Query 043613
Match_columns 90
No_of_seqs 110 out of 1005
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:38:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043613.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043613hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01281 Ribosomal_L9_N: Ribos 99.9 1.4E-25 3E-30 137.0 2.9 48 39-86 1-48 (48)
2 CHL00160 rpl9 ribosomal protei 99.9 1.6E-24 3.5E-29 156.8 4.0 53 37-89 4-56 (153)
3 TIGR00158 L9 ribosomal protein 99.9 4E-24 8.8E-29 153.4 3.7 51 39-89 1-51 (148)
4 PRK00137 rplI 50S ribosomal pr 99.9 5E-24 1.1E-28 152.2 4.1 51 39-89 1-51 (147)
5 COG0359 RplI Ribosomal protein 99.8 9.4E-22 2E-26 143.0 3.9 51 39-89 1-51 (148)
6 KOG4607 Mitochondrial ribosoma 99.7 2.5E-18 5.3E-23 132.3 2.9 59 26-84 36-94 (222)
7 PRK14538 putative bifunctional 99.7 5.4E-18 1.2E-22 147.3 0.3 51 38-89 688-738 (838)
8 TIGR00074 hypC_hupF hydrogenas 63.1 10 0.00022 24.9 3.0 30 37-70 26-55 (76)
9 PF01455 HupF_HypC: HupF/HypC 53.7 6.7 0.00014 25.0 0.9 29 36-68 27-55 (68)
10 PRK10413 hydrogenase 2 accesso 50.3 22 0.00048 23.6 3.0 31 37-68 29-60 (82)
11 PF06560 GPI: Glucose-6-phosph 49.6 14 0.0003 27.8 2.2 27 40-66 94-129 (182)
12 PRK10409 hydrogenase assembly 35.2 49 0.0011 22.4 2.9 34 37-70 26-61 (90)
13 PF07726 AAA_3: ATPase family 35.1 10 0.00023 27.3 -0.4 12 42-53 2-13 (131)
14 PRK06461 single-stranded DNA-b 29.7 83 0.0018 21.7 3.4 30 38-67 52-81 (129)
15 PF09926 DUF2158: Uncharacteri 29.2 39 0.00084 20.8 1.5 11 52-62 2-12 (53)
16 COG0298 HypC Hydrogenase matur 27.5 71 0.0015 21.8 2.6 27 37-67 28-55 (82)
17 KOG3416 Predicted nucleic acid 27.4 78 0.0017 23.4 3.0 37 39-77 50-86 (134)
18 PRK07218 replication factor A; 25.8 78 0.0017 26.6 3.1 30 37-67 208-237 (423)
19 cd04491 SoSSB_OBF SoSSB_OBF: A 24.8 51 0.0011 20.3 1.5 32 37-68 34-66 (82)
20 COG0035 Upp Uracil phosphoribo 22.4 38 0.00082 26.3 0.6 48 10-57 143-206 (210)
21 PF08415 NRPS: Nonribosomal pe 21.1 99 0.0021 18.4 2.2 23 7-29 6-28 (58)
No 1
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.91 E-value=1.4e-25 Score=137.04 Aligned_cols=48 Identities=40% Similarity=0.607 Sum_probs=44.8
Q ss_pred eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHH
Q 043613 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIR 86 (90)
Q Consensus 39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~ 86 (90)
|+|||++||||+|++||+|+|++|||||||+|+++|+|||++++++++
T Consensus 1 m~ViL~~dv~~lG~~Gdiv~V~~Gy~RN~L~p~~~A~~at~~~~~~~e 48 (48)
T PF01281_consen 1 MKVILLKDVPGLGKKGDIVEVKPGYARNFLIPQGLAVYATPENLKQLE 48 (48)
T ss_dssp -EEEESSCCTTSBSTTEEEE-SHHHHHHTTTTTTSEEECSHHHHHHHH
T ss_pred CEEEEcccccccCCCCCEEEEccceeeehccCCCceeeCCHHHHHhcC
Confidence 799999999999999999999999999999999999999999999874
No 2
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=99.90 E-value=1.6e-24 Score=156.77 Aligned_cols=53 Identities=30% Similarity=0.529 Sum_probs=50.1
Q ss_pred eeeEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR 89 (90)
Q Consensus 37 ~km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~ 89 (90)
++|+|||++||++||+.||+|+|+||||||||||+|+|++||+.++++++..+
T Consensus 4 kkmkVIL~~dV~~LGk~Gdiv~Vk~GYaRNyLiP~glA~~AT~~n~~~~e~~~ 56 (153)
T CHL00160 4 KKIQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQ 56 (153)
T ss_pred ceEEEEEcccccccCCCCCEEEEcCchHhhhhcccCchhhCCHHHHHHHHHHH
Confidence 57999999999999999999999999999999999999999999999877654
No 3
>TIGR00158 L9 ribosomal protein L9. Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.
