Query 035053
Match_columns 74
No_of_seqs 127 out of 285
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:49:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035053.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035053hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1668 Elongation factor 1 be 100.0 2.5E-37 5.5E-42 226.3 4.0 71 1-74 161-231 (231)
2 cd00292 EF1B Elongation factor 100.0 1.6E-28 3.5E-33 157.3 6.5 70 1-74 19-88 (88)
3 PF00736 EF1_GNE: EF-1 guanine 99.9 9.1E-28 2E-32 153.8 6.0 71 1-74 17-89 (89)
4 PRK00435 ef1B elongation facto 99.9 2.5E-27 5.4E-32 152.2 6.0 70 1-74 19-88 (88)
5 TIGR00489 aEF-1_beta translati 99.9 6.3E-23 1.4E-27 131.8 5.9 70 1-74 19-88 (88)
6 COG2092 EFB1 Translation elong 99.7 1.4E-16 3E-21 103.1 5.8 70 1-74 19-88 (88)
7 COG3702 VirB3 Type IV secretor 54.4 6.4 0.00014 26.3 0.9 25 3-29 75-99 (105)
8 TIGR03116 cas_csf3 CRISPR-asso 52.4 7.5 0.00016 28.9 1.1 21 12-32 59-79 (214)
9 COG1730 GIM5 Predicted prefold 43.7 20 0.00044 24.8 2.1 26 19-47 55-81 (145)
10 COG1152 CdhA CO dehydrogenase/ 39.5 8 0.00017 33.2 -0.5 30 13-42 611-642 (772)
11 TIGR02934 nifT_nitrog probable 32.8 16 0.00034 22.7 0.1 19 2-21 20-38 (67)
12 PF07292 NID: Nmi/IFP 35 domai 28.3 30 0.00064 22.1 0.9 40 29-73 40-79 (88)
13 PF05639 Pup: Pup-like protein 23.5 49 0.0011 20.6 1.2 21 45-65 40-62 (69)
14 PF14790 THDPS_N: Tetrahydrodi 23.5 57 0.0012 23.5 1.7 14 22-35 16-29 (167)
15 PF04650 YSIRK_signal: YSIRK t 23.3 31 0.00067 17.7 0.2 11 27-37 6-16 (27)
16 PF00543 P-II: Nitrogen regula 22.3 1.8E+02 0.0039 17.9 3.7 50 2-53 11-74 (102)
17 COG4668 MtlA Mannitol/fructose 21.0 67 0.0014 22.5 1.6 20 12-31 80-99 (142)
18 PF09314 DUF1972: Domain of un 20.1 34 0.00073 24.3 -0.1 16 11-26 123-138 (185)
No 1
>KOG1668 consensus Elongation factor 1 beta/delta chain [Transcription]
Probab=100.00 E-value=2.5e-37 Score=226.34 Aligned_cols=71 Identities=70% Similarity=0.999 Sum_probs=67.5
Q ss_pred ChHHHHhhhccccCceeeccceeeeeeeeeeeEEEEEEEecCccChhhhhhhhhcccCCCCceeeeeeeccccC
Q 035053 1 MKKLEEAVRSVEMPGLFWGASKLVPVGYGIKKLQIMITIVDDLVSVDSLIEEHLTVEPCNEYVQSCDIVAFNKI 74 (74)
Q Consensus 1 m~~le~~Vr~I~~dGL~WG~sKlvpv~yGikKLqi~cvveDdkVs~ddl~ee~i~~e~~ed~VQS~Di~afnKi 74 (74)
|++||++||+|+|+||+||+|||+|||||||||||+|||+|||||+|+|+|++ +. ||||||||||+|||||
T Consensus 161 m~~~e~~vrsi~~~gl~wgasklvpvGygikKlqi~~vveddkvs~D~l~e~i-~~--~e~~Vqs~di~afnki 231 (231)
