Query 038380
Match_columns 261
No_of_seqs 111 out of 120
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 10:25:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038380.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038380hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04927 SMP: Seed maturation 99.8 3.8E-19 8.2E-24 132.1 6.4 61 199-260 1-61 (62)
2 PF04927 SMP: Seed maturation 99.8 6.8E-19 1.5E-23 130.8 6.6 61 135-195 1-62 (62)
3 PF09018 Phage_Capsid_P3: P3 m 63.0 2.8 6E-05 39.9 0.4 14 16-29 135-148 (394)
4 cd07046 BMC_PduU-EutS 1,2-prop 25.5 57 0.0012 27.1 2.3 23 101-123 1-24 (110)
5 TIGR00388 glyQ glycyl-tRNA syn 15.0 55 0.0012 31.6 0.1 9 18-26 186-194 (293)
6 COG0752 GlyQ Glycyl-tRNA synth 13.0 68 0.0015 30.9 0.1 10 17-26 189-198 (298)
7 PF15142 INCA1: INCA1 11.6 83 0.0018 28.2 0.1 12 18-29 26-39 (178)
8 KOG1783 Small nuclear ribonucl 11.3 1.1E+02 0.0024 24.3 0.7 11 15-25 53-63 (77)
9 PF07896 DUF1674: Protein of u 10.8 89 0.0019 22.6 0.1 9 16-24 30-38 (47)
10 PF11005 DUF2844: Protein of u 10.7 2.8E+02 0.006 23.8 3.0 34 85-118 26-60 (132)
No 1
>PF04927 SMP: Seed maturation protein; InterPro: IPR007011 Late embryogenesis abundant (LEA) proteins accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. LEA proteins have been grouped into at least six families on the basis of sequence similarity. Although significant similarity has not been detected between the members of the different classes, a unifying and outstanding feature of these proteins is their high hydrophilicity and high percentage of glycines. Amino acid sequence analysis allows one to predict that these proteins exist primarily as random coils. This property has been confirmed in few cases with purified proteins and is supported by the fact that proteins of this type do not coagulate upon heating. LEA protein families have been identified in a wide range of different plant species to the extent that they can be considered ubiquitous in plants. Moreover, it has been shown that members of at least one of the LEA protein families, the so-called dehydrins, are present in a range of photosynthetic organisms, including lower plants, algae, and cyanobacteria. In addition similar proteins, the hydrophilins are induced in a variety of different taxons, of non-photosynthetic organsims, in response to osmotic stress. All of these proteins have a high hydrophilicity index, generally greater than 1.0 []. This conserved region identifies a set of plant seed maturation proteins described as LEA D34.
Probab=99.78 E-value=3.8e-19 Score=132.15 Aligned_cols=61 Identities=48% Similarity=0.622 Sum_probs=58.0
Q ss_pred cchHHHHHhhhhhccccCcccCHhhHHHHHHHHHhcCCCCCCCCCcHHHHHHHHHHhccccC
Q 038380 199 KIKLNQVLAGATAKLAADKAVTRQDAEGIASAEQRNNPNADTHPGGVAASVAAAARLNENVN 260 (261)
Q Consensus 199 kitigdvL~~Atakl~~DK~Vt~eDAaaV~aAE~Ra~g~~~~~PGGVAAa~qaAA~lN~~~~ 260 (261)
||||||||+ |+.++++|||||+|||++||+||+|++|...+.||||++++|+||++|++..
T Consensus 1 ~vt~gdvl~-A~a~~~~~kpVt~eDAa~iqsAE~r~~g~~~~~~GGvAa~~qsAA~~N~~~~ 61 (62)
T PF04927_consen 1 KVTIGDVLE-AAAGLPGDKPVTPEDAAAIQSAEARATGGAQTQPGGVAAAAQSAADKNERAG 61 (62)
T ss_pred CccHHHHHH-HHhcccccCCCCHHHHHHHHHHHHhhCCCCCCCCCCHHHHHHHHHHHhhhcc
Confidence 699999995 9999999999999999999999999999988999999999999999999753
No 2
>PF04927 SMP: Seed maturation protein; InterPro: IPR007011 Late embryogenesis abundant (LEA) proteins accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. LEA proteins have been grouped into at least six families on the basis of sequence similarity. Although significant similarity has not been detected between the members of the different classes, a unifying and outstanding feature of these proteins is their high hydrophilicity and high percentage of glycines. Amino acid sequence analysis allows one to predict that these proteins exist primarily as random coils. This property has been confirmed in few cases with purified proteins and is supported by the fact that proteins of this type do not coagulate upon heating. LEA protein families have been identified in a wide range of different plant species to the extent that they can be considered ubiquitous in plants. Moreover, it has been shown that members of at least one of the LEA protein families, the so-called dehydrins, are present in a range of photosynthetic organisms, including lower plants, algae, and cyanobacteria. In addition similar proteins, the hydrophilins are induced in a variety of different taxons, of non-photosynthetic organsims, in response to osmotic stress. All of these proteins have a high hydrophilicity index, generally greater than 1.0 []. This conserved region identifies a set of plant seed maturation proteins described as LEA D34.
