Query psy14411
Match_columns 85
No_of_seqs 101 out of 124
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 19:11:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14411hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06732 Pescadillo_N: Pescadi 100.0 5.3E-45 1.2E-49 282.7 6.2 81 5-85 1-81 (281)
2 KOG2481|consensus 100.0 2E-43 4.3E-48 292.2 5.8 84 2-85 1-84 (570)
3 COG5163 NOP7 Protein required 100.0 1.2E-36 2.6E-41 250.0 6.0 83 3-85 2-84 (591)
4 PF00867 XPG_I: XPG I-region; 89.4 0.3 6.4E-06 31.5 2.1 30 12-41 63-92 (94)
5 TIGR01764 excise DNA binding d 87.5 0.66 1.4E-05 25.0 2.4 46 16-72 1-46 (49)
6 PF12728 HTH_17: Helix-turn-he 85.6 2.2 4.8E-05 24.1 4.0 47 16-73 1-47 (51)
7 cd04762 HTH_MerR-trunc Helix-T 82.9 4.1 9E-05 21.5 4.2 47 17-73 1-47 (49)
8 cd04761 HTH_MerR-SF Helix-Turn 80.5 5.1 0.00011 21.8 4.1 47 17-73 1-47 (49)
9 PRK03980 flap endonuclease-1; 69.8 3.9 8.5E-05 31.9 2.3 28 14-41 160-187 (292)
10 cd00080 HhH2_motif Helix-hairp 68.1 2.5 5.3E-05 26.6 0.8 24 25-48 2-29 (75)
11 PF02042 RWP-RK: RWP-RK domain 65.7 12 0.00025 23.0 3.4 33 17-50 16-48 (52)
12 cd00128 XPG Xeroderma pigmento 57.3 9.4 0.0002 29.2 2.4 29 13-41 193-221 (316)
13 PF05930 Phage_AlpA: Prophage 57.3 9.1 0.0002 22.1 1.8 47 15-70 2-48 (51)
14 PTZ00217 flap endonuclease-1; 55.6 11 0.00024 30.7 2.6 28 14-41 206-233 (393)
15 PF08127 Propeptide_C1: Peptid 54.9 6.1 0.00013 22.9 0.8 18 27-47 24-41 (41)
16 KOG2518|consensus 53.8 7 0.00015 34.0 1.3 32 10-42 189-224 (556)
17 TIGR03674 fen_arch flap struct 52.4 12 0.00026 29.5 2.3 28 15-42 208-235 (338)
18 cd01106 HTH_TipAL-Mta Helix-Tu 51.2 37 0.0008 21.8 4.1 47 18-73 2-48 (103)
19 cd04763 HTH_MlrA-like Helix-Tu 50.1 45 0.00097 19.7 4.1 48 18-74 2-49 (68)
20 PF02887 PK_C: Pyruvate kinase 49.6 7.3 0.00016 25.5 0.6 17 29-45 48-64 (117)
21 smart00422 HTH_MERR helix_turn 49.6 50 0.0011 19.0 4.3 48 17-73 1-48 (70)
22 PF08569 Mo25: Mo25-like; Int 47.8 8.6 0.00019 30.7 0.8 16 12-27 219-234 (335)
23 PF05997 Nop52: Nucleolar prot 47.2 8.8 0.00019 28.5 0.8 27 15-43 13-48 (217)
24 PF06627 DUF1153: Protein of u 44.0 15 0.00033 25.1 1.4 22 15-36 48-69 (90)
25 PF05356 Phage_Coat_B: Phage C 42.1 8.5 0.00018 26.0 0.0 14 29-42 13-26 (83)
26 PF07021 MetW: Methionine bios 38.4 18 0.00039 27.3 1.3 16 28-43 146-161 (193)
27 PF13411 MerR_1: MerR HTH fami 38.0 82 0.0018 18.2 4.1 47 17-73 1-47 (69)
28 PF03683 UPF0175: Uncharacteri 37.4 43 0.00094 21.0 2.7 28 16-43 34-61 (76)
29 PF14898 DUF4491: Domain of un 37.3 16 0.00034 25.1 0.8 13 38-50 82-94 (94)
30 PF06709 DUF1196: Protein of u 36.4 12 0.00026 23.2 0.0 14 31-46 18-31 (51)
31 KOG1266|consensus 36.2 20 0.00044 30.5 1.3 36 9-45 155-192 (458)
32 KOG3911|consensus 36.0 23 0.00049 29.6 1.6 28 14-43 19-57 (378)
33 smart00878 Biotin_carb_C Bioti 35.0 14 0.00031 24.8 0.3 17 18-34 60-76 (107)
34 smart00475 53EXOc 5'-3' exonuc 33.9 37 0.00081 25.9 2.4 34 15-48 156-193 (259)
35 PF12418 AcylCoA_DH_N: Acyl-Co 32.2 17 0.00038 19.8 0.3 12 65-76 6-17 (34)
36 KOG3981|consensus 31.8 25 0.00054 28.6 1.2 18 30-48 73-90 (326)
37 KOG1566|consensus 29.8 24 0.00052 29.1 0.8 18 10-27 220-237 (342)
38 PRK13182 racA polar chromosome 28.9 1.3E+02 0.0028 22.1 4.4 46 18-73 2-47 (175)
39 cd00008 53EXOc 5'-3' exonuclea 27.8 56 0.0012 24.4 2.4 33 15-47 153-189 (240)
40 cd00592 HTH_MerR-like Helix-Tu 26.4 1.4E+02 0.0029 18.7 3.7 46 18-73 2-47 (100)
41 PF02785 Biotin_carb_C: Biotin 25.9 25 0.00055 23.7 0.2 17 18-34 60-76 (107)
42 TIGR03277 methan_mark_9 putati 25.5 54 0.0012 23.2 1.8 19 18-36 29-47 (109)
43 PF07766 LETM1: LETM1-like pro 25.1 66 0.0014 24.6 2.4 27 20-46 209-238 (268)
44 PRK14976 5'-3' exonuclease; Pr 24.9 73 0.0016 24.6 2.6 35 14-48 160-198 (281)
45 cd01105 HTH_GlnR-like Helix-Tu 24.7 1.7E+02 0.0038 18.4 4.0 48 17-73 2-49 (88)
46 cd04773 HTH_TioE_rpt2 Second H 23.6 1.9E+02 0.0041 18.9 4.1 48 17-73 1-48 (108)
47 smart00279 HhH2 Helix-hairpin- 23.3 49 0.0011 18.4 1.0 14 31-44 2-15 (36)
48 cd04766 HTH_HspR Helix-Turn-He 23.2 2E+02 0.0043 18.0 4.2 48 16-73 1-48 (91)
49 PF10206 WRW: Mitochondrial F1 22.6 33 0.00072 23.7 0.3 29 41-72 4-32 (104)
50 PF02002 TFIIE_alpha: TFIIE al 22.5 77 0.0017 20.3 2.0 23 15-37 26-48 (105)
51 COG2177 FtsX Cell division pro 22.5 43 0.00094 26.4 1.0 19 13-31 89-107 (297)
52 PRK02515 psbU photosystem II c 21.4 39 0.00085 24.4 0.5 42 24-72 51-92 (132)
53 cd04985 IgC_CH1 CH1 domain (fi 21.2 26 0.00056 22.6 -0.4 12 36-47 22-33 (95)
