Query psy5735
Match_columns 247
No_of_seqs 209 out of 1350
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 16:40:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5735.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5735hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2084|consensus 99.6 1.6E-14 3.4E-19 135.8 14.0 150 9-168 168-319 (482)
2 PF00856 SET: SET domain; Int 99.5 6.7E-14 1.4E-18 111.5 5.5 52 38-89 107-162 (162)
3 smart00317 SET SET (Su(var)3-9 99.2 1.7E-11 3.7E-16 93.3 3.7 46 43-88 67-116 (116)
4 KOG2589|consensus 98.7 1E-08 2.2E-13 92.8 3.9 64 45-120 191-256 (453)
5 COG2940 Proteins containing SE 98.1 1.7E-06 3.6E-11 82.9 3.1 70 49-120 405-478 (480)
6 KOG4442|consensus 98.1 2.3E-06 5.1E-11 83.1 3.4 50 42-91 185-239 (729)
7 KOG1080|consensus 98.0 3.7E-06 8E-11 85.9 3.6 42 48-89 938-983 (1005)
8 KOG1082|consensus 97.4 9E-05 2E-09 68.7 3.1 53 40-92 262-323 (364)
9 KOG1083|consensus 96.7 0.0012 2.6E-08 67.2 3.1 50 40-89 1234-1294(1306)
10 KOG1085|consensus 96.5 0.0017 3.7E-08 57.7 2.8 42 50-91 334-379 (392)
11 KOG1141|consensus 96.4 0.0015 3.3E-08 65.0 2.0 56 50-115 1190-1253(1262)
12 KOG1337|consensus 96.4 0.0022 4.7E-08 61.5 2.8 60 44-111 231-291 (472)
13 KOG1079|consensus 94.9 0.022 4.8E-07 55.9 3.4 43 49-91 665-711 (739)
14 PF13424 TPR_12: Tetratricopep 89.4 0.97 2.1E-05 31.4 5.0 55 181-236 8-62 (78)
15 KOG1081|consensus 89.2 0.15 3.3E-06 48.9 0.8 50 41-90 362-416 (463)
16 KOG1338|consensus 87.7 0.38 8.3E-06 44.9 2.4 54 38-91 207-261 (466)
17 KOG2461|consensus 84.7 0.44 9.5E-06 44.8 1.2 27 66-92 120-146 (396)
18 PF13374 TPR_10: Tetratricopep 75.0 6.2 0.00013 23.4 3.8 34 184-217 8-41 (42)
19 PF13414 TPR_11: TPR repeat; P 73.3 19 0.00042 23.9 6.4 49 178-234 3-51 (69)
20 cd02684 MIT_2 MIT: domain cont 72.6 6.2 0.00013 28.1 3.8 42 175-216 3-45 (75)
21 PF13719 zinc_ribbon_5: zinc-r 70.3 2 4.2E-05 26.4 0.6 30 135-166 3-35 (37)
22 cd02680 MIT_calpain7_2 MIT: do 68.8 9.3 0.0002 27.4 4.0 34 176-209 4-37 (75)
23 PRK00398 rpoP DNA-directed RNA 67.8 3.7 8E-05 26.2 1.6 30 134-167 3-32 (46)
24 PF04212 MIT: MIT (microtubule 65.5 11 0.00024 26.0 3.8 36 177-212 4-39 (69)
25 PF13432 TPR_16: Tetratricopep 64.8 22 0.00048 23.4 5.1 45 184-236 3-47 (65)
26 PF08271 TF_Zn_Ribbon: TFIIB z 63.5 3.3 7.1E-05 26.1 0.7 30 135-167 1-30 (43)
27 PF13174 TPR_6: Tetratricopept 63.5 14 0.0003 20.6 3.5 27 181-207 3-29 (33)
28 cd02683 MIT_1 MIT: domain cont 62.6 12 0.00027 26.7 3.6 40 177-216 5-45 (77)
29 cd02681 MIT_calpain7_1 MIT: do 62.5 33 0.00071 24.6 5.8 35 177-211 5-39 (76)
30 cd02678 MIT_VPS4 MIT: domain c 62.1 16 0.00034 25.8 4.1 42 175-216 3-45 (75)
31 cd02677 MIT_SNX15 MIT: domain 61.5 15 0.00034 26.1 4.0 41 176-216 4-45 (75)
32 PF06957 COPI_C: Coatomer (COP 61.3 27 0.00058 33.3 6.6 52 181-232 207-258 (422)
33 PF09986 DUF2225: Uncharacteri 60.7 21 0.00045 30.6 5.4 80 155-235 47-133 (214)
34 PF13717 zinc_ribbon_4: zinc-r 60.5 4.9 0.00011 24.5 1.1 29 135-165 3-34 (36)
35 smart00661 RPOL9 RNA polymeras 59.2 6.5 0.00014 25.4 1.6 29 140-168 4-32 (52)
36 PF08666 SAF: SAF domain; Int 58.9 6.8 0.00015 26.1 1.7 18 71-88 3-20 (63)
37 PF10579 Rapsyn_N: Rapsyn N-te 58.9 20 0.00043 26.1 4.1 55 180-234 8-71 (80)
38 PF02150 RNA_POL_M_15KD: RNA p 58.1 3.6 7.8E-05 25.0 0.2 29 137-168 4-32 (35)
39 TIGR02059 swm_rep_I cyanobacte 57.6 16 0.00034 27.7 3.5 23 69-91 76-98 (101)
40 PF01485 IBR: IBR domain; Int 57.5 7.1 0.00015 25.9 1.6 31 135-165 19-49 (64)
41 smart00745 MIT Microtubule Int 56.1 53 0.0011 22.8 6.1 37 176-212 6-42 (77)
42 TIGR02098 MJ0042_CXXC MJ0042 f 55.9 4.2 9E-05 24.7 0.2 30 135-166 3-35 (38)
43 PF14803 Nudix_N_2: Nudix N-te 54.5 6.9 0.00015 23.6 1.0 26 140-165 4-31 (34)
44 cd02682 MIT_AAA_Arch MIT: doma 54.3 22 0.00048 25.5 3.7 37 177-213 5-41 (75)
45 TIGR02795 tol_pal_ybgF tol-pal 52.7 49 0.0011 23.8 5.7 51 181-236 42-92 (119)
46 PF07719 TPR_2: Tetratricopept 52.4 33 0.00071 19.2 3.8 27 181-207 4-30 (34)
47 cd02656 MIT MIT: domain contai 52.1 77 0.0017 21.9 6.4 36 177-212 5-40 (75)
48 TIGR03302 OM_YfiO outer membra 51.8 36 0.00078 28.5 5.4 25 181-205 36-60 (235)
49 PF00515 TPR_1: Tetratricopept 51.5 35 0.00075 19.3 3.8 28 181-208 4-31 (34)
50 PF05191 ADK_lid: Adenylate ki 51.3 10 0.00022 23.2 1.4 28 135-164 2-29 (36)
51 PF04810 zf-Sec23_Sec24: Sec23 49.8 6.6 0.00014 24.4 0.4 31 135-167 3-35 (40)
52 PF10122 Mu-like_Com: Mu-like 49.6 6.6 0.00014 26.0 0.4 32 134-167 4-35 (51)
53 PF08472 S6PP_C: Sucrose-6-pho 49.0 30 0.00065 27.6 4.0 47 187-233 37-85 (133)
54 PF14559 TPR_19: Tetratricopep 48.2 39 0.00084 22.2 4.1 40 189-236 2-41 (68)
55 PF13525 YfiO: Outer membrane 48.0 73 0.0016 26.6 6.6 52 179-235 6-57 (203)
56 PF13176 TPR_7: Tetratricopept 47.2 37 0.00079 20.0 3.5 22 185-206 6-27 (36)
57 smart00834 CxxC_CXXC_SSSS Puta 45.8 13 0.00028 22.6 1.3 29 134-164 5-34 (41)
58 PF09723 Zn-ribbon_8: Zinc rib 44.5 15 0.00032 23.1 1.4 29 134-164 5-34 (42)
59 PF13181 TPR_8: Tetratricopept 44.2 48 0.001 18.6 3.6 27 181-207 4-30 (34)
60 KOG0545|consensus 42.5 48 0.001 29.7 4.7 61 181-241 181-244 (329)
61 smart00647 IBR In Between Ring 41.4 20 0.00043 23.7 1.8 30 135-164 19-48 (64)
62 TIGR01206 lysW lysine biosynth 40.7 16 0.00034 24.5 1.1 32 135-168 3-34 (54)
63 KOG0553|consensus 38.8 1E+02 0.0022 28.1 6.3 32 177-208 80-111 (304)
64 PF14561 TPR_20: Tetratricopep 37.9 58 0.0012 23.8 3.9 51 178-236 22-74 (90)
65 TIGR01053 LSD1 zinc finger dom 36.6 23 0.00051 20.9 1.3 27 135-165 2-28 (31)
66 PF10516 SHNi-TPR: SHNi-TPR; 35.9 64 0.0014 19.8 3.3 25 188-212 11-35 (38)
67 TIGR02795 tol_pal_ybgF tol-pal 35.8 1.3E+02 0.0028 21.5 5.7 12 192-203 90-101 (119)
68 PF01599 Ribosomal_S27: Riboso 35.5 21 0.00045 23.3 1.1 29 134-164 18-46 (47)
69 PF12895 Apc3: Anaphase-promot 34.4 1.1E+02 0.0024 21.2 4.9 48 180-236 27-74 (84)
70 smart00858 SAF This domain fam 33.0 29 0.00062 22.9 1.5 16 71-86 3-18 (64)
71 cd00350 rubredoxin_like Rubred 31.5 37 0.00081 20.0 1.7 26 135-166 2-27 (33)
72 PLN03098 LPA1 LOW PSII ACCUMUL 31.4 1.2E+02 0.0026 29.2 5.9 54 178-236 75-128 (453)
73 PF04216 FdhE: Protein involve 31.3 20 0.00043 32.1 0.6 46 111-167 197-249 (290)
74 PF01807 zf-CHC2: CHC2 zinc fi 30.8 57 0.0012 24.1 3.0 17 155-171 53-69 (97)
75 COG1594 RPB9 DNA-directed RNA 30.4 26 0.00057 27.0 1.1 31 137-169 5-35 (113)
76 COG1998 RPS31 Ribosomal protei 29.8 30 0.00065 22.8 1.1 26 136-165 21-46 (51)
77 PF07975 C1_4: TFIIH C1-like d 29.6 22 0.00047 23.6 0.4 47 114-163 2-50 (51)
78 PF03604 DNA_RNApol_7kD: DNA d 29.3 53 0.0011 19.5 2.0 8 157-164 18-25 (32)
79 TIGR02605 CxxC_CxxC_SSSS putat 29.2 36 0.00079 21.9 1.5 29 134-164 5-34 (52)
80 PRK15363 pathogenicity island 28.7 1.2E+02 0.0026 24.9 4.7 28 178-205 35-62 (157)
81 PRK10866 outer membrane biogen 28.5 1.8E+02 0.004 25.1 6.2 28 179-206 33-60 (243)
82 smart00659 RPOLCX RNA polymera 28.3 40 0.00087 21.5 1.5 27 135-166 3-29 (44)
83 CHL00033 ycf3 photosystem I as 27.6 2.4E+02 0.0052 22.3 6.4 29 179-207 36-64 (168)
84 PRK03564 formate dehydrogenase 27.5 51 0.0011 30.1 2.6 46 111-167 212-263 (309)
85 PF13240 zinc_ribbon_2: zinc-r 27.3 34 0.00073 18.6 0.9 19 140-164 3-21 (23)
86 TIGR00373 conserved hypothetic 26.8 52 0.0011 26.8 2.3 10 156-165 128-137 (158)
87 PRK00420 hypothetical protein; 26.4 1.9E+02 0.0042 22.3 5.2 28 135-167 24-51 (112)
88 PF13428 TPR_14: Tetratricopep 26.4 1.2E+02 0.0026 18.4 3.5 23 184-206 7-29 (44)
89 PF00301 Rubredoxin: Rubredoxi 25.8 61 0.0013 21.0 2.0 13 154-166 32-44 (47)
90 PF12760 Zn_Tnp_IS1595: Transp 25.7 43 0.00093 21.2 1.3 28 134-164 18-45 (46)
91 PF09862 DUF2089: Protein of u 25.2 98 0.0021 24.0 3.4 17 194-210 63-79 (113)
92 PF02748 PyrI_C: Aspartate car 25.2 50 0.0011 21.8 1.6 36 135-170 7-49 (52)
