Query 040053
Match_columns 74
No_of_seqs 110 out of 266
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 04:38:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040053.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040053hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3380 Predicted NAD/FAD-depe 99.7 9.3E-19 2E-23 122.2 3.2 68 5-74 46-113 (331)
2 PF13450 NAD_binding_8: NAD(P) 89.0 0.24 5.1E-06 27.4 1.2 26 5-30 41-68 (68)
3 PF15320 RAM: mRNA cap methyla 80.4 0.58 1.3E-05 27.4 0.2 27 16-42 11-38 (81)
4 PF05678 VQ: VQ motif; InterP 77.7 1.6 3.4E-05 21.1 1.2 21 13-33 5-25 (31)
5 COG1759 5-formaminoimidazole-4 59.5 7.6 0.00017 28.4 2.0 26 12-37 163-189 (361)
6 PF04468 PSP1: PSP1 C-terminal 52.3 19 0.0004 20.9 2.6 19 15-33 59-78 (88)
7 PF09106 SelB-wing_2: Elongati 50.5 19 0.00041 19.1 2.2 20 19-38 33-52 (59)
8 TIGR03467 HpnE squalene-associ 41.5 24 0.00051 24.6 2.2 24 7-30 36-59 (419)
9 PF09397 Ftsk_gamma: Ftsk gamm 41.1 29 0.00063 19.3 2.1 19 23-41 37-55 (65)
10 PF06258 Mito_fiss_Elm1: Mitoc 40.8 24 0.00051 25.0 2.1 31 12-42 249-283 (311)
11 PHA02591 hypothetical protein; 40.1 39 0.00085 19.8 2.6 25 12-36 37-61 (83)
12 PF10557 Cullin_Nedd8: Cullin 35.9 15 0.00033 20.1 0.4 26 14-39 38-63 (68)
13 PTZ00043 cytochrome c oxidase 35.3 30 0.00064 24.3 1.8 59 6-67 104-162 (268)
14 PF14178 YppF: YppF-like prote 35.3 28 0.0006 19.3 1.4 18 21-38 40-57 (60)
15 PF01593 Amino_oxidase: Flavin 35.0 29 0.00062 23.6 1.7 27 6-32 39-65 (450)
16 PF14021 DUF4237: Protein of u 34.4 25 0.00054 20.7 1.2 21 12-38 68-88 (90)
17 TIGR00562 proto_IX_ox protopor 33.5 24 0.00052 25.3 1.2 26 5-30 51-76 (462)
18 KOG1635 Peptide methionine sul 33.5 32 0.0007 23.1 1.7 35 9-45 110-148 (191)
19 smart00843 Ftsk_gamma This dom 30.7 42 0.0009 18.6 1.6 20 22-41 35-54 (63)
20 PRK07208 hypothetical protein; 29.2 39 0.00084 24.5 1.7 27 5-31 49-75 (479)
21 PF08672 APC2: Anaphase promot 28.3 19 0.0004 19.6 -0.1 27 12-38 27-53 (60)
22 PRK09409 IS2 transposase TnpB; 27.4 66 0.0014 22.5 2.6 28 7-40 195-222 (301)
23 PF13463 HTH_27: Winged helix 27.3 13 0.00027 19.6 -0.9 20 18-37 30-49 (68)
24 KOG2292 Oligosaccharyltransfer 27.0 48 0.001 26.3 1.9 21 28-48 318-338 (751)
25 PF09292 Neil1-DNA_bind: Endon 26.5 24 0.00052 17.8 0.2 12 61-73 11-22 (39)
26 cd03715 RT_ZFREV_like RT_ZFREV 25.9 53 0.0012 21.3 1.8 19 22-40 16-34 (210)
27 smart00345 HTH_GNTR helix_turn 25.8 21 0.00046 17.8 -0.1 26 13-38 27-52 (60)
28 PRK12416 protoporphyrinogen ox 25.3 28 0.0006 25.2 0.4 25 6-30 53-77 (463)
29 smart00420 HTH_DEOR helix_turn 25.2 23 0.00049 17.2 -0.1 26 13-38 21-46 (53)
30 PLN02576 protoporphyrinogen ox 24.7 34 0.00074 24.9 0.7 25 5-29 58-82 (496)
31 PF12970 DUF3858: Domain of Un 24.0 22 0.00048 22.1 -0.3 21 14-34 89-110 (116)
32 cd00537 MTHFR Methylenetetrahy 23.9 67 0.0015 21.8 2.1 27 9-35 157-187 (274)
33 PF13591 MerR_2: MerR HTH fami 23.7 71 0.0015 18.1 1.8 18 24-41 14-31 (84)
34 PRK14702 insertion element IS2 23.5 79 0.0017 21.6 2.3 28 7-40 156-183 (262)
35 PF07277 SapC: SapC; InterPro 23.1 55 0.0012 22.1 1.5 23 23-45 147-169 (221)
36 PLN02268 probable polyamine ox 22.5 78 0.0017 22.6 2.2 25 6-30 46-72 (435)
37 cd07377 WHTH_GntR Winged helix 22.3 28 0.0006 17.8 -0.1 24 15-38 34-57 (66)
38 smart00419 HTH_CRP helix_turn_ 22.0 27 0.00058 16.8 -0.2 21 18-38 20-40 (48)
