Query psy10008
Match_columns 214
No_of_seqs 224 out of 1258
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 15:31:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10008hhsearch_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; 98.9 6.2E-10 1.3E-14 69.5 1.4 37 124-163 1-37 (37)
2 KOG2084|consensus 97.6 4E-05 8.6E-10 70.5 3.6 70 87-163 22-91 (482)
3 KOG1710|consensus 97.4 5.8E-05 1.3E-09 67.3 0.9 44 121-167 319-362 (396)
4 PF00856 SET: SET domain; Int 97.2 0.00021 4.5E-09 55.1 2.5 24 90-113 1-24 (162)
5 smart00317 SET SET (Su(var)3-9 96.7 0.0026 5.6E-08 46.9 4.3 34 81-114 2-35 (116)
6 PF13824 zf-Mss51: Zinc-finger 93.9 0.099 2.1E-06 35.5 3.8 45 124-170 2-48 (55)
7 PLN03158 methionine aminopepti 93.0 0.075 1.6E-06 49.5 2.8 37 121-160 9-52 (396)
8 PF04438 zf-HIT: HIT zinc fing 92.9 0.074 1.6E-06 31.6 1.7 28 122-152 3-30 (30)
9 KOG3612|consensus 92.5 0.03 6.4E-07 53.6 -0.5 38 121-163 527-564 (588)
10 KOG1085|consensus 86.4 0.83 1.8E-05 41.1 3.6 34 76-109 253-286 (392)
11 PF09889 DUF2116: Uncharacteri 83.6 0.84 1.8E-05 31.4 1.9 27 121-155 3-29 (59)
12 PF12855 Ecl1: Life-span regul 83.4 0.67 1.5E-05 29.9 1.3 32 121-157 6-37 (43)
13 KOG2857|consensus 82.6 0.57 1.2E-05 37.8 0.9 36 121-163 5-42 (157)
14 PF08666 SAF: SAF domain; Int 77.3 1.5 3.3E-05 29.2 1.5 15 91-105 2-16 (63)
15 PRK00418 DNA gyrase inhibitor; 75.8 1.7 3.7E-05 30.2 1.4 12 143-154 25-36 (62)
16 PRK01343 zinc-binding protein; 75.7 1.8 3.8E-05 29.6 1.5 27 121-154 9-35 (57)
17 KOG3362|consensus 75.6 1 2.2E-05 36.4 0.4 31 121-154 118-148 (156)
18 PF03884 DUF329: Domain of unk 72.0 2.5 5.4E-05 28.9 1.5 13 142-154 20-32 (57)
19 KOG4317|consensus 70.9 1.7 3.6E-05 39.5 0.6 31 121-153 7-37 (383)
20 smart00317 SET SET (Su(var)3-9 69.6 7.9 0.00017 27.9 3.9 29 79-107 83-114 (116)
21 COG2075 RPL24A Ribosomal prote 66.8 4.4 9.6E-05 28.4 1.9 33 121-153 3-39 (66)
22 KOG4442|consensus 64.5 6.8 0.00015 39.0 3.4 30 78-107 119-148 (729)
23 PLN03144 Carbon catabolite rep 58.1 6 0.00013 39.0 1.8 19 142-161 89-107 (606)
24 COG3024 Uncharacterized protei 57.7 4.9 0.00011 28.1 0.8 13 142-154 25-37 (65)
25 PF14949 ARF7EP_C: ARF7 effect 56.7 10 0.00022 29.0 2.4 29 120-155 66-95 (103)
26 smart00858 SAF This domain fam 55.2 7.8 0.00017 25.5 1.5 17 91-107 2-18 (64)
27 TIGR03586 PseI pseudaminic aci 54.4 8.5 0.00018 35.1 2.0 21 89-109 274-294 (327)
28 PF00856 SET: SET domain; Int 52.0 22 0.00048 26.6 3.8 28 80-107 129-159 (162)
29 PRK14891 50S ribosomal protein 51.7 12 0.00027 29.6 2.2 34 121-154 4-41 (131)
30 PF04570 DUF581: Protein of un 51.1 11 0.00023 25.9 1.6 35 121-155 16-51 (58)
31 TIGR03569 NeuB_NnaB N-acetylne 49.8 11 0.00025 34.3 2.1 21 89-109 276-296 (329)
32 PF14803 Nudix_N_2: Nudix N-te 49.6 6.9 0.00015 23.8 0.4 23 123-145 2-33 (34)
33 PF08189 Meleagrin: Meleagrin/ 45.8 5.6 0.00012 24.7 -0.4 19 140-159 6-25 (39)
34 KOG1338|consensus 45.6 13 0.00029 34.9 1.8 21 88-108 39-59 (466)
35 COG4068 Uncharacterized protei 42.6 15 0.00032 25.4 1.2 25 121-153 8-32 (64)
36 PF10013 DUF2256: Uncharacteri 40.4 7.8 0.00017 24.8 -0.3 30 121-152 8-40 (42)
37 PRK00807 50S ribosomal protein 39.9 23 0.0005 23.5 1.9 33 122-154 2-38 (52)
38 COG1096 Predicted RNA-binding 37.9 32 0.0007 29.0 2.8 47 96-142 116-173 (188)
39 PF08394 Arc_trans_TRASH: Arch 36.8 28 0.00062 21.6 1.8 30 124-153 1-32 (37)
40 smart00154 ZnF_AN1 AN1-like Zi 36.2 24 0.00051 22.0 1.4 24 124-148 1-25 (39)
41 KOG2061|consensus 35.4 31 0.00068 31.9 2.6 40 122-163 137-176 (362)
42 KOG0438|consensus 34.7 39 0.00085 30.6 3.0 22 91-112 129-152 (312)
43 PF04945 YHS: YHS domain; Int 34.1 23 0.0005 22.5 1.1 13 141-153 23-35 (47)
44 cd02249 ZZ Zinc finger, ZZ typ 33.9 28 0.0006 22.1 1.5 32 123-155 2-34 (46)
45 KOG2858|consensus 33.3 15 0.00032 34.0 0.2 35 118-154 14-48 (390)
46 PF04640 PLATZ: PLATZ transcri 33.1 35 0.00076 24.3 2.0 24 120-151 48-71 (72)
47 PF09538 FYDLN_acid: Protein o 32.5 29 0.00063 26.6 1.6 23 120-142 8-34 (108)
48 PF00181 Ribosomal_L2: Ribosom 32.2 62 0.0013 22.9 3.2 39 63-106 37-76 (77)
49 PRK12618 flgA flagellar basal 30.7 31 0.00068 27.5 1.6 23 86-108 15-37 (141)
50 KOG2738|consensus 30.5 25 0.00054 32.1 1.1 33 125-160 12-49 (369)
51 COG1579 Zn-ribbon protein, pos 30.0 19 0.00041 31.5 0.3 26 120-145 196-232 (239)
52 cd00472 Ribosomal_L24e_L24 Rib 29.2 49 0.0011 22.2 2.1 33 121-154 3-40 (54)
53 PF03277 Herpes_UL4: Herpesvir 29.1 37 0.0008 28.7 1.8 56 98-154 46-107 (188)
54 PRK09612 rpl2p 50S ribosomal p 29.1 59 0.0013 28.4 3.1 43 61-107 41-83 (238)
55 cd02337 ZZ_CBP Zinc finger, ZZ 28.4 21 0.00047 22.4 0.2 37 123-161 2-38 (41)
56 PF13717 zinc_ribbon_4: zinc-r 28.3 34 0.00074 20.8 1.1 24 122-145 3-36 (36)
57 PF01428 zf-AN1: AN1-like Zinc 28.2 39 0.00084 21.2 1.4 21 127-148 6-26 (43)
58 PF07975 C1_4: TFIIH C1-like d 28.0 27 0.00058 23.3 0.6 28 123-152 1-37 (51)
59 smart00746 TRASH metallochaper 27.4 61 0.0013 17.5 2.1 14 141-154 22-35 (39)
60 COG2089 SpsE Sialic acid synth 27.0 30 0.00064 31.8 1.0 22 89-110 288-309 (347)
61 PF07295 DUF1451: Protein of u 25.6 39 0.00085 27.2 1.4 25 121-145 112-141 (146)
