Query psy14482
Match_columns 95
No_of_seqs 138 out of 1202
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 20:57:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14482.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14482hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01753 zf-MYND: MYND finger; 99.5 3.3E-15 7.1E-20 73.9 1.8 37 6-42 1-37 (37)
2 KOG1710|consensus 99.0 2.1E-11 4.6E-16 84.0 -1.9 42 4-45 320-362 (396)
3 KOG2084|consensus 97.8 2.1E-05 4.5E-10 56.8 3.9 62 33-94 3-70 (482)
4 PF13824 zf-Mss51: Zinc-finger 97.6 1.6E-05 3.5E-10 42.1 0.7 45 5-49 1-49 (55)
5 KOG3612|consensus 97.6 7.9E-06 1.7E-10 60.4 -1.4 38 6-45 530-567 (588)
6 PF00856 SET: SET domain; Int 97.4 0.00015 3.2E-09 44.4 2.4 27 54-80 1-27 (162)
7 KOG2061|consensus 96.6 0.0011 2.3E-08 47.4 1.7 46 3-48 136-182 (362)
8 PF04438 zf-HIT: HIT zinc fing 96.1 0.0031 6.8E-08 29.4 1.1 28 4-32 3-30 (30)
9 PLN03158 methionine aminopepti 96.1 0.0041 8.8E-08 45.2 2.1 37 4-40 10-53 (396)
10 PF12855 Ecl1: Life-span regul 94.9 0.012 2.6E-07 29.7 0.8 33 2-37 5-37 (43)
11 KOG3362|consensus 94.4 0.013 2.8E-07 36.9 0.3 33 4-37 119-151 (156)
12 smart00317 SET SET (Su(var)3-9 94.1 0.077 1.7E-06 30.8 3.2 30 50-79 7-36 (116)
13 KOG2857|consensus 92.8 0.077 1.7E-06 33.4 1.7 37 5-46 7-46 (157)
14 PRK01343 zinc-binding protein; 87.3 0.69 1.5E-05 24.7 2.2 30 3-37 9-38 (57)
15 PF09889 DUF2116: Uncharacteri 86.1 0.51 1.1E-05 25.3 1.4 32 3-40 3-34 (59)
16 PF10013 DUF2256: Uncharacteri 81.7 0.27 5.8E-06 24.6 -0.8 31 2-32 7-40 (42)
17 PF08666 SAF: SAF domain; Int 77.9 1.8 3.8E-05 22.6 1.6 15 55-69 2-16 (63)
18 KOG4442|consensus 77.5 1.7 3.6E-05 34.0 1.9 44 26-71 105-148 (729)
19 COG4338 Uncharacterized protei 75.0 0.13 2.8E-06 26.6 -3.2 31 3-33 12-45 (54)
20 KOG1085|consensus 73.8 4.5 9.9E-05 28.7 3.1 33 38-70 251-283 (392)
21 PF09297 zf-NADH-PPase: NADH p 73.0 2 4.2E-05 19.8 0.8 23 3-25 3-32 (32)
22 KOG2738|consensus 65.2 3 6.4E-05 29.8 0.7 40 4-43 7-53 (369)
23 PF03884 DUF329: Domain of unk 63.1 6.2 0.00013 21.0 1.6 32 5-37 4-35 (57)
24 PLN03144 Carbon catabolite rep 61.1 5.4 0.00012 30.9 1.5 36 5-40 61-107 (606)
25 smart00858 SAF This domain fam 59.7 7 0.00015 20.2 1.5 15 55-69 2-16 (64)
26 KOG4317|consensus 55.1 4.2 9.1E-05 29.1 0.1 28 5-33 9-37 (383)
27 COG3024 Uncharacterized protei 54.7 12 0.00026 20.4 1.8 35 2-37 6-40 (65)
28 KOG4215|consensus 54.2 9.4 0.0002 28.0 1.7 35 3-43 19-59 (432)
29 PF14803 Nudix_N_2: Nudix N-te 54.0 5.4 0.00012 18.9 0.4 22 4-25 1-33 (34)
30 TIGR03569 NeuB_NnaB N-acetylne 49.7 13 0.00029 26.6 1.9 27 53-79 276-302 (329)
31 TIGR03586 PseI pseudaminic aci 49.7 12 0.00026 26.7 1.7 21 53-73 274-294 (327)
32 cd06955 NR_DBD_VDR DNA-binding 48.1 12 0.00025 22.5 1.2 27 1-27 4-36 (107)
33 PF08189 Meleagrin: Meleagrin/ 48.0 4.7 0.0001 19.5 -0.4 20 20-39 6-26 (39)
34 PRK00418 DNA gyrase inhibitor; 46.9 19 0.00042 19.5 1.9 33 4-37 7-39 (62)
35 PF12879 SICA_C: SICA C-termin 46.5 4 8.6E-05 25.4 -1.0 53 27-81 75-127 (138)
36 PRK12618 flgA flagellar basal 45.4 15 0.00032 23.0 1.5 20 50-69 15-34 (141)
37 PF13240 zinc_ribbon_2: zinc-r 44.0 14 0.00031 15.7 0.9 17 5-21 1-20 (23)
38 COG3357 Predicted transcriptio 42.9 14 0.0003 21.7 1.0 24 1-24 56-86 (97)
39 PF06945 DUF1289: Protein of u 42.4 9.7 0.00021 19.6 0.3 12 83-94 13-24 (51)
40 PF00181 Ribosomal_L2: Ribosom 41.3 23 0.00049 19.7 1.7 19 52-70 58-76 (77)
41 PF05766 NinG: Bacteriophage L 39.1 37 0.0008 22.5 2.6 31 3-36 6-36 (189)
42 PRK14890 putative Zn-ribbon RN 37.2 8.7 0.00019 20.6 -0.4 8 4-11 8-15 (59)
43 PF00643 zf-B_box: B-box zinc 35.5 40 0.00086 15.9 1.9 35 3-39 3-38 (42)
44 cd06962 NR_DBD_FXR DNA-binding 34.7 23 0.00051 20.1 1.1 24 4-27 2-31 (84)
45 PF07591 PT-HINT: Pretoxin HIN 34.4 32 0.00069 21.1 1.7 20 54-73 68-87 (130)
46 PF13248 zf-ribbon_3: zinc-rib 33.6 28 0.0006 15.1 1.0 18 4-21 3-23 (26)
47 KOG1338|consensus 33.2 33 0.00072 25.6 1.8 20 52-71 39-58 (466)
48 PF13717 zinc_ribbon_4: zinc-r 30.5 28 0.00062 16.4 0.8 11 14-24 25-35 (36)
49 PF13878 zf-C2H2_3: zinc-finge 29.8 64 0.0014 15.6 2.1 15 14-28 13-27 (41)
50 PF09416 UPF1_Zn_bind: RNA hel 29.4 23 0.00051 22.6 0.5 25 5-30 2-29 (152)
51 PF04570 DUF581: Protein of un 29.4 40 0.00087 17.9 1.4 12 23-34 39-50 (58)
52 cd06970 NR_DBD_PNR DNA-binding 28.7 30 0.00065 20.0 0.9 25 2-26 5-35 (92)
53 PRK06005 flgA flagellar basal 28.3 38 0.00082 21.6 1.3 16 54-69 33-48 (160)
54 PF13842 Tnp_zf-ribbon_2: DDE_ 27.5 23 0.00049 16.4 0.2 22 5-27 2-28 (32)
55 COG2089 SpsE Sialic acid synth 27.5 42 0.00091 24.3 1.5 29 52-80 287-315 (347)
56 PRK01103 formamidopyrimidine/5 27.5 15 0.00032 25.4 -0.7 27 5-32 247-273 (274)
57 COG1261 FlgA Flagellar basal b 27.4 40 0.00088 22.8 1.4 18 52-69 93-110 (220)
58 cd07170 NR_DBD_ERR DNA-binding 27.4 23 0.0005 20.7 0.2 23 3-25 4-32 (97)
59 COG4050 Uncharacterized protei 27.0 58 0.0013 20.2 1.9 7 87-93 100-106 (152)
60 TIGR03170 flgA_cterm flagella 26.8 39 0.00086 20.0 1.2 13 57-69 2-14 (122)
61 cd06964 NR_DBD_RAR DNA-binding 26.7 39 0.00085 19.2 1.1 25 3-27 4-34 (85)
62 PRK14891 50S ribosomal protein 26.7 64 0.0014 20.1 2.1 36 2-37 3-44 (131)
63 KOG2858|consensus 26.5 19 0.00042 26.2 -0.2 31 3-34 17-48 (390)
64 cd07157 2DBD_NR_DBD1 The first 26.0 37 0.00079 19.3 0.9 22 5-26 2-29 (86)
65 PF09885 DUF2112: Uncharacteri 25.7 20 0.00044 22.5 -0.2 18 68-93 85-102 (143)
66 PRK00807 50S ribosomal protein 25.7 60 0.0013 16.7 1.6 32 4-35 2-39 (52)
67 KOG0438|consensus 25.6 50 0.0011 23.6 1.6 17 55-71 129-145 (312)
68 PF02069 Metallothio_Pro: Prok 24.7 55 0.0012 17.1 1.3 12 23-34 28-39 (52)
69 cd06966 NR_DBD_CAR DNA-binding 24.4 39 0.00084 19.6 0.8 22 5-26 2-29 (94)
70 cd06967 NR_DBD_TR2_like DNA-bi 24.2 41 0.00089 19.2 0.9 26 3-28 3-34 (87)
71 cd07160 NR_DBD_LXR DNA-binding 24.0 39 0.00085 19.9 0.8 24 3-26 18-47 (101)
72 PRK04016 DNA-directed RNA poly 24.0 37 0.00081 18.4 0.6 12 1-12 2-13 (62)
73 PRK11479 hypothetical protein; 23.8 45 0.00097 23.4 1.1 18 57-74 59-76 (274)
74 PF00098 zf-CCHC: Zinc knuckle 23.8 67 0.0014 12.7 1.7 9 5-13 2-10 (18)
75 PRK14350 ligA NAD-dependent DN 23.6 86 0.0019 24.8 2.7 35 61-95 363-409 (669)
76 smart00154 ZnF_AN1 AN1-like Zi 23.4 56 0.0012 15.7 1.2 21 6-27 1-24 (39)
77 PF08792 A2L_zn_ribbon: A2L zi 23.2 60 0.0013 15.1 1.2 13 1-13 1-13 (33)
78 COG2888 Predicted Zn-ribbon RN 23.2 20 0.00043 19.3 -0.5 20 14-33 27-47 (61)
79 cd07172 NR_DBD_GR_PR DNA-bindi 23.0 31 0.00066 19.3 0.2 22 3-24 2-29 (78)
80 PF10571 UPF0547: Uncharacteri 22.8 82 0.0018 13.8 1.5 18 5-22 2-22 (26)
81 KOG4217|consensus 22.7 38 0.00083 25.9 0.7 22 2-23 268-295 (605)
