Query psy12714
Match_columns 117
No_of_seqs 136 out of 1014
Neff 8.7
Searched_HMMs 46136
Date Fri Aug 16 17:50:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12714.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12714hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00412 LIM: LIM domain; Int 99.6 2E-15 4.3E-20 84.7 4.4 57 35-91 1-58 (58)
2 KOG1701|consensus 99.4 1.6E-14 3.5E-19 107.3 -1.6 84 28-112 330-430 (468)
3 KOG1044|consensus 99.4 1.7E-13 3.7E-18 105.1 3.3 83 29-112 130-216 (670)
4 KOG1701|consensus 99.3 3.7E-13 8.1E-18 100.2 -0.7 81 30-111 272-362 (468)
5 KOG2272|consensus 99.2 5E-13 1.1E-17 93.9 -1.3 84 30-113 10-98 (332)
6 KOG1703|consensus 99.2 2.4E-12 5.3E-17 99.1 1.8 82 29-111 360-452 (479)
7 KOG4577|consensus 99.2 6.6E-13 1.4E-17 94.8 -2.8 64 31-95 32-95 (383)
8 KOG2272|consensus 98.9 1.6E-10 3.6E-15 81.4 -0.5 80 29-109 192-280 (332)
9 smart00132 LIM Zinc-binding do 98.7 7.8E-09 1.7E-13 52.8 2.5 37 34-70 1-38 (39)
10 KOG1700|consensus 98.7 2.5E-09 5.5E-14 74.0 0.1 85 28-112 104-188 (200)
11 KOG1703|consensus 98.6 2.4E-08 5.1E-13 77.2 3.8 81 30-110 301-390 (479)
12 KOG1700|consensus 98.6 1.4E-08 3.1E-13 70.2 1.5 66 30-95 5-70 (200)
13 KOG4577|consensus 98.4 5.1E-08 1.1E-12 70.1 0.4 68 28-95 88-158 (383)
14 KOG1702|consensus 98.4 1.1E-08 2.3E-13 70.4 -3.2 58 33-90 5-62 (264)
15 KOG1044|consensus 98.2 2.3E-06 4.9E-11 66.6 4.1 80 29-111 13-93 (670)
16 KOG0490|consensus 95.1 0.0026 5.6E-08 44.3 -1.7 57 38-95 2-62 (235)
17 PF09943 DUF2175: Uncharacteri 90.3 0.089 1.9E-06 32.6 0.1 33 34-66 4-37 (101)
18 COG4357 Zinc finger domain con 86.5 0.087 1.9E-06 32.3 -1.7 58 35-96 38-95 (105)
19 PF08394 Arc_trans_TRASH: Arch 81.6 0.58 1.3E-05 23.6 0.4 31 35-68 1-32 (37)
20 PF10367 Vps39_2: Vacuolar sor 80.8 1.2 2.6E-05 27.1 1.7 30 31-60 77-107 (109)
21 PF14471 DUF4428: Domain of un 80.0 1.7 3.6E-05 23.5 1.9 29 61-90 1-30 (51)
22 PF11781 RRN7: RNA polymerase 74.8 1.9 4.2E-05 21.5 1.1 23 61-87 10-32 (36)
23 PF14446 Prok-RING_1: Prokaryo 72.8 2.1 4.6E-05 23.5 1.1 29 32-60 5-36 (54)
24 COG1645 Uncharacterized Zn-fin 72.3 1.6 3.5E-05 28.4 0.6 21 62-87 31-51 (131)
25 COG4847 Uncharacterized protei 71.6 1.4 3.1E-05 26.9 0.2 37 32-68 6-43 (103)
26 PF13240 zinc_ribbon_2: zinc-r 71.1 2.3 4.9E-05 19.0 0.8 8 35-42 2-9 (23)
27 PF12674 Zn_ribbon_2: Putative 70.9 2.4 5.2E-05 25.2 1.1 28 61-88 2-34 (81)
28 COG2191 Formylmethanofuran deh 67.0 2 4.4E-05 30.0 0.2 31 60-90 173-203 (206)
29 PF01258 zf-dskA_traR: Prokary 61.9 3.2 7E-05 20.4 0.4 27 62-88 6-32 (36)
30 PF00645 zf-PARP: Poly(ADP-rib 59.8 4.6 9.9E-05 23.6 0.8 17 30-46 5-21 (82)
31 PF06677 Auto_anti-p27: Sjogre 59.3 3.8 8.3E-05 21.1 0.4 21 62-86 20-40 (41)
32 cd02336 ZZ_RSC8 Zinc finger, Z 57.9 8.5 0.00018 20.2 1.6 29 61-89 2-32 (45)
33 PF02069 Metallothio_Pro: Prok 56.4 7.3 0.00016 21.2 1.2 28 61-88 9-37 (52)
34 KOG3579|consensus 53.8 13 0.00029 27.4 2.5 50 30-84 266-315 (352)
35 PRK00420 hypothetical protein; 53.0 5.6 0.00012 25.2 0.4 10 33-42 24-33 (112)
36 PF13248 zf-ribbon_3: zinc-rib 48.4 10 0.00022 17.2 0.8 9 34-42 4-12 (26)
37 smart00291 ZnF_ZZ Zinc-binding 45.6 19 0.00041 18.4 1.7 11 79-89 26-36 (44)
38 PF00628 PHD: PHD-finger; Int 44.3 16 0.00035 18.9 1.3 46 35-87 2-49 (51)
39 cd02249 ZZ Zinc finger, ZZ typ 44.0 19 0.00041 18.6 1.6 10 79-88 22-31 (46)
40 PF00320 GATA: GATA zinc finge 42.9 34 0.00074 16.7 2.3 26 62-87 1-27 (36)
41 PF14835 zf-RING_6: zf-RING of 42.6 17 0.00036 20.7 1.3 35 61-95 9-43 (65)
42 smart00504 Ubox Modified RING 41.4 36 0.00078 18.2 2.6 31 60-91 2-32 (63)
43 PRK00807 50S ribosomal protein 37.7 20 0.00043 19.3 1.0 24 33-56 2-28 (52)
44 PF14569 zf-UDP: Zinc-binding 35.7 44 0.00096 19.8 2.3 21 31-55 8-28 (80)
45 PF13834 DUF4193: Domain of un 34.3 12 0.00026 23.1 -0.2 28 59-86 70-98 (99)
46 PF00569 ZZ: Zinc finger, ZZ t 33.4 36 0.00078 17.6 1.6 11 79-89 27-37 (46)
47 PF10235 Cript: Microtubule-as 33.2 41 0.00088 20.4 2.0 39 28-72 40-82 (90)
48 PF05502 Dynactin_p62: Dynacti 32.7 25 0.00054 27.8 1.3 39 32-71 26-64 (483)
49 PF13923 zf-C3HC4_2: Zinc fing 32.1 52 0.0011 16.0 2.1 30 63-92 2-31 (39)
50 PF10886 DUF2685: Protein of u 32.1 35 0.00075 18.7 1.4 16 34-49 3-18 (54)
51 PF08746 zf-RING-like: RING-li 32.1 7.7 0.00017 20.0 -1.1 26 35-60 1-28 (43)
52 PF07754 DUF1610: Domain of un 31.5 31 0.00068 15.6 1.0 9 35-43 1-9 (24)
53 KOG0955|consensus 31.5 40 0.00087 29.4 2.3 68 30-108 217-289 (1051)
54 COG0266 Nei Formamidopyrimidin 30.7 25 0.00054 25.8 0.9 15 28-42 241-255 (273)
55 PF10080 DUF2318: Predicted me 29.2 26 0.00055 21.8 0.7 29 55-87 31-59 (102)
56 PF07503 zf-HYPF: HypF finger; 28.5 16 0.00034 18.1 -0.3 30 35-69 2-31 (35)
57 PF12855 Ecl1: Life-span regul 27.1 31 0.00068 17.9 0.7 22 62-87 9-31 (43)
58 TIGR02098 MJ0042_CXXC MJ0042 f 27.0 24 0.00053 17.2 0.2 9 34-42 4-12 (38)
59 KOG2893|consensus 26.8 27 0.00059 25.3 0.5 52 30-89 8-60 (341)
60 PRK00398 rpoP DNA-directed RNA 26.3 31 0.00068 17.7 0.6 28 33-69 4-31 (46)
61 cd02341 ZZ_ZZZ3 Zinc finger, Z 25.7 65 0.0014 17.0 1.8 10 80-89 26-35 (48)
62 COG5152 Uncharacterized conser 25.2 40 0.00087 23.7 1.1 49 59-111 196-246 (259)
63 cd00162 RING RING-finger (Real 25.0 35 0.00076 16.3 0.6 7 35-41 2-8 (45)
64 COG1998 RPS31 Ribosomal protei 25.0 33 0.00072 18.5 0.5 9 78-86 35-43 (51)
65 COG4416 Com Mu-like prophage p 24.8 17 0.00038 19.9 -0.6 12 32-43 4-15 (60)
66 PF06750 DiS_P_DiS: Bacterial 24.7 24 0.00053 21.3 -0.0 41 29-71 30-70 (92)
67 PF05570 DUF765: Circovirus pr 24.6 88 0.0019 14.4 2.0 23 2-24 2-24 (29)
68 cd02340 ZZ_NBR1_like Zinc fing 24.3 72 0.0016 16.3 1.8 9 80-88 23-31 (43)
69 KOG0978|consensus 24.1 33 0.00071 28.5 0.6 33 60-94 644-677 (698)
70 PRK00085 recO DNA repair prote 23.4 32 0.0007 24.1 0.4 28 60-87 150-177 (247)
71 TIGR00373 conserved hypothetic 23.1 22 0.00047 23.7 -0.5 32 31-70 108-139 (158)
72 PF00130 C1_1: Phorbol esters/ 22.9 28 0.0006 18.2 -0.0 12 31-42 10-21 (53)
73 PF04810 zf-Sec23_Sec24: Sec23 22.7 68 0.0015 16.0 1.4 11 33-43 3-13 (40)
74 PF06689 zf-C4_ClpX: ClpX C4-t 22.6 1.2E+02 0.0026 15.2 2.6 28 61-88 3-32 (41)
