Query psy4931
Match_columns 186
No_of_seqs 227 out of 455
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 21:33:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4931hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1723|consensus 100.0 4.5E-49 9.8E-54 323.1 5.9 148 1-148 1-148 (162)
2 PTZ00033 60S ribosomal protein 100.0 7.1E-45 1.5E-49 287.9 11.8 115 1-124 1-119 (125)
3 KOG1722|consensus 100.0 7.2E-38 1.6E-42 253.5 7.5 99 1-108 1-100 (155)
4 PF01246 Ribosomal_L24e: Ribos 100.0 4.5E-37 9.7E-42 223.0 2.2 67 1-67 1-67 (71)
5 PRK14891 50S ribosomal protein 100.0 2.5E-36 5.4E-41 240.5 6.0 62 1-62 2-63 (131)
6 COG2075 RPL24A Ribosomal prote 100.0 3.3E-35 7.2E-40 211.0 5.7 65 1-65 1-65 (66)
7 cd00472 Ribosomal_L24e_L24 Rib 100.0 5.2E-33 1.1E-37 192.6 4.3 54 1-54 1-54 (54)
8 PRK00807 50S ribosomal protein 100.0 2.2E-29 4.9E-34 172.6 3.7 52 3-54 1-52 (52)
9 smart00746 TRASH metallochaper 98.6 9.5E-08 2.1E-12 54.9 4.0 37 6-43 1-38 (39)
10 PF08394 Arc_trans_TRASH: Arch 97.2 0.00056 1.2E-08 44.7 3.7 36 6-43 1-36 (37)
11 PF04945 YHS: YHS domain; Int 97.1 0.00057 1.2E-08 44.9 3.0 36 6-42 3-38 (47)
12 PF06467 zf-FCS: MYM-type Zinc 96.2 0.002 4.4E-08 40.9 0.9 37 3-40 6-43 (43)
13 PF09889 DUF2116: Uncharacteri 94.6 0.0067 1.5E-07 43.1 -0.7 36 4-51 4-40 (59)
14 PF05573 NosL: NosL; InterPro 94.5 0.029 6.2E-07 44.9 2.5 39 4-42 26-67 (149)
15 COG3350 Uncharacterized conser 94.0 0.077 1.7E-06 37.3 3.5 38 7-46 6-43 (53)
16 PF09943 DUF2175: Uncharacteri 91.9 0.052 1.1E-06 42.5 0.3 28 4-32 3-30 (101)
17 cd01057 AAMH_A Aromatic and Al 82.5 1.5 3.2E-05 41.8 3.7 53 5-59 382-441 (465)
18 PF04570 DUF581: Protein of un 80.9 1.5 3.2E-05 31.2 2.4 34 4-40 17-50 (58)
19 PHA03073 late transcription fa 79.1 1.1 2.5E-05 37.3 1.5 53 3-61 49-102 (150)
20 COG4068 Uncharacterized protei 78.2 0.84 1.8E-05 33.2 0.4 23 4-38 9-31 (64)
21 COG4314 NosL Predicted lipopro 77.9 2.5 5.4E-05 36.0 3.2 47 4-50 36-86 (176)
22 PF15585 Imm46: Immunity prote 67.6 3.2 7E-05 33.8 1.5 26 12-37 79-113 (129)
23 COG4847 Uncharacterized protei 64.3 2.5 5.4E-05 33.3 0.3 29 1-30 4-32 (103)
24 PF00412 LIM: LIM domain; Int 58.9 10 0.00022 24.6 2.4 25 5-34 28-52 (58)
25 PF08384 NPP: Pro-opiomelanoco 57.9 5 0.00011 27.5 0.8 11 10-20 31-41 (45)
26 PRK09710 lar restriction allev 54.4 9.5 0.00021 27.8 1.9 31 3-39 6-36 (64)
27 smart00132 LIM Zinc-binding do 50.1 14 0.00029 21.6 1.8 25 5-31 1-25 (39)
28 PF06689 zf-C4_ClpX: ClpX C4-t 49.6 9.1 0.0002 24.8 1.0 13 4-16 2-14 (41)
29 TIGR00270 conserved hypothetic 47.6 15 0.00032 30.2 2.2 31 6-39 3-33 (154)
30 PRK08359 transcription factor; 44.3 16 0.00035 30.9 2.0 33 5-40 8-40 (176)
31 PF14353 CpXC: CpXC protein 42.4 28 0.0006 26.7 2.9 33 3-35 38-70 (128)
32 PF07754 DUF1610: Domain of un 39.0 21 0.00045 21.4 1.4 18 6-23 1-19 (24)
33 COG1997 RPL43A Ribosomal prote 37.3 16 0.00034 28.3 0.8 29 4-41 36-64 (89)
34 PF12156 ATPase-cat_bd: Putati 35.5 42 0.00091 24.9 2.8 36 5-41 2-37 (88)
35 PF01197 Ribosomal_L31: Riboso 34.4 13 0.00029 26.7 0.0 30 1-32 34-63 (69)
36 KOG3710|consensus 33.5 32 0.00069 31.3 2.2 22 12-33 148-178 (280)
37 KOG2963|consensus 32.8 1E+02 0.0022 29.5 5.5 27 96-122 318-344 (405)
38 PF13408 Zn_ribbon_recom: Reco 32.6 34 0.00073 22.1 1.7 29 3-36 5-33 (58)
39 PF14447 Prok-RING_4: Prokaryo 32.5 23 0.00049 25.1 0.9 14 4-17 40-53 (55)
40 PRK14890 putative Zn-ribbon RN 27.5 41 0.00088 24.2 1.5 40 1-40 5-46 (59)
41 PF03884 DUF329: Domain of unk 27.4 37 0.0008 24.0 1.3 29 4-39 3-31 (57)
42 PF06221 zf-C2HC5: Putative zi 26.4 30 0.00066 24.4 0.7 12 4-15 36-47 (57)
43 PLN02469 hydroxyacylglutathion 26.1 51 0.0011 28.5 2.2 21 64-84 211-231 (258)
44 KOG4135|consensus 25.7 25 0.00055 30.1 0.3 23 163-185 46-68 (185)
45 PF11672 DUF3268: Protein of u 25.3 38 0.00083 26.4 1.2 36 3-39 2-40 (102)
46 PF14354 Lar_restr_allev: Rest 24.8 38 0.00082 22.6 0.9 10 3-12 3-12 (61)
47 KOG1549|consensus 24.2 40 0.00088 32.3 1.3 25 1-25 232-258 (428)
48 PF14777 BBIP10: Cilia BBSome 24.0 52 0.0011 24.1 1.6 23 12-35 10-32 (65)
49 COG2888 Predicted Zn-ribbon RN 23.8 83 0.0018 22.8 2.6 37 3-39 9-47 (61)
50 TIGR01922 purO_arch IMP cycloh 23.5 45 0.00097 29.1 1.4 27 13-39 1-30 (199)
51 PRK13446 atpC F0F1 ATP synthas 23.0 80 0.0017 25.0 2.6 10 11-20 33-42 (136)
52 TIGR03666 Rv2061_F420 PPOX cla 22.8 78 0.0017 24.7 2.5 28 20-47 32-59 (132)
53 KOG0402|consensus 22.3 28 0.0006 27.0 -0.1 29 4-41 37-65 (92)
54 PRK05342 clpX ATP-dependent pr 22.3 39 0.00085 31.6 0.8 13 2-14 8-20 (412)
55 PF08789 PBCV_basic_adap: PBCV 22.1 51 0.0011 22.0 1.1 18 9-26 7-25 (40)
56 PF01753 zf-MYND: MYND finger; 20.9 89 0.0019 19.1 2.0 28 6-39 1-28 (37)
57 PF01321 Creatinase_N: Creatin 20.8 67 0.0015 23.1 1.7 35 5-40 25-62 (132)
58 TIGR03550 F420_cofG 7,8-dideme 20.5 45 0.00098 29.5 0.8 22 3-24 15-36 (322)
59 PRK00398 rpoP DNA-directed RNA 20.2 44 0.00096 21.6 0.5 11 4-14 22-32 (46)
