Query psy11667
Match_columns 119
No_of_seqs 121 out of 391
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 15:47:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11667.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11667hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3173|consensus 99.9 2.4E-26 5.3E-31 175.8 6.5 69 50-119 99-167 (167)
2 smart00154 ZnF_AN1 AN1-like Zi 99.5 5.8E-15 1.3E-19 89.3 2.2 38 59-97 1-39 (39)
3 PF01428 zf-AN1: AN1-like Zinc 99.1 1.2E-11 2.6E-16 75.5 1.4 38 59-98 1-41 (43)
4 KOG3183|consensus 97.7 9.6E-06 2.1E-10 66.2 -0.2 45 49-93 91-138 (250)
5 COG3582 Predicted nucleic acid 97.6 2.8E-05 6.1E-10 60.0 1.7 38 58-97 99-137 (162)
6 KOG3183|consensus 97.0 0.00027 5.7E-09 57.9 1.1 39 57-97 9-50 (250)
7 PF01363 FYVE: FYVE zinc finge 94.0 0.034 7.4E-07 35.7 1.7 31 54-84 7-39 (69)
8 cd00065 FYVE FYVE domain; Zinc 92.0 0.069 1.5E-06 32.9 0.8 27 57-83 3-31 (57)
9 PF10571 UPF0547: Uncharacteri 91.8 0.086 1.9E-06 29.3 1.0 23 57-80 1-24 (26)
10 smart00064 FYVE Protein presen 91.7 0.1 2.2E-06 33.3 1.4 29 56-84 10-40 (68)
11 KOG1818|consensus 86.1 0.3 6.5E-06 44.8 0.7 44 54-97 163-219 (634)
12 PF15135 UPF0515: Uncharacteri 80.4 0.94 2E-05 37.8 1.4 29 52-81 128-166 (278)
13 PF00130 C1_1: Phorbol esters/ 80.1 1.2 2.5E-05 27.0 1.5 26 54-80 9-38 (53)
14 PF02928 zf-C5HC2: C5HC2 zinc 76.1 1.4 2.9E-05 27.8 0.9 27 59-86 1-29 (54)
15 KOG0320|consensus 72.7 3.7 8.1E-05 32.7 2.8 47 49-95 124-173 (187)
16 KOG1729|consensus 72.5 0.85 1.8E-05 38.1 -0.8 34 54-88 166-202 (288)
17 KOG2807|consensus 70.9 2.7 5.9E-05 36.4 1.8 30 54-83 328-358 (378)
18 PHA00626 hypothetical protein 68.3 2.6 5.7E-05 27.9 1.0 21 58-81 13-34 (59)
19 KOG1819|consensus 67.7 3 6.5E-05 38.6 1.5 29 56-84 901-931 (990)
20 PF13240 zinc_ribbon_2: zinc-r 67.1 3.2 6.9E-05 22.2 1.0 21 58-79 1-22 (23)
21 PRK14890 putative Zn-ribbon RN 64.2 2.8 6.2E-05 27.7 0.5 21 56-79 36-57 (59)
22 COG2888 Predicted Zn-ribbon RN 63.6 2.7 5.9E-05 28.0 0.3 19 57-78 39-58 (61)
23 PF07975 C1_4: TFIIH C1-like d 63.3 3.3 7.1E-05 26.5 0.7 36 59-94 2-48 (51)
24 KOG1812|consensus 59.9 4.7 0.0001 34.6 1.2 32 54-85 304-338 (384)
25 PRK00398 rpoP DNA-directed RNA 59.3 5.7 0.00012 23.8 1.2 31 57-87 4-38 (46)
26 PF02148 zf-UBP: Zn-finger in 58.4 5.8 0.00013 25.2 1.2 23 59-83 1-24 (63)
27 PF13842 Tnp_zf-ribbon_2: DDE_ 57.6 8.6 0.00019 22.0 1.7 27 58-84 2-30 (32)
28 COG3582 Predicted nucleic acid 56.1 6.3 0.00014 30.6 1.2 49 59-109 3-52 (162)
29 PTZ00303 phosphatidylinositol 54.3 6.2 0.00014 38.2 1.1 27 57-83 461-494 (1374)
30 cd04476 RPA1_DBD_C RPA1_DBD_C: 54.1 5.9 0.00013 29.2 0.8 42 53-94 31-81 (166)
31 cd00029 C1 Protein kinase C co 52.6 8.3 0.00018 22.4 1.1 24 56-79 11-37 (50)
32 smart00109 C1 Protein kinase C 52.6 8.9 0.00019 21.9 1.2 25 55-79 10-36 (49)
33 COG1571 Predicted DNA-binding 52.5 7.3 0.00016 34.4 1.2 52 55-106 349-405 (421)
34 PF02318 FYVE_2: FYVE-type zin 52.4 9.9 0.00022 27.1 1.7 33 55-87 53-88 (118)
35 smart00290 ZnF_UBP Ubiquitin C 52.2 4.9 0.00011 24.0 0.1 24 58-84 1-25 (50)
36 TIGR00622 ssl1 transcription f 51.8 13 0.00028 27.3 2.3 36 57-94 56-108 (112)
37 PF13978 DUF4223: Protein of u 51.5 7.1 0.00015 25.5 0.7 18 80-97 19-36 (56)
38 PF03107 C1_2: C1 domain; Int 51.2 12 0.00026 20.8 1.6 21 58-79 2-24 (30)
39 COG1996 RPC10 DNA-directed RNA 50.1 8.6 0.00019 24.5 0.9 33 56-88 6-42 (49)
40 PF05207 zf-CSL: CSL zinc fing 50.0 8 0.00017 24.5 0.8 12 71-82 18-29 (55)
41 PF07649 C1_3: C1-like domain; 49.3 7.9 0.00017 21.3 0.6 23 58-80 2-25 (30)
42 PF03604 DNA_RNApol_7kD: DNA d 48.4 8.8 0.00019 22.2 0.7 22 58-79 2-26 (32)
43 PF01485 IBR: IBR domain; Int 47.7 11 0.00023 22.8 1.1 31 57-87 19-57 (64)
44 PHA02768 hypothetical protein; 47.7 7.9 0.00017 25.1 0.5 13 70-82 4-17 (55)
45 PF13248 zf-ribbon_3: zinc-rib 47.7 11 0.00024 20.3 1.1 21 57-78 3-24 (26)
46 KOG3507|consensus 46.6 5 0.00011 26.8 -0.5 33 51-83 15-50 (62)
47 PRK07218 replication factor A; 46.5 9.3 0.0002 33.5 0.9 21 56-79 297-318 (423)
48 PF10367 Vps39_2: Vacuolar sor 46.0 14 0.0003 24.5 1.6 25 56-80 78-102 (109)
49 PF09723 Zn-ribbon_8: Zinc rib 45.7 12 0.00025 22.3 1.0 23 71-93 5-30 (42)
50 PRK08402 replication factor A; 45.7 10 0.00022 32.5 1.0 30 56-86 212-245 (355)
51 PHA03073 late transcription fa 45.2 4.2 9.2E-05 31.3 -1.2 21 48-68 41-61 (150)
52 PF14471 DUF4428: Domain of un 43.9 8.5 0.00018 24.2 0.2 23 58-80 1-30 (51)
53 PF04438 zf-HIT: HIT zinc fing 43.7 12 0.00025 21.2 0.7 23 57-83 3-26 (30)
54 smart00647 IBR In Between Ring 43.6 15 0.00033 22.2 1.3 32 56-87 18-57 (64)
55 PF00096 zf-C2H2: Zinc finger, 43.5 11 0.00023 18.9 0.5 10 72-81 1-11 (23)
56 KOG1074|consensus 43.4 18 0.0004 34.9 2.4 35 49-83 346-394 (958)
57 PF01780 Ribosomal_L37ae: Ribo 43.1 8.6 0.00019 27.3 0.2 36 52-87 31-70 (90)
58 COG1997 RPL43A Ribosomal prote 41.9 13 0.00029 26.4 0.9 37 51-87 30-70 (89)
59 smart00659 RPOLCX RNA polymera 41.4 13 0.00028 22.8 0.7 29 57-85 3-34 (44)
60 KOG3362|consensus 40.6 13 0.00028 28.9 0.8 28 52-83 114-142 (156)
61 PF10122 Mu-like_Com: Mu-like 40.5 10 0.00022 24.4 0.2 25 56-80 4-34 (51)
62 PF13717 zinc_ribbon_4: zinc-r 40.2 14 0.0003 21.5 0.7 10 71-80 25-35 (36)
63 PF09538 FYDLN_acid: Protein o 39.7 18 0.0004 26.0 1.4 29 55-83 8-39 (108)
64 KOG1842|consensus 39.2 7.5 0.00016 35.0 -0.8 25 57-81 181-207 (505)
65 PF14446 Prok-RING_1: Prokaryo 38.7 22 0.00047 23.0 1.5 25 55-80 4-31 (54)
66 PF01529 zf-DHHC: DHHC palmito 38.6 34 0.00073 24.7 2.7 46 50-100 42-87 (174)
67 PF06750 DiS_P_DiS: Bacterial 38.6 19 0.0004 25.0 1.3 25 54-78 31-66 (92)
68 PF11781 RRN7: RNA polymerase 38.0 17 0.00036 21.4 0.8 23 57-79 9-34 (36)
69 PF13912 zf-C2H2_6: C2H2-type 37.7 16 0.00034 19.0 0.6 12 71-82 1-13 (27)
70 PF13894 zf-C2H2_4: C2H2-type 37.6 15 0.00033 17.7 0.5 9 72-80 1-10 (24)
71 KOG1074|consensus 37.4 23 0.0005 34.2 2.0 48 49-96 598-672 (958)
72 PRK12366 replication factor A; 36.8 15 0.00032 33.5 0.7 31 55-86 531-563 (637)
73 COG1439 Predicted nucleic acid 36.4 15 0.00031 29.0 0.5 30 49-79 132-162 (177)
74 PF01194 RNA_pol_N: RNA polyme 36.1 16 0.00035 24.1 0.6 13 56-68 4-16 (60)
75 PF13824 zf-Mss51: Zinc-finger 35.7 22 0.00047 23.1 1.2 25 58-82 1-27 (55)
76 PF13465 zf-H2C2_2: Zinc-finge 35.4 18 0.00039 19.3 0.6 11 70-80 13-24 (26)
77 PRK04136 rpl40e 50S ribosomal 35.1 22 0.00048 22.7 1.1 25 53-78 11-36 (48)
78 PF15227 zf-C3HC4_4: zinc fing 34.8 22 0.00047 21.1 1.0 22 59-82 1-22 (42)
79 PF09416 UPF1_Zn_bind: RNA hel 34.8 20 0.00044 27.6 1.1 26 58-84 2-28 (152)
80 PLN02569 threonine synthase 34.3 35 0.00076 30.2 2.6 35 52-86 45-80 (484)
81 COG5574 PEX10 RING-finger-cont 34.3 15 0.00032 30.8 0.3 28 56-86 215-243 (271)
82 PF08882 Acetone_carb_G: Aceto 34.0 22 0.00047 26.3 1.1 32 61-95 17-48 (112)
83 smart00661 RPOL9 RNA polymeras 33.6 28 0.00061 20.7 1.4 22 58-79 2-29 (52)
84 PRK04016 DNA-directed RNA poly 33.6 15 0.00033 24.5 0.2 13 56-68 4-16 (62)
85 COG3357 Predicted transcriptio 33.4 16 0.00035 26.3 0.3 18 64-82 52-70 (97)
86 PF09862 DUF2089: Protein of u 32.8 21 0.00047 26.1 0.9 28 59-87 1-29 (113)
87 PRK00464 nrdR transcriptional 32.5 26 0.00055 26.7 1.3 14 72-85 29-43 (154)
88 TIGR00280 L37a ribosomal prote 32.4 22 0.00047 25.3 0.8 34 52-86 31-69 (91)
89 PTZ00255 60S ribosomal protein 32.3 24 0.00053 25.0 1.1 34 51-84 31-68 (90)
90 PF01927 Mut7-C: Mut7-C RNAse 31.8 34 0.00074 25.1 1.8 29 53-81 88-135 (147)
91 PF15549 PGC7_Stella: PGC7/Ste 31.5 27 0.00058 27.2 1.3 20 70-91 122-141 (160)
92 PF14369 zf-RING_3: zinc-finge 31.4 26 0.00056 20.4 0.9 23 58-80 4-31 (35)
93 PF07282 OrfB_Zn_ribbon: Putat 31.4 34 0.00073 21.6 1.5 25 55-79 27-55 (69)
94 PRK05978 hypothetical protein; 31.3 26 0.00057 26.7 1.2 27 54-80 31-62 (148)
95 PRK03976 rpl37ae 50S ribosomal 31.1 25 0.00053 25.0 0.9 31 52-83 32-67 (90)
96 PLN00032 DNA-directed RNA poly 30.9 18 0.0004 24.7 0.2 13 56-68 4-16 (71)
97 KOG2462|consensus 30.3 85 0.0019 26.5 4.1 49 51-101 125-199 (279)
98 PRK12496 hypothetical protein; 30.3 24 0.00051 26.8 0.8 31 49-79 120-152 (164)
99 TIGR00627 tfb4 transcription f 29.1 39 0.00085 28.0 1.9 28 55-84 241-269 (279)
100 PF13771 zf-HC5HC2H: PHD-like 29.1 39 0.00084 22.1 1.6 24 50-75 30-53 (90)
101 PRK06386 replication factor A; 28.9 25 0.00055 30.3 0.8 20 56-78 236-256 (358)
102 PF13832 zf-HC5HC2H_2: PHD-zin 28.6 39 0.00085 23.1 1.6 20 54-75 53-72 (110)