62 KOG4236|consensus 24.4 31 0.00067 34.2 0.6 48 94-141 117-180 (888)
63 PF13719 zinc_ribbon_5: zinc-r 23.8 52 0.0011 20.0 1.4 23 122-144 3-35 (37)
64 TIGR03170 flgA_cterm flagella 23.1 45 0.00098 25.2 1.2 15 93-107 2-16 (122)
65 TIGR02098 MJ0042_CXXC MJ0042 f 22.5 55 0.0012 19.6 1.3 22 123-144 4-35 (38)
66 PF07282 OrfB_Zn_ribbon: Putat 22.4 1.1E+02 0.0024 20.6 2.9 27 116-142 23-54 (69)
67 cd02340 ZZ_NBR1_like Zinc fing 22.4 58 0.0013 20.5 1.4 31 123-154 2-33 (43)
68 PF07754 DUF1610: Domain of un 22.3 64 0.0014 18.2 1.4 18 124-141 1-23 (24)
69 PF01246 Ribosomal_L24e: Ribos 22.1 71 0.0015 22.7 1.9 33 121-153 3-39 (71)
70 PF09297 zf-NADH-PPase: NADH p 21.9 60 0.0013 18.9 1.3 25 121-145 3-32 (32)
71 KOG1082|consensus 21.5 1.1E+02 0.0023 28.1 3.5 33 75-107 172-204 (364)
72 cd02341 ZZ_ZZZ3 Zinc finger, Z 21.4 46 0.001 21.7 0.8 31 123-154 2-36 (48)
73 smart00109 C1 Protein kinase C 20.6 97 0.0021 18.8 2.2 31 120-152 10-43 (49)
74 CHL00044 rpl16 ribosomal prote 20.4 75 0.0016 25.2 2.0 41 69-109 67-107 (135)
75 PF13240 zinc_ribbon_2: zinc-r 20.1 58 0.0013 17.9 0.9 18 123-140 1-19 (23)
76 PRK14559 putative protein seri 20.0 65 0.0014 32.2 1.9 32 120-153 14-50 (645)
77 TIGR02300 FYDLN_acid conserved 20.0 71 0.0015 25.4 1.7 24 120-143 8-35 (129)
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=98.88 E-value=6.2e-10 Score=69.47 Aligned_cols=37 Identities=43% Similarity=1.139 Sum_probs=32.2
Q ss_pred cccCCCCCCCcccCCCCCceeecChHHHhHhhhcchHHhh
Q psy10008 124 CNHCCTSISAPIPCNECILAVYCSESCRREAWLRYHRWEC 163 (214)
Q Consensus 124 C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~EC 163 (214)
|.+|++. ...+|++|+.++|||++||+.+| ..|+.+|
T Consensus 1 C~~C~~~--~~~~C~~C~~~~YCs~~Cq~~~w-~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGKP--ALKRCSRCKSVYYCSEECQRADW-PYHKFEC 37 (37)
T ss_dssp -TTTSSC--SSEEETTTSSSEESSHHHHHHHH-HHHCCTH
T ss_pred CcCCCCC--cCCcCCCCCCEEecCHHHHHHHH-HHHhhhC
Confidence 7888884 34499999999999999999999 9999887
No 2
>KOG2084|consensus
Probab=97.64 E-value=4e-05 Score=70.50 Aligned_cols=70 Identities=21% Similarity=0.652 Sum_probs=54.1
Q ss_pred CCCccEEEEccCCCCCCEEEEeccceeeecCCCCCCccccCCCCCCCcccCCCCCceeecChHHHhHhhhcchHHhh
Q psy10008 87 NAKGRHVIAVEDVHKGDTLFVEKPVAFVILPPCSMSNCNHCCTSISAPIPCNECILAVYCSESCRREAWLRYHRWEC 163 (214)
Q Consensus 87 ~~~GRgl~Atrdi~~GevIl~e~P~~~v~~~~~~~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~EC 163 (214)
+..|||++|+++|++|++|+.|.|++..+.. ..|..|+.. ....|.+|....+|+. |+..+|...|+++|
T Consensus 22 ~~~Gr~~~a~~~i~~g~~i~~e~p~~~~p~~----~~~~~c~~~--~~~~C~~~~~~~~~~~-~~~~~~~~~~~~~~ 91 (482)
T KOG2084|consen 22 PELGRGLVATQAIEAGEVILEEEPLVVGPAS----KSCSRCLGC--SCDHCRRCLEAIECNK-CQQRGWALCGKFAC 91 (482)
T ss_pred cccCcceeeecccCCCceEEecCcceeeecc----cCCcccccc--chhhhhcCCccHhhhh-hhccCccccchhhc
Confidence 6899999999999999999999999977765 455555543 4556888888899986 55544446666666
No 3
>KOG1710|consensus
Probab=97.36 E-value=5.8e-05 Score=67.27 Aligned_cols=44 Identities=27% Similarity=0.717 Sum_probs=37.8
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhHhhhcchHHhhHHHH
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRREAWLRYHRWECHGAL 167 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~EC~~~l 167 (214)
..+|+.|+.+. ...+|+.|+.+.||+.+||+-+| ..|+.-| .++
T Consensus 319 ~~fCstCG~~g-a~KrCs~CKav~YCdqeCQk~hW-f~HKK~C-~~L 362 (396)
T KOG1710|consen 319 CQFCSTCGHPG-AKKRCSQCKAVAYCDQECQKFHW-FIHKKVC-SFL 362 (396)
T ss_pred cccccccCCCC-ccchhhhhHHHHHHHHHHHHhhh-HHHHHHH-HHH
Confidence 46788888764 45789999999999999999999 9999999 554
No 4
>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=97.23 E-value=0.00021 Score=55.11 Aligned_cols=24 Identities=25% Similarity=0.719 Sum_probs=18.8
Q ss_pred ccEEEEccCCCCCCEEEEecccee
Q psy10008 90 GRHVIAVEDVHKGDTLFVEKPVAF 113 (214)
Q Consensus 90 GRgl~Atrdi~~GevIl~e~P~~~ 113 (214)
||||||++||++||+|++..|++.
T Consensus 1 GrGl~At~dI~~Ge~I~~p~~~~~ 24 (162)
T PF00856_consen 1 GRGLFATRDIKAGEVILIPRPAIL 24 (162)
T ss_dssp SEEEEESS-B-TTEEEEEESEEEE
T ss_pred CEEEEECccCCCCCEEEEECcceE
Confidence 999999999999999996666653
No 5
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=96.68 E-value=0.0026 Score=46.94 Aligned_cols=34 Identities=26% Similarity=0.234 Sum_probs=29.5
Q ss_pred EEEEEcCCCccEEEEccCCCCCCEEEEeccceee
Q psy10008 81 IKMQTSNAKGRHVIAVEDVHKGDTLFVEKPVAFV 114 (214)
Q Consensus 81 vei~~s~~~GRgl~Atrdi~~GevIl~e~P~~~v 114 (214)
+++..++.+|+||+|+++|++|++|+...+.+..
T Consensus 2 ~~~~~~~~~G~gl~a~~~i~~g~~i~~~~g~~~~ 35 (116)
T smart00317 2 LEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIIT 35 (116)
T ss_pred cEEEecCCCcEEEEECCccCCCCEEEEEEeEEEC
Confidence 5677778999999999999999999988887644
No 6
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=93.91 E-value=0.099 Score=35.49 Aligned_cols=45 Identities=27% Similarity=0.629 Sum_probs=35.3
Q ss_pred cccCCCCC--CCcccCCCCCceeecChHHHhHhhhcchHHhhHHHHHhh
Q psy10008 124 CNHCCTSI--SAPIPCNECILAVYCSESCRREAWLRYHRWECHGALRLL 170 (214)
Q Consensus 124 C~~C~~~~--~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~EC~~~l~~l 170 (214)
|..|.... ...+.|+.|+...|||++=...+. ..|+.-| ..|+..
