Query psy4232
Match_columns 130
No_of_seqs 136 out of 415
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 20:12:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4232hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00033 60S ribosomal protein 100.0 5.9E-58 1.3E-62 341.9 12.8 119 1-119 1-123 (125)
2 KOG1722|consensus 100.0 3E-58 6.4E-63 350.6 10.8 127 1-127 1-128 (155)
3 PF01246 Ribosomal_L24e: Ribos 100.0 2.6E-40 5.7E-45 226.5 0.1 71 1-71 1-71 (71)
4 PRK14891 50S ribosomal protein 100.0 6.6E-37 1.4E-41 229.9 5.9 63 1-63 2-64 (131)
5 COG2075 RPL24A Ribosomal prote 100.0 1.1E-35 2.4E-40 201.1 5.3 65 1-65 1-65 (66)
6 cd00472 Ribosomal_L24e_L24 Rib 100.0 2.5E-34 5.3E-39 188.0 4.1 54 1-54 1-54 (54)
7 PRK00807 50S ribosomal protein 100.0 4.9E-30 1.1E-34 166.2 3.7 51 3-53 1-51 (52)
8 KOG1723|consensus 99.9 2.2E-28 4.9E-33 189.7 4.8 91 1-91 1-94 (162)
9 smart00746 TRASH metallochaper 98.7 4.1E-08 9E-13 53.8 4.1 37 6-43 1-38 (39)
10 PF04945 YHS: YHS domain; Int 97.3 0.0003 6.5E-09 43.6 3.1 36 6-42 3-38 (47)
11 PF08394 Arc_trans_TRASH: Arch 97.2 0.00055 1.2E-08 41.9 3.7 36 6-43 1-36 (37)
12 PF06467 zf-FCS: MYM-type Zinc 96.4 0.0011 2.4E-08 39.8 0.5 37 3-40 6-43 (43)
13 PF05573 NosL: NosL; InterPro 95.2 0.014 3.1E-07 44.0 2.4 39 4-42 26-67 (149)
14 PF09889 DUF2116: Uncharacteri 94.9 0.0055 1.2E-07 40.8 -0.5 26 4-41 4-29 (59)
15 COG3350 Uncharacterized conser 94.5 0.061 1.3E-06 35.4 3.7 39 6-46 5-43 (53)
16 PF09943 DUF2175: Uncharacteri 90.8 0.077 1.7E-06 38.9 0.2 29 3-32 2-30 (101)
17 cd01057 AAMH_A Aromatic and Al 87.2 0.66 1.4E-05 41.5 3.5 51 5-57 382-439 (465)
18 COG4314 NosL Predicted lipopro 86.8 0.74 1.6E-05 36.6 3.2 46 4-49 36-85 (176)
19 PF04570 DUF581: Protein of un 80.3 1.7 3.6E-05 28.9 2.4 35 4-41 17-51 (58)
20 COG4068 Uncharacterized protei 76.7 1 2.2E-05 30.6 0.5 23 4-38 9-31 (64)
21 PHA03073 late transcription fa 74.4 1.9 4E-05 33.7 1.5 38 3-41 49-87 (150)
22 PRK09710 lar restriction allev 71.0 3.6 7.7E-05 28.0 2.0 30 3-38 6-35 (64)
23 PF00412 LIM: LIM domain; Int 67.4 6.6 0.00014 23.9 2.6 25 5-34 28-52 (58)
24 COG4847 Uncharacterized protei 67.1 1.8 3.9E-05 31.9 -0.0 23 1-23 4-26 (103)
25 PF15585 Imm46: Immunity prote 65.7 4.1 8.9E-05 31.1 1.7 26 12-37 79-113 (129)
26 PF14353 CpXC: CpXC protein 65.3 7.3 0.00016 28.1 2.9 33 3-35 38-70 (128)
27 TIGR00270 conserved hypothetic 64.9 5.5 0.00012 30.6 2.3 31 6-39 3-33 (154)
28 PRK08359 transcription factor; 62.7 5.8 0.00013 31.4 2.1 30 5-37 8-37 (176)
29 PF08384 NPP: Pro-opiomelanoco 60.1 4.5 9.7E-05 25.8 0.8 11 10-20 31-41 (45)
30 PF06689 zf-C4_ClpX: ClpX C4-t 58.9 5.9 0.00013 24.1 1.2 20 4-24 2-21 (41)
31 smart00132 LIM Zinc-binding do 55.2 10 0.00023 20.7 1.8 25 5-31 1-25 (39)
32 KOG3710|consensus 52.7 11 0.00025 31.9 2.3 23 12-34 148-179 (280)
33 PF07754 DUF1610: Domain of un 52.7 10 0.00022 21.1 1.4 17 6-22 1-18 (24)
34 KOG1549|consensus 52.6 7.6 0.00016 34.9 1.3 29 1-29 232-262 (428)
35 PF12156 ATPase-cat_bd: Putati 45.9 23 0.0005 24.6 2.7 36 5-41 2-37 (88)
36 PF14447 Prok-RING_4: Prokaryo 44.2 12 0.00026 24.8 0.9 14 4-17 40-53 (55)
37 COG2888 Predicted Zn-ribbon RN 44.0 27 0.00058 23.6 2.6 37 3-39 9-47 (61)
38 PRK14890 putative Zn-ribbon RN 41.2 19 0.00041 24.1 1.6 40 1-40 5-46 (59)
39 PF08789 PBCV_basic_adap: PBCV 40.6 16 0.00035 22.7 1.1 18 9-26 7-25 (40)
40 PF01197 Ribosomal_L31: Riboso 40.3 7.6 0.00016 26.2 -0.5 30 1-32 34-63 (69)
41 PF13408 Zn_ribbon_recom: Reco 38.6 22 0.00048 21.6 1.5 28 4-36 6-33 (58)
42 TIGR01922 purO_arch IMP cycloh 37.7 19 0.00042 29.3 1.4 27 13-39 1-30 (199)
43 PRK13446 atpC F0F1 ATP synthas 36.8 35 0.00077 25.3 2.6 25 10-34 32-66 (136)
44 COG1997 RPL43A Ribosomal prote 36.6 17 0.00038 26.2 0.9 29 4-41 36-64 (89)
45 KOG0402|consensus 36.2 12 0.00025 27.1 -0.0 29 4-41 37-65 (92)
46 PRK00420 hypothetical protein; 34.6 23 0.0005 26.3 1.3 30 1-30 21-51 (112)
47 PF06221 zf-C2HC5: Putative zi 33.9 19 0.00042 23.7 0.7 12 4-15 36-47 (57)
48 PF00319 SRF-TF: SRF-type tran 32.8 20 0.00043 22.9 0.6 26 4-33 26-51 (51)
49 PRK14012 cysteine desulfurase; 32.6 21 0.00044 29.9 0.9 24 3-26 197-222 (404)
50 TIGR03550 F420_cofG 7,8-dideme 32.2 21 0.00045 29.8 0.8 21 4-24 16-36 (322)
51 COG3467 Predicted flavin-nucle 32.2 42 0.00092 25.8 2.5 41 7-47 29-69 (166)
52 PF10517 DM13: Electron transf 31.9 41 0.00089 23.7 2.2 26 7-33 2-29 (108)
53 PRK04151 IMP cyclohydrolase; P 31.6 28 0.0006 28.4 1.4 26 13-38 1-29 (197)
54 PF13240 zinc_ribbon_2: zinc-r 31.1 26 0.00056 18.9 0.8 11 6-16 2-12 (23)
55 PRK05342 clpX ATP-dependent pr 30.6 23 0.00049 31.1 0.8 13 2-14 8-20 (412)
56 PRK08445 hypothetical protein; 30.3 29 0.00062 29.6 1.4 20 4-23 54-73 (348)
57 TIGR03666 Rv2061_F420 PPOX cla 30.2 52 0.0011 24.1 2.6 28 20-47 32-59 (132)
58 PF14354 Lar_restr_allev: Rest 30.1 33 0.00072 21.5 1.3 10 3-12 3-12 (61)
59 PF01321 Creatinase_N: Creatin 30.0 31 0.00068 23.4 1.3 35 4-39 24-61 (132)
60 PF03884 DUF329: Domain of unk 29.7 30 0.00065 22.8 1.1 29 5-40 4-32 (57)
61 COG0520 csdA Selenocysteine ly 29.7 27 0.00058 30.4 1.1 24 3-26 215-241 (405)
62 PRK08444 hypothetical protein; 29.0 27 0.0006 29.9 1.0 19 4-22 61-79 (353)
63 PF14777 BBIP10: Cilia BBSome 28.5 40 0.00087 23.0 1.6 23 12-35 10-32 (65)
64 PF13248 zf-ribbon_3: zinc-rib 28.0 31 0.00066 18.8 0.8 13 4-16 3-15 (26)
65 PF11672 DUF3268: Protein of u 28.0 32 0.00069 25.1 1.1 37 3-40 2-41 (102)
66 smart00696 DM9 Repeats found i 27.9 45 0.00098 22.3 1.8 20 12-31 43-62 (71)
67 PF03604 DNA_RNApol_7kD: DNA d 27.4 26 0.00056 20.5 0.4 9 5-13 19-27 (32)
68 cd04867 TGS_YchF_C TGS_YchF_C: 27.0 47 0.001 23.6 1.8 16 17-32 67-82 (83)
69 cd00655 RNAP_Rpb7_N_like RNAP_ 27.0 52 0.0011 22.3 2.0 24 8-31 53-76 (80)
70 COG1996 RPC10 DNA-directed RNA 26.6 24 0.00053 22.7 0.2 9 5-13 26-34 (49)
71 KOG2361|consensus 26.4 47 0.001 28.2 2.0 23 18-40 202-225 (264)
72 PRK06424 transcription factor; 26.3 48 0.001 25.3 1.9 31 6-40 3-33 (144)
73 PRK00398 rpoP DNA-directed RNA 26.0 29 0.00063 21.0 0.5 11 4-14 22-32 (46)
74 PF09416 UPF1_Zn_bind: RNA hel 24.8 55 0.0012 25.6 2.0 29 5-37 2-30 (152)
75 cd06926 RNAP_II_RPB11 RPB11 su 24.4 42 0.00092 23.6 1.2 25 2-26 40-67 (93)
76 PF07826 IMP_cyclohyd: IMP cyc 24.3 53 0.0012 26.7 1.8 26 13-38 1-28 (199)
77 KOG2996|consensus 24.0 49 0.0011 31.7 1.8 46 7-52 612-660 (865)
78 TIGR03831 YgiT_finger YgiT-typ 23.8 1E+02 0.0023 17.6 2.7 28 6-33 1-29 (46)
79 PF03119 DNA_ligase_ZBD: NAD-d 23.7 60 0.0013 18.2 1.5 19 16-34 4-22 (28)
80 COG1060 ThiH Thiamine biosynth 23.7 37 0.00081 29.6 0.9 20 4-23 71-90 (370)
81 TIGR03403 nifS_epsilon cystein 22.7 43 0.00093 27.6 1.1 23 3-25 193-217 (382)
82 PF13395 HNH_4: HNH endonuclea 22.6 38 0.00082 21.2 0.6 12 6-17 1-12 (54)
83 PF07921 Fibritin_C: Fibritin 22.5 59 0.0013 23.5 1.6 14 14-27 73-86 (93)
84 COG3564 Uncharacterized protei 22.4 58 0.0013 24.3 1.6 23 12-34 84-106 (116)
85 PF11811 DUF3331: Domain of un 22.2 40 0.00087 24.5 0.7 15 3-17 54-68 (96)
86 cd07029 RNAP_I_III_AC19 AC19 s 22.1 45 0.00097 23.2 0.9 25 2-26 32-59 (85)
87 PRK12495 hypothetical protein; 21.7 47 0.001 27.6 1.1 21 1-21 40-60 (226)
88 PF13186 SPASM: Iron-sulfur cl 21.5 68 0.0015 19.2 1.6 17 16-32 4-20 (64)
89 COG1104 NifS Cysteine sulfinat 21.5 48 0.001 29.4 1.1 24 2-25 193-218 (386)
90 PF05132 RNA_pol_Rpc4: RNA pol 21.1 66 0.0014 23.6 1.7 23 11-33 62-85 (131)
91 PF15279 SOBP: Sine oculis-bin 21.1 33 0.00071 29.5 0.1 27 17-43 10-38 (306)
92 cd04331 RNAP_E_N RNAP_E_N: Rpo 21.1 96 0.0021 21.1 2.4 26 6-31 51-76 (80)
93 smart00659 RPOLCX RNA polymera 20.8 38 0.00083 20.9 0.3 9 5-13 21-29 (44)
94 COG3114 CcmD Heme exporter pro 20.0 2E+02 0.0044 19.7 3.7 26 88-113 36-62 (67)
No 1
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=100.00 E-value=5.9e-58 Score=341.90 Aligned_cols=119 Identities=33% Similarity=0.618 Sum_probs=117.1
Q ss_pred CceeecccCCCCccCCCcceEEe----ecCceEEEechhHHhhhhcccCCccchhhHHHHHHhcccchHHHHHHhhcccc