103 PF14835 zf-RING_6: zf-RING of 28.0 32 0.0007 23.1 1.0 25 57-83 8-33 (65)
104 COG0675 Transposase and inacti 27.5 36 0.00078 26.2 1.4 24 54-79 307-331 (364)
105 TIGR02098 MJ0042_CXXC MJ0042 f 27.3 28 0.00061 19.7 0.6 9 72-80 26-35 (38)
106 smart00834 CxxC_CXXC_SSSS Puta 26.3 31 0.00068 19.4 0.7 23 71-93 5-30 (41)
107 PF02207 zf-UBR: Putative zinc 26.1 38 0.00083 22.0 1.1 15 71-85 50-71 (71)
108 COG5432 RAD18 RING-finger-cont 25.8 23 0.00051 30.6 0.1 26 56-83 25-50 (391)
109 PRK00432 30S ribosomal protein 25.4 38 0.00083 21.1 1.0 28 54-81 18-48 (50)
110 KOG0193|consensus 25.3 26 0.00057 32.7 0.3 49 59-112 192-243 (678)
111 KOG3497|consensus 24.9 26 0.00056 23.7 0.1 13 56-68 4-16 (69)
112 COG1933 Archaeal DNA polymeras 24.5 28 0.0006 29.0 0.3 26 54-79 165-192 (253)
113 PF06689 zf-C4_ClpX: ClpX C4-t 24.1 31 0.00068 20.5 0.4 11 57-67 2-12 (41)
114 smart00132 LIM Zinc-binding do 24.0 44 0.00094 17.8 0.9 6 59-64 2-7 (39)
115 PF09779 Ima1_N: Ima1 N-termin 23.4 47 0.001 24.3 1.3 22 58-79 2-29 (131)
116 TIGR02300 FYDLN_acid conserved 23.4 47 0.001 25.1 1.3 26 55-80 8-36 (129)
117 COG1644 RPB10 DNA-directed RNA 23.2 27 0.00059 23.4 -0.0 13 56-68 4-16 (63)
118 TIGR02605 CxxC_CxxC_SSSS putat 22.8 41 0.00089 20.1 0.7 23 71-93 5-30 (52)
119 PF04236 Transp_Tc5_C: Tc5 tra 22.2 40 0.00088 22.2 0.7 32 57-92 28-63 (63)
120 PF08646 Rep_fac-A_C: Replicat 22.1 29 0.00062 25.0 -0.1 32 55-86 17-54 (146)
121 COG3877 Uncharacterized protei 22.0 59 0.0013 24.2 1.5 33 54-87 4-37 (122)
122 TIGR00373 conserved hypothetic 21.6 39 0.00085 25.4 0.6 26 54-79 107-137 (158)
123 COG1656 Uncharacterized conser 20.9 42 0.00091 26.2 0.6 16 53-68 94-109 (165)
124 PF06467 zf-FCS: MYM-type Zinc 20.8 40 0.00086 19.3 0.4 15 54-68 4-18 (43)
125 PF14803 Nudix_N_2: Nudix N-te 20.7 49 0.0011 19.2 0.8 11 58-68 2-12 (34)
126 PF00412 LIM: LIM domain; Int 20.7 34 0.00074 20.3 0.1 25 58-83 28-52 (58)
127 PF08073 CHDNT: CHDNT (NUC034) 20.6 36 0.00079 22.1 0.2 20 98-117 21-40 (55)
128 PF12773 DZR: Double zinc ribb 20.4 70 0.0015 18.9 1.4 26 54-79 10-38 (50)
129 PF00628 PHD: PHD-finger; Int 20.4 66 0.0014 18.8 1.3 22 58-79 1-23 (51)
130 PRK08329 threonine synthase; V 20.2 61 0.0013 26.9 1.5 31 57-87 2-32 (347)
No 1
>KOG3173|consensus
Probab=99.93 E-value=2.4e-26 Score=175.78 Aligned_cols=69 Identities=45% Similarity=0.962 Sum_probs=64.9
Q ss_pred ccCCcCCCcccccccccccccceeeccCCcccCCCCCCCCCCCccccHHhhHHHHHHhCCcccccccccC
Q psy11667 50 KKTKHKRSRCAQCNAKLTVCSSFTCRCRKLFCPRHRHPEEHACTFDYKAYGRHLLAATNPLVVADKVVRI 119 (119)
Q Consensus 50 ~~~~~~k~RC~~C~kkl~Ls~~f~CrCg~~FC~~HR~pe~H~C~fDyk~~gr~~Lak~NP~v~~~Kl~ki 119 (119)
....+.++||+.|+|++|| ++|.||||++||..|||+|.|+|.||||.+||+.|+++||+|+++||.||
T Consensus 99 ~~~~~~~~rC~~C~kk~gl-tgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 99 ESKPKKKKRCFKCRKKVGL-TGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKANPVVKADKLQKI 167 (167)
T ss_pred ccccccchhhhhhhhhhcc-cccccccCCcccccccCCccccccccHHHHHHHHHHHhCCeeeccccccC
Confidence 4455677889999999999 78999999999999999999999999999999999999999999999998
No 2
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.51 E-value=5.8e-15 Score=89.32 Aligned_cols=38 Identities=50% Similarity=1.170 Sum_probs=36.1
Q ss_pred ccccccccccccceeec-cCCcccCCCCCCCCCCCccccH
Q psy11667 59 CAQCNAKLTVCSSFTCR-CRKLFCPRHRHPEEHACTFDYK 97 (119)
Q Consensus 59 C~~C~kkl~Ls~~f~Cr-Cg~~FC~~HR~pe~H~C~fDyk 97 (119)
|+.|+++++| ++|+|+ |+++||+.||++|+|+|++||+
T Consensus 1 C~~C~~~~~l-~~f~C~~C~~~FC~~HR~~e~H~C~~~~k 39 (39)
T smart00154 1 CHFCRKKVGL-TGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39 (39)
T ss_pred CcccCCcccc-cCeECCccCCccccccCCccccCCccccC
Confidence 7889999999 699999 9999999999999999999985
No 3
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.15 E-value=1.2e-11 Score=75.51 Aligned_cols=38 Identities=42% Similarity=0.947 Sum_probs=27.7
Q ss_pred ccc--cccccccccceeec-cCCcccCCCCCCCCCCCccccHH
Q psy11667 59 CAQ--CNAKLTVCSSFTCR-CRKLFCPRHRHPEEHACTFDYKA 98 (119)
Q Consensus 59 C~~--C~kkl~Ls~~f~Cr-Cg~~FC~~HR~pe~H~C~fDyk~ 98 (119)
|+. |++++.| +|.|+ |+..||.+||++++|.|+++++.
T Consensus 1 C~~~~C~~~~~~--~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDFL--PFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCTS--HEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccCC--CeECCCCCcccCccccCccccCCcchhhc
Confidence 566 9998875 99999 99999999999999999998763
No 4
>KOG3183|consensus
Probab=97.65 E-value=9.6e-06 Score=66.22 Aligned_cols=45 Identities=40% Similarity=0.927 Sum_probs=41.1
Q ss_pred cccCCcCCCcccc--cccccccccceeec-cCCcccCCCCCCCCCCCc
Q psy11667 49 VKKTKHKRSRCAQ--CNAKLTVCSSFTCR-CRKLFCPRHRHPEEHACT 93 (119)
Q Consensus 49 ~~~~~~~k~RC~~--C~kkl~Ls~~f~Cr-Cg~~FC~~HR~pe~H~C~ 93 (119)
..+++..+++|.. |++++.+++.+.|+ |+..||.+||++-+|.|.
T Consensus 91 ~~~~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 91 QKKRKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred hhhcccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 4567788889997 99999998889999 999999999999999998
No 5
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=97.60 E-value=2.8e-05 Score=60.04 Aligned_cols=38 Identities=29% Similarity=0.504 Sum_probs=32.0
Q ss_pred cccccccccccccceeec-cCCcccCCCCCCCCCCCccccH
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKLFCPRHRHPEEHACTFDYK 97 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~HR~pe~H~C~fDyk 97 (119)
.|..|++..+| .++|. |++.||+.||+++.|+|.+-..
T Consensus 99 ~~~~~g~~s~l--~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 99 TPQCTGKGSTL--AGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred cceeccCCccc--cccccCCCCcceeceecccccccccHHH
Confidence 34447777777 89999 9999999999999999997543
No 6
>KOG3183|consensus
Probab=96.99 E-value=0.00027 Score=57.90 Aligned_cols=39 Identities=31% Similarity=0.761 Sum_probs=32.9
Q ss_pred Cccc--ccccccccccceeec-cCCcccCCCCCCCCCCCccccH
Q psy11667 57 SRCA--QCNAKLTVCSSFTCR-CRKLFCPRHRHPEEHACTFDYK 97 (119)
Q Consensus 57 ~RC~--~C~kkl~Ls~~f~Cr-Cg~~FC~~HR~pe~H~C~fDyk 97 (119)
..|. .|+..-- ++|+|- |+..||+.||.-+.|.|++-+.
T Consensus 9 kHCs~~~CkqlDF--LPf~Cd~C~~~FC~eHrsye~H~Cp~~~~ 50 (250)
T KOG3183|consen 9 KHCSVPYCKQLDF--LPFKCDGCSGIFCLEHRSYESHHCPKGLR 50 (250)
T ss_pred cccCcchhhhccc--cceeeCCccchhhhccchHhhcCCCcccc
Confidence 3677 5887543 499999 9999999999999999998665
No 7
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=94.00 E-value=0.034 Score=35.66 Aligned_cols=31 Identities=26% Similarity=0.773 Sum_probs=17.5
Q ss_pred cCCCcccccccccccc-cceeec-cCCcccCCC
Q psy11667 54 HKRSRCAQCNAKLTVC-SSFTCR-CRKLFCPRH 84 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls-~~f~Cr-Cg~~FC~~H 84 (119)
.....|..|+++.++. .-..|| ||.+||+.+
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCC
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCch
Confidence 4456899999998874 578999 999999654
No 8
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=91.98 E-value=0.069 Score=32.86 Aligned_cols=27 Identities=33% Similarity=1.005 Sum_probs=22.7
Q ss_pred Ccccccccccccc-cceeec-cCCcccCC
Q psy11667 57 SRCAQCNAKLTVC-SSFTCR-CRKLFCPR 83 (119)
Q Consensus 57 ~RC~~C~kkl~Ls-~~f~Cr-Cg~~FC~~ 83 (119)
..|..|++.+++. ....|+ ||.+||..
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~ 31 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSK 31 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChH
Confidence 5799999988874 488999 99999874
No 9
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=91.82 E-value=0.086 Score=29.34 Aligned_cols=23 Identities=30% Similarity=0.706 Sum_probs=20.2
Q ss_pred Ccccccccccccccceeec-cCCcc
Q psy11667 57 SRCAQCNAKLTVCSSFTCR-CRKLF 80 (119)
Q Consensus 57 ~RC~~C~kkl~Ls~~f~Cr-Cg~~F 80 (119)
.+|..|++.+.+ ....|- ||+.|
T Consensus 1 K~CP~C~~~V~~-~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPE-SAKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchh-hcCcCCCCCCCC
Confidence 379999999988 788999 99887
No 10
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1818|consensus
Probab=86.05 E-value=0.3 Score=44.84 Aligned_cols=44 Identities=23% Similarity=0.658 Sum_probs=33.4
Q ss_pred cCCCcccccccccccc-cceeec-cCCcccCCCC-----------CCCCCCCccccH
Q psy11667 54 HKRSRCAQCNAKLTVC-SSFTCR-CRKLFCPRHR-----------HPEEHACTFDYK 97 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls-~~f~Cr-Cg~~FC~~HR-----------~pe~H~C~fDyk 97 (119)
.....|..|+.+.++. ....|| ||.+||..|= |-+.--|..+|.
