Query 033081
Match_columns 128
No_of_seqs 37 out of 39
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 09:35:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033081.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033081hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13991 BssS: BssS protein fa 87.0 0.75 1.6E-05 32.5 3.0 43 40-93 2-55 (73)
2 PRK12301 bssS biofilm formatio 57.8 9.1 0.0002 28.0 2.2 45 39-94 11-66 (84)
3 KOG3389 NADH:ubiquinone oxidor 50.0 7.9 0.00017 31.5 0.9 16 36-51 107-122 (178)
4 cd08915 V_Alix_like Protein-in 48.1 22 0.00048 29.1 3.3 32 79-110 10-41 (342)
5 KOG1610 Corticosteroid 11-beta 41.9 10 0.00022 33.2 0.4 19 74-93 56-74 (322)
6 PF04800 ETC_C1_NDUFA4: ETC co 41.1 12 0.00026 27.4 0.7 19 35-53 31-49 (101)
7 KOG1268 Glucosamine 6-phosphat 37.2 18 0.00038 34.5 1.2 21 99-119 363-397 (670)
8 cd09237 V_ScBro1_like Protein- 36.6 44 0.00096 27.8 3.4 30 79-109 10-39 (356)
9 KOG4108 Dynein light chain [Ce 35.4 2E+02 0.0044 23.3 6.8 39 80-119 71-109 (174)
10 PF10925 DUF2680: Protein of u 35.3 47 0.001 22.1 2.7 23 77-99 30-52 (59)
11 PRK15441 peptidyl-prolyl cis-t 34.8 32 0.00069 23.3 1.9 23 79-101 12-34 (93)
12 cd00483 HPPK 7,8-dihydro-6-hyd 34.6 16 0.00035 26.7 0.5 24 33-56 34-57 (128)
13 PF00771 FHIPEP: FHIPEP family 33.6 14 0.0003 34.3 0.0 29 75-103 139-167 (658)
14 PLN03052 acetate--CoA ligase; 33.5 38 0.00082 30.6 2.7 11 97-107 63-73 (728)
15 PRK13658 hypothetical protein; 33.4 20 0.00043 24.8 0.7 13 96-108 14-30 (59)
16 PRK10239 2-amino-4-hydroxy-6-h 31.9 23 0.00049 27.4 0.9 23 33-55 37-59 (159)
17 PF01756 ACOX: Acyl-CoA oxidas 30.2 30 0.00066 25.9 1.3 32 78-109 104-149 (187)
18 PRK15337 type III secretion sy 29.6 36 0.00077 32.4 1.9 26 77-102 161-186 (686)
19 PF12513 SUV3_C: Mitochondrial 28.1 42 0.0009 20.9 1.5 20 74-94 20-40 (49)
20 PF15361 RIC3: Resistance to i 28.0 44 0.00095 25.7 1.9 20 78-97 126-145 (152)
21 TIGR01398 FlhA flagellar biosy 26.7 43 0.00094 31.8 2.0 26 77-102 155-180 (678)
22 TIGR01498 folK 2-amino-4-hydro 25.8 31 0.00068 25.4 0.7 24 32-55 32-55 (127)
23 TIGR01399 hrcV type III secret 25.6 46 0.001 31.6 1.9 26 77-102 151-176 (677)
24 KOG3894 SNARE protein Syntaxin 25.5 60 0.0013 28.5 2.5 25 79-103 226-252 (316)
25 PF02217 T_Ag_DNA_bind: Origin 25.5 46 0.001 24.6 1.6 16 79-94 27-42 (94)
26 PHA02417 hypothetical protein 24.9 57 0.0012 23.8 1.9 15 100-114 51-66 (83)
27 PRK06012 flhA flagellar biosyn 24.5 51 0.0011 31.1 2.0 26 77-102 172-197 (697)
28 PRK05910 type III secretion sy 24.0 53 0.0011 30.8 2.0 26 77-102 156-181 (584)
29 PF12209 SAC3: Leucine permeas 23.6 95 0.0021 21.6 2.8 36 75-110 21-63 (79)
30 cd00307 RuBisCO_small_like Rib 23.4 32 0.0007 24.4 0.4 11 36-46 31-41 (84)
31 PF10231 DUF2315: Uncharacteri 23.3 1.3E+02 0.0029 22.8 3.7 45 48-103 2-47 (126)
32 PF08153 NGP1NT: NGP1NT (NUC09 22.5 12 0.00027 28.8 -2.0 30 73-102 71-100 (130)
33 PRK12792 flhA flagellar biosyn 22.1 61 0.0013 30.9 2.0 26 77-102 169-194 (694)
34 PRK09767 hypothetical protein; 21.5 45 0.00097 24.6 0.8 16 82-97 6-21 (117)
35 COG4003 Uncharacterized protei 21.4 75 0.0016 23.8 2.0 17 78-94 61-77 (98)
36 cd09236 V_AnPalA_UmRIM20_like 21.1 1.1E+02 0.0025 25.6 3.3 32 79-110 10-41 (353)
No 1
>PF13991 BssS: BssS protein family
Probab=86.99 E-value=0.75 Score=32.48 Aligned_cols=43 Identities=30% Similarity=0.516 Sum_probs=29.5
Q ss_pred cccCCCCC-----------CcccCCCCCCCCCchhhHhhhcCCCCCcCCCcccHHHHHHHHHHhh
Q 033081 40 PLFGWSSE-----------ADYIDSESKPENRSESDLEAKSSRSSRFSPGCFTEEKAKQLRLMTK 93 (128)
Q Consensus 40 PLfGWS~~-----------~DYi~~~~~~~~~~e~e~~~~~~r~srF~~G~lTEEKAkqLR~~~~ 93 (128)
|+.||--. .+|++........ +. . .+|. +||.|-||||...+.
