Query psy4350
Match_columns 107
No_of_seqs 115 out of 1072
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 23:20:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4350.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4350hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.8 7.4E-21 1.6E-25 134.4 -0.6 91 9-104 267-359 (468)
2 PF00412 LIM: LIM domain; Int 99.6 1.5E-15 3.2E-20 81.8 4.6 56 19-75 1-58 (58)
3 KOG1044|consensus 99.6 5.2E-16 1.1E-20 113.4 2.4 85 14-103 131-216 (670)
4 KOG1701|consensus 99.6 1.9E-16 4.2E-21 112.2 -1.2 86 13-102 331-424 (468)
5 KOG4577|consensus 99.5 9.5E-16 2.1E-20 104.3 -2.6 83 15-102 32-117 (383)
6 KOG2272|consensus 99.5 1E-14 2.2E-19 97.9 0.5 86 15-104 11-98 (332)
7 KOG2272|consensus 99.5 8.1E-15 1.8E-19 98.3 -0.1 84 15-103 194-278 (332)
8 KOG1703|consensus 99.3 9.9E-13 2.2E-17 96.7 2.6 85 14-103 361-448 (479)
9 KOG1703|consensus 99.1 1.3E-10 2.9E-15 85.6 6.0 87 14-104 301-388 (479)
10 smart00132 LIM Zinc-binding do 98.8 3.7E-09 8E-14 51.9 3.0 37 18-54 1-38 (39)
11 KOG1044|consensus 98.7 1.2E-08 2.6E-13 75.5 3.3 80 9-103 9-89 (670)
12 KOG4577|consensus 98.5 2.8E-08 6E-13 68.3 1.1 64 16-80 92-158 (383)
13 KOG1700|consensus 98.2 3.7E-07 8E-12 60.5 0.7 65 12-77 3-68 (200)
14 KOG1700|consensus 98.1 6.2E-07 1.3E-11 59.5 -0.6 64 10-74 102-165 (200)
15 KOG1702|consensus 97.9 7.1E-07 1.5E-11 58.9 -2.8 59 17-76 5-64 (264)
16 KOG0490|consensus 95.5 0.0067 1.5E-07 40.5 1.2 76 22-100 2-82 (235)
17 PF00412 LIM: LIM domain; Int 90.0 0.13 2.9E-06 26.7 0.7 47 46-100 1-48 (58)
18 PF14446 Prok-RING_1: Prokaryo 88.2 0.52 1.1E-05 24.8 2.1 29 16-44 5-36 (54)
19 PF08394 Arc_trans_TRASH: Arch 87.2 0.47 1E-05 23.0 1.5 25 19-43 1-26 (37)
20 PF09943 DUF2175: Uncharacteri 77.7 1 2.2E-05 26.8 0.6 32 17-48 3-35 (101)
21 COG2191 Formylmethanofuran deh 76.4 1 2.2E-05 30.1 0.4 30 44-74 173-202 (206)
22 KOG3579|consensus 75.6 2.4 5.2E-05 29.9 2.1 51 12-68 264-314 (352)
23 PF14471 DUF4428: Domain of un 73.6 3.7 8E-05 21.2 2.0 29 45-74 1-29 (51)
24 PF14835 zf-RING_6: zf-RING of 73.3 2.7 5.8E-05 22.9 1.5 43 44-90 8-51 (65)
25 PF13240 zinc_ribbon_2: zinc-r 73.2 2.3 5E-05 18.2 1.0 9 19-27 2-10 (23)
26 smart00504 Ubox Modified RING 72.8 9.8 0.00021 19.7 3.7 43 44-90 2-46 (63)
27 PF04810 zf-Sec23_Sec24: Sec23 72.5 3.1 6.8E-05 20.2 1.5 31 16-51 2-32 (40)
28 PF13920 zf-C3HC4_3: Zinc fing 70.9 10 0.00022 19.0 3.4 43 45-91 4-49 (50)
29 PF10367 Vps39_2: Vacuolar sor 70.6 3 6.4E-05 24.2 1.4 30 15-44 77-107 (109)
30 KOG0320|consensus 66.0 5.9 0.00013 26.1 2.2 50 40-91 128-179 (187)
31 PF07754 DUF1610: Domain of un 65.9 5.1 0.00011 17.4 1.3 12 19-30 1-12 (24)
32 PF10235 Cript: Microtubule-as 63.9 5.4 0.00012 23.2 1.6 44 37-91 38-81 (90)
33 PF13248 zf-ribbon_3: zinc-rib 63.3 5.9 0.00013 17.3 1.3 9 18-26 4-12 (26)
34 PF01258 zf-dskA_traR: Prokary 62.9 1.4 3E-05 20.9 -0.9 27 46-73 6-32 (36)
35 COG4357 Zinc finger domain con 59.6 0.81 1.7E-05 26.9 -2.4 36 19-54 38-73 (105)
36 PF11781 RRN7: RNA polymerase 59.4 6 0.00013 18.9 1.0 22 45-71 10-31 (36)
37 PF00645 zf-PARP: Poly(ADP-rib 59.0 6.7 0.00015 21.9 1.4 16 15-30 6-21 (82)
38 KOG1813|consensus 57.8 6.6 0.00014 27.9 1.4 46 43-92 241-288 (313)
39 PRK14890 putative Zn-ribbon RN 57.3 16 0.00034 19.6 2.5 29 15-52 6-34 (59)
40 COG1645 Uncharacterized Zn-fin 57.0 5.3 0.00011 24.9 0.8 21 45-71 30-50 (131)
41 COG5152 Uncharacterized conser 55.8 5 0.00011 26.9 0.6 47 42-92 195-243 (259)
42 PF02069 Metallothio_Pro: Prok 55.3 7.4 0.00016 20.3 1.0 28 45-73 9-37 (52)
43 PF06677 Auto_anti-p27: Sjogre 55.2 5.6 0.00012 19.6 0.5 21 45-70 19-39 (41)
44 cd02336 ZZ_RSC8 Zinc finger, Z 53.2 16 0.00034 18.4 2.0 29 45-74 2-32 (45)
45 PF13834 DUF4193: Domain of un 53.0 3.6 7.8E-05 24.4 -0.4 28 44-71 71-98 (99)
46 smart00291 ZnF_ZZ Zinc-binding 51.0 20 0.00042 17.6 2.2 9 66-74 28-36 (44)
47 PF05502 Dynactin_p62: Dynacti 50.4 9.1 0.0002 29.0 1.2 40 15-55 25-64 (483)
48 cd02249 ZZ Zinc finger, ZZ typ 48.8 20 0.00043 17.7 2.0 8 67-74 25-32 (46)
49 COG4847 Uncharacterized protei 48.4 7.3 0.00016 22.9 0.4 36 17-52 7-43 (103)
50 PF04570 DUF581: Protein of un 45.6 15 0.00033 19.5 1.3 25 45-69 18-43 (58)
51 PF07503 zf-HYPF: HypF finger; 45.2 7.2 0.00016 18.5 0.0 30 19-53 2-31 (35)
52 PF06689 zf-C4_ClpX: ClpX C4-t 44.7 39 0.00085 16.4 2.7 30 45-74 3-33 (41)
53 PF00130 C1_1: Phorbol esters/ 43.8 16 0.00035 18.3 1.3 13 14-26 9-21 (53)
54 PF14255 Cys_rich_CPXG: Cystei 43.5 9.7 0.00021 19.8 0.4 29 18-46 2-30 (52)
55 COG2888 Predicted Zn-ribbon RN 42.0 30 0.00064 18.6 2.1 28 16-52 9-36 (61)
56 KOG0978|consensus 41.6 11 0.00024 29.9 0.6 43 44-90 644-689 (698)
57 PF10886 DUF2685: Protein of u 40.9 28 0.00061 18.3 1.8 26 17-42 2-27 (54)
58 PF08746 zf-RING-like: RING-li 40.7 11 0.00024 18.6 0.3 11 19-29 1-11 (43)
59 cd02335 ZZ_ADA2 Zinc finger, Z 40.6 32 0.0007 17.3 2.1 8 67-74 26-33 (49)
60 PRK08359 transcription factor; 39.7 30 0.00064 22.7 2.2 31 45-76 8-41 (176)
61 PF12674 Zn_ribbon_2: Putative 38.6 19 0.0004 20.5 1.1 30 45-74 2-35 (81)
62 PLN03208 E3 ubiquitin-protein 38.3 57 0.0012 21.8 3.4 12 78-91 69-80 (193)
63 PF01286 XPA_N: XPA protein N- 37.6 9.8 0.00021 18.0 -0.2 15 16-30 3-17 (34)
64 PRK00420 hypothetical protein; 37.4 16 0.00034 22.2 0.6 20 44-68 24-43 (112)
65 TIGR00270 conserved hypothetic 37.0 33 0.00072 21.9 2.1 30 46-76 3-34 (154)
66 PRK00019 rpmE 50S ribosomal pr 36.8 18 0.00039 20.1 0.8 8 100-107 40-47 (72)
67 PF10083 DUF2321: Uncharacteri 35.9 22 0.00048 22.9 1.2 10 79-90 70-79 (158)
68 PF14634 zf-RING_5: zinc-RING 35.5 58 0.0012 15.7 3.0 39 46-86 2-43 (44)
69 COG1885 Uncharacterized protei 34.8 22 0.00048 21.3 1.0 29 2-30 35-63 (115)
70 KOG4739|consensus 34.0 28 0.0006 24.0 1.5 31 58-91 18-49 (233)
71 cd00162 RING RING-finger (Real 33.4 55 0.0012 14.9 2.4 24 63-88 18-44 (45)
72 PF00569 ZZ: Zinc finger, ZZ t 33.3 35 0.00075 16.9 1.5 9 66-74 29-37 (46)
73 PF10764 Gin: Inhibitor of sig 33.2 46 0.001 16.7 1.9 10 64-73 17-26 (46)
74 KOG3002|consensus 33.0 48 0.001 23.6 2.6 46 43-92 48-93 (299)
75 PF10080 DUF2318: Predicted me 32.9 22 0.00048 21.1 0.8 33 37-74 29-61 (102)
76 PF14569 zf-UDP: Zinc-binding 32.8 64 0.0014 18.3 2.6 23 65-89 36-61 (80)
77 PF13923 zf-C3HC4_2: Zinc fing 32.2 62 0.0013 15.0 2.7 27 47-74 2-28 (39)
78 PF06750 DiS_P_DiS: Bacterial 31.5 22 0.00047 20.6 0.6 12 78-91 59-70 (92)
79 PRK01397 50S ribosomal protein 31.3 25 0.00054 19.9 0.8 9 99-107 38-46 (78)
80 PRK03922 hypothetical protein; 31.1 32 0.0007 20.8 1.3 29 2-30 35-63 (113)
81 PRK01678 rpmE2 50S ribosomal p 31.1 25 0.00053 20.4 0.7 15 39-53 9-23 (87)
82 PF00628 PHD: PHD-finger; Int 30.8 33 0.00071 17.0 1.1 26 19-44 2-29 (51)
83 KOG2893|consensus 29.9 13 0.00028 25.8 -0.6 38 16-56 10-47 (341)
84 PF11077 DUF2616: Protein of u 29.8 22 0.00048 23.3 0.5 34 40-74 136-169 (173)
85 PF01927 Mut7-C: Mut7-C RNAse 29.7 33 0.00071 21.5 1.2 36 16-51 91-132 (147)
86 CHL00136 rpl31 ribosomal prote 28.4 26 0.00057 19.2 0.5 7 101-107 41-47 (68)
87 smart00249 PHD PHD zinc finger 28.4 42 0.00091 15.6 1.3 26 19-44 2-29 (47)
88 cd02341 ZZ_ZZZ3 Zinc finger, Z 28.3 68 0.0015 16.2 2.0 8 67-74 28-35 (48)
89 PLN02195 cellulose synthase A 28.3 55 0.0012 27.3 2.5 53 14-90 4-59 (977)
90 COG0254 RpmE Ribosomal protein 27.7 31 0.00068 19.4 0.8 10 98-107 40-49 (75)
91 PF12773 DZR: Double zinc ribb 27.5 85 0.0018 15.4 2.4 13 15-27 11-23 (50)
92 PF14149 YhfH: YhfH-like prote 27.2 16 0.00035 17.6 -0.4 20 71-92 6-26 (37)
93 PF08792 A2L_zn_ribbon: A2L zi 26.3 41 0.00089 15.6 0.9 7 62-68 18-24 (33)
94 PF04475 DUF555: Protein of un 25.4 39 0.00084 20.1 0.9 25 6-30 37-61 (102)
95 PLN00162 transport protein sec 24.7 1.2E+02 0.0027 24.5 3.8 34 13-51 50-83 (761)
96 PF01194 RNA_pol_N: RNA polyme 24.7 43 0.00094 18.0 0.9 13 16-28 4-16 (60)
97 PRK14559 putative protein seri 24.4 56 0.0012 25.9 1.9 9 18-26 3-11 (645)
98 PF08271 TF_Zn_Ribbon: TFIIB z 24.4 37 0.0008 16.5 0.6 9 45-53 21-29 (43)
99 PLN02915 cellulose synthase A 24.3 1.1E+02 0.0023 25.9 3.4 21 15-39 14-34 (1044)
100 TIGR00105 L31 ribosomal protei 24.1 34 0.00074 18.7 0.5 9 99-107 39-47 (68)
101 PF01197 Ribosomal_L31: Riboso 23.2 40 0.00086 18.4 0.7 7 101-107 42-48 (69)
102 COG1813 Predicted transcriptio 23.1 76 0.0017 20.6 2.0 30 46-76 6-36 (165)
103 PRK00807 50S ribosomal protein 23.0 53 0.0012 16.9 1.1 24 17-40 2-28 (52)
104 PF06827 zf-FPG_IleRS: Zinc fi 22.3 23 0.0005 15.7 -0.3 12 17-28 2-13 (30)
