Query 035373
Match_columns 66
No_of_seqs 18 out of 20
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 02:32:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035373hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10138 vWA-TerF-like: vWA fo 62.1 4.2 9.1E-05 29.5 1.1 31 28-58 5-35 (200)
2 PRK12620 flgB flagellar basal 46.2 15 0.00034 23.6 1.7 17 47-63 23-39 (132)
3 PRK07182 flgB flagellar basal 45.8 15 0.00033 24.5 1.7 17 47-63 23-39 (148)
4 PRK12685 flgB flagellar basal 44.5 15 0.00032 23.7 1.4 17 47-63 23-39 (116)
5 PF13820 Nucleic_acid_bd: Puta 41.8 36 0.00079 23.7 3.1 38 7-44 16-55 (149)
6 COG1710 Uncharacterized protei 34.4 27 0.00058 24.9 1.5 17 36-52 3-19 (139)
7 PRK12622 flgB flagellar basal 32.8 33 0.00071 22.8 1.7 18 46-63 21-38 (135)
8 PRK12621 flgB flagellar basal 30.8 36 0.00079 21.9 1.6 17 47-63 23-39 (136)
9 PRK12624 flgB flagellar basal 28.5 43 0.00093 22.5 1.7 19 45-63 23-41 (143)
10 PRK12627 flgB flagellar basal 28.1 44 0.00096 22.0 1.7 19 45-63 20-38 (128)
11 PRK05680 flgB flagellar basal 27.3 46 0.001 21.7 1.6 18 46-63 22-39 (137)
12 PF00673 Ribosomal_L5_C: ribos 26.2 90 0.0019 19.5 2.8 22 36-57 3-24 (95)
13 COG5503 Uncharacterized conser 26.2 58 0.0013 20.9 1.9 22 32-53 18-40 (69)
14 PRK12625 flgB flagellar basal 25.0 55 0.0012 21.7 1.7 18 46-63 22-39 (132)
15 PF07006 DUF1310: Protein of u 24.9 51 0.0011 22.1 1.6 20 40-59 35-54 (122)
16 COG1815 FlgB Flagellar basal b 24.7 49 0.0011 22.6 1.5 18 46-63 21-38 (133)
17 PF11002 RDM: RFPL defining mo 24.7 25 0.00053 20.6 0.0 12 4-15 12-23 (42)
18 PRK12619 flgB flagellar basal 24.4 58 0.0013 21.2 1.7 18 46-63 22-39 (130)
19 PRK06003 flgB flagellar basal 23.1 62 0.0013 21.0 1.7 19 46-64 20-38 (126)
20 COG0186 RpsQ Ribosomal protein 23.1 44 0.00095 21.8 0.9 15 28-42 17-31 (87)
21 TIGR01396 FlgB flagellar basal 22.6 64 0.0014 21.1 1.7 18 46-63 18-35 (131)
22 PRK12623 flgB flagellar basal 22.6 52 0.0011 21.9 1.2 17 47-63 27-43 (131)
No 1
>PF10138 vWA-TerF-like: vWA found in TerF C terminus ; InterPro: IPR019303 This entry represents the N-terminal domain of a family of proteins that confer resistance to the metalloid element tellurium and its salts.