75 PRK01103 formamidopyrimidine/5 22.4 45 0.00098 24.1 1.0 15 28-42 241-255 (274)
76 PRK14811 formamidopyrimidine-D 22.2 45 0.00097 24.2 1.0 15 28-42 231-245 (269)
77 PF02591 DUF164: Putative zinc 22.0 20 0.00044 19.3 -0.7 12 61-72 24-35 (56)
78 PF11571 Med27: Mediator compl 21.9 45 0.00097 19.9 0.8 14 29-42 51-64 (90)
79 PF01927 Mut7-C: Mut7-C RNAse 21.8 46 0.001 21.7 0.9 38 32-69 91-134 (147)
80 KOG2186|consensus 21.6 21 0.00046 25.9 -0.8 44 33-77 4-47 (276)
81 PF09723 Zn-ribbon_8: Zinc rib 21.4 22 0.00049 18.0 -0.6 11 32-42 5-15 (42)
82 PRK06266 transcription initiat 21.4 28 0.00061 23.7 -0.2 33 31-71 116-148 (178)
83 smart00531 TFIIE Transcription 21.0 28 0.00061 22.7 -0.3 38 30-70 97-134 (147)
84 PF14255 Cys_rich_CPXG: Cystei 21.0 26 0.00057 19.0 -0.4 29 34-62 2-30 (52)
85 TIGR00270 conserved hypothetic 20.9 72 0.0016 21.2 1.7 9 35-43 3-11 (154)
86 cd02335 ZZ_ADA2 Zinc finger, Z 20.9 89 0.0019 16.3 1.7 10 80-89 24-33 (49)
87 PRK14810 formamidopyrimidine-D 20.1 53 0.0011 23.8 0.9 15 28-42 240-254 (272)
88 PRK13945 formamidopyrimidine-D 20.1 49 0.0011 24.1 0.8 15 28-42 250-264 (282)
89 smart00249 PHD PHD zinc finger 20.0 82 0.0018 15.2 1.5 26 35-60 2-29 (47)
No 1
>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=99.58 E-value=2e-15 Score=84.75 Aligned_cols=57 Identities=30% Similarity=0.799 Sum_probs=52.2
Q ss_pred ccccccccccCccE-EeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhh
Q psy12714 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91 (117)
Q Consensus 35 C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~ 91 (117)
|.+|+++|...+.+ .+.++.||..||+|..|+..|....++..++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999877765 6999999999999999999999888888999999999998876
No 2
>KOG1701|consensus
Probab=99.40 E-value=1.6e-14 Score=107.31 Aligned_cols=84 Identities=23% Similarity=0.514 Sum_probs=72.1
Q ss_pred CCcccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccc-cCCeeccHHHHHhhhCCCC-----------
Q psy12714 28 TGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTM-NNGHLYCLPHFKQLFISRG----------- 95 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~-~~g~~~C~~~y~~~~~~kc----------- 95 (117)
+++...+|..|++.|. ..++.+.++.||..||+|..|.+.|....|.. .++.+||-.||.++|+|||
T Consensus 330 yq~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~ 408 (468)
T KOG1701|consen 330 YQDTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRD 408 (468)
T ss_pred HHHHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCC
Confidence 5666789999999995 45578999999999999999999999888887 5899999999999999998
Q ss_pred -----ccccccCccccccCCcc
Q psy12714 96 -----NYDEGFGSDQHKRKWQP 112 (117)
Q Consensus 96 -----~~~~~~~~~~~~~~~~~ 112 (117)
..+.++++.||-+-||=
T Consensus 409 G~~etvRvvamdr~fHv~CY~C 430 (468)
T KOG1701|consen 409 GKDETVRVVAMDRDFHVNCYKC 430 (468)
T ss_pred CCcceEEEEEccccccccceeh
Confidence 34567778888777763
No 3
>KOG1044|consensus
Probab=99.39 E-value=1.7e-13 Score=105.06 Aligned_cols=83 Identities=22% Similarity=0.502 Sum_probs=68.7
Q ss_pred CcccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC----ccccccCcc
Q psy12714 29 GNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG----NYDEGFGSD 104 (117)
Q Consensus 29 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc----~~~~~~~~~ 104 (117)
..+...|++|++.|..++.+.++++.||..||+|..|+..| .+.|..++|.+||+.||.+.|+-|| .||.|..-.
T Consensus 130 ~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL-~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLq 208 (670)
T KOG1044|consen 130 SYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVL-NGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQ 208 (670)
T ss_pred ccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccc-cceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhh
Confidence 35667899999999888889999999999999999999999 4579999999999999999999998 455544443
Q ss_pred ccccCCcc
Q psy12714 105 QHKRKWQP 112 (117)
Q Consensus 105 ~~~~~~~~ 112 (117)
.-..||||
T Consensus 209 ag~kh~HP 216 (670)
T KOG1044|consen 209 AGDKHFHP 216 (670)
T ss_pred ccCcccCc
Confidence 33355554
No 4
>KOG1701|consensus
Probab=99.28 E-value=3.7e-13 Score=100.16 Aligned_cols=81 Identities=23% Similarity=0.485 Sum_probs=68.6
Q ss_pred cccccccccccccccCcc-EEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC---------cccc
Q psy12714 30 NPSSLCFACNKKVYPLEK-IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG---------NYDE 99 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc---------~~~~ 99 (117)
.....|.+|+|.|+..+. +.++++.||..||.|..|.+.|..+.||..++++||+.||++.+ .|| ..+.
T Consensus 272 ~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLr 350 (468)
T KOG1701|consen 272 DYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILR 350 (468)
T ss_pred hhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHH
Confidence 334599999999976554 57999999999999999999999999999999999999998765 344 4567
Q ss_pred ccCccccccCCc
Q psy12714 100 GFGSDQHKRKWQ 111 (117)
Q Consensus 100 ~~~~~~~~~~~~ 111 (117)
++|++||..-|.
T Consensus 351 A~GkayHp~CF~ 362 (468)
T KOG1701|consen 351 ALGKAYHPGCFT 362 (468)
T ss_pred hcccccCCCceE
Confidence 889999987664
No 5
>KOG2272|consensus
Probab=99.25 E-value=5e-13 Score=93.89 Aligned_cols=84 Identities=26% Similarity=0.579 Sum_probs=74.4
Q ss_pred cccccccccccccccCcc-EEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC----ccccccCcc
Q psy12714 30 NPSSLCFACNKKVYPLEK-IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG----NYDEGFGSD 104 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc----~~~~~~~~~ 104 (117)
.....|.+|.......+. +...+..||..||.|..|-.++.++.|+..+|+.||+.+|..+|+|.| .|+.|....
T Consensus 10 ~~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVik 89 (332)
T KOG2272|consen 10 LANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIK 89 (332)
T ss_pred HHHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHH
Confidence 345689999998877665 468899999999999999999999999999999999999999999987 688888888
Q ss_pred ccccCCccc
Q psy12714 105 QHKRKWQPV 113 (117)
Q Consensus 105 ~~~~~~~~~ 113 (117)
..++.|||.