105 PRK00398 rpoP DNA-directed RNA 21.9 46 0.001 16.3 0.7 9 18-26 5-13 (46)
106 PF02591 DUF164: Putative zinc 21.9 13 0.00029 19.2 -1.4 10 45-54 24-33 (56)
107 PLN02638 cellulose synthase A 21.7 1.4E+02 0.0031 25.3 3.6 15 12-26 13-27 (1079)
108 PF06906 DUF1272: Protein of u 20.8 1.5E+02 0.0033 15.7 3.1 42 46-90 8-52 (57)
109 KOG3497|consensus 20.6 32 0.0007 18.5 -0.0 12 17-28 5-16 (69)
110 PRK14873 primosome assembly pr 20.4 68 0.0015 25.5 1.6 27 59-88 404-431 (665)
111 COG1644 RPB10 DNA-directed RNA 20.1 41 0.00088 18.2 0.3 13 16-28 4-16 (63)
No 1
>KOG1701|consensus
Probab=99.79 E-value=7.4e-21 Score=134.37 Aligned_cols=91 Identities=19% Similarity=0.436 Sum_probs=83.3
Q ss_pred CCCCCCCCCccccccccccCceE-EeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCC
Q psy4350 9 SSPCPEEKSSCGGCGQPIIDRFY-LLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIP 86 (107)
Q Consensus 9 ~~~~~~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~ 86 (107)
++..+..+..|.+|+|.|+.... +.++++.||..||+|..|++.|.++ .||..++++||+.||.. .. +|.. |+
T Consensus 267 ~~p~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq-~FY~v~~k~~CE~cyq~tle--kC~~--Cg 341 (468)
T KOG1701|consen 267 AEPVEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQ-SFYQVDGKPYCEGCYQDTLE--KCNK--CG 341 (468)
T ss_pred CChhhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccc-cccccCCcccchHHHHHHHH--HHhh--hh
Confidence 45566677799999999987654 6999999999999999999999998 89999999999999999 77 8999 99
Q ss_pred CcchhhhhhhccccCCCC
Q psy4350 87 KTLVSFLYDKQGAASEPL 104 (107)
Q Consensus 87 ~~i~~~~~~~~g~~~~p~ 104 (107)
++|+++++++.|++|||.
T Consensus 342 ~~I~d~iLrA~GkayHp~ 359 (468)
T KOG1701|consen 342 EPIMDRILRALGKAYHPG 359 (468)
T ss_pred hHHHHHHHHhcccccCCC
Confidence 999999999999999995
No 2
>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=99.60 E-value=1.5e-15 Score=81.77 Aligned_cols=56 Identities=30% Similarity=0.894 Sum_probs=51.2
Q ss_pred cccccccccCceEE-eecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-h
Q psy4350 19 CGGCGQPIIDRFYL-LAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-Y 75 (107)
Q Consensus 19 C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~ 75 (107)
|.+|+++|.+.+.+ .+.++.||+.||+|..|+++|.+. .++..++++||+.||.+ |
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDG-DFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTS-SEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCC-eeEeECCEEECHHHHhhhC
Confidence 78999999987765 699999999999999999999988 58999999999999987 5
No 3
>KOG1044|consensus
Probab=99.58 E-value=5.2e-16 Score=113.42 Aligned_cols=85 Identities=27% Similarity=0.665 Sum_probs=79.7
Q ss_pred CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhh
Q psy4350 14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSF 92 (107)
Q Consensus 14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~ 92 (107)
.++..|++|++.|..+..+.++++.||..||+|..|+..|.+ .+..+++.+||+.||.. |++ +|.. |.+.|+|.
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g--ey~skdg~pyce~dy~~~fgv-kc~~--c~~fisgk 205 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG--EYMSKDGVPYCEKDYQAKFGV-KCEE--CEKFISGK 205 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc--eeeccCCCcchhhhhhhhcCe-ehHH--hhhhhhhh
Confidence 467789999999998888899999999999999999999987 48899999999999999 995 9999 99999999
Q ss_pred hhhhccccCCC
Q psy4350 93 LYDKQGAASEP 103 (107)
Q Consensus 93 ~~~~~g~~~~p 103 (107)
++.+.|+-|||
T Consensus 206 vLqag~kh~HP 216 (670)
T KOG1044|consen 206 VLQAGDKHFHP 216 (670)
T ss_pred hhhccCcccCc
Confidence 99999999999
No 4
>KOG1701|consensus
Probab=99.57 E-value=1.9e-16 Score=112.24 Aligned_cols=86 Identities=24% Similarity=0.551 Sum_probs=72.3
Q ss_pred CCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchh
Q psy4350 13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVS 91 (107)
Q Consensus 13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~ 91 (107)
+....+|..|++.|.+.. +.++|+.||+.||+|..|.+.|.+..+....++++||..||++ |+ ++|+. |+++|+.
T Consensus 331 q~tlekC~~Cg~~I~d~i-LrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA-PrCs~--C~~PI~P 406 (468)
T KOG1701|consen 331 QDTLEKCNKCGEPIMDRI-LRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA-PRCSV--CGNPILP 406 (468)
T ss_pred HHHHHHHhhhhhHHHHHH-HHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC-cchhh--ccCCccC
Confidence 345678999999999984 8999999999999999999999988334677899999999999 99 79999 9999974
Q ss_pred h-------hhhhccccCC
Q psy4350 92 F-------LYDKQGAASE 102 (107)
Q Consensus 92 ~-------~~~~~g~~~~ 102 (107)
. -+.++++.||
T Consensus 407 ~~G~~etvRvvamdr~fH 424 (468)
T KOG1701|consen 407 RDGKDETVRVVAMDRDFH 424 (468)
T ss_pred CCCCcceEEEEEcccccc
Confidence 2 2334566666
No 5
>KOG4577|consensus
Probab=99.49 E-value=9.5e-16 Score=104.34 Aligned_cols=83 Identities=39% Similarity=0.903 Sum_probs=73.8
Q ss_pred CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchh--
Q psy4350 15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVS-- 91 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~-- 91 (107)
..++|+.|.+.|.+++++.++++.||..|++|+.|..+|.. .++.+++.+||+.+|++ || .+|.. |+..|..
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d--rCFsR~~s~yCkedFfKrfG-TKCsa--C~~GIpPtq 106 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD--RCFSREGSVYCKEDFFKRFG-TKCSA--CQEGIPPTQ 106 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH--HHhhcCCceeehHHHHHHhC-Ccchh--hcCCCChHH
Confidence 56789999999999998899999999999999999999988 57899999999999999 99 59999 9999964
Q ss_pred hhhhhccccCC
Q psy4350 92 FLYDKQGAASE 102 (107)
Q Consensus 92 ~~~~~~g~~~~ 102 (107)
.+-+++...||
T Consensus 107 VVRkAqd~VYH 117 (383)
T KOG4577|consen 107 VVRKAQDFVYH 117 (383)
T ss_pred HHHHhhcceee
Confidence 55566666666
No 6
>KOG2272|consensus
Probab=99.46 E-value=1e-14 Score=97.86 Aligned_cols=86 Identities=17% Similarity=0.426 Sum_probs=77.8
Q ss_pred CCCccccccccccCceE-EeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhh
Q psy4350 15 EKSSCGGCGQPIIDRFY-LLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSF 92 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~ 92 (107)
....|.+|.....+.+. +...+..||..||.|..|-.++.++ .|++-+|+.||+.+|.. |+ |-|+. |++.|.|.
T Consensus 11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g-~~~efEgRkYCEhDF~~Lfa-PcC~k--C~EFiiGr 86 (332)
T KOG2272|consen 11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDG-IFYEFEGRKYCEHDFHVLFA-PCCGK--CGEFIIGR 86 (332)
T ss_pred HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCc-eeEEecCcccccccchhhhc-hhhcc--cccchhhH
Confidence 34569999988876665 4677889999999999999999988 89999999999999999 99 79999 99999999
Q ss_pred hhhhccccCCCC
Q psy4350 93 LYDKQGAASEPL 104 (107)
Q Consensus 93 ~~~~~g~~~~p~ 104 (107)
++.++.++|||-
T Consensus 87 VikamnnSwHp~ 98 (332)
T KOG2272|consen 87 VIKAMNNSWHPA 98 (332)
T ss_pred HHHhhccccCcc
Confidence 999999999994
No 7
>KOG2272|consensus
Probab=99.46 E-value=8.1e-15 Score=98.29 Aligned_cols=84 Identities=20% Similarity=0.515 Sum_probs=77.5
Q ss_pred CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhhh
Q psy4350 15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSFL 93 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~~ 93 (107)
+.++|..|.++|.++ ++.++|+.||...|+|+.|.++.-+- ..|++.|..||+.+|.+ || ..|.. |+..|-|.+
T Consensus 194 gipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFlGH-rHYEkkGlaYCe~h~~qLfG-~~CF~--C~~~i~G~v 268 (332)
T KOG2272|consen 194 GIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFLGH-RHYEKKGLAYCETHYHQLFG-NLCFI--CNRVIGGDV 268 (332)
T ss_pred CCcccccccCchHHH-HHHHhccccchhheeehhcCCcccch-hhhhhcCchhHHHHHHHHhh-hhhee--cCCccCccH
Confidence 567899999999876 48999999999999999999998776 78999999999999999 99 69999 999999999
Q ss_pred hhhccccCCC
Q psy4350 94 YDKQGAASEP 103 (107)
Q Consensus 94 ~~~~g~~~~p 103 (107)
+.+.++||-|
T Consensus 269 v~al~KawCv 278 (332)
T KOG2272|consen 269 VSALNKAWCV 278 (332)
T ss_pred HHHhhhhhcc
Confidence 9999999876
No 8
>KOG1703|consensus
Probab=99.30 E-value=9.9e-13 Score=96.75 Aligned_cols=85 Identities=26% Similarity=0.592 Sum_probs=76.8
Q ss_pred CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch--
Q psy4350 14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV-- 90 (107)
Q Consensus 14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~-- 90 (107)
...+.|.+|.+.|.+.. |.+.+..||+.||+|..|.+.+... .|+..++.+||+.||.+ +. ++|.. |..++.