T Consensus 2 Pv~GW~i~pv~~~dal~lrl~yls~~~q~~e~------a~--~-~~~~--~lT~e~Ar~Li~~L~ 55 (73)
T PF13991_consen 2 PVTGWDIGPVDSYDALMLRLHYLSSPDQPPEE------AQ--V-GRTY--WLTTEMARQLISILE 55 (73)
T ss_pred CcccceeccccccceeEEEecccCCCCCCccc------cc--c-Ccee--EecHHHHHHHHHHHH
Confidence 88899544 3888886655322 11 2 3565 799999999998764
No 2
>PRK12301 bssS biofilm formation regulatory protein BssS; Reviewed
Probab=57.75 E-value=9.1 Score=28.01 Aligned_cols=45 Identities=18% Similarity=0.364 Sum_probs=27.9
Q ss_pred ccccCCCCCC-----------cccCCCCCCCCCchhhHhhhcCCCCCcCCCcccHHHHHHHHHHhhh
Q 033081 39 SPLFGWSSEA-----------DYIDSESKPENRSESDLEAKSSRSSRFSPGCFTEEKAKQLRLMTKD 94 (128)
Q Consensus 39 aPLfGWS~~~-----------DYi~~~~~~~~~~e~e~~~~~~r~srF~~G~lTEEKAkqLR~~~~e 94 (128)
-|+.||--.+ +|+..+..++.. +.. -||. .||.+-||||=..+-+
T Consensus 11 hPvvGWdistvd~YDAmmirlhyLss~~Q~~e~-------A~v--~~tl--wLTtdvArqlI~iLea 66 (84)
T PRK12301 11 HPLVGWDISTVDSYDALMLRLHYQSPNDQEPEG-------AEV--GQTL--WLTTDVARQFISILEA 66 (84)
T ss_pred cccccccccCcccHhhHHHhhhhcCCCCCCccc-------ccc--cceE--EecHHHHHHHHHHHHH
Confidence 3899997653 466554433222 111 2465 6999999999776643
No 3
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=49.95 E-value=7.9 Score=31.45 Aligned_cols=16 Identities=50% Similarity=1.155 Sum_probs=13.7
Q ss_pred CccccccCCCCCCccc
Q 033081 36 NWWSPLFGWSSEADYI 51 (128)
Q Consensus 36 ~WWaPLfGWS~~~DYi 51 (128)
+|=.||.||++.+|=+
T Consensus 107 rWENPLMGWtsTaDPl 122 (178)
T KOG3389|consen 107 RWENPLMGWTSTADPL 122 (178)
T ss_pred hccCccccccccCCcc
Confidence 6889999999998744
No 4
>cd08915 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains
Probab=48.06 E-value=22 Score=29.13 Aligned_cols=32 Identities=16% Similarity=0.252 Sum_probs=27.3
Q ss_pred cccHHHHHHHHHHhhhhhhhHHHHHHHHHHHH
Q 033081 79 CFTEEKAKQLRLMTKDTASFHDAMYHSAIASR 110 (128)
Q Consensus 79 ~lTEEKAkqLR~~~~etesFHD~MYHSAIASR 110 (128)
.++|+||+.+|..+++----++.++++.++|.
T Consensus 10 ~Y~E~k~~lvr~e~~~~~e~~~~~l~~~L~sl 41 (342)
T cd08915 10 AYNERQDDYVREHIVEPIEALNKLLNSFLAER 41 (342)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 36899999999998566677899999999885
No 5
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=41.90 E-value=10 Score=33.16 Aligned_cols=19 Identities=58% Similarity=0.817 Sum_probs=16.6
Q ss_pred CcCCCcccHHHHHHHHHHhh
Q 033081 74 RFSPGCFTEEKAKQLRLMTK 93 (128)
Q Consensus 74 rF~~G~lTEEKAkqLR~~~~ 93 (128)
-|. ||||||.|++||..+.