54 TIGR01064 pyruv_kin pyruvate k 20.8 41 0.00088 28.0 0.6 19 29-47 405-423 (473)
55 smart00684 DM15 Tandem repeat 20.5 53 0.0012 18.9 0.8 8 31-38 8-15 (39)
56 cd04789 HTH_Cfa Helix-Turn-Hel 20.3 2.6E+02 0.0055 18.1 4.8 47 17-73 2-48 (102)
No 1
>PF06732 Pescadillo_N: Pescadillo N-terminus; InterPro: IPR010613 Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest []. ; GO: 0042254 ribosome biogenesis, 0005730 nucleolus
Probab=100.00 E-value=5.3e-45 Score=282.70 Aligned_cols=81 Identities=57% Similarity=0.894 Sum_probs=79.4
Q ss_pred cccccccccchhccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhhcChhHHHhhhc
Q psy14411 5 QKKYEAGEAVRYITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLLHEPNLVIMRQQ 84 (85)
Q Consensus 5 ~kk~~~G~~~~yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~hePil~kfRe~ 84 (85)
+|||++|++++||||+||+++|||||+||||||||||||||||++++++|+||++++||||+|||+||+||||+++|||+
T Consensus 1 kkK~~~g~a~~yiTR~qAlkkLQlsl~dFRRLCILKGIyPrePk~k~k~~kg~~~~ktyY~~KDI~~L~hepil~kfRe~ 80 (281)
T PF06732_consen 1 KKKGEKGEAKNYITRNQALKKLQLSLKDFRRLCILKGIYPREPKKKKKVNKGSTAPKTYYHIKDIKFLAHEPILQKFREI 80 (281)
T ss_pred CCCcccccccccccHHHHHHHhcCCHHHHhhHHhhcCccCCCCCcccccccCCCCCceEEEHHHHHHHhccHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred C
Q psy14411 85 R 85 (85)
Q Consensus 85 r 85 (85)
|
T Consensus 81 k 81 (281)
T PF06732_consen 81 K 81 (281)
T ss_pred H
Confidence 5
No 2
>KOG2481|consensus
Probab=100.00 E-value=2e-43 Score=292.24 Aligned_cols=84 Identities=52% Similarity=0.910 Sum_probs=81.5
Q ss_pred ccccccccccccchhccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhhcChhHHHh
Q psy14411 2 VIRQKKYEAGEAVRYITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLLHEPNLVIM 81 (85)
Q Consensus 2 ~~~~kk~~~G~~~~yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~hePil~kf 81 (85)
++.++|+++|+|+|||||+||+|+|||||+||||||||||||||||++++|+|||||+++||||+|||+||+||||+|||
T Consensus 1 ~r~kkk~~~G~A~~YiTr~qAlKkLQLsLaDFRRLCIlKGIYP~EPKhkkK~NKGSta~~tfY~~kDI~fLlHEpIv~Kf 80 (570)
T KOG2481|consen 1 GREKKKYERGSATNYITRSQALKKLQLSLADFRRLCILKGIYPREPKHKKKVNKGSTAAQTFYYIKDIRFLLHEPIVNKF 80 (570)
T ss_pred CCccccccccchhhhhhHHHHHHHhcccHHHHhhHhhhccccCCCcchhhhcccCCCCcceeeeHhHHHHHhhhHHHHHH
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcC
Q psy14411 82 RQQR 85 (85)
Q Consensus 82 Re~r 85 (85)
||++
T Consensus 81 reyK 84 (570)
T KOG2481|consen 81 REYK 84 (570)
T ss_pred HHHH
Confidence 9975
No 3
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-36 Score=250.01 Aligned_cols=83 Identities=48% Similarity=0.799 Sum_probs=80.5
Q ss_pred cccccccccccchhccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhhcChhHHHhh
Q psy14411 3 IRQKKYEAGEAVRYITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLLHEPNLVIMR 82 (85)
Q Consensus 3 ~~~kk~~~G~~~~yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~hePil~kfR 82 (85)
+.++|++.|+|.+||||+||+++|||+|+||||||||||||||||++++|+|+|||++.|||+++||++|+|||++.+||
T Consensus 2 rik~kn~~g~ar~yItr~qa~kkLql~ladFrrlcilkGvYPrePknkkKankGstap~tfYy~kDiqyL~Hepv~~kfr 81 (591)
T COG5163 2 RIKGKNYIGPARKYITRGQAMKKLQLRLADFRRLCILKGVYPREPKNKKKANKGSTAPGTFYYIKDIQYLAHEPVYRKFR 81 (591)
T ss_pred cccccCcccchhhheeHHHHHHHhcccHHHHhhHhhhcccccCCCccchhcccCCCCceeEEEehhhHHHhccHHHHHHH
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q psy14411 83 QQR 85 (85)
Q Consensus 83 e~r 85 (85)
|++
T Consensus 82 e~K 84 (591)
T COG5163 82 ENK 84 (591)
T ss_pred HhH
Confidence 974
No 4
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=89.39 E-value=0.3 Score=31.53 Aligned_cols=30 Identities=43% Similarity=0.600 Sum_probs=27.0
Q ss_pred ccchhccHHHHHHHhcCChhhhhhhhhhcc
Q psy14411 12 EAVRYITRRGALKKLQVTLKQFRTLCILKG 41 (85)
Q Consensus 12 ~~~~yitR~qAlkkLQlsl~dFRRLCILKG 41 (85)
.....++....++.|++|.++|.-+|||=|
T Consensus 63 ~~~~~~~~~~i~~~l~l~~~~fi~~~iL~G 92 (94)
T PF00867_consen 63 KEVEVIDLDDILKELGLTREQFIDLCILCG 92 (94)
T ss_dssp SEEEEEEHHHHHHHHTTSHHHHHHHHHHHH
T ss_pred cceEEEEHHHHHHHcCCCHHHHHHHheecC
Confidence 346789999999999999999999999977
No 5
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=87.48 E-value=0.66 Score=24.99 Aligned_cols=46 Identities=24% Similarity=0.239 Sum_probs=35.5
Q ss_pred hccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHh
Q psy14411 16 YITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFL 72 (85)
Q Consensus 16 yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L 72 (85)
|+|-.+|.+.|++|..-++++|- .|..|.. +. | ....|...||.-.