T Consensus 361 ~~~p~C~~C~~~i~~~~-v~a~~~~wH~~cf~C~~C~~~~~~~-~~~~~~~~pyce~~~~~~~~-~~~~~--~~~p~~~~ 435 (479)
T KOG1703|consen 361 PFRPNCKRCLLPILEEG-VCALGRLWHPECFVCADCGKPLKNS-SFFESDGEPYCEDHYKKLFT-TKCDY--CKKPVEFG 435 (479)
T ss_pred hhCccccccCCchHHhH-hhhccCeechhceeeecccCCCCCC-cccccCCccchhhhHhhhcc-ccchh--ccchhHhh
Confidence 45788999999998885 7777999999999999999999887 89999999999999999 98 69999 999987
Q ss_pred hhhhhhccccCCC
Q psy4350 91 SFLYDKQGAASEP 103 (107)
Q Consensus 91 ~~~~~~~g~~~~p 103 (107)
+..+.++|..||+
T Consensus 436 ~~~ie~~~~~~h~ 448 (479)
T KOG1703|consen 436 SRQIEADGSPFHG 448 (479)
T ss_pred hhHhhccCccccc
Confidence 7889999999886
No 9
>KOG1703|consensus
Probab=99.12 E-value=1.3e-10 Score=85.62 Aligned_cols=87 Identities=17% Similarity=0.331 Sum_probs=78.8
Q ss_pred CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhh
Q psy4350 14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSF 92 (107)
Q Consensus 14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~ 92 (107)
...+.|..|+..|.....+.++++.||+.+|.|..|...+... .+...++++||..||.. +. +.|.. |+++|.+.
T Consensus 301 ~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~-~~~~~~g~~~c~~~~~~~~~-p~C~~--C~~~i~~~ 376 (479)
T KOG1703|consen 301 VTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDG-GPRELDGKILCHECFHAPFR-PNCKR--CLLPILEE 376 (479)
T ss_pred cccccccccccCcccceeEeeccccccccceeeccccccccCC-CccccCCCccHHHHHHHhhC-ccccc--cCCchHHh
Confidence 3458899999999884468999999999999999999998877 67888999999999999 88 79999 99999999
Q ss_pred hhhhccccCCCC
Q psy4350 93 LYDKQGAASEPL 104 (107)
Q Consensus 93 ~~~~~g~~~~p~ 104 (107)
.+.+.+..|||-
T Consensus 377 ~v~a~~~~wH~~ 388 (479)
T KOG1703|consen 377 GVCALGRLWHPE 388 (479)
T ss_pred HhhhccCeechh
Confidence 999999999984
No 10
>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=98.83 E-value=3.7e-09 Score=51.88 Aligned_cols=37 Identities=41% Similarity=1.068 Sum_probs=32.7
Q ss_pred ccccccccccCc-eEEeecCcccccccccccccCCCCC
Q psy4350 18 SCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCHVPLH 54 (107)
Q Consensus 18 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~ 54 (107)
+|.+|++.|.+. ..+.+.++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 488999999886 5578899999999999999999885
No 11
>KOG1044|consensus
Probab=98.70 E-value=1.2e-08 Score=75.51 Aligned_cols=80 Identities=23% Similarity=0.458 Sum_probs=64.7
Q ss_pred CCCCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCC
Q psy4350 9 SSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPK 87 (107)
Q Consensus 9 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~ 87 (107)
+........+|.+|.+.-... ++.+.++.||..||+|..|+..|... .|+.+++. + ++ + .. |..
T Consensus 9 s~~~~~~~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~-gff~k~~~--------~~yg-t--~~--c~~ 73 (670)
T KOG1044|consen 9 SPQTGKQGIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEG-GFFTKPEN--------RLYG-T--DD--CRA 73 (670)
T ss_pred CccccccceehhhhCCccccc-eeEeeccccceeeeeccccCCCcccc-cceecccc--------eeec-c--cc--hhh
Confidence 334445567899999988765 68999999999999999999999887 67666554 3 44 2 44 778
Q ss_pred cchhhhhhhccccCCC
Q psy4350 88 TLVSFLYDKQGAASEP 103 (107)
Q Consensus 88 ~i~~~~~~~~g~~~~p 103 (107)
.|.+.++.+.|++|||
T Consensus 74 ~~~gevvsa~gktyh~ 89 (670)
T KOG1044|consen 74 FVEGEVVSTLGKTYHP 89 (670)
T ss_pred hccceeEecccceecc
Confidence 9999999999999998
No 12
>KOG4577|consensus
Probab=98.53 E-value=2.8e-08 Score=68.32 Aligned_cols=64 Identities=22% Similarity=0.449 Sum_probs=53.4
Q ss_pred CCccccccccccCceEE-eecCcccccccccccccCCCCCCCCce-eccCCeeccHHHHhh-hCCCCC
Q psy4350 16 KSSCGGCGQPIIDRFYL-LAVDRQWHLGCLQCAHCHVPLHSELSC-FSRHGNIYCKQDFFR-YSQARY 80 (107)
Q Consensus 16 ~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~~~~~~C~~~y~~-~~~~~C 80 (107)
.-+|..|.+.|.+..++ .+.+..||..||.|..|.+.|..+..| ...+.++.|+.+|+. -. +.|
T Consensus 92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~-k~~ 158 (383)
T KOG4577|consen 92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQ-KHC 158 (383)
T ss_pred CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHh-ccc
Confidence 45799999999988766 788899999999999999999854444 577889999999998 55 455
No 13
>KOG1700|consensus
Probab=98.21 E-value=3.7e-07 Score=60.52 Aligned_cols=65 Identities=18% Similarity=0.452 Sum_probs=55.4
Q ss_pred CCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCC
Q psy4350 12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQ 77 (107)
Q Consensus 12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~ 77 (107)
.......|..|++.++..+.+...+..||+.||.|..|.+.|... .+..+++.+||+.+|.. +++
T Consensus 3 ~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~-~~~~~e~~~yc~~~~~~~~~~ 68 (200)
T KOG1700|consen 3 FTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLS-GYSEHEGVPYCKNCHVAQFGP 68 (200)
T ss_pred cccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccc-cccccccccccccchHhhhCc
Confidence 344566899999999988777888999999999999999999876 67789999999998777 773
No 14
>KOG1700|consensus
Probab=98.06 E-value=6.2e-07 Score=59.46 Aligned_cols=64 Identities=23% Similarity=0.565 Sum_probs=55.0
Q ss_pred CCCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350 10 SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74 (107)
Q Consensus 10 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~ 74 (107)
.+.......|..|.+.+++.+.+...+..||..||+|..|+..|... .+....+.++|...+..
T Consensus 102 ~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~-~~~~~~g~l~~~~~~~~ 165 (200)
T KOG1700|consen 102 QVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPK-NYAALEGVLYCKHHFAQ 165 (200)
T ss_pred HhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCc-chhhcCCccccchhhhe
Confidence 34556678899999999998888999999999999999999999987 78888888888776665
No 15
>KOG1702|consensus
Probab=97.88 E-value=7.1e-07 Score=58.86 Aligned_cols=59 Identities=19% Similarity=0.536 Sum_probs=52.2
Q ss_pred CccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350 17 SSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS 76 (107)
Q Consensus 17 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~ 76 (107)
..|..|++.+++.+.+..+++.||..||+|..|+..|... .+-..+.++||..+|.+ .+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmK-nyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMK-NYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhh-hccccccCCCcCccccccee
Confidence 4578899999998888999999999999999999999877 67778889999999987 54
No 16
>KOG0490|consensus
Probab=95.46 E-value=0.0067 Score=40.51 Aligned_cols=76 Identities=41% Similarity=0.848 Sum_probs=56.1
Q ss_pred ccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh---hCCCCCCCCCCCCcch--hhhhhh
Q psy4350 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR---YSQARYPDLPIPKTLV--SFLYDK 96 (107)
Q Consensus 22 C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~---~~~~~C~~~~C~~~i~--~~~~~~ 96 (107)
|+..|.+...+...+..||..|..|..|...+......+..++..||..+|.+ +. .+|.. |...|. ..+..+
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~-~rr~r--t~~~~~ql~~ler~ 78 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFS-KRCAR--CKFTISQLDELERA 78 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhcc-ccccC--CCCCcCHHHHHHHh
Confidence 66777777666777899999999999999998722234444999999999985 44 68999 888873 344444
Q ss_pred cccc
Q psy4350 97 QGAA 100 (107)
Q Consensus 97 ~g~~ 100 (107)
..+.