39 PF13412 HTH_24: Winged helix- 21.6 98 0.0021 15.1 2.0 17 21-37 32-48 (48)
40 PF14541 TAXi_C: Xylanase inhi 21.3 60 0.0013 20.1 1.3 30 5-34 30-59 (161)
41 PRK10265 chaperone-modulator p 20.9 86 0.0019 18.5 1.9 18 23-40 20-37 (101)
42 PRK11883 protoporphyrinogen ox 20.8 40 0.00087 23.9 0.4 26 5-30 47-72 (451)
43 TIGR02731 phytoene_desat phyto 20.7 79 0.0017 22.8 2.0 25 6-30 46-70 (453)
44 PF09756 DDRGK: DDRGK domain; 20.5 36 0.00078 22.7 0.1 45 15-73 122-166 (188)
45 PF00265 TK: Thymidine kinase; 20.0 60 0.0013 21.0 1.1 21 13-36 85-105 (176)
No 1
>COG3380 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]
Probab=99.74 E-value=9.3e-19 Score=122.20 Aligned_cols=68 Identities=26% Similarity=0.366 Sum_probs=57.7
Q ss_pred CCcccccCCceeEeCCCchHHHHHHHHHcCceeccCCceeeeecCCcccCCCCCCCcEEeCCCCCccccC
Q 040053 5 QPLIFGHAAQFITVNDYRFHPSVNGWLERGLVRPWGGMIGELEVGDQFTPFPFLRPRYIGVNGLHPLANS 74 (74)
Q Consensus 5 ~~~~~DhGAQyfta~~~~f~~~v~~~~~~G~v~~W~~~~~~~~~~~~~~~~~~~~~ryVg~pgM~al~k~ 74 (74)
+++.||||||||+++++.|.++|+.|.++|+|.+|+..++++..++ .++..++.+ |||.|||++|+|+
T Consensus 46 ~~g~~DhGAqYfk~~~~~F~~~Ve~~~~~glV~~W~~~~~~~~~~~-~~~~~d~~p-yvg~pgmsalak~ 113 (331)
T COG3380 46 DGGRFDHGAQYFKPRDELFLRAVEALRDDGLVDVWTPAVWTFTGDG-SPPRGDEDP-YVGEPGMSALAKF 113 (331)
T ss_pred CCccccccceeecCCchHHHHHHHHHHhCCceeeccccccccccCC-CCCCCCCCc-cccCcchHHHHHH
Confidence 3567999999999999999999999999999999999888887665 333333343 9999999999984
No 2
>PF13450 NAD_binding_8: NAD(P)-binding Rossmann-like domain; PDB: 3KA7_A 1V0J_D 3INR_B 3KYB_B 3GF4_A 2BI8_A 3INT_B 1WAM_A 2BI7_A 3MJ4_G ....
Probab=89.01 E-value=0.24 Score=27.37 Aligned_cols=26 Identities=8% Similarity=0.005 Sum_probs=19.3
Q ss_pred CCcccccCCceeEeC--CCchHHHHHHH
Q 040053 5 QPLIFGHAAQFITVN--DYRFHPSVNGW 30 (74)
Q Consensus 5 ~~~~~DhGAQyfta~--~~~f~~~v~~~ 30 (74)
++..+|+|+.+|... .+.+.+++++|
T Consensus 41 ~g~~~d~g~~~~~~~~~~~~~~~l~~~L 68 (68)
T PF13450_consen 41 PGYRFDLGAHYFFPPDDYPNLFRLLREL 68 (68)
T ss_dssp TTEEEETSS-SEEETTSCHHHHHHHHTT
T ss_pred CCEEEeeccEEEeCCCCchHHHHHHcCC
Confidence 348899999999884 47787877764
No 3
>PF15320 RAM: mRNA cap methylation, RNMT-activating mini protein
Probab=80.38 E-value=0.58 Score=27.37 Aligned_cols=27 Identities=19% Similarity=0.404 Sum_probs=23.2
Q ss_pred eEeCCCchHHHHH-HHHHcCceeccCCc
Q 040053 16 ITVNDYRFHPSVN-GWLERGLVRPWGGM 42 (74)
Q Consensus 16 fta~~~~f~~~v~-~~~~~G~v~~W~~~ 42 (74)
||..+++|+++++ +...-=||.+|..+
T Consensus 11 fTe~D~ey~~~~~~~~~~PPIV~~W~~r 38 (81)
T PF15320_consen 11 FTEDDEEYMEYCKRPFPPPPIVEPWNSR 38 (81)
T ss_pred ccccCHHHHHHHhCCCCCCCEecCcccC
Confidence 8999999999997 56777899999863
No 4
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=77.68 E-value=1.6 Score=21.06 Aligned_cols=21 Identities=14% Similarity=0.153 Sum_probs=17.7
Q ss_pred CceeEeCCCchHHHHHHHHHc
Q 040053 13 AQFITVNDYRFHPSVNGWLER 33 (74)
Q Consensus 13 AQyfta~~~~f~~~v~~~~~~ 33 (74)
..++.++...|+++|++|.-.
T Consensus 5 p~vi~~d~~~Fr~lVQ~LTG~ 25 (31)
T PF05678_consen 5 PTVIHTDPSNFRALVQRLTGA 25 (31)
T ss_pred CEEEEeCHHHHHHHHHHhHCc
Confidence 468889999999999998643
No 5
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=59.48 E-value=7.6 Score=28.42 Aligned_cols=26 Identities=15% Similarity=0.367 Sum_probs=22.7
Q ss_pred CCceeEeCC-CchHHHHHHHHHcCcee
Q 040053 12 AAQFITVND-YRFHPSVNGWLERGLVR 37 (74)
Q Consensus 12 GAQyfta~~-~~f~~~v~~~~~~G~v~ 37 (74)
|==||.|++ .+|...++.|++.|++.