T Consensus 90 amnnSwHp~ 98 (332)
T KOG2272|consen 90 AMNNSWHPA 98 (332)
T ss_pred hhccccCcc
Confidence 888899885
No 6
>KOG1703|consensus
Probab=99.24 E-value=2.4e-12 Score=99.11 Aligned_cols=82 Identities=28% Similarity=0.536 Sum_probs=71.7
Q ss_pred CcccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC-----------cc
Q psy12714 29 GNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG-----------NY 97 (117)
Q Consensus 29 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc-----------~~ 97 (117)
....+.|.+|+++|. .+.|.+.+..||+.||.|..|.+.|....|+..++.+||+.||..+++++| ..
T Consensus 360 ~~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ 438 (479)
T KOG1703|consen 360 APFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQ 438 (479)
T ss_pred HhhCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhH
Confidence 566789999999995 566778899999999999999999999999999999999999999998776 34
Q ss_pred ccccCccccccCCc
Q psy12714 98 DEGFGSDQHKRKWQ 111 (117)
Q Consensus 98 ~~~~~~~~~~~~~~ 111 (117)
+++.+..||...|.
T Consensus 439 ie~~~~~~h~~~F~ 452 (479)
T KOG1703|consen 439 IEADGSPFHGDCFR 452 (479)
T ss_pred hhccCcccccccee
Confidence 56778888888875
No 7
>KOG4577|consensus
Probab=99.20 E-value=6.6e-13 Score=94.78 Aligned_cols=64 Identities=19% Similarity=0.527 Sum_probs=58.8
Q ss_pred ccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC
Q psy12714 31 PSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG 95 (117)
Q Consensus 31 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc 95 (117)
..+.|++|.+.|.+..++.++++.||-.|++|+.|..+|.. ..+.+++.+||+.+|.++|++||
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKC 95 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKC 95 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcc
Confidence 57899999999976666789999999999999999999965 58889999999999999999999
No 8
>KOG2272|consensus
Probab=98.91 E-value=1.6e-10 Score=81.35 Aligned_cols=80 Identities=21% Similarity=0.316 Sum_probs=65.1
Q ss_pred CcccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC---------cccc
Q psy12714 29 GNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG---------NYDE 99 (117)
Q Consensus 29 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc---------~~~~ 99 (117)
..+.+.|..|.++|. ...+.++++.||.+.|+|.+|-+++-+-..|.+.|..||+.+|.++|+--| ..++
T Consensus 192 ~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~ 270 (332)
T KOG2272|consen 192 KMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVS 270 (332)
T ss_pred ccCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHH
Confidence 456788999999994 344679999999999999999999877788999999999999999999876 3445
Q ss_pred ccCccccccC
Q psy12714 100 GFGSDQHKRK 109 (117)
Q Consensus 100 ~~~~~~~~~~ 109 (117)
+++.+|=.+.
T Consensus 271 al~KawCv~c 280 (332)
T KOG2272|consen 271 ALNKAWCVEC 280 (332)
T ss_pred Hhhhhhcccc
Confidence 5555554443
No 9
>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=98.74 E-value=7.8e-09 Score=52.84 Aligned_cols=37 Identities=30% Similarity=0.716 Sum_probs=32.4
Q ss_pred cccccccccccC-ccEEeCCCcccccCcccccCCcccc
Q psy12714 34 LCFACNKKVYPL-EKIETDGKLFHRACFRCTQCCTVLR 70 (117)
Q Consensus 34 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~L~ 70 (117)
+|.+|++.|... ..+...++.||..||.|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999776 5567899999999999999999884
No 10
>KOG1700|consensus
Probab=98.71 E-value=2.5e-09 Score=73.99 Aligned_cols=85 Identities=44% Similarity=0.892 Sum_probs=73.7
Q ss_pred CCcccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCCccccccCccccc
Q psy12714 28 TGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRGNYDEGFGSDQHK 107 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc~~~~~~~~~~~~ 107 (117)
.......|..|.+.+++.+.+...+..||+.||+|..|+..|....+...++.+||..++.+++-.+..|..+.+...+.
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNEGFGARENK 183 (200)
T ss_pred hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcccccchhhhhh
Confidence 45556789999999999999999999999999999999999999999999999999998888888888888887776666
Q ss_pred cCCcc
Q psy12714 108 RKWQP 112 (117)
Q Consensus 108 ~~~~~ 112 (117)
+.|-.
T Consensus 184 ~~~~~ 188 (200)
T KOG1700|consen 184 EAAAA 188 (200)
T ss_pred hhhhh
Confidence 65543
No 11
>KOG1703|consensus
Probab=98.65 E-value=2.4e-08 Score=77.21 Aligned_cols=81 Identities=23% Similarity=0.418 Sum_probs=67.1
Q ss_pred cccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC---------ccccc
Q psy12714 30 NPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG---------NYDEG 100 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc---------~~~~~ 100 (117)
...+.|..|+..|.....+..+++.||+.+|.|..|...+....+...+|.+||..||.+.+.++| ..+.+
T Consensus 301 ~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a 380 (479)
T KOG1703|consen 301 VTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCA 380 (479)
T ss_pred cccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhh
Confidence 456899999999965466789999999999999999999998888888999999999999999998 34444
Q ss_pred cCccccccCC
Q psy12714 101 FGSDQHKRKW 110 (117)
Q Consensus 101 ~~~~~~~~~~ 110 (117)
++..||.+.|
T Consensus 381 ~~~~wH~~cf 390 (479)
T KOG1703|consen 381 LGRLWHPECF 390 (479)
T ss_pred ccCeechhce
Confidence 4555555544
No 12
>KOG1700|consensus
Probab=98.61 E-value=1.4e-08 Score=70.23 Aligned_cols=66 Identities=35% Similarity=0.778 Sum_probs=60.2
Q ss_pred cccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCC
Q psy12714 30 NPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG 95 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc 95 (117)
.....|..|++.++..+++...+..||+.||+|..|...|....+...++.+||..+|...++|+.
T Consensus 5 ~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~ 70 (200)
T KOG1700|consen 5 GTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKG 70 (200)
T ss_pred cccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccc
Confidence 345699999999998888888899999999999999999999899999999999998889999987
No 13
>KOG4577|consensus
Probab=98.43 E-value=5.1e-08 Score=70.06 Aligned_cols=68 Identities=19% Similarity=0.452 Sum_probs=55.9
Q ss_pred CCcccccccccccccccCccE-EeCCCcccccCcccccCCccccCC-Ccc-ccCCeeccHHHHHhhhCCCC
Q psy12714 28 TGNPSSLCFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRME-SYT-MNNGHLYCLPHFKQLFISRG 95 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~~C~~~y~~~~~~kc 95 (117)
+..+..+|..|...|.....+ .+.+..||..||.|..|..+|..+ .|| +.|+++.|+.+|+.--...|
T Consensus 88 fKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 88 FKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred HHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 456677999999999777766 489999999999999999999855 344 47999999999987655555
No 14
>KOG1702|consensus
Probab=98.41 E-value=1.1e-08 Score=70.39 Aligned_cols=58 Identities=33% Similarity=0.780 Sum_probs=53.2
Q ss_pred ccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhh
Q psy12714 33 SLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQL 90 (117)
Q Consensus 33 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~ 90 (117)
..|..|++.++..+.+..+++.||..||.|..|+..|....|.+-+.++||..+|...
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence 4678899999999999999999999999999999999999999999999999999543
No 15
>KOG1044|consensus
Probab=98.16 E-value=2.3e-06 Score=66.63 Aligned_cols=80 Identities=24% Similarity=0.510 Sum_probs=62.6
Q ss_pred CcccccccccccccccCccEEeCCCcccccCcccccCCccccCCCcccc-CCeeccHHHHHhhhCCCCccccccCccccc
Q psy12714 29 GNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMN-NGHLYCLPHFKQLFISRGNYDEGFGSDQHK 107 (117)
Q Consensus 29 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~-~g~~~C~~~y~~~~~~kc~~~~~~~~~~~~ 107 (117)
....-.|..|++.- .++.+.+.++.||..||.|..|+..|..+.|+.+ +.++|+.....+ | ..|..+.++|+.+|+
T Consensus 13 ~~~~i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~-~-~~gevvsa~gktyh~ 89 (670)
T KOG1044|consen 13 GKQGIKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRA-F-VEGEVVSTLGKTYHP 89 (670)
T ss_pred cccceehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhh-h-ccceeEecccceecc
Confidence 34456899999988 5788999999999999999999999999888886 467777633222 1 246678888888888
Q ss_pred cCCc
Q psy12714 108 RKWQ 111 (117)
Q Consensus 108 ~~~~ 111 (117)
+.+.