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVK----VDGKSFTFINSKCESSFKMRRNPRKVTWTVLYRRKQKKGQEEEATRKRTRRTH 76 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr----~Dgkv~~F~ssKc~~~~~~krnPrki~WT~~yRr~~KK~~~~~~~kkr~rr~~ 76 (130)
|++++|+|||++||||||++||+ +||+||+|||+||+++|++++|||+|.||++||++|+||+++++.++|+++|+
T Consensus 1 Mk~~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~~~~krnPRkl~WT~~yRr~~kK~~~e~~~kkR~~rtv 80 (125)
T PTZ00033 1 MRTIACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYMRKKNPRFLPWTRTYRRINRKTTTDRVQRRRAARTV 80 (125)
T ss_pred CceeEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHHHHCcCCCccchHHHHHHHHhCCcchhHHHHHHhcCCc
Confidence 89999999999999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred chhhhHHHhhHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Q psy4232 77 KFQRAIVGASINDILAKRNVKPEIRKAQREQAIKAAKEQKRAQ 119 (130)
Q Consensus 77 K~~Raivg~sle~I~~kR~qk~e~r~a~r~~a~~~~Ke~kk~~ 119 (130)
+|||+|||+||++|+++|||+|||+.|++++||+++||+++++
T Consensus 81 K~qRaivg~sLe~I~~kR~~k~evr~aar~~a~r~~Ke~~~~~ 123 (125)
T PTZ00033 81 KVQRAIVGADLSYIQEVRAYVQKVDRSAKAKAVRAEKAERKAA 123 (125)
T ss_pred cchHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999998865
No 2
>KOG1722|consensus
Probab=100.00 E-value=3e-58 Score=350.59 Aligned_cols=127 Identities=67% Similarity=1.068 Sum_probs=121.6
Q ss_pred CceeecccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCccchhhHHHHHHhcccchHHHHHHhhccccc-hh
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPRKVTWTVLYRRKQKKGQEEEATRKRTRRTHK-FQ 79 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki~WT~~yRr~~KK~~~~~~~kkr~rr~~K-~~ 79 (130)
|++|+|+||||+||||||++|||.||+||.|+|+||+++|++++|||+|.||++||+.|+||.++|.+++|++++++ ||
T Consensus 1 MKvElCsFSG~KIyPG~G~r~vR~D~Kvf~Fln~Kc~~~f~~rrnPr~l~WTvLyR~khkKg~~ee~~kkrtrrt~k~~q 80 (155)
T KOG1722|consen 1 MKVELCSFSGYKIYPGHGRRFVRGDGKVFRFLNSKCESLFLQRRNPRRLAWTVLYRKKHKKGIQEEAAKKRTRRTVKKFQ 80 (155)
T ss_pred CceeEeeccCceecCCCceeEEecCCeeeeehhhhhHHHHHhccChhhhhHHHHHHHHhhcchhHHHHHHHhhhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999776 99
Q ss_pred hhHHHhhHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q psy4232 80 RAIVGASINDILAKRNVKPEIRKAQREQAIKAAKEQKRAQKEAKKPPP 127 (130)
Q Consensus 80 Raivg~sle~I~~kR~qk~e~r~a~r~~a~~~~Ke~kk~~~~~kk~~~ 127 (130)
|+|||+||++|+++|||+||||+||||||++++||+.++.++++++.+
T Consensus 81 RaI~GasL~~I~~KRn~kpevR~a~Re~alK~aKe~~ka~k~ak~A~K 128 (155)
T KOG1722|consen 81 RAIVGASLDVILEKRNQKPEVRKAAREAALKKAKEKKKATKAAKKAKK 128 (155)
T ss_pred hhhccccHHHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999999999999988877765443
No 3
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=100.00 E-value=2.6e-40 Score=226.53 Aligned_cols=71 Identities=65% Similarity=1.158 Sum_probs=56.9
Q ss_pred CceeecccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCccchhhHHHHHHhcccchHHHHHHh
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPRKVTWTVLYRRKQKKGQEEEATRKR 71 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki~WT~~yRr~~KK~~~~~~~kkr 71 (130)
|++++|+|||++||||||.|||++||++|+|||+||++||++++|||+|.||++||++|||+++++++++|
T Consensus 1 mk~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~~~~krnPrkl~WT~~~Rr~~kK~~~~~~~kkr 71 (71)
T PF01246_consen 1 MKTEKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKLFKLKRNPRKLKWTVAYRRQHKKGQSEEAAKKR 71 (71)
T ss_dssp SSSEE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTTCHHH-----SSSSSSS
T ss_pred CceEEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHHHHccCCcccchhHHHHHHHhCchhhhhHhhcC
Confidence 89999999999999999999999999999999999999999999999999999999999999999988654
No 4
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=100.00 E-value=6.6e-37 Score=229.90 Aligned_cols=63 Identities=32% Similarity=0.707 Sum_probs=61.5
Q ss_pred CceeecccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCccchhhHHHHHHhcccc
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPRKVTWTVLYRRKQKKGQ 63 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki~WT~~yRr~~KK~~ 63 (130)
|++++|+|||++||||||+||||+||+||+||||||++||+++||||+|+||++||+.++|..
T Consensus 2 m~~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT~~yRk~~g~~~ 64 (131)
T PRK14891 2 VETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWTEAGRAEKGPAA 64 (131)
T ss_pred CceeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHHccCCCccchhHHHHHHHcCchh
Confidence 799999999999999999999999999999999999999999999999999999999999974
No 5
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-35 Score=201.05 Aligned_cols=65 Identities=49% Similarity=0.889 Sum_probs=63.0
Q ss_pred CceeecccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCccchhhHHHHHHhcccchH
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPRKVTWTVLYRRKQKKGQEE 65 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki~WT~~yRr~~KK~~~~ 65 (130)
|+++.|+|||.+||||+|+|||++||++|+|||+||+++|.+++|||+|+||..||++++++..+
T Consensus 1 m~~~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k~~~~~rnPRk~~WT~~~~~~~~k~~~~ 65 (66)
T COG2075 1 MKVRVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEKLFKLGRNPRKLKWTKKYRKMHKKEIKE 65 (66)
T ss_pred CceeEecCcCCccCCCceEEEEecCCeEEEEechhHHHHHHccCCCccchhHHHHHHHHHhhhcc
Confidence 78999999999999999999999999999999999999999999999999999999999998764
No 6
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=100.00 E-value=2.5e-34 Score=188.03 Aligned_cols=54 Identities=59% Similarity=1.129 Sum_probs=52.7
Q ss_pred CceeecccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCccchhhHH
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPRKVTWTVL 54 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki~WT~~ 54 (130)
|++++|+|||++||||||+|||++||++|+|||+||+++|++++|||+|+||++
T Consensus 1 m~~~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~~~krnPRkv~WT~~ 54 (54)
T cd00472 1 MKTEKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNFLRKRNPRKLKWTVA 54 (54)
T ss_pred CcEEEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHHHCcCCCCcceeecC
Confidence 899999999999999999999999999999999999999999999999999973
No 7
>PRK00807 50S ribosomal protein L24e; Validated
Probab=99.96 E-value=4.9e-30 Score=166.18 Aligned_cols=51 Identities=45% Similarity=0.864 Sum_probs=49.5
Q ss_pred eeecccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCccchhhH
Q psy4232 3 LGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPRKVTWTV 53 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki~WT~ 53 (130)
+++|+|||++||||||++||++||++|+|||+||+++|++++|||+|+||.
T Consensus 1 ~~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f~~~~nprk~~WT~ 51 (52)
T PRK00807 1 TRTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNYKLGRVPRKLKWTK 51 (52)
T ss_pred CcccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHHHccCCCCcccccc
Confidence 468999999999999999999999999999999999999999999999996
No 8
>KOG1723|consensus
Probab=99.95 E-value=2.2e-28 Score=189.66 Aligned_cols=91 Identities=35% Similarity=0.725 Sum_probs=85.6
Q ss_pred CceeecccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCccchhhHHHHHHhcccchHHHH---HHhhccccc
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPRKVTWTVLYRRKQKKGQEEEAT---RKRTRRTHK 77 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki~WT~~yRr~~KK~~~~~~~---kkr~rr~~K 77 (130)
|+++.|+||+.+||||||.|||+||.++|.||.++|+++|.+++||+++.||.++|++++++...+.+ .++++.+++
T Consensus 1 Mri~kc~fcss~IyPgHgi~Fv~Nd~k~f~Fc~skc~k~f~~k~nPrk~~~tka~rKaagre~~~d~~~e~~~rrn~~~~ 80 (162)
T KOG1723|consen 1 MRIEKCYFCSSPIYPGHGIMFVRNDCKVFRFCKSKCHKNFKQKKNPRKVGWTKAFRKAAGRELVTDSTFEFEKRRNVPRK 80 (162)
T ss_pred CceeeeeeecCcccCCCceEEEecCcchhHHHHhhhhhhhhhhcCCCccchHHHHHHHhhhhHhhhhhHHHHHhcCcchh
Confidence 89999999999999999999999999999999999999999999999999999999999999988877 557788999
Q ss_pred hhhhHHHhhHHHHH
Q psy4232 78 FQRAIVGASINDIL 91 (130)
Q Consensus 78 ~~Raivg~sle~I~ 91 (130)
|+|+.++.|++.++
T Consensus 81 y~r~~~~~Ti~a~k 94 (162)
T KOG1723|consen 81 YDRELINKTIDAMK 94 (162)
T ss_pred hcccchhhHHHHHH
Confidence 99999999986554
No 9
>smart00746 TRASH metallochaperone-like domain.