82 TIGR03271 methan_mark_5 putati 22.3 27 0.0006 21.9 -0.1 18 68-93 84-101 (142)
83 TIGR02219 phage_NlpC_fam putat 22.2 53 0.0011 20.1 1.1 15 58-72 72-86 (134)
84 PRK14811 formamidopyrimidine-D 21.5 24 0.00052 24.4 -0.5 29 4-33 236-264 (269)
85 cd00064 FU Furin-like repeats. 21.3 75 0.0016 15.5 1.4 22 4-25 4-25 (49)
86 cd07168 NR_DBD_DHR4_like DNA-b 21.0 38 0.00083 19.4 0.3 24 3-26 6-35 (90)
87 PF10948 DUF2635: Protein of u 21.0 56 0.0012 16.6 0.9 15 60-74 32-46 (47)
88 cd06960 NR_DBD_HNF4A DNA-bindi 20.5 50 0.0011 18.1 0.7 21 6-26 1-27 (76)
89 PRK00241 nudC NADH pyrophospha 20.5 62 0.0014 22.2 1.3 11 3-13 99-109 (256)
90 KOG4846|consensus 20.4 34 0.00073 25.7 -0.0 41 5-46 134-182 (538)
91 cd07161 NR_DBD_EcR DNA-binding 20.3 35 0.00076 19.7 0.1 22 4-25 2-29 (91)
92 COG0361 InfA Translation initi 20.1 74 0.0016 17.9 1.3 12 62-73 46-57 (75)
No 1
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=99.53 E-value=3.3e-15 Score=73.91 Aligned_cols=37 Identities=43% Similarity=1.162 Sum_probs=33.9
Q ss_pred CcccCccccCCCCCCCceeecCHHHHHhhhhcccccc
Q psy14482 6 CGLCGETAKQKCSGCQLIYYCCREHQKIHWKKHKSHC 42 (95)
Q Consensus 6 C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~Hk~~C 42 (95)
|.+|+++++.+|++|+.++|||++||+.||..|+.+|
T Consensus 1 C~~C~~~~~~~C~~C~~~~YCs~~Cq~~~w~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGKPALKRCSRCKSVYYCSEECQRADWPYHKFEC 37 (37)
T ss_dssp -TTTSSCSSEEETTTSSSEESSHHHHHHHHHHHCCTH
T ss_pred CcCCCCCcCCcCCCCCCEEecCHHHHHHHHHHHhhhC
Confidence 7889998888999999999999999999998899876
No 2
>KOG1710|consensus
Probab=99.01 E-value=2.1e-11 Score=83.99 Aligned_cols=42 Identities=43% Similarity=0.993 Sum_probs=39.6
Q ss_pred CcCcccCcc-ccCCCCCCCceeecCHHHHHhhhhccccccCCc
Q psy14482 4 NICGLCGET-AKQKCSGCQLIYYCCREHQKIHWKKHKSHCRPM 45 (95)
Q Consensus 4 ~~C~~C~~~-~~~~C~~c~~~~ycs~~cq~~~w~~Hk~~C~~i 45 (95)
+.|..||++ +.++||.|+.+.||+.+||+.||..||+.|..+
T Consensus 320 ~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf~HKK~C~~L 362 (396)
T KOG1710|consen 320 QFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWFIHKKVCSFL 362 (396)
T ss_pred ccccccCCCCccchhhhhHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 579999998 599999999999999999999999999999987
No 3
>KOG2084|consensus
Probab=97.83 E-value=2.1e-05 Score=56.75 Aligned_cols=62 Identities=34% Similarity=0.599 Sum_probs=46.6
Q ss_pred hhhhccccccCCcccccc-ccccceEEEcCCCCCCcEEEeeCCceEccCCCCcccccc-----ccccc
Q psy14482 33 IHWKKHKSHCRPMKLCED-KVLGRYYIASRSIKAGEVVLREPPLVQGPCQMTGPVCLG-----CLKAI 94 (95)
Q Consensus 33 ~~w~~Hk~~C~~i~~~~~-~~~gR~~va~r~i~~geii~~E~p~~~~p~~~~~~~c~~-----C~~~~ 94 (95)
.+|..++......+.... +..||+++|+++|..|++|+.|.|++.+|.......|.+ |++..
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~Gr~~~a~~~i~~g~~i~~e~p~~~~p~~~~~~~c~~~~~~~C~~~~ 70 (482)
T KOG2084|consen 3 KDLKSDPRNGLNVEEVANSPELGRGLVATQAIEAGEVILEEEPLVVGPASKSCSRCLGCSCDHCRRCL 70 (482)
T ss_pred chhccCccccCCcccccCccccCcceeeecccCCCceEEecCcceeeecccCCccccccchhhhhcCC
Confidence 456665554444443333 478999999999999999999999999999976666665 76653
No 4
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=97.65 E-value=1.6e-05 Score=42.12 Aligned_cols=45 Identities=20% Similarity=0.666 Sum_probs=39.1
Q ss_pred cCcccCc----cccCCCCCCCceeecCHHHHHhhhhccccccCCccccc
Q psy14482 5 ICGLCGE----TAKQKCSGCQLIYYCCREHQKIHWKKHKSHCRPMKLCE 49 (95)
Q Consensus 5 ~C~~C~~----~~~~~C~~c~~~~ycs~~cq~~~w~~Hk~~C~~i~~~~ 49 (95)
.|.+|++ .....|..|...+|||+++-..|.+.|++.|..++...
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D~e~H~~~c~~LRqvN 49 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDDYEEHRQLCERLRQVN 49 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHHHHHHhHHHHHHHHHHHHHhc
Confidence 3777887 56889999999999999999999999999998887543
No 5
>KOG3612|consensus
Probab=97.59 E-value=7.9e-06 Score=60.42 Aligned_cols=38 Identities=37% Similarity=0.797 Sum_probs=32.3
Q ss_pred CcccCccccCCCCCCCceeecCHHHHHhhhhccccccCCc
Q psy14482 6 CGLCGETAKQKCSGCQLIYYCCREHQKIHWKKHKSHCRPM 45 (95)
Q Consensus 6 C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~Hk~~C~~i 45 (95)
|++|...+..-| |-...|||.+||+.||..|+..|+.-
T Consensus 530 C~nC~~EAiy~C--CWNTSYCsveCQQ~HW~~H~ksCrrk 567 (588)
T KOG3612|consen 530 CYNCLDEAIYHC--CWNTSYCSVECQQGHWPEHRKSCRRK 567 (588)
T ss_pred HHhhhHHHHHHh--hccccccCcchhhccchhHhhhhccc
Confidence 777887777666 55789999999999999999999753
No 6
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=97.36 E-value=0.00015 Score=44.45 Aligned_cols=27 Identities=48% Similarity=0.680 Sum_probs=22.1
Q ss_pred cceEEEcCCCCCCcEEEeeCCceEccC
Q psy14482 54 GRYYIASRSIKAGEVVLREPPLVQGPC 80 (95)
Q Consensus 54 gR~~va~r~i~~geii~~E~p~~~~p~ 80 (95)
||+++|+++|++||+|+.+.++++.+.
T Consensus 1 GrGl~At~dI~~Ge~I~~p~~~~~~~~ 27 (162)
T PF00856_consen 1 GRGLFATRDIKAGEVILIPRPAILTPD 27 (162)
T ss_dssp SEEEEESS-B-TTEEEEEESEEEEEHH
T ss_pred CEEEEECccCCCCCEEEEECcceEEeh
Confidence 899999999999999998888887754
No 7
>KOG2061|consensus
Probab=96.63 E-value=0.0011 Score=47.36 Aligned_cols=46 Identities=37% Similarity=0.912 Sum_probs=40.7
Q ss_pred CCcCcccCccccCCCCCCCceeecCHHHHHhhhhc-cccccCCcccc
Q psy14482 3 DNICGLCGETAKQKCSGCQLIYYCCREHQKIHWKK-HKSHCRPMKLC 48 (95)
Q Consensus 3 ~~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~-Hk~~C~~i~~~ 48 (95)
+..|..|+..+...|+.|+.+.|||..+|..||.. |+..|...+..
T Consensus 136 ~~~~~~~~~~a~~~~~~~~~a~~~S~~~q~~d~~~~~~~a~aq~~~~ 182 (362)
T KOG2061|consen 136 ADLCGSCGCSAPAACSPCKAAAYCSKKHQSLDWPKGHKDACAQPSTL 182 (362)
T ss_pred cchhccCcccCcccccccchhhhcCchhhcccccccccccccCcccc
Confidence 45688888888999999999999999999999999 99999876644
No 8
>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=96.10 E-value=0.0031 Score=29.38 Aligned_cols=28 Identities=36% Similarity=0.942 Sum_probs=21.8
Q ss_pred CcCcccCccccCCCCCCCceeecCHHHHH
Q psy14482 4 NICGLCGETAKQKCSGCQLIYYCCREHQK 32 (95)
Q Consensus 4 ~~C~~C~~~~~~~C~~c~~~~ycs~~cq~ 32 (95)
..|.+|+.++..+|.+|. ..|||-+|-+
T Consensus 3 ~~C~vC~~~~kY~Cp~C~-~~~CSl~C~k 30 (30)
T PF04438_consen 3 KLCSVCGNPAKYRCPRCG-ARYCSLACYK 30 (30)
T ss_dssp EEETSSSSEESEE-TTT---EESSHHHHH
T ss_pred CCCccCcCCCEEECCCcC-CceeCcEeEC
Confidence 578999998899999998 6799998864
No 9
>PLN03158 methionine aminopeptidase; Provisional
Probab=96.05 E-value=0.0041 Score=45.17 Aligned_cols=37 Identities=30% Similarity=0.736 Sum_probs=32.4
Q ss_pred CcCcccCccccCCCCCCCc-------eeecCHHHHHhhhhcccc
Q psy14482 4 NICGLCGETAKQKCSGCQL-------IYYCCREHQKIHWKKHKS 40 (95)
Q Consensus 4 ~~C~~C~~~~~~~C~~c~~-------~~ycs~~cq~~~w~~Hk~ 40 (95)
..|..|++++.+.|-.|.. .++||.+|=+..|+.||.