T Consensus 1 ~lt~~e~a~~lgis~~ti~~~~~-~g~i~~~-~~------g---~~~~~~~~~l~~~ 46 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKDTVYRLIH-EGELPAY-RV------G---RHYRIPREDVDEY 46 (49)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH-cCCCCeE-Ee------C---CeEEEeHHHHHHH
Confidence 78999999999999999999974 5766642 11 1 2578888888654
No 6
>PF12728 HTH_17: Helix-turn-helix domain
Probab=85.58 E-value=2.2 Score=24.08 Aligned_cols=47 Identities=19% Similarity=0.167 Sum_probs=35.7
Q ss_pred hccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 16 YITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 16 yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
|+|-.||...|+||...++++|-=. -.|.- + . ..+.+|...||.-.+
T Consensus 1 ~lt~~e~a~~l~is~~tv~~~~~~g-~i~~~---~----~---g~~~~~~~~~l~~~~ 47 (51)
T PF12728_consen 1 YLTVKEAAELLGISRSTVYRWIRQG-KIPPF---K----I---GRKWRIPKSDLDRWL 47 (51)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHcC-CCCeE---E----e---CCEEEEeHHHHHHHH
Confidence 7899999999999999999999644 44333 1 1 236999999986543
No 7
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=82.93 E-value=4.1 Score=21.49 Aligned_cols=47 Identities=21% Similarity=0.270 Sum_probs=34.4
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
+|..++.+.|+||...+++++= .|..|.. +. . .....|...||.-++
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~-~g~~~~~--~~--~-----~~~~~~~~~ei~~~~ 47 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVK-EGKLKAI--RT--P-----GGHRRFPEEDLERLL 47 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-cCCCCce--eC--C-----CCceecCHHHHHHHH
Confidence 4778999999999999999964 6777632 11 0 135789999987654
No 8
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=80.49 E-value=5.1 Score=21.83 Aligned_cols=47 Identities=23% Similarity=0.206 Sum_probs=34.8
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
+|-.++-+.|+||..-+|++ +=+|.-| |.... ...-+|...||.-|.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~-~~~g~l~--~~~~~-------~~~~~y~~~~v~~l~ 47 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYY-ERIGLLS--PARTE-------GGYRLYSDADLERLR 47 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHH-HHCCCCC--CCcCC-------CCCEEeCHHHHHHhh
Confidence 46788999999999999976 6788887 43211 135688999987763
No 9
>PRK03980 flap endonuclease-1; Provisional
Probab=69.81 E-value=3.9 Score=31.86 Aligned_cols=28 Identities=32% Similarity=0.412 Sum_probs=25.7
Q ss_pred chhccHHHHHHHhcCChhhhhhhhhhcc
Q psy14411 14 VRYITRRGALKKLQVTLKQFRTLCILKG 41 (85)
Q Consensus 14 ~~yitR~qAlkkLQlsl~dFRRLCILKG 41 (85)
..+++.+..+..|+|+.++|--+|||=|
T Consensus 160 ~e~~~~~~vl~~lgl~~~q~id~~iL~G 187 (292)
T PRK03980 160 PELIELEEVLKELGITREQLIDIAILVG 187 (292)
T ss_pred ceeeeHHHHHHHhCCCHHHHHHHHHhcC
Confidence 3479999999999999999999999987
No 10
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=68.07 E-value=2.5 Score=26.60 Aligned_cols=24 Identities=46% Similarity=0.542 Sum_probs=19.4
Q ss_pred HhcCChhhhhhhhhhcc----cCCCCCc
Q psy14411 25 KLQVTLKQFRTLCILKG----VYPREPI 48 (85)
Q Consensus 25 kLQlsl~dFRRLCILKG----IyPreP~ 48 (85)
+++++.++|..+|+|-| -.|-.|.
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~g 29 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPG 29 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCc
Confidence 57899999999999999 2366663
No 11
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=65.73 E-value=12 Score=22.96 Aligned_cols=33 Identities=27% Similarity=0.555 Sum_probs=28.7
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKR 50 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k 50 (85)
++-++|-+.|+||...+-|+|=-=|| ||=|-.+
T Consensus 16 lp~~eAA~~Lgv~~T~LKr~CR~~GI-~RWP~Rk 48 (52)
T PF02042_consen 16 LPIKEAAKELGVSVTTLKRRCRRLGI-PRWPYRK 48 (52)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHcCC-CCCCchh
Confidence 67789999999999999999999998 7777554
No 12
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=57.31 E-value=9.4 Score=29.15 Aligned_cols=29 Identities=34% Similarity=0.398 Sum_probs=25.8
Q ss_pred cchhccHHHHHHHhcCChhhhhhhhhhcc
Q psy14411 13 AVRYITRRGALKKLQVTLKQFRTLCILKG 41 (85)
Q Consensus 13 ~~~yitR~qAlkkLQlsl~dFRRLCILKG 41 (85)
....++.+..++.|+|+.++|--+|||=|
T Consensus 193 ~~~~~~~~~~~~~lgl~~~q~id~~~L~G 221 (316)
T cd00128 193 PVEEIDLEKILKELGLTREKLIDLAILLG 221 (316)
T ss_pred ceEEEEHHHHHHHcCCCHHHHHHHHHhcC
Confidence 44568899999999999999999999876
No 13
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=57.30 E-value=9.1 Score=22.11 Aligned_cols=47 Identities=17% Similarity=0.327 Sum_probs=23.7
Q ss_pred hhccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhh
Q psy14411 15 RYITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDIN 70 (85)
Q Consensus 15 ~yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~ 70 (85)
++|+.++..+.+++|..-+.+++= .|-||.--+= | ...+.|...||+
T Consensus 2 rll~~~ev~~~~g~s~~ti~~~~k-~g~FP~pvkl------g--~r~~~W~~~eV~ 48 (51)
T PF05930_consen 2 RLLRIKEVAELLGVSRSTIYRLIK-DGKFPKPVKL------G--GRAVRWRESEVE 48 (51)
T ss_dssp -EE-HHHHHHHHSS-HHHHHHHHH-HHH---SEES------S--S-----------
T ss_pred ccccHHHHHHHHCCCHHHHHHHHh-cccCCCCEEE------C--CCcccccccccc
Confidence 589999999999999999999955 8989865321 1 124667766664
No 14
>PTZ00217 flap endonuclease-1; Provisional
Probab=55.57 E-value=11 Score=30.65 Aligned_cols=28 Identities=36% Similarity=0.638 Sum_probs=25.8
Q ss_pred chhccHHHHHHHhcCChhhhhhhhhhcc
Q psy14411 14 VRYITRRGALKKLQVTLKQFRTLCILKG 41 (85)
Q Consensus 14 ~~yitR~qAlkkLQlsl~dFRRLCILKG 41 (85)
..+++.+..+..|+|+..+|--+|||=|
T Consensus 206 ~~~~~~~~v~~~~gl~~~q~id~~iL~G 233 (393)
T PTZ00217 206 IQEINLSTVLEELGLSMDQFIDLCILCG 233 (393)
T ss_pred eEEEEHHHHHHHhCCCHHHHHHHHHHhC
Confidence 4578999999999999999999999988
No 15
>PF08127 Propeptide_C1: Peptidase family C1 propeptide; InterPro: IPR012599 This domain is found at the N-terminal of cathepsin B and cathepsin B-like peptidases that belong to MEROPS peptidase subfamily C1A. Cathepsin B are lysosomal cysteine proteinases belonging to the papain superfamily and are unique in their ability to act as both an endo- and an exopeptidases. They are synthesized as inactive zymogens. Activation of the peptidases occurs with the removal of the propeptide [, ]. ; GO: 0004197 cysteine-type endopeptidase activity, 0050790 regulation of catalytic activity; PDB: 1MIR_A 1PBH_A 2PBH_A 3PBH_A.