T Consensus 56 V~A-gcl~~~gae~L~~~~~ 74 (322)
T KOG1610|consen 56 VFA-GCLTEEGAESLRGETK 74 (322)
T ss_pred EEE-EeecCchHHHHhhhhc
Confidence 354 9999999999999985
No 6
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=41.13 E-value=12 Score=27.38 Aligned_cols=19 Identities=37% Similarity=0.977 Sum_probs=11.0
Q ss_pred CCccccccCCCCCCcccCC
Q 033081 35 SNWWSPLFGWSSEADYIDS 53 (128)
Q Consensus 35 ~~WWaPLfGWS~~~DYi~~ 53 (128)
.+|=-||.||.+..|.+.-
T Consensus 31 ~~~~~PLMGWtss~D~~~q 49 (101)
T PF04800_consen 31 ARWENPLMGWTSSGDPLSQ 49 (101)
T ss_dssp SS---TTT-SSSS--SEEE
T ss_pred CCcCCCccCCCCCCChhhC
Confidence 3788999999999998874
No 7
>KOG1268 consensus Glucosamine 6-phosphate synthetases, contain amidotransferase and phosphosugar isomerase domains [Cell wall/membrane/envelope biogenesis]
Probab=37.20 E-value=18 Score=34.50 Aligned_cols=21 Identities=57% Similarity=0.759 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHH--------------Hhhhhcccc
Q 033081 99 HDAMYHSAIASR--------------LASDFKIRS 119 (128)
Q Consensus 99 HD~MYHSAIASR--------------LAsd~~~r~ 119 (128)
+-+-||||+|.| |||||-.|.
T Consensus 363 cgtSyhs~~A~R~ilEEL~eiPV~vElAsDflDR~ 397 (670)
T KOG1268|consen 363 CGTSYHSALATRPILEELSEIPVSVELASDFLDRN 397 (670)
T ss_pred ecchHHHHHHHHHHHHHHhcCCeeeehhhhhHhcC
Confidence 455699999999 788886653
No 8
>cd09237 V_ScBro1_like Protein-interacting V-domain of Saccharomyces cerevisiae Bro1 and related domains. This family contains the V-shaped (V) domain of Saccharomyces cerevisiae Bro1, and related domains. It belongs to the V_Alix_like superfamily which also includes the V-domain of Saccharomyces cerevisiae Rim20 (also known as PalA), mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Bro1 interacts with the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in endosomal trafficking. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Bro1 also has an N-terminal Bro1-like domain, which binds Snf7, a component of the ESCRT-III complex, and a C-terminal proline-rich
Probab=36.55 E-value=44 Score=27.84 Aligned_cols=30 Identities=30% Similarity=0.374 Sum_probs=24.2
Q ss_pred cccHHHHHHHHHHhhhhhhhHHHHHHHHHHH
Q 033081 79 CFTEEKAKQLRLMTKDTASFHDAMYHSAIAS 109 (128)
Q Consensus 79 ~lTEEKAkqLR~~~~etesFHD~MYHSAIAS 109 (128)
..+||||+.+|..+.+ --.++..+|+.+++
T Consensus 10 ~YsE~ka~lvr~e~~~-~e~a~~~~~~~L~~ 39 (356)
T cd09237 10 LYSEEKAKLLRAEVER-VEVANEEYASFLEY 39 (356)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence 3689999999999644 45678888988876
No 9
>KOG4108 consensus Dynein light chain [Cell motility]
Probab=35.37 E-value=2e+02 Score=23.29 Aligned_cols=39 Identities=21% Similarity=0.277 Sum_probs=26.9
Q ss_pred ccHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhhhhcccc
Q 033081 80 FTEEKAKQLRLMTKDTASFHDAMYHSAIASRLASDFKIRS 119 (128)
Q Consensus 80 lTEEKAkqLR~~~~etesFHD~MYHSAIASRLAsd~~~r~ 119 (128)
|..+-++..=+..+ +|..||.+||+--|.+|+..+....
