Query psy4887
Match_columns 100
No_of_seqs 126 out of 637
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:20:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4887.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4887hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3461|consensus 100.0 8.6E-37 1.9E-41 220.6 4.2 95 6-100 31-132 (132)
2 smart00704 ZnF_CDGSH CDGSH-typ 99.7 5.6E-17 1.2E-21 95.9 3.4 34 51-85 5-38 (38)
3 PF09360 zf-CDGSH: Iron-bindin 99.6 3.4E-16 7.4E-21 92.3 2.5 37 43-80 2-38 (38)
4 COG3369 Zinc finger domain con 99.3 4.5E-13 9.9E-18 90.3 2.8 28 58-85 28-55 (78)
5 KOG4605|consensus 99.3 3.6E-12 7.8E-17 92.4 4.1 75 8-86 30-122 (129)
6 KOG4605|consensus 99.1 2E-10 4.4E-15 83.3 5.9 55 38-99 39-93 (129)
7 PF10660 MitoNEET_N: Iron-cont 98.4 5.4E-08 1.2E-12 63.5 0.3 33 5-37 31-63 (64)
8 PRK00750 lysK lysyl-tRNA synth 46.0 34 0.00073 29.4 4.2 54 23-85 169-223 (510)
9 cd00674 LysRS_core_class_I cat 32.4 73 0.0016 26.4 4.0 54 23-85 163-216 (353)
10 PLN02961 alanine-tRNA ligase 28.2 56 0.0012 24.8 2.5 58 36-98 139-210 (223)
11 PF05207 zf-CSL: CSL zinc fing 23.8 67 0.0014 19.7 1.8 12 58-69 15-26 (55)
12 TIGR00467 lysS_arch lysyl-tRNA 21.3 95 0.0021 27.0 2.9 52 23-85 162-214 (515)
No 1
>KOG3461|consensus
Probab=100.00 E-value=8.6e-37 Score=220.59 Aligned_cols=95 Identities=46% Similarity=0.835 Sum_probs=87.9
Q ss_pred chhhhhhhhh--hheeeeeeEeeEEeeecC-----CCccccccccccceEEEeeeccCCCceEEEEeeCCCCCCccccCC
Q psy4887 6 PLADFVKYVP--YALVLGGISYGVYKVISP-----KGHINPNIQKSNSKVVNVINIEDIADTLALCRCWRSKTFPKCDGS 78 (100)
Q Consensus 6 ~~~dwl~l~p--~~~~~~~~gY~~~~~f~~-----~~~vN~~I~k~~pkvv~~~~~e~~~~~~~~CrCg~S~~~PfCDGS 78 (100)
++++|..+.| +.++.|+.+|..|+.|.. +.++|..|+|++||+|+.||+|||+++.+|||||+|++|||||||
T Consensus 31 ~~~~~~~v~~p~v~~~ta~~~y~ay~r~~~k~~~n~a~iN~hIqkd~pKIVd~~d~eDl~~ka~yCrCWrs~kfP~CDGs 110 (132)
T KOG3461|consen 31 TVKDIAAVTPPCVAAGTAATAYLAYKRFYVKDHQNKARINLHIQKDNPKIVDAFDMEDLGDKAAYCRCWRSKKFPLCDGS 110 (132)
T ss_pred cccchhhcCCcceecchhhhhhhhheeeeeeecccCccccceeecCCCceeEEEehhhhcccceEEEeeccCCcccccCc
Confidence 4589999998 666777899999988776 788999999999999999999999999999999999999999999
Q ss_pred CcCCcccCCCcccceEEEeccC
Q psy4887 79 HAQHNQCTGDNVGPVLIKRNAA 100 (100)
Q Consensus 79 H~~~~~~~gdnvgPl~~~~~~~ 100 (100)
|.+||+++|||||||++|+++.
T Consensus 111 h~KhNk~tgdNvgpliikk~~~ 132 (132)
T KOG3461|consen 111 HGKHNKETGDNVGPLIIKKKET 132 (132)
T ss_pred ccccccccccccccceeeeccC
Confidence 9999999999999999999863
No 2
>smart00704 ZnF_CDGSH CDGSH-type zinc finger. Function unknown.
