Query T0539 HR4710B, , 81 residues
Match_columns 81
No_of_seqs 127 out of 4952
Neff 7.3
Searched_HMMs 11830
Date Fri May 21 18:06:23 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0539.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0539.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00097 zf-C3HC4: Zinc finger 99.0 1.3E-11 1.1E-15 75.3 1.0 40 33-73 1-42 (42)
2 PF11793 FANCL_C: FANCL C-term 98.8 5.5E-10 4.6E-14 67.2 1.6 50 29-78 1-66 (70)
3 PF05883 Baculo_RING: Baculovi 98.6 3.8E-09 3.2E-13 63.1 0.4 47 30-76 26-78 (134)
4 PF04564 U-box: U-box domain; 98.4 3.3E-08 2.8E-12 58.3 1.2 50 27-79 2-52 (75)
5 PF11789 zf-Nse: Zinc-finger o 97.7 2.5E-06 2.1E-10 48.9 0.6 44 28-73 9-56 (57)
6 PF04641 Rtf2: Replication ter 97.2 7.5E-05 6.4E-09 41.6 3.0 49 27-77 109-158 (258)
7 PF10367 Vps39_2: Vacuolar sor 96.3 0.00044 3.7E-08 37.7 1.3 36 26-62 74-109 (109)
8 PF10272 Tmpp129: Putative tra 95.5 0.0014 1.2E-07 35.3 0.9 29 49-77 309-350 (358)
9 PF07800 DUF1644: Protein of u 95.4 0.0042 3.5E-07 32.9 3.1 47 29-78 1-91 (162)
10 PF08746 zf-RING-like: RING-li 94.9 0.0016 1.4E-07 34.9 -0.2 41 33-73 1-43 (43)
11 PF03854 zf-P11: P-11 zinc fin 90.9 0.025 2.1E-06 29.0 0.8 32 50-81 17-49 (50)
12 PF02891 zf-MIZ: MIZ/SP-RING z 90.8 0.031 2.6E-06 28.5 1.2 44 30-76 2-50 (50)
13 PF11261 IRF-2BP1_2: Interfero 83.3 0.15 1.2E-05 25.1 1.0 40 29-68 442-482 (516)
14 PF05290 Baculo_IE-1: Baculovi 80.9 0.18 1.5E-05 24.7 0.7 49 30-78 80-132 (140)
15 PF07191 DUF1407: Protein of u 75.1 0.091 7.7E-06 26.2 -2.2 40 30-77 1-40 (70)
16 PF06906 DUF1272: Protein of u 68.4 1.4 0.00012 20.3 2.6 45 32-80 7-55 (57)
17 PF00628 PHD: PHD-finger; Int 65.4 0.78 6.6E-05 21.5 0.9 44 32-75 1-50 (51)
18 PF10497 zf-4CXXC_R1: Zinc-fin 55.7 1.2 0.0001 20.5 0.5 27 49-75 31-69 (105)
19 PF01363 FYVE: FYVE zinc finge 55.5 2 0.00017 19.5 1.6 39 28-66 7-46 (69)
20 PF05605 Di19: Drought induced 51.9 1.1 9.1E-05 20.8 -0.3 43 27-77 30-72 (210)
21 PF06844 DUF1244: Protein of u 50.2 1.4 0.00012 20.2 0.1 13 54-66 11-23 (68)
22 PF04423 Rad50_zn_hook: Rad50 40.4 2.9 0.00024 18.7 0.4 10 69-78 22-31 (54)
23 PF04216 FdhE: Protein involve 38.8 1.3 0.00011 20.4 -1.6 47 29-76 171-220 (290)
24 PF06937 EURL: EURL protein; 33.3 9.9 0.00084 16.0 2.2 42 31-74 31-77 (285)
25 PF06750 DiS_P_DiS: Bacterial 32.6 8.4 0.00071 16.4 1.8 22 58-79 49-70 (92)
26 PF01485 IBR: IBR domain; Int 28.1 1.6 0.00013 20.0 -2.6 33 31-63 19-58 (64)
27 PF07975 C1_4: TFIIH C1-like d 27.7 4.8 0.00041 17.6 -0.1 42 33-74 2-50 (51)
28 PF09943 DUF2175: Uncharacteri 21.3 13 0.0011 15.5 1.0 35 31-66 3-37 (101)
29 PF06044 DRP: Dam-replacing fa 20.3 15 0.0013 15.1 1.2 32 27-63 28-63 (254)
No 1
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR001841 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents RING-type zinc finger domains. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions. , , . There are two different variants, the C3HC4-type and a C3H2C3-type, which are clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain that has been implicated in a range of diverse biological processes. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain. E3 ubiquitin-protein ligases determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 . Various RING fingers also exhibit binding to E2 ubiquitin-conjugating enzymes (Ubc's) , , . Several 3D-structures for RING-fingers are known , . The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C. Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second, as illustrated in the following schematic representation: Note that in the older literature, some RING-fingers are denoted as LIM-domains. The LIM-domain Zn-finger is a fundamentally different family, albeit with similar Cys-spacing (see IPR001781 from INTERPRO). More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0005515 protein binding, 0008270 zinc ion binding; PDB: 1x4j_A 2ep4_A 2ect_A 2djb_A 2ckl_A 2h0d_A 2k4d_A 1fbv_A 1chc_A 2ecn_A ....