T Consensus 71 F~~~~v~~iI~~vl-~e~L~~~~Y~~~~a~~lt~elae~I 109 (174)
T KOG4108|consen 71 FPAERVEKIIEAVL-TEKLADAEYDPDEALQLTKELAEEI 109 (174)
T ss_pred CCHHHHHHHHHHHH-HHHhhhhccCHHHHHHHHHHHHHHH
Confidence 33444443333333 6888999999999999999776543
No 10
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=35.26 E-value=47 Score=22.09 Aligned_cols=23 Identities=17% Similarity=0.384 Sum_probs=18.7
Q ss_pred CCcccHHHHHHHHHHhhhhhhhH
Q 033081 77 PGCFTEEKAKQLRLMTKDTASFH 99 (128)
Q Consensus 77 ~G~lTEEKAkqLR~~~~etesFH 99 (128)
.|.+|.|+|..+...|-+-..++
T Consensus 30 ~G~iTqeqAd~ik~~id~~~~~~ 52 (59)
T PF10925_consen 30 AGVITQEQADAIKKHIDQRQEYM 52 (59)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999999999987655554
No 11
>PRK15441 peptidyl-prolyl cis-trans isomerase C; Provisional
Probab=34.81 E-value=32 Score=23.25 Aligned_cols=23 Identities=26% Similarity=0.147 Sum_probs=19.5
Q ss_pred cccHHHHHHHHHHhhhhhhhHHH
Q 033081 79 CFTEEKAKQLRLMTKDTASFHDA 101 (128)
Q Consensus 79 ~lTEEKAkqLR~~~~etesFHD~ 101 (128)
+-+|++|++|+.++.+.++|=++
T Consensus 12 ~~~~~~A~~i~~~l~~g~~F~~l 34 (93)
T PRK15441 12 VKEEKLALDLLEQIKNGADFGKL 34 (93)
T ss_pred ECCHHHHHHHHHHHHCCCCHHHH
Confidence 45899999999999988998653
No 12
>cd00483 HPPK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is HPPK which catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The functional enzyme is a monomer. Mammals lack many of the enzymes in the folate pathway including, HPPK.
Probab=34.59 E-value=16 Score=26.66 Aligned_cols=24 Identities=13% Similarity=0.383 Sum_probs=20.4
Q ss_pred CCCCccccccCCCCCCcccCCCCC
Q 033081 33 ASSNWWSPLFGWSSEADYIDSESK 56 (128)
Q Consensus 33 ~~~~WWaPLfGWS~~~DYi~~~~~ 56 (128)
.|.-||+|-+|..+++||+|+-..
T Consensus 34 ~S~~y~T~p~g~~~~~~FlN~v~~ 57 (128)
T cd00483 34 VSPLYETAPVGFTDQPDFLNAVVE 57 (128)
T ss_pred ECCCEEeCCCCCCCChHHHheEEE
Confidence 466899999999999999998543
No 13
>PF00771 FHIPEP: FHIPEP family; InterPro: IPR001712 The Flagellar/Hr/Invasion Proteins Export Pore (FHIPEP) family [, ] consists of a number of proteins that constitute the type III secretion (or signal peptide-independent) pathway apparatus [, ]. This mechanism translocates proteins lacking an N-terminal signal peptide across the cell membrane in one step, as it does not require an intermediate periplasmic process to cleave the signal peptide. It is a common pathway amongst Gram-negative bacteria for secreting toxic and flagellar proteins. The pathway apparatus comprises three components: two within the inner membrane and one within the outer []. An FHIPEP protein is located within the inner membrane, although it is unknown which component it constitutes. FHIPEP proteins have all about 700 amino-acid residues. Within the sequence, the N terminus is highly conserved and hydrophobic, suggesting that this terminus is embedded within the membrane, with 6-8 transmembrane (TM) domains, while the C terminus is less conserved and appears to be devoid of TM regions. It is possible that members of the FHIPEP family serve as pores for the export of specific proteins.; GO: 0009306 protein secretion, 0016020 membrane; PDB: 3MIX_A 2X4A_A 3LW9_A 2X49_A 3MYD_A 3A5I_A.
Probab=33.55 E-value=14 Score=34.34 Aligned_cols=29 Identities=31% Similarity=0.383 Sum_probs=0.0
Q ss_pred cCCCcccHHHHHHHHHHhhhhhhhHHHHH
Q 033081 75 FSPGCFTEEKAKQLRLMTKDTASFHDAMY 103 (128)
Q Consensus 75 F~~G~lTEEKAkqLR~~~~etesFHD~MY 103 (128)
+-.|..|||.||..|+++..-+.|+-+|=
T Consensus 139 l~aG~I~~~eA~~rR~~l~~E~~fyGaMD 167 (658)
T PF00771_consen 139 LNAGLIDEEEARRRREELEREADFYGAMD 167 (658)
T ss_dssp -----------------------------
T ss_pred hhcCCCCHHHHHHHHHHHHHHhhhhhhcc
Confidence 34589999999999999998899999983
No 14
>PLN03052 acetate--CoA ligase; Provisional
Probab=33.54 E-value=38 Score=30.59 Aligned_cols=11 Identities=36% Similarity=0.627 Sum_probs=9.2
Q ss_pred hhHHHHHHHHH
Q 033081 97 SFHDAMYHSAI 107 (128)
Q Consensus 97 sFHD~MYHSAI 107 (128)
+||++||||--
T Consensus 63 ~~~~~~~~~~~ 73 (728)
T PLN03052 63 ALHQLMYYSCY 73 (728)
T ss_pred cHHHHhhhhcc
Confidence 69999999853
No 15
>PRK13658 hypothetical protein; Provisional
Probab=33.37 E-value=20 Score=24.80 Aligned_cols=13 Identities=46% Similarity=0.710 Sum_probs=9.4
Q ss_pred hhhHHHH----HHHHHH
Q 033081 96 ASFHDAM----YHSAIA 108 (128)
Q Consensus 96 esFHD~M----YHSAIA 108 (128)
.+.-|++ |||||-
T Consensus 14 DTVLDILVAGdyHSAI~ 30 (59)
T PRK13658 14 DTVLDILVAGDYHSAIH 30 (59)
T ss_pred hHHHHHHhcccHHHHHH
Confidence 4556765 999994
No 16
>PRK10239 2-amino-4-hydroxy-6-hydroxymethyldihyropteridine pyrophosphokinase; Provisional
Probab=31.92 E-value=23 Score=27.37 Aligned_cols=23 Identities=26% Similarity=0.502 Sum_probs=20.2
Q ss_pred CCCCccccccCCCCCCcccCCCC
Q 033081 33 ASSNWWSPLFGWSSEADYIDSES 55 (128)
Q Consensus 33 ~~~~WWaPLfGWS~~~DYi~~~~ 55 (128)
.|.-|+++-+|..+++||+|+-.
