Query 039251
Match_columns 89
No_of_seqs 60 out of 62
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:49:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039251.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039251hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06232 ATS3: Embryo-specific 100.0 2.3E-47 4.9E-52 269.8 7.4 79 1-79 46-125 (125)
2 cd00113 PLAT PLAT (Polycystin- 99.2 1.1E-10 2.3E-15 77.1 7.5 66 14-79 44-114 (116)
3 cd01754 PLAT_plant_stress PLAT 98.6 2.1E-07 4.5E-12 65.7 6.7 62 8-69 46-115 (129)
4 cd01753 PLAT_LOX PLAT domain o 98.4 1.7E-06 3.8E-11 58.9 7.0 66 6-72 37-106 (113)
5 cd01756 PLAT_repeat PLAT/LH2 d 98.2 8E-06 1.7E-10 55.3 7.5 66 6-71 37-107 (120)
6 cd01752 PLAT_polycystin PLAT/L 97.8 9.2E-05 2E-09 50.2 6.7 66 6-71 37-107 (120)
7 smart00308 LH2 Lipoxygenase ho 97.6 0.0004 8.7E-09 45.1 7.0 57 12-68 43-102 (105)
8 cd02899 PLAT_SR Scavenger rece 97.4 0.00049 1.1E-08 47.4 5.9 57 13-69 40-97 (109)
9 PF01477 PLAT: PLAT/LH2 domain 97.0 0.0023 5E-08 41.2 5.7 56 17-72 44-104 (113)
10 cd01757 PLAT_RAB6IP1 PLAT/LH2 92.9 0.52 1.1E-05 32.7 6.2 50 21-70 44-97 (114)
11 cd01755 PLAT_lipase PLAT/ LH2 62.2 40 0.00087 22.8 5.9 51 13-63 41-103 (120)
12 KOG3123 Diphthine synthase [Tr 59.5 4.8 0.0001 32.1 1.1 19 31-49 119-145 (272)
13 PF05727 UPF0228: Uncharacteri 48.8 8.9 0.00019 27.8 1.0 17 32-49 85-102 (127)
14 COG3411 Ferredoxin [Energy pro 35.7 16 0.00035 23.6 0.5 15 58-76 17-31 (64)
15 KOG4714 Nucleoporin [Nuclear s 35.2 25 0.00054 28.9 1.7 24 16-39 290-316 (319)
16 PF03394 Pox_E8: Poxvirus E8 p 33.8 16 0.00034 28.9 0.4 20 35-54 4-23 (242)
17 PHA03004 putative membrane pro 32.3 17 0.00037 29.1 0.3 21 34-54 34-54 (270)
18 PF08695 Coa1: Cytochrome oxid 31.7 1.5E+02 0.0033 19.4 5.2 40 20-59 71-111 (116)
19 KOG3646 Acetylcholine receptor 27.6 57 0.0012 28.3 2.7 40 31-74 163-202 (486)
20 PF14326 DUF4384: Domain of un 26.0 1.1E+02 0.0024 19.1 3.2 28 21-54 10-37 (83)
21 PF06347 SH3_4: Bacterial SH3 24.9 75 0.0016 18.2 2.1 28 19-49 24-51 (55)
22 TIGR01221 rmlC dTDP-4-dehydror 22.4 41 0.00089 24.7 0.8 12 67-78 109-120 (176)
23 PF14237 DUF4339: Domain of un 20.6 51 0.0011 18.6 0.8 12 36-47 33-44 (45)
24 PF00932 LTD: Lamin Tail Domai 20.1 79 0.0017 20.3 1.7 12 48-59 26-37 (116)
No 1
>PF06232 ATS3: Embryo-specific protein 3, (ATS3); InterPro: IPR010417 This is a family of plant seed-specific proteins identified in Arabidopsis thaliana (Mouse-ear cress). ATS3 is expressed in a pattern similar to the Arabidopsis seed storage protein genes [].