Probab=99.04 E-value=1.3e-11 Score=75.33 Aligned_cols=40 Identities=48% Similarity=1.138 Sum_probs=36.2
Q ss_pred CCEECCCCCCCCEEEECCCCCCCCCCCHHHHHH--CCCCCCCC
Q ss_conf 421346677897156500344337732168986--08998802
Q T0539 33 CPICCSEYVKGEVATELPCHHYFHKPCVSIWLQ--KSGTCPVC 73 (81)
Q Consensus 33 C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~--~~~~CP~C 73 (81)
|+||++++++++ +..++|||.||.+||.+|++ .+.+||+|
T Consensus 1 C~IC~~~~~~~~-~~~~~C~H~fc~~Cl~~~~~~~~~~~CP~C 42 (42)
T PF00097_consen 1 CPICLDEFEDPE-VLLLPCGHSFCKKCLEKWLKSSKNFKCPIC 42 (42)
T ss_dssp ETTTTSBBSSEE-EEETTTTEEEEHHHHHHHHHHHHSSCTTTT
T ss_pred CCCCCCCCCCCC-EEEECCCCCHHHHHHHHHHCCCCCCCCCCC
T ss_conf 965786736898-586068981429999999836878999289
No 2
>PF11793 FANCL_C: FANCL C-terminal domain
Probab=98.78 E-value=5.5e-10 Score=67.25 Aligned_cols=50 Identities=40% Similarity=0.826 Sum_probs=37.8
Q ss_pred CCCCCCEECCCCCCCCEE--EEC---CCCCCCCCCCHHHHHHCC-----------CCCCCCCCCCC
Q ss_conf 776042134667789715--650---034433773216898608-----------99880267588
Q T0539 29 QEMCCPICCSEYVKGEVA--TEL---PCHHYFHKPCVSIWLQKS-----------GTCPVCRCMFP 78 (81)
Q Consensus 29 ~~~~C~ICl~~~~~~~~~--~~l---~C~H~Fh~~Ci~~Wl~~~-----------~~CP~CR~~~p 78 (81)
++.+|+||+..+..++.+ ..- .|++.||..||.+||... ++||+||.+|-
T Consensus 1 ~~~~C~IC~~~~~~~~~~p~~~C~~~~C~~~fH~~CL~~Wf~~~~~~r~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 1 QELECPICYSYRLDDGELPDVVCPNPSCGNKFHMLCLSEWFLSSEKSRQSFNPIFGTCPYCRSPIS 66 (70)
T ss_pred CCCCCCCCCCEEECCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf 995266847176459963604879876684999999999998677777012626779979998406
No 3
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several baculovirus proteins of around 130 residues in length. The function of this family is unknown.
Probab=98.56 E-value=3.8e-09 Score=63.05 Aligned_cols=47 Identities=17% Similarity=0.449 Sum_probs=41.9
Q ss_pred CCCCCEECCCCCCCCEEEECCCC------CCCCCCCHHHHHHCCCCCCCCCCC
Q ss_conf 76042134667789715650034------433773216898608998802675
Q T0539 30 EMCCPICCSEYVKGEVATELPCH------HYFHKPCVSIWLQKSGTCPVCRCM 76 (81)
Q Consensus 30 ~~~C~ICl~~~~~~~~~~~l~C~------H~Fh~~Ci~~Wl~~~~~CP~CR~~ 76 (81)
..+|+||++.+..++.++.++|| |.||.+|+.+|.+.++..|+.|.-
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~~~lnLEkmFc~~C~krw~~~~~rDPf~R~I 78 (134)
T PF05883_consen 26 NVECAICFDRINDNDGVVAVTDGGTLNLEKMFCAECIKRWKRENNRDPFNRNI 78 (134)
T ss_pred CCCCHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCE
T ss_conf 75307668876069998998269712388999999999998644899864645
No 4
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 . Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families . Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins , . Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues . ; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1t1h_A 2oxq_C 2f42_A 2c2v_S 2c2l_D 2qiz_A 2qj0_A 1wgm_A 2yur_A.