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D~-e~H~~~c-~~LRqv 48 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDDY-EEHRQLC-ERLRQV 48 (55)
T ss_pred CCCCccccccccCCcCCCCCCcCccCHHHHHHhH-HHHHHHH-HHHHHh
Confidence 66666644 246889999999999998888875 7898899 777654
No 7
>PLN03158 methionine aminopeptidase; Provisional
Probab=92.95 E-value=0.075 Score=49.48 Aligned_cols=37 Identities=30% Similarity=0.883 Sum_probs=29.3
Q ss_pred CCccccCCCCCCCcccCCCCC-------ceeecChHHHhHhhhcchH
Q psy10008 121 MSNCNHCCTSISAPIPCNECI-------LAVYCSESCRREAWLRYHR 160 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~-------~~~YCS~~C~~~aw~~~H~ 160 (214)
...|..|.+.. ...|+.|. ..+|||.+|-+.+| ..|+
T Consensus 9 ~~~c~~c~~~a--~l~Cp~C~k~~~~~~~s~fCsq~CFk~~w-~~Hk 52 (396)
T PLN03158 9 PLACARCSKPA--HLQCPKCLELKLPREGASFCSQDCFKAAW-SSHK 52 (396)
T ss_pred cccccCCCCcc--cccCccchhcCCCCCCceeECHHHHHHHH-HHHH
Confidence 45688999864 48899885 37999999999999 5553
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=92.87 E-value=0.074 Score=31.61 Aligned_cols=28 Identities=36% Similarity=0.819 Sum_probs=20.5
Q ss_pred CccccCCCCCCCcccCCCCCceeecChHHHh
Q psy10008 122 SNCNHCCTSISAPIPCNECILAVYCSESCRR 152 (214)
Q Consensus 122 ~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~ 152 (214)
..|.-|.. ...+.|++| ...|||.+|.+
T Consensus 3 ~~C~vC~~--~~kY~Cp~C-~~~~CSl~C~k 30 (30)
T PF04438_consen 3 KLCSVCGN--PAKYRCPRC-GARYCSLACYK 30 (30)
T ss_dssp EEETSSSS--EESEE-TTT---EESSHHHHH
T ss_pred CCCccCcC--CCEEECCCc-CCceeCcEeEC
Confidence 46778887 678899999 88999999964
No 9
>KOG3612|consensus
Probab=92.50 E-value=0.03 Score=53.64 Aligned_cols=38 Identities=34% Similarity=0.830 Sum_probs=31.9
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhHhhhcchHHhh
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRREAWLRYHRWEC 163 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~EC 163 (214)
..-|.+|... +.+-| |-...|||.+||+.+| ..|+.-|
T Consensus 527 KQWC~nC~~E--Aiy~C--CWNTSYCsveCQQ~HW-~~H~ksC 564 (588)
T KOG3612|consen 527 KQWCYNCLDE--AIYHC--CWNTSYCSVECQQGHW-PEHRKSC 564 (588)
T ss_pred HHHHHhhhHH--HHHHh--hccccccCcchhhccc-hhHhhhh
Confidence 5678888873 45666 7789999999999999 7999999
No 10
>KOG1085|consensus
Probab=86.38 E-value=0.83 Score=41.13 Aligned_cols=34 Identities=21% Similarity=0.245 Sum_probs=28.6
Q ss_pred cCCCcEEEEEcCCCccEEEEccCCCCCCEEEEec
Q psy10008 76 CASNKIKMQTSNAKGRHVIAVEDVHKGDTLFVEK 109 (214)
Q Consensus 76 ~~s~~vei~~s~~~GRgl~Atrdi~~GevIl~e~ 109 (214)
.-..++.+.+..++||||+|+++|+.||-|..-.
T Consensus 253 g~~egl~~~~~dgKGRGv~a~~~F~rgdFVVEY~ 286 (392)
T KOG1085|consen 253 GTNEGLLEVYKDGKGRGVRAKVNFERGDFVVEYR 286 (392)
T ss_pred ccccceeEEeeccccceeEeecccccCceEEEEe
Confidence 3456778888889999999999999999987543
No 11
>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=83.61 E-value=0.84 Score=31.40 Aligned_cols=27 Identities=30% Similarity=0.656 Sum_probs=21.3
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhHhh
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRREAW 155 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw 155 (214)
..+|-+|+++.+. .-.|||++|++..+
T Consensus 3 HkHC~~CG~~Ip~--------~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 3 HKHCPVCGKPIPP--------DESFCSPKCREEYR 29 (59)
T ss_pred CCcCCcCCCcCCc--------chhhhCHHHHHHHH
Confidence 4689999988754 46799999998865
No 12
>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=83.42 E-value=0.67 Score=29.86 Aligned_cols=32 Identities=28% Similarity=0.474 Sum_probs=22.7
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhHhhhc
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRREAWLR 157 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~ 157 (214)
..+|-.|-+.+.. .-....|||++|+..++..
T Consensus 6 ~~yC~~Cdk~~~~-----~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 6 NDYCIVCDKQIDP-----PDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hhHHHHhhccccC-----CCCCccccCHHHHhHhhhc
Confidence 3567777776633 2237899999999998744
No 13
>KOG2857|consensus
Probab=82.57 E-value=0.57 Score=37.76 Aligned_cols=36 Identities=31% Similarity=0.765 Sum_probs=27.5
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhHhhhcchHH--hh
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRREAWLRYHRW--EC 163 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~--EC 163 (214)
..+|.-|.+.. ..++|+.| .+.|||-.|.+ .|+. +|
T Consensus 5 t~tC~ic~e~~-~KYKCpkC-~vPYCSl~CfK-----iHk~tPq~ 42 (157)
T KOG2857|consen 5 TTTCVICLESE-IKYKCPKC-SVPYCSLPCFK-----IHKSTPQC 42 (157)
T ss_pred eeeehhhhcch-hhccCCCC-CCccccchhhh-----hccCCccc
Confidence 45788888753 35899999 89999999954 5554 67
No 14
>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=77.26 E-value=1.5 Score=29.18 Aligned_cols=15 Identities=33% Similarity=0.618 Sum_probs=11.7
Q ss_pred cEEEEccCCCCCCEE
Q psy10008 91 RHVIAVEDVHKGDTL 105 (214)
Q Consensus 91 Rgl~Atrdi~~GevI 105 (214)
+.++|++||++|++|
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 468999999999998
No 15
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=75.80 E-value=1.7 Score=30.21 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=10.3
Q ss_pred eeecChHHHhHh
Q psy10008 143 AVYCSESCRREA 154 (214)
Q Consensus 143 ~~YCS~~C~~~a 154 (214)
-.|||+.|+..+
T Consensus 25 rPFCS~RCk~ID 36 (62)
T PRK00418 25 RPFCSKRCQLID 36 (62)
T ss_pred CCcccHHHHhhh
Confidence 479999999876
No 16
>PRK01343 zinc-binding protein; Provisional
Probab=75.74 E-value=1.8 Score=29.64 Aligned_cols=27 Identities=26% Similarity=0.564 Sum_probs=19.7
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhHh
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRREA 154 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~a 154 (214)
...|..|.++... ....|||+.|+..|
T Consensus 9 ~~~CP~C~k~~~~-------~~rPFCS~RC~~iD 35 (57)
T PRK01343 9 TRPCPECGKPSTR-------EAYPFCSERCRDID 35 (57)
T ss_pred CCcCCCCCCcCcC-------CCCcccCHHHhhhh
Confidence 4567777776542 25689999999876
No 17
>KOG3362|consensus
Probab=75.57 E-value=1 Score=36.38 Aligned_cols=31 Identities=26% Similarity=0.653 Sum_probs=26.4
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhHh
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRREA 154 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~a 154 (214)
..+|.-|+ ....+.|.+| ...|||..|.+.+
T Consensus 118 r~fCaVCG--~~S~ysC~~C-G~kyCsv~C~~~H 148 (156)
T KOG3362|consen 118 RKFCAVCG--YDSKYSCVNC-GTKYCSVRCLKTH 148 (156)
T ss_pred chhhhhcC--CCchhHHHhc-CCceeechhhhhc
Confidence 47899999 4578899999 8999999998765
No 18
>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=72.01 E-value=2.5 Score=28.89 Aligned_cols=13 Identities=31% Similarity=0.789 Sum_probs=9.8
Q ss_pred ceeecChHHHhHh
Q psy10008 142 LAVYCSESCRREA 154 (214)
Q Consensus 142 ~~~YCS~~C~~~a 154 (214)
.-.|||+.|+..+
T Consensus 20 ~rPFCS~RCk~iD 32 (57)
T PF03884_consen 20 FRPFCSERCKLID 32 (57)
T ss_dssp --SSSSHHHHHHH
T ss_pred cCCcccHhhcccC
Confidence 3469999999876
No 19
>KOG4317|consensus
Probab=70.94 E-value=1.7 Score=39.53 Aligned_cols=31 Identities=29% Similarity=0.751 Sum_probs=25.0
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhH
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRRE 153 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~ 153 (214)
...|+-|...... +.|++| ...|||-.|.+.
T Consensus 7 ~~~C~ic~vq~~~-YtCPRC-n~~YCsl~CYr~ 37 (383)
T KOG4317|consen 7 FLACGICGVQKRE-YTCPRC-NLLYCSLKCYRN 37 (383)
T ss_pred eeecccccccccc-ccCCCC-CccceeeeeecC
Confidence 4578888776544 999999 899999999764
No 20
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=69.60 E-value=7.9 Score=27.91 Aligned_cols=29 Identities=17% Similarity=0.376 Sum_probs=19.7
Q ss_pred CcEEEEEcCCCc---cEEEEccCCCCCCEEEE
Q psy10008 79 NKIKMQTSNAKG---RHVIAVEDVHKGDTLFV 107 (214)
Q Consensus 79 ~~vei~~s~~~G---Rgl~Atrdi~~GevIl~ 107 (214)
...++......| =.++|+|+|++||.|+.