Probab=100.00 E-value=2.3e-47 Score=269.76 Aligned_cols=79 Identities=67% Similarity=1.442 Sum_probs=78.0
Q ss_pred CccCCCCCCCC-CCcccccccceeeecccccCceEEEEEEeCCCCCeecEEEEeccCCCceeEEeccccCCCcceeeccC
Q 039251 1 VYAPRLDDPYS-RTFESCSTDTYTLYGPCTYQICYLYLYRSGYDGWKPESVTVYGYYTRSISFYYNTWIPDDIWYGFNYC 79 (89)
Q Consensus 1 vy~~rLDdp~~-~~FerCstDtF~V~G~C~~~ICylyL~r~G~dgW~Pe~V~Iy~~~~~~vtF~f~~~iP~~vwyG~n~C 79 (89)
||+||||||.+ ++||||++|+|+|+|+|+++||||||+|+|+|||+||||+||+++++|++||||+|||+|+|||||+|
T Consensus 46 v~~~~Ld~p~~~~~FErCs~DtF~v~G~C~~~IC~lyL~r~G~dGW~Pe~V~Iy~~~~~~~~F~~~~~lp~~vwyG~n~C 125 (125)
T PF06232_consen 46 VYVPRLDDPGSGDTFERCSTDTFQVTGPCLYQICYLYLYRSGSDGWKPEWVQIYGSGSKPVTFYFNTFLPNGVWYGFNYC 125 (125)
T ss_pred EEEccCCCCCccCchhcCCcceeEeecccCCcccEEEEEEccCCCCEeCeEEEEEcCCCCeEEECCCcCCCCCcccccCC
Confidence 79999999998 99999999999999999999999999999999999999999999999999999999999999999999
No 2
>cd00113 PLAT PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates.
Probab=99.19 E-value=1.1e-10 Score=77.15 Aligned_cols=66 Identities=33% Similarity=0.497 Sum_probs=59.8
Q ss_pred cccccccceeeecc-cccCceEEEEEEeCCC---CCeecEEEEeccC-CCceeEEeccccCCCcceeeccC
Q 039251 14 FESCSTDTYTLYGP-CTYQICYLYLYRSGYD---GWKPESVTVYGYY-TRSISFYYNTWIPDDIWYGFNYC 79 (89)
Q Consensus 14 FerCstDtF~V~G~-C~~~ICylyL~r~G~d---gW~Pe~V~Iy~~~-~~~vtF~f~~~iP~~vwyG~n~C 79 (89)
|||.++|+|.|..+ .++.|+.|.|.+.+.. +|.+++|+|.... ....+|.++.||..+.++...+|
T Consensus 44 f~~g~~~~f~v~~~~~lG~i~~v~l~~d~~g~~~~W~l~~V~V~~~~~~~~~~F~~~~Wl~~~~~~~~~r~ 114 (116)
T cd00113 44 FERGSTDTFQIDLKLDIGDITKVYLRRDGSGLSDGWYCESITVQALGTKKVYTFPVNRWVLGGKWYTSVRS 114 (116)
T ss_pred ccCCCceEEEEeccCCCcCeEEEEEEECCCCCCCCEEEeEEEEEeCCCCCEEEEEeCCCcccCCCCCceee
Confidence 99999999999999 7789999999999774 9999999999765 47899999999999999888765
No 3
>cd01754 PLAT_plant_stress PLAT/LH2 domain of plant-specific single domain protein family with unknown function. Many of its members are stress induced. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.
Probab=98.58 E-value=2.1e-07 Score=65.67 Aligned_cols=62 Identities=24% Similarity=0.432 Sum_probs=52.0
Q ss_pred CCCCCCcccccccceeeecccc-cCceEEEEEEe--CC-CCCeecEEEEeccCC----CceeEEeccccC
Q 039251 8 DPYSRTFESCSTDTYTLYGPCT-YQICYLYLYRS--GY-DGWKPESVTVYGYYT----RSISFYYNTWIP 69 (89)
Q Consensus 8 dp~~~~FerCstDtF~V~G~C~-~~ICylyL~r~--G~-dgW~Pe~V~Iy~~~~----~~vtF~f~~~iP 69 (89)
++....|||.++|+|.|+.++. +.||+|.|.++ |. ++|..++|+|-.... ....|-.|+||-
T Consensus 46 ~~~~~~FerG~~d~F~v~~~~~lG~l~~irI~HDn~G~~p~W~l~~V~V~d~~~~~~~~~~~F~c~rWLa 115 (129)
T cd01754 46 GAGHDYFERGNLDRFSGRGPCLPSPPCWMNLTSDGTGNHPGWYVNYVEVTQAGQHAPCMQHLFAVEQWLA 115 (129)
T ss_pred ccccccccCCCccEEEEEeccCCCCeEEEEEEECCCCCCCCcccCEEEEEeCCCCCcCcEEEEEecEecc
Confidence 4556799999999999999985 89999999998 44 799999999986432 357788899986
No 4
>cd01753 PLAT_LOX PLAT domain of 12/15-lipoxygenase. As a unique subfamily of the mammalian lipoxygenases, they catalyze enzymatic lipid peroxidation in complex biological structures via direct dioxygenation of phospholipids and cholesterol esters of biomembranes and plasma lipoproteins. Both types of enzymes are cytosolic but need this domain to access their sequestered membrane or micelle bound substrates.