No 1
>KOG1723|consensus
Probab=100.00 E-value=4.5e-49 Score=323.12 Aligned_cols=148 Identities=57% Similarity=1.053 Sum_probs=144.8
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCCccchhhHHHHHHhCCcccccchhhhhhhhCCccc
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAVDPSFEFAKRRNVPLK 80 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnPRKl~WT~~~Rr~~kKe~~~d~~~efekRRn~~vK 80 (186)
||+++|+||+++||||||+|||+||.++|.||+|+|+++|++++|||++.||.++|+++||++.+|++++|++|||.|++
T Consensus 1 Mri~kc~fcss~IyPgHgi~Fv~Nd~k~f~Fc~skc~k~f~~k~nPrk~~~tka~rKaagre~~~d~~~e~~~rrn~~~~ 80 (162)
T KOG1723|consen 1 MRIEKCYFCSSPIYPGHGIMFVRNDCKVFRFCKSKCHKNFKQKKNPRKVGWTKAFRKAAGRELVTDSTFEFEKRRNVPRK 80 (162)
T ss_pred CceeeeeeecCcccCCCceEEEecCcchhHHHHhhhhhhhhhhcCCCccchHHHHHHHhhhhHhhhhhHHHHHhcCcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHhHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhcccccCCchHHHHHHHHHh
Q psy4931 81 YDREFWNKTVEAIKKVEHIKTKRQNLYLAQRLRKAREVETARDIKAVQRDIAILNDPTEAIKAKKKRM 148 (186)
Q Consensus 81 y~R~lv~~tl~amkrve~Ik~kR~~~~~~~R~~~~k~~~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~ 148 (186)
|+|+.++.|++||++|.+|+.+|++.||.+||+++++.++..|+++|.+|+|||++|.++.+++....
T Consensus 81 y~r~~~~~Ti~a~k~v~~i~~~~~~~~i~~rL~~~ke~~~~~d~k~v~~n~~li~~~~~~~~~~~~~~ 148 (162)
T KOG1723|consen 81 YDRELINKTIDAMKRVLEIKQKREAHFIGNRLKKGKEAQLVQDIKEVKQNIHLIRAPEAGKEKQLAEK 148 (162)
T ss_pred hcccchhhHHHHHHHHHhhcccchhhhhhhccCccchhccchhHHHHHhhhhhhcchhhhhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999998876544
No 2
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=100.00 E-value=7.1e-45 Score=287.90 Aligned_cols=115 Identities=30% Similarity=0.511 Sum_probs=104.4
Q ss_pred CceeecccCCCCccCCccceEEe----eCCceeEEechhHHHhhhcccCCccchhhHHHHHHhCCcccccchhhhhhhhC
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVR----NDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAVDPSFEFAKRRN 76 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVr----nDgkvf~FcssKC~k~f~~KrnPRKl~WT~~~Rr~~kKe~~~d~~~efekRRn 76 (186)
|+++.|+|||++||||||++||+ +||+||+||||||+++|++++|||+|.||.+||++|||+++++ + +++|++
T Consensus 1 Mk~~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~~~~krnPRkl~WT~~yRr~~kK~~~e~-~--~kkR~~ 77 (125)
T PTZ00033 1 MRTIACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYMRKKNPRFLPWTRTYRRINRKTTTDR-V--QRRRAA 77 (125)
T ss_pred CceeEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHHHHCcCCCccchHHHHHHHHhCCcchhH-H--HHHHhc
Confidence 89999999999999999999999 9999999999999999999999999999999999999997654 3 478889
Q ss_pred CcccchhhHHHHhHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Q psy4931 77 VPLKYDREFWNKTVEAIKKVEHIKTKRQNLYLAQRLRKAREVETARDI 124 (186)
Q Consensus 77 ~~vKy~R~lv~~tl~amkrve~Ik~kR~~~~~~~R~~~~k~~~~~~~~ 124 (186)
+||+|||+|||+|| ++|+++|++....++++...+.+.+.+.
T Consensus 78 rtvK~qRaivg~sL------e~I~~kR~~k~evr~aar~~a~r~~Ke~ 119 (125)
T PTZ00033 78 RTVKVQRAIVGADL------SYIQEVRAYVQKVDRSAKAKAVRAEKAE 119 (125)
T ss_pred CCccchHHHHHHHH------HHHHHHHhcCHHHHHHHHHHHHHHHHHH
Confidence 99999999999997 8899999999999888776665544443
No 3
>KOG1722|consensus
Probab=100.00 E-value=7.2e-38 Score=253.48 Aligned_cols=99 Identities=41% Similarity=0.749 Sum_probs=87.8
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCCccchhhHHHHHHhCCcccccchhhhhhhhCCcc-
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAVDPSFEFAKRRNVPL- 79 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnPRKl~WT~~~Rr~~kKe~~~d~~~efekRRn~~v- 79 (186)
|++++|+|||++||||||+.|||.||+||+|+|+||.++|++++|||+|.||.+||+.|+|+.+++. ..+|+++++
T Consensus 1 MKvElCsFSG~KIyPG~G~r~vR~D~Kvf~Fln~Kc~~~f~~rrnPr~l~WTvLyR~khkKg~~ee~---~kkrtrrt~k 77 (155)
T KOG1722|consen 1 MKVELCSFSGYKIYPGHGRRFVRGDGKVFRFLNSKCESLFLQRRNPRRLAWTVLYRKKHKKGIQEEA---AKKRTRRTVK 77 (155)
T ss_pred CceeEeeccCceecCCCceeEEecCCeeeeehhhhhHHHHHhccChhhhhHHHHHHHHhhcchhHHH---HHHHhhhhhh
Confidence 8999999999999999999999999999999999999999999999999999999999999977642 245555655
Q ss_pred cchhhHHHHhHHHHHhHHHHHHHHHHHHH
Q psy4931 80 KYDREFWNKTVEAIKKVEHIKTKRQNLYL 108 (186)
Q Consensus 80 Ky~R~lv~~tl~amkrve~Ik~kR~~~~~ 108 (186)
+|||+|+|+|| +.|.++|++..-
T Consensus 78 ~~qRaI~GasL------~~I~~KRn~kpe 100 (155)
T KOG1722|consen 78 KFQRAIVGASL------DVILEKRNQKPE 100 (155)
T ss_pred hhhhhhccccH------HHHHHHhccChH
Confidence 59999999998 777888877544
No 4
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=100.00 E-value=4.5e-37 Score=223.03 Aligned_cols=67 Identities=55% Similarity=1.014 Sum_probs=53.5
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCCccchhhHHHHHHhCCcccccc
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAVDP 67 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnPRKl~WT~~~Rr~~kKe~~~d~ 67 (186)
|++++|+|||++||||||+|||++||++|+|||+||.+||++++|||+|+||.+||++|+|+++++.