Probab=98.36 E-value=3.3e-08 Score=58.32 Aligned_cols=50 Identities=26% Similarity=0.607 Sum_probs=42.6
Q ss_pred CCCCCCCCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHC-CCCCCCCCCCCCC
Q ss_conf 6777604213466778971565003443377321689860-8998802675888
Q T0539 27 VGQEMCCPICCSEYVKGEVATELPCHHYFHKPCVSIWLQK-SGTCPVCRCMFPP 79 (81)
Q Consensus 27 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~~p~ 79 (81)
..++..|+|+.+-|.+. +++++||.|.+.+|.+|+.. +++||++|+.+..
T Consensus 2 iP~~f~CpIt~~lm~dP---Vi~~~g~tyer~~I~~~l~~~~~~~P~t~~~l~~ 52 (75)
T PF04564_consen 2 IPEEFLCPITGELMKDP---VILPSGHTYERSAIEKWLRQGNPTCPITRQPLTS 52 (75)
T ss_dssp SSGGGC-TTTSSB-SSE---EE-TTT-EEEHHHHHHHHCTSSSB-TTT-SB-SC
T ss_pred CCHHHCCCCCCCHHCCC---EECCCCCEECHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 73263686766642198---4878898865799999998199989998982781
No 5
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2yu4_A.
Probab=97.71 E-value=2.5e-06 Score=48.95 Aligned_cols=44 Identities=27% Similarity=0.643 Sum_probs=36.4
Q ss_pred CCCCCCCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHC--CCCCCC--C
Q ss_conf 777604213466778971565003443377321689860--899880--2
Q T0539 28 GQEMCCPICCSEYVKGEVATELPCHHYFHKPCVSIWLQK--SGTCPV--C 73 (81)
Q Consensus 28 ~~~~~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~--~~~CP~--C 73 (81)
..+..|+|++..|+ ++++...|||+|.+++|.+|++. +..||+ |
T Consensus 9 ~~~l~CPit~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv~GC 56 (57)
T PF11789_consen 9 VISLKCPITLKPFE--DPVRSKKCGHVFEKEAIEQYIKNNGSIRCPVAGC 56 (57)
T ss_dssp ----B-TTT-SB-S--SEEEES----EEEHHHHHHHHTTT--B-------
T ss_pred EEECCCCCCCCCCC--CCCCCCCCCCEECHHHHHHHHHHCCCCCCCCCCC
T ss_conf 41048878467213--8856487888775999999998469988998768
No 6
>PF04641 Rtf2: Replication termination factor 2; InterPro: IPR006735 This family represents several uncharacterised eukaryotic proteins.
Probab=97.22 E-value=7.5e-05 Score=41.58 Aligned_cols=49 Identities=31% Similarity=0.602 Sum_probs=39.1
Q ss_pred CCCCCCCCEECCCCCCCCEEEEC-CCCCCCCCCCHHHHHHCCCCCCCCCCCC
Q ss_conf 67776042134667789715650-0344337732168986089988026758
Q T0539 27 VGQEMCCPICCSEYVKGEVATEL-PCHHYFHKPCVSIWLQKSGTCPVCRCMF 77 (81)
Q Consensus 27 ~~~~~~C~ICl~~~~~~~~~~~l-~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~~ 77 (81)
......|||...+|......+.+ +|||+|...+|++- ....||+|-..|
T Consensus 109 ~~~~~~CPvt~~~~~~~~~fv~l~~CG~V~S~~al~e~--k~~~C~~C~~~f 158 (258)
T PF04641_consen 109 SDGEFICPVTGKEFNGNTKFVALRPCGCVFSEKALKEL--KSKKCPVCGEPF 158 (258)
T ss_pred CCCCEECCCCCCCCCCCEEEEEEECCCCEECHHHHHHH--CCCCCCCCCCCC
T ss_conf 67865789866255796459999188789429999976--007685547736
No 7
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2
Probab=96.32 E-value=0.00044 Score=37.74 Aligned_cols=36 Identities=19% Similarity=0.459 Sum_probs=28.9
Q ss_pred CCCCCCCCCEECCCCCCCCEEEECCCCCCCCCCCHHH
Q ss_conf 6677760421346677897156500344337732168
Q T0539 26 AVGQEMCCPICCSEYVKGEVATELPCHHYFHKPCVSI 62 (81)
Q Consensus 26 ~~~~~~~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~ 62 (81)
..+++..|++|-..+.. ......||||.||..|+.+
T Consensus 74 ~i~~~~~C~~C~k~l~~-~~f~~~P~~~~~H~~C~~r 109 (109)
T PF10367_consen 74 VIDEDTKCSVCHKPLGN-SVFVVFPNGHVVHYHCAKR 109 (109)
T ss_pred EECCCCCCHHHCCCCCC-CEEEEECCCEEEEHHHCCC
T ss_conf 97999887655896699-8599968994871221349
No 8
>PF10272 Tmpp129: Putative transmembrane protein precursor
Probab=95.52 E-value=0.0014 Score=35.30 Aligned_cols=29 Identities=28% Similarity=0.841 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCHHHHHHCC-------------CCCCCCCCCC
Q ss_conf 0034433773216898608-------------9988026758
Q T0539 49 LPCHHYFHKPCVSIWLQKS-------------GTCPVCRCMF 77 (81)
Q Consensus 49 l~C~H~Fh~~Ci~~Wl~~~-------------~~CP~CR~~~ 77 (81)
.-|...+|.+|+-+|+..+ -.||+||+.|
T Consensus 309 CyCRPmWC~~C~~~wFasrQ~~~~~~~wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 309 CYCRPMWCLDCMAKWFASRQDQQHRETWLSSKCPCPTCRAKF 350 (358)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCCCEECCCCCCCCCCCEE
T ss_conf 525030898887777510456468773314767898642136
No 9
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=95.44 E-value=0.0042 Score=32.88 Aligned_cols=47 Identities=26% Similarity=0.698 Sum_probs=31.3
Q ss_pred CCCCCCEECCCCCCCCEEEECC------------CCCCC-CCCCHHHHHHC-----------------------------
Q ss_conf 7760421346677897156500------------34433-77321689860-----------------------------
Q T0539 29 QEMCCPICCSEYVKGEVATELP------------CHHYF-HKPCVSIWLQK----------------------------- 66 (81)
Q Consensus 29 ~~~~C~ICl~~~~~~~~~~~l~------------C~H~F-h~~Ci~~Wl~~----------------------------- 66 (81)
++..|+||||---++ +.|- |+-.| |..|+++.-+.
T Consensus 1 ed~~CpiCme~PHNA---VLL~CSS~~kgcRPymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 77 (162)
T PF07800_consen 1 EDVTCPICMEHPHNA---VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSTSQSASSAPLDSNSSESSEKCE 77 (162)
T ss_pred CCCCCCEECCCCCCE---EEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 986674001589861---78884366788764245666413179999998625777766655445766654445633456
Q ss_pred --CCCCCCCCCCCC
Q ss_conf --899880267588
Q T0539 67 --SGTCPVCRCMFP 78 (81)
Q Consensus 67 --~~~CP~CR~~~p 78 (81)
.-.||+||.++-
T Consensus 78 ~~~L~CPLCRG~V~ 91 (162)
T PF07800_consen 78 QPELACPLCRGEVK 91 (162)
T ss_pred CCCCCCCCCCCCEE
T ss_conf 67455887467100
No 10
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 2ct0_A.
Probab=94.92 E-value=0.0016 Score=34.89 Aligned_cols=41 Identities=22% Similarity=0.720 Sum_probs=33.7
Q ss_pred CCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHCCC--CCCCC
Q ss_conf 421346677897156500344337732168986089--98802
Q T0539 33 CPICCSEYVKGEVATELPCHHYFHKPCVSIWLQKSG--TCPVC 73 (81)
Q Consensus 33 C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~~~--~CP~C 73 (81)
|.+|.+.+..|..-..-.|+=.+|..|+.++++.+. +||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~~~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEVCKEIVTQGQRCSNRDCPIRLHDDCFKKYFRHRSNPRCPSC 43 (43)
T ss_dssp -SSS--B-----B-S------B--HHHHHHHSTT-SS---TTT
T ss_pred CCHHHHHHEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 9112177813044899765710799999999964799999687
No 11
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions. , , . There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known , . The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E , . It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell . This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication . More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0003723 RNA binding, 0008270 zinc ion binding
Probab=90.93 E-value=0.025 Score=28.99 Aligned_cols=32 Identities=31% Similarity=0.908 Sum_probs=28.6
Q ss_pred CCC-CCCCCCCHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 034-43377321689860899880267588889
Q T0539 50 PCH-HYFHKPCVSIWLQKSGTCPVCRCMFPPPL 81 (81)
Q Consensus 50 ~C~-H~Fh~~Ci~~Wl~~~~~CP~CR~~~p~p~ 81 (81)
.|. |..|..|+...+..++.||+|..++|.-+
T Consensus 17 ~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt~i 49 (50)
T PF03854_consen 17 KCSDHYLCLNCLTLMLSRSDRCPICGKPLPTKI 49 (50)
T ss_pred EECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 134115799999999732678773567676555
No 12
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 . Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding
Probab=90.75 E-value=0.031 Score=28.53 Aligned_cols=44 Identities=18% Similarity=0.443 Sum_probs=31.3
Q ss_pred CCCCCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHCCC-----CCCCCCCC
Q ss_conf 760421346677897156500344337732168986089-----98802675
Q T0539 30 EMCCPICCSEYVKGEVATELPCHHYFHKPCVSIWLQKSG-----TCPVCRCM 76 (81)
Q Consensus 30 ~~~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~~~-----~CP~CR~~ 76 (81)
...|+|....+.. +++...|.|..|.+- ..|++.+. .||+|++.