Probab=98.38 E-value=1.7e-06 Score=58.85 Aligned_cols=66 Identities=26% Similarity=0.320 Sum_probs=55.7
Q ss_pred CCCCCCCCcccccccceeeecc-cccCceEEEEEEeC--C-CCCeecEEEEeccCCCceeEEeccccCCCc
Q 039251 6 LDDPYSRTFESCSTDTYTLYGP-CTYQICYLYLYRSG--Y-DGWKPESVTVYGYYTRSISFYYNTWIPDDI 72 (89)
Q Consensus 6 LDdp~~~~FerCstDtF~V~G~-C~~~ICylyL~r~G--~-dgW~Pe~V~Iy~~~~~~vtF~f~~~iP~~v 72 (89)
|+++.. .|||-++|+|.|+.+ .++.|++|-|.+++ . ++|..++|+|-+.......|..++||..+.
T Consensus 37 L~~~~~-~FerG~~d~F~v~~~~~lG~l~~i~i~~d~~g~~~~W~l~~V~V~~~~~~~~~F~c~rWl~~~~ 106 (113)
T cd01753 37 LDRPGY-DFERGAVDEYKVKVPEDLGELLLVRLRKRKYLLFDAWFCNYITVTGPGGDEYHFPCYRWIEGYG 106 (113)
T ss_pred cCCCCC-ccCCCCeeEEEEecccCCCCcEEEEEEECCCCCCCCeeecEEEEEcCCCCEEEEEhHHeECCCC
Confidence 666553 599999999999986 67999999999994 3 899999999998776667888899998543
No 5
>cd01756 PLAT_repeat PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins.
Probab=98.22 E-value=8e-06 Score=55.33 Aligned_cols=66 Identities=20% Similarity=0.297 Sum_probs=57.1
Q ss_pred CCCC-CCCCcccccccceeeecccccCceEEEEEEeCC---CCCeecEEEEeccC-CCceeEEeccccCCC
Q 039251 6 LDDP-YSRTFESCSTDTYTLYGPCTYQICYLYLYRSGY---DGWKPESVTVYGYY-TRSISFYYNTWIPDD 71 (89)
Q Consensus 6 LDdp-~~~~FerCstDtF~V~G~C~~~ICylyL~r~G~---dgW~Pe~V~Iy~~~-~~~vtF~f~~~iP~~ 71 (89)
|+++ ....|||-++|+|.|...-++.|.+|-|.+++. ++|..+.|+|-... .+..+|..++||-.+
T Consensus 37 L~~~~~~~~FerGs~d~F~i~~~~lG~l~~i~i~~d~~g~~~~W~~~~V~V~~~~~~~~~~F~~~~Wl~~~ 107 (120)
T cd01756 37 LKKSNNKNKFERGQTDKFTVEAVDLGKLKKIRIGHDNSGLGAGWFLDKVEIREPGTGDEYTFPCNRWLDKD 107 (120)
T ss_pred ccCCCcCCcccCCCeEEEEEEecCCCCeEEEEEEECCCCCCCCcEEeEEEEEECCCceEEEEEeCCccCCC
Confidence 6665 557999999999999999999999999999954 79999999999764 566889999999854
No 6
>cd01752 PLAT_polycystin PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological functions remain poorly defined. In human, mutations in polycystin-1 (PKD1) and polycystin-2 (PKD2) have been shown to be the cause for autosomal dominant polycystic kidney disease (ADPKD). The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=97.82 E-value=9.2e-05 Score=50.24 Aligned_cols=66 Identities=24% Similarity=0.407 Sum_probs=55.2
Q ss_pred CCCCCCCCcccccccceeeecc-cccCceEEEEEEeC--C-CCCeecEEEEeccC-CCceeEEeccccCCC
Q 039251 6 LDDPYSRTFESCSTDTYTLYGP-CTYQICYLYLYRSG--Y-DGWKPESVTVYGYY-TRSISFYYNTWIPDD 71 (89)
Q Consensus 6 LDdp~~~~FerCstDtF~V~G~-C~~~ICylyL~r~G--~-dgW~Pe~V~Iy~~~-~~~vtF~f~~~iP~~ 71 (89)
|+++....|||-++|+|.|..+ =++.|.+|-|.+++ . ++|.-++|+|-... ..-..|..++||-.+
T Consensus 37 L~~~~~~~F~rG~~~~f~i~~~~dlG~l~~i~l~hd~~g~~~~W~l~~V~V~~~~t~~~~~F~~~rWl~~~ 107 (120)
T cd01752 37 LRDPEKPIFERGSVDSFLLTTPFPLGELQSIRLWHDNSGLSPSWYLSRVIVRDLQTGKKWFFLCNDWLSVE 107 (120)
T ss_pred cCCCCccceeCCCeeEEEecCccCCCCccEEEEEECCCCCCCCeEEEEEEEEECCCCcEEEEEeCcEECCc
Confidence 5666556899999999999987 46899999999984 4 89999999999764 556789999999743
No 7
>smart00308 LH2 Lipoxygenase homology 2 (beta barrel) domain.
