Query 025376
Match_columns 253
No_of_seqs 156 out of 246
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 05:11:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025376hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2997 F-box protein FBX9 [Ge 100.0 6.9E-62 1.5E-66 447.2 12.0 221 1-241 127-366 (366)
2 PF12937 F-box-like: F-box-lik 98.3 5.1E-07 1.1E-11 61.1 2.5 32 1-32 16-47 (47)
3 PF00646 F-box: F-box domain; 97.0 0.0006 1.3E-08 45.6 2.7 31 1-31 18-48 (48)
4 smart00256 FBOX A Receptor for 96.8 0.001 2.2E-08 42.5 2.6 28 1-28 13-40 (41)
5 KOG3926 F-box proteins [Amino 94.3 0.033 7.2E-07 51.9 2.9 58 2-60 219-276 (332)
6 KOG2120 SCF ubiquitin ligase, 84.9 0.35 7.6E-06 46.3 0.7 29 3-31 115-143 (419)
7 KOG0281 Beta-TrCP (transducin 83.7 0.88 1.9E-05 44.2 2.8 32 1-32 94-125 (499)
8 PF06881 Elongin_A: RNA polyme 81.4 1.9 4E-05 34.3 3.5 52 2-60 20-71 (109)
9 KOG0274 Cdc4 and related F-box 76.8 1.6 3.5E-05 44.1 2.2 32 1-32 123-154 (537)
10 KOG2997 F-box protein FBX9 [Ge 72.0 4.9 0.00011 38.6 4.0 18 87-104 254-271 (366)
11 KOG4408 Putative Mg2+ and Co2+ 66.8 1.9 4.2E-05 41.5 0.1 65 1-73 23-87 (386)
12 PHA02123 hypothetical protein 51.1 11 0.00023 31.1 1.9 41 63-114 97-139 (146)
13 KOG4341 F-box protein containi 42.4 11 0.00023 37.7 0.7 36 1-36 87-122 (483)
14 PF13924 Lipocalin_5: Lipocali 35.8 2.4E+02 0.0052 23.0 9.3 51 99-149 31-89 (140)
15 PF11794 HpaB_N: 4-hydroxyphen 34.2 19 0.00041 33.4 1.0 13 159-171 206-218 (264)
16 COG2826 Tra8 Transposase and i 28.0 18 0.00039 34.4 -0.2 28 100-127 270-297 (318)
17 PF07661 MORN_2: MORN repeat v 25.1 82 0.0018 17.0 2.3 14 98-111 5-18 (22)
18 TIGR03067 Planc_TIGR03067 Plan 21.7 1.9E+02 0.0041 22.8 4.6 29 131-159 76-106 (107)
19 TIGR02310 HpaB-2 4-hydroxyphen 21.2 29 0.00063 35.2 -0.3 8 228-235 271-278 (519)
20 cd06537 CIDE_N_B CIDE_N domain 20.8 42 0.00091 25.9 0.6 20 96-115 54-73 (81)
21 PF09367 CpeS: CpeS-like prote 20.7 1.6E+02 0.0034 25.4 4.2 53 130-183 108-166 (170)
No 1
>KOG2997 consensus F-box protein FBX9 [General function prediction only]
Probab=100.00 E-value=6.9e-62 Score=447.25 Aligned_cols=221 Identities=36% Similarity=0.596 Sum_probs=204.3
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHHHHHhhccCCCchhhhhhhccCCCCcHHHHHHhcccCccCeEEEeecceeeCC
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACLKAWQLSGVVENYKILQSRYEGSWRKMWLLRPRIRIDGLYVSRNTYIRAG 80 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~~w~~~~~~~~~~~~~~~y~~sWr~Mf~~RPRIRfdG~YIS~~~Y~R~G 80 (253)
||.+||+++|+|||+|++++++|++||.+|+++|+..++..+.+++++.|.+|||+||++||||||||||||+|+|+|+|
T Consensus 127 ~d~rsL~~~s~vCr~F~~~~R~~~lwR~aC~KvW~~s~~~ln~~~~~sky~~SWR~Mfl~RpRvrFdG~YIS~~tYiR~G 206 (366)
T KOG2997|consen 127 LDLRSLEQLSLVCRGFYKCARDPELWRLACLKVWQRSCIKLNPKILQSKYYTSWREMFLERPRVRFDGVYISKTTYIRQG 206 (366)
T ss_pred cchhhHHHhHhhHHHHHHHHcChHHHHHHHHHHHHHhhhccchhhhhhHHHhHHHHHHhhCcceeecceEEEEEeEeecC