Probab=54.90 E-value=6.1 Score=22.90 Aligned_cols=18 Identities=28% Similarity=0.646 Sum_probs=10.3
Q ss_pred cCChhhhhhhhhhcccCCCCC
Q psy14411 27 QVTLKQFRTLCILKGVYPREP 47 (85)
Q Consensus 27 Qlsl~dFRRLCILKGIyPreP 47 (85)
..|++++|+|| |+.|..|
T Consensus 24 ~~~~~~ik~Ll---Gv~~~~p 41 (41)
T PF08127_consen 24 NTSIEYIKRLL---GVLPDPP 41 (41)
T ss_dssp SB-HHHHHHCS----B-TTS-
T ss_pred CCCHHHHHHHc---CCCCCCC
Confidence 46788999998 5555443
No 16
>KOG2518|consensus
Probab=53.77 E-value=7 Score=33.98 Aligned_cols=32 Identities=28% Similarity=0.505 Sum_probs=21.8
Q ss_pred ccccchhccHHHHHHHhcC----Chhhhhhhhhhccc
Q psy14411 10 AGEAVRYITRRGALKKLQV----TLKQFRTLCILKGV 42 (85)
Q Consensus 10 ~G~~~~yitR~qAlkkLQl----sl~dFRRLCILKGI 42 (85)
.|.+..+ .+++.-..-++ +.+.||++|||=|-
T Consensus 189 ~G~~le~-~~~~l~~~~~l~~~~~~ekfr~mciLSGC 224 (556)
T KOG2518|consen 189 FGNGLEI-NRSKLPECKPLGDKFTEEKFRRMCILSGC 224 (556)
T ss_pred CCCcccc-cHhhhhhccccccccCHHHHHHHHHhcCC
Confidence 4555555 55555544444 68899999999884
No 17
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=52.44 E-value=12 Score=29.50 Aligned_cols=28 Identities=29% Similarity=0.396 Sum_probs=25.4
Q ss_pred hhccHHHHHHHhcCChhhhhhhhhhccc
Q psy14411 15 RYITRRGALKKLQVTLKQFRTLCILKGV 42 (85)
Q Consensus 15 ~yitR~qAlkkLQlsl~dFRRLCILKGI 42 (85)
..++.+..+..|+|+.++|--+|||=|=
T Consensus 208 e~~~~~~v~~~lgl~~~q~id~~iL~G~ 235 (338)
T TIGR03674 208 ELIELEEVLSELGITREQLIDIAILVGT 235 (338)
T ss_pred eeeeHHHHHHHhCCCHHHHHHHHHhcCC
Confidence 3589999999999999999999999775
No 18
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=51.19 E-value=37 Score=21.85 Aligned_cols=47 Identities=19% Similarity=0.176 Sum_probs=34.0
Q ss_pred cHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 18 TRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 18 tR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
|-+++-+.++||..-+|.. .=.|+.|-. .+.. ...-+|...||..|.
T Consensus 2 ti~eva~~~gvs~~tlR~y-e~~Gll~~~--~~~~------~g~R~y~~~di~~l~ 48 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYY-DEIGLLKPS--RRTE------NGYRLYTEEDLERLQ 48 (103)
T ss_pred CHHHHHHHHCcCHHHHHHH-HHCCCCCCC--ccCC------CCceeeCHHHHHHHH
Confidence 5578889999999999965 468988632 1111 135789999998774
No 19
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=50.11 E-value=45 Score=19.66 Aligned_cols=48 Identities=17% Similarity=0.100 Sum_probs=33.9
Q ss_pred cHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhhc
Q psy14411 18 TRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLLH 74 (85)
Q Consensus 18 tR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~h 74 (85)
|=.++-+.++||..-.|..|=--|+-|- ++. . ...-+|...||..|..
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~gl~~~-~r~-~-------~g~R~yt~~di~~l~~ 49 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREFGLLKP-QRS-D-------GGHRLFNDADIDRILE 49 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhcCCCCC-CcC-C-------CCCcccCHHHHHHHHH
Confidence 5578899999999999999764475421 221 1 1246899999998754
No 20
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=49.62 E-value=7.3 Score=25.54 Aligned_cols=17 Identities=35% Similarity=0.501 Sum_probs=14.2
Q ss_pred ChhhhhhhhhhcccCCC
Q psy14411 29 TLKQFRTLCILKGVYPR 45 (85)
Q Consensus 29 sl~dFRRLCILKGIyPr 45 (85)
+..-.|+||+..||+|.
T Consensus 48 ~~~~~r~l~l~~GV~p~ 64 (117)
T PF02887_consen 48 NESVARQLSLYWGVYPV 64 (117)
T ss_dssp SHHHHHHGGGSTTEEEE
T ss_pred cHHHHhhhhcccceEEE
Confidence 44567999999999994
No 21
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=49.59 E-value=50 Score=19.03 Aligned_cols=48 Identities=23% Similarity=0.202 Sum_probs=33.9
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
+|-.++.+.++||....|+++= .|+-|-+-+. . ...-+|...||..|.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~-~gli~~~~~~--~------~g~r~y~~~dl~~l~ 48 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER-IGLLPPPIRT--E------GGYRLYSDEDLERLR 48 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccC--C------CCCEecCHHHHHHHH
Confidence 3567888999999999998864 7887632111 1 135689999988664
No 22
>PF08569 Mo25: Mo25-like; InterPro: IPR013878 Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localised alternately to the spindle pole body and to the site of cell division in a cell cycle dependent manner [, ]. ; PDB: 2WTK_A 1UPK_A 3GNI_A 1UPL_A.