Probab=97.60 E-value=0.0004 Score=45.06 Aligned_cols=57 Identities=19% Similarity=0.206 Sum_probs=51.0
Q ss_pred CCcccccccceeeeccc-ccCceEEEEEEeC-CCCCeecEEEEecc-CCCceeEEecccc
Q 039251 12 RTFESCSTDTYTLYGPC-TYQICYLYLYRSG-YDGWKPESVTVYGY-YTRSISFYYNTWI 68 (89)
Q Consensus 12 ~~FerCstDtF~V~G~C-~~~ICylyL~r~G-~dgW~Pe~V~Iy~~-~~~~vtF~f~~~i 68 (89)
..|||-++|+|.|..+. ++.+..|.|.+.+ .+.|..++|+|-+. .....+|-.+.||
T Consensus 43 ~~f~~g~~~~f~v~~~~~lG~l~~v~v~~d~~~~~w~l~~V~V~~~~~~~~~~F~c~~Wl 102 (105)
T smart00308 43 GIFARGSTYEFTFDVDEDFGELGAVKIKNEHRHPEWFLKSITVKDLPTGGKYHFPCNSWV 102 (105)
T ss_pred ccccCCceEEEEEecccCCCCcEEEEEEeCCCCCCeEEEEEEEEECCCCCEEEEEcCcee
Confidence 35999999999999975 8999999999999 79999999999874 6678999999988
No 8
>cd02899 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1.
Probab=97.43 E-value=0.00049 Score=47.41 Aligned_cols=57 Identities=18% Similarity=0.233 Sum_probs=51.0
Q ss_pred CcccccccceeeecccccCceEEEEEEeCC-CCCeecEEEEeccCCCceeEEeccccC
Q 039251 13 TFESCSTDTYTLYGPCTYQICYLYLYRSGY-DGWKPESVTVYGYYTRSISFYYNTWIP 69 (89)
Q Consensus 13 ~FerCstDtF~V~G~C~~~ICylyL~r~G~-dgW~Pe~V~Iy~~~~~~vtF~f~~~iP 69 (89)
.|||=+.|+|.|++..++.|=.|-|.+.|. |+|.-++|+|-.+..+...|-.++||=
T Consensus 40 ~F~~G~~d~F~v~~~dLG~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~~~Fpc~rWla 97 (109)
T cd02899 40 GFYPGSLKRIRFRAADVGDINAIILSNTALNDPWYCDYVRIKSEDGKVFAFNVKRWIG 97 (109)
T ss_pred ccCCCceEEEEECccccCceEEEEEECCCCCCCceeeEEEEECCCCCEEEEEcceeeC
Confidence 599999999999999999999999988887 899999999998766667788888873
No 9
>PF01477 PLAT: PLAT/LH2 domain; InterPro: IPR001024 Lipoxygenases (1.13.11.- from EC) are a class of iron-containing dioxygenases which catalyses the hydroperoxidation of lipids, containing a cis,cis-1,4-pentadiene structure. They are common in plants where they may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. In mammals a number of lipoxygenases isozymes are involved in the metabolism of prostaglandins and leukotrienes []. Sequence data is available for the following lipoxygenases: Plant lipoxygenases (1.13.11.12 from EC, IPR001246 from INTERPRO). Plants express a variety of cytosolic isozymes as well as what seems to be a chloroplast isozyme []. Mammalian arachidonate 5-lipoxygenase (1.13.11.34 from EC, IPR001885 from INTERPRO). Mammalian arachidonate 12-lipoxygenase (1.13.11.31 from EC, IPR001885 from INTERPRO). Mammalian erythroid cell-specific 15-lipoxygenase (1.13.11.33 from EC, IPR001885 from INTERPRO). The iron atom in lipoxygenases is bound by four ligands, three of which are histidine residues []. Six histidines are conserved in all lipoxygenase sequences, five of them are found clustered in a stretch of 40 amino acids. This region contains two of the three iron-ligands; the other histidines have been shown [] to be important for the activity of lipoxygenases. This entry represents a domain found in lipoxygenases and other enzymes. It is known as the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain, is found in a variety of membrane or lipid associated proteins. Structurally, this domain forms a beta-sandwich composed of two sheets of four strands each [, , ]. The most highly conserved regions coincide with the beta-strands, with most of the highly conserved residues being buried within the protein. An exception to this is a surface lysine or arginine that occurs on the surface of the fifth beta-strand of the eukaryotic domains. In pancreatic lipase, the lysine in this position forms a salt bridge with the procolipase protein. The conservation of a charged surface residue may indicate the location of a conserved ligand-binding site. It is thought that this domain may mediate membrane attachment via other protein binding partners.; GO: 0005515 protein binding; PDB: 3FG3_D 3FG1_C 3FG4_D 3DY5_A 2FNQ_B 3O8Y_B 3V99_B 3V92_A 3V98_B 1HPL_A ....
