Query 027886
Match_columns 217
No_of_seqs 113 out of 124
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 02:57:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027886.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027886hhsearch_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 1.5E-20 3.1E-25 136.3 6.5 62 92-153 1-62 (62)
2 PF04927 SMP: Seed maturation 99.8 7.8E-20 1.7E-24 132.5 4.9 59 157-216 1-59 (62)
3 cd07046 BMC_PduU-EutS 1,2-prop 22.6 58 0.0013 26.2 1.8 23 59-81 1-24 (110)
4 PF12218 End_N_terminal: N ter 10.8 2E+02 0.0044 21.6 2.0 31 43-73 26-61 (67)
5 PF11005 DUF2844: Protein of u 10.1 2.9E+02 0.0063 23.0 2.9 25 43-68 27-51 (132)
6 PRK10386 curli assembly protei 9.8 4.4E+02 0.0095 22.0 3.8 35 44-79 56-91 (130)
7 PRK15468 carboxysome structura 7.6 2.2E+02 0.0049 23.3 1.2 78 59-148 4-94 (111)
8 smart00685 DM14 Repeats in fly 5.8 4.6E+02 0.01 19.0 1.9 19 94-115 36-54 (59)
9 TIGR03687 pupylate_cterm ubiqu 5.3 2.1E+02 0.0045 18.9 -0.1 14 3-16 19-32 (33)
10 cd01208 X11 X11 Phosphotyrosin 4.7 3.9E+02 0.0085 23.0 1.1 13 92-104 136-148 (156)
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=99.82 E-value=1.5e-20 Score=136.34 Aligned_cols=62 Identities=52% Similarity=0.659 Sum_probs=59.0
Q ss_pred CchHhHHHHHhhhhhcCCCCChhHHHHHHHHHHhhccCCCCCCCcHHHHHhhHHHhcccccC
Q 027886 92 QSTIGEALEATALSAGDKAVDQRDAAAIYAAEARASATNEIKPGGIGSRAQSAATQNERTTF 153 (217)
Q Consensus 92 ~itiGealeaaa~~~g~kPV~~~DAAaiqaAE~ratG~~~~~~GG~AA~aQsAA~~N~r~~~ 153 (217)
+|||||+|++++..+++|||+++||+.||+||+|.+|.+.++|||++++||||+++|++.++
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 59999999988888999999999999999999999999889999999999999999998764
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=99.79 E-value=7.8e-20 Score=132.55 Aligned_cols=59 Identities=47% Similarity=0.628 Sum_probs=57.3
Q ss_pred cchhhhhhhhccccCCCCCCCCHhhHhhhhchhhhcCCCCCCCCCcHHHHHHHHHHhccC
Q 027886 157 KITISDVSGDATTKLSDDKPVTREDAEGIISPEIRNKPDMRTTPGGVASSMAAAARLNQS 216 (217)
Q Consensus 157 kitigdvL~~At~kl~~Dk~vt~eDAaaV~aAE~R~~g~~~~~pGGVAaa~qaAA~~N~~ 216 (217)
|||||||| +|+.++++|||||+|||++||+||+|++|...+.||||+++||+||++|++
T Consensus 1 ~vt~gdvl-~A~a~~~~~kpVt~eDAa~iqsAE~r~~g~~~~~~GGvAa~~qsAA~~N~~ 59 (62)
T PF04927_consen 1 KVTIGDVL-EAAAGLPGDKPVTPEDAAAIQSAEARATGGAQTQPGGVAAAAQSAADKNER 59 (62)
T ss_pred CccHHHHH-HHHhcccccCCCCHHHHHHHHHHHHhhCCCCCCCCCCHHHHHHHHHHHhhh
Confidence 69999999 999999999999999999999999999999889999999999999999986
No 3
>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=22.63 E-value=58 Score=26.21 Aligned_cols=23 Identities=22% Similarity=0.209 Sum_probs=19.8
Q ss_pred CeeEeeeecc-eeceeeccCCCCc
Q 027886 59 NRIITEAIGD-QVLAQYATPEVPT 81 (217)
Q Consensus 59 ~RivTE~VaG-QVvgq~~~p~~~~ 81 (217)
.|||-|+|.| |++..|+-|.+..