Probab=98.66 E-value=4.1e-08 Score=53.79 Aligned_cols=37 Identities=51% Similarity=0.978 Sum_probs=33.7
Q ss_pred cccCCCCcc-CCCcceEEeecCceEEEechhHHhhhhcc
Q psy4232 6 CAYSGYKIY-PGHGKTLVKVDGKSFTFINSKCESSFKMR 43 (130)
Q Consensus 6 C~Fsg~~Iy-PG~G~~~Vr~Dgkv~~F~ssKc~~~~~~k 43 (130)
|.+||..|+ |+.+..++ .||++++|||..|...|...
T Consensus 1 c~~C~~~~~~~~~~~~~~-~~g~~~~FCs~~c~~~~~~~ 38 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVV-NDGKVFYFCSSKCLSKFKKK 38 (39)
T ss_pred CCCCCCCccCCCCceEEE-ECCEEEEEeCHHHHHHHHhc
Confidence 899999999 88899888 99999999999999988753
No 10
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=97.27 E-value=0.0003 Score=43.63 Aligned_cols=36 Identities=25% Similarity=0.615 Sum_probs=26.8
Q ss_pred cccCCCCccCCCcceEEeecCceEEEechhHHhhhhc
Q psy4232 6 CAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKM 42 (130)
Q Consensus 6 C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~ 42 (130)
+..||-.| ||.....+.-+|++++|||.-|...|..
T Consensus 3 DPvcg~~v-~~~~~~~~~y~G~~Y~FCS~~C~~~F~~ 38 (47)
T PF04945_consen 3 DPVCGMKV-PGNAAYSVEYNGRTYYFCSEGCKEKFEA 38 (47)
T ss_dssp B-GGG-BE------EEEEETTEEEEESSHHHHHHHHC
T ss_pred CCCCCCEE-ccCccEEEEECCEEEEEcCHHHHHHHHH
Confidence 56799999 9999999999999999999999999864
No 11
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=97.21 E-value=0.00055 Score=41.91 Aligned_cols=36 Identities=33% Similarity=0.644 Sum_probs=30.8
Q ss_pred cccCCCCccCCCcceEEeecCceEEEechhHHhhhhcc
Q psy4232 6 CAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMR 43 (130)
Q Consensus 6 C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~k 43 (130)
|.+||..|. |.+..| +.+|++++||..-|.+-|..+
T Consensus 1 Cd~CG~~I~-~eP~~~-k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVV-KIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred CCccCCccc-CCEEEE-EECCeEEEEECHHHHHHHHhh
Confidence 899999998 777654 559999999999999998765
No 12
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=96.38 E-value=0.0011 Score=39.79 Aligned_cols=37 Identities=30% Similarity=0.410 Sum_probs=26.6
Q ss_pred eeecccCCCCccCCC-cceEEeecCceEEEechhHHhhh
Q psy4232 3 LGLCAYSGYKIYPGH-GKTLVKVDGKSFTFINSKCESSF 40 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~-G~~~Vr~Dgkv~~F~ssKc~~~~ 40 (130)
...|++|+..|+.+. + .-+..||.+..|||.-|...|
T Consensus 6 ~~~C~~C~~~~~~~~~~-~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPTM-IEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp CEE-TTT--EEECCC-----EE-TTTTSCCSSHHHHHHH
T ss_pred CCcCcccCCcccCCCcc-ccccccCcccChhCHHHHhhC
Confidence 457999999999888 5 888999999999999998765
No 13
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=95.23 E-value=0.014 Score=43.99 Aligned_cols=39 Identities=26% Similarity=0.514 Sum_probs=17.3
Q ss_pred eecccCCCCc--cCCC-cceEEeecCceEEEechhHHhhhhc
Q psy4232 4 GLCAYSGYKI--YPGH-GKTLVKVDGKSFTFINSKCESSFKM 42 (130)
Q Consensus 4 ~~C~Fsg~~I--yPG~-G~~~Vr~Dgkv~~F~ssKc~~~~~~ 42 (130)
..|.+||-.| |||. |.++..+.+++++|||-.|.-.|.+
T Consensus 26 ~~C~~CgM~i~d~p~~~aqi~~~~g~~~~~Fdsi~c~~~~~~ 67 (149)
T PF05573_consen 26 DRCPVCGMVISDYPGFAAQIIYKDGEKVYKFDSIGCMFAYLK 67 (149)
T ss_dssp -----------------EEEEETT-SSEEEES-HHHHHHHHT
T ss_pred CccCCCCCEeccCCCccEEEEECCCCEEEEECCHHHHHHHHh
Confidence 5799999999 6885 5555554449999999999877764
No 14
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=94.92 E-value=0.0055 Score=40.84 Aligned_cols=26 Identities=27% Similarity=0.621 Sum_probs=22.5
Q ss_pred eecccCCCCccCCCcceEEeecCceEEEechhHHhhhh
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFK 41 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~ 41 (130)
..|-+||.+|+|. -.|||.+|+..|.
T Consensus 4 kHC~~CG~~Ip~~------------~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKPIPPD------------ESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCcCCcc------------hhhhCHHHHHHHH
Confidence 4699999999994 5799999998876
No 15
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=94.52 E-value=0.061 Score=35.38 Aligned_cols=39 Identities=26% Similarity=0.499 Sum_probs=31.5
Q ss_pred cccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCC
Q psy4232 6 CAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNP 46 (130)
Q Consensus 6 C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnP 46 (130)
-..||..|.+-.-..=.--+|++++|||..|...|. .||
T Consensus 5 DPVcgm~v~~~~a~~k~~Y~GktYYFcse~~~~~F~--~~P 43 (53)
T COG3350 5 DPVCGMKVDNENAEYKSSYGGKTYYFCSEECKEKFK--DNP 43 (53)
T ss_pred cCCcCccccccccceeEEeCCEEEEEeCHHHHHHHH--HCH
Confidence 356888888777777777899999999999988875 455
No 16
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=90.84 E-value=0.077 Score=38.93 Aligned_cols=29 Identities=28% Similarity=0.229 Sum_probs=22.8
Q ss_pred eeecccCCCCccCCCcceEEeecCceEEEe
Q psy4232 3 LGLCAYSGYKIYPGHGKTLVKVDGKSFTFI 32 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ 32 (130)
...|++||.+||-|-...|..+ |-|.|-|
T Consensus 2 kWkC~iCg~~I~~gqlFTF~~k-G~VH~~C 30 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFTKK-GPVHYEC 30 (101)
T ss_pred ceEEEecCCeeeecceEEEecC-CcEeHHH
Confidence 3579999999998888777777 7766544
No 17
>cd01057 AAMH_A Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit A (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds, however, the beta-subunit lacks critical diiron ligands and a C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphtho
Probab=87.17 E-value=0.66 Score=41.50 Aligned_cols=51 Identities=20% Similarity=0.452 Sum_probs=39.1
Q ss_pred ecccCCCCccC----CCcc-eEEeecCceEEEechhHHhhhhcccCCccc--hhhHHHHH
Q psy4232 5 LCAYSGYKIYP----GHGK-TLVKVDGKSFTFINSKCESSFKMRRNPRKV--TWTVLYRR 57 (130)
Q Consensus 5 ~C~Fsg~~IyP----G~G~-~~Vr~Dgkv~~F~ssKc~~~~~~krnPrki--~WT~~yRr 57 (130)
+|..||-+|-| +... .-.--||+.++|||--|+..|.+ +|-+- .|+..-|-
T Consensus 382 ~c~vC~~p~~~~~~~~~~~~~~~ey~G~~y~FCS~~C~~~F~~--ePerY~~~~~~~~~~ 439 (465)
T cd01057 382 LCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSEGCEWIFEQ--EPERYAGHWNPVDRF 439 (465)
T ss_pred CCCCCCCeeccccCcccccceEEEECCEEEEecCHHHHHHHHH--CHHHHhcCCCHHHHH
Confidence 79999999985 4443 44566999999999999999986 78766 45554443
No 18
>COG4314 NosL Predicted lipoprotein involved in nitrous oxide reduction [Energy production and conversion]
Probab=86.81 E-value=0.74 Score=36.63 Aligned_cols=46 Identities=17% Similarity=0.455 Sum_probs=37.2
Q ss_pred eecccCCCCc--cCCC-cceEEeecCceEEEechhHHhhhh-cccCCccc
Q psy4232 4 GLCAYSGYKI--YPGH-GKTLVKVDGKSFTFINSKCESSFK-MRRNPRKV 49 (130)
Q Consensus 4 ~~C~Fsg~~I--yPG~-G~~~Vr~Dgkv~~F~ssKc~~~~~-~krnPrki 49 (130)
..|.|||-.| |||- |.+|..-+-...||||.+--=.|. +=-+|+.|
T Consensus 36 s~g~ycgMnl~ehpGPKgQi~l~g~~qP~wfsst~e~f~~tllPEepk~i 85 (176)
T COG4314 36 SMGHYCGMNLLEHPGPKGQIILNGKPQPIWFSSTREMFGFTLLPEEPKGI 85 (176)
T ss_pred ccccccceeeecCCCCcceEeeCCCCCceeeecHHHHhhHhcCCcCcCce
Confidence 3699999877 7997 999999888899999999766554 66667655
No 19
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=80.34 E-value=1.7 Score=28.89 Aligned_cols=35 Identities=23% Similarity=0.437 Sum_probs=28.2
Q ss_pred eecccCCCCccCCCcceEEeecCceEEEechhHHhhhh
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFK 41 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~ 41 (130)
..|++|..+|-||..+-.-|-|. -|||.-|+...+
T Consensus 17 ~~C~~C~k~L~~~~DiymYrGd~---aFCS~ECR~~qi 51 (58)
T PF04570_consen 17 SFCYLCKKKLDPGKDIYMYRGDK---AFCSEECRSQQI 51 (58)
T ss_pred HHHHccCCCCCCCCCeeeecccc---ccccHHHHHHHH
Confidence 46999999999999876666664 499999987643
No 20
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=76.69 E-value=1 Score=30.59 Aligned_cols=23 Identities=22% Similarity=0.479 Sum_probs=19.9
Q ss_pred eecccCCCCccCCCcceEEeecCceEEEechhHHh
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCES 38 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~ 38 (130)
..|..||..|+||. .|||-+|..
T Consensus 9 ~HC~VCg~aIp~de------------~~CSe~C~e 31 (64)
T COG4068 9 RHCVVCGKAIPPDE------------QVCSEECGE 31 (64)
T ss_pred ccccccCCcCCCcc------------chHHHHHHH
Confidence 46999999999985 689999984
No 21
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=74.43 E-value=1.9 Score=33.73 Aligned_cols=38 Identities=16% Similarity=0.264 Sum_probs=29.3
Q ss_pred eeecccCCCCccCCCcceEEeecC-ceEEEechhHHhhhh
Q psy4232 3 LGLCAYSGYKIYPGHGKTLVKVDG-KSFTFINSKCESSFK 41 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~G~~~Vr~Dg-kv~~F~ssKc~~~~~ 41 (130)
...|+||+..+-+-. ...=..+| .+=.|||.=|+-.|-
T Consensus 49 ~~~CwfC~q~~~~~~-~~iETl~g~~vg~FCS~ICRDSfa 87 (150)
T PHA03073 49 NDYCWFCKQDLIIAP-LFIETLKGGAVGYFCSKICRDSFA 87 (150)
T ss_pred CCcEEeeccccccCc-eEEEeecCchhhhHhHHHHHHHHH
Confidence 457999999987766 33334466 899999999998885
No 22
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=70.96 E-value=3.6 Score=28.02 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=24.2
Q ss_pred eeecccCCCCccCCCcceEEeecCceEEEechhHHh
Q psy4232 3 LGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCES 38 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~ 38 (130)
+..|.|||..+ ..|+.+|-.|+|+..+|..