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E 219 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYE 219 (634)
T ss_pred ccccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHH
Confidence 4456899999999985 367999 9999999884 334556766664
No 12
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=80.36 E-value=0.94 Score=37.83 Aligned_cols=29 Identities=31% Similarity=0.855 Sum_probs=23.1
Q ss_pred CCcCCCcccccccc---------cccccceeec-cCCccc
Q psy11667 52 TKHKRSRCAQCNAK---------LTVCSSFTCR-CRKLFC 81 (119)
Q Consensus 52 ~~~~k~RC~~C~kk---------l~Ls~~f~Cr-Cg~~FC 81 (119)
..+..+||..|+++ +|+ .-|.|. |+..|=
T Consensus 128 ~rKeVSRCr~C~~rYDPVP~dkmwG~-aef~C~~C~h~F~ 166 (278)
T PF15135_consen 128 QRKEVSRCRKCRKRYDPVPCDKMWGI-AEFHCPKCRHNFR 166 (278)
T ss_pred cccccccccccccccCCCccccccce-eeeecccccccch
Confidence 35667899999876 777 689997 999873
No 13
>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=80.10 E-value=1.2 Score=27.00 Aligned_cols=26 Identities=19% Similarity=0.589 Sum_probs=18.8
Q ss_pred cCCCccccccccc---ccccceeec-cCCcc
Q psy11667 54 HKRSRCAQCNAKL---TVCSSFTCR-CRKLF 80 (119)
Q Consensus 54 ~~k~RC~~C~kkl---~Ls~~f~Cr-Cg~~F 80 (119)
.....|..|++.+ ++ .++.|. |+..+
T Consensus 9 ~~~~~C~~C~~~i~g~~~-~g~~C~~C~~~~ 38 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGK-QGYRCSWCGLVC 38 (53)
T ss_dssp SSTEB-TTSSSBECSSSS-CEEEETTTT-EE
T ss_pred CCCCCCcccCcccCCCCC-CeEEECCCCChH
Confidence 3456899999988 44 799999 98763
No 14
>PF02928 zf-C5HC2: C5HC2 zinc finger; InterPro: IPR004198 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 predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [], and may have a DNA binding function. The mouse jumonji protein is required for neural tube formation, and is essential for normal heart development. It also plays a role in the down-regulation of cell proliferation signalling. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005634 nucleus
Probab=76.09 E-value=1.4 Score=27.78 Aligned_cols=27 Identities=41% Similarity=0.926 Sum_probs=22.9
Q ss_pred ccccccccccccceeecc--CCcccCCCCC
Q psy11667 59 CAQCNAKLTVCSSFTCRC--RKLFCPRHRH 86 (119)
Q Consensus 59 C~~C~kkl~Ls~~f~CrC--g~~FC~~HR~ 86 (119)
|..|+.-.-| ..+.|.| +.++|..|-.
T Consensus 1 C~~Ck~~~yL-S~v~C~C~~~~~~CL~H~~ 29 (54)
T PF02928_consen 1 CSICKAYCYL-SAVTCSCKPDKVVCLRHAK 29 (54)
T ss_pred CcccCCchhh-cccccCCCCCcEEccccch
Confidence 7789998888 6889997 8899999954
No 15
>KOG0320|consensus
Probab=72.71 E-value=3.7 Score=32.68 Aligned_cols=47 Identities=15% Similarity=0.396 Sum_probs=27.8
Q ss_pred cccCCcCCCcccccccccccccceeeccCCcccCC---CCCCCCCCCccc
Q psy11667 49 VKKTKHKRSRCAQCNAKLTVCSSFTCRCRKLFCPR---HRHPEEHACTFD 95 (119)
Q Consensus 49 ~~~~~~~k~RC~~C~kkl~Ls~~f~CrCg~~FC~~---HR~pe~H~C~fD 95 (119)
.+..+.....|..|-..+.--..+.=+||.+||.. -=+...|.|+.=
T Consensus 124 ~~~~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C 173 (187)
T KOG0320|consen 124 DPLRKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTC 173 (187)
T ss_pred cccccccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCc
Confidence 34445556789998654443234666799999964 223334555543
No 16
>KOG1729|consensus
Probab=72.48 E-value=0.85 Score=38.08 Aligned_cols=34 Identities=21% Similarity=0.679 Sum_probs=26.4
Q ss_pred cCCCccccccc-ccccc-cceeec-cCCcccCCCCCCC
Q psy11667 54 HKRSRCAQCNA-KLTVC-SSFTCR-CRKLFCPRHRHPE 88 (119)
Q Consensus 54 ~~k~RC~~C~k-kl~Ls-~~f~Cr-Cg~~FC~~HR~pe 88 (119)
...+.|..|.+ .-.|+ .--+|| ||.+||. |....
T Consensus 166 ~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n 202 (288)
T KOG1729|consen 166 SEATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRN 202 (288)
T ss_pred ccceecccCCCccccHHHHHHHHHhcchHhhh-hhhcC
Confidence 35679999999 66664 467899 9999999 76554
No 17
>KOG2807|consensus
Probab=70.95 E-value=2.7 Score=36.44 Aligned_cols=30 Identities=23% Similarity=0.788 Sum_probs=23.1
Q ss_pred cCCCcccccccccccccceeec-cCCcccCC
Q psy11667 54 HKRSRCAQCNAKLTVCSSFTCR-CRKLFCPR 83 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~ 83 (119)
...++|+.|.-.+.-+..|.|. |.++||..
T Consensus 328 ~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 328 NGSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CCCcceeeeccccCCCCcEEchhccceeecc
Confidence 4556799995544444799999 99999974
No 18
>PHA00626 hypothetical protein
Probab=68.31 E-value=2.6 Score=27.88 Aligned_cols=21 Identities=10% Similarity=0.195 Sum_probs=14.4
Q ss_pred cccccccccccccceeec-cCCccc
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKLFC 81 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~FC 81 (119)
||.+|++. ++.|.|. ||+.|-
T Consensus 13 rcg~cr~~---snrYkCkdCGY~ft 34 (59)
T PHA00626 13 KEKTMRGW---SDDYVCCDCGYNDS 34 (59)
T ss_pred eeceeccc---CcceEcCCCCCeec
Confidence 55666653 3679999 987774
No 19
>KOG1819|consensus
Probab=67.65 E-value=3 Score=38.61 Aligned_cols=29 Identities=24% Similarity=0.808 Sum_probs=20.9
Q ss_pred CCcccccccccccc-cceeec-cCCcccCCC
Q psy11667 56 RSRCAQCNAKLTVC-SSFTCR-CRKLFCPRH 84 (119)
Q Consensus 56 k~RC~~C~kkl~Ls-~~f~Cr-Cg~~FC~~H 84 (119)
-.+|..|....... ....|| ||++||.+-
T Consensus 901 a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 901 AEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred chhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 45888888755432 356899 999999763
No 20
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=67.05 E-value=3.2 Score=22.22 Aligned_cols=21 Identities=24% Similarity=0.651 Sum_probs=14.3
Q ss_pred cccccccccccccceeec-cCCc
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKL 79 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~ 79 (119)
+|..|+..+.- ....|. ||..
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC-cCcchhhhCCc
Confidence 47778888766 555577 7653
No 21
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=64.19 E-value=2.8 Score=27.70 Aligned_cols=21 Identities=29% Similarity=0.751 Sum_probs=13.3
Q ss_pred CCcccccccccccccceeec-cCCc
Q psy11667 56 RSRCAQCNAKLTVCSSFTCR-CRKL 79 (119)
Q Consensus 56 k~RC~~C~kkl~Ls~~f~Cr-Cg~~ 79 (119)
-.||..||+ +++.|.|- ||+.
T Consensus 36 I~RC~~CRk---~~~~Y~CP~CGF~ 57 (59)
T PRK14890 36 IYRCEKCRK---QSNPYTCPKCGFE 57 (59)
T ss_pred EeechhHHh---cCCceECCCCCCc
Confidence 346767766 33578885 8763
No 22
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.56 E-value=2.7 Score=28.01 Aligned_cols=19 Identities=32% Similarity=0.936 Sum_probs=11.4
Q ss_pred Ccccccccccccccceeec-cCC
Q psy11667 57 SRCAQCNAKLTVCSSFTCR-CRK 78 (119)
Q Consensus 57 ~RC~~C~kkl~Ls~~f~Cr-Cg~ 78 (119)
.||..||+ |++.|.|- ||+
T Consensus 39 ~Rc~~CRk---~g~~Y~Cp~CGF 58 (61)
T COG2888 39 YRCAKCRK---LGNPYRCPKCGF 58 (61)
T ss_pred ehhhhHHH---cCCceECCCcCc
Confidence 45666665 33577774 775
No 23
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=63.33 E-value=3.3 Score=26.46 Aligned_cols=36 Identities=28% Similarity=0.694 Sum_probs=17.1
Q ss_pred ccccccccccc-------cceeec-cCCcccCC---CCCCCCCCCcc
Q psy11667 59 CAQCNAKLTVC-------SSFTCR-CRKLFCPR---HRHPEEHACTF 94 (119)
Q Consensus 59 C~~C~kkl~Ls-------~~f~Cr-Cg~~FC~~---HR~pe~H~C~f 94 (119)
|+.|.+.+... ..|.|. |+..||.. --+-.-|+|++
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPG 48 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPG 48 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSST
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcC
Confidence 66676666542 479999 99999863 22233377764
No 24
>KOG1812|consensus
Probab=59.90 E-value=4.7 Score=34.56 Aligned_cols=32 Identities=25% Similarity=0.744 Sum_probs=25.9
Q ss_pred cCCCcccccccccccc---cceeeccCCcccCCCC
Q psy11667 54 HKRSRCAQCNAKLTVC---SSFTCRCRKLFCPRHR 85 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls---~~f~CrCg~~FC~~HR 85 (119)
+.-.+|..|+-.+.++ +-++||||..||..=.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 4556899999877775 5789999999998766
No 25
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=59.26 E-value=5.7 Score=23.85 Aligned_cols=31 Identities=23% Similarity=0.620 Sum_probs=21.4
Q ss_pred Ccccccccccccc---cceeec-cCCcccCCCCCC
Q psy11667 57 SRCAQCNAKLTVC---SSFTCR-CRKLFCPRHRHP 87 (119)
Q Consensus 57 ~RC~~C~kkl~Ls---~~f~Cr-Cg~~FC~~HR~p 87 (119)
.+|..|+..+.+. ..+.|. ||..+--++|-+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKERPP 38 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccCCC
Confidence 4788888876442 267888 888777666643
No 26
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=58.45 E-value=5.8 Score=25.24 Aligned_cols=23 Identities=26% Similarity=0.778 Sum_probs=15.0
Q ss_pred ccccccccccccceeec-cCCcccCC
Q psy11667 59 CAQCNAKLTVCSSFTCR-CRKLFCPR 83 (119)
Q Consensus 59 C~~C~kkl~Ls~~f~Cr-Cg~~FC~~ 83 (119)
|..|+.. +- .-+.|- ||.++|..
T Consensus 1 C~~C~~~-~~-~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NS-NLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SS-SEEEETTTS-EEETT
T ss_pred CCCCCCc-CC-ceEEeCCCCcccccC
Confidence 5667755 22 457799 99999994
No 27
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=57.62 E-value=8.6 Score=22.00 Aligned_cols=27 Identities=26% Similarity=0.711 Sum_probs=19.1
Q ss_pred cccccccccc-cccceeec-cCCcccCCC
Q psy11667 58 RCAQCNAKLT-VCSSFTCR-CRKLFCPRH 84 (119)
Q Consensus 58 RC~~C~kkl~-Ls~~f~Cr-Cg~~FC~~H 84 (119)
||..|.++-. -.+.|.|. |+-..|..|
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVEP 30 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCCC
Confidence 6777876432 22689999 987788776
No 28
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=56.09 E-value=6.3 Score=30.62 Aligned_cols=49 Identities=6% Similarity=-0.023 Sum_probs=31.5
Q ss_pred ccccccccccccceeec-cCCcccCCCCCCCCCCCccccHHhhHHHHHHhCC
Q psy11667 59 CAQCNAKLTVCSSFTCR-CRKLFCPRHRHPEEHACTFDYKAYGRHLLAATNP 109 (119)
Q Consensus 59 C~~C~kkl~Ls~~f~Cr-Cg~~FC~~HR~pe~H~C~fDyk~~gr~~Lak~NP 109 (119)
|..|...+.| ++.|. |+.+||..|++.-.|.|.+--..-.|..|++.-|
T Consensus 3 ~~s~~~~~~l--P~r~~~~~kv~s~~~~~~~~~~f~~~i~~~~r~~i~k~~~ 52 (162)
T COG3582 3 RDSRVSETRL--PSRGNITAKVSSTDNSLTLFSPFKLFIQLCDRKKIKKPDP 52 (162)
T ss_pred ccccceeccC--CccccceeeeccCccccccccccchhhhhhhhhccccCCC
Confidence 3445556666 77888 8888888888888888876423333444444433
No 29
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=54.26 E-value=6.2 Score=38.25 Aligned_cols=27 Identities=22% Similarity=0.673 Sum_probs=19.9
Q ss_pred Cccccccccccc------ccceeec-cCCcccCC
Q psy11667 57 SRCAQCNAKLTV------CSSFTCR-CRKLFCPR 83 (119)
Q Consensus 57 ~RC~~C~kkl~L------s~~f~Cr-Cg~~FC~~ 83 (119)
..|..|+++-.. .....|| ||.+||..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~ 494 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVF 494 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCcc
Confidence 469999997752 1356799 99988754
No 30
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=54.10 E-value=5.9 Score=29.18 Aligned_cols=42 Identities=24% Similarity=0.483 Sum_probs=28.8
Q ss_pred CcCCCcccccccccccc--cceeec-cCCcc-cCCCCCC-----CCCCCcc
Q psy11667 53 KHKRSRCAQCNAKLTVC--SSFTCR-CRKLF-CPRHRHP-----EEHACTF 94 (119)
Q Consensus 53 ~~~k~RC~~C~kkl~Ls--~~f~Cr-Cg~~F-C~~HR~p-----e~H~C~f 94 (119)
.-.-..|..|+|||... ..|.|. |+..+ =..+||- .||....
