Query 042443
Match_columns 95
No_of_seqs 103 out of 125
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:14:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042443.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042443hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02988 YaaA_near_RecF S4 do 97.2 0.00026 5.7E-09 43.0 2.3 27 69-95 7-33 (59)
2 PF01479 S4: S4 domain; Inter 96.8 0.0014 3E-08 37.8 2.7 25 71-95 1-25 (48)
3 PLN00051 RNA-binding S4 domain 96.4 0.0024 5.2E-08 50.2 2.7 25 70-95 191-215 (267)
4 COG0564 RluA Pseudouridylate s 95.7 0.0081 1.8E-07 47.1 2.7 26 69-95 11-36 (289)
5 cd00165 S4 S4/Hsp/ tRNA synthe 95.3 0.022 4.7E-07 32.1 2.7 25 71-95 1-25 (70)
6 PRK11180 rluD 23S rRNA pseudou 94.7 0.027 5.8E-07 43.9 2.8 27 69-95 16-42 (325)
7 PRK11025 23S rRNA pseudouridyl 94.6 0.043 9.3E-07 42.8 3.6 27 69-95 18-44 (317)
8 smart00363 S4 S4 RNA-binding d 94.0 0.066 1.4E-06 29.3 2.6 25 71-95 1-25 (60)
9 TIGR03069 PS_II_S4 photosystem 93.7 0.056 1.2E-06 42.0 2.7 26 69-95 182-207 (257)
10 PF06353 DUF1062: Protein of u 91.8 0.16 3.5E-06 37.1 2.7 25 70-95 102-126 (142)
11 TIGR01017 rpsD_bact ribosomal 79.6 1.8 3.9E-05 32.6 2.6 26 70-95 89-114 (200)
12 COG2302 Uncharacterized conser 79.1 1.8 3.8E-05 35.2 2.6 25 70-95 180-204 (257)
13 PRK05327 rpsD 30S ribosomal pr 78.6 2 4.4E-05 32.3 2.6 26 70-95 92-117 (203)
14 COG4332 Uncharacterized protei 77.8 2.2 4.8E-05 33.7 2.7 30 63-94 132-161 (203)
15 CHL00113 rps4 ribosomal protei 74.8 2.9 6.2E-05 31.9 2.6 25 71-95 89-113 (201)
16 PF02845 CUE: CUE domain; Int 70.8 3.6 7.9E-05 23.5 1.8 20 75-94 6-25 (42)
17 PRK10348 ribosome-associated h 55.5 13 0.00027 27.2 2.6 26 70-95 8-33 (133)
18 PF13518 HTH_28: Helix-turn-he 46.9 22 0.00048 19.7 2.2 23 70-94 12-34 (52)
19 PRK04051 rps4p 30S ribosomal p 44.9 21 0.00045 27.1 2.5 26 70-95 102-127 (177)
20 TIGR01764 excise DNA binding d 43.0 25 0.00055 18.8 2.1 17 78-95 8-24 (49)
21 smart00546 CUE Domain that may 42.3 30 0.00065 19.5 2.4 19 76-94 8-26 (43)
22 PF03474 DMA: DMRTA motif; In 41.2 30 0.00065 20.9 2.3 19 75-93 6-24 (39)
23 PF13384 HTH_23: Homeodomain-l 34.6 51 0.0011 18.4 2.5 18 76-94 22-39 (50)
24 cd04762 HTH_MerR-trunc Helix-T 31.5 50 0.0011 17.3 2.0 17 78-95 7-23 (49)
25 PF12728 HTH_17: Helix-turn-he 30.6 51 0.0011 18.6 2.1 17 78-95 8-24 (51)
26 PF09607 BrkDBD: Brinker DNA-b 29.7 64 0.0014 20.9 2.6 20 75-95 29-48 (58)
27 PF14502 HTH_41: Helix-turn-he 25.7 56 0.0012 20.5 1.7 25 69-94 2-28 (48)
28 PF09916 DUF2145: Uncharacteri 24.2 84 0.0018 24.7 2.8 46 48-94 101-148 (201)
29 TIGR00250 RNAse_H_YqgF RNAse H 20.8 87 0.0019 21.9 2.1 22 65-93 108-129 (130)
30 PF12091 DUF3567: Protein of u 20.6 70 0.0015 22.2 1.6 22 70-95 39-60 (85)
No 1
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=97.21 E-value=0.00026 Score=42.99 Aligned_cols=27 Identities=11% Similarity=-0.079 Sum_probs=22.7
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.+.|||++|++....+||+++|.||++
T Consensus 7 ~~~rLd~~L~~~~~~~SR~~~k~li~~ 33 (59)
T TIGR02988 7 EYITLGQLLKELGIIDSGGQAKWFLQE 33 (59)
T ss_pred hHHHHHHHHHHcCCccCHHHHHHHHHc
Confidence 579999999999333499999999974
No 2
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=96.79 E-value=0.0014 Score=37.82 Aligned_cols=25 Identities=28% Similarity=0.131 Sum_probs=23.4
Q ss_pred ChhHHHHHHhchhchHHHHHHHHhC
Q 042443 71 RRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 71 ~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.|||.+|+++.+.-||+.+++||++
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~ 25 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQ 25 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHT
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCC
Confidence 4999999999999999999999975
No 3
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=96.43 E-value=0.0024 Score=50.21 Aligned_cols=25 Identities=28% Similarity=0.392 Sum_probs=23.7