T Consensus 37 ~S~~y~T~P~g~~~q~~FlN~v~ 59 (159)
T PRK10239 37 VSSFYRTPPLGPQDQPDYLNAAV 59 (159)
T ss_pred ECCCEEeCCCCCCCCCCceEEEE
Confidence 46789999999999999999854
No 17
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=30.21 E-value=30 Score=25.90 Aligned_cols=32 Identities=31% Similarity=0.432 Sum_probs=21.8
Q ss_pred CcccHHHHHHHHHHh--------------hhhhhhHHHHHHHHHHH
Q 033081 78 GCFTEEKAKQLRLMT--------------KDTASFHDAMYHSAIAS 109 (128)
Q Consensus 78 G~lTEEKAkqLR~~~--------------~etesFHD~MYHSAIAS 109 (128)
|.+|.++++.||... +++=-|+|.+.+|+|++
T Consensus 104 g~ls~~~~~~l~~~i~~l~~~lrp~av~LVDAF~~~D~~L~S~iG~ 149 (187)
T PF01756_consen 104 GYLSPEQIKALRKAIEELCAELRPNAVALVDAFDFPDFFLNSPIGR 149 (187)
T ss_dssp TSS-HHHHHHHHHHHHHHHHHHGGGHHHHHHTT---HHHHT-STT-
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHhHHHHHHHhcCCCHHHHcChhcc
Confidence 789999999999864 55667899999999975
No 18
>PRK15337 type III secretion system protein InvA; Provisional
Probab=29.58 E-value=36 Score=32.38 Aligned_cols=26 Identities=12% Similarity=0.243 Sum_probs=23.9
Q ss_pred CCcccHHHHHHHHHHhhhhhhhHHHH
Q 033081 77 PGCFTEEKAKQLRLMTKDTASFHDAM 102 (128)
Q Consensus 77 ~G~lTEEKAkqLR~~~~etesFHD~M 102 (128)
.|..||+-||+-|+++.+-+.|+-+|
T Consensus 161 AG~Ide~eAr~RR~~l~~EadFyGAM 186 (686)
T PRK15337 161 AGIIDADGVKERRSVLERESQLYGSF 186 (686)
T ss_pred cCCCCHHHHHHHHHHHHHHHHhccCc
Confidence 48999999999999999888999887
No 19
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=28.06 E-value=42 Score=20.87 Aligned_cols=20 Identities=35% Similarity=0.713 Sum_probs=15.0
Q ss_pred CcCCCcccH-HHHHHHHHHhhh
Q 033081 74 RFSPGCFTE-EKAKQLRLMTKD 94 (128)
Q Consensus 74 rF~~G~lTE-EKAkqLR~~~~e 94 (128)
|| |+.|++ |+|.++|..+.+
T Consensus 20 Rf-p~~F~d~e~a~~~k~~~~~ 40 (49)
T PF12513_consen 20 RF-PDVFPDRELAEELKKRVEE 40 (49)
T ss_dssp C--TTTSTTHHHHHHHHHHHHH
T ss_pred Hc-ccccCCHHHHHHHHHHHHH
Confidence 67 567776 999999998754
No 20
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=27.96 E-value=44 Score=25.69 Aligned_cols=20 Identities=20% Similarity=0.077 Sum_probs=18.2
Q ss_pred CcccHHHHHHHHHHhhhhhh
Q 033081 78 GCFTEEKAKQLRLMTKDTAS 97 (128)
Q Consensus 78 G~lTEEKAkqLR~~~~etes 97 (128)
..+|+.+-.||+.|+.|||.
T Consensus 126 ~~~~~~eL~qLq~rL~qTE~ 145 (152)
T PF15361_consen 126 RKITDYELAQLQERLAQTER 145 (152)
T ss_pred ccchHHHHHHHHHHHHHHHH
Confidence 46899999999999999995
No 21
>TIGR01398 FlhA flagellar biosynthesis protein FlhA. This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this model.