T Consensus 2 sL~Cpls~~~i~~--P~Rg~~C~H~qCFDl-~~fl~~~~~~~~w~CPiC~~~ 50 (50)
T PF02891_consen 2 SLRCPLSFQRIKI--PVRGKNCQHLQCFDL-ESFLESNQQTNKWKCPICNKP 50 (50)
T ss_pred CCCCCCCCCEEEE--CCCCCCCCCCCEECH-HHHHHHHHCCCCCCCCCCCCC
T ss_conf 4258788878776--662686898777688-999999752897099487997
No 13
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein 1 & 2; PDB: 2cs3_A.
Probab=83.32 E-value=0.15 Score=25.15 Aligned_cols=40 Identities=23% Similarity=0.539 Sum_probs=30.0
Q ss_pred CCCCCCEECCCCCCCCEEEECC-CCCCCCCCCHHHHHHCCC
Q ss_conf 7760421346677897156500-344337732168986089
Q T0539 29 QEMCCPICCSEYVKGEVATELP-CHHYFHKPCVSIWLQKSG 68 (81)
Q Consensus 29 ~~~~C~ICl~~~~~~~~~~~l~-C~H~Fh~~Ci~~Wl~~~~ 68 (81)
..+.|.||.|.+++..-+..-. =+|.||+.|-+..++.+.
T Consensus 442 ~~l~ctlc~e~ledthfvqcpsv~~hkfcfpc~r~~ik~q~ 482 (516)
T PF11261_consen 442 APLCCTLCQERLEDTHFVQCPSVPHHKFCFPCSRESIKQQG 482 (516)
T ss_dssp -----SSS-S--SSTTSEE-SS-SS-EE-HHHHHHHHHH--
T ss_pred CCEEEECCHHHHCCCCEEECCCCCCCCEECCCCHHHHHHCC
T ss_conf 86244251445237734426777777113223689997337
No 14
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=80.85 E-value=0.18 Score=24.75 Aligned_cols=49 Identities=20% Similarity=0.415 Sum_probs=33.5
Q ss_pred CCCCCEECCCCCCCCEEEE-CCCCCCCCCCCHHHHHHCC---CCCCCCCCCCC
Q ss_conf 7604213466778971565-0034433773216898608---99880267588
Q T0539 30 EMCCPICCSEYVKGEVATE-LPCHHYFHKPCVSIWLQKS---GTCPVCRCMFP 78 (81)
Q Consensus 30 ~~~C~ICl~~~~~~~~~~~-l~C~H~Fh~~Ci~~Wl~~~---~~CP~CR~~~p 78 (81)
--+|-||.|.-.+..=+.- .-||=..|..|-..-++.. ..||+|+..+-
T Consensus 80 lYeCnIC~etS~e~~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFK 132 (140)
T PF05290_consen 80 LYECNICKETSTEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFK 132 (140)
T ss_pred CEECCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 23503753433112037962231327999999999987355878986556545
No 15
>PF07191 DUF1407: Protein of unknown function (DUF1407); InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2jne_A 2jrp_A.
Probab=75.07 E-value=0.091 Score=26.19 Aligned_cols=40 Identities=33% Similarity=0.595 Sum_probs=27.8
Q ss_pred CCCCCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHCCCCCCCCCCCC
Q ss_conf 760421346677897156500344337732168986089988026758
Q T0539 30 EMCCPICCSEYVKGEVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 77 (81)
Q Consensus 30 ~~~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~~ 77 (81)
+..||.|..+++... +|.+|..|-.. ++....||-|.++|
T Consensus 1 e~~CP~C~~el~~~~-------~~~~C~~C~~~-~~~~~~CPdC~~~L 40 (70)
T PF07191_consen 1 ENICPQCQQELEWKG-------GHYHCSQCQKD-FQKEAYCPDCGQEL 40 (70)
T ss_dssp --B-SSS-SBEEE----------EEEETTT--E-EEEEEE-TTT-SB-
T ss_pred CCCCCCCCCEEEECC-------CEEECHHHCCC-EEEEECCCCCCHHH
T ss_conf 986865574303648-------85884030411-05657288520599
No 16
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=68.38 E-value=1.4 Score=20.32 Aligned_cols=45 Identities=27% Similarity=0.575 Sum_probs=31.9
Q ss_pred CCCEECCCCCCCC-EEEECCCC--CCCCCCCHHHHHHCCCCCCCCCCCC-CCC
Q ss_conf 0421346677897-15650034--4337732168986089988026758-888
Q T0539 32 CCPICCSEYVKGE-VATELPCH--HYFHKPCVSIWLQKSGTCPVCRCMF-PPP 80 (81)
Q Consensus 32 ~C~ICl~~~~~~~-~~~~l~C~--H~Fh~~Ci~~Wl~~~~~CP~CR~~~-p~p 80 (81)
.|-.|-.++..+. .+.+ |. ..||.+|.+..| ++.||.|-.+| +.|
T Consensus 7 nCE~C~~dLp~ds~eA~I--CsfECTFC~~C~e~~l--~~~CPNCgG~lv~RP 55 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYI--CSFECTFCADCAETML--HGVCPNCGGELVRRP 55 (57)
T ss_pred CCCCCCCCCCCCCCCCEE--EEEECCCCHHHHHHHH--CCCCCCCCCCCCCCC
T ss_conf 876468979889985468--8777844578998886--584939998035588
No 17
>PF00628 PHD: PHD-finger; InterPro: IPR001965 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents the PHD (homeodomain) zinc finger domain ,, which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0005515 protein binding, 0008270 zinc ion binding; PDB: 2k16_A 2k17_A 1wep_A 2f6n_A 2f6j_A 2ri7_A 2fui_A 2fsa_B 2fuu_A 1we9_A ....