T Consensus 163 gRGyFiA~s~eef~ek~e~l~~~gvi~ 189 (361)
T COG1759 163 GRGYFIASSPEEFYEKAERLLKRGVIT 189 (361)
T ss_pred CceEEEEcCHHHHHHHHHHHHHcCCcc
Confidence 556999998 67999999999999983
No 6
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=52.30 E-value=19 Score=20.89 Aligned_cols=19 Identities=16% Similarity=0.260 Sum_probs=15.6
Q ss_pred eeEeCC-CchHHHHHHHHHc
Q 040053 15 FITVND-YRFHPSVNGWLER 33 (74)
Q Consensus 15 yfta~~-~~f~~~v~~~~~~ 33 (74)
||++.+ ..|+.++++|...
T Consensus 59 yy~a~~rvDFR~Lvr~L~~~ 78 (88)
T PF04468_consen 59 YYTAESRVDFRELVRDLARE 78 (88)
T ss_pred EEEeCCcCcHHHHHHHHHHH
Confidence 788766 8899999998754
No 7
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=50.47 E-value=19 Score=19.05 Aligned_cols=20 Identities=10% Similarity=0.207 Sum_probs=16.6
Q ss_pred CCCchHHHHHHHHHcCceec
Q 040053 19 NDYRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 19 ~~~~f~~~v~~~~~~G~v~~ 38 (74)
..+.|..+++.|.++|.|..
T Consensus 33 ~~k~~~~ll~~l~~~g~l~~ 52 (59)
T PF09106_consen 33 PPKLFNALLEALVAEGRLKV 52 (59)
T ss_dssp -HCCHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHHHCCCeee
Confidence 45789999999999999854
No 8
>TIGR03467 HpnE squalene-associated FAD-dependent desaturase. The sequences in this family are members of the pfam01593 superfamily of flavin-containing amine oxidases which include the phytoene desaturases. These sequences also include a FAD-dependent oxidoreductase domain, pfam01266. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of squalene, the condensation product of the polyisoprenoid farnesyl pyrophosphate. This gene and its association with hopene biosynthesis in Zymomonas mobilis has been noted in the literature where the gene symbol hpnE was assigned. This gene is also found in contexts where the downstream conversion of squalene to hopenes is not evidence. The precise nature of the reaction catalyzed by this enzyme is unknown at this time.
Probab=41.52 E-value=24 Score=24.60 Aligned_cols=24 Identities=0% Similarity=-0.097 Sum_probs=20.4
Q ss_pred cccccCCceeEeCCCchHHHHHHH
Q 040053 7 LIFGHAAQFITVNDYRFHPSVNGW 30 (74)
Q Consensus 7 ~~~DhGAQyfta~~~~f~~~v~~~ 30 (74)
..||.|+++|....+.+.++++++
T Consensus 36 ~~~d~G~~~~~~~~~~~~~l~~~l 59 (419)
T TIGR03467 36 QTIDNGQHVLLGAYTNLLALLRRI 59 (419)
T ss_pred cceecCCEEEEcccHHHHHHHHHh
Confidence 349999999988888888888876
No 9
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=41.06 E-value=29 Score=19.27 Aligned_cols=19 Identities=26% Similarity=0.398 Sum_probs=13.8
Q ss_pred hHHHHHHHHHcCceeccCC
Q 040053 23 FHPSVNGWLERGLVRPWGG 41 (74)
Q Consensus 23 f~~~v~~~~~~G~v~~W~~ 41 (74)
=.++++.|.+.|+|.|-.+
T Consensus 37 Aariid~LE~~GiVs~~~~ 55 (65)
T PF09397_consen 37 AARIIDQLEEEGIVSPANG 55 (65)
T ss_dssp HHHHHHHHHHCTSBE---T
T ss_pred HHHHHHHHHHCCCCCCCCC
Confidence 3578999999999988875
No 10
>PF06258 Mito_fiss_Elm1: Mitochondrial fission ELM1; InterPro: IPR009367 This family consists of several hypothetical eukaryotic and prokaryotic proteins. The function of this family is unknown.
Probab=40.83 E-value=24 Score=25.04 Aligned_cols=31 Identities=29% Similarity=0.427 Sum_probs=24.2
Q ss_pred CCceeEe----CCCchHHHHHHHHHcCceeccCCc
Q 040053 12 AAQFITV----NDYRFHPSVNGWLERGLVRPWGGM 42 (74)
Q Consensus 12 GAQyfta----~~~~f~~~v~~~~~~G~v~~W~~~ 42 (74)
|++-+.. +..+|+++++.|.+.|.++++.+.