93 PF09788 Tmemb_55A: Transmembr 25.1 42 0.00092 29.7 1.5 36 133-170 156-191 (256)
94 PF06943 zf-LSD1: LSD1 zinc fi 25.0 59 0.0013 18.3 1.6 23 140-164 2-24 (25)
95 TIGR01562 FdhE formate dehydro 24.9 60 0.0013 29.5 2.5 48 110-168 209-264 (305)
96 PF13453 zf-TFIIB: Transcripti 24.9 50 0.0011 20.4 1.4 7 113-119 1-7 (41)
97 PRK06266 transcription initiat 24.8 52 0.0011 27.4 2.0 10 156-165 136-145 (178)
98 PF07282 OrfB_Zn_ribbon: Putat 24.6 53 0.0011 22.4 1.7 32 132-167 26-57 (69)
99 smart00028 TPR Tetratricopepti 24.3 1.1E+02 0.0023 15.2 3.1 24 183-206 6-29 (34)
100 PRK00415 rps27e 30S ribosomal 24.2 40 0.00086 23.1 0.9 32 131-166 8-40 (59)
101 PF08969 USP8_dimer: USP8 dime 23.7 1.2E+02 0.0027 22.9 3.8 34 176-209 36-69 (115)
102 KOG0739|consensus 23.5 1.1E+02 0.0025 28.2 4.0 35 174-208 6-40 (439)
103 COG2051 RPS27A Ribosomal prote 23.2 40 0.00086 23.6 0.8 31 131-165 16-47 (67)
104 PRK02603 photosystem I assembl 22.9 3.1E+02 0.0066 21.8 6.2 24 182-205 39-62 (172)
105 PF10058 DUF2296: Predicted in 22.7 49 0.0011 22.1 1.1 31 132-164 20-52 (54)
106 PF08996 zf-DNA_Pol: DNA Polym 22.6 90 0.0019 26.1 3.0 20 156-175 45-64 (188)
107 PRK12380 hydrogenase nickel in 22.5 47 0.001 25.5 1.2 7 157-163 87-93 (113)
108 cd00189 TPR Tetratricopeptide 22.4 2E+02 0.0044 18.2 4.4 38 191-236 47-84 (100)
109 PF14369 zf-RING_3: zinc-finge 22.1 70 0.0015 19.3 1.7 28 134-164 2-29 (35)
110 PF09082 DUF1922: Domain of un 22.1 54 0.0012 23.1 1.3 30 135-170 4-33 (68)
111 KOG2155|consensus 22.0 2.5E+02 0.0054 27.3 6.0 57 47-105 202-264 (631)
112 PRK14066 exodeoxyribonuclease 21.9 83 0.0018 22.5 2.3 10 194-203 27-36 (75)
113 TIGR00100 hypA hydrogenase nic 21.8 50 0.0011 25.4 1.2 9 112-120 71-79 (115)
114 COG2956 Predicted N-acetylgluc 21.8 1.6E+02 0.0034 27.5 4.5 42 188-236 224-265 (389)
115 PF13512 TPR_18: Tetratricopep 21.5 3.4E+02 0.0073 21.8 6.0 26 180-205 12-37 (142)
116 COG1997 RPL43A Ribosomal prote 20.7 57 0.0012 24.1 1.2 29 134-166 35-63 (89)
117 smart00400 ZnF_CHCC zinc finge 20.2 92 0.002 20.3 2.1 17 155-171 22-38 (55)
No 1
>KOG2084|consensus
Probab=99.59 E-value=1.6e-14 Score=135.81 Aligned_cols=150 Identities=23% Similarity=0.411 Sum_probs=114.6
Q ss_pred HHHHHHHHhhhhhcccccccccccCCCCCCceeeeEEeccccccccCCCccCcEEEEeCCEEEEEEcccccCCC-eeeec
Q psy5735 9 IGGLLLHQIQCLQFNCHEVADLVGTGESSKTRFIGAGIFPTLSMFNHSCEPNIVRYFRGTMVYVNLCKNFKKGD-QICEN 87 (247)
Q Consensus 9 ~~~~ll~~~~~l~~Na~~i~~~~~~~~~~~~~~~g~glyp~~sl~NHSC~PN~~~~~~~~~~~~~A~r~I~~Ge-ei~~~ 87 (247)
.+..+..++..+..|++.+...... .....+|.|+||..+++||||.||+...|++....+++...+.+++ +++++
T Consensus 168 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~hsC~pn~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 244 (482)
T KOG2084|consen 168 AADCISKLFPSLLCNSITNASSLRV---PEPLFLGRGLFPGSSLFNHSCFPNISVIFDGRGLALLVPAGIDAGEEELTIS 244 (482)
T ss_pred HHHHHHHHHHHHHHhhhhhhhhhhc---cccccceeeecccchhcccCCCCCeEEEECCceeEEEeecccCCCCCEEEEe
Confidence 3445556666667777776553210 0111589999999999999999999999999999999999998887 99999
Q ss_pred cccccccCCHHHHHHHHhcCCCeeEeecCCCCCCcchhhhhhhhhccccccCCCCCCcccccCCc-ccccccccccccch
Q psy5735 88 YGPLYSQVRKTERQNTLKSQYWFDCHCIACEHDWPLFEEMQAAQDLRFRCETENCHNVVKVATNT-TQFMIKCDKCDQFI 166 (247)
Q Consensus 88 Y~~~~~~~~~~~R~~~L~~~~~F~C~C~~C~~~~~~~~~~~~~~~~~~~C~~~~C~~~~~~~~~~-~~~~~~C~~C~~~~ 166 (247)
|++.. +++..|++.|+..|.|.|.|++|.++...+. ...+++|.+..|.+.+...... ....|.|..|....
T Consensus 245 y~~~~--~~~~~r~~~l~~~~~f~c~c~rc~d~~~~~~-----~~~~~~c~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~ 317 (482)
T KOG2084|consen 245 YTDPL--LSTASRQKQLRQSKLFSCQCPRCLDPTELGT-----FLSSLRCENCTCGGLLGTSFLDKEDLQWPCTECALVR 317 (482)
T ss_pred ecccc--cCHHHHHHHHhhccceeeecCCCCCCCcccc-----chhhhhhcCCCCCCccCCCcccccCCCccccccccch
Confidence 99875 6899999999999999999999998765433 3456888777777766433222 24589999999876
Q ss_pred hh
Q psy5735 167 NI 168 (247)
Q Consensus 167 ~~ 168 (247)
..
T Consensus 318 ~~ 319 (482)
T KOG2084|consen 318 LK 319 (482)
T ss_pred hH
Confidence 53
No 2
>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=99.46 E-value=6.7e-14 Score=111.49 Aligned_cols=52 Identities=35% Similarity=0.660 Sum_probs=46.5
Q ss_pred CceeeeEEeccccccccCCCccCcEEEEe----CCEEEEEEcccccCCCeeeeccc
Q psy5735 38 KTRFIGAGIFPTLSMFNHSCEPNIVRYFR----GTMVYVNLCKNFKKGDQICENYG 89 (247)
Q Consensus 38 ~~~~~g~glyp~~sl~NHSC~PN~~~~~~----~~~~~~~A~r~I~~Geei~~~Y~ 89 (247)
.....+.++||.++++||||.||+.+.++ ++.+.++|.|+|++||||+++||
T Consensus 107 ~~~~~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 107 EDDRDGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp TEEEEEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEEEST
T ss_pred cccccccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEEEEC
Confidence 34567899999999999999999999998 78999999999999999999997
No 3
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.17 E-value=1.7e-11 Score=93.31 Aligned_cols=46 Identities=24% Similarity=0.395 Sum_probs=40.8
Q ss_pred eEEeccccccccCCCccCcEEEEeC--C--EEEEEEcccccCCCeeeecc
Q psy5735 43 GAGIFPTLSMFNHSCEPNIVRYFRG--T--MVYVNLCKNFKKGDQICENY 88 (247)
Q Consensus 43 g~glyp~~sl~NHSC~PN~~~~~~~--~--~~~~~A~r~I~~Geei~~~Y 88 (247)
+..++|.++++||||.||+...+.. + .+.++|+|+|++||||+++|
T Consensus 67 ~~~~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 67 ARRKGNIARFINHSCEPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred CCccCcHHHeeCCCCCCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 4457899999999999999988753 2 69999999999999999998
No 4
>KOG2589|consensus
Probab=98.71 E-value=1e-08 Score=92.75 Aligned_cols=64 Identities=23% Similarity=0.542 Sum_probs=54.5
Q ss_pred Eecc-ccccccCCCccCcEEEEeC-CEEEEEEcccccCCCeeeeccccccccCCHHHHHHHHhcCCCeeEeecCCCCC
Q psy5735 45 GIFP-TLSMFNHSCEPNIVRYFRG-TMVYVNLCKNFKKGDQICENYGPLYSQVRKTERQNTLKSQYWFDCHCIACEHD 120 (247)
Q Consensus 45 glyp-~~sl~NHSC~PN~~~~~~~-~~~~~~A~r~I~~Geei~~~Y~~~~~~~~~~~R~~~L~~~~~F~C~C~~C~~~ 120 (247)
-||. -++++||.|.|||..+-.| +++.|+++|||++|||||.-|+..|+. ..+-.|.|..|...
T Consensus 191 qLwLGPaafINHDCrpnCkFvs~g~~tacvkvlRDIePGeEITcFYgs~fFG------------~~N~~CeC~TCER~ 256 (453)
T KOG2589|consen 191 QLWLGPAAFINHDCRPNCKFVSTGRDTACVKVLRDIEPGEEITCFYGSGFFG------------ENNEECECVTCERR 256 (453)
T ss_pred hheeccHHhhcCCCCCCceeecCCCceeeeehhhcCCCCceeEEeecccccC------------CCCceeEEeecccc
Confidence 3444 3578999999999988888 899999999999999999999998864 24578999999864
No 5
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=98.10 E-value=1.7e-06 Score=82.92 Aligned_cols=70 Identities=23% Similarity=0.451 Sum_probs=56.1
Q ss_pred ccccccCCCccCcEEEEeCC----EEEEEEcccccCCCeeeeccccccccCCHHHHHHHHhcCCCeeEeecCCCCC
Q psy5735 49 TLSMFNHSCEPNIVRYFRGT----MVYVNLCKNFKKGDQICENYGPLYSQVRKTERQNTLKSQYWFDCHCIACEHD 120 (247)
Q Consensus 49 ~~sl~NHSC~PN~~~~~~~~----~~~~~A~r~I~~Geei~~~Y~~~~~~~~~~~R~~~L~~~~~F~C~C~~C~~~ 120 (247)
...++||||.||+.....+. .+.++|++||.+||||+..|...... ...+...+...+...|.|.+|...
T Consensus 405 ~~r~~nHS~~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~ 478 (480)
T COG2940 405 VARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLED--NRELKKLLEKRWGCACGEDRCSHT 478 (480)
T ss_pred ccceeecCCCCCcceecccccccceeeecccccchhhhhhcccccccccc--chhhhhhhhhhhccccCCCccCCC
Confidence 45689999999999887643 89999999999999999999976542 122355666678899999999764
No 6
>KOG4442|consensus
Probab=98.08 E-value=2.3e-06 Score=83.08 Aligned_cols=50 Identities=30% Similarity=0.298 Sum_probs=38.0
Q ss_pred eeEEecccc-ccccCCCccCcEE---EEeC-CEEEEEEcccccCCCeeeeccccc
Q psy5735 42 IGAGIFPTL-SMFNHSCEPNIVR---YFRG-TMVYVNLCKNFKKGDQICENYGPL 91 (247)
Q Consensus 42 ~g~glyp~~-sl~NHSC~PN~~~---~~~~-~~~~~~A~r~I~~Geei~~~Y~~~ 91 (247)
|....+-.+ .++||||+|||.+ +..| -+|-++|.++|++|||||+.|.-.