Probab=62.08 E-value=4.2 Score=29.48 Aligned_cols=31 Identities=19% Similarity=0.454 Sum_probs=28.0
Q ss_pred chhccCccceeeeeehHHHHHHHHHhhhhcc
Q 035373 28 YIKMDKSSSVKVEIRSRKAKKLIDKTLQVAD 58 (66)
Q Consensus 28 Y~Km~Ks~SmrVEIRSRkArkLI~ktL~~AD 58 (66)
|-=+|+|-||+=.-++...|.+.+.+|..|-
T Consensus 5 ~LVLD~SGSM~~~yk~G~vQ~~~Er~lalA~ 35 (200)
T PF10138_consen 5 YLVLDISGSMRPLYKDGTVQRVVERILALAA 35 (200)
T ss_pred EEEEeCCCCCchhhhCccHHHHHHHHHHHHh
Confidence 4558999999999999999999999999883
No 2
>PRK12620 flgB flagellar basal body rod protein FlgB; Provisional
Probab=46.15 E-value=15 Score=23.61 Aligned_cols=17 Identities=41% Similarity=0.618 Sum_probs=15.3
Q ss_pred HHHHHHhhhhccCCCCc
Q 035373 47 KKLIDKTLQVADRPGKR 63 (66)
Q Consensus 47 rkLI~ktL~~ADs~~~r 63 (66)
+++|+.|++=||.||=+
T Consensus 23 q~via~NIANadTPgYk 39 (132)
T PRK12620 23 MKLIASNLSNVDTPGYK 39 (132)
T ss_pred HHHHHHHHHhcCCCCcC
Confidence 68999999999999854
No 3
>PRK07182 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=45.77 E-value=15 Score=24.54 Aligned_cols=17 Identities=18% Similarity=0.356 Sum_probs=15.4
Q ss_pred HHHHHHhhhhccCCCCc
Q 035373 47 KKLIDKTLQVADRPGKR 63 (66)
Q Consensus 47 rkLI~ktL~~ADs~~~r 63 (66)
|++|+.|++=||.||=+
T Consensus 23 q~vIa~NIANadTPGYk 39 (148)
T PRK07182 23 AELLSANLANVNTPNFQ 39 (148)
T ss_pred HHHHHHhHHhcCCCCCC
Confidence 78999999999999954
No 4
>PRK12685 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=44.54 E-value=15 Score=23.75 Aligned_cols=17 Identities=29% Similarity=0.579 Sum_probs=15.4
Q ss_pred HHHHHHhhhhccCCCCc
Q 035373 47 KKLIDKTLQVADRPGKR 63 (66)
Q Consensus 47 rkLI~ktL~~ADs~~~r 63 (66)
|++|+.|++-||-||=+
T Consensus 23 q~via~NIANadTPgYk 39 (116)
T PRK12685 23 SKVLASNLANAETPGYK 39 (116)
T ss_pred HHHHHhhhhccCCCCcC
Confidence 78999999999999954
No 5
>PF13820 Nucleic_acid_bd: Putative nucleic acid-binding region
Probab=41.83 E-value=36 Score=23.74 Aligned_cols=38 Identities=21% Similarity=0.218 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHhhhccCC--cchhccCccceeeeeehH
Q 035373 7 ENLVESIKSKVRALKKKKNK--PYIKMDKSSSVKVEIRSR 44 (66)
Q Consensus 7 g~lv~~iKsk~r~~~~k~kk--~Y~Km~Ks~SmrVEIRSR 44 (66)
+.=+|.||..|+.+-...++ -+.+.++-.|++||+-.-
T Consensus 16 ~~~ld~i~~~l~~L~~~~~~~l~~~~~~~~~sv~V~f~ip 55 (149)
T PF13820_consen 16 QYKLDDIKNWLASLYKPRISDLKVRKVEPWNSVRVTFSIP 55 (149)
T ss_pred HHHHHHHHHHHHHHHhcccccceeeccccCceEEEEEech
Confidence 34467788888888654444 489999999999998764
No 6
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.38 E-value=27 Score=24.91 Aligned_cols=17 Identities=29% Similarity=0.714 Sum_probs=15.8
Q ss_pred ceeeeeehHHHHHHHHH
Q 035373 36 SVKVEIRSRKAKKLIDK 52 (66)
Q Consensus 36 SmrVEIRSRkArkLI~k 52 (66)
-|+|||.+|.-+.|+++
