Query psy7234
Match_columns 164
No_of_seqs 107 out of 280
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 21:30:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7234.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7234hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07701 HNOBA: Heme NO bindin 100.0 6.7E-52 1.5E-56 335.2 9.4 152 9-163 2-177 (219)
2 KOG4171|consensus 100.0 1.5E-44 3.3E-49 325.0 10.4 155 8-163 231-388 (671)
3 PF13426 PAS_9: PAS domain; PD 82.8 3 6.6E-05 27.3 4.5 89 27-120 5-96 (104)
4 PF13596 PAS_10: PAS domain; P 71.5 2.9 6.3E-05 28.8 1.9 44 18-61 3-47 (106)
5 PF00989 PAS: PAS fold; Inter 62.3 18 0.00039 23.9 4.4 44 19-62 7-51 (113)
6 PF08448 PAS_4: PAS fold; Int 57.1 26 0.00057 23.0 4.4 59 27-86 9-69 (110)
7 PF08534 Redoxin: Redoxin; In 48.6 13 0.00029 26.9 2.0 22 22-43 114-135 (146)
8 PF08447 PAS_3: PAS fold; Int 39.7 12 0.00026 24.4 0.4 86 35-122 1-90 (91)
9 cd03012 TlpA_like_DipZ_like Tl 38.0 28 0.00062 24.7 2.3 18 22-39 105-122 (126)
10 PF14061 Mtf2_C: Polycomb-like 34.8 37 0.00079 21.4 2.0 26 80-116 22-47 (50)
11 PF08446 PAS_2: PAS fold; Int 34.8 22 0.00048 25.3 1.3 37 26-62 18-59 (110)
12 cd06583 PGRP Peptidoglycan rec 32.5 38 0.00081 23.8 2.1 19 23-41 36-54 (126)
13 cd02971 PRX_family Peroxiredox 31.4 33 0.00072 24.3 1.7 22 22-43 109-130 (140)
14 cd02967 mauD Methylamine utili 28.9 53 0.0012 22.4 2.4 18 22-39 95-112 (114)
15 PF13691 Lactamase_B_4: tRNase 27.3 90 0.0019 20.4 3.1 37 25-62 15-52 (63)
16 PF13905 Thioredoxin_8: Thiore 27.0 50 0.0011 21.8 1.9 15 21-35 81-95 (95)
17 smart00644 Ami_2 Ami_2. 26.0 58 0.0013 23.1 2.2 22 23-44 33-54 (126)
18 KOG3561|consensus 25.4 48 0.001 32.1 2.1 53 23-78 105-158 (803)
19 COG3695 Predicted methylated D 25.1 30 0.00065 25.0 0.5 38 22-60 54-91 (103)
20 TIGR02661 MauD methylamine deh 24.8 64 0.0014 25.0 2.4 19 22-40 146-164 (189)
21 cd02966 TlpA_like_family TlpA- 24.5 70 0.0015 20.9 2.3 17 22-38 97-113 (116)
22 PF01510 Amidase_2: N-acetylmu 24.0 50 0.0011 23.4 1.5 21 21-41 35-55 (132)
23 PF07310 PAS_5: PAS domain; I 23.6 95 0.0021 22.7 3.0 65 10-76 24-92 (137)
24 COG5148 RPN10 26S proteasome r 23.2 58 0.0013 26.4 1.8 41 115-158 109-149 (243)
25 KOG1145|consensus 23.1 68 0.0015 30.2 2.5 35 108-142 194-228 (683)
26 PF15249 GLTSCR1: Glioma tumor 20.9 41 0.00089 24.1 0.5 20 16-35 25-44 (109)
27 PF04355 SmpA_OmlA: SmpA / Oml 20.9 85 0.0018 20.2 2.0 16 24-39 56-71 (71)
28 PRK11789 N-acetyl-anhydromuran 20.1 81 0.0018 25.0 2.1 22 25-46 76-97 (185)
No 1
>PF07701 HNOBA: Heme NO binding associated; InterPro: IPR011645 The HNOBA (Haem NO Binding) domain is found associated with the HNOB domain and IPR001054 from INTERPRO in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a haem-dependent sensor for gaseous ligands, and transduce diverse downstream signals in both bacteria and animals.; GO: 0004383 guanylate cyclase activity, 0006182 cGMP biosynthetic process; PDB: 2P04_B 2P08_A 3HLS_E.