Probab=99.89 E-value=4e-24 Score=153.43 Aligned_cols=51 Identities=41% Similarity=0.607 Sum_probs=48.7
Q ss_pred eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR 89 (90)
Q Consensus 39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~ 89 (90)
|+|||++||++||++||+|+|+||||||||||+|+|++||++++++++.++
T Consensus 1 MkVIL~~dV~~lGk~GdiV~Vk~GYaRNyLiP~g~A~~aT~~nl~~~e~~~ 51 (148)
T TIGR00158 1 MKVILLEDVANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFFEARR 51 (148)
T ss_pred CeEEEcccccccCCCCCEEEEcccchhhhhcccCchhhCCHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999987654
No 4
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=99.89 E-value=5e-24 Score=152.19 Aligned_cols=51 Identities=35% Similarity=0.523 Sum_probs=48.7
Q ss_pred eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR 89 (90)
Q Consensus 39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~ 89 (90)
|+|||++||+|||++||+|+|+||||||||||+|+|+|||++++++++..+
T Consensus 1 mkVIL~~dv~~lGk~Gdiv~Vk~GYaRNyLiP~~lA~~aT~~~~~~~~~~~ 51 (147)
T PRK00137 1 MKVILLEDVKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARR 51 (147)
T ss_pred CeEEEcccccccCCCCCEEEEcCcchhhhhccCCceeeCCHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999987654
No 5
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=9.4e-22 Score=142.96 Aligned_cols=51 Identities=41% Similarity=0.593 Sum_probs=48.9
Q ss_pred eEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR 89 (90)
Q Consensus 39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~ 89 (90)
|+|||++||++||+.||+|+|++|||||||||+|+|+.||+.+++.+..++
T Consensus 1 MkVILl~dV~~lGk~Gdiv~VkdGYarNfLiPkglAv~At~~n~~~~e~~r 51 (148)
T COG0359 1 MKVILLEDVKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARR 51 (148)
T ss_pred CeEEEecchhhcCCCCCEEEecchhhhhhhccccchhhCCHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999887754
No 6
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=2.5e-18 Score=132.28 Aligned_cols=59 Identities=46% Similarity=0.548 Sum_probs=55.6
Q ss_pred hheeeecceeeeeeEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHH
Q 043613 26 PLLFSCQGVKYRRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHL 84 (90)
Q Consensus 26 p~~~~~q~~r~~km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~ 84 (90)
+++.-+|++.+..++|||++||+|||+.||+|+|++||+||+|+|+|+|+|+++.+.++
T Consensus 36 ~lv~~~~~k~k~~levIL~~~Ve~lG~qGdvVsVk~g~~RN~Llp~glAvy~tp~~~~~ 94 (222)
T KOG4607|consen 36 ELVEFTQKKPKPNLEVILKTDVEKLGKQGDVVSVKRGYFRNFLLPKGLAVYNTPLNLKK 94 (222)
T ss_pred hHhHhhhccCCcceeeeeehhhhhhcccCcEEEeecchhhhhcccccccccCChhhHHH
Confidence 78888999999999999999999999999999999999999999999999999999444
No 7
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=99.68 E-value=5.4e-18 Score=147.26 Aligned_cols=51 Identities=31% Similarity=0.440 Sum_probs=48.5
Q ss_pred eeEEEEeccccccCCCCcEEEecCcceecccccccccccchHHHHHHHHHhh
Q 043613 38 RLEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLNIEKFAHLIREQR 89 (90)
Q Consensus 38 km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~At~~~~~~l~~~~ 89 (90)
.|+|||++||++||++||+|+|+|||| |||||+|+|++||++++++++.++
T Consensus 688 ~MkVIL~~dv~~lGk~Gdvv~Vk~GYa-NfLiP~~~A~~aT~~nlk~~e~~~ 738 (838)