T Consensus 1 mk~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~~~~krnPrkl~WT~~~Rr~~kK~~~~~~ 67 (71)
T PF01246_consen 1 MKTEKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKLFKLKRNPRKLKWTVAYRRQHKKGQSEEA 67 (71)
T ss_dssp SSSEE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTTCHHH-----SSS
T ss_pred CceEEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHHHHccCCcccchhHHHHHHHhCchhhhhH
Confidence 8999999999999999999999999999999999999999999999999999999999999988753
No 5
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=100.00 E-value=2.5e-36 Score=240.55 Aligned_cols=62 Identities=34% Similarity=0.674 Sum_probs=61.1
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCCccchhhHHHHHHhCCc
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKD 62 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnPRKl~WT~~~Rr~~kKe 62 (186)
|++++|+|||++||||||+|||||||+||+||||||++||++|||||||+||++||+.+||.
T Consensus 2 m~~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT~~yRk~~g~~ 63 (131)
T PRK14891 2 VETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWTEAGRAEKGPA 63 (131)
T ss_pred CceeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHHccCCCccchhHHHHHHHcCch
Confidence 79999999999999999999999999999999999999999999999999999999999996
No 6
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-35 Score=211.03 Aligned_cols=65 Identities=55% Similarity=1.089 Sum_probs=62.9
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCCccchhhHHHHHHhCCcccc
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAV 65 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnPRKl~WT~~~Rr~~kKe~~~ 65 (186)
|+++.|+|||.+||||||+|||+|||++|+||||||+++|+++||||+|+||..||++++|+...
T Consensus 1 m~~~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k~~~~~rnPRk~~WT~~~~~~~~k~~~~ 65 (66)
T COG2075 1 MKVRVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEKLFKLGRNPRKLKWTKKYRKMHKKEIKE 65 (66)
T ss_pred CceeEecCcCCccCCCceEEEEecCCeEEEEechhHHHHHHccCCCccchhHHHHHHHHHhhhcc
Confidence 88999999999999999999999999999999999999999999999999999999999998754
No 7
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=99.97 E-value=5.2e-33 Score=192.62 Aligned_cols=54 Identities=65% Similarity=1.229 Sum_probs=52.7
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCCccchhhHH
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKA 54 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnPRKl~WT~~ 54 (186)
|++++|+|||++||||||+||||+||++|+|||+||+++|.+|+|||+|+||.+
T Consensus 1 m~~~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~~~krnPRkv~WT~~ 54 (54)
T cd00472 1 MKTEKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNFLRKRNPRKLKWTVA 54 (54)
T ss_pred CcEEEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHHHCcCCCCcceeecC
Confidence 899999999999999999999999999999999999999999999999999963
No 8
>PRK00807 50S ribosomal protein L24e; Validated
Probab=99.95 E-value=2.2e-29 Score=172.64 Aligned_cols=52 Identities=48% Similarity=0.943 Sum_probs=49.9
Q ss_pred eeecccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCCccchhhHH
Q psy4931 3 IETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKA 54 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnPRKl~WT~~ 54 (186)
+++|+|||++||||||++||++||++|+|||+||+++|++|+|||+|+||.+
T Consensus 1 ~~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f~~~~nprk~~WT~~ 52 (52)
T PRK00807 1 TRTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNYKLGRVPRKLKWTKA 52 (52)
T ss_pred CcccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHHHccCCCCccccccC
Confidence 4689999999999999999999999999999999999999999999999974
No 9
>smart00746 TRASH metallochaperone-like domain.
Probab=98.56 E-value=9.5e-08 Score=54.93 Aligned_cols=37 Identities=59% Similarity=1.199 Sum_probs=33.9
Q ss_pred cccCCCCcc-CCccceEEeeCCceeEEechhHHHhhhcc
Q psy4931 6 CYFCSSKIY-PGHGIQFVRNDCKIFRFCRSKCHKLFKRK 43 (186)
Q Consensus 6 C~Fcg~~Iy-PGhG~~fVrnDgkvf~FcssKC~k~f~~K 43 (186)
|.+||..|+ |+.|..++ .||++++||+..|...|..+
T Consensus 1 c~~C~~~~~~~~~~~~~~-~~g~~~~FCs~~c~~~~~~~ 38 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVV-NDGKVFYFCSSKCLSKFKKK 38 (39)
T ss_pred CCCCCCCccCCCCceEEE-ECCEEEEEeCHHHHHHHHhc
Confidence 899999999 88899998 99999999999999998754
No 10
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=97.17 E-value=0.00056 Score=44.68 Aligned_cols=36 Identities=33% Similarity=0.798 Sum_probs=31.6
Q ss_pred cccCCCCccCCccceEEeeCCceeEEechhHHHhhhcc
Q psy4931 6 CYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRK 43 (186)
Q Consensus 6 C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~K 43 (186)
|.+||.+|. |.++.| +-++++++||..-|.+-|+.+
T Consensus 1 Cd~CG~~I~-~eP~~~-k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVV-KIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred CCccCCccc-CCEEEE-EECCeEEEEECHHHHHHHHhh
Confidence 899999998 777765 458999999999999999865
No 11
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=97.06 E-value=0.00057 Score=44.94 Aligned_cols=36 Identities=25% Similarity=0.606 Sum_probs=26.8
Q ss_pred cccCCCCccCCccceEEeeCCceeEEechhHHHhhhc
Q psy4931 6 CYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKR 42 (186)
Q Consensus 6 C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~ 42 (186)
+.-||-.| ||.....+.-+|++|+|||.-|...|..