Probab=26.75 E-value=43 Score=31.76 Aligned_cols=26 Identities=42% Similarity=0.479 Sum_probs=23.9
Q ss_pred CCcccHHHHHHHHHHhhhhhhhHHHH
Q 033081 77 PGCFTEEKAKQLRLMTKDTASFHDAM 102 (128)
Q Consensus 77 ~G~lTEEKAkqLR~~~~etesFHD~M 102 (128)
.|..||+-||+-|+++.+-+.|+-+|
T Consensus 155 AG~I~~~eAr~RR~~l~~Ea~FyGAM 180 (678)
T TIGR01398 155 AGLITEEEAKKRREELEQEADFYGAM 180 (678)
T ss_pred CCCCCHHHHHHHHHHHHHHHHhcccc
Confidence 48999999999999999888999887
No 22
>TIGR01498 folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. This model describes the folate biosynthesis enzyme 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. Alternate names include 6-hydroxymethyl-7,8-dihydropterin diphosphokinase and 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (HPPK). The extreme C-terminal region, of typically eight to thirty residues, is not included in the model. This enzyme may be found as a fusion protein with other enzymes of folate biosynthesis.
Probab=25.83 E-value=31 Score=25.39 Aligned_cols=24 Identities=21% Similarity=0.505 Sum_probs=20.1
Q ss_pred CCCCCccccccCCCCCCcccCCCC
Q 033081 32 NASSNWWSPLFGWSSEADYIDSES 55 (128)
Q Consensus 32 ~~~~~WWaPLfGWS~~~DYi~~~~ 55 (128)
..|.-+++|-+|...+|||+|+..
T Consensus 32 ~~S~~y~T~p~g~~~q~~FlN~v~ 55 (127)
T TIGR01498 32 IVSSIYETPPWGFTDQPDFLNAVV 55 (127)
T ss_pred EEccCEEEcCCCCCCCchhheEEE
Confidence 346789999999999999999754
No 23
>TIGR01399 hrcV type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane.
Probab=25.61 E-value=46 Score=31.58 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=23.8
Q ss_pred CCcccHHHHHHHHHHhhhhhhhHHHH
Q 033081 77 PGCFTEEKAKQLRLMTKDTASFHDAM 102 (128)
Q Consensus 77 ~G~lTEEKAkqLR~~~~etesFHD~M 102 (128)
.|..||+-||+-|+++.+-+.|+-+|
T Consensus 151 AGlI~~~eAr~RR~~l~~Ea~FyGAM 176 (677)
T TIGR01399 151 AGVIDADEARRRRSTLEKESQLYGAM 176 (677)
T ss_pred cCCCCHHHHHHHHHHHHHHHHhccCc
Confidence 48999999999999999888998877
No 24
>KOG3894 consensus SNARE protein Syntaxin 18/UFE1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.55 E-value=60 Score=28.50 Aligned_cols=25 Identities=8% Similarity=0.183 Sum_probs=21.9
Q ss_pred ccc--HHHHHHHHHHhhhhhhhHHHHH
Q 033081 79 CFT--EEKAKQLRLMTKDTASFHDAMY 103 (128)
Q Consensus 79 ~lT--EEKAkqLR~~~~etesFHD~MY 103 (128)
.+. -++++|++++++|-+..||+|-
T Consensus 226 ~~n~~~devrqie~~lvEI~~Lq~ifs 252 (316)
T KOG3894|consen 226 ELNELLDEVRQIEKRLVEISALQDIFS 252 (316)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455 5889999999999999999984
No 25
>PF02217 T_Ag_DNA_bind: Origin of replication binding protein; InterPro: IPR003133 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []. Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the central origin-binding domain (OBD). The overall fold of the ~130-residue T-ag OBD can be described as a central five-stranded antiparallel beta-sheet flanked by two alpha-helices on one side and one alpha-helix and one 3(10)-helix on the other. Both faces of the central beta-sheet are largely hydrophobic and are protected from solvent by the helices, thus forming two hydrophobic cores []. The T-ag OBD molecules are arranged as a spiral with a left-handed twist having six T-ag OBD's per turn. The spiral surrounds a central channel, the inner wall of which consists of alpha helices []. ; GO: 0003688 DNA replication origin binding, 0006260 DNA replication; PDB: 2IPR_B 2ITL_B 1Z1D_B 2FUF_A 2TBD_A 3QK2_A 2ITJ_A 2IF9_A 2NL8_A 2NTC_A ....