T KOG1668|consen 161 MKELEECVRSIEMDGLVWGASKLVPVGYGIKKLQIQCVVEDDKVSIDDLIEEI-TK--FEDHVQSVDIAAFNKI 231 (231)
T ss_pred HHHHHHHHHHhhhccceeccccccccccceeeEEEEEEEEcCccccchhHHHh-hh--hhcceeeehhhhcccC
Confidence 78999999999999999999999999999999999999999999999998874 33 8999999999999997
No 2
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=99.95 E-value=1.6e-28 Score=157.28 Aligned_cols=70 Identities=44% Similarity=0.746 Sum_probs=65.0
Q ss_pred ChHHHHhhhccccCceeeccceeeeeeeeeeeEEEEEEEecCccChhhhhhhhhcccCCCCceeeeeeeccccC
Q 035053 1 MKKLEEAVRSVEMPGLFWGASKLVPVGYGIKKLQIMITIVDDLVSVDSLIEEHLTVEPCNEYVQSCDIVAFNKI 74 (74)
Q Consensus 1 m~~le~~Vr~I~~dGL~WG~sKlvpv~yGikKLqi~cvveDdkVs~ddl~ee~i~~e~~ed~VQS~Di~afnKi 74 (74)
|++|+++||++.++||+||+++++|+||||||||+.|+|+|+++|+|++.|. |.. +|+||||||++||||
T Consensus 19 l~~l~~~Ik~~~~~gl~~~~~~~epiaFGlk~L~i~~vv~D~~~~td~lee~-i~~---~d~VqsveI~~~~ki 88 (88)
T cd00292 19 LDELEEKIRAILMDGLLWGKSKLEPIAFGLKALQIYCVVEDDEGGTDELEEA-ISE---EDGVQSVDVEAFNKL 88 (88)
T ss_pred HHHHHHHHHHhCcCCcEEEEEEEEEeeeEeeEEEEEEEEEeCCcCcHHHHHH-Hhc---cCCceEEEEEEEEeC
Confidence 5789999999999999999999999999999999999999999999998665 444 689999999999996
No 3
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=99.94 E-value=9.1e-28 Score=153.78 Aligned_cols=71 Identities=42% Similarity=0.695 Sum_probs=63.9
Q ss_pred ChHHHHhh-hccccCceeec-cceeeeeeeeeeeEEEEEEEecCccChhhhhhhhhcccCCCCceeeeeeeccccC
Q 035053 1 MKKLEEAV-RSVEMPGLFWG-ASKLVPVGYGIKKLQIMITIVDDLVSVDSLIEEHLTVEPCNEYVQSCDIVAFNKI 74 (74)
Q Consensus 1 m~~le~~V-r~I~~dGL~WG-~sKlvpv~yGikKLqi~cvveDdkVs~ddl~ee~i~~e~~ed~VQS~Di~afnKi 74 (74)
|++|+++| |+|+++||+|| +++++|+|||+|+||+.|+++|+++|+|++.+. + +.+++.||||||.+||||
T Consensus 17 l~~l~~~Ik~~i~~~gl~w~~~~~~epIaFGlk~L~v~~vv~D~~~~~d~lee~-i--~~~~e~Vqsvei~~~~rl 89 (89)
T PF00736_consen 17 LEKLEKKIKRKIPMEGLKWGEKSKEEPIAFGLKALQVSCVVEDDEGSTDDLEEA-I--ESFEEGVQSVEIESFNRL 89 (89)
T ss_dssp HHHHHHHHHHHS-TTTEEEEEEEEEEEECTTEEEEEEEEEECTTTCGHHHHHHH-H--TTCTTTEEEEEEEEEEE-
T ss_pred HHHHHHHHHHhchhcceeeeeeeeeeeecccEEEEEEEEEEEcCccChHHHHHH-H--HhcCCCccEEEEEEEEcC
Confidence 57899999 99999999999 799999999999999999999999999998665 4 338999999999999996
No 4
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=99.94 E-value=2.5e-27 Score=152.23 Aligned_cols=70 Identities=19% Similarity=0.384 Sum_probs=65.2
Q ss_pred ChHHHHhhhccccCceeeccceeeeeeeeeeeEEEEEEEecCccChhhhhhhhhcccCCCCceeeeeeeccccC