Probab=100.00 E-value=6.7e-52 Score=335.20 Aligned_cols=152 Identities=43% Similarity=0.793 Sum_probs=98.3
Q ss_pred cccceeCHHHHHhhCCeEEEEcCCccEEEcChhhHhhhccccccCCCccceeEEEccCccceeehhhhhhccCCcEEEEE
Q psy7234 9 VLDLKIGVASFCKAFPWHFIVDRKLELVQLGAGYMRLFGRCLKHLGSSVNNYFEIRRPNLLTVTFSSILKRVNSPFVIAI 88 (164)
Q Consensus 9 ~~~l~i~~~~F~~lFPfHivfd~~l~I~~~G~~L~r~l~~~~~~~g~~~~d~F~l~rP~~i~~tf~~i~~~~~~~f~L~~ 88 (164)
+++++|++++||++|||||+||+||+|+|+|.+|+|++|+. ..|.+++|+|+|+||. +.+||++|+.++|+.|+|++
T Consensus 2 ~~~l~i~~~~F~~lFPFHi~fd~dl~I~~~G~~L~~~~p~~--~~g~~~~d~F~l~rP~-i~~tf~~I~~~~n~~F~L~~ 78 (219)
T PF07701_consen 2 PEDLPISSSTFCKLFPFHIVFDRDLKIVQVGEGLQRLLPDL--LLGKSLTDIFELVRPK-IEFTFDNILSHINNVFELES 78 (219)
T ss_dssp -------HCCHHHHSTT-EEEETT-BEEEE-HHHHHC-SS----TTSBGGGTEEEEESS---S-HHHHHT-TTS-EEEEE
T ss_pred CcCCcCCHHHHHhhCCeEEEECCCCEEEECchHHHHhCccc--ccCCCcceEEEecCCC-CcccHHHHHHhcCCeEEEEE
Confidence 57889999999999999999999999999999999999985 4688899999999999 99999999999999999999
Q ss_pred ecCCCCC------------------------CCCCcceeeeeeEEEeCCCCeEEEeecCCCCchhhHhhcCCcccCCCCC
Q psy7234 89 RLPQSLQ------------------------NSPVEGLEFKGQMVYCPESESLLFVASPFLDALDNLTSRGLFISDIPLH 144 (164)
Q Consensus 89 ~~~~~~~------------------------~~~~~~l~LkGqm~~~~e~~~ilFL~SP~v~~le~l~~~gL~lsD~~~h 144 (164)
+.+.... ....+.++|||||+|++||++|+|||||+++++++|.++||||||||+|
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LkGQM~y~~e~~~ilFl~sP~v~~l~el~~~gl~lsD~p~H 158 (219)
T PF07701_consen 79 KSPVMSTAKNNIPSNSKSTPRSSDQSSRSTVNDEARSLKLKGQMVYLEEWDSILFLGSPVVSSLEELRERGLYLSDLPLH 158 (219)
T ss_dssp -----------------------------------T--EEEEEEEEETTTTEEEEEEEE---TT----------------
T ss_pred CchhhcccccccccccccccccccccccccccccCCceEEEEEEEEecCCCeEEEEcccccCCHHHHHHcCCCccccCCc
Confidence 8743210 0012459999999999999999999999999999999999999999999
Q ss_pred ccchhhhhhhhhHHhhhcc
Q psy7234 145 DATRDVILVGEQARAQLAQ 163 (164)
Q Consensus 145 D~~rDlll~~eq~~ae~~~ 163 (164)
|++||+||+++|++||+++
T Consensus 159 d~~Rdlvl~~~q~~a~~~l 177 (219)
T PF07701_consen 159 DATRDLVLLGQQQSAELKL 177 (219)
T ss_dssp -EHHHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHHH
Confidence 9999999999999999875
No 2
>KOG4171|consensus
Probab=100.00 E-value=1.5e-44 Score=324.96 Aligned_cols=155 Identities=46% Similarity=0.843 Sum_probs=146.0
Q ss_pred CcccceeCHHHHHhhCCeEEEEcCCccEEEcChhhHhhhccccccCCCccceeEEEccCccceeehhhhhhccCCcEEEE
Q psy7234 8 SVLDLKIGVASFCKAFPWHFIVDRKLELVQLGAGYMRLFGRCLKHLGSSVNNYFEIRRPNLLTVTFSSILKRVNSPFVIA 87 (164)
Q Consensus 8 ~~~~l~i~~~~F~~lFPfHivfd~~l~I~~~G~~L~r~l~~~~~~~g~~~~d~F~l~rP~~i~~tf~~i~~~~~~~f~L~ 87 (164)
..+.+.|++++||++||||++||++|+|+|+|.++.|.+|+.....+..+.|+|++.||+ ++++|++|+.++|++|+++
T Consensus 231 ~~~~l~i~~~~F~~~fPfHf~fd~~~~i~q~G~~l~n~~~~~~~~~~~~~~~~fe~~rP~-i~~~fe~I~~~~Nt~Fvl~ 309 (671)