T Consensus 90 ~cf~ 93 (670)
T KOG1044|consen 90 KCFS 93 (670)
T ss_pred ccce
Confidence 7654
No 16
>KOG0490|consensus
Probab=95.14 E-value=0.0026 Score=44.35 Aligned_cols=57 Identities=19% Similarity=0.631 Sum_probs=44.1
Q ss_pred cccccccCccEEeCCCcccccCcccccCCcccc--CCCccccCCeeccHHHHHh--hhCCCC
Q psy12714 38 CNKKVYPLEKIETDGKLFHRACFRCTQCCTVLR--MESYTMNNGHLYCLPHFKQ--LFISRG 95 (117)
Q Consensus 38 C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~~C~~~y~~--~~~~kc 95 (117)
|+..|.+...+...+..||..|..|..|...|. ...+.. +|..||..+|.. .+..+|
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr 62 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRC 62 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccc
Confidence 555665444455668999999999999999997 444555 999999999987 666666
No 17
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=90.27 E-value=0.089 Score=32.59 Aligned_cols=33 Identities=24% Similarity=0.508 Sum_probs=25.4
Q ss_pred cccccccccccCccEEe-CCCcccccCcccccCC
Q psy12714 34 LCFACNKKVYPLEKIET-DGKLFHRACFRCTQCC 66 (117)
Q Consensus 34 ~C~~C~~~i~~~~~~~~-~~~~~H~~Cf~C~~C~ 66 (117)
+|..|++.|+.++.+.+ .+...|..||.=..-.
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~ 37 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKASK 37 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHhh
Confidence 69999999999998874 3456799998755443
No 18
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=86.45 E-value=0.087 Score=32.29 Aligned_cols=58 Identities=19% Similarity=0.383 Sum_probs=36.9
Q ss_pred ccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCCCCc
Q psy12714 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRGN 96 (117)
Q Consensus 35 C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc~ 96 (117)
|..|+..+..--.....-..++..+..|..|...|+-..|..-..-+|| +..|.|+|.
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C----~spFNp~Ck 95 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC----QSPFNPGCK 95 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc----CCCCCcccc
Confidence 4455555532222233445678888999999999987777766665555 355677774
No 19
>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=81.61 E-value=0.58 Score=23.65 Aligned_cols=31 Identities=19% Similarity=0.533 Sum_probs=19.7
Q ss_pred ccccccccccCcc-EEeCCCcccccCcccccCCcc
Q psy12714 35 CFACNKKVYPLEK-IETDGKLFHRACFRCTQCCTV 68 (117)
Q Consensus 35 C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~ 68 (117)
|..||..|.+.-. +...++.|+ |.|..|...
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHH
Confidence 6778998864332 467888887 444455443
No 20
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=80.79 E-value=1.2 Score=27.07 Aligned_cols=30 Identities=23% Similarity=0.412 Sum_probs=18.9
Q ss_pred ccccccccccccccCccE-EeCCCcccccCc
Q psy12714 31 PSSLCFACNKKVYPLEKI-ETDGKLFHRACF 60 (117)
Q Consensus 31 ~~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf 60 (117)
....|..|++.|.....+ -..+..+|..|+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 345788888888543322 244566787775
No 21
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=79.97 E-value=1.7 Score=23.51 Aligned_cols=29 Identities=21% Similarity=0.647 Sum_probs=19.0
Q ss_pred ccccCCccccCCC-ccccCCeeccHHHHHhh
Q psy12714 61 RCTQCCTVLRMES-YTMNNGHLYCLPHFKQL 90 (117)
Q Consensus 61 ~C~~C~~~L~~~~-~~~~~g~~~C~~~y~~~ 90 (117)
.|..|+..++.-. +...|| ..|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 3667777765433 445666 6888888765
No 22
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=74.80 E-value=1.9 Score=21.51 Aligned_cols=23 Identities=22% Similarity=0.515 Sum_probs=15.5
Q ss_pred ccccCCccccCCCccccCCeeccHHHH
Q psy12714 61 RCTQCCTVLRMESYTMNNGHLYCLPHF 87 (117)
Q Consensus 61 ~C~~C~~~L~~~~~~~~~g~~~C~~~y 87 (117)
.|..|+.. .+...+|..||..|-
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCc
Confidence 46667653 366678888886653
No 23
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.78 E-value=2.1 Score=23.45 Aligned_cols=29 Identities=28% Similarity=0.584 Sum_probs=19.1
Q ss_pred ccccccccccccc-CccEE--eCCCcccccCc
Q psy12714 32 SSLCFACNKKVYP-LEKIE--TDGKLFHRACF 60 (117)
Q Consensus 32 ~~~C~~C~~~i~~-~~~~~--~~~~~~H~~Cf 60 (117)
..+|..|++.+.. ++++. .=+..||++|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 4588999998864 33333 34566787776
No 24
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=72.35 E-value=1.6 Score=28.35 Aligned_cols=21 Identities=29% Similarity=0.793 Sum_probs=14.9
Q ss_pred cccCCccccCCCccccCCeeccHHHH
Q psy12714 62 CTQCCTVLRMESYTMNNGHLYCLPHF 87 (117)
Q Consensus 62 C~~C~~~L~~~~~~~~~g~~~C~~~y 87 (117)
|..|+.+| |- ++|.+||..|-
T Consensus 31 Cp~Cg~PL----F~-KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL----FR-KDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc----ee-eCCeEECCCCC
Confidence 66777776 33 78888887774
No 25
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=71.64 E-value=1.4 Score=26.95 Aligned_cols=37 Identities=14% Similarity=0.269 Sum_probs=27.2
Q ss_pred cccccccccccccCccEEeC-CCcccccCcccccCCcc
Q psy12714 32 SSLCFACNKKVYPLEKIETD-GKLFHRACFRCTQCCTV 68 (117)
Q Consensus 32 ~~~C~~C~~~i~~~~~~~~~-~~~~H~~Cf~C~~C~~~ 68 (117)
.-+|..|+..|..++++..- ....|..||.-+.-+++
T Consensus 6 ewkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eeeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 45799999999888887643 34578888876665543
No 26
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=71.07 E-value=2.3 Score=19.01 Aligned_cols=8 Identities=25% Similarity=0.966 Sum_probs=4.4
Q ss_pred cccccccc
Q psy12714 35 CFACNKKV 42 (117)
Q Consensus 35 C~~C~~~i 42 (117)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 55555555
No 27
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=70.86 E-value=2.4 Score=25.17 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=20.3
Q ss_pred ccccCCccccCCCcccc-----CCeeccHHHHH
Q psy12714 61 RCTQCCTVLRMESYTMN-----NGHLYCLPHFK 88 (117)
Q Consensus 61 ~C~~C~~~L~~~~~~~~-----~g~~~C~~~y~ 88 (117)
.|..|+.+|.....+.. ...-||..||.
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 48889999986654432 35779999994
No 28
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=66.99 E-value=2 Score=29.95 Aligned_cols=31 Identities=23% Similarity=0.497 Sum_probs=22.2
Q ss_pred cccccCCccccCCCccccCCeeccHHHHHhh
Q psy12714 60 FRCTQCCTVLRMESYTMNNGHLYCLPHFKQL 90 (117)
Q Consensus 60 f~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~ 90 (117)
-+|..|+-..-...-...+|++.|..||...
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 4678888766555555578899999998643
No 29
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=61.90 E-value=3.2 Score=20.41 Aligned_cols=27 Identities=19% Similarity=0.421 Sum_probs=12.3
Q ss_pred cccCCccccCCCccccCCeeccHHHHH
Q psy12714 62 CTQCCTVLRMESYTMNNGHLYCLPHFK 88 (117)
Q Consensus 62 C~~C~~~L~~~~~~~~~g~~~C~~~y~ 88 (117)
|..|+..+.........+..+|..|..