T Consensus 6 lKPCPFCG~~~------~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 6 VKPCPFCGCPS------VTVKAISGYYRAKCNGCES 35 (64)
T ss_pred ccCCCCCCCce------eEEEecCceEEEEcCCCCc
Confidence 56799998875 4677778888898889976
No 23
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=67.39 E-value=6.6 Score=23.91 Aligned_cols=25 Identities=24% Similarity=0.539 Sum_probs=17.9
Q ss_pred ecccCCCCccCCCcceEEeecCceEEEech
Q psy4232 5 LCAYSGYKIYPGHGKTLVKVDGKSFTFINS 34 (130)
Q Consensus 5 ~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ss 34 (130)
.|+-|+..|.++. |.-.||+ .||..
T Consensus 28 ~C~~C~~~l~~~~---~~~~~~~--~~C~~ 52 (58)
T PF00412_consen 28 KCSKCGKPLNDGD---FYEKDGK--PYCKD 52 (58)
T ss_dssp BETTTTCBTTTSS---EEEETTE--EEEHH
T ss_pred ccCCCCCccCCCe---eEeECCE--EECHH
Confidence 5888999998777 7777774 44443
No 24
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=67.13 E-value=1.8 Score=31.87 Aligned_cols=23 Identities=30% Similarity=0.320 Sum_probs=16.9
Q ss_pred CceeecccCCCCccCCCcceEEe
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVK 23 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr 23 (130)
|+...|+.||..|--|.-..|..
T Consensus 4 lkewkC~VCg~~iieGqkFTF~~ 26 (103)
T COG4847 4 LKEWKCYVCGGTIIEGQKFTFTK 26 (103)
T ss_pred cceeeEeeeCCEeeeccEEEEee
Confidence 67889999999997654444444
No 25
>PF15585 Imm46: Immunity protein 46
Probab=65.72 E-value=4.1 Score=31.12 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=21.2
Q ss_pred CccCCC-cceEEeecC--------ceEEEechhHH
Q psy4232 12 KIYPGH-GKTLVKVDG--------KSFTFINSKCE 37 (130)
Q Consensus 12 ~IyPG~-G~~~Vr~Dg--------kv~~F~ssKc~ 37 (130)
.|-||+ |.+|||.|- +||.++..+|.
T Consensus 79 e~aPGSYGlLy~rDDEd~~~~neFrV~vl~RG~~t 113 (129)
T PF15585_consen 79 EIAPGSYGLLYIRDDEDPEHFNEFRVFVLARGELT 113 (129)
T ss_pred HhCCCceeEEEEecCCCCCCCCceEEEEEEccEEe
Confidence 467887 999999876 78888888874
No 26
>PF14353 CpXC: CpXC protein
Probab=65.31 E-value=7.3 Score=28.10 Aligned_cols=33 Identities=12% Similarity=0.000 Sum_probs=29.7
Q ss_pred eeecccCCCCccCCCcceEEeecCceEEEechh
Q psy4232 3 LGLCAYSGYKIYPGHGKTLVKVDGKSFTFINSK 35 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssK 35 (130)
.-+|..||..++..+..+|+..+.+.+.|....
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 357999999999999999999999988887766
No 27
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=64.87 E-value=5.5 Score=30.64 Aligned_cols=31 Identities=29% Similarity=0.617 Sum_probs=25.8
Q ss_pred cccCCCCccCCCcceEEeecCceEEEechhHHhh
Q psy4232 6 CAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESS 39 (130)
Q Consensus 6 C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~ 39 (130)
|--||..|. |.| .-|.-||..+..|.+ |.++
T Consensus 3 CEiCG~~i~-~~~-~~v~iega~l~vC~~-C~k~ 33 (154)
T TIGR00270 3 CEICGRKIK-GKG-FKIVIEGSEMTVCGE-CRKF 33 (154)
T ss_pred cccCCCccC-CCC-eEEEEcCeEEehhhh-HHhc
Confidence 999999996 665 789999999999976 5543
No 28
>PRK08359 transcription factor; Validated
Probab=62.68 E-value=5.8 Score=31.44 Aligned_cols=30 Identities=23% Similarity=0.631 Sum_probs=25.4
Q ss_pred ecccCCCCccCCCcceEEeecCceEEEechhHH
Q psy4232 5 LCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCE 37 (130)
Q Consensus 5 ~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~ 37 (130)
.|--||..|. |.| ..|.-||..+.-|++ |.
T Consensus 8 ~CEiCG~~i~-g~~-~~v~ieGael~VC~~-Ca 37 (176)
T PRK08359 8 YCEICGAEIR-GPG-HRIRIEGAELLVCDR-CY 37 (176)
T ss_pred eeecCCCccC-CCC-eEEEEcCeEEehHHH-HH
Confidence 4999999995 665 789999999999976 55
No 29
>PF08384 NPP: Pro-opiomelanocortin, N-terminal region; InterPro: IPR013593 This domain represents the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity [].
Probab=60.10 E-value=4.5 Score=25.81 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=9.5
Q ss_pred CCCccCCCcce
Q psy4232 10 GYKIYPGHGKT 20 (130)
Q Consensus 10 g~~IyPG~G~~ 20 (130)
+.+||||+|.+
T Consensus 31 EsPv~PGn~hl 41 (45)
T PF08384_consen 31 ESPVFPGNGHL 41 (45)
T ss_pred CCCccCCCccc
Confidence 68999999965
No 30
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=58.88 E-value=5.9 Score=24.05 Aligned_cols=20 Identities=15% Similarity=0.288 Sum_probs=9.5
Q ss_pred eecccCCCCccCCCcceEEee
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKV 24 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~ 24 (130)
..|||||.+-... +.|+.-.
T Consensus 2 ~~CSFCgr~~~~v-~~li~g~ 21 (41)
T PF06689_consen 2 KRCSFCGRPESEV-GRLISGP 21 (41)
T ss_dssp -B-TTT--BTTTS-SSEEEES
T ss_pred CCccCCCCCHHHH-hceecCC
Confidence 4699999987654 3443333
No 31
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=55.16 E-value=10 Score=20.74 Aligned_cols=25 Identities=28% Similarity=0.396 Sum_probs=18.9
Q ss_pred ecccCCCCccCCCcceEEeecCceEEE
Q psy4232 5 LCAYSGYKIYPGHGKTLVKVDGKSFTF 31 (130)
Q Consensus 5 ~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F 31 (130)
.|.-|+..|+|+ ..++..+|..|..
T Consensus 1 ~C~~C~~~i~~~--~~~~~~~~~~~H~ 25 (39)
T smart00132 1 KCAGCGKPIRGG--ELVLRALGKVWHP 25 (39)
T ss_pred CccccCCcccCC--cEEEEeCCccccc
Confidence 488899999998 5566677776653
No 32
>KOG3710|consensus
Probab=52.71 E-value=11 Score=31.87 Aligned_cols=23 Identities=35% Similarity=0.819 Sum_probs=17.7
Q ss_pred CccCCCcceEEee------cCceE---EEech
Q psy4232 12 KIYPGHGKTLVKV------DGKSF---TFINS 34 (130)
Q Consensus 12 ~IyPG~G~~~Vr~------Dgkv~---~F~ss 34 (130)
.+|||.|.-|||. ||+.+ |+||.
T Consensus 148 AcYPGNGtgYVrHVDNP~gDGRcITcIYYlNq 179 (280)
T KOG3710|consen 148 ACYPGNGTGYVRHVDNPHGDGRCITCIYYLNQ 179 (280)
T ss_pred EEecCCCceeeEeccCCCCCceEEEEEEEccc
Confidence 4799999999996 88754 55553
No 33
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=52.69 E-value=10 Score=21.14 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=14.3
Q ss_pred cccCCCCccCCC-cceEE
Q psy4232 6 CAYSGYKIYPGH-GKTLV 22 (130)
Q Consensus 6 C~Fsg~~IyPG~-G~~~V 22 (130)
|+-||..|.|.. |..|.
T Consensus 1 C~sC~~~i~~r~~~v~f~ 18 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFP 18 (24)
T ss_pred CccCCCcccCcccCceEe
Confidence 788999999977 87775
No 34
>KOG1549|consensus
Probab=52.61 E-value=7.6 Score=34.86 Aligned_cols=29 Identities=28% Similarity=0.468 Sum_probs=23.8
Q ss_pred CceeecccCCCCcc--CCCcceEEeecCceE
Q psy4232 1 MKLGLCAYSGYKIY--PGHGKTLVKVDGKSF 29 (130)
Q Consensus 1 mk~~~C~Fsg~~Iy--PG~G~~~Vr~Dgkv~ 29 (130)
|.++.|++|+++|| ||-|-+|||.|..-.
T Consensus 232 ln~D~~s~s~HK~ygp~~iGaLYvr~~~~~~ 262 (428)
T KOG1549|consen 232 LNADFLSISAHKIYGPPGIGALYVRRKRPRL 262 (428)
T ss_pred cCchheeeecccccCCCcceEEEEccCCCcc
Confidence 56788999999997 778999999855543
No 35
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=45.92 E-value=23 Score=24.61 Aligned_cols=36 Identities=25% Similarity=0.540 Sum_probs=29.9
Q ss_pred ecccCCCCccCCCcceEEeecCceEEEechhHHhhhh
Q psy4232 5 LCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFK 41 (130)
Q Consensus 5 ~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~ 41 (130)
.|+-||.+|++|. .+-+..||....||=.=|..-+.
T Consensus 2 ~C~HCg~~~p~~~-~~~~~~~g~~~~FCC~GC~~V~~ 37 (88)
T PF12156_consen 2 KCYHCGLPVPEGA-KITVEIDGEERPFCCPGCQAVYQ 37 (88)
T ss_pred CCCCCCCCCCCCC-CeeeeeCCCccccccHHHHHHHH
Confidence 5999999997555 56677899999999999988654
No 36
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=44.18 E-value=12 Score=24.77 Aligned_cols=14 Identities=14% Similarity=0.290 Sum_probs=11.4
Q ss_pred eecccCCCCccCCC
Q psy4232 4 GLCAYSGYKIYPGH 17 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~ 17 (130)
.-|.|||.+|.+|.
T Consensus 40 ngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 40 NGCPFCGTPFEFDD 53 (55)
T ss_pred cCCCCCCCcccCCC
Confidence 34999999999874
No 37
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=43.98 E-value=27 Score=23.61 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=28.1
Q ss_pred eeecccCCCCccCCCc-ceEE-eecCceEEEechhHHhh
Q psy4232 3 LGLCAYSGYKIYPGHG-KTLV-KVDGKSFTFINSKCESS 39 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~G-~~~V-r~Dgkv~~F~ssKc~~~ 39 (130)
...|+-||..|.||.+ ..|. -|=|.+...=..+|+++
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~ 47 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKL 47 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHc
Confidence 4689999999999974 4443 45577888878888775
No 38
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=41.25 E-value=19 Score=24.15 Aligned_cols=40 Identities=20% Similarity=0.392 Sum_probs=28.4
Q ss_pred CceeecccCCCCccCCC-cceEEeec-CceEEEechhHHhhh
Q psy4232 1 MKLGLCAYSGYKIYPGH-GKTLVKVD-GKSFTFINSKCESSF 40 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~-G~~~Vr~D-gkv~~F~ssKc~~~~ 40 (130)
|....|+-||..|.|+- |..|.=-| |.+...=-.+|+++.