Probab=97.04 E-value=0.0023 Score=41.16 Aligned_cols=56 Identities=29% Similarity=0.400 Sum_probs=48.3
Q ss_pred ccccceeeec-ccccCceEEEEEEeCC---CCCeecEEEEecc-CCCceeEEeccccCCCc
Q 039251 17 CSTDTYTLYG-PCTYQICYLYLYRSGY---DGWKPESVTVYGY-YTRSISFYYNTWIPDDI 72 (89)
Q Consensus 17 CstDtF~V~G-~C~~~ICylyL~r~G~---dgW~Pe~V~Iy~~-~~~~vtF~f~~~iP~~v 72 (89)
=++|+|.|.. .-++.|..|-|.+.|. ++|..++|+|-.. .....+|..|.||-.+.
T Consensus 44 g~~d~F~i~~~~~lG~i~~i~i~~~~~~~~~~W~l~~V~V~~~~~~~~~~F~~~~Wl~~~~ 104 (113)
T PF01477_consen 44 GSTDTFTIETPEDLGEIQKIRIWHDGSGPSPSWYLDSVVVTDGETGRTYTFPCNRWLDPDK 104 (113)
T ss_dssp TEEEEEEEEESSCGCSEEEEEEEEESSSSSSEEEEEEEEEEETTTSEEEEEEEEEEESTTE
T ss_pred CceEEeeeeecccCCCCcEEEEEEccCCCccceEEEEEEEEeCCCCcEEEEEcCCEECCCC
Confidence 5799999998 4789999999999933 8999999999884 56789999999998654
No 10
>cd01757 PLAT_RAB6IP1 PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed function of mediating interaction with lipids or membrane bound proteins.
Probab=92.91 E-value=0.52 Score=32.71 Aligned_cols=50 Identities=16% Similarity=0.238 Sum_probs=41.7
Q ss_pred ceeeecccccCceEEEEEEe--CC-CCCeecEEEEec-cCCCceeEEeccccCC
Q 039251 21 TYTLYGPCTYQICYLYLYRS--GY-DGWKPESVTVYG-YYTRSISFYYNTWIPD 70 (89)
Q Consensus 21 tF~V~G~C~~~ICylyL~r~--G~-dgW~Pe~V~Iy~-~~~~~vtF~f~~~iP~ 70 (89)
.|.|....++.+-+|-|.|+ |. ++|.-++|+|-. ....-..|--|+||-.
T Consensus 44 ~~~v~~~~LG~L~~irIwHDnsG~~~~Wfl~~V~V~d~~t~~~~~FpC~rWLa~ 97 (114)
T cd01757 44 EMTFDCQNLGKLTTVQIGHDNSGLLAKWLVEYVMVRNEITGHTYKFPCGRWLGE 97 (114)
T ss_pred EEEEecCCcCCcEEEEEEECCCCCCCCeeeeEEEEEeCCCCCEEEEecCceecC
Confidence 57777788899999999998 55 899999999998 4556677888988863
No 11
>cd01755 PLAT_lipase PLAT/ LH2 domain present in connection with a lipase domain. This family contains two major subgroups, the lipoprotein lipase (LPL) and the pancreatic triglyceride lipase. LPL is a key enzyme in catabolism of plasma lipoprotein triglycerides (TGs). The central role of triglyceride lipases is in energy production. In general, PLAT/LH2 domain's proposed function is to mediate interaction with lipids or membrane bound proteins.