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhC
Confidence 455555544333333455666666654
No 30
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=59.76 E-value=4.6 Score=23.55 Aligned_cols=17 Identities=29% Similarity=0.491 Sum_probs=12.0
Q ss_pred cccccccccccccccCc
Q psy12714 30 NPSSLCFACNKKVYPLE 46 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~ 46 (117)
+....|..|++.|..++
T Consensus 5 s~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGE 21 (82)
T ss_dssp SSTEBETTTSCBE-TTS
T ss_pred CCCccCcccCCcCCCCC
Confidence 34568999999996544
No 31
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=59.34 E-value=3.8 Score=21.10 Aligned_cols=21 Identities=33% Similarity=0.873 Sum_probs=10.8
Q ss_pred cccCCccccCCCccccCCeeccHHH
Q psy12714 62 CTQCCTVLRMESYTMNNGHLYCLPH 86 (117)
Q Consensus 62 C~~C~~~L~~~~~~~~~g~~~C~~~ 86 (117)
|..|+.+|- -.++++.||..|
T Consensus 20 Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCeeE----EecCCCEECCCC
Confidence 445555552 234566666543
No 32
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=57.88 E-value=8.5 Score=20.18 Aligned_cols=29 Identities=14% Similarity=0.276 Sum_probs=18.0
Q ss_pred ccccCCccccCCCcccc--CCeeccHHHHHh
Q psy12714 61 RCTQCCTVLRMESYTMN--NGHLYCLPHFKQ 89 (117)
Q Consensus 61 ~C~~C~~~L~~~~~~~~--~g~~~C~~~y~~ 89 (117)
.|..|+..++...|... .+..+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 46667776654333332 357889999953
No 33
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=56.38 E-value=7.3 Score=21.20 Aligned_cols=28 Identities=25% Similarity=0.590 Sum_probs=14.8
Q ss_pred ccccCCccccCCCccccCCeecc-HHHHH
Q psy12714 61 RCTQCCTVLRMESYTMNNGHLYC-LPHFK 88 (117)
Q Consensus 61 ~C~~C~~~L~~~~~~~~~g~~~C-~~~y~ 88 (117)
.|..|...+....-+.++|+.|| +.|-.
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 46677777765566678899998 55543
No 34
>KOG3579|consensus
Probab=53.83 E-value=13 Score=27.44 Aligned_cols=50 Identities=18% Similarity=0.493 Sum_probs=33.1
Q ss_pred cccccccccccccccCccEEeCCCcccccCcccccCCccccCCCccccCCeeccH
Q psy12714 30 NPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCL 84 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~ 84 (117)
...-.|..|++.+.+...+..-.-.-|+-||-|+.=. | +--...|.+||.
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRes--I---K~Qg~sgevYCP 315 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRES--I---KQQGASGEVYCP 315 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHH--H---HhhcCCCceeCC
Confidence 3346799999999777666666666799899776421 1 112234688884
No 35
>PRK00420 hypothetical protein; Validated
Probab=52.98 E-value=5.6 Score=25.16 Aligned_cols=10 Identities=20% Similarity=0.567 Sum_probs=5.3
Q ss_pred cccccccccc
Q psy12714 33 SLCFACNKKV 42 (117)
Q Consensus 33 ~~C~~C~~~i 42 (117)
..|..|+.++
T Consensus 24 ~~CP~Cg~pL 33 (112)
T PRK00420 24 KHCPVCGLPL 33 (112)
T ss_pred CCCCCCCCcc
Confidence 4555555544
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=48.38 E-value=10 Score=17.20 Aligned_cols=9 Identities=22% Similarity=0.933 Sum_probs=5.1
Q ss_pred ccccccccc
Q psy12714 34 LCFACNKKV 42 (117)
Q Consensus 34 ~C~~C~~~i 42 (117)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 466666544
No 37
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=45.56 E-value=19 Score=18.43 Aligned_cols=11 Identities=18% Similarity=0.335 Sum_probs=7.4
Q ss_pred CeeccHHHHHh
Q psy12714 79 GHLYCLPHFKQ 89 (117)
Q Consensus 79 g~~~C~~~y~~ 89 (117)
+--+|..||.+
T Consensus 26 d~dlC~~Cf~~ 36 (44)
T smart00291 26 DYDLCQSCFAK 36 (44)
T ss_pred CccchHHHHhC
Confidence 45578888854
No 38
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the 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; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=44.32 E-value=16 Score=18.94 Aligned_cols=46 Identities=17% Similarity=0.395 Sum_probs=22.2
Q ss_pred ccccccccccCccEEe--CCCcccccCcccccCCccccCCCccccCCeeccHHHH
Q psy12714 35 CFACNKKVYPLEKIET--DGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87 (117)
Q Consensus 35 C~~C~~~i~~~~~~~~--~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y 87 (117)
|..|+..-...+.|.- =+..||..|..-. ........+..+|..|-
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~-------~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVGPP-------EKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTSTSS-------HSHHSHHSSSBSSHHHH
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCCCC-------hhhccCCCCcEECcCCc
Confidence 6667763333333332 2356787774211 11112223477777764
No 39
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=43.97 E-value=19 Score=18.58 Aligned_cols=10 Identities=10% Similarity=0.308 Sum_probs=6.7
Q ss_pred CeeccHHHHH
Q psy12714 79 GHLYCLPHFK 88 (117)
Q Consensus 79 g~~~C~~~y~ 88 (117)
+--+|..||.
T Consensus 22 d~dLC~~Cf~ 31 (46)
T cd02249 22 DFDLCSSCYA 31 (46)
T ss_pred CCcCHHHHHC
Confidence 3556888875
No 40
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=42.93 E-value=34 Score=16.73 Aligned_cols=26 Identities=23% Similarity=0.309 Sum_probs=13.4
Q ss_pred cccCCccccCCCccccCCee-ccHHHH
Q psy12714 62 CTQCCTVLRMESYTMNNGHL-YCLPHF 87 (117)
Q Consensus 62 C~~C~~~L~~~~~~~~~g~~-~C~~~y 87 (117)
|..|+..-+.......+|.. +|..|+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg 27 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACG 27 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHH
Confidence 44555544444444446666 899887
No 41
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=42.56 E-value=17 Score=20.71 Aligned_cols=35 Identities=20% Similarity=0.457 Sum_probs=10.1
Q ss_pred ccccCCccccCCCccccCCeeccHHHHHhhhCCCC
Q psy12714 61 RCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISRG 95 (117)
Q Consensus 61 ~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~kc 95 (117)
+|+.|...|........=..+||..|-...++..|
T Consensus 9 rCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~C 43 (65)
T PF14835_consen 9 RCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSEC 43 (65)
T ss_dssp S-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-
T ss_pred CCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCC
Confidence 44445444432211122234555555544444444
No 42
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=41.42 E-value=36 Score=18.22 Aligned_cols=31 Identities=16% Similarity=0.354 Sum_probs=20.2
Q ss_pred cccccCCccccCCCccccCCeeccHHHHHhhh
Q psy12714 60 FRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91 (117)
Q Consensus 60 f~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~ 91 (117)
|.|..|...+.. ......|..||..+..+.+
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~ 32 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWL 32 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHH
Confidence 456777777654 3444567888888876544
No 43
>PRK00807 50S ribosomal protein L24e; Validated
Probab=37.68 E-value=20 Score=19.35 Aligned_cols=24 Identities=25% Similarity=0.584 Sum_probs=15.7
Q ss_pred ccccccccccccCcc---EEeCCCccc
Q psy12714 33 SLCFACNKKVYPLEK---IETDGKLFH 56 (117)
Q Consensus 33 ~~C~~C~~~i~~~~~---~~~~~~~~H 56 (117)
..|..|+..|+++.. +...++.|.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 368888888875443 345667665
No 44
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=35.69 E-value=44 Score=19.76 Aligned_cols=21 Identities=24% Similarity=0.703 Sum_probs=8.0
Q ss_pred ccccccccccccccCccEEeCCCcc
Q psy12714 31 PSSLCFACNKKVYPLEKIETDGKLF 55 (117)
Q Consensus 31 ~~~~C~~C~~~i~~~~~~~~~~~~~ 55 (117)
....|..|+..|- +...+..|
T Consensus 8 ~~qiCqiCGD~VG----l~~~Ge~F 28 (80)
T PF14569_consen 8 NGQICQICGDDVG----LTENGEVF 28 (80)
T ss_dssp SS-B-SSS--B------B-SSSSB-
T ss_pred CCcccccccCccc----cCCCCCEE
Confidence 3457888888773 34455544
No 45
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=34.26 E-value=12 Score=23.11 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=16.8
Q ss_pred CcccccCCccccCCCcc-ccCCeeccHHH
Q psy12714 59 CFRCTQCCTVLRMESYT-MNNGHLYCLPH 86 (117)
Q Consensus 59 Cf~C~~C~~~L~~~~~~-~~~g~~~C~~~ 86 (117)
=|.|..|-..-..+... ..+|.++|..|
T Consensus 70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhccccCCCEecccc
Confidence 37777775533222222 35789999876
No 46
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=33.38 E-value=36 Score=17.58 Aligned_cols=11 Identities=18% Similarity=0.280 Sum_probs=7.5
Q ss_pred CeeccHHHHHh
Q psy12714 79 GHLYCLPHFKQ 89 (117)
Q Consensus 79 g~~~C~~~y~~ 89 (117)
+--+|..||.+
T Consensus 27 d~dLC~~C~~~ 37 (46)
T PF00569_consen 27 DYDLCEDCFSK 37 (46)
T ss_dssp S-EEEHHHHHH
T ss_pred CCchhhHHHhC
Confidence 45679999865
No 47
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=33.17 E-value=41 Score=20.44 Aligned_cols=39 Identities=26% Similarity=0.420 Sum_probs=20.9
Q ss_pred CCcccccccccccccccCccEEeCCCcccccC----cccccCCccccCC
Q psy12714 28 TGNPSSLCFACNKKVYPLEKIETDGKLFHRAC----FRCTQCCTVLRME 72 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~C----f~C~~C~~~L~~~ 72 (117)
+......|..|...|+.. +..|-..| -.|..|++.|.+.