T Consensus 79 f~~~ 82 (235)
T KOG0490|consen 79 FEKV 82 (235)
T ss_pred hcCC
Confidence 4444
No 17
>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=90.00 E-value=0.13 Score=26.70 Aligned_cols=47 Identities=23% Similarity=0.469 Sum_probs=32.1
Q ss_pred ccccCCCCCCCCceeccCCeeccHHHHhhhCCCCCCCCCCCCcchhh-hhhhcccc
Q psy4350 46 CAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSF-LYDKQGAA 100 (107)
Q Consensus 46 C~~C~~~l~~~~~~~~~~~~~~C~~~y~~~~~~~C~~~~C~~~i~~~-~~~~~g~~ 100 (107)
|..|++++.+........++.|...|| .|.. |+.+|.+. .+..+|+.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf------~C~~--C~~~l~~~~~~~~~~~~ 48 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECF------KCSK--CGKPLNDGDFYEKDGKP 48 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTS------BETT--TTCBTTTSSEEEETTEE
T ss_pred CCCCCCCccCcEEEEEeCCcEEEcccc------ccCC--CCCccCCCeeEeECCEE
Confidence 677888887663444578888887773 5888 99998765 34444543
No 18
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.18 E-value=0.52 Score=24.78 Aligned_cols=29 Identities=21% Similarity=0.524 Sum_probs=20.6
Q ss_pred CCcccccccccc--CceEE-eecCcccccccc
Q psy4350 16 KSSCGGCGQPII--DRFYL-LAVDRQWHLGCL 44 (107)
Q Consensus 16 ~~~C~~C~~~i~--~~~~~-~~~~~~~H~~Cf 44 (107)
..+|..|++.+. +..++ ..-+..||++|+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 457999999995 33222 456788999887
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=87.21 E-value=0.47 Score=22.97 Aligned_cols=25 Identities=20% Similarity=0.481 Sum_probs=17.9
Q ss_pred cccccccccCceE-EeecCccccccc
Q psy4350 19 CGGCGQPIIDRFY-LLAVDRQWHLGC 43 (107)
Q Consensus 19 C~~C~~~i~~~~~-~~~~~~~~H~~C 43 (107)
|..|+.+|.+... +...++.|+.-|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCC 26 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEEC
Confidence 6778999976654 477788887443
No 20
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=77.75 E-value=1 Score=26.77 Aligned_cols=32 Identities=22% Similarity=0.423 Sum_probs=23.1
Q ss_pred CccccccccccCceEEeecC-cccccccccccc
Q psy4350 17 SSCGGCGQPIIDRFYLLAVD-RQWHLGCLQCAH 48 (107)
Q Consensus 17 ~~C~~C~~~i~~~~~~~~~~-~~~H~~Cf~C~~ 48 (107)
-.|..|++.|+.+++..+.. ..-|..||.=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 36888999998888776644 456888886543
No 21
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=76.37 E-value=1 Score=30.10 Aligned_cols=30 Identities=17% Similarity=0.364 Sum_probs=24.1
Q ss_pred ccccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350 44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74 (107)
Q Consensus 44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~ 74 (107)
-+|+.|+...... .....+|++.|..||.+
T Consensus 173 v~C~kCGE~~~e~-~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEP-RAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccc-hhhhcCCceeccccccc
Confidence 5788899877655 56778999999999875
No 22
>KOG3579|consensus
Probab=75.62 E-value=2.4 Score=29.93 Aligned_cols=51 Identities=20% Similarity=0.525 Sum_probs=35.0
Q ss_pred CCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeecc
Q psy4350 12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYC 68 (107)
Q Consensus 12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C 68 (107)
.+...-.|.-|++.+.+...+..-.-.-|+.||-|+. ..+-. ....+++||
T Consensus 264 A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR--esIK~----Qg~sgevYC 314 (352)
T KOG3579|consen 264 APSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR--ESIKQ----QGASGEVYC 314 (352)
T ss_pred CCCCceeehhhhhhhccCceeecCCCcccceecccCH--HHHHh----hcCCCceeC
Confidence 3344567899999999887777777788999998763 11211 233457787
No 23
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=73.62 E-value=3.7 Score=21.21 Aligned_cols=29 Identities=21% Similarity=0.349 Sum_probs=19.5
Q ss_pred cccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350 45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~ 74 (107)
.|..|+..++--..+-..+| ..|.+|+.+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~K 29 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKK 29 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHH
Confidence 36778877764323556666 579999876
No 24
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=73.33 E-value=2.7 Score=22.95 Aligned_cols=43 Identities=19% Similarity=0.403 Sum_probs=19.5
Q ss_pred ccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch
Q psy4350 44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV 90 (107)
Q Consensus 44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~ 90 (107)
++|+.|...|... .....=..+||..|-.. ++ ..|-. |+.|-.
T Consensus 8 LrCs~C~~~l~~p-v~l~~CeH~fCs~Ci~~~~~-~~CPv--C~~Paw 51 (65)
T PF14835_consen 8 LRCSICFDILKEP-VCLGGCEHIFCSSCIRDCIG-SECPV--CHTPAW 51 (65)
T ss_dssp TS-SSS-S--SS--B---SSS--B-TTTGGGGTT-TB-SS--S--B-S
T ss_pred cCCcHHHHHhcCC-ceeccCccHHHHHHhHHhcC-CCCCC--cCChHH
Confidence 5677777766543 23455567788888877 77 57888 887754
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.23 E-value=2.3 Score=18.16 Aligned_cols=9 Identities=44% Similarity=1.073 Sum_probs=4.2
Q ss_pred ccccccccc
Q psy4350 19 CGGCGQPII 27 (107)
Q Consensus 19 C~~C~~~i~ 27 (107)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 444544443
No 26
>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=72.76 E-value=9.8 Score=19.72 Aligned_cols=43 Identities=12% Similarity=0.207 Sum_probs=29.9
Q ss_pred ccccccCCCCCCCCceeccCCeeccHHHHhh-hC-CCCCCCCCCCCcch
Q psy4350 44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS-QARYPDLPIPKTLV 90 (107)
Q Consensus 44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~-~~~C~~~~C~~~i~ 90 (107)
|.|..|...+.. ......|.+||+.+..+ +. ...|-. |++++.
T Consensus 2 ~~Cpi~~~~~~~--Pv~~~~G~v~~~~~i~~~~~~~~~cP~--~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD--PVILPSGQTYERRAIEKWLLSHGTDPV--TGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC--CEECCCCCEEeHHHHHHHHHHCCCCCC--CcCCCC
Confidence 467777777765 35567789999999887 43 245766 777764
No 27
>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=72.49 E-value=3.1 Score=20.20 Aligned_cols=31 Identities=16% Similarity=0.423 Sum_probs=15.2
Q ss_pred CCccccccccccCceEEeecCcccccccccccccCC
Q psy4350 16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHV 51 (107)
Q Consensus 16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~ 51 (107)
+.+|..|+..|.+-..+...++.| +|..|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 467888888887654455555555 5555553
No 28
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=70.88 E-value=10 Score=18.98 Aligned_cols=43 Identities=16% Similarity=0.392 Sum_probs=27.4
Q ss_pred cccccCCCCCCCCceeccCCee-ccHHHHhh-h-CCCCCCCCCCCCcchh
Q psy4350 45 QCAHCHVPLHSELSCFSRHGNI-YCKQDFFR-Y-SQARYPDLPIPKTLVS 91 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~~~~~~~-~C~~~y~~-~-~~~~C~~~~C~~~i~~ 91 (107)
.|..|...... .....=+.. +|..|..+ + ..+.|-. |.++|..
T Consensus 4 ~C~iC~~~~~~--~~~~pCgH~~~C~~C~~~~~~~~~~CP~--Cr~~i~~ 49 (50)
T PF13920_consen 4 ECPICFENPRD--VVLLPCGHLCFCEECAERLLKRKKKCPI--CRQPIES 49 (50)
T ss_dssp B-TTTSSSBSS--EEEETTCEEEEEHHHHHHHHHTTSBBTT--TTBB-SE
T ss_pred CCccCCccCCc--eEEeCCCChHHHHHHhHHhcccCCCCCc--CChhhcC
Confidence 45555555433 345556667 99999987 3 3468999 9988863
No 29
>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=70.56 E-value=3 Score=24.24 Aligned_cols=30 Identities=23% Similarity=0.756 Sum_probs=16.3
Q ss_pred CCCccccccccccCceEE-eecCcccccccc
Q psy4350 15 EKSSCGGCGQPIIDRFYL-LAVDRQWHLGCL 44 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf 44 (107)
....|..|++.|.....+ -..+..+|..|.
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 344577777777554322 333445666554
No 30
>KOG0320|consensus
Probab=66.02 E-value=5.9 Score=26.08 Aligned_cols=50 Identities=16% Similarity=0.442 Sum_probs=36.6
Q ss_pred ccccccccccCCCCCCCCceeccCCeeccHHHHhh-h-CCCCCCCCCCCCcchh
Q psy4350 40 HLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-Y-SQARYPDLPIPKTLVS 91 (107)
Q Consensus 40 H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~-~~~~C~~~~C~~~i~~ 91 (107)
...++.|..|-........+.-.-|.+||+.|-.. . .+.+|-. |++-|+.
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~--C~kkIt~ 179 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPT--CRKKITH 179 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCC--cccccch
Confidence 34578888887777665445567889999999876 3 2368999 9987763
No 31
>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=65.89 E-value=5.1 Score=17.42 Aligned_cols=12 Identities=50% Similarity=1.146 Sum_probs=6.5
Q ss_pred cccccccccCce
Q psy4350 19 CGGCGQPIIDRF 30 (107)
Q Consensus 19 C~~C~~~i~~~~ 30 (107)
|..|+..|.+++
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 455666665543
No 32
>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=63.87 E-value=5.4 Score=23.22 Aligned_cols=44 Identities=16% Similarity=0.377 Sum_probs=29.4
Q ss_pred cccccccccccccCCCCCCCCceeccCCeeccHHHHhhhCCCCCCCCCCCCcchh
Q psy4350 37 RQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVS 91 (107)
Q Consensus 37 ~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~~~~~~C~~~~C~~~i~~ 91 (107)
+.|-..--.|..|...+.+ .+.-||..|-++-+ .|+- |++.|.+
T Consensus 38 nPy~~~~~~C~~CK~~v~q-------~g~~YCq~CAYkkG--iCam--CGKki~d 81 (90)
T PF10235_consen 38 NPYAPYSSKCKICKTKVHQ-------PGAKYCQTCAYKKG--ICAM--CGKKILD 81 (90)
T ss_pred CcccccCcccccccccccc-------CCCccChhhhcccC--cccc--cCCeecc
Confidence 4454433466777765533 25679999966545 8999 9999854
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.34 E-value=5.9 Score=17.26 Aligned_cols=9 Identities=44% Similarity=1.069 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy4350 18 SCGGCGQPI 26 (107)
Q Consensus 18 ~C~~C~~~i 26 (107)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 355555543
No 34
>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=62.94 E-value=1.4 Score=20.89 Aligned_cols=27 Identities=22% Similarity=0.459 Sum_probs=11.6
Q ss_pred ccccCCCCCCCCceeccCCeeccHHHHh
Q psy4350 46 CAHCHVPLHSELSCFSRHGNIYCKQDFF 73 (107)
Q Consensus 46 C~~C~~~l~~~~~~~~~~~~~~C~~~y~ 73 (107)
|..|+..+... ......+..+|..|..
T Consensus 6 C~~CGe~I~~~-Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 6 CEDCGEPIPEE-RLVAVPGATLCVECQE 32 (36)
T ss_dssp -TTTSSBEEHH-HHHHCTTECS-HHHHH
T ss_pred ccccCChHHHH-HHHhCCCcEECHHHhC
Confidence 44555544433 3333445555555543
No 35
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=59.64 E-value=0.81 Score=26.94 Aligned_cols=36 Identities=17% Similarity=0.326 Sum_probs=18.7
Q ss_pred cccccccccCceEEeecCcccccccccccccCCCCC
Q psy4350 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLH 54 (107)
Q Consensus 19 C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 54 (107)
|..|+..+.......+.-..+++.+..|..|...|.
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT 73 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLT 73 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhh
Confidence 334444444333233334456666666666666664
No 36
>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=59.42 E-value=6 Score=18.87 Aligned_cols=22 Identities=27% Similarity=0.637 Sum_probs=13.8
Q ss_pred cccccCCCCCCCCceeccCCeeccHHH
Q psy4350 45 QCAHCHVPLHSELSCFSRHGNIYCKQD 71 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~ 71 (107)
.|..|+.. .+...+|..||..|
T Consensus 10 ~C~~C~~~-----~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 10 PCPVCGSR-----WFYSDDGFYYCDRC 31 (36)
T ss_pred cCCCCCCe-----EeEccCCEEEhhhC
Confidence 35556543 35667888888655
No 37
>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=58.98 E-value=6.7 Score=21.89 Aligned_cols=16 Identities=25% Similarity=0.630 Sum_probs=11.5
Q ss_pred CCCccccccccccCce
Q psy4350 15 EKSSCGGCGQPIIDRF 30 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~ 30 (107)
+-..|..|++.|...+
T Consensus 6 ~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGE 21 (82)
T ss_dssp STEBETTTSCBE-TTS
T ss_pred CCccCcccCCcCCCCC
Confidence 4457999999997555
No 38
>KOG1813|consensus
Probab=57.76 E-value=6.6 Score=27.87 Aligned_cols=46 Identities=11% Similarity=0.293 Sum_probs=34.2
Q ss_pred cccccccCCCCCCCCceeccCCeeccHHHHhh-hCC-CCCCCCCCCCcchhh
Q psy4350 43 CLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQ-ARYPDLPIPKTLVSF 92 (107)
Q Consensus 43 Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~-~~C~~~~C~~~i~~~ 92 (107)
-|.|..|++..... ..-.-+.-||+.|..+ |.. +.|.. |++++.|.