T Consensus 3 ~m~v~l~ar~i~ELlek 19 (139)
T COG1710 3 KMRVELTARNIRELLEK 19 (139)
T ss_pred ceeeehhhhhHHHHHHH
Confidence 58999999999999987
No 7
>PRK12622 flgB flagellar basal body rod protein FlgB; Provisional
Probab=32.81 E-value=33 Score=22.81 Aligned_cols=18 Identities=17% Similarity=0.370 Sum_probs=15.5
Q ss_pred HHHHHHHhhhhccCCCCc
Q 035373 46 AKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 46 ArkLI~ktL~~ADs~~~r 63 (66)
=+++|+.|++-||.||=+
T Consensus 21 r~~via~NiAN~~Tp~yk 38 (135)
T PRK12622 21 RQSVIADNIANVDTPNFK 38 (135)
T ss_pred HHHHHHHHHHhcCCcccC
Confidence 378999999999999854
No 8
>PRK12621 flgB flagellar basal body rod protein FlgB; Provisional
Probab=30.81 E-value=36 Score=21.92 Aligned_cols=17 Identities=18% Similarity=0.458 Sum_probs=15.1
Q ss_pred HHHHHHhhhhccCCCCc
Q 035373 47 KKLIDKTLQVADRPGKR 63 (66)
Q Consensus 47 rkLI~ktL~~ADs~~~r 63 (66)
++.|+.|++-||.||=+
T Consensus 23 q~viA~NIAN~nTPgYk 39 (136)
T PRK12621 23 QNVVMSNLANVNTPGYK 39 (136)
T ss_pred HHHHHHhhhhcCCCCCC
Confidence 68999999999999854
No 9
>PRK12624 flgB flagellar basal body rod protein FlgB; Provisional
Probab=28.51 E-value=43 Score=22.54 Aligned_cols=19 Identities=26% Similarity=0.447 Sum_probs=15.9
Q ss_pred HHHHHHHHhhhhccCCCCc
Q 035373 45 KAKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 45 kArkLI~ktL~~ADs~~~r 63 (66)
+=+++|+.|++-||.||=+
T Consensus 23 ~R~~via~NiANa~Tp~yk 41 (143)
T PRK12624 23 QKRKVISDNIANADVPHFK 41 (143)
T ss_pred HHHHHHHHHHHhcCCCCCC
Confidence 3478999999999999854
No 10
>PRK12627 flgB flagellar basal body rod protein FlgB; Provisional
Probab=28.06 E-value=44 Score=21.95 Aligned_cols=19 Identities=26% Similarity=0.573 Sum_probs=16.1
Q ss_pred HHHHHHHHhhhhccCCCCc
Q 035373 45 KAKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 45 kArkLI~ktL~~ADs~~~r 63 (66)
.=+++|+.|++-||.||=+
T Consensus 20 ~r~~~ia~NiAN~~tp~y~ 38 (128)
T PRK12627 20 ERQAVVARNVANADTPGYR 38 (128)
T ss_pred HHHHHHHHHHHccCCCCCC
Confidence 3478999999999999855
No 11
>PRK05680 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=27.25 E-value=46 Score=21.73 Aligned_cols=18 Identities=28% Similarity=0.562 Sum_probs=15.5
Q ss_pred HHHHHHHhhhhccCCCCc
Q 035373 46 AKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 46 ArkLI~ktL~~ADs~~~r 63 (66)
=+++|+.|++-||.||=+
T Consensus 22 r~~~ia~NiAN~~Tpgyk 39 (137)
T PRK05680 22 RQEVIASNIANADTPGYK 39 (137)
T ss_pred HHHHHHHhHHhcCCCCcC
Confidence 478999999999999854
No 12
>PF00673 Ribosomal_L5_C: ribosomal L5P family C-terminus; InterPro: IPR002132 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 L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 2ZJR_D 2ZJP_D 3PIO_D 3CF5_D 2ZJQ_D 3DLL_D 3PIP_D 2WDL_G 3UZN_G ....