T Consensus 40 y~~~~~~C~~CK~~v~q~------g~~YCq~CAYkkGiCamCGKki~dt 82 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQP------GAKYCQTCAYKKGICAMCGKKILDT 82 (90)
T ss_pred ccccCccccccccccccC------CCccChhhhcccCcccccCCeeccc
Confidence 444455777777666431 12233333 2577777776443
No 48
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=32.72 E-value=25 Score=27.83 Aligned_cols=39 Identities=28% Similarity=0.554 Sum_probs=26.0
Q ss_pred cccccccccccccCccEEeCCCcccccCcccccCCccccC
Q psy12714 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRM 71 (117)
Q Consensus 32 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~ 71 (117)
...|..|-..+...+ +...+....+.||.|-.|...|..
T Consensus 26 ~~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 26 SYYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred eeECccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 456777776664333 334444556699999999988853
No 49
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=32.11 E-value=52 Score=15.98 Aligned_cols=30 Identities=20% Similarity=0.360 Sum_probs=16.0
Q ss_pred ccCCccccCCCccccCCeeccHHHHHhhhC
Q psy12714 63 TQCCTVLRMESYTMNNGHLYCLPHFKQLFI 92 (117)
Q Consensus 63 ~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~ 92 (117)
..|...+........=|..||..|..+.+.
T Consensus 2 ~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 2 PICLDELRDPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp TTTTSB-SSEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCcccCcCEECCCCCchhHHHHHHHHH
Confidence 345444433212334478888888765543
No 50
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=32.10 E-value=35 Score=18.69 Aligned_cols=16 Identities=19% Similarity=0.590 Sum_probs=8.6
Q ss_pred cccccccccccCccEE
Q psy12714 34 LCFACNKKVYPLEKIE 49 (117)
Q Consensus 34 ~C~~C~~~i~~~~~~~ 49 (117)
+|..|+.+|.....+.
T Consensus 3 ~CvVCKqpi~~a~~v~ 18 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVE 18 (54)
T ss_pred eeeeeCCccCcceEEE
Confidence 5666666664443333
No 51
>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: 3NW0_A 2CT0_A.
Probab=32.10 E-value=7.7 Score=20.00 Aligned_cols=26 Identities=27% Similarity=0.526 Sum_probs=9.1
Q ss_pred ccccccccccCccEE--eCCCcccccCc
Q psy12714 35 CFACNKKVYPLEKIE--TDGKLFHRACF 60 (117)
Q Consensus 35 C~~C~~~i~~~~~~~--~~~~~~H~~Cf 60 (117)
|..|++.+..+.+-. .=+..||..|+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~ 28 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCF 28 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHH
Confidence 556777665443321 11223565554
No 52
>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=31.53 E-value=31 Score=15.57 Aligned_cols=9 Identities=22% Similarity=0.936 Sum_probs=4.8
Q ss_pred ccccccccc
Q psy12714 35 CFACNKKVY 43 (117)
Q Consensus 35 C~~C~~~i~ 43 (117)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 445655554
No 53
>KOG0955|consensus
Probab=31.48 E-value=40 Score=29.39 Aligned_cols=68 Identities=12% Similarity=0.165 Sum_probs=41.5
Q ss_pred ccccccccccccccc--CccEEe--CCCcccccCcccccCCccccCCCccccCCeeccHHHHHhhhCC-CCccccccCcc
Q psy12714 30 NPSSLCFACNKKVYP--LEKIET--DGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFIS-RGNYDEGFGSD 104 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~--~~~~~~--~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~~~-kc~~~~~~~~~ 104 (117)
....+|..|.+.-.. ..++-. -+..+|..|.. .-++.+|+++|..|.....++ +|.+....+++
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg-----------i~~ipeg~WlCr~Cl~s~~~~v~c~~cp~~~gA 285 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYG-----------IPFIPEGQWLCRRCLQSPQRPVRCLLCPSKGGA 285 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCCCcchhhhhccC-----------CCCCCCCcEeehhhccCcCcccceEeccCCCCc
Confidence 445688888775432 112221 23445666642 234578999999999766566 77666666666
Q ss_pred cccc
Q psy12714 105 QHKR 108 (117)
Q Consensus 105 ~~~~ 108 (117)
|.++
T Consensus 286 Fkqt 289 (1051)
T KOG0955|consen 286 FKQT 289 (1051)
T ss_pred ceec
Confidence 5543
No 54
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=30.73 E-value=25 Score=25.78 Aligned_cols=15 Identities=20% Similarity=0.574 Sum_probs=10.7
Q ss_pred CCccccccccccccc
Q psy12714 28 TGNPSSLCFACNKKV 42 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i 42 (117)
++.....|..|+..|
T Consensus 241 YgR~GepC~~CGt~I 255 (273)
T COG0266 241 YGRAGEPCRRCGTPI 255 (273)
T ss_pred ecCCCCCCCccCCEe
Confidence 555566788888777
No 55
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=29.18 E-value=26 Score=21.76 Aligned_cols=29 Identities=21% Similarity=0.367 Sum_probs=19.7
Q ss_pred ccccCcccccCCccccCCCccccCCeeccHHHH
Q psy12714 55 FHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87 (117)
Q Consensus 55 ~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y 87 (117)
+...-=.|..| ....|+.+++.+.|..|-
T Consensus 31 ~~va~daCeiC----~~~GY~q~g~~lvC~~C~ 59 (102)
T PF10080_consen 31 YRVAFDACEIC----GPKGYYQEGDQLVCKNCG 59 (102)
T ss_pred EEEEEEecccc----CCCceEEECCEEEEecCC
Confidence 33333356777 456788888888888885
No 56
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=28.53 E-value=16 Score=18.10 Aligned_cols=30 Identities=27% Similarity=0.679 Sum_probs=17.0
Q ss_pred ccccccccccCccEEeCCCcccccCcccccCCccc
Q psy12714 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVL 69 (117)
Q Consensus 35 C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L 69 (117)
|..|.+.+. ...++.||-.-..|..|+-.+
T Consensus 2 C~~C~~Ey~-----~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEYF-----DPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHHC-----STTSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHHc-----CCCCCcccCcCccCCCCCCCE
Confidence 556665543 245678898888899998765
No 57
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=27.13 E-value=31 Score=17.88 Aligned_cols=22 Identities=27% Similarity=0.611 Sum_probs=11.7
Q ss_pred cccCCccccCCCccccCCeecc-HHHH
Q psy12714 62 CTQCCTVLRMESYTMNNGHLYC-LPHF 87 (117)
Q Consensus 62 C~~C~~~L~~~~~~~~~g~~~C-~~~y 87 (117)
|..|.+.+.. ..++.+|| +.|-
T Consensus 9 C~~Cdk~~~~----~~~~~lYCSe~Cr 31 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCSEECR 31 (43)
T ss_pred HHHhhccccC----CCCCccccCHHHH
Confidence 4455554422 34667888 4553
No 58
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=26.96 E-value=24 Score=17.16 Aligned_cols=9 Identities=22% Similarity=0.682 Sum_probs=5.9
Q ss_pred ccccccccc
Q psy12714 34 LCFACNKKV 42 (117)
Q Consensus 34 ~C~~C~~~i 42 (117)
.|..|+..+
T Consensus 4 ~CP~C~~~~ 12 (38)
T TIGR02098 4 QCPNCKTSF 12 (38)
T ss_pred ECCCCCCEE
Confidence 577777654
No 59
>KOG2893|consensus
Probab=26.82 E-value=27 Score=25.26 Aligned_cols=52 Identities=27% Similarity=0.483 Sum_probs=29.7
Q ss_pred cccccccccccccccCccEEeC-CCcccccCcccccCCccccCCCccccCCeeccHHHHHh
Q psy12714 30 NPSSLCFACNKKVYPLEKIETD-GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQ 89 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~~~~~~-~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~ 89 (117)
...+-|-.|+... +.|+|.+. .+.=| |+|..|.+.|- ..-.-.+.|..-+.+
T Consensus 8 ~~kpwcwycnref-ddekiliqhqkakh---fkchichkkl~----sgpglsihcmqvhke 60 (341)
T KOG2893|consen 8 VDKPWCWYCNREF-DDEKILIQHQKAKH---FKCHICHKKLF----SGPGLSIHCMQVHKE 60 (341)
T ss_pred cCCceeeeccccc-chhhhhhhhhhhcc---ceeeeehhhhc----cCCCceeehhhhhhh
Confidence 3455688898877 45555433 33334 77888887763 233344556444433
No 60
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=26.27 E-value=31 Score=17.70 Aligned_cols=28 Identities=29% Similarity=0.526 Sum_probs=15.6
Q ss_pred ccccccccccccCccEEeCCCcccccCcccccCCccc
Q psy12714 33 SLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVL 69 (117)
Q Consensus 33 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L 69 (117)
-+|..||..+...+. .. -+.|..|+..+
T Consensus 4 y~C~~CG~~~~~~~~----~~-----~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEY----GT-----GVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCC----CC-----ceECCCCCCeE
Confidence 468888776632221 11 25677777655
No 61
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=25.67 E-value=65 Score=16.99 Aligned_cols=10 Identities=10% Similarity=0.125 Sum_probs=6.7
Q ss_pred eeccHHHHHh
Q psy12714 80 HLYCLPHFKQ 89 (117)
Q Consensus 80 ~~~C~~~y~~ 89 (117)
--+|..||..