T Consensus 83 pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i 114 (116)
T smart00317 83 PNCELLFVEVNGDSRIVIFALRDIKPGEELTI 114 (116)
T ss_pred CCEEEEEEEECCCcEEEEEECCCcCCCCEEee
Confidence 344444443344 35679999999999975
No 21
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=66.82 E-value=4.4 Score=28.44 Aligned_cols=33 Identities=21% Similarity=0.511 Sum_probs=22.9
Q ss_pred CCccccCCCCCCC----cccCCCCCceeecChHHHhH
Q psy10008 121 MSNCNHCCTSISA----PIPCNECILAVYCSESCRRE 153 (214)
Q Consensus 121 ~~~C~~C~~~~~~----~~~C~~C~~~~YCS~~C~~~ 153 (214)
..+|++|...++. .+-=..=+..+|||..|.+.
T Consensus 3 ~~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k~ 39 (66)
T COG2075 3 VRVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEKL 39 (66)
T ss_pred eeEecCcCCccCCCceEEEEecCCeEEEEechhHHHH
Confidence 3579999998853 22222345889999999873
No 22
>KOG4442|consensus
Probab=64.54 E-value=6.8 Score=39.04 Aligned_cols=30 Identities=27% Similarity=0.366 Sum_probs=27.7
Q ss_pred CCcEEEEEcCCCccEEEEccCCCCCCEEEE
Q psy10008 78 SNKIKMQTSNAKGRHVIAVEDVHKGDTLFV 107 (214)
Q Consensus 78 s~~vei~~s~~~GRgl~Atrdi~~GevIl~ 107 (214)
..+|+|..++.+|=||.|..||++|.-|+.
T Consensus 119 yA~vevF~Te~KG~GLRA~~dI~~g~FI~E 148 (729)
T KOG4442|consen 119 YAKVEVFLTEKKGCGLRAEEDIPKGQFILE 148 (729)
T ss_pred cCceeEEEecCcccceeeccccCCCcEEee
Confidence 368999999999999999999999999985
No 23
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=58.13 E-value=6 Score=39.04 Aligned_cols=19 Identities=42% Similarity=0.824 Sum_probs=15.8
Q ss_pred ceeecChHHHhHhhhcchHH
Q psy10008 142 LAVYCSESCRREAWLRYHRW 161 (214)
Q Consensus 142 ~~~YCS~~C~~~aw~~~H~~ 161 (214)
..+|||.+|-+.+| ..|+.
T Consensus 89 ~s~fCsq~CFk~~w-~~Hk~ 107 (606)
T PLN03144 89 KSYHCSPKCFSDAW-RHHRV 107 (606)
T ss_pred cceeeCHHHHHHHH-HHHHH
Confidence 37899999999999 66654
No 24
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.68 E-value=4.9 Score=28.11 Aligned_cols=13 Identities=23% Similarity=0.728 Sum_probs=10.8
Q ss_pred ceeecChHHHhHh
Q psy10008 142 LAVYCSESCRREA 154 (214)
Q Consensus 142 ~~~YCS~~C~~~a 154 (214)
.-.|||+.|+..+
T Consensus 25 frPFCSkRCklID 37 (65)
T COG3024 25 FRPFCSKRCKLID 37 (65)
T ss_pred cCcchhHhhhhcc
Confidence 4579999999876
No 25
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=56.71 E-value=10 Score=29.01 Aligned_cols=29 Identities=31% Similarity=0.917 Sum_probs=22.3
Q ss_pred CCCccccCCCCCCCcccCCCCCceeecChHHHhH-hh
Q psy10008 120 SMSNCNHCCTSISAPIPCNECILAVYCSESCRRE-AW 155 (214)
Q Consensus 120 ~~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~-aw 155 (214)
....|..|| +||+.| ...-|+.+|+.. -|
T Consensus 66 L~~~C~GC~------~PC~~C-~S~KCG~~CR~nRkw 95 (103)
T PF14949_consen 66 LDEDCPGCH------YPCPKC-GSRKCGPECRCNRKW 95 (103)
T ss_pred cCCCCCCcc------ccCCCC-CCCccChhhCcCCce
Confidence 345688887 689999 788999999753 44
No 26
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=55.25 E-value=7.8 Score=25.52 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=14.4
Q ss_pred cEEEEccCCCCCCEEEE
Q psy10008 91 RHVIAVEDVHKGDTLFV 107 (214)
Q Consensus 91 Rgl~Atrdi~~GevIl~ 107 (214)
+.++|+++|++|++|-.
T Consensus 2 ~v~va~~~i~~G~~i~~ 18 (64)
T smart00858 2 RVVVAARDLPAGEVITA 18 (64)
T ss_pred CEEEEeCccCCCCCcch
Confidence 46899999999999863
No 27
>TIGR03586 PseI pseudaminic acid synthase.
Probab=54.39 E-value=8.5 Score=35.06 Aligned_cols=21 Identities=33% Similarity=0.504 Sum_probs=18.1
Q ss_pred CccEEEEccCCCCCCEEEEec
Q psy10008 89 KGRHVIAVEDVHKGDTLFVEK 109 (214)
Q Consensus 89 ~GRgl~Atrdi~~GevIl~e~ 109 (214)
.+|+|||++||++|++|-.+.
T Consensus 274 ~rrsl~a~~di~~G~~it~~~ 294 (327)
T TIGR03586 274 FRRSLYVVKDIKKGETFTEEN 294 (327)
T ss_pred eeEEEEEccCcCCCCEecHHh
Confidence 489999999999999986554
No 28
>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=51.99 E-value=22 Score=26.59 Aligned_cols=28 Identities=21% Similarity=0.405 Sum_probs=19.2
Q ss_pred cEEEEEc---CCCccEEEEccCCCCCCEEEE
Q psy10008 80 KIKMQTS---NAKGRHVIAVEDVHKGDTLFV 107 (214)
Q Consensus 80 ~vei~~s---~~~GRgl~Atrdi~~GevIl~ 107 (214)
.+.+... ....=.++|+|+|++||.|+.
T Consensus 129 n~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i 159 (162)
T PF00856_consen 129 NCEVSFDFDGDGGCLVVRATRDIKKGEEIFI 159 (162)
T ss_dssp SEEEEEEEETTTTEEEEEESS-B-TTSBEEE
T ss_pred ccceeeEeecccceEEEEECCccCCCCEEEE
Confidence 5666665 455556789999999999985
No 29
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=51.67 E-value=12 Score=29.63 Aligned_cols=34 Identities=9% Similarity=0.262 Sum_probs=23.7
Q ss_pred CCccccCCCCCCC----cccCCCCCceeecChHHHhHh
Q psy10008 121 MSNCNHCCTSISA----PIPCNECILAVYCSESCRREA 154 (214)
Q Consensus 121 ~~~C~~C~~~~~~----~~~C~~C~~~~YCS~~C~~~a 154 (214)
...|+||...+.. .+-=...+..+|||.+|.+..
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f 41 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNY 41 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHH
Confidence 3579999988742 222235678999999997653
No 30
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=51.12 E-value=11 Score=25.86 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=22.4
Q ss_pred CCccccCCCCCCC-cccCCCCCceeecChHHHhHhh
Q psy10008 121 MSNCNHCCTSISA-PIPCNECILAVYCSESCRREAW 155 (214)
Q Consensus 121 ~~~C~~C~~~~~~-~~~C~~C~~~~YCS~~C~~~aw 155 (214)
...|..|-+.+.. .--+---.-..|||.+|+....
T Consensus 16 L~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi 51 (58)
T PF04570_consen 16 LSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQI 51 (58)
T ss_pred HHHHHccCCCCCCCCCeeeeccccccccHHHHHHHH
Confidence 3689999998852 1001112356899999998753
No 31
>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=49.81 E-value=11 Score=34.28 Aligned_cols=21 Identities=19% Similarity=0.499 Sum_probs=18.1
Q ss_pred CccEEEEccCCCCCCEEEEec
Q psy10008 89 KGRHVIAVEDVHKGDTLFVEK 109 (214)
Q Consensus 89 ~GRgl~Atrdi~~GevIl~e~ 109 (214)
..|+|||++||++|++|-.+.