T Consensus 249 G~pV~v~~l~~~~~r~~r~~~~L~~~g~~r~~~~~ 283 (311)
T PF06258_consen 249 GKPVYVLPLPGRSGRFRRFHQSLEERGAVRPFTGW 283 (311)
T ss_pred CCCEEEecCCCcchHHHHHHHHHHHCCCEEECCCc
Confidence 4444443 345799999999999999999974
No 11
>PHA02591 hypothetical protein; Provisional
Probab=40.14 E-value=39 Score=19.81 Aligned_cols=25 Identities=4% Similarity=0.215 Sum_probs=22.1
Q ss_pred CCceeEeCCCchHHHHHHHHHcCce
Q 040053 12 AAQFITVNDYRFHPSVNGWLERGLV 36 (74)
Q Consensus 12 GAQyfta~~~~f~~~v~~~~~~G~v 36 (74)
|..||--+.+...++..+|.+.|.=
T Consensus 37 ~~ryfi~~~dd~~~vA~eL~eqGlS 61 (83)
T PHA02591 37 QTRYFVESEDDLISVTHELARKGFT 61 (83)
T ss_pred CEEEEEeccchHHHHHHHHHHcCCC
Confidence 5789999999999999999999863
No 12
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=35.92 E-value=15 Score=20.08 Aligned_cols=26 Identities=4% Similarity=0.049 Sum_probs=19.9
Q ss_pred ceeEeCCCchHHHHHHHHHcCceecc
Q 040053 14 QFITVNDYRFHPSVNGWLERGLVRPW 39 (74)
Q Consensus 14 Qyfta~~~~f~~~v~~~~~~G~v~~W 39 (74)
+.|.++...|++-++.|++.+.|++=
T Consensus 38 ~~f~~~~~~ik~~Ie~LIekeyi~Rd 63 (68)
T PF10557_consen 38 KRFPPSVSDIKKRIESLIEKEYIERD 63 (68)
T ss_dssp TTS---HHHHHHHHHHHHHTTSEEEE
T ss_pred CCcCCCHHHHHHHHHHHHHhhhhhcC
Confidence 37888889999999999999998764
No 13
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=35.33 E-value=30 Score=24.29 Aligned_cols=59 Identities=15% Similarity=0.156 Sum_probs=36.4
Q ss_pred CcccccCCceeEeCCCchHHHHHHHHHcCceeccCCceeeeecCCcccCCCCCCCcEEeCCC
Q 040053 6 PLIFGHAAQFITVNDYRFHPSVNGWLERGLVRPWGGMIGELEVGDQFTPFPFLRPRYIGVNG 67 (74)
Q Consensus 6 ~~~~DhGAQyfta~~~~f~~~v~~~~~~G~v~~W~~~~~~~~~~~~~~~~~~~~~ryVg~pg 67 (74)
++..|+|.|-.+-.++..+++++-..--. ..+-.+.+++.+..- +.+ .....||||-.|
T Consensus 104 qla~d~gmqi~~~~~~hm~~~le~y~~Lk-~~~~~GPfGTkEdPi-LVp-Sy~deRyVGCTG 162 (268)
T PTZ00043 104 QLARDMGMQIVNEPSEHMLGLLELYEYLK-SSSFVGPFGTIENPV-LVP-SVGTERVVGCTG 162 (268)
T ss_pred HHHHHhCceecCCchHHHHHHHHHHHhcC-cCCCCCCCCCccCCe-Eec-cCCCceEEeccC
Confidence 45679999998888888887777543211 133344555554322 122 224679999988
No 14
>PF14178 YppF: YppF-like protein
Probab=35.29 E-value=28 Score=19.29 Aligned_cols=18 Identities=22% Similarity=0.327 Sum_probs=15.3
Q ss_pred CchHHHHHHHHHcCceec
Q 040053 21 YRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 21 ~~f~~~v~~~~~~G~v~~ 38 (74)
.+++.++.+|..+|.+.|
T Consensus 40 ~eYR~lvreLE~~GA~~p 57 (60)
T PF14178_consen 40 NEYRNLVRELEANGAVSP 57 (60)
T ss_pred HHHHHHHHHHHHhCCCCC
Confidence 468899999999998765
No 15
>PF01593 Amino_oxidase: Flavin containing amine oxidoreductase This is a subset of the Pfam family; InterPro: IPR002937 This entry consists of various amine oxidases, including maize polyamine oxidase (PAO) [], L-amino acid oxidases (LAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. In vertebrates MAO plays an important role in regulating the intracellular levels of amines via their oxidation; these include various neurotransmitters, neurotoxins and trace amines []. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium []. PAOs in plants, bacteria and protozoa oxidise spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines []. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2Z5U_A ....
Probab=34.98 E-value=29 Score=23.59 Aligned_cols=27 Identities=7% Similarity=-0.165 Sum_probs=21.5
Q ss_pred CcccccCCceeEeCCCchHHHHHHHHH
Q 040053 6 PLIFGHAAQFITVNDYRFHPSVNGWLE 32 (74)
Q Consensus 6 ~~~~DhGAQyfta~~~~f~~~v~~~~~ 32 (74)
+..+|+|+.+|+...+.+..++.++..
T Consensus 39 g~~~e~G~~~~~~~~~~~~~~~~~l~~ 65 (450)
T PF01593_consen 39 GFTFELGAHRFFGMYPNLLNLIDELGL 65 (450)
T ss_dssp TEEEESSS-EEETTSHHHHHHHHHHTH
T ss_pred ceeecCCcccccccchhhHHHHHHhhh
Confidence 688999999999887778888887654
No 16
>PF14021 DUF4237: Protein of unknown function (DUF4237)
Probab=34.38 E-value=25 Score=20.68 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=15.8
Q ss_pred CCceeEeCCCchHHHHHHHHHcCceec
Q 040053 12 AAQFITVNDYRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 12 GAQyfta~~~~f~~~v~~~~~~G~v~~ 38 (74)
|.||.+ ..-++.|++.|.|++
T Consensus 68 G~Qy~~------~~~i~~L~~~G~L~~ 88 (90)
T PF14021_consen 68 GTQYKL------PRSIQELLENGYLRE 88 (90)
T ss_pred eEEEEe------cCcHHHHHHCCceEE
Confidence 678865 455788999998865
No 17
>TIGR00562 proto_IX_ox protoporphyrinogen oxidase. This protein is a flavoprotein and has a beta-alpha-beta dinucleotide binding motif near the amino end.