T Consensus 10 ~~c~~c~~~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~ 53 (396)
T PLN03158 10 LACARCSKPAHLQCPKCLELKLPREGASFCSQDCFKAAWSSHKS 53 (396)
T ss_pred ccccCCCCcccccCccchhcCCCCCCceeECHHHHHHHHHHHHH
Confidence 4699999999999999853 689999999999999875
No 10
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=94.92 E-value=0.012 Score=29.69 Aligned_cols=33 Identities=21% Similarity=0.437 Sum_probs=24.9
Q ss_pred CCCcCcccCccccCCCCCCCceeecCHHHHHhhhhc
Q psy14482 2 FDNICGLCGETAKQKCSGCQLIYYCCREHQKIHWKK 37 (95)
Q Consensus 2 ~~~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~ 37 (95)
|.+.|..|.+.-.. .-...-|||++|+..|+..
T Consensus 5 F~~yC~~Cdk~~~~---~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 5 FNDYCIVCDKQIDP---PDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hhhHHHHhhccccC---CCCCccccCHHHHhHhhhc
Confidence 67788888875322 3345789999999999876
No 11
>KOG3362|consensus
Probab=94.44 E-value=0.013 Score=36.89 Aligned_cols=33 Identities=30% Similarity=0.743 Sum_probs=29.1
Q ss_pred CcCcccCccccCCCCCCCceeecCHHHHHhhhhc
Q psy14482 4 NICGLCGETAKQKCSGCQLIYYCCREHQKIHWKK 37 (95)
Q Consensus 4 ~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~ 37 (95)
..|++||-.+...|..|. ..|||..|...|...
T Consensus 119 ~fCaVCG~~S~ysC~~CG-~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 119 KFCAVCGYDSKYSCVNCG-TKYCSVRCLKTHNET 151 (156)
T ss_pred hhhhhcCCCchhHHHhcC-Cceeechhhhhcccc
Confidence 469999988999999998 899999999888653
No 12
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=94.09 E-value=0.077 Score=30.76 Aligned_cols=30 Identities=17% Similarity=0.011 Sum_probs=24.9
Q ss_pred cccccceEEEcCCCCCCcEEEeeCCceEcc
Q psy14482 50 DKVLGRYYIASRSIKAGEVVLREPPLVQGP 79 (95)
Q Consensus 50 ~~~~gR~~va~r~i~~geii~~E~p~~~~p 79 (95)
.+..|++++|+++|++|++|+...+.+..+
T Consensus 7 ~~~~G~gl~a~~~i~~g~~i~~~~g~~~~~ 36 (116)
T smart00317 7 SPGKGWGVRATEDIPKGEFIGEYVGEIITS 36 (116)
T ss_pred cCCCcEEEEECCccCCCCEEEEEEeEEECH
Confidence 357799999999999999888777776654
No 13
>KOG2857|consensus
Probab=92.80 E-value=0.077 Score=33.40 Aligned_cols=37 Identities=38% Similarity=0.876 Sum_probs=29.4
Q ss_pred cCcccCccc-cCCCCCCCceeecCHHHHHhhhhcccc--ccCCcc
Q psy14482 5 ICGLCGETA-KQKCSGCQLIYYCCREHQKIHWKKHKS--HCRPMK 46 (95)
Q Consensus 5 ~C~~C~~~~-~~~C~~c~~~~ycs~~cq~~~w~~Hk~--~C~~i~ 46 (95)
.|..|.+.. ..+|..|. +.|||-.| |+.||. .|.+.+
T Consensus 7 tC~ic~e~~~KYKCpkC~-vPYCSl~C----fKiHk~tPq~~~ve 46 (157)
T KOG2857|consen 7 TCVICLESEIKYKCPKCS-VPYCSLPC----FKIHKSTPQCETVE 46 (157)
T ss_pred eehhhhcchhhccCCCCC-Cccccchh----hhhccCCccccccC
Confidence 578888865 88999996 99999998 666776 676654
No 14
>PRK01343 zinc-binding protein; Provisional
Probab=87.31 E-value=0.69 Score=24.70 Aligned_cols=30 Identities=17% Similarity=0.545 Sum_probs=21.2
Q ss_pred CCcCcccCccccCCCCCCCceeecCHHHHHhhhhc
Q psy14482 3 DNICGLCGETAKQKCSGCQLIYYCCREHQKIHWKK 37 (95)
Q Consensus 3 ~~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~ 37 (95)
...|-.|+++... ....|||+.|+..|--.
T Consensus 9 ~~~CP~C~k~~~~-----~~rPFCS~RC~~iDLg~ 38 (57)
T PRK01343 9 TRPCPECGKPSTR-----EAYPFCSERCRDIDLNR 38 (57)
T ss_pred CCcCCCCCCcCcC-----CCCcccCHHHhhhhHHH
Confidence 3468888876542 34679999999997543
No 15
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=86.12 E-value=0.51 Score=25.35 Aligned_cols=32 Identities=19% Similarity=0.438 Sum_probs=23.8
Q ss_pred CCcCcccCccccCCCCCCCceeecCHHHHHhhhhcccc
Q psy14482 3 DNICGLCGETAKQKCSGCQLIYYCCREHQKIHWKKHKS 40 (95)
Q Consensus 3 ~~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~Hk~ 40 (95)
...|-+||++-.. .-.|||++|+...++..+.
T Consensus 3 HkHC~~CG~~Ip~------~~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 3 HKHCPVCGKPIPP------DESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCcCCcCCCcCCc------chhhhCHHHHHHHHHHHHH
Confidence 4568888886432 3679999999988887554
No 16
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=81.70 E-value=0.27 Score=24.58 Aligned_cols=31 Identities=26% Similarity=0.742 Sum_probs=19.9
Q ss_pred CCCcCcccCccc--cCCCCCC-CceeecCHHHHH
Q psy14482 2 FDNICGLCGETA--KQKCSGC-QLIYYCCREHQK 32 (95)
Q Consensus 2 ~~~~C~~C~~~~--~~~C~~c-~~~~ycs~~cq~ 32 (95)
....|.+|+.+. .++-..+ ..|.|||+.|..
T Consensus 7 p~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR~ 40 (42)
T PF10013_consen 7 PSKICPVCGRPFTWRKKWARCWDEVKYCSDRCRR 40 (42)
T ss_pred CCCcCcccCCcchHHHHHHHhchhhccHHHHhcc
Confidence 345788888764 3333333 258899998865
No 17
>PF08666 SAF: SAF domain; InterPro: IPR013974 This entry includes a range of different proteins, such as antifreeze proteins, flagellar FlgA proteins, and CpaB pilus proteins. ; PDB: 1C89_A 3NLA_A 3RDN_A 1C8A_A 3FRN_A 1WVO_A 3K3S_H 3G8R_B 1XUU_A 1XUZ_A ....
Probab=77.86 E-value=1.8 Score=22.63 Aligned_cols=15 Identities=47% Similarity=0.736 Sum_probs=11.3
Q ss_pred ceEEEcCCCCCCcEE
Q psy14482 55 RYYIASRSIKAGEVV 69 (95)
Q Consensus 55 R~~va~r~i~~geii 69 (95)
+.++|+++|++|++|
T Consensus 2 ~vvVA~~di~~G~~i 16 (63)
T PF08666_consen 2 RVVVAARDIPAGTVI 16 (63)
T ss_dssp SEEEESSTB-TT-BE
T ss_pred cEEEEeCccCCCCEE
Confidence 468899999999988
No 18
>KOG4442|consensus
Probab=77.52 E-value=1.7 Score=34.00 Aligned_cols=44 Identities=16% Similarity=0.242 Sum_probs=34.5
Q ss_pred cCHHHHHhhhhccccccCCccccccccccceEEEcCCCCCCcEEEe
Q psy14482 26 CCREHQKIHWKKHKSHCRPMKLCEDKVLGRYYIASRSIKAGEVVLR 71 (95)
Q Consensus 26 cs~~cq~~~w~~Hk~~C~~i~~~~~~~~gR~~va~r~i~~geii~~ 71 (95)
|+..|+.+-.+.| ++.+.++-..+..|-++.|..+|++|+.|+.
T Consensus 105 cg~~C~NQRFQkk--qyA~vevF~Te~KG~GLRA~~dI~~g~FI~E 148 (729)
T KOG4442|consen 105 CGVYCKNQRFQKK--QYAKVEVFLTEKKGCGLRAEEDIPKGQFILE 148 (729)
T ss_pred ccccccchhhhhh--ccCceeEEEecCcccceeeccccCCCcEEee
Confidence 5567777766654 4556677777889999999999999998863
No 19
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.03 E-value=0.13 Score=26.56 Aligned_cols=31 Identities=26% Similarity=0.745 Sum_probs=21.6
Q ss_pred CCcCcccCccc--cCCCCCCC-ceeecCHHHHHh
Q psy14482 3 DNICGLCGETA--KQKCSGCQ-LIYYCCREHQKI 33 (95)
Q Consensus 3 ~~~C~~C~~~~--~~~C~~c~-~~~ycs~~cq~~ 33 (95)
..+|.+|+.+. .++-.+|- .|.|||+.|.+.