T Consensus 241 Pf~c~icr~~f~~p--Vvt~c~h~fc~~ca~~~~qk~~~c~v--C~~~t~g~ 288 (313)
T KOG1813|consen 241 PFKCFICRKYFYRP--VVTKCGHYFCEVCALKPYQKGEKCYV--CSQQTHGS 288 (313)
T ss_pred Cccccccccccccc--hhhcCCceeehhhhccccccCCccee--cccccccc
Confidence 47788888776542 3445567789999988 663 69999 99998763
No 39
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.28 E-value=16 Score=19.58 Aligned_cols=29 Identities=28% Similarity=0.503 Sum_probs=19.3
Q ss_pred CCCccccccccccCceEEeecCcccccccccccccCCC
Q psy4350 15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVP 52 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~ 52 (107)
..+.|..|+..|.+.+. ---|.|..|+..
T Consensus 6 ~~~~CtSCg~~i~~~~~---------~~~F~CPnCG~~ 34 (59)
T PRK14890 6 EPPKCTSCGIEIAPREK---------AVKFLCPNCGEV 34 (59)
T ss_pred cCccccCCCCcccCCCc---------cCEeeCCCCCCe
Confidence 35679999998876641 122677777765
No 40
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=56.98 E-value=5.3 Score=24.91 Aligned_cols=21 Identities=33% Similarity=1.064 Sum_probs=14.8
Q ss_pred cccccCCCCCCCCceeccCCeeccHHH
Q psy4350 45 QCAHCHVPLHSELSCFSRHGNIYCKQD 71 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~ 71 (107)
.|..|+.+| +.++|.+||-.|
T Consensus 30 hCp~Cg~PL------F~KdG~v~CPvC 50 (131)
T COG1645 30 HCPKCGTPL------FRKDGEVFCPVC 50 (131)
T ss_pred hCcccCCcc------eeeCCeEECCCC
Confidence 577888776 237889999444
No 41
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=55.80 E-value=5 Score=26.93 Aligned_cols=47 Identities=17% Similarity=0.252 Sum_probs=34.3
Q ss_pred ccccccccCCCCCCCCceeccCCeeccHHHHhh-hC-CCCCCCCCCCCcchhh
Q psy4350 42 GCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS-QARYPDLPIPKTLVSF 92 (107)
Q Consensus 42 ~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~-~~~C~~~~C~~~i~~~ 92 (107)
.-|.|..|.+.... ...-.-|.-||..|+.+ +. .+.|.. |++...|.
T Consensus 195 IPF~C~iCKkdy~s--pvvt~CGH~FC~~Cai~~y~kg~~C~~--Cgk~t~G~ 243 (259)
T COG5152 195 IPFLCGICKKDYES--PVVTECGHSFCSLCAIRKYQKGDECGV--CGKATYGR 243 (259)
T ss_pred Cceeehhchhhccc--hhhhhcchhHHHHHHHHHhccCCccee--cchhhccc
Confidence 35788888887655 23445667899999988 54 369999 99877653
No 42
>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=55.28 E-value=7.4 Score=20.29 Aligned_cols=28 Identities=21% Similarity=0.579 Sum_probs=14.4
Q ss_pred cccccCCCCCCCCceeccCCeeccH-HHHh
Q psy4350 45 QCAHCHVPLHSELSCFSRHGNIYCK-QDFF 73 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~~~~~~~~C~-~~y~ 73 (107)
.|..|...+... ..+.++|+.||- .|-.
T Consensus 9 aC~~C~C~V~~~-~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEE-EAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TT-TSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECch-HhHHhCCEeeecHHHhc
Confidence 466677666644 567889999984 4443
No 43
>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=55.19 E-value=5.6 Score=19.61 Aligned_cols=21 Identities=38% Similarity=1.005 Sum_probs=11.9
Q ss_pred cccccCCCCCCCCceeccCCeeccHH
Q psy4350 45 QCAHCHVPLHSELSCFSRHGNIYCKQ 70 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~~~~~~~~C~~ 70 (107)
.|..|+.+|- ..+++++||-.
T Consensus 19 ~Cp~C~~PL~-----~~k~g~~~Cv~ 39 (41)
T PF06677_consen 19 HCPDCGTPLM-----RDKDGKIYCVS 39 (41)
T ss_pred ccCCCCCeeE-----EecCCCEECCC
Confidence 4556665552 23567777743
No 44
>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=53.23 E-value=16 Score=18.36 Aligned_cols=29 Identities=10% Similarity=0.199 Sum_probs=17.3
Q ss_pred cccccCCCCCCCCcee--ccCCeeccHHHHhh
Q psy4350 45 QCAHCHVPLHSELSCF--SRHGNIYCKQDFFR 74 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~--~~~~~~~C~~~y~~ 74 (107)
.|..|+..+... .+. ...+..+|..||.+
T Consensus 2 ~C~~Cg~D~t~v-ryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRV-RYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCce-EEEecCCCccccChHHHhC
Confidence 466677666543 231 12335589999987
No 45
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=52.98 E-value=3.6 Score=24.36 Aligned_cols=28 Identities=18% Similarity=0.509 Sum_probs=16.1
Q ss_pred ccccccCCCCCCCCceeccCCeeccHHH
Q psy4350 44 LQCAHCHVPLHSELSCFSRHGNIYCKQD 71 (107)
Q Consensus 44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~ 71 (107)
|+|+.|-.---.+......++.++|..|
T Consensus 71 FTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 71 FTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred eeeeeeeeEechhhhccccCCCEecccc
Confidence 7777776322111123456788888776
No 46
>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=51.01 E-value=20 Score=17.61 Aligned_cols=9 Identities=22% Similarity=0.504 Sum_probs=6.3
Q ss_pred eccHHHHhh
Q psy4350 66 IYCKQDFFR 74 (107)
Q Consensus 66 ~~C~~~y~~ 74 (107)
-+|..||.+
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 358888765
No 47
>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=50.37 E-value=9.1 Score=29.01 Aligned_cols=40 Identities=18% Similarity=0.419 Sum_probs=29.2
Q ss_pred CCCccccccccccCceEEeecCcccccccccccccCCCCCC
Q psy4350 15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS 55 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 55 (107)
....|..|-..+...+ +...++.-..+||.|..|...|..
T Consensus 25 ~~~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 25 DSYYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred ceeECccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 3455777777665554 555666677799999999999864
No 48
>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=48.80 E-value=20 Score=17.73 Aligned_cols=8 Identities=13% Similarity=0.588 Sum_probs=4.5
Q ss_pred ccHHHHhh
Q psy4350 67 YCKQDFFR 74 (107)
Q Consensus 67 ~C~~~y~~ 74 (107)
+|..||..
T Consensus 25 LC~~Cf~~ 32 (46)
T cd02249 25 LCSSCYAK 32 (46)
T ss_pred CHHHHHCc
Confidence 46666554
No 49
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=48.38 E-value=7.3 Score=22.92 Aligned_cols=36 Identities=25% Similarity=0.392 Sum_probs=23.9
Q ss_pred CccccccccccCceEEeecC-cccccccccccccCCC
Q psy4350 17 SSCGGCGQPIIDRFYLLAVD-RQWHLGCLQCAHCHVP 52 (107)
Q Consensus 17 ~~C~~C~~~i~~~~~~~~~~-~~~H~~Cf~C~~C~~~ 52 (107)
-.|..|+++|..++...+-. .+-|-.||.-+.-+++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 46888888887777665533 3568788766554443
No 50
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=45.63 E-value=15 Score=19.53 Aligned_cols=25 Identities=20% Similarity=0.456 Sum_probs=16.1
Q ss_pred cccccCCCCC-CCCceeccCCeeccH
Q psy4350 45 QCAHCHVPLH-SELSCFSRHGNIYCK 69 (107)
Q Consensus 45 ~C~~C~~~l~-~~~~~~~~~~~~~C~ 69 (107)
.|..|++.|. +...|.-++.+.||.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 4567778887 343555666677774
No 51
>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=45.25 E-value=7.2 Score=18.52 Aligned_cols=30 Identities=23% Similarity=0.698 Sum_probs=15.7
Q ss_pred cccccccccCceEEeecCcccccccccccccCCCC
Q psy4350 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL 53 (107)
Q Consensus 19 C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l 53 (107)
|..|.+.+.+. .++.||-.-..|..|+-.+
T Consensus 2 C~~C~~Ey~~p-----~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEYFDP-----SNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHHCST-----TSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHHcCC-----CCCcccCcCccCCCCCCCE
Confidence 45555544332 3677888888888888655
No 52
>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=44.66 E-value=39 Score=16.38 Aligned_cols=30 Identities=20% Similarity=0.396 Sum_probs=14.1
Q ss_pred cccccCCCCCCCCceec-cCCeeccHHHHhh
Q psy4350 45 QCAHCHVPLHSELSCFS-RHGNIYCKQDFFR 74 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~~~-~~~~~~C~~~y~~ 74 (107)
.|+.|+++-........ .++...|..|-..
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 46777776654323332 3355667777554
No 53
>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=43.83 E-value=16 Score=18.32 Aligned_cols=13 Identities=31% Similarity=0.731 Sum_probs=8.9
Q ss_pred CCCCccccccccc
Q psy4350 14 EEKSSCGGCGQPI 26 (107)
Q Consensus 14 ~~~~~C~~C~~~i 26 (107)
..+..|..|++.|
T Consensus 9 ~~~~~C~~C~~~i 21 (53)
T PF00130_consen 9 SKPTYCDVCGKFI 21 (53)
T ss_dssp SSTEB-TTSSSBE
T ss_pred CCCCCCcccCccc
Confidence 3456788898888
No 54
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=43.50 E-value=9.7 Score=19.79 Aligned_cols=29 Identities=31% Similarity=0.560 Sum_probs=17.6
Q ss_pred ccccccccccCceEEeecCcccccccccc
Q psy4350 18 SCGGCGQPIIDRFYLLAVDRQWHLGCLQC 46 (107)
Q Consensus 18 ~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C 46 (107)
.|+.|++.+.-.--.+..++.|-..|-.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc
Confidence 58888887743211344566777777544
No 55
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=42.03 E-value=30 Score=18.59 Aligned_cols=28 Identities=21% Similarity=0.457 Sum_probs=18.5
Q ss_pred CCccccccccccCceEEeecCcccccccccccccCCC
Q psy4350 16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVP 52 (107)
Q Consensus 16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~ 52 (107)
.+.|..|+..|.+.+. -.-|.|..|+..
T Consensus 9 ~~~CtSCg~~i~p~e~---------~v~F~CPnCGe~ 36 (61)
T COG2888 9 PPVCTSCGREIAPGET---------AVKFPCPNCGEV 36 (61)
T ss_pred CceeccCCCEeccCCc---------eeEeeCCCCCce
Confidence 6789999998866542 122667777743
No 56
>KOG0978|consensus
Probab=41.62 E-value=11 Score=29.91 Aligned_cols=43 Identities=19% Similarity=0.583 Sum_probs=30.9
Q ss_pred ccccccCCCCCCCCceeccCCeeccHHHHhh-hC--CCCCCCCCCCCcch
Q psy4350 44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS--QARYPDLPIPKTLV 90 (107)
Q Consensus 44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~--~~~C~~~~C~~~i~ 90 (107)
++|+.|...+-+ .....-+.+||..|-.. +. ..+|-. |+.+..