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
+.|||.++|..+ .+|||++|+||++
T Consensus 191 s~RLD~vla~~~-~~SRsk~~~lI~~ 215 (267)
T PLN00051 191 SLRLDALASAGF-RMSRSKLVDLISS 215 (267)
T ss_pred cccHHHHHHHHh-ccCHHHHHHHHHc
Confidence 799999999999 9999999999974
No 4
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=95.74 E-value=0.0081 Score=47.13 Aligned_cols=26 Identities=31% Similarity=0.373 Sum_probs=24.0
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.|+|||++|+++++ +||++++.||++
T Consensus 11 ~g~rld~~L~~l~~-~sr~~~~~~i~~ 36 (289)
T COG0564 11 AGQRLDKFLAKLLP-ISRSRIQKLIRK 36 (289)
T ss_pred cCCCHHHHHHHccC-cCHHHHHHHHHC
Confidence 48999999999888 999999999974
No 5
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=95.26 E-value=0.022 Score=32.10 Aligned_cols=25 Identities=28% Similarity=0.153 Sum_probs=22.7
Q ss_pred ChhHHHHHHhchhchHHHHHHHHhC
Q 042443 71 RRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 71 ~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.|||.+|.+.++..||+.+++||.+
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~ 25 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKH 25 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHc
Confidence 4899999999889999999999974
No 6
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=94.73 E-value=0.027 Score=43.94 Aligned_cols=27 Identities=44% Similarity=0.768 Sum_probs=24.8
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
-|.|||++|++.++.+||+.++++|.+
T Consensus 16 ~g~RLd~~L~~~~~~~Sr~~~~~lI~~ 42 (325)
T PRK11180 16 LGQRLDQALAELFPDYSRSRIKEWILD 42 (325)
T ss_pred CCccHHHHHHhhccccCHHHHHHHHHC
Confidence 378999999999999999999999974
No 7
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=94.57 E-value=0.043 Score=42.77 Aligned_cols=27 Identities=11% Similarity=0.249 Sum_probs=24.8
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.|.|||++|+..++.+||+.++.+|++
T Consensus 18 ~g~RLd~~L~~~~~~~sr~~i~~li~~ 44 (317)
T PRK11025 18 AGQRIDNFLRTQLKGVPKSMIYRILRK 44 (317)
T ss_pred CCchHHHHHHHhcccCCHHHHHHHHHc
Confidence 378999999999999999999999974
No 8
>smart00363 S4 S4 RNA-binding domain.
Probab=94.02 E-value=0.066 Score=29.34 Aligned_cols=25 Identities=32% Similarity=0.220 Sum_probs=22.0
Q ss_pred ChhHHHHHHhchhchHHHHHHHHhC
Q 042443 71 RRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 71 ~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.|||+++.+.+..+||+.++.+|.+
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~ 25 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQ 25 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHc
Confidence 4899999998788999999999863
No 9
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=93.73 E-value=0.056 Score=41.98 Aligned_cols=26 Identities=31% Similarity=0.327 Sum_probs=23.5
Q ss_pred ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443 69 KKRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.+.|||.+++..+ .+||+.+++||++
T Consensus 182 ~s~RLD~lls~~~-~~SRs~a~~lI~~ 207 (257)
T TIGR03069 182 ASLRIDAIASAGF-GLSRSKIVDQIKA 207 (257)
T ss_pred ccccHHHHHHhhh-hhhHHHHHHHHHC
Confidence 4789999999999 8999999999974
No 10
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=91.76 E-value=0.16 Score=37.15 Aligned_cols=25 Identities=28% Similarity=0.373 Sum_probs=23.4
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.+||+.+ ..|||+|+++|++
T Consensus 102 ~~Rld~lLa~~L-~lSrs~l~~l~~~ 126 (142)
T PF06353_consen 102 PLRLDRLLARQL-GLSRSRLKRLIEQ 126 (142)
T ss_pred CccHHHHHHHHh-CcCHHHHHHHHHC
Confidence 789999999999 8999999999974
No 11
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=79.57 E-value=1.8 Score=32.56 Aligned_cols=26 Identities=15% Similarity=0.126 Sum_probs=23.0
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.+|....-..||+.+++||..
