Query 031225
Match_columns 163
No_of_seqs 159 out of 454
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 11:03:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031225.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031225hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1722 60s ribosomal protein 100.0 1.1E-61 2.3E-66 382.4 10.4 154 3-160 1-155 (155)
2 PTZ00033 60S ribosomal protein 100.0 3.2E-54 6.9E-59 333.4 11.4 120 3-123 1-124 (125)
3 PF01246 Ribosomal_L24e: Ribos 100.0 9.8E-39 2.1E-43 226.6 -0.9 70 3-72 1-70 (71)
4 PRK14891 50S ribosomal protein 100.0 2.6E-36 5.7E-41 234.8 5.7 63 2-64 1-63 (131)
5 COG2075 RPL24A Ribosomal prote 100.0 9.6E-35 2.1E-39 203.4 5.1 65 3-67 1-65 (66)
6 cd00472 Ribosomal_L24e_L24 Rib 100.0 2.3E-33 5.1E-38 189.9 3.7 54 3-56 1-54 (54)
7 KOG1723 60s ribosomal protein 100.0 4E-30 8.7E-35 206.7 5.2 121 3-130 1-123 (162)
8 PRK00807 50S ribosomal protein 100.0 3.1E-29 6.8E-34 168.2 3.6 51 5-55 1-51 (52)
9 smart00746 TRASH metallochaper 98.6 8.6E-08 1.9E-12 54.5 3.9 37 8-45 1-38 (39)
10 PF08394 Arc_trans_TRASH: Arch 97.1 0.00064 1.4E-08 43.1 3.6 36 8-45 1-36 (37)
11 PF04945 YHS: YHS domain; Int 97.0 0.00062 1.3E-08 43.8 2.7 36 8-44 3-38 (47)
12 PF06467 zf-FCS: MYM-type Zinc 96.3 0.0016 3.6E-08 40.5 1.1 37 5-42 6-43 (43)
13 PF05573 NosL: NosL; InterPro 94.8 0.025 5.4E-07 44.4 2.7 40 5-44 25-67 (149)
14 PF09889 DUF2116: Uncharacteri 94.0 0.012 2.5E-07 40.8 -0.5 36 6-53 4-40 (59)
15 COG3350 Uncharacterized conser 93.8 0.088 1.9E-06 35.9 3.5 39 8-48 5-43 (53)
16 PF09943 DUF2175: Uncharacteri 89.5 0.12 2.5E-06 39.5 0.2 29 6-35 3-31 (101)
17 cd01057 AAMH_A Aromatic and Al 86.0 0.72 1.6E-05 42.9 3.2 51 7-59 382-439 (465)
18 COG4314 NosL Predicted lipopro 83.3 1.4 3E-05 36.4 3.4 47 6-52 36-86 (176)
19 PHA03073 late transcription fa 78.8 1.3 2.8E-05 35.9 1.7 39 4-43 48-87 (150)
20 PF04570 DUF581: Protein of un 78.1 1.9 4.2E-05 29.7 2.2 34 6-42 17-50 (58)
21 COG4847 Uncharacterized protei 77.7 0.76 1.7E-05 35.1 0.1 31 1-32 2-32 (103)
22 COG4068 Uncharacterized protei 75.9 1.3 2.8E-05 31.2 0.9 27 2-40 5-31 (64)
23 TIGR00270 conserved hypothetic 62.5 5.9 0.00013 31.7 2.1 31 8-41 3-33 (154)
24 PRK08359 transcription factor; 60.1 6.4 0.00014 32.4 2.0 29 8-39 9-37 (176)
25 PRK09710 lar restriction allev 59.0 7.4 0.00016 27.5 1.9 30 5-40 6-35 (64)
26 PF00412 LIM: LIM domain; Int 57.1 11 0.00023 23.9 2.3 25 7-36 28-52 (58)
27 PF15585 Imm46: Immunity prote 53.7 7.4 0.00016 30.9 1.3 26 14-39 79-113 (129)
28 PF01197 Ribosomal_L31: Riboso 53.7 6.8 0.00015 27.4 1.0 32 2-35 33-64 (69)
29 PF06689 zf-C4_ClpX: ClpX C4-t 52.4 9.6 0.00021 24.0 1.5 20 6-26 2-21 (41)
30 PF08384 NPP: Pro-opiomelanoco 51.5 7.5 0.00016 25.8 0.9 12 11-22 30-41 (45)
31 PF14353 CpXC: CpXC protein 49.8 17 0.00037 27.2 2.7 33 5-37 38-70 (128)
32 smart00132 LIM Zinc-binding do 48.0 15 0.00033 20.9 1.8 25 7-33 1-25 (39)
33 PF07754 DUF1610: Domain of un 43.3 17 0.00036 21.0 1.4 17 8-24 1-18 (24)
34 PRK14890 putative Zn-ribbon RN 42.9 17 0.00037 25.3 1.6 41 2-42 4-46 (59)
35 COG2888 Predicted Zn-ribbon RN 40.6 31 0.00067 24.2 2.6 37 5-41 9-47 (61)
36 KOG3710 EGL-Nine (EGLN) protei 36.7 25 0.00055 31.0 2.1 22 14-35 148-178 (280)
37 PF00319 SRF-TF: SRF-type tran 34.9 19 0.00042 23.9 0.9 26 6-35 26-51 (51)
38 PF14447 Prok-RING_4: Prokaryo 33.6 22 0.00047 24.5 1.0 14 6-19 40-53 (55)
39 PF12156 ATPase-cat_bd: Putati 32.5 49 0.0011 23.9 2.7 36 7-43 2-37 (88)
40 KOG1549 Cysteine desulfurase N 32.4 24 0.00053 33.0 1.4 27 3-29 232-260 (428)
41 PF08789 PBCV_basic_adap: PBCV 30.2 30 0.00065 22.4 1.1 18 11-28 7-25 (40)
42 TIGR01922 purO_arch IMP cycloh 29.8 27 0.00058 29.6 1.1 27 15-41 1-30 (199)
43 COG1997 RPL43A Ribosomal prote 29.6 21 0.00046 26.8 0.4 30 5-43 35-64 (89)
44 PF13408 Zn_ribbon_recom: Reco 28.2 39 0.00085 21.3 1.5 29 5-38 5-33 (58)
45 PF11672 DUF3268: Protein of u 27.0 31 0.00068 26.2 0.9 36 5-41 2-40 (102)
46 PRK05342 clpX ATP-dependent pr 26.9 28 0.00061 31.8 0.8 14 3-16 7-20 (412)
47 PRK13446 atpC F0F1 ATP synthas 26.8 54 0.0012 25.3 2.3 18 12-29 32-58 (136)
48 PF15279 SOBP: Sine oculis-bin 26.2 24 0.00053 31.5 0.3 28 19-46 10-39 (306)
49 PRK06424 transcription factor; 26.2 45 0.00097 26.5 1.7 30 8-41 3-32 (144)
50 PF06221 zf-C2HC5: Putative zi 26.0 32 0.00069 23.6 0.7 12 6-17 36-47 (57)
51 TIGR03550 F420_cofG 7,8-dideme 26.0 19 0.00041 31.3 -0.4 22 6-27 16-37 (322)
52 KOG0402 60S ribosomal protein 25.7 23 0.0005 26.6 0.0 29 6-43 37-65 (92)
53 PF01321 Creatinase_N: Creatin 25.5 49 0.0011 23.4 1.7 49 6-55 24-76 (132)
54 TIGR03666 Rv2061_F420 PPOX cla 25.4 56 0.0012 24.9 2.1 28 22-49 32-59 (132)
55 PRK04151 IMP cyclohydrolase; P 24.3 39 0.00084 28.6 1.1 26 15-40 1-29 (197)
56 PF13240 zinc_ribbon_2: zinc-r 22.7 45 0.00099 18.6 0.8 11 8-18 2-12 (23)
57 PRK08445 hypothetical protein; 22.2 50 0.0011 29.3 1.4 20 6-25 54-73 (348)
58 PF03884 DUF329: Domain of unk 22.1 64 0.0014 22.1 1.6 29 6-41 3-31 (57)