T Consensus 12 ~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCrr~ 45 (54)
T COG4338 12 DKICPVCQRPFSWRKKWARCWDEVKYCSERCRRL 45 (54)
T ss_pred hhhhhhhcCchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788888774 45555553 578999998753
No 20
>KOG1085|consensus
Probab=73.77 E-value=4.5 Score=28.74 Aligned_cols=33 Identities=18% Similarity=0.109 Sum_probs=28.6
Q ss_pred cccccCCccccccccccceEEEcCCCCCCcEEE
Q psy14482 38 HKSHCRPMKLCEDKVLGRYYIASRSIKAGEVVL 70 (95)
Q Consensus 38 Hk~~C~~i~~~~~~~~gR~~va~r~i~~geii~ 70 (95)
.+..|..+.+.+.+..||+++|.+++..||.|+
T Consensus 251 l~g~~egl~~~~~dgKGRGv~a~~~F~rgdFVV 283 (392)
T KOG1085|consen 251 LKGTNEGLLEVYKDGKGRGVRAKVNFERGDFVV 283 (392)
T ss_pred HhccccceeEEeeccccceeEeecccccCceEE
Confidence 445688888888899999999999999999774
No 21
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=73.00 E-value=2 Score=19.83 Aligned_cols=23 Identities=30% Similarity=0.927 Sum_probs=12.2
Q ss_pred CCcCcccCccc-------cCCCCCCCceee
Q psy14482 3 DNICGLCGETA-------KQKCSGCQLIYY 25 (95)
Q Consensus 3 ~~~C~~C~~~~-------~~~C~~c~~~~y 25 (95)
...|..||.+. .+.|..|....|
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~~y 32 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHEHY 32 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-EE-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCEeC
Confidence 45788899873 567888876655
No 22
>KOG2738|consensus
Probab=65.19 E-value=3 Score=29.79 Aligned_cols=40 Identities=35% Similarity=0.738 Sum_probs=32.0
Q ss_pred CcC--cccCccccCCCCCCC-----ceeecCHHHHHhhhhccccccC
Q psy14482 4 NIC--GLCGETAKQKCSGCQ-----LIYYCCREHQKIHWKKHKSHCR 43 (95)
Q Consensus 4 ~~C--~~C~~~~~~~C~~c~-----~~~ycs~~cq~~~w~~Hk~~C~ 43 (95)
..| ..|++++.+.|..|. ..++|+.+|-+.-|..||..-.
T Consensus 7 ~~c~~~~c~~~a~l~Cp~c~~~~i~~~~fc~q~cf~~~w~~hK~~h~ 53 (369)
T KOG2738|consen 7 ISCEGLQCGSEASLQCPTCLKLGIKSAYFCAQECFKNSWLSHKKLHR 53 (369)
T ss_pred ceeeccccCChhhccCchhhhcCCCcccccCchhhhcchhhhhhhcc
Confidence 456 568888888898874 3589999999999999987653
No 23
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=63.12 E-value=6.2 Score=21.00 Aligned_cols=32 Identities=16% Similarity=0.453 Sum_probs=16.4
Q ss_pred cCcccCccccCCCCCCCceeecCHHHHHhhhhc
Q psy14482 5 ICGLCGETAKQKCSGCQLIYYCCREHQKIHWKK 37 (95)
Q Consensus 5 ~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~ 37 (95)
.|..|+++....=.. ....+||+.|+.+|--+
T Consensus 4 ~CP~C~k~~~~~~~n-~~rPFCS~RCk~iDLg~ 35 (57)
T PF03884_consen 4 KCPICGKPVEWSPEN-PFRPFCSERCKLIDLGR 35 (57)
T ss_dssp E-TTT--EEE-SSSS-S--SSSSHHHHHHHHS-
T ss_pred cCCCCCCeecccCCC-CcCCcccHhhcccCHHH
Confidence 577777764332111 34569999999997554
No 24
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=61.13 E-value=5.4 Score=30.93 Aligned_cols=36 Identities=25% Similarity=0.647 Sum_probs=26.4
Q ss_pred cCcccCcc----ccCCCCCCC-------ceeecCHHHHHhhhhcccc
Q psy14482 5 ICGLCGET----AKQKCSGCQ-------LIYYCCREHQKIHWKKHKS 40 (95)
Q Consensus 5 ~C~~C~~~----~~~~C~~c~-------~~~ycs~~cq~~~w~~Hk~ 40 (95)
.+.+|... +.+.|-.|. ..++||.+|=+..|+.||.
T Consensus 61 ~~~~c~~h~~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~ 107 (606)
T PLN03144 61 KVAVCSVHPSEPATLQCVGCVKAKLPVSKSYHCSPKCFSDAWRHHRV 107 (606)
T ss_pred cceeEeecCCCcccccCccchhcCCCcCcceeeCHHHHHHHHHHHHH
Confidence 44566553 356777763 2579999999999999876
No 25
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=59.67 E-value=7 Score=20.19 Aligned_cols=15 Identities=47% Similarity=0.791 Sum_probs=12.6
Q ss_pred ceEEEcCCCCCCcEE
Q psy14482 55 RYYIASRSIKAGEVV 69 (95)
Q Consensus 55 R~~va~r~i~~geii 69 (95)
+.++++++|.+|++|
T Consensus 2 ~v~va~~~i~~G~~i 16 (64)
T smart00858 2 RVVVAARDLPAGEVI 16 (64)
T ss_pred CEEEEeCccCCCCCc
Confidence 457889999999987
No 26
>KOG4317|consensus
Probab=55.14 E-value=4.2 Score=29.14 Aligned_cols=28 Identities=29% Similarity=0.910 Sum_probs=22.1
Q ss_pred cCcccCcc-ccCCCCCCCceeecCHHHHHh
Q psy14482 5 ICGLCGET-AKQKCSGCQLIYYCCREHQKI 33 (95)
Q Consensus 5 ~C~~C~~~-~~~~C~~c~~~~ycs~~cq~~ 33 (95)
.|..|++. .-.+|.+|. ..|||-.|-+.
T Consensus 9 ~C~ic~vq~~~YtCPRCn-~~YCsl~CYr~ 37 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCN-LLYCSLKCYRN 37 (383)
T ss_pred eccccccccccccCCCCC-ccceeeeeecC
Confidence 68888886 478999997 78888777554
No 27
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.66 E-value=12 Score=20.41 Aligned_cols=35 Identities=14% Similarity=0.347 Sum_probs=20.2
Q ss_pred CCCcCcccCccccCCCCCCCceeecCHHHHHhhhhc
Q psy14482 2 FDNICGLCGETAKQKCSGCQLIYYCCREHQKIHWKK 37 (95)
Q Consensus 2 ~~~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~ 37 (95)
....|..|+++..-. ..=...-+||+.||..|-.+
T Consensus 6 ~~v~CP~Cgkpv~w~-~~s~frPFCSkRCklIDLg~ 40 (65)
T COG3024 6 ITVPCPTCGKPVVWG-EESPFRPFCSKRCKLIDLGE 40 (65)
T ss_pred ccccCCCCCCccccc-ccCCcCcchhHhhhhcchhh
Confidence 345677777753110 00113458999999987554
No 28
>KOG4215|consensus
Probab=54.20 E-value=9.4 Score=28.01 Aligned_cols=35 Identities=31% Similarity=0.874 Sum_probs=22.7
Q ss_pred CCcCcccCccc------cCCCCCCCceeecCHHHHHhhhhccccccC
Q psy14482 3 DNICGLCGETA------KQKCSGCQLIYYCCREHQKIHWKKHKSHCR 43 (95)
Q Consensus 3 ~~~C~~C~~~~------~~~C~~c~~~~ycs~~cq~~~w~~Hk~~C~ 43 (95)
...|++||-.+ ...|-+|+-++- +.-|+.|+..|+
T Consensus 19 ~~~CaICGDkaTGKHYGA~SCdGCKGFFR------RSVrk~~~YtCR 59 (432)
T KOG4215|consen 19 AEFCAICGDKATGKHYGAISCDGCKGFFR------RSVRKNHQYTCR 59 (432)
T ss_pred cchhheeCCcccccccceeecCcchHHHH------HHHHhcceeeee
Confidence 45799999874 569999985442 334555544443
No 29
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=54.04 E-value=5.4 Score=18.90 Aligned_cols=22 Identities=32% Similarity=0.911 Sum_probs=11.8
Q ss_pred CcCcccCccc-----------cCCCCCCCceee
Q psy14482 4 NICGLCGETA-----------KQKCSGCQLIYY 25 (95)
Q Consensus 4 ~~C~~C~~~~-----------~~~C~~c~~~~y 25 (95)
+.|..|+.+. ...|..|..+-|
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCEEe
Confidence 3688888752 357888887766
No 30
>TIGR03569 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Probab=49.74 E-value=13 Score=26.57 Aligned_cols=27 Identities=26% Similarity=0.463 Sum_probs=20.4
Q ss_pred ccceEEEcCCCCCCcEEEeeCCceEcc
Q psy14482 53 LGRYYIASRSIKAGEVVLREPPLVQGP 79 (95)
Q Consensus 53 ~gR~~va~r~i~~geii~~E~p~~~~p 79 (95)
..|.+++.++|++|+++-.|.-.+.-|
T Consensus 276 ~rrsl~a~~di~~G~~lt~~~l~~~RP 302 (329)
T TIGR03569 276 ARKSLVAAKDIKKGEIFTEDNLTVKRP 302 (329)
T ss_pred cceEEEEccCcCCCCEecHHheeeeCC
Confidence 478999999999999996654333333
No 31
>TIGR03586 PseI pseudaminic acid synthase.
Probab=49.72 E-value=12 Score=26.75 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=18.0
Q ss_pred ccceEEEcCCCCCCcEEEeeC
Q psy14482 53 LGRYYIASRSIKAGEVVLREP 73 (95)
Q Consensus 53 ~gR~~va~r~i~~geii~~E~ 73 (95)
..|.+++.++|++|+++-.|.
T Consensus 274 ~rrsl~a~~di~~G~~it~~~ 294 (327)
T TIGR03586 274 FRRSLYVVKDIKKGETFTEEN 294 (327)
T ss_pred eeEEEEEccCcCCCCEecHHh
Confidence 478999999999999996554
No 32
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=48.13 E-value=12 Score=22.46 Aligned_cols=27 Identities=33% Similarity=0.891 Sum_probs=20.0
Q ss_pred CCCCcCcccCccc------cCCCCCCCceeecC
Q psy14482 1 MFDNICGLCGETA------KQKCSGCQLIYYCC 27 (95)
Q Consensus 1 ~~~~~C~~C~~~~------~~~C~~c~~~~ycs 27 (95)
|.+..|.+|+.++ ...|.+|+..+-.+
T Consensus 4 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~ 36 (107)
T cd06955 4 NVPRICGVCGDRATGFHFNAMTCEGCKGFFRRS 36 (107)
T ss_pred CCCCCCeecCCcCcccEECcceeeeecceecce
Confidence 3567899999864 67899998765443
No 33
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=47.96 E-value=4.7 Score=19.50 Aligned_cols=20 Identities=30% Similarity=0.722 Sum_probs=14.9
Q ss_pred CCceeecCHHHHHhh-hhccc
Q psy14482 20 CQLIYYCCREHQKIH-WKKHK 39 (95)
Q Consensus 20 c~~~~ycs~~cq~~~-w~~Hk 39 (95)
|-.+.|||..|-+.| |..|.