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 45668999999999876 77775443 666455566777654
No 39
>PF08789 PBCV_basic_adap: PBCV-specific basic adaptor domain; InterPro: IPR014897 The small PBCV-specific basic adaptor protein is found fused to S/T protein kinases and the 2-Cysteine domain [].
Probab=40.56 E-value=16 Score=22.69 Aligned_cols=18 Identities=50% Similarity=0.804 Sum_probs=15.6
Q ss_pred CCCCccCC-CcceEEeecC
Q psy4232 9 SGYKIYPG-HGKTLVKVDG 26 (130)
Q Consensus 9 sg~~IyPG-~G~~~Vr~Dg 26 (130)
-|..||-| .|..||..|+
T Consensus 7 kgR~i~~g~rGg~yV~~~~ 25 (40)
T PF08789_consen 7 KGRKIFKGPRGGTYVISDG 25 (40)
T ss_pred cCCEEEECCCCCEEEeCCC
Confidence 37889999 5999999996
No 40
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=40.29 E-value=7.6 Score=26.17 Aligned_cols=30 Identities=27% Similarity=0.551 Sum_probs=22.6
Q ss_pred CceeecccCCCCccCCCcceEEeecCceEEEe
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTLVKVDGKSFTFI 32 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ 32 (130)
|.+++||-| .+.|=|...+ |..+|+|=.|-
T Consensus 34 ~~vdi~s~~-HPfytG~~~~-~~~~Grv~KF~ 63 (69)
T PF01197_consen 34 IKVDICSNC-HPFYTGKQKV-VDTAGRVEKFN 63 (69)
T ss_dssp EEECSCSSS-SCTTCSCSSC-SCCCCCCTSCC
T ss_pred EEEeecCCC-CEEEcCcEEE-EccccCHHHHH
Confidence 467889888 7889896554 88888876553
No 41
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=38.63 E-value=22 Score=21.57 Aligned_cols=28 Identities=11% Similarity=0.072 Sum_probs=19.3
Q ss_pred eecccCCCCccCCCcceEEeecCceEEEechhH
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKC 36 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc 36 (130)
-.|..||..... ..++.+..+|.|++.-
T Consensus 6 l~C~~CG~~m~~-----~~~~~~~~yy~C~~~~ 33 (58)
T PF13408_consen 6 LRCGHCGSKMTR-----RKRKGKYRYYRCSNRR 33 (58)
T ss_pred EEcccCCcEeEE-----EECCCCceEEEcCCCc
Confidence 469999988775 2233556888888763
No 42
>TIGR01922 purO_arch IMP cyclohydrolase. This model represents IMP cyclohydrolase, the final step in the biosynthesis of inosine monophosphate (IMP) in archaea. In bacteria this step is catalyzed by a bifunctional enzyme (purH).
Probab=37.73 E-value=19 Score=29.33 Aligned_cols=27 Identities=22% Similarity=0.281 Sum_probs=22.5
Q ss_pred ccCCCcceEEee-cCc--eEEEechhHHhh
Q psy4232 13 IYPGHGKTLVKV-DGK--SFTFINSKCESS 39 (130)
Q Consensus 13 IyPG~G~~~Vr~-Dgk--v~~F~ssKc~~~ 39 (130)
+|||+|...=+. ||+ +.||++|.++-+
T Consensus 1 MY~GR~ivvG~s~dG~~~~aY~V~sRSfpn 30 (199)
T TIGR01922 1 MYIGRFLVVGKLEDGTPFAAYRVSSRSFPN 30 (199)
T ss_pred CCCCCEEEEccCCCCCeEEEEEEecCCCCC
Confidence 599999999887 997 778998887655
No 43
>PRK13446 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=36.81 E-value=35 Score=25.29 Aligned_cols=25 Identities=32% Similarity=0.715 Sum_probs=15.4
Q ss_pred CCCccCCC---------cceEEeecCce-EEEech
Q psy4232 10 GYKIYPGH---------GKTLVKVDGKS-FTFINS 34 (130)
Q Consensus 10 g~~IyPG~---------G~~~Vr~Dgkv-~~F~ss 34 (130)
++-|.||| |.+.|+.||.. ++|+++
T Consensus 32 ~~gILp~H~p~it~L~~G~l~i~~~~~~~~~~v~g 66 (136)
T PRK13446 32 EFGVLPGHAPFLTALKIGELTYKKGGKTHYVAVNG 66 (136)
T ss_pred CeEEcCCCcceEEEeeccEEEEEeCCcEEEEEEcC
Confidence 35689998 56666666663 344443
No 44
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=36.56 E-value=17 Score=26.19 Aligned_cols=29 Identities=24% Similarity=0.445 Sum_probs=23.1
Q ss_pred eecccCCCCccCCCcceEEeecCceEEEechhHHhhhh
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFK 41 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~ 41 (130)
..|.|||.+. |++-+.-+|-|+ ||..-|.
T Consensus 36 ~~Cp~C~~~~--------VkR~a~GIW~C~-kCg~~fA 64 (89)
T COG1997 36 HVCPFCGRTT--------VKRIATGIWKCR-KCGAKFA 64 (89)
T ss_pred CcCCCCCCcc--------eeeeccCeEEcC-CCCCeec
Confidence 5699998763 788888899998 8877665
No 45
>KOG0402|consensus
Probab=36.22 E-value=12 Score=27.09 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=19.1
Q ss_pred eecccCCCCccCCCcceEEeecCceEEEechhHHhhhh
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFK 41 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~ 41 (130)
.+|+|||.. -|.+.---+|-|+ .|.+-+-
T Consensus 37 y~CsfCGK~--------~vKR~AvGiW~C~-~C~kv~a 65 (92)
T KOG0402|consen 37 YTCSFCGKK--------TVKRKAVGIWKCG-SCKKVVA 65 (92)
T ss_pred hhhhhcchh--------hhhhhceeEEecC-Cccceec
Confidence 579999864 3555556677777 6666543
No 46
>PRK00420 hypothetical protein; Validated
Probab=34.63 E-value=23 Score=26.27 Aligned_cols=30 Identities=23% Similarity=0.520 Sum_probs=20.8
Q ss_pred CceeecccCCCCccC-CCcceEEeecCceEE
Q psy4232 1 MKLGLCAYSGYKIYP-GHGKTLVKVDGKSFT 30 (130)
Q Consensus 1 mk~~~C~Fsg~~IyP-G~G~~~Vr~Dgkv~~ 30 (130)
|-.+.|..||+++.- =+|..|--+=|.++.
T Consensus 21 ml~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 21 MLSKHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred HccCCCCCCCCcceecCCCceECCCCCCeee
Confidence 345789999999885 456777666666433
No 47
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=33.92 E-value=19 Score=23.73 Aligned_cols=12 Identities=25% Similarity=0.794 Sum_probs=10.1
Q ss_pred eecccCCCCccC
Q psy4232 4 GLCAYSGYKIYP 15 (130)
Q Consensus 4 ~~C~Fsg~~IyP 15 (130)
..|.|||.++++
T Consensus 36 ~pC~fCg~~l~~ 47 (57)
T PF06221_consen 36 GPCPFCGTPLLS 47 (57)
T ss_pred CcCCCCCCcccC
Confidence 579999998875
No 48
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=32.79 E-value=20 Score=22.94 Aligned_cols=26 Identities=27% Similarity=0.433 Sum_probs=18.5
Q ss_pred eecccCCCCccCCCcceEEeecCceEEEec
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKVDGKSFTFIN 33 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~s 33 (130)
|+|..||-.|. .+....||+++.|+|
T Consensus 26 ELs~LC~~~v~----~iv~~~~g~~~~f~s 51 (51)
T PF00319_consen 26 ELSTLCGVDVA----LIVFSPDGKLYTFPS 51 (51)
T ss_dssp HHHHHHT-EEE----EEEEETTSEEEEEES
T ss_pred eeeeecCCeEE----EEEECCCCCEEEecC
Confidence 56677777775 455667899999986
No 49
>PRK14012 cysteine desulfurase; Provisional
Probab=32.59 E-value=21 Score=29.90 Aligned_cols=24 Identities=38% Similarity=0.647 Sum_probs=18.9
Q ss_pred eeecccCCCCcc-C-CCcceEEeecC
Q psy4232 3 LGLCAYSGYKIY-P-GHGKTLVKVDG 26 (130)
Q Consensus 3 ~~~C~Fsg~~Iy-P-G~G~~~Vr~Dg 26 (130)
.+.++||+++++ | |-|-+||++|-
T Consensus 197 ~D~~~~s~~K~~gp~g~G~l~~~~~~ 222 (404)
T PRK14012 197 VDLMSFSAHKIYGPKGIGALYVRRKP 222 (404)
T ss_pred CCEEEEehhhccCCCceEEEEEecCC
Confidence 456789999988 5 45899999873
No 50
>TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit. This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria.
Probab=32.18 E-value=21 Score=29.77 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=16.5
Q ss_pred eecccCCCCccCCCcceEEee
Q psy4232 4 GLCAYSGYKIYPGHGKTLVKV 24 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~ 24 (130)
..|.||++...||.-..|.+.
T Consensus 16 ~~C~fCaf~~~~g~~~~~~l~ 36 (322)
T TIGR03550 16 NRCGYCTFRRPPGELEAALLS 36 (322)
T ss_pred CCCccCCccccCCCcccccCC
Confidence 569999999999986656543
No 51
>COG3467 Predicted flavin-nucleotide-binding protein [General function prediction only]
Probab=32.16 E-value=42 Score=25.84 Aligned_cols=41 Identities=15% Similarity=0.031 Sum_probs=30.6
Q ss_pred ccCCCCccCCCcceEEeecCceEEEechhHHhhhhcccCCc
Q psy4232 7 AYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSFKMRRNPR 47 (130)
Q Consensus 7 ~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~~~krnPr 47 (130)
+|++...+=.....|+..+|..++|.+..-++.-.++.||.
T Consensus 29 a~~~~~~PyivP~~y~~~~~~lY~h~~~~grk~~~l~~~p~ 69 (166)
T COG3467 29 AFAGDGQPYVVPLNYGYEGGHLYFHGSPEGRKIELLRKNPL 69 (166)
T ss_pred EEcCCCCcEEEEeEeEEeCCeEEEEeCCcchhhHHhhcCCc
Confidence 56655554467899999999966666665788888888885
No 52
>PF10517 DM13: Electron transfer DM13; InterPro: IPR019545 This domain of unknown function is present in proteins of Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. In some proteins it is found in either one or two copies, N-terminal to the DOMON domain. Proteins with the DM13 and DOMON domains include Skeletor, which is part of a macromolecular complex that forms the spindle matrix []. The DM13 domain is also a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins []. It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme [].