Probab=47.76 E-value=8.6 Score=30.70 Aligned_cols=16 Identities=44% Similarity=0.688 Sum_probs=13.3
Q ss_pred ccchhccHHHHHHHhc
Q psy14411 12 EAVRYITRRGALKKLQ 27 (85)
Q Consensus 12 ~~~~yitR~qAlkkLQ 27 (85)
.+.||+||.|++|-|+
T Consensus 219 ~s~NYvtkrqslkLL~ 234 (335)
T PF08569_consen 219 ESSNYVTKRQSLKLLG 234 (335)
T ss_dssp T-SSHHHHHHHHHHHH
T ss_pred cCCCeEeehhhHHHHH
Confidence 3579999999999886
No 23
>PF05997 Nop52: Nucleolar protein,Nop52; InterPro: IPR010301 Nop52 is believed to be involved in the generation of 28S rRNA [].; GO: 0006364 rRNA processing, 0030688 preribosome, small subunit precursor
Probab=47.16 E-value=8.8 Score=28.51 Aligned_cols=27 Identities=37% Similarity=0.447 Sum_probs=19.3
Q ss_pred hhccHHHHHHHhc--------C-ChhhhhhhhhhcccC
Q psy14411 15 RYITRRGALKKLQ--------V-TLKQFRTLCILKGVY 43 (85)
Q Consensus 15 ~yitR~qAlkkLQ--------l-sl~dFRRLCILKGIy 43 (85)
+=-||++|++.|. . +..||.+|| ||+|
T Consensus 13 d~~~R~~al~~l~~~l~~~~~~~~~~~~~kLW--KGLf 48 (217)
T PF05997_consen 13 DKKTRDRALKSLRKWLSKRSQLLTELDMLKLW--KGLF 48 (217)
T ss_pred ChhHHHHHHHHHHHHHHhccccCCHHHHHHHH--HHHH
Confidence 3457888888774 2 677887766 8876
No 24
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=43.99 E-value=15 Score=25.10 Aligned_cols=22 Identities=14% Similarity=0.289 Sum_probs=18.2
Q ss_pred hhccHHHHHHHhcCChhhhhhh
Q psy14411 15 RYITRRGALKKLQVTLKQFRTL 36 (85)
Q Consensus 15 ~yitR~qAlkkLQlsl~dFRRL 36 (85)
--||.++|+++-.||.++|-..
T Consensus 48 Glis~~EA~~rY~Ls~eEf~~W 69 (90)
T PF06627_consen 48 GLISVEEACRRYGLSEEEFESW 69 (90)
T ss_dssp TTS-HHHHHHCTTSSHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHH
Confidence 3589999999999999999753
No 25
>PF05356 Phage_Coat_B: Phage Coat protein B ; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 1QL1_A 2XKM_A 4IFM_A 1QL2_A 1IFM_A 2KLV_A 1IFN_A 2IFN_A 3IFM_A 2KSJ_A ....
Probab=42.06 E-value=8.5 Score=25.98 Aligned_cols=14 Identities=43% Similarity=0.828 Sum_probs=0.0
Q ss_pred Chhhhhhhhhhccc
Q psy14411 29 TLKQFRTLCILKGV 42 (85)
Q Consensus 29 sl~dFRRLCILKGI 42 (85)
+-..||+|||-=|+
T Consensus 13 ~v~sfr~~~iag~V 26 (83)
T PF05356_consen 13 PVPSFRNLCIAGAV 26 (83)
T ss_dssp --------------
T ss_pred CcHHHHHHHHHHHH
Confidence 56789999997665
No 26
>PF07021 MetW: Methionine biosynthesis protein MetW; InterPro: IPR010743 This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In P. putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells [].
Probab=38.41 E-value=18 Score=27.29 Aligned_cols=16 Identities=38% Similarity=0.686 Sum_probs=13.8
Q ss_pred CChhhhhhhhhhcccC
Q psy14411 28 VTLKQFRTLCILKGVY 43 (85)
Q Consensus 28 lsl~dFRRLCILKGIy 43 (85)
+|.+||+.||=-.||-
T Consensus 146 ~Ti~DFe~lc~~~~i~ 161 (193)
T PF07021_consen 146 CTIKDFEDLCRELGIR 161 (193)
T ss_pred ccHHHHHHHHHHCCCE
Confidence 6899999999888873
No 27
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.02 E-value=82 Score=18.18 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=32.8
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
+|-+++-+.++||...-|..+= .|+.|- .+.. ....+|...||..|.
T Consensus 1 yti~eva~~~gvs~~tlr~y~~-~gll~~--~~~~-------~g~r~y~~~dv~~l~ 47 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYER-EGLLPP--PRDE-------NGYRYYSEEDVERLR 47 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHH-TTSSTT--BEST-------TSSEEE-HHHHHHHH
T ss_pred CcHHHHHHHHCcCHHHHHHHHH-hcCccc--cccc-------CceeeccHHHHHHHH
Confidence 3667899999999998888865 566332 2211 235999999998875
No 28
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=37.37 E-value=43 Score=20.97 Aligned_cols=28 Identities=18% Similarity=0.096 Sum_probs=25.9
Q ss_pred hccHHHHHHHhcCChhhhhhhhhhcccC
Q psy14411 16 YITRRGALKKLQVTLKQFRTLCILKGVY 43 (85)
Q Consensus 16 yitR~qAlkkLQlsl~dFRRLCILKGIy 43 (85)
-||=.+|-+-+++|.-+|..++-=+||.
T Consensus 34 ~iS~gkAAelag~s~~eF~~~L~~~gI~ 61 (76)
T PF03683_consen 34 KISLGKAAELAGMSRWEFLELLKERGIP 61 (76)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence 4788899999999999999999999997
No 29
>PF14898 DUF4491: Domain of unknown function (DUF4491)
Probab=37.33 E-value=16 Score=25.13 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=10.9
Q ss_pred hhcccCCCCCchh
Q psy14411 38 ILKGVYPREPIKR 50 (85)
Q Consensus 38 ILKGIyPreP~~k 50 (85)
.-||-||+.|++|
T Consensus 82 V~kGWFP~NPkrK 94 (94)
T PF14898_consen 82 VEKGWFPKNPKRK 94 (94)
T ss_pred HHcCCCCCCCCCC
Confidence 4599999999875
No 30
>PF06709 DUF1196: Protein of unknown function (DUF1196); InterPro: IPR009585 This family consists of several hypothetical bacterial proteins of around 51 residues in length which seem to be specific to Vibrio cholerae. The function of this family is unknown.
Probab=36.37 E-value=12 Score=23.18 Aligned_cols=14 Identities=29% Similarity=0.809 Sum_probs=10.9
Q ss_pred hhhhhhhhhcccCCCC
Q psy14411 31 KQFRTLCILKGVYPRE 46 (85)
Q Consensus 31 ~dFRRLCILKGIyPre 46 (85)
.-|.+.| ||||-..