Probab=99.66 E-value=5.6e-17 Score=95.86 Aligned_cols=34 Identities=53% Similarity=1.037 Sum_probs=28.9
Q ss_pred eeeccCCCceEEEEeeCCCCCCccccCCCcCCccc
Q psy4887 51 VINIEDIADTLALCRCWRSKTFPKCDGSHAQHNQC 85 (100)
Q Consensus 51 ~~~~e~~~~~~~~CrCg~S~~~PfCDGSH~~~~~~ 85 (100)
.+++|+ ++.++|||||+|+|+|||||||...+++
T Consensus 5 ~~~~e~-~~~~~lC~C~~S~~~PfCDGsH~~~~~~ 38 (38)
T smart00704 5 EVEVEK-REKYALCRCGRSKNFPYCDGSHKKHNEQ 38 (38)
T ss_pred EEEecC-CCEEEEeeCCCCCCCCccCCcccCcCcC
Confidence 455565 6889999999999999999999987753
No 3
>PF09360 zf-CDGSH: Iron-binding zinc finger CDGSH type; InterPro: IPR018967 This entry represents iron-sulphur domain containing proteins that have a CDGSH sequence motif (although the Ser residue can also be an Ala or Thr), and is found in proteins from a wide range of organisms with the exception of fungi. The CDGSH-type domain binds a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family []. CDGSH-type domains are found in mitoNEET, an iron-containing integral protein of the outer mitochondrian membrane (OMM). MitoNEET forms a dimeric structure with a NEET fold, and contains two domains: a beta-cap region and a cluster-binding domain that coordinated two acid-labile 2Fe-2S clusters (one bound to each protomer) []. The CDGSH iron-sulphur domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, (IPR019610 from INTERPRO) [, ]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM. ; GO: 0051537 2 iron, 2 sulfur cluster binding, 0043231 intracellular membrane-bounded organelle; PDB: 3TBO_A 3FNV_B 3TBM_B 3TBN_A 3S2R_A 3S2Q_A 3LPQ_A 2QH7_A 3EW0_A 2R13_A ....
Probab=99.60 E-value=3.4e-16 Score=92.28 Aligned_cols=37 Identities=43% Similarity=0.635 Sum_probs=24.4
Q ss_pred cccceEEEeeeccCCCceEEEEeeCCCCCCccccCCCc
Q psy4887 43 KSNSKVVNVINIEDIADTLALCRCWRSKTFPKCDGSHA 80 (100)
Q Consensus 43 k~~pkvv~~~~~e~~~~~~~~CrCg~S~~~PfCDGSH~ 80 (100)
+++|.+++. +.+...++++|||||+|+|+|||||||+
T Consensus 2 ~~~P~~v~g-~~~~~~~~~~lC~Cg~S~~~PfCDGsH~ 38 (38)
T PF09360_consen 2 DNGPYKVEG-DTELEKGTYALCRCGKSKNKPFCDGSHK 38 (38)
T ss_dssp TTSSEEEEE-CGGCSTSEEEE-SSS--TTTTB--SHHH
T ss_pred CCcCEEEEe-eEEecCCEEEEecCCCCCCCCccCCcCC
Confidence 457888766 2222258999999999999999999995
No 4
>COG3369 Zinc finger domain containing protein (CDGSH-type) [Function unknown]
Probab=99.35 E-value=4.5e-13 Score=90.27 Aligned_cols=28 Identities=39% Similarity=0.744 Sum_probs=25.9
Q ss_pred CceEEEEeeCCCCCCccccCCCcCCccc
Q psy4887 58 ADTLALCRCWRSKTFPKCDGSHAQHNQC 85 (100)
Q Consensus 58 ~~~~~~CrCg~S~~~PfCDGSH~~~~~~ 85 (100)
...+++||||+|.|+|||||||.+..++
T Consensus 28 ~~~~~LCrCG~S~NKPfCDGtH~k~gf~ 55 (78)
T COG3369 28 DEQAALCRCGHSENKPFCDGTHKKTGFD 55 (78)
T ss_pred ceEEEEEeccCcCCCCccCCcccccccc
Confidence 4789999999999999999999999885
No 5
>KOG4605|consensus
Probab=99.27 E-value=3.6e-12 Score=92.35 Aligned_cols=75 Identities=19% Similarity=0.289 Sum_probs=57.3