T Consensus 3 DPvcg~~v-~~~~~~~~~y~G~~Y~FCS~~C~~~F~~ 38 (47)
T PF04945_consen 3 DPVCGMKV-PGNAAYSVEYNGRTYYFCSEGCKEKFEA 38 (47)
T ss_dssp B-GGG-BE------EEEEETTEEEEESSHHHHHHHHC
T ss_pred CCCCCCEE-ccCccEEEEECCEEEEEcCHHHHHHHHH
Confidence 56799999 9999999999999999999999999964
No 12
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=96.18 E-value=0.002 Score=40.93 Aligned_cols=37 Identities=27% Similarity=0.545 Sum_probs=26.7
Q ss_pred eeecccCCCCccCCc-cceEEeeCCceeEEechhHHHhh
Q psy4931 3 IETCYFCSSKIYPGH-GIQFVRNDCKIFRFCRSKCHKLF 40 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGh-G~~fVrnDgkvf~FcssKC~k~f 40 (186)
...|++|+..|+.+. + .-+..||++..|||.-|...|
T Consensus 6 ~~~C~~C~~~~~~~~~~-~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPTM-IEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp CEE-TTT--EEECCC-----EE-TTTTSCCSSHHHHHHH
T ss_pred CCcCcccCCcccCCCcc-ccccccCcccChhCHHHHhhC
Confidence 457999999999888 5 888999999999999998765
No 13
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=94.64 E-value=0.0067 Score=43.10 Aligned_cols=36 Identities=36% Similarity=0.806 Sum_probs=26.4
Q ss_pred eecccCCCCccCCccceEEeeCCceeEEechhHHHhhh-cccCCccchh
Q psy4931 4 ETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFK-RKKNPRKTAW 51 (186)
Q Consensus 4 e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~-~KrnPRKl~W 51 (186)
..|-+||.+|.|. -.|||.+|+..+. ..+..++..|
T Consensus 4 kHC~~CG~~Ip~~------------~~fCS~~C~~~~~k~qk~~~~~~~ 40 (59)
T PF09889_consen 4 KHCPVCGKPIPPD------------ESFCSPKCREEYRKRQKRMRKTQY 40 (59)
T ss_pred CcCCcCCCcCCcc------------hhhhCHHHHHHHHHHHHHHHHHHH
Confidence 4699999999994 4799999998875 3333444444
No 14
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=94.48 E-value=0.029 Score=44.91 Aligned_cols=39 Identities=23% Similarity=0.603 Sum_probs=17.9
Q ss_pred eecccCCCCc--cCCc-cceEEeeCCceeEEechhHHHhhhc
Q psy4931 4 ETCYFCSSKI--YPGH-GIQFVRNDCKIFRFCRSKCHKLFKR 42 (186)
Q Consensus 4 e~C~Fcg~~I--yPGh-G~~fVrnDgkvf~FcssKC~k~f~~ 42 (186)
..|.+||-.| |||. |.++..+.+++++||+-.|--.|.+
T Consensus 26 ~~C~~CgM~i~d~p~~~aqi~~~~g~~~~~Fdsi~c~~~~~~ 67 (149)
T PF05573_consen 26 DRCPVCGMVISDYPGFAAQIIYKDGEKVYKFDSIGCMFAYLK 67 (149)
T ss_dssp -----------------EEEEETT-SSEEEES-HHHHHHHHT
T ss_pred CccCCCCCEeccCCCccEEEEECCCCEEEEECCHHHHHHHHh
Confidence 5799999999 7885 5666555449999999999877764
No 15
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=94.01 E-value=0.077 Score=37.31 Aligned_cols=38 Identities=26% Similarity=0.507 Sum_probs=30.3
Q ss_pred ccCCCCccCCccceEEeeCCceeEEechhHHHhhhcccCC
Q psy4931 7 YFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNP 46 (186)
Q Consensus 7 ~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~~KrnP 46 (186)
..||.+|.+-.-..=.--+|++|+|||..|.-.|+ .||
T Consensus 6 PVcgm~v~~~~a~~k~~Y~GktYYFcse~~~~~F~--~~P 43 (53)
T COG3350 6 PVCGMKVDNENAEYKSSYGGKTYYFCSEECKEKFK--DNP 43 (53)
T ss_pred CCcCccccccccceeEEeCCEEEEEeCHHHHHHHH--HCH
Confidence 46888888777666666789999999999999885 455
No 16
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=91.94 E-value=0.052 Score=42.46 Aligned_cols=28 Identities=29% Similarity=0.713 Sum_probs=23.2
Q ss_pred eecccCCCCccCCccceEEeeCCceeEEe
Q psy4931 4 ETCYFCSSKIYPGHGIQFVRNDCKIFRFC 32 (186)
Q Consensus 4 e~C~Fcg~~IyPGhG~~fVrnDgkvf~Fc 32 (186)
-+|++||.+||-|-...|..+ |-|.|=|
T Consensus 3 WkC~iCg~~I~~gqlFTF~~k-G~VH~~C 30 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKK-GPVHYEC 30 (101)
T ss_pred eEEEecCCeeeecceEEEecC-CcEeHHH
Confidence 479999999999998888888 7765544
No 17
>cd01057 AAMH_A Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit A (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds, however, the beta-subunit lacks critical diiron ligands and a C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphtho
Probab=82.52 E-value=1.5 Score=41.85 Aligned_cols=53 Identities=17% Similarity=0.499 Sum_probs=40.5
Q ss_pred ecccCCCCccC----Cccc-eEEeeCCceeEEechhHHHhhhcccCCccc--hhhHHHHHHh
Q psy4931 5 TCYFCSSKIYP----GHGI-QFVRNDCKIFRFCRSKCHKLFKRKKNPRKT--AWTKAYRKVR 59 (186)
Q Consensus 5 ~C~Fcg~~IyP----GhG~-~fVrnDgkvf~FcssKC~k~f~~KrnPRKl--~WT~~~Rr~~ 59 (186)
.|.-|+-||-| +... .-.--+|+.|+|||--|+.-|.+ +|-+- .|+..-|-..
T Consensus 382 ~c~vC~~p~~~~~~~~~~~~~~~ey~G~~y~FCS~~C~~~F~~--ePerY~~~~~~~~~~~~ 441 (465)
T cd01057 382 LCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSEGCEWIFEQ--EPERYAGHWNPVDRFLG 441 (465)
T ss_pred CCCCCCCeeccccCcccccceEEEECCEEEEecCHHHHHHHHH--CHHHHhcCCCHHHHHhc
Confidence 79999999985 4443 44556999999999999999986 88776 5665555444
No 18
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=80.91 E-value=1.5 Score=31.19 Aligned_cols=34 Identities=35% Similarity=0.845 Sum_probs=27.9
Q ss_pred eecccCCCCccCCccceEEeeCCceeEEechhHHHhh
Q psy4931 4 ETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLF 40 (186)
Q Consensus 4 e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f 40 (186)
..|++|..++-||..+-.-|-|.- |||.-|+...
T Consensus 17 ~~C~~C~k~L~~~~DiymYrGd~a---FCS~ECR~~q 50 (58)
T PF04570_consen 17 SFCYLCKKKLDPGKDIYMYRGDKA---FCSEECRSQQ 50 (58)
T ss_pred HHHHccCCCCCCCCCeeeeccccc---cccHHHHHHH
Confidence 469999999999998766666654 9999998764
No 19
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=79.06 E-value=1.1 Score=37.25 Aligned_cols=53 Identities=17% Similarity=0.319 Sum_probs=36.3
Q ss_pred eeecccCCCCccCCccceEEeeCC-ceeEEechhHHHhhhcccCCccchhhHHHHHHhCC
Q psy4931 3 IETCYFCSSKIYPGHGIQFVRNDC-KIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGK 61 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGhG~~fVrnDg-kvf~FcssKC~k~f~~KrnPRKl~WT~~~Rr~~kK 61 (186)
...||||+..+-+-. ...=..+| .+=.|||.=|.-+|-. -|+-+.|-|..-|=
T Consensus 49 ~~~CwfC~q~~~~~~-~~iETl~g~~vg~FCS~ICRDSfa~-----~Vk~~vALREePKi 102 (150)
T PHA03073 49 NDYCWFCKQDLIIAP-LFIETLKGGAVGYFCSKICRDSFAS-----MVKSHVALREEPKI 102 (150)
T ss_pred CCcEEeeccccccCc-eEEEeecCchhhhHhHHHHHHHHHH-----HHHHHhhhccCCce
Confidence 457999999988766 33334566 8999999999999852 23445555544433
No 20
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=78.15 E-value=0.84 Score=33.15 Aligned_cols=23 Identities=26% Similarity=0.823 Sum_probs=20.1
Q ss_pred eecccCCCCccCCccceEEeeCCceeEEechhHHH
Q psy4931 4 ETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHK 38 (186)
Q Consensus 4 e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k 38 (186)
..|-.||.+|+||. .|||-+|..