T Consensus 644 LkCs~Cn~R~Kd--~vI~kC~H~FC~~Cvq~r~etRqRKCP~--Cn~aFg 689 (698)
T KOG0978|consen 644 LKCSVCNTRWKD--AVITKCGHVFCEECVQTRYETRQRKCPK--CNAAFG 689 (698)
T ss_pred eeCCCccCchhh--HHHHhcchHHHHHHHHHHHHHhcCCCCC--CCCCCC
Confidence 578888865544 34566677899999876 55 358888 888764
No 57
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=40.93 E-value=28 Score=18.27 Aligned_cols=26 Identities=31% Similarity=0.436 Sum_probs=16.1
Q ss_pred CccccccccccCceEEeecCcccccc
Q psy4350 17 SSCGGCGQPIIDRFYLLAVDRQWHLG 42 (107)
Q Consensus 17 ~~C~~C~~~i~~~~~~~~~~~~~H~~ 42 (107)
.+|..|+.+|.++..+...+..-|+.
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcH
Confidence 35778888887764455455555553
No 58
>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=40.75 E-value=11 Score=18.58 Aligned_cols=11 Identities=18% Similarity=0.700 Sum_probs=4.3
Q ss_pred cccccccccCc
Q psy4350 19 CGGCGQPIIDR 29 (107)
Q Consensus 19 C~~C~~~i~~~ 29 (107)
|..|++.+.-+
T Consensus 1 C~~C~~iv~~G 11 (43)
T PF08746_consen 1 CEACKEIVTQG 11 (43)
T ss_dssp -TTT-SB-SSS
T ss_pred CcccchhHeee
Confidence 44566655544
No 59
>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=40.57 E-value=32 Score=17.26 Aligned_cols=8 Identities=25% Similarity=0.480 Sum_probs=4.7
Q ss_pred ccHHHHhh
Q psy4350 67 YCKQDFFR 74 (107)
Q Consensus 67 ~C~~~y~~ 74 (107)
+|.+||..
T Consensus 26 LC~~Cf~~ 33 (49)
T cd02335 26 LCLECFSA 33 (49)
T ss_pred hhHHhhhC
Confidence 46666654
No 60
>PRK08359 transcription factor; Validated
Probab=39.75 E-value=30 Score=22.72 Aligned_cols=31 Identities=13% Similarity=0.468 Sum_probs=18.6
Q ss_pred cccccCCCCCCCCce-e-ccCCee-ccHHHHhhhC
Q psy4350 45 QCAHCHVPLHSELSC-F-SRHGNI-YCKQDFFRYS 76 (107)
Q Consensus 45 ~C~~C~~~l~~~~~~-~-~~~~~~-~C~~~y~~~~ 76 (107)
.|..|+..+.+. .+ . ..+..+ .|..|+.+||
T Consensus 8 ~CEiCG~~i~g~-~~~v~ieGael~VC~~Ca~k~G 41 (176)
T PRK08359 8 YCEICGAEIRGP-GHRIRIEGAELLVCDRCYEKYG 41 (176)
T ss_pred eeecCCCccCCC-CeEEEEcCeEEehHHHHHHHhC
Confidence 377888877654 22 2 223333 5888886666
No 61
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=38.64 E-value=19 Score=20.46 Aligned_cols=30 Identities=20% Similarity=0.483 Sum_probs=18.5
Q ss_pred cccccCCCCCCCC----ceeccCCeeccHHHHhh
Q psy4350 45 QCAHCHVPLHSEL----SCFSRHGNIYCKQDFFR 74 (107)
Q Consensus 45 ~C~~C~~~l~~~~----~~~~~~~~~~C~~~y~~ 74 (107)
.|..|+-+|.... ......+.-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 3677888876542 11223335689999886
No 62
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=38.31 E-value=57 Score=21.78 Aligned_cols=12 Identities=8% Similarity=0.185 Sum_probs=7.7
Q ss_pred CCCCCCCCCCcchh
Q psy4350 78 ARYPDLPIPKTLVS 91 (107)
Q Consensus 78 ~~C~~~~C~~~i~~ 91 (107)
+.|-. |...|..
T Consensus 69 ~~CPv--CR~~Is~ 80 (193)
T PLN03208 69 PKCPV--CKSDVSE 80 (193)
T ss_pred CcCCC--CCCcCCh
Confidence 36777 7777643
No 63
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=37.63 E-value=9.8 Score=17.99 Aligned_cols=15 Identities=33% Similarity=1.099 Sum_probs=6.5
Q ss_pred CCccccccccccCce
Q psy4350 16 KSSCGGCGQPIIDRF 30 (107)
Q Consensus 16 ~~~C~~C~~~i~~~~ 30 (107)
.+.|..|+++..+.+
T Consensus 3 ~~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 3 YPKCDECGKPFMDSY 17 (34)
T ss_dssp -EE-TTT--EES-SS
T ss_pred CchHhHhCCHHHHHH
Confidence 346777777766654
No 64
>PRK00420 hypothetical protein; Validated
Probab=37.41 E-value=16 Score=22.20 Aligned_cols=20 Identities=30% Similarity=0.839 Sum_probs=10.8
Q ss_pred ccccccCCCCCCCCceeccCCeecc
Q psy4350 44 LQCAHCHVPLHSELSCFSRHGNIYC 68 (107)
Q Consensus 44 f~C~~C~~~l~~~~~~~~~~~~~~C 68 (107)
-.|..|+.+|- ...+|+.||
T Consensus 24 ~~CP~Cg~pLf-----~lk~g~~~C 43 (112)
T PRK00420 24 KHCPVCGLPLF-----ELKDGEVVC 43 (112)
T ss_pred CCCCCCCCcce-----ecCCCceEC
Confidence 34566665542 225666666
No 65
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=37.03 E-value=33 Score=21.88 Aligned_cols=30 Identities=13% Similarity=0.363 Sum_probs=15.2
Q ss_pred ccccCCCCCCCCceeccCC-ee-ccHHHHhhhC
Q psy4350 46 CAHCHVPLHSELSCFSRHG-NI-YCKQDFFRYS 76 (107)
Q Consensus 46 C~~C~~~l~~~~~~~~~~~-~~-~C~~~y~~~~ 76 (107)
|..|++.+.+.-.....+| .+ .|..|+ +||
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~-k~G 34 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR-KFG 34 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH-hcC
Confidence 6667766655411122222 22 577777 555
No 66
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=36.78 E-value=18 Score=20.11 Aligned_cols=8 Identities=38% Similarity=0.783 Sum_probs=5.3
Q ss_pred cCCCCcCC
Q psy4350 100 ASEPLLTG 107 (107)
Q Consensus 100 ~~~p~~~~ 107 (107)
..||+.||
T Consensus 40 ~~HPFyTG 47 (72)
T PRK00019 40 KCHPFYTG 47 (72)
T ss_pred CCCCcCcC
Confidence 46777776
No 67
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=35.90 E-value=22 Score=22.85 Aligned_cols=10 Identities=10% Similarity=-0.077 Sum_probs=5.1
Q ss_pred CCCCCCCCCcch
Q psy4350 79 RYPDLPIPKTLV 90 (107)
Q Consensus 79 ~C~~~~C~~~i~ 90 (107)
-|.. |+++-.
T Consensus 70 YC~~--CGkpyP 79 (158)
T PF10083_consen 70 YCHN--CGKPYP 79 (158)
T ss_pred hHHh--CCCCCc
Confidence 4555 555543
No 68
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=35.50 E-value=58 Score=15.70 Aligned_cols=39 Identities=15% Similarity=0.410 Sum_probs=21.3
Q ss_pred ccccCCCCC-CCCceeccCCeeccHHHHhh-h-CCCCCCCCCCC
Q psy4350 46 CAHCHVPLH-SELSCFSRHGNIYCKQDFFR-Y-SQARYPDLPIP 86 (107)
Q Consensus 46 C~~C~~~l~-~~~~~~~~~~~~~C~~~y~~-~-~~~~C~~~~C~ 86 (107)
|..|..... ....+...=+.++|..|..+ . ....|-. |+
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~--C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPI--CR 43 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcC--CC
Confidence 444555442 11134555667788888777 5 1136665 54
No 69
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.84 E-value=22 Score=21.33 Aligned_cols=29 Identities=28% Similarity=0.496 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCCCCCCccccccccccCce
Q psy4350 2 LKDRDDSSSPCPEEKSSCGGCGQPIIDRF 30 (107)
Q Consensus 2 ~~~~~~~~~~~~~~~~~C~~C~~~i~~~~ 30 (107)
|++-+..-.-..-+...|+.|+..+...+
T Consensus 35 Ln~~~LdyV~ie~G~t~CP~Cg~~~e~~f 63 (115)
T COG1885 35 LNKPDLDYVEIEVGSTSCPKCGEPFESAF 63 (115)
T ss_pred hccCCCCeEEEecccccCCCCCCccceeE
Confidence 33334444444556677999988876654
No 70
>KOG4739|consensus
Probab=34.01 E-value=28 Score=23.95 Aligned_cols=31 Identities=10% Similarity=0.164 Sum_probs=23.5
Q ss_pred ceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchh
Q psy4350 58 SCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVS 91 (107)
Q Consensus 58 ~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~ 91 (107)
.|.-.-..++|..|... .+ ..|.. |+++|..
T Consensus 18 f~LTaC~HvfC~~C~k~~~~-~~C~l--Ckk~ir~ 49 (233)
T KOG4739|consen 18 FFLTACRHVFCEPCLKASSP-DVCPL--CKKSIRI 49 (233)
T ss_pred eeeeechhhhhhhhcccCCc-ccccc--ccceeee
Confidence 44555668899999877 77 58999 9998764
No 71
>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=33.43 E-value=55 Score=14.85 Aligned_cols=24 Identities=13% Similarity=0.383 Sum_probs=12.2
Q ss_pred CCeeccHHHHhh-hC--CCCCCCCCCCCc
Q psy4350 63 HGNIYCKQDFFR-YS--QARYPDLPIPKT 88 (107)
Q Consensus 63 ~~~~~C~~~y~~-~~--~~~C~~~~C~~~ 88 (107)
-+..||..|..+ +. ...|-. |+..
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~--C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPL--CRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCC--CCCc
Confidence 445566666654 32 134655 5543
No 72
>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=33.32 E-value=35 Score=16.90 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=6.7
Q ss_pred eccHHHHhh
Q psy4350 66 IYCKQDFFR 74 (107)
Q Consensus 66 ~~C~~~y~~ 74 (107)
-+|..||.+
T Consensus 29 dLC~~C~~~ 37 (46)
T PF00569_consen 29 DLCEDCFSK 37 (46)
T ss_dssp EEEHHHHHH
T ss_pred chhhHHHhC
Confidence 458888876
No 73
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=33.19 E-value=46 Score=16.72 Aligned_cols=10 Identities=20% Similarity=0.328 Sum_probs=4.5
Q ss_pred CeeccHHHHh
Q psy4350 64 GNIYCKQDFF 73 (107)
Q Consensus 64 ~~~~C~~~y~ 73 (107)
++..|..|-.