T PRK14538 688 NMEIILLTDIKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKK 738 (838)
T ss_pred hhhHHHHHHHHhcCCCCCEEEECCCch-hhhccCCchhhcCHHHHHHHHHHH
Confidence 599999999999999999999999999 999999999999999999977664
No 8
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=63.06 E-value=10 Score=24.86 Aligned_cols=30 Identities=33% Similarity=0.386 Sum_probs=23.7
Q ss_pred eeeEEEEeccccccCCCCcEEEecCcceeccccc
Q 043613 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNHLMP 70 (90)
Q Consensus 37 ~km~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP 70 (90)
+.+.+.|+.++ +.||.|-|..|||+..+=+
T Consensus 26 ~~v~l~lv~~~----~vGD~VLVH~G~Ai~~ide 55 (76)
T TIGR00074 26 RDVSLDLVGEV----KVGDYVLVHVGFAISVLDE 55 (76)
T ss_pred EEEEEEeeCCC----CCCCEEEEecChhhhhCCH
Confidence 45777888775 5899999999999975543
No 9
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=53.74 E-value=6.7 Score=25.01 Aligned_cols=29 Identities=31% Similarity=0.507 Sum_probs=20.9
Q ss_pred eeeeEEEEeccccccCCCCcEEEecCcceeccc
Q 043613 36 YRRLEVILTTKVDKLGKVGETVKVAPGYFHNHL 68 (90)
Q Consensus 36 ~~km~VILl~dV~gLGk~GdvV~Vk~GYARN~L 68 (90)
.+.+.+-|+.|+ ..||.|-|..|||...+
T Consensus 27 ~~~V~~~lv~~v----~~Gd~VLVHaG~Ai~~i 55 (68)
T PF01455_consen 27 RREVSLALVPDV----KVGDYVLVHAGFAIEKI 55 (68)
T ss_dssp EEEEEGTTCTSB-----TT-EEEEETTEEEEEE
T ss_pred EEEEEEEEeCCC----CCCCEEEEecChhheeC
Confidence 345666677773 78999999999998755
No 10
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=50.34 E-value=22 Score=23.62 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=24.2
Q ss_pred eeeEEEEeccc-cccCCCCcEEEecCcceeccc
Q 043613 37 RRLEVILTTKV-DKLGKVGETVKVAPGYFHNHL 68 (90)
Q Consensus 37 ~km~VILl~dV-~gLGk~GdvV~Vk~GYARN~L 68 (90)
+.+.+-|+.+. |. -..||.|-|..|||++-+
T Consensus 29 r~V~l~Lv~~~~~~-~~vGDyVLVHaGfAi~~i 60 (82)
T PRK10413 29 RDVNIALICEGNPA-DLLGQWVLVHVGFAMSII 60 (82)
T ss_pred EEEEeeeeccCCcc-cccCCEEEEecchhhhhC
Confidence 44788888765 33 378999999999999854
No 11
>PF06560 GPI: Glucose-6-phosphate isomerase (GPI); InterPro: IPR010551 This entry consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (5.3.1.9 from EC), which are involved in glycolysis and in gluconeogenesis and catalyse the conversion of D-glucose 6-phosphate to D-fructose 6-phosphate. The deduced amino acid sequence of the first archaeal PGI isolated from Pyrococcus furiosus revealed that it is not related to its eukaryotic and many of its bacterial counterparts. In contrast, this archaeal PGI shares similarity with the cupin superfamily that consists of a variety of proteins that are generally involved in sugar metabolism in both prokaryotes and eukaryotes [].; GO: 0004347 glucose-6-phosphate isomerase activity, 0006094 gluconeogenesis, 0006096 glycolysis, 0005737 cytoplasm; PDB: 1J3Q_B 1J3R_B 1J3P_A 2GC0_A 1X8E_A 1X82_A 1QY4_B 2GC2_B 1QXJ_A 1QXR_B ....
Probab=49.59 E-value=14 Score=27.78 Aligned_cols=27 Identities=37% Similarity=0.614 Sum_probs=17.0
Q ss_pred EEEEeccccc---------cCCCCcEEEecCcceec
Q 043613 40 EVILTTKVDK---------LGKVGETVKVAPGYFHN 66 (90)
Q Consensus 40 ~VILl~dV~g---------LGk~GdvV~Vk~GYARN 66 (90)
-++|+++.++ -.++||+|-|.||||..