T Consensus 18 ~~FK~v~--KGI~~K~ 31 (51)
T PF06709_consen 18 LPFKGVA--KGIYAKQ 31 (51)
T ss_pred chHHHHH--HHHHHhh
Confidence 4588999 9999653
No 31
>KOG1266|consensus
Probab=36.15 E-value=20 Score=30.46 Aligned_cols=36 Identities=17% Similarity=0.363 Sum_probs=26.3
Q ss_pred cccccchhccHHHHHHHhcCChhhhhhhh--hhcccCCC
Q psy14411 9 EAGEAVRYITRRGALKKLQVTLKQFRTLC--ILKGVYPR 45 (85)
Q Consensus 9 ~~G~~~~yitR~qAlkkLQlsl~dFRRLC--ILKGIyPr 45 (85)
.+|+.+.|+-|..- ..-.++.++|+|+| ||-||||-
T Consensus 155 ssgs~~~fLkrt~~-~~~a~~~~~wkkw~tqIlsal~yL 192 (458)
T KOG1266|consen 155 SSGSLKQFLKRTKK-NQKALFQKAWKKWCTQILSALSYL 192 (458)
T ss_pred cchhHHHHHHHHHH-hhhhhhHHHHHHHHHHHHhhhhhh
Confidence 56777777766432 22346789999999 99999985
No 32
>KOG3911|consensus
Probab=36.01 E-value=23 Score=29.60 Aligned_cols=28 Identities=36% Similarity=0.507 Sum_probs=20.5
Q ss_pred chhccHHHHHHHhc-----------CChhhhhhhhhhcccC
Q psy14411 14 VRYITRRGALKKLQ-----------VTLKQFRTLCILKGVY 43 (85)
Q Consensus 14 ~~yitR~qAlkkLQ-----------lsl~dFRRLCILKGIy 43 (85)
.+=.||+.||+.|+ -+-.||=+|| ||.|
T Consensus 19 ne~~tRdrAlr~Lrkyi~ak~~k~~F~~~dflklW--KGLf 57 (378)
T KOG3911|consen 19 NERKTRDRALRKLRKYISAKTQKEGFDQDDFLKLW--KGLF 57 (378)
T ss_pred CChHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHH--HhhH
Confidence 34569999999886 5666777766 7765
No 33
>smart00878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.
Probab=35.04 E-value=14 Score=24.82 Aligned_cols=17 Identities=41% Similarity=0.712 Sum_probs=15.2
Q ss_pred cHHHHHHHhcCChhhhh
Q psy14411 18 TRRGALKKLQVTLKQFR 34 (85)
Q Consensus 18 tR~qAlkkLQlsl~dFR 34 (85)
+|.+|+++|.-.|.+|+
T Consensus 60 ~R~~A~~rl~~aL~e~~ 76 (107)
T smart00878 60 TREEAIARLRRALDEFR 76 (107)
T ss_pred CHHHHHHHHHHHHHhCE
Confidence 69999999999998875
No 34
>smart00475 53EXOc 5'-3' exonuclease.
Probab=33.90 E-value=37 Score=25.91 Aligned_cols=34 Identities=24% Similarity=0.224 Sum_probs=29.7
Q ss_pred hhccHHHHHHHhcCChhhhhhhhhhccc----CCCCCc
Q psy14411 15 RYITRRGALKKLQVTLKQFRTLCILKGV----YPREPI 48 (85)
Q Consensus 15 ~yitR~qAlkkLQlsl~dFRRLCILKGI----yPreP~ 48 (85)
..++.+....+++++.++|--+|+|-|= +|-.|.
T Consensus 156 ~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~G 193 (259)
T smart00475 156 ELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPG 193 (259)
T ss_pred EEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCC
Confidence 5799999999999999999999999992 577763
No 35
>PF12418 AcylCoA_DH_N: Acyl-CoA dehydrogenase N terminal ; InterPro: IPR020953 This entry represents the N-terminal domain of Acyl-CoA dehydrogenase, which is one of the enzymes involved in AcylCoA interaction in beta-oxidation []. The protein is found in association with PF02770 from PFAM, PF00441 from PFAM, PF02771 from PFAM.
Probab=32.23 E-value=17 Score=19.84 Aligned_cols=12 Identities=33% Similarity=0.481 Sum_probs=9.7
Q ss_pred ehhhhhHhhcCh
Q psy14411 65 YRKDINFLLHEP 76 (85)
Q Consensus 65 ~~KDI~~L~heP 76 (85)
-..|++|++||=
T Consensus 6 p~rD~~F~L~Ev 17 (34)
T PF12418_consen 6 PLRDMRFVLYEV 17 (34)
T ss_pred cHHHHHHHHHHH
Confidence 368999999873
No 36
>KOG3981|consensus
Probab=31.84 E-value=25 Score=28.58 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=15.2
Q ss_pred hhhhhhhhhhcccCCCCCc
Q psy14411 30 LKQFRTLCILKGVYPREPI 48 (85)
Q Consensus 30 l~dFRRLCILKGIyPreP~ 48 (85)
...-+||| ++.+||.||-
T Consensus 73 asnv~rLc-~rA~yP~~p~ 90 (326)
T KOG3981|consen 73 ASNVVRLC-KRAIYPVEPQ 90 (326)
T ss_pred HHHHHHHH-HHhcCCCCHH
Confidence 46789999 5999999994
No 37
>KOG1566|consensus
Probab=29.82 E-value=24 Score=29.11 Aligned_cols=18 Identities=33% Similarity=0.432 Sum_probs=15.5
Q ss_pred ccccchhccHHHHHHHhc
Q psy14411 10 AGEAVRYITRRGALKKLQ 27 (85)
Q Consensus 10 ~G~~~~yitR~qAlkkLQ 27 (85)
-|++.||+||.|+++-|+
T Consensus 220 Ll~s~Nyvtkrqs~kllg 237 (342)
T KOG1566|consen 220 LLRSENYVTKRQSLKLLG 237 (342)
T ss_pred HhcccceehHHHHHHhHH
Confidence 367889999999999876
No 38
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=28.92 E-value=1.3e+02 Score=22.07 Aligned_cols=46 Identities=17% Similarity=0.119 Sum_probs=33.7
Q ss_pred cHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 18 TRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 18 tR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
|=.++-+.++||..--|+.+- +|..| ..+.. ...-.|.-.||.+|-
T Consensus 2 ti~evA~~lGVS~~TLRrw~k-~g~L~-~~R~~--------~G~R~y~~~dl~~L~ 47 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVK-QLNLP-CEKNE--------YGHYIFTEEDLQLLE 47 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-cCCCC-CCcCC--------CCCEEECHHHHHHHH
Confidence 557889999999999998886 45556 22211 236889999998874
No 39
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=27.82 E-value=56 Score=24.37 Aligned_cols=33 Identities=27% Similarity=0.358 Sum_probs=28.4
Q ss_pred hhccHHHHHHHhcCChhhhhhhhhhcc----cCCCCC
Q psy14411 15 RYITRRGALKKLQVTLKQFRTLCILKG----VYPREP 47 (85)
Q Consensus 15 ~yitR~qAlkkLQlsl~dFRRLCILKG----IyPreP 47 (85)
..++...-.++++++.+.|-.+|+|.| =+|-.|
T Consensus 153 ~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~ 189 (240)
T cd00008 153 KLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVP 189 (240)
T ss_pred eEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCC
Confidence 468888889999999999999999999 356666
No 40
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.39 E-value=1.4e+02 Score=18.70 Aligned_cols=46 Identities=28% Similarity=0.354 Sum_probs=33.0
Q ss_pred cHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 18 TRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 18 tR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
|=.++.+.++|+..-.|.++= .|+-| |.+.. ...-+|...||..|.