T Consensus 26 ~DlC~~C~~~ 35 (48)
T cd02341 26 FDLCQDCVVK 35 (48)
T ss_pred CccCHHHHhC
Confidence 4468888754
No 62
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=25.16 E-value=40 Score=23.73 Aligned_cols=49 Identities=18% Similarity=0.281 Sum_probs=29.8
Q ss_pred CcccccCCccccCCCccccCCeeccHHHHHhhh--CCCCccccccCccccccCCc
Q psy12714 59 CFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF--ISRGNYDEGFGSDQHKRKWQ 111 (117)
Q Consensus 59 Cf~C~~C~~~L~~~~~~~~~g~~~C~~~y~~~~--~~kc~~~~~~~~~~~~~~~~ 111 (117)
=|.|..|.+.... .....=|.-+|..|+.+.| ++.| .-.|.+.+..-|+
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C---~~Cgk~t~G~f~V 246 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDEC---GVCGKATYGRFWV 246 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcc---eecchhhccceeH
Confidence 4678888776533 2333457889999997665 4556 4445555544443
No 63
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=25.03 E-value=35 Score=16.28 Aligned_cols=7 Identities=29% Similarity=0.847 Sum_probs=2.8
Q ss_pred ccccccc
Q psy12714 35 CFACNKK 41 (117)
Q Consensus 35 C~~C~~~ 41 (117)
|..|.+.
T Consensus 2 C~iC~~~ 8 (45)
T cd00162 2 CPICLEE 8 (45)
T ss_pred CCcCchh
Confidence 3344433
No 64
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.96 E-value=33 Score=18.46 Aligned_cols=9 Identities=11% Similarity=0.143 Sum_probs=4.0
Q ss_pred CCeeccHHH
Q psy12714 78 NGHLYCLPH 86 (117)
Q Consensus 78 ~g~~~C~~~ 86 (117)
.++++|..|
T Consensus 35 ~dR~~CGkC 43 (51)
T COG1998 35 KDRWACGKC 43 (51)
T ss_pred CceeEeccc
Confidence 344455443
No 65
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=24.76 E-value=17 Score=19.90 Aligned_cols=12 Identities=33% Similarity=0.620 Sum_probs=8.7
Q ss_pred cccccccccccc
Q psy12714 32 SSLCFACNKKVY 43 (117)
Q Consensus 32 ~~~C~~C~~~i~ 43 (117)
+-+|..|++.+.
T Consensus 4 tiRC~~CnKlLa 15 (60)
T COG4416 4 TIRCAKCNKLLA 15 (60)
T ss_pred eeehHHHhHHHH
Confidence 347888888774
No 66
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. 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 localised 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=24.73 E-value=24 Score=21.28 Aligned_cols=41 Identities=20% Similarity=0.225 Sum_probs=26.4
Q ss_pred CcccccccccccccccCccEEeCCCcccccCcccccCCccccC
Q psy12714 29 GNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRM 71 (117)
Q Consensus 29 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~ 71 (117)
......|..|++.+...+.+-+.+ |-..--+|..|+.++..
T Consensus 30 ~~~rS~C~~C~~~L~~~~lIPi~S--~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 30 IFPRSHCPHCGHPLSWWDLIPILS--YLLLRGRCRYCGAPIPP 70 (92)
T ss_pred cCCCCcCcCCCCcCcccccchHHH--HHHhCCCCcccCCCCCh
Confidence 344679999999986555443332 33333578888888743
No 67
>PF05570 DUF765: Circovirus protein of unknown function (DUF765); InterPro: IPR008484 This family consists of several short (27-30aa) porcine and bovine circovirus ORF6 proteins of unknown function.
Probab=24.58 E-value=88 Score=14.35 Aligned_cols=23 Identities=17% Similarity=0.169 Sum_probs=12.3
Q ss_pred ccccCCCCCchhhhhccCCCCCC
Q psy12714 2 SFFVPATSSKIAVKIILNQPEAP 24 (117)
Q Consensus 2 ~~~~p~~~~~~~~~~~~~~~~~~ 24 (117)
--+.|.++.++.+-...++...+
T Consensus 2 asstpaspapsdils~~pqs~rp 24 (29)
T PF05570_consen 2 ASSTPASPAPSDILSSKPQSKRP 24 (29)
T ss_pred CcCCCCCCCcHHHHhcCccccCC
Confidence 34556666665555555554444
No 68
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=24.29 E-value=72 Score=16.27 Aligned_cols=9 Identities=11% Similarity=-0.097 Sum_probs=5.1
Q ss_pred eeccHHHHH
Q psy12714 80 HLYCLPHFK 88 (117)
Q Consensus 80 ~~~C~~~y~ 88 (117)
--+|..||.
T Consensus 23 ~dLC~~C~~ 31 (43)
T cd02340 23 YDLCESCEA 31 (43)
T ss_pred ccchHHhhC
Confidence 345666664
No 69
>KOG0978|consensus
Probab=24.15 E-value=33 Score=28.49 Aligned_cols=33 Identities=21% Similarity=0.618 Sum_probs=19.9
Q ss_pred cccccCCccccCCCccc-cCCeeccHHHHHhhhCCC
Q psy12714 60 FRCTQCCTVLRMESYTM-NNGHLYCLPHFKQLFISR 94 (117)
Q Consensus 60 f~C~~C~~~L~~~~~~~-~~g~~~C~~~y~~~~~~k 94 (117)
++|..|.... ....+ .=+.+||..|-..+|..|
T Consensus 644 LkCs~Cn~R~--Kd~vI~kC~H~FC~~Cvq~r~etR 677 (698)
T KOG0978|consen 644 LKCSVCNTRW--KDAVITKCGHVFCEECVQTRYETR 677 (698)
T ss_pred eeCCCccCch--hhHHHHhcchHHHHHHHHHHHHHh
Confidence 4677776432 22333 346778888887777654
No 70
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=23.37 E-value=32 Score=24.09 Aligned_cols=28 Identities=14% Similarity=0.224 Sum_probs=15.2
Q ss_pred cccccCCccccCCCccccCCeeccHHHH
Q psy12714 60 FRCTQCCTVLRMESYTMNNGHLYCLPHF 87 (117)
Q Consensus 60 f~C~~C~~~L~~~~~~~~~g~~~C~~~y 87 (117)
..|..|+..+....+...+|.++|..|.
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 3566666665422222356666676664
No 71
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.14 E-value=22 Score=23.67 Aligned_cols=32 Identities=22% Similarity=0.350 Sum_probs=21.7
Q ss_pred ccccccccccccccCccEEeCCCcccccCcccccCCcccc
Q psy12714 31 PSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLR 70 (117)
Q Consensus 31 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 70 (117)
.--.|..|+......+.+. .-|.|..|+..|.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred CeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 3457888987665444332 2489999999885
No 72
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=22.91 E-value=28 Score=18.18 Aligned_cols=12 Identities=25% Similarity=0.647 Sum_probs=8.3
Q ss_pred cccccccccccc
Q psy12714 31 PSSLCFACNKKV 42 (117)
Q Consensus 31 ~~~~C~~C~~~i 42 (117)
....|..|++.|
T Consensus 10 ~~~~C~~C~~~i 21 (53)
T PF00130_consen 10 KPTYCDVCGKFI 21 (53)
T ss_dssp STEB-TTSSSBE
T ss_pred CCCCCcccCccc
Confidence 345888888888
No 73
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=22.67 E-value=68 Score=16.01 Aligned_cols=11 Identities=18% Similarity=0.431 Sum_probs=4.0
Q ss_pred ccccccccccc
Q psy12714 33 SLCFACNKKVY 43 (117)
Q Consensus 33 ~~C~~C~~~i~ 43 (117)
.+|..|+-.|-
T Consensus 3 ~rC~~C~aylN 13 (40)
T PF04810_consen 3 VRCRRCRAYLN 13 (40)
T ss_dssp -B-TTT--BS-
T ss_pred cccCCCCCEEC
Confidence 46777766653
No 74
>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=22.56 E-value=1.2e+02 Score=15.22 Aligned_cols=28 Identities=21% Similarity=0.364 Sum_probs=12.5
Q ss_pred ccccCCccccCCCccc--cCCeeccHHHHH
Q psy12714 61 RCTQCCTVLRMESYTM--NNGHLYCLPHFK 88 (117)
Q Consensus 61 ~C~~C~~~L~~~~~~~--~~g~~~C~~~y~ 88 (117)
.|+.|++........+ .++...|..|-.