T Consensus 94 g~~lLq~~~~~~~~~~~~v~~~~G~~v~IPp~yaH~ 129 (182)
T PF06560_consen 94 GLILLQKEEGDDVGDVIAVEAKPGDVVYIPPGYAHR 129 (182)
T ss_dssp EEEEEE-TTS-----EEEEEE-TTEEEEE-TT-EEE
T ss_pred EEEEEEecCCCcceeEEEEEeCCCCEEEECCCceEE
Confidence 4678888776 14678889999998864
No 12
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=35.25 E-value=49 Score=22.44 Aligned_cols=34 Identities=24% Similarity=0.331 Sum_probs=24.7
Q ss_pred eeeEEEEecccc--ccCCCCcEEEecCcceeccccc
Q 043613 37 RRLEVILTTKVD--KLGKVGETVKVAPGYFHNHLMP 70 (90)
Q Consensus 37 ~km~VILl~dV~--gLGk~GdvV~Vk~GYARN~LiP 70 (90)
+.+.+.|+.+.+ .=-+.||.|-|..|||...+=+
T Consensus 26 reV~l~Lv~~~~~~~~~~vGDyVLVHaGfAi~~ide 61 (90)
T PRK10409 26 RDVDLTLVGSCDENGQPRVGQWVLVHVGFAMSVINE 61 (90)
T ss_pred EEEEEeeecccCCCCccCCCCEEEEecChHHhhCCH
Confidence 447888886432 1248999999999999975544
No 13
>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model. AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.
Probab=35.12 E-value=10 Score=27.34 Aligned_cols=12 Identities=33% Similarity=0.495 Sum_probs=6.8
Q ss_pred EEeccccccCCC
Q 043613 42 ILTTKVDKLGKV 53 (90)
Q Consensus 42 ILl~dV~gLGk~ 53 (90)
+|++|+||+||.
T Consensus 2 vLleg~PG~GKT 13 (131)
T PF07726_consen 2 VLLEGVPGVGKT 13 (131)
T ss_dssp EEEES---HHHH
T ss_pred EeeECCCccHHH
Confidence 688888888873
No 14
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=29.73 E-value=83 Score=21.68 Aligned_cols=30 Identities=20% Similarity=0.172 Sum_probs=20.6
Q ss_pred eeEEEEeccccccCCCCcEEEecCcceecc
Q 043613 38 RLEVILTTKVDKLGKVGETVKVAPGYFHNH 67 (90)
Q Consensus 38 km~VILl~dV~gLGk~GdvV~Vk~GYARN~ 67 (90)
++.+.|=.+-...=..||+|.|+.||.+-|
T Consensus 52 ~I~~tlW~~~a~~l~~GdvV~I~na~v~~f 81 (129)
T PRK06461 52 RVKLTLWGEQAGSLKEGEVVEIENAWTTLY 81 (129)
T ss_pred EEEEEEeCCccccCCCCCEEEEECcEEeee
Confidence 355555554333337899999999998754
No 15
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=29.23 E-value=39 Score=20.78 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=9.1
Q ss_pred CCCcEEEecCc
Q 043613 52 KVGETVKVAPG 62 (90)
Q Consensus 52 k~GdvV~Vk~G 62 (90)
+.||+|..|.|
T Consensus 2 ~~GDvV~LKSG 12 (53)
T PF09926_consen 2 KIGDVVQLKSG 12 (53)
T ss_pred CCCCEEEEccC
Confidence 47899998887
No 16
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=27.51 E-value=71 Score=21.80 Aligned_cols=27 Identities=33% Similarity=0.482 Sum_probs=20.2
Q ss_pred eeeEEEEec-cccccCCCCcEEEecCcceecc
Q 043613 37 RRLEVILTT-KVDKLGKVGETVKVAPGYFHNH 67 (90)
Q Consensus 37 ~km~VILl~-dV~gLGk~GdvV~Vk~GYARN~ 67 (90)
+.+++=|+. ++ +.||.|-|.-|||-+.