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~-~Gll~--~~~~~-------~g~r~y~~~dv~~l~ 47 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE-KGLLP--PERSE-------NGYRLYSEEDLERLR 47 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CCCcC--CCcCC-------CCCcccCHHHHHHHH
Confidence 556888999999999888864 78887 43211 135678888887664
No 41
>PF02785 Biotin_carb_C: Biotin carboxylase C-terminal domain; InterPro: IPR005482 Acetyl-CoA carboxylase is found in all animals, plants, and bacteria and catalyzes the first committed step in fatty acid synthesis. It is a multicomponent enzyme containing a biotin carboxylase activity, a biotin carboxyl carrier protein, and a carboxyltransferase functionality. The "B-domain" extends from the main body of the subunit where it folds into two alpha-helical regions and three strands of beta-sheet. Following the excursion into the B-domain, the polypeptide chain folds back into the body of the protein where it forms an eight-stranded antiparallel beta-sheet. In addition to this major secondary structural element, the C-terminal domain also contains a smaller three-stranded antiparallel beta-sheet and seven alpha-helices []. ; GO: 0016874 ligase activity; PDB: 1W96_B 1W93_A 3VA7_A 2GPW_A 2W70_A 3G8D_A 1DV2_A 2VR1_B 2J9G_B 1DV1_A ....
Probab=25.94 E-value=25 Score=23.73 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=15.6
Q ss_pred cHHHHHHHhcCChhhhh
Q psy14411 18 TRRGALKKLQVTLKQFR 34 (85)
Q Consensus 18 tR~qAlkkLQlsl~dFR 34 (85)
||.+|+.+|.--|.+|+
T Consensus 60 ~R~~Ai~~l~~AL~e~~ 76 (107)
T PF02785_consen 60 DREEAIARLRRALAETV 76 (107)
T ss_dssp SHHHHHHHHHHHHHHHE
T ss_pred chHHHHHHHHhhcceEE
Confidence 79999999999999886
No 42
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=25.47 E-value=54 Score=23.16 Aligned_cols=19 Identities=16% Similarity=0.280 Sum_probs=15.9
Q ss_pred cHHHHHHHhcCChhhhhhh
Q psy14411 18 TRRGALKKLQVTLKQFRTL 36 (85)
Q Consensus 18 tR~qAlkkLQlsl~dFRRL 36 (85)
.=-.|+.+|++|.+||.++
T Consensus 29 p~~~al~~~~~sp~ef~~~ 47 (109)
T TIGR03277 29 PIHPKLAELGLSPQEFVRI 47 (109)
T ss_pred ccHHHHHHcCCCHHHHHHH
Confidence 3347999999999999886
No 43
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=25.12 E-value=66 Score=24.57 Aligned_cols=27 Identities=11% Similarity=0.322 Sum_probs=18.1
Q ss_pred HHHHHHh---cCChhhhhhhhhhcccCCCC
Q psy14411 20 RGALKKL---QVTLKQFRTLCILKGVYPRE 46 (85)
Q Consensus 20 ~qAlkkL---Qlsl~dFRRLCILKGIyPre 46 (85)
+++|.+- ++|.+|.+..|..+||-|..
T Consensus 209 D~~i~~eGv~~Ls~~EL~~Ac~~RGl~~~~ 238 (268)
T PF07766_consen 209 DRLIKREGVDSLSEEELQDACYERGLRSTG 238 (268)
T ss_dssp HHHHHHH-GGGS-HHHHHHHHHHTT---TT
T ss_pred HHHHHHhccccCCHHHHHHHHHHhCCCcCC
Confidence 3455555 67999999999999998764
No 44
>PRK14976 5'-3' exonuclease; Provisional
Probab=24.95 E-value=73 Score=24.63 Aligned_cols=35 Identities=11% Similarity=-0.083 Sum_probs=29.8
Q ss_pred chhccHHHHHHHhcCChhhhhhhhhhcc----cCCCCCc
Q psy14411 14 VRYITRRGALKKLQVTLKQFRTLCILKG----VYPREPI 48 (85)
Q Consensus 14 ~~yitR~qAlkkLQlsl~dFRRLCILKG----IyPreP~ 48 (85)
...++..+...+++++.+.|--+|+|-| =+|-.|.
T Consensus 160 ~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpG 198 (281)
T PRK14976 160 HFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKG 198 (281)
T ss_pred cEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCc
Confidence 3578999999999999999999999999 3566663
No 45
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.74 E-value=1.7e+02 Score=18.38 Aligned_cols=48 Identities=27% Similarity=0.259 Sum_probs=34.8
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
+|=.++-+.++||....|...= +|+.| |..... ...-||...||..|.
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~-~Gll~--p~r~~~------~g~R~Ys~~dv~~l~ 49 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEE-KGLIK--SIRSDG------GGQRKYSLADVDRLL 49 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCCC--CCccCC------CCceecCHHHHHHHH
Confidence 4667889999999999988754 68776 432211 146799999988765
No 46
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=23.65 E-value=1.9e+02 Score=18.88 Aligned_cols=48 Identities=15% Similarity=0.073 Sum_probs=34.7
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
+|=.++-+.++||..-.|..+= .|+-|-.. +.. ...-+|...||..|.
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~-~Gll~p~~--~~~------~g~R~Y~~~dl~~l~ 48 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEK-EGLLSPDR--EPE------TGYRVYDPSDVRDAR 48 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCc--CCC------CCceeeCHHHHHHHH
Confidence 3567888999999999998876 58876322 111 135789999998774
No 47
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=23.30 E-value=49 Score=18.38 Aligned_cols=14 Identities=36% Similarity=0.529 Sum_probs=11.4
Q ss_pred hhhhhhhhhcccCC
Q psy14411 31 KQFRTLCILKGVYP 44 (85)
Q Consensus 31 ~dFRRLCILKGIyP 44 (85)
++|..+|||-|-|=
T Consensus 2 ~q~~~~~~L~GD~~ 15 (36)
T smart00279 2 EQLIDYAILVGDYS 15 (36)
T ss_pred HHHHHHHHHhCcCC
Confidence 57899999999653
No 48
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.21 E-value=2e+02 Score=17.98 Aligned_cols=48 Identities=19% Similarity=0.151 Sum_probs=35.6
Q ss_pred hccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 16 YITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 16 yitR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
|+|=.++.+.++||...-|.+.= .|+.| |.... ...-+|...||..|.