T Consensus 185 IDAT~KGnlaRFiNHSC~PNa~~~KWtV~~~lRvGiFakk~I~~GEEITFDYqf~ 239 (729)
T KOG4442|consen 185 IDATKKGNLARFINHSCDPNAEVQKWTVPDELRVGIFAKKVIKPGEEITFDYQFD 239 (729)
T ss_pred ecccccCcHHHhhcCCCCCCceeeeeeeCCeeEEEEeEecccCCCceeeEecccc
Confidence 445555554 4679999999953 3333 478899999999999999999643
No 7
>KOG1080|consensus
Probab=98.01 E-value=3.7e-06 Score=85.93 Aligned_cols=42 Identities=21% Similarity=0.451 Sum_probs=36.0
Q ss_pred cccccccCCCccCcEEEEe---C-CEEEEEEcccccCCCeeeeccc
Q psy5735 48 PTLSMFNHSCEPNIVRYFR---G-TMVYVNLCKNFKKGDQICENYG 89 (247)
Q Consensus 48 p~~sl~NHSC~PN~~~~~~---~-~~~~~~A~r~I~~Geei~~~Y~ 89 (247)
-.+.++||||.|||..... | .+|+++|.|+|.+|||||..|-
T Consensus 938 niAr~InHsC~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYk 983 (1005)
T KOG1080|consen 938 NIARFINHSCNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYK 983 (1005)
T ss_pred chhheeecccCCCceeeEEEecCeeEEEEEEecccccCceeeeecc
Confidence 3578999999999976653 4 5899999999999999998884
No 8
>KOG1082|consensus
Probab=97.44 E-value=9e-05 Score=68.69 Aligned_cols=53 Identities=23% Similarity=0.419 Sum_probs=40.6
Q ss_pred eeeeEEecccc-ccccCCCccCcEEEEe--C------CEEEEEEcccccCCCeeeecccccc
Q psy5735 40 RFIGAGIFPTL-SMFNHSCEPNIVRYFR--G------TMVYVNLCKNFKKGDQICENYGPLY 92 (247)
Q Consensus 40 ~~~g~glyp~~-sl~NHSC~PN~~~~~~--~------~~~~~~A~r~I~~Geei~~~Y~~~~ 92 (247)
..|....+... -++||||.||+.+... + -++.+.|+++|++|+|+|..|+..+
T Consensus 262 ~~ida~~~GNv~RfinHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~ 323 (364)
T KOG1082|consen 262 LLIDAKPHGNVARFINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAY 323 (364)
T ss_pred eEEchhhcccccccccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhcccc
Confidence 34444455544 4789999999976653 2 2789999999999999999999754
No 9
>KOG1083|consensus
Probab=96.68 E-value=0.0012 Score=67.21 Aligned_cols=50 Identities=28% Similarity=0.535 Sum_probs=38.2
Q ss_pred eeeeEEecccc-------ccccCCCccCcE---EEEeC-CEEEEEEcccccCCCeeeeccc
Q psy5735 40 RFIGAGIFPTL-------SMFNHSCEPNIV---RYFRG-TMVYVNLCKNFKKGDQICENYG 89 (247)
Q Consensus 40 ~~~g~glyp~~-------sl~NHSC~PN~~---~~~~~-~~~~~~A~r~I~~Geei~~~Y~ 89 (247)
..|..++|+.+ ..+||||.|||. +..+| .++.|+|+|||++||||+..|-
T Consensus 1234 L~I~p~l~id~~R~~n~~RfinhscKPNc~~qkwSVNG~~Rv~L~A~rDi~kGEELtYDYN 1294 (1306)
T KOG1083|consen 1234 LVIDPGLFIDIPRMGNGARFINHSCKPNCEMQKWSVNGEYRVGLFALRDLPKGEELTYDYN 1294 (1306)
T ss_pred cccCccccCChhhccccccccccccCCCCccccccccceeeeeeeecCCCCCCceEEEecc
Confidence 34555555433 467999999995 33455 5899999999999999999984
No 10
>KOG1085|consensus
Probab=96.54 E-value=0.0017 Score=57.73 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=35.9
Q ss_pred cccccCCCccCcEEEE---eC-CEEEEEEcccccCCCeeeeccccc
Q psy5735 50 LSMFNHSCEPNIVRYF---RG-TMVYVNLCKNFKKGDQICENYGPL 91 (247)
Q Consensus 50 ~sl~NHSC~PN~~~~~---~~-~~~~~~A~r~I~~Geei~~~Y~~~ 91 (247)
..|+|||=.+|+.... +| ..+++.|.|+|.+||||+..||+-
T Consensus 334 GRLINHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDR 379 (392)
T KOG1085|consen 334 GRLINHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDR 379 (392)
T ss_pred hhhhcccccCcceeeEEEecCCceEEEEeccccccchhhhhhcccc
Confidence 3589999999995443 44 589999999999999999999975
No 11
>KOG1141|consensus
Probab=96.42 E-value=0.0015 Score=65.03 Aligned_cols=56 Identities=30% Similarity=0.427 Sum_probs=39.8
Q ss_pred cccccCCCccCcEE--EEeC------CEEEEEEcccccCCCeeeeccccccccCCHHHHHHHHhcCCCeeEeec
Q psy5735 50 LSMFNHSCEPNIVR--YFRG------TMVYVNLCKNFKKGDQICENYGPLYSQVRKTERQNTLKSQYWFDCHCI 115 (247)
Q Consensus 50 ~sl~NHSC~PN~~~--~~~~------~~~~~~A~r~I~~Geei~~~Y~~~~~~~~~~~R~~~L~~~~~F~C~C~ 115 (247)
..++||||+||..+ +|.+ .-+.+.|.+-|++|+|||..|........ ..-..|+|-
T Consensus 1190 GRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~----------~keL~C~CG 1253 (1262)
T KOG1141|consen 1190 GRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVA----------TKELTCHCG 1253 (1262)
T ss_pred hhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccc----------cceEEEecC
Confidence 35789999999854 3432 24667888999999999999986543211 234778885
No 12
>KOG1337|consensus
Probab=96.39 E-value=0.0022 Score=61.48 Aligned_cols=60 Identities=25% Similarity=0.380 Sum_probs=47.0
Q ss_pred EEeccccccccCCCccCcEEEEe-CCEEEEEEcccccCCCeeeeccccccccCCHHHHHHHHhcCCCee
Q psy5735 44 AGIFPTLSMFNHSCEPNIVRYFR-GTMVYVNLCKNFKKGDQICENYGPLYSQVRKTERQNTLKSQYWFD 111 (247)
Q Consensus 44 ~glyp~~sl~NHSC~PN~~~~~~-~~~~~~~A~r~I~~Geei~~~Y~~~~~~~~~~~R~~~L~~~~~F~ 111 (247)
.++.|.+-++||++.+....... +..+.+++.++|.+|+||+++||+.- ...|...|||.
T Consensus 231 ~~L~P~~D~~NH~~~~~~~~~~~~d~~~~l~~~~~v~~geevfi~YG~~~--------N~eLL~~YGFv 291 (472)
T KOG1337|consen 231 EALAPLIDLLNHSPEVIKAGYNQEDEAVELVAERDVSAGEEVFINYGPKS--------NAELLLHYGFV 291 (472)
T ss_pred hhhhhhHHhhccCchhccccccCCCCcEEEEEeeeecCCCeEEEecCCCc--------hHHHHHhcCCC
Confidence 68999999999999993333332 34899999999999999999999842 12355579994
No 13
>KOG1079|consensus
Probab=94.93 E-value=0.022 Score=55.90 Aligned_cols=43 Identities=19% Similarity=0.288 Sum_probs=35.1
Q ss_pred ccccccCCCccCcEEEE---eC-CEEEEEEcccccCCCeeeeccccc
Q psy5735 49 TLSMFNHSCEPNIVRYF---RG-TMVYVNLCKNFKKGDQICENYGPL 91 (247)
Q Consensus 49 ~~sl~NHSC~PN~~~~~---~~-~~~~~~A~r~I~~Geei~~~Y~~~ 91 (247)
.+-+.|||=.|||.... .| .+|-++|.|.|.+|||||+.|...
T Consensus 665 k~rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYrYs 711 (739)
T KOG1079|consen 665 KIRFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYRYS 711 (739)
T ss_pred hhhhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeeccC
Confidence 34577999999996443 34 589999999999999999999743
No 14
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=89.42 E-value=0.97 Score=31.43 Aligned_cols=55 Identities=25% Similarity=0.462 Sum_probs=43.3
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
+...+..+...|++++|+..|.+.+.. ...+.+.+.++..+...|..||..+|+.
T Consensus 8 ~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~~a~~~~~lg~~~~~~g~~ 62 (78)
T PF13424_consen 8 YNNLARVYRELGRYDEALDYYEKALDI-EEQLGDDHPDTANTLNNLGECYYRLGDY 62 (78)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTTTHHHHHHHHHHHHHHHHHHTTHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHcCCH
Confidence 344455667889999999999999998 5556666677889999999999998874
No 15
>KOG1081|consensus
Probab=89.15 E-value=0.15 Score=48.88 Aligned_cols=50 Identities=30% Similarity=0.418 Sum_probs=39.9
Q ss_pred eeeEEeccccc-cccCCCccCcEEEEe----CCEEEEEEcccccCCCeeeecccc
Q psy5735 41 FIGAGIFPTLS-MFNHSCEPNIVRYFR----GTMVYVNLCKNFKKGDQICENYGP 90 (247)
Q Consensus 41 ~~g~glyp~~s-l~NHSC~PN~~~~~~----~~~~~~~A~r~I~~Geei~~~Y~~ 90 (247)
.+..+.++..| ++||||.||+.-.-. ...+.+.|.+.|+.|+|+|++|.-
T Consensus 362 ~id~~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g~e~t~~~n~ 416 (463)
T KOG1081|consen 362 IIDAGPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAGEELTFNYNG 416 (463)
T ss_pred ccccccccchhhhhcccCCCceeechhheecccccccccccccccchhhhheeec
Confidence 45567777665 569999999965432 357899999999999999999964
No 16
>KOG1338|consensus
Probab=87.71 E-value=0.38 Score=44.90 Aligned_cols=54 Identities=19% Similarity=0.232 Sum_probs=46.8
Q ss_pred CceeeeEEeccccccccCCCc-cCcEEEEeCCEEEEEEcccccCCCeeeeccccc
Q psy5735 38 KTRFIGAGIFPTLSMFNHSCE-PNIVRYFRGTMVYVNLCKNFKKGDQICENYGPL 91 (247)
Q Consensus 38 ~~~~~g~glyp~~sl~NHSC~-PN~~~~~~~~~~~~~A~r~I~~Geei~~~Y~~~ 91 (247)
+....|-..-|.+.++||.=. -|+...+..+.+.+.|.|+|++|+++..+||.+
T Consensus 207 e~e~ngk~m~p~ad~lNhd~~k~nanl~y~~NcL~mva~r~iekgdev~n~dg~~ 261 (466)
T KOG1338|consen 207 EIECNGKLMTPIADFLNHDGLKANANLRYEDNCLEMVADRNIEKGDEVDNSDGLK 261 (466)
T ss_pred ccccCcccccchhhhhccchhhcccceeccCcceeeeecCCCCCccccccccccC
Confidence 344577888899999999877 778888888999999999999999999999843
No 17
>KOG2461|consensus
Probab=84.70 E-value=0.44 Score=44.83 Aligned_cols=27 Identities=15% Similarity=0.437 Sum_probs=24.3
Q ss_pred eCCEEEEEEcccccCCCeeeecccccc
Q psy5735 66 RGTMVYVNLCKNFKKGDQICENYGPLY 92 (247)
Q Consensus 66 ~~~~~~~~A~r~I~~Geei~~~Y~~~~ 92 (247)
.+..|..+|+|+|++||||.+-|++.+
T Consensus 120 ~~~~Ifyrt~r~I~p~eELlVWY~~e~ 146 (396)
T KOG2461|consen 120 IGENIFYRTIRDIRPNEELLVWYGSEY 146 (396)
T ss_pred ccCceEEEecccCCCCCeEEEEeccch
Confidence 456899999999999999999999765
No 18
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=75.01 E-value=6.2 Score=23.36 Aligned_cols=34 Identities=35% Similarity=0.553 Sum_probs=20.1
Q ss_pred HHhhhhccchHHHHHHHHHHHHhhhhhccCCCcc
Q psy5735 184 LANNYKENGLYEKALEKFTQLMTLLDENLVPPYR 217 (247)
Q Consensus 184 ~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~ 217 (247)
.+..+...|++++|+..+.+.+.....++.+.|.
T Consensus 8 la~~~~~~g~~~~A~~~~~~al~~~~~~~G~~Hp 41 (42)
T PF13374_consen 8 LANAYRAQGRYEEALELLEEALEIRERLLGPDHP 41 (42)
T ss_dssp HHHHHHHCT-HHHHHHHHHHHHHHH---------
T ss_pred HHHHHHhhhhcchhhHHHHHHHHHHHHHhccccc
Confidence 4556677899999999999999888777766553
No 19
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=73.29 E-value=19 Score=23.91 Aligned_cols=49 Identities=24% Similarity=0.445 Sum_probs=33.6
Q ss_pred HHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhc
Q psy5735 178 TESLFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLG 234 (247)
Q Consensus 178 ~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g 234 (247)
++.+...+..++..+++++|+..|.+.+... .+-..+.-.+..|+..+|
T Consensus 3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~--------p~~~~~~~~~g~~~~~~~ 51 (69)
T PF13414_consen 3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD--------PNNAEAYYNLGLAYMKLG 51 (69)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS--------TTHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--------CCCHHHHHHHHHHHHHhC
Confidence 3445566778888999999999999988652 122335555666666666
No 20
>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.
Probab=72.64 E-value=6.2 Score=28.13 Aligned_cols=42 Identities=17% Similarity=0.129 Sum_probs=32.4
Q ss_pred hHhHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhcc-CCCc
Q psy5735 175 LQDTESLFRLANNYKENGLYEKALEKFTQLMTLLDENL-VPPY 216 (247)
Q Consensus 175 lq~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l-~~p~ 216 (247)
++++..++.+|......|++++|+..|.+.|..+..++ ..++
T Consensus 3 l~~Ai~lv~~Av~~D~~g~y~eA~~lY~~ale~~~~~~k~e~~ 45 (75)
T cd02684 3 LEKAIALVVQAVKKDQRGDAAAALSLYCSALQYFVPALHYETD 45 (75)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 44566677888888889999999999999998776554 3344
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=70.31 E-value=2 Score=26.39 Aligned_cols=30 Identities=23% Similarity=0.701 Sum_probs=18.0
Q ss_pred ccccCCCCCCcccccCC---cccccccccccccch
Q psy5735 135 FRCETENCHNVVKVATN---TTQFMIKCDKCDQFI 166 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~---~~~~~~~C~~C~~~~ 166 (247)
+.| ++|+..+.++.+ ......+|.+|+...
T Consensus 3 i~C--P~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITC--PNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEC--CCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 457 677776665543 223456788887643
No 22
>cd02680 MIT_calpain7_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=68.84 E-value=9.3 Score=27.39 Aligned_cols=34 Identities=26% Similarity=0.264 Sum_probs=27.0
Q ss_pred HhHHHHHHHHhhhhccchHHHHHHHHHHHHhhhh
Q psy5735 176 QDTESLFRLANNYKENGLYEKALEKFTQLMTLLD 209 (247)
Q Consensus 176 q~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~ 209 (247)
.++..++++|..--..|++++|++.|.+.|..+-
T Consensus 4 ~kai~Lv~~A~~eD~~gny~eA~~lY~~ale~~~ 37 (75)
T cd02680 4 ERAHFLVTQAFDEDEKGNAEEAIELYTEAVELCI 37 (75)
T ss_pred HHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHH
Confidence 3455677777777788999999999999887654
No 23
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=67.85 E-value=3.7 Score=26.22 Aligned_cols=30 Identities=20% Similarity=0.539 Sum_probs=21.1
Q ss_pred cccccCCCCCCcccccCCcccccccccccccchh
Q psy5735 134 RFRCETENCHNVVKVATNTTQFMIKCDKCDQFIN 167 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~ 167 (247)
.|+| ++|+..+..+... ..+.|+.||....