Probab=31.92 E-value=41 Score=23.66 Aligned_cols=26 Identities=35% Similarity=0.502 Sum_probs=17.8
Q ss_pred ccCC--CCccCCCcceEEeecCceEEEec
Q psy4232 7 AYSG--YKIYPGHGKTLVKVDGKSFTFIN 33 (130)
Q Consensus 7 ~Fsg--~~IyPG~G~~~Vr~Dgkv~~F~s 33 (130)
+|+| ..-|+.+|..+| .|++.+...+
T Consensus 2 ~F~~~~~~~h~vsG~v~i-~d~~t~~i~~ 29 (108)
T PF10517_consen 2 TFSGQLSGGHGVSGTVTI-VDGKTFLIFN 29 (108)
T ss_pred eeEcccCCCceeeEEEEE-eCCCeEEEec
Confidence 4776 556999999999 5555554443
No 53
>PRK04151 IMP cyclohydrolase; Provisional
Probab=31.59 E-value=28 Score=28.36 Aligned_cols=26 Identities=23% Similarity=0.281 Sum_probs=21.4
Q ss_pred ccCCCcceEEee-cCc--eEEEechhHHh
Q psy4232 13 IYPGHGKTLVKV-DGK--SFTFINSKCES 38 (130)
Q Consensus 13 IyPG~G~~~Vr~-Dgk--v~~F~ssKc~~ 38 (130)
.|||+|.+-=+. ||+ +.||++|.++-
T Consensus 1 MY~GR~ivvG~s~dG~~~~aY~V~sRSfp 29 (197)
T PRK04151 1 MYVGRFLVVGKTEEGKPFAAYRVSSRSFP 29 (197)
T ss_pred CCCCCEEEEccCCCCCeEEEEEEecCCCC
Confidence 599999988776 598 77999998765
No 54
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=31.08 E-value=26 Score=18.86 Aligned_cols=11 Identities=27% Similarity=0.510 Sum_probs=9.2
Q ss_pred cccCCCCccCC
Q psy4232 6 CAYSGYKIYPG 16 (130)
Q Consensus 6 C~Fsg~~IyPG 16 (130)
|..||..|.++
T Consensus 2 Cp~CG~~~~~~ 12 (23)
T PF13240_consen 2 CPNCGAEIEDD 12 (23)
T ss_pred CcccCCCCCCc
Confidence 88899999875
No 55
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=30.57 E-value=23 Score=31.14 Aligned_cols=13 Identities=31% Similarity=0.542 Sum_probs=9.7
Q ss_pred ceeecccCCCCcc
Q psy4232 2 KLGLCAYSGYKIY 14 (130)
Q Consensus 2 k~~~C~Fsg~~Iy 14 (130)
....|||||.+=.
T Consensus 8 ~~~~CSFCGr~~~ 20 (412)
T PRK05342 8 KLLYCSFCGKSQH 20 (412)
T ss_pred CccccCCCCCChh
Confidence 4567999998633
No 56
>PRK08445 hypothetical protein; Provisional
Probab=30.27 E-value=29 Score=29.57 Aligned_cols=20 Identities=5% Similarity=0.120 Sum_probs=16.5
Q ss_pred eecccCCCCccCCCcceEEe
Q psy4232 4 GLCAYSGYKIYPGHGKTLVK 23 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr 23 (130)
+.|.||++.-.|+++..|+.
T Consensus 54 ~~C~FCa~~~~~~~~~~y~l 73 (348)
T PRK08445 54 VDCKFCAFYRHLKEDDAYIL 73 (348)
T ss_pred cCCccCCCccCCCCCCCeeC
Confidence 57999999999888877743
No 57
>TIGR03666 Rv2061_F420 PPOX class probable F420-dependent enzyme, Rv2061 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN.
Probab=30.24 E-value=52 Score=24.10 Aligned_cols=28 Identities=18% Similarity=0.118 Sum_probs=22.1
Q ss_pred eEEeecCceEEEechhHHhhhhcccCCc
Q psy4232 20 TLVKVDGKSFTFINSKCESSFKMRRNPR 47 (130)
Q Consensus 20 ~~Vr~Dgkv~~F~ssKc~~~~~~krnPr 47 (130)
.|+.-||.++++++..-.+.-..+.||+
T Consensus 32 ~~~~d~g~l~f~t~~~~~K~~nl~~np~ 59 (132)
T TIGR03666 32 WAAVDGDKLLVRTKEDSWKVKRIRNNPR 59 (132)
T ss_pred EEEEECCEEEEEECCcCHHHHHHHhCCC
Confidence 4666688888778777778888899997
No 58
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.10 E-value=33 Score=21.48 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=7.4
Q ss_pred eeecccCCCC
Q psy4232 3 LGLCAYSGYK 12 (130)
Q Consensus 3 ~~~C~Fsg~~ 12 (130)
+..|.|||..
T Consensus 3 LkPCPFCG~~ 12 (61)
T PF14354_consen 3 LKPCPFCGSA 12 (61)
T ss_pred CcCCCCCCCc
Confidence 4579999754
No 59
>PF01321 Creatinase_N: Creatinase/Prolidase N-terminal domain; InterPro: IPR000587 Creatinase or creatine amidinohydrolase (3.5.3.3 from EC) catalyses the conversion of creatine and water to sarcosine and urea. The enzyme works as a homodimer, and is induced by choline chloride. Each monomer of creatinase has two clearly defined domains, a small N-terminal domain, and a large C-terminal domain. The structure of the C-terminal region represents the "pita-bread" fold. The fold contains both alpha helices and an anti-parallel beta sheet within two structurally similar domains that are thought to be derived from an ancient gene duplication. The active site, where conserved, is located between the two domains. The fold is common to methionine aminopeptidase (3.4.11.18 from EC), aminopeptidase P (3.4.11.9 from EC), prolidase (3.4.13.9 from EC), agropine synthase and creatinase (3.5.3.3 from EC). Though many of these peptidases require a divalent cation, creatinase is not a metal-dependent enzyme [, , ]. ; GO: 0016787 hydrolase activity; PDB: 1PV9_A 3CTZ_A 3IL0_B 3PN9_A 2HOW_A 1WN1_B 3I7M_A 1CHM_B 3QOC_D 1KP0_B ....
Probab=29.98 E-value=31 Score=23.41 Aligned_cols=35 Identities=23% Similarity=0.522 Sum_probs=22.6
Q ss_pred eecccCCCCccCCCcceEE--eecCceEEEec-hhHHhh
Q psy4232 4 GLCAYSGYKIYPGHGKTLV--KVDGKSFTFIN-SKCESS 39 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~V--r~Dgkv~~F~s-sKc~~~ 39 (130)
...+|||+...||.+-.++ ..||. ++|++ .-....
T Consensus 24 ni~YltG~~~~~~~~~~~l~i~~~~~-~l~~~~~~~~~~ 61 (132)
T PF01321_consen 24 NIRYLTGFRWQPGERPVLLVITADGA-VLFVPKGEYERA 61 (132)
T ss_dssp HHHHHHS--ST-TSSEEEEEEESSSE-EEEEEGGGHHHH
T ss_pred hceEecCCCcCCCcceEEEEecccCc-EEEeccccHHHH
Confidence 3568999988888866655 88999 77777 555444
No 60
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=29.73 E-value=30 Score=22.83 Aligned_cols=29 Identities=14% Similarity=0.212 Sum_probs=15.0
Q ss_pred ecccCCCCccCCCcceEEeecCceEEEechhHHhhh
Q psy4232 5 LCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSF 40 (130)
Q Consensus 5 ~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~ 40 (130)
.|.-||..+.+.. +...+=|||..|...=
T Consensus 4 ~CP~C~k~~~~~~-------~n~~rPFCS~RCk~iD 32 (57)
T PF03884_consen 4 KCPICGKPVEWSP-------ENPFRPFCSERCKLID 32 (57)
T ss_dssp E-TTT--EEE-SS-------SSS--SSSSHHHHHHH
T ss_pred cCCCCCCeecccC-------CCCcCCcccHhhcccC
Confidence 5777777666532 2233449999998653
No 61
>COG0520 csdA Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]
Probab=29.69 E-value=27 Score=30.45 Aligned_cols=24 Identities=33% Similarity=0.521 Sum_probs=19.0
Q ss_pred eeecccCCCC-cc-C-CCcceEEeecC
Q psy4232 3 LGLCAYSGYK-IY-P-GHGKTLVKVDG 26 (130)
Q Consensus 3 ~~~C~Fsg~~-Iy-P-G~G~~~Vr~Dg 26 (130)
.+-+.|||++ +| | |-|.+||+.|.
T Consensus 215 ~Df~afsgHKwl~gP~GiGvLy~r~~~ 241 (405)
T COG0520 215 CDFLAFSGHKWLLGPTGIGVLYVRKEL 241 (405)
T ss_pred CCEEEEcccccccCCCceEEEEEchHH
Confidence 3456899999 54 6 88999999983
No 62
>PRK08444 hypothetical protein; Provisional
Probab=28.98 E-value=27 Score=29.94 Aligned_cols=19 Identities=5% Similarity=0.342 Sum_probs=15.7
Q ss_pred eecccCCCCccCCCcceEE
Q psy4232 4 GLCAYSGYKIYPGHGKTLV 22 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~V 22 (130)
+.|.||++...++++..|.
T Consensus 61 ~~C~FCaf~~~~~~~~~y~ 79 (353)
T PRK08444 61 DVCKFCAFSAHRKNPNPYT 79 (353)
T ss_pred cCCccCCCccCCCCCcccc
Confidence 5799999999999876564
No 63
>PF14777 BBIP10: Cilia BBSome complex subunit 10
Probab=28.50 E-value=40 Score=23.01 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=19.9
Q ss_pred CccCCCcceEEeecCceEEEechh
Q psy4232 12 KIYPGHGKTLVKVDGKSFTFINSK 35 (130)
Q Consensus 12 ~IyPG~G~~~Vr~Dgkv~~F~ssK 35 (130)
.|-|-.|.+|.. |-..+.||..|
T Consensus 10 eVlPk~G~l~~E-~~~~~vlCKPK 32 (65)
T PF14777_consen 10 EVLPKQGLLFQE-DKLTPVLCKPK 32 (65)
T ss_pred HhccccCceeec-cccceeeeccc
Confidence 378999999987 78999999877
No 64
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.00 E-value=31 Score=18.78 Aligned_cols=13 Identities=31% Similarity=0.603 Sum_probs=10.4
Q ss_pred eecccCCCCccCC
Q psy4232 4 GLCAYSGYKIYPG 16 (130)
Q Consensus 4 ~~C~Fsg~~IyPG 16 (130)
..|..||..|.++
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 3699999988776
No 65
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=27.99 E-value=32 Score=25.11 Aligned_cols=37 Identities=16% Similarity=0.250 Sum_probs=23.7
Q ss_pred eeecccCCCCccCCC-cceEEee--cCceEEEechhHHhhh
Q psy4232 3 LGLCAYSGYKIYPGH-GKTLVKV--DGKSFTFINSKCESSF 40 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~-G~~~Vr~--Dgkv~~F~ssKc~~~~ 40 (130)
...|.|||.++.=-. -.+|-+. ++..||.|+. |....
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~-C~AyV 41 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTP-CDAYV 41 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCC-CCcee
Confidence 467999987643222 2334433 5788899998 87653
No 66
>smart00696 DM9 Repeats found in Drosophila proteins.