Probab=26.24 E-value=90 Score=19.55 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=19.4
Q ss_pred ceeeeeehHHHHHHHHHhhhhc
Q 035373 36 SVKVEIRSRKAKKLIDKTLQVA 57 (66)
Q Consensus 36 SmrVEIRSRkArkLI~ktL~~A 57 (66)
.++|.+|-.+|-..+++-+.++
T Consensus 3 G~kvTLRg~~m~~FL~kli~~v 24 (95)
T PF00673_consen 3 GCKVTLRGKKMYEFLDKLITIV 24 (95)
T ss_dssp EEEEEEEHHHHHHHHHHHHHTT
T ss_pred EEEEEEccHHHHHHHHHHHHHh
Confidence 3789999999999999988874
No 13
>COG5503 Uncharacterized conserved small protein [Function unknown]
Probab=26.15 E-value=58 Score=20.87 Aligned_cols=22 Identities=23% Similarity=0.448 Sum_probs=18.8
Q ss_pred cCccceeeeeeh-HHHHHHHHHh
Q 035373 32 DKSSSVKVEIRS-RKAKKLIDKT 53 (66)
Q Consensus 32 ~Ks~SmrVEIRS-RkArkLI~kt 53 (66)
++|+|.-||+-| .+||+|+.+|
T Consensus 18 E~T~sLYle~~se~~vR~ll~e~ 40 (69)
T COG5503 18 ETTDSLYLEADSETKVRQLLKEN 40 (69)
T ss_pred cccceEEEechhHHHHHHHHhcc
Confidence 688999999975 6899999876
No 14
>PRK12625 flgB flagellar basal body rod protein FlgB; Provisional
Probab=24.96 E-value=55 Score=21.65 Aligned_cols=18 Identities=22% Similarity=0.394 Sum_probs=15.5
Q ss_pred HHHHHHHhhhhccCCCCc
Q 035373 46 AKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 46 ArkLI~ktL~~ADs~~~r 63 (66)
=+++|+.||+-||.||=+
T Consensus 22 r~~~~a~NiAN~~tp~y~ 39 (132)
T PRK12625 22 RAEVISSNIANADTPHYK 39 (132)
T ss_pred HHHHHHHHHHhcCCCCcC
Confidence 378999999999999854
No 15
>PF07006 DUF1310: Protein of unknown function (DUF1310); InterPro: IPR010738 This family consists of several hypothetical proteins of around 125 residues in length. Members of this family seem to be specific to Listeria and Streptococcus species. The function of this family is unknown.
Probab=24.93 E-value=51 Score=22.11 Aligned_cols=20 Identities=40% Similarity=0.556 Sum_probs=17.8
Q ss_pred eeehHHHHHHHHHhhhhccC
Q 035373 40 EIRSRKAKKLIDKTLQVADR 59 (66)
Q Consensus 40 EIRSRkArkLI~ktL~~ADs 59 (66)
-+.|..|+++|++.|+.-|+
T Consensus 35 Iv~S~E~k~~~E~~Lk~lD~ 54 (122)
T PF07006_consen 35 IVKSEEAKKVIEKDLKNLDP 54 (122)
T ss_pred HhcCHHHHHHHHHHHHHhCh
Confidence 35799999999999999886
No 16
>COG1815 FlgB Flagellar basal body protein [Cell motility and secretion]
Probab=24.72 E-value=49 Score=22.61 Aligned_cols=18 Identities=28% Similarity=0.575 Sum_probs=15.9
Q ss_pred HHHHHHHhhhhccCCCCc
Q 035373 46 AKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 46 ArkLI~ktL~~ADs~~~r 63 (66)
-|++|+-|++-||-||=+
T Consensus 21 Rq~via~NIANadTP~yK 38 (133)
T COG1815 21 RQEVIANNIANADTPGYK 38 (133)
T ss_pred HHHHHHhhhccCCCCCCC
Confidence 478999999999999855
No 17
>PF11002 RDM: RFPL defining motif (RDM); InterPro: IPR022723 The RFPL defining motif (RDM) is a domain found on RFPL (Ret finger protein like) proteins. In humans, RFPL transcripts can be detected at the onset of neurogenesis in differentiating human embryonic stem cells, and in the developing human neocortex []. The RDM domain is thought to have emerged from a neofunctionalisation event. It is found N-terminal to the SPRY domain (PF00622 from PFAM). ; PDB: 2FBE_B.