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 4566666554333222 235667776653
No 75
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.41 E-value=45 Score=24.13 Aligned_cols=15 Identities=20% Similarity=0.556 Sum_probs=9.5
Q ss_pred CCccccccccccccc
Q psy12714 28 TGNPSSLCFACNKKV 42 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i 42 (117)
+......|..|+..|
T Consensus 241 y~R~g~pC~~Cg~~I 255 (274)
T PRK01103 241 YGREGEPCRRCGTPI 255 (274)
T ss_pred cCCCCCCCCCCCCee
Confidence 444445677777776
No 76
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.19 E-value=45 Score=24.15 Aligned_cols=15 Identities=20% Similarity=0.543 Sum_probs=9.6
Q ss_pred CCccccccccccccc
Q psy12714 28 TGNPSSLCFACNKKV 42 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i 42 (117)
+......|..|+..|
T Consensus 231 y~R~g~pC~~Cg~~I 245 (269)
T PRK14811 231 YGREGQPCPRCGTPI 245 (269)
T ss_pred cCCCcCCCCcCCCee
Confidence 444455677777777
No 77
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.97 E-value=20 Score=19.27 Aligned_cols=12 Identities=25% Similarity=0.609 Sum_probs=5.6
Q ss_pred ccccCCccccCC
Q psy12714 61 RCTQCCTVLRME 72 (117)
Q Consensus 61 ~C~~C~~~L~~~ 72 (117)
.|..|...|..+
T Consensus 24 ~C~gC~~~l~~~ 35 (56)
T PF02591_consen 24 TCSGCHMELPPQ 35 (56)
T ss_pred ccCCCCEEcCHH
Confidence 444555554433
No 78
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=21.88 E-value=45 Score=19.94 Aligned_cols=14 Identities=29% Similarity=0.420 Sum_probs=11.1
Q ss_pred Cccccccccccccc
Q psy12714 29 GNPSSLCFACNKKV 42 (117)
Q Consensus 29 ~~~~~~C~~C~~~i 42 (117)
..+...|..|++.+
T Consensus 51 ~lfs~pC~~C~klL 64 (90)
T PF11571_consen 51 NLFSTPCKKCGKLL 64 (90)
T ss_pred hhccchhhHHHhHh
Confidence 55567899999988
No 79
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=21.81 E-value=46 Score=21.68 Aligned_cols=38 Identities=26% Similarity=0.486 Sum_probs=21.1
Q ss_pred cccccccccccccCccEEe----CCCc--ccccCcccccCCccc
Q psy12714 32 SSLCFACNKKVYPLEKIET----DGKL--FHRACFRCTQCCTVL 69 (117)
Q Consensus 32 ~~~C~~C~~~i~~~~~~~~----~~~~--~H~~Cf~C~~C~~~L 69 (117)
..+|..|+..+.....-.+ .... .+...+.|..|++..
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 5689999987744222111 1111 234456788887743
No 80
>KOG2186|consensus
Probab=21.59 E-value=21 Score=25.89 Aligned_cols=44 Identities=23% Similarity=0.448 Sum_probs=27.5
Q ss_pred ccccccccccccCccEEeCCCcccccCcccccCCccccCCCcccc
Q psy12714 33 SLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMN 77 (117)
Q Consensus 33 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~ 77 (117)
..|..||+.|-- ..+.----..|-.+|.|-.|++.+....|..+
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~~sYknH 47 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFERVSYKNH 47 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeecccccccchhhhh
Confidence 468889987732 11211111235578999999998877666554
No 81
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.41 E-value=22 Score=18.03 Aligned_cols=11 Identities=18% Similarity=0.531 Sum_probs=6.8
Q ss_pred ccccccccccc
Q psy12714 32 SSLCFACNKKV 42 (117)
Q Consensus 32 ~~~C~~C~~~i 42 (117)
.-+|..|+...
T Consensus 5 ey~C~~Cg~~f 15 (42)
T PF09723_consen 5 EYRCEECGHEF 15 (42)
T ss_pred EEEeCCCCCEE
Confidence 34677777554
No 82
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.38 E-value=28 Score=23.68 Aligned_cols=33 Identities=27% Similarity=0.457 Sum_probs=22.2
Q ss_pred ccccccccccccccCccEEeCCCcccccCcccccCCccccC
Q psy12714 31 PSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRM 71 (117)
Q Consensus 31 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~~ 71 (117)
..-.|..|+......+.+ . .-|.|..|+..|..
T Consensus 116 ~~Y~Cp~C~~rytf~eA~---~-----~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAM---E-----YGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHh---h-----cCCcCCCCCCCCee
Confidence 345788888776544432 2 24899999998853
No 83
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.02 E-value=28 Score=22.72 Aligned_cols=38 Identities=26% Similarity=0.398 Sum_probs=22.7
Q ss_pred cccccccccccccccCccEEeCCCcccccCcccccCCcccc
Q psy12714 30 NPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLR 70 (117)
Q Consensus 30 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 70 (117)
...-.|..|+......+.+...+. ..=|.|..|+..|.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 335578889877754443322221 12288888888774
No 84
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.96 E-value=26 Score=18.95 Aligned_cols=29 Identities=17% Similarity=0.398 Sum_probs=15.4
Q ss_pred cccccccccccCccEEeCCCcccccCccc
Q psy12714 34 LCFACNKKVYPLEKIETDGKLFHRACFRC 62 (117)
Q Consensus 34 ~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C 62 (117)
.|..||+.+...-=.+..++.|-..|-.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc
Confidence 47788887742111123455666665544
No 85
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.91 E-value=72 Score=21.18 Aligned_cols=9 Identities=33% Similarity=0.947 Sum_probs=4.5
Q ss_pred ccccccccc
Q psy12714 35 CFACNKKVY 43 (117)
Q Consensus 35 C~~C~~~i~ 43 (117)
|..||..|.
T Consensus 3 CEiCG~~i~ 11 (154)
T TIGR00270 3 CEICGRKIK 11 (154)
T ss_pred cccCCCccC
Confidence 455555543
No 86
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=20.85 E-value=89 Score=16.28 Aligned_cols=10 Identities=30% Similarity=0.550 Sum_probs=6.3
Q ss_pred eeccHHHHHh
Q psy12714 80 HLYCLPHFKQ 89 (117)
Q Consensus 80 ~~~C~~~y~~ 89 (117)
--+|..||..
T Consensus 24 ~dLC~~Cf~~ 33 (49)
T cd02335 24 FDLCLECFSA 33 (49)
T ss_pred cchhHHhhhC
Confidence 4467777753
No 87
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.08 E-value=53 Score=23.81 Aligned_cols=15 Identities=13% Similarity=0.532 Sum_probs=9.5
Q ss_pred CCccccccccccccc
Q psy12714 28 TGNPSSLCFACNKKV 42 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i 42 (117)
+......|..|+..|
T Consensus 240 y~R~g~pCprCG~~I 254 (272)
T PRK14810 240 YQRTGEPCLNCKTPI 254 (272)
T ss_pred cCCCCCcCCCCCCee
Confidence 344455677777766
No 88
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.05 E-value=49 Score=24.08 Aligned_cols=15 Identities=13% Similarity=0.403 Sum_probs=9.3
Q ss_pred CCccccccccccccc
Q psy12714 28 TGNPSSLCFACNKKV 42 (117)
Q Consensus 28 ~~~~~~~C~~C~~~i 42 (117)
+......|..|+..|
T Consensus 250 y~R~g~pC~~Cg~~I 264 (282)
T PRK13945 250 YRRTGKPCRKCGTPI 264 (282)
T ss_pred eCCCcCCCCcCCCee
Confidence 334445677777776
No 89
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the