T Consensus 276 ~rrsl~a~~di~~G~~lt~~~ 296 (329)
T TIGR03569 276 ARKSLVAAKDIKKGEIFTEDN 296 (329)
T ss_pred cceEEEEccCcCCCCEecHHh
Confidence 379999999999999986554
No 32
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.62 E-value=6.9 Score=23.84 Aligned_cols=23 Identities=22% Similarity=0.647 Sum_probs=12.5
Q ss_pred ccccCCCCCCC---------cccCCCCCceee
Q psy10008 123 NCNHCCTSISA---------PIPCNECILAVY 145 (214)
Q Consensus 123 ~C~~C~~~~~~---------~~~C~~C~~~~Y 145 (214)
+|..|..++.. -..|+.|..+.|
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE-
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEEe
Confidence 68888887743 245888887766
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=45.81 E-value=5.6 Score=24.74 Aligned_cols=19 Identities=32% Similarity=0.992 Sum_probs=14.3
Q ss_pred CCceeecChHHHhHh-hhcch
Q psy10008 140 CILAVYCSESCRREA-WLRYH 159 (214)
Q Consensus 140 C~~~~YCS~~C~~~a-w~~~H 159 (214)
|..+-|||..|.+.+ | .+|
T Consensus 6 cpkiGYCS~~CsKt~vW-a~s 25 (39)
T PF08189_consen 6 CPKIGYCSSKCSKTDVW-AFS 25 (39)
T ss_pred Ccccceeccccccccee-eec
Confidence 557889999998865 6 444
No 34
>KOG1338|consensus
Probab=45.65 E-value=13 Score=34.92 Aligned_cols=21 Identities=33% Similarity=0.670 Sum_probs=18.8
Q ss_pred CCccEEEEccCCCCCCEEEEe
Q psy10008 88 AKGRHVIAVEDVHKGDTLFVE 108 (214)
Q Consensus 88 ~~GRgl~Atrdi~~GevIl~e 108 (214)
..|+|++|+.+|++|+.+|.-
T Consensus 39 ~~G~g~vAtesIkkgE~Lf~~ 59 (466)
T KOG1338|consen 39 IAGAGIVATESIKKGESLFAY 59 (466)
T ss_pred hcccceeeehhhcCCceEEEe
Confidence 469999999999999999973
No 35
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=42.59 E-value=15 Score=25.36 Aligned_cols=25 Identities=28% Similarity=0.554 Sum_probs=18.4
Q ss_pred CCccccCCCCCCCcccCCCCCceeecChHHHhH
Q psy10008 121 MSNCNHCCTSISAPIPCNECILAVYCSESCRRE 153 (214)
Q Consensus 121 ~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~ 153 (214)
..+|--|.++++. .-.+||++|+..
T Consensus 8 H~HC~VCg~aIp~--------de~~CSe~C~ei 32 (64)
T COG4068 8 HRHCVVCGKAIPP--------DEQVCSEECGEI 32 (64)
T ss_pred CccccccCCcCCC--------ccchHHHHHHHH
Confidence 3578888887754 456799999964
No 36
>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=40.38 E-value=7.8 Score=24.84 Aligned_cols=30 Identities=30% Similarity=0.567 Sum_probs=19.7
Q ss_pred CCccccCCCCCCC---cccCCCCCceeecChHHHh
Q psy10008 121 MSNCNHCCTSISA---PIPCNECILAVYCSESCRR 152 (214)
Q Consensus 121 ~~~C~~C~~~~~~---~~~C~~C~~~~YCS~~C~~ 152 (214)
.-.|..|.++..= --.|= ..|.|||+.|+.
T Consensus 8 ~K~C~~C~rpf~WRKKW~~~W--d~VkYCS~rCR~ 40 (42)
T PF10013_consen 8 SKICPVCGRPFTWRKKWARCW--DEVKYCSDRCRR 40 (42)
T ss_pred CCcCcccCCcchHHHHHHHhc--hhhccHHHHhcc
Confidence 3578888887741 12221 268999999975
No 37
>PRK00807 50S ribosomal protein L24e; Validated
Probab=39.89 E-value=23 Score=23.48 Aligned_cols=33 Identities=18% Similarity=0.536 Sum_probs=22.2
Q ss_pred CccccCCCCCCC----cccCCCCCceeecChHHHhHh
Q psy10008 122 SNCNHCCTSISA----PIPCNECILAVYCSESCRREA 154 (214)
Q Consensus 122 ~~C~~C~~~~~~----~~~C~~C~~~~YCS~~C~~~a 154 (214)
..|++|...+.. .+-=.+.+..+|||..|.+.-
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f 38 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNY 38 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHH
Confidence 368999887742 111134568999999998753
No 38
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.91 E-value=32 Score=29.01 Aligned_cols=47 Identities=15% Similarity=0.318 Sum_probs=30.7
Q ss_pred ccCCCCCCEEE----E-eccc-eeeecCCC--CCCccccCCCCCC---CcccCCCCCc
Q psy10008 96 VEDVHKGDTLF----V-EKPV-AFVILPPC--SMSNCNHCCTSIS---APIPCNECIL 142 (214)
Q Consensus 96 trdi~~GevIl----~-e~P~-~~v~~~~~--~~~~C~~C~~~~~---~~~~C~~C~~ 142 (214)
+..|++||+|- . ..|+ ++...+++ ....|+.|...+. ....|++|..
T Consensus 116 ~d~f~~GDivrA~Vis~~~~~~Lst~~~dlGVI~A~CsrC~~~L~~~~~~l~Cp~Cg~ 173 (188)
T COG1096 116 SDAFRIGDIVRARVISTGDPIQLSTKGNDLGVIYARCSRCRAPLVKKGNMLKCPNCGN 173 (188)
T ss_pred ccccccccEEEEEEEecCCCeEEEecCCcceEEEEEccCCCcceEEcCcEEECCCCCC
Confidence 36899999985 2 1333 33333443 2478999988774 4678999864
No 39
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=36.76 E-value=28 Score=21.63 Aligned_cols=30 Identities=23% Similarity=0.656 Sum_probs=19.2
Q ss_pred cccCCCCCCC-cccCC-CCCceeecChHHHhH
Q psy10008 124 CNHCCTSISA-PIPCN-ECILAVYCSESCRRE 153 (214)
Q Consensus 124 C~~C~~~~~~-~~~C~-~C~~~~YCS~~C~~~ 153 (214)
|++|...+.. ++.=. +=+..+||+..|.+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHH
Confidence 7888887742 11110 334788999999865
No 40
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=36.23 E-value=24 Score=21.96 Aligned_cols=24 Identities=25% Similarity=0.897 Sum_probs=18.0
Q ss_pred cccCCCCCCC-cccCCCCCceeecCh
Q psy10008 124 CNHCCTSISA-PIPCNECILAVYCSE 148 (214)
Q Consensus 124 C~~C~~~~~~-~~~C~~C~~~~YCS~ 148 (214)
|+.|.+...- ++.|..| .-.||+.
T Consensus 1 C~~C~~~~~l~~f~C~~C-~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHC-GNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCcc-CCccccc
Confidence 6677776655 7889999 6778874
No 41
>KOG2061|consensus
Probab=35.42 E-value=31 Score=31.92 Aligned_cols=40 Identities=35% Similarity=0.815 Sum_probs=35.4
Q ss_pred CccccCCCCCCCcccCCCCCceeecChHHHhHhhhcchHHhh
Q psy10008 122 SNCNHCCTSISAPIPCNECILAVYCSESCRREAWLRYHRWEC 163 (214)
Q Consensus 122 ~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~EC 163 (214)
..|..|+-. ....|..|+.+.|||..=|..+|...|+.+|
T Consensus 137 ~~~~~~~~~--a~~~~~~~~~a~~~S~~~q~~d~~~~~~~a~ 176 (362)
T KOG2061|consen 137 DLCGSCGCS--APAACSPCKAAAYCSKKHQSLDWPKGHKDAC 176 (362)
T ss_pred chhccCccc--CcccccccchhhhcCchhhcccccccccccc
Confidence 677777765 6778999999999999999999988999999
No 42
>KOG0438|consensus
Probab=34.70 E-value=39 Score=30.56 Aligned_cols=22 Identities=32% Similarity=0.610 Sum_probs=18.0
Q ss_pred cEEEEccCCCCCCEEEE--eccce
Q psy10008 91 RHVIAVEDVHKGDTLFV--EKPVA 112 (214)
Q Consensus 91 Rgl~Atrdi~~GevIl~--e~P~~ 112 (214)
|+++|++.+++||+|+. +-|+.
T Consensus 129 ~~Ila~egm~aGD~i~ss~~i~~~ 152 (312)
T KOG0438|consen 129 RYILATEGLKAGDTILSSRKIPFM 152 (312)
T ss_pred eEEEEecCCCCCCccccccccccc
Confidence 59999999999999984 44554
No 43
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=34.06 E-value=23 Score=22.47 Aligned_cols=13 Identities=31% Similarity=0.810 Sum_probs=10.9
Q ss_pred CceeecChHHHhH
Q psy10008 141 ILAVYCSESCRRE 153 (214)
Q Consensus 141 ~~~~YCS~~C~~~ 153 (214)
+..+|||+.|+..
T Consensus 23 ~~Y~FCS~~C~~~ 35 (47)
T PF04945_consen 23 RTYYFCSEGCKEK 35 (47)
T ss_dssp EEEEESSHHHHHH
T ss_pred EEEEEcCHHHHHH
Confidence 3689999999876
No 44
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=33.86 E-value=28 Score=22.09 Aligned_cols=32 Identities=28% Similarity=0.558 Sum_probs=25.5
Q ss_pred ccccCCCCCC-CcccCCCCCceeecChHHHhHhh
Q psy10008 123 NCNHCCTSIS-APIPCNECILAVYCSESCRREAW 155 (214)
Q Consensus 123 ~C~~C~~~~~-~~~~C~~C~~~~YCS~~C~~~aw 155 (214)
.|+.|.+++. ..+.|..|...-.|. .|-....