Probab=24.66 E-value=25 Score=20.63 Aligned_cols=12 Identities=50% Similarity=0.520 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHH
Q 035373 4 NQLENLVESIKS 15 (66)
Q Consensus 4 ~qLg~lv~~iKs 15 (66)
-|||.||.-||.
T Consensus 12 ~qLg~Lvs~iKe 23 (42)
T PF11002_consen 12 FQLGKLVSKIKE 23 (42)
T ss_dssp ------------
T ss_pred HHHHHHHHHHHH
Confidence 489999987775
No 18
>PRK12619 flgB flagellar basal body rod protein FlgB; Provisional
Probab=24.44 E-value=58 Score=21.19 Aligned_cols=18 Identities=6% Similarity=0.272 Sum_probs=15.6
Q ss_pred HHHHHHHhhhhccCCCCc
Q 035373 46 AKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 46 ArkLI~ktL~~ADs~~~r 63 (66)
-++.|+.||+-+|.||=+
T Consensus 22 r~~via~NiAN~~Tpgyk 39 (130)
T PRK12619 22 RASVLANNIANVNTPNFK 39 (130)
T ss_pred HHHHHHHHHHhcCCCCcC
Confidence 478999999999999854
No 19
>PRK06003 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=23.12 E-value=62 Score=21.01 Aligned_cols=19 Identities=21% Similarity=0.424 Sum_probs=16.1
Q ss_pred HHHHHHHhhhhccCCCCcc
Q 035373 46 AKKLIDKTLQVADRPGKRS 64 (66)
Q Consensus 46 ArkLI~ktL~~ADs~~~rt 64 (66)
=+++|+.|++=||-||=+.
T Consensus 20 rq~viA~NiAN~~TPgyk~ 38 (126)
T PRK06003 20 RQATVAGNIANANTPGYRA 38 (126)
T ss_pred HHHHHHHhHHhcCCCCccc
Confidence 3789999999999999653
No 20
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=23.05 E-value=44 Score=21.79 Aligned_cols=15 Identities=47% Similarity=0.470 Sum_probs=12.9
Q ss_pred chhccCccceeeeee
Q 035373 28 YIKMDKSSSVKVEIR 42 (66)
Q Consensus 28 Y~Km~Ks~SmrVEIR 42 (66)
=|||+||-.|+||-+
T Consensus 17 S~Km~KTvvV~ve~~ 31 (87)
T COG0186 17 SDKMDKTVVVEVERK 31 (87)
T ss_pred EccCceeEEEEEEEE
Confidence 489999999999864
No 21
>TIGR01396 FlgB flagellar basal-body rod protein FlgB. This model represents FlgB, one of several components of bacterial flagella that share a domain described by pfam model pfam00460. FlgB is part of the basal body.
Probab=22.62 E-value=64 Score=21.14 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=15.4
Q ss_pred HHHHHHHhhhhccCCCCc
Q 035373 46 AKKLIDKTLQVADRPGKR 63 (66)
Q Consensus 46 ArkLI~ktL~~ADs~~~r 63 (66)
-++.|+.|++-||.||=+
T Consensus 18 r~~~ia~NiAN~~Tpgyk 35 (131)
T TIGR01396 18 RQEVIANNIANVDTPGYK 35 (131)
T ss_pred HHHHHHHHHHhcCCCccc
Confidence 367999999999999854
No 22
>PRK12623 flgB flagellar basal body rod protein FlgB; Provisional
Probab=22.60 E-value=52 Score=21.87 Aligned_cols=17 Identities=18% Similarity=0.370 Sum_probs=14.9
Q ss_pred HHHHHHhhhhccCCCCc
Q 035373 47 KKLIDKTLQVADRPGKR 63 (66)
Q Consensus 47 rkLI~ktL~~ADs~~~r 63 (66)
++.|+.|++-||.||=+
T Consensus 27 ~~via~NiAN~~Tpgyk 43 (131)
T PRK12623 27 GKVISNNIANVNTKGYK 43 (131)
T ss_pred HHHHHhcchhcCCcccC
Confidence 67899999999999854
Done!