T Consensus 9 ~HC~VCg~aIp~de------------~~CSe~C~e 31 (64)
T COG4068 9 RHCVVCGKAIPPDE------------QVCSEECGE 31 (64)
T ss_pred ccccccCCcCCCcc------------chHHHHHHH
Confidence 46999999999985 689999984
No 21
>COG4314 NosL Predicted lipoprotein involved in nitrous oxide reduction [Energy production and conversion]
Probab=77.94 E-value=2.5 Score=36.01 Aligned_cols=47 Identities=17% Similarity=0.313 Sum_probs=38.3
Q ss_pred eecccCCCCc--cCCc-cceEEeeCCceeEEechhHHHhhh-cccCCccch
Q psy4931 4 ETCYFCSSKI--YPGH-GIQFVRNDCKIFRFCRSKCHKLFK-RKKNPRKTA 50 (186)
Q Consensus 4 e~C~Fcg~~I--yPGh-G~~fVrnDgkvf~FcssKC~k~f~-~KrnPRKl~ 50 (186)
..|.|||-.| |||- |..|..-+-...|||+.+---+|. +=-+|+.|+
T Consensus 36 s~g~ycgMnl~ehpGPKgQi~l~g~~qP~wfsst~e~f~~tllPEepk~ia 86 (176)
T COG4314 36 SMGHYCGMNLLEHPGPKGQIILNGKPQPIWFSSTREMFGFTLLPEEPKGIA 86 (176)
T ss_pred ccccccceeeecCCCCcceEeeCCCCCceeeecHHHHhhHhcCCcCcCcee
Confidence 3699999887 7996 999999888889999999877775 556676653
No 22
>PF15585 Imm46: Immunity protein 46
Probab=67.64 E-value=3.2 Score=33.79 Aligned_cols=26 Identities=31% Similarity=0.761 Sum_probs=22.2
Q ss_pred CccCCc-cceEEeeCC--------ceeEEechhHH
Q psy4931 12 KIYPGH-GIQFVRNDC--------KIFRFCRSKCH 37 (186)
Q Consensus 12 ~IyPGh-G~~fVrnDg--------kvf~FcssKC~ 37 (186)
.|-||. |.+|||.|- +||.+++.+|-
T Consensus 79 e~aPGSYGlLy~rDDEd~~~~neFrV~vl~RG~~t 113 (129)
T PF15585_consen 79 EIAPGSYGLLYIRDDEDPEHFNEFRVFVLARGELT 113 (129)
T ss_pred HhCCCceeEEEEecCCCCCCCCceEEEEEEccEEe
Confidence 467887 999999876 89999999884
No 23
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=64.29 E-value=2.5 Score=33.28 Aligned_cols=29 Identities=21% Similarity=0.580 Sum_probs=21.4
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeE
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFR 30 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~ 30 (186)
|+.-+||.||.+|--|.-..|.. -|.|.|
T Consensus 4 lkewkC~VCg~~iieGqkFTF~~-kGsVH~ 32 (103)
T COG4847 4 LKEWKCYVCGGTIIEGQKFTFTK-KGSVHY 32 (103)
T ss_pred cceeeEeeeCCEeeeccEEEEee-CCcchH
Confidence 67789999999998776666665 355443
No 24
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=58.93 E-value=10 Score=24.57 Aligned_cols=25 Identities=28% Similarity=0.765 Sum_probs=17.7
Q ss_pred ecccCCCCccCCccceEEeeCCceeEEech
Q psy4931 5 TCYFCSSKIYPGHGIQFVRNDCKIFRFCRS 34 (186)
Q Consensus 5 ~C~Fcg~~IyPGhG~~fVrnDgkvf~Fcss 34 (186)
.|+-|+.+|.++. |.-.||+ .||..
T Consensus 28 ~C~~C~~~l~~~~---~~~~~~~--~~C~~ 52 (58)
T PF00412_consen 28 KCSKCGKPLNDGD---FYEKDGK--PYCKD 52 (58)
T ss_dssp BETTTTCBTTTSS---EEEETTE--EEEHH
T ss_pred ccCCCCCccCCCe---eEeECCE--EECHH
Confidence 5888999998777 6667775 34443
No 25
>PF08384 NPP: Pro-opiomelanocortin, N-terminal region; InterPro: IPR013593 This domain represents the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity [].
Probab=57.91 E-value=5 Score=27.47 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=9.4
Q ss_pred CCCccCCccce
Q psy4931 10 SSKIYPGHGIQ 20 (186)
Q Consensus 10 g~~IyPGhG~~ 20 (186)
..|||||+|.+
T Consensus 31 EsPv~PGn~hl 41 (45)
T PF08384_consen 31 ESPVFPGNGHL 41 (45)
T ss_pred CCCccCCCccc
Confidence 68999999964
No 26
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=54.41 E-value=9.5 Score=27.79 Aligned_cols=31 Identities=19% Similarity=0.411 Sum_probs=24.6
Q ss_pred eeecccCCCCccCCccceEEeeCCceeEEechhHHHh
Q psy4931 3 IETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKL 39 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~ 39 (186)
+.-|.|||..+ ..|+.++-.|+|+-.+|...
T Consensus 6 lKPCPFCG~~~------~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPS------VTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCce------eEEEecCceEEEEcCCCCcC
Confidence 56799998775 46667788888999999873
No 27
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=50.15 E-value=14 Score=21.60 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=19.2
Q ss_pred ecccCCCCccCCccceEEeeCCceeEE
Q psy4931 5 TCYFCSSKIYPGHGIQFVRNDCKIFRF 31 (186)
Q Consensus 5 ~C~Fcg~~IyPGhG~~fVrnDgkvf~F 31 (186)
.|.-|+.+|+|+ ..++..+|+.|..
T Consensus 1 ~C~~C~~~i~~~--~~~~~~~~~~~H~ 25 (39)
T smart00132 1 KCAGCGKPIRGG--ELVLRALGKVWHP 25 (39)
T ss_pred CccccCCcccCC--cEEEEeCCccccc
Confidence 488999999998 5566677777753
No 28
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=49.59 E-value=9.1 Score=24.83 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=6.9
Q ss_pred eecccCCCCccCC
Q psy4931 4 ETCYFCSSKIYPG 16 (186)
Q Consensus 4 e~C~Fcg~~IyPG 16 (186)
..|||||.+-...
T Consensus 2 ~~CSFCgr~~~~v 14 (41)
T PF06689_consen 2 KRCSFCGRPESEV 14 (41)
T ss_dssp -B-TTT--BTTTS
T ss_pred CCccCCCCCHHHH
Confidence 4699999987654
No 29
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=47.58 E-value=15 Score=30.16 Aligned_cols=31 Identities=29% Similarity=0.650 Sum_probs=25.9
Q ss_pred cccCCCCccCCccceEEeeCCceeEEechhHHHh
Q psy4931 6 CYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKL 39 (186)
Q Consensus 6 C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~ 39 (186)
|--||.+|. |.| .-|.-||..+.-|.+ |.+.
T Consensus 3 CEiCG~~i~-~~~-~~v~iega~l~vC~~-C~k~ 33 (154)
T TIGR00270 3 CEICGRKIK-GKG-FKIVIEGSEMTVCGE-CRKF 33 (154)
T ss_pred cccCCCccC-CCC-eEEEEcCeEEehhhh-HHhc
Confidence 999999995 665 789999999999976 6543
No 30
>PRK08359 transcription factor; Validated
Probab=44.32 E-value=16 Score=30.85 Aligned_cols=33 Identities=24% Similarity=0.621 Sum_probs=26.8
Q ss_pred ecccCCCCccCCccceEEeeCCceeEEechhHHHhh
Q psy4931 5 TCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLF 40 (186)
Q Consensus 5 ~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f 40 (186)
.|--||.+|. |.| .-|+-||..+.-|++ |..-|
T Consensus 8 ~CEiCG~~i~-g~~-~~v~ieGael~VC~~-Ca~k~ 40 (176)
T PRK08359 8 YCEICGAEIR-GPG-HRIRIEGAELLVCDR-CYEKY 40 (176)
T ss_pred eeecCCCccC-CCC-eEEEEcCeEEehHHH-HHHHh
Confidence 3999999995 665 789999999999976 66334
No 31
>PF14353 CpXC: CpXC protein
Probab=42.38 E-value=28 Score=26.69 Aligned_cols=33 Identities=15% Similarity=0.187 Sum_probs=29.5
Q ss_pred eeecccCCCCccCCccceEEeeCCceeEEechh
Q psy4931 3 IETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSK 35 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssK 35 (186)
.-+|..||..++..+..+|.-.+.+.+.|....