T Consensus 3 ~y~C--~~CG~~~~~~~~~--~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKC--ARCGREVELDEYG--TGVRCPYCGYRIL 32 (46)
T ss_pred EEEC--CCCCCEEEECCCC--CceECCCCCCeEE
Confidence 3788 8898877655432 2688999987554
No 24
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=65.52 E-value=11 Score=25.96 Aligned_cols=36 Identities=31% Similarity=0.422 Sum_probs=27.7
Q ss_pred hHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhcc
Q psy5735 177 DTESLFRLANNYKENGLYEKALEKFTQLMTLLDENL 212 (247)
Q Consensus 177 ~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l 212 (247)
++..+..+|...-..|++++|+..|.+.+..+...+
T Consensus 4 ~A~~~~~~Av~~D~~g~~~~A~~~Y~~ai~~l~~~~ 39 (69)
T PF04212_consen 4 KAIELIKKAVEADEAGNYEEALELYKEAIEYLMQAL 39 (69)
T ss_dssp HHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 344456667777789999999999999998766443
No 25
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=64.80 E-value=22 Score=23.39 Aligned_cols=45 Identities=20% Similarity=0.224 Sum_probs=30.5
Q ss_pred HHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 184 LANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 184 ~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
.+..++..|++++|++.|..++... .+-..+.-.+..|+...|+.
T Consensus 3 ~a~~~~~~g~~~~A~~~~~~~l~~~--------P~~~~a~~~lg~~~~~~g~~ 47 (65)
T PF13432_consen 3 LARALYQQGDYDEAIAAFEQALKQD--------PDNPEAWYLLGRILYQQGRY 47 (65)
T ss_dssp HHHHHHHCTHHHHHHHHHHHHHCCS--------TTHHHHHHHHHHHHHHTT-H
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHC--------CCCHHHHHHHHHHHHHcCCH
Confidence 3556778899999999999877543 22455666667777666654
No 26
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=63.54 E-value=3.3 Score=26.09 Aligned_cols=30 Identities=17% Similarity=0.504 Sum_probs=16.9
Q ss_pred ccccCCCCCCcccccCCcccccccccccccchh
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQFIN 167 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~ 167 (247)
|+| +.|+.... -.+.......|..||.+.+
T Consensus 1 m~C--p~Cg~~~~-~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKC--PNCGSKEI-VFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp ESB--TTTSSSEE-EEETTTTEEEETTT-BBEE
T ss_pred CCC--cCCcCCce-EEcCCCCeEECCCCCCEee
Confidence 467 77776531 1122334578888887664
No 27
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=63.49 E-value=14 Score=20.58 Aligned_cols=27 Identities=41% Similarity=0.698 Sum_probs=20.7
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhh
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTL 207 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~ 207 (247)
++..+.-....|++++|++.|..++..
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~ 29 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRLIKR 29 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence 455566666778999999999988753
No 28
>cd02683 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear.
Probab=62.63 E-value=12 Score=26.74 Aligned_cols=40 Identities=18% Similarity=0.261 Sum_probs=30.7
Q ss_pred hHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhcc-CCCc
Q psy5735 177 DTESLFRLANNYKENGLYEKALEKFTQLMTLLDENL-VPPY 216 (247)
Q Consensus 177 ~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l-~~p~ 216 (247)
.+..++.+|...-..|++++|+..|.+.|..+..++ ..|+
T Consensus 5 ~a~~l~~~Ave~D~~g~y~eAl~~Y~~aie~l~~~lk~e~d 45 (77)
T cd02683 5 AAKEVLKRAVELDQEGRFQEALVCYQEGIDLLMQVLKGTKD 45 (77)
T ss_pred HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 344567778888889999999999999998876654 3443
No 29
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=62.48 E-value=33 Score=24.55 Aligned_cols=35 Identities=26% Similarity=0.308 Sum_probs=29.2
Q ss_pred hHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhc
Q psy5735 177 DTESLFRLANNYKENGLYEKALEKFTQLMTLLDEN 211 (247)
Q Consensus 177 ~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~ 211 (247)
++..+..+|+..-..|++++|+..|.+.+..+...
T Consensus 5 ~Ai~~a~~Ave~D~~g~y~eA~~~Y~~aie~l~~~ 39 (76)
T cd02681 5 DAVQFARLAVQRDQEGRYSEAVFYYKEAAQLLIYA 39 (76)
T ss_pred HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHH
Confidence 45567778888889999999999999999877653
No 30
>cd02678 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
Probab=62.11 E-value=16 Score=25.80 Aligned_cols=42 Identities=24% Similarity=0.296 Sum_probs=32.2
Q ss_pred hHhHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhcc-CCCc
Q psy5735 175 LQDTESLFRLANNYKENGLYEKALEKFTQLMTLLDENL-VPPY 216 (247)
Q Consensus 175 lq~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l-~~p~ 216 (247)
++++..++.+|...-..|++++|+..|.+.+..+-..+ ..|+
T Consensus 3 ~~~A~~l~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~~k~e~~ 45 (75)
T cd02678 3 LQKAIELVKKAIEEDNAGNYEEALRLYQHALEYFMHALKYEKN 45 (75)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 44566677788888889999999999999998776554 3344
No 31
>cd02677 MIT_SNX15 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear.
Probab=61.48 E-value=15 Score=26.11 Aligned_cols=41 Identities=29% Similarity=0.352 Sum_probs=30.6
Q ss_pred HhHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhcc-CCCc
Q psy5735 176 QDTESLFRLANNYKENGLYEKALEKFTQLMTLLDENL-VPPY 216 (247)
Q Consensus 176 q~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l-~~p~ 216 (247)
.++..++.+|...-..+++++|+..|.+.|..+-..+ ..++
T Consensus 4 ~~A~~l~~~Ave~d~~~~y~eA~~~Y~~~i~~~~~~~k~e~~ 45 (75)
T cd02677 4 EQAAELIRLALEKEEEGDYEAAFEFYRAGVDLLLKGVQGDSS 45 (75)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhccCCC
Confidence 4455567777777788999999999999998776544 3443
No 32
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=61.31 E-value=27 Score=33.26 Aligned_cols=52 Identities=15% Similarity=0.195 Sum_probs=40.7
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHH
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLN 232 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~ 232 (247)
.++.+-++...|+|++|+..|..+|+..--+......+...+++.|..|.--
T Consensus 207 ~Lk~gyk~~t~gKF~eA~~~Fr~iL~~i~l~vv~~~~E~~e~~eli~icrEY 258 (422)
T PF06957_consen 207 RLKEGYKLFTAGKFEEAIEIFRSILHSIPLLVVESREEEDEAKELIEICREY 258 (422)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHHHC--BSSCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHhheeeecCHHHHHHHHHHHHHHHHH
Confidence 4556777889999999999999999987767777788888888888888643
No 33
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=60.70 E-value=21 Score=30.65 Aligned_cols=80 Identities=11% Similarity=0.070 Sum_probs=47.2
Q ss_pred ccccccccccchhhh--hhhhhhH--hHHHHHH---HHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHH
Q psy5735 155 FMIKCDKCDQFINIF--KGLKNLQ--DTESLFR---LANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQ 227 (247)
Q Consensus 155 ~~~~C~~C~~~~~~~--~~l~~lq--~~~~l~~---~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~ 227 (247)
..|.|+.||...... ..+...+ .+...+. +...+.....+++|++.|.-.|-. ..+...++...+...--|+
T Consensus 47 ~V~vCP~CgyA~~~~~F~~l~~~~~~~i~~~i~~~~~~~~~~~~Rt~~~ai~~YkLAll~-~~~~~~~~s~~A~l~LrlA 125 (214)
T PF09986_consen 47 EVWVCPHCGYAAFEEDFEKLSPEQKEKIKENISSRWKPRDFSGERTLEEAIESYKLALLC-AQIKKEKPSKKAGLCLRLA 125 (214)
T ss_pred eEEECCCCCCcccccccccCCHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHHHH-HHHhCCCHHHHHHHHHHHH
Confidence 369999999654311 1111111 1111111 122344566899999999866643 2334456667777778889
Q ss_pred HHHHHhcc
Q psy5735 228 TCFLNLGQ 235 (247)
Q Consensus 228 ~c~~~~g~ 235 (247)
|+|-.+|+
T Consensus 126 WlyR~~~~ 133 (214)
T PF09986_consen 126 WLYRDLGD 133 (214)
T ss_pred HHhhccCC
Confidence 99988887
No 34
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=60.50 E-value=4.9 Score=24.50 Aligned_cols=29 Identities=21% Similarity=0.674 Sum_probs=16.6
Q ss_pred ccccCCCCCCcccccCC---cccccccccccccc
Q psy5735 135 FRCETENCHNVVKVATN---TTQFMIKCDKCDQF 165 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~---~~~~~~~C~~C~~~ 165 (247)
+.| ++|...+.++.. +.....+|..|+..
T Consensus 3 i~C--p~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITC--PNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EEC--CCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 456 667666655433 12335678777754
No 35
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=59.18 E-value=6.5 Score=25.36 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=18.5
Q ss_pred CCCCCcccccCCcccccccccccccchhh
Q psy5735 140 ENCHNVVKVATNTTQFMIKCDKCDQFINI 168 (247)
Q Consensus 140 ~~C~~~~~~~~~~~~~~~~C~~C~~~~~~ 168 (247)
+.|++.+..........+.|+.|+....+
T Consensus 4 p~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 4 PKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 78888665443322236889999976543
No 36
>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=58.92 E-value=6.8 Score=26.08 Aligned_cols=18 Identities=17% Similarity=0.206 Sum_probs=12.9
Q ss_pred EEEEcccccCCCeeeecc
Q psy5735 71 YVNLCKNFKKGDQICENY 88 (247)
Q Consensus 71 ~~~A~r~I~~Geei~~~Y 88 (247)
++.|.++|++|+.|+-.-
T Consensus 3 vvVA~~di~~G~~i~~~d 20 (63)
T PF08666_consen 3 VVVAARDIPAGTVITAED 20 (63)
T ss_dssp EEEESSTB-TT-BECTTT
T ss_pred EEEEeCccCCCCEEccCC
Confidence 578999999999986444
No 37
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=58.90 E-value=20 Score=26.06 Aligned_cols=55 Identities=9% Similarity=0.117 Sum_probs=41.5
Q ss_pred HHHHHHhhhhccchHHHHHHHHHHHHhhhh---------hccCCCcccHHHHHHHHHHHHHHhc
Q psy5735 180 SLFRLANNYKENGLYEKALEKFTQLMTLLD---------ENLVPPYRDYILCQRSIQTCFLNLG 234 (247)
Q Consensus 180 ~l~~~a~~~~~~~~~e~al~~~~~~L~~~~---------~~l~~p~~~~~~~~~~l~~c~~~~g 234 (247)
..++++.+++...+.++||.++.+.|.... ..|..-|.++++..++|+.-..+++
T Consensus 8 ~~ie~GlkLY~~~~~~~Al~~W~~aL~k~~~~~~rf~~lG~l~qA~~e~Gkyr~~L~fA~~Q~~ 71 (80)
T PF10579_consen 8 QQIEKGLKLYHQNETQQALQKWRKALEKITDREDRFRVLGYLIQAHMEWGKYREMLAFALQQLE 71 (80)
T ss_pred HHHHHHHHHhccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567778888899999999999987432 2356778888888888887776654
No 38
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=58.12 E-value=3.6 Score=24.97 Aligned_cols=29 Identities=21% Similarity=0.511 Sum_probs=18.1
Q ss_pred ccCCCCCCcccccCCcccccccccccccchhh
Q psy5735 137 CETENCHNVVKVATNTTQFMIKCDKCDQFINI 168 (247)
Q Consensus 137 C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~~ 168 (247)
| +.|++.+.+..+..... .|..|+....+
T Consensus 4 C--p~C~nlL~p~~~~~~~~-~C~~C~Y~~~~ 32 (35)
T PF02150_consen 4 C--PECGNLLYPKEDKEKRV-ACRTCGYEEPI 32 (35)
T ss_dssp E--TTTTSBEEEEEETTTTE-EESSSS-EEE-
T ss_pred C--CCCCccceEcCCCccCc-CCCCCCCccCC
Confidence 7 88999876554333223 79999976554
No 39
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=57.59 E-value=16 Score=27.75 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=21.2
Q ss_pred EEEEEEcccccCCCeeeeccccc
Q psy5735 69 MVYVNLCKNFKKGDQICENYGPL 91 (247)
Q Consensus 69 ~~~~~A~r~I~~Geei~~~Y~~~ 91 (247)
.+.+.-.++|+.|++++++|.+.
T Consensus 76 tVTLTL~~~V~~Gq~VTVsYt~p 98 (101)
T TIGR02059 76 TITLTLAQVVEDGDEVTLSYTKN 98 (101)
T ss_pred EEEEEecccccCCCEEEEEeeCC
Confidence 88999999999999999999864
No 40
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=57.45 E-value=7.1 Score=25.94 Aligned_cols=31 Identities=13% Similarity=0.489 Sum_probs=14.7
Q ss_pred ccccCCCCCCcccccCCcccccccccccccc
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQF 165 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (247)
..||++.|...+............|..|+..