T Consensus 17 ~~fIC~~CE~ 26 (46)
T PF10764_consen 17 GKFICSDCEK 26 (46)
T ss_pred CeEehHHHHH
Confidence 3444544443
No 74
>KOG3002|consensus
Probab=32.95 E-value=48 Score=23.62 Aligned_cols=46 Identities=20% Similarity=0.377 Sum_probs=34.7
Q ss_pred cccccccCCCCCCCCceeccCCeeccHHHHhhhCCCCCCCCCCCCcchhh
Q psy4350 43 CLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSF 92 (107)
Q Consensus 43 Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~~~~~~C~~~~C~~~i~~~ 92 (107)
=+.|..|...|... .+.-.+|.+.|..|-.+.. .+|-. |..+|...
T Consensus 48 lleCPvC~~~l~~P-i~QC~nGHlaCssC~~~~~-~~CP~--Cr~~~g~~ 93 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPP-IFQCDNGHLACSSCRTKVS-NKCPT--CRLPIGNI 93 (299)
T ss_pred hccCchhhccCccc-ceecCCCcEehhhhhhhhc-ccCCc--cccccccH
Confidence 46777778777765 6777888999999986633 28888 98888753
No 75
>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=32.94 E-value=22 Score=21.13 Aligned_cols=33 Identities=15% Similarity=0.412 Sum_probs=22.9
Q ss_pred cccccccccccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350 37 RQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74 (107)
Q Consensus 37 ~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~ 74 (107)
..+...-=.|..| ++. .|++.++.+.|..|-.+
T Consensus 29 g~~~va~daCeiC----~~~-GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 29 GSYRVAFDACEIC----GPK-GYYQEGDQLVCKNCGVR 61 (102)
T ss_pred CCEEEEEEecccc----CCC-ceEEECCEEEEecCCCE
Confidence 3444444467777 344 78899999999999654
No 76
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=32.79 E-value=64 Score=18.30 Aligned_cols=23 Identities=9% Similarity=0.086 Sum_probs=10.0
Q ss_pred eeccHHHHhh---hCCCCCCCCCCCCcc
Q psy4350 65 NIYCKQDFFR---YSQARYPDLPIPKTL 89 (107)
Q Consensus 65 ~~~C~~~y~~---~~~~~C~~~~C~~~i 89 (107)
-+.|+.||.. -+.+.|-+ |+..-
T Consensus 36 fPvCr~CyEYErkeg~q~Cpq--Ckt~y 61 (80)
T PF14569_consen 36 FPVCRPCYEYERKEGNQVCPQ--CKTRY 61 (80)
T ss_dssp ----HHHHHHHHHTS-SB-TT--T--B-
T ss_pred CccchhHHHHHhhcCcccccc--cCCCc
Confidence 4569999863 45567888 87653
No 77
>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=32.22 E-value=62 Score=15.05 Aligned_cols=27 Identities=19% Similarity=0.389 Sum_probs=16.0
Q ss_pred cccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350 47 AHCHVPLHSELSCFSRHGNIYCKQDFFR 74 (107)
Q Consensus 47 ~~C~~~l~~~~~~~~~~~~~~C~~~y~~ 74 (107)
..|...+... .....=|..||..|..+
T Consensus 2 ~iC~~~~~~~-~~~~~CGH~fC~~C~~~ 28 (39)
T PF13923_consen 2 PICLDELRDP-VVVTPCGHSFCKECIEK 28 (39)
T ss_dssp TTTTSB-SSE-EEECTTSEEEEHHHHHH
T ss_pred CCCCCcccCc-CEECCCCCchhHHHHHH
Confidence 3444444442 24566778888888776
No 78
>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=31.49 E-value=22 Score=20.61 Aligned_cols=12 Identities=8% Similarity=-0.014 Sum_probs=8.0
Q ss_pred CCCCCCCCCCcchh
Q psy4350 78 ARYPDLPIPKTLVS 91 (107)
Q Consensus 78 ~~C~~~~C~~~i~~ 91 (107)
.+|.. |+.+|.-
T Consensus 59 GrCr~--C~~~I~~ 70 (92)
T PF06750_consen 59 GRCRY--CGAPIPP 70 (92)
T ss_pred CCCcc--cCCCCCh
Confidence 37777 7777754
No 79
>PRK01397 50S ribosomal protein L31; Provisional
Probab=31.33 E-value=25 Score=19.91 Aligned_cols=9 Identities=11% Similarity=0.102 Sum_probs=5.9
Q ss_pred ccCCCCcCC
Q psy4350 99 AASEPLLTG 107 (107)
Q Consensus 99 ~~~~p~~~~ 107 (107)
...||+.||
T Consensus 38 s~~HPFyTG 46 (78)
T PRK01397 38 FRKHPAWNK 46 (78)
T ss_pred CCCCCcCcC
Confidence 346777776
No 80
>PRK03922 hypothetical protein; Provisional
Probab=31.13 E-value=32 Score=20.78 Aligned_cols=29 Identities=24% Similarity=0.426 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCCCCCccccccccccCce
Q psy4350 2 LKDRDDSSSPCPEEKSSCGGCGQPIIDRF 30 (107)
Q Consensus 2 ~~~~~~~~~~~~~~~~~C~~C~~~i~~~~ 30 (107)
|+..+....-.+-+...|+.|++++.+..
T Consensus 35 Ln~~~l~yVeievG~~~cP~cge~~~~af 63 (113)
T PRK03922 35 LNPEDLDYVEVEVGLTICPKCGEPFDSAF 63 (113)
T ss_pred cCcccCCeEEEecCcccCCCCCCcCCcEE
Confidence 33434444445567778999999886654
No 81
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=31.06 E-value=25 Score=20.36 Aligned_cols=15 Identities=0% Similarity=-0.018 Sum_probs=8.7
Q ss_pred cccccccccccCCCC
Q psy4350 39 WHLGCLQCAHCHVPL 53 (107)
Q Consensus 39 ~H~~Cf~C~~C~~~l 53 (107)
|+.-.|.|..|+..+
T Consensus 9 y~~v~~~~~t~g~~f 23 (87)
T PRK01678 9 YRPVVFHDTSTGFKF 23 (87)
T ss_pred CEEEEEEECCCCCEE
Confidence 455566666666544
No 82
>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=30.79 E-value=33 Score=16.95 Aligned_cols=26 Identities=31% Similarity=0.599 Sum_probs=14.9
Q ss_pred cccccccccCceEEe--ecCcccccccc
Q psy4350 19 CGGCGQPIIDRFYLL--AVDRQWHLGCL 44 (107)
Q Consensus 19 C~~C~~~i~~~~~~~--~~~~~~H~~Cf 44 (107)
|..|++.-.+..++. .-++.||..|.
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTS
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccC
Confidence 556666444444443 23467888775
No 83
>KOG2893|consensus
Probab=29.85 E-value=13 Score=25.77 Aligned_cols=38 Identities=26% Similarity=0.467 Sum_probs=24.0
Q ss_pred CCccccccccccCceEEeecCcccccccccccccCCCCCCC
Q psy4350 16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSE 56 (107)
Q Consensus 16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 56 (107)
.+-|-.|+....+..++..-.+. ..|+|..|.+.|...
T Consensus 10 kpwcwycnrefddekiliqhqka---khfkchichkkl~sg 47 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKA---KHFKCHICHKKLFSG 47 (341)
T ss_pred Cceeeecccccchhhhhhhhhhh---ccceeeeehhhhccC
Confidence 34588888887666433222222 358889999887543
No 84
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=29.76 E-value=22 Score=23.25 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=21.2
Q ss_pred ccccccccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350 40 HLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74 (107)
Q Consensus 40 H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~ 74 (107)
|..|++|..-....+.. .++.-+.+++|..|..-
T Consensus 136 ~~kC~QC~~~~~~~~~~-~~~~F~~~lFC~~ClFP 169 (173)
T PF11077_consen 136 YDKCVQCSQKCENVGAK-IFTYFNFNLFCKNCLFP 169 (173)
T ss_pred ccccCcCCCCcccccce-eEEecChhhcccccCcc
Confidence 34566665543333333 36777889999988764
No 85
>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=29.67 E-value=33 Score=21.48 Aligned_cols=36 Identities=17% Similarity=0.158 Sum_probs=18.6
Q ss_pred CCccccccccccCceEEeec------CcccccccccccccCC
Q psy4350 16 KSSCGGCGQPIIDRFYLLAV------DRQWHLGCLQCAHCHV 51 (107)
Q Consensus 16 ~~~C~~C~~~i~~~~~~~~~------~~~~H~~Cf~C~~C~~ 51 (107)
..+|..||..+.....-.+. -...+...+.|..|++
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~k 132 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGK 132 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCC
Confidence 56788888866322111111 1112444667777775
No 86
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=28.43 E-value=26 Score=19.24 Aligned_cols=7 Identities=43% Similarity=0.952 Sum_probs=4.4
Q ss_pred CCCCcCC
Q psy4350 101 SEPLLTG 107 (107)
Q Consensus 101 ~~p~~~~ 107 (107)
.||+.||
T Consensus 41 ~HPfyTG 47 (68)
T CHL00136 41 NHPFYTG 47 (68)
T ss_pred CCccCcC
Confidence 5666665
No 87
>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 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=28.27 E-value=68 Score=16.20 Aligned_cols=8 Identities=13% Similarity=0.567 Sum_probs=5.2
Q ss_pred ccHHHHhh
Q psy4350 67 YCKQDFFR 74 (107)
Q Consensus 67 ~C~~~y~~ 74 (107)
+|..||.+
T Consensus 28 lC~~C~~~ 35 (48)
T cd02341 28 LCQDCVVK 35 (48)
T ss_pred cCHHHHhC
Confidence 47777665
No 89
>PLN02195 cellulose synthase A
Probab=28.26 E-value=55 Score=27.25 Aligned_cols=53 Identities=13% Similarity=0.262 Sum_probs=30.0
Q ss_pred CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHh--h-hCCCCCCCCCCCCcch
Q psy4350 14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF--R-YSQARYPDLPIPKTLV 90 (107)
Q Consensus 14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~--~-~~~~~C~~~~C~~~i~ 90 (107)
++...|.-|+..|. +...|..| -.|..|+- +.|++||+ + -|.+.|-+ |+..-.
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~--------------pvCrpCyeyer~eg~q~Cpq--Ckt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF----VACHECSY--------------PLCKACLEYEIKEGRKVCLR--CGGPYD 59 (977)
T ss_pred CCCccceecccccC----cCCCCCeE----EEeccCCC--------------ccccchhhhhhhcCCccCCc--cCCccc
Confidence 44567888877663 23345444 23444432 34777775 3 44567888 876654
No 90
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=27.69 E-value=31 Score=19.37 Aligned_cols=10 Identities=30% Similarity=0.597 Sum_probs=6.4
Q ss_pred cccCCCCcCC
Q psy4350 98 GAASEPLLTG 107 (107)
Q Consensus 98 g~~~~p~~~~ 107 (107)
-...||+.||
T Consensus 40 ~s~~HPFyTG 49 (75)
T COG0254 40 CSKCHPFYTG 49 (75)
T ss_pred CCCCCCcCcC
Confidence 3446777776
No 91
>PF12773 DZR: Double zinc ribbon
Probab=27.47 E-value=85 Score=15.42 Aligned_cols=13 Identities=31% Similarity=0.871 Sum_probs=6.5
Q ss_pred CCCcccccccccc
Q psy4350 15 EKSSCGGCGQPII 27 (107)
Q Consensus 15 ~~~~C~~C~~~i~ 27 (107)
....|..|+..+.