Probab=99.77 E-value=6.8e-19 Score=130.79 Aligned_cols=61 Identities=59% Similarity=0.785 Sum_probs=56.1
Q ss_pred cchHHHHHHHHHhhhCCCCCChhHHHHHHHHHHHhcCCCCCCC-cHHHHHHHHHHhcccCCC
Q 038380 135 AITIGEALETTAQTAGDKPVDQSDAAAIQAAEVRATGSTVTTP-GLAASAQSAAAHNETVDR 195 (261)
Q Consensus 135 ~ItiGealeA~a~~~g~kPV~~sDAAaiQaAE~ratG~~~~~~-G~AA~aQsAA~~N~r~~~ 195 (261)
+|||||+|++++..+++|||+++||++||+||+|++|.....+ |++++|||||++|++.+|
T Consensus 1 ~vt~gdvl~A~a~~~~~kpVt~eDAa~iqsAE~r~~g~~~~~~GGvAa~~qsAA~~N~~~~~ 62 (62)
T PF04927_consen 1 KVTIGDVLEAAAGLPGDKPVTPEDAAAIQSAEARATGGAQTQPGGVAAAAQSAADKNERAGR 62 (62)
T ss_pred CccHHHHHHHHhcccccCCCCHHHHHHHHHHHHhhCCCCCCCCCCHHHHHHHHHHHhhhccC
Confidence 5999999999999999999999999999999999999755555 799999999999998764
No 3
>PF09018 Phage_Capsid_P3: P3 major capsid protein; InterPro: IPR015108 The major capsid protein p3 from Bacteriophage PRD1 adopts a double-barrel structure comprising two eight-stranded viral beta-barrels or jelly rolls, each of which contains a 12-residue alpha-helix. This protein then trimerises through a 'trimerisation loop' sequence, and is incorporated within the viral capsid []. ; PDB: 1HX6_A 1HQN_C 1GW8_K 1GW7_J 1HB7_L 1HB5_B 1HB9_L 1W8X_B 1CJD_C.
Probab=63.04 E-value=2.8 Score=39.94 Aligned_cols=14 Identities=57% Similarity=1.004 Sum_probs=7.7
Q ss_pred CCCCccCceeeccc
Q 038380 16 QQPIKYGDFFNVSG 29 (261)
Q Consensus 16 ~~pikYgdvF~v~G 29 (261)
+.|||||||.||-.
T Consensus 135 dspikygdvmnvid 148 (394)
T PF09018_consen 135 DSPIKYGDVMNVID 148 (394)
T ss_dssp --SS--BSSS-SSB
T ss_pred CCCccccceeeecc
Confidence 57999999999853
No 4
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=25.51 E-value=57 Score=27.05 Aligned_cols=23 Identities=39% Similarity=0.457 Sum_probs=19.7
Q ss_pred ceeEEeeecc-eeeeeeecCCCCC
Q 038380 101 RRIITESVGG-QVVGRHEEPTPVS 123 (261)
Q Consensus 101 ~RIvTE~VaG-QVvgq~~~p~~~~ 123 (261)
.|||-|+|.| |++..|+-|.+..
T Consensus 1 ~r~~~~~v~gk~i~~~~vI~~v~~ 24 (110)
T cd07046 1 QRIIQEYVPGKQITLAHLIANPDP 24 (110)
T ss_pred CcceEEecCcceEEEEEEecCCCH
Confidence 3899999988 9999999988844
No 5
>TIGR00388 glyQ glycyl-tRNA synthetase, tetrameric type, alpha subunit. This tetrameric form of glycyl-tRNA synthetase (2 alpha, 2 beta) is found in the majority of completed eubacterial genomes, with the two genes fused in a few species. A substantially different homodimeric form (not recognized by this model) replaces this form in the Archaea, animals, yeasts, and some eubacteria.