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTE 49 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCc
Confidence 3788888988876554433223678877753
No 41
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=56.08 E-value=53 Score=22.83 Aligned_cols=37 Identities=30% Similarity=0.407 Sum_probs=28.0
Q ss_pred HhHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhcc
Q psy5735 176 QDTESLFRLANNYKENGLYEKALEKFTQLMTLLDENL 212 (247)
Q Consensus 176 q~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l 212 (247)
+++..++.+|...-..|++++|+..|.+.+..+...+
T Consensus 6 ~~A~~li~~Av~~d~~g~~~eAl~~Y~~a~e~l~~~~ 42 (77)
T smart00745 6 SKAKELISKALKADEAGDYEEALELYKKAIEYLLEGI 42 (77)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence 3444566667776678999999999999998776554
No 42
>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=55.90 E-value=4.2 Score=24.70 Aligned_cols=30 Identities=23% Similarity=0.675 Sum_probs=17.2
Q ss_pred ccccCCCCCCcccccCCc---ccccccccccccch
Q psy5735 135 FRCETENCHNVVKVATNT---TQFMIKCDKCDQFI 166 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~---~~~~~~C~~C~~~~ 166 (247)
+.| ++|+..+.++.+. ......|..|+...
T Consensus 3 ~~C--P~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQC--PNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEC--CCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 567 6777766544321 12246788887653
No 43
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=54.52 E-value=6.9 Score=23.65 Aligned_cols=26 Identities=12% Similarity=0.424 Sum_probs=12.5
Q ss_pred CCCCCccc--ccCCcccccccccccccc
Q psy5735 140 ENCHNVVK--VATNTTQFMIKCDKCDQF 165 (247)
Q Consensus 140 ~~C~~~~~--~~~~~~~~~~~C~~C~~~ 165 (247)
+.|++.+. ++..++...+.|..|+.+
T Consensus 4 ~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 4 PQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccChhhhhcCCCCCccceECCCCCCE
Confidence 77887663 233333446889888853
No 44
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=54.32 E-value=22 Score=25.46 Aligned_cols=37 Identities=14% Similarity=0.156 Sum_probs=29.8
Q ss_pred hHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhccC
Q psy5735 177 DTESLFRLANNYKENGLYEKALEKFTQLMTLLDENLV 213 (247)
Q Consensus 177 ~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~ 213 (247)
.+..+..+|..+-..|++++|+..|.+.+..+..++.
T Consensus 5 ~A~~~a~~AVe~D~~gr~~eAi~~Y~~aIe~L~q~~~ 41 (75)
T cd02682 5 MARKYAINAVKAEKEGNAEDAITNYKKAIEVLSQIVK 41 (75)
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 3445667788888899999999999999988876643
No 45
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=52.66 E-value=49 Score=23.84 Aligned_cols=51 Identities=20% Similarity=0.287 Sum_probs=32.4
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
.+..+..++..+++++|+..|..++. ..|.+.....+...+..++..+|+.
T Consensus 42 ~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~p~~~~~~~~~~~~~~~~~~~~~~ 92 (119)
T TIGR02795 42 HYWLGEAYYAQGKYADAAKAFLAVVK-----KYPKSPKAPDALLKLGMSLQELGDK 92 (119)
T ss_pred HHHHHHHHHhhccHHHHHHHHHHHHH-----HCCCCCcccHHHHHHHHHHHHhCCh
Confidence 33345555666777777777777663 2344444556677777888777664
No 46
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=52.37 E-value=33 Score=19.15 Aligned_cols=27 Identities=33% Similarity=0.602 Sum_probs=20.2
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhh
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTL 207 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~ 207 (247)
.+..+.-.+..|++++|++.|.+.+..
T Consensus 4 ~~~lg~~~~~~~~~~~A~~~~~~al~l 30 (34)
T PF07719_consen 4 WYYLGQAYYQLGNYEEAIEYFEKALEL 30 (34)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 445566677889999999999988754
No 47
>cd02656 MIT MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear.
Probab=52.06 E-value=77 Score=21.95 Aligned_cols=36 Identities=31% Similarity=0.479 Sum_probs=27.5
Q ss_pred hHHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhcc
Q psy5735 177 DTESLFRLANNYKENGLYEKALEKFTQLMTLLDENL 212 (247)
Q Consensus 177 ~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l 212 (247)
++..+..+|...-..|++++|+..|.+.+..+...+
T Consensus 5 ~a~~l~~~Av~~D~~g~~~~Al~~Y~~a~e~l~~~~ 40 (75)
T cd02656 5 QAKELIKQAVKEDEDGNYEEALELYKEALDYLLQAL 40 (75)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence 344455666666678999999999999998877654
No 48
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=51.82 E-value=36 Score=28.51 Aligned_cols=25 Identities=28% Similarity=0.462 Sum_probs=13.1
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHH
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLM 205 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L 205 (247)
++..+..++..+++++|+..|.+++
T Consensus 36 ~~~~g~~~~~~~~~~~A~~~~~~~~ 60 (235)
T TIGR03302 36 LYEEAKEALDSGDYTEAIKYFEALE 60 (235)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 4444444555555555555555544
No 49
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=51.47 E-value=35 Score=19.31 Aligned_cols=28 Identities=36% Similarity=0.570 Sum_probs=21.1
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhhh
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTLL 208 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~~ 208 (247)
++.++.-.+..+++++|+.-|.+.|...
T Consensus 4 ~~~~g~~~~~~~~~~~A~~~~~~al~~~ 31 (34)
T PF00515_consen 4 YYNLGNAYFQLGDYEEALEYYQRALELD 31 (34)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHC
Confidence 4556667778899999999999888643
No 50
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=51.25 E-value=10 Score=23.18 Aligned_cols=28 Identities=21% Similarity=0.538 Sum_probs=18.4
Q ss_pred ccccCCCCCCcccccCCccccccccccccc
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (247)
..| +.|+..+.....+......|+.||.
T Consensus 2 r~C--~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RIC--PKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEE--TTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCc--CCCCCccccccCCCCCCCccCCCCC
Confidence 347 7888877554444445678999986
No 51
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=49.77 E-value=6.6 Score=24.41 Aligned_cols=31 Identities=16% Similarity=0.338 Sum_probs=14.9
Q ss_pred ccccCCCCCCccccc--CCcccccccccccccchh
Q psy5735 135 FRCETENCHNVVKVA--TNTTQFMIKCDKCDQFIN 167 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~--~~~~~~~~~C~~C~~~~~ 167 (247)
+|| +.|+..+..- .+.....|.|+-|+....
T Consensus 3 ~rC--~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 3 VRC--RRCRAYLNPFCQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp -B---TTT--BS-TTSEEETTTTEEEETTT--EEE
T ss_pred ccc--CCCCCEECCcceEcCCCCEEECcCCCCcCC
Confidence 578 7888766311 112345799999997543
No 52
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=49.56 E-value=6.6 Score=26.01 Aligned_cols=32 Identities=25% Similarity=0.713 Sum_probs=21.0
Q ss_pred cccccCCCCCCcccccCCcccccccccccccchh
Q psy5735 134 RFRCETENCHNVVKVATNTTQFMIKCDKCDQFIN 167 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~ 167 (247)
.+|| +.|...+..........++|+.|+....
T Consensus 4 eiRC--~~CnklLa~~g~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 4 EIRC--GHCNKLLAKAGEVIELEIKCPRCKTINH 35 (51)
T ss_pred ceec--cchhHHHhhhcCccEEEEECCCCCccce
Confidence 4788 8888766442222335689999997544
No 53
>PF08472 S6PP_C: Sucrose-6-phosphate phosphohydrolase C-terminal; InterPro: IPR013679 This is the Sucrose-6-phosphate phosphohydrolase (S6PP or SPP) C-terminal domain [] as found in plant sucrose phosphatases. These enzymes irreversibly catalyse the last step in sucrose synthesis following the formation of Sucrose-6-Phosphate via sucrose-phosphate synthase (SPS). ; GO: 0000287 magnesium ion binding, 0050307 sucrose-phosphate phosphatase activity, 0005986 sucrose biosynthetic process
Probab=49.05 E-value=30 Score=27.61 Aligned_cols=47 Identities=9% Similarity=0.105 Sum_probs=40.2
Q ss_pred hhhccchHHHHHHHHHHHHhhhhhccCCCc--ccHHHHHHHHHHHHHHh
Q psy5735 187 NYKENGLYEKALEKFTQLMTLLDENLVPPY--RDYILCQRSIQTCFLNL 233 (247)
Q Consensus 187 ~~~~~~~~e~al~~~~~~L~~~~~~l~~p~--~~~~~~~~~l~~c~~~~ 233 (247)
+.-+..+.+.+++.++..+++...++||.. +.++.+-++|+.||.+-
T Consensus 37 rrgEVe~se~~~~~LK~~~~~~g~~vhPsGvE~slh~~Id~Lr~~yGdk 85 (133)
T PF08472_consen 37 RRGEVENSEEYFQRLKSVCHPNGTFVHPSGVEKSLHDSIDALRSCYGDK 85 (133)
T ss_pred hhcccCCcHHHHHHhhhhhccCcCEEccccccccHHHHHHHHHHHhhhh
Confidence 334566788999999999999999999975 77889999999999875
No 54
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=48.18 E-value=39 Score=22.22 Aligned_cols=40 Identities=23% Similarity=0.468 Sum_probs=23.3
Q ss_pred hccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 189 KENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 189 ~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
+..|++++|++.|.+.+.. .|.+.+ +.-.++.|+...|+.
T Consensus 2 l~~~~~~~A~~~~~~~l~~-----~p~~~~---~~~~la~~~~~~g~~ 41 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQR-----NPDNPE---ARLLLAQCYLKQGQY 41 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHH-----TTTSHH---HHHHHHHHHHHTT-H
T ss_pred hhccCHHHHHHHHHHHHHH-----CCCCHH---HHHHHHHHHHHcCCH
Confidence 4567888888888877643 222222 222466777776654
No 55
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=47.97 E-value=73 Score=26.57 Aligned_cols=52 Identities=23% Similarity=0.322 Sum_probs=28.8
Q ss_pred HHHHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhcc
Q psy5735 179 ESLFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQ 235 (247)
Q Consensus 179 ~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~ 235 (247)
+.++..+...+..|++++|++.|..++.. +|......+++=.|+.++...|+
T Consensus 6 ~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~-----~P~s~~a~~A~l~la~a~y~~~~ 57 (203)
T PF13525_consen 6 EALYQKALEALQQGDYEEAIKLFEKLIDR-----YPNSPYAPQAQLMLAYAYYKQGD 57 (203)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHHHHHHHH------TTSTTHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHH-----CCCChHHHHHHHHHHHHHHHcCC
Confidence 44666677777777777777777776542 33333344444445555544443
No 56
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=47.21 E-value=37 Score=19.97 Aligned_cols=22 Identities=36% Similarity=0.678 Sum_probs=16.5
Q ss_pred HhhhhccchHHHHHHHHHHHHh
Q psy5735 185 ANNYKENGLYEKALEKFTQLMT 206 (247)
Q Consensus 185 a~~~~~~~~~e~al~~~~~~L~ 206 (247)
+.-....|++++|++.|.+.|.
T Consensus 6 g~~~~~~g~~~~Ai~~y~~aL~ 27 (36)
T PF13176_consen 6 GRIYRQQGDYEKAIEYYEQALA 27 (36)
T ss_dssp HHHHHHCT-HHHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHHHHH
Confidence 4445678899999999999764
No 57
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=45.78 E-value=13 Score=22.60 Aligned_cols=29 Identities=24% Similarity=0.763 Sum_probs=17.7
Q ss_pred cccccCCCCCCcccccCC-ccccccccccccc
Q psy5735 134 RFRCETENCHNVVKVATN-TTQFMIKCDKCDQ 164 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~~-~~~~~~~C~~C~~ 164 (247)
.|+| +.|+..+..... .......|+.||.
T Consensus 5 ~y~C--~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRC--EDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEc--CCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 4778 788876532221 1134567999987
No 58
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=44.54 E-value=15 Score=23.06 Aligned_cols=29 Identities=24% Similarity=0.684 Sum_probs=18.3
Q ss_pred cccccCCCCCCccccc-CCccccccccccccc
Q psy5735 134 RFRCETENCHNVVKVA-TNTTQFMIKCDKCDQ 164 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~-~~~~~~~~~C~~C~~ 164 (247)
.|+| ..|+..+..- .........|+.|+.
T Consensus 5 ey~C--~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRC--EECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEe--CCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4788 8888665221 111135678999987
No 59
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=44.21 E-value=48 Score=18.58 Aligned_cols=27 Identities=37% Similarity=0.650 Sum_probs=20.1
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhh
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTL 207 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~ 207 (247)
++..+.-....|++++|++.|.+.+..
T Consensus 4 ~~~lg~~y~~~~~~~~A~~~~~~a~~~ 30 (34)
T PF13181_consen 4 YYNLGKIYEQLGDYEEALEYFEKALEL 30 (34)
T ss_dssp HHHHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 344455666788999999999988764
No 60
>KOG0545|consensus
Probab=42.45 E-value=48 Score=29.68 Aligned_cols=61 Identities=25% Similarity=0.320 Sum_probs=40.1
Q ss_pred HHHHHhhhhccchHHHHHHHHHHHHhhhhhccC---CCcccHHHHHHHHHHHHHHhcccccccc
Q psy5735 181 LFRLANNYKENGLYEKALEKFTQLMTLLDENLV---PPYRDYILCQRSIQTCFLNLGQKCLNKE 241 (247)
Q Consensus 181 l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~---~p~~~~~~~~~~l~~c~~~~g~~~l~~~ 241 (247)
+-.++-+++-.++|.+|..+|.+.+-.+..+.. |.-.+|......+.--+++...+.|+++
T Consensus 181 l~q~GN~lfk~~~ykEA~~~YreAi~~l~~L~lkEkP~e~eW~eLdk~~tpLllNy~QC~L~~~ 244 (329)
T KOG0545|consen 181 LHQEGNRLFKLGRYKEASSKYREAIICLRNLQLKEKPGEPEWLELDKMITPLLLNYCQCLLKKE 244 (329)
T ss_pred HHHhhhhhhhhccHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHhhhHHHHhHHHHHhhHH
Confidence 444567788899999999999999887765533 4446677666655444444444444433
No 61
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=41.38 E-value=20 Score=23.74 Aligned_cols=30 Identities=20% Similarity=0.480 Sum_probs=17.8
Q ss_pred ccccCCCCCCcccccCCccccccccccccc
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (247)
.+||.++|...+....+.......|..|+.