Probab=25.50 E-value=46 Score=24.57 Aligned_cols=16 Identities=38% Similarity=0.254 Sum_probs=13.5
Q ss_pred cccHHHHHHHHHHhhh
Q 033081 79 CFTEEKAKQLRLMTKD 94 (128)
Q Consensus 79 ~lTEEKAkqLR~~~~e 94 (128)
.=|-||+++|+.++.|
T Consensus 27 yTT~eK~~~Ly~kl~~ 42 (94)
T PF02217_consen 27 YTTKEKAEQLYKKLLE 42 (94)
T ss_dssp EEEHHHHHHHHHHCHH
T ss_pred EEcHHHHHHHHHHHHH
Confidence 4589999999999864
No 26
>PHA02417 hypothetical protein
Probab=24.88 E-value=57 Score=23.78 Aligned_cols=15 Identities=40% Similarity=0.328 Sum_probs=11.9
Q ss_pred HHHHHHH-HHHHHhhh
Q 033081 100 DAMYHSA-IASRLASD 114 (128)
Q Consensus 100 D~MYHSA-IASRLAsd 114 (128)
.+|.|+| ||.||||-
T Consensus 51 s~~l~aAv~ARR~A~L 66 (83)
T PHA02417 51 EAAIRAAVIARRRARL 66 (83)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 4688886 79999983
No 27
>PRK06012 flhA flagellar biosynthesis protein FlhA; Validated
Probab=24.52 E-value=51 Score=31.14 Aligned_cols=26 Identities=38% Similarity=0.460 Sum_probs=23.8
Q ss_pred CCcccHHHHHHHHHHhhhhhhhHHHH
Q 033081 77 PGCFTEEKAKQLRLMTKDTASFHDAM 102 (128)
Q Consensus 77 ~G~lTEEKAkqLR~~~~etesFHD~M 102 (128)
.|..||+-||.-|+++.+-+.|+-+|
T Consensus 172 aG~I~~~eAr~rR~~l~~Es~fyGaM 197 (697)
T PRK06012 172 AGLIDEEEAKKRRKELQQEADFYGAM 197 (697)
T ss_pred cCCCCHHHHHHHHHHHHHHHhhcccc
Confidence 48999999999999999888998887
No 28
>PRK05910 type III secretion system protein; Validated
Probab=23.97 E-value=53 Score=30.81 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=23.8
Q ss_pred CCcccHHHHHHHHHHhhhhhhhHHHH
Q 033081 77 PGCFTEEKAKQLRLMTKDTASFHDAM 102 (128)
Q Consensus 77 ~G~lTEEKAkqLR~~~~etesFHD~M 102 (128)
.|..||+-||+-|+++.+-+.|+-+|
T Consensus 156 aG~Id~~eAr~RR~~l~~EadFyGAM 181 (584)
T PRK05910 156 SGRASYSRVSKQKNSLLEESDFFSAM 181 (584)
T ss_pred CCCCCHHHHHHHHHHHHHHHHhcccc
Confidence 48999999999999999888998887
No 29
>PF12209 SAC3: Leucine permease transcriptional regulator helical domain; InterPro: IPR024293 This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [].; PDB: 3FWC_N 3FWB_B.
Probab=23.62 E-value=95 Score=21.62 Aligned_cols=36 Identities=19% Similarity=0.342 Sum_probs=24.1
Q ss_pred cCCCcccHHHHHHHHHHhhhhhh-------hHHHHHHHHHHHH
Q 033081 75 FSPGCFTEEKAKQLRLMTKDTAS-------FHDAMYHSAIASR 110 (128)
Q Consensus 75 F~~G~lTEEKAkqLR~~~~etes-------FHD~MYHSAIASR 110 (128)
++.-+|.++.+++.|+++.++=+ +|+.||.-..-|+
T Consensus 21 ~l~~~l~~~n~~~~R~~iI~sLs~ELy~AFi~E~~Y~~~lesk 63 (79)
T PF12209_consen 21 ILKNLLRRQNARKERKQIIDSLSEELYDAFIHEQLYQIYLESK 63 (79)
T ss_dssp HHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33347889999999999976544 5888888777665
No 30
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=23.43 E-value=32 Score=24.41 Aligned_cols=11 Identities=9% Similarity=0.090 Sum_probs=9.2
Q ss_pred CccccccCCCC
Q 033081 36 NWWSPLFGWSS 46 (128)
Q Consensus 36 ~WWaPLfGWS~ 46 (128)
.||.|+||-.+
T Consensus 31 ~w~lp~f~~~~ 41 (84)
T cd00307 31 SSWQSCGPIEG 41 (84)
T ss_pred hhcCCCCCCCC
Confidence 69999999843
No 31
>PF10231 DUF2315: Uncharacterised conserved protein (DUF2315); InterPro: IPR018796 This entry consists of small conserved proteins found from worms to humans. Their function is not known.
Probab=23.34 E-value=1.3e+02 Score=22.75 Aligned_cols=45 Identities=24% Similarity=0.432 Sum_probs=27.5
Q ss_pred CcccCCCCCCCCCchhhHhhhcCCCCCcC-CCcccHHHHHHHHHHhhhhhhhHHHHH
Q 033081 48 ADYIDSESKPENRSESDLEAKSSRSSRFS-PGCFTEEKAKQLRLMTKDTASFHDAMY 103 (128)
Q Consensus 48 ~DYi~~~~~~~~~~e~e~~~~~~r~srF~-~G~lTEEKAkqLR~~~~etesFHD~MY 103 (128)
-|||+++.+-++. |.=.|. +...| +-.++||..-.||..||..-.