Probab=15.02 E-value=55 Score=31.56 Aligned_cols=9 Identities=44% Similarity=0.973 Sum_probs=7.9
Q ss_pred CCccCceee
Q 038380 18 PIKYGDFFN 26 (261)
Q Consensus 18 pikYgdvF~ 26 (261)
+|+|||||-
T Consensus 186 ~vtYgdv~~ 194 (293)
T TIGR00388 186 KTTYGDVFH 194 (293)
T ss_pred ccchhhccc
Confidence 699999994
No 6
>COG0752 GlyQ Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=13.05 E-value=68 Score=30.87 Aligned_cols=10 Identities=40% Similarity=0.826 Sum_probs=8.5
Q ss_pred CCCccCceee
Q 038380 17 QPIKYGDFFN 26 (261)
Q Consensus 17 ~pikYgdvF~ 26 (261)
+.|+|||||-
T Consensus 189 ~~~tYgdvf~ 198 (298)
T COG0752 189 GKVTYGDVFL 198 (298)
T ss_pred Cceehhhhhh
Confidence 4799999994
No 7
>PF15142 INCA1: INCA1
Probab=11.55 E-value=83 Score=28.16 Aligned_cols=12 Identities=58% Similarity=1.173 Sum_probs=9.4
Q ss_pred CCccCcee--eccc
Q 038380 18 PIKYGDFF--NVSG 29 (261)
Q Consensus 18 pikYgdvF--~v~G 29 (261)
|-+|||+| |.|-
T Consensus 26 pq~Ygd~FWenLsq 39 (178)
T PF15142_consen 26 PQRYGDIFWENLSQ 39 (178)
T ss_pred cchhhhHHHHhhcc
Confidence 78999999 5543
No 8
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=11.28 E-value=1.1e+02 Score=24.35 Aligned_cols=11 Identities=55% Similarity=0.718 Sum_probs=9.7
Q ss_pred CCCCCccCcee
Q 038380 15 QQQPIKYGDFF 25 (261)
Q Consensus 15 ~~~pikYgdvF 25 (261)
+|+|=||||+|
T Consensus 53 gql~n~ygdaF 63 (77)
T KOG1783|consen 53 GQLKNKYGDAF 63 (77)
T ss_pred Cccccccccee
Confidence 47899999999
No 9
>PF07896 DUF1674: Protein of unknown function (DUF1674); InterPro: IPR012875 The members of this family are sequences derived from hypothetical eukaryotic and bacterial proteins. The region in question is approximately 60 residues long. ; PDB: 2K5K_A.
Probab=10.80 E-value=89 Score=22.61 Aligned_cols=9 Identities=44% Similarity=1.254 Sum_probs=1.0
Q ss_pred CCCCccCce
Q 038380 16 QQPIKYGDF 24 (261)
Q Consensus 16 ~~pikYgdv 24 (261)
.||.+|||-
T Consensus 30 ~ePtRyGDW 38 (47)
T PF07896_consen 30 PEPTRYGDW 38 (47)
T ss_dssp ----S----
T ss_pred CCCcccccc
Confidence 489999984
No 10
>PF11005 DUF2844: Protein of unknown function (DUF2844); InterPro: IPR021267 This bacterial family of proteins has no known function.
Probab=10.66 E-value=2.8e+02 Score=23.78 Aligned_cols=34 Identities=21% Similarity=0.055 Sum_probs=25.6
Q ss_pred cccCCCeeEEeecCCCceeEEeeecc-eeeeeeec
Q 038380 85 VAGDQGVTVTETDVPGRRIITESVGG-QVVGRHEE 118 (261)
Q Consensus 85 ~a~d~GV~Vtet~vpG~RIvTE~VaG-QVvgq~~~ 118 (261)
.....+++|.|+..++...|.||+.. =+|.-+.=
T Consensus 26 ~~~~~~ytv~~~t~~~Gt~VrEY~~~~G~VFAvaW 60 (132)
T PF11005_consen 26 STSAAAYTVRETTDASGTTVREYVTPDGIVFAVAW 60 (132)
T ss_pred ccCCCceEEEEEEcCCCcEEEEEEcCCCcEEEEEe
Confidence 34668999999999999999999975 34443333
Done!