T Consensus 6 cpkiGYCS~~CsKt~vWa~s~ 26 (39)
T PF08189_consen 6 CPKIGYCSSKCSKTDVWAFSQ 26 (39)
T ss_pred CcccceecccccccceeeecC
Confidence 445899999998875 66654
No 34
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=46.95 E-value=19 Score=19.46 Aligned_cols=33 Identities=18% Similarity=0.358 Sum_probs=20.2
Q ss_pred CcCcccCccccCCCCCCCceeecCHHHHHhhhhc
Q psy14482 4 NICGLCGETAKQKCSGCQLIYYCCREHQKIHWKK 37 (95)
Q Consensus 4 ~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~~ 37 (95)
..|-.|+++..-.=.. ...-+||+.|+..|--+
T Consensus 7 v~CP~C~k~~~w~~~~-~~rPFCS~RCk~IDLg~ 39 (62)
T PRK00418 7 VNCPTCGKPVEWGEIS-PFRPFCSKRCQLIDLGE 39 (62)
T ss_pred ccCCCCCCcccccCCC-CcCCcccHHHHhhhHHH
Confidence 4677777764321111 23468999999997554
No 35
>PF12879 SICA_C: SICA C-terminal inner membrane domain ; InterPro: IPR024288 The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain []. The conserved C-terminal domain is thought to remain within the cytoplasm of the infected erythrocyte.
Probab=46.47 E-value=4 Score=25.45 Aligned_cols=53 Identities=23% Similarity=0.453 Sum_probs=32.0
Q ss_pred CHHHHHhhhhccccccCCccccccccccceEEEcCCCCCCcEEEeeCCceEccCC
Q psy14482 27 CREHQKIHWKKHKSHCRPMKLCEDKVLGRYYIASRSIKAGEVVLREPPLVQGPCQ 81 (95)
Q Consensus 27 s~~cq~~~w~~Hk~~C~~i~~~~~~~~gR~~va~r~i~~geii~~E~p~~~~p~~ 81 (95)
-.+||+.+|+.++. ..+++...+-.|.-......+...++.+.-.|+-.+|..
T Consensus 75 LdEcqk~~~~ln~~--DFLei~v~EFm~~e~~~~EqVpkE~v~me~vpme~vp~E 127 (138)
T PF12879_consen 75 LDECQKGEWELNKK--DFLEICVEEFMGSENMEEEQVPKEEVLMEGVPMEQVPME 127 (138)
T ss_pred HHHHHcccchhhhh--HHHHHHHHHHhcccccccccCcHhhcccccCcccccchh
Confidence 36899999999776 334443333334444455566666666655666666654
No 36
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=45.38 E-value=15 Score=22.99 Aligned_cols=20 Identities=25% Similarity=0.351 Sum_probs=16.9
Q ss_pred cccccceEEEcCCCCCCcEE
Q psy14482 50 DKVLGRYYIASRSIKAGEVV 69 (95)
Q Consensus 50 ~~~~gR~~va~r~i~~geii 69 (95)
.+..+..++|+++|.+|++|
T Consensus 15 ~~~~~~VvVA~r~L~rGevI 34 (141)
T PRK12618 15 QPAAAETVVAARTIRALTVI 34 (141)
T ss_pred ccceeEEEEEccCcCCCCCc
Confidence 35567889999999999988
No 37
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.99 E-value=14 Score=15.73 Aligned_cols=17 Identities=29% Similarity=0.872 Sum_probs=11.0
Q ss_pred cCcccCcc---ccCCCCCCC
Q psy14482 5 ICGLCGET---AKQKCSGCQ 21 (95)
Q Consensus 5 ~C~~C~~~---~~~~C~~c~ 21 (95)
.|.+|++. ..+.|..|.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCCcCcchhhhC
Confidence 47778876 256676665
No 38
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=42.87 E-value=14 Score=21.66 Aligned_cols=24 Identities=21% Similarity=0.563 Sum_probs=17.0
Q ss_pred CCCCcCcccCccc-------cCCCCCCCcee
Q psy14482 1 MFDNICGLCGETA-------KQKCSGCQLIY 24 (95)
Q Consensus 1 ~~~~~C~~C~~~~-------~~~C~~c~~~~ 24 (95)
|-|..|.+||-.. ..+|..|++-|
T Consensus 56 v~Pa~CkkCGfef~~~~ik~pSRCP~CKSE~ 86 (97)
T COG3357 56 VRPARCKKCGFEFRDDKIKKPSRCPKCKSEW 86 (97)
T ss_pred ecChhhcccCccccccccCCcccCCcchhhc
Confidence 4578899998752 45788887644
No 39
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=42.44 E-value=9.7 Score=19.55 Aligned_cols=12 Identities=33% Similarity=0.902 Sum_probs=10.1
Q ss_pred Cccccccccccc
Q psy14482 83 TGPVCLGCLKAI 94 (95)
Q Consensus 83 ~~~~c~~C~~~~ 94 (95)
..-+|.+|+|++
T Consensus 13 ~~~~C~GC~RT~ 24 (51)
T PF06945_consen 13 SDGVCRGCGRTL 24 (51)
T ss_pred CCCccCCCCCcH
Confidence 478999999975
No 40
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=41.34 E-value=23 Score=19.71 Aligned_cols=19 Identities=32% Similarity=0.539 Sum_probs=15.7
Q ss_pred cccceEEEcCCCCCCcEEE
Q psy14482 52 VLGRYYIASRSIKAGEVVL 70 (95)
Q Consensus 52 ~~gR~~va~r~i~~geii~ 70 (95)
..-++++|+..++.||+|.
T Consensus 58 g~~~yiiA~eg~~vGd~I~ 76 (77)
T PF00181_consen 58 GEKRYIIAPEGMKVGDIIE 76 (77)
T ss_dssp SEEEEEEEBTTEBTTEEEE
T ss_pred CcEEEEEeECCCcCCCEEE
Confidence 3457899999999999885
No 41
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=39.08 E-value=37 Score=22.50 Aligned_cols=31 Identities=26% Similarity=0.251 Sum_probs=21.5
Q ss_pred CCcCcccCccccCCCCCCCceeecCHHHHHhhhh
Q psy14482 3 DNICGLCGETAKQKCSGCQLIYYCCREHQKIHWK 36 (95)
Q Consensus 3 ~~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~~w~ 36 (95)
+..|.+|+....-.=+ ..++||++|-...++
T Consensus 6 ~rKCKvCg~~F~P~~s---~q~vCSpeCa~a~~k 36 (189)
T PF05766_consen 6 RRKCKVCGEWFVPARS---NQKVCSPECAIALAK 36 (189)
T ss_pred CCcCcccCCccccCCC---ceeeeCHHHHhHHHH
Confidence 4678888876433222 468999999976665
No 42
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=37.17 E-value=8.7 Score=20.62 Aligned_cols=8 Identities=38% Similarity=0.862 Sum_probs=3.9
Q ss_pred CcCcccCc
Q psy14482 4 NICGLCGE 11 (95)
Q Consensus 4 ~~C~~C~~ 11 (95)
..|.-|+.
T Consensus 8 ~~CtSCg~ 15 (59)
T PRK14890 8 PKCTSCGI 15 (59)
T ss_pred ccccCCCC
Confidence 34555554
No 43
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=35.45 E-value=40 Score=15.91 Aligned_cols=35 Identities=26% Similarity=0.370 Sum_probs=23.1
Q ss_pred CCcCcccCcc-ccCCCCCCCceeecCHHHHHhhhhccc
Q psy14482 3 DNICGLCGET-AKQKCSGCQLIYYCCREHQKIHWKKHK 39 (95)
Q Consensus 3 ~~~C~~C~~~-~~~~C~~c~~~~ycs~~cq~~~w~~Hk 39 (95)
...|..+... ....|..|+. ..| ..|...+-+.|+
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~-~~C-~~C~~~~H~~H~ 38 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNE-PLC-SECTVSGHKGHK 38 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTE-EEE-HHHHHTSTTTSE
T ss_pred CccCccCCccceEEEecCCCC-ccC-ccCCCCCCCCCE
Confidence 4678888877 6788999885 666 567666544443
No 44
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=34.74 E-value=23 Score=20.07 Aligned_cols=24 Identities=29% Similarity=0.891 Sum_probs=18.0
Q ss_pred CcCcccCccc------cCCCCCCCceeecC
Q psy14482 4 NICGLCGETA------KQKCSGCQLIYYCC 27 (95)
Q Consensus 4 ~~C~~C~~~~------~~~C~~c~~~~ycs 27 (95)
..|.+|+.++ ...|.+|+..+-.+
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~ 31 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRS 31 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeee
Confidence 5689998864 67899998766544
No 45
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=34.43 E-value=32 Score=21.05 Aligned_cols=20 Identities=20% Similarity=0.547 Sum_probs=11.4
Q ss_pred cceEEEcCCCCCCcEEEeeC
Q psy14482 54 GRYYIASRSIKAGEVVLREP 73 (95)
Q Consensus 54 gR~~va~r~i~~geii~~E~ 73 (95)
++.++.+.+|++||.++.+.