T Consensus 89 e~RLD~~L~~~g~~~SR~~ArqlI~~ 114 (200)
T TIGR01017 89 ESRLDNVVYRLGFAPTRFAARQLVSH 114 (200)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHC
Confidence 47999999988888899999999964
No 12
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=79.10 E-value=1.8 Score=35.15 Aligned_cols=25 Identities=36% Similarity=0.367 Sum_probs=23.0
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.++++.| ..||+..+++|+.
T Consensus 180 SlRLD~vis~~~-~~SR~~a~~lIe~ 204 (257)
T COG2302 180 SLRLDVVISEGF-GLSRAKAQQLIEK 204 (257)
T ss_pred hhhHHHHHHHHH-hhhHHHHHHHHHc
Confidence 689999999999 8999999999974
No 13
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=78.58 E-value=2 Score=32.35 Aligned_cols=26 Identities=15% Similarity=0.158 Sum_probs=22.8
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.++.+.....||+.++++|..
T Consensus 92 E~RLD~iL~~~g~~~SR~~arqlI~~ 117 (203)
T PRK05327 92 ESRLDNVVYRLGFAPTRRQARQLVSH 117 (203)
T ss_pred HHHHHHHHHHcCccCCHHHHHHHHHC
Confidence 36999999988878999999999963
No 14
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.82 E-value=2.2 Score=33.72 Aligned_cols=30 Identities=30% Similarity=0.393 Sum_probs=25.5
Q ss_pred ccccCcccChhHHHHHHhchhchHHHHHHHHh
Q 042443 63 KIQLPKKKRRLDEICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 63 k~q~~~~G~RLDqvLAeLfPeySRSrIQ~WI~ 94 (95)
++.+|- ..|||..|++.+ ..|||.+|++|+
T Consensus 132 ~~~~p~-qlrl~~Ll~seL-~LSrS~lq~lie 161 (203)
T COG4332 132 RISRPF-QLRLDRLLASEL-GLSRSELQRLIE 161 (203)
T ss_pred cccCcc-hhHHHHHHHHHh-CcCHHHHHHHHH
Confidence 444444 889999999999 899999999996
No 15
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=74.82 E-value=2.9 Score=31.94 Aligned_cols=25 Identities=16% Similarity=0.060 Sum_probs=22.9
Q ss_pred ChhHHHHHHhchhchHHHHHHHHhC
Q 042443 71 RRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 71 ~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
.|||.+|.++....||+.+++||..
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~ 113 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNH 113 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHC
Confidence 5999999999989999999999963
No 16
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=70.85 E-value=3.6 Score=23.46 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=15.7
Q ss_pred HHHHHhchhchHHHHHHHHh
Q 042443 75 EICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 75 qvLAeLfPeySRSrIQ~WI~ 94 (95)
+.|.++||++++..|+.-++
T Consensus 6 ~~L~~mFP~~~~~~I~~~L~ 25 (42)
T PF02845_consen 6 QQLQEMFPDLDREVIEAVLQ 25 (42)
T ss_dssp HHHHHHSSSS-HHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHH
Confidence 35789999999999998763
No 17
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=55.54 E-value=13 Score=27.21 Aligned_cols=26 Identities=19% Similarity=0.086 Sum_probs=23.4
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||++|...----||+..|.+|+.