T Consensus 11 ~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 11 DAKFCPHCGTPLP 23 (50)
T ss_pred cccCChhhcCChh
Confidence 3444555555444
No 92
>PF14149 YhfH: YhfH-like protein
Probab=27.16 E-value=16 Score=17.63 Aligned_cols=20 Identities=20% Similarity=0.419 Sum_probs=14.7
Q ss_pred HHhh-hCCCCCCCCCCCCcchhh
Q psy4350 71 DFFR-YSQARYPDLPIPKTLVSF 92 (107)
Q Consensus 71 ~y~~-~~~~~C~~~~C~~~i~~~ 92 (107)
.|.+ ++.+.|.. |++.|...
T Consensus 6 eFfrnLp~K~C~~--CG~~i~EQ 26 (37)
T PF14149_consen 6 EFFRNLPPKKCTE--CGKEIEEQ 26 (37)
T ss_pred HHHHhCCCcccHH--HHHHHHHH
Confidence 4566 66688999 99888653
No 93
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.34 E-value=41 Score=15.60 Aligned_cols=7 Identities=14% Similarity=0.344 Sum_probs=3.0
Q ss_pred cCCeecc
Q psy4350 62 RHGNIYC 68 (107)
Q Consensus 62 ~~~~~~C 68 (107)
.++..+|
T Consensus 18 ~~~~~~C 24 (33)
T PF08792_consen 18 EDDYEVC 24 (33)
T ss_pred cCCeEEc
Confidence 3444444
No 94
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=25.37 E-value=39 Score=20.09 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCccccccccccCce
Q psy4350 6 DDSSSPCPEEKSSCGGCGQPIIDRF 30 (107)
Q Consensus 6 ~~~~~~~~~~~~~C~~C~~~i~~~~ 30 (107)
+....-.+.+...|+.|++++....
T Consensus 37 ~~~~VeIevG~~~cP~Cge~~~~a~ 61 (102)
T PF04475_consen 37 DLDYVEIEVGDTICPKCGEELDSAF 61 (102)
T ss_pred CCCeEEEecCcccCCCCCCccCceE
Confidence 3444445567778999999887654
No 95
>PLN00162 transport protein sec23; Provisional
Probab=24.67 E-value=1.2e+02 Score=24.51 Aligned_cols=34 Identities=18% Similarity=0.451 Sum_probs=22.6
Q ss_pred CCCCCccccccccccCceEEeecCcccccccccccccCC
Q psy4350 13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHV 51 (107)
Q Consensus 13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~ 51 (107)
+..+.+|.+|+..|.+--.+...++.| +|..|..
T Consensus 50 ~~~pvRC~~CraylNPf~~~d~~~~~W-----~C~~C~~ 83 (761)
T PLN00162 50 PYDPLRCRTCRAVLNPYCRVDFQAKIW-----ICPFCFQ 83 (761)
T ss_pred CCCCCccCCCcCEECCceEEecCCCEE-----EccCCCC
Confidence 446788999999887754455556666 5555554
No 96
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=24.67 E-value=43 Score=17.96 Aligned_cols=13 Identities=31% Similarity=0.588 Sum_probs=7.5
Q ss_pred CCccccccccccC
Q psy4350 16 KSSCGGCGQPIID 28 (107)
Q Consensus 16 ~~~C~~C~~~i~~ 28 (107)
+.+|..|+++|.+
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 4567777777643
No 97
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.40 E-value=56 Score=25.90 Aligned_cols=9 Identities=22% Similarity=0.434 Sum_probs=4.6
Q ss_pred ccccccccc
Q psy4350 18 SCGGCGQPI 26 (107)
Q Consensus 18 ~C~~C~~~i 26 (107)
.|..|+..+
T Consensus 3 ~Cp~Cg~~n 11 (645)
T PRK14559 3 ICPQCQFEN 11 (645)
T ss_pred cCCCCCCcC
Confidence 455555544
No 98
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=24.37 E-value=37 Score=16.45 Aligned_cols=9 Identities=33% Similarity=0.947 Sum_probs=3.7
Q ss_pred cccccCCCC
Q psy4350 45 QCAHCHVPL 53 (107)
Q Consensus 45 ~C~~C~~~l 53 (107)
.|..|+..|
T Consensus 21 vC~~CG~Vl 29 (43)
T PF08271_consen 21 VCPNCGLVL 29 (43)
T ss_dssp EETTT-BBE
T ss_pred ECCCCCCEe
Confidence 444554444
No 99
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=24.26 E-value=1.1e+02 Score=25.90 Aligned_cols=21 Identities=14% Similarity=0.477 Sum_probs=12.9
Q ss_pred CCCccccccccccCceEEeecCccc
Q psy4350 15 EKSSCGGCGQPIIDRFYLLAVDRQW 39 (107)
Q Consensus 15 ~~~~C~~C~~~i~~~~~~~~~~~~~ 39 (107)
....|.-|+..|. +.+.|..|
T Consensus 14 ~~~~c~iCGd~vg----~~~~Ge~F 34 (1044)
T PLN02915 14 DAKTCRVCGDEVG----VKEDGQPF 34 (1044)
T ss_pred CcchhhccccccC----cCCCCCEE
Confidence 4567888888763 23445554
No 100
>TIGR00105 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.
Probab=24.15 E-value=34 Score=18.68 Aligned_cols=9 Identities=33% Similarity=0.737 Sum_probs=5.4
Q ss_pred ccCCCCcCC
Q psy4350 99 AASEPLLTG 107 (107)
Q Consensus 99 ~~~~p~~~~ 107 (107)
...||+.||
T Consensus 39 s~~HPfyTG 47 (68)
T TIGR00105 39 SKCHPFYTG 47 (68)
T ss_pred CCCcccCCC
Confidence 346677665
No 101
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=23.16 E-value=40 Score=18.44 Aligned_cols=7 Identities=43% Similarity=0.914 Sum_probs=4.2
Q ss_pred CCCCcCC
Q psy4350 101 SEPLLTG 107 (107)
Q Consensus 101 ~~p~~~~ 107 (107)
.||+.||
T Consensus 42 ~HPfytG 48 (69)
T PF01197_consen 42 CHPFYTG 48 (69)
T ss_dssp SSCTTCS
T ss_pred CCEEEcC
Confidence 4666665
No 102
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=23.12 E-value=76 Score=20.65 Aligned_cols=30 Identities=10% Similarity=0.404 Sum_probs=15.7
Q ss_pred ccccCCCCCCCCceeccCCee-ccHHHHhhhC
Q psy4350 46 CAHCHVPLHSELSCFSRHGNI-YCKQDFFRYS 76 (107)
Q Consensus 46 C~~C~~~l~~~~~~~~~~~~~-~C~~~y~~~~ 76 (107)
|..|++...........+..+ .|..|+ +||
T Consensus 6 CEiCG~~i~~~~~v~vegsel~VC~~Ca-k~G 36 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAELTVCDDCA-KFG 36 (165)
T ss_pred eeccccccCCCeeEEeecceeehhHHHH-Hhc
Confidence 666776665331222333333 577777 555
No 103
>PRK00807 50S ribosomal protein L24e; Validated
Probab=23.01 E-value=53 Score=16.90 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=14.4
Q ss_pred CccccccccccCceE---EeecCcccc
Q psy4350 17 SSCGGCGQPIIDRFY---LLAVDRQWH 40 (107)
Q Consensus 17 ~~C~~C~~~i~~~~~---~~~~~~~~H 40 (107)
..|..|+..|+++.- +...|+.|.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 458888888874432 234455554
No 104
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=22.29 E-value=23 Score=15.68 Aligned_cols=12 Identities=33% Similarity=0.564 Sum_probs=6.0
Q ss_pred CccccccccccC
Q psy4350 17 SSCGGCGQPIID 28 (107)
Q Consensus 17 ~~C~~C~~~i~~ 28 (107)
..|.+|+..|..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 358888887644
No 105
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.92 E-value=46 Score=16.32 Aligned_cols=9 Identities=33% Similarity=1.232 Sum_probs=5.1
Q ss_pred ccccccccc
Q psy4350 18 SCGGCGQPI 26 (107)
Q Consensus 18 ~C~~C~~~i 26 (107)
+|..|+..+
T Consensus 5 ~C~~CG~~~ 13 (46)
T PRK00398 5 KCARCGREV 13 (46)
T ss_pred ECCCCCCEE
Confidence 466666644
No 106
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.87 E-value=13 Score=19.21 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=4.4
Q ss_pred cccccCCCCC
Q psy4350 45 QCAHCHVPLH 54 (107)
Q Consensus 45 ~C~~C~~~l~ 54 (107)
+|..|...|.
T Consensus 24 ~C~gC~~~l~ 33 (56)
T PF02591_consen 24 TCSGCHMELP 33 (56)
T ss_pred ccCCCCEEcC
Confidence 3444444443
No 107
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=21.72 E-value=1.4e+02 Score=25.33 Aligned_cols=15 Identities=20% Similarity=0.441 Sum_probs=9.9
Q ss_pred CCCCCCccccccccc
Q psy4350 12 CPEEKSSCGGCGQPI 26 (107)
Q Consensus 12 ~~~~~~~C~~C~~~i 26 (107)
.......|.-|+..|
T Consensus 13 ~~~~~qiCqICGD~v 27 (1079)
T PLN02638 13 KHGGGQVCQICGDNV 27 (1079)
T ss_pred cccCCceeeeccccc
Confidence 344455788888766
No 108
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=20.83 E-value=1.5e+02 Score=15.69 Aligned_cols=42 Identities=17% Similarity=0.331 Sum_probs=22.1
Q ss_pred ccccCCCCCCCC--ceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch
Q psy4350 46 CAHCHVPLHSEL--SCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV 90 (107)
Q Consensus 46 C~~C~~~l~~~~--~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~ 90 (107)
|..|.+.|.... .++-.-.=-||.+|-.. +. ..|-. |++.++
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~-~~CPN--CgGelv 52 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLN-GVCPN--CGGELV 52 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc-CcCcC--CCCccc
Confidence 455555554321 22222223367777777 66 47777 776654
No 109
>KOG3497|consensus
Probab=20.63 E-value=32 Score=18.52 Aligned_cols=12 Identities=42% Similarity=0.700 Sum_probs=7.0
Q ss_pred CccccccccccC
Q psy4350 17 SSCGGCGQPIID 28 (107)
Q Consensus 17 ~~C~~C~~~i~~ 28 (107)
.+|..|++.|.+
T Consensus 5 iRCFtCGKvig~ 16 (69)
T KOG3497|consen 5 IRCFTCGKVIGD 16 (69)
T ss_pred eEeeeccccccc
Confidence 456666666644
No 110
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.43 E-value=68 Score=25.52 Aligned_cols=27 Identities=19% Similarity=-0.003 Sum_probs=19.2
Q ss_pred eeccCCeeccHHHHhh-hCCCCCCCCCCCCc
Q psy4350 59 CFSRHGNIYCKQDFFR-YSQARYPDLPIPKT 88 (107)
Q Consensus 59 ~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~ 88 (107)
+....+.+.|.-|-.. .. ..|.. |+..
T Consensus 404 ~h~~~~~l~Ch~CG~~~~p-~~Cp~--Cgs~ 431 (665)
T PRK14873 404 LPSAGGTPRCRWCGRAAPD-WRCPR--CGSD 431 (665)
T ss_pred EecCCCeeECCCCcCCCcC-ccCCC--CcCC
Confidence 3344567889888666 54 68999 9875
No 111
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=20.08 E-value=41 Score=18.19 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=8.5
Q ss_pred CCccccccccccC
Q psy4350 16 KSSCGGCGQPIID 28 (107)
Q Consensus 16 ~~~C~~C~~~i~~ 28 (107)
+.+|..|+++|.+
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 4567777777743
Done!