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~ 48 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGF 48 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCC
Confidence 468777887766544222334566776764
No 62
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=40.70 E-value=16 Score=24.55 Aligned_cols=32 Identities=19% Similarity=0.661 Sum_probs=22.8
Q ss_pred ccccCCCCCCcccccCCcccccccccccccchhh
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQFINI 168 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~~ 168 (247)
++| +.|+..+.++.........|+.||....+
T Consensus 3 ~~C--P~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FEC--PDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred cCC--CCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 678 88998887665433345689999976654
No 63
>KOG0553|consensus
Probab=38.82 E-value=1e+02 Score=28.07 Aligned_cols=32 Identities=31% Similarity=0.371 Sum_probs=25.6
Q ss_pred hHHHHHHHHhhhhccchHHHHHHHHHHHHhhh
Q psy5735 177 DTESLFRLANNYKENGLYEKALEKFTQLMTLL 208 (247)
Q Consensus 177 ~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~ 208 (247)
.++.+-.++.++|..++|++|+.+|.+.|...
T Consensus 80 ~AE~LK~eGN~~m~~~~Y~eAv~kY~~AI~l~ 111 (304)
T KOG0553|consen 80 LAESLKNEGNKLMKNKDYQEAVDKYTEAIELD 111 (304)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence 34555556788899999999999999988643
No 64
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=37.88 E-value=58 Score=23.84 Aligned_cols=51 Identities=27% Similarity=0.436 Sum_probs=35.4
Q ss_pred HHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccH--HHHHHHHHHHHHHhccc
Q psy5735 178 TESLFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDY--ILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 178 ~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~--~~~~~~l~~c~~~~g~~ 236 (247)
.+..+..+..++..|++++|++.+.+++.. ++.| ..+...+-..|..+|..
T Consensus 22 ~~ar~~lA~~~~~~g~~e~Al~~Ll~~v~~--------dr~~~~~~ar~~ll~~f~~lg~~ 74 (90)
T PF14561_consen 22 LDARYALADALLAAGDYEEALDQLLELVRR--------DRDYEDDAARKRLLDIFELLGPG 74 (90)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHCC---------TTCCCCHHHHHHHHHHHHH-TT
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CccccccHHHHHHHHHHHHcCCC
Confidence 456677788889999999999999986632 2233 56677777777777764
No 65
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=36.61 E-value=23 Score=20.88 Aligned_cols=27 Identities=15% Similarity=0.573 Sum_probs=19.2
Q ss_pred ccccCCCCCCcccccCCcccccccccccccc
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQF 165 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (247)
+.| ..|+..+..|.. ...++|..|+..
T Consensus 2 ~~C--~~C~t~L~yP~g--A~~vrCs~C~~v 28 (31)
T TIGR01053 2 VVC--GGCRTLLMYPRG--ASSVRCALCQTV 28 (31)
T ss_pred cCc--CCCCcEeecCCC--CCeEECCCCCeE
Confidence 457 788888877754 446888888754
No 66
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=35.90 E-value=64 Score=19.82 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=17.8
Q ss_pred hhccchHHHHHHHHHHHHhhhhhcc
Q psy5735 188 YKENGLYEKALEKFTQLMTLLDENL 212 (247)
Q Consensus 188 ~~~~~~~e~al~~~~~~L~~~~~~l 212 (247)
.+..++|++|+.-|.+.|....+++
T Consensus 11 sle~e~f~qA~~D~~~aL~i~~~l~ 35 (38)
T PF10516_consen 11 SLENENFEQAIEDYEKALEIQEELL 35 (38)
T ss_pred HHHhccHHHHHHHHHHHHHHHHHhc
Confidence 3456678888888888887665544
No 67
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=35.79 E-value=1.3e+02 Score=21.46 Aligned_cols=12 Identities=42% Similarity=0.346 Sum_probs=4.8
Q ss_pred chHHHHHHHHHH
Q psy5735 192 GLYEKALEKFTQ 203 (247)
Q Consensus 192 ~~~e~al~~~~~ 203 (247)
+++++|++.+..
T Consensus 90 ~~~~~A~~~~~~ 101 (119)
T TIGR02795 90 GDKEKAKATLQQ 101 (119)
T ss_pred CChHHHHHHHHH
Confidence 334444444433
No 68
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=35.51 E-value=21 Score=23.27 Aligned_cols=29 Identities=28% Similarity=0.478 Sum_probs=17.8
Q ss_pred cccccCCCCCCcccccCCccccccccccccc
Q psy5735 134 RFRCETENCHNVVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (247)
+-.||++.|+.++..... ...+.|.+|+.
T Consensus 18 rk~CP~~~CG~GvFMA~H--~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEH--KDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE---SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeec--CCCccCCCccc
Confidence 456977799976432321 23689999984
No 69
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=34.41 E-value=1.1e+02 Score=21.17 Aligned_cols=48 Identities=29% Similarity=0.477 Sum_probs=30.8
Q ss_pred HHHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 180 SLFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 180 ~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
.++..|.-++..|++++|+..+.. +.... .+ ..+.-.+++|+..+|..
T Consensus 27 ~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-----~~---~~~~~l~a~~~~~l~~y 74 (84)
T PF12895_consen 27 YLYNLAQCYFQQGKYEEAIELLQK-LKLDP-----SN---PDIHYLLARCLLKLGKY 74 (84)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-----CH---HHHHHHHHHHHHHTT-H
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-----CC---HHHHHHHHHHHHHhCCH
Confidence 344456677889999999999876 21111 11 34444668888888864
No 70
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=33.01 E-value=29 Score=22.87 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=13.8
Q ss_pred EEEEcccccCCCeeee
Q psy5735 71 YVNLCKNFKKGDQICE 86 (247)
Q Consensus 71 ~~~A~r~I~~Geei~~ 86 (247)
+++|.++|++|+.|+-
T Consensus 3 v~va~~~i~~G~~i~~ 18 (64)
T smart00858 3 VVVAARDLPAGEVITA 18 (64)
T ss_pred EEEEeCccCCCCCcch
Confidence 5688999999999884
No 71
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.45 E-value=37 Score=19.98 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=17.0
Q ss_pred ccccCCCCCCcccccCCcccccccccccccch
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQFI 166 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (247)
++| ..|+-.+... ...|.|+.|+...
T Consensus 2 ~~C--~~CGy~y~~~----~~~~~CP~Cg~~~ 27 (33)
T cd00350 2 YVC--PVCGYIYDGE----EAPWVCPVCGAPK 27 (33)
T ss_pred EEC--CCCCCEECCC----cCCCcCcCCCCcH
Confidence 567 7787654322 2468999998643
No 72
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=31.43 E-value=1.2e+02 Score=29.17 Aligned_cols=54 Identities=17% Similarity=0.178 Sum_probs=35.7
Q ss_pred HHHHHHHHhhhhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 178 TESLFRLANNYKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 178 ~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
.+..+..+..++..++|++|+..|...|... |.+.+...+.--++-||+.+|+.
T Consensus 75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL~-----Pd~aeA~~A~yNLAcaya~LGr~ 128 (453)
T PLN03098 75 AEDAVNLGLSLFSKGRVKDALAQFETALELN-----PNPDEAQAAYYNKACCHAYREEG 128 (453)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-----CCchHHHHHHHHHHHHHHHcCCH
Confidence 4455666777888999999999999877532 33333334555666666666654
No 73
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=31.25 E-value=20 Score=32.06 Aligned_cols=46 Identities=22% Similarity=0.647 Sum_probs=23.5
Q ss_pred eEeecCCCCCCcchhhhhhhhhccccccCCCCCCcccc-------cCCcccccccccccccchh
Q psy5735 111 DCHCIACEHDWPLFEEMQAAQDLRFRCETENCHNVVKV-------ATNTTQFMIKCDKCDQFIN 167 (247)
Q Consensus 111 ~C~C~~C~~~~~~~~~~~~~~~~~~~C~~~~C~~~~~~-------~~~~~~~~~~C~~C~~~~~ 167 (247)
...|..|...|. +.+++| +.|++.-.. ...+....-.|..|+....
T Consensus 197 ~L~Cs~C~t~W~---------~~R~~C--p~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 197 YLHCSLCGTEWR---------FVRIKC--PYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp EEEETTT--EEE-----------TTS---TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred EEEcCCCCCeee---------ecCCCC--cCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 468999999883 456889 899863211 1112233468999997654
No 74
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=30.82 E-value=57 Score=24.15 Aligned_cols=17 Identities=18% Similarity=0.204 Sum_probs=9.6
Q ss_pred ccccccccccchhhhhh
Q psy5735 155 FMIKCDKCDQFINIFKG 171 (247)
Q Consensus 155 ~~~~C~~C~~~~~~~~~ 171 (247)
..|.|-.|+..-++-+.
T Consensus 53 ~~~~Cf~Cg~~Gd~i~~ 69 (97)
T PF01807_consen 53 NRFKCFGCGKGGDVIDF 69 (97)
T ss_dssp TEEEETTT--EE-HHHH
T ss_pred CeEEECCCCCCCcHHhH
Confidence 46899999876655443
No 75
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=30.41 E-value=26 Score=27.00 Aligned_cols=31 Identities=16% Similarity=0.354 Sum_probs=22.2
Q ss_pred ccCCCCCCcccccCCcccccccccccccchhhh
Q psy5735 137 CETENCHNVVKVATNTTQFMIKCDKCDQFINIF 169 (247)
Q Consensus 137 C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~~~ 169 (247)
| +.|++.+....+.....+.|.+|+....+.
T Consensus 5 C--p~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 5 C--PKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred c--CCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 7 788887765544344578999999876544
No 76
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=29.77 E-value=30 Score=22.82 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=16.0
Q ss_pred cccCCCCCCcccccCCcccccccccccccc
Q psy5735 136 RCETENCHNVVKVATNTTQFMIKCDKCDQF 165 (247)
Q Consensus 136 ~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~ 165 (247)
.| +.|+.+..... ....|.|.+|+..
T Consensus 21 ~C--PrCG~gvfmA~--H~dR~~CGkCgyT 46 (51)
T COG1998 21 FC--PRCGPGVFMAD--HKDRWACGKCGYT 46 (51)
T ss_pred cC--CCCCCcchhhh--cCceeEeccccce
Confidence 47 77885433222 2347999999864
No 77
>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=29.60 E-value=22 Score=23.57 Aligned_cols=47 Identities=26% Similarity=0.702 Sum_probs=18.5
Q ss_pred ecCCCCCCcchhhhhhhhhccccccCCCCCCcccccCC--cccccccccccc
Q psy5735 114 CIACEHDWPLFEEMQAAQDLRFRCETENCHNVVKVATN--TTQFMIKCDKCD 163 (247)
Q Consensus 114 C~~C~~~~~~~~~~~~~~~~~~~C~~~~C~~~~~~~~~--~~~~~~~C~~C~ 163 (247)
|-.|..+.+....-.. ...+|+| ++|.+.+..+=+ ..+..-.|+.|.
T Consensus 2 CfgC~~~~~~~~~~~~-~~~~y~C--~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKA-DSSRYRC--PKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS--------EEE----TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccc-cCCeEEC--CCCCCccccCcChhhhccccCCcCCC
Confidence 5667665443221111 2357999 899988765432 123344566653
No 78
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=29.25 E-value=53 Score=19.50 Aligned_cols=8 Identities=38% Similarity=1.311 Sum_probs=4.4
Q ss_pred cccccccc
Q psy5735 157 IKCDKCDQ 164 (247)
Q Consensus 157 ~~C~~C~~ 164 (247)
.+|..||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 56666664
No 79
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=29.25 E-value=36 Score=21.88 Aligned_cols=29 Identities=21% Similarity=0.635 Sum_probs=16.8
Q ss_pred cccccCCCCCCcccccC-Cccccccccccccc
Q psy5735 134 RFRCETENCHNVVKVAT-NTTQFMIKCDKCDQ 164 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~-~~~~~~~~C~~C~~ 164 (247)
.|+| ..|+..+..-. ........|+.|+.
T Consensus 5 ey~C--~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRC--TACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEe--CCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 4788 78887542211 11123467999986
No 80
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=28.65 E-value=1.2e+02 Score=24.88 Aligned_cols=28 Identities=25% Similarity=0.290 Sum_probs=17.5
Q ss_pred HHHHHHHHhhhhccchHHHHHHHHHHHH
Q psy5735 178 TESLFRLANNYKENGLYEKALEKFTQLM 205 (247)
Q Consensus 178 ~~~l~~~a~~~~~~~~~e~al~~~~~~L 205 (247)
.+.++..+..+++.|++++|.+.|.-+.
T Consensus 35 l~~lY~~A~~ly~~G~l~~A~~~f~~L~ 62 (157)
T PRK15363 35 LNTLYRYAMQLMEVKEFAGAARLFQLLT 62 (157)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445556666777777777776665433
No 81
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=28.46 E-value=1.8e+02 Score=25.13 Aligned_cols=28 Identities=14% Similarity=0.360 Sum_probs=19.9
Q ss_pred HHHHHHHhhhhccchHHHHHHHHHHHHh
Q psy5735 179 ESLFRLANNYKENGLYEKALEKFTQLMT 206 (247)
Q Consensus 179 ~~l~~~a~~~~~~~~~e~al~~~~~~L~ 206 (247)
+..+..+...+..|++++|++.|.+++.