59 cd06926 RNAP_II_RPB11 RPB11 su 22.1 39 0.00085 24.8 0.6 26 3-28 39-67 (93)
60 PRK08444 hypothetical protein; 21.4 47 0.001 29.7 1.1 20 6-25 61-80 (353)
61 COG1996 RPC10 DNA-directed RNA 21.3 35 0.00076 22.9 0.2 9 7-15 26-34 (49)
62 KOG2361 Predicted methyltransf 21.0 74 0.0016 28.1 2.2 24 20-43 202-226 (264)
63 smart00696 DM9 Repeats found i 20.7 64 0.0014 22.5 1.5 20 14-33 43-62 (71)
64 PF03604 DNA_RNApol_7kD: DNA d 20.5 43 0.00094 20.3 0.5 9 7-15 19-27 (32)
No 1
>KOG1722 consensus 60s ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-61 Score=382.38 Aligned_cols=154 Identities=53% Similarity=0.857 Sum_probs=143.1
Q ss_pred eeeccccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCCccchhhHHHHHhhchhhhHHHHHHHhhcCCCccc
Q 031225 3 LKTELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKKRRSTKKPYS 82 (163)
Q Consensus 3 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki~WT~~yRr~~kK~~~~e~~kkrrr~~~~k~~ 82 (163)
|++|+|+||||+||||||++|||.||+||.|+|+||+++|++++|||+|.||++||+.|+||+++|.+++|+|+++++||
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 88999999999999999999999999999999999999999999999999999999999999999999999999998999
Q ss_pred hhhhhhcHHHHHHHhccChHHHHHHHHHHHHHHHHHhhhchHHHHhhhhhhhhccccccC-CCCCCCCCCCCCCCCCCC
Q 031225 83 RSIVGATLEVIQKRRTEKPEVRDAAREAALREIKERIKKTKDEKRAKKAEVTSKSKTQSK-GSMPKGAAPKGPKLGGGG 160 (163)
Q Consensus 83 Raivg~Sl~~I~~kr~qkpevr~a~Re~a~~~~Ker~k~~~~~kk~~~~~~~~~~~~~~k-~~~~k~~~~~~p~~ggk~ 160 (163)
|+|||+||++|+++|||+||||+|+||||++.+||+.++.++++++.+++. ..+++ +++.++++.++|+|||+.
T Consensus 81 RaI~GasL~~I~~KRn~kpevR~a~Re~alK~aKe~~ka~k~ak~A~K~~~----as~~k~qk~~k~~k~aaprVggkr 155 (155)
T KOG1722|consen 81 RAIVGASLDVILEKRNQKPEVRKAAREAALKKAKEKKKATKAAKKAKKAKS----ASAPKKQKAKKNAKVAAPRVGGKR 155 (155)
T ss_pred hhhccccHHHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc----cccccccchhhhhhhhcccccCCC
Confidence 999999999999999999999999999999999999999888886544432 22333 889999999999999974
No 2
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=100.00 E-value=3.2e-54 Score=333.35 Aligned_cols=120 Identities=31% Similarity=0.523 Sum_probs=113.1
Q ss_pred eeeccccccCCCccCCCCceEEe----cCCceeEeechHHHHhhhccCCCccchhhHHHHHhhchhhhHHHHHHHhhcCC
Q 031225 3 LKTELCRFSGAKIYPGKGIRFIR----SDSQVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKKRRSTK 78 (163)
Q Consensus 3 mk~~~C~Fsg~~IyPG~G~~~Vr----~Dgkvf~F~ssKc~~~f~~krnPRki~WT~~yRr~~kK~~~~e~~kkrrr~~~ 78 (163)
|++++|+|||++||||||++||+ +||+||+|||+||+++|++++|||+|.||++||++|+||+++|+. +++++.+
T Consensus 1 Mk~~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~~~~krnPRkl~WT~~yRr~~kK~~~e~~~-kkR~~rt 79 (125)
T PTZ00033 1 MRTIACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYMRKKNPRFLPWTRTYRRINRKTTTDRVQ-RRRAART 79 (125)
T ss_pred CceeEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHHHHCcCCCccchHHHHHHHHhCCcchhHHH-HHHhcCC
Confidence 78999999999999999999999 999999999999999999999999999999999999999887765 5556667
Q ss_pred CccchhhhhhcHHHHHHHhccChHHHHHHHHHHHHHHHHHhhhch
Q 031225 79 KPYSRSIVGATLEVIQKRRTEKPEVRDAAREAALREIKERIKKTK 123 (163)
Q Consensus 79 ~k~~Raivg~Sl~~I~~kr~qkpevr~a~Re~a~~~~Ker~k~~~ 123 (163)
++|||+|||+||++|+++|||+|||+.++|++|++++||++++++
T Consensus 80 vK~qRaivg~sLe~I~~kR~~k~evr~aar~~a~r~~Ke~~~~~k 124 (125)
T PTZ00033 80 VKVQRAIVGADLSYIQEVRAYVQKVDRSAKAKAVRAEKAERKAAK 124 (125)
T ss_pred ccchHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 799999999999999999999999999999999999999988653
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=9.8e-39 Score=226.58 Aligned_cols=70 Identities=53% Similarity=0.976 Sum_probs=55.6
Q ss_pred eeeccccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCCccchhhHHHHHhhchhhhHHHHHH
Q 031225 3 LKTELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKK 72 (163)
Q Consensus 3 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki~WT~~yRr~~kK~~~~e~~kk 72 (163)
|++++|+|||++||||||+|||++||+||+|||+||++||++++|||+|.||++||++|+|++++|++++
T Consensus 1 mk~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~~~~krnPrkl~WT~~~Rr~~kK~~~~~~~kk 70 (71)
T PF01246_consen 1 MKTEKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKLFKLKRNPRKLKWTVAYRRQHKKGQSEEAAKK 70 (71)
T ss_dssp SSSEE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTTCHHH-----SSSSSS
T ss_pred CceEEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHHHHccCCcccchhHHHHHHHhCchhhhhHhhc
Confidence 7899999999999999999999999999999999999999999999999999999999999999887644
No 4
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=100.00 E-value=2.6e-36 Score=234.76 Aligned_cols=63 Identities=30% Similarity=0.665 Sum_probs=61.3
Q ss_pred ceeeccccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCCccchhhHHHHHhhchh
Q 031225 2 VLKTELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKD 64 (163)
Q Consensus 2 vmk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki~WT~~yRr~~kK~ 64 (163)
+|++++|+|||++||||||+|||||||+||+||||||++||+++||||+|+||++||+.++|.