Probab=27.89 E-value=45 Score=22.35 Aligned_cols=20 Identities=25% Similarity=0.589 Sum_probs=17.8
Q ss_pred CccCCCcceEEeecCceEEE
Q psy4232 12 KIYPGHGKTLVKVDGKSFTF 31 (130)
Q Consensus 12 ~IyPG~G~~~Vr~Dgkv~~F 31 (130)
+|.|+||..||--||.-+.+
T Consensus 43 Kv~p~~~~~yi~~~g~E~~~ 62 (71)
T smart00696 43 KVVPSHGCAYIPYGGQEVRL 62 (71)
T ss_pred EEEccCCEEEEEECCEEEEc
Confidence 58899999999999998776
No 67
>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=27.42 E-value=26 Score=20.49 Aligned_cols=9 Identities=33% Similarity=0.670 Sum_probs=6.5
Q ss_pred ecccCCCCc
Q psy4232 5 LCAYSGYKI 13 (130)
Q Consensus 5 ~C~Fsg~~I 13 (130)
.|.+||+.|
T Consensus 19 rC~~CG~RI 27 (32)
T PF03604_consen 19 RCPECGHRI 27 (32)
T ss_dssp SBSSSS-SE
T ss_pred ECCcCCCeE
Confidence 588898887
No 68
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=27.01 E-value=47 Score=23.58 Aligned_cols=16 Identities=38% Similarity=0.503 Sum_probs=14.4
Q ss_pred CcceEEeecCceEEEe
Q psy4232 17 HGKTLVKVDGKSFTFI 32 (130)
Q Consensus 17 ~G~~~Vr~Dgkv~~F~ 32 (130)
.|+-||-.||.|++|.
T Consensus 67 eGK~Yiv~DGDi~~f~ 82 (83)
T cd04867 67 EGKDYVVQDGDIIFFK 82 (83)
T ss_pred hCCceEeeCCeEEEEE
Confidence 5889999999999995
No 69
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=26.96 E-value=52 Score=22.33 Aligned_cols=24 Identities=29% Similarity=0.451 Sum_probs=18.3
Q ss_pred cCCCCccCCCcceEEeecCceEEE
Q psy4232 8 YSGYKIYPGHGKTLVKVDGKSFTF 31 (130)
Q Consensus 8 Fsg~~IyPG~G~~~Vr~Dgkv~~F 31 (130)
-+...|.||.|..|+...-+.+.|
T Consensus 53 i~~G~I~~gdG~~~~~V~F~~ivF 76 (80)
T cd00655 53 IPEGAIRPGDGSAYVNVSFRAVVF 76 (80)
T ss_pred EcCCEEECCCCCEEEEEEEEEEEE
Confidence 467789999999998876555544
No 70
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=26.62 E-value=24 Score=22.72 Aligned_cols=9 Identities=44% Similarity=1.069 Sum_probs=7.3
Q ss_pred ecccCCCCc
Q psy4232 5 LCAYSGYKI 13 (130)
Q Consensus 5 ~C~Fsg~~I 13 (130)
-|.+||++|
T Consensus 26 rCp~Cg~rI 34 (49)
T COG1996 26 RCPYCGSRI 34 (49)
T ss_pred eCCCCCcEE
Confidence 488998887
No 71
>KOG2361|consensus
Probab=26.42 E-value=47 Score=28.22 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=18.1
Q ss_pred cceEEeecCce-EEEechhHHhhh
Q psy4232 18 GKTLVKVDGKS-FTFINSKCESSF 40 (130)
Q Consensus 18 G~~~Vr~Dgkv-~~F~ssKc~~~~ 40 (130)
+..|||-||+. |+|+.-.-..+|
T Consensus 202 ~nfYVRgDGT~~YfF~~eeL~~~f 225 (264)
T KOG2361|consen 202 ENFYVRGDGTRAYFFTEEELDELF 225 (264)
T ss_pred cceEEccCCceeeeccHHHHHHHH
Confidence 67899999997 778777666555
No 72
>PRK06424 transcription factor; Provisional
Probab=26.25 E-value=48 Score=25.28 Aligned_cols=31 Identities=26% Similarity=0.438 Sum_probs=25.7
Q ss_pred cccCCCCccCCCcceEEeecCceEEEechhHHhhh
Q psy4232 6 CAYSGYKIYPGHGKTLVKVDGKSFTFINSKCESSF 40 (130)
Q Consensus 6 C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~~~~ 40 (130)
|--||..|. |...|..||-.+..|. .|.++=
T Consensus 3 CE~CG~~~~---~~~~v~ieg~~l~vC~-~Ca~~G 33 (144)
T PRK06424 3 CEMCGKKVP---QTTKVMIDGAILNVCD-DCAKFG 33 (144)
T ss_pred ccccCcccC---CceEEEEcCeeeehhH-HHHHcC
Confidence 999999997 4489999999999986 466653
No 73
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=25.97 E-value=29 Score=20.99 Aligned_cols=11 Identities=45% Similarity=1.068 Sum_probs=7.7
Q ss_pred eecccCCCCcc
Q psy4232 4 GLCAYSGYKIY 14 (130)
Q Consensus 4 ~~C~Fsg~~Iy 14 (130)
-.|.|||.++-
T Consensus 22 ~~Cp~CG~~~~ 32 (46)
T PRK00398 22 VRCPYCGYRIL 32 (46)
T ss_pred eECCCCCCeEE
Confidence 46888887653
No 74
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=24.77 E-value=55 Score=25.58 Aligned_cols=29 Identities=28% Similarity=0.373 Sum_probs=15.3
Q ss_pred ecccCCCCccCCCcceEEeecCceEEEechhHH
Q psy4232 5 LCAYSGYKIYPGHGKTLVKVDGKSFTFINSKCE 37 (130)
Q Consensus 5 ~C~Fsg~~IyPG~G~~~Vr~Dgkv~~F~ssKc~ 37 (130)
-|+|||..-+ .-.|+=..--.||||++..
T Consensus 2 aC~YCG~~~p----~~vv~C~~c~kWFCNg~~~ 30 (152)
T PF09416_consen 2 ACAYCGIHDP----SCVVKCNTCNKWFCNGRGN 30 (152)
T ss_dssp S-TTT----C----CCEEEETTTTEEEES--TT
T ss_pred CccccCCCCc----ccEeEcCCCCcEeecCCCC
Confidence 4999995443 2356666677899999864
No 75
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=24.43 E-value=42 Score=23.64 Aligned_cols=25 Identities=32% Similarity=0.489 Sum_probs=16.5
Q ss_pred ceeecccCCCCc-cCCCcce--EEeecC
Q psy4232 2 KLGLCAYSGYKI-YPGHGKT--LVKVDG 26 (130)
Q Consensus 2 k~~~C~Fsg~~I-yPG~G~~--~Vr~Dg 26 (130)
+...+.||||.| +|-...+ +|..||
T Consensus 40 ~~~~V~fagY~vpHPl~~~~~l~i~t~~ 67 (93)
T cd06926 40 KDPNVLFAGYKVPHPLEHKIELRIQTDG 67 (93)
T ss_pred cCCCeeEEeeccCCCCCCceEEEEEeCC
Confidence 344578999999 5765544 455565
No 76
>PF07826 IMP_cyclohyd: IMP cyclohydrolase-like protein; InterPro: IPR020600 This entry represents inosine monophosphate (IMP) cyclohydrolase, found in archaeal species, as well as some bacterial proteins of unknown function. IMP cyclohydrolase catalyses the cyclisation of 5-formylamidoimidazole-4-carboxamide ribonucleotide to IMP, a reaction which is important in de novo purine biosynthesis in archaeal species []. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family []. In bacteria this step is catalysed by a bifunctional enzyme (purH).; GO: 0003937 IMP cyclohydrolase activity; PDB: 2NTL_B 1KUU_A 2NTM_B 2NTK_A.
Probab=24.29 E-value=53 Score=26.68 Aligned_cols=26 Identities=35% Similarity=0.439 Sum_probs=14.6
Q ss_pred ccCCCcceEEee-cC-ceEEEechhHHh
Q psy4232 13 IYPGHGKTLVKV-DG-KSFTFINSKCES 38 (130)
Q Consensus 13 IyPG~G~~~Vr~-Dg-kv~~F~ssKc~~ 38 (130)
+|||+|.+.=+. || =+.||+++.++-
T Consensus 1 MY~GR~ivvG~t~dg~~~aY~I~sRSf~ 28 (199)
T PF07826_consen 1 MYPGRGIVVGKTEDGAFVAYRIMSRSFP 28 (199)
T ss_dssp ----SEEEEEEETTEEEEEEEEE-SS--
T ss_pred CCCCCEEEEeecCCCCEEEEEEecCCCC
Confidence 599999998887 44 377888887653
No 77
>KOG2996|consensus
Probab=24.01 E-value=49 Score=31.75 Aligned_cols=46 Identities=30% Similarity=0.391 Sum_probs=39.3
Q ss_pred ccCCCCccCCC-cceEEeecCceEEEechhHHhhhhcccCC--ccchhh
Q psy4232 7 AYSGYKIYPGH-GKTLVKVDGKSFTFINSKCESSFKMRRNP--RKVTWT 52 (130)
Q Consensus 7 ~Fsg~~IyPG~-G~~~Vr~Dgkv~~F~ssKc~~~~~~krnP--rki~WT 52 (130)
.|||.+-+||+ |-..+++.|.|+-.+..-.+++|...+|- +.+.|-
T Consensus 612 ~ysg~p~Pag~igP~l~~~~gdvlel~~~d~~s~~w~gr~~~sr~sg~f 660 (865)
T KOG2996|consen 612 NYSGIPPPAGSIGPRLVLQEGDVLELLKGDAESSWWEGRNHGSRESGNF 660 (865)
T ss_pred ccCCCCCCCccCCCceEecCCceeehhcCCCCCcccccCCccCCccCCC
Confidence 68999999999 99999999999999999999999877763 444443
No 78
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=23.83 E-value=1e+02 Score=17.65 Aligned_cols=28 Identities=18% Similarity=0.293 Sum_probs=18.7
Q ss_pred cccCCCCccCCCc-ceEEeecCceEEEec
Q psy4232 6 CAYSGYKIYPGHG-KTLVKVDGKSFTFIN 33 (130)
Q Consensus 6 C~Fsg~~IyPG~G-~~~Vr~Dgkv~~F~s 33 (130)
|.+||....++.- .+.+.-+|.++.+-+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~ 29 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVIEN 29 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEEeC
Confidence 8889766666664 555556777776644
No 79
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=23.70 E-value=60 Score=18.18 Aligned_cols=19 Identities=21% Similarity=0.186 Sum_probs=10.4
Q ss_pred CCcceEEeecCceEEEech
Q psy4232 16 GHGKTLVKVDGKSFTFINS 34 (130)
Q Consensus 16 G~G~~~Vr~Dgkv~~F~ss 34 (130)
-=|...++.+|.+.+||-.
T Consensus 4 ~C~s~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 4 VCGSKLVREEGEVDIRCPN 22 (28)
T ss_dssp TT--BEEE-CCTTCEEE--
T ss_pred CCCCEeEcCCCCEeEECCC
Confidence 3355567888888888753
No 80
>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]
Probab=23.68 E-value=37 Score=29.56 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=16.1
Q ss_pred eecccCCCCccCCCcceEEe
Q psy4232 4 GLCAYSGYKIYPGHGKTLVK 23 (130)
Q Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr 23 (130)
..|.||++.-.||+...|.-
T Consensus 71 ~~C~fCaF~~~~~~~~~y~L 90 (370)
T COG1060 71 NDCTFCAFYRKPGDPKAYTL 90 (370)
T ss_pred CCCCccccccCCCCcccccc
Confidence 46999999999988866643
No 81
>TIGR03403 nifS_epsilon cysteine desulfurase, NifS family, epsilon proteobacteria type. Members of this family are the NifS-like cysteine desulfurase of the epsilon division of the Proteobacteria, similar to the NifS protein of nitrogen-fixing bacteria. Like NifS, and unlike IscS, this protein is found as part of a system of just two proteins, a cysteine desulfurase and a scaffold, for iron-sulfur cluster biosynthesis. This protein is called NifS by Olsen, et al. (PubMed:11123951), so we use this designation.