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 457999999999999999999999988887766
No 32
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=38.95 E-value=21 Score=21.37 Aligned_cols=18 Identities=28% Similarity=0.613 Sum_probs=15.1
Q ss_pred cccCCCCccCCc-cceEEe
Q psy4931 6 CYFCSSKIYPGH-GIQFVR 23 (186)
Q Consensus 6 C~Fcg~~IyPGh-G~~fVr 23 (186)
|.-||..|.|.. |..|.=
T Consensus 1 C~sC~~~i~~r~~~v~f~C 19 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPC 19 (24)
T ss_pred CccCCCcccCcccCceEeC
Confidence 788999999987 888863
No 33
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=37.34 E-value=16 Score=28.29 Aligned_cols=29 Identities=31% Similarity=0.637 Sum_probs=23.8
Q ss_pred eecccCCCCccCCccceEEeeCCceeEEechhHHHhhh
Q psy4931 4 ETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFK 41 (186)
Q Consensus 4 e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~ 41 (186)
..|.||+.+. |++-+.-.|-|+ ||..-|.
T Consensus 36 ~~Cp~C~~~~--------VkR~a~GIW~C~-kCg~~fA 64 (89)
T COG1997 36 HVCPFCGRTT--------VKRIATGIWKCR-KCGAKFA 64 (89)
T ss_pred CcCCCCCCcc--------eeeeccCeEEcC-CCCCeec
Confidence 4799998763 788888899998 8988775
No 34
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=35.48 E-value=42 Score=24.90 Aligned_cols=36 Identities=25% Similarity=0.575 Sum_probs=29.6
Q ss_pred ecccCCCCccCCccceEEeeCCceeEEechhHHHhhh
Q psy4931 5 TCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFK 41 (186)
Q Consensus 5 ~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~ 41 (186)
.|+-||.+|.+|. ..-+.-||....||=.=|...+.
T Consensus 2 ~C~HCg~~~p~~~-~~~~~~~g~~~~FCC~GC~~V~~ 37 (88)
T PF12156_consen 2 KCYHCGLPVPEGA-KITVEIDGEERPFCCPGCQAVYQ 37 (88)
T ss_pred CCCCCCCCCCCCC-CeeeeeCCCccccccHHHHHHHH
Confidence 5999999997555 55677789999999999987653
No 35
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=34.44 E-value=13 Score=26.69 Aligned_cols=30 Identities=20% Similarity=0.558 Sum_probs=23.1
Q ss_pred CceeecccCCCCccCCccceEEeeCCceeEEe
Q psy4931 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFC 32 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGhG~~fVrnDgkvf~Fc 32 (186)
|++++|+-| .|.|=|...+ |..+|+|=.|-
T Consensus 34 ~~vdi~s~~-HPfytG~~~~-~~~~Grv~KF~ 63 (69)
T PF01197_consen 34 IKVDICSNC-HPFYTGKQKV-VDTAGRVEKFN 63 (69)
T ss_dssp EEECSCSSS-SCTTCSCSSC-SCCCCCCTSCC
T ss_pred EEEeecCCC-CEEEcCcEEE-EccccCHHHHH
Confidence 467889888 8999996555 88888886663
No 36
>KOG3710|consensus
Probab=33.46 E-value=32 Score=31.26 Aligned_cols=22 Identities=32% Similarity=0.735 Sum_probs=16.9
Q ss_pred CccCCccceEEee------CCcee---EEec
Q psy4931 12 KIYPGHGIQFVRN------DCKIF---RFCR 33 (186)
Q Consensus 12 ~IyPGhG~~fVrn------Dgkvf---~Fcs 33 (186)
.+|||.|.-|||. ||+.. ++||
T Consensus 148 AcYPGNGtgYVrHVDNP~gDGRcITcIYYlN 178 (280)
T KOG3710|consen 148 ACYPGNGTGYVRHVDNPHGDGRCITCIYYLN 178 (280)
T ss_pred EEecCCCceeeEeccCCCCCceEEEEEEEcc
Confidence 3799999999996 88754 4554
No 37
>KOG2963|consensus
Probab=32.81 E-value=1e+02 Score=29.48 Aligned_cols=27 Identities=30% Similarity=0.363 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHH
Q psy4931 96 VEHIKTKRQNLYLAQRLRKAREVETAR 122 (186)
Q Consensus 96 ve~Ik~kR~~~~~~~R~~~~k~~~~~~ 122 (186)
-|+|++.|+...-+.||+..+..+.++
T Consensus 318 ~eEi~~l~~~~ekk~~lKeqRkkeQ~e 344 (405)
T KOG2963|consen 318 EEEIKALRKRHEKKRRLKEQRKKEQEE 344 (405)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999998776655444
No 38
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=32.58 E-value=34 Score=22.12 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=19.7
Q ss_pred eeecccCCCCccCCccceEEeeCCceeEEechhH
Q psy4931 3 IETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKC 36 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC 36 (186)
+-.|..||.+... ..++.+..++.|++.-
T Consensus 5 ~l~C~~CG~~m~~-----~~~~~~~~yy~C~~~~ 33 (58)
T PF13408_consen 5 LLRCGHCGSKMTR-----RKRKGKYRYYRCSNRR 33 (58)
T ss_pred cEEcccCCcEeEE-----EECCCCceEEEcCCCc
Confidence 3469999988776 2233566888888653
No 39
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=32.46 E-value=23 Score=25.14 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=11.6
Q ss_pred eecccCCCCccCCc
Q psy4931 4 ETCYFCSSKIYPGH 17 (186)
Q Consensus 4 e~C~Fcg~~IyPGh 17 (186)
.-|.|||.+|.+|.
T Consensus 40 ngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 40 NGCPFCGTPFEFDD 53 (55)
T ss_pred cCCCCCCCcccCCC
Confidence 35999999999874
No 40
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.48 E-value=41 Score=24.20 Aligned_cols=40 Identities=23% Similarity=0.480 Sum_probs=28.2
Q ss_pred CceeecccCCCCccCCc-cceEEeeC-CceeEEechhHHHhh
Q psy4931 1 MRIETCYFCSSKIYPGH-GIQFVRND-CKIFRFCRSKCHKLF 40 (186)
Q Consensus 1 Mr~e~C~Fcg~~IyPGh-G~~fVrnD-gkvf~FcssKC~k~f 40 (186)
|....|.-||..|.|+- |..|.=-+ |.+...=-.+|+++.
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 35668999999999876 88887655 455333356777664
No 41
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=27.38 E-value=37 Score=24.01 Aligned_cols=29 Identities=17% Similarity=0.477 Sum_probs=15.3
Q ss_pred eecccCCCCccCCccceEEeeCCceeEEechhHHHh
Q psy4931 4 ETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKL 39 (186)
Q Consensus 4 e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~ 39 (186)
-.|.-||.++.+..+ ...+=|||..|.-.