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~ 81 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTGEA 81 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCCCE
Confidence 34445788899999763 368999 88875 4566664 5566553
No 31
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=52.63 E-value=8.3 Score=22.40 Aligned_cols=24 Identities=17% Similarity=0.499 Sum_probs=18.7
Q ss_pred CCccccccccccc--ccceeec-cCCc
Q psy11667 56 RSRCAQCNAKLTV--CSSFTCR-CRKL 79 (119)
Q Consensus 56 k~RC~~C~kkl~L--s~~f~Cr-Cg~~ 79 (119)
...|..|++.+.. ..+++|. |+..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCc
Confidence 4579999998774 3799999 8654
No 32
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=52.60 E-value=8.9 Score=21.95 Aligned_cols=25 Identities=20% Similarity=0.650 Sum_probs=18.4
Q ss_pred CCCcccccccccccc-cceeec-cCCc
Q psy11667 55 KRSRCAQCNAKLTVC-SSFTCR-CRKL 79 (119)
Q Consensus 55 ~k~RC~~C~kkl~Ls-~~f~Cr-Cg~~ 79 (119)
....|..|++.+... .+++|. |+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~ 36 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVK 36 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCch
Confidence 355799999988753 388898 7654
No 33
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=52.48 E-value=7.3 Score=34.41 Aligned_cols=52 Identities=13% Similarity=0.349 Sum_probs=29.3
Q ss_pred CCCcccccccccccc--cceeec-cCCcccCCCCCCCCCCCc--cccHHhhHHHHHH
Q psy11667 55 KRSRCAQCNAKLTVC--SSFTCR-CRKLFCPRHRHPEEHACT--FDYKAYGRHLLAA 106 (119)
Q Consensus 55 ~k~RC~~C~kkl~Ls--~~f~Cr-Cg~~FC~~HR~pe~H~C~--fDyk~~gr~~Lak 106 (119)
.+.+|..|+..+.-. ++|.|+ ||..+=..-+..-.++=. +++...+|..|.|
T Consensus 349 ~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arRHLsk 405 (421)
T COG1571 349 VNPVCPRCGGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARRHLSK 405 (421)
T ss_pred cCCCCCccCCchhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhhhccC
Confidence 345999999876543 499999 987654333222222221 2234455655544
No 34
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=52.37 E-value=9.9 Score=27.07 Aligned_cols=33 Identities=18% Similarity=0.515 Sum_probs=24.8
Q ss_pred CCCcccccccccccc--cceeec-cCCcccCCCCCC
Q psy11667 55 KRSRCAQCNAKLTVC--SSFTCR-CRKLFCPRHRHP 87 (119)
Q Consensus 55 ~k~RC~~C~kkl~Ls--~~f~Cr-Cg~~FC~~HR~p 87 (119)
....|..|.+.+|+. .+..|. |+..+|.+=+.-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 456899999988874 488999 999999876654
No 35
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=52.22 E-value=4.9 Score=23.96 Aligned_cols=24 Identities=29% Similarity=0.755 Sum_probs=17.8
Q ss_pred cccccccccccccceeec-cCCcccCCC
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKLFCPRH 84 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~H 84 (119)
||..|..... -+.|- |+.++|...
T Consensus 1 ~C~~C~~~~~---l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIEN---LWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcCC---eEEecCCCCcccCCC
Confidence 6888886443 46788 999999764
No 36
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.77 E-value=13 Score=27.28 Aligned_cols=36 Identities=25% Similarity=0.722 Sum_probs=25.1
Q ss_pred Ccccccccccc-----------cccceeec-cCCccc-----CCCCCCCCCCCcc
Q psy11667 57 SRCAQCNAKLT-----------VCSSFTCR-CRKLFC-----PRHRHPEEHACTF 94 (119)
Q Consensus 57 ~RC~~C~kkl~-----------Ls~~f~Cr-Cg~~FC-----~~HR~pe~H~C~f 94 (119)
..|+.|.+.+. .+..|.|. |...|| -.|= .-|+|++
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe--~Lh~CPG 108 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE--SLHCCPG 108 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh--hccCCcC
Confidence 35999988553 23579999 999999 4454 3377764
No 37
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=51.46 E-value=7.1 Score=25.53 Aligned_cols=18 Identities=33% Similarity=0.840 Sum_probs=16.1
Q ss_pred ccCCCCCCCCCCCccccH
Q psy11667 80 FCPRHRHPEEHACTFDYK 97 (119)
Q Consensus 80 FC~~HR~pe~H~C~fDyk 97 (119)
-|.-|-|..+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999995
No 38
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=51.22 E-value=12 Score=20.77 Aligned_cols=21 Identities=24% Similarity=0.591 Sum_probs=16.3
Q ss_pred ccccccccccccc-ceeec-cCCc
Q psy11667 58 RCAQCNAKLTVCS-SFTCR-CRKL 79 (119)
Q Consensus 58 RC~~C~kkl~Ls~-~f~Cr-Cg~~ 79 (119)
.|..|++++.- . .|.|. |+..
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~c~f~ 24 (30)
T PF03107_consen 2 WCDVCRRKIDG-FYFYHCSECCFT 24 (30)
T ss_pred CCCCCCCCcCC-CEeEEeCCCCCe
Confidence 58899998876 5 88998 7644
No 39
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=50.06 E-value=8.6 Score=24.48 Aligned_cols=33 Identities=18% Similarity=0.519 Sum_probs=24.5
Q ss_pred CCcccccccccccc---cceeec-cCCcccCCCCCCC
Q psy11667 56 RSRCAQCNAKLTVC---SSFTCR-CRKLFCPRHRHPE 88 (119)
Q Consensus 56 k~RC~~C~kkl~Ls---~~f~Cr-Cg~~FC~~HR~pe 88 (119)
..+|..|++.+.+. .+..|. ||.-.--+-|-+.
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R~~~ 42 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSRILVKERPKV 42 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcEEEEeccCCc
Confidence 45899999988742 588999 9887766666553
No 40
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=50.01 E-value=8 Score=24.53 Aligned_cols=12 Identities=42% Similarity=0.877 Sum_probs=9.9
Q ss_pred ceeeccCCcccC
Q psy11667 71 SFTCRCRKLFCP 82 (119)
Q Consensus 71 ~f~CrCg~~FC~ 82 (119)
.+.||||..|-.
T Consensus 18 ~y~CRCG~~f~i 29 (55)
T PF05207_consen 18 SYPCRCGGEFEI 29 (55)
T ss_dssp EEEETTSSEEEE
T ss_pred EEcCCCCCEEEE
Confidence 788999998753
No 41
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=49.34 E-value=7.9 Score=21.29 Aligned_cols=23 Identities=22% Similarity=0.582 Sum_probs=8.6
Q ss_pred cccccccccccccceeec-cCCcc
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKLF 80 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~F 80 (119)
+|..|++.+.....|.|. |.+.+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 688999977643589999 87664
No 42
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=48.41 E-value=8.8 Score=22.18 Aligned_cols=22 Identities=23% Similarity=0.738 Sum_probs=12.7
Q ss_pred cccccccccccc--cceeec-cCCc
Q psy11667 58 RCAQCNAKLTVC--SSFTCR-CRKL 79 (119)
Q Consensus 58 RC~~C~kkl~Ls--~~f~Cr-Cg~~ 79 (119)
.|..|+..+.|. ....|+ ||+-
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCe
Confidence 366777766653 356777 7654
No 43
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=47.70 E-value=11 Score=22.84 Aligned_cols=31 Identities=29% Similarity=0.686 Sum_probs=18.9
Q ss_pred Ccccc--cccccccc---cc--eeec-cCCcccCCCCCC
Q psy11667 57 SRCAQ--CNAKLTVC---SS--FTCR-CRKLFCPRHRHP 87 (119)
Q Consensus 57 ~RC~~--C~kkl~Ls---~~--f~Cr-Cg~~FC~~HR~p 87 (119)
..|.. |...+... .. +.|. |+..||..++.+
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcc
Confidence 37876 87655442 23 7899 999999998865
No 44
>PHA02768 hypothetical protein; Provisional
Probab=47.69 E-value=7.9 Score=25.11 Aligned_cols=13 Identities=15% Similarity=0.815 Sum_probs=10.1
Q ss_pred cceeec-cCCcccC
Q psy11667 70 SSFTCR-CRKLFCP 82 (119)
Q Consensus 70 ~~f~Cr-Cg~~FC~ 82 (119)
.||.|. ||..|-.
T Consensus 4 ~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 4 LGYECPICGEIYIK 17 (55)
T ss_pred cccCcchhCCeecc
Confidence 588888 8888754
No 45
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=47.68 E-value=11 Score=20.27 Aligned_cols=21 Identities=24% Similarity=0.654 Sum_probs=13.9
Q ss_pred Ccccccccccccccceeec-cCC
Q psy11667 57 SRCAQCNAKLTVCSSFTCR-CRK 78 (119)
Q Consensus 57 ~RC~~C~kkl~Ls~~f~Cr-Cg~ 78 (119)
..|..|++.+.. ....|. ||.
T Consensus 3 ~~Cp~Cg~~~~~-~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP-DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc-ccccChhhCC
Confidence 468888886655 555676 664
No 46
>KOG3507|consensus
Probab=46.61 E-value=5 Score=26.80 Aligned_cols=33 Identities=21% Similarity=0.430 Sum_probs=23.7
Q ss_pred cCCcCCCcccccccccccc--cceeec-cCCcccCC
Q psy11667 51 KTKHKRSRCAQCNAKLTVC--SSFTCR-CRKLFCPR 83 (119)
Q Consensus 51 ~~~~~k~RC~~C~kkl~Ls--~~f~Cr-Cg~~FC~~ 83 (119)
....-..-|.-|+.+..|. ..+.|| ||+-.--+
T Consensus 15 r~~~miYiCgdC~~en~lk~~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLKRGDVIRCRECGYRILYK 50 (62)
T ss_pred CcccEEEEeccccccccccCCCcEehhhcchHHHHH
Confidence 3445567899999987774 589999 98654433
No 47
>PRK07218 replication factor A; Provisional
Probab=46.54 E-value=9.3 Score=33.47 Aligned_cols=21 Identities=24% Similarity=0.613 Sum_probs=16.8
Q ss_pred CCcccccccccccccceeec-cCCc
Q psy11667 56 RSRCAQCNAKLTVCSSFTCR-CRKL 79 (119)
Q Consensus 56 k~RC~~C~kkl~Ls~~f~Cr-Cg~~ 79 (119)
-.||..|++.|. .+.|+ ||.+
T Consensus 297 i~rCP~C~r~v~---~~~C~~hG~v 318 (423)
T PRK07218 297 IERCPECGRVIQ---KGQCRSHGAV 318 (423)
T ss_pred eecCcCcccccc---CCcCCCCCCc
Confidence 369999999984 47899 8765
No 48
>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=45.99 E-value=14 Score=24.53 Aligned_cols=25 Identities=16% Similarity=0.460 Sum_probs=16.1
Q ss_pred CCcccccccccccccceeeccCCcc
Q psy11667 56 RSRCAQCNAKLTVCSSFTCRCRKLF 80 (119)
Q Consensus 56 k~RC~~C~kkl~Ls~~f~CrCg~~F 80 (119)
...|..|+++++.+.-....||.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE
Confidence 4579999999988322223355544
No 49
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=45.73 E-value=12 Score=22.32 Aligned_cols=23 Identities=22% Similarity=0.544 Sum_probs=17.1
Q ss_pred ceeec-cCCcccCCCCCCC--CCCCc
Q psy11667 71 SFTCR-CRKLFCPRHRHPE--EHACT 93 (119)
Q Consensus 71 ~f~Cr-Cg~~FC~~HR~pe--~H~C~ 93 (119)
.|.|. ||..|=..+.+.+ ...|+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP 30 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCP 30 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCC
Confidence 58899 9988877777766 55554
No 50
>PRK08402 replication factor A; Reviewed
Probab=45.71 E-value=10 Score=32.47 Aligned_cols=30 Identities=13% Similarity=0.346 Sum_probs=20.8
Q ss_pred CCccccccccccc---ccceeec-cCCcccCCCCC
Q psy11667 56 RSRCAQCNAKLTV---CSSFTCR-CRKLFCPRHRH 86 (119)
Q Consensus 56 k~RC~~C~kkl~L---s~~f~Cr-Cg~~FC~~HR~ 86 (119)
-.+|..|+|++-. ...+.|. ||.+-+ .|||
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 3699999999952 1367888 776544 5664
No 51
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=45.18 E-value=4.2 Score=31.34 Aligned_cols=21 Identities=24% Similarity=0.415 Sum_probs=17.1
Q ss_pred ccccCCcCCCccccccccccc
Q psy11667 48 CVKKTKHKRSRCAQCNAKLTV 68 (119)
Q Consensus 48 ~~~~~~~~k~RC~~C~kkl~L 68 (119)
...+.....+.||+|+..+..
T Consensus 41 ~~l~~ns~~~~CwfC~q~~~~ 61 (150)
T PHA03073 41 VRLKTNSDNDYCWFCKQDLII 61 (150)
T ss_pred hheecccCCCcEEeecccccc
Confidence 456677888999999998876
No 52
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=43.90 E-value=8.5 Score=24.19 Aligned_cols=23 Identities=30% Similarity=0.928 Sum_probs=17.0
Q ss_pred cccccccccccc------cceeec-cCCcc
Q psy11667 58 RCAQCNAKLTVC------SSFTCR-CRKLF 80 (119)
Q Consensus 58 RC~~C~kkl~Ls------~~f~Cr-Cg~~F 80 (119)
+|..|++++||- .+|-|. |-...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 589999999873 367888 75444
No 53
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=43.73 E-value=12 Score=21.24 Aligned_cols=23 Identities=22% Similarity=0.836 Sum_probs=15.5
Q ss_pred Ccccccccccccccceeec-cCCcccCC
Q psy11667 57 SRCAQCNAKLTVCSSFTCR-CRKLFCPR 83 (119)
Q Consensus 57 ~RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~ 83 (119)
..|.+|+. . ..|.|. |+..||+.