T Consensus 28 reV~l~Lv~~~v----~~GdyVLVHvGfAi~~ 55 (82)
T COG0298 28 REVNLDLVGEEV----KVGDYVLVHVGFAMSK 55 (82)
T ss_pred EEEEeeeecCcc----ccCCEEEEEeeEEEee
Confidence 456666665 43 7899999999999763
No 17
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=27.38 E-value=78 Score=23.37 Aligned_cols=37 Identities=14% Similarity=0.291 Sum_probs=27.2
Q ss_pred eEEEEeccccccCCCCcEEEecCcceecccccccccccc
Q 043613 39 LEVILTTKVDKLGKVGETVKVAPGYFHNHLMPKLLAVLN 77 (90)
Q Consensus 39 m~VILl~dV~gLGk~GdvV~Vk~GYARN~LiP~glA~~A 77 (90)
+.+-+-.|+-.+=..||||....||+- ++-.+|-.|+
T Consensus 50 I~isvW~e~~~~~~PGDIirLt~Gy~S--i~qg~LtL~~ 86 (134)
T KOG3416|consen 50 INISVWDEEGCLIQPGDIIRLTGGYAS--IFQGCLTLYV 86 (134)
T ss_pred EEEEEecCcCcccCCccEEEecccchh--hhcCceEEEe
Confidence 666677777778899999999999984 3334555553
No 18
>PRK07218 replication factor A; Provisional
Probab=25.81 E-value=78 Score=26.64 Aligned_cols=30 Identities=13% Similarity=0.380 Sum_probs=26.6
Q ss_pred eeeEEEEeccccccCCCCcEEEecCcceecc
Q 043613 37 RRLEVILTTKVDKLGKVGETVKVAPGYFHNH 67 (90)
Q Consensus 37 ~km~VILl~dV~gLGk~GdvV~Vk~GYARN~ 67 (90)
.++++.|=.|.+++ ..||+|.|..+|.+.|
T Consensus 208 G~Ir~tlW~~~~~l-~~Gd~v~I~na~v~e~ 237 (423)
T PRK07218 208 GRLPFTDWDPLPEI-EIGASIRIEDAYVREF 237 (423)
T ss_pred ceEEEEEecccccC-CCCCEEEEeeeEEecc
Confidence 56888888888877 8999999999999987
No 19
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=24.76 E-value=51 Score=20.28 Aligned_cols=32 Identities=13% Similarity=0.180 Sum_probs=22.3
Q ss_pred eeeEEEEeccc-cccCCCCcEEEecCcceeccc
Q 043613 37 RRLEVILTTKV-DKLGKVGETVKVAPGYFHNHL 68 (90)
Q Consensus 37 ~km~VILl~dV-~gLGk~GdvV~Vk~GYARN~L 68 (90)
..+++.+-.+- ...=..||+|.++.||.+.|-
T Consensus 34 G~i~~~~W~~~~~~~~~~G~vv~i~~~~v~~~~ 66 (82)
T cd04491 34 GTIRFTLWDEKAADDLEPGDVVRIENAYVREFN 66 (82)
T ss_pred CEEEEEEECchhcccCCCCCEEEEEeEEEEecC
Confidence 34566665543 223478999999999999873
No 20
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=22.36 E-value=38 Score=26.31 Aligned_cols=48 Identities=25% Similarity=0.422 Sum_probs=28.0
Q ss_pred HHHHHHHh-hcccceechheeeeccee-----eeeeEEE-------Eecc---ccccCCCCcEE
Q 043613 10 ALRQITKE-SSDRVLHHPLLFSCQGVK-----YRRLEVI-------LTTK---VDKLGKVGETV 57 (90)
Q Consensus 10 ~~~~~~~~-~s~~~~~~p~~~~~q~~r-----~~km~VI-------Ll~d---V~gLGk~GdvV 57 (90)
|++-+.++ ..-+..+=.++....|++ +..+++. |.+. |||||..||..
T Consensus 143 ai~~L~~~G~~~~I~~v~~vAapeGi~~v~~~~p~v~I~ta~iD~~Lne~gYIvPGLGDaGDR~ 206 (210)
T COG0035 143 AIDLLKKRGGPKNIKVVSLVAAPEGIKAVEKAHPDVEIYTAAIDEGLNEKGYIVPGLGDAGDRL 206 (210)
T ss_pred HHHHHHHhCCCceEEEEEEEecHHHHHHHHHhCCCCeEEEEEeccccccCCCCccCCCcccccc
Confidence 55666666 445544444444444432 2333333 5666 99999999965
No 21
>PF08415 NRPS: Nonribosomal peptide synthase; InterPro: IPR013624 This domain is found in bacterial non-ribosomal peptide synthetases (NRPS). NRPS are megaenzymes organised as iterative modules, one for each amino acid to be built into the peptide product []. NRPS modules are involved in epothilone biosynthesis (EpoB), myxothiazol biosynthesis (MtaC and MtaD), and other functions []. The NRPS domain tends to be found together with the condensation domain (IPR001242 from INTERPRO) and the phosphopantetheine binding domain (IPR006163 from INTERPRO).
Probab=21.11 E-value=99 Score=18.38 Aligned_cols=23 Identities=26% Similarity=0.608 Sum_probs=18.8
Q ss_pred hHHHHHHHHHhhcccceechhee
Q 043613 7 GRNALRQITKESSDRVLHHPLLF 29 (90)
Q Consensus 7 ~~~~~~~~~~~~s~~~~~~p~~~ 29 (90)
|-+.||.+.+......++.|.++
T Consensus 6 Gv~vlRel~r~~~~~~~~~PVVF 28 (58)
T PF08415_consen 6 GVEVLRELARRGGGRAAVMPVVF 28 (58)
T ss_pred HHHHHHHHHHhcCCCCCcCCEEE
Confidence 77889999998777777777776
Done!