Confidence 68999999999999999999999999999999999988888888888999999999999999999999999999999999
Q ss_pred cccc-cccCceEEEEEeeeEEEecCCcEEEeeccccHHHHhhhhcccccCCCceEEEEEEEeCCEEEEEEecCC------
Q 025376 81 VAEW-KITNPVHIVCYYRYMRFFPSGRFIYKNSSQKIKDVAKIMNFRAAKADCVFTGHYTLSEEKVEAAVLYPG------ 153 (253)
Q Consensus 81 ~~~~-~~~~Pvh~VtYYRYLRFfpDGtvl~llS~~~P~~VV~~l~~~~~~~~~~~~G~~~l~~d~v~~~v~~~g------ 153 (253)
++++ +|++|||+|||||||||||||+||+++|++||++||++|+.++.+...++.|+|+++++.|++++..++
T Consensus 207 ~~~~~~~~~PVHlV~YYRYiRFyP~G~~l~~~SsdEP~dvVk~~s~~Nt~~~s~~~g~y~ls~~dv~~al~~~~~~~ps~ 286 (366)
T KOG2997|consen 207 ENSLDSFYRPVHLVEYYRYIRFYPDGHVLMLTSSDEPQDVVKRLSTRNTRRDSILLGHYRLSQSDVFAALTKSKERTPSD 286 (366)
T ss_pred chhhhhhcCcceeeEEEEEEEecCCCcEEEEeCCcChHHHHHhhhhccCcchhhhcccccccCCchhhhhccCcccCchh
Confidence 9999 999999999999999999999999999999999999999999988899999999999988877776321
Q ss_pred ------------CcceEEEEEEEEecCCCCccceeEEeEeEEecCCCCCCCCCCCcccccccccccCCCCCCCCCccccc
Q 025376 154 ------------LRPTVLRIRLRLRGTTAGANNRMDLLSLVTSGMNDNEVNGHDEDILGVVEGWQDDETHNPDVPAVSHK 221 (253)
Q Consensus 154 ------------~~~~~f~~~L~lrs~~~g~nnkL~w~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (253)
..+++|.++|+|++++..+.|+|+|.++. +++|+..|+++++.|++.|+
T Consensus 287 ~~~~r~~~~~v~~~s~tfl~~l~l~~~g~rr~~~L~W~~~~-------------------~~~~~d~et~~se~~l~~~k 347 (366)
T KOG2997|consen 287 YKYRRGRRVPVQEASQTFLVELQLCGSGHRRFNKLKWIHHS-------------------ITYKSDKETAVSEFPLTKMK 347 (366)
T ss_pred hhhhcccccccccccceeEEEEEEecccchhhhhheeeeee-------------------eeEeecccccccCCcccccc
Confidence 12467999999999999999999998876 14677889999999999999
Q ss_pred CCCcceeeeecccccccccC
Q 025376 222 RGLTPFVFVPFEEVETSVLN 241 (253)
Q Consensus 222 rg~~~~~fvp~e~~~~~~ln 241 (253)
+| .-|++||+++++.++||
T Consensus 348 ~~-~~FsrV~Sy~~d~e~l~ 366 (366)
T KOG2997|consen 348 TP-LFFSRVKSYTADSERLL 366 (366)
T ss_pred Cc-ceEEEeeeeeccccccC
Confidence 99 88999999999988875
No 2
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=98.27 E-value=5.1e-07 Score=61.11 Aligned_cols=32 Identities=38% Similarity=0.941 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHHHHHh
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACLK 32 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~ 32 (253)
||+.++.++|+|||+|+.++.++.+||++|.+
T Consensus 16 L~~~dl~~~~~vcr~w~~~~~~~~lW~~~~~r 47 (47)
T PF12937_consen 16 LDPRDLLRLSLVCRRWRRIANDNSLWRRLCLR 47 (47)
T ss_dssp S-HHHHHHHTTSSHHHHHHHTCCCHHHHHC--
T ss_pred CCHHHHHHHHHHHHHHHHHHCChhhhhhhccC
Confidence 68999999999999999999999999999974
No 3
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=96.99 E-value=0.0006 Score=45.62 Aligned_cols=31 Identities=26% Similarity=0.675 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHHHHH
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACL 31 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~lC~ 31 (253)
||+.++.++++|||+|+.++.+..+|+..|.