Probab=65.39 E-value=0.78 Score=21.52 Aligned_cols=44 Identities=32% Similarity=0.672 Sum_probs=30.0
Q ss_pred CCCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHC------CCCCCCCCC
Q ss_conf 04213466778971565003443377321689860------899880267
Q T0539 32 CCPICCSEYVKGEVATELPCHHYFHKPCVSIWLQK------SGTCPVCRC 75 (81)
Q Consensus 32 ~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~------~~~CP~CR~ 75 (81)
.|.||...-..++.+.--.|+..||..|+..-... .=.||.|+.
T Consensus 1 ~C~iC~~~~~~~~~i~Cd~C~~w~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPICGKSDDDGDMIQCDGCDRWFHQSCVGPPESSEEIPEGEWFCPDCRP 50 (51)
T ss_dssp ETTTTTECETTSTEEEBSTSSSEEETTTSSSTSSHHSCHSTSBSTHHHHH
T ss_pred CCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHCCCCCCCEECCCCCC
T ss_conf 98568888899848781999845980348978101558997089938828
No 18
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1
Probab=55.69 E-value=1.2 Score=20.53 Aligned_cols=27 Identities=26% Similarity=0.533 Sum_probs=20.8
Q ss_pred CCC---CCCCCCCCHHHHHHCC---------CCCCCCCC
Q ss_conf 003---4433773216898608---------99880267
Q T0539 49 LPC---HHYFHKPCVSIWLQKS---------GTCPVCRC 75 (81)
Q Consensus 49 l~C---~H~Fh~~Ci~~Wl~~~---------~~CP~CR~ 75 (81)
..| .-.||..||..+...+ -.||.||.
T Consensus 31 ~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CRg 69 (105)
T PF10497_consen 31 SSCHSCRGKFCYGCLFNRYGENPEEVMENPEWICPKCRG 69 (105)
T ss_pred CCCCCCCCHHHHHHHHHHHCCCHHHHHHCCCCCCCCCCC
T ss_conf 987657323219999988052589997377740877777
No 19
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn^2+ ions . The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding; PDB: 1joc_A 1hyj_A 1hyi_A 2yw8_A 2yqm_A 1x4u_A 1wfk_A 1vfy_A 1dvp_A.
Probab=55.54 E-value=2 Score=19.48 Aligned_cols=39 Identities=18% Similarity=0.232 Sum_probs=28.3
Q ss_pred CCCCCCCEECCCCCCCCE-EEECCCCCCCCCCCHHHHHHC
Q ss_conf 777604213466778971-565003443377321689860
Q T0539 28 GQEMCCPICCSEYVKGEV-ATELPCHHYFHKPCVSIWLQK 66 (81)
Q Consensus 28 ~~~~~C~ICl~~~~~~~~-~~~l~C~H~Fh~~Ci~~Wl~~ 66 (81)
.+...|.+|-..|..-.. -.--.||++||.+|...++..
T Consensus 7 ~~~~~C~~C~~~Fs~~~rrhhCr~CG~v~C~~C~~~~~~~ 46 (69)
T PF01363_consen 7 SEVSNCMICGKPFSLFRRRHHCRNCGRVFCSSCSSNRSPL 46 (69)
T ss_dssp CC-SB-TTT--B-BSSS-EEE-S----EEECGGS-EEEEE
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCEECHHHHCCCCCC
T ss_conf 8789184779835812156027998888696683886556
No 20
>PF05605 Di19: Drought induced 19 protein (Di19); InterPro: IPR008598 This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought . The precise function of Di19 is unknown.