Probab=62.17 E-value=40 Score=22.82 Aligned_cols=51 Identities=8% Similarity=0.066 Sum_probs=38.9
Q ss_pred Ccccccccceee-ecccccCceEEEEEEeCC----------CCCeecEEEEe-ccCCCceeEE
Q 039251 13 TFESCSTDTYTL-YGPCTYQICYLYLYRSGY----------DGWKPESVTVY-GYYTRSISFY 63 (89)
Q Consensus 13 ~FerCstDtF~V-~G~C~~~ICylyL~r~G~----------dgW~Pe~V~Iy-~~~~~~vtF~ 63 (89)
.||+.++++|-| .-..++.+-.|-|.++.+ ..|.-+.|.|- +...+-.+|=
T Consensus 41 ~~~~g~~~sfli~t~~~lG~l~~v~~~~dn~~~~~~~~~~~p~~~~~~I~Vq~get~~~~~FC 103 (120)
T cd01755 41 ELKPNKTYSFLIDTEVDIGDLLKVKFKWENNVINSNSGETLPKLGARKIRVKSGETQKKFTFC 103 (120)
T ss_pred cccCCCEEEEEEEcCCCccceEEEEEEEcCCCcccccccCCCcEEEEEEEEEECCCCCEEEEE
Confidence 589999999999 678889999999999744 36667788886 4455444443
No 12
>KOG3123 consensus Diphthine synthase [Translation, ribosomal structure and biogenesis]
Probab=59.45 E-value=4.8 Score=32.14 Aligned_cols=19 Identities=53% Similarity=0.987 Sum_probs=16.1
Q ss_pred CceEEEEEEeCC--------CCCeecE
Q 039251 31 QICYLYLYRSGY--------DGWKPES 49 (89)
Q Consensus 31 ~ICylyL~r~G~--------dgW~Pe~ 49 (89)
+.|-|+||.+|. |.|+|++
T Consensus 119 G~CGLqlY~fGetVSiv~ftd~wrP~S 145 (272)
T KOG3123|consen 119 GCCGLQLYNFGETVSIVFFTDNWRPES 145 (272)
T ss_pred ccceeeeeccCcEEEEEEEccCcCchh
Confidence 689999999984 6888876
No 13
>PF05727 UPF0228: Uncharacterised protein family (UPF0228); InterPro: IPR008887 This small family of proteins is currently restricted to Methanosarcina species. Members of this family are about 200 residues in length, except for Q8TMK1 from SWISSPROT that has two copies of this region. Although the function of this region is unknown the pattern of conservation suggests that this may be an enzyme, including multiple conserved aspartate and glutamate residues. The most conserved motif in these proteins is NEL/MEXNE/D, where X can be any amino acid, and is found at the C terminus of these proteins.
Probab=48.78 E-value=8.9 Score=27.75 Aligned_cols=17 Identities=35% Similarity=0.874 Sum_probs=14.5
Q ss_pred ceEEEEEEeCCC-CCeecE
Q 039251 32 ICYLYLYRSGYD-GWKPES 49 (89)
Q Consensus 32 ICylyL~r~G~d-gW~Pe~ 49 (89)
.||+.+ ++|+- .|+||.
T Consensus 85 wCyI~f-~dgs~nywIpe~ 102 (127)
T PF05727_consen 85 WCYIRF-GDGSKNYWIPEK 102 (127)
T ss_pred EEEEEc-CCCCcccccchH
Confidence 699999 88885 699986
No 14
>COG3411 Ferredoxin [Energy production and conversion]
Probab=35.74 E-value=16 Score=23.60 Aligned_cols=15 Identities=27% Similarity=0.853 Sum_probs=10.6
Q ss_pred CceeEEeccccCCCcceee
Q 039251 58 RSISFYYNTWIPDDIWYGF 76 (89)
Q Consensus 58 ~~vtF~f~~~iP~~vwyG~ 76 (89)
.|+-+.| |+|+||+.
T Consensus 17 gPvl~vY----pegvWY~~ 31 (64)
T COG3411 17 GPVLVVY----PEGVWYTR 31 (64)
T ss_pred CCEEEEe----cCCeeEec
Confidence 4566655 78899985
No 15
>KOG4714 consensus Nucleoporin [Nuclear structure]
Probab=35.20 E-value=25 Score=28.89 Aligned_cols=24 Identities=33% Similarity=0.663 Sum_probs=19.4
Q ss_pred cccccceeeecccc---cCceEEEEEE
Q 039251 16 SCSTDTYTLYGPCT---YQICYLYLYR 39 (89)
Q Consensus 16 rCstDtF~V~G~C~---~~ICylyL~r 39 (89)
+=|.++|+|.|||+ ..+=-+||+|
T Consensus 290 ~~SinsfDV~g~~lVcgtd~eaIyl~~ 316 (319)
T KOG4714|consen 290 SLSINSFDVLGPCLVCGTDAEAIYLTR 316 (319)
T ss_pred ceeeeeeeccCceEEeccccceEEEec
Confidence 45889999999998 3577788877
No 16
>PF03394 Pox_E8: Poxvirus E8 protein; InterPro: IPR005057 This family of poxvirus E8 proteins have no known function.