T Consensus 3 ~~C~vC~~-~---~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 3 KLCSVCGN-P---AKYRCPRCGARYCSL 26 (30)
T ss_dssp EEETSSSS-E---ESEE-TTT--EESSH
T ss_pred CCCccCcC-C---CEEECCCcCCceeCc
Confidence 46888988 3 379999 99999974
No 54
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=43.64 E-value=15 Score=22.24 Aligned_cols=32 Identities=38% Similarity=0.932 Sum_probs=21.8
Q ss_pred CCccc--cccccccc-----ccceee-ccCCcccCCCCCC
Q psy11667 56 RSRCA--QCNAKLTV-----CSSFTC-RCRKLFCPRHRHP 87 (119)
Q Consensus 56 k~RC~--~C~kkl~L-----s~~f~C-rCg~~FC~~HR~p 87 (119)
...|. .|..-+.+ .....| .|+..||..++.+
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCc
Confidence 34576 56543322 247899 6999999998866
No 55
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=43.47 E-value=11 Score=18.86 Aligned_cols=10 Identities=40% Similarity=1.148 Sum_probs=6.2
Q ss_pred eeec-cCCccc
Q psy11667 72 FTCR-CRKLFC 81 (119)
Q Consensus 72 f~Cr-Cg~~FC 81 (119)
|.|. |+..|=
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 5676 766663
No 56
>KOG1074|consensus
Probab=43.45 E-value=18 Score=34.86 Aligned_cols=35 Identities=17% Similarity=0.505 Sum_probs=26.2
Q ss_pred cccCCcCCCcccccccccccc-------------cceeec-cCCcccCC
Q psy11667 49 VKKTKHKRSRCAQCNAKLTVC-------------SSFTCR-CRKLFCPR 83 (119)
Q Consensus 49 ~~~~~~~k~RC~~C~kkl~Ls-------------~~f~Cr-Cg~~FC~~ 83 (119)
..+..-.+++|.+|.|-.|-. ..|+|+ ||+.|-.+
T Consensus 346 ~~~~~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTk 394 (958)
T KOG1074|consen 346 PSEKPFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTK 394 (958)
T ss_pred CCccccccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccc
Confidence 345567788999998866531 289999 99998764
No 57
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=43.10 E-value=8.6 Score=27.28 Aligned_cols=36 Identities=25% Similarity=0.645 Sum_probs=22.7
Q ss_pred CCcCCCccccccccc-c-cc-cceeec-cCCcccCCCCCC
Q psy11667 52 TKHKRSRCAQCNAKL-T-VC-SSFTCR-CRKLFCPRHRHP 87 (119)
Q Consensus 52 ~~~~k~RC~~C~kkl-~-Ls-~~f~Cr-Cg~~FC~~HR~p 87 (119)
.+..+..|.+|++.. . .+ .-.+|+ |+.+|-+-=-.|
T Consensus 31 ~q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGAy~~ 70 (90)
T PF01780_consen 31 SQHAKYTCPFCGKTSVKRVATGIWKCKKCGKKFAGGAYTP 70 (90)
T ss_dssp HHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSS
T ss_pred HHhCCCcCCCCCCceeEEeeeEEeecCCCCCEEeCCCccc
Confidence 346678999999743 1 11 347999 999987654433
No 58
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=41.92 E-value=13 Score=26.44 Aligned_cols=37 Identities=19% Similarity=0.548 Sum_probs=25.1
Q ss_pred cCCcCCCcccccccccc--cc-cceeec-cCCcccCCCCCC
Q psy11667 51 KTKHKRSRCAQCNAKLT--VC-SSFTCR-CRKLFCPRHRHP 87 (119)
Q Consensus 51 ~~~~~k~RC~~C~kkl~--Ls-~~f~Cr-Cg~~FC~~HR~p 87 (119)
.++..+..|..|+++.- ++ .--.|+ ||.+|=.---.|
T Consensus 30 ~~~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 30 AQQRAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred HHHhcCCcCCCCCCcceeeeccCeEEcCCCCCeeccccccc
Confidence 34567789999998521 12 346899 999987655444
No 59
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=41.45 E-value=13 Score=22.76 Aligned_cols=29 Identities=21% Similarity=0.521 Sum_probs=19.5
Q ss_pred Ccccccccccccc--cceeec-cCCcccCCCC
Q psy11667 57 SRCAQCNAKLTVC--SSFTCR-CRKLFCPRHR 85 (119)
Q Consensus 57 ~RC~~C~kkl~Ls--~~f~Cr-Cg~~FC~~HR 85 (119)
.+|..|+..+.+. .+..|+ ||.-.--+-|
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRILYKKR 34 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceEEEEeC
Confidence 4688888877664 578887 8765544443
No 60
>KOG3362|consensus
Probab=40.59 E-value=13 Score=28.89 Aligned_cols=28 Identities=32% Similarity=0.720 Sum_probs=21.8
Q ss_pred CCcCCCcccccccccccccceeec-cCCcccCC
Q psy11667 52 TKHKRSRCAQCNAKLTVCSSFTCR-CRKLFCPR 83 (119)
Q Consensus 52 ~~~~k~RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~ 83 (119)
-++...-|++|+- . ..|.|- ||..||+.
T Consensus 114 ~KP~r~fCaVCG~---~-S~ysC~~CG~kyCsv 142 (156)
T KOG3362|consen 114 FKPLRKFCAVCGY---D-SKYSCVNCGTKYCSV 142 (156)
T ss_pred CCCcchhhhhcCC---C-chhHHHhcCCceeec
Confidence 3466778999992 2 468899 99999986
No 61
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=40.48 E-value=10 Score=24.44 Aligned_cols=25 Identities=28% Similarity=0.753 Sum_probs=18.1
Q ss_pred CCcccccccccccc-----cceeec-cCCcc
Q psy11667 56 RSRCAQCNAKLTVC-----SSFTCR-CRKLF 80 (119)
Q Consensus 56 k~RC~~C~kkl~Ls-----~~f~Cr-Cg~~F 80 (119)
.-||..|++.|..+ ..++|- |+..+
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 45999999987653 366887 87654
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=40.25 E-value=14 Score=21.51 Aligned_cols=10 Identities=30% Similarity=1.039 Sum_probs=5.9
Q ss_pred ceeec-cCCcc
Q psy11667 71 SFTCR-CRKLF 80 (119)
Q Consensus 71 ~f~Cr-Cg~~F 80 (119)
..+|. ||.+|
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 35666 66655
No 63
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=39.68 E-value=18 Score=26.03 Aligned_cols=29 Identities=28% Similarity=0.684 Sum_probs=19.5
Q ss_pred CCCccccccccccc-c-cceeec-cCCcccCC
Q psy11667 55 KRSRCAQCNAKLTV-C-SSFTCR-CRKLFCPR 83 (119)
Q Consensus 55 ~k~RC~~C~kkl~L-s-~~f~Cr-Cg~~FC~~ 83 (119)
.|..|..|++|..- . .+..|- ||..|=..
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 46788888886542 1 477788 87776444
No 64
>KOG1842|consensus
Probab=39.22 E-value=7.5 Score=34.99 Aligned_cols=25 Identities=24% Similarity=0.895 Sum_probs=21.1
Q ss_pred Ccccccccccccc-cceeec-cCCccc
Q psy11667 57 SRCAQCNAKLTVC-SSFTCR-CRKLFC 81 (119)
Q Consensus 57 ~RC~~C~kkl~Ls-~~f~Cr-Cg~~FC 81 (119)
.-|..|..+.+|+ ..-.|| ||.+.|
T Consensus 181 ~~CP~Ca~~F~l~rRrHHCRLCG~VmC 207 (505)
T KOG1842|consen 181 QFCPECANSFGLTRRRHHCRLCGRVMC 207 (505)
T ss_pred cccccccchhhhHHHhhhhhhcchHHH
Confidence 3799999999986 477999 999966
No 65
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.71 E-value=22 Score=23.04 Aligned_cols=25 Identities=20% Similarity=0.644 Sum_probs=19.0
Q ss_pred CCCccccccccc--ccccceeec-cCCcc
Q psy11667 55 KRSRCAQCNAKL--TVCSSFTCR-CRKLF 80 (119)
Q Consensus 55 ~k~RC~~C~kkl--~Ls~~f~Cr-Cg~~F 80 (119)
...+|..|++++ +. ....|. ||..+
T Consensus 4 ~~~~C~~Cg~~~~~~d-DiVvCp~Cgapy 31 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGD-DIVVCPECGAPY 31 (54)
T ss_pred cCccChhhCCcccCCC-CEEECCCCCCcc
Confidence 456899999998 44 567888 87653
No 66
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=38.62 E-value=34 Score=24.67 Aligned_cols=46 Identities=22% Similarity=0.445 Sum_probs=32.2
Q ss_pred ccCCcCCCcccccccccccccceeeccCCcccCCCCCCCCCCCccccHHhh
Q psy11667 50 KKTKHKRSRCAQCNAKLTVCSSFTCRCRKLFCPRHRHPEEHACTFDYKAYG 100 (119)
Q Consensus 50 ~~~~~~k~RC~~C~kkl~Ls~~f~CrCg~~FC~~HR~pe~H~C~fDyk~~g 100 (119)
........-|..|+..-.. ....|+ +|.+=-+.=||.|++--.=.|
T Consensus 42 ~~~~~~~~~C~~C~~~kp~-Rs~HC~----~C~~CV~~~DHHC~w~~~cIG 87 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKPP-RSHHCR----VCNRCVLRFDHHCPWLGNCIG 87 (174)
T ss_pred cccCCCCEECcccCCcCCC-cceecc----ccccccccccccchhhccccc
Confidence 3355667789999987777 799999 444444556799997554444
No 67
>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=38.61 E-value=19 Score=24.99 Aligned_cols=25 Identities=32% Similarity=0.677 Sum_probs=18.2
Q ss_pred cCCCcccccccccccc----------cceeec-cCC
Q psy11667 54 HKRSRCAQCNAKLTVC----------SSFTCR-CRK 78 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls----------~~f~Cr-Cg~ 78 (119)
..+++|..|+++|..- ...+|| |+.
T Consensus 31 ~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~ 66 (92)
T PF06750_consen 31 FPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGA 66 (92)
T ss_pred CCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCC
Confidence 3468999999988752 267888 644
No 68
>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=38.04 E-value=17 Score=21.36 Aligned_cols=23 Identities=22% Similarity=0.694 Sum_probs=16.6
Q ss_pred Ccccccccccccc--cceee-ccCCc
Q psy11667 57 SRCAQCNAKLTVC--SSFTC-RCRKL 79 (119)
Q Consensus 57 ~RC~~C~kkl~Ls--~~f~C-rCg~~ 79 (119)
-+|..|+..+..+ .-|.| +||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 3699999886654 36789 58865
No 69
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=37.72 E-value=16 Score=18.96 Aligned_cols=12 Identities=42% Similarity=1.065 Sum_probs=8.6
Q ss_pred ceeec-cCCcccC
Q psy11667 71 SFTCR-CRKLFCP 82 (119)
Q Consensus 71 ~f~Cr-Cg~~FC~ 82 (119)
.|+|. |+..|-.
T Consensus 1 ~~~C~~C~~~F~~ 13 (27)
T PF13912_consen 1 PFECDECGKTFSS 13 (27)
T ss_dssp SEEETTTTEEESS
T ss_pred CCCCCccCCccCC
Confidence 36788 8887754
No 70
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=37.59 E-value=15 Score=17.71 Aligned_cols=9 Identities=56% Similarity=1.339 Sum_probs=3.7
Q ss_pred eeec-cCCcc
Q psy11667 72 FTCR-CRKLF 80 (119)
Q Consensus 72 f~Cr-Cg~~F 80 (119)
|.|. |+..|
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 4565 65554
No 71
>KOG1074|consensus
Probab=37.37 E-value=23 Score=34.25 Aligned_cols=48 Identities=19% Similarity=0.631 Sum_probs=33.0
Q ss_pred cccCCcCCCcccccccccc------cc-------cceeec-cCCcccCC---------CC----CCCCCCCcccc
Q psy11667 49 VKKTKHKRSRCAQCNAKLT------VC-------SSFTCR-CRKLFCPR---------HR----HPEEHACTFDY 96 (119)
Q Consensus 49 ~~~~~~~k~RC~~C~kkl~------Ls-------~~f~Cr-Cg~~FC~~---------HR----~pe~H~C~fDy 96 (119)
...+....|.|-+|.+-|. |. ..|+|+ ||+-|--+ || +--.|.|++.|
T Consensus 598 ~~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 598 SENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred cccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 4556677899999877553 21 389999 99998632 33 34678898543
No 72
>PRK12366 replication factor A; Reviewed
Probab=36.82 E-value=15 Score=33.51 Aligned_cols=31 Identities=16% Similarity=0.535 Sum_probs=22.3
Q ss_pred CCCcccccccccccc-cceeec-cCCcccCCCCC
Q psy11667 55 KRSRCAQCNAKLTVC-SSFTCR-CRKLFCPRHRH 86 (119)
Q Consensus 55 ~k~RC~~C~kkl~Ls-~~f~Cr-Cg~~FC~~HR~ 86 (119)
.-.+|..|+|||-.. ..|.|. ||.. =..|||
T Consensus 531 ~y~aCp~CnkKv~~~~g~~~C~~c~~~-~p~~~~ 563 (637)
T PRK12366 531 ILYLCPNCRKRVEEVDGEYICEFCGEV-EPNELL 563 (637)
T ss_pred EEecccccCeEeEcCCCcEECCCCCCC-CCcEEE
Confidence 346999999999652 347898 9887 335666
No 73
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=36.42 E-value=15 Score=29.04 Aligned_cols=30 Identities=27% Similarity=0.543 Sum_probs=24.0
Q ss_pred cccCCcCCCcccccccccccccceeec-cCCc
Q psy11667 49 VKKTKHKRSRCAQCNAKLTVCSSFTCR-CRKL 79 (119)
Q Consensus 49 ~~~~~~~k~RC~~C~kkl~Ls~~f~Cr-Cg~~ 79 (119)
..+..++..||..|++.... ....|- ||..
