-.=..|+
T Consensus 325 ligtvvSDyl 334 (416)
T KOG2765|consen 325 LIGTVVSDYL 334 (416)
T ss_pred HHHHHHHHHH
Confidence 9986544443
No 18
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=22.05 E-value=63 Score=21.97 Aligned_cols=15 Identities=20% Similarity=0.038 Sum_probs=10.8
Q ss_pred CCCCCCcccccccCC
Q psy12148 70 LIPEAMVPVAYFLNT 84 (116)
Q Consensus 70 ~~~~~~~HHCpWinN 84 (116)
...+..|-+|||.+|
T Consensus 8 p~~~~~d~~cpf~g~ 22 (102)
T TIGR03630 8 PERECNDPKCPFHGH 22 (102)
T ss_pred CCccccCCCCCccce
Confidence 344556788999985
Done!