Q 035053 1 MKKLEEAVRSVEMPGLFWGASKLVPVGYGIKKLQIMITIVDDLVSVDSLIEEHLTVEPCNEYVQSCDIVAFNKI 74 (74)
Q Consensus 1 m~~le~~Vr~I~~dGL~WG~sKlvpv~yGikKLqi~cvveDdkVs~ddl~ee~i~~e~~ed~VQS~Di~afnKi 74 (74)
|++|+++||++.++||.||+++++|+|||||+||+.|+++|+++|+|++.|. ++. ||| |||+||++||++
T Consensus 19 l~~L~~~ik~~~~~g~~~~~~~~ePIaFGLkaL~i~~vv~D~~~~td~lee~-i~~--~e~-Vqsvei~~~~r~ 88 (88)
T PRK00435 19 LDELKEKIKEVLPEGYKINGIEEEPIAFGLKALKLYVIMPDEEGGTEPVEEA-FAN--VEG-VESVEVEEVSRI 88 (88)
T ss_pred HHHHHHHHHHhCcCCcEEeEeEEEEeeccceeEEEEEEEEcCCcCcHHHHHH-Hhc--cCC-CcEEEEEEEecC
Confidence 5789999999999999999999999999999999999999999999987554 555 999 999999999986
No 5
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=99.88 E-value=6.3e-23 Score=131.81 Aligned_cols=70 Identities=16% Similarity=0.285 Sum_probs=64.3
Q ss_pred ChHHHHhhhccccCceeeccceeeeeeeeeeeEEEEEEEecCccChhhhhhhhhcccCCCCceeeeeeeccccC
Q 035053 1 MKKLEEAVRSVEMPGLFWGASKLVPVGYGIKKLQIMITIVDDLVSVDSLIEEHLTVEPCNEYVQSCDIVAFNKI 74 (74)
Q Consensus 1 m~~le~~Vr~I~~dGL~WG~sKlvpv~yGikKLqi~cvveDdkVs~ddl~ee~i~~e~~ed~VQS~Di~afnKi 74 (74)
|++|++++|++.++|+.||.++.+|+|||+++||+.|+++|+++++|++.+ .+.. +|+ |||+||.+|+++
T Consensus 19 le~L~~~ik~~~~~g~~~~~~~~ePiaFGLkaL~~~~vv~D~~g~td~lee-~i~~--ve~-V~svev~~~~r~ 88 (88)
T TIGR00489 19 LEALKEKIKERIPEGVEIRKIDEEPIAFGLVAINVMVVMGDAEGGTEAAEE-SLSG--IEG-VESVEVTDVRLL 88 (88)
T ss_pred HHHHHHHHHHhCcCCcEEeeeEEEeeeccceeeEEEEEEecCCcChHHHHH-HHhc--CCC-ccEEEEEEEEcC
Confidence 578999999999999999999999999999999999999999999998744 4655 885 999999999986
No 6
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=99.66 E-value=1.4e-16 Score=103.07 Aligned_cols=70 Identities=21% Similarity=0.368 Sum_probs=60.7
Q ss_pred ChHHHHhhhccccCceeeccceeeeeeeeeeeEEEEEEEecCccChhhhhhhhhcccCCCCceeeeeeeccccC
Q 035053 1 MKKLEEAVRSVEMPGLFWGASKLVPVGYGIKKLQIMITIVDDLVSVDSLIEEHLTVEPCNEYVQSCDIVAFNKI 74 (74)
Q Consensus 1 m~~le~~Vr~I~~dGL~WG~sKlvpv~yGikKLqi~cvveDdkVs~ddl~ee~i~~e~~ed~VQS~Di~afnKi 74 (74)
+++|++.||++.++|+.|+.+..+|+|||+|+|++.|+++|.--++|++.+. +.. +++ |||++++++++|
T Consensus 19 l~~L~~~ik~~l~~g~~~~~~~~epIaFGLkal~l~vvv~D~Eg~td~~ee~-l~~--veg-V~sveve~vsrl 88 (88)
T COG2092 19 LEELEEKIKEKLPEGYELIKIEEEPIAFGLKALKLYVVVEDKEGGTDALEEA-LEE--VEG-VESVEVENVSRL 88 (88)
T ss_pred HHHHHHHHHHhccccceeccceeEeeeeeeeeEEEEEEEcccccCcHHHHHH-Hhh--ccC-cceEEEEEEEeC