T Consensus 68 ~~gWv~A~~L~~GD~L~~~~ 87 (130)
T PF07591_consen 68 GKGWVEAEDLKVGDRLLTAD 87 (130)
T ss_dssp ----EEGGG--TTSEEEEE-
T ss_pred hHhhhhHhhCCCCCEEEcCC
Confidence 56789999999999887653
No 46
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=33.59 E-value=28 Score=15.07 Aligned_cols=18 Identities=28% Similarity=0.815 Sum_probs=11.5
Q ss_pred CcCcccCcc---ccCCCCCCC
Q psy14482 4 NICGLCGET---AKQKCSGCQ 21 (95)
Q Consensus 4 ~~C~~C~~~---~~~~C~~c~ 21 (95)
..|..|++. ..+.|..|.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG 23 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCG 23 (26)
T ss_pred CCCcccCCcCCcccccChhhC
Confidence 467788875 255666664
No 47
>KOG1338|consensus
Probab=33.16 E-value=33 Score=25.58 Aligned_cols=20 Identities=35% Similarity=0.534 Sum_probs=17.6
Q ss_pred cccceEEEcCCCCCCcEEEe
Q psy14482 52 VLGRYYIASRSIKAGEVVLR 71 (95)
Q Consensus 52 ~~gR~~va~r~i~~geii~~ 71 (95)
..|++++|+.+|+.|+.+|.
T Consensus 39 ~~G~g~vAtesIkkgE~Lf~ 58 (466)
T KOG1338|consen 39 IAGAGIVATESIKKGESLFA 58 (466)
T ss_pred hcccceeeehhhcCCceEEE
Confidence 46999999999999998764
No 48
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.49 E-value=28 Score=16.41 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=7.7
Q ss_pred cCCCCCCCcee
Q psy14482 14 KQKCSGCQLIY 24 (95)
Q Consensus 14 ~~~C~~c~~~~ 24 (95)
..+|+.|..++
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 45788887665
No 49
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=29.80 E-value=64 Score=15.64 Aligned_cols=15 Identities=20% Similarity=0.605 Sum_probs=12.7
Q ss_pred cCCCCCCCceeecCH
Q psy14482 14 KQKCSGCQLIYYCCR 28 (95)
Q Consensus 14 ~~~C~~c~~~~ycs~ 28 (95)
...|+.|.+.|.-+.
T Consensus 13 ~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGS 27 (41)
T ss_pred CcCCCCCCCEECCCC
Confidence 679999999998774
No 50
>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=29.41 E-value=23 Score=22.62 Aligned_cols=25 Identities=28% Similarity=0.867 Sum_probs=15.4
Q ss_pred cCcccCcc---ccCCCCCCCceeecCHHH
Q psy14482 5 ICGLCGET---AKQKCSGCQLIYYCCREH 30 (95)
Q Consensus 5 ~C~~C~~~---~~~~C~~c~~~~ycs~~c 30 (95)
.|++||-. .+-+|..|+ .|||+...
T Consensus 2 aC~YCG~~~p~~vv~C~~c~-kWFCNg~~ 29 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCN-KWFCNGRG 29 (152)
T ss_dssp S-TTT----CCCEEEETTTT-EEEES--T
T ss_pred CccccCCCCcccEeEcCCCC-cEeecCCC
Confidence 59999954 377999997 88997543
No 51
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=29.37 E-value=40 Score=17.94 Aligned_cols=12 Identities=17% Similarity=0.445 Sum_probs=9.1
Q ss_pred eeecCHHHHHhh
Q psy14482 23 IYYCCREHQKIH 34 (95)
Q Consensus 23 ~~ycs~~cq~~~ 34 (95)
..+||.+|...+
T Consensus 39 ~aFCS~ECR~~q 50 (58)
T PF04570_consen 39 KAFCSEECRSQQ 50 (58)
T ss_pred cccccHHHHHHH
Confidence 468999997654
No 52
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=28.70 E-value=30 Score=20.02 Aligned_cols=25 Identities=28% Similarity=0.756 Sum_probs=18.3
Q ss_pred CCCcCcccCccc------cCCCCCCCceeec
Q psy14482 2 FDNICGLCGETA------KQKCSGCQLIYYC 26 (95)
Q Consensus 2 ~~~~C~~C~~~~------~~~C~~c~~~~yc 26 (95)
+...|.+|+.++ ...|.+|+..+-.
T Consensus 5 p~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR 35 (92)
T cd06970 5 PGLLCRVCGDTSSGKHYGIYACNGCSGFFKR 35 (92)
T ss_pred CCCCCeecCCcCcccEECccEEeeeeeEeee
Confidence 345799998864 6789999876544
No 53
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.26 E-value=38 Score=21.63 Aligned_cols=16 Identities=25% Similarity=0.445 Sum_probs=14.2
Q ss_pred cceEEEcCCCCCCcEE
Q psy14482 54 GRYYIASRSIKAGEVV 69 (95)
Q Consensus 54 gR~~va~r~i~~geii 69 (95)
-+.++++++|.+||+|
T Consensus 33 v~vvVa~r~I~rGevI 48 (160)
T PRK06005 33 IAFVVPSTTIYPGETI 48 (160)
T ss_pred EEEEEEccCcCCCCCc
Confidence 4678999999999988
No 54
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=27.55 E-value=23 Score=16.37 Aligned_cols=22 Identities=27% Similarity=0.904 Sum_probs=13.0
Q ss_pred cCcccCcc-----ccCCCCCCCceeecC
Q psy14482 5 ICGLCGET-----AKQKCSGCQLIYYCC 27 (95)
Q Consensus 5 ~C~~C~~~-----~~~~C~~c~~~~ycs 27 (95)
.|.+|.+. +...|+.|. ++-|.
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~-v~lC~ 28 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCD-VPLCV 28 (32)
T ss_pred CCeECCcCCccceeEEEccCCC-CcccC
Confidence 46677664 355677774 55543
No 55
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=27.53 E-value=42 Score=24.32 Aligned_cols=29 Identities=28% Similarity=0.402 Sum_probs=21.7
Q ss_pred cccceEEEcCCCCCCcEEEeeCCceEccC
Q psy14482 52 VLGRYYIASRSIKAGEVVLREPPLVQGPC 80 (95)
Q Consensus 52 ~~gR~~va~r~i~~geii~~E~p~~~~p~ 80 (95)
...|.++++++|+.||+.-.|.-.+.-|.
T Consensus 287 ~~~Rsl~~~kdikkGe~ls~~Nl~~~RP~ 315 (347)
T COG2089 287 FARRSLVATKDIKKGEILSEDNLKVLRPG 315 (347)
T ss_pred HHhhheeeecccccCccccccceEEeCCC
Confidence 45799999999999998855554444444
No 56
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=27.51 E-value=15 Score=25.43 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=16.3
Q ss_pred cCcccCccccCCCCCCCceeecCHHHHH
Q psy14482 5 ICGLCGETAKQKCSGCQLIYYCCREHQK 32 (95)
Q Consensus 5 ~C~~C~~~~~~~C~~c~~~~ycs~~cq~ 32 (95)
.|..|+.+-.+.=-+-+..+|| +.||+
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~C-P~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEKIKQGGRSTFFC-PRCQK 273 (274)
T ss_pred CCCCCCCeeEEEEECCCCcEEC-cCCCC
Confidence 5777776543333334677888 57775
No 57
>COG1261 FlgA Flagellar basal body P-ring biosynthesis protein [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=27.36 E-value=40 Score=22.82 Aligned_cols=18 Identities=33% Similarity=0.525 Sum_probs=15.8
Q ss_pred cccceEEEcCCCCCCcEE
Q psy14482 52 VLGRYYIASRSIKAGEVV 69 (95)
Q Consensus 52 ~~gR~~va~r~i~~geii 69 (95)
..|+++++.+.|.+||.|
T Consensus 93 ~~~~~~va~r~I~~Ge~i 110 (220)
T COG1261 93 APGEVVVAARTIYRGEKI 110 (220)
T ss_pred ccceEEEEecccCCCCcc
Confidence 456899999999999988
No 58
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=27.36 E-value=23 Score=20.74 Aligned_cols=23 Identities=26% Similarity=0.888 Sum_probs=17.2
Q ss_pred CCcCcccCccc------cCCCCCCCceee
Q psy14482 3 DNICGLCGETA------KQKCSGCQLIYY 25 (95)
Q Consensus 3 ~~~C~~C~~~~------~~~C~~c~~~~y 25 (95)
...|.+|+.++ ...|.+|+..+-
T Consensus 4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFR 32 (97)
T cd07170 4 KRLCLVCGDIASGYHYGVASCEACKAFFK 32 (97)
T ss_pred CCCCeecCCcCcceEECceeehhhhHHHH
Confidence 45799998864 678999986553
No 59
>COG4050 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.96 E-value=58 Score=20.19 Aligned_cols=7 Identities=43% Similarity=1.640 Sum_probs=4.8
Q ss_pred ccccccc
Q psy14482 87 CLGCLKA 93 (95)
Q Consensus 87 c~~C~~~ 93 (95)
|.+|-|+
T Consensus 100 CiGC~RT 106 (152)
T COG4050 100 CIGCART 106 (152)
T ss_pred eeccccc
Confidence 7777664
No 60
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=26.81 E-value=39 Score=20.00 Aligned_cols=13 Identities=46% Similarity=0.813 Sum_probs=10.9
Q ss_pred EEEcCCCCCCcEE
Q psy14482 57 YIASRSIKAGEVV 69 (95)
Q Consensus 57 ~va~r~i~~geii 69 (95)
++|+++|++|++|
T Consensus 2 ~Va~r~I~~G~~i 14 (122)
T TIGR03170 2 VVAKRPLKRGEVI 14 (122)
T ss_pred EEECcccCCCCCc
Confidence 5788999999877
No 61
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=26.66 E-value=39 Score=19.16 Aligned_cols=25 Identities=20% Similarity=0.602 Sum_probs=18.2
Q ss_pred CCcCcccCccc------cCCCCCCCceeecC
Q psy14482 3 DNICGLCGETA------KQKCSGCQLIYYCC 27 (95)
Q Consensus 3 ~~~C~~C~~~~------~~~C~~c~~~~ycs 27 (95)
...|.+|+.++ ...|.+|+..+-.+
T Consensus 4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~ 34 (85)
T cd06964 4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRS 34 (85)
T ss_pred CCCCcccCCcCcccEECcceeeeeeeEEeee
Confidence 35699998864 67899998766443
No 62
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=26.66 E-value=64 Score=20.10 Aligned_cols=36 Identities=11% Similarity=0.021 Sum_probs=24.8
Q ss_pred CCCcCcccCccc------cCCCCCCCceeecCHHHHHhhhhc
Q psy14482 2 FDNICGLCGETA------KQKCSGCQLIYYCCREHQKIHWKK 37 (95)
Q Consensus 2 ~~~~C~~C~~~~------~~~C~~c~~~~ycs~~cq~~~w~~ 37 (95)
--..|..|+.+- ...-.-.++.+|||..|.+.....