T Consensus 3 v~CP~C~k~~~~~~~-------n~~rPFCS~RCk~i 31 (57)
T PF03884_consen 3 VKCPICGKPVEWSPE-------NPFRPFCSERCKLI 31 (57)
T ss_dssp EE-TTT--EEE-SSS-------SS--SSSSHHHHHH
T ss_pred ccCCCCCCeecccCC-------CCcCCcccHhhccc
Confidence 458888877766322 23344999999854
No 42
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.44 E-value=30 Score=24.44 Aligned_cols=12 Identities=25% Similarity=0.852 Sum_probs=10.3
Q ss_pred eecccCCCCccC
Q psy4931 4 ETCYFCSSKIYP 15 (186)
Q Consensus 4 e~C~Fcg~~IyP 15 (186)
..|.|||.++++
T Consensus 36 ~pC~fCg~~l~~ 47 (57)
T PF06221_consen 36 GPCPFCGTPLLS 47 (57)
T ss_pred CcCCCCCCcccC
Confidence 579999999886
No 43
>PLN02469 hydroxyacylglutathione hydrolase
Probab=26.05 E-value=51 Score=28.53 Aligned_cols=21 Identities=19% Similarity=0.139 Sum_probs=12.5
Q ss_pred cccchhhhhhhhCCcccchhh
Q psy4931 64 AVDPSFEFAKRRNVPLKYDRE 84 (186)
Q Consensus 64 ~~d~~~efekRRn~~vKy~R~ 84 (186)
+.-+|+..|++-|-=.+.+..
T Consensus 211 t~pstl~~E~~~Npflr~~~~ 231 (258)
T PLN02469 211 TVPSTIEEELETNPFMRVDLP 231 (258)
T ss_pred cCCccHHHHHhhCCeecCCCH
Confidence 445677778887843444333
No 44
>KOG4135|consensus
Probab=25.73 E-value=25 Score=30.09 Aligned_cols=23 Identities=39% Similarity=0.780 Sum_probs=16.9
Q ss_pred hhhhccccccccccccCccceec
Q psy4931 163 EAEENMEVDTHWETNEDKLTYIK 185 (186)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~ 185 (186)
.-+++-+..-.|.++|||||||-
T Consensus 46 tLdeEyeMQ~sW~~DeDKlTFIV 68 (185)
T KOG4135|consen 46 TLDEEYEMQKSWREDEDKLTFIV 68 (185)
T ss_pred chhHHHHhhhhhccCCcceEEEE
Confidence 33444555667999999999984
No 45
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=25.27 E-value=38 Score=26.40 Aligned_cols=36 Identities=14% Similarity=0.316 Sum_probs=22.6
Q ss_pred eeecccCCCCccCCc-cceEEee--CCceeEEechhHHHh
Q psy4931 3 IETCYFCSSKIYPGH-GIQFVRN--DCKIFRFCRSKCHKL 39 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGh-G~~fVrn--Dgkvf~FcssKC~k~ 39 (186)
...|.|||.++.=-. -.+|-+. ++..|+.|+. |...
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~-C~Ay 40 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTP-CDAY 40 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCC-CCce
Confidence 457999987643222 2334433 5777899988 7654
No 46
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=24.79 E-value=38 Score=22.65 Aligned_cols=10 Identities=40% Similarity=1.105 Sum_probs=7.3
Q ss_pred eeecccCCCC
Q psy4931 3 IETCYFCSSK 12 (186)
Q Consensus 3 ~e~C~Fcg~~ 12 (186)
+.-|.|||.+
T Consensus 3 LkPCPFCG~~ 12 (61)
T PF14354_consen 3 LKPCPFCGSA 12 (61)
T ss_pred CcCCCCCCCc
Confidence 4579999754
No 47
>KOG1549|consensus
Probab=24.24 E-value=40 Score=32.35 Aligned_cols=25 Identities=32% Similarity=0.622 Sum_probs=21.1
Q ss_pred CceeecccCCCCcc--CCccceEEeeC
Q psy4931 1 MRIETCYFCSSKIY--PGHGIQFVRND 25 (186)
Q Consensus 1 Mr~e~C~Fcg~~Iy--PGhG~~fVrnD 25 (186)
|.++.|++|+.+|| ||=|-+|||.+
T Consensus 232 ln~D~~s~s~HK~ygp~~iGaLYvr~~ 258 (428)
T KOG1549|consen 232 LNADFLSISAHKIYGPPGIGALYVRRK 258 (428)
T ss_pred cCchheeeecccccCCCcceEEEEccC
Confidence 56788999999998 77899999873
No 48
>PF14777 BBIP10: Cilia BBSome complex subunit 10
Probab=23.99 E-value=52 Score=24.12 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=19.4
Q ss_pred CccCCccceEEeeCCceeEEechh
Q psy4931 12 KIYPGHGIQFVRNDCKIFRFCRSK 35 (186)
Q Consensus 12 ~IyPGhG~~fVrnDgkvf~FcssK 35 (186)
.|-|-.|.+|.. |-..+.||..|
T Consensus 10 eVlPk~G~l~~E-~~~~~vlCKPK 32 (65)
T PF14777_consen 10 EVLPKQGLLFQE-DKLTPVLCKPK 32 (65)
T ss_pred HhccccCceeec-cccceeeeccc
Confidence 378999999987 78999999765
No 49
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.79 E-value=83 Score=22.84 Aligned_cols=37 Identities=30% Similarity=0.559 Sum_probs=27.2
Q ss_pred eeecccCCCCccCCc-cceEEe-eCCceeEEechhHHHh
Q psy4931 3 IETCYFCSSKIYPGH-GIQFVR-NDCKIFRFCRSKCHKL 39 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGh-G~~fVr-nDgkvf~FcssKC~k~ 39 (186)
...|.-||..|.||. +..|.- |=|.+...=..+|+++
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~ 47 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKL 47 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHc
Confidence 468999999999997 455554 4465777777778765
No 50
>TIGR01922 purO_arch IMP cyclohydrolase. This model represents IMP cyclohydrolase, the final step in the biosynthesis of inosine monophosphate (IMP) in archaea. In bacteria this step is catalyzed by a bifunctional enzyme (purH).
Probab=23.54 E-value=45 Score=29.12 Aligned_cols=27 Identities=15% Similarity=0.043 Sum_probs=22.2
Q ss_pred ccCCccceEEee-CCc--eeEEechhHHHh
Q psy4931 13 IYPGHGIQFVRN-DCK--IFRFCRSKCHKL 39 (186)
Q Consensus 13 IyPGhG~~fVrn-Dgk--vf~FcssKC~k~ 39 (186)
+|||+|++-=+. ||+ +.+|.+|....|
T Consensus 1 MY~GR~ivvG~s~dG~~~~aY~V~sRSfpn 30 (199)
T TIGR01922 1 MYIGRFLVVGKLEDGTPFAAYRVSSRSFPN 30 (199)
T ss_pred CCCCCEEEEccCCCCCeEEEEEEecCCCCC
Confidence 599999999888 897 678888877655
No 51
>PRK13446 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=22.97 E-value=80 Score=24.95 Aligned_cols=10 Identities=30% Similarity=0.491 Sum_probs=7.0
Q ss_pred CCccCCccce
Q psy4931 11 SKIYPGHGIQ 20 (186)
Q Consensus 11 ~~IyPGhG~~ 20 (186)
.-|+|||.-+
T Consensus 33 ~gILp~H~p~ 42 (136)
T PRK13446 33 FGVLPGHAPF 42 (136)
T ss_pred eEEcCCCcce
Confidence 5689999433
No 52
>TIGR03666 Rv2061_F420 PPOX class probable F420-dependent enzyme, Rv2061 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN.