T Consensus 33 ~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~ 60 (243)
T PRK10866 33 SEIYATAQQKLQDGNWKQAITQLEALDN 60 (243)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3456667777777888888888777664
No 82
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=28.32 E-value=40 Score=21.47 Aligned_cols=27 Identities=19% Similarity=0.661 Sum_probs=14.8
Q ss_pred ccccCCCCCCcccccCCcccccccccccccch
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQFI 166 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (247)
|.| ..|+..+.... .....|+.||..+
T Consensus 3 Y~C--~~Cg~~~~~~~---~~~irC~~CG~rI 29 (44)
T smart00659 3 YIC--GECGRENEIKS---KDVVRCRECGYRI 29 (44)
T ss_pred EEC--CCCCCEeecCC---CCceECCCCCceE
Confidence 566 66666543331 2346777777543
No 83
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=27.59 E-value=2.4e+02 Score=22.27 Aligned_cols=29 Identities=24% Similarity=0.421 Sum_probs=18.2
Q ss_pred HHHHHHHhhhhccchHHHHHHHHHHHHhh
Q psy5735 179 ESLFRLANNYKENGLYEKALEKFTQLMTL 207 (247)
Q Consensus 179 ~~l~~~a~~~~~~~~~e~al~~~~~~L~~ 207 (247)
..++..+......+++++|+..|...+..
T Consensus 36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l 64 (168)
T CHL00033 36 FTYYRDGMSAQSEGEYAEALQNYYEAMRL 64 (168)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence 33444455556667777777777776654
No 84
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.50 E-value=51 Score=30.08 Aligned_cols=46 Identities=26% Similarity=0.744 Sum_probs=29.8
Q ss_pred eEeecCCCCCCcchhhhhhhhhccccccCCCCCCccc-----ccCC-cccccccccccccchh
Q psy5735 111 DCHCIACEHDWPLFEEMQAAQDLRFRCETENCHNVVK-----VATN-TTQFMIKCDKCDQFIN 167 (247)
Q Consensus 111 ~C~C~~C~~~~~~~~~~~~~~~~~~~C~~~~C~~~~~-----~~~~-~~~~~~~C~~C~~~~~ 167 (247)
.+.|..|...|. +.+.+| +.|++.-. +... .....-.|..|+....
T Consensus 212 yL~CslC~teW~---------~~R~~C--~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 212 YLHCNLCESEWH---------VVRVKC--SNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred EEEcCCCCCccc---------ccCccC--CCCCCCCceeeeeecCCCcceEeeecccccccce
Confidence 588999999993 457899 88986321 1111 1123357999997654
No 85
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=27.26 E-value=34 Score=18.64 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=10.8
Q ss_pred CCCCCcccccCCccccccccccccc
Q psy5735 140 ENCHNVVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 140 ~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (247)
++|+..+.. ..-.|..||.
T Consensus 3 p~CG~~~~~------~~~fC~~CG~ 21 (23)
T PF13240_consen 3 PNCGAEIED------DAKFCPNCGT 21 (23)
T ss_pred cccCCCCCC------cCcchhhhCC
Confidence 667665431 2335777775
No 86
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=26.80 E-value=52 Score=26.80 Aligned_cols=10 Identities=20% Similarity=0.846 Sum_probs=5.0
Q ss_pred cccccccccc
Q psy5735 156 MIKCDKCDQF 165 (247)
Q Consensus 156 ~~~C~~C~~~ 165 (247)
.+.|+.||..
T Consensus 128 ~F~Cp~Cg~~ 137 (158)
T TIGR00373 128 NFTCPRCGAM 137 (158)
T ss_pred CCcCCCCCCE
Confidence 3455555543
No 87
>PRK00420 hypothetical protein; Validated
Probab=26.41 E-value=1.9e+02 Score=22.30 Aligned_cols=28 Identities=11% Similarity=0.097 Sum_probs=14.7
Q ss_pred ccccCCCCCCcccccCCcccccccccccccchh
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQFIN 167 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~ 167 (247)
-.| |.|+..+.-. ......|+.||....
T Consensus 24 ~~C--P~Cg~pLf~l---k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHC--PVCGLPLFEL---KDGEVVCPVHGKVYI 51 (112)
T ss_pred CCC--CCCCCcceec---CCCceECCCCCCeee
Confidence 456 5666554321 123456777776543
No 88
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=26.39 E-value=1.2e+02 Score=18.41 Aligned_cols=23 Identities=22% Similarity=0.342 Sum_probs=18.5
Q ss_pred HHhhhhccchHHHHHHHHHHHHh
Q psy5735 184 LANNYKENGLYEKALEKFTQLMT 206 (247)
Q Consensus 184 ~a~~~~~~~~~e~al~~~~~~L~ 206 (247)
.+..+...|++++|++.|...|.
T Consensus 7 la~~~~~~G~~~~A~~~~~~~l~ 29 (44)
T PF13428_consen 7 LARAYRRLGQPDEAERLLRRALA 29 (44)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHH
Confidence 34556678999999999998885
No 89
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=25.76 E-value=61 Score=20.99 Aligned_cols=13 Identities=15% Similarity=0.089 Sum_probs=7.5
Q ss_pred cccccccccccch
Q psy5735 154 QFMIKCDKCDQFI 166 (247)
Q Consensus 154 ~~~~~C~~C~~~~ 166 (247)
...|.|+.|+...
T Consensus 32 p~~w~CP~C~a~K 44 (47)
T PF00301_consen 32 PDDWVCPVCGAPK 44 (47)
T ss_dssp -TT-B-TTTSSBG
T ss_pred CCCCcCcCCCCcc
Confidence 3579999998643
No 90
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.66 E-value=43 Score=21.21 Aligned_cols=28 Identities=21% Similarity=0.555 Sum_probs=16.4
Q ss_pred cccccCCCCCCcccccCCccccccccccccc
Q psy5735 134 RFRCETENCHNVVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (247)
.+.| +.|+..-.... .....|+|..|++
T Consensus 18 g~~C--P~Cg~~~~~~~-~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVC--PHCGSTKHYRL-KTRGRYRCKACRK 45 (46)
T ss_pred CCCC--CCCCCeeeEEe-CCCCeEECCCCCC
Confidence 4668 77876421111 1135688998875
No 91
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.21 E-value=98 Score=23.97 Aligned_cols=17 Identities=12% Similarity=0.333 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHhhhhh
Q psy5735 194 YEKALEKFTQLMTLLDE 210 (247)
Q Consensus 194 ~e~al~~~~~~L~~~~~ 210 (247)
|=.+..++-+++..+..
T Consensus 63 YPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 63 YPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cHHHHHHHHHHHHHhCC
Confidence 33444455555555543
No 92
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=25.17 E-value=50 Score=21.83 Aligned_cols=36 Identities=19% Similarity=0.579 Sum_probs=17.4
Q ss_pred ccccCCCCCCcc--cccC-----Ccccccccccccccchhhhh
Q psy5735 135 FRCETENCHNVV--KVAT-----NTTQFMIKCDKCDQFINIFK 170 (247)
Q Consensus 135 ~~C~~~~C~~~~--~~~~-----~~~~~~~~C~~C~~~~~~~~ 170 (247)
++|+|++|...- .++. +......+|.-|.+..+.+.
T Consensus 7 l~C~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~~~~e 49 (52)
T PF02748_consen 7 LKCPNPNCITNSNEPVESRFYVIDKEPIKLRCHYCERIITEDE 49 (52)
T ss_dssp SE-SSTTBTTT-TSSS--EEEEEETTTCEEEETTT--EEEHHH
T ss_pred EEcCCCCcccCCCCCCCceEEEEeCCCCEEEeeCCCCEecccE
Confidence 677777776441 1110 01234578999988765543
No 93
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=25.11 E-value=42 Score=29.68 Aligned_cols=36 Identities=22% Similarity=0.491 Sum_probs=24.9
Q ss_pred ccccccCCCCCCcccccCCcccccccccccccchhhhh
Q psy5735 133 LRFRCETENCHNVVKVATNTTQFMIKCDKCDQFINIFK 170 (247)
Q Consensus 133 ~~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~~~~ 170 (247)
.++.| .+|...|..+....+...+|+.|++...+-.
T Consensus 156 ~rv~C--ghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~ 191 (256)
T PF09788_consen 156 CRVIC--GHCSNTFLFNTLTSNTLARCPHCRKVSSVGP 191 (256)
T ss_pred eeEEC--CCCCCcEeccCCCCCccccCCCCceeccccc
Confidence 45778 7888777666544345678999998776543
No 94
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=25.02 E-value=59 Score=18.27 Aligned_cols=23 Identities=13% Similarity=0.501 Sum_probs=15.1
Q ss_pred CCCCCcccccCCccccccccccccc
Q psy5735 140 ENCHNVVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 140 ~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (247)
.+|+..+..|.. ...++|..|+.
T Consensus 2 ~~Cr~~L~yp~G--A~sVrCa~C~~ 24 (25)
T PF06943_consen 2 GGCRTLLMYPRG--APSVRCACCHT 24 (25)
T ss_pred CCCCceEEcCCC--CCCeECCccCc
Confidence 567777766643 34678888764
No 95
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=24.89 E-value=60 Score=29.54 Aligned_cols=48 Identities=21% Similarity=0.656 Sum_probs=30.6
Q ss_pred eeEeecCCCCCCcchhhhhhhhhccccccCCCCCCccc-----ccCC---cccccccccccccchhh
Q psy5735 110 FDCHCIACEHDWPLFEEMQAAQDLRFRCETENCHNVVK-----VATN---TTQFMIKCDKCDQFINI 168 (247)
Q Consensus 110 F~C~C~~C~~~~~~~~~~~~~~~~~~~C~~~~C~~~~~-----~~~~---~~~~~~~C~~C~~~~~~ 168 (247)
=...|..|...|. +.+.+| +.|++.-. +..+ +.-..-.|..|+....+
T Consensus 209 RyL~CslC~teW~---------~~R~~C--~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 209 RYLSCSLCATEWH---------YVRVKC--SHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred eEEEcCCCCCccc---------ccCccC--CCCCCCCceeeEeecCCCCCcceEEeeccccccchhh
Confidence 3589999999993 457899 88886321 1110 11123479999976653
No 96
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.89 E-value=50 Score=20.35 Aligned_cols=7 Identities=29% Similarity=0.918 Sum_probs=4.0
Q ss_pred eecCCCC
Q psy5735 113 HCIACEH 119 (247)
Q Consensus 113 ~C~~C~~ 119 (247)
+|++|..
T Consensus 1 ~CP~C~~ 7 (41)
T PF13453_consen 1 KCPRCGT 7 (41)
T ss_pred CcCCCCc
Confidence 3666654
No 97
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.81 E-value=52 Score=27.40 Aligned_cols=10 Identities=20% Similarity=0.913 Sum_probs=5.1
Q ss_pred cccccccccc
Q psy5735 156 MIKCDKCDQF 165 (247)
Q Consensus 156 ~~~C~~C~~~ 165 (247)
.+.|+.||..
T Consensus 136 ~F~Cp~Cg~~ 145 (178)
T PRK06266 136 GFRCPQCGEM 145 (178)
T ss_pred CCcCCCCCCC
Confidence 4555555543
No 98
>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=24.60 E-value=53 Score=22.38 Aligned_cols=32 Identities=16% Similarity=0.359 Sum_probs=21.1
Q ss_pred hccccccCCCCCCcccccCCcccccccccccccchh
Q psy5735 132 DLRFRCETENCHNVVKVATNTTQFMIKCDKCDQFIN 167 (247)
Q Consensus 132 ~~~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~ 167 (247)
..+-.| +.|+..... ......+.|+.||...+
T Consensus 26 ~TSq~C--~~CG~~~~~--~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 26 YTSQTC--PRCGHRNKK--RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CCccCc--cCccccccc--ccccceEEcCCCCCEEC
Confidence 345668 788776543 22345789999998754
No 99
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=24.29 E-value=1.1e+02 Score=15.22 Aligned_cols=24 Identities=33% Similarity=0.589 Sum_probs=16.6
Q ss_pred HHHhhhhccchHHHHHHHHHHHHh
Q psy5735 183 RLANNYKENGLYEKALEKFTQLMT 206 (247)
Q Consensus 183 ~~a~~~~~~~~~e~al~~~~~~L~ 206 (247)
..+.-.+..+++++|+..+...+.
T Consensus 6 ~~a~~~~~~~~~~~a~~~~~~~~~ 29 (34)
T smart00028 6 NLGNAYLKLGDYDEALEYYEKALE 29 (34)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHc
Confidence 334455667788888888877664
No 100
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=24.23 E-value=40 Score=23.07 Aligned_cols=32 Identities=19% Similarity=0.563 Sum_probs=17.5
Q ss_pred hhccccccCCCCCCccc-ccCCcccccccccccccch
Q psy5735 131 QDLRFRCETENCHNVVK-VATNTTQFMIKCDKCDQFI 166 (247)
Q Consensus 131 ~~~~~~C~~~~C~~~~~-~~~~~~~~~~~C~~C~~~~ 166 (247)
.+..++| +.|.+.-. +... .....|..|+...