Probab=33.53 E-value=24 Score=25.30 Aligned_cols=26 Identities=4% Similarity=-0.055 Sum_probs=21.9
Q ss_pred CCcccccCCceeEeCCCchHHHHHHH
Q 040053 5 QPLIFGHAAQFITVNDYRFHPSVNGW 30 (74)
Q Consensus 5 ~~~~~DhGAQyfta~~~~f~~~v~~~ 30 (74)
.+..||.|++.|..+.+.+.++++++
T Consensus 51 ~g~~~e~G~~~~~~~~~~~~~l~~~l 76 (462)
T TIGR00562 51 DGYLIERGPDSFLERKKSAPDLVKDL 76 (462)
T ss_pred CCEEEecCccccccCChHHHHHHHHc
Confidence 35779999999999888888888776
No 18
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=33.48 E-value=32 Score=23.11 Aligned_cols=35 Identities=11% Similarity=0.058 Sum_probs=17.9
Q ss_pred cccCCceeE----eCCCchHHHHHHHHHcCceeccCCceee
Q 040053 9 FGHAAQFIT----VNDYRFHPSVNGWLERGLVRPWGGMIGE 45 (74)
Q Consensus 9 ~DhGAQyft----a~~~~f~~~v~~~~~~G~v~~W~~~~~~ 45 (74)
=|+|.||=+ .+++..+-..+.+...... |.+++.+
T Consensus 110 ~D~GtQYRS~I~~~s~eq~k~A~~s~e~~Q~k--~~~kI~T 148 (191)
T KOG1635|consen 110 NDVGTQYRSGIYTYSPEQEKLARESKEREQKK--WNGKIVT 148 (191)
T ss_pred CcccceeeeeeeeCCHHHHHHHHHHHHHHHhc--cCCcceE
Confidence 499999944 3443333222223222222 7777664
No 19
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=30.66 E-value=42 Score=18.59 Aligned_cols=20 Identities=30% Similarity=0.438 Sum_probs=15.8
Q ss_pred chHHHHHHHHHcCceeccCC
Q 040053 22 RFHPSVNGWLERGLVRPWGG 41 (74)
Q Consensus 22 ~f~~~v~~~~~~G~v~~W~~ 41 (74)
+=.++++.|.+.|+|.|=.+
T Consensus 35 rAariid~lE~~GiV~p~~g 54 (63)
T smart00843 35 RAARLIDQLEEEGIVGPANG 54 (63)
T ss_pred HHHHHHHHHHHCcCCCCCCC
Confidence 34678999999999977654
No 20
>PRK07208 hypothetical protein; Provisional
Probab=29.19 E-value=39 Score=24.51 Aligned_cols=27 Identities=11% Similarity=-0.079 Sum_probs=23.7
Q ss_pred CCcccccCCceeEeCCCchHHHHHHHH
Q 040053 5 QPLIFGHAAQFITVNDYRFHPSVNGWL 31 (74)
Q Consensus 5 ~~~~~DhGAQyfta~~~~f~~~v~~~~ 31 (74)
.+..+|.|++.|..+++...++++++.
T Consensus 49 ~g~~~d~G~h~~~~~~~~~~~l~~~l~ 75 (479)
T PRK07208 49 KGNRFDIGGHRFFSKSPEVMDLWNEIL 75 (479)
T ss_pred CCceEccCCceeccCCHHHHHHHHHhc
Confidence 457899999999999999999999985
No 21
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=28.34 E-value=19 Score=19.64 Aligned_cols=27 Identities=7% Similarity=0.032 Sum_probs=18.6
Q ss_pred CCceeEeCCCchHHHHHHHHHcCceec
Q 040053 12 AAQFITVNDYRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 12 GAQyfta~~~~f~~~v~~~~~~G~v~~ 38 (74)
+++++..+.++.+++++.+.+.|.+.-
T Consensus 27 ~~~~~~~s~~eL~~fL~~lv~e~~L~~ 53 (60)
T PF08672_consen 27 DPGGYDISLEELQEFLDRLVEEGKLEC 53 (60)
T ss_dssp GG--TT--HHHHHHHHHHHHHTTSEE-
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCcEEe
Confidence 456777788899999999999988753
No 22
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=27.44 E-value=66 Score=22.49 Aligned_cols=28 Identities=7% Similarity=-0.075 Sum_probs=17.2
Q ss_pred cccccCCceeEeCCCchHHHHHHHHHcCceeccC
Q 040053 7 LIFGHAAQFITVNDYRFHPSVNGWLERGLVRPWG 40 (74)
Q Consensus 7 ~~~DhGAQyfta~~~~f~~~v~~~~~~G~v~~W~ 40 (74)
..-|+|.||-.. +|.+++ .+.|+...-+
T Consensus 195 ihSDrGsqy~s~---~~~~~l---~~~gI~~Sms 222 (301)
T PRK09409 195 WLTDNGSCYRAN---ETRQFA---RMLGLEPKNT 222 (301)
T ss_pred EecCCCcccccH---HHHHHH---HHcCCeEeeC
Confidence 446999999743 354444 4567765544
No 23
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=27.31 E-value=13 Score=19.57 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=15.0
Q ss_pred eCCCchHHHHHHHHHcCcee
Q 040053 18 VNDYRFHPSVNGWLERGLVR 37 (74)
Q Consensus 18 a~~~~f~~~v~~~~~~G~v~ 37 (74)
.+.+...+.++.|.+.|+|.
T Consensus 30 ~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 30 ISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp --HHHHHHHHHHHHHTTSEE
T ss_pred cCHHHHHHHHHHHHHCCCEE
Confidence 34456778999999999983
No 24
>KOG2292 consensus Oligosaccharyltransferase, STT3 subunit [Posttranslational modification, protein turnover, chaperones]
Probab=27.05 E-value=48 Score=26.27 Aligned_cols=21 Identities=24% Similarity=0.425 Sum_probs=17.1
Q ss_pred HHHHHcCceeccCCceeeeec
Q 040053 28 NGWLERGLVRPWGGMIGELEV 48 (74)
Q Consensus 28 ~~~~~~G~v~~W~~~~~~~~~ 48 (74)
.-|...|.+.||+|++..+-+
T Consensus 318 ~~Lt~~g~iaPWtGRfySL~D 338 (751)
T KOG2292|consen 318 AALTATGYIAPWTGRFYSLWD 338 (751)
T ss_pred HHHHhcceecccccceeeccC
Confidence 346778999999999998744
No 25
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=26.46 E-value=24 Score=17.80 Aligned_cols=12 Identities=33% Similarity=0.681 Sum_probs=6.4
Q ss_pred cEEeCCCCCcccc
Q 040053 61 RYIGVNGLHPLAN 73 (74)
Q Consensus 61 ryVg~pgM~al~k 73 (74)
+| .+|||++|-.