T KOG4171|consen 231 LDSTLRISTSDFCKAFPFHFMFDKDLEIVQAGNGLLNLMPPNLLQGGTNLEDYFEIVRPK-IPFTFENIMSHINTVFVLQ 309 (671)
T ss_pred cccccccchHhhHhhCcEEEEEcCCcEehHhhHHHHHhcchhhcccCCcHHHHHhhcCCC-ccccHHHHHHhhcccEEEE
Confidence 457899999999999999999999999999999999999776667889999999999999 9999999999999999999
Q ss_pred EecCCCCCC---CCCcceeeeeeEEEeCCCCeEEEeecCCCCchhhHhhcCCcccCCCCCccchhhhhhhhhHHhhhcc
Q psy7234 88 IRLPQSLQN---SPVEGLEFKGQMVYCPESESLLFVASPFLDALDNLTSRGLFISDIPLHDATRDVILVGEQARAQLAQ 163 (164)
Q Consensus 88 ~~~~~~~~~---~~~~~l~LkGqm~~~~e~~~ilFL~SP~v~~le~l~~~gL~lsD~~~hD~~rDlll~~eq~~ae~~~ 163 (164)
++.+..... ...+.+.|||||+|++|+++|||||||.|+++++|.++||||||+|+||+|||+||+|||++||+|+
T Consensus 310 ~k~~~~~~~~~~~~~~~l~LKGQM~~i~e~~sIlflcSP~V~~LdeL~~~GLyLsDiplHDatRDlILl~~Q~~aq~el 388 (671)
T KOG4171|consen 310 LKPEPMSVERDSESLRVLKLKGQMMYIPESDSILFLCSPVVDNLDELTGRGLYLSDIPLHDATRDLVLLGQQRRAQLEL 388 (671)
T ss_pred ecCCcccccccccccceEEEeeeEEEecCCCeEEEEcCcccCchHHHHhCCceeccCCccccchhheecchHHHHHHHH
Confidence 997665544 5678899999999999999999999999999999999999999999999999999999999999986
No 3
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=82.83 E-value=3 Score=27.33 Aligned_cols=89 Identities=18% Similarity=0.288 Sum_probs=49.9
Q ss_pred EEEcCCccEEEcChhhHhhhccc-cccCCCccceeEEEc-cCccceeehhhhhh-ccCCcEEEEEecCCCCCCCCCccee
Q psy7234 27 FIVDRKLELVQLGAGYMRLFGRC-LKHLGSSVNNYFEIR-RPNLLTVTFSSILK-RVNSPFVIAIRLPQSLQNSPVEGLE 103 (164)
Q Consensus 27 ivfd~~l~I~~~G~~L~r~l~~~-~~~~g~~~~d~F~l~-rP~~i~~tf~~i~~-~~~~~f~L~~~~~~~~~~~~~~~l~ 103 (164)
+++|.+|+|+.+-+...++++-. ....|+++.++|.-. ++. ..-.+.+... .....+++..+... .....+.
T Consensus 5 ~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~~----g~~~~~~ 79 (104)
T PF13426_consen 5 FILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPE-FEEQIERALEEGGSWSGEVRLRRKD----GETFWVE 79 (104)
T ss_dssp EEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHH-HHHHHHHHHHHTSSEEEEEEEEETT----SEEEEEE
T ss_pred EEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchh-hHHHHHHHHhcCCceeEEEEEEcCC----CCEEEEE
Confidence 68999999999999999999732 236789998888521 122 2233333322 22233344443211 1123366
Q ss_pred eeeeEEEeCCCCeEEEe
Q psy7234 104 FKGQMVYCPESESLLFV 120 (164)
Q Consensus 104 LkGqm~~~~e~~~ilFL 120 (164)
+.+.-++-++++..-++
T Consensus 80 ~~~~~i~~~~g~~~~~i 96 (104)
T PF13426_consen 80 VSASPIRDEDGEITGII 96 (104)
T ss_dssp EEEEEEEETTSSEEEEE
T ss_pred EEEEEEECCCCCEEEEE
Confidence 66666666666543333
No 4
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=71.53 E-value=2.9 Score=28.83 Aligned_cols=44 Identities=20% Similarity=0.375 Sum_probs=30.3
Q ss_pred HHHhhCCeEE-EEcCCccEEEcChhhHhhhccccccCCCccceeE
Q psy7234 18 SFCKAFPWHF-IVDRKLELVQLGAGYMRLFGRCLKHLGSSVNNYF 61 (164)
Q Consensus 18 ~F~~lFPfHi-vfd~~l~I~~~G~~L~r~l~~~~~~~g~~~~d~F 61 (164)
.+.+..|.-+ ++|++++|+..-+..+++++-.....|+++.++.
T Consensus 3 ~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~~~iGr~l~~~~ 47 (106)
T PF13596_consen 3 NILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSPSDIGRPLFDIH 47 (106)
T ss_dssp HHHHHSSSEEEEEETTSBEEEE-SCGC-SS---GGGTTSBCCCSS
T ss_pred HHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCChHHCCCCHHHcC
Confidence 3455566665 5799999999999999888654346899998874
No 5
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=62.32 E-value=18 Score=23.91 Aligned_cols=44 Identities=14% Similarity=0.214 Sum_probs=34.3
Q ss_pred HHhhCCeEEEEcCCccEEEcChhhHhhhccc-cccCCCccceeEE
Q psy7234 19 FCKAFPWHFIVDRKLELVQLGAGYMRLFGRC-LKHLGSSVNNYFE 62 (164)
Q Consensus 19 F~~lFPfHivfd~~l~I~~~G~~L~r~l~~~-~~~~g~~~~d~F~ 62 (164)
+..+=-.-+++|++|+|+.+-++..++++-. ....|+++.|++.
T Consensus 7 ~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~ 51 (113)
T PF00989_consen 7 LENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIH 51 (113)
T ss_dssp HHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCS
T ss_pred HhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcC
Confidence 4444456789999999999999999999643 2478999988854
No 6
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=57.06 E-value=26 Score=22.97 Aligned_cols=59 Identities=19% Similarity=0.283 Sum_probs=36.5
Q ss_pred EEEcCCccEEEcChhhHhhhccc-cccCCCccceeEEE-ccCccceeehhhhhhccCCcEEE
Q psy7234 27 FIVDRKLELVQLGAGYMRLFGRC-LKHLGSSVNNYFEI-RRPNLLTVTFSSILKRVNSPFVI 86 (164)
Q Consensus 27 ivfd~~l~I~~~G~~L~r~l~~~-~~~~g~~~~d~F~l-~rP~~i~~tf~~i~~~~~~~f~L 86 (164)
+++|++++|+.+-....++++.. ....|+++.|+|.= .++. ..--++.........+..
T Consensus 9 ~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 69 (110)
T PF08448_consen 9 FVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREE-FQAALRRALAGGEPVFFE 69 (110)
T ss_dssp EEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHH-HHHHHHHHHHHTSEEEEE
T ss_pred EEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhh-hHHHHHHhhccCceEEEE
Confidence 56799999999999999977543 24789999985443 2222 334444554443333333
No 7
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=48.63 E-value=13 Score=26.86 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=19.5
Q ss_pred hCCeEEEEcCCccEEEcChhhH
Q psy7234 22 AFPWHFIVDRKLELVQLGAGYM 43 (164)
Q Consensus 22 lFPfHivfd~~l~I~~~G~~L~ 43 (164)
..|..+++|++|+|+..+.+..
T Consensus 114 ~~P~~~lId~~G~V~~~~~g~~ 135 (146)
T PF08534_consen 114 GIPTTFLIDKDGKVVYRHVGPD 135 (146)
T ss_dssp SSSEEEEEETTSBEEEEEESSB
T ss_pred eecEEEEEECCCEEEEEEeCCC
Confidence 6899999999999999987754
No 8
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=39.66 E-value=12 Score=24.37 Aligned_cols=86 Identities=13% Similarity=0.321 Sum_probs=47.8
Q ss_pred EEEcChhhHhhhccccccC-CCccceeEEEccCccceeehhhhhh---ccCCcEEEEEecCCCCCCCCCcceeeeeeEEE
Q psy7234 35 LVQLGAGYMRLFGRCLKHL-GSSVNNYFEIRRPNLLTVTFSSILK---RVNSPFVIAIRLPQSLQNSPVEGLEFKGQMVY 110 (164)
Q Consensus 35 I~~~G~~L~r~l~~~~~~~-g~~~~d~F~l~rP~~i~~tf~~i~~---~~~~~f~L~~~~~~~~~~~~~~~l~LkGqm~~ 110 (164)
|+.+.+...++++-..... -....+...+++|.+...-.+.+.. ..+..+.++.|-- .++....-+..+|+.++
T Consensus 1 ~i~~s~~~~~i~G~~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~--~~~G~~~wi~~~~~~~~ 78 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEIGKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIR--RKDGEYRWIEVRGRPIF 78 (91)
T ss_dssp -EEE-THHHHHHTS-HHHHTCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEE--GTTSTEEEEEEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHhccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEE--CCCCCEEEEEEEEEEEE
Confidence 4556666677765431111 2445567788899865555555544 2344666554420 12223456999999999
Q ss_pred eCCCCeEEEeec
Q psy7234 111 CPESESLLFVAS 122 (164)
Q Consensus 111 ~~e~~~ilFL~S 122 (164)
-++++.+-.+|+
T Consensus 79 d~~g~~~~~~Gv 90 (91)
T PF08447_consen 79 DENGKPIRIIGV 90 (91)
T ss_dssp TTTS-EEEEEEE
T ss_pred CCCCCEEEEEEE
Confidence 778887777764
No 9
>cd03012 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
Probab=38.02 E-value=28 Score=24.68 Aligned_cols=18 Identities=11% Similarity=0.303 Sum_probs=15.5
Q ss_pred hCCeEEEEcCCccEEEcC
Q psy7234 22 AFPWHFIVDRKLELVQLG 39 (164)
Q Consensus 22 lFPfHivfd~~l~I~~~G 39 (164)
-.|..++||++|+|++.-
T Consensus 105 ~~P~~~vid~~G~v~~~~ 122 (126)
T cd03012 105 YWPALYLIDPTGNVRHVH 122 (126)
T ss_pred cCCeEEEECCCCcEEEEE
Confidence 389999999999998753
No 10
>PF14061 Mtf2_C: Polycomb-like MTF2 factor 2
Probab=34.84 E-value=37 Score=21.37 Aligned_cols=26 Identities=19% Similarity=0.300 Sum_probs=19.8
Q ss_pred cCCcEEEEEecCCCCCCCCCcceeeeeeEEEeCCCCe
Q psy7234 80 VNSPFVIAIRLPQSLQNSPVEGLEFKGQMVYCPESES 116 (164)
Q Consensus 80 ~~~~f~L~~~~~~~~~~~~~~~l~LkGqm~~~~e~~~ 116 (164)
++..|.+.+| ++...|++.|+-||+.
T Consensus 22 ~GE~~~VlAr-----------RV~~dG~vQYLvEWeg 47 (50)
T PF14061_consen 22 CGEKYRVLAR-----------RVTPDGKVQYLVEWEG 47 (50)
T ss_pred cCCeeEEEEE-----------EEcCCCcEEEEEEecC
Confidence 5566666665 4889999999999963
No 11
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
Probab=34.79 E-value=22 Score=25.31 Aligned_cols=37 Identities=22% Similarity=0.330 Sum_probs=29.2
Q ss_pred EEEEcC-CccEEEcChhhHhhhccc----cccCCCccceeEE
Q psy7234 26 HFIVDR-KLELVQLGAGYMRLFGRC----LKHLGSSVNNYFE 62 (164)
Q Consensus 26 Hivfd~-~l~I~~~G~~L~r~l~~~----~~~~g~~~~d~F~ 62 (164)
=+++|+ +++|++++.....+++.. ....|+++.++|.
T Consensus 18 LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~ 59 (110)
T PF08446_consen 18 LLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLSELLG 59 (110)
T ss_dssp EEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSC
T ss_pred EEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhC
Confidence 467875 699999999999999753 1368999999883
No 12
>cd06583 PGRP Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of
Probab=32.50 E-value=38 Score=23.77 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=16.6
Q ss_pred CCeEEEEcCCccEEEcChh
Q psy7234 23 FPWHFIVDRKLELVQLGAG 41 (164)
Q Consensus 23 FPfHivfd~~l~I~~~G~~ 41 (164)
..+|+++|++|+|.++-+-
T Consensus 36 ~~~H~~I~~~G~i~q~~~~ 54 (126)
T cd06583 36 ISYHFLVGGDGRIYQGRGW 54 (126)
T ss_pred cCceEEEcCCCEEEEECCC
Confidence 6799999999999997753
No 13
>cd02971 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a
Probab=31.39 E-value=33 Score=24.31 Aligned_cols=22 Identities=18% Similarity=0.147 Sum_probs=18.1
Q ss_pred hCCeEEEEcCCccEEEcChhhH
Q psy7234 22 AFPWHFIVDRKLELVQLGAGYM 43 (164)
Q Consensus 22 lFPfHivfd~~l~I~~~G~~L~ 43 (164)
..|+.+++|++|+|+..+.+..
T Consensus 109 ~~p~~~lid~~g~i~~~~~~~~ 130 (140)
T cd02971 109 AARATFIIDPDGKIRYVEVEPL 130 (140)
T ss_pred eeEEEEEECCCCcEEEEEecCC
Confidence 3578999999999999887753
No 14
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=28.92 E-value=53 Score=22.41 Aligned_cols=18 Identities=17% Similarity=0.423 Sum_probs=16.0
Q ss_pred hCCeEEEEcCCccEEEcC
Q psy7234 22 AFPWHFIVDRKLELVQLG 39 (164)
Q Consensus 22 lFPfHivfd~~l~I~~~G 39 (164)
.+|--+++|++|+|++-|
T Consensus 95 ~~P~~~vid~~G~v~~~~ 112 (114)
T cd02967 95 KLPYAVLLDEAGVIAAKG 112 (114)
T ss_pred CcCeEEEECCCCeEEecc
Confidence 469999999999999877
No 15
>PF13691 Lactamase_B_4: tRNase Z endonuclease
Probab=27.33 E-value=90 Score=20.38 Aligned_cols=37 Identities=24% Similarity=0.242 Sum_probs=28.4
Q ss_pred eEEEEcCCccEE-EcChhhHhhhccccccCCCccceeEE
Q psy7234 25 WHFIVDRKLELV-QLGAGYMRLFGRCLKHLGSSVNNYFE 62 (164)
Q Consensus 25 fHivfd~~l~I~-~~G~~L~r~l~~~~~~~g~~~~d~F~ 62 (164)
..+.+|.+-=+. .+|++-||.+.+. ..+=.++.++|-
T Consensus 15 l~l~~d~~rYlFGn~gEGtQR~~~e~-~ikl~kl~~IFl 52 (63)
T PF13691_consen 15 LLLFFDSRRYLFGNCGEGTQRACNEH-KIKLSKLNDIFL 52 (63)
T ss_pred EEEEeCCceEEeccCCcHHHHHHHHc-CCCccccceEEE
Confidence 567788877778 8999999999874 344477777773
No 16
>PF13905 Thioredoxin_8: Thioredoxin-like; PDB: 1FG4_A 1I5G_A 1OC8_B 1O6J_A 1OC9_B 1O81_A 3FKF_A 1O85_A 1O7U_A 1O8W_A ....
Probab=26.97 E-value=50 Score=21.83 Aligned_cols=15 Identities=13% Similarity=0.293 Sum_probs=13.2
Q ss_pred hhCCeEEEEcCCccE
Q psy7234 21 KAFPWHFIVDRKLEL 35 (164)
Q Consensus 21 ~lFPfHivfd~~l~I 35 (164)
...|.-+++|++|+|
T Consensus 81 ~~iP~~~lld~~G~I 95 (95)
T PF13905_consen 81 NGIPTLVLLDPDGKI 95 (95)
T ss_dssp TSSSEEEEEETTSBE
T ss_pred CcCCEEEEECCCCCC
Confidence 458999999999987
No 17
>smart00644 Ami_2 Ami_2.
Probab=26.05 E-value=58 Score=23.08 Aligned_cols=22 Identities=18% Similarity=0.107 Sum_probs=18.7
Q ss_pred CCeEEEEcCCccEEEcChhhHh
Q psy7234 23 FPWHFIVDRKLELVQLGAGYMR 44 (164)
Q Consensus 23 FPfHivfd~~l~I~~~G~~L~r 44 (164)
-.+|+.+|+||+|.+..+.-.+
T Consensus 33 ~~~H~~I~~dG~i~~~~~~~~~ 54 (126)
T smart00644 33 IGYHFLVGGDGRVYQGVGWNYV 54 (126)
T ss_pred eeeEEEEcCCCEEEEccCCccc
Confidence 4699999999999999886544
No 18
>KOG3561|consensus
Probab=25.44 E-value=48 Score=32.15 Aligned_cols=53 Identities=15% Similarity=0.159 Sum_probs=41.3
Q ss_pred CCeEEEEcCCccEEEcChhhHhhhccc-cccCCCccceeEEEccCccceeehhhhhh
Q psy7234 23 FPWHFIVDRKLELVQLGAGYMRLFGRC-LKHLGSSVNNYFEIRRPNLLTVTFSSILK 78 (164)
Q Consensus 23 FPfHivfd~~l~I~~~G~~L~r~l~~~-~~~~g~~~~d~F~l~rP~~i~~tf~~i~~ 78 (164)
==|-++++.+|+|+.|..++-.+|+-. ..+.|..+. .|.+|.+...-|+.+..
T Consensus 105 DGF~fvV~cdG~IvyVSeSVT~~L~y~QsDL~~qSly---~ilhp~d~~~~~~ql~~ 158 (803)
T KOG3561|consen 105 DGFLFVVNCDGRIVYVSESVTSVLGYLQSDLMGQSLY---DILHPLDNDKPREQLSP 158 (803)
T ss_pred cCeEEEEecCceEEEEecchHHhhCcCHHHHhcchHH---HhcCccccCcccccccc
Confidence 348999999999999999999888643 135666654 45599988888888774
No 19
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=25.07 E-value=30 Score=25.02 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=27.2
Q ss_pred hCCeEEEEcCCccEEEcChhhHhhhccccccCCCcccee
Q psy7234 22 AFPWHFIVDRKLELVQLGAGYMRLFGRCLKHLGSSVNNY 60 (164)
Q Consensus 22 lFPfHivfd~~l~I~~~G~~L~r~l~~~~~~~g~~~~d~ 60 (164)
..|||=|++.+|+|..-|+.-++-..- +..+|.-|.+.
T Consensus 54 ~lPWhRVvns~G~isl~~~~~~~Q~~l-L~aEGv~~~~~ 91 (103)
T COG3695 54 DLPWHRVVNSDGRISLPGPDKQRQREL-LLAEGVEFSDT 91 (103)
T ss_pred CCChhheecCCCcccCCCccHHHHHHH-HHHcCceeccC
Confidence 469999999999999998866554332 23556666554
No 20
>TIGR02661 MauD methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded.
Probab=24.79 E-value=64 Score=24.95 Aligned_cols=19 Identities=16% Similarity=0.405 Sum_probs=16.6
Q ss_pred hCCeEEEEcCCccEEEcCh
Q psy7234 22 AFPWHFIVDRKLELVQLGA 40 (164)
Q Consensus 22 lFPfHivfd~~l~I~~~G~ 40 (164)
-.|.-+++|++|+|++.|.
T Consensus 146 ~~P~~~lID~~G~I~~~g~ 164 (189)
T TIGR02661 146 KIPYGVLLDQDGKIRAKGL 164 (189)
T ss_pred ccceEEEECCCCeEEEccC
Confidence 4799999999999998764
No 21
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=24.46 E-value=70 Score=20.90 Aligned_cols=17 Identities=24% Similarity=0.462 Sum_probs=14.4
Q ss_pred hCCeEEEEcCCccEEEc
Q psy7234 22 AFPWHFIVDRKLELVQL 38 (164)
Q Consensus 22 lFPfHivfd~~l~I~~~ 38 (164)
-.|..+++|++|+|++.
T Consensus 97 ~~P~~~l~d~~g~v~~~ 113 (116)
T cd02966 97 GLPTTFLIDRDGRIRAR 113 (116)
T ss_pred ccceEEEECCCCcEEEE
Confidence 57889999999998863
No 22
>PF01510 Amidase_2: N-acetylmuramoyl-L-alanine amidase; InterPro: IPR002502 Proteins families containing this domain include zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity 3.5.1.28 from EC This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the Bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.; GO: 0008745 N-acetylmuramoyl-L-alanine amidase activity, 0009253 peptidoglycan catabolic process; PDB: 2RKQ_A 2EAV_A 2EAX_B 2XZ4_A 3TRU_A 3NKW_B 3QS0_B 3NW3_C 2Z9N_C 3NNO_B ....
Probab=23.97 E-value=50 Score=23.36 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=16.3
Q ss_pred hhCCeEEEEcCCccEEEcChh
Q psy7234 21 KAFPWHFIVDRKLELVQLGAG 41 (164)
Q Consensus 21 ~lFPfHivfd~~l~I~~~G~~ 41 (164)
.---+|+++|+||+|.++-+.
T Consensus 35 ~~~s~H~~I~~dG~i~q~~~~ 55 (132)
T PF01510_consen 35 SGASYHYVIDRDGTIYQGVPE 55 (132)
T ss_dssp SS-SSSEEEETTSEEEESSTT
T ss_pred CCceEEEEEecCCeEEEeecc
Confidence 345699999999999887544
No 23
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=23.56 E-value=95 Score=22.71 Aligned_cols=65 Identities=18% Similarity=0.344 Sum_probs=48.2
Q ss_pred ccceeCHHHHHhhCCeEEEEcC----CccEEEcChhhHhhhccccccCCCccceeEEEccCccceeehhhh
Q psy7234 10 LDLKIGVASFCKAFPWHFIVDR----KLELVQLGAGYMRLFGRCLKHLGSSVNNYFEIRRPNLLTVTFSSI 76 (164)
Q Consensus 10 ~~l~i~~~~F~~lFPfHivfd~----~l~I~~~G~~L~r~l~~~~~~~g~~~~d~F~l~rP~~i~~tf~~i 76 (164)
.--.|++..+-.+.|.-++++. +.+..-+|..+.++++. ...|+.+.|+|.-.......-.++.+
T Consensus 24 ~R~didP~~i~~~Lp~i~ile~~~~~~~r~RLaGt~i~~~~G~--d~tG~~~~el~~~~~~~~~~~~~~~v 92 (137)
T PF07310_consen 24 SRSDIDPADIPRLLPHIFILEVDDPGDFRYRLAGTRIVELFGR--DLTGRRLSELFPPEDRERVRRAYRAV 92 (137)
T ss_pred chhcCCHHHHHHHhCCeEEEEEeCCCceEEEEecHHHHHHhCC--CCCCCCHHHhcChHhHHHHHHHHHHH
Confidence 3345788899999999999874 55788899999999987 46899999997665443233334443
No 24
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=23.19 E-value=58 Score=26.44 Aligned_cols=41 Identities=27% Similarity=0.422 Sum_probs=29.0
Q ss_pred CeEEEeecCCCCchhhHhhcCCcccCCCCCccchhhhhhhhhHH
Q psy7234 115 ESLLFVASPFLDALDNLTSRGLFISDIPLHDATRDVILVGEQAR 158 (164)
Q Consensus 115 ~~ilFL~SP~v~~le~l~~~gL~lsD~~~hD~~rDlll~~eq~~ 158 (164)
..+.|+|||+..+-++|.+.--.+- -...+.|++..||.+.
T Consensus 109 riVaFvgSpi~esedeLirlak~lk---knnVAidii~fGE~~n 149 (243)
T COG5148 109 RIVAFVGSPIQESEDELIRLAKQLK---KNNVAIDIIFFGEAAN 149 (243)
T ss_pred EEEEEecCcccccHHHHHHHHHHHH---hcCeeEEEEehhhhhh
Confidence 4689999999999998866433322 2245678888887763
No 25
>KOG1145|consensus
Probab=23.07 E-value=68 Score=30.18 Aligned_cols=35 Identities=29% Similarity=0.472 Sum_probs=31.9
Q ss_pred EEEeCCCCeEEEeecCCCCchhhHhhcCCcccCCC
Q psy7234 108 MVYCPESESLLFVASPFLDALDNLTSRGLFISDIP 142 (164)
Q Consensus 108 m~~~~e~~~ilFL~SP~v~~le~l~~~gL~lsD~~ 142 (164)
-+.++++..|-||-||+-.--.+|+.+|-.+.|+-
T Consensus 194 ~V~~p~G~~iTFLDTPGHaAF~aMRaRGA~vtDIv 228 (683)
T KOG1145|consen 194 TVTLPSGKSITFLDTPGHAAFSAMRARGANVTDIV 228 (683)
T ss_pred EEecCCCCEEEEecCCcHHHHHHHHhccCccccEE
Confidence 35678889999999999999999999999999984
No 26
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=20.92 E-value=41 Score=24.12 Aligned_cols=20 Identities=10% Similarity=0.283 Sum_probs=16.0
Q ss_pred HHHHHhhCCeEEEEcCCccE
Q psy7234 16 VASFCKAFPWHFIVDRKLEL 35 (164)
Q Consensus 16 ~~~F~~lFPfHivfd~~l~I 35 (164)
.+.+.+|.|||++-..+..-
T Consensus 25 ~DA~~RLLPYHv~~~~~~~~ 44 (109)
T PF15249_consen 25 EDAVERLLPYHVFQEPEEDE 44 (109)
T ss_pred HHHHHHhcchhhhcCCCCCh
Confidence 47899999999998776443
No 27
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=20.89 E-value=85 Score=20.15 Aligned_cols=16 Identities=13% Similarity=0.158 Sum_probs=14.1
Q ss_pred CeEEEEcCCccEEEcC
Q psy7234 24 PWHFIVDRKLELVQLG 39 (164)
Q Consensus 24 PfHivfd~~l~I~~~G 39 (164)
.+.|.||+++++..+|
T Consensus 56 ~l~V~Fd~~~~v~~~~ 71 (71)
T PF04355_consen 56 QLKVYFDDDGVVKSIG 71 (71)
T ss_dssp EEEEEECTTSBEEEEE
T ss_pred EEEEEEcCCCEEEEeC
Confidence 5789999999999876
No 28
>PRK11789 N-acetyl-anhydromuranmyl-L-alanine amidase; Provisional
Probab=20.11 E-value=81 Score=24.96 Aligned_cols=22 Identities=32% Similarity=0.368 Sum_probs=17.4
Q ss_pred eEEEEcCCccEEEcChhhHhhh
Q psy7234 25 WHFIVDRKLELVQLGAGYMRLF 46 (164)
Q Consensus 25 fHivfd~~l~I~~~G~~L~r~l 46 (164)
.|+++++||+|.|.=+--.+-+
T Consensus 76 aHy~I~rdG~I~Q~V~~~~~Aw 97 (185)
T PRK11789 76 AHFLIRRDGEIVQFVSFDDRAW 97 (185)
T ss_pred EEEEECCCCeEEEecccccccc
Confidence 7999999999998776544443
Done!