T Consensus 1 Mm~~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT~~yRk~~g~~ 63 (131)
T PRK14891 1 MVETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWTEAGRAEKGPA 63 (131)
T ss_pred CCceeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHHccCCCccchhHHHHHHHcCch
Confidence 468999999999999999999999999999999999999999999999999999999999996
No 5
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.6e-35 Score=203.35 Aligned_cols=65 Identities=46% Similarity=0.917 Sum_probs=62.6
Q ss_pred eeeccccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCCccchhhHHHHHhhchhhhH
Q 031225 3 LKTELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAA 67 (163)
Q Consensus 3 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki~WT~~yRr~~kK~~~~ 67 (163)
|+++.|+|||..||||||+|||+|||+||+|||+||+++|.++||||+|+||..||+.++++..+
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 67899999999999999999999999999999999999999999999999999999999998754
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=99.98 E-value=2.3e-33 Score=189.90 Aligned_cols=54 Identities=48% Similarity=0.976 Sum_probs=52.5
Q ss_pred eeeccccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCCccchhhHH
Q 031225 3 LKTELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKPSKLTWTSM 56 (163)
Q Consensus 3 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki~WT~~ 56 (163)
|++++|+|||++||||||+|||++||+||+|||+||+++|++++|||+|+||++
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 789999999999999999999999999999999999999999999999999973
No 7
>KOG1723 consensus 60s ribosomal protein L30 isolog [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=4e-30 Score=206.70 Aligned_cols=121 Identities=33% Similarity=0.717 Sum_probs=106.4
Q ss_pred eeeccccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCCccchhhHHHHHhhchhhhHHHH--HHHhhcCCCc
Q 031225 3 LKTELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAV--KKKRRSTKKP 80 (163)
Q Consensus 3 mk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki~WT~~yRr~~kK~~~~e~~--kkrrr~~~~k 80 (163)
|+++.|+||+.+||||||+|||+||.++|.||.|+|+++|.+++|||++.||.++|+.+++++..|.+ ++.+|+.+.+
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 77999999999999999999999999999999999999999999999999999999999999999987 4668899999
Q ss_pred cchhhhhhcHHHHHHHhccChHHHHHHHHHHHHHHHHHhhhchHHHHhhh
Q 031225 81 YSRSIVGATLEVIQKRRTEKPEVRDAAREAALREIKERIKKTKDEKRAKK 130 (163)
Q Consensus 81 ~~Raivg~Sl~~I~~kr~qkpevr~a~Re~a~~~~Ker~k~~~~~kk~~~ 130 (163)
|+|+.++.|+++|+..- +++ ..+++ .++..+++.+++.+....
T Consensus 81 y~r~~~~~Ti~a~k~v~----~i~-~~~~~--~~i~~rL~~~ke~~~~~d 123 (162)
T KOG1723|consen 81 YDRELINKTIDAMKRVL----EIK-QKREA--HFIGNRLKKGKEAQLVQD 123 (162)
T ss_pred hcccchhhHHHHHHHHH----hhc-ccchh--hhhhhccCccchhccchh
Confidence 99999999999998875 333 33443 578888887777666533
No 8
>PRK00807 50S ribosomal protein L24e; Validated
Probab=99.95 E-value=3.1e-29 Score=168.17 Aligned_cols=51 Identities=35% Similarity=0.811 Sum_probs=49.5
Q ss_pred eccccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCCccchhhH
Q 031225 5 TELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKPSKLTWTS 55 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki~WT~ 55 (163)
+++|+|||++||||||++||++||+||+|||+||+++|++++|||+|+||.
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 9
>smart00746 TRASH metallochaperone-like domain.
Probab=98.57 E-value=8.6e-08 Score=54.47 Aligned_cols=37 Identities=46% Similarity=1.019 Sum_probs=33.7
Q ss_pred ccccCCCcc-CCCCceEEecCCceeEeechHHHHhhhcc
Q 031225 8 CRFSGAKIY-PGKGIRFIRSDSQVFLFANSKCKRYFHNR 45 (163)
Q Consensus 8 C~Fsg~~Iy-PG~G~~~Vr~Dgkvf~F~ssKc~~~f~~k 45 (163)
|.+||..|+ |+.+..++ .||++++|||..|...|...
T Consensus 1 c~~C~~~~~~~~~~~~~~-~~g~~~~FCs~~c~~~~~~~ 38 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVV-NDGKVFYFCSSKCLSKFKKK 38 (39)
T ss_pred CCCCCCCccCCCCceEEE-ECCEEEEEeCHHHHHHHHhc
Confidence 899999999 88899988 99999999999999988753
No 10
>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=97.14 E-value=0.00064 Score=43.14 Aligned_cols=36 Identities=25% Similarity=0.665 Sum_probs=31.0
Q ss_pred ccccCCCccCCCCceEEecCCceeEeechHHHHhhhcc
Q 031225 8 CRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNR 45 (163)
Q Consensus 8 C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~k 45 (163)
|+|||..|. |.++.| +.++++++||..-|.+-|+.+
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 777665 458999999999999998865
No 11
>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=97.01 E-value=0.00062 Score=43.81 Aligned_cols=36 Identities=22% Similarity=0.527 Sum_probs=26.8
Q ss_pred ccccCCCccCCCCceEEecCCceeEeechHHHHhhhc
Q 031225 8 CRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHN 44 (163)
Q Consensus 8 C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~ 44 (163)
+..||-.| ||.-...+.-+|++|+|||.-|...|..