T Consensus 1 ~r~~~~~v~gk~i~~~~vI~~v~~ 24 (110)
T cd07046 1 QRIIQEYVPGKQITLAHLIANPDP 24 (110)
T ss_pred CcceEEecCcceEEEEEEecCCCH
Confidence 3899999988 8999999998854
No 4
>PF12218 End_N_terminal: N terminal extension of bacteriophage endosialidase; InterPro: IPR024429 This entry represents the N-terminal extension domain of endosialidases which is approximately 70 amino acids in length. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain [].; PDB: 3JU4_A 3GVL_A 3GVK_B 3GVJ_A 1V0E_B 1V0F_E.
Probab=10.83 E-value=2e+02 Score=21.63 Aligned_cols=31 Identities=29% Similarity=0.333 Sum_probs=17.9
Q ss_pred ccCCCeeeEecccCC-----CCeeEeeeecceecee
Q 027886 43 ARDQGVTVSESTVAD-----GNRIITEAIGDQVLAQ 73 (217)
Q Consensus 43 a~d~GV~VtEt~vp~-----G~RivTE~VaGQVvgq 73 (217)
....|.+-.-+.+|+ ..|++-|.+.||++--
T Consensus 26 IDg~GlTykVs~lPd~srf~N~rF~~eri~gqpl~y 61 (67)
T PF12218_consen 26 IDGAGLTYKVSSLPDISRFKNARFVYERIPGQPLYY 61 (67)
T ss_dssp EE-TT-EEEESS---GGGEES-EEEE-SSTT--EEE
T ss_pred EecCCceEEEeeCccHHhhccceEEEeecCCCceEe
Confidence 447788888888997 6799999999998753
No 5
>PF11005 DUF2844: Protein of unknown function (DUF2844); InterPro: IPR021267 This bacterial family of proteins has no known function.
Probab=10.08 E-value=2.9e+02 Score=22.98 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=21.6
Q ss_pred ccCCCeeeEecccCCCCeeEeeeecc
Q 027886 43 ARDQGVTVSESTVADGNRIITEAIGD 68 (217)
Q Consensus 43 a~d~GV~VtEt~vp~G~RivTE~VaG 68 (217)
.....++|.|+..+ +...|.|++..
T Consensus 27 ~~~~~ytv~~~t~~-~Gt~VrEY~~~ 51 (132)
T PF11005_consen 27 TSAAAYTVRETTDA-SGTTVREYVTP 51 (132)
T ss_pred cCCCceEEEEEEcC-CCcEEEEEEcC
Confidence 45789999999999 88889999875
No 6
>PRK10386 curli assembly protein CsgE; Provisional
Probab=9.77 E-value=4.4e+02 Score=22.03 Aligned_cols=35 Identities=26% Similarity=0.243 Sum_probs=28.4
Q ss_pred cCCCeeeEecccCC-CCeeEeeeecceeceeeccCCC
Q 027886 44 RDQGVTVSESTVAD-GNRIITEAIGDQVLAQYATPEV 79 (217)
Q Consensus 44 ~d~GV~VtEt~vp~-G~RivTE~VaGQVvgq~~~p~~ 79 (217)
-+..|+|.|..-|. |. +||=.+..+||-|+..++.