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~-~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCS-SCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHH-HHHCcCc
Confidence 5999999765 367899998899997 5987664
No 45
>KOG2858|consensus
Probab=33.32 E-value=15 Score=33.98 Aligned_cols=35 Identities=26% Similarity=0.557 Sum_probs=27.9
Q ss_pred CCCCCccccCCCCCCCcccCCCCCceeecChHHHhHh
Q psy10008 118 PCSMSNCNHCCTSISAPIPCNECILAVYCSESCRREA 154 (214)
Q Consensus 118 ~~~~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~a 154 (214)
......|.-|++.- ..+.|++| .+.+||-+|-+++
T Consensus 14 ~~~~vlCgVClknE-~KYkCPRC-l~rtCsLeCskkH 48 (390)
T KOG2858|consen 14 GLHSVLCGVCLKNE-PKYKCPRC-LARTCSLECSKKH 48 (390)
T ss_pred ccchhhhhhcccCc-ccccCcch-hhhheeccccccc
Confidence 34557899999874 45889999 9999999997653
No 46
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=33.09 E-value=35 Score=24.34 Aligned_cols=24 Identities=33% Similarity=0.690 Sum_probs=18.0
Q ss_pred CCCccccCCCCCCCcccCCCCCceeecChHHH
Q psy10008 120 SMSNCNHCCTSISAPIPCNECILAVYCSESCR 151 (214)
Q Consensus 120 ~~~~C~~C~~~~~~~~~C~~C~~~~YCS~~C~ 151 (214)
....|..|.+.+.. ...|||-.|.
T Consensus 48 ~~~~C~~C~R~L~d--------~~~fCSl~CK 71 (72)
T PF04640_consen 48 SGNICETCHRSLQD--------PYRFCSLSCK 71 (72)
T ss_pred CCCccCCCCCCCCC--------CCeEEeeeEE
Confidence 46789999998864 2568888774
No 47
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=32.50 E-value=29 Score=26.57 Aligned_cols=23 Identities=26% Similarity=0.683 Sum_probs=18.0
Q ss_pred CCCccccCCCCCC----CcccCCCCCc
Q psy10008 120 SMSNCNHCCTSIS----APIPCNECIL 142 (214)
Q Consensus 120 ~~~~C~~C~~~~~----~~~~C~~C~~ 142 (214)
...+|..|.+++. .++.|+.|+.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGT 34 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCC
Confidence 3589999999885 4677998853
No 48
>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=32.22 E-value=62 Score=22.94 Aligned_cols=39 Identities=18% Similarity=0.305 Sum_probs=26.0
Q ss_pred CCcccCCCCcccccCCCcEE-EEEcCCCccEEEEccCCCCCCEEE
Q psy10008 63 LPSLACGESHTLMCASNKIK-MQTSNAKGRHVIAVEDVHKGDTLF 106 (214)
Q Consensus 63 ~p~l~~~~n~~ip~~s~~ve-i~~s~~~GRgl~Atrdi~~GevIl 106 (214)
+.++.+++|.. ..+. |++.+..-+++.|+..+++||+|.
T Consensus 37 V~~i~~DP~Rs-----a~iAlV~~~~g~~~yiiA~eg~~vGd~I~ 76 (77)
T PF00181_consen 37 VIDIEYDPNRS-----APIALVKYEDGEKRYIIAPEGMKVGDIIE 76 (77)
T ss_dssp EEEEEEETTTS-----SEEEEEEETTSEEEEEEEBTTEBTTEEEE
T ss_pred EEEEEecCCcC-----ccEEEEEecCCcEEEEEeECCCcCCCEEE
Confidence 33444454444 4444 344455668999999999999986
No 49
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=30.68 E-value=31 Score=27.50 Aligned_cols=23 Identities=17% Similarity=0.169 Sum_probs=18.8
Q ss_pred cCCCccEEEEccCCCCCCEEEEe
Q psy10008 86 SNAKGRHVIAVEDVHKGDTLFVE 108 (214)
Q Consensus 86 s~~~GRgl~Atrdi~~GevIl~e 108 (214)
.+..+..++|+++|.+|++|-.+
T Consensus 15 ~~~~~~VvVA~r~L~rGevIt~~ 37 (141)
T PRK12618 15 QPAAAETVVAARTIRALTVIGAE 37 (141)
T ss_pred ccceeEEEEEccCcCCCCCcCHH
Confidence 35678889999999999998544
No 50
>KOG2738|consensus
Probab=30.54 E-value=25 Score=32.09 Aligned_cols=33 Identities=27% Similarity=0.896 Sum_probs=22.9
Q ss_pred ccCCCCCCCcccCCCCC-----ceeecChHHHhHhhhcchH
Q psy10008 125 NHCCTSISAPIPCNECI-----LAVYCSESCRREAWLRYHR 160 (214)
Q Consensus 125 ~~C~~~~~~~~~C~~C~-----~~~YCS~~C~~~aw~~~H~ 160 (214)
..|.+... ..|+.|- .++||+.+|.+..| ..|+
T Consensus 12 ~~c~~~a~--l~Cp~c~~~~i~~~~fc~q~cf~~~w-~~hK 49 (369)
T KOG2738|consen 12 LQCGSEAS--LQCPTCLKLGIKSAYFCAQECFKNSW-LSHK 49 (369)
T ss_pred cccCChhh--ccCchhhhcCCCcccccCchhhhcch-hhhh
Confidence 45665433 6677663 46899999999999 4444
No 51
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=29.95 E-value=19 Score=31.47 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=19.2
Q ss_pred CCCccccCCCCCC-----------CcccCCCCCceee
Q psy10008 120 SMSNCNHCCTSIS-----------APIPCNECILAVY 145 (214)
Q Consensus 120 ~~~~C~~C~~~~~-----------~~~~C~~C~~~~Y 145 (214)
.+.+|..|+..++ ..+.||.|+...|
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy 232 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILY 232 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhcCCCCccCCccchHHH
Confidence 4778999998775 2678998875544
No 52
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=29.18 E-value=49 Score=22.24 Aligned_cols=33 Identities=21% Similarity=0.547 Sum_probs=23.2
Q ss_pred CCccccCCCCCCC-----cccCCCCCceeecChHHHhHh
Q psy10008 121 MSNCNHCCTSISA-----PIPCNECILAVYCSESCRREA 154 (214)
Q Consensus 121 ~~~C~~C~~~~~~-----~~~C~~C~~~~YCS~~C~~~a 154 (214)
...|++|...+.. .++ .+.+...|||..|.+..
T Consensus 3 ~~~C~f~g~~I~PG~G~~~Vr-~Dgkv~~F~s~Kc~~~~ 40 (54)
T cd00472 3 TEKCSFCGYKIYPGHGKMYVR-NDGKVFRFCSSKCEKNF 40 (54)
T ss_pred EEEecCcCCeecCCCccEEEe-cCCCEEEEECHHHHHHH
Confidence 3578999887742 222 25668999999998654
No 53
>PF03277 Herpes_UL4: Herpesvirus UL4 family; InterPro: IPR004958 This is a family of Herpes virus UL4 proteins, which are related to Human herpesvirus 1 (HHV-1), Human herpesvirus 2 (HHV-2), Equid herpesvirus 1 (Equine herpesvirus 1, EHV-1) 58, and Human herpesvirus 3 VZV-32 56 proteins.
Probab=29.10 E-value=37 Score=28.66 Aligned_cols=56 Identities=18% Similarity=0.317 Sum_probs=40.6
Q ss_pred CCCCCCEEEEeccceeeecCCCCCCccccCCCCCC---CcccCC---CCCceeecChHHHhHh
Q psy10008 98 DVHKGDTLFVEKPVAFVILPPCSMSNCNHCCTSIS---APIPCN---ECILAVYCSESCRREA 154 (214)
Q Consensus 98 di~~GevIl~e~P~~~v~~~~~~~~~C~~C~~~~~---~~~~C~---~C~~~~YCS~~C~~~a 154 (214)
.|++|.+|+...|.+.++--+....+|.|+|.... .+.+.. -| .+.|++..|...+
T Consensus 46 ~Lp~G~vViQh~P~gtli~VDc~~efCsY~f~~~~~~~~~~~~~~~~~~-v~PF~sw~~~~~~ 107 (188)
T PF03277_consen 46 HLPPGNVVIQHGPVGTLIVVDCGAEFCSYRFTGRESRRRPLSWWPGSTC-VYPFDSWVVSGRD 107 (188)
T ss_pred cCCCCeEEEEeCCeEEEEEEecccceeEEEEeccccccccccCCCCCEE-EEecceeEEeCCC
Confidence 79999999999999988887888899999996321 122222 34 6778876665443
No 54
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=29.08 E-value=59 Score=28.44 Aligned_cols=43 Identities=14% Similarity=0.178 Sum_probs=31.5
Q ss_pred cCCCcccCCCCcccccCCCcEEEEEcCCCccEEEEccCCCCCCEEEE
Q psy10008 61 ASLPSLACGESHTLMCASNKIKMQTSNAKGRHVIAVEDVHKGDTLFV 107 (214)
Q Consensus 61 ~~~p~l~~~~n~~ip~~s~~vei~~s~~~GRgl~Atrdi~~GevIl~ 107 (214)
..+-++-|++|...+-+ .|.+.+..-+++.|+..++.||+|..