Probab=22.82 E-value=78 Score=24.71 Aligned_cols=28 Identities=18% Similarity=0.226 Sum_probs=22.9
Q ss_pred eEEeeCCceeEEechhHHHhhhcccCCc
Q psy4931 20 QFVRNDCKIFRFCRSKCHKLFKRKKNPR 47 (186)
Q Consensus 20 ~fVrnDgkvf~FcssKC~k~f~~KrnPR 47 (186)
.|+.-||.+|.+++..-.|.-..++||+
T Consensus 32 ~~~~d~g~l~f~t~~~~~K~~nl~~np~ 59 (132)
T TIGR03666 32 WAAVDGDKLLVRTKEDSWKVKRIRNNPR 59 (132)
T ss_pred EEEEECCEEEEEECCcCHHHHHHHhCCC
Confidence 5677788888888887778888888998
No 53
>KOG0402|consensus
Probab=22.28 E-value=28 Score=27.02 Aligned_cols=29 Identities=31% Similarity=0.622 Sum_probs=21.1
Q ss_pred eecccCCCCccCCccceEEeeCCceeEEechhHHHhhh
Q psy4931 4 ETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFK 41 (186)
Q Consensus 4 e~C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~f~ 41 (186)
.+|+|||.. -|++..--.|-|+ .|++-|.
T Consensus 37 y~CsfCGK~--------~vKR~AvGiW~C~-~C~kv~a 65 (92)
T KOG0402|consen 37 YTCSFCGKK--------TVKRKAVGIWKCG-SCKKVVA 65 (92)
T ss_pred hhhhhcchh--------hhhhhceeEEecC-Cccceec
Confidence 579999764 3566666778887 7877664
No 54
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=22.26 E-value=39 Score=31.58 Aligned_cols=13 Identities=23% Similarity=0.651 Sum_probs=9.7
Q ss_pred ceeecccCCCCcc
Q psy4931 2 RIETCYFCSSKIY 14 (186)
Q Consensus 2 r~e~C~Fcg~~Iy 14 (186)
....|||||.+-.
T Consensus 8 ~~~~CSFCGr~~~ 20 (412)
T PRK05342 8 KLLYCSFCGKSQH 20 (412)
T ss_pred CccccCCCCCChh
Confidence 4568999998643
No 55
>PF08789 PBCV_basic_adap: PBCV-specific basic adaptor domain; InterPro: IPR014897 The small PBCV-specific basic adaptor protein is found fused to S/T protein kinases and the 2-Cysteine domain [].
Probab=22.10 E-value=51 Score=22.04 Aligned_cols=18 Identities=33% Similarity=0.521 Sum_probs=15.3
Q ss_pred CCCCccCC-ccceEEeeCC
Q psy4931 9 CSSKIYPG-HGIQFVRNDC 26 (186)
Q Consensus 9 cg~~IyPG-hG~~fVrnDg 26 (186)
-|..||-| .|..||..|+
T Consensus 7 kgR~i~~g~rGg~yV~~~~ 25 (40)
T PF08789_consen 7 KGRKIFKGPRGGTYVISDG 25 (40)
T ss_pred cCCEEEECCCCCEEEeCCC
Confidence 37889999 5999999986
No 56
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=20.91 E-value=89 Score=19.14 Aligned_cols=28 Identities=25% Similarity=0.764 Sum_probs=18.3
Q ss_pred cccCCCCccCCccceEEeeCCceeEEechhHHHh
Q psy4931 6 CYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKL 39 (186)
Q Consensus 6 C~Fcg~~IyPGhG~~fVrnDgkvf~FcssKC~k~ 39 (186)
|.+|+. |+ ...=...+..+|||..|...
T Consensus 1 C~~C~~---~~---~~~C~~C~~~~YCs~~Cq~~ 28 (37)
T PF01753_consen 1 CAVCGK---PA---LKRCSRCKSVYYCSEECQRA 28 (37)
T ss_dssp -TTTSS---CS---SEEETTTSSSEESSHHHHHH
T ss_pred CcCCCC---Cc---CCcCCCCCCEEecCHHHHHH
Confidence 566766 11 11445678899999999765
No 57
>PF01321 Creatinase_N: Creatinase/Prolidase N-terminal domain; InterPro: IPR000587 Creatinase or creatine amidinohydrolase (3.5.3.3 from EC) catalyses the conversion of creatine and water to sarcosine and urea. The enzyme works as a homodimer, and is induced by choline chloride. Each monomer of creatinase has two clearly defined domains, a small N-terminal domain, and a large C-terminal domain. The structure of the C-terminal region represents the "pita-bread" fold. The fold contains both alpha helices and an anti-parallel beta sheet within two structurally similar domains that are thought to be derived from an ancient gene duplication. The active site, where conserved, is located between the two domains. The fold is common to methionine aminopeptidase (3.4.11.18 from EC), aminopeptidase P (3.4.11.9 from EC), prolidase (3.4.13.9 from EC), agropine synthase and creatinase (3.5.3.3 from EC). Though many of these peptidases require a divalent cation, creatinase is not a metal-dependent enzyme [, , ]. ; GO: 0016787 hydrolase activity; PDB: 1PV9_A 3CTZ_A 3IL0_B 3PN9_A 2HOW_A 1WN1_B 3I7M_A 1CHM_B 3QOC_D 1KP0_B ....
Probab=20.80 E-value=67 Score=23.10 Aligned_cols=35 Identities=14% Similarity=0.222 Sum_probs=23.1
Q ss_pred ecccCCCCccCCccceEE--eeCCceeEEec-hhHHHhh
Q psy4931 5 TCYFCSSKIYPGHGIQFV--RNDCKIFRFCR-SKCHKLF 40 (186)
Q Consensus 5 ~C~Fcg~~IyPGhG~~fV--rnDgkvf~Fcs-sKC~k~f 40 (186)
..||||+..+||.+-.++ ..||. +.|++ .-....-
T Consensus 25 i~YltG~~~~~~~~~~~l~i~~~~~-~l~~~~~~~~~~~ 62 (132)
T PF01321_consen 25 IRYLTGFRWQPGERPVLLVITADGA-VLFVPKGEYERAA 62 (132)
T ss_dssp HHHHHS--ST-TSSEEEEEEESSSE-EEEEEGGGHHHHH
T ss_pred ceEecCCCcCCCcceEEEEecccCc-EEEeccccHHHHH
Confidence 468999988888866655 88998 77887 5555443
No 58
>TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit. This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria.
Probab=20.45 E-value=45 Score=29.54 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=16.9
Q ss_pred eeecccCCCCccCCccceEEee
Q psy4931 3 IETCYFCSSKIYPGHGIQFVRN 24 (186)
Q Consensus 3 ~e~C~Fcg~~IyPGhG~~fVrn 24 (186)
...|.||++...||.-..|.+.
T Consensus 15 ~~~C~fCaf~~~~g~~~~~~l~ 36 (322)
T TIGR03550 15 RNRCGYCTFRRPPGELEAALLS 36 (322)
T ss_pred CCCCccCCccccCCCcccccCC
Confidence 3579999999999886656544
No 59
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=20.24 E-value=44 Score=21.59 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=7.7
Q ss_pred eecccCCCCcc
Q psy4931 4 ETCYFCSSKIY 14 (186)
Q Consensus 4 e~C~Fcg~~Iy 14 (186)
-.|.|||.++-
T Consensus 22 ~~Cp~CG~~~~ 32 (46)
T PRK00398 22 VRCPYCGYRIL 32 (46)
T ss_pred eECCCCCCeEE
Confidence 46888887653
Done!