T Consensus 3 ~~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~~k 44 (131)
T PRK14891 3 ETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLG 44 (131)
T ss_pred ceeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHHcc
Confidence 445788888751 333344668899999998776544
No 63
>KOG2858|consensus
Probab=26.45 E-value=19 Score=26.22 Aligned_cols=31 Identities=35% Similarity=0.750 Sum_probs=22.8
Q ss_pred CCcCcccCccc-cCCCCCCCceeecCHHHHHhh
Q psy14482 3 DNICGLCGETA-KQKCSGCQLIYYCCREHQKIH 34 (95)
Q Consensus 3 ~~~C~~C~~~~-~~~C~~c~~~~ycs~~cq~~~ 34 (95)
+..|.+|++.. ..+|-+|. +..||=+|.+.|
T Consensus 17 ~vlCgVClknE~KYkCPRCl-~rtCsLeCskkH 48 (390)
T KOG2858|consen 17 SVLCGVCLKNEPKYKCPRCL-ARTCSLECSKKH 48 (390)
T ss_pred hhhhhhcccCcccccCcchh-hhheeccccccc
Confidence 56799999985 77999996 556666665543
No 64
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=26.05 E-value=37 Score=19.34 Aligned_cols=22 Identities=32% Similarity=0.892 Sum_probs=16.5
Q ss_pred cCcccCccc------cCCCCCCCceeec
Q psy14482 5 ICGLCGETA------KQKCSGCQLIYYC 26 (95)
Q Consensus 5 ~C~~C~~~~------~~~C~~c~~~~yc 26 (95)
.|.+|+.++ ...|.+|+..+-.
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEec
Confidence 588998763 6789999876644
No 65
>PF09885 DUF2112: Uncharacterized protein conserved in archaea (DUF2112); InterPro: IPR012356 The exact function of this protein is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=25.75 E-value=20 Score=22.51 Aligned_cols=18 Identities=28% Similarity=1.117 Sum_probs=11.0
Q ss_pred EEEeeCCceEccCCCCcccccccccc
Q psy14482 68 VVLREPPLVQGPCQMTGPVCLGCLKA 93 (95)
Q Consensus 68 ii~~E~p~~~~p~~~~~~~c~~C~~~ 93 (95)
||+.+.|+..| |.+|.|+
T Consensus 85 IIv~~~p~~FG--------C~GCart 102 (143)
T PF09885_consen 85 IIVEDAPIAFG--------CMGCART 102 (143)
T ss_pred eEecCCCcccc--------ccccccH
Confidence 44555555555 8888764
No 66
>PRK00807 50S ribosomal protein L24e; Validated
Probab=25.72 E-value=60 Score=16.71 Aligned_cols=32 Identities=19% Similarity=0.509 Sum_probs=21.5
Q ss_pred CcCcccCccc------cCCCCCCCceeecCHHHHHhhh
Q psy14482 4 NICGLCGETA------KQKCSGCQLIYYCCREHQKIHW 35 (95)
Q Consensus 4 ~~C~~C~~~~------~~~C~~c~~~~ycs~~cq~~~w 35 (95)
..|..||..- ...=...+..++||..|++...
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f~ 39 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNYK 39 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHHH
Confidence 3688888751 2233445678999999987653
No 67
>KOG0438|consensus
Probab=25.59 E-value=50 Score=23.56 Aligned_cols=17 Identities=41% Similarity=0.860 Sum_probs=15.1
Q ss_pred ceEEEcCCCCCCcEEEe
Q psy14482 55 RYYIASRSIKAGEVVLR 71 (95)
Q Consensus 55 R~~va~r~i~~geii~~ 71 (95)
+|++|++++++||+|+.
T Consensus 129 ~~Ila~egm~aGD~i~s 145 (312)
T KOG0438|consen 129 RYILATEGLKAGDTILS 145 (312)
T ss_pred eEEEEecCCCCCCcccc
Confidence 58999999999999963
No 68
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=24.67 E-value=55 Score=17.05 Aligned_cols=12 Identities=33% Similarity=0.730 Sum_probs=10.0
Q ss_pred eeecCHHHHHhh
Q psy14482 23 IYYCCREHQKIH 34 (95)
Q Consensus 23 ~~ycs~~cq~~~ 34 (95)
.+|||+.|-..|
T Consensus 28 k~YCS~aCA~gH 39 (52)
T PF02069_consen 28 KYYCSEACANGH 39 (52)
T ss_dssp -EESSHHHHHTS
T ss_pred EeeecHHHhccC
Confidence 489999998877
No 69
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=24.45 E-value=39 Score=19.60 Aligned_cols=22 Identities=36% Similarity=1.075 Sum_probs=16.6
Q ss_pred cCcccCccc------cCCCCCCCceeec
Q psy14482 5 ICGLCGETA------KQKCSGCQLIYYC 26 (95)
Q Consensus 5 ~C~~C~~~~------~~~C~~c~~~~yc 26 (95)
.|.+|+.++ ...|.+|+..+--
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehh
Confidence 588898763 6789999876644
No 70
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=24.25 E-value=41 Score=19.17 Aligned_cols=26 Identities=27% Similarity=0.752 Sum_probs=19.0
Q ss_pred CCcCcccCccc------cCCCCCCCceeecCH
Q psy14482 3 DNICGLCGETA------KQKCSGCQLIYYCCR 28 (95)
Q Consensus 3 ~~~C~~C~~~~------~~~C~~c~~~~ycs~ 28 (95)
...|.+|+.++ ...|.+|+..+-.+.
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v 34 (87)
T cd06967 3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSI 34 (87)
T ss_pred CCCCeecCCcCCcCEeCcceEeeeeeEeeeee
Confidence 45699998863 668999987765543
No 71
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=24.03 E-value=39 Score=19.93 Aligned_cols=24 Identities=29% Similarity=0.958 Sum_probs=17.7
Q ss_pred CCcCcccCccc------cCCCCCCCceeec
Q psy14482 3 DNICGLCGETA------KQKCSGCQLIYYC 26 (95)
Q Consensus 3 ~~~C~~C~~~~------~~~C~~c~~~~yc 26 (95)
...|.+|+..+ ...|.+|+..+-.
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhh
Confidence 35699998863 6789999876544
No 72
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=23.98 E-value=37 Score=18.37 Aligned_cols=12 Identities=33% Similarity=0.675 Sum_probs=8.7
Q ss_pred CCCCcCcccCcc
Q psy14482 1 MFDNICGLCGET 12 (95)
Q Consensus 1 ~~~~~C~~C~~~ 12 (95)
|+|-+|..||+.
T Consensus 2 iiPvRCFTCGkv 13 (62)
T PRK04016 2 MIPVRCFTCGKV 13 (62)
T ss_pred CCCeEecCCCCC
Confidence 477778888774
No 73
>PRK11479 hypothetical protein; Provisional
Probab=23.78 E-value=45 Score=23.40 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=14.3
Q ss_pred EEEcCCCCCCcEEEeeCC
Q psy14482 57 YIASRSIKAGEVVLREPP 74 (95)
Q Consensus 57 ~va~r~i~~geii~~E~p 74 (95)
.+...++++||+||.+..
T Consensus 59 ~Vs~~~LqpGDLVFfst~ 76 (274)
T PRK11479 59 EITAPDLKPGDLLFSSSL 76 (274)
T ss_pred ccChhhCCCCCEEEEecC
Confidence 455678999999998754
No 74
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=23.77 E-value=67 Score=12.65 Aligned_cols=9 Identities=44% Similarity=0.870 Sum_probs=6.3
Q ss_pred cCcccCccc
Q psy14482 5 ICGLCGETA 13 (95)
Q Consensus 5 ~C~~C~~~~ 13 (95)
.|..|++..
T Consensus 2 ~C~~C~~~G 10 (18)
T PF00098_consen 2 KCFNCGEPG 10 (18)
T ss_dssp BCTTTSCSS
T ss_pred cCcCCCCcC
Confidence 577777764
No 75
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=23.59 E-value=86 Score=24.83 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=24.3
Q ss_pred CCCCCCcEEEeeC-----CceEccCCC-------CcccccccccccC
Q psy14482 61 RSIKAGEVVLREP-----PLVQGPCQM-------TGPVCLGCLKAIV 95 (95)
Q Consensus 61 r~i~~geii~~E~-----p~~~~p~~~-------~~~~c~~C~~~~~ 95 (95)
.+|..||.|++++ |.+....+. .+..|..|..+||
T Consensus 363 ~di~iGD~V~V~raGdVIP~I~~v~~~~r~~~~~~P~~CP~C~s~l~ 409 (669)
T PRK14350 363 IGLNVGDVVKISRRGDVIPAVELVIEKLSVGFFKIPDNCPSCKTALI 409 (669)
T ss_pred cCCCCCCEEEEEecCCCCCceeeecccccCCCCCCCCCCCCCCCEee
Confidence 3888999998886 555443321 3678999987764
No 76
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=23.42 E-value=56 Score=15.69 Aligned_cols=21 Identities=29% Similarity=0.884 Sum_probs=12.7
Q ss_pred CcccCccc---cCCCCCCCceeecC
Q psy14482 6 CGLCGETA---KQKCSGCQLIYYCC 27 (95)
Q Consensus 6 C~~C~~~~---~~~C~~c~~~~ycs 27 (95)
|..|++.. ...|..|+ ..||+
T Consensus 1 C~~C~~~~~l~~f~C~~C~-~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCG-NLFCG 24 (39)
T ss_pred CcccCCcccccCeECCccC-Ccccc
Confidence 56677653 45677776 44554
No 77
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.22 E-value=60 Score=15.08 Aligned_cols=13 Identities=23% Similarity=0.470 Sum_probs=8.8
Q ss_pred CCCCcCcccCccc
Q psy14482 1 MFDNICGLCGETA 13 (95)
Q Consensus 1 ~~~~~C~~C~~~~ 13 (95)
|....|.+|+...