T Consensus 11 CY-~v~gM~sl~D 22 (39)
T PF09292_consen 11 CY-SVPGMKSLRD 22 (39)
T ss_dssp ST-T-TT-EEEE-
T ss_pred Hh-cccccccccc
Confidence 44 6889998753
No 26
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=25.93 E-value=53 Score=21.31 Aligned_cols=19 Identities=26% Similarity=0.548 Sum_probs=15.5
Q ss_pred chHHHHHHHHHcCceeccC
Q 040053 22 RFHPSVNGWLERGLVRPWG 40 (74)
Q Consensus 22 ~f~~~v~~~~~~G~v~~W~ 40 (74)
..+..|++++++|+|++..
T Consensus 16 ~~~~~v~~ll~~G~I~~~~ 34 (210)
T cd03715 16 GITPHIQELLEAGILVPCQ 34 (210)
T ss_pred HHHHHHHHHHHCCCeECCC
Confidence 4567899999999998664
No 27
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=25.79 E-value=21 Score=17.83 Aligned_cols=26 Identities=19% Similarity=0.229 Sum_probs=19.4
Q ss_pred CceeEeCCCchHHHHHHHHHcCceec
Q 040053 13 AQFITVNDYRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 13 AQyfta~~~~f~~~v~~~~~~G~v~~ 38 (74)
|+.|-++.+...+.++.|.+.|+|..
T Consensus 27 a~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 27 AAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 44555555677888999999999854
No 28
>PRK12416 protoporphyrinogen oxidase; Provisional
Probab=25.28 E-value=28 Score=25.20 Aligned_cols=25 Identities=20% Similarity=0.259 Sum_probs=21.0
Q ss_pred CcccccCCceeEeCCCchHHHHHHH
Q 040053 6 PLIFGHAAQFITVNDYRFHPSVNGW 30 (74)
Q Consensus 6 ~~~~DhGAQyfta~~~~f~~~v~~~ 30 (74)
+..+|.|++.|..+.+.+.+++++|
T Consensus 53 g~~~e~G~~~i~~~~~~~~~l~~~l 77 (463)
T PRK12416 53 DFIMESGADSIVARNEHVMPLVKDL 77 (463)
T ss_pred CEEEecCcHHHhcCCHHHHHHHHHc
Confidence 5679999999988888887888876
No 29
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=25.20 E-value=23 Score=17.23 Aligned_cols=26 Identities=23% Similarity=0.424 Sum_probs=18.7
Q ss_pred CceeEeCCCchHHHHHHHHHcCceec
Q 040053 13 AQFITVNDYRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 13 AQyfta~~~~f~~~v~~~~~~G~v~~ 38 (74)
|+.|.++.......++.|.+.|+|..
T Consensus 21 ~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 21 AELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 34455555677888999999988853
No 30
>PLN02576 protoporphyrinogen oxidase
Probab=24.72 E-value=34 Score=24.93 Aligned_cols=25 Identities=12% Similarity=0.248 Sum_probs=20.4
Q ss_pred CCcccccCCceeEeCCCchHHHHHH
Q 040053 5 QPLIFGHAAQFITVNDYRFHPSVNG 29 (74)
Q Consensus 5 ~~~~~DhGAQyfta~~~~f~~~v~~ 29 (74)
.+..||+|++.|...++.+..+++.
T Consensus 58 ~g~~~d~G~~~~~~~~~~~~~l~~~ 82 (496)
T PLN02576 58 DGFIWEEGPNSFQPSDPELTSAVDS 82 (496)
T ss_pred CCeEEecCCchhccCcHHHHHHHHc
Confidence 3678999999999888877777665
No 31
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=24.00 E-value=22 Score=22.14 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=14.2
Q ss_pred ceeEeCC-CchHHHHHHHHHcC
Q 040053 14 QFITVND-YRFHPSVNGWLERG 34 (74)
Q Consensus 14 Qyfta~~-~~f~~~v~~~~~~G 34 (74)
|-+|..+ ++|++++.+|.+.+
T Consensus 89 qlitPaEY~afr~L~~eW~d~~ 110 (116)
T PF12970_consen 89 QLITPAEYPAFRSLMTEWTDVD 110 (116)
T ss_dssp SEE-HHHHHHHHHHHHHHH-GG
T ss_pred eeeCchhHHHHHHHHHHhccCC
Confidence 5555555 78999999998754
No 32
>cd00537 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease.
Probab=23.94 E-value=67 Score=21.84 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=21.7
Q ss_pred cccCCceeEeCC----CchHHHHHHHHHcCc
Q 040053 9 FGHAAQFITVND----YRFHPSVNGWLERGL 35 (74)
Q Consensus 9 ~DhGAQyfta~~----~~f~~~v~~~~~~G~ 35 (74)
.|.||.||...- +.|.++++.+.+.|+
T Consensus 157 i~aGA~f~iTQ~~fd~~~~~~~~~~~~~~gi 187 (274)
T cd00537 157 VDAGADFIITQLFFDNDAFLRFVDRCRAAGI 187 (274)
T ss_pred HHCCCCEEeecccccHHHHHHHHHHHHHcCC
Confidence 578999987643 778889999888885
No 33
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=23.75 E-value=71 Score=18.12 Aligned_cols=18 Identities=28% Similarity=0.468 Sum_probs=14.7
Q ss_pred HHHHHHHHHcCceeccCC
Q 040053 24 HPSVNGWLERGLVRPWGG 41 (74)
Q Consensus 24 ~~~v~~~~~~G~v~~W~~ 41 (74)
.+++..|.+.|+|.|=..