Probab=22.71 E-value=43 Score=27.56 Aligned_cols=23 Identities=17% Similarity=0.342 Sum_probs=17.9
Q ss_pred eeecccCCCCcc--CCCcceEEeec
Q psy4232 3 LGLCAYSGYKIY--PGHGKTLVKVD 25 (130)
Q Consensus 3 ~~~C~Fsg~~Iy--PG~G~~~Vr~D 25 (130)
.+.+.||+++++ ||-|.+||+.+
T Consensus 193 ~D~~~~s~~K~~gp~G~g~l~vr~~ 217 (382)
T TIGR03403 193 VDFLSFSAHKFHGPKGVGGLYIRKG 217 (382)
T ss_pred CCEEEEcchhhCCCCceEEEEECCC
Confidence 355678888876 68899999876
No 82
>PF13395 HNH_4: HNH endonuclease
Probab=22.61 E-value=38 Score=21.21 Aligned_cols=12 Identities=33% Similarity=0.653 Sum_probs=10.6
Q ss_pred cccCCCCccCCC
Q psy4232 6 CAYSGYKIYPGH 17 (130)
Q Consensus 6 C~Fsg~~IyPG~ 17 (130)
|.|||..|-++.
T Consensus 1 C~Y~g~~i~~~~ 12 (54)
T PF13395_consen 1 CPYCGKPISIEN 12 (54)
T ss_pred CCCCCCCCChhh
Confidence 899999998876
No 83
>PF07921 Fibritin_C: Fibritin C-terminal region; InterPro: IPR012473 This family features sequences bearing similarity to the C-terminal portion of the Bacteriophage T4 protein fibritin (P10104 from SWISSPROT). This protein is responsible for attachment of long tail fibres to virus particle, and forms the, "whiskers", or fibres on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerisation and folding []. This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilised by hydrogen bonds, salt bridges and hydrophobic interactions []. ; PDB: 2WW7_C 2WW6_C 1U0P_A 2IBL_A 1AVY_A 1V1H_B 1RFO_B 1OX3_A 1AA0_A 1V1I_C ....
Probab=22.55 E-value=59 Score=23.54 Aligned_cols=14 Identities=43% Similarity=0.655 Sum_probs=11.0
Q ss_pred cCCCcceEEeecCc
Q psy4232 14 YPGHGKTLVKVDGK 27 (130)
Q Consensus 14 yPG~G~~~Vr~Dgk 27 (130)
.|-.|..|||.||-
T Consensus 73 ~p~dg~~Y~r~~g~ 86 (93)
T PF07921_consen 73 APDDGKWYVRKDGA 86 (93)
T ss_dssp --SSSSEEEEETTE
T ss_pred cchhhhhhhccCce
Confidence 47789999999996
No 84
>COG3564 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.40 E-value=58 Score=24.29 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=19.9
Q ss_pred CccCCCcceEEeecCceEEEech
Q psy4232 12 KIYPGHGKTLVKVDGKSFTFINS 34 (130)
Q Consensus 12 ~IyPG~G~~~Vr~Dgkv~~F~ss 34 (130)
.+-||+|-||.-.+|.--+|+.+
T Consensus 84 DVVpGRGGmFSLdng~E~RFLtR 106 (116)
T COG3564 84 DVVPGRGGMFSLDNGREKRFLTR 106 (116)
T ss_pred EEecCCCceeEccCCcceeeeee
Confidence 36799999999999999998865
No 85
>PF11811 DUF3331: Domain of unknown function (DUF3331); InterPro: IPR021769 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family vary in length from 96 to 160 amino acids.
Probab=22.20 E-value=40 Score=24.51 Aligned_cols=15 Identities=47% Similarity=0.775 Sum_probs=12.8
Q ss_pred eeecccCCCCccCCC
Q psy4232 3 LGLCAYSGYKIYPGH 17 (130)
Q Consensus 3 ~~~C~Fsg~~IyPG~ 17 (130)
-..|..||.+|.+|-
T Consensus 54 ~G~CaLSG~~I~rGD 68 (96)
T PF11811_consen 54 SGVCALSGRPIRRGD 68 (96)
T ss_pred CCEEeCCCCEecCCC
Confidence 367999999999985
No 86
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=22.14 E-value=45 Score=23.19 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=16.6
Q ss_pred ceeecccCCCCc-cCCCcceEEe--ecC
Q psy4232 2 KLGLCAYSGYKI-YPGHGKTLVK--VDG 26 (130)
Q Consensus 2 k~~~C~Fsg~~I-yPG~G~~~Vr--~Dg 26 (130)
+-....||||.| +|--..+.+| .||
T Consensus 32 ~~p~V~fagY~vpHPl~~~~~lriqT~~ 59 (85)
T cd07029 32 KNPEVEFCGYSIPHPSENKINLRIQTKG 59 (85)
T ss_pred hCCCceEEeecccCCCCCccEEEEEeCC
Confidence 344568999999 5776665544 454
No 87
>PRK12495 hypothetical protein; Provisional
Probab=21.72 E-value=47 Score=27.64 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=13.7
Q ss_pred CceeecccCCCCccCCCcceE
Q psy4232 1 MKLGLCAYSGYKIYPGHGKTL 21 (130)
Q Consensus 1 mk~~~C~Fsg~~IyPG~G~~~ 21 (130)
|--..|..||.+|+-=.|..|
T Consensus 40 msa~hC~~CG~PIpa~pG~~~ 60 (226)
T PRK12495 40 MTNAHCDECGDPIFRHDGQEF 60 (226)
T ss_pred cchhhcccccCcccCCCCeeE
Confidence 445679999999983334333
No 88
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=21.54 E-value=68 Score=19.22 Aligned_cols=17 Identities=18% Similarity=0.411 Sum_probs=14.2
Q ss_pred CCcceEEeecCceEEEe
Q psy4232 16 GHGKTLVKVDGKSFTFI 32 (130)
Q Consensus 16 G~G~~~Vr~Dgkv~~F~ 32 (130)
|...++|--||.|+-.+
T Consensus 4 ~~~~~~I~~dG~v~pC~ 20 (64)
T PF13186_consen 4 GWNSLYIDPDGDVYPCC 20 (64)
T ss_pred cCeEEEEeeCccEEeCC
Confidence 56789999999998863
No 89
>COG1104 NifS Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
Probab=21.47 E-value=48 Score=29.41 Aligned_cols=24 Identities=25% Similarity=0.325 Sum_probs=19.0
Q ss_pred ceeecccCCCCcc--CCCcceEEeec
Q psy4232 2 KLGLCAYSGYKIY--PGHGKTLVKVD 25 (130)
Q Consensus 2 k~~~C~Fsg~~Iy--PG~G~~~Vr~D 25 (130)
-++..+|||.+|| .|-|-+||+.+
T Consensus 193 ~vD~ls~SaHK~~GpkGiGaLyv~~~ 218 (386)
T COG1104 193 GVDLLSFSAHKFGGPKGIGALYVRPG 218 (386)
T ss_pred CcceEEeehhhccCCCceEEEEECCC
Confidence 3577899999998 46689999554
No 90
>PF05132 RNA_pol_Rpc4: RNA polymerase III RPC4; InterPro: IPR007811 This family comprises a specific subunit for Pol III, the tRNA specific polymerase.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006383 transcription from RNA polymerase III promoter, 0005666 DNA-directed RNA polymerase III complex
Probab=21.11 E-value=66 Score=23.57 Aligned_cols=23 Identities=30% Similarity=0.307 Sum_probs=18.2
Q ss_pred CCccCCC-cceEEeecCceEEEec
Q psy4232 11 YKIYPGH-GKTLVKVDGKSFTFIN 33 (130)
Q Consensus 11 ~~IyPG~-G~~~Vr~Dgkv~~F~s 33 (130)
....+|+ |.+.|+.+|++-.-+.
T Consensus 62 ~~~~~G~iGkL~V~kSGkv~l~iG 85 (131)
T PF05132_consen 62 SDLPEGQIGKLRVHKSGKVTLKIG 85 (131)
T ss_pred ccCCCCeeEEEEEEeCCcEEEEEC
Confidence 3457888 9999999999876543
No 91
>PF15279 SOBP: Sine oculis-binding protein
Probab=21.10 E-value=33 Score=29.49 Aligned_cols=27 Identities=37% Similarity=0.770 Sum_probs=19.4
Q ss_pred CcceEEee-cC-ceEEEechhHHhhhhcc
Q psy4232 17 HGKTLVKV-DG-KSFTFINSKCESSFKMR 43 (130)
Q Consensus 17 ~G~~~Vr~-Dg-kv~~F~ssKc~~~~~~k 43 (130)
|-.-||.- || .-+.|||.||..-|+|-
T Consensus 10 h~~~y~d~~~g~~~lqfcs~kclnqykm~ 38 (306)
T PF15279_consen 10 HTKSYVDFQDGERQLQFCSDKCLNQYKMD 38 (306)
T ss_pred chhheeccccchHHhhhccHHHHhHHHHH
Confidence 44445543 66 46899999999988874
No 92
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=21.08 E-value=96 Score=21.14 Aligned_cols=26 Identities=23% Similarity=0.224 Sum_probs=19.6
Q ss_pred cccCCCCccCCCcceEEeecCceEEE
Q psy4232 6 CAYSGYKIYPGHGKTLVKVDGKSFTF 31 (130)
Q Consensus 6 C~Fsg~~IyPG~G~~~Vr~Dgkv~~F 31 (130)
..-+...|.||.|-.|....-+.+.|
T Consensus 51 ~~i~eG~I~~gdG~~~~~V~F~~ivF 76 (80)
T cd04331 51 KDVGEGKIVHGDGAVYHEVRFDALVF 76 (80)
T ss_pred EEecCCEEEcCCCCEEEEEEEEEEEE
Confidence 45577889999999998776655555
No 93
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=20.78 E-value=38 Score=20.93 Aligned_cols=9 Identities=44% Similarity=1.006 Sum_probs=5.9
Q ss_pred ecccCCCCc
Q psy4232 5 LCAYSGYKI 13 (130)
Q Consensus 5 ~C~Fsg~~I 13 (130)
.|..||++|
T Consensus 21 rC~~CG~rI 29 (44)
T smart00659 21 RCRECGYRI 29 (44)
T ss_pred ECCCCCceE
Confidence 477777665
No 94
>COG3114 CcmD Heme exporter protein D [Intracellular trafficking and secretion]
Probab=20.04 E-value=2e+02 Score=19.71 Aligned_cols=26 Identities=27% Similarity=0.538 Sum_probs=16.4
Q ss_pred HHHHHHhcC-CHHHHHHHHHHHHHHHH
Q psy4232 88 NDILAKRNV-KPEIRKAQREQAIKAAK 113 (130)
Q Consensus 88 e~I~~kR~q-k~e~r~a~r~~a~~~~K 113 (130)
..++++|.- ..+.|+.+||+.+++++
T Consensus 36 ~sv~qrr~iL~~v~r~~aReaR~~~aq 62 (67)
T COG3114 36 HSVLQRRAILRGVARQRAREARLRAAQ 62 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444433 44557888888888876
Done!