T Consensus 18 l~~~~~~~l~~vsk~~~~~~~~~~~~~~~~r 48 (48)
T PF00646_consen 18 LDPKDLLRLSLVSKRWRSLVDSPRLWKKIIR 48 (48)
T ss_dssp S-HHHHHHHCTT-HHHHHHHTTHHHHHHHH-
T ss_pred CcHHHHHHHHHHhhHHHHHHcCCCccHHHhC
Confidence 6899999999999999999999999999874
No 4
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=96.83 E-value=0.001 Score=42.51 Aligned_cols=28 Identities=32% Similarity=0.661 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHH
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRN 28 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~ 28 (253)
|++.++.++++|||.|+.++.++.+|+.
T Consensus 13 l~~~d~~~~~~vc~~~~~~~~~~~~~~~ 40 (41)
T smart00256 13 LPPKDLLRLRKVSRRWRSLIDSHDFWFK 40 (41)
T ss_pred CCHHHHHHHHHHHHHHHHHhcChhhhhc
Confidence 6889999999999999999999999975
No 5
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=94.33 E-value=0.033 Score=51.93 Aligned_cols=58 Identities=14% Similarity=0.303 Sum_probs=44.3
Q ss_pred CHHHHHHHHHhChHHHHhccCchHHHHHHHhhccCCCchhhhhhhccCCCCcHHHHHHh
Q 025376 2 SPYDLGKASCVCRKWKYTIRNPVFWRNACLKAWQLSGVVENYKILQSRYEGSWRKMWLL 60 (253)
Q Consensus 2 Dp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~~w~~~~~~~~~~~~~~~y~~sWr~Mf~~ 60 (253)
|-+||+.+|+|=-.++.|..+..|||.||...|+.-.+. ..+++.+.+.-+||+||-+
T Consensus 219 Dh~dL~s~aqa~etl~~l~~e~~iWkkLcqfHF~erQi~-~~l~l~k~~q~dWkqmyf~ 276 (332)
T KOG3926|consen 219 DHRDLESLAQAWETLAKLSEERRIWKKLCQFHFNERQIH-TILILSKKGQKDWKQMYFQ 276 (332)
T ss_pred CcchHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhHHHHH-HhhhhccccchhHHHHHHH
Confidence 668999999999999999998899999999877542221 1223445555789999865
No 6
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=84.92 E-value=0.35 Score=46.32 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=25.7
Q ss_pred HHHHHHHHHhChHHHHhccCchHHHHHHH
Q 025376 3 PYDLGKASCVCRKWKYTIRNPVFWRNACL 31 (253)
Q Consensus 3 p~sL~rlS~VCk~f~~l~~~~~lWR~lC~ 31 (253)
-.+|.++|.|||+|+.++.++.+|..+=+
T Consensus 115 kk~LL~~~~VC~Rfyr~~~de~lW~~lDl 143 (419)
T KOG2120|consen 115 KKELLKVSGVCKRFYRLASDESLWQTLDL 143 (419)
T ss_pred HHHHHHHHHHHHHHhhccccccceeeecc
Confidence 35799999999999999999999987754
No 7
>KOG0281 consensus Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown]
Probab=83.66 E-value=0.88 Score=44.16 Aligned_cols=32 Identities=19% Similarity=0.640 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHHHHHh
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACLK 32 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~ 32 (253)
||..||..+-+|||.|..+..++.+||+|-.+
T Consensus 94 ld~~sLc~celv~k~W~r~l~dg~~WKkLie~ 125 (499)
T KOG0281|consen 94 LDALSLCACELVCKEWKRVLSDGMLWKKLIER 125 (499)
T ss_pred cchhhhhHHHHHHHHHHHHhccchHHHHHHHH
Confidence 68999999999999999999999999999765