T Consensus 8 ~~RlDk~L~~~rl~ktRs~A~~lI~~ 33 (133)
T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEG 33 (133)
T ss_pred cccHHHHHHHcCccccHHHHHHHHHC
Confidence 47999999998889999999999974
No 18
>PF13518 HTH_28: Helix-turn-helix domain
Probab=46.87 E-value=22 Score=19.74 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=15.8
Q ss_pred cChhHHHHHHhchhchHHHHHHHHh
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~ 94 (95)
|.-+.+ +|+.| ..|++.|..||+
T Consensus 12 g~s~~~-~a~~~-gis~~tv~~w~~ 34 (52)
T PF13518_consen 12 GESVRE-IAREF-GISRSTVYRWIK 34 (52)
T ss_pred CCCHHH-HHHHH-CCCHhHHHHHHH
Confidence 333444 55555 569999999996
No 19
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=44.94 E-value=21 Score=27.06 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=23.4
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..|||.+|.++----||+..++||.+
T Consensus 102 erRLd~il~r~gla~S~~~Ar~lI~h 127 (177)
T PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVH 127 (177)
T ss_pred HhHHHHHHHHccCcCCHHHHHHHHHc
Confidence 34999999999999999999999974
No 20
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=43.05 E-value=25 Score=18.77 Aligned_cols=17 Identities=18% Similarity=0.155 Sum_probs=12.5
Q ss_pred HHhchhchHHHHHHHHhC
Q 042443 78 LERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 78 AeLfPeySRSrIQ~WI~~ 95 (95)
|+++ ..||+.|.+||.+
T Consensus 8 a~~l-gis~~ti~~~~~~ 24 (49)
T TIGR01764 8 AEYL-GVSKDTVYRLIHE 24 (49)
T ss_pred HHHH-CCCHHHHHHHHHc
Confidence 4444 6899999998864
No 21
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=42.31 E-value=30 Score=19.54 Aligned_cols=19 Identities=11% Similarity=0.086 Sum_probs=15.5
Q ss_pred HHHHhchhchHHHHHHHHh
Q 042443 76 ICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 76 vLAeLfPeySRSrIQ~WI~ 94 (95)
.|.++||++++..|+.-++
T Consensus 8 ~L~~mFP~l~~~~I~~~L~ 26 (43)
T smart00546 8 DLKDMFPNLDEEVIKAVLE 26 (43)
T ss_pred HHHHHCCCCCHHHHHHHHH
Confidence 5678999999999986553
No 22
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=41.23 E-value=30 Score=20.92 Aligned_cols=19 Identities=16% Similarity=0.303 Sum_probs=16.0
Q ss_pred HHHHHhchhchHHHHHHHH
Q 042443 75 EICLERFQQYSRTYIQSWI 93 (95)
Q Consensus 75 qvLAeLfPeySRSrIQ~WI 93 (95)
.+|+.+||+.-|+.++..+
T Consensus 6 diL~rvFP~~kr~~Le~iL 24 (39)
T PF03474_consen 6 DILTRVFPHQKRSVLELIL 24 (39)
T ss_pred HHHHHHCCCCChHHHHHHH
Confidence 4789999999999998654
No 23
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=34.58 E-value=51 Score=18.41 Aligned_cols=18 Identities=28% Similarity=0.457 Sum_probs=13.2
Q ss_pred HHHHhchhchHHHHHHHHh
Q 042443 76 ICLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 76 vLAeLfPeySRSrIQ~WI~ 94 (95)
-+|+.+ ..||+.|..|++
T Consensus 22 ~ia~~l-gvs~~Tv~~w~k 39 (50)
T PF13384_consen 22 EIAKRL-GVSRSTVYRWIK 39 (50)
T ss_dssp HHHHHH-TS-HHHHHHHHT
T ss_pred HHHHHH-CcCHHHHHHHHH
Confidence 355555 799999999986
No 24
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=31.51 E-value=50 Score=17.34 Aligned_cols=17 Identities=18% Similarity=0.432 Sum_probs=12.7
Q ss_pred HHhchhchHHHHHHHHhC
Q 042443 78 LERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 78 AeLfPeySRSrIQ~WI~~ 95 (95)
|+.+ ..|++.|..|+++
T Consensus 7 a~~l-gvs~~tl~~~~~~ 23 (49)
T cd04762 7 AELL-GVSPSTLRRWVKE 23 (49)
T ss_pred HHHH-CcCHHHHHHHHHc
Confidence 4444 7899999999864
No 25