Confidence 4789999999999999999999999999999999999995555559987554 444 877 999999999876
No 7
>COG3702 VirB3 Type IV secretory pathway, VirB3 components [Intracellular trafficking and secretion]
Probab=54.45 E-value=6.4 Score=26.34 Aligned_cols=25 Identities=40% Similarity=0.694 Sum_probs=19.2
Q ss_pred HHHHhhhccccCceeeccceeeeeeee
Q 035053 3 KLEEAVRSVEMPGLFWGASKLVPVGYG 29 (74)
Q Consensus 3 ~le~~Vr~I~~dGL~WG~sKlvpv~yG 29 (74)
.++.+-|+ .+|+.||++-+-|+++-
T Consensus 75 ~~~~~~~~--rn~~fWga~Sysp~~~~ 99 (105)
T COG3702 75 WLSTTGRS--RNGLFWGAASYSPLALK 99 (105)
T ss_pred HHHHcCCC--CCcceecccccCccccc
Confidence 45555555 89999999999888753
No 8
>TIGR03116 cas_csf3 CRISPR-associated protein, Csf3 family. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf3 (CRISPR/cas Subtype as in A. ferrooxidans protein 3), as it lies third closest to the repeats.
Probab=52.39 E-value=7.5 Score=28.88 Aligned_cols=21 Identities=24% Similarity=0.281 Sum_probs=18.0
Q ss_pred ccCceeeccceeeeeeeeeee
Q 035053 12 EMPGLFWGASKLVPVGYGIKK 32 (74)
Q Consensus 12 ~~dGL~WG~sKlvpv~yGikK 32 (74)
+-|+-+|-+|+|.+++|+=+-
T Consensus 59 ~~d~W~Wkas~l~v~~f~~~~ 79 (214)
T TIGR03116 59 EGDSWVWKASRLEVLAFLPYP 79 (214)
T ss_pred CCCeEEEEecceeeeecCccc
Confidence 468899999999999998653
No 9
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=43.75 E-value=20 Score=24.83 Aligned_cols=26 Identities=42% Similarity=0.626 Sum_probs=18.5
Q ss_pred ccceeeeeeeeeeeEEEEEEEec-CccChh
Q 035053 19 GASKLVPVGYGIKKLQIMITIVD-DLVSVD 47 (74)
Q Consensus 19 G~sKlvpv~yGikKLqi~cvveD-dkVs~d 47 (74)
|.-.|||+|.|.. +...|.| |+|-++
T Consensus 55 g~E~LVpvGag~f---v~~kv~~~~kviV~ 81 (145)
T COG1730 55 GKEVLVPVGAGLF---VKAKVKDMDKVIVS 81 (145)
T ss_pred CceEEEEcCCCce---EEEEeccCceEEEE
Confidence 6689999999974 5666666 665443
No 10
>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]
Probab=39.54 E-value=8 Score=33.21 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=25.7
Q ss_pred cCceeecc-c-eeeeeeeeeeeEEEEEEEecC
Q 035053 13 MPGLFWGA-S-KLVPVGYGIKKLQIMITIVDD 42 (74)
Q Consensus 13 ~dGL~WG~-s-Klvpv~yGikKLqi~cvveDd 42 (74)
.=|+-||+ | |...+|+|..++=|+.|+-.+
T Consensus 611 AcgvAWGaySqkaasiatG~nr~GIPvVlGPh 642 (772)
T COG1152 611 ACGVAWGAYSQKAASIATGCNRWGIPVVLGPH 642 (772)
T ss_pred eeEEeehhhhHHHHHHhcCccccCCceEECCC
Confidence 34899998 4 999999999999999997554
No 11
>TIGR02934 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein.