Q ss_pred hhhhhhhhhheeee------------------eeEeeEEeeecCCCccccccccccceEEEeeeccCCCceEEEEeeCCC
Q psy4887 8 ADFVKYVPYALVLG------------------GISYGVYKVISPKGHINPNIQKSNSKVVNVINIEDIADTLALCRCWRS 69 (100)
Q Consensus 8 ~dwl~l~p~~~~~~------------------~~gY~~~~~f~~~~~vN~~I~k~~pkvv~~~~~e~~~~~~~~CrCg~S 69 (100)
+.|..++|....++ .+||+..|||||+++.|+. +.+-++|.+.. |. ...|++|.|+++
T Consensus 30 ~~ta~~lp~~g~v~~k~p~KVhL~a~KtY~WCsCG~S~sQPfCDGsHk~~~--~tklrPvrFkv-ek-tg~~wlCnCKqT 105 (129)
T KOG4605|consen 30 AQTAPRLPARGVVALKTPIKVHLVAGKTYRWCSCGRSKSQPFCDGSHKFQG--RTKLRPVRFKV-EK-TGMVWLCNCKQT 105 (129)
T ss_pred cccccccccCceecccCceEEEEecCCEEEEEeccccCCCccccccccccc--cccccceEeEe-cc-cceEEeeccccc
Confidence 56666777666543 4788999999999999886 44445555543 43 689999999999
Q ss_pred CCCccccCCCcCCcccC
Q psy4887 70 KTFPKCDGSHAQHNQCT 86 (100)
Q Consensus 70 ~~~PfCDGSH~~~~~~~ 86 (100)
.+.|||||.|+....+.
T Consensus 106 ~~rP~CDGtH~~~~~q~ 122 (129)
T KOG4605|consen 106 QRRPYCDGTHRSERVQK 122 (129)
T ss_pred CCCCccCCcccccccch
Confidence 99999999999776543
No 6
>KOG4605|consensus
Probab=99.09 E-value=2e-10 Score=83.29 Aligned_cols=55 Identities=29% Similarity=0.481 Sum_probs=40.3
Q ss_pred ccccccccceEEEeeeccCCCceEEEEeeCCCCCCccccCCCcCCcccCCCcccceEEEecc
Q psy4887 38 NPNIQKSNSKVVNVINIEDIADTLALCRCWRSKTFPKCDGSHAQHNQCTGDNVGPVLIKRNA 99 (100)
Q Consensus 38 N~~I~k~~pkvv~~~~~e~~~~~~~~CrCg~S~~~PfCDGSH~~~~~~~gdnvgPl~~~~~~ 99 (100)
|-.|....|..|+.. -++.|.||.||+|+.+|||||||+... -.++-|+-++-++
T Consensus 39 ~g~v~~k~p~KVhL~----a~KtY~WCsCG~S~sQPfCDGsHk~~~---~tklrPvrFkvek 93 (129)
T KOG4605|consen 39 RGVVALKTPIKVHLV----AGKTYRWCSCGRSKSQPFCDGSHKFQG---RTKLRPVRFKVEK 93 (129)
T ss_pred CceecccCceEEEEe----cCCEEEEEeccccCCCccccccccccc---cccccceEeEecc
Confidence 334444445554442 268899999999999999999999554 5678888877654
No 7
>PF10660 MitoNEET_N: Iron-containing outer mitochondrial membrane protein N-terminus ; InterPro: IPR019610 The CDGSH iron sulphur domain are a group of iron-sulphur (Fe-S) clusters and a unique 39 amino acid CDGSH domain [C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H]. The CDGSH iron sulphur domain protein (also referred to as mitoNEET) is an integral membrane protein located in the outer mitochondrial membrane and whose function may be to transport iron into the mitochondria []. Iron in turn is essential for the function of several mitochondrial enzymes. This entry represents the N-terminal of the mitoNEET and Miner-type proteins that carry a CDGSH-type cluster-binding domain (IPR018967 from INTERPRO) that coordinate a redox-active 2Fe-2S cluster. In the outer mitochondrian membrane (OMM), the CDGSH 2Fe-2S-containing domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by the N-terminal domain found in higher vertebrates [, , ]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM.; GO: 0051537 2 iron, 2 sulfur cluster binding, 0043231 intracellular membrane-bounded organelle; PDB: 2R13_A 3REE_A 2QD0_B.