Probab=33.82 E-value=16 Score=28.90 Aligned_cols=20 Identities=35% Similarity=0.627 Sum_probs=16.3
Q ss_pred EEEEEeCCCCCeecEEEEec
Q 039251 35 LYLYRSGYDGWKPESVTVYG 54 (89)
Q Consensus 35 lyL~r~G~dgW~Pe~V~Iy~ 54 (89)
-|||+.=+=||+||++--+.
T Consensus 4 TylyhnYayGWIPETaiWsS 23 (242)
T PF03394_consen 4 TYLYHNYAYGWIPETAIWSS 23 (242)
T ss_pred ceeeccccccCcchhhHhhh
Confidence 48899888999999976544
No 17
>PHA03004 putative membrane protein; Provisional
Probab=32.33 E-value=17 Score=29.12 Aligned_cols=21 Identities=33% Similarity=0.575 Sum_probs=17.1
Q ss_pred EEEEEEeCCCCCeecEEEEec
Q 039251 34 YLYLYRSGYDGWKPESVTVYG 54 (89)
Q Consensus 34 ylyL~r~G~dgW~Pe~V~Iy~ 54 (89)
+-|||+.=+=||+||++--+.
T Consensus 34 nTylyhnYaYGWIPETaiWsS 54 (270)
T PHA03004 34 NTYLYHNYAYGWIPETAIWSS 54 (270)
T ss_pred cceeeccccccCcchhhhhhh
Confidence 458999988999999986544
No 18
>PF08695 Coa1: Cytochrome oxidase complex assembly protein 1; InterPro: IPR014807 Coa1 is an inner mitochondrial membrane protein that associates with Shy1 and is required for cytochrome oxidase complex IV assembly. It contains a conserved hydrophobic segment (amino acids 74-92) with the potential to form a membrane-spanning helix. The N terminus of Coa1 is rich in positively charged amino acids and could form an amphipathic alpha helix, characteristic of a mitochondrial presequence. A cleavage site for the mitochondrial processing peptidase is predicted adjacent to the presequence. Upon in vitro import into mitochondria, Coa1 is processed to a mature form, indicating that it possesses a cleavable presequence []. The eukaryotic cytochrome oxidase complex consists of 12-13 subunits, with three mitochondrial encoded subunits, Cox1-Cox3, forming the core enzyme. Translation of the Cox1 transcript requires the two promoters, Pet309 and Mss51, and the latter has an additional role in translational elongation. Coa1 is necessary for linking the activity of Mss51 to Cox1 insertion into the assembly complex [].
Probab=31.71 E-value=1.5e+02 Score=19.38 Aligned_cols=40 Identities=23% Similarity=0.226 Sum_probs=33.3
Q ss_pred cceeeecccccCceEEEEEEeCC-CCCeecEEEEeccCCCc
Q 039251 20 DTYTLYGPCTYQICYLYLYRSGY-DGWKPESVTVYGYYTRS 59 (89)
Q Consensus 20 DtF~V~G~C~~~ICylyL~r~G~-dgW~Pe~V~Iy~~~~~~ 59 (89)
-+|.|+|+=....-|+.-.|.+. +.|..+.++|.-.....
T Consensus 71 ~~~pV~G~k~~G~v~~~a~r~~~~~~W~~~~~~v~~~~g~~ 111 (116)
T PF08695_consen 71 LSFPVKGPKGKGTVYVEATRSGGKDPWEILRLEVEIDDGQV 111 (116)
T ss_pred EEEEEEcCCCcEEEEEEEEecCCCCceEEEEEEEEeCCCCE
Confidence 47889999988999999999966 68999999997664433
No 19
>KOG3646 consensus Acetylcholine receptor [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.58 E-value=57 Score=28.27 Aligned_cols=40 Identities=25% Similarity=0.336 Sum_probs=24.2
Q ss_pred CceEEEEEEeCCCCCeecEEEEeccCCCceeEEeccccCCCcce
Q 039251 31 QICYLYLYRSGYDGWKPESVTVYGYYTRSISFYYNTWIPDDIWY 74 (89)
Q Consensus 31 ~ICylyL~r~G~dgW~Pe~V~Iy~~~~~~vtF~f~~~iP~~vwy 74 (89)
|+|+|=+=.--.+||.-+=.-.-..+. |+..++||+|-|+
T Consensus 163 Q~C~mKFGSWTY~G~~lDL~~~~~~g~----~Dls~yi~NGEW~ 202 (486)
T KOG3646|consen 163 QVCYLKFGSWTYAGILLDLRIDDEDGG----IDLSTYIPNGEWD 202 (486)
T ss_pred cEEEEEeeeEEEcceeeeeeeccccCC----cchhhcccCCcee
Confidence 677663322222788776332222222 8889999999994