Probab=32.76 E-value=16 Score=22.66 Aligned_cols=19 Identities=53% Similarity=0.782 Sum_probs=15.7
Q ss_pred hHHHHhhhccccCceeeccc
Q 035053 2 KKLEEAVRSVEMPGLFWGAS 21 (74)
Q Consensus 2 ~~le~~Vr~I~~dGL~WG~s 21 (74)
+.||+.|-+++.+++ ||..
T Consensus 20 KDLEE~Vv~~e~~~~-WGG~ 38 (67)
T TIGR02934 20 KDLEEVIVSVEKEEL-WGGW 38 (67)
T ss_pred CcchhheeeeecCcc-ccCE
Confidence 468999999997776 9975
No 12
>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi). This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].
Probab=28.28 E-value=30 Score=22.15 Aligned_cols=40 Identities=20% Similarity=0.346 Sum_probs=27.3
Q ss_pred eeeeEEEEEEEecCccChhhhhhhhhcccCCCCceeeeeeecccc
Q 035053 29 GIKKLQIMITIVDDLVSVDSLIEEHLTVEPCNEYVQSCDIVAFNK 73 (74)
Q Consensus 29 GikKLqi~cvveDdkVs~ddl~ee~i~~e~~ed~VQS~Di~afnK 73 (74)
-+.|+|+.+.+-..+|-+..|-+ .+.+|.+.|.+. .+|+|
T Consensus 40 ~~~k~qv~~~vs~rtVlvsgip~-~l~ee~l~D~Le----IhFqK 79 (88)
T PF07292_consen 40 HLQKFQVFSGVSKRTVLVSGIPD-VLDEEELRDKLE----IHFQK 79 (88)
T ss_pred CceEEEEEEcccCCEEEEeCCCC-CCChhhheeeEE----EEEec
Confidence 46899999999888888777655 355555555543 45554
No 13
>PF05639 Pup: Pup-like protein; InterPro: IPR008515 This family consists of several short bacterial proteins formely known as (DUF797). It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD) []. Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages []. The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup []). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier. ; PDB: 3M91_D 3M9D_I.
Probab=23.49 E-value=49 Score=20.57 Aligned_cols=21 Identities=33% Similarity=0.553 Sum_probs=7.5
Q ss_pred Chhhhhhhh--hcccCCCCceee
Q 035053 45 SVDSLIEEH--LTVEPCNEYVQS 65 (74)
Q Consensus 45 s~ddl~ee~--i~~e~~ed~VQS 65 (74)
.+|+|+++| +-++-=|+||+|
T Consensus 40 ~vD~lLDeID~vLE~NAeeFVr~ 62 (69)
T PF05639_consen 40 DVDDLLDEIDSVLETNAEEFVRS 62 (69)
T ss_dssp CHHHHHHHHTTTSSSC-------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 478888875 111223566665
No 14
>PF14790 THDPS_N: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 2RIJ_A 3R5A_F 3R5B_A 3R5C_B 3R5D_D.
Probab=23.46 E-value=57 Score=23.47 Aligned_cols=14 Identities=21% Similarity=0.503 Sum_probs=8.3
Q ss_pred eeeeeeeeeeeEEE
Q 035053 22 KLVPVGYGIKKLQI 35 (74)
Q Consensus 22 Klvpv~yGikKLqi 35 (74)
-..|+||||.+.+.
T Consensus 16 Yk~PlaFGIaRvd~ 29 (167)
T PF14790_consen 16 YKDPLAFGIARVDR 29 (167)
T ss_dssp ----SEEEEEEEEE
T ss_pred CCCcceeeeeeeee
Confidence 46799999987764
No 15
>PF04650 YSIRK_signal: YSIRK type signal peptide; InterPro: IPR005877 Many surface proteins found in Streptococcus, Staphylococcus, and related lineages share apparently homologous signal sequences. A motif resembling [YF]SIRKxxxGxxS[VIA] appears at the start of the transmembrane domain. The GxxS motif appears perfectly conserved, suggesting a specific function and not just homology. ; GO: 0016020 membrane
Probab=23.33 E-value=31 Score=17.71 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=8.5
Q ss_pred eeeeeeEEEEE
Q 035053 27 GYGIKKLQIMI 37 (74)
Q Consensus 27 ~yGikKLqi~c 37 (74)
-|+|+||.+..