T Consensus 41 g~V~~IeyDPnRsa~IA----lv~~~~g~~~YIiAp~gl~~Gd~I~s 83 (238)
T PRK09612 41 GKVVDILHDPGRNAPVA----KVKFENGEEFLILAPEGLYVGQEIEI 83 (238)
T ss_pred EEEEEEEECCCCCCeEE----EEEeCCCCEEEEEccCCCCCCCEEEe
Confidence 34556777777775422 34566667789999999999999985
No 55
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=28.40 E-value=21 Score=22.42 Aligned_cols=37 Identities=22% Similarity=0.511 Sum_probs=26.8
Q ss_pred ccccCCCCCCCcccCCCCCceeecChHHHhHhhhcchHH
Q psy10008 123 NCNHCCTSISAPIPCNECILAVYCSESCRREAWLRYHRW 161 (214)
Q Consensus 123 ~C~~C~~~~~~~~~C~~C~~~~YCS~~C~~~aw~~~H~~ 161 (214)
.|+.|.......++|..|...-.|. .|....- ..|++
T Consensus 2 ~C~~C~~~~~~r~~C~~C~dfDLC~-~C~~~~~-H~H~~ 38 (41)
T cd02337 2 TCNECKHHVETRWHCTVCEDYDLCI-TCYNTKN-HPHKM 38 (41)
T ss_pred cCCCCCCcCCCceECCCCcchhhHH-HHhCCCC-CCccc
Confidence 4888877666778999998888886 5887643 44543
No 56
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=28.27 E-value=34 Score=20.78 Aligned_cols=24 Identities=17% Similarity=0.623 Sum_probs=15.6
Q ss_pred CccccCCCCCC----------CcccCCCCCceee
Q psy10008 122 SNCNHCCTSIS----------APIPCNECILAVY 145 (214)
Q Consensus 122 ~~C~~C~~~~~----------~~~~C~~C~~~~Y 145 (214)
..|.+|..... ..++|++|+.+++
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 35777776542 2578999976653
No 57
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=28.22 E-value=39 Score=21.17 Aligned_cols=21 Identities=24% Similarity=0.686 Sum_probs=12.7
Q ss_pred CCCCCCCcccCCCCCceeecCh
Q psy10008 127 CCTSISAPIPCNECILAVYCSE 148 (214)
Q Consensus 127 C~~~~~~~~~C~~C~~~~YCS~ 148 (214)
|.+....++.|+.| .-.||.+
T Consensus 6 C~~~~~~~~~C~~C-~~~FC~~ 26 (43)
T PF01428_consen 6 CKKKDFLPFKCKHC-GKSFCLK 26 (43)
T ss_dssp T--BCTSHEE-TTT-S-EE-TT
T ss_pred CcCccCCCeECCCC-CcccCcc
Confidence 77766678899999 7889974
No 58
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=28.03 E-value=27 Score=23.27 Aligned_cols=28 Identities=21% Similarity=0.681 Sum_probs=14.8
Q ss_pred ccccCCCCCCC---------cccCCCCCceeecChHHHh
Q psy10008 123 NCNHCCTSISA---------PIPCNECILAVYCSESCRR 152 (214)
Q Consensus 123 ~C~~C~~~~~~---------~~~C~~C~~~~YCS~~C~~ 152 (214)
.|..|.+++.. .+.|++| ...||- +|-.
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C-~~~FC~-dCD~ 37 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKC-KNHFCI-DCDV 37 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTT-T--B-H-HHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCC-CCcccc-CcCh
Confidence 37778877754 4789999 677884 5754
No 59
>smart00746 TRASH metallochaperone-like domain.
Probab=27.43 E-value=61 Score=17.49 Aligned_cols=14 Identities=21% Similarity=0.558 Sum_probs=10.6
Q ss_pred CceeecChHHHhHh
Q psy10008 141 ILAVYCSESCRREA 154 (214)
Q Consensus 141 ~~~~YCS~~C~~~a 154 (214)
....|||..|....
T Consensus 22 ~~~~FCs~~c~~~~ 35 (39)
T smart00746 22 KVFYFCSSKCLSKF 35 (39)
T ss_pred EEEEEeCHHHHHHH
Confidence 36689999998753
No 60
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=27.02 E-value=30 Score=31.81 Aligned_cols=22 Identities=27% Similarity=0.492 Sum_probs=18.4
Q ss_pred CccEEEEccCCCCCCEEEEecc
Q psy10008 89 KGRHVIAVEDVHKGDTLFVEKP 110 (214)
Q Consensus 89 ~GRgl~Atrdi~~GevIl~e~P 110 (214)
.-|+||+++||++|+++=.+.-
T Consensus 288 ~~Rsl~~~kdikkGe~ls~~Nl 309 (347)
T COG2089 288 ARRSLVATKDIKKGEILSEDNL 309 (347)
T ss_pred HhhheeeecccccCccccccce
Confidence 5799999999999998766653
No 61
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=25.65 E-value=39 Score=27.23 Aligned_cols=25 Identities=20% Similarity=0.590 Sum_probs=17.9
Q ss_pred CCccccCCCCC-----CCcccCCCCCceee
Q psy10008 121 MSNCNHCCTSI-----SAPIPCNECILAVY 145 (214)
Q Consensus 121 ~~~C~~C~~~~-----~~~~~C~~C~~~~Y 145 (214)
.-+|.+|.... ..+-+|+.|....|
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHTEF 141 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCCee
Confidence 45788888655 24678999976555
No 62
>KOG4236|consensus
Probab=24.36 E-value=31 Score=34.20 Aligned_cols=48 Identities=21% Similarity=0.445 Sum_probs=29.9
Q ss_pred EEccCCCCCCEEE---Eeccce--eeecCC-------CCCCccccCCCCCCC----cccCCCCC
Q psy10008 94 IAVEDVHKGDTLF---VEKPVA--FVILPP-------CSMSNCNHCCTSISA----PIPCNECI 141 (214)
Q Consensus 94 ~Atrdi~~GevIl---~e~P~~--~v~~~~-------~~~~~C~~C~~~~~~----~~~C~~C~ 141 (214)
-+..||..||+|- ...|.. +.+.|. ....+|++|+..+.. .+.|.+|+
T Consensus 117 tsasdI~eG~lvEvvl~~~at~ed~~i~PH~l~vhSY~~PtFCD~CGEmL~GLvrQGlKC~gCg 180 (888)
T KOG4236|consen 117 TSASDITEGDLVEVVLSASATFEDFQIRPHTLFVHSYKAPTFCDFCGEMLFGLVRQGLKCEGCG 180 (888)
T ss_pred ccccccccCceEEEEeeccccccceeeecceeeeecccCchHHHHHHHHHHHHHHccccccCCC
Confidence 3556999998764 222221 112221 245899999988854 46799984
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.82 E-value=52 Score=19.99 Aligned_cols=23 Identities=22% Similarity=0.592 Sum_probs=14.9
Q ss_pred CccccCCCCCC----------CcccCCCCCcee
Q psy10008 122 SNCNHCCTSIS----------APIPCNECILAV 144 (214)
Q Consensus 122 ~~C~~C~~~~~----------~~~~C~~C~~~~ 144 (214)
..|.+|..... ..++|+.|+.++
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 35777765441 267899997654
No 64
>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=23.07 E-value=45 Score=25.16 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=12.8
Q ss_pred EEEccCCCCCCEEEE
Q psy10008 93 VIAVEDVHKGDTLFV 107 (214)
Q Consensus 93 l~Atrdi~~GevIl~ 107 (214)
++|+++|++|++|-.