Probab=51.87 E-value=1.1 Score=20.82 Aligned_cols=43 Identities=26% Similarity=0.613 Sum_probs=24.9
Q ss_pred CCCCCCCCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHCCCCCCCCCCCC
Q ss_conf 677760421346677897156500344337732168986089988026758
Q T0539 27 VGQEMCCPICCSEYVKGEVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 77 (81)
Q Consensus 27 ~~~~~~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~~ 77 (81)
......||.|.++|+. ..-|.|+--.++.. .+...||+|-..+
T Consensus 30 ~~~~f~CP~C~~~~d~-----~~L~~H~~~eH~~~---~~~~vCPvC~~~v 72 (210)
T PF05605_consen 30 LREEFTCPFCYEDFDV-----VSLCCHLEDEHPFE---SKNVVCPVCAAKV 72 (210)
T ss_pred CCCEEECCCCCCCCCH-----HHHHHHHHHHCCCC---CCCCCCCCHHHHC
T ss_conf 7761168998876558-----99999989747577---8666577204022
No 21
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 3fyb_B 2o35_A.
Probab=50.25 E-value=1.4 Score=20.23 Aligned_cols=13 Identities=31% Similarity=0.825 Sum_probs=11.2
Q ss_pred CCCCCCHHHHHHC
Q ss_conf 3377321689860
Q T0539 54 YFHKPCVSIWLQK 66 (81)
Q Consensus 54 ~Fh~~Ci~~Wl~~ 66 (81)
.||+.||.+|...
T Consensus 11 GFCRNCLs~Wy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRA 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
T ss_conf 8999987999999
No 22
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair, 0030870 Mre11 complex; PDB: 1l8d_A.
Probab=40.37 E-value=2.9 Score=18.68 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q ss_conf 9880267588
Q T0539 69 TCPVCRCMFP 78 (81)
Q Consensus 69 ~CP~CR~~~p 78 (81)
.||+|.+.|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp --S-------
T ss_pred CCCCCCCCCC
T ss_conf 7899999798
No 23
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex . The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; PDB: 2fiy_A.
Probab=38.82 E-value=1.3 Score=20.44 Aligned_cols=47 Identities=26% Similarity=0.420 Sum_probs=30.7
Q ss_pred CCCCCCEECCCCCCCCEEEECC---CCCCCCCCCHHHHHHCCCCCCCCCCC
Q ss_conf 7760421346677897156500---34433773216898608998802675
Q T0539 29 QEMCCPICCSEYVKGEVATELP---CHHYFHKPCVSIWLQKSGTCPVCRCM 76 (81)
Q Consensus 29 ~~~~C~ICl~~~~~~~~~~~l~---C~H~Fh~~Ci~~Wl~~~~~CP~CR~~ 76 (81)
....||||-..-..+ .+..-. =.+.+|.-|-..|--.+..||.|-.+
T Consensus 171 ~~g~CPVCGs~P~~s-~l~~~~~~G~R~L~Cs~C~teW~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 171 QRGYCPVCGSPPVAS-VLRGEERQGKRYLHCSLCGTEWHFVRVKCPYCGNE 220 (290)
T ss_dssp T-SS-S-----EEE--EE--------EEEEETTT--EEE--TTS-TTT---
T ss_pred CCCCCCCCCCCCCEE-EEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf 589799999857668-89438988617887799988243117768599999
No 24
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation .
Probab=33.29 E-value=9.9 Score=16.02 Aligned_cols=42 Identities=24% Similarity=0.522 Sum_probs=22.6
Q ss_pred CCCCEECCCCCCCCEEEECCCCC----CCCCCCHHHHHHC-CCCCCCCC
Q ss_conf 60421346677897156500344----3377321689860-89988026
Q T0539 31 MCCPICCSEYVKGEVATELPCHH----YFHKPCVSIWLQK-SGTCPVCR 74 (81)
Q Consensus 31 ~~C~ICl~~~~~~~~~~~l~C~H----~Fh~~Ci~~Wl~~-~~~CP~CR 74 (81)
.-|+||++.=..|.. .+.=-| .=|.+|+.+|-.. +.+||-=|
T Consensus 31 ~~C~iC~el~iegv~--~~~~~Ht~s~rGH~~CFEk~H~Ia~q~~~rsk 77 (285)
T PF06937_consen 31 SFCHICFELSIEGVP--KSDLLHTKSLRGHRDCFEKWHLIANQDCPRSK 77 (285)
T ss_pred EECHHHHHCCCCCCC--CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf 144346534815586--43454421323247899999999706786555
No 25
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. 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-, 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. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised . More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin and archaean preflagellin have been described , . Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional , and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme , . The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue .
Probab=32.59 E-value=8.4 Score=16.37 Aligned_cols=22 Identities=23% Similarity=0.473 Sum_probs=18.3
Q ss_pred CCHHHHHHCCCCCCCCCCCCCC
Q ss_conf 3216898608998802675888
Q T0539 58 PCVSIWLQKSGTCPVCRCMFPP 79 (81)
Q Consensus 58 ~Ci~~Wl~~~~~CP~CR~~~p~ 79 (81)
-=|..|+-.++.|-.|++.+++
T Consensus 49 IPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 49 IPILSYLLLRGRCRYCGAPISP 70 (92)
T ss_pred CHHHHHHHHCCCCCCCCCCCCH
T ss_conf 8599999868798124999780
No 26
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins . More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding; PDB: 1wim_A 2jmo_A 2ct7_A 1wd2_A.
Probab=28.11 E-value=1.6 Score=19.99 Aligned_cols=33 Identities=27% Similarity=0.542 Sum_probs=22.0
Q ss_pred CCCCE--ECCCCCCCCE--E--EECC-CCCCCCCCCHHHH
Q ss_conf 60421--3466778971--5--6500-3443377321689
Q T0539 31 MCCPI--CCSEYVKGEV--A--TELP-CHHYFHKPCVSIW 63 (81)
Q Consensus 31 ~~C~I--Cl~~~~~~~~--~--~~l~-C~H~Fh~~Ci~~W 63 (81)
.-|+. |-.-+...+. . +.-+ |++.||..|-..|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCGYIIEKEDGCNQSSVQCPKCGYEFCFNCKEPW 58 (64)
T ss_dssp ---TTSST----C--SSTTS--CC-TTCGSEECSSTTCE-
T ss_pred CCCCCCCCCCEEEECCCCCCCCEECCCCCCEECCCCCCCC
T ss_conf 6896879885088688999881199869762742609364
No 27
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C .; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1z60_A.
Probab=27.68 E-value=4.8 Score=17.58 Aligned_cols=42 Identities=21% Similarity=0.458 Sum_probs=23.1
Q ss_pred CCEECCCCCCC-------CEEEECCCCCCCCCCCHHHHHHCCCCCCCCC
Q ss_conf 42134667789-------7156500344337732168986089988026
Q T0539 33 CPICCSEYVKG-------EVATELPCHHYFHKPCVSIWLQKSGTCPVCR 74 (81)
Q Consensus 33 C~ICl~~~~~~-------~~~~~l~C~H~Fh~~Ci~~Wl~~~~~CP~CR 74 (81)
|.=|+..|..+ ..-+-..|++.||.+|=.=.=+.=.+||-|-
T Consensus 2 C~~C~~~~~~~~~~~~~s~~y~C~~C~~~FCidCDvfiHE~LHnCPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPDKKTDSSRYRCPKCKQHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp --------TTS-------EEE--TTTT--B-HHHHHTTTTTS-S-----
T ss_pred CCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCHHHHHHCCCCCCCC
T ss_conf 5234767787632334456468967787401656855553223795978
No 28
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175)
Probab=21.26 E-value=13 Score=15.46 Aligned_cols=35 Identities=26% Similarity=0.280 Sum_probs=25.4
Q ss_pred CCCCEECCCCCCCCEEEECCCCCCCCCCCHHHHHHC
Q ss_conf 604213466778971565003443377321689860
Q T0539 31 MCCPICCSEYVKGEVATELPCHHYFHKPCVSIWLQK 66 (81)
Q Consensus 31 ~~C~ICl~~~~~~~~~~~l~C~H~Fh~~Ci~~Wl~~ 66 (81)
-.|.||-..+..|+....+. +-.-|++|+..=...
T Consensus 3 wkC~iCg~~I~~gelFTF~k-~G~VH~~C~~~~~~~ 37 (101)
T PF09943_consen 3 WKCYICGKPIYEGELFTFTK-KGPVHYECFEEDASK 37 (101)
T ss_pred EEEEECCCCEEECCEEEEEC-CCCEEHHHHHHHHHC
T ss_conf 27995498305063578826-986509999988741
No 29
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis .
Probab=20.32 E-value=15 Score=15.10 Aligned_cols=32 Identities=19% Similarity=0.586 Sum_probs=16.2
Q ss_pred CCCCCCCCEECCC----CCCCCEEEECCCCCCCCCCCHHHH
Q ss_conf 6777604213466----778971565003443377321689
Q T0539 27 VGQEMCCPICCSE----YVKGEVATELPCHHYFHKPCVSIW 63 (81)
Q Consensus 27 ~~~~~~C~ICl~~----~~~~~~~~~l~C~H~Fh~~Ci~~W 63 (81)
++.+.-||+|-.. |.++.++. -.||..|-.++
T Consensus 28 v~~n~yCP~CG~~~l~~f~NN~PVa-----DFyC~~C~e~f 63 (254)
T PF06044_consen 28 VEKNSYCPNCGSNPLSHFANNKPVA-----DFYCLNCHEQF 63 (254)
T ss_pred HHHCCCCCCCCCCHHHHCCCCCCEE-----EEECCCCCHHH
T ss_conf 9865779988980333045898125-----78758751887
Done!