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 9999999999999999999999999874
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=96.34 E-value=0.0016 Score=40.51 Aligned_cols=37 Identities=14% Similarity=0.252 Sum_probs=26.5
Q ss_pred eccccccCCCccCCC-CceEEecCCceeEeechHHHHhh
Q 031225 5 TELCRFSGAKIYPGK-GIRFIRSDSQVFLFANSKCKRYF 42 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG~-G~~~Vr~Dgkvf~F~ssKc~~~f 42 (163)
...|++|+..|+.+. + ..+..||.+..|||.-|...|
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 457999999998888 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=94.76 E-value=0.025 Score=44.40 Aligned_cols=40 Identities=23% Similarity=0.497 Sum_probs=16.7
Q ss_pred eccccccCCCc--cCCC-CceEEecCCceeEeechHHHHhhhc
Q 031225 5 TELCRFSGAKI--YPGK-GIRFIRSDSQVFLFANSKCKRYFHN 44 (163)
Q Consensus 5 ~~~C~Fsg~~I--yPG~-G~~~Vr~Dgkvf~F~ssKc~~~f~~ 44 (163)
...|.+||-.| |||. |.++..+.+++++||+-.|--.|.+
T Consensus 25 ~~~C~~CgM~i~d~p~~~aqi~~~~g~~~~~Fdsi~c~~~~~~ 67 (149)
T PF05573_consen 25 DDRCPVCGMVISDYPGFAAQIIYKDGEKVYKFDSIGCMFAYLK 67 (149)
T ss_dssp ------------------EEEEETT-SSEEEES-HHHHHHHHT
T ss_pred CCccCCCCCEeccCCCccEEEEECCCCEEEEECCHHHHHHHHh
Confidence 46799999999 7886 5555544449999999999866654
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=94.05 E-value=0.012 Score=40.77 Aligned_cols=36 Identities=22% Similarity=0.498 Sum_probs=26.4
Q ss_pred ccccccCCCccCCCCceEEecCCceeEeechHHHHhhh-ccCCCccchh
Q 031225 6 ELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFH-NRLKPSKLTW 53 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~-~krnPRki~W 53 (163)
..|-+||.+|.|. -.|||.+|+..|. ..+..++..|
T Consensus 4 kHC~~CG~~Ip~~------------~~fCS~~C~~~~~k~qk~~~~~~~ 40 (59)
T PF09889_consen 4 KHCPVCGKPIPPD------------ESFCSPKCREEYRKRQKRMRKTQY 40 (59)
T ss_pred CcCCcCCCcCCcc------------hhhhCHHHHHHHHHHHHHHHHHHH
Confidence 4699999999983 5799999987766 3344444444
No 15
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=93.83 E-value=0.088 Score=35.95 Aligned_cols=39 Identities=18% Similarity=0.303 Sum_probs=31.1
Q ss_pred ccccCCCccCCCCceEEecCCceeEeechHHHHhhhccCCC
Q 031225 8 CRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFHNRLKP 48 (163)
Q Consensus 8 C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~~krnP 48 (163)
-..||.+|.+-.-..=.--+|++++|||..|...|. .||
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 457888888777666667789999999999988875 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=89.49 E-value=0.12 Score=39.46 Aligned_cols=29 Identities=24% Similarity=0.369 Sum_probs=23.3
Q ss_pred ccccccCCCccCCCCceEEecCCceeEeec
Q 031225 6 ELCRFSGAKIYPGKGIRFIRSDSQVFLFAN 35 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~s 35 (163)
..|++||.+||-|-...|..+ |-|.|-|-
T Consensus 3 WkC~iCg~~I~~gqlFTF~~k-G~VH~~C~ 31 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKK-GPVHYECF 31 (101)
T ss_pred eEEEecCCeeeecceEEEecC-CcEeHHHH
Confidence 579999999998888777777 77766553
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=85.97 E-value=0.72 Score=42.92 Aligned_cols=51 Identities=18% Similarity=0.445 Sum_probs=38.6
Q ss_pred cccccCCCccC----CCC-ceEEecCCceeEeechHHHHhhhccCCCccc--hhhHHHHH
Q 031225 7 LCRFSGAKIYP----GKG-IRFIRSDSQVFLFANSKCKRYFHNRLKPSKL--TWTSMYRK 59 (163)
Q Consensus 7 ~C~Fsg~~IyP----G~G-~~~Vr~Dgkvf~F~ssKc~~~f~~krnPRki--~WT~~yRr 59 (163)
+|..|+-+|-| ..- ..-.--||+.|+|||--|+..|.+ +|-+. .|+..-|-
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 443 344566999999999999999986 77665 45544433
No 18
>COG4314 NosL Predicted lipoprotein involved in nitrous oxide reduction [Energy production and conversion]
Probab=83.34 E-value=1.4 Score=36.42 Aligned_cols=47 Identities=17% Similarity=0.352 Sum_probs=37.7
Q ss_pred ccccccCCCc--cCCC-CceEEecCCceeEeechHHHHhhh-ccCCCccch
Q 031225 6 ELCRFSGAKI--YPGK-GIRFIRSDSQVFLFANSKCKRYFH-NRLKPSKLT 52 (163)
Q Consensus 6 ~~C~Fsg~~I--yPG~-G~~~Vr~Dgkvf~F~ssKc~~~f~-~krnPRki~ 52 (163)
..|.|||-.| |||- |.+|..-+-...||||.+---+|. +=-+|+.|.
T Consensus 36 s~g~ycgMnl~ehpGPKgQi~l~g~~qP~wfsst~e~f~~tllPEepk~ia 86 (176)
T COG4314 36 SMGHYCGMNLLEHPGPKGQIILNGKPQPIWFSSTREMFGFTLLPEEPKGIA 86 (176)
T ss_pred ccccccceeeecCCCCcceEeeCCCCCceeeecHHHHhhHhcCCcCcCcee
Confidence 4699999877 7997 999999888889999999855444 666777653
No 19
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=78.75 E-value=1.3 Score=35.93 Aligned_cols=39 Identities=15% Similarity=0.330 Sum_probs=29.7
Q ss_pred eeccccccCCCccCCCCceEEecCC-ceeEeechHHHHhhh
Q 031225 4 KTELCRFSGAKIYPGKGIRFIRSDS-QVFLFANSKCKRYFH 43 (163)
Q Consensus 4 k~~~C~Fsg~~IyPG~G~~~Vr~Dg-kvf~F~ssKc~~~f~ 43 (163)
....|+||+..+-+-. ...=-.+| .|=.|||.=|+-+|-
T Consensus 48 ~~~~CwfC~q~~~~~~-~~iETl~g~~vg~FCS~ICRDSfa 87 (150)
T PHA03073 48 DNDYCWFCKQDLIIAP-LFIETLKGGAVGYFCSKICRDSFA 87 (150)
T ss_pred CCCcEEeeccccccCc-eEEEeecCchhhhHhHHHHHHHHH
Confidence 3567999999887766 33334466 899999999997775
No 20
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=78.10 E-value=1.9 Score=29.71 Aligned_cols=34 Identities=29% Similarity=0.633 Sum_probs=27.8
Q ss_pred ccccccCCCccCCCCceEEecCCceeEeechHHHHhh
Q 031225 6 ELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYF 42 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f 42 (163)
..|++|..+|.||.-+..-|-|. -|||.-|+...
T Consensus 17 ~~C~~C~k~L~~~~DiymYrGd~---aFCS~ECR~~q 50 (58)
T PF04570_consen 17 SFCYLCKKKLDPGKDIYMYRGDK---AFCSEECRSQQ 50 (58)
T ss_pred HHHHccCCCCCCCCCeeeecccc---ccccHHHHHHH
Confidence 46999999999999876666664 49999998654
No 21
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=77.72 E-value=0.76 Score=35.05 Aligned_cols=31 Identities=29% Similarity=0.462 Sum_probs=22.0
Q ss_pred CceeeccccccCCCccCCCCceEEecCCceeE
Q 031225 1 MVLKTELCRFSGAKIYPGKGIRFIRSDSQVFL 32 (163)
Q Consensus 1 mvmk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~ 32 (163)
|-|+...|+.||.+|--|.-..|.. .|.|.|
T Consensus 2 ~~lkewkC~VCg~~iieGqkFTF~~-kGsVH~ 32 (103)
T COG4847 2 MGLKEWKCYVCGGTIIEGQKFTFTK-KGSVHY 32 (103)
T ss_pred CccceeeEeeeCCEeeeccEEEEee-CCcchH
Confidence 6689999999999998765555544 344433
No 22
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=75.87 E-value=1.3 Score=31.17 Aligned_cols=27 Identities=22% Similarity=0.497 Sum_probs=22.0
Q ss_pred ceeeccccccCCCccCCCCceEEecCCceeEeechHHHH
Q 031225 2 VLKTELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKR 40 (163)
Q Consensus 2 vmk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~ 40 (163)
|.--..|-.||..|+||. .|||-+|..