T Consensus 2 ~d~igPPd~~SNl----------Rpi~~~~~~nEt-~lE~klR~~Rqe~~~wNq~FW 47 (126)
T PF10231_consen 2 HDWIGPPDPVSNL----------RPIIFHIPENET-PLERKLRLLRQETQEWNQEFW 47 (126)
T ss_pred CCCcCCCCccCCc----------ceeeccCCCCCC-HHHHHHHHHHHHHHHHHHHHH
Confidence 3778776666554 211222 22334 456788888889999977544
No 32
>PF08153 NGP1NT: NGP1NT (NUC091) domain; InterPro: IPR012971 This N-terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1 [].
Probab=22.46 E-value=12 Score=28.78 Aligned_cols=30 Identities=23% Similarity=0.383 Sum_probs=25.1
Q ss_pred CCcCCCcccHHHHHHHHHHhhhhhhhHHHH
Q 033081 73 SRFSPGCFTEEKAKQLRLMTKDTASFHDAM 102 (128)
Q Consensus 73 srF~~G~lTEEKAkqLR~~~~etesFHD~M 102 (128)
++.=++.|++.+.|+-|..+.+||+|.|+.
T Consensus 71 ~KLPmsLL~d~~~k~~~~~il~te~F~~tF 100 (130)
T PF08153_consen 71 SKLPMSLLQDSGTKQKRVHILETEPFEDTF 100 (130)
T ss_pred CcCCHHHhcccccccCCcceeecCCHHHHh
Confidence 566667777777999999999999999974
No 33
>PRK12792 flhA flagellar biosynthesis protein FlhA; Reviewed
Probab=22.07 E-value=61 Score=30.91 Aligned_cols=26 Identities=19% Similarity=0.415 Sum_probs=23.7
Q ss_pred CCcccHHHHHHHHHHhhhhhhhHHHH
Q 033081 77 PGCFTEEKAKQLRLMTKDTASFHDAM 102 (128)
Q Consensus 77 ~G~lTEEKAkqLR~~~~etesFHD~M 102 (128)
.|..||+-||+-|+++..-+.|+-+|
T Consensus 169 AGlI~~~eAr~RR~~l~~Ea~FyGAM 194 (694)
T PRK12792 169 AGLIDDKEAQRRRRELEEESAFFGSM 194 (694)
T ss_pred cCCCCHHHHHHHHHHHHHHHhhcccc
Confidence 48999999999999999888898877
No 34
>PRK09767 hypothetical protein; Provisional
Probab=21.46 E-value=45 Score=24.61 Aligned_cols=16 Identities=19% Similarity=0.150 Sum_probs=13.0
Q ss_pred HHHHHHHHHHhhhhhh
Q 033081 82 EEKAKQLRLMTKDTAS 97 (128)
Q Consensus 82 EEKAkqLR~~~~etes 97 (128)
-+.||+||++|.+.|.
T Consensus 6 ~~~ar~lR~~~T~aE~ 21 (117)
T PRK09767 6 KSNARDLRRNLTLQER 21 (117)
T ss_pred HHHHHHHHcCCCHHHH
Confidence 3689999999977664
No 35
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.42 E-value=75 Score=23.84 Aligned_cols=17 Identities=41% Similarity=0.423 Sum_probs=15.1
Q ss_pred CcccHHHHHHHHHHhhh
Q 033081 78 GCFTEEKAKQLRLMTKD 94 (128)
Q Consensus 78 G~lTEEKAkqLR~~~~e 94 (128)
|-+|+|-|+.||..+++
T Consensus 61 GEi~~E~A~~L~~~~~~ 77 (98)
T COG4003 61 GEITPEMAKALRVTLVH 77 (98)
T ss_pred CCCCHHHHHHHHhhHHH
Confidence 88999999999988764
No 36
>cd09236 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas Pa
Probab=21.10 E-value=1.1e+02 Score=25.58 Aligned_cols=32 Identities=16% Similarity=0.116 Sum_probs=26.3
Q ss_pred cccHHHHHHHHHHhhhhhhhHHHHHHHHHHHH
Q 033081 79 CFTEEKAKQLRLMTKDTASFHDAMYHSAIASR 110 (128)
Q Consensus 79 ~lTEEKAkqLR~~~~etesFHD~MYHSAIASR 110 (128)
.++|+|++.+|....+---.++.+.|+.++|.
T Consensus 10 ~Y~erk~~lVr~~~~~~le~~~~~l~~~L~sl 41 (353)
T cd09236 10 IYDDRKDRLVNESIIDELEELTNRAHSTLRSL 41 (353)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC
Confidence 46899999999998666667788888888875
Done!