No 20
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=25.96 E-value=1.1e+02 Score=19.09 Aligned_cols=28 Identities=21% Similarity=0.451 Sum_probs=20.6
Q ss_pred ceeeecccccCceEEEEEEeCCCCCeecEEEEec
Q 039251 21 TYTLYGPCTYQICYLYLYRSGYDGWKPESVTVYG 54 (89)
Q Consensus 21 tF~V~G~C~~~ICylyL~r~G~dgW~Pe~V~Iy~ 54 (89)
.|.|+. .+-|||||+-.+.|| +...++-
T Consensus 10 ~~~~~~---~~~~Yl~l~~~~~~G---~v~~L~P 37 (83)
T PF14326_consen 10 RFRVTS---NRDGYLYLFYIDADG---KVTLLFP 37 (83)
T ss_pred EEEEEe---CCCeEEEEEEECCCC---CEEEEec
Confidence 455655 688999999999999 4445553
No 21
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=24.93 E-value=75 Score=18.18 Aligned_cols=28 Identities=21% Similarity=0.422 Sum_probs=21.8
Q ss_pred ccceeeecccccCceEEEEEEeCCCCCeecE
Q 039251 19 TDTYTLYGPCTYQICYLYLYRSGYDGWKPES 49 (89)
Q Consensus 19 tDtF~V~G~C~~~ICylyL~r~G~dgW~Pe~ 49 (89)
-...+|. .|..+=|.+- ..|..||++.+
T Consensus 24 g~~v~v~-~~~~~W~~V~--~~g~~GWv~~~ 51 (55)
T PF06347_consen 24 GVPVRVI-ECRGGWCKVR--ADGRTGWVHKS 51 (55)
T ss_pred CCEEEEE-EccCCeEEEE--ECCeEEeEEee
Confidence 3455666 8888888888 78999999875
No 22
>TIGR01221 rmlC dTDP-4-dehydrorhamnose 3,5-epimerase. This enzyme participates in the biosynthesis of dTDP-L-rhamnose, often as a precursor to LPS O-antigen
Probab=22.36 E-value=41 Score=24.71 Aligned_cols=12 Identities=42% Similarity=0.946 Sum_probs=10.5
Q ss_pred ccCCCcceeecc
Q 039251 67 WIPDDIWYGFNY 78 (89)
Q Consensus 67 ~iP~~vwyG~n~ 78 (89)
+||.|+++||-.
T Consensus 109 ~IP~G~aHGF~~ 120 (176)
T TIGR01221 109 WIPEGFAHGFVV 120 (176)
T ss_pred EeCCcceeEEEE
Confidence 899999999853
No 23
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=20.60 E-value=51 Score=18.56 Aligned_cols=12 Identities=33% Similarity=1.132 Sum_probs=9.0
Q ss_pred EEEEeCCCCCee
Q 039251 36 YLYRSGYDGWKP 47 (89)
Q Consensus 36 yL~r~G~dgW~P 47 (89)
++.+.|-++|+|
T Consensus 33 lvw~~g~~~W~p 44 (45)
T PF14237_consen 33 LVWKEGMSDWKP 44 (45)
T ss_pred eEeCCChhhceE
Confidence 456678888887
No 24
>PF00932 LTD: Lamin Tail Domain; InterPro: IPR001322 Intermediate filaments (IF) are primordial components of the cytoskeleton and the nuclear envelope []. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups, type I: acidic cytokeratins, type II: basic cytokeratins, type III: vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin, type IV: neurofilaments L, H and M, alpha-internexin and nestin, and type V: nuclear lamins A, B1, B2 and C. The lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane that may provide a framework for the nuclear envelope and may interact with chromatin. All IF proteins are structurally similar in that they consist of a central rod domain arranged in coiled-coil alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. The C-terminal domain has been charcterised for the lamins.; PDB: 3UMN_A 2KPW_A 3JT0_A 2LLL_A 1UFG_A 3GEF_D 1IFR_A 1IVT_A.
Probab=20.07 E-value=79 Score=20.25 Aligned_cols=12 Identities=25% Similarity=0.218 Sum_probs=8.4
Q ss_pred cEEEEeccCCCc
Q 039251 48 ESVTVYGYYTRS 59 (89)
Q Consensus 48 e~V~Iy~~~~~~ 59 (89)
|||+||+..+.+
T Consensus 26 e~VEl~N~~~~~ 37 (116)
T PF00932_consen 26 EWVELYNPGDST 37 (116)
T ss_dssp SEEEEEE-SSS-
T ss_pred EEEEEEECCCCc
Confidence 999999876543
Done!