T Consensus 5 v~PH~HC~VCg~aIp~de------------~~CSe~C~e 31 (64)
T COG4068 5 VVPHRHCVVCGKAIPPDE------------QVCSEECGE 31 (64)
T ss_pred CCCCccccccCCcCCCcc------------chHHHHHHH
Confidence 344567999999999985 689999973
No 23
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=62.54 E-value=5.9 Score=31.71 Aligned_cols=31 Identities=29% Similarity=0.636 Sum_probs=25.9
Q ss_pred ccccCCCccCCCCceEEecCCceeEeechHHHHh
Q 031225 8 CRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRY 41 (163)
Q Consensus 8 C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~ 41 (163)
|.-||..|. |.| .-|.-||.++.-|.+ |.++
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 789999999999986 5543
No 24
>PRK08359 transcription factor; Validated
Probab=60.14 E-value=6.4 Score=32.45 Aligned_cols=29 Identities=34% Similarity=0.705 Sum_probs=25.0
Q ss_pred ccccCCCccCCCCceEEecCCceeEeechHHH
Q 031225 8 CRFSGAKIYPGKGIRFIRSDSQVFLFANSKCK 39 (163)
Q Consensus 8 C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~ 39 (163)
|--||..|. |.| .-|.-||..+.-|++ |.
T Consensus 9 CEiCG~~i~-g~~-~~v~ieGael~VC~~-Ca 37 (176)
T PRK08359 9 CEICGAEIR-GPG-HRIRIEGAELLVCDR-CY 37 (176)
T ss_pred eecCCCccC-CCC-eEEEEcCeEEehHHH-HH
Confidence 999999995 655 789999999999986 55
No 25
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=58.96 E-value=7.4 Score=27.50 Aligned_cols=30 Identities=17% Similarity=0.346 Sum_probs=24.1
Q ss_pred eccccccCCCccCCCCceEEecCCceeEeechHHHH
Q 031225 5 TELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKR 40 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~ 40 (163)
++-|.|||..+ ..|+.++-.|+|+..+|..
T Consensus 6 lKPCPFCG~~~------~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 6 VKPCPFCGCPS------VTVKAISGYYRAKCNGCES 35 (64)
T ss_pred ccCCCCCCCce------eEEEecCceEEEEcCCCCc
Confidence 56799999875 4677778888898889976
No 26
>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=57.11 E-value=11 Score=23.90 Aligned_cols=25 Identities=20% Similarity=0.499 Sum_probs=18.1
Q ss_pred cccccCCCccCCCCceEEecCCceeEeech
Q 031225 7 LCRFSGAKIYPGKGIRFIRSDSQVFLFANS 36 (163)
Q Consensus 7 ~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ss 36 (163)
.|+-|+..|.++. |.-.||+ .||..
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 5899999998777 6667774 44543
No 27
>PF15585 Imm46: Immunity protein 46
Probab=53.69 E-value=7.4 Score=30.88 Aligned_cols=26 Identities=38% Similarity=0.799 Sum_probs=21.3
Q ss_pred CccCCC-CceEEecCC--------ceeEeechHHH
Q 031225 14 KIYPGK-GIRFIRSDS--------QVFLFANSKCK 39 (163)
Q Consensus 14 ~IyPG~-G~~~Vr~Dg--------kvf~F~ssKc~ 39 (163)
.|-||+ |.+|||.|= +||.++..+|.
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 999999875 78888888874
No 28
>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=53.68 E-value=6.8 Score=27.44 Aligned_cols=32 Identities=25% Similarity=0.482 Sum_probs=24.9
Q ss_pred ceeeccccccCCCccCCCCceEEecCCceeEeec
Q 031225 2 VLKTELCRFSGAKIYPGKGIRFIRSDSQVFLFAN 35 (163)
Q Consensus 2 vmk~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~s 35 (163)
+|.+++|+-| .+.|-|...+ +..+|+|=.|-+
T Consensus 33 ~~~vdi~s~~-HPfytG~~~~-~~~~Grv~KF~k 64 (69)
T PF01197_consen 33 VIKVDICSNC-HPFYTGKQKV-VDTAGRVEKFNK 64 (69)
T ss_dssp -EEECSCSSS-SCTTCSCSSC-SCCCCCCTSCCT
T ss_pred EEEEeecCCC-CEEEcCcEEE-EccccCHHHHHH
Confidence 4789999999 7999996554 888999877643
No 29
>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=52.43 E-value=9.6 Score=24.02 Aligned_cols=20 Identities=20% Similarity=0.252 Sum_probs=9.6
Q ss_pred ccccccCCCccCCCCceEEec
Q 031225 6 ELCRFSGAKIYPGKGIRFIRS 26 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~ 26 (163)
..|||||.+-... +.|+.-.
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 4699999987644 4444433
No 30
>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=51.53 E-value=7.5 Score=25.76 Aligned_cols=12 Identities=25% Similarity=0.728 Sum_probs=9.9
Q ss_pred cCCCccCCCCce
Q 031225 11 SGAKIYPGKGIR 22 (163)
Q Consensus 11 sg~~IyPG~G~~ 22 (163)
-..+||||+|.+
T Consensus 30 aEsPv~PGn~hl 41 (45)
T PF08384_consen 30 AESPVFPGNGHL 41 (45)
T ss_pred CCCCccCCCccc
Confidence 378999999965
No 31
>PF14353 CpXC: CpXC protein
Probab=49.75 E-value=17 Score=27.22 Aligned_cols=33 Identities=9% Similarity=0.191 Sum_probs=29.5
Q ss_pred eccccccCCCccCCCCceEEecCCceeEeechH
Q 031225 5 TELCRFSGAKIYPGKGIRFIRSDSQVFLFANSK 37 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssK 37 (163)
.-.|..||..++..+..+|...+.+.+.|....
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 32
>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=48.05 E-value=15 Score=20.91 Aligned_cols=25 Identities=24% Similarity=0.262 Sum_probs=19.0
Q ss_pred cccccCCCccCCCCceEEecCCceeEe
Q 031225 7 LCRFSGAKIYPGKGIRFIRSDSQVFLF 33 (163)
Q Consensus 7 ~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F 33 (163)
.|.-|+..|+++ ..++..+|..|+.
T Consensus 1 ~C~~C~~~i~~~--~~~~~~~~~~~H~ 25 (39)
T smart00132 1 KCAGCGKPIRGG--ELVLRALGKVWHP 25 (39)
T ss_pred CccccCCcccCC--cEEEEeCCccccc
Confidence 488899999998 5566677777754
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=43.32 E-value=17 Score=21.04 Aligned_cols=17 Identities=29% Similarity=0.602 Sum_probs=14.3
Q ss_pred ccccCCCccCCC-CceEE
Q 031225 8 CRFSGAKIYPGK-GIRFI 24 (163)
Q Consensus 8 C~Fsg~~IyPG~-G~~~V 24 (163)
|+-||..|.|.. |..|.