T Consensus 2 ~Va~r~I~~G~~i~~ 16 (122)
T TIGR03170 2 VVAKRPLKRGEVISP 16 (122)
T ss_pred EEECcccCCCCCcCH
Confidence 689999999998753
No 65
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=22.50 E-value=55 Score=19.57 Aligned_cols=22 Identities=27% Similarity=0.674 Sum_probs=13.5
Q ss_pred ccccCCCCCC----------CcccCCCCCcee
Q psy10008 123 NCNHCCTSIS----------APIPCNECILAV 144 (214)
Q Consensus 123 ~C~~C~~~~~----------~~~~C~~C~~~~ 144 (214)
.|.+|..... ..+.|++|+...
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 5777776431 146788886554
No 66
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.37 E-value=1.1e+02 Score=20.64 Aligned_cols=27 Identities=15% Similarity=0.408 Sum_probs=18.0
Q ss_pred cCCCCCCccccCCCCCCC-----cccCCCCCc
Q psy10008 116 LPPCSMSNCNHCCTSISA-----PIPCNECIL 142 (214)
Q Consensus 116 ~~~~~~~~C~~C~~~~~~-----~~~C~~C~~ 142 (214)
++.+....|+.|...... .+.|+.|+.
T Consensus 23 ~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 23 DEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CCCCCccCccCcccccccccccceEEcCCCCC
Confidence 334457789999977643 466777743
No 67
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=22.36 E-value=58 Score=20.55 Aligned_cols=31 Identities=26% Similarity=0.561 Sum_probs=24.4
Q ss_pred ccccCCCCCC-CcccCCCCCceeecChHHHhHh
Q psy10008 123 NCNHCCTSIS-APIPCNECILAVYCSESCRREA 154 (214)
Q Consensus 123 ~C~~C~~~~~-~~~~C~~C~~~~YCS~~C~~~a 154 (214)
.|+.|.+++. ..++|..|...-+|. +|....
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~-~C~~~~ 33 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCE-SCEAKG 33 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchH-HhhCcC
Confidence 5899998764 468999998899997 587654
No 68
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=22.28 E-value=64 Score=18.16 Aligned_cols=18 Identities=39% Similarity=1.136 Sum_probs=10.8
Q ss_pred cccCCCCCC-----CcccCCCCC
Q psy10008 124 CNHCCTSIS-----APIPCNECI 141 (214)
Q Consensus 124 C~~C~~~~~-----~~~~C~~C~ 141 (214)
|..|...+. ..++|++|.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 455654442 367888884
No 69
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=22.07 E-value=71 Score=22.68 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=20.1
Q ss_pred CCccccCCCCCCC----cccCCCCCceeecChHHHhH
Q psy10008 121 MSNCNHCCTSISA----PIPCNECILAVYCSESCRRE 153 (214)
Q Consensus 121 ~~~C~~C~~~~~~----~~~C~~C~~~~YCS~~C~~~ 153 (214)
...|++|...+.. .+-=.+.....|||..|.+.
T Consensus 3 ~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~ 39 (71)
T PF01246_consen 3 TEKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKL 39 (71)
T ss_dssp SEE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHH
T ss_pred eEEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHH
Confidence 4579999987742 11124566899999999865
No 70
>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=21.85 E-value=60 Score=18.90 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=13.2
Q ss_pred CCccccCCCCCC-----CcccCCCCCceee
Q psy10008 121 MSNCNHCCTSIS-----APIPCNECILAVY 145 (214)
Q Consensus 121 ~~~C~~C~~~~~-----~~~~C~~C~~~~Y 145 (214)
..+|..|..+.. ....|+.|....|
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 457888887763 2567888876655
No 71
>KOG1082|consensus
Probab=21.45 E-value=1.1e+02 Score=28.09 Aligned_cols=33 Identities=12% Similarity=0.169 Sum_probs=29.2
Q ss_pred ccCCCcEEEEEcCCCccEEEEccCCCCCCEEEE
Q psy10008 75 MCASNKIKMQTSNAKGRHVIAVEDVHKGDTLFV 107 (214)
Q Consensus 75 p~~s~~vei~~s~~~GRgl~Atrdi~~GevIl~ 107 (214)
..+...++|..++.+|=||.+...|++|+-|..
T Consensus 172 ~g~~~~leIfrt~~kGwgvRs~~~I~~G~fvcE 204 (364)
T KOG1082|consen 172 KGLQFHLEVFRTPEKGWGVRTLDPIPAGEFVCE 204 (364)
T ss_pred cccccceEEEecCCceeeecccccccCCCeeEE
Confidence 446789999999889999999999999998874
No 72
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.40 E-value=46 Score=21.69 Aligned_cols=31 Identities=26% Similarity=0.665 Sum_probs=23.5
Q ss_pred ccccCCC-CCC-CcccCCCCC--ceeecChHHHhHh
Q psy10008 123 NCNHCCT-SIS-APIPCNECI--LAVYCSESCRREA 154 (214)
Q Consensus 123 ~C~~C~~-~~~-~~~~C~~C~--~~~YCS~~C~~~a 154 (214)
.|+.|.. ++. .-+.|..|. ..-.|+ .|....
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~-~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQ-DCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCH-HHHhCc
Confidence 4889988 543 357899998 788997 587654
No 73
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=20.60 E-value=97 Score=18.79 Aligned_cols=31 Identities=29% Similarity=0.683 Sum_probs=20.2
Q ss_pred CCCccccCCCCCCC---cccCCCCCceeecChHHHh
Q psy10008 120 SMSNCNHCCTSISA---PIPCNECILAVYCSESCRR 152 (214)
Q Consensus 120 ~~~~C~~C~~~~~~---~~~C~~C~~~~YCS~~C~~ 152 (214)
....|..|.+.+.. .+.|..|+ ..|-..|..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~--~~~H~~C~~ 43 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCK--VKCHKKCAE 43 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCC--chHHHHHHh
Confidence 45689999988863 56777773 234444543
No 74
>CHL00044 rpl16 ribosomal protein L16
Probab=20.35 E-value=75 Score=25.24 Aligned_cols=41 Identities=15% Similarity=0.045 Sum_probs=31.8
Q ss_pred CCCcccccCCCcEEEEEcCCCccEEEEccCCCCCCEEEEec
Q psy10008 69 GESHTLMCASNKIKMQTSNAKGRHVIAVEDVHKGDTLFVEK 109 (214)
Q Consensus 69 ~~n~~ip~~s~~vei~~s~~~GRgl~Atrdi~~GevIl~e~ 109 (214)
-..+.+|--..+.+++...++|.-..-...+++|++||+-.
T Consensus 67 rv~P~~pvtkkp~e~RMGkGKG~~~~~va~V~~G~ilfEi~ 107 (135)
T CHL00044 67 RIFPDKPVTMRPAETRMGSGKGSPEYWVAVVKPGRILYEMG 107 (135)
T ss_pred EECCCcceEeCcccccccCCCCCccEEEEEECCCcEEEEEe
Confidence 34566666667788888888888877778899999999654
No 75
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.08 E-value=58 Score=17.85 Aligned_cols=18 Identities=28% Similarity=0.778 Sum_probs=10.3
Q ss_pred ccccCCCCCCC-cccCCCC
Q psy10008 123 NCNHCCTSISA-PIPCNEC 140 (214)
Q Consensus 123 ~C~~C~~~~~~-~~~C~~C 140 (214)
.|.+|...+.. ...|+.|
T Consensus 1 ~Cp~CG~~~~~~~~fC~~C 19 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNC 19 (23)
T ss_pred CCcccCCCCCCcCcchhhh
Confidence 36777776643 3445555
No 76
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.05 E-value=65 Score=32.15 Aligned_cols=32 Identities=31% Similarity=0.739 Sum_probs=22.7
Q ss_pred CCCccccCCCCCCCcccCCCCC-----ceeecChHHHhH
Q psy10008 120 SMSNCNHCCTSISAPIPCNECI-----LAVYCSESCRRE 153 (214)
Q Consensus 120 ~~~~C~~C~~~~~~~~~C~~C~-----~~~YCS~~C~~~ 153 (214)
...+|..|+..+.. ..|+.|+ .+.||. +|-..
T Consensus 14 ~akFC~~CG~~l~~-~~Cp~CG~~~~~~~~fC~-~CG~~ 50 (645)
T PRK14559 14 NNRFCQKCGTSLTH-KPCPQCGTEVPVDEAHCP-NCGAE 50 (645)
T ss_pred CCccccccCCCCCC-CcCCCCCCCCCccccccc-ccCCc
Confidence 35689999887743 5799996 457886 47653
No 77
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.02 E-value=71 Score=25.36 Aligned_cols=24 Identities=8% Similarity=0.002 Sum_probs=18.4
Q ss_pred CCCccccCCCCCC----CcccCCCCCce
Q psy10008 120 SMSNCNHCCTSIS----APIPCNECILA 143 (214)
Q Consensus 120 ~~~~C~~C~~~~~----~~~~C~~C~~~ 143 (214)
....|..|.+++. .++.|+.|+..
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCc
Confidence 3579999999885 46789888644
Done!