T Consensus 1 ~~~~~C~~C~~~~ 13 (33)
T PF08792_consen 1 SNLKKCSKCGGNG 13 (33)
T ss_pred CCceEcCCCCCCe
Confidence 4566788887753
No 78
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.20 E-value=20 Score=19.33 Aligned_cols=20 Identities=30% Similarity=0.752 Sum_probs=9.1
Q ss_pred cCCCCCCC-ceeecCHHHHHh
Q psy14482 14 KQKCSGCQ-LIYYCCREHQKI 33 (95)
Q Consensus 14 ~~~C~~c~-~~~ycs~~cq~~ 33 (95)
...|-.|. ..-|....|.++
T Consensus 27 ~F~CPnCGe~~I~Rc~~CRk~ 47 (61)
T COG2888 27 KFPCPNCGEVEIYRCAKCRKL 47 (61)
T ss_pred EeeCCCCCceeeehhhhHHHc
Confidence 34555555 333444444443
No 79
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=22.95 E-value=31 Score=19.28 Aligned_cols=22 Identities=27% Similarity=0.931 Sum_probs=16.3
Q ss_pred CCcCcccCccc------cCCCCCCCcee
Q psy14482 3 DNICGLCGETA------KQKCSGCQLIY 24 (95)
Q Consensus 3 ~~~C~~C~~~~------~~~C~~c~~~~ 24 (95)
...|.+|+.++ ...|.+|+..+
T Consensus 2 ~~~C~VCg~~a~g~hyGv~sC~aC~~FF 29 (78)
T cd07172 2 QKICLVCSDEASGCHYGVLTCGSCKVFF 29 (78)
T ss_pred CCCCeecCCcCcceEECceeehhhHHhH
Confidence 35699998864 66888887654
No 80
>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=22.79 E-value=82 Score=13.78 Aligned_cols=18 Identities=28% Similarity=0.822 Sum_probs=11.6
Q ss_pred cCcccCcc---ccCCCCCCCc
Q psy14482 5 ICGLCGET---AKQKCSGCQL 22 (95)
Q Consensus 5 ~C~~C~~~---~~~~C~~c~~ 22 (95)
.|-.|++. ..+.|..|..
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCC
Confidence 46667765 3667777754
No 81
>KOG4217|consensus
Probab=22.69 E-value=38 Score=25.86 Aligned_cols=22 Identities=32% Similarity=1.043 Sum_probs=17.1
Q ss_pred CCCcCcccCccc------cCCCCCCCce
Q psy14482 2 FDNICGLCGETA------KQKCSGCQLI 23 (95)
Q Consensus 2 ~~~~C~~C~~~~------~~~C~~c~~~ 23 (95)
.+..|++||-.+ .+.|.+|+-.
T Consensus 268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGF 295 (605)
T KOG4217|consen 268 AEGLCAVCGDNAACQHYGVRTCEGCKGF 295 (605)
T ss_pred ccceeeecCChHHhhhcCccccccchHH
Confidence 367899988763 8899999743
No 82
>TIGR03271 methan_mark_5 putative methanogenesis marker protein 5. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=22.29 E-value=27 Score=21.87 Aligned_cols=18 Identities=39% Similarity=1.198 Sum_probs=10.8
Q ss_pred EEEeeCCceEccCCCCcccccccccc
Q psy14482 68 VVLREPPLVQGPCQMTGPVCLGCLKA 93 (95)
Q Consensus 68 ii~~E~p~~~~p~~~~~~~c~~C~~~ 93 (95)
||+.+.|+..| |.+|.|+
T Consensus 84 IIv~~ap~~FG--------C~GCart 101 (142)
T TIGR03271 84 IIVREAPFAFG--------CMGCART 101 (142)
T ss_pred EEecCCCcccc--------ccccccH
Confidence 44455565555 7888764
No 83
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=22.25 E-value=53 Score=20.07 Aligned_cols=15 Identities=13% Similarity=0.419 Sum_probs=11.2
Q ss_pred EEcCCCCCCcEEEee
Q psy14482 58 IASRSIKAGEVVLRE 72 (95)
Q Consensus 58 va~r~i~~geii~~E 72 (95)
+...++++||+||.-
T Consensus 72 v~~~~~qpGDlvff~ 86 (134)
T TIGR02219 72 VPCDAAQPGDVLVFR 86 (134)
T ss_pred cchhcCCCCCEEEEe
Confidence 345679999999864
No 84
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.55 E-value=24 Score=24.40 Aligned_cols=29 Identities=21% Similarity=0.491 Sum_probs=17.9
Q ss_pred CcCcccCccccCCCCCCCceeecCHHHHHh
Q psy14482 4 NICGLCGETAKQKCSGCQLIYYCCREHQKI 33 (95)
Q Consensus 4 ~~C~~C~~~~~~~C~~c~~~~ycs~~cq~~ 33 (95)
..|..|+.+-.+.=-+-+..+|| +.||+.
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~C-p~CQ~~ 264 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFC-PQCQPL 264 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEEC-CCCcCC
Confidence 35777877643333334677888 577764
No 85
>cd00064 FU Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Probab=21.29 E-value=75 Score=15.51 Aligned_cols=22 Identities=23% Similarity=0.801 Sum_probs=17.0
Q ss_pred CcCcccCccccCCCCCCCceee
Q psy14482 4 NICGLCGETAKQKCSGCQLIYY 25 (95)
Q Consensus 4 ~~C~~C~~~~~~~C~~c~~~~y 25 (95)
..|..|..+....|..|+..+|
T Consensus 4 ~~C~~C~g~~~~~C~~C~~~~~ 25 (49)
T cd00064 4 PSCATCTGPGPDQCTSCRHGFY 25 (49)
T ss_pred CccCCCcCcCcCcCccCcCccC
Confidence 4677787777788999987776
No 86
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=21.03 E-value=38 Score=19.43 Aligned_cols=24 Identities=25% Similarity=0.809 Sum_probs=17.9
Q ss_pred CCcCcccCccc------cCCCCCCCceeec
Q psy14482 3 DNICGLCGETA------KQKCSGCQLIYYC 26 (95)
Q Consensus 3 ~~~C~~C~~~~------~~~C~~c~~~~yc 26 (95)
...|.+|+.++ ...|.+|+..+..
T Consensus 6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 6 PKLCSICEDKATGLHYGIITCEGCKGFFKR 35 (90)
T ss_pred CCCCcccCCcCcceEECceehhhhhHhhhh
Confidence 45799998863 6789999876544
No 87
>PF10948 DUF2635: Protein of unknown function (DUF2635); InterPro: IPR024400 This family consists of uncharacterised proteins found in bacteria and bacteriophages. It includes protein Gp38 from Enterobacteria phage Mu.
Probab=21.02 E-value=56 Score=16.60 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=11.5
Q ss_pred cCCCCCCcEEEeeCC
Q psy14482 60 SRSIKAGEVVLREPP 74 (95)
Q Consensus 60 ~r~i~~geii~~E~p 74 (95)
.|-++.|||++.+.+
T Consensus 32 ~RRl~dGDV~~v~~~ 46 (47)
T PF10948_consen 32 LRRLADGDVVEVTPK 46 (47)
T ss_pred HHhhhcCCEEEecCC
Confidence 456888999988765
No 88
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=20.54 E-value=50 Score=18.13 Aligned_cols=21 Identities=33% Similarity=1.004 Sum_probs=14.1
Q ss_pred CcccCccc------cCCCCCCCceeec
Q psy14482 6 CGLCGETA------KQKCSGCQLIYYC 26 (95)
Q Consensus 6 C~~C~~~~------~~~C~~c~~~~yc 26 (95)
|.+|+.++ ...|.+|+..+-.
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR 27 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRR 27 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCc
Confidence 56777653 6678888766544
No 89
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.46 E-value=62 Score=22.19 Aligned_cols=11 Identities=36% Similarity=1.141 Sum_probs=8.2
Q ss_pred CCcCcccCccc
Q psy14482 3 DNICGLCGETA 13 (95)
Q Consensus 3 ~~~C~~C~~~~ 13 (95)
...|..||.+.
T Consensus 99 ~~fC~~CG~~~ 109 (256)
T PRK00241 99 HRFCGYCGHPM 109 (256)
T ss_pred CccccccCCCC
Confidence 35788999864
No 90
>KOG4846|consensus
Probab=20.38 E-value=34 Score=25.72 Aligned_cols=41 Identities=27% Similarity=0.766 Sum_probs=28.3
Q ss_pred cCcccCccc------cCCCCCCCceeecCHHHHHhhhhc--cccccCCcc
Q psy14482 5 ICGLCGETA------KQKCSGCQLIYYCCREHQKIHWKK--HKSHCRPMK 46 (95)
Q Consensus 5 ~C~~C~~~~------~~~C~~c~~~~ycs~~cq~~~w~~--Hk~~C~~i~ 46 (95)
.|.+|+-.+ ...|.+|+-.+.. .--|+.++++ -.+.|...+
T Consensus 134 lCkVCgDkASGfHYGV~aCEGCKGFFRR-SIQqkI~YrrClk~e~C~I~R 182 (538)
T KOG4846|consen 134 LCKVCGDKASGFHYGVTACEGCKGFFRR-SIQQKIDYRRCLKQEVCEIKR 182 (538)
T ss_pred eehhhccccccceeceeecccchHHHHH-HHHHhhhHHHHhhhhceehhh
Confidence 699999864 7799999955544 4567888876 334555443
No 91
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=20.31 E-value=35 Score=19.67 Aligned_cols=22 Identities=32% Similarity=0.982 Sum_probs=15.9
Q ss_pred CcCcccCccc------cCCCCCCCceee
Q psy14482 4 NICGLCGETA------KQKCSGCQLIYY 25 (95)
Q Consensus 4 ~~C~~C~~~~------~~~C~~c~~~~y 25 (95)
..|.+|+.++ ...|.+|+..+-
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFR 29 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFR 29 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHH
Confidence 4589998864 668888876543
No 92
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=20.07 E-value=74 Score=17.86 Aligned_cols=12 Identities=50% Similarity=0.595 Sum_probs=9.5
Q ss_pred CCCCCcEEEeeC
Q psy14482 62 SIKAGEVVLREP 73 (95)
Q Consensus 62 ~i~~geii~~E~ 73 (95)
-|.+||+|++|.
T Consensus 46 ~I~~GD~V~Ve~ 57 (75)
T COG0361 46 RILPGDVVLVEL 57 (75)
T ss_pred EeCCCCEEEEEe
Confidence 478999998773
Done!