T Consensus 6 rysIRK~svGv 16 (27)
T PF04650_consen 6 RYSIRKLSVGV 16 (27)
T ss_pred EEeEEccccch
Confidence 58999998654
No 16
>PF00543 P-II: Nitrogen regulatory protein P-II members of this family.; InterPro: IPR002187 In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity []. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of GS, thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed. P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein []. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome. Other proteins highly similar to glnB are: Bacillus subtilis protein nrgB []. Escherichia coli hypothetical protein ybaI []. ; GO: 0030234 enzyme regulator activity, 0006808 regulation of nitrogen utilization; PDB: 1V3S_B 1V3R_C 2XZW_A 2XUL_A 2V5H_J 2XG8_C 2JJ4_F 1QY7_C 4AFF_A 2XBP_A ....
Probab=22.29 E-value=1.8e+02 Score=17.90 Aligned_cols=50 Identities=26% Similarity=0.367 Sum_probs=31.4
Q ss_pred hHHHHhhhccccCceeecc------ce-----eeeeeee---eeeEEEEEEEecCccChhhhhhhh
Q 035053 2 KKLEEAVRSVEMPGLFWGA------SK-----LVPVGYG---IKKLQIMITIVDDLVSVDSLIEEH 53 (74)
Q Consensus 2 ~~le~~Vr~I~~dGL~WG~------sK-----lvpv~yG---ikKLqi~cvveDdkVs~ddl~ee~ 53 (74)
+++.++.+..-..|+++.. .+ ..-..|. ..|.++.+++.|+. ++++++-+
T Consensus 11 ~~v~~aL~~~G~~g~Tv~~v~G~G~~~~~~~~~~g~~~~~~~~~k~~i~ivv~d~~--v~~iv~~I 74 (102)
T PF00543_consen 11 EEVIEALREAGVPGMTVSEVRGRGRQKGQAEIYRGDEYFVEFSPKVKIEIVVPDED--VEEIVEAI 74 (102)
T ss_dssp HHHHHHHHHTTGSCEEEEEEEEESSTTTEEEEETTEEECCCEEEEEEEEEEEEGGG--HHHHHHHH
T ss_pred HHHHHHHHHCCCCeEEEEEeEEecccccccceeeeeeeeecccccEEEEEEECHHh--HHHHHHHH
Confidence 4566677777788888732 11 1111222 57889999999986 56666643
No 17
>COG4668 MtlA Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]
Probab=21.01 E-value=67 Score=22.46 Aligned_cols=20 Identities=25% Similarity=0.456 Sum_probs=15.6
Q ss_pred ccCceeeccceeeeeeeeee
Q 035053 12 EMPGLFWGASKLVPVGYGIK 31 (74)
Q Consensus 12 ~~dGL~WG~sKlvpv~yGik 31 (74)
-.+|+.||....+-+.+||-
T Consensus 80 ~p~GV~wg~g~~a~~viGIA 99 (142)
T COG4668 80 FPEGVDWGDGQIAYLVIGIA 99 (142)
T ss_pred CCCccccCCCceEEEEEEEe
Confidence 45999999777777777874
No 18
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=20.06 E-value=34 Score=24.33 Aligned_cols=16 Identities=38% Similarity=0.516 Sum_probs=13.0
Q ss_pred cccCceeeccceeeee
Q 035053 11 VEMPGLFWGASKLVPV 26 (74)
Q Consensus 11 I~~dGL~WG~sKlvpv 26 (74)
+++|||.|-.+|.-+.
T Consensus 123 vN~DGlEWkR~KW~~~ 138 (185)
T PF09314_consen 123 VNMDGLEWKRAKWGRP 138 (185)
T ss_pred ECCCcchhhhhhcCHH
Confidence 5999999998887543
Done!