T Consensus 8 ~F~~VkC--p~C~n~q~vFsha--~t~V~C~~Cg~~L 40 (59)
T PRK00415 8 RFLKVKC--PDCGNEQVVFSHA--STVVRCLVCGKTL 40 (59)
T ss_pred eEEEEEC--CCCCCeEEEEecC--CcEEECcccCCCc
Confidence 4556777 67776432 2211 2345677777643
No 101
>PF08969 USP8_dimer: USP8 dimerisation domain; InterPro: IPR015063 This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It has no known function. ; PDB: 2XZE_B 2A9U_A.
Probab=23.72 E-value=1.2e+02 Score=22.89 Aligned_cols=34 Identities=26% Similarity=0.511 Sum_probs=27.4
Q ss_pred HhHHHHHHHHhhhhccchHHHHHHHHHHHHhhhh
Q psy5735 176 QDTESLFRLANNYKENGLYEKALEKFTQLMTLLD 209 (247)
Q Consensus 176 q~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~~ 209 (247)
+-+..+++.|.....+|+.|.|--.|..++....
T Consensus 36 rsa~~l~~~A~~~~~egd~E~AYvl~~R~~~L~~ 69 (115)
T PF08969_consen 36 RSANKLLREAEEYRQEGDEEQAYVLYMRYLTLVE 69 (115)
T ss_dssp HHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3455578888888999999999999999998884
No 102
>KOG0739|consensus
Probab=23.50 E-value=1.1e+02 Score=28.22 Aligned_cols=35 Identities=23% Similarity=0.286 Sum_probs=28.6
Q ss_pred hhHhHHHHHHHHhhhhccchHHHHHHHHHHHHhhh
Q psy5735 174 NLQDTESLFRLANNYKENGLYEKALEKFTQLMTLL 208 (247)
Q Consensus 174 ~lq~~~~l~~~a~~~~~~~~~e~al~~~~~~L~~~ 208 (247)
.+|++.++.++|..-...++|++|+..|...|.-+
T Consensus 6 ~l~kaI~lv~kA~~eD~a~nY~eA~~lY~~aleYF 40 (439)
T KOG0739|consen 6 FLQKAIDLVKKAIDEDNAKNYEEALRLYQNALEYF 40 (439)
T ss_pred HHHHHHHHHHHHhhhcchhchHHHHHHHHHHHHHH
Confidence 46677778888888778899999999999888643
No 103
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=23.24 E-value=40 Score=23.62 Aligned_cols=31 Identities=23% Similarity=0.524 Sum_probs=17.4
Q ss_pred hhccccccCCCCCCccc-ccCCcccccccccccccc
Q psy5735 131 QDLRFRCETENCHNVVK-VATNTTQFMIKCDKCDQF 165 (247)
Q Consensus 131 ~~~~~~C~~~~C~~~~~-~~~~~~~~~~~C~~C~~~ 165 (247)
.+..++| +.|++.-. +... .....|..||..
T Consensus 16 ~Fl~VkC--pdC~N~q~vFsha--st~V~C~~CG~~ 47 (67)
T COG2051 16 RFLRVKC--PDCGNEQVVFSHA--STVVTCLICGTT 47 (67)
T ss_pred eEEEEEC--CCCCCEEEEeccC--ceEEEecccccE
Confidence 4556777 77776432 2211 234677777764
No 104
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=22.87 E-value=3.1e+02 Score=21.82 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=11.3
Q ss_pred HHHHhhhhccchHHHHHHHHHHHH
Q psy5735 182 FRLANNYKENGLYEKALEKFTQLM 205 (247)
Q Consensus 182 ~~~a~~~~~~~~~e~al~~~~~~L 205 (247)
+..+..+...|++++|+..|.+.+
T Consensus 39 ~~lg~~~~~~g~~~~A~~~~~~al 62 (172)
T PRK02603 39 YRDGMSAQADGEYAEALENYEEAL 62 (172)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHH
Confidence 333434444455555555555444
No 105
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=22.70 E-value=49 Score=22.07 Aligned_cols=31 Identities=13% Similarity=0.449 Sum_probs=19.0
Q ss_pred hccccccCCCCCC--cccccCCccccccccccccc
Q psy5735 132 DLRFRCETENCHN--VVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 132 ~~~~~C~~~~C~~--~~~~~~~~~~~~~~C~~C~~ 164 (247)
..++-| ++|.. ++..........|.|..|+.
T Consensus 20 r~aLIC--~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 20 RYALIC--SKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred ceeEEC--cccchhhcccccccCCceEEEcCCCCC
Confidence 446678 77774 33323333345789999985
No 106
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=22.56 E-value=90 Score=26.08 Aligned_cols=20 Identities=15% Similarity=0.374 Sum_probs=8.7
Q ss_pred cccccccccchhhhhhhhhh
Q psy5735 156 MIKCDKCDQFINIFKGLKNL 175 (247)
Q Consensus 156 ~~~C~~C~~~~~~~~~l~~l 175 (247)
.+.|+.|+.......+.+++
T Consensus 45 ~~~C~~C~~~~~~~~l~Nql 64 (188)
T PF08996_consen 45 GLQCPNCSTPLSPASLVNQL 64 (188)
T ss_dssp EEEETTT--B--HHHHHHHH
T ss_pred cCcCCCCCCcCCHHHHHHHH
Confidence 46777777755544433333
No 107
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=22.46 E-value=47 Score=25.49 Aligned_cols=7 Identities=29% Similarity=1.141 Sum_probs=3.6
Q ss_pred ccccccc
Q psy5735 157 IKCDKCD 163 (247)
Q Consensus 157 ~~C~~C~ 163 (247)
+.|+.|+
T Consensus 87 ~~CP~Cg 93 (113)
T PRK12380 87 AQCPHCH 93 (113)
T ss_pred ccCcCCC
Confidence 3455555
No 108
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=22.45 E-value=2e+02 Score=18.17 Aligned_cols=38 Identities=26% Similarity=0.441 Sum_probs=19.4
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 191 NGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 191 ~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
.+++++|++.+...+... |... .+.-.++.++...|+.
T Consensus 47 ~~~~~~a~~~~~~~~~~~-----~~~~---~~~~~~~~~~~~~~~~ 84 (100)
T cd00189 47 LGKYEEALEDYEKALELD-----PDNA---KAYYNLGLAYYKLGKY 84 (100)
T ss_pred HHHHHHHHHHHHHHHhCC-----Ccch---hHHHHHHHHHHHHHhH
Confidence 355666666555544321 1111 4455666666666653
No 109
>PF14369 zf-RING_3: zinc-finger
Probab=22.12 E-value=70 Score=19.27 Aligned_cols=28 Identities=25% Similarity=0.808 Sum_probs=14.7
Q ss_pred cccccCCCCCCcccccCCccccccccccccc
Q psy5735 134 RFRCETENCHNVVKVATNTTQFMIKCDKCDQ 164 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~ 164 (247)
+|+| -.|...+....... ....|+.|+.
T Consensus 2 ~ywC--h~C~~~V~~~~~~~-~~~~CP~C~~ 29 (35)
T PF14369_consen 2 RYWC--HQCNRFVRIAPSPD-SDVACPRCHG 29 (35)
T ss_pred CEeC--ccCCCEeEeCcCCC-CCcCCcCCCC
Confidence 3667 67776654432211 1235777763
No 110
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=22.08 E-value=54 Score=23.09 Aligned_cols=30 Identities=23% Similarity=0.630 Sum_probs=17.1
Q ss_pred ccccCCCCCCcccccCCcccccccccccccchhhhh
Q psy5735 135 FRCETENCHNVVKVATNTTQFMIKCDKCDQFINIFK 170 (247)
Q Consensus 135 ~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~~~~~ 170 (247)
||| .|+..+..+.. ...-+| .||+..++.+
T Consensus 4 frC---~Cgr~lya~e~--~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 4 FRC---DCGRYLYAKEG--AKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp EEE---TTS--EEEETT---SEEEE-TTTEEEE--S
T ss_pred EEe---cCCCEEEecCC--cceeEe-cCCCeeeeee
Confidence 788 48887654432 234579 9999887654
No 111
>KOG2155|consensus
Probab=22.05 E-value=2.5e+02 Score=27.27 Aligned_cols=57 Identities=21% Similarity=0.152 Sum_probs=41.0
Q ss_pred ccccccccCCCccCcEEE---EeC---CEEEEEEcccccCCCeeeeccccccccCCHHHHHHHHh
Q psy5735 47 FPTLSMFNHSCEPNIVRY---FRG---TMVYVNLCKNFKKGDQICENYGPLYSQVRKTERQNTLK 105 (247)
Q Consensus 47 yp~~sl~NHSC~PN~~~~---~~~---~~~~~~A~r~I~~Geei~~~Y~~~~~~~~~~~R~~~L~ 105 (247)
--.+|.+.||=.||.... |-. .--++.-++++..|||||-.+..... ....|.-.|.
T Consensus 202 DefGsrvrHsdePnf~~aPf~fmPq~vaYsimwp~k~~~tgeE~trDfasg~~--~p~~Rk~~l~ 264 (631)
T KOG2155|consen 202 DEFGSRVRHSDEPNFRIAPFMFMPQNVAYSIMWPTKPVNTGEEITRDFASGVI--HPEWRKYILQ 264 (631)
T ss_pred hhhhhhhccCCCCcceeeeheecchhcceeEEeeccCCCCchHHHHHHhhcCC--CHHHHHHHhc
Confidence 346789999999998643 333 24567889999999999988865542 4556655554
No 112
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=21.95 E-value=83 Score=22.47 Aligned_cols=10 Identities=20% Similarity=0.591 Sum_probs=4.5
Q ss_pred HHHHHHHHHH
Q psy5735 194 YEKALEKFTQ 203 (247)
Q Consensus 194 ~e~al~~~~~ 203 (247)
++++++.|.+
T Consensus 27 Leesl~lyee 36 (75)
T PRK14066 27 LDDSLKAFEE 36 (75)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 113
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=21.83 E-value=50 Score=25.39 Aligned_cols=9 Identities=33% Similarity=1.302 Sum_probs=4.3
Q ss_pred EeecCCCCC
Q psy5735 112 CHCIACEHD 120 (247)
Q Consensus 112 C~C~~C~~~ 120 (247)
..|..|...
T Consensus 71 ~~C~~Cg~~ 79 (115)
T TIGR00100 71 CECEDCSEE 79 (115)
T ss_pred EEcccCCCE
Confidence 345555543
No 114
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=21.83 E-value=1.6e+02 Score=27.47 Aligned_cols=42 Identities=19% Similarity=0.321 Sum_probs=31.1
Q ss_pred hhccchHHHHHHHHHHHHhhhhhccCCCcccHHHHHHHHHHHHHHhccc
Q psy5735 188 YKENGLYEKALEKFTQLMTLLDENLVPPYRDYILCQRSIQTCFLNLGQK 236 (247)
Q Consensus 188 ~~~~~~~e~al~~~~~~L~~~~~~l~~p~~~~~~~~~~l~~c~~~~g~~ 236 (247)
.+..|+|++|++.+..++.-++ -.+...-+.|..||..+|..
T Consensus 224 ~~~~g~y~~AV~~~e~v~eQn~-------~yl~evl~~L~~~Y~~lg~~ 265 (389)
T COG2956 224 ELAKGDYQKAVEALERVLEQNP-------EYLSEVLEMLYECYAQLGKP 265 (389)
T ss_pred HHhccchHHHHHHHHHHHHhCh-------HHHHHHHHHHHHHHHHhCCH
Confidence 3667788888888887666554 34567788999999998863
No 115
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=21.51 E-value=3.4e+02 Score=21.84 Aligned_cols=26 Identities=27% Similarity=0.475 Sum_probs=17.5
Q ss_pred HHHHHHhhhhccchHHHHHHHHHHHH
Q psy5735 180 SLFRLANNYKENGLYEKALEKFTQLM 205 (247)
Q Consensus 180 ~l~~~a~~~~~~~~~e~al~~~~~~L 205 (247)
+++..|...+..|+|++|++.+..+.
T Consensus 12 ~ly~~a~~~l~~~~Y~~A~~~le~L~ 37 (142)
T PF13512_consen 12 ELYQEAQEALQKGNYEEAIKQLEALD 37 (142)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 35666666777777777777766544
No 116
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.66 E-value=57 Score=24.11 Aligned_cols=29 Identities=21% Similarity=0.427 Sum_probs=18.5
Q ss_pred cccccCCCCCCcccccCCcccccccccccccch
Q psy5735 134 RFRCETENCHNVVKVATNTTQFMIKCDKCDQFI 166 (247)
Q Consensus 134 ~~~C~~~~C~~~~~~~~~~~~~~~~C~~C~~~~ 166 (247)
.+.| +.|+..-+.- .....|.|.+|+...
T Consensus 35 ~~~C--p~C~~~~VkR--~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVC--PFCGRTTVKR--IATGIWKCRKCGAKF 63 (89)
T ss_pred CCcC--CCCCCcceee--eccCeEEcCCCCCee
Confidence 4678 7887653211 123579999998754
No 117
>smart00400 ZnF_CHCC zinc finger.
Probab=20.21 E-value=92 Score=20.32 Aligned_cols=17 Identities=18% Similarity=0.217 Sum_probs=11.5
Q ss_pred ccccccccccchhhhhh
Q psy5735 155 FMIKCDKCDQFINIFKG 171 (247)
Q Consensus 155 ~~~~C~~C~~~~~~~~~ 171 (247)
..|.|-.|+.--++-..
T Consensus 22 n~~~Cf~cg~gGd~i~f 38 (55)
T smart00400 22 QFFHCFGCGAGGNVISF 38 (55)
T ss_pred CEEEEeCCCCCCCHHHH
Confidence 46899999866554433
Done!