No 8
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=81.36 E-value=1.9 Score=34.27 Aligned_cols=52 Identities=13% Similarity=0.238 Sum_probs=31.9
Q ss_pred CHHHHHHHHHhChHHHHhccCchHHHHHHHhhccCCCchhhhhhhccCCCCcHHHHHHh
Q 025376 2 SPYDLGKASCVCRKWKYTIRNPVFWRNACLKAWQLSGVVENYKILQSRYEGSWRKMWLL 60 (253)
Q Consensus 2 Dp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~~w~~~~~~~~~~~~~~~y~~sWr~Mf~~ 60 (253)
.|.-|.++-.-|..+ .-.++.||+++|.+-|+...... .. .-..+||.||..
T Consensus 20 ~~~QL~~iE~~np~l--~~~tdeLW~~~i~rdFp~~~~~~----~~-~~~~~Wr~~Y~~ 71 (109)
T PF06881_consen 20 SPEQLRRIEDNNPHL--IEDTDELWKKLIKRDFPEESKRQ----KP-KEPESWRELYEK 71 (109)
T ss_pred CHHHHHHHHHhCCCc--chhhHHHHHHHHHhHCcChhhcc----cc-cccchHHHHHHH
Confidence 455566666666322 23366999999999997521111 11 123699999875
No 9
>KOG0274 consensus Cdc4 and related F-box and WD-40 proteins [General function prediction only]
Probab=76.80 E-value=1.6 Score=44.06 Aligned_cols=32 Identities=25% Similarity=0.609 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHHHHHh
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACLK 32 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~ 32 (253)
||+++|.++++||+.|+.++.+...|.+.|..
T Consensus 123 Ld~~~l~~~~~v~~~w~~~~~~~~~~~~~~~~ 154 (537)
T KOG0274|consen 123 LDGRDLLAVRQVCRNWNKLLDDDKVWWRMCRE 154 (537)
T ss_pred CCHHHhhhhhhhcchhhhhhhccchhhhhhhh
Confidence 79999999999999999999999888877765
No 10
>KOG2997 consensus F-box protein FBX9 [General function prediction only]
Probab=72.04 E-value=4.9 Score=38.62 Aligned_cols=18 Identities=6% Similarity=-0.103 Sum_probs=10.5
Q ss_pred cCceEEEEEeeeEEEecC
Q 025376 87 TNPVHIVCYYRYMRFFPS 104 (253)
Q Consensus 87 ~~Pvh~VtYYRYLRFfpD 104 (253)
+++-|-+-=++|.-|--|
T Consensus 254 Nt~~~s~~~g~y~ls~~d 271 (366)
T KOG2997|consen 254 NTRRDSILLGHYRLSQSD 271 (366)
T ss_pred cCcchhhhcccccccCCc
Confidence 455565556666655555
No 11
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=66.81 E-value=1.9 Score=41.46 Aligned_cols=65 Identities=18% Similarity=0.215 Sum_probs=46.2
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHHHHHhhccCCCchhhhhhhccCCCCcHHHHHHhcccCccCeEEEee
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACLKAWQLSGVVENYKILQSRYEGSWRKMWLLRPRIRIDGLYVSR 73 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~~w~~~~~~~~~~~~~~~y~~sWr~Mf~~RPRIRfdG~YIS~ 73 (253)
|+++.+.+.|.|.+++..+..+..+|++.|.+.|.......+ .++ .+|| .|+++++ -+-|+|+.-
T Consensus 23 ~~~~~~~~~a~vs~rLk~~~s~~~lw~r~c~k~l~is~e~~~-----~~~-etgq-sF~h~~f-~yvgvv~~~ 87 (386)
T KOG4408|consen 23 LLYRDLINCAYVSRRLKELGSHLPLWNRPCKKYLLISEEEKT-----QKY-ETGQ-SFLHDTF-GYVGVVLFP 87 (386)
T ss_pred cchhhhhcceeechHHhhhhhccccccccccccccccccccC-----Ccc-cccc-eeeeeec-ccceEEEEe