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
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.91 E-value=17 Score=25.29 Aligned_cols=41 Identities=20% Similarity=0.551 Sum_probs=28.8
Q ss_pred ceeeccccccCCCccCCC-CceEEe-cCCceeEeechHHHHhh
Q 031225 2 VLKTELCRFSGAKIYPGK-GIRFIR-SDSQVFLFANSKCKRYF 42 (163)
Q Consensus 2 vmk~~~C~Fsg~~IyPG~-G~~~Vr-~Dgkvf~F~ssKc~~~f 42 (163)
.|....|+-||..|.|+- +..|.= |=|.+...=-.+|+++.
T Consensus 4 ~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 4 MMEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred cccCccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 356778999999999876 777754 44566444456776654
No 35
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=40.57 E-value=31 Score=24.25 Aligned_cols=37 Identities=24% Similarity=0.632 Sum_probs=28.2
Q ss_pred eccccccCCCccCCCC-ceE-EecCCceeEeechHHHHh
Q 031225 5 TELCRFSGAKIYPGKG-IRF-IRSDSQVFLFANSKCKRY 41 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG~G-~~~-Vr~Dgkvf~F~ssKc~~~ 41 (163)
...|+-||..|.||.+ ..| --|=|.+...=..+|+++
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 5789999999999974 444 346677888878888765
No 36
>KOG3710 consensus EGL-Nine (EGLN) protein [Signal transduction mechanisms]
Probab=36.71 E-value=25 Score=31.00 Aligned_cols=22 Identities=32% Similarity=0.822 Sum_probs=17.1
Q ss_pred CccCCCCceEEec------CCcee---Eeec
Q 031225 14 KIYPGKGIRFIRS------DSQVF---LFAN 35 (163)
Q Consensus 14 ~IyPG~G~~~Vr~------Dgkvf---~F~s 35 (163)
.+|||.|.-|||. ||... ++||
T Consensus 148 AcYPGNGtgYVrHVDNP~gDGRcITcIYYlN 178 (280)
T KOG3710|consen 148 ACYPGNGTGYVRHVDNPHGDGRCITCIYYLN 178 (280)
T ss_pred EEecCCCceeeEeccCCCCCceEEEEEEEcc
Confidence 4799999999995 88754 4555
No 37
>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=34.87 E-value=19 Score=23.92 Aligned_cols=26 Identities=19% Similarity=0.511 Sum_probs=19.6
Q ss_pred ccccccCCCccCCCCceEEecCCceeEeec
Q 031225 6 ELCRFSGAKIYPGKGIRFIRSDSQVFLFAN 35 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~s 35 (163)
|+|..||-.|. .+....||++|.|+|
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 67788888875 455668899999986
No 38
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=33.63 E-value=22 Score=24.46 Aligned_cols=14 Identities=21% Similarity=0.380 Sum_probs=11.4
Q ss_pred ccccccCCCccCCC
Q 031225 6 ELCRFSGAKIYPGK 19 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~ 19 (163)
.-|.|||.+|.+|.
T Consensus 40 ngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 40 NGCPFCGTPFEFDD 53 (55)
T ss_pred cCCCCCCCcccCCC
Confidence 34999999999874
No 39
>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=32.48 E-value=49 Score=23.88 Aligned_cols=36 Identities=17% Similarity=0.326 Sum_probs=29.5
Q ss_pred cccccCCCccCCCCceEEecCCceeEeechHHHHhhh
Q 031225 7 LCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFH 43 (163)
Q Consensus 7 ~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~ 43 (163)
.|+-||.+|.+|. .+.+..||....||=.=|...+.
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 4999999997554 56677889999999999987554
No 40
>KOG1549 consensus Cysteine desulfurase NFS1 [Amino acid transport and metabolism]
Probab=32.38 E-value=24 Score=32.98 Aligned_cols=27 Identities=33% Similarity=0.677 Sum_probs=22.7
Q ss_pred eeeccccccCCCcc--CCCCceEEecCCc
Q 031225 3 LKTELCRFSGAKIY--PGKGIRFIRSDSQ 29 (163)
Q Consensus 3 mk~~~C~Fsg~~Iy--PG~G~~~Vr~Dgk 29 (163)
|.++.|++|+.+|| ||=|-+|||.|..
T Consensus 232 ln~D~~s~s~HK~ygp~~iGaLYvr~~~~ 260 (428)
T KOG1549|consen 232 LNADFLSISAHKIYGPPGIGALYVRRKRP 260 (428)
T ss_pred cCchheeeecccccCCCcceEEEEccCCC
Confidence 56789999999998 7789999998543
No 41
>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=30.22 E-value=30 Score=22.38 Aligned_cols=18 Identities=39% Similarity=0.779 Sum_probs=15.6
Q ss_pred cCCCccCC-CCceEEecCC
Q 031225 11 SGAKIYPG-KGIRFIRSDS 28 (163)
Q Consensus 11 sg~~IyPG-~G~~~Vr~Dg 28 (163)
-|..||-| .|..||..|+
T Consensus 7 kgR~i~~g~rGg~yV~~~~ 25 (40)
T PF08789_consen 7 KGRKIFKGPRGGTYVISDG 25 (40)
T ss_pred cCCEEEECCCCCEEEeCCC
Confidence 47889999 5999999996
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=29.80 E-value=27 Score=29.63 Aligned_cols=27 Identities=15% Similarity=0.112 Sum_probs=22.7
Q ss_pred ccCCCCceEEec-CCc--eeEeechHHHHh
Q 031225 15 IYPGKGIRFIRS-DSQ--VFLFANSKCKRY 41 (163)
Q Consensus 15 IyPG~G~~~Vr~-Dgk--vf~F~ssKc~~~ 41 (163)
+|||+|.+.=+. ||+ +.+|++|..+.+
T Consensus 1 MY~GR~ivvG~s~dG~~~~aY~V~sRSfpn 30 (199)
T TIGR01922 1 MYIGRFLVVGKLEDGTPFAAYRVSSRSFPN 30 (199)
T ss_pred CCCCCEEEEccCCCCCeEEEEEEecCCCCC
Confidence 599999999888 997 778999887655
No 43
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=29.64 E-value=21 Score=26.76 Aligned_cols=30 Identities=20% Similarity=0.445 Sum_probs=23.4
Q ss_pred eccccccCCCccCCCCceEEecCCceeEeechHHHHhhh
Q 031225 5 TELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFH 43 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~ 43 (163)
...|.|||.++ |++-+.-.|-|+ ||..-|.
T Consensus 35 ~~~Cp~C~~~~--------VkR~a~GIW~C~-kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRTT--------VKRIATGIWKCR-KCGAKFA 64 (89)
T ss_pred CCcCCCCCCcc--------eeeeccCeEEcC-CCCCeec
Confidence 34699998874 777888899998 8877665
No 44
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=28.17 E-value=39 Score=21.29 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=19.8
Q ss_pred eccccccCCCccCCCCceEEecCCceeEeechHH
Q 031225 5 TELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKC 38 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc 38 (163)
.-.|..||..... ..++.+..+|.|++.-
T Consensus 5 ~l~C~~CG~~m~~-----~~~~~~~~yy~C~~~~ 33 (58)
T PF13408_consen 5 LLRCGHCGSKMTR-----RKRKGKYRYYRCSNRR 33 (58)
T ss_pred cEEcccCCcEeEE-----EECCCCceEEEcCCCc
Confidence 3469999988775 2233556888888763
No 45
>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=26.99 E-value=31 Score=26.16 Aligned_cols=36 Identities=14% Similarity=0.326 Sum_probs=22.7
Q ss_pred eccccccCCCccCC-CCceEEec--CCceeEeechHHHHh
Q 031225 5 TELCRFSGAKIYPG-KGIRFIRS--DSQVFLFANSKCKRY 41 (163)
Q Consensus 5 ~~~C~Fsg~~IyPG-~G~~~Vr~--Dgkvf~F~ssKc~~~ 41 (163)
...|.|||.++.== .-.+|-+. |+..||.|+. |...