T Consensus 132 I~~v~~w~~rC~GC~~~f~~-~~~~Cp~CG~~ 162 (177)
T COG1439 132 IKKVRKWRLRCHGCKRIFPE-PKDFCPICGSP 162 (177)
T ss_pred cceEeeeeEEEecCceecCC-CCCcCCCCCCc
Confidence 46677888999999998774 577798 8865
No 74
>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=36.11 E-value=16 Score=24.12 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=9.3
Q ss_pred CCccccccccccc
Q psy11667 56 RSRCAQCNAKLTV 68 (119)
Q Consensus 56 k~RC~~C~kkl~L 68 (119)
+-||++|++-++-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 4599999998753
No 75
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=35.71 E-value=22 Score=23.14 Aligned_cols=25 Identities=28% Similarity=0.782 Sum_probs=19.2
Q ss_pred cccccccccccccceeec-cCCc-ccC
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKL-FCP 82 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~-FC~ 82 (119)
.|.+|.+++.....|.|. ||.. +|+
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCS 27 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccC
Confidence 488888877766799999 9875 444
No 76
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=35.39 E-value=18 Score=19.27 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=7.7
Q ss_pred cceeec-cCCcc
Q psy11667 70 SSFTCR-CRKLF 80 (119)
Q Consensus 70 ~~f~Cr-Cg~~F 80 (119)
..|.|. |+..|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 467787 77766
No 77
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=35.07 E-value=22 Score=22.66 Aligned_cols=25 Identities=28% Similarity=0.667 Sum_probs=20.2
Q ss_pred CcCCCcccccccccccccceeec-cCC
Q psy11667 53 KHKRSRCAQCNAKLTVCSSFTCR-CRK 78 (119)
Q Consensus 53 ~~~k~RC~~C~kkl~Ls~~f~Cr-Cg~ 78 (119)
.-.+.-|..|..++.. ..-.|| ||.
T Consensus 11 ~~~k~ICrkC~ARnp~-~A~~CRKCg~ 36 (48)
T PRK04136 11 VFNKKICMRCNARNPW-RATKCRKCGY 36 (48)
T ss_pred hhcccchhcccCCCCc-cccccccCCC
Confidence 3456678899999988 788999 875
No 78
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=34.83 E-value=22 Score=21.09 Aligned_cols=22 Identities=23% Similarity=0.679 Sum_probs=13.4
Q ss_pred ccccccccccccceeeccCCcccC
Q psy11667 59 CAQCNAKLTVCSSFTCRCRKLFCP 82 (119)
Q Consensus 59 C~~C~kkl~Ls~~f~CrCg~~FC~ 82 (119)
|..|..-+. .+..-.||.+||.
T Consensus 1 CpiC~~~~~--~Pv~l~CGH~FC~ 22 (42)
T PF15227_consen 1 CPICLDLFK--DPVSLPCGHSFCR 22 (42)
T ss_dssp ETTTTSB-S--SEEE-SSSSEEEH
T ss_pred CCccchhhC--CccccCCcCHHHH
Confidence 455555443 3677789999994
No 79
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=34.80 E-value=20 Score=27.60 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=15.7
Q ss_pred cccccccccccccceeec-cCCcccCCC
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKLFCPRH 84 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~H 84 (119)
.|..|+-.-.- ...+|. |++.||..-
T Consensus 2 aC~YCG~~~p~-~vv~C~~c~kWFCNg~ 28 (152)
T PF09416_consen 2 ACAYCGIHDPS-CVVKCNTCNKWFCNGR 28 (152)
T ss_dssp S-TTT----CC-CEEEETTTTEEEES--
T ss_pred CccccCCCCcc-cEeEcCCCCcEeecCC
Confidence 58889865544 468899 999999874
No 80
>PLN02569 threonine synthase
Probab=34.34 E-value=35 Score=30.15 Aligned_cols=35 Identities=14% Similarity=0.170 Sum_probs=25.5
Q ss_pred CCcCCCcccccccccccc-cceeeccCCcccCCCCC
Q psy11667 52 TKHKRSRCAQCNAKLTVC-SSFTCRCRKLFCPRHRH 86 (119)
Q Consensus 52 ~~~~k~RC~~C~kkl~Ls-~~f~CrCg~~FC~~HR~ 86 (119)
......+|..|++...+. ..+.|.||..+=..|.|
T Consensus 45 ~~~~~l~C~~Cg~~y~~~~~~~~C~cgg~l~~~~d~ 80 (484)
T PLN02569 45 KYVPFLECPLTGEKYSLDEVVYRSKSGGLLDVRHDM 80 (484)
T ss_pred ccccccEeCCCCCcCCCccccccCCCCCeEEEecch
Confidence 345568999999987764 35789998887666554
No 81
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.30 E-value=15 Score=30.84 Aligned_cols=28 Identities=25% Similarity=0.589 Sum_probs=21.2
Q ss_pred CCcccccccccccccceeec-cCCcccCCCCC
Q psy11667 56 RSRCAQCNAKLTVCSSFTCR-CRKLFCPRHRH 86 (119)
Q Consensus 56 k~RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~HR~ 86 (119)
-.+|+.|-.-. ..+.|. ||++||+.--+
T Consensus 215 d~kC~lC~e~~---~~ps~t~CgHlFC~~Cl~ 243 (271)
T COG5574 215 DYKCFLCLEEP---EVPSCTPCGHLFCLSCLL 243 (271)
T ss_pred ccceeeeeccc---CCcccccccchhhHHHHH
Confidence 46899997743 467899 99999986433
No 82
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=33.95 E-value=22 Score=26.30 Aligned_cols=32 Identities=19% Similarity=0.323 Sum_probs=23.0
Q ss_pred ccccccccccceeeccCCcccCCCCCCCCCCCccc
Q psy11667 61 QCNAKLTVCSSFTCRCRKLFCPRHRHPEEHACTFD 95 (119)
Q Consensus 61 ~C~kkl~Ls~~f~CrCg~~FC~~HR~pe~H~C~fD 95 (119)
.|+++-. ..+|.||..||.-+.--..|.--++
T Consensus 17 i~~~~~k---~vkc~CGh~f~d~r~NwK~~alv~v 48 (112)
T PF08882_consen 17 IVQKKDK---VVKCDCGHEFCDARENWKLGALVYV 48 (112)
T ss_pred EEEecCc---eeeccCCCeecChhcChhhCcEEEe
Confidence 4555441 5789999999998877776665544
No 83
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.63 E-value=28 Score=20.67 Aligned_cols=22 Identities=32% Similarity=0.720 Sum_probs=13.4
Q ss_pred cccccccccccc-----cceeec-cCCc
Q psy11667 58 RCAQCNAKLTVC-----SSFTCR-CRKL 79 (119)
Q Consensus 58 RC~~C~kkl~Ls-----~~f~Cr-Cg~~ 79 (119)
-|..|+..|... .-+.|. ||+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCe
Confidence 477787755432 147788 7753
No 84
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=33.58 E-value=15 Score=24.47 Aligned_cols=13 Identities=23% Similarity=0.598 Sum_probs=10.3
Q ss_pred CCccccccccccc
Q psy11667 56 RSRCAQCNAKLTV 68 (119)
Q Consensus 56 k~RC~~C~kkl~L 68 (119)
+-||++|+|-++-
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 4599999998754
No 85
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.41 E-value=16 Score=26.32 Aligned_cols=18 Identities=28% Similarity=0.534 Sum_probs=13.3
Q ss_pred cccccccceeec-cCCcccC
Q psy11667 64 AKLTVCSSFTCR-CRKLFCP 82 (119)
Q Consensus 64 kkl~Ls~~f~Cr-Cg~~FC~ 82 (119)
+.|-+ .+-.|+ ||++|=.
T Consensus 52 ~~Llv-~Pa~CkkCGfef~~ 70 (97)
T COG3357 52 KRLLV-RPARCKKCGFEFRD 70 (97)
T ss_pred ceEEe-cChhhcccCccccc
Confidence 34444 688999 9999966
No 86
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=32.79 E-value=21 Score=26.11 Aligned_cols=28 Identities=25% Similarity=0.666 Sum_probs=22.4
Q ss_pred ccccccccccccceeec-cCCcccCCCCCC
Q psy11667 59 CAQCNAKLTVCSSFTCR-CRKLFCPRHRHP 87 (119)
Q Consensus 59 C~~C~kkl~Ls~~f~Cr-Cg~~FC~~HR~p 87 (119)
|..|+..|-. +..+|. |+-.+-+.-.++
T Consensus 1 CPvCg~~l~v-t~l~C~~C~t~i~G~F~l~ 29 (113)
T PF09862_consen 1 CPVCGGELVV-TRLKCPSCGTEIEGEFELP 29 (113)
T ss_pred CCCCCCceEE-EEEEcCCCCCEEEeeeccc
Confidence 8899999988 899999 988776655443
No 87
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=32.49 E-value=26 Score=26.75 Aligned_cols=14 Identities=36% Similarity=0.619 Sum_probs=9.7
Q ss_pred eeec-cCCcccCCCC
Q psy11667 72 FTCR-CRKLFCPRHR 85 (119)
Q Consensus 72 f~Cr-Cg~~FC~~HR 85 (119)
++|. ||+.|=..-+
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 7788 8888765444
No 88
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=32.45 E-value=22 Score=25.29 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=23.0
Q ss_pred CCcCCCcccccccc----cccccceeec-cCCcccCCCCC
Q psy11667 52 TKHKRSRCAQCNAK----LTVCSSFTCR-CRKLFCPRHRH 86 (119)
Q Consensus 52 ~~~~k~RC~~C~kk----l~Ls~~f~Cr-Cg~~FC~~HR~ 86 (119)
.+..+..|.+|++. +.. .--+|+ |+.+|-.-=-.