Confidence 578899999999999999999999999999988865432221 223 6666 5555552 233665544
No 12
>PHA02123 hypothetical protein
Probab=51.09 E-value=11 Score=31.06 Aligned_cols=41 Identities=34% Similarity=0.613 Sum_probs=29.5
Q ss_pred cCccCeEEEeecceeeCCccc--ccccCceEEEEEeeeEEEecCCcEEEeeccc
Q 025376 63 RIRIDGLYVSRNTYIRAGVAE--WKITNPVHIVCYYRYMRFFPSGRFIYKNSSQ 114 (253)
Q Consensus 63 RIRfdG~YIS~~~Y~R~G~~~--~~~~~Pvh~VtYYRYLRFfpDGtvl~llS~~ 114 (253)
-|-|||+ +-.+.|+|.|.+- |...||- |-|=|.|++.+|+.
T Consensus 97 mis~~gi-vqnv~yirsgsaivi~r~dnp~----------fnp~g~v~sitt~~ 139 (146)
T PHA02123 97 MISLNGI-VQNVDYIRSGSAIVIRRMDNPT----------FNPIGDVLSITTSS 139 (146)
T ss_pred EEEecce-EeeeEEEecCcEEEEEecCCCC----------CCcccceEEEecCC
Confidence 3466775 3446799999763 3456776 88999999998874
No 13
>KOG4341 consensus F-box protein containing LRR [General function prediction only]
Probab=42.36 E-value=11 Score=37.70 Aligned_cols=36 Identities=19% Similarity=0.401 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHhChHHHHhccCchHHHHHHHhhccC
Q 025376 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACLKAWQL 36 (253)
Q Consensus 1 LDp~sL~rlS~VCk~f~~l~~~~~lWR~lC~~~w~~ 36 (253)
||..+|.|.|++|+.|+.++.+-.-|.++=+-.++.
T Consensus 87 LDtksl~r~a~~c~~~n~~AlD~~~~q~idL~t~~r 122 (483)
T KOG4341|consen 87 LDTKSLCRAAQCCTMWNKLALDGSCWQHIDLFTFQR 122 (483)
T ss_pred HhHHHHHHHHHHHHHhhhhhhccccceeeehhcchh
Confidence 688999999999999999999999999988876664
No 14
>PF13924 Lipocalin_5: Lipocalin-like domain
Probab=35.83 E-value=2.4e+02 Score=22.98 Aligned_cols=51 Identities=20% Similarity=0.317 Sum_probs=27.7
Q ss_pred EEEecCCcEEEeeccccHHHHhhhhccc--------ccCCCceEEEEEEEeCCEEEEEE
Q 025376 99 MRFFPSGRFIYKNSSQKIKDVAKIMNFR--------AAKADCVFTGHYTLSEEKVEAAV 149 (253)
Q Consensus 99 LRFfpDGtvl~llS~~~P~~VV~~l~~~--------~~~~~~~~~G~~~l~~d~v~~~v 149 (253)
|=|-|||.+-..++...+......-... ..+.--++.|+|+++++.|+-.+
T Consensus 31 l~Yt~dG~ms~~i~~~~r~~~~~~~~~~~t~~e~~~~~~~~~aY~G~y~v~~~~v~h~v 89 (140)
T PF13924_consen 31 LIYTPDGYMSAQIMRPDRPPFASPDKWNATDAEWAAAARGYLAYSGRYEVDEDTVTHHV 89 (140)
T ss_pred EEECCCCeEEEEEecCCCCCcCcCccccCCHHHHHHHhhhheEEEEEEEEcCcEEEEEE
Confidence 3368999975555444332211111000 11234688999999999554444
No 15
>PF11794 HpaB_N: 4-hydroxyphenylacetate 3-hydroxylase N terminal; InterPro: IPR024674 This domain is found in the N terminus of HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []. The enzyme is NADH-dependent and uses FAD as the redox chromophore. The domain is also found in pyoverdin chromophore biosynthetic protein (PvcC), which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [] and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate [].; PDB: 3HWC_D 1U8V_D 2YYM_A 2YYI_A 2YYJ_A 2YYL_A 2YYG_A 2YYK_A.