T Consensus 1 ~~~i~e~A~~~gvs~~tLr~ye~-~Gli~--p~r~~-------~g~R~y~~~dv~~l~ 48 (91)
T cd04766 1 VYVISVAAELSGMHPQTLRLYER-LGLLS--PSRTD-------GGTRRYSERDIERLR 48 (91)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH-CCCcC--CCcCC-------CCCeeECHHHHHHHH
Confidence 56778999999999998888764 68886 32111 235789999998774
No 49
>PF10206 WRW: Mitochondrial F1F0-ATP synthase, subunit f; InterPro: IPR019344 This entry represents small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known.
Probab=22.57 E-value=33 Score=23.71 Aligned_cols=29 Identities=28% Similarity=0.424 Sum_probs=23.4
Q ss_pred ccCCCCCchhhhhcCCCCCceeeeehhhhhHh
Q psy14411 41 GVYPREPIKRKRAQRGKPGVKILYYRKDINFL 72 (85)
Q Consensus 41 GIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L 72 (85)
|-||.|-..+ -+|...+..||-++|..++
T Consensus 4 G~~p~eyn~~---vhGpy~p~ryYGk~Dt~l~ 32 (104)
T PF10206_consen 4 GDYPKEYNPK---VHGPYDPARYYGKKDTPLM 32 (104)
T ss_pred CCCchhhCcc---ccCCCCchhhcCCCCCchh
Confidence 7788887754 3688999999999998753
No 50
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=22.54 E-value=77 Score=20.34 Aligned_cols=23 Identities=26% Similarity=0.284 Sum_probs=17.1
Q ss_pred hhccHHHHHHHhcCChhhhhhhh
Q psy14411 15 RYITRRGALKKLQVTLKQFRTLC 37 (85)
Q Consensus 15 ~yitR~qAlkkLQlsl~dFRRLC 37 (85)
..||-++-.+.++++.++.|++|
T Consensus 26 ~~l~de~la~~~~l~~~~vRkiL 48 (105)
T PF02002_consen 26 GELTDEDLAKKLGLKPKEVRKIL 48 (105)
T ss_dssp --B-HHHHHHTT-S-HHHHHHHH
T ss_pred CCcCHHHHHHHhCCCHHHHHHHH
Confidence 35788899999999999999999
No 51
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=22.49 E-value=43 Score=26.41 Aligned_cols=19 Identities=53% Similarity=0.688 Sum_probs=15.7
Q ss_pred cchhccHHHHHHHhcCChh
Q psy14411 13 AVRYITRRGALKKLQVTLK 31 (85)
Q Consensus 13 ~~~yitR~qAlkkLQlsl~ 31 (85)
+.+|+||+|+++.|+=.+.
T Consensus 89 ~v~~~sre~~l~~L~~~lg 107 (297)
T COG2177 89 SVRFISREEALKELQPWLG 107 (297)
T ss_pred eEEEeCHHHHHHHHHHHcC
Confidence 4799999999999985444
No 52
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=21.44 E-value=39 Score=24.40 Aligned_cols=42 Identities=19% Similarity=0.225 Sum_probs=30.3
Q ss_pred HHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHh
Q psy14411 24 KKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFL 72 (85)
Q Consensus 24 kkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L 72 (85)
.++.|+.++=+.|+=|.||||.--++.-+ + --|-.+.|+.-+
T Consensus 51 ~kIdiN~A~~~el~~lpGigP~~A~~IV~--n-----Gpf~sveDL~~V 92 (132)
T PRK02515 51 EKIDLNNSSVRAFRQFPGMYPTLAGKIVK--N-----APYDSVEDVLNL 92 (132)
T ss_pred CcccCCccCHHHHHHCCCCCHHHHHHHHH--C-----CCCCCHHHHHcC
Confidence 45577777778888899999987766652 3 356777777655
No 53
>cd04985 IgC_CH1 CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin. IgC_CH1: The first immunoglobulin constant domain (IgC), of immunoglobulin (Ig) heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.
Probab=21.19 E-value=26 Score=22.60 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=10.6
Q ss_pred hhhhcccCCCCC
Q psy14411 36 LCILKGVYPREP 47 (85)
Q Consensus 36 LCILKGIyPreP 47 (85)
.|...|.||++-
T Consensus 22 ~C~a~gFyP~~i 33 (95)
T cd04985 22 GCLATGFLPEPV 33 (95)
T ss_pred EEEEeeEECCCc
Confidence 399999999977
No 54
>TIGR01064 pyruv_kin pyruvate kinase. This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars.
Probab=20.83 E-value=41 Score=27.95 Aligned_cols=19 Identities=26% Similarity=0.352 Sum_probs=16.1
Q ss_pred ChhhhhhhhhhcccCCCCC
Q psy14411 29 TLKQFRTLCILKGVYPREP 47 (85)
Q Consensus 29 sl~dFRRLCILKGIyPreP 47 (85)
+..-+|+|++..||||.-.
T Consensus 405 ~~~v~R~L~L~wGV~Pil~ 423 (473)
T TIGR01064 405 NERVARQLALYWGVFPFLV 423 (473)
T ss_pred CHHHHHHhhccCCcEEEEe
Confidence 5677899999999999743
No 55
>smart00684 DM15 Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function.
Probab=20.51 E-value=53 Score=18.90 Aligned_cols=8 Identities=50% Similarity=1.369 Sum_probs=6.6
Q ss_pred hhhhhhhh
Q psy14411 31 KQFRTLCI 38 (85)
Q Consensus 31 ~dFRRLCI 38 (85)
.+||++|+
T Consensus 8 ~eFr~lal 15 (39)
T smart00684 8 EEFRQLCL 15 (39)
T ss_pred HHHHHHHH
Confidence 57999996
No 56
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.29 E-value=2.6e+02 Score=18.08 Aligned_cols=47 Identities=19% Similarity=0.118 Sum_probs=35.6
Q ss_pred ccHHHHHHHhcCChhhhhhhhhhcccCCCCCchhhhhcCCCCCceeeeehhhhhHhh
Q psy14411 17 ITRRGALKKLQVTLKQFRTLCILKGVYPREPIKRKRAQRGKPGVKILYYRKDINFLL 73 (85)
Q Consensus 17 itR~qAlkkLQlsl~dFRRLCILKGIyPreP~~k~k~~kg~~~~ktyY~~KDI~~L~ 73 (85)
+|=.+.-+.++||..-.|..+=. |+.|- ++ .. ...-+|.-.||..|.
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~~-~r--~~------~g~R~Y~~~~l~~l~ 48 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLITG-TR--NA------NGYRLYPDSDLQRLL 48 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCC-Cc--CC------CCCeeCCHHHHHHHH
Confidence 46678899999999999988874 99873 22 11 246899999998876
Done!