T Consensus 31 ~q~a~y~CpfCgk~~vkR~a~-GIW~C~~C~~~~AGGAy~ 69 (91)
T TIGR00280 31 QQKAKYVCPFCGKKTVKRGST-GIWTCRKCGAKFAGGAYT 69 (91)
T ss_pred HHhcCccCCCCCCCceEEEee-EEEEcCCCCCEEeCCccc
Confidence 45677899999752 222 346999 99998765433
No 89
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=32.32 E-value=24 Score=24.97 Aligned_cols=34 Identities=18% Similarity=0.543 Sum_probs=22.7
Q ss_pred cCCcCCCcccccccc-ccc-c-cceeec-cCCcccCCC
Q psy11667 51 KTKHKRSRCAQCNAK-LTV-C-SSFTCR-CRKLFCPRH 84 (119)
Q Consensus 51 ~~~~~k~RC~~C~kk-l~L-s-~~f~Cr-Cg~~FC~~H 84 (119)
..+..+..|.+|++. +.- + .--+|+ |+.+|-.-=
T Consensus 31 ~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 31 ISQHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred HHHhCCccCCCCCCCceeeeeeEEEEcCCCCCEEeCCc
Confidence 345678899999752 221 1 346999 999987643
No 90
>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=31.75 E-value=34 Score=25.10 Aligned_cols=29 Identities=31% Similarity=0.730 Sum_probs=19.2
Q ss_pred CcCCCcccccccccccc------------------cceeec-cCCccc
Q psy11667 53 KHKRSRCAQCNAKLTVC------------------SSFTCR-CRKLFC 81 (119)
Q Consensus 53 ~~~k~RC~~C~kkl~Ls------------------~~f~Cr-Cg~~FC 81 (119)
.....||..|+..|... .-+.|. ||.+|=
T Consensus 88 ~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW 135 (147)
T PF01927_consen 88 DPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYW 135 (147)
T ss_pred CCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEec
Confidence 34468999999766331 135788 888763
No 91
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=31.55 E-value=27 Score=27.23 Aligned_cols=20 Identities=40% Similarity=1.129 Sum_probs=16.3
Q ss_pred cceeeccCCcccCCCCCCCCCC
Q psy11667 70 SSFTCRCRKLFCPRHRHPEEHA 91 (119)
Q Consensus 70 ~~f~CrCg~~FC~~HR~pe~H~ 91 (119)
+.|.|.| .||-.||.+.+-+
T Consensus 122 ~~FrC~C--~yC~~~~~~~~~n 141 (160)
T PF15549_consen 122 NRFRCEC--HYCQSHRNPGERN 141 (160)
T ss_pred Cceeeee--eeecccCCCcccc
Confidence 4789998 6999999776666
No 92
>PF14369 zf-RING_3: zinc-finger
Probab=31.41 E-value=26 Score=20.40 Aligned_cols=23 Identities=35% Similarity=0.736 Sum_probs=14.9
Q ss_pred cccccccccccc---ccee-ec-cCCcc
Q psy11667 58 RCAQCNAKLTVC---SSFT-CR-CRKLF 80 (119)
Q Consensus 58 RC~~C~kkl~Ls---~~f~-Cr-Cg~~F 80 (119)
=|+.|++.+.+. .... |- |+..|
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 377888777652 2334 87 87776
No 93
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.39 E-value=34 Score=21.58 Aligned_cols=25 Identities=24% Similarity=0.611 Sum_probs=17.4
Q ss_pred CCCccccccccccc--c-cceeec-cCCc
Q psy11667 55 KRSRCAQCNAKLTV--C-SSFTCR-CRKL 79 (119)
Q Consensus 55 ~k~RC~~C~kkl~L--s-~~f~Cr-Cg~~ 79 (119)
+...|+.|+..+.. . ..|.|. ||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45689999875544 2 478888 7665
No 94
>PRK05978 hypothetical protein; Provisional
Probab=31.26 E-value=26 Score=26.69 Aligned_cols=27 Identities=33% Similarity=0.652 Sum_probs=18.3
Q ss_pred cCCCccccccc-ccc---cccceeec-cCCcc
Q psy11667 54 HKRSRCAQCNA-KLT---VCSSFTCR-CRKLF 80 (119)
Q Consensus 54 ~~k~RC~~C~k-kl~---Ls~~f~Cr-Cg~~F 80 (119)
--+.||..|++ ++- |...-.|. ||..|
T Consensus 31 Gl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 31 GFRGRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred HHcCcCCCCCCCcccccccccCCCccccCCcc
Confidence 34579999998 441 22466888 87765
No 95
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=31.07 E-value=25 Score=24.96 Aligned_cols=31 Identities=19% Similarity=0.598 Sum_probs=21.7
Q ss_pred CCcCCCccccccc----ccccccceeec-cCCcccCC
Q psy11667 52 TKHKRSRCAQCNA----KLTVCSSFTCR-CRKLFCPR 83 (119)
Q Consensus 52 ~~~~k~RC~~C~k----kl~Ls~~f~Cr-Cg~~FC~~ 83 (119)
.+..+..|.+|++ +... .--+|+ |+.+|-.-
T Consensus 32 ~q~a~y~CpfCgk~~vkR~a~-GIW~C~~C~~~~AGG 67 (90)
T PRK03976 32 KMRAKHVCPVCGRPKVKRVGT-GIWECRKCGAKFAGG 67 (90)
T ss_pred HHhcCccCCCCCCCceEEEEE-EEEEcCCCCCEEeCC
Confidence 4567789999965 2222 346999 99998664
No 96
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=30.85 E-value=18 Score=24.69 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=10.4
Q ss_pred CCccccccccccc
Q psy11667 56 RSRCAQCNAKLTV 68 (119)
Q Consensus 56 k~RC~~C~kkl~L 68 (119)
+-||++|+|-++-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 4599999998763
No 97
>KOG2462|consensus
Probab=30.34 E-value=85 Score=26.49 Aligned_cols=49 Identities=33% Similarity=0.792 Sum_probs=32.2
Q ss_pred cCCcCCCccccccccccccc----------------ceeec-cCCcccCC---------CCCCCCCCCccccHHhhH
Q psy11667 51 KTKHKRSRCAQCNAKLTVCS----------------SFTCR-CRKLFCPR---------HRHPEEHACTFDYKAYGR 101 (119)
Q Consensus 51 ~~~~~k~RC~~C~kkl~Ls~----------------~f~Cr-Cg~~FC~~---------HR~pe~H~C~fDyk~~gr 101 (119)
..+..+..|..|+|...-+. .|.|. ||++|-++ |-++ |.|.|=-|.+-|
T Consensus 125 ~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~--c~C~iCGKaFSR 199 (279)
T KOG2462|consen 125 AAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLP--CECGICGKAFSR 199 (279)
T ss_pred cccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCC--cccccccccccc
Confidence 45666778888998765433 58899 99987653 4444 777765554443
No 98
>PRK12496 hypothetical protein; Provisional
Probab=30.29 E-value=24 Score=26.83 Aligned_cols=31 Identities=26% Similarity=0.475 Sum_probs=21.6
Q ss_pred cccCCcCCCcccccccccccc-cceeec-cCCc
Q psy11667 49 VKKTKHKRSRCAQCNAKLTVC-SSFTCR-CRKL 79 (119)
Q Consensus 49 ~~~~~~~k~RC~~C~kkl~Ls-~~f~Cr-Cg~~ 79 (119)
.++...|+.+|..|++..... ....|- ||..
T Consensus 120 i~~~~~w~~~C~gC~~~~~~~~~~~~C~~CG~~ 152 (164)
T PRK12496 120 IKKVIKWRKVCKGCKKKYPEDYPDDVCEICGSP 152 (164)
T ss_pred chhheeeeEECCCCCccccCCCCCCcCCCCCCh
Confidence 456667889999999876431 345688 8764
No 99
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.13 E-value=39 Score=28.05 Aligned_cols=28 Identities=29% Similarity=0.814 Sum_probs=21.9
Q ss_pred CCCcccccccccccccceeec-cCCcccCCC
Q psy11667 55 KRSRCAQCNAKLTVCSSFTCR-CRKLFCPRH 84 (119)
Q Consensus 55 ~k~RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~H 84 (119)
.+..|+ |.+++.. .||.|. |.-.||...
T Consensus 241 ~ra~Cf-Ch~k~v~-~GyvCs~Clsi~C~~p 269 (279)
T TIGR00627 241 YRASCF-CHHQLVS-IGFVCSVCLSVLCQYT 269 (279)
T ss_pred Ccceee-ecCcccc-ceEECCCccCCcCCCC
Confidence 345775 7887766 799999 999999864
No 100
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=29.10 E-value=39 Score=22.13 Aligned_cols=24 Identities=17% Similarity=0.559 Sum_probs=17.4
Q ss_pred ccCCcCCCcccccccccccccceeec
Q psy11667 50 KKTKHKRSRCAQCNAKLTVCSSFTCR 75 (119)
Q Consensus 50 ~~~~~~k~RC~~C~kkl~Ls~~f~Cr 75 (119)
......+.+|..|+++.|. ...|.
T Consensus 30 ~~~~~~~~~C~~C~~~~Ga--~i~C~ 53 (90)
T PF13771_consen 30 EIKRRRKLKCSICKKKGGA--CIGCS 53 (90)
T ss_pred HHHHHhCCCCcCCCCCCCe--EEEEe
Confidence 3445667799999999777 55565
No 101
>PRK06386 replication factor A; Reviewed
Probab=28.90 E-value=25 Score=30.25 Aligned_cols=20 Identities=20% Similarity=0.534 Sum_probs=14.7
Q ss_pred CCcccccccccccccceeec-cCC
Q psy11667 56 RSRCAQCNAKLTVCSSFTCR-CRK 78 (119)
Q Consensus 56 k~RC~~C~kkl~Ls~~f~Cr-Cg~ 78 (119)
-.||+.|++.|.. ..|+ ||.
T Consensus 236 i~rCP~C~R~l~~---g~C~~HG~ 256 (358)
T PRK06386 236 FTKCSVCNKIIED---GVCKDHPD 256 (358)
T ss_pred EecCcCCCeEccC---CcCCCCCC
Confidence 3799999999853 3676 654
No 102
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=28.64 E-value=39 Score=23.05 Aligned_cols=20 Identities=15% Similarity=0.501 Sum_probs=15.6
Q ss_pred cCCCcccccccccccccceeec
Q psy11667 54 HKRSRCAQCNAKLTVCSSFTCR 75 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls~~f~Cr 75 (119)
....+|.+|++..|. ..+|.
T Consensus 53 ~~~~~C~iC~~~~G~--~i~C~ 72 (110)
T PF13832_consen 53 RFKLKCSICGKSGGA--CIKCS 72 (110)
T ss_pred hcCCcCcCCCCCCce--eEEcC
Confidence 467899999999887 55555
No 103
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=27.96 E-value=32 Score=23.11 Aligned_cols=25 Identities=28% Similarity=0.689 Sum_probs=10.6
Q ss_pred Ccccccccccccccce-eeccCCcccCC
Q psy11667 57 SRCAQCNAKLTVCSSF-TCRCRKLFCPR 83 (119)
Q Consensus 57 ~RC~~C~kkl~Ls~~f-~CrCg~~FC~~ 83 (119)
-||+.|..-+.. ++ .-.|...||+.
T Consensus 8 LrCs~C~~~l~~--pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 8 LRCSICFDILKE--PVCLGGCEHIFCSS 33 (65)
T ss_dssp TS-SSS-S--SS---B---SSS--B-TT
T ss_pred cCCcHHHHHhcC--CceeccCccHHHHH
Confidence 589999876544 32 24489999975
No 104
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.49 E-value=36 Score=26.23 Aligned_cols=24 Identities=25% Similarity=0.621 Sum_probs=16.6
Q ss_pred cCCCcccccccccccccceeec-cCCc
Q psy11667 54 HKRSRCAQCNAKLTVCSSFTCR-CRKL 79 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls~~f~Cr-Cg~~ 79 (119)
.....|+.|+. +.- ..|.|. ||..
T Consensus 307 ~tS~~C~~cg~-~~~-r~~~C~~cg~~ 331 (364)
T COG0675 307 YTSKTCPCCGH-LSG-RLFKCPRCGFV 331 (364)
T ss_pred CCcccccccCC-ccc-eeEECCCCCCe
Confidence 34468999998 322 468898 8765
No 105
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=27.34 E-value=28 Score=19.67 Aligned_cols=9 Identities=22% Similarity=0.995 Sum_probs=5.0
Q ss_pred eeec-cCCcc
Q psy11667 72 FTCR-CRKLF 80 (119)
Q Consensus 72 f~Cr-Cg~~F 80 (119)
+.|. ||..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4565 65554
No 106
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=26.34 E-value=31 Score=19.40 Aligned_cols=23 Identities=17% Similarity=0.521 Sum_probs=15.0
Q ss_pred ceeec-cCCcccCCCCC--CCCCCCc
Q psy11667 71 SFTCR-CRKLFCPRHRH--PEEHACT 93 (119)
Q Consensus 71 ~f~Cr-Cg~~FC~~HR~--pe~H~C~ 93 (119)
.|.|. ||..|=..+.. .+...|+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP 30 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCP 30 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCC
Confidence 68999 99987544433 4455565
No 107
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=26.06 E-value=38 Score=22.00 Aligned_cols=15 Identities=33% Similarity=0.975 Sum_probs=8.4
Q ss_pred ceeeccCCc-------ccCCCC
Q psy11667 71 SFTCRCRKL-------FCPRHR 85 (119)
Q Consensus 71 ~f~CrCg~~-------FC~~HR 85 (119)
++.|-||.. ||..||
T Consensus 50 ~~~CDCG~~~~~k~~~~C~~H~ 71 (71)
T PF02207_consen 50 GGCCDCGDPEAWKKEGFCKKHK 71 (71)
T ss_dssp CEBB-TT-GGGBSS--S-TTT-
T ss_pred CeEEeCCCCccccCCCCCCCCC
Confidence 688888876 677775
No 108
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=25.78 E-value=23 Score=30.64 Aligned_cols=26 Identities=23% Similarity=0.763 Sum_probs=18.5
Q ss_pred CCcccccccccccccceeeccCCcccCC
Q psy11667 56 RSRCAQCNAKLTVCSSFTCRCRKLFCPR 83 (119)
Q Consensus 56 k~RC~~C~kkl~Ls~~f~CrCg~~FC~~ 83 (119)
--||..|.-.+.. .-.=.||.+||+.
T Consensus 25 ~lrC~IC~~~i~i--p~~TtCgHtFCsl 50 (391)
T COG5432 25 MLRCRICDCRISI--PCETTCGHTFCSL 50 (391)
T ss_pred HHHhhhhhheeec--ceecccccchhHH
Confidence 3599999887755 3333499999874
No 109
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.43 E-value=38 Score=21.13 Aligned_cols=28 Identities=18% Similarity=0.511 Sum_probs=18.7
Q ss_pred cCCCcccccccc-cccc-cceeec-cCCccc
Q psy11667 54 HKRSRCAQCNAK-LTVC-SSFTCR-CRKLFC 81 (119)
Q Consensus 54 ~~k~RC~~C~kk-l~Ls-~~f~Cr-Cg~~FC 81 (119)
....-|..|+.. +... ..+.|. ||.++-
T Consensus 18 ~~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred EccCcCcCCCcchheccCCcEECCCcCCEEe
Confidence 445589899873 3222 478898 888763
No 110
>KOG0193|consensus
Probab=25.34 E-value=26 Score=32.74 Aligned_cols=49 Identities=31% Similarity=0.582 Sum_probs=27.9
Q ss_pred ccccccccccccceeec-cCCcc--cCCCCCCCCCCCccccHHhhHHHHHHhCCccc
Q psy11667 59 CAQCNAKLTVCSSFTCR-CRKLF--CPRHRHPEEHACTFDYKAYGRHLLAATNPLVV 112 (119)
Q Consensus 59 C~~C~kkl~Ls~~f~Cr-Cg~~F--C~~HR~pe~H~C~fDyk~~gr~~Lak~NP~v~ 112 (119)
|..|..++-+ ++|+|+ |++.| .+.-|.|. .|. ++ .-.++.+...+|-+.