T Consensus 14 ~~~l~~lve~Gli~p~~~ 31 (84)
T PF13591_consen 14 PEFLRELVEEGLIEPEGE 31 (84)
T ss_pred HHHHHHHHHCCCeeecCC
Confidence 478899999999988543
No 34
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=23.51 E-value=79 Score=21.64 Aligned_cols=28 Identities=7% Similarity=-0.065 Sum_probs=17.2
Q ss_pred cccccCCceeEeCCCchHHHHHHHHHcCceeccC
Q 040053 7 LIFGHAAQFITVNDYRFHPSVNGWLERGLVRPWG 40 (74)
Q Consensus 7 ~~~DhGAQyfta~~~~f~~~v~~~~~~G~v~~W~ 40 (74)
..-|.|.||-. ..|.+++ .+.|+....+
T Consensus 156 ihSD~Gsqy~s---~~~~~~l---~~~gI~~Sms 183 (262)
T PRK14702 156 WLTDNGSCYRA---NETRQFA---RMLGLEPKNT 183 (262)
T ss_pred EEcCCCcccch---HHHHHHH---HHcCCeeccC
Confidence 44699999953 3454444 4567765544
No 35
>PF07277 SapC: SapC; InterPro: IPR010836 This family contains a number of bacterial SapC proteins approximately 250 residues long. In Campylobacter fetus, SapC forms part of a paracrystalline surface layer (S-layer) that confers serum resistance [].
Probab=23.15 E-value=55 Score=22.06 Aligned_cols=23 Identities=22% Similarity=0.408 Sum_probs=18.5
Q ss_pred hHHHHHHHHHcCceeccCCceee
Q 040053 23 FHPSVNGWLERGLVRPWGGMIGE 45 (74)
Q Consensus 23 f~~~v~~~~~~G~v~~W~~~~~~ 45 (74)
-+++++.|.+.|++++|+-.+..
T Consensus 147 T~~f~~~L~~~~Ll~~~~l~v~~ 169 (221)
T PF07277_consen 147 TQAFIKALAELGLLEPWTLTVTL 169 (221)
T ss_pred HHHHHHHHHHcCCCcccEEEEEe
Confidence 45678899999999999975544
No 36
>PLN02268 probable polyamine oxidase
Probab=22.48 E-value=78 Score=22.61 Aligned_cols=25 Identities=8% Similarity=0.126 Sum_probs=17.5
Q ss_pred CcccccCCceeEeC--CCchHHHHHHH
Q 040053 6 PLIFGHAAQFITVN--DYRFHPSVNGW 30 (74)
Q Consensus 6 ~~~~DhGAQyfta~--~~~f~~~v~~~ 30 (74)
+..+|.|+++|.-. .+.+.++++++
T Consensus 46 g~~~d~G~~~i~~~~~~~~~~~l~~~l 72 (435)
T PLN02268 46 GFPVDMGASWLHGVCNENPLAPLIGRL 72 (435)
T ss_pred CcccCCCCeeEeccCCCchHHHHHHHh
Confidence 46799999999743 33466666664
No 37
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=22.30 E-value=28 Score=17.76 Aligned_cols=24 Identities=17% Similarity=0.178 Sum_probs=17.9
Q ss_pred eeEeCCCchHHHHHHHHHcCceec
Q 040053 15 FITVNDYRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 15 yfta~~~~f~~~v~~~~~~G~v~~ 38 (74)
.|-++.+...+.+..|.+.|+|..
T Consensus 34 ~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 34 ELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred HHCCCHHHHHHHHHHHHHCCCEEe
Confidence 344555677888999999999853
No 38
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=21.98 E-value=27 Score=16.81 Aligned_cols=21 Identities=10% Similarity=0.191 Sum_probs=16.3
Q ss_pred eCCCchHHHHHHHHHcCceec
Q 040053 18 VNDYRFHPSVNGWLERGLVRP 38 (74)
Q Consensus 18 a~~~~f~~~v~~~~~~G~v~~ 38 (74)
.+.+...+.++.|.+.|+|..
T Consensus 20 ~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 20 LTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred CCHHHHHHHHHHHHHCCCEEE
Confidence 344667788999999999863
No 39
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.62 E-value=98 Score=15.11 Aligned_cols=17 Identities=18% Similarity=0.292 Sum_probs=12.8
Q ss_pred CchHHHHHHHHHcCcee
Q 040053 21 YRFHPSVNGWLERGLVR 37 (74)
Q Consensus 21 ~~f~~~v~~~~~~G~v~ 37 (74)
+.-.+.++.|.+.|+|+
T Consensus 32 ~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 32 STVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHCcCcC
Confidence 34567788899999874
No 40
>PF14541 TAXi_C: Xylanase inhibitor C-terminal; PDB: 3AUP_D 3HD8_A 1T6G_A 1T6E_X 2B42_A 3VLB_A 3VLA_A.