T Consensus 56 ~~~nltI~E~p~a~~GS-~ItV~~n~~vIy~t~l~p~ 91 (130)
T PRK10386 56 YDGNLTINERPSARWGS-WITITVNQDVIYQTFLFPN 91 (130)
T ss_pred CCCcEEEEEEEcCCCCc-EEEEEECCEEEEEEecCcc
Confidence 35789999998886 55 7888999999999887644
No 7
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=7.56 E-value=2.2e+02 Score=23.34 Aligned_cols=78 Identities=21% Similarity=0.223 Sum_probs=41.1
Q ss_pred CeeEeeeecc-eeceeeccCCCCccCCCcccCCCCchHhHHHHHhhhhhcCCCCChhHHHHHHH------HHH------h
Q 027886 59 NRIITEAIGD-QVLAQYATPEVPTRASGAALGRDQSTIGEALEATALSAGDKAVDQRDAAAIYA------AEA------R 125 (217)
Q Consensus 59 ~RivTE~VaG-QVvgq~~~p~~~~~~~~~a~~~~~itiGealeaaa~~~g~kPV~~~DAAaiqa------AE~------r 125 (217)
.|||-|+|-| ||---.+-..|....-. ++| |+.. .++|==-|+|++++-|.+ +.. |
T Consensus 4 ~RiIQE~VPGKQvTlAHiIa~P~~~iy~--------klG--l~~~-~AIGIlTiTP~E~aIIAaDIA~Kaa~V~igF~DR 72 (111)
T PRK15468 4 ERIIQEFVPGKQVTLAHLIAHPGEELAK--------KIG--VPDA-GAIGIMTLTPGETAMIAGDLALKAADVHIGFLDR 72 (111)
T ss_pred cceEEeecCCceeeeeeeecCCcHHHHH--------HhC--CCcc-CceEEEEeCcchHHHHHHHhhhhccCcEEeeeec
Confidence 4899999988 77655554433211000 000 1111 145556677777765543 221 3
Q ss_pred hccCCCCCCCcHHHHHhhHHHhc
Q 027886 126 ASATNEIKPGGIGSRAQSAATQN 148 (217)
Q Consensus 126 atG~~~~~~GG~AA~aQsAA~~N 148 (217)
.+| ...+-|.++++..+--..+
T Consensus 73 FsG-slvitGdvs~Ve~Al~~V~ 94 (111)
T PRK15468 73 FSG-ALVIYGSVGAVEEALSQTV 94 (111)
T ss_pred cce-eEEEEccHHHHHHHHHHHH
Confidence 444 3346777877766655554
No 8
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=5.79 E-value=4.6e+02 Score=19.02 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=13.1
Q ss_pred hHhHHHHHhhhhhcCCCCChhH
Q 027886 94 TIGEALEATALSAGDKAVDQRD 115 (217)
Q Consensus 94 tiGealeaaa~~~g~kPV~~~D 115 (217)
+|.++++++- .++||+.++
T Consensus 36 ~~~~~I~~~~---aG~pVd~~~ 54 (59)
T smart00685 36 QFDDAIKAAR---AGRPVDLSE 54 (59)
T ss_pred hHHHHHHHHH---CCCCCChhc
Confidence 4666776653 579998875
No 9
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=5.34 E-value=2.1e+02 Score=18.91 Aligned_cols=14 Identities=43% Similarity=0.667 Sum_probs=11.7
Q ss_pred hhhhhhhcccCCCC
Q 027886 3 AAENMALGKTQRGG 16 (217)
Q Consensus 3 sAE~~v~G~tqkgG 16 (217)
.||.-|-|-.||||
T Consensus 19 NAe~FV~~fVQKGG 32 (33)
T TIGR03687 19 NAEEFVRGFVQKGG 32 (33)
T ss_pred hHHHHHHHHHHccC
Confidence 47888888899998
No 10
>cd01208 X11 X11 Phosphotyrosine-binding (PTB) domain. X11 Phosphotyrosine-binding (PTB) domain. The neuronal protein X11 has a PTB domain followed by two PDZ domains. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether. X11 binds to the cytoplasmic domain of the beta-amyloid precursor protein (beta-APP) and does not require the substrate to be tyrosine-phosphorylated for binding.
Probab=4.71 E-value=3.9e+02 Score=22.98 Aligned_cols=13 Identities=23% Similarity=0.432 Sum_probs=10.4
Q ss_pred CchHhHHHHHhhh
Q 027886 92 QSTIGEALEATAL 104 (217)
Q Consensus 92 ~itiGealeaaa~ 104 (217)
..|||+||+.+=+
T Consensus 136 a~TIGQAF~lAY~ 148 (156)
T cd01208 136 AQSIGQAFQVAYQ 148 (156)
T ss_pred HHHHHHHHHHHHH
Confidence 4699999998743
Done!