>PF12728 HTH_17: Helix-turn-helix domain
Probab=30.61 E-value=51 Score=18.65 Aligned_cols=17 Identities=35% Similarity=0.528 Sum_probs=12.3
Q ss_pred HHhchhchHHHHHHHHhC
Q 042443 78 LERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 78 AeLfPeySRSrIQ~WI~~ 95 (95)
|+++ ..|++.|.+||.+
T Consensus 8 a~~l-~is~~tv~~~~~~ 24 (51)
T PF12728_consen 8 AELL-GISRSTVYRWIRQ 24 (51)
T ss_pred HHHH-CcCHHHHHHHHHc
Confidence 4444 5899999998863
No 26
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=29.71 E-value=64 Score=20.92 Aligned_cols=20 Identities=25% Similarity=0.512 Sum_probs=15.0
Q ss_pred HHHHHhchhchHHHHHHHHhC
Q 042443 75 EICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 75 qvLAeLfPeySRSrIQ~WI~~ 95 (95)
++.|.-| ..+|..||.|.++
T Consensus 29 RAaarkf-~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 29 RAAARKF-NVSRRQVRKWRKQ 48 (58)
T ss_dssp HHHHHHT-TS-HHHHHHHHTT
T ss_pred HHHHHHh-CccHHHHHHHHHH
Confidence 4567777 6799999999864
No 27
>PF14502 HTH_41: Helix-turn-helix domain
Probab=25.67 E-value=56 Score=20.50 Aligned_cols=25 Identities=32% Similarity=0.332 Sum_probs=17.3
Q ss_pred ccChhHHH--HHHhchhchHHHHHHHHh
Q 042443 69 KKRRLDEI--CLERFQQYSRTYIQSWIL 94 (95)
Q Consensus 69 ~G~RLDqv--LAeLfPeySRSrIQ~WI~ 94 (95)
.|.||+.+ +++.| +.||-.||.-|+
T Consensus 2 ~GdRi~tI~e~~~~~-~vs~GtiQ~Alk 28 (48)
T PF14502_consen 2 VGDRIPTISEYSEKF-GVSRGTIQNALK 28 (48)
T ss_pred CCcccCCHHHHHHHh-CcchhHHHHHHH
Confidence 46666644 45555 789999998764
No 28
>PF09916 DUF2145: Uncharacterized protein conserved in bacteria (DUF2145); InterPro: IPR014547 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.17 E-value=84 Score=24.68 Aligned_cols=46 Identities=13% Similarity=0.206 Sum_probs=39.3
Q ss_pred cCCccceeeccccccccccCcccChhHHHHHHhch--hchHHHHHHHHh
Q 042443 48 YPIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQ--QYSRTYIQSWIL 94 (95)
Q Consensus 48 ~~~r~fa~a~~~k~~k~q~~~~G~RLDqvLAeLfP--eySRSrIQ~WI~ 94 (95)
.+-..|.+.+|+=+.+-|.-. .-=||.+.+.+.| .-+|.++|.|++
T Consensus 101 Lh~~~YS~vAyp~~~~YQNcn-qw~LE~laaA~~~~~~~~r~~aqawl~ 148 (201)
T PF09916_consen 101 LHNPRYSMVAYPFSTRYQNCN-QWVLEVLAAAMYPAGTDDRAQAQAWLR 148 (201)
T ss_pred hcCCCcceeecccCCccccch-HHHHHHHHHHhcccccCCHHHHHHHHH
Confidence 344567778888889988887 8889999999999 899999999986
No 29
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=20.81 E-value=87 Score=21.89 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=15.2
Q ss_pred ccCcccChhHHHHHHhchhchHHHHHHHH
Q 042443 65 QLPKKKRRLDEICLERFQQYSRTYIQSWI 93 (95)
Q Consensus 65 q~~~~G~RLDqvLAeLfPeySRSrIQ~WI 93 (95)
.++++..++|++.|.++ ||+|+
T Consensus 108 ~~~~~k~~vD~~AA~iI-------Lq~yL 129 (130)
T TIGR00250 108 FRALRKGKIDKAAAVII-------LQSYL 129 (130)
T ss_pred ChhhccccHhHHHHHHH-------HHHHh
Confidence 33334568999999987 66665
No 30
>PF12091 DUF3567: Protein of unknown function (DUF3567); InterPro: IPR021951 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif.
Probab=20.60 E-value=70 Score=22.25 Aligned_cols=22 Identities=27% Similarity=0.277 Sum_probs=18.3
Q ss_pred cChhHHHHHHhchhchHHHHHHHHhC
Q 042443 70 KRRLDEICLERFQQYSRTYIQSWILQ 95 (95)
Q Consensus 70 G~RLDqvLAeLfPeySRSrIQ~WI~~ 95 (95)
..=||=.+|+.| |..||.||.+
T Consensus 39 Eifi~G~~Ae~F----r~~V~~li~~ 60 (85)
T PF12091_consen 39 EIFIDGSWAEMF----REDVQALIAS 60 (85)
T ss_pred eEEeCcHHHHHH----HHHHHHHHhc
Confidence 445888999999 8899999974
Done!