T Consensus 192 C~~~~~~~l~-~gfrC~~C~~KfHq~Cs~~vp~--~C~-~~-~~~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 192 CDSCCNKFLF-TGFRCQTCGYKFHQSCSPRVPT--SCV-NP-DHLRQLLVFEFPAVG 243 (678)
T ss_pred hhhhcchhhh-cccccCCCCCccccccCCCCCC--CCC-Cc-chHhhhhhhcccccc
Confidence 4434556645 799999 99976 22334553 343 22 234455666666553
No 111
>KOG3497|consensus
Probab=24.93 E-value=26 Score=23.71 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=10.1
Q ss_pred CCccccccccccc
Q psy11667 56 RSRCAQCNAKLTV 68 (119)
Q Consensus 56 k~RC~~C~kkl~L 68 (119)
+-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 4599999997763
No 112
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=24.55 E-value=28 Score=29.01 Aligned_cols=26 Identities=27% Similarity=0.571 Sum_probs=19.5
Q ss_pred cCCCcccccccccccc-cceeec-cCCc
Q psy11667 54 HKRSRCAQCNAKLTVC-SSFTCR-CRKL 79 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls-~~f~Cr-Cg~~ 79 (119)
.+.-||..|+++++-. +..+|. ||+.
T Consensus 165 rq~~rc~~c~~k~rr~pl~g~c~kcg~~ 192 (253)
T COG1933 165 RQEFRCVKCNTKFRRPPLDGKCPICGGK 192 (253)
T ss_pred hheeehHhhhhhhcCCCccccccccCCe
Confidence 4456899999887743 578888 8875
No 113
>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=24.07 E-value=31 Score=20.50 Aligned_cols=11 Identities=27% Similarity=0.733 Sum_probs=5.2
Q ss_pred Ccccccccccc
Q psy11667 57 SRCAQCNAKLT 67 (119)
Q Consensus 57 ~RC~~C~kkl~ 67 (119)
.+|++|++...
T Consensus 2 ~~CSFCgr~~~ 12 (41)
T PF06689_consen 2 KRCSFCGRPES 12 (41)
T ss_dssp -B-TTT--BTT
T ss_pred CCccCCCCCHH
Confidence 58999998553
No 114
>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=23.96 E-value=44 Score=17.82 Aligned_cols=6 Identities=50% Similarity=1.353 Sum_probs=2.6
Q ss_pred cccccc
Q psy11667 59 CAQCNA 64 (119)
Q Consensus 59 C~~C~k 64 (119)
|..|++
T Consensus 2 C~~C~~ 7 (39)
T smart00132 2 CAGCGK 7 (39)
T ss_pred ccccCC
Confidence 444444
No 115
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=23.40 E-value=47 Score=24.30 Aligned_cols=22 Identities=32% Similarity=0.751 Sum_probs=14.7
Q ss_pred cccccccccccc----cc-eeec-cCCc
Q psy11667 58 RCAQCNAKLTVC----SS-FTCR-CRKL 79 (119)
Q Consensus 58 RC~~C~kkl~Ls----~~-f~Cr-Cg~~ 79 (119)
+||+|+++..+. +. |.|. |+.+
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q~ 29 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQY 29 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCCc
Confidence 699998764432 34 8888 7643
No 116
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=23.35 E-value=47 Score=25.07 Aligned_cols=26 Identities=12% Similarity=0.192 Sum_probs=19.1
Q ss_pred CCCcccccccccccc--cceeec-cCCcc
Q psy11667 55 KRSRCAQCNAKLTVC--SSFTCR-CRKLF 80 (119)
Q Consensus 55 ~k~RC~~C~kkl~Ls--~~f~Cr-Cg~~F 80 (119)
.|..|..|++|..-- .+..|- ||..|
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCcc
Confidence 467899999875521 578888 88776
No 117
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=23.23 E-value=27 Score=23.41 Aligned_cols=13 Identities=23% Similarity=0.557 Sum_probs=10.3
Q ss_pred CCccccccccccc
Q psy11667 56 RSRCAQCNAKLTV 68 (119)
Q Consensus 56 k~RC~~C~kkl~L 68 (119)
+-||+.|++.++-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 4599999998764
No 118
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=22.78 E-value=41 Score=20.14 Aligned_cols=23 Identities=17% Similarity=0.574 Sum_probs=16.5
Q ss_pred ceeec-cCCcccCCCCCCC--CCCCc
Q psy11667 71 SFTCR-CRKLFCPRHRHPE--EHACT 93 (119)
Q Consensus 71 ~f~Cr-Cg~~FC~~HR~pe--~H~C~ 93 (119)
.|.|. ||..|=..+.+.+ .-.|+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP 30 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCP 30 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCC
Confidence 68999 9998877766553 34566
No 119
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.22 E-value=40 Score=22.18 Aligned_cols=32 Identities=38% Similarity=0.824 Sum_probs=23.4
Q ss_pred Ccccc--cccccccccceeec-cCCcccCCCCC-CCCCCC
Q psy11667 57 SRCAQ--CNAKLTVCSSFTCR-CRKLFCPRHRH-PEEHAC 92 (119)
Q Consensus 57 ~RC~~--C~kkl~Ls~~f~Cr-Cg~~FC~~HR~-pe~H~C 92 (119)
..|.. |+.- .-..|. |.+.+|-.|-+ .+.|.|
T Consensus 28 ~~C~~~gC~~~----s~I~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 28 GDCDITGCNNT----SFIRCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred CcCCCCCCCCc----CEEEccccCCcccccceeeeeeEcC
Confidence 34554 6552 245798 99999999999 578877
No 120
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=22.05 E-value=29 Score=25.02 Aligned_cols=32 Identities=34% Similarity=0.728 Sum_probs=19.5
Q ss_pred CCCccc--ccccccccc--cceeec-cCCcc-cCCCCC
Q psy11667 55 KRSRCA--QCNAKLTVC--SSFTCR-CRKLF-CPRHRH 86 (119)
Q Consensus 55 ~k~RC~--~C~kkl~Ls--~~f~Cr-Cg~~F-C~~HR~ 86 (119)
.=.-|. .|+|||... ..+.|. |+..+ =..+||
T Consensus 17 ~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry 54 (146)
T PF08646_consen 17 YYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRY 54 (146)
T ss_dssp EEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEE
T ss_pred EECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEE
Confidence 334688 899998763 247997 98775 446776
No 121
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.01 E-value=59 Score=24.24 Aligned_cols=33 Identities=24% Similarity=0.584 Sum_probs=26.2
Q ss_pred cCCCcccccccccccccceeec-cCCcccCCCCCC
Q psy11667 54 HKRSRCAQCNAKLTVCSSFTCR-CRKLFCPRHRHP 87 (119)
Q Consensus 54 ~~k~RC~~C~kkl~Ls~~f~Cr-Cg~~FC~~HR~p 87 (119)
+-.++|..|++++-. +.-+|. |+-+.=+.-|..
T Consensus 4 ~~~~~cPvcg~~~iV-TeL~c~~~etTVrg~F~~s 37 (122)
T COG3877 4 KVINRCPVCGRKLIV-TELKCSNCETTVRGNFKMS 37 (122)
T ss_pred CCCCCCCccccccee-EEEecCCCCceEecceecc
Confidence 456899999999966 899999 988876666554
No 122
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=21.57 E-value=39 Score=25.38 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=19.9
Q ss_pred cCCCccccccccccc----ccceeec-cCCc
Q psy11667 54 HKRSRCAQCNAKLTV----CSSFTCR-CRKL 79 (119)
Q Consensus 54 ~~k~RC~~C~kkl~L----s~~f~Cr-Cg~~ 79 (119)
..--.|..|+.+... ..+|.|- ||..
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 445679999988764 2599999 9886
No 123
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.91 E-value=42 Score=26.24 Aligned_cols=16 Identities=38% Similarity=0.692 Sum_probs=11.9
Q ss_pred CcCCCccccccccccc
Q psy11667 53 KHKRSRCAQCNAKLTV 68 (119)
Q Consensus 53 ~~~k~RC~~C~kkl~L 68 (119)
....+||..|+-.|..
T Consensus 94 ~~e~~RCp~CN~~L~~ 109 (165)
T COG1656 94 FPEFSRCPECNGELEK 109 (165)
T ss_pred ccccccCcccCCEecc
Confidence 3557899999976654
No 124
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=20.76 E-value=40 Score=19.28 Aligned_cols=15 Identities=20% Similarity=0.465 Sum_probs=7.6
Q ss_pred cCCCccccccccccc
Q psy11667 54 HKRSRCAQCNAKLTV 68 (119)
Q Consensus 54 ~~k~RC~~C~kkl~L 68 (119)
...++|..|++.+..
T Consensus 4 ~~~~~C~~C~~~~~~ 18 (43)
T PF06467_consen 4 LKMKTCSYCKKYIPN 18 (43)
T ss_dssp -SCEE-TTT--EEEC
T ss_pred CcCCcCcccCCcccC
Confidence 346789999886643
No 125
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.72 E-value=49 Score=19.24 Aligned_cols=11 Identities=36% Similarity=0.757 Sum_probs=4.2
Q ss_pred ccccccccccc
Q psy11667 58 RCAQCNAKLTV 68 (119)
Q Consensus 58 RC~~C~kkl~L 68 (119)
-|..|+..|.+
T Consensus 2 fC~~CG~~l~~ 12 (34)
T PF14803_consen 2 FCPQCGGPLER 12 (34)
T ss_dssp B-TTT--B-EE
T ss_pred ccccccChhhh
Confidence 36667766654
No 126
>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=20.66 E-value=34 Score=20.32 Aligned_cols=25 Identities=24% Similarity=0.632 Sum_probs=12.3
Q ss_pred cccccccccccccceeeccCCcccCC
Q psy11667 58 RCAQCNAKLTVCSSFTCRCRKLFCPR 83 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~CrCg~~FC~~ 83 (119)
+|..|++.|.. ..|.=.=|..||..
T Consensus 28 ~C~~C~~~l~~-~~~~~~~~~~~C~~ 52 (58)
T PF00412_consen 28 KCSKCGKPLND-GDFYEKDGKPYCKD 52 (58)
T ss_dssp BETTTTCBTTT-SSEEEETTEEEEHH
T ss_pred ccCCCCCccCC-CeeEeECCEEECHH
Confidence 44457777665 23433334445443
No 127
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.57 E-value=36 Score=22.11 Aligned_cols=20 Identities=35% Similarity=0.376 Sum_probs=15.9
Q ss_pred HhhHHHHHHhCCcccccccc
Q psy11667 98 AYGRHLLAATNPLVVADKVV 117 (119)
Q Consensus 98 ~~gr~~Lak~NP~v~~~Kl~ 117 (119)
+.=|-.|+++||++.-.||-
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34577889999999888874
No 128
>PF12773 DZR: Double zinc ribbon
Probab=20.42 E-value=70 Score=18.88 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=17.1
Q ss_pred cCCCcccccccccc--cccceeec-cCCc
Q psy11667 54 HKRSRCAQCNAKLT--VCSSFTCR-CRKL 79 (119)
Q Consensus 54 ~~k~RC~~C~kkl~--Ls~~f~Cr-Cg~~ 79 (119)
.....|..|+.+|. ......|. ||..
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCC
Confidence 34567888888887 33456787 6653
No 129
>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=20.37 E-value=66 Score=18.84 Aligned_cols=22 Identities=18% Similarity=0.554 Sum_probs=12.6
Q ss_pred cccccccccccccceeec-cCCc
Q psy11667 58 RCAQCNAKLTVCSSFTCR-CRKL 79 (119)
Q Consensus 58 RC~~C~kkl~Ls~~f~Cr-Cg~~ 79 (119)
+|.+|++......-..|. |+..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~ 23 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRW 23 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCE
T ss_pred eCcCCCCcCCCCCeEEcCCCChh
Confidence 366777733333456677 6655
No 130
>PRK08329 threonine synthase; Validated
Probab=20.19 E-value=61 Score=26.86 Aligned_cols=31 Identities=16% Similarity=0.404 Sum_probs=21.3
Q ss_pred CcccccccccccccceeeccCCcccCCCCCC
Q psy11667 57 SRCAQCNAKLTVCSSFTCRCRKLFCPRHRHP 87 (119)
Q Consensus 57 ~RC~~C~kkl~Ls~~f~CrCg~~FC~~HR~p 87 (119)
-+|..|++.......+.|.||..|=..+.|.
T Consensus 2 l~C~~Cg~~~~~~~~~~C~c~~~l~~~~~~~ 32 (347)
T PRK08329 2 LRCTKCGRTYEEKFKLRCDCGGTLLVEREYG 32 (347)
T ss_pred cCcCCCCCCcCCCCceecCCCCcEEEEeccc
Confidence 4799999877654457899887665554443
Done!