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~-C~Ay 40 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTP-CDAY 40 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCC-CCce
Confidence 46799998764321 12334433 5788899998 8764
No 46
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=26.88 E-value=28 Score=31.80 Aligned_cols=14 Identities=29% Similarity=0.420 Sum_probs=10.5
Q ss_pred eeeccccccCCCcc
Q 031225 3 LKTELCRFSGAKIY 16 (163)
Q Consensus 3 mk~~~C~Fsg~~Iy 16 (163)
+....|||||.+=.
T Consensus 7 ~~~~~CSFCGr~~~ 20 (412)
T PRK05342 7 KKLLYCSFCGKSQH 20 (412)
T ss_pred CCccccCCCCCChh
Confidence 45678999998633
No 47
>PRK13446 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=26.81 E-value=54 Score=25.29 Aligned_cols=18 Identities=17% Similarity=0.322 Sum_probs=12.0
Q ss_pred CCCccCCC---------CceEEecCCc
Q 031225 12 GAKIYPGK---------GIRFIRSDSQ 29 (163)
Q Consensus 12 g~~IyPG~---------G~~~Vr~Dgk 29 (163)
++-|+||| |.+.|+.||.
T Consensus 32 ~~gILp~H~p~it~L~~G~l~i~~~~~ 58 (136)
T PRK13446 32 EFGVLPGHAPFLTALKIGELTYKKGGK 58 (136)
T ss_pred CeEEcCCCcceEEEeeccEEEEEeCCc
Confidence 35789999 5555655555
No 48
>PF15279 SOBP: Sine oculis-binding protein
Probab=26.24 E-value=24 Score=31.48 Aligned_cols=28 Identities=14% Similarity=0.405 Sum_probs=20.0
Q ss_pred CCceEEec-CC-ceeEeechHHHHhhhccC
Q 031225 19 KGIRFIRS-DS-QVFLFANSKCKRYFHNRL 46 (163)
Q Consensus 19 ~G~~~Vr~-Dg-kvf~F~ssKc~~~f~~kr 46 (163)
|-.=||.- || .-+.|||.||-+-|+|-.
T Consensus 10 h~~~y~d~~~g~~~lqfcs~kclnqykm~i 39 (306)
T PF15279_consen 10 HTKSYVDFQDGERQLQFCSDKCLNQYKMDI 39 (306)
T ss_pred chhheeccccchHHhhhccHHHHhHHHHHH
Confidence 44455543 66 468999999999888753
No 49
>PRK06424 transcription factor; Provisional
Probab=26.22 E-value=45 Score=26.49 Aligned_cols=30 Identities=17% Similarity=0.520 Sum_probs=25.4
Q ss_pred ccccCCCccCCCCceEEecCCceeEeechHHHHh
Q 031225 8 CRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRY 41 (163)
Q Consensus 8 C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~ 41 (163)
|..||..|. |...|..||..+..|.+ |.++
T Consensus 3 CE~CG~~~~---~~~~v~ieg~~l~vC~~-Ca~~ 32 (144)
T PRK06424 3 CEMCGKKVP---QTTKVMIDGAILNVCDD-CAKF 32 (144)
T ss_pred ccccCcccC---CceEEEEcCeeeehhHH-HHHc
Confidence 999999997 44899999999999964 6554
No 50
>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=26.03 E-value=32 Score=23.62 Aligned_cols=12 Identities=25% Similarity=0.678 Sum_probs=10.1
Q ss_pred ccccccCCCccC
Q 031225 6 ELCRFSGAKIYP 17 (163)
Q Consensus 6 ~~C~Fsg~~IyP 17 (163)
..|.|||.++++
T Consensus 36 ~pC~fCg~~l~~ 47 (57)
T PF06221_consen 36 GPCPFCGTPLLS 47 (57)
T ss_pred CcCCCCCCcccC
Confidence 579999998875
No 51
>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=26.01 E-value=19 Score=31.25 Aligned_cols=22 Identities=18% Similarity=0.239 Sum_probs=17.1
Q ss_pred ccccccCCCccCCCCceEEecC
Q 031225 6 ELCRFSGAKIYPGKGIRFIRSD 27 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~D 27 (163)
..|.||++...||+-..|.+..
T Consensus 16 ~~C~fCaf~~~~g~~~~~~l~~ 37 (322)
T TIGR03550 16 NRCGYCTFRRPPGELEAALLSP 37 (322)
T ss_pred CCCccCCccccCCCcccccCCH
Confidence 5699999999998866665543
No 52
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=25.71 E-value=23 Score=26.57 Aligned_cols=29 Identities=21% Similarity=0.433 Sum_probs=19.3
Q ss_pred ccccccCCCccCCCCceEEecCCceeEeechHHHHhhh
Q 031225 6 ELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRYFH 43 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~f~ 43 (163)
.+|+|||.. -|.+.---.|-|+ .|.+.|-
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 479999864 3555556677777 6765543
No 53
>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=25.52 E-value=49 Score=23.41 Aligned_cols=49 Identities=14% Similarity=0.295 Sum_probs=29.0
Q ss_pred ccccccCCCccCCCCceEE--ecCCceeEeec-hHHHHhhhcc-CCCccchhhH
Q 031225 6 ELCRFSGAKIYPGKGIRFI--RSDSQVFLFAN-SKCKRYFHNR-LKPSKLTWTS 55 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~V--r~Dgkvf~F~s-sKc~~~f~~k-rnPRki~WT~ 55 (163)
...+|||+..+||.+-.++ ..||. +.|++ .-....-..- ....-+.|+.