Probab=98.41 E-value=5.4e-08 Score=63.50 Aligned_cols=33 Identities=33% Similarity=0.638 Sum_probs=3.4
Q ss_pred cchhhhhhhhhhheeeeeeEeeEEeeecCCCcc
Q psy4887 5 SPLADFVKYVPYALVLGGISYGVYKVISPKGHI 37 (100)
Q Consensus 5 ~~~~dwl~l~p~~~~~~~~gY~~~~~f~~~~~v 37 (100)
.+++||++|+|+++++|++||+.+++|+++.+.
T Consensus 31 Ls~kdWl~Lvp~~~~va~igYlayk~f~pk~~~ 63 (64)
T PF10660_consen 31 LSVKDWLALVPFAAAVAGIGYLAYKPFCPKKKC 63 (64)
T ss_dssp -------------------------CC---STT
T ss_pred ccHHHHHHHHhHHHHHHHHHHHhheeecccccC
Confidence 467999999999999999999999999996553
No 8
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=45.99 E-value=34 Score=29.43 Aligned_cols=54 Identities=22% Similarity=0.359 Sum_probs=35.3
Q ss_pred eEeeEEeeecCC-CccccccccccceEEEeeeccCCCceEEEEeeCCCCCCccccCCCcCCccc
Q psy4887 23 ISYGVYKVISPK-GHINPNIQKSNSKVVNVINIEDIADTLALCRCWRSKTFPKCDGSHAQHNQC 85 (100)
Q Consensus 23 ~gY~~~~~f~~~-~~vN~~I~k~~pkvv~~~~~e~~~~~~~~CrCg~S~~~PfCDGSH~~~~~~ 85 (100)
-+|+-+.|+|++ +++++ .++..+|.+. +...+-|.||+....++=+| |.|++++
T Consensus 169 ~~~~P~~pic~~cg~~~~-------~~~~~~d~~~-~~v~y~~~cG~~~~~~~~~g-~~KL~Wr 223 (510)
T PRK00750 169 ATYSPFLPICPKCGKVLT-------TPVISYDAEA-GTVTYDCECGHEGEVPVTGG-HGKLQWK 223 (510)
T ss_pred CCeeeeeeeCCCCCccce-------EEEEEEeCCC-CEEEEEcCCCCEEEEecCCC-CcccCCC
Confidence 467777788874 44443 2333455553 34455799999999999886 6677654
No 9
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=32.40 E-value=73 Score=26.40 Aligned_cols=54 Identities=11% Similarity=0.111 Sum_probs=33.3
Q ss_pred eEeeEEeeecCCCccccccccccceEEEeeeccCCCceEEEEeeCCCCCCccccCCCcCCccc
Q psy4887 23 ISYGVYKVISPKGHINPNIQKSNSKVVNVINIEDIADTLALCRCWRSKTFPKCDGSHAQHNQC 85 (100)
Q Consensus 23 ~gY~~~~~f~~~~~vN~~I~k~~pkvv~~~~~e~~~~~~~~CrCg~S~~~PfCDGSH~~~~~~ 85 (100)
-+|+-+.|+|++-- +++ ..|..+|.+. +...+-|.||+....++=+| +.|++++
T Consensus 163 ~~~~P~~p~c~~cg---~~~----~~v~~~d~~~-~~v~y~c~cG~~g~~~~~~g-~~KL~Wr 216 (353)
T cd00674 163 ETWYPFMPYCEKCG---KDT----TTVEAYDAKA-GTVTYKCECGHEETVDIRTG-RGKLTWR 216 (353)
T ss_pred CCceeeeeecCCcC---cce----eEEEEEeCCC-CeEEEEcCCCCEEEEeecCC-CcccCCC
Confidence 45666677776422 221 3334455543 45677899999999988765 4566543