Probab=34.21 E-value=19 Score=33.40 Aligned_cols=13 Identities=15% Similarity=0.273 Sum_probs=8.0
Q ss_pred EEEEEEEecCCCC
Q 025376 159 LRIRLRLRGTTAG 171 (253)
Q Consensus 159 f~~~L~lrs~~~g 171 (253)
|-+-+.+-...+|
T Consensus 206 yAv~FavP~~tpG 218 (264)
T PF11794_consen 206 YAVAFAVPMNTPG 218 (264)
T ss_dssp G-EEEEEETT-TT
T ss_pred eEEEEEccCCCCC
Confidence 4567777777777
No 16
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=27.95 E-value=18 Score=34.42 Aligned_cols=28 Identities=25% Similarity=0.575 Sum_probs=25.9
Q ss_pred EEecCCcEEEeeccccHHHHhhhhcccc
Q 025376 100 RFFPSGRFIYKNSSQKIKDVAKIMNFRA 127 (253)
Q Consensus 100 RFfpDGtvl~llS~~~P~~VV~~l~~~~ 127 (253)
||||-||.+...|+++...|...|+.++
T Consensus 270 rf~PKgTdla~vt~~el~~i~~~lN~rP 297 (318)
T COG2826 270 RFLPKGTDLAAVTQEELAAIADLLNHRP 297 (318)
T ss_pred HhCCCCCchhhCCHHHHHHHHHHHhcCc
Confidence 7999999999999999999999998753
No 17
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=25.13 E-value=82 Score=17.02 Aligned_cols=14 Identities=7% Similarity=0.453 Sum_probs=10.5
Q ss_pred eEEEecCCcEEEee
Q 025376 98 YMRFFPSGRFIYKN 111 (253)
Q Consensus 98 YLRFfpDGtvl~ll 111 (253)
+..|++||.+.+..
T Consensus 5 ~~~yy~nG~l~~~~ 18 (22)
T PF07661_consen 5 WKFYYENGKLKSEG 18 (22)
T ss_pred EEEEeCCCCEEEEE
Confidence 46799999977654
No 18
>TIGR03067 Planc_TIGR03067 Planctomycetes uncharacterized domain TIGR03067. This domain occurs in several species, mostly from the Planctomycetes division of the bacteria. It is expanded into a paralogous family of at least twenty-five members in Gemmata obscuriglobus UQM 2246. This family appears related to TIGR03066, which also is expanded into a large paralogous family in Gemmata obscuriglobus.