T Consensus 24 ni~YltG~~~~~~~~~~~l~i~~~~~-~l~~~~~~~~~~~~~~~~~~~v~~~~~ 76 (132)
T PF01321_consen 24 NIRYLTGFRWQPGERPVLLVITADGA-VLFVPKGEYERAAEESAPDDEVVEYED 76 (132)
T ss_dssp HHHHHHS--ST-TSSEEEEEEESSSE-EEEEEGGGHHHHHHHHTTSSEEEEEST
T ss_pred hceEecCCCcCCCcceEEEEecccCc-EEEeccccHHHHHHhhcCCceEEEEec
Confidence 4578999988888866655 88999 77777 5555443322 3344444444
No 54
>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=25.38 E-value=56 Score=24.93 Aligned_cols=28 Identities=7% Similarity=0.038 Sum_probs=22.0
Q ss_pred eEEecCCceeEeechHHHHhhhccCCCc
Q 031225 22 RFIRSDSQVFLFANSKCKRYFHNRLKPS 49 (163)
Q Consensus 22 ~~Vr~Dgkvf~F~ssKc~~~f~~krnPR 49 (163)
.|+.-||.+++|++..-.+.-..++||+
T Consensus 32 ~~~~d~g~l~f~t~~~~~K~~nl~~np~ 59 (132)
T TIGR03666 32 WAAVDGDKLLVRTKEDSWKVKRIRNNPR 59 (132)
T ss_pred EEEEECCEEEEEECCcCHHHHHHHhCCC
Confidence 5666788888888777777778888997
No 55
>PRK04151 IMP cyclohydrolase; Provisional
Probab=24.33 E-value=39 Score=28.63 Aligned_cols=26 Identities=12% Similarity=0.184 Sum_probs=21.6
Q ss_pred ccCCCCceEEec-CCc--eeEeechHHHH
Q 031225 15 IYPGKGIRFIRS-DSQ--VFLFANSKCKR 40 (163)
Q Consensus 15 IyPG~G~~~Vr~-Dgk--vf~F~ssKc~~ 40 (163)
.|||+|.+.=+. ||+ +.+|.+|..+.
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 56
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.66 E-value=45 Score=18.62 Aligned_cols=11 Identities=36% Similarity=0.561 Sum_probs=9.1
Q ss_pred ccccCCCccCC
Q 031225 8 CRFSGAKIYPG 18 (163)
Q Consensus 8 C~Fsg~~IyPG 18 (163)
|..||..|.++
T Consensus 2 Cp~CG~~~~~~ 12 (23)
T PF13240_consen 2 CPNCGAEIEDD 12 (23)
T ss_pred CcccCCCCCCc
Confidence 88899998865
No 57
>PRK08445 hypothetical protein; Provisional
Probab=22.20 E-value=50 Score=29.30 Aligned_cols=20 Identities=15% Similarity=0.124 Sum_probs=16.5
Q ss_pred ccccccCCCccCCCCceEEe
Q 031225 6 ELCRFSGAKIYPGKGIRFIR 25 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr 25 (163)
+.|.||+..-.++++..|+.
T Consensus 54 ~~C~FCa~~~~~~~~~~y~l 73 (348)
T PRK08445 54 VDCKFCAFYRHLKEDDAYIL 73 (348)
T ss_pred cCCccCCCccCCCCCCCeeC
Confidence 57999999998888877744
No 58
>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=22.14 E-value=64 Score=22.13 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=15.0
Q ss_pred ccccccCCCccCCCCceEEecCCceeEeechHHHHh
Q 031225 6 ELCRFSGAKIYPGKGIRFIRSDSQVFLFANSKCKRY 41 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr~Dgkvf~F~ssKc~~~ 41 (163)
-.|.-||..+.+. .+...+=|||..|...
T Consensus 3 v~CP~C~k~~~~~-------~~n~~rPFCS~RCk~i 31 (57)
T PF03884_consen 3 VKCPICGKPVEWS-------PENPFRPFCSERCKLI 31 (57)
T ss_dssp EE-TTT--EEE-S-------SSSS--SSSSHHHHHH
T ss_pred ccCCCCCCeeccc-------CCCCcCCcccHhhccc
Confidence 3587777766653 2234455999999753
No 59
>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=22.12 E-value=39 Score=24.79 Aligned_cols=26 Identities=31% Similarity=0.331 Sum_probs=18.0
Q ss_pred eeeccccccCCCc-cCCCCc--eEEecCC
Q 031225 3 LKTELCRFSGAKI-YPGKGI--RFIRSDS 28 (163)
Q Consensus 3 mk~~~C~Fsg~~I-yPG~G~--~~Vr~Dg 28 (163)
|+...+.||||.| +|-... ++|..||
T Consensus 39 ~~~~~V~fagY~vpHPl~~~~~l~i~t~~ 67 (93)
T cd06926 39 LKDPNVLFAGYKVPHPLEHKIELRIQTDG 67 (93)
T ss_pred hcCCCeeEEeeccCCCCCCceEEEEEeCC
Confidence 5667789999999 576544 4455565
No 60
>PRK08444 hypothetical protein; Provisional
Probab=21.36 E-value=47 Score=29.71 Aligned_cols=20 Identities=10% Similarity=0.291 Sum_probs=16.2
Q ss_pred ccccccCCCccCCCCceEEe
Q 031225 6 ELCRFSGAKIYPGKGIRFIR 25 (163)
Q Consensus 6 ~~C~Fsg~~IyPG~G~~~Vr 25 (163)
+.|.||++...+++..-|.-
T Consensus 61 ~~C~FCaf~~~~~~~~~y~l 80 (353)
T PRK08444 61 DVCKFCAFSAHRKNPNPYTM 80 (353)
T ss_pred cCCccCCCccCCCCCccccC
Confidence 67999999999998765643
No 61
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.28 E-value=35 Score=22.85 Aligned_cols=9 Identities=33% Similarity=1.036 Sum_probs=7.0
Q ss_pred cccccCCCc
Q 031225 7 LCRFSGAKI 15 (163)
Q Consensus 7 ~C~Fsg~~I 15 (163)
-|.+||++|
T Consensus 26 rCp~Cg~rI 34 (49)
T COG1996 26 RCPYCGSRI 34 (49)
T ss_pred eCCCCCcEE
Confidence 488888876
No 62
>KOG2361 consensus Predicted methyltransferase [General function prediction only]
Probab=21.02 E-value=74 Score=28.14 Aligned_cols=24 Identities=17% Similarity=0.455 Sum_probs=19.0
Q ss_pred CceEEecCCce-eEeechHHHHhhh
Q 031225 20 GIRFIRSDSQV-FLFANSKCKRYFH 43 (163)
Q Consensus 20 G~~~Vr~Dgkv-f~F~ssKc~~~f~ 43 (163)
+..|||-||+. |+|+.-.-..+|.
T Consensus 202 ~nfYVRgDGT~~YfF~~eeL~~~f~ 226 (264)
T KOG2361|consen 202 ENFYVRGDGTRAYFFTEEELDELFT 226 (264)
T ss_pred cceEEccCCceeeeccHHHHHHHHH
Confidence 67899999996 8888877665553
No 63
>smart00696 DM9 Repeats found in Drosophila proteins.
Probab=20.68 E-value=64 Score=22.50 Aligned_cols=20 Identities=25% Similarity=0.438 Sum_probs=17.7
Q ss_pred CccCCCCceEEecCCceeEe
Q 031225 14 KIYPGKGIRFIRSDSQVFLF 33 (163)
Q Consensus 14 ~IyPG~G~~~Vr~Dgkvf~F 33 (163)
+|.|.||..||--||.-+.+
T Consensus 43 Kv~p~~~~~yi~~~g~E~~~ 62 (71)
T smart00696 43 KVVPSHGCAYIPYGGQEVRL 62 (71)
T ss_pred EEEccCCEEEEEECCEEEEc
Confidence 58899999999999998776
No 64
>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=20.49 E-value=43 Score=20.33 Aligned_cols=9 Identities=33% Similarity=0.634 Sum_probs=6.7
Q ss_pred cccccCCCc
Q 031225 7 LCRFSGAKI 15 (163)
Q Consensus 7 ~C~Fsg~~I 15 (163)
.|.+||+.|
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 699999887
Done!