No 10
>PLN02961 alanine-tRNA ligase
Probab=28.22 E-value=56 Score=24.78 Aligned_cols=58 Identities=16% Similarity=0.244 Sum_probs=33.2
Q ss_pred ccccccccccceEEEeeeccCC--------------CceEEEEeeCCCCCCccccCCCcCCcccCCCcccceEEEec
Q psy4887 36 HINPNIQKSNSKVVNVINIEDI--------------ADTLALCRCWRSKTFPKCDGSHAQHNQCTGDNVGPVLIKRN 98 (100)
Q Consensus 36 ~vN~~I~k~~pkvv~~~~~e~~--------------~~~~~~CrCg~S~~~PfCDGSH~~~~~~~gdnvgPl~~~~~ 98 (100)
.+|..|+.+.|..+..++.++. ++.+-+-.-+-+.-. .|=|+|.. .|++ +|++.|.+.
T Consensus 139 ~~N~~I~~~~~V~~~~~~~~ea~~~~~~~~~~~~~~~~~vRiV~I~~~d~~-~CgGTHv~---nT~e-ig~i~I~~~ 210 (223)
T PLN02961 139 EANELIAEGGKVSAAVLPYDEAAELCGGSLPDYIAKDSTPRIVKIGDSPGC-PCGGTHVA---DVSE-ITSVKVTQI 210 (223)
T ss_pred HHHHHHHcCCceeEEEeCHHHHHHhcCCcCCCcCCCCCceEEEEECCCccC-ccCCcccC---chhc-cccEEEEEE
Confidence 4677888887777766554321 122333333332222 28999994 3444 888887653
No 11
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=23.83 E-value=67 Score=19.72 Aligned_cols=12 Identities=25% Similarity=0.335 Sum_probs=8.9
Q ss_pred CceEEEEeeCCC
Q psy4887 58 ADTLALCRCWRS 69 (100)
Q Consensus 58 ~~~~~~CrCg~S 69 (100)
+.-++-||||..
T Consensus 15 ~~~~y~CRCG~~ 26 (55)
T PF05207_consen 15 GVYSYPCRCGGE 26 (55)
T ss_dssp TEEEEEETTSSE
T ss_pred CEEEEcCCCCCE
Confidence 456788999864
No 12
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=21.30 E-value=95 Score=27.03 Aligned_cols=52 Identities=13% Similarity=0.094 Sum_probs=32.9
Q ss_pred eEeeEEeeecCC-CccccccccccceEEEeeeccCCCceEEEEeeCCCCCCccccCCCcCCccc
Q psy4887 23 ISYGVYKVISPK-GHINPNIQKSNSKVVNVINIEDIADTLALCRCWRSKTFPKCDGSHAQHNQC 85 (100)
Q Consensus 23 ~gY~~~~~f~~~-~~vN~~I~k~~pkvv~~~~~e~~~~~~~~CrCg~S~~~PfCDGSH~~~~~~ 85 (100)
-+|+=+.|+|++ +++.+ .++ .+|.+. ...+-|.||+....++=+| +.|++++
T Consensus 162 ~~~~P~~pic~~cGrv~~-------~~~-~~~~~~--~v~Y~c~cG~~g~~~~~~g-~~KL~Wk 214 (515)
T TIGR00467 162 ENWYPISVFCENCGRDTT-------TVN-NYDNEY--SIEYSCECGNQESVDIYTG-AIKLPWR 214 (515)
T ss_pred CCceeeeeecCCcCccCc-------eEE-EecCCc--eEEEEcCCCCEEEEeecCC-CcccCCC
Confidence 456667777774 44433 222 344443 3556799999999999655 5576654
Done!