Probab=21.28 E-value=60 Score=20.15 Aligned_cols=30 Identities=7% Similarity=0.018 Sum_probs=24.2
Q ss_pred CCcccccCCceeEeCCCchHHHHHHHHHcC
Q 040053 5 QPLIFGHAAQFITVNDYRFHPSVNGWLERG 34 (74)
Q Consensus 5 ~~~~~DhGAQyfta~~~~f~~~v~~~~~~G 34 (74)
-+..+|-|..|--..++.|..+++++.++-
T Consensus 30 g~~iiDSGT~~T~L~~~~y~~l~~al~~~~ 59 (161)
T PF14541_consen 30 GGTIIDSGTTYTYLPPPVYDALVQALDAQM 59 (161)
T ss_dssp CSEEE-SSSSSEEEEHHHHHHHHHHHHHHH
T ss_pred CCEEEECCCCccCCcHHHHHHHHHHHHHHh
Confidence 356799999999999999999998887743
No 41
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=20.88 E-value=86 Score=18.46 Aligned_cols=18 Identities=17% Similarity=0.302 Sum_probs=14.6
Q ss_pred hHHHHHHHHHcCceeccC
Q 040053 23 FHPSVNGWLERGLVRPWG 40 (74)
Q Consensus 23 f~~~v~~~~~~G~v~~W~ 40 (74)
-.+++.+|.+.|+|.|=.
T Consensus 20 ~~~~l~eLve~GlIep~~ 37 (101)
T PRK10265 20 SEEELNEIVGLGVIEPRE 37 (101)
T ss_pred CHHHHHHHHHCCCeecCC
Confidence 357899999999998743
No 42
>PRK11883 protoporphyrinogen oxidase; Reviewed
Probab=20.75 E-value=40 Score=23.89 Aligned_cols=26 Identities=4% Similarity=-0.106 Sum_probs=19.5
Q ss_pred CCcccccCCceeEeCCCchHHHHHHH
Q 040053 5 QPLIFGHAAQFITVNDYRFHPSVNGW 30 (74)
Q Consensus 5 ~~~~~DhGAQyfta~~~~f~~~v~~~ 30 (74)
.+..+|+|++.|....+...++++++
T Consensus 47 ~g~~~d~G~~~~~~~~~~~~~l~~~l 72 (451)
T PRK11883 47 DGFPIELGPESFLARKPSAPALVKEL 72 (451)
T ss_pred CCeEEecChHHhcCCcHHHHHHHHHc
Confidence 35679999997776666677777765
No 43
>TIGR02731 phytoene_desat phytoene desaturase. Plants and cyanobacteria (and, supposedly, Chlorobium tepidum) have a conserved pathway from two molecules geranylgeranyl-PP to one of all-trans-lycopene. Members of this family are the enzyme pytoene desaturase (also called phytoene dehydrogenase). This model does not include the region of the chloroplast transit peptide in plants. A closely related family, excluded by this model, is zeta-carotene desaturase, another enzyme in the same pathway.
Probab=20.70 E-value=79 Score=22.76 Aligned_cols=25 Identities=0% Similarity=-0.181 Sum_probs=21.0
Q ss_pred CcccccCCceeEeCCCchHHHHHHH
Q 040053 6 PLIFGHAAQFITVNDYRFHPSVNGW 30 (74)
Q Consensus 6 ~~~~DhGAQyfta~~~~f~~~v~~~ 30 (74)
+..+|+|.+.|....+.+.+++++|
T Consensus 46 g~~~d~G~~~~~~~~~~~~~l~~~l 70 (453)
T TIGR02731 46 GDWYETGLHIFFGAYPNMLQLLKEL 70 (453)
T ss_pred CCEEEcCcceeccCCchHHHHHHHc
Confidence 4678999999998888888888875
No 44
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=20.46 E-value=36 Score=22.73 Aligned_cols=45 Identities=11% Similarity=0.152 Sum_probs=17.6
Q ss_pred eeEeCCCchHHHHHHHHHcCceeccCCceeeeecCCcccCCCCCCCcEEeCCCCCcccc
Q 040053 15 FITVNDYRFHPSVNGWLERGLVRPWGGMIGELEVGDQFTPFPFLRPRYIGVNGLHPLAN 73 (74)
Q Consensus 15 yfta~~~~f~~~v~~~~~~G~v~~W~~~~~~~~~~~~~~~~~~~~~ryVg~pgM~al~k 73 (74)
-|.+++..-...++.|.+.|.| ++.++..| .=-||.+.-|.+|++
T Consensus 122 ~f~l~t~~~i~ri~~L~~~g~l------tGv~DdrG--------kfIyIs~eE~~~va~ 166 (188)
T PF09756_consen 122 EFGLRTQDVINRIQELEAEGRL------TGVIDDRG--------KFIYISEEEMEAVAK 166 (188)
T ss_dssp HH-S-HHHHHHHHHHHHHHSSS-------EEE-TT----------EEE-----------
T ss_pred HcCCCHHHHHHHHHHHHHCCCc------eeeEcCCC--------CeEEecHHHHHHHHH
Confidence 3455556666778888888876 23444433 224666666776665
No 45
>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2.7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....
Probab=20.03 E-value=60 Score=21.03 Aligned_cols=21 Identities=24% Similarity=0.283 Sum_probs=15.4
Q ss_pred CceeEeCCCchHHHHHHHHHcCce
Q 040053 13 AQFITVNDYRFHPSVNGWLERGLV 36 (74)
Q Consensus 13 AQyfta~~~~f~~~v~~~~~~G~v 36 (74)
||||+ +....+++.+.+.|+.
T Consensus 85 aQFf~---~~i~~l~~~~~~~g~~ 105 (176)
T PF00265_consen 85 AQFFD---EQIVQLVEILANKGIP 105 (176)
T ss_dssp GGGST---TTHHHHHHHHHHTT-E
T ss_pred hHhhH---HHHHHHHHHHHhCCCe
Confidence 78886 5677788888887774
Done!