Probab=21.73 E-value=1.9e+02 Score=22.83 Aligned_cols=29 Identities=24% Similarity=0.339 Sum_probs=21.4
Q ss_pred CceEEEEEEEeCCEEEEEEecCCC--cceEE
Q 025376 131 DCVFTGHYTLSEEKVEAAVLYPGL--RPTVL 159 (253)
Q Consensus 131 ~~~~~G~~~l~~d~v~~~v~~~g~--~~~~f 159 (253)
...+.|-|+|++|+..+-...+|. +++.|
T Consensus 76 g~~~~gIY~l~gd~L~vC~~~~g~~~RPt~F 106 (107)
T TIGR03067 76 GKTIKGIYKLDGDTLTVCFSGGGDKPRPTEF 106 (107)
T ss_pred CCEEEEEEEEcCCEEEEEECCCCCCCCCCCC
Confidence 357899999999977776555554 66654
No 19
>TIGR02310 HpaB-2 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Shigella, Photorhabdus and Pasteurella. The family modelled by this alignment is narrowly limited to gammaproteobacteria to exclude other aromatic hydroxylases involved in various secondary metabolic pathways. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241).
Probab=21.22 E-value=29 Score=35.18 Aligned_cols=8 Identities=63% Similarity=1.356 Sum_probs=7.4
Q ss_pred eeeecccc
Q 025376 228 VFVPFEEV 235 (253)
Q Consensus 228 ~fvp~e~~ 235 (253)
||||||.|
T Consensus 271 VfVPWErV 278 (519)
T TIGR02310 271 VFIPWENV 278 (519)
T ss_pred cccchHHc
Confidence 89999988
No 20
>cd06537 CIDE_N_B CIDE_N domain of CIDE-B proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45 and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance.
Probab=20.82 E-value=42 Score=25.95 Aligned_cols=20 Identities=0% Similarity=0.102 Sum_probs=16.7
Q ss_pred eeeEEEecCCcEEEeecccc
Q 025376 96 YRYMRFFPSGRFIYKNSSQK 115 (253)
Q Consensus 96 YRYLRFfpDGtvl~llS~~~ 115 (253)
=-||...||.|++++|.+.+
T Consensus 54 EeyF~tLpdnT~lm~L~~gq 73 (81)
T cd06537 54 EDFFELLEDDTCLMVLEQGQ 73 (81)
T ss_pred HHHHhhCCCCCEEEEECCCC
Confidence 35889999999999998764
No 21
>PF09367 CpeS: CpeS-like protein; InterPro: IPR018536 This family contains Ycf58, which is encoded in the chlorplast genomes of red algae and CpeS its cyanobacterial homologue. CpeS is annotated as a phycoerythrin linkerprotein; although encoded in the phycoerythrin linker-polypeptide operon (cpeCDESTR), the function and role of CpeS remains unknown []. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis. Phycoerythrin is a red protein from the light-harvesting phycobiliprotein family, present in cyanobacteria, red algae and cryptomonads.; PDB: 3BDR_A.
Probab=20.74 E-value=1.6e+02 Score=25.42 Aligned_cols=53 Identities=21% Similarity=0.294 Sum_probs=22.0
Q ss_pred CCceEEEEEEEeCC-EEEEEEecCCCcceEEEEE-----EEEecCCCCccceeEEeEeEE
Q 025376 130 ADCVFTGHYTLSEE-KVEAAVLYPGLRPTVLRIR-----LRLRGTTAGANNRMDLLSLVT 183 (253)
Q Consensus 130 ~~~~~~G~~~l~~d-~v~~~v~~~g~~~~~f~~~-----L~lrs~~~g~nnkL~w~~~~s 183 (253)
.+.-..|+|.++.| .+.++..|.+....+ +++ |++|++-....+.....+|+|
T Consensus 108 e~~pv~~~y~~~~d~~L~L~T~y~~~~~eE-riwF~~pnlRlR~Siv~~~~g~~~~sF~s 166 (170)
T PF09367_consen 108 EKKPVVGRYRFDEDGTLTLTTEYERSVSEE-RIWFASPNLRLRTSIVKRSGGFSQTSFCS 166 (170)
T ss_dssp -------EEEE-TTS-EEEEEE-SS-EEEE-EEEEEETTEEEEEEEEEETTEEEEEEEEE
T ss_pred ccCceeEEEEECCCCeEEEEEEeCCEEEEE-EEEecCCCEEEEEEEEEcCCCceeeEEEE
Confidence 34566